Accurate analytic solution of chemical master equations for gene regulation networks in a single cell

NASA Astrophysics Data System (ADS)

Huang, Guan-Rong; Saakian, David B.; Hu, Chin-Kun

2018-01-01

Studying gene regulation networks in a single cell is an important, interesting, and hot research topic of molecular biology. Such process can be described by chemical master equations (CMEs). We propose a Hamilton-Jacobi equation method with finite-size corrections to solve such CMEs accurately at the intermediate region of switching, where switching rate is comparable to fast protein production rate. We applied this approach to a model of self-regulating proteins [H. Ge et al., Phys. Rev. Lett. 114, 078101 (2015), 10.1103/PhysRevLett.114.078101] and found that as a parameter related to inducer concentration increases the probability of protein production changes from unimodal to bimodal, then to unimodal, consistent with phenotype switching observed in a single cell.

Stochastic switching in biology: from genotype to phenotype

NASA Astrophysics Data System (ADS)

Bressloff, Paul C.

2017-03-01

There has been a resurgence of interest in non-equilibrium stochastic processes in recent years, driven in part by the observation that the number of molecules (genes, mRNA, proteins) involved in gene expression are often of order 1-1000. This means that deterministic mass-action kinetics tends to break down, and one needs to take into account the discrete, stochastic nature of biochemical reactions. One of the major consequences of molecular noise is the occurrence of stochastic biological switching at both the genotypic and phenotypic levels. For example, individual gene regulatory networks can switch between graded and binary responses, exhibit translational/transcriptional bursting, and support metastability (noise-induced switching between states that are stable in the deterministic limit). If random switching persists at the phenotypic level then this can confer certain advantages to cell populations growing in a changing environment, as exemplified by bacterial persistence in response to antibiotics. Gene expression at the single-cell level can also be regulated by changes in cell density at the population level, a process known as quorum sensing. In contrast to noise-driven phenotypic switching, the switching mechanism in quorum sensing is stimulus-driven and thus noise tends to have a detrimental effect. A common approach to modeling stochastic gene expression is to assume a large but finite system and to approximate the discrete processes by continuous processes using a system-size expansion. However, there is a growing need to have some familiarity with the theory of stochastic processes that goes beyond the standard topics of chemical master equations, the system-size expansion, Langevin equations and the Fokker-Planck equation. Examples include stochastic hybrid systems (piecewise deterministic Markov processes), large deviations and the Wentzel-Kramers-Brillouin (WKB) method, adiabatic reductions, and queuing/renewal theory. The major aim of this review is to provide a self-contained survey of these mathematical methods, mainly within the context of biological switching processes at both the genotypic and phenotypic levels. However, applications to other examples of biological switching are also discussed, including stochastic ion channels, diffusion in randomly switching environments, bacterial chemotaxis, and stochastic neural networks.

Systematic Genetic Screen for Transcriptional Regulators of the Candida albicans White-Opaque Switch.

PubMed

Lohse, Matthew B; Ene, Iuliana V; Craik, Veronica B; Hernday, Aaron D; Mancera, Eugenio; Morschhäuser, Joachim; Bennett, Richard J; Johnson, Alexander D

2016-08-01

The human fungal pathogen Candida albicans can reversibly switch between two cell types named "white" and "opaque," each of which is stable through many cell divisions. These two cell types differ in their ability to mate, their metabolic preferences and their interactions with the mammalian innate immune system. A highly interconnected network of eight transcriptional regulators has been shown to control switching between these two cell types. To identify additional regulators of the switch, we systematically and quantitatively measured white-opaque switching rates of 196 strains, each deleted for a specific transcriptional regulator. We identified 19 new regulators with at least a 10-fold effect on switching rates and an additional 14 new regulators with more subtle effects. To investigate how these regulators affect switching rates, we examined several criteria, including the binding of the eight known regulators of switching to the control region of each new regulatory gene, differential expression of the newly found genes between cell types, and the growth rate of each mutant strain. This study highlights the complexity of the transcriptional network that regulates the white-opaque switch and the extent to which switching is linked to a variety of metabolic processes, including respiration and carbon utilization. In addition to revealing specific insights, the information reported here provides a foundation to understand the highly complex coupling of white-opaque switching to cellular physiology. Copyright © 2016 by the Genetics Society of America.

Sex determination in insects: a binary decision based on alternative splicing.

PubMed

Salz, Helen K

2011-08-01

The gene regulatory networks that control sex determination vary between species. Despite these differences, comparative studies in insects have found that alternative splicing is reiteratively used in evolution to control expression of the key sex-determining genes. Sex determination is best understood in Drosophila where activation of the RNA binding protein-encoding gene Sex-lethal is the central female-determining event. Sex-lethal serves as a genetic switch because once activated it controls its own expression by a positive feedback splicing mechanism. Sex fate choice in is also maintained by self-sustaining positive feedback splicing mechanisms in other dipteran and hymenopteran insects, although different RNA binding protein-encoding genes function as the binary switch. Studies exploring the mechanisms of sex-specific splicing have revealed the extent to which sex determination is integrated with other developmental regulatory networks. Copyright © 2011 Elsevier Ltd. All rights reserved.

Stochastic Switching Induced Adaptation in a Starved Escherichia coli Population

PubMed Central

Ito, Yoichiro; Ying, Bei-Wen; Yomo, Tetsuya

2011-01-01

Population adaptation can be determined by stochastic switching in living cells. To examine how stochastic switching contributes to the fate decision for a population under severe stress, we constructed an Escherichia coli strain crucially dependent on the expression of a rewired gene. The gene essential for tryptophan biosynthesis, trpC, was removed from the native regulatory unit, the Trp operon, and placed under the extraneous control of the lactose utilisation network. Bistability of the network provided the cells two discrete phenotypes: the induced and suppressed level of trpC. The two phenotypes permitted the cells to grow or not, respectively, under conditions of tryptophan depletion. We found that stochastic switching between the two states allowed the initially suppressed cells to form a new population with induced trpC in response to tryptophan starvation. However, the frequency of the transition from suppressed to induced state dropped off dramatically in the starved population, in comparison to that in the nourished population. This reduced switching rate was compensated by increasing the initial population size, which probably provided the cell population more chances to wait for the rarely appearing fit cells from the unfit cells. Taken together, adaptation of a starved bacterial population because of stochasticity in the gene rewired from the ancient regulon was experimentally confirmed, and the nutritional status and the population size played a great role in stochastic adaptation. PMID:21931628

Large-Scale Analysis of Network Bistability for Human Cancers

PubMed Central

Shiraishi, Tetsuya; Matsuyama, Shinako; Kitano, Hiroaki

2010-01-01

Protein–protein interaction and gene regulatory networks are likely to be locked in a state corresponding to a disease by the behavior of one or more bistable circuits exhibiting switch-like behavior. Sets of genes could be over-expressed or repressed when anomalies due to disease appear, and the circuits responsible for this over- or under-expression might persist for as long as the disease state continues. This paper shows how a large-scale analysis of network bistability for various human cancers can identify genes that can potentially serve as drug targets or diagnosis biomarkers. PMID:20628618

Modulation of dynamic modes by interplay between positive and negative feedback loops in gene regulatory networks

NASA Astrophysics Data System (ADS)

Wang, Liu-Suo; Li, Ning-Xi; Chen, Jing-Jia; Zhang, Xiao-Peng; Liu, Feng; Wang, Wei

2018-04-01

A positive and a negative feedback loop can induce bistability and oscillation, respectively, in biological networks. Nevertheless, they are frequently interlinked to perform more elaborate functions in many gene regulatory networks. Coupled positive and negative feedback loops may exhibit either oscillation or bistability depending on the intensity of the stimulus in some particular networks. It is less understood how the transition between the two dynamic modes is modulated by the positive and negative feedback loops. We developed an abstract model of such systems, largely based on the core p53 pathway, to explore the mechanism for the transformation of dynamic behaviors. Our results show that enhancing the positive feedback may promote or suppress oscillations depending on the strength of both feedback loops. We found that the system oscillates with low amplitudes in response to a moderate stimulus and switches to the on state upon a strong stimulus. When the positive feedback is activated much later than the negative one in response to a strong stimulus, the system exhibits long-term oscillations before switching to the on state. We explain this intriguing phenomenon using quasistatic approximation. Moreover, early switching to the on state may occur when the system starts from a steady state in the absence of stimuli. The interplay between the positive and negative feedback plays a key role in the transitions between oscillation and bistability. Of note, our conclusions should be applicable only to some specific gene regulatory networks, especially the p53 network, in which both oscillation and bistability exist in response to a certain type of stimulus. Our work also underscores the significance of transient dynamics in determining cellular outcome.

Markov State Models of gene regulatory networks.

PubMed

Chu, Brian K; Tse, Margaret J; Sato, Royce R; Read, Elizabeth L

2017-02-06

Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understanding of network dynamics have the potential to guide cell-reprogramming strategies. Networks are often modeled by the stochastic Chemical Master Equation, but methods for systematic identification of key properties of the global dynamics are currently lacking. The method identifies the number, phenotypes, and lifetimes of long-lived states for a set of common gene regulatory network models. Application of transition path theory to the constructed Markov State Model decomposes global dynamics into a set of dominant transition paths and associated relative probabilities for stochastic state-switching. In this proof-of-concept study, we found that the Markov State Model provides a general framework for analyzing and visualizing stochastic multistability and state-transitions in gene networks. Our results suggest that this framework-adopted from the field of atomistic Molecular Dynamics-can be a useful tool for quantitative Systems Biology at the network scale.

Distinguishing the rates of gene activation from phenotypic variations.

PubMed

Chen, Ye; Lv, Cheng; Li, Fangting; Li, Tiejun

2015-06-18

Stochastic genetic switching driven by intrinsic noise is an important process in gene expression. When the rates of gene activation/inactivation are relatively slow, fast, or medium compared with the synthesis/degradation rates of mRNAs and proteins, the variability of protein and mRNA levels may exhibit very different dynamical patterns. It is desirable to provide a systematic approach to identify their key dynamical features in different regimes, aiming at distinguishing which regime a considered gene regulatory network is in from their phenotypic variations. We studied a gene expression model with positive feedbacks when genetic switching rates vary over a wide range. With the goal of providing a method to distinguish the regime of the switching rates, we first focus on understanding the essential dynamics of gene expression system in different cases. In the regime of slow switching rates, we found that the effective dynamics can be reduced to independent evolutions on two separate layers corresponding to gene activation and inactivation states, and the transitions between two layers are rare events, after which the system goes mainly along deterministic ODE trajectories on a particular layer to reach new steady states. The energy landscape in this regime can be well approximated by using Gaussian mixture model. In the regime of intermediate switching rates, we analyzed the mean switching time to investigate the stability of the system in different parameter ranges. We also discussed the case of fast switching rates from the viewpoint of transition state theory. Based on the obtained results, we made a proposal to distinguish these three regimes in a simulation experiment. We identified the intermediate regime from the fact that the strength of cellular memory is lower than the other two cases, and the fast and slow regimes can be distinguished by their different perturbation-response behavior with respect to the switching rates perturbations. We proposed a simulation experiment to distinguish the slow, intermediate and fast regimes, which is the main point of our paper. In order to achieve this goal, we systematically studied the essential dynamics of gene expression system when the switching rates are in different regimes. Our theoretical understanding provides new insights on the gene expression experiments.

Analysis of continuous-time switching networks

NASA Astrophysics Data System (ADS)

Edwards, R.

2000-11-01

Models of a number of biological systems, including gene regulation and neural networks, can be formulated as switching networks, in which the interactions between the variables depend strongly on thresholds. An idealized class of such networks in which the switching takes the form of Heaviside step functions but variables still change continuously in time has been proposed as a useful simplification to gain analytic insight. These networks, called here Glass networks after their originator, are simple enough mathematically to allow significant analysis without restricting the range of dynamics found in analogous smooth systems. A number of results have been obtained before, particularly regarding existence and stability of periodic orbits in such networks, but important cases were not considered. Here we present a coherent method of analysis that summarizes previous work and fills in some of the gaps as well as including some new results. Furthermore, we apply this analysis to a number of examples, including surprising long and complex limit cycles involving sequences of hundreds of threshold transitions. Finally, we show how the above methods can be extended to investigate aperiodic behaviour in specific networks, though a complete analysis will have to await new results in matrix theory and symbolic dynamics.

Classification of Genes and Putative Biomarker Identification Using Distribution Metrics on Expression Profiles

PubMed Central

Huang, Hung-Chung; Jupiter, Daniel; VanBuren, Vincent

2010-01-01

Background Identification of genes with switch-like properties will facilitate discovery of regulatory mechanisms that underlie these properties, and will provide knowledge for the appropriate application of Boolean networks in gene regulatory models. As switch-like behavior is likely associated with tissue-specific expression, these gene products are expected to be plausible candidates as tissue-specific biomarkers. Methodology/Principal Findings In a systematic classification of genes and search for biomarkers, gene expression profiles (GEPs) of more than 16,000 genes from 2,145 mouse array samples were analyzed. Four distribution metrics (mean, standard deviation, kurtosis and skewness) were used to classify GEPs into four categories: predominantly-off, predominantly-on, graded (rheostatic), and switch-like genes. The arrays under study were also grouped and examined by tissue type. For example, arrays were categorized as ‘brain group’ and ‘non-brain group’; the Kolmogorov-Smirnov distance and Pearson correlation coefficient were then used to compare GEPs between brain and non-brain for each gene. We were thus able to identify tissue-specific biomarker candidate genes. Conclusions/Significance The methodology employed here may be used to facilitate disease-specific biomarker discovery. PMID:20140228

Gene regulatory networks in lactation: identification of global principles using bioinformatics.

PubMed

Lemay, Danielle G; Neville, Margaret C; Rudolph, Michael C; Pollard, Katherine S; German, J Bruce

2007-11-27

The molecular events underlying mammary development during pregnancy, lactation, and involution are incompletely understood. Mammary gland microarray data, cellular localization data, protein-protein interactions, and literature-mined genes were integrated and analyzed using statistics, principal component analysis, gene ontology analysis, pathway analysis, and network analysis to identify global biological principles that govern molecular events during pregnancy, lactation, and involution. Several key principles were derived: (1) nearly a third of the transcriptome fluctuates to build, run, and disassemble the lactation apparatus; (2) genes encoding the secretory machinery are transcribed prior to lactation; (3) the diversity of the endogenous portion of the milk proteome is derived from fewer than 100 transcripts; (4) while some genes are differentially transcribed near the onset of lactation, the lactation switch is primarily post-transcriptionally mediated; (5) the secretion of materials during lactation occurs not by up-regulation of novel genomic functions, but by widespread transcriptional suppression of functions such as protein degradation and cell-environment communication; (6) the involution switch is primarily transcriptionally mediated; and (7) during early involution, the transcriptional state is partially reverted to the pre-lactation state. A new hypothesis for secretory diminution is suggested - milk production gradually declines because the secretory machinery is not transcriptionally replenished. A comprehensive network of protein interactions during lactation is assembled and new regulatory gene targets are identified. Less than one fifth of the transcriptionally regulated nodes in this lactation network have been previously explored in the context of lactation. Implications for future research in mammary and cancer biology are discussed.

PRODIGEN: visualizing the probability landscape of stochastic gene regulatory networks in state and time space.

PubMed

Ma, Chihua; Luciani, Timothy; Terebus, Anna; Liang, Jie; Marai, G Elisabeta

2017-02-15

Visualizing the complex probability landscape of stochastic gene regulatory networks can further biologists' understanding of phenotypic behavior associated with specific genes. We present PRODIGEN (PRObability DIstribution of GEne Networks), a web-based visual analysis tool for the systematic exploration of probability distributions over simulation time and state space in such networks. PRODIGEN was designed in collaboration with bioinformaticians who research stochastic gene networks. The analysis tool combines in a novel way existing, expanded, and new visual encodings to capture the time-varying characteristics of probability distributions: spaghetti plots over one dimensional projection, heatmaps of distributions over 2D projections, enhanced with overlaid time curves to display temporal changes, and novel individual glyphs of state information corresponding to particular peaks. We demonstrate the effectiveness of the tool through two case studies on the computed probabilistic landscape of a gene regulatory network and of a toggle-switch network. Domain expert feedback indicates that our visual approach can help biologists: 1) visualize probabilities of stable states, 2) explore the temporal probability distributions, and 3) discover small peaks in the probability landscape that have potential relation to specific diseases.

Fast randomization of large genomic datasets while preserving alteration counts.

PubMed

Gobbi, Andrea; Iorio, Francesco; Dawson, Kevin J; Wedge, David C; Tamborero, David; Alexandrov, Ludmil B; Lopez-Bigas, Nuria; Garnett, Mathew J; Jurman, Giuseppe; Saez-Rodriguez, Julio

2014-09-01

Studying combinatorial patterns in cancer genomic datasets has recently emerged as a tool for identifying novel cancer driver networks. Approaches have been devised to quantify, for example, the tendency of a set of genes to be mutated in a 'mutually exclusive' manner. The significance of the proposed metrics is usually evaluated by computing P-values under appropriate null models. To this end, a Monte Carlo method (the switching-algorithm) is used to sample simulated datasets under a null model that preserves patient- and gene-wise mutation rates. In this method, a genomic dataset is represented as a bipartite network, to which Markov chain updates (switching-steps) are applied. These steps modify the network topology, and a minimal number of them must be executed to draw simulated datasets independently under the null model. This number has previously been deducted empirically to be a linear function of the total number of variants, making this process computationally expensive. We present a novel approximate lower bound for the number of switching-steps, derived analytically. Additionally, we have developed the R package BiRewire, including new efficient implementations of the switching-algorithm. We illustrate the performances of BiRewire by applying it to large real cancer genomics datasets. We report vast reductions in time requirement, with respect to existing implementations/bounds and equivalent P-value computations. Thus, we propose BiRewire to study statistical properties in genomic datasets, and other data that can be modeled as bipartite networks. BiRewire is available on BioConductor at http://www.bioconductor.org/packages/2.13/bioc/html/BiRewire.html. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Circuit-Host Coupling Induces Multifaceted Behavioral Modulations of a Gene Switch.

PubMed

Blanchard, Andrew E; Liao, Chen; Lu, Ting

2018-02-06

Quantitative modeling of gene circuits is fundamentally important to synthetic biology, as it offers the potential to transform circuit engineering from trial-and-error construction to rational design and, hence, facilitates the advance of the field. Currently, typical models regard gene circuits as isolated entities and focus only on the biochemical processes within the circuits. However, such a standard paradigm is getting challenged by increasing experimental evidence suggesting that circuits and their host are intimately connected, and their interactions can potentially impact circuit behaviors. Here we systematically examined the roles of circuit-host coupling in shaping circuit dynamics by using a self-activating gene switch as a model circuit. Through a combination of deterministic modeling, stochastic simulation, and Fokker-Planck equation formalism, we found that circuit-host coupling alters switch behaviors across multiple scales. At the single-cell level, it slows the switch dynamics in the high protein production regime and enlarges the difference between stable steady-state values. At the population level, it favors cells with low protein production through differential growth amplification. Together, the two-level coupling effects induce both quantitative and qualitative modulations of the switch, with the primary component of the effects determined by the circuit's architectural parameters. This study illustrates the complexity and importance of circuit-host coupling in modulating circuit behaviors, demonstrating the need for a new paradigm-integrated modeling of the circuit-host system-for quantitative understanding of engineered gene networks. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Eliminating fast reactions in stochastic simulations of biochemical networks: A bistable genetic switch

NASA Astrophysics Data System (ADS)

Morelli, Marco J.; Allen, Rosalind J.; Tǎnase-Nicola, Sorin; ten Wolde, Pieter Rein

2008-01-01

In many stochastic simulations of biochemical reaction networks, it is desirable to "coarse grain" the reaction set, removing fast reactions while retaining the correct system dynamics. Various coarse-graining methods have been proposed, but it remains unclear which methods are reliable and which reactions can safely be eliminated. We address these issues for a model gene regulatory network that is particularly sensitive to dynamical fluctuations: a bistable genetic switch. We remove protein-DNA and/or protein-protein association-dissociation reactions from the reaction set using various coarse-graining strategies. We determine the effects on the steady-state probability distribution function and on the rate of fluctuation-driven switch flipping transitions. We find that protein-protein interactions may be safely eliminated from the reaction set, but protein-DNA interactions may not. We also find that it is important to use the chemical master equation rather than macroscopic rate equations to compute effective propensity functions for the coarse-grained reactions.

Switch-connected HyperX network

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Dong; Heidelberger, Philip

A network system includes a plurality of sub-network planes and global switches. The sub-network planes have a same network topology as each other. Each of the sub-network planes includes edge switches. Each of the edge switches has N ports. Each of the global switches is configured to connect a group of edge switches at a same location in the sub-network planes. In each of the sub-network planes, some of the N ports of each of the edge switches are connected to end nodes, and others of the N ports are connected to other edge switches in the same sub-network plane,more » other of the N ports are connected to at least one of the global switches.« less

How to turn a genetic circuit into a synthetic tunable oscillator, or a bistable switch.

PubMed

Marucci, Lucia; Barton, David A W; Cantone, Irene; Ricci, Maria Aurelia; Cosma, Maria Pia; Santini, Stefania; di Bernardo, Diego; di Bernardo, Mario

2009-12-07

Systems and Synthetic Biology use computational models of biological pathways in order to study in silico the behaviour of biological pathways. Mathematical models allow to verify biological hypotheses and to predict new possible dynamical behaviours. Here we use the tools of non-linear analysis to understand how to change the dynamics of the genes composing a novel synthetic network recently constructed in the yeast Saccharomyces cerevisiae for In-vivo Reverse-engineering and Modelling Assessment (IRMA). Guided by previous theoretical results that make the dynamics of a biological network depend on its topological properties, through the use of simulation and continuation techniques, we found that the network can be easily turned into a robust and tunable synthetic oscillator or a bistable switch. Our results provide guidelines to properly re-engineering in vivo the network in order to tune its dynamics.

Programmable cells: Interfacing natural and engineered gene networks

NASA Astrophysics Data System (ADS)

Kobayashi, Hideki; Kærn, Mads; Araki, Michihiro; Chung, Kristy; Gardner, Timothy S.; Cantor, Charles R.; Collins, James J.

2004-06-01

Novel cellular behaviors and characteristics can be obtained by coupling engineered gene networks to the cell's natural regulatory circuitry through appropriately designed input and output interfaces. Here, we demonstrate how an engineered genetic circuit can be used to construct cells that respond to biological signals in a predetermined and programmable fashion. We employ a modular design strategy to create Escherichia coli strains where a genetic toggle switch is interfaced with: (i) the SOS signaling pathway responding to DNA damage, and (ii) a transgenic quorum sensing signaling pathway from Vibrio fischeri. The genetic toggle switch endows these strains with binary response dynamics and an epigenetic inheritance that supports a persistent phenotypic alteration in response to transient signals. These features are exploited to engineer cells that form biofilms in response to DNA-damaging agents and cells that activate protein synthesis when the cell population reaches a critical density. Our work represents a step toward the development of "plug-and-play" genetic circuitry that can be used to create cells with programmable behaviors. heterologous gene expression | synthetic biology | Escherichia coli

Paper-based Synthetic Gene Networks

PubMed Central

Pardee, Keith; Green, Alexander A.; Ferrante, Tom; Cameron, D. Ewen; DaleyKeyser, Ajay; Yin, Peng; Collins, James J.

2014-01-01

Synthetic gene networks have wide-ranging uses in reprogramming and rewiring organisms. To date, there has not been a way to harness the vast potential of these networks beyond the constraints of a laboratory or in vivo environment. Here, we present an in vitro paper-based platform that provides a new venue for synthetic biologists to operate, and a much-needed medium for the safe deployment of engineered gene circuits beyond the lab. Commercially available cell-free systems are freeze-dried onto paper, enabling the inexpensive, sterile and abiotic distribution of synthetic biology-based technologies for the clinic, global health, industry, research and education. For field use, we create circuits with colorimetric outputs for detection by eye, and fabricate a low-cost, electronic optical interface. We demonstrate this technology with small molecule and RNA actuation of genetic switches, rapid prototyping of complex gene circuits, and programmable in vitro diagnostics, including glucose sensors and strain-specific Ebola virus sensors. PMID:25417167

Paper-based synthetic gene networks.

PubMed

Pardee, Keith; Green, Alexander A; Ferrante, Tom; Cameron, D Ewen; DaleyKeyser, Ajay; Yin, Peng; Collins, James J

2014-11-06

Synthetic gene networks have wide-ranging uses in reprogramming and rewiring organisms. To date, there has not been a way to harness the vast potential of these networks beyond the constraints of a laboratory or in vivo environment. Here, we present an in vitro paper-based platform that provides an alternate, versatile venue for synthetic biologists to operate and a much-needed medium for the safe deployment of engineered gene circuits beyond the lab. Commercially available cell-free systems are freeze dried onto paper, enabling the inexpensive, sterile, and abiotic distribution of synthetic-biology-based technologies for the clinic, global health, industry, research, and education. For field use, we create circuits with colorimetric outputs for detection by eye and fabricate a low-cost, electronic optical interface. We demonstrate this technology with small-molecule and RNA actuation of genetic switches, rapid prototyping of complex gene circuits, and programmable in vitro diagnostics, including glucose sensors and strain-specific Ebola virus sensors.

Criticality Is an Emergent Property of Genetic Networks that Exhibit Evolvability

PubMed Central

Torres-Sosa, Christian; Huang, Sui; Aldana, Maximino

2012-01-01

Accumulating experimental evidence suggests that the gene regulatory networks of living organisms operate in the critical phase, namely, at the transition between ordered and chaotic dynamics. Such critical dynamics of the network permits the coexistence of robustness and flexibility which are necessary to ensure homeostatic stability (of a given phenotype) while allowing for switching between multiple phenotypes (network states) as occurs in development and in response to environmental change. However, the mechanisms through which genetic networks evolve such critical behavior have remained elusive. Here we present an evolutionary model in which criticality naturally emerges from the need to balance between the two essential components of evolvability: phenotype conservation and phenotype innovation under mutations. We simulated the Darwinian evolution of random Boolean networks that mutate gene regulatory interactions and grow by gene duplication. The mutating networks were subjected to selection for networks that both (i) preserve all the already acquired phenotypes (dynamical attractor states) and (ii) generate new ones. Our results show that this interplay between extending the phenotypic landscape (innovation) while conserving the existing phenotypes (conservation) suffices to cause the evolution of all the networks in a population towards criticality. Furthermore, the networks produced by this evolutionary process exhibit structures with hubs (global regulators) similar to the observed topology of real gene regulatory networks. Thus, dynamical criticality and certain elementary topological properties of gene regulatory networks can emerge as a byproduct of the evolvability of the phenotypic landscape. PMID:22969419

Shape-dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks

NASA Technical Reports Server (NTRS)

Huang, S.; Ingber, D. E.

2000-01-01

Development of characteristic tissue patterns requires that individual cells be switched locally between different phenotypes or "fates;" while one cell may proliferate, its neighbors may differentiate or die. Recent studies have revealed that local switching between these different gene programs is controlled through interplay between soluble growth factors, insoluble extracellular matrix molecules, and mechanical forces which produce cell shape distortion. Although the precise molecular basis remains unknown, shape-dependent control of cell growth and function appears to be mediated by tension-dependent changes in the actin cytoskeleton. However, the question remains: how can a generalized physical stimulus, such as cell distortion, activate the same set of genes and signaling proteins that are triggered by molecules which bind to specific cell surface receptors. In this article, we use computer simulations based on dynamic Boolean networks to show that the different cell fates that a particular cell can exhibit may represent a preprogrammed set of common end programs or "attractors" which self-organize within the cell's regulatory networks. In this type of dynamic network model of information processing, generalized stimuli (e.g., mechanical forces) and specific molecular cues elicit signals which follow different trajectories, but eventually converge onto one of a small set of common end programs (growth, quiescence, differentiation, apoptosis, etc.). In other words, if cells use this type of information processing system, then control of cell function would involve selection of preexisting (latent) behavioral modes of the cell, rather than instruction by specific binding molecules. Importantly, the results of the computer simulation closely mimic experimental data obtained with living endothelial cells. The major implication of this finding is that current methods used for analysis of cell function that rely on characterization of linear signaling pathways or clusters of genes with common activity profiles may overlook the most critical features of cellular information processing which normally determine how signal specificity is established and maintained in living cells. Copyright 2000 Academic Press.

Software-defined networking control plane for seamless integration of multiple silicon photonic switches in Datacom networks.

PubMed

Shen, Yiwen; Hattink, Maarten H N; Samadi, Payman; Cheng, Qixiang; Hu, Ziyiz; Gazman, Alexander; Bergman, Keren

2018-04-16

Silicon photonics based switches offer an effective option for the delivery of dynamic bandwidth for future large-scale Datacom systems while maintaining scalable energy efficiency. The integration of a silicon photonics-based optical switching fabric within electronic Datacom architectures requires novel network topologies and arbitration strategies to effectively manage the active elements in the network. We present a scalable software-defined networking control plane to integrate silicon photonic based switches with conventional Ethernet or InfiniBand networks. Our software-defined control plane manages both electronic packet switches and multiple silicon photonic switches for simultaneous packet and circuit switching. We built an experimental Dragonfly network testbed with 16 electronic packet switches and 2 silicon photonic switches to evaluate our control plane. Observed latencies occupied by each step of the switching procedure demonstrate a total of 344 µs control plane latency for data-center and high performance computing platforms.

Reconstructing the regulatory circuit of cell fate determination in yeast mating response.

PubMed

Shao, Bin; Yuan, Haiyu; Zhang, Rongfei; Wang, Xuan; Zhang, Shuwen; Ouyang, Qi; Hao, Nan; Luo, Chunxiong

2017-07-01

Massive technological advances enabled high-throughput measurements of proteomic changes in biological processes. However, retrieving biological insights from large-scale protein dynamics data remains a challenging task. Here we used the mating differentiation in yeast Saccharomyces cerevisiae as a model and developed integrated experimental and computational approaches to analyze the proteomic dynamics during the process of cell fate determination. When exposed to a high dose of mating pheromone, the yeast cell undergoes growth arrest and forms a shmoo-like morphology; however, at intermediate doses, chemotropic elongated growth is initialized. To understand the gene regulatory networks that control this differentiation switch, we employed a high-throughput microfluidic imaging system that allows real-time and simultaneous measurements of cell growth and protein expression. Using kinetic modeling of protein dynamics, we classified the stimulus-dependent changes in protein abundance into two sources: global changes due to physiological alterations and gene-specific changes. A quantitative framework was proposed to decouple gene-specific regulatory modes from the growth-dependent global modulation of protein abundance. Based on the temporal patterns of gene-specific regulation, we established the network architectures underlying distinct cell fates using a reverse engineering method and uncovered the dose-dependent rewiring of gene regulatory network during mating differentiation. Furthermore, our results suggested a potential crosstalk between the pheromone response pathway and the target of rapamycin (TOR)-regulated ribosomal biogenesis pathway, which might underlie a cell differentiation switch in yeast mating response. In summary, our modeling approach addresses the distinct impacts of the global and gene-specific regulation on the control of protein dynamics and provides new insights into the mechanisms of cell fate determination. We anticipate that our integrated experimental and modeling strategies could be widely applicable to other biological systems.

Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters.

PubMed

Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo

2005-02-01

cis-Acting regulatory elements are important molecular switches involved in the transcriptional regulation of a dynamic network of gene activities controlling various biological processes, including abiotic stress responses, hormone responses and developmental processes. In particular, understanding regulatory gene networks in stress response cascades depends on successful functional analyses of cis-acting elements. The ever-improving accuracy of transcriptome expression profiling has led to the identification of various combinations of cis-acting elements in the promoter regions of stress-inducible genes involved in stress and hormone responses. Here we discuss major cis-acting elements, such as the ABA-responsive element (ABRE) and the dehydration-responsive element/C-repeat (DRE/CRT), that are a vital part of ABA-dependent and ABA-independent gene expression in osmotic and cold stress responses.

Analysis of the SWI/SNF chromatin-remodeling complex during early heart development and BAF250a repression cardiac gene transcription during P19 cell differentiation

PubMed Central

Singh, Ajeet Pratap; Archer, Trevor K.

2014-01-01

The regulatory networks of differentiation programs and the molecular mechanisms of lineage-specific gene regulation in mammalian embryos remain only partially defined. We document differential expression and temporal switching of BRG1-associated factor (BAF) subunits, core pluripotency factors and cardiac-specific genes during post-implantation development and subsequent early organogenesis. Using affinity purification of BRG1 ATPase coupled to mass spectrometry, we characterized the cardiac-enriched remodeling complexes present in E8.5 mouse embryos. The relative abundance and combinatorial assembly of the BAF subunits provides functional specificity to Switch/Sucrose NonFermentable (SWI/SNF) complexes resulting in a unique gene expression profile in the developing heart. Remarkably, the specific depletion of the BAF250a subunit demonstrated differential effects on cardiac-specific gene expression and resulted in arrhythmic contracting cardiomyocytes in vitro. Indeed, the BAF250a physically interacts and functionally cooperates with Nucleosome Remodeling and Histone Deacetylase (NURD) complex subunits to repressively regulate chromatin structure of the cardiac genes by switching open and poised chromatin marks associated with active and repressed gene expression. Finally, BAF250a expression modulates BRG1 occupancy at the loci of cardiac genes regulatory regions in P19 cell differentiation. These findings reveal specialized and novel cardiac-enriched SWI/SNF chromatin-remodeling complexes, which are required for heart formation and critical for cardiac gene expression regulation at the early stages of heart development. PMID:24335282

Derivation of large-scale cellular regulatory networks from biological time series data.

PubMed

de Bivort, Benjamin L

2010-01-01

Pharmacological agents and other perturbants of cellular homeostasis appear to nearly universally affect the activity of many genes, proteins, and signaling pathways. While this is due in part to nonspecificity of action of the drug or cellular stress, the large-scale self-regulatory behavior of the cell may also be responsible, as this typically means that when a cell switches states, dozens or hundreds of genes will respond in concert. If many genes act collectively in the cell during state transitions, rather than every gene acting independently, models of the cell can be created that are comprehensive of the action of all genes, using existing data, provided that the functional units in the model are collections of genes. Techniques to develop these large-scale cellular-level models are provided in detail, along with methods of analyzing them, and a brief summary of major conclusions about large-scale cellular networks to date.

Global dynamics for switching systems and their extensions by linear differential equations

NASA Astrophysics Data System (ADS)

Huttinga, Zane; Cummins, Bree; Gedeon, Tomáš; Mischaikow, Konstantin

2018-03-01

Switching systems use piecewise constant nonlinearities to model gene regulatory networks. This choice provides advantages in the analysis of behavior and allows the global description of dynamics in terms of Morse graphs associated to nodes of a parameter graph. The parameter graph captures spatial characteristics of a decomposition of parameter space into domains with identical Morse graphs. However, there are many cellular processes that do not exhibit threshold-like behavior and thus are not well described by a switching system. We consider a class of extensions of switching systems formed by a mixture of switching interactions and chains of variables governed by linear differential equations. We show that the parameter graphs associated to the switching system and any of its extensions are identical. For each parameter graph node, there is an order-preserving map from the Morse graph of the switching system to the Morse graph of any of its extensions. We provide counterexamples that show why possible stronger relationships between the Morse graphs are not valid.

Global dynamics for switching systems and their extensions by linear differential equations.

PubMed

Huttinga, Zane; Cummins, Bree; Gedeon, Tomáš; Mischaikow, Konstantin

2018-03-15

Switching systems use piecewise constant nonlinearities to model gene regulatory networks. This choice provides advantages in the analysis of behavior and allows the global description of dynamics in terms of Morse graphs associated to nodes of a parameter graph. The parameter graph captures spatial characteristics of a decomposition of parameter space into domains with identical Morse graphs. However, there are many cellular processes that do not exhibit threshold-like behavior and thus are not well described by a switching system. We consider a class of extensions of switching systems formed by a mixture of switching interactions and chains of variables governed by linear differential equations. We show that the parameter graphs associated to the switching system and any of its extensions are identical. For each parameter graph node, there is an order-preserving map from the Morse graph of the switching system to the Morse graph of any of its extensions. We provide counterexamples that show why possible stronger relationships between the Morse graphs are not valid.

Back to the biology in systems biology: what can we learn from biomolecular networks?

PubMed

Huang, Sui

2004-02-01

Genome-scale molecular networks, including protein interaction and gene regulatory networks, have taken centre stage in the investigation of the burgeoning disciplines of systems biology and biocomplexity. What do networks tell us? Some see in networks simply the comprehensive, detailed description of all cellular pathways, others seek in networks simple, higher-order qualities that emerge from the collective action of the individual pathways. This paper discusses networks from an encompassing category of thinking that will hopefully help readers to bridge the gap between these polarised viewpoints. Systems biology so far has emphasised the characterisation of large pathway maps. Now one has to ask: where is the actual biology in 'systems biology'? As structures midway between genome and phenome, and by serving as an 'extended genotype' or an 'elementary phenotype', molecular networks open a new window to the study of evolution and gene function in complex living systems. For the study of evolution, features in network topology offer a novel starting point for addressing the old debate on the relative contributions of natural selection versus intrinsic constraints to a particular trait. To study the function of genes, it is necessary not only to see them in the context of gene networks, but also to reach beyond describing network topology and to embrace the global dynamics of networks that will reveal higher-order, collective behaviour of the interacting genes. This will pave the way to understanding how the complexity of genome-wide molecular networks collapses to produce a robust whole-cell behaviour that manifests as tightly-regulated switching between distinct cell fates - the basis for multicellular life.

Tuning stochastic transition rates in a bistable genetic network.

NASA Astrophysics Data System (ADS)

Chickarmane, Vijay; Peterson, Carsten

2009-03-01

We investigate the stochastic dynamics of a simple genetic network, a toggle switch, in which the system makes transitions between the two alternative states. Our interest is in exploring whether such stochastic transitions, which occur due to the intrinsic noise such as transcriptional and degradation events, can be slowed down/speeded up, without changing the mean expression levels of the two genes, which comprise the toggle network. Such tuning is achieved by linking a signaling network to the toggle switch. The signaling network comprises of a protein, which can exist either in an active (phosphorylated) or inactive (dephosphorylated) form, and where its state is determined by one of the genetic network components. The active form of the protein in turn feeds back on the dynamics of the genetic network. We find that the rate of stochastic transitions from one state to the other, is determined essentially by the speed of phosphorylation, and hence the rate can be modulated by varying the phosphatase levels. We hypothesize that such a network architecture can be implemented as a general mechanism for controlling transition rates and discuss applications in population studies of two differentiated cell lineages, ex: the myeloid/erythroid lineage in hematopoiesis.

Bistable switch in let-7 miRNA biogenesis pathway involving Lin28.

PubMed

Shi, Fei; Yu, Wenbao; Wang, Xia

2014-10-21

miRNAs are small noncoding RNAs capable of regulating gene expression at the post-transcriptional level. A growing body of evidence demonstrated that let-7 family of miRNAs, as one of the highly conserved miRNAs, plays an important role in cell differentiation and development, as well as tumor suppressor function depending on their levels of expression. To explore the physiological significance of let-7 in regulating cell fate decisions, we present a coarse grained model of let-7 biogenesis network, in which let-7 and its regulator Lin28 inhibit mutually. The dynamics of this minimal network architecture indicates that, as the concentration of Lin28 increases, the system undergoes a transition from monostability to a bistability and then to a one-way switch with increasing strength of positive feedback of let-7, while in the absence of Lin28 inhibition, the system loses bistability. Moreover, the ratio of degradation rates of let-7 and Lin28 is critical for the switching sensitivity and resistance to stimulus fluctuations. These findings may highlight why let-7 is required for normal gene expression in the context of embryonic development and oncogenesis, which will facilitate the development of approaches to exploit this regulatory pathway by manipulating Lin28/let-7 axis for novel treatments of human diseases.

Coactivation of cognitive control networks during task switching.

PubMed

Yin, Shouhang; Deák, Gedeon; Chen, Antao

2018-01-01

The ability to flexibly switch between tasks is considered an important component of cognitive control that involves frontal and parietal cortical areas. The present study was designed to characterize network dynamics across multiple brain regions during task switching. Functional magnetic resonance images (fMRI) were captured during a standard rule-switching task to identify switching-related brain regions. Multiregional psychophysiological interaction (PPI) analysis was used to examine effective connectivity between these regions. During switching trials, behavioral performance declined and activation of a generic cognitive control network increased. Concurrently, task-related connectivity increased within and between cingulo-opercular and fronto-parietal cognitive control networks. Notably, the left inferior frontal junction (IFJ) was most consistently coactivated with the 2 cognitive control networks. Furthermore, switching-dependent effective connectivity was negatively correlated with behavioral switch costs. The strength of effective connectivity between left IFJ and other regions in the networks predicted individual differences in switch costs. Task switching was supported by coactivated connections within cognitive control networks, with left IFJ potentially acting as a key hub between the fronto-parietal and cingulo-opercular networks. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Integrating mitosis, toxicity, and transgene expression in a telecommunications packet-switched network model of lipoplex-mediated gene delivery.

PubMed

Martin, Timothy M; Wysocki, Beata J; Beyersdorf, Jared P; Wysocki, Tadeusz A; Pannier, Angela K

2014-08-01

Gene delivery systems transport exogenous genetic information to cells or biological systems with the potential to directly alter endogenous gene expression and behavior with applications in functional genomics, tissue engineering, medical devices, and gene therapy. Nonviral systems offer advantages over viral systems because of their low immunogenicity, inexpensive synthesis, and easy modification but suffer from lower transfection levels. The representation of gene transfer using models offers perspective and interpretation of complex cellular mechanisms,including nonviral gene delivery where exact mechanisms are unknown. Here, we introduce a novel telecommunications model of the nonviral gene delivery process in which the delivery of the gene to a cell is synonymous with delivery of a packet of information to a destination computer within a packet-switched computer network. Such a model uses nodes and layers to simplify the complexity of modeling the transfection process and to overcome several challenges of existing models. These challenges include a limited scope and limited time frame, which often does not incorporate biological effects known to affect transfection. The telecommunication model was constructed in MATLAB to model lipoplex delivery of the gene encoding the green fluorescent protein to HeLa cells. Mitosis and toxicity events were included in the model resulting in simulation outputs of nuclear internalization and transfection efficiency that correlated with experimental data. A priori predictions based on model sensitivity analysis suggest that increasing endosomal escape and decreasing lysosomal degradation, protein degradation, and GFP-induced toxicity can improve transfection efficiency by three-fold. Application of the telecommunications model to nonviral gene delivery offers insight into the development of new gene delivery systems with therapeutically relevant transfection levels.

Software Defined Networking (SDN) controlled all optical switching networks with multi-dimensional switching architecture

NASA Astrophysics Data System (ADS)

Zhao, Yongli; Ji, Yuefeng; Zhang, Jie; Li, Hui; Xiong, Qianjin; Qiu, Shaofeng

2014-08-01

Ultrahigh throughout capacity requirement is challenging the current optical switching nodes with the fast development of data center networks. Pbit/s level all optical switching networks need to be deployed soon, which will cause the high complexity of node architecture. How to control the future network and node equipment together will become a new problem. An enhanced Software Defined Networking (eSDN) control architecture is proposed in the paper, which consists of Provider NOX (P-NOX) and Node NOX (N-NOX). With the cooperation of P-NOX and N-NOX, the flexible control of the entire network can be achieved. All optical switching network testbed has been experimentally demonstrated with efficient control of enhanced Software Defined Networking (eSDN). Pbit/s level all optical switching nodes in the testbed are implemented based on multi-dimensional switching architecture, i.e. multi-level and multi-planar. Due to the space and cost limitation, each optical switching node is only equipped with four input line boxes and four output line boxes respectively. Experimental results are given to verify the performance of our proposed control and switching architecture.

Predicting effects of structural stress in a genome-reduced model bacterial metabolism

NASA Astrophysics Data System (ADS)

Güell, Oriol; Sagués, Francesc; Serrano, M. Ángeles

2012-08-01

Mycoplasma pneumoniae is a human pathogen recently proposed as a genome-reduced model for bacterial systems biology. Here, we study the response of its metabolic network to different forms of structural stress, including removal of individual and pairs of reactions and knockout of genes and clusters of co-expressed genes. Our results reveal a network architecture as robust as that of other model bacteria regarding multiple failures, although less robust against individual reaction inactivation. Interestingly, metabolite motifs associated to reactions can predict the propagation of inactivation cascades and damage amplification effects arising in double knockouts. We also detect a significant correlation between gene essentiality and damages produced by single gene knockouts, and find that genes controlling high-damage reactions tend to be expressed independently of each other, a functional switch mechanism that, simultaneously, acts as a genetic firewall to protect metabolism. Prediction of failure propagation is crucial for metabolic engineering or disease treatment.

An Arabidopsis Gene Regulatory Network for Secondary Cell Wall Synthesis

PubMed Central

Taylor-Teeples, M; Lin, L; de Lucas, M; Turco, G; Toal, TW; Gaudinier, A; Young, NF; Trabucco, GM; Veling, MT; Lamothe, R; Handakumbura, PP; Xiong, G; Wang, C; Corwin, J; Tsoukalas, A; Zhang, L; Ware, D; Pauly, M; Kliebenstein, DJ; Dehesh, K; Tagkopoulos, I; Breton, G; Pruneda-Paz, JL; Ahnert, SE; Kay, SA; Hazen, SP; Brady, SM

2014-01-01

Summary The plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and vital to cell function. A regulatory hierarchy of developmental switches has been proposed, although the full complement of regulators remains unknown. Here, we present a protein-DNA network between Arabidopsis transcription factors and secondary cell wall metabolic genes with gene expression regulated by a series of feed-forward loops. This model allowed us to develop and validate new hypotheses about secondary wall gene regulation under abiotic stress. Distinct stresses are able to perturb targeted genes to potentially promote functional adaptation. These interactions will serve as a foundation for understanding the regulation of a complex, integral plant component. PMID:25533953

A programmable synthetic lineage-control network that differentiates human IPSCs into glucose-sensitive insulin-secreting beta-like cells

PubMed Central

Saxena, Pratik; Heng, Boon Chin; Bai, Peng; Folcher, Marc; Zulewski, Henryk; Fussenegger, Martin

2016-01-01

Synthetic biology has advanced the design of standardized transcription control devices that programme cellular behaviour. By coupling synthetic signalling cascade- and transcription factor-based gene switches with reverse and differential sensitivity to the licensed food additive vanillic acid, we designed a synthetic lineage-control network combining vanillic acid-triggered mutually exclusive expression switches for the transcription factors Ngn3 (neurogenin 3; OFF-ON-OFF) and Pdx1 (pancreatic and duodenal homeobox 1; ON-OFF-ON) with the concomitant induction of MafA (V-maf musculoaponeurotic fibrosarcoma oncogene homologue A; OFF-ON). This designer network consisting of different network topologies orchestrating the timely control of transgenic and genomic Ngn3, Pdx1 and MafA variants is able to programme human induced pluripotent stem cells (hIPSCs)-derived pancreatic progenitor cells into glucose-sensitive insulin-secreting beta-like cells, whose glucose-stimulated insulin-release dynamics are comparable to human pancreatic islets. Synthetic lineage-control networks may provide the missing link to genetically programme somatic cells into autologous cell phenotypes for regenerative medicine. PMID:27063289

Software-defined networking control plane for seamless integration of multiple silicon photonic switches in Datacom networks

DOE PAGES

Shen, Yiwen; Hattink, Maarten; Samadi, Payman; ...

2018-04-13

Silicon photonics based switches offer an effective option for the delivery of dynamic bandwidth for future large-scale Datacom systems while maintaining scalable energy efficiency. The integration of a silicon photonics-based optical switching fabric within electronic Datacom architectures requires novel network topologies and arbitration strategies to effectively manage the active elements in the network. Here, we present a scalable software-defined networking control plane to integrate silicon photonic based switches with conventional Ethernet or InfiniBand networks. Our software-defined control plane manages both electronic packet switches and multiple silicon photonic switches for simultaneous packet and circuit switching. We built an experimental Dragonfly networkmore » testbed with 16 electronic packet switches and 2 silicon photonic switches to evaluate our control plane. Observed latencies occupied by each step of the switching procedure demonstrate a total of 344 microsecond control plane latency for data-center and high performance computing platforms.« less

Software-defined networking control plane for seamless integration of multiple silicon photonic switches in Datacom networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shen, Yiwen; Hattink, Maarten; Samadi, Payman

Silicon photonics based switches offer an effective option for the delivery of dynamic bandwidth for future large-scale Datacom systems while maintaining scalable energy efficiency. The integration of a silicon photonics-based optical switching fabric within electronic Datacom architectures requires novel network topologies and arbitration strategies to effectively manage the active elements in the network. Here, we present a scalable software-defined networking control plane to integrate silicon photonic based switches with conventional Ethernet or InfiniBand networks. Our software-defined control plane manages both electronic packet switches and multiple silicon photonic switches for simultaneous packet and circuit switching. We built an experimental Dragonfly networkmore » testbed with 16 electronic packet switches and 2 silicon photonic switches to evaluate our control plane. Observed latencies occupied by each step of the switching procedure demonstrate a total of 344 microsecond control plane latency for data-center and high performance computing platforms.« less

Maximal switchability of centralized networks

NASA Astrophysics Data System (ADS)

Vakulenko, Sergei; Morozov, Ivan; Radulescu, Ovidiu

2016-08-01

We consider continuous time Hopfield-like recurrent networks as dynamical models for gene regulation and neural networks. We are interested in networks that contain n high-degree nodes preferably connected to a large number of N s weakly connected satellites, a property that we call n/N s -centrality. If the hub dynamics is slow, we obtain that the large time network dynamics is completely defined by the hub dynamics. Moreover, such networks are maximally flexible and switchable, in the sense that they can switch from a globally attractive rest state to any structurally stable dynamics when the response time of a special controller hub is changed. In particular, we show that a decrease of the controller hub response time can lead to a sharp variation in the network attractor structure: we can obtain a set of new local attractors, whose number can increase exponentially with N, the total number of nodes of the nework. These new attractors can be periodic or even chaotic. We provide an algorithm, which allows us to design networks with the desired switching properties, or to learn them from time series, by adjusting the interactions between hubs and satellites. Such switchable networks could be used as models for context dependent adaptation in functional genetics or as models for cognitive functions in neuroscience.

Bistability in a Metabolic Network Underpins the De Novo Evolution of Colony Switching in Pseudomonas fluorescens

PubMed Central

Gallie, Jenna; Libby, Eric; Bertels, Frederic; Remigi, Philippe; Jendresen, Christian B.; Ferguson, Gayle C.; Desprat, Nicolas; Buffing, Marieke F.; Sauer, Uwe; Beaumont, Hubertus J. E.; Martinussen, Jan; Kilstrup, Mogens; Rainey, Paul B.

2015-01-01

Phenotype switching is commonly observed in nature. This prevalence has allowed the elucidation of a number of underlying molecular mechanisms. However, little is known about how phenotypic switches arise and function in their early evolutionary stages. The first opportunity to provide empirical insight was delivered by an experiment in which populations of the bacterium Pseudomonas fluorescens SBW25 evolved, de novo, the ability to switch between two colony phenotypes. Here we unravel the molecular mechanism behind colony switching, revealing how a single nucleotide change in a gene enmeshed in central metabolism (carB) generates such a striking phenotype. We show that colony switching is underpinned by ON/OFF expression of capsules consisting of a colanic acid-like polymer. We use molecular genetics, biochemical analyses, and experimental evolution to establish that capsule switching results from perturbation of the pyrimidine biosynthetic pathway. Of central importance is a bifurcation point at which uracil triphosphate is partitioned towards either nucleotide metabolism or polymer production. This bifurcation marks a cell-fate decision point whereby cells with relatively high pyrimidine levels favour nucleotide metabolism (capsule OFF), while cells with lower pyrimidine levels divert resources towards polymer biosynthesis (capsule ON). This decision point is present and functional in the wild-type strain. Finally, we present a simple mathematical model demonstrating that the molecular components of the decision point are capable of producing switching. Despite its simple mutational cause, the connection between genotype and phenotype is complex and multidimensional, offering a rare glimpse of how noise in regulatory networks can provide opportunity for evolution. PMID:25763575

Design framework for entanglement-distribution switching networks

NASA Astrophysics Data System (ADS)

Drost, Robert J.; Brodsky, Michael

2016-09-01

The distribution of quantum entanglement appears to be an important component of applications of quantum communications and networks. The ability to centralize the sourcing of entanglement in a quantum network can provide for improved efficiency and enable a variety of network structures. A necessary feature of an entanglement-sourcing network node comprising several sources of entangled photons is the ability to reconfigurably route the generated pairs of photons to network neighbors depending on the desired entanglement sharing of the network users at a given time. One approach to such routing is the use of a photonic switching network. The requirements for an entanglement distribution switching network are less restrictive than for typical conventional applications, leading to design freedom that can be leveraged to optimize additional criteria. In this paper, we present a mathematical framework defining the requirements of an entanglement-distribution switching network. We then consider the design of such a switching network using a number of 2 × 2 crossbar switches, addressing the interconnection of these switches and efficient routing algorithms. In particular, we define a worst-case loss metric and consider 6 × 6, 8 × 8, and 10 × 10 network designs that optimize both this metric and the number of crossbar switches composing the network. We pay particular attention to the 10 × 10 network, detailing novel results proving the optimality of the proposed design. These optimized network designs have great potential for use in practical quantum networks, thus advancing the concept of quantum networks toward reality.

Antagonistic control of a dual-input mammalian gene switch by food additives.

PubMed

Xie, Mingqi; Ye, Haifeng; Hamri, Ghislaine Charpin-El; Fussenegger, Martin

2014-08-01

Synthetic biology has significantly advanced the design of mammalian trigger-inducible transgene-control devices that are able to programme complex cellular behaviour. Fruit-based benzoate derivatives licensed as food additives, such as flavours (e.g. vanillate) and preservatives (e.g. benzoate), are a particularly attractive class of trigger compounds for orthogonal mammalian transgene control devices because of their innocuousness, physiological compatibility and simple oral administration. Capitalizing on the genetic componentry of the soil bacterium Comamonas testosteroni, which has evolved to catabolize a variety of aromatic compounds, we have designed different mammalian gene expression systems that could be induced and repressed by the food additives benzoate and vanillate. When implanting designer cells engineered for gene switch-driven expression of the human placental secreted alkaline phosphatase (SEAP) into mice, blood SEAP levels of treated animals directly correlated with a benzoate-enriched drinking programme. Additionally, the benzoate-/vanillate-responsive device was compatible with other transgene control systems and could be assembled into higher-order control networks providing expression dynamics reminiscent of a lap-timing stopwatch. Designer gene switches using licensed food additives as trigger compounds to achieve antagonistic dual-input expression profiles and provide novel control topologies and regulation dynamics may advance future gene- and cell-based therapies. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Network topology mapper

DOEpatents

Quist, Daniel A [Los Alamos, NM; Gavrilov, Eugene M [Los Alamos, NM; Fisk, Michael E [Jemez, NM

2008-01-15

A method enables the topology of an acyclic fully propagated network to be discovered. A list of switches that comprise the network is formed and the MAC address cache for each one of the switches is determined. For each pair of switches, from the MAC address caches the remaining switches that see the pair of switches are located. For each pair of switches the remaining switches are determined that see one of the pair of switches on a first port and the second one of the pair of switches on a second port. A list of insiders is formed for every pair of switches. It is determined whether the insider for each pair of switches is a graph edge and adjacent ones of the graph edges are determined. A symmetric adjacency matrix is formed from the graph edges to represent the topology of the data link network.

Genomics of sex determination.

PubMed

Zhang, Jisen; Boualem, Adnane; Bendahmane, Abdelhafid; Ming, Ray

2014-04-01

Sex determination is a major switch in the evolutionary history of angiosperm, resulting 11% monoecious and dioecious species. The genomic sequences of papaya sex chromosomes unveiled the molecular basis of recombination suppression in the sex determination region, and candidate genes for sex determination. Identification and analyses of sex determination genes in cucurbits and maize demonstrated conservation of sex determination mechanism in one lineage and divergence between the two systems. Epigenetic control and hormonal influence of sex determination were elucidated in both plants and animals. Intensive investigation of potential sex determination genes in model species will improve our understanding of sex determination gene network. Such network will in turn accelerate the identification of sex determination genes in dioecious species with sex chromosomes, which are burdensome due to no recombination in sex determining regions. The sex determination genes in dioecious species are crucial for understanding the origin of dioecy and sex chromosomes, particularly in their early stage of evolution. Copyright © 2014 Elsevier Ltd. All rights reserved.

Finite-time synchronization of uncertain coupled switched neural networks under asynchronous switching.

PubMed

Wu, Yuanyuan; Cao, Jinde; Li, Qingbo; Alsaedi, Ahmed; Alsaadi, Fuad E

2017-01-01

This paper deals with the finite-time synchronization problem for a class of uncertain coupled switched neural networks under asynchronous switching. By constructing appropriate Lyapunov-like functionals and using the average dwell time technique, some sufficient criteria are derived to guarantee the finite-time synchronization of considered uncertain coupled switched neural networks. Meanwhile, the asynchronous switching feedback controller is designed to finite-time synchronize the concerned networks. Finally, two numerical examples are introduced to show the validity of the main results. Copyright © 2016 Elsevier Ltd. All rights reserved.

Voltage control in pulsed system by predict-ahead control

DOEpatents

Payne, Anthony N.; Watson, James A.; Sampayan, Stephen E.

1994-01-01

A method and apparatus for predict-ahead pulse-to-pulse voltage control in a pulsed power supply system is disclosed. A DC power supply network is coupled to a resonant charging network via a first switch. The resonant charging network is coupled at a node to a storage capacitor. An output load is coupled to the storage capacitor via a second switch. A de-Q-ing network is coupled to the resonant charging network via a third switch. The trigger for the third switch is a derived function of the initial voltage of the power supply network, the initial voltage of the storage capacitor, and the present voltage of the storage capacitor. A first trigger closes the first switch and charges the capacitor. The third trigger is asserted according to the derived function to close the third switch. When the third switch is closed, the first switch opens and voltage on the node is regulated. The second trigger may be thereafter asserted to discharge the capacitor into the output load.

Voltage control in pulsed system by predict-ahead control

DOEpatents

Payne, A.N.; Watson, J.A.; Sampayan, S.E.

1994-09-13

A method and apparatus for predict-ahead pulse-to-pulse voltage control in a pulsed power supply system is disclosed. A DC power supply network is coupled to a resonant charging network via a first switch. The resonant charging network is coupled at a node to a storage capacitor. An output load is coupled to the storage capacitor via a second switch. A de-Q-ing network is coupled to the resonant charging network via a third switch. The trigger for the third switch is a derived function of the initial voltage of the power supply network, the initial voltage of the storage capacitor, and the present voltage of the storage capacitor. A first trigger closes the first switch and charges the capacitor. The third trigger is asserted according to the derived function to close the third switch. When the third switch is closed, the first switch opens and voltage on the node is regulated. The second trigger may be thereafter asserted to discharge the capacitor into the output load. 4 figs.

A Temperature-Responsive Network Links Cell Shape and Virulence Traits in a Primary Fungal Pathogen

PubMed Central

Beyhan, Sinem; Gutierrez, Matias; Voorhies, Mark; Sil, Anita

2013-01-01

Survival at host temperature is a critical trait for pathogenic microbes of humans. Thermally dimorphic fungal pathogens, including Histoplasma capsulatum, are soil fungi that undergo dramatic changes in cell shape and virulence gene expression in response to host temperature. How these organisms link changes in temperature to both morphologic development and expression of virulence traits is unknown. Here we elucidate a temperature-responsive transcriptional network in H. capsulatum, which switches from a filamentous form in the environment to a pathogenic yeast form at body temperature. The circuit is driven by three highly conserved factors, Ryp1, Ryp2, and Ryp3, that are required for yeast-phase growth at 37°C. Ryp factors belong to distinct families of proteins that control developmental transitions in fungi: Ryp1 is a member of the WOPR family of transcription factors, and Ryp2 and Ryp3 are both members of the Velvet family of proteins whose molecular function is unknown. Here we provide the first evidence that these WOPR and Velvet proteins interact, and that Velvet proteins associate with DNA to drive gene expression. Using genome-wide chromatin immunoprecipitation studies, we determine that Ryp1, Ryp2, and Ryp3 associate with a large common set of genomic loci that includes known virulence genes, indicating that the Ryp factors directly control genes required for pathogenicity in addition to their role in regulating cell morphology. We further dissect the Ryp regulatory circuit by determining that a fourth transcription factor, which we name Ryp4, is required for yeast-phase growth and gene expression, associates with DNA, and displays interdependent regulation with Ryp1, Ryp2, and Ryp3. Finally, we define cis-acting motifs that recruit the Ryp factors to their interwoven network of temperature-responsive target genes. Taken together, our results reveal a positive feedback circuit that directs a broad transcriptional switch between environmental and pathogenic states in response to temperature. PMID:23935449

Emergent adaptive behaviour of GRN-controlled simulated robots in a changing environment.

PubMed

Yao, Yao; Storme, Veronique; Marchal, Kathleen; Van de Peer, Yves

2016-01-01

We developed a bio-inspired robot controller combining an artificial genome with an agent-based control system. The genome encodes a gene regulatory network (GRN) that is switched on by environmental cues and, following the rules of transcriptional regulation, provides output signals to actuators. Whereas the genome represents the full encoding of the transcriptional network, the agent-based system mimics the active regulatory network and signal transduction system also present in naturally occurring biological systems. Using such a design that separates the static from the conditionally active part of the gene regulatory network contributes to a better general adaptive behaviour. Here, we have explored the potential of our platform with respect to the evolution of adaptive behaviour, such as preying when food becomes scarce, in a complex and changing environment and show through simulations of swarm robots in an A-life environment that evolution of collective behaviour likely can be attributed to bio-inspired evolutionary processes acting at different levels, from the gene and the genome to the individual robot and robot population.

Emergent adaptive behaviour of GRN-controlled simulated robots in a changing environment

PubMed Central

Yao, Yao; Storme, Veronique; Marchal, Kathleen

2016-01-01

We developed a bio-inspired robot controller combining an artificial genome with an agent-based control system. The genome encodes a gene regulatory network (GRN) that is switched on by environmental cues and, following the rules of transcriptional regulation, provides output signals to actuators. Whereas the genome represents the full encoding of the transcriptional network, the agent-based system mimics the active regulatory network and signal transduction system also present in naturally occurring biological systems. Using such a design that separates the static from the conditionally active part of the gene regulatory network contributes to a better general adaptive behaviour. Here, we have explored the potential of our platform with respect to the evolution of adaptive behaviour, such as preying when food becomes scarce, in a complex and changing environment and show through simulations of swarm robots in an A-life environment that evolution of collective behaviour likely can be attributed to bio-inspired evolutionary processes acting at different levels, from the gene and the genome to the individual robot and robot population. PMID:28028477

Defense switched network technology and experiments program

NASA Astrophysics Data System (ADS)

Weinstein, C. J.

1983-09-01

This report documents work performed during FY 1983 on the DCA-sponsored Defense Switched Network Technology and Experiments Program. The areas of work reported are: (1) development of routing algorithms for application in the Defense Switched Network (DSN); (2) instrumentation and integration of the Experimental Integrated Switched Network (EISN) test facility; (3) development and test of data communication techniques using DoD-standard data protocols in an integrated voice/data network; and (4) EISN system coordination and experiment planning.

Neural network for control of rearrangeable Clos networks.

PubMed

Park, Y K; Cherkassky, V

1994-09-01

Rapid evolution in the field of communication networks requires high speed switching technologies. This involves a high degree of parallelism in switching control and routing performed at the hardware level. The multistage crossbar networks have always been attractive to switch designers. In this paper a neural network approach to controlling a three-stage Clos network in real time is proposed. This controller provides optimal routing of communication traffic requests on a call-by-call basis by rearranging existing connections, with a minimum length of rearrangement sequence so that a new blocked call request can be accommodated. The proposed neural network controller uses Paull's rearrangement algorithm, along with the special (least used) switch selection rule in order to minimize the length of rearrangement sequences. The functional behavior of our model is verified by simulations and it is shown that the convergence time required for finding an optimal solution is constant, regardless of the switching network size. The performance is evaluated for random traffic with various traffic loads. Simulation results show that applying the least used switch selection rule increases the efficiency in switch rearrangements, reducing the network convergence time. The implementation aspects are also discussed to show the feasibility of the proposed approach.

Dynamical predictors of an imminent phenotypic switch in bacteria

NASA Astrophysics Data System (ADS)

Wang, Huijing; Ray, J. Christian J.

2017-08-01

Single cells can stochastically switch across thresholds imposed by regulatory networks. Such thresholds can act as a tipping point, drastically changing global phenotypic states. In ecology and economics, imminent transitions across such tipping points can be predicted using dynamical early warning indicators. A typical example is ‘flickering’ of a fast variable, predicting a longer-lasting switch from a low to a high state or vice versa. Considering the different timescales between metabolite and protein fluctuations in bacteria, we hypothesized that metabolic early warning indicators predict imminent transitions across a network threshold caused by enzyme saturation. We used stochastic simulations to determine if flickering predicts phenotypic transitions, accounting for a variety of molecular physiological parameters, including enzyme affinity, burstiness of enzyme gene expression, homeostatic feedback, and rates of metabolic precursor influx. In most cases, we found that metabolic flickering rates are robustly peaked near the enzyme saturation threshold. The degree of fluctuation was amplified by product inhibition of the enzyme. We conclude that sensitivity to flickering in fast variables may be a possible natural or synthetic strategy to prepare physiological states for an imminent transition.

An Arabidopsis gene regulatory network for secondary cell wall synthesis

DOE PAGES

Taylor-Teeples, M.; Lin, L.; de Lucas, M.; ...

2014-12-24

The plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and vital to cell function. A regulatory hierarchy of developmental switches has been proposed, although the full complement of regulators remains unknown. In this paper, we present a protein–DNA network between Arabidopsis thaliana transcription factors and secondary cell wall metabolic genes with gene expression regulated bymore » a series of feed-forward loops. This model allowed us to develop and validate new hypotheses about secondary wall gene regulation under abiotic stress. Distinct stresses are able to perturb targeted genes to potentially promote functional adaptation. Finally, these interactions will serve as a foundation for understanding the regulation of a complex, integral plant component.« less

Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Faria, Jose P.; Overbeek, Ross; Taylor, Ronald C.

Here, we introduce a manually constructed and curated regulatory network model that describes the current state of knowledge of transcriptional regulation of B. subtilis. The model corresponds to an updated and enlarged version of the regulatory model of central metabolism originally proposed in 2008. We extended the original network to the whole genome by integration of information from DBTBS, a compendium of regulatory data that includes promoters, transcription factors (TFs), binding sites, motifs and regulated operons. Additionally, we consolidated our network with all the information on regulation included in the SporeWeb and Subtiwiki community-curated resources on B. subtilis. Finally, wemore » reconciled our network with data from RegPrecise, which recently released their own less comprehensive reconstruction of the regulatory network for B. subtilis. Our model describes 275 regulators and their target genes, representing 30 different mechanisms of regulation such as TFs, RNA switches, Riboswitches and small regulatory RNAs. Overall, regulatory information is included in the model for approximately 2500 of the ~4200 genes in B. subtilis 168. In an effort to further expand our knowledge of B. subtilis regulation, we reconciled our model with expression data. For this process, we reconstructed the Atomic Regulons (ARs) for B. subtilis, which are the sets of genes that share the same “ON” and “OFF” gene expression profiles across multiple samples of experimental data. We show how atomic regulons for B. subtilis are able to capture many sets of genes corresponding to regulated operons in our manually curated network. Additionally, we demonstrate how atomic regulons can be used to help expand or validate the knowledge of the regulatory networks by looking at highly correlated genes in the ARs for which regulatory information is lacking. During this process, we were also able to infer novel stimuli for hypothetical genes by exploring the genome expression metadata relating to experimental conditions, gaining insights into novel biology.« less

Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data

DOE PAGES

Faria, Jose P.; Overbeek, Ross; Taylor, Ronald C.; ...

2016-03-18

Here, we introduce a manually constructed and curated regulatory network model that describes the current state of knowledge of transcriptional regulation of B. subtilis. The model corresponds to an updated and enlarged version of the regulatory model of central metabolism originally proposed in 2008. We extended the original network to the whole genome by integration of information from DBTBS, a compendium of regulatory data that includes promoters, transcription factors (TFs), binding sites, motifs and regulated operons. Additionally, we consolidated our network with all the information on regulation included in the SporeWeb and Subtiwiki community-curated resources on B. subtilis. Finally, wemore » reconciled our network with data from RegPrecise, which recently released their own less comprehensive reconstruction of the regulatory network for B. subtilis. Our model describes 275 regulators and their target genes, representing 30 different mechanisms of regulation such as TFs, RNA switches, Riboswitches and small regulatory RNAs. Overall, regulatory information is included in the model for approximately 2500 of the ~4200 genes in B. subtilis 168. In an effort to further expand our knowledge of B. subtilis regulation, we reconciled our model with expression data. For this process, we reconstructed the Atomic Regulons (ARs) for B. subtilis, which are the sets of genes that share the same “ON” and “OFF” gene expression profiles across multiple samples of experimental data. We show how atomic regulons for B. subtilis are able to capture many sets of genes corresponding to regulated operons in our manually curated network. Additionally, we demonstrate how atomic regulons can be used to help expand or validate the knowledge of the regulatory networks by looking at highly correlated genes in the ARs for which regulatory information is lacking. During this process, we were also able to infer novel stimuli for hypothetical genes by exploring the genome expression metadata relating to experimental conditions, gaining insights into novel biology.« less

Complex regulatory network encompassing the Csr, c-di-GMP and motility systems of Salmonella Typhimurium.

PubMed

Jonas, Kristina; Edwards, Adrianne N; Ahmad, Irfan; Romeo, Tony; Römling, Ute; Melefors, Ojar

2010-02-01

Bacterial survival depends on the ability to switch between sessile and motile lifestyles in response to changing environmental conditions. In many species, this switch is governed by (3'-5')-cyclic-diguanosine monophosphate (c-di-GMP), a signalling molecule, which is metabolized by proteins containing GGDEF and/or EAL domains. Salmonella Typhimurium contains 20 such proteins. Here, we show that the RNA-binding protein CsrA regulates the expression of eight genes encoding GGDEF, GGDEF-EAL and EAL domain proteins. CsrA bound directly to the mRNA leaders of five of these genes, suggesting that it may regulate these genes post-transcriptionally. The c-di-GMP-specific phosphodiesterase STM3611, which reciprocally controls flagella function and production of biofilm matrix components, was regulated by CsrA binding to the mRNA, but was also indirectly regulated by CsrA through the FlhDC/FliA flagella cascade and STM1344. STM1344 is an unconventional (c-di-GMP-inactive) EAL domain protein, recently identified as a negative regulator of flagella gene expression. Here, we demonstrate that CsrA directly downregulates expression of STM1344, which in turn regulates STM3611 through fliA and thus reciprocally controls motility and biofilm factors. Altogether, our data reveal that the concerted and complex regulation of several genes encoding GGDEF/EAL domain proteins allows CsrA to control the motility-sessility switch in S. Typhimurium at multiple levels.

Experimental demonstration of OSPF-TE extensions in muiti-domain OBS networks connected by GMPLS network

NASA Astrophysics Data System (ADS)

Tian, Chunlei; Yin, Yawei; Wu, Jian; Lin, Jintong

2008-11-01

The interworking network of Generalized Multi-Protocol Label Switching (GMPLS) and Optical Burst Switching (OBS) is attractive network architecture for the future IP/DWDM network nowadays. In this paper, OSPF-TE extensions for multi-domain Optical Burst Switching networks connected by GMPLS controlled WDM network are proposed, the corresponding experimental results such as the advertising latency are also presented by using an OBS network testbed. The experimental results show that it works effectively on the OBS/GMPLS networks.

Synchronization of Switched Neural Networks With Communication Delays via the Event-Triggered Control.

PubMed

Wen, Shiping; Zeng, Zhigang; Chen, Michael Z Q; Huang, Tingwen

2017-10-01

This paper addresses the issue of synchronization of switched delayed neural networks with communication delays via event-triggered control. For synchronizing coupled switched neural networks, we propose a novel event-triggered control law which could greatly reduce the number of control updates for synchronization tasks of coupled switched neural networks involving embedded microprocessors with limited on-board resources. The control signals are driven by properly defined events, which depend on the measurement errors and current-sampled states. By using a delay system method, a novel model of synchronization error system with delays is proposed with the communication delays and event-triggered control in the unified framework for coupled switched neural networks. The criteria are derived for the event-triggered synchronization analysis and control synthesis of switched neural networks via the Lyapunov-Krasovskii functional method and free weighting matrix approach. A numerical example is elaborated on to illustrate the effectiveness of the derived results.

Network speech systems technology program

NASA Astrophysics Data System (ADS)

Weinstein, C. J.

1981-09-01

This report documents work performed during FY 1981 on the DCA-sponsored Network Speech Systems Technology Program. The two areas of work reported are: (1) communication system studies in support of the evolving Defense Switched Network (DSN) and (2) design and implementation of satellite/terrestrial interfaces for the Experimental Integrated Switched Network (EISN). The system studies focus on the development and evaluation of economical and endurable network routing procedures. Satellite/terrestrial interface development includes circuit-switched and packet-switched connections to the experimental wideband satellite network. Efforts in planning and coordination of EISN experiments are reported in detail in a separate EISN Experiment Plan.

A three-sided rearrangeable switching network for a binary fat tree

NASA Astrophysics Data System (ADS)

Yen, Mao-Hsu; Yu, Chu; Shin, Haw-Yun; Chen, Sao-Jie

2011-06-01

A binary fat tree needs an internal node to interconnect the left-children, right-children and parent terminals to each other. In this article, we first propose a three-stage, 3-sided rearrangeable switching network for the implementation of a binary fat tree. The main component of this 3-sided switching network (3SSN) consists of a polygonal switch block (PSB) interconnected by crossbars. With the same size and the same number of switches as our 3SSN, a three-stage, 3-sided clique-based switching network is shown to be not rearrangeable. Also, the effects of the rearrangeable structure and the number of terminals on the network switch-efficiency are explored and a proper set of parameters has been determined to minimise the number of switches. We derive that a rearrangeable 3-sided switching network with switches proportional to N 3/2 is most suitable to interconnect N terminals. Moreover, we propose a new Polygonal Field Programmable Gate Array (PFPGA) that consists of logic blocks interconnected by our 3SSN, such that the logic blocks in this PFPGA can be grouped into clusters to implement different logic functions. Since the programmable switches usually have high resistance and capacitance and occupy a large area, we have to consider the effect of the 3SSN structure and the granularity of its cluster logic blocks on the switch efficiency of PFPGA. Experiments on benchmark circuits show that the switch and speed performances are significantly improved. Based on the experimental results, we can determine the parameters of PFPGA for the VLSI implementation.

The Rsb Phosphoregulatory Network Controls Availability of the Primary Sigma Factor in Chlamydia trachomatis and Influences the Kinetics of Growth and Development

PubMed Central

Thompson, Christopher C.; Griffiths, Cherry; Nicod, Sophie S.; Lowden, Nicole M.; Wigneshweraraj, Sivaramesh; Fisher, Derek J.; McClure, Myra O.

2015-01-01

Chlamydia trachomatis is an obligate intracellular human pathogen that exhibits stage-specific gene transcription throughout a biphasic developmental cycle. The mechanisms that control modulation in transcription and associated phenotypic changes are poorly understood. This study provides evidence that a switch-protein kinase regulatory network controls availability of σ66 , the main sigma subunit for transcription in Chlamydia. In vitro analysis revealed that a putative switch-protein kinase regulator, RsbW, is capable of interacting directly with σ66, as well as phosphorylating its own antagonist, RsbV1, rendering it inactive. Conversely, the putative PP2C-like phosphatase domain of chlamydial RsbU was capable of reverting RsbV1 into its active state. Recent advances in genetic manipulation of Chlamydia were employed to inactivate rsbV1, as well as to increase the expression levels of rsbW or rsbV1, in vivo. Representative σ66-dependent gene transcription was repressed in the absence of rsbV1 or upon increased expression of RsbW, and increased upon elevated expression of RsbV1. These effects on housekeeping transcription were also correlated to several measures of growth and development. A model is proposed where the relative levels of active antagonist (RsbV1) and switch-protein anti-sigma factor (RsbW) control the availability of σ66 and subsequently act as a molecular 'throttle' for Chlamydia growth and development. PMID:26313645

Heteroclinic switching between chimeras

NASA Astrophysics Data System (ADS)

Bick, Christian

2018-05-01

Functional oscillator networks, such as neuronal networks in the brain, exhibit switching between metastable states involving many oscillators. We give exact results how such global dynamics can arise in paradigmatic phase oscillator networks: Higher-order network interactions give rise to metastable chimeras—localized frequency synchrony patterns—which are joined by heteroclinic connections. Moreover, we illuminate the mechanisms that underly the switching dynamics in these experimentally accessible networks.

Generating and repairing genetically programmed DNA breaks during immunoglobulin class switch recombination

PubMed Central

Nicolas, Laura; Cols, Montserrat; Choi, Jee Eun; Chaudhuri, Jayanta; Vuong, Bao

2018-01-01

Adaptive immune responses require the generation of a diverse repertoire of immunoglobulins (Igs) that can recognize and neutralize a seemingly infinite number of antigens. V(D)J recombination creates the primary Ig repertoire, which subsequently is modified by somatic hypermutation (SHM) and class switch recombination (CSR). SHM promotes Ig affinity maturation whereas CSR alters the effector function of the Ig. Both SHM and CSR require activation-induced cytidine deaminase (AID) to produce dU:dG mismatches in the Ig locus that are transformed into untemplated mutations in variable coding segments during SHM or DNA double-strand breaks (DSBs) in switch regions during CSR. Within the Ig locus, DNA repair pathways are diverted from their canonical role in maintaining genomic integrity to permit AID-directed mutation and deletion of gene coding segments. Recently identified proteins, genes, and regulatory networks have provided new insights into the temporally and spatially coordinated molecular interactions that control the formation and repair of DSBs within the Ig locus. Unravelling the genetic program that allows B cells to selectively alter the Ig coding regions while protecting non-Ig genes from DNA damage advances our understanding of the molecular processes that maintain genomic integrity as well as humoral immunity. PMID:29744038

Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters

PubMed Central

Rhodius, Virgil A; Segall-Shapiro, Thomas H; Sharon, Brian D; Ghodasara, Amar; Orlova, Ekaterina; Tabakh, Hannah; Burkhardt, David H; Clancy, Kevin; Peterson, Todd C; Gross, Carol A; Voigt, Christopher A

2013-01-01

Cells react to their environment through gene regulatory networks. Network integrity requires minimization of undesired crosstalk between their biomolecules. Similar constraints also limit the use of regulators when building synthetic circuits for engineering applications. Here, we mapped the promoter specificities of extracytoplasmic function (ECF) σs as well as the specificity of their interaction with anti-σs. DNA synthesis was used to build 86 ECF σs (two from every subgroup), their promoters, and 62 anti-σs identified from the genomes of diverse bacteria. A subset of 20 σs and promoters were found to be highly orthogonal to each other. This set can be increased by combining the −35 and −10 binding domains from different subgroups to build chimeras that target sequences unrepresented in any subgroup. The orthogonal σs, anti-σs, and promoters were used to build synthetic genetic switches in Escherichia coli. This represents a genome-scale resource of the properties of ECF σs and a resource for synthetic biology, where this set of well-characterized regulatory parts will enable the construction of sophisticated gene expression programs. PMID:24169405

Stochastic dynamics of genetic broadcasting networks

NASA Astrophysics Data System (ADS)

Potoyan, Davit; Wolynes, Peter

The complex genetic programs of eukaryotic cells are often regulated by key transcription factors occupying or clearing out of a large number of genomic locations. Orchestrating the residence times of these factors is therefore important for the well organized functioning of a large network. The classic models of genetic switches sidestep this timing issue by assuming the binding of transcription factors to be governed entirely by thermodynamic protein-DNA affinities. Here we show that relying on passive thermodynamics and random release times can lead to a ''time-scale crisis'' of master genes that broadcast their signals to large number of binding sites. We demonstrate that this ''time-scale crisis'' can be resolved by actively regulating residence times through molecular stripping. We illustrate these ideas by studying the stochastic dynamics of the genetic network of the central eukaryotic master regulator NFκB which broadcasts its signals to many downstream genes that regulate immune response, apoptosis etc.

Feasibility study of an integrated optic switching center. [satellite tracking application

NASA Technical Reports Server (NTRS)

1979-01-01

The design of a high data rate switching center for a satellite tracking station is discussed. The feasibility of a switching network using an integrated switching matrix is assessed. The preferred integrated optical switching scheme was found to be an electro-optic Bragg diffraction switch. To ascertain the advantages of the integrated optics switching center, its properties are compared to those of opto-electronic and to electronics switching networks.

Stochastic dynamics of genetic broadcasting networks

NASA Astrophysics Data System (ADS)

Potoyan, Davit A.; Wolynes, Peter G.

2017-11-01

The complex genetic programs of eukaryotic cells are often regulated by key transcription factors occupying or clearing out of a large number of genomic locations. Orchestrating the residence times of these factors is therefore important for the well organized functioning of a large network. The classic models of genetic switches sidestep this timing issue by assuming the binding of transcription factors to be governed entirely by thermodynamic protein-DNA affinities. Here we show that relying on passive thermodynamics and random release times can lead to a "time-scale crisis" for master genes that broadcast their signals to a large number of binding sites. We demonstrate that this time-scale crisis for clearance in a large broadcasting network can be resolved by actively regulating residence times through molecular stripping. We illustrate these ideas by studying a model of the stochastic dynamics of the genetic network of the central eukaryotic master regulator NFκ B which broadcasts its signals to many downstream genes that regulate immune response, apoptosis, etc.

Hypoxia induces a HIF-1α dependent signaling cascade to make a complex metabolic switch in SGBS-adipocytes☆

PubMed Central

Leiherer, Andreas; Geiger, Kathrin; Muendlein, Axel; Drexel, Heinz

2014-01-01

To elucidate the complex impact of hypoxia on adipose tissue, resulting in biased metabolism, insulin resistance and finally diabetes we used mature adipocytes derived from a Simpson-Golabi-Behmel syndrome patient for microarray analysis. We found a significantly increased transcription rate of genes involved in glycolysis and a striking association between the pattern of upregulated genes and disease biomarkers for diabetes mellitus and insulin resistance. Although their upregulation turned out to be HIF-1α-dependent, we identified further transcription factors mainly AP-1 components to play also an important role in hypoxia response. Analyzing the regulatory network of mentioned transcription factors and glycolysis targets we revealed a clear hint for directing glycolysis to glutathione and glycogen synthesis. This metabolic switch in adipocytes enables the cell to prevent oxidative damage in the short term but might induce lipogenesis and establish systemic metabolic disorders in the long run. PMID:24275182

Three-tier multi-granularity switching system based on PCE

NASA Astrophysics Data System (ADS)

Wang, Yubao; Sun, Hao; Liu, Yanfei

2017-10-01

With the growing demand for business communications, electrical signal processing optical path switching can't meet the demand. The multi-granularity switch system that can improve node routing and switching capabilities came into being. In the traditional network, each node is responsible for calculating the path; synchronize the whole network state, which will increase the burden on the network, so the concept of path calculation element (PCE) is proposed. The PCE is responsible for routing and allocating resources in the network1. In the traditional band-switched optical network, the wavelength is used as the basic routing unit, resulting in relatively low wavelength utilization. Due to the limitation of wavelength continuity, the routing design of the band technology becomes complicated, which directly affects the utilization of the system. In this paper, optical code granularity is adopted. There is no continuity of the optical code, and the number of optical codes is more flexible than the wavelength. For the introduction of optical code switching, we propose a Code Group Routing Entity (CGRE) algorithm. In short, the combination of three-tier multi-granularity optical switching system and PCE can simplify the network structure, reduce the node load, and enhance the network scalability and survivability. Realize the intelligentization of optical network.

Parallel Algorithms for Switching Edges in Heterogeneous Graphs.

PubMed

Bhuiyan, Hasanuzzaman; Khan, Maleq; Chen, Jiangzhuo; Marathe, Madhav

2017-06-01

An edge switch is an operation on a graph (or network) where two edges are selected randomly and one of their end vertices are swapped with each other. Edge switch operations have important applications in graph theory and network analysis, such as in generating random networks with a given degree sequence, modeling and analyzing dynamic networks, and in studying various dynamic phenomena over a network. The recent growth of real-world networks motivates the need for efficient parallel algorithms. The dependencies among successive edge switch operations and the requirement to keep the graph simple (i.e., no self-loops or parallel edges) as the edges are switched lead to significant challenges in designing a parallel algorithm. Addressing these challenges requires complex synchronization and communication among the processors leading to difficulties in achieving a good speedup by parallelization. In this paper, we present distributed memory parallel algorithms for switching edges in massive networks. These algorithms provide good speedup and scale well to a large number of processors. A harmonic mean speedup of 73.25 is achieved on eight different networks with 1024 processors. One of the steps in our edge switch algorithms requires the computation of multinomial random variables in parallel. This paper presents the first non-trivial parallel algorithm for the problem, achieving a speedup of 925 using 1024 processors.

Parallel Algorithms for Switching Edges in Heterogeneous Graphs☆

PubMed Central

Khan, Maleq; Chen, Jiangzhuo; Marathe, Madhav

2017-01-01

An edge switch is an operation on a graph (or network) where two edges are selected randomly and one of their end vertices are swapped with each other. Edge switch operations have important applications in graph theory and network analysis, such as in generating random networks with a given degree sequence, modeling and analyzing dynamic networks, and in studying various dynamic phenomena over a network. The recent growth of real-world networks motivates the need for efficient parallel algorithms. The dependencies among successive edge switch operations and the requirement to keep the graph simple (i.e., no self-loops or parallel edges) as the edges are switched lead to significant challenges in designing a parallel algorithm. Addressing these challenges requires complex synchronization and communication among the processors leading to difficulties in achieving a good speedup by parallelization. In this paper, we present distributed memory parallel algorithms for switching edges in massive networks. These algorithms provide good speedup and scale well to a large number of processors. A harmonic mean speedup of 73.25 is achieved on eight different networks with 1024 processors. One of the steps in our edge switch algorithms requires the computation of multinomial random variables in parallel. This paper presents the first non-trivial parallel algorithm for the problem, achieving a speedup of 925 using 1024 processors. PMID:28757680

77 FR 21996 - Certain Equipment for Communications Networks, Including Switches, Routers, Gateways, Bridges...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-12

... INTERNATIONAL TRADE COMMISSION [Investigation No. 337-TA-778] Certain Equipment for Communications Networks, Including Switches, Routers, Gateways, Bridges, Wireless Access Points, Cable Modems, IP Phones... networks, including switches, routers, gateways, bridges, wireless access points, cable modems, IP phones...

Optical burst switching based satellite backbone network

NASA Astrophysics Data System (ADS)

Li, Tingting; Guo, Hongxiang; Wang, Cen; Wu, Jian

2018-02-01

We propose a novel time slot based optical burst switching (OBS) architecture for GEO/LEO based satellite backbone network. This architecture can provide high speed data transmission rate and high switching capacity . Furthermore, we design the control plane of this optical satellite backbone network. The software defined network (SDN) and network slice (NS) technologies are introduced. Under the properly designed control mechanism, this backbone network is flexible to support various services with diverse transmission requirements. Additionally, the LEO access and handoff management in this network is also discussed.

Switch for serial or parallel communication networks

DOEpatents

Crosette, D.B.

1994-07-19

A communication switch apparatus and a method for use in a geographically extensive serial, parallel or hybrid communication network linking a multi-processor or parallel processing system has a very low software processing overhead in order to accommodate random burst of high density data. Associated with each processor is a communication switch. A data source and a data destination, a sensor suite or robot for example, may also be associated with a switch. The configuration of the switches in the network are coordinated through a master processor node and depends on the operational phase of the multi-processor network: data acquisition, data processing, and data exchange. The master processor node passes information on the state to be assumed by each switch to the processor node associated with the switch. The processor node then operates a series of multi-state switches internal to each communication switch. The communication switch does not parse and interpret communication protocol and message routing information. During a data acquisition phase, the communication switch couples sensors producing data to the processor node associated with the switch, to a downlink destination on the communications network, or to both. It also may couple an uplink data source to its processor node. During the data exchange phase, the switch couples its processor node or an uplink data source to a downlink destination (which may include a processor node or a robot), or couples an uplink source to its processor node and its processor node to a downlink destination. 9 figs.

Switch for serial or parallel communication networks

DOEpatents

Crosette, Dario B.

1994-01-01

A communication switch apparatus and a method for use in a geographically extensive serial, parallel or hybrid communication network linking a multi-processor or parallel processing system has a very low software processing overhead in order to accommodate random burst of high density data. Associated with each processor is a communication switch. A data source and a data destination, a sensor suite or robot for example, may also be associated with a switch. The configuration of the switches in the network are coordinated through a master processor node and depends on the operational phase of the multi-processor network: data acquisition, data processing, and data exchange. The master processor node passes information on the state to be assumed by each switch to the processor node associated with the switch. The processor node then operates a series of multi-state switches internal to each communication switch. The communication switch does not parse and interpret communication protocol and message routing information. During a data acquisition phase, the communication switch couples sensors producing data to the processor node associated with the switch, to a downlink destination on the communications network, or to both. It also may couple an uplink data source to its processor node. During the data exchange phase, the switch couples its processor node or an uplink data source to a downlink destination (which may include a processor node or a robot), or couples an uplink source to its processor node and its processor node to a downlink destination.

Artificial Epigenetic Networks: Automatic Decomposition of Dynamical Control Tasks Using Topological Self-Modification.

PubMed

Turner, Alexander P; Caves, Leo S D; Stepney, Susan; Tyrrell, Andy M; Lones, Michael A

2017-01-01

This paper describes the artificial epigenetic network, a recurrent connectionist architecture that is able to dynamically modify its topology in order to automatically decompose and solve dynamical problems. The approach is motivated by the behavior of gene regulatory networks, particularly the epigenetic process of chromatin remodeling that leads to topological change and which underlies the differentiation of cells within complex biological organisms. We expected this approach to be useful in situations where there is a need to switch between different dynamical behaviors, and do so in a sensitive and robust manner in the absence of a priori information about problem structure. This hypothesis was tested using a series of dynamical control tasks, each requiring solutions that could express different dynamical behaviors at different stages within the task. In each case, the addition of topological self-modification was shown to improve the performance and robustness of controllers. We believe this is due to the ability of topological changes to stabilize attractors, promoting stability within a dynamical regime while allowing rapid switching between different regimes. Post hoc analysis of the controllers also demonstrated how the partitioning of the networks could provide new insights into problem structure.

Recognizing and engineering digital-like logic gates and switches in gene regulatory networks.

PubMed

Bradley, Robert W; Buck, Martin; Wang, Baojun

2016-10-01

A central aim of synthetic biology is to build organisms that can perform useful activities in response to specified conditions. The digital computing paradigm which has proved so successful in electrical engineering is being mapped to synthetic biological systems to allow them to make such decisions. However, stochastic molecular processes have graded input-output functions, thus, bioengineers must select those with desirable characteristics and refine their transfer functions to build logic gates with digital-like switching behaviour. Recent efforts in genome mining and the development of programmable RNA-based switches, especially CRISPRi, have greatly increased the number of parts available to synthetic biologists. Improvements to the digital characteristics of these parts are required to enable robust predictable design of deeply layered logic circuits. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Secure videoconferencing equipment switching system and method

DOEpatents

Hansen, Michael E [Livermore, CA

2009-01-13

A switching system and method are provided to facilitate use of videoconference facilities over a plurality of security levels. The system includes a switch coupled to a plurality of codecs and communication networks. Audio/Visual peripheral components are connected to the switch. The switch couples control and data signals between the Audio/Visual peripheral components and one but nor both of the plurality of codecs. The switch additionally couples communication networks of the appropriate security level to each of the codecs. In this manner, a videoconferencing facility is provided for use on both secure and non-secure networks.

Programmable on-chip and off-chip network architecture on demand for flexible optical intra-datacenters.

PubMed

Rofoee, Bijan Rahimzadeh; Zervas, Georgios; Yan, Yan; Amaya, Norberto; Qin, Yixuan; Simeonidou, Dimitra

2013-03-11

The paper presents a novel network architecture on demand approach using on-chip and-off chip implementations, enabling programmable, highly efficient and transparent networking, well suited for intra-datacenter communications. The implemented FPGA-based adaptable line-card with on-chip design along with an architecture on demand (AoD) based off-chip flexible switching node, deliver single chip dual L2-Packet/L1-time shared optical network (TSON) server Network Interface Cards (NIC) interconnected through transparent AoD based switch. It enables hitless adaptation between Ethernet over wavelength switched network (EoWSON), and TSON based sub-wavelength switching, providing flexible bitrates, while meeting strict bandwidth, QoS requirements. The on and off-chip performance results show high throughput (9.86Ethernet, 8.68Gbps TSON), high QoS, as well as hitless switch-over.

Clustering and Flow Conservation Monitoring Tool for Software Defined Networks.

PubMed

Puente Fernández, Jesús Antonio; García Villalba, Luis Javier; Kim, Tai-Hoon

2018-04-03

Prediction systems present some challenges on two fronts: the relation between video quality and observed session features and on the other hand, dynamics changes on the video quality. Software Defined Networks (SDN) is a new concept of network architecture that provides the separation of control plane (controller) and data plane (switches) in network devices. Due to the existence of the southbound interface, it is possible to deploy monitoring tools to obtain the network status and retrieve a statistics collection. Therefore, achieving the most accurate statistics depends on a strategy of monitoring and information requests of network devices. In this paper, we propose an enhanced algorithm for requesting statistics to measure the traffic flow in SDN networks. Such an algorithm is based on grouping network switches in clusters focusing on their number of ports to apply different monitoring techniques. Such grouping occurs by avoiding monitoring queries in network switches with common characteristics and then, by omitting redundant information. In this way, the present proposal decreases the number of monitoring queries to switches, improving the network traffic and preventing the switching overload. We have tested our optimization in a video streaming simulation using different types of videos. The experiments and comparison with traditional monitoring techniques demonstrate the feasibility of our proposal maintaining similar values decreasing the number of queries to the switches.

High speed all optical networks

NASA Technical Reports Server (NTRS)

Chlamtac, Imrich; Ganz, Aura

1990-01-01

An inherent problem of conventional point-to-point wide area network (WAN) architectures is that they cannot translate optical transmission bandwidth into comparable user available throughput due to the limiting electronic processing speed of the switching nodes. The first solution to wavelength division multiplexing (WDM) based WAN networks that overcomes this limitation is presented. The proposed Lightnet architecture takes into account the idiosyncrasies of WDM switching/transmission leading to an efficient and pragmatic solution. The Lightnet architecture trades the ample WDM bandwidth for a reduction in the number of processing stages and a simplification of each switching stage, leading to drastically increased effective network throughputs. The principle of the Lightnet architecture is the construction and use of virtual topology networks, embedded in the original network in the wavelength domain. For this construction Lightnets utilize the new concept of lightpaths which constitute the links of the virtual topology. Lightpaths are all-optical, multihop, paths in the network that allow data to be switched through intermediate nodes using high throughput passive optical switches. The use of the virtual topologies and the associated switching design introduce a number of new ideas, which are discussed in detail.

Butyrate Infusions in the Ovine Fetus Delay the Biologic Clock for Globin Gene Switching

NASA Astrophysics Data System (ADS)

Perrine, Susan P.; Rudolph, Abraham; Faller, Douglas V.; Roman, Christine; Cohen, Ruth A.; Chen, Shao-Jing; Kan, Yuet Wai

1988-11-01

The switch from fetal to adult hemoglobin expression is regulated in many mammalian species by a developmental clock-like mechanism and determined by the gestational age of the fetus. Prolonging fetal globin gene expression is of considerable interest for therapeutic potential in diseases caused by abnormal β -globin genes. Butyric acid, which is found in increased plasma concentrations in infants of diabetic mothers who have delayed globin gene switching, was infused into catheterized fetal lambs in utero during the time of the normal globin gene switch period. The globin gene switch was significantly delayed in three of four butyrate-treated fetuses compared with controls and was entirely prevented in one fetus in whom the infusion was begun before the globin switch was under way. These data provide a model for investigating and arresting the biologic clock of hemoglobin switching.

The formation of the light-sensing compartment of cone photoreceptors coincides with a transcriptional switch

PubMed Central

Daum, Janine M; Keles, Özkan; Holwerda, Sjoerd JB; Kohler, Hubertus; Rijli, Filippo M

2017-01-01

High-resolution daylight vision is mediated by cone photoreceptors. The molecular program responsible for the formation of their light sensor, the outer segment, is not well understood. We correlated daily changes in ultrastructure and gene expression in postmitotic mouse cones, between birth and eye opening, using serial block-face electron microscopy (EM) and RNA sequencing. Outer segments appeared rapidly at postnatal day six and their appearance coincided with a switch in gene expression. The switch affected over 14% of all expressed genes. Genes that switched off were rich in transcription factors and neurogenic genes. Those that switched on contained genes relevant for cone function. Chromatin rearrangements in enhancer regions occurred before the switch was completed, but not after. We provide a resource comprised of correlated EM, RNAseq, and ATACseq data, showing that the growth of a key compartment of a postmitotic cell involves an extensive switch in gene expression and chromatin accessibility. PMID:29106373

Dynamic Testing and Automatic Repair of Reconfigurable Wiring Harnesses

DTIC Science & Technology

2006-11-27

Switch An M ×N grid of switches configured to provide a M -input, N -output routing network. Permutation Network A permutation network performs an...wiring reduces the effective advantage of their reduced switch count, particularly when considering that regular grids (crossbar switches being a...are connected to. The outline circuit shown in Fig. 20 shows how a suitable ‘discovery probe’ might be implemented. The circuit shows a UART

The Hippo signal transduction network for exercise physiologists

PubMed Central

Hamilton, D. Lee; Tremblay, Annie M.

2016-01-01

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

47 CFR 90.477 - Interconnected systems.

Code of Federal Regulations, 2013 CFR

2013-10-01

...) Applicants for new land stations to be interconnected with the public switched telephone network must... switched telephone network only after modifying their license. See § 1.929 of this chapter. In all cases a..., 896-901 MHz, and 935-940 MHz, interconnection with the public switched telephone network is authorized...

47 CFR 90.477 - Interconnected systems.

Code of Federal Regulations, 2011 CFR

2011-10-01

...) Applicants for new land stations to be interconnected with the public switched telephone network must... switched telephone network only after modifying their license. See § 1.929 of this chapter. In all cases a..., 896-901 MHz, and 935-940 MHz, interconnection with the public switched telephone network is authorized...

47 CFR 90.477 - Interconnected systems.

Code of Federal Regulations, 2014 CFR

2014-10-01

...) Applicants for new land stations to be interconnected with the public switched telephone network must... switched telephone network only after modifying their license. See § 1.929 of this chapter. In all cases a..., 896-901 MHz, and 935-940 MHz, interconnection with the public switched telephone network is authorized...

47 CFR 90.477 - Interconnected systems.

Code of Federal Regulations, 2012 CFR

2012-10-01

...) Applicants for new land stations to be interconnected with the public switched telephone network must... switched telephone network only after modifying their license. See § 1.929 of this chapter. In all cases a..., 896-901 MHz, and 935-940 MHz, interconnection with the public switched telephone network is authorized...

Optical Circuit Switched Protocol

NASA Technical Reports Server (NTRS)

Monacos, Steve P. (Inventor)

2000-01-01

The present invention is a system and method embodied in an optical circuit switched protocol for the transmission of data through a network. The optical circuit switched protocol is an all-optical circuit switched network and includes novel optical switching nodes for transmitting optical data packets within a network. Each optical switching node comprises a detector for receiving the header, header detection logic for translating the header into routing information and eliminating the header, and a controller for receiving the routing information and configuring an all optical path within the node. The all optical path located within the node is solely an optical path without having electronic storage of the data and without having optical delay of the data. Since electronic storage of the header is not necessary and the initial header is eliminated by the first detector of the first switching node. multiple identical headers are sent throughout the network so that subsequent switching nodes can receive and read the header for setting up an optical data path.

An absorptive single-pole four-throw switch using multiple-contact MEMS switches and its application to a monolithic millimeter-wave beam-forming network

NASA Astrophysics Data System (ADS)

Lee, Sanghyo; Kim, Jong-Man; Kim, Yong-Kweon; Kwon, Youngwoo

2009-01-01

In this paper, a new absorptive single-pole four-throw (SP4T) switch based on multiple-contact switching is proposed and integrated with a Butler matrix to demonstrate a monolithic beam-forming network at millimeter waves (mm waves). In order to simplify the switching driving circuit and reduce the number of unit switches in an absorptive SP4T switch, the individual switches were replaced with long-span multiple-contact switches using stress-free single-crystalline-silicon MEMS technology. This approach improves the mechanical stability as well as the manufacturing yield, thereby allowing successful integration into a monolithic beam former. The fabricated absorptive SP4T MEMS switch shows insertion loss less than 1.3 dB, return losses better than 11 dB at 30 GHz and wideband isolation performance higher than 39 dB from 20 to 40 GHz. The absorptive SP4T MEMS switch is integrated with a 4 × 4 Butler matrix on a single chip to implement a monolithic beam-forming network, directing beam into four distinct angles. Array factors from the measured data show that the proposed absorptive SPnT MEMS switch can be effectively used for high-performance mm-wave beam-switching systems. This work corresponds to the first demonstration of a monolithic beam-forming network using switched beams.

Clustering promotes switching dynamics in networks of noisy neurons

NASA Astrophysics Data System (ADS)

Franović, Igor; Klinshov, Vladimir

2018-02-01

Macroscopic variability is an emergent property of neural networks, typically manifested in spontaneous switching between the episodes of elevated neuronal activity and the quiescent episodes. We investigate the conditions that facilitate switching dynamics, focusing on the interplay between the different sources of noise and heterogeneity of the network topology. We consider clustered networks of rate-based neurons subjected to external and intrinsic noise and derive an effective model where the network dynamics is described by a set of coupled second-order stochastic mean-field systems representing each of the clusters. The model provides an insight into the different contributions to effective macroscopic noise and qualitatively indicates the parameter domains where switching dynamics may occur. By analyzing the mean-field model in the thermodynamic limit, we demonstrate that clustering promotes multistability, which gives rise to switching dynamics in a considerably wider parameter region compared to the case of a non-clustered network with sparse random connection topology.

WDM Network and Multicasting Protocol Strategies

PubMed Central

Zaim, Abdul Halim

2014-01-01

Optical technology gains extensive attention and ever increasing improvement because of the huge amount of network traffic caused by the growing number of internet users and their rising demands. However, with wavelength division multiplexing (WDM), it is easier to take the advantage of optical networks and optical burst switching (OBS) and to construct WDM networks with low delay rates and better data transparency these technologies are the best choices. Furthermore, multicasting in WDM is an urgent solution for bandwidth-intensive applications. In the paper, a new multicasting protocol with OBS is proposed. The protocol depends on a leaf initiated structure. The network is composed of source, ingress switches, intermediate switches, edge switches, and client nodes. The performance of the protocol is examined with Just Enough Time (JET) and Just In Time (JIT) reservation protocols. Also, the paper involves most of the recent advances about WDM multicasting in optical networks. WDM multicasting in optical networks is given as three common subtitles: Broadcast and-select networks, wavelength-routed networks, and OBS networks. Also, in the paper, multicast routing protocols are briefly summarized and optical burst switched WDM networks are investigated with the proposed multicast schemes. PMID:24744683

Learning a Markov Logic network for supervised gene regulatory network inference

PubMed Central

2013-01-01

Background Gene regulatory network inference remains a challenging problem in systems biology despite the numerous approaches that have been proposed. When substantial knowledge on a gene regulatory network is already available, supervised network inference is appropriate. Such a method builds a binary classifier able to assign a class (Regulation/No regulation) to an ordered pair of genes. Once learnt, the pairwise classifier can be used to predict new regulations. In this work, we explore the framework of Markov Logic Networks (MLN) that combine features of probabilistic graphical models with the expressivity of first-order logic rules. Results We propose to learn a Markov Logic network, e.g. a set of weighted rules that conclude on the predicate “regulates”, starting from a known gene regulatory network involved in the switch proliferation/differentiation of keratinocyte cells, a set of experimental transcriptomic data and various descriptions of genes all encoded into first-order logic. As training data are unbalanced, we use asymmetric bagging to learn a set of MLNs. The prediction of a new regulation can then be obtained by averaging predictions of individual MLNs. As a side contribution, we propose three in silico tests to assess the performance of any pairwise classifier in various network inference tasks on real datasets. A first test consists of measuring the average performance on balanced edge prediction problem; a second one deals with the ability of the classifier, once enhanced by asymmetric bagging, to update a given network. Finally our main result concerns a third test that measures the ability of the method to predict regulations with a new set of genes. As expected, MLN, when provided with only numerical discretized gene expression data, does not perform as well as a pairwise SVM in terms of AUPR. However, when a more complete description of gene properties is provided by heterogeneous sources, MLN achieves the same performance as a black-box model such as a pairwise SVM while providing relevant insights on the predictions. Conclusions The numerical studies show that MLN achieves very good predictive performance while opening the door to some interpretability of the decisions. Besides the ability to suggest new regulations, such an approach allows to cross-validate experimental data with existing knowledge. PMID:24028533

Learning a Markov Logic network for supervised gene regulatory network inference.

PubMed

Brouard, Céline; Vrain, Christel; Dubois, Julie; Castel, David; Debily, Marie-Anne; d'Alché-Buc, Florence

2013-09-12

Gene regulatory network inference remains a challenging problem in systems biology despite the numerous approaches that have been proposed. When substantial knowledge on a gene regulatory network is already available, supervised network inference is appropriate. Such a method builds a binary classifier able to assign a class (Regulation/No regulation) to an ordered pair of genes. Once learnt, the pairwise classifier can be used to predict new regulations. In this work, we explore the framework of Markov Logic Networks (MLN) that combine features of probabilistic graphical models with the expressivity of first-order logic rules. We propose to learn a Markov Logic network, e.g. a set of weighted rules that conclude on the predicate "regulates", starting from a known gene regulatory network involved in the switch proliferation/differentiation of keratinocyte cells, a set of experimental transcriptomic data and various descriptions of genes all encoded into first-order logic. As training data are unbalanced, we use asymmetric bagging to learn a set of MLNs. The prediction of a new regulation can then be obtained by averaging predictions of individual MLNs. As a side contribution, we propose three in silico tests to assess the performance of any pairwise classifier in various network inference tasks on real datasets. A first test consists of measuring the average performance on balanced edge prediction problem; a second one deals with the ability of the classifier, once enhanced by asymmetric bagging, to update a given network. Finally our main result concerns a third test that measures the ability of the method to predict regulations with a new set of genes. As expected, MLN, when provided with only numerical discretized gene expression data, does not perform as well as a pairwise SVM in terms of AUPR. However, when a more complete description of gene properties is provided by heterogeneous sources, MLN achieves the same performance as a black-box model such as a pairwise SVM while providing relevant insights on the predictions. The numerical studies show that MLN achieves very good predictive performance while opening the door to some interpretability of the decisions. Besides the ability to suggest new regulations, such an approach allows to cross-validate experimental data with existing knowledge.

Global exponential stability for switched memristive neural networks with time-varying delays.

PubMed

Xin, Youming; Li, Yuxia; Cheng, Zunshui; Huang, Xia

2016-08-01

This paper considers the problem of exponential stability for switched memristive neural networks (MNNs) with time-varying delays. Different from most of the existing papers, we model a memristor as a continuous system, and view switched MNNs as switched neural networks with uncertain time-varying parameters. Based on average dwell time technique, mode-dependent average dwell time technique and multiple Lyapunov-Krasovskii functional approach, two conditions are derived to design the switching signal and guarantee the exponential stability of the considered neural networks, which are delay-dependent and formulated by linear matrix inequalities (LMIs). Finally, the effectiveness of the theoretical results is demonstrated by two numerical examples. Copyright © 2016 Elsevier Ltd. All rights reserved.

Switching synchronization in one-dimensional memristive networks

NASA Astrophysics Data System (ADS)

Slipko, Valeriy A.; Shumovskyi, Mykola; Pershin, Yuriy V.

2015-11-01

We report on a switching synchronization phenomenon in one-dimensional memristive networks, which occurs when several memristive systems with different switching constants are switched from the high- to low-resistance state. Our numerical simulations show that such a collective behavior is especially pronounced when the applied voltage slightly exceeds the combined threshold voltage of memristive systems. Moreover, a finite increase in the network switching time is found compared to the average switching time of individual systems. An analytical model is presented to explain our observations. Using this model, we have derived asymptotic expressions for memory resistances at short and long times, which are in excellent agreement with results of our numerical simulations.

Controlled Photon Switch Assisted by Coupled Quantum Dots

PubMed Central

Luo, Ming-Xing; Ma, Song-Ya; Chen, Xiu-Bo; Wang, Xiaojun

2015-01-01

Quantum switch is a primitive element in quantum network communication. In contrast to previous switch schemes on one degree of freedom (DOF) of quantum systems, we consider controlled switches of photon system with two DOFs. These controlled photon switches are constructed by exploring the optical selection rules derived from the quantum-dot spins in one-sided optical microcavities. Several double controlled-NOT gate on different joint systems are greatly simplified with an auxiliary DOF of the controlling photon. The photon switches show that two DOFs of photons can be independently transmitted in quantum networks. This result reduces the quantum resources for quantum network communication. PMID:26095049

Call for Papers: Photonics in Switching

NASA Astrophysics Data System (ADS)

Wosinska, Lena; Glick, Madeleine

2006-04-01

Call for Papers: Photonics in Switching

Guest Editors:

Lena Wosinska, Royal Institute of Technology (KTH) / ICT Sweden Madeleine Glick, Intel Research, Cambridge, UK

Scope of Submission

• WDM node architectures
• Novel device technologies enabling photonics in switching, such as optical switch fabrics, optical memory, and wavelength conversion
• Routing protocols
• WDM switching and routing
• Quality of service
• Performance measurement and evaluation
• Next-generation optical networks: architecture, signaling, and control
• Traffic measurement and field trials
• Optical burst and packet switching
• OBS/OPS node architectures
• Burst/Packet scheduling and routing algorithms
• Contention resolution/avoidance strategies
• Services and applications for OBS/OPS (e.g., grid networks, storage-area networks, etc.)
• Burst assembly and ingress traffic shaping
• Hybrid OBS/TDM or OBS/wavelength routing

Manuscript Submission

Apollo Ring Optical Switch

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maestas, J.H.

1987-03-01

An optical switch was designed, built, and installed at Sandia National Laboratories in Albuquerque, New Mexico, to facilitate the integration of two Apollo computer networks into a single network. This report presents an overview of the optical switch as well as its layout, switch testing procedure and test data, and installation.

GLOBECOM '88 - IEEE Global Telecommunications Conference and Exhibition, Hollywood, FL, Nov. 28-Dec. 1, 1988, Conference Record. Volumes 1, 2, & 3

NASA Astrophysics Data System (ADS)

Various papers on communications for the information age are presented. Among the general topics considered are: telematic services and terminals, satellite communications, telecommunications mangaement network, control of integrated broadband networks, advances in digital radio systems, the intelligent network, broadband networks and services deployment, future switch architectures, performance analysis of computer networks, advances in spread spectrum, optical high-speed LANs, and broadband switching and networks. Also addressed are: multiple access protocols, video coding techniques, modulation and coding, photonic switching, SONET terminals and applications, standards for video coding, digital switching, progress in MANs, mobile and portable radio, software design for improved maintainability, multipath propagation and advanced countermeasure, data communication, network control and management, fiber in the loop, network algorithm and protocols, and advances in computer communications.

Low threshold all-optical crossbar switch on GaAs-GaAlAs channel waveguide arrays

NASA Astrophysics Data System (ADS)

Jannson, Tomasz; Kostrzewski, Andrew

1994-09-01

During the Phase 2 project entitled 'Low Threshold All-Optical Crossbar Switch on GaAs - GaAlAs Channel Waveguide Array,' Physical Optics Corporation (POC) developed the basic principles for the fabrication of all-optical crossbar switches. Based on this development. POC fabricated a 2 x 2 GaAs/GaAlAs switch that changes the direction of incident light with minimum insertion loss and nonlinear distortion. This unique technology can be used in both analog and digital networks. The applications of this technology are widespread. Because the all-optical network does not have any speed limitations (RC time constant), POC's approach will be beneficial to SONET networks, phased array radar networks, very high speed oscilloscopes, all-optical networks, IR countermeasure systems, BER equipment, and the fast growing video conferencing network market. The novel all-optical crossbar switch developed in this program will solve interconnect problems. and will be a key component in the widely proposed all-optical 200 Gb/s SONET/ATM networks.

Clustering and Flow Conservation Monitoring Tool for Software Defined Networks

PubMed Central

Puente Fernández, Jesús Antonio

2018-01-01

Prediction systems present some challenges on two fronts: the relation between video quality and observed session features and on the other hand, dynamics changes on the video quality. Software Defined Networks (SDN) is a new concept of network architecture that provides the separation of control plane (controller) and data plane (switches) in network devices. Due to the existence of the southbound interface, it is possible to deploy monitoring tools to obtain the network status and retrieve a statistics collection. Therefore, achieving the most accurate statistics depends on a strategy of monitoring and information requests of network devices. In this paper, we propose an enhanced algorithm for requesting statistics to measure the traffic flow in SDN networks. Such an algorithm is based on grouping network switches in clusters focusing on their number of ports to apply different monitoring techniques. Such grouping occurs by avoiding monitoring queries in network switches with common characteristics and then, by omitting redundant information. In this way, the present proposal decreases the number of monitoring queries to switches, improving the network traffic and preventing the switching overload. We have tested our optimization in a video streaming simulation using different types of videos. The experiments and comparison with traditional monitoring techniques demonstrate the feasibility of our proposal maintaining similar values decreasing the number of queries to the switches. PMID:29614049

Fault tolerant high-performance PACS network design and implementation

NASA Astrophysics Data System (ADS)

Chimiak, William J.; Boehme, Johannes M.

1998-07-01

The Wake Forest University School of Medicine and the Wake Forest University/Baptist Medical Center (WFUBMC) are implementing a second generation PACS. The first generation PACS provided helpful information about the functional and temporal requirements of the system. It highlighted the importance of image retrieval speed, system availability, RIS/HIS integration, the ability to rapidly view images on any PACS workstation, network bandwidth, equipment redundancy, and the ability for the system to evolve using standards-based components. This paper deals with the network design and implementation of the PACS. The physical layout of the hospital areas served by the PACS, the choice of network equipment and installation issues encountered are addressed. Efforts to optimize fault tolerance are discussed. The PACS network is a gigabit, mixed-media network based on LAN emulation over ATM (LANE) with a rapid migration from LANE to Multiple Protocols Over ATM (MPOA) planned. Two fault-tolerant backbone ATM switches serve to distribute network accesses with two load-balancing 622 megabit per second (Mbps) OC-12 interconnections. The switch was sized to be upgradable to provide a 2.54 Gbps OC-48 interconnection with an OC-12 interconnection as a load-balancing backup. Modalities connect with legacy network interface cards to a switched-ethernet device. This device has two 155 Mbps OC-3 load-balancing uplinks to each of the backbone ATM switches of the PACS. This provides a fault-tolerant logical connection to the modality servers which pass verified DICOM images to the PACS servers and proper PACS diagnostic workstations. Where fiber pulls were prohibitively expensive, edge ATM switches were installed with an OC-12 uplink to a backbone ATM switches. The PACS and data base servers are fault-tolerant, hot-swappable Sun Enterprise Servers with an OC-12 connection to a backbone ATM switch and a fast-ethernet connection to a back-up network. The workstations come with 10/100 BASET autosense cards. A redundant switched-ethernet network will be installed to provide yet another degree of network fault-tolerance. The switched-ethernet devices are connected to each of the backbone ATM switches with two-load-balancing OC-3 connections to provide fault-tolerant connectivity in the event of a primary network failure.

Scalable Active Optical Access Network Using Variable High-Speed PLZT Optical Switch/Splitter

NASA Astrophysics Data System (ADS)

Ashizawa, Kunitaka; Sato, Takehiro; Tokuhashi, Kazumasa; Ishii, Daisuke; Okamoto, Satoru; Yamanaka, Naoaki; Oki, Eiji

This paper proposes a scalable active optical access network using high-speed Plumbum Lanthanum Zirconate Titanate (PLZT) optical switch/splitter. The Active Optical Network, called ActiON, using PLZT switching technology has been presented to increase the number of subscribers and the maximum transmission distance, compared to the Passive Optical Network (PON). ActiON supports the multicast slot allocation realized by running the PLZT switch elements in the splitter mode, which forces the switch to behave as an optical splitter. However, the previous ActiON creates a tradeoff between the network scalability and the power loss experienced by the optical signal to each user. It does not use the optical power efficiently because the optical power is simply divided into 0.5 to 0.5 without considering transmission distance from OLT to each ONU. The proposed network adopts PLZT switch elements in the variable splitter mode, which controls the split ratio of the optical power considering the transmission distance from OLT to each ONU, in addition to PLZT switch elements in existing two modes, the switching mode and the splitter mode. The proposed network introduces the flexible multicast slot allocation according to the transmission distance from OLT to each user and the number of required users using three modes, while keeping the advantages of ActiON, which are to support scalable and secure access services. Numerical results show that the proposed network dramatically reduces the required number of slots and supports high bandwidth efficiency services and extends the coverage of access network, compared to the previous ActiON, and the required computation time for selecting multicast users is less than 30msec, which is acceptable for on-demand broadcast services.

76 FR 36154 - In the Matter of Certain Equipment for Communications Networks, Including Switches, Routers...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-21

... Communications Networks, Including Switches, Routers, Gateways, Bridges, Wireless Access Points, Cable Modems, IP... networks, including switches, routers, gateways, bridges, wireless access points, cable modems, IP phones... points, cable modems, IP phones, and products containing same that infringe one or more of claims 1, 5, 9...

Remote Optical Switch for Localized and Selective Control of Gene Interference

PubMed Central

Lee, Somin Eunice; Liu, Gang Logan; Kim, Franklin; Lee, Luke P.

2009-01-01

Near infrared-absorbing gold nanoplasmonic particles (GNPs) are used as optical switches of gene interference and are remotely controlled using light. We have tuned optical switches to a wavelength where cellular photodamage is minimized. Optical switches are functionalized with double-stranded oligonucleotides. At desired times and at specific intracellular locations, remote optical excitation is used to liberate gene-interfering oligonucleotides. We demonstrate a novel gene-interfering technique offering spatial and temporal control, which is otherwise impossible using conventional gene-interfering techniques. PMID:19128006

Prioritized retransmission in slotted all-optical packet-switched networks

NASA Astrophysics Data System (ADS)

Ghaffar Pour Rahbar, Akbar; Yang, Oliver

2006-12-01

We consider an all-optical slotted packet-switched network interconnected by a number of bufferless all-optical switches with contention-based operation. One approach to reduce the cost of the expensive contention resolution hardware could be retransmission in which each ingress switch keeps a copy of the transmitted traffic in the electronic buffer and retransmits whenever required. The conventional retransmission technique may need a higher number of retransmissions until traffic passes through the network. This in turn may lead to a retransmission at a higher layer and reduce the network throughput. In this paper, we propose and analyze a simple but effective prioritized retransmission technique in which dropped traffic is prioritized when retransmitted from ingress switches so that the core switch can process them with a higher priority. We present the analysis of both techniques in multifiber network architecture and verify it via simulation to demonstrate that our proposed algorithm can limit the number of retransmissions significantly and can improve TCP throughput better than the conventional retransmission technique.

Neural networks supporting switching, hypothesis testing, and rule application

PubMed Central

Liu, Zhiya; Braunlich, Kurt; Wehe, Hillary S.; Seger, Carol A.

2015-01-01

We identified dynamic changes in recruitment of neural connectivity networks across three phases of a flexible rule learning and set-shifting task similar to the Wisconsin Card Sort Task: switching, rule learning via hypothesis testing, and rule application. During fMRI scanning, subjects viewed pairs of stimuli that differed across four dimensions (letter, color, size, screen location), chose one stimulus, and received feedback. Subjects were informed that the correct choice was determined by a simple unidimensional rule, for example “choose the blue letter.” Once each rule had been learned and correctly applied for 4-7 trials, subjects were cued via either negative feedback or visual cues to switch to learning a new rule. Task performance was divided into three phases: Switching (first trial after receiving the switch cue), hypothesis testing (subsequent trials through the last error trial), and rule application (correct responding after the rule was learned). We used both univariate analysis to characterize activity occurring within specific regions of the brain, and a multivariate method, constrained principal component analysis for fMRI (fMRI-CPCA), to investigate how distributed regions coordinate to subserve different processes. As hypothesized, switching was subserved by a limbic network including the ventral striatum, thalamus, and parahippocampal gyrus, in conjunction with cortical salience network regions including the anterior cingulate and frontoinsular cortex. Activity in the ventral striatum was associated with switching regardless of how switching was cued; visually cued shifts were associated with additional visual cortical activity. After switching, as subjects moved into the hypothesis testing phase, a broad fronto-parietal-striatal network (associated with the cognitive control, dorsal attention, and salience networks) increased in activity. This network was sensitive to rule learning speed, with greater extended activity for the slowest learning speed late in the time course of learning. As subjects shifted from hypothesis testing to rule application, activity in this network decreased and activity in the somatomotor and default mode networks increased. PMID:26197092

Neural networks supporting switching, hypothesis testing, and rule application.

PubMed

Liu, Zhiya; Braunlich, Kurt; Wehe, Hillary S; Seger, Carol A

2015-10-01

We identified dynamic changes in recruitment of neural connectivity networks across three phases of a flexible rule learning and set-shifting task similar to the Wisconsin Card Sort Task: switching, rule learning via hypothesis testing, and rule application. During fMRI scanning, subjects viewed pairs of stimuli that differed across four dimensions (letter, color, size, screen location), chose one stimulus, and received feedback. Subjects were informed that the correct choice was determined by a simple unidimensional rule, for example "choose the blue letter". Once each rule had been learned and correctly applied for 4-7 trials, subjects were cued via either negative feedback or visual cues to switch to learning a new rule. Task performance was divided into three phases: Switching (first trial after receiving the switch cue), hypothesis testing (subsequent trials through the last error trial), and rule application (correct responding after the rule was learned). We used both univariate analysis to characterize activity occurring within specific regions of the brain, and a multivariate method, constrained principal component analysis for fMRI (fMRI-CPCA), to investigate how distributed regions coordinate to subserve different processes. As hypothesized, switching was subserved by a limbic network including the ventral striatum, thalamus, and parahippocampal gyrus, in conjunction with cortical salience network regions including the anterior cingulate and frontoinsular cortex. Activity in the ventral striatum was associated with switching regardless of how switching was cued; visually cued shifts were associated with additional visual cortical activity. After switching, as subjects moved into the hypothesis testing phase, a broad fronto-parietal-striatal network (associated with the cognitive control, dorsal attention, and salience networks) increased in activity. This network was sensitive to rule learning speed, with greater extended activity for the slowest learning speed late in the time course of learning. As subjects shifted from hypothesis testing to rule application, activity in this network decreased and activity in the somatomotor and default mode networks increased. Copyright © 2015 Elsevier Ltd. All rights reserved.

A Lossless Network for Data Acquisition

NASA Astrophysics Data System (ADS)

Jereczek, Grzegorz; Lehmann Miotto, Giovanna; Malone, David; Walukiewicz, Miroslaw

2017-06-01

The bursty many-to-one communication pattern, typical for data acquisition systems, is particularly demanding for commodity TCP/IP and Ethernet technologies. We expand the study of lossless switching in software running on commercial off-the-shelf servers, using the ATLAS experiment as a case study. In this paper, we extend the popular software switch, Open vSwitch, with a dedicated, throughput-oriented buffering mechanism for data acquisition. We compare the performance under heavy congestion on typical Ethernet switches to a commodity server acting as a switch. Our results indicate that software switches with large buffers perform significantly better. Next, we evaluate the scalability of the system when building a larger topology of interconnected software switches, exploiting the integration with software-defined networking technologies. We build an IP-only leaf-spine network consisting of eight software switches running on distinct physical servers as a demonstrator.

Neural correlates of task switching in paternal 15q11-q13 deletion Prader-Willi syndrome.

PubMed

Woodcock, Kate A; Humphreys, Glyn W; Oliver, Chris; Hansen, Peter C

2010-12-02

We report a first study of brain activity linked to task switching in individuals with Prader-Willi syndrome (PWS). PWS individuals show a specific cognitive deficit in task switching which may be associated with the display of temper outbursts and repetitive questioning. The performance of participants with PWS and typically developing controls was matched in a cued task switching procedure, and brain activity was contrasted on switching and non-switching blocks using fMRI. Individuals with PWS did not show the typical frontal-parietal pattern of neural activity associated with switching blocks, with significantly reduced activation in regions of the posterior parietal and ventromedial prefrontal cortices. We suggest that this is linked to a difficulty in PWS in setting appropriate attentional weights to enable task-set reconfiguration. In addition to this, PWS individuals did not show the typical pattern of deactivation, with significantly less deactivation in an anterior region of the ventromedial prefrontal cortex. One plausible explanation for this is that individuals with PWS show dysfunction within the default mode network, which has been linked to attentional control. The data point to functional changes in the neural circuitry supporting task switching in PWS even when behavioural performance is matched to controls and thus highlight neural mechanisms that may be involved in a specific pathway between genes, cognition and behaviour. Copyright © 2010 Elsevier B.V. All rights reserved.

Structural Controllability of Temporal Networks with a Single Switching Controller

PubMed Central

Yao, Peng; Hou, Bao-Yu; Pan, Yu-Jian; Li, Xiang

2017-01-01

Temporal network, whose topology evolves with time, is an important class of complex networks. Temporal trees of a temporal network describe the necessary edges sustaining the network as well as their active time points. By a switching controller which properly selects its location with time, temporal trees are used to improve the controllability of the network. Therefore, more nodes are controlled within the limited time. Several switching strategies to efficiently select the location of the controller are designed, which are verified with synthetic and empirical temporal networks to achieve better control performance. PMID:28107538

ATM encryption testing

NASA Astrophysics Data System (ADS)

Capell, Joyce; Deeth, David

1996-01-01

This paper describes why encryption was selected by Lockheed Martin Missiles & Space as the means for securing ATM networks. The ATM encryption testing program is part of an ATM network trial provided by Pacific Bell under the California Research Education Network (CalREN). The problem being addressed is the threat to data security which results when changing from a packet switched network infrastructure to a circuit switched ATM network backbone. As organizations move to high speed cell-based networks, there is a break down in the traditional security model which is designed to protect packet switched data networks from external attacks. This is due to the fact that most data security firewalls filter IP packets, restricting inbound and outbound protocols, e.g. ftp. ATM networks, based on cell-switching over virtual circuits, does not support this method for restricting access since the protocol information is not carried by each cell. ATM switches set up multiple virtual connections, thus there is no longer a single point of entry into the internal network. The problem is further complicated by the fact that ATM networks support high speed multi-media applications, including real time video and video teleconferencing which are incompatible with packet switched networks. The ability to restrict access to Lockheed Martin networks in support of both unclassified and classified communications is required before ATM network technology can be fully deployed. The Lockheed Martin CalREN ATM testbed provides the opportunity to test ATM encryption prototypes with actual applications to assess the viability of ATM encryption methodologies prior to installing large scale ATM networks. Two prototype ATM encryptors are being tested: (1) `MILKBUSH' a prototype encryptor developed by NSA for transmission of government classified data over ATM networks, and (2) a prototype ATM encryptor developed by Sandia National Labs in New Mexico, for the encryption of proprietary data.

Mathematical model of a gene regulatory network reconciles effects of genetic perturbations on hematopoietic stem cell emergence.

PubMed

Narula, Jatin; Williams, C J; Tiwari, Abhinav; Marks-Bluth, Jonathon; Pimanda, John E; Igoshin, Oleg A

2013-07-15

Interlinked gene regulatory networks (GRNs) are vital for the spatial and temporal control of gene expression during development. The hematopoietic transcription factors (TFs) Scl, Gata2 and Fli1 form one such densely connected GRN which acts as a master regulator of embryonic hematopoiesis. This triad has been shown to direct the specification of the hemogenic endothelium and emergence of hematopoietic stem cells (HSCs) in response to Notch1 and Bmp4-Smad signaling. Here we employ previously published data to construct a mathematical model of this GRN network and use this model to systematically investigate the network dynamical properties. Our model uses a statistical-thermodynamic framework to describe the combinatorial regulation of gene expression and reconciles, mechanistically, several previously published but unexplained results from different genetic perturbation experiments. In particular, our results demonstrate how the interactions of Runx1, an essential hematopoietic TF, with components of the Bmp4 signaling pathway allow it to affect triad activation and acts as a key regulator of HSC emergence. We also explain why heterozygous deletion of this essential TF, Runx1, speeds up the network dynamics leading to accelerated HSC emergence. Taken together our results demonstrate that the triad, a master-level controller of definitive hematopoiesis, is an irreversible bistable switch whose dynamical properties are modulated by Runx1 and components of the Bmp4 signaling pathway. Copyright © 2013 Elsevier Inc. All rights reserved.

Fast packet switch architectures for broadband integrated services digital networks

NASA Technical Reports Server (NTRS)

Tobagi, Fouad A.

1990-01-01

Background information on networking and switching is provided, and the various architectures that have been considered for fast packet switches are described. The focus is solely on switches designed to be implemented electronically. A set of definitions and a brief description of the functionality required of fast packet switches are given. Three basic types of packet switches are identified: the shared-memory, shared-medium, and space-division types. Each of these is described, and examples are given.

Local area network with fault-checking, priorities, and redundant backup

NASA Technical Reports Server (NTRS)

Morales, Sergio (Inventor); Friedman, Gary L. (Inventor)

1989-01-01

This invention is a redundant error detecting and correcting local area networked computer system having a plurality of nodes each including a network connector board within the node for connecting to an interfacing transceiver operably attached to a network cable. There is a first network cable disposed along a path to interconnect the nodes. The first network cable includes a plurality of first interfacing transceivers attached thereto. A second network cable is disposed in parallel with the first cable and, in like manner, includes a plurality of second interfacing transceivers attached thereto. There are a plurality of three position switches each having a signal input, three outputs for individual selective connection to the input, and a control input for receiving signals designating which of the outputs is to be connected to the signal input. Each of the switches includes means for designating a response address for responding to addressed signals appearing at the control input and each of the switches further has its signal input connected to a respective one of the input/output lines from the nodes. Also, one of the three outputs is connected to a repective one of the plurality of first interfacing transceivers. There is master switch control means having an output connected to the control inputs of the plurality of three position switches and an input for receiving directive signals for outputting addressed switch position signals to the three position switches as well as monitor and control computer means having a pair of network connector boards therein connected to respective ones of one of the first interfacing transceivers and one of the second interfacing transceivers and an output connected to the input of the master switch means for monitoring the status of the networked computer system by sending messages to the nodes and receiving and verifying messages therefrom and for sending control signals to the master switch to cause the master switch to cause respective ones of the nodes to use a desired one of the first and second cables for transmitting and receiving messages and for disconnecting desired ones of the nodes from both cables.

An efficient platform for genetic selection and screening of gene switches in Escherichia coli

PubMed Central

Muranaka, Norihito; Sharma, Vandana; Nomura, Yoko; Yokobayashi, Yohei

2009-01-01

Engineered gene switches and circuits that can sense various biochemical and physical signals, perform computation, and produce predictable outputs are expected to greatly advance our ability to program complex cellular behaviors. However, rational design of gene switches and circuits that function in living cells is challenging due to the complex intracellular milieu. Consequently, most successful designs of gene switches and circuits have relied, to some extent, on high-throughput screening and/or selection from combinatorial libraries of gene switch and circuit variants. In this study, we describe a generic and efficient platform for selection and screening of gene switches and circuits in Escherichia coli from large libraries. The single-gene dual selection marker tetA was translationally fused to green fluorescent protein (gfpuv) via a flexible peptide linker and used as a dual selection and screening marker for laboratory evolution of gene switches. Single-cycle (sequential positive and negative selections) enrichment efficiencies of >7000 were observed in mock selections of model libraries containing functional riboswitches in liquid culture. The technique was applied to optimize various parameters affecting the selection outcome, and to isolate novel thiamine pyrophosphate riboswitches from a complex library. Artificial riboswitches with excellent characteristics were isolated that exhibit up to 58-fold activation as measured by fluorescent reporter gene assay. PMID:19190095

Stabilizing Motifs in Autonomous Boolean Networks and the Yeast Cell Cycle Oscillator

NASA Astrophysics Data System (ADS)

Sevim, Volkan; Gong, Xinwei; Socolar, Joshua

2009-03-01

Synchronously updated Boolean networks are widely used to model gene regulation. Some properties of these model networks are known to be artifacts of the clocking in the update scheme. Autonomous updating is a less artificial scheme that allows one to introduce small timing perturbations and study stability of the attractors. We argue that the stabilization of a limit cycle in an autonomous Boolean network requires a combination of motifs such as feed-forward loops and auto-repressive links that can correct small fluctuations in the timing of switching events. A recently published model of the transcriptional cell-cycle oscillator in yeast contains the motifs necessary for stability under autonomous updating [1]. [1] D. A. Orlando, et al. Nature (London), 4530 (7197):0 944--947, 2008.

Architecture design and performance evaluation of multigranularity optical networks based on optical code division multiplexing

NASA Astrophysics Data System (ADS)

Huang, Shaowei; Baba, Ken-Ichi; Murata, Masayuki; Kitayama, Ken-Ichi

2006-12-01

In traditional lambda-based multigranularity optical networks, a lambda is always treated as the basic routing unit, resulting in low wavelength utilization. On the basis of optical code division multiplexing (OCDM) technology, a novel OCDM-based multigranularity optical cross-connect (MG-OXC) is proposed. Compared with the traditional lambda-based MG-OXC, its switching capability has been extended to support fiber switching, waveband switching, lambda switching, and OCDM switching. In a network composed of OCDM-based MG-OXCs, a single wavelength can be shared by distinct label switched paths (LSPs) called OCDM-LSPs, and OCDM-LSP switching can be implemented in the optical domain. To improve the network flexibility for an OCDM-LSP provisioning, two kinds of switches enabling hybrid optical code (OC)-wavelength conversion are designed. Simulation results indicate that a blocking probability reduction of 2 orders can be obtained by deploying only five OCs to a single wavelength. Furthermore, compared with time-division-multiplexing LSP (TDM-LSP), owing to the asynchronous accessibility and the OC conversion, OCDM-LSPs have been shown to permit a simpler switch architecture and achieve better blocking performance than TDM-LSPs.

Performance of highly connected photonic switching lossless metro-access optical networks

NASA Astrophysics Data System (ADS)

Martins, Indayara Bertoldi; Martins, Yara; Barbosa, Felipe Rudge

2018-03-01

The present work analyzes the performance of photonic switching networks, optical packet switching (OPS) and optical burst switching (OBS), in mesh topology of different sizes and configurations. The "lossless" photonic switching node is based on a semiconductor optical amplifier, demonstrated and validated with experimental results on optical power gain, noise figure, and spectral range. The network performance was evaluated through computer simulations based on parameters such as average number of hops, optical packet loss fraction, and optical transport delay (Am). The combination of these elements leads to a consistent account of performance, in terms of network traffic and packet delivery for OPS and OBS metropolitan networks. Results show that a combination of highly connected mesh topologies having an ingress e-buffer present high efficiency and throughput, with very low packet loss and low latency, ensuring fast data delivery to the final receiver.

Developmental Progression in the Coral Acropora digitifera Is Controlled by Differential Expression of Distinct Regulatory Gene Networks

PubMed Central

Reyes-Bermudez, Alejandro; Villar-Briones, Alejandro; Ramirez-Portilla, Catalina; Hidaka, Michio; Mikheyev, Alexander S.

2016-01-01

Corals belong to the most basal class of the Phylum Cnidaria, which is considered the sister group of bilaterian animals, and thus have become an emerging model to study the evolution of developmental mechanisms. Although cell renewal, differentiation, and maintenance of pluripotency are cellular events shared by multicellular animals, the cellular basis of these fundamental biological processes are still poorly understood. To understand how changes in gene expression regulate morphogenetic transitions at the base of the eumetazoa, we performed quantitative RNA-seq analysis during Acropora digitifera’s development. We collected embryonic, larval, and adult samples to characterize stage-specific transcription profiles, as well as broad expression patterns. Transcription profiles reconstructed development revealing two main expression clusters. The first cluster grouped blastula and gastrula and the second grouped subsequent developmental time points. Consistently, we observed clear differences in gene expression between early and late developmental transitions, with higher numbers of differentially expressed genes and fold changes around gastrulation. Furthermore, we identified three coexpression clusters that represented discrete gene expression patterns. During early transitions, transcriptional networks seemed to regulate cellular fate and morphogenesis of the larval body. In late transitions, these networks seemed to play important roles preparing planulae for switch in lifestyle and regulation of adult processes. Although developmental progression in A. digitifera is regulated to some extent by differential coexpression of well-defined gene networks, stage-specific transcription profiles appear to be independent entities. While negative regulation of transcription is predominant in early development, cell differentiation was upregulated in larval and adult stages. PMID:26941230

Asynchronous Transfer Mode (ATM) Switch Technology and Vendor Survey

NASA Technical Reports Server (NTRS)

Berry, Noemi

1995-01-01

Asynchronous Transfer Mode (ATM) switch and software features are described and compared in order to make switch comparisons meaningful. An ATM switch's performance cannot be measured solely based on its claimed switching capacity; traffic management and congestion control are emerging as the determining factors in an ATM network's ultimate throughput. Non-switch ATM products and experiences with actual installations of ATM networks are described. A compilation of select vendor offerings as of October 1994 is provided in chart form.

Six-port optical switch for cluster-mesh photonic network-on-chip

NASA Astrophysics Data System (ADS)

Jia, Hao; Zhou, Ting; Zhao, Yunchou; Xia, Yuhao; Dai, Jincheng; Zhang, Lei; Ding, Jianfeng; Fu, Xin; Yang, Lin

2018-05-01

Photonic network-on-chip for high-performance multi-core processors has attracted substantial interest in recent years as it offers a systematic method to meet the demand of large bandwidth, low latency and low power dissipation. In this paper we demonstrate a non-blocking six-port optical switch for cluster-mesh photonic network-on-chip. The architecture is constructed by substituting three optical switching units of typical Spanke-Benes network to optical waveguide crossings. Compared with Spanke-Benes network, the number of optical switching units is reduced by 20%, while the connectivity of routing path is maintained. By this way the footprint and power consumption can be reduced at the expense of sacrificing the network latency performance in some cases. The device is realized by 12 thermally tuned silicon Mach-Zehnder optical switching units. Its theoretical spectral responses are evaluated by establishing a numerical model. The experimental spectral responses are also characterized, which indicates that the optical signal-to-noise ratios of the optical switch are larger than 13.5 dB in the wavelength range from 1525 nm to 1565 nm. Data transmission experiment with the data rate of 32 Gbps is implemented for each optical link.

Shipboard Calibration Network Extension Utilizing COTS Products

DTIC Science & Technology

2014-09-01

to emulate the MCS system console. C. KEYBOARD VIDEO AND MOUSE (KVM) SWITCH A ServSwitch Wizard IP Plus KVM switch is used to allow remote access...9 C. KEYBOARD VIDEO AND MOUSE (KVM) SWITCH .......................... 10 D. ROUTER...mechanical, and electrical KVM Keyboard Video and Mouse LAN Local Area Network MCS Machinery Control Systems NIST National Institute of Standards and

QKD-Based Secured Burst Integrity Design for Optical Burst Switched Networks

NASA Astrophysics Data System (ADS)

Balamurugan, A. M.; Sivasubramanian, A.; Parvathavarthini, B.

2016-03-01

The field of optical transmission has undergone numerous advancements and is still being researched mainly due to the fact that optical data transmission can be done at enormous speeds. It is quite evident that people prefer optical communication when it comes to large amount of data involving its transmission. The concept of switching in networks has matured enormously with several researches, architecture to implement and methods starting with Optical circuit switching to Optical Burst Switching. Optical burst switching is regarded as viable solution for switching bursts over networks but has several security vulnerabilities. However, this work exploited the security issues associated with Optical Burst Switching with respect to integrity of burst. This proposed Quantum Key based Secure Hash Algorithm (QKBSHA-512) with enhanced compression function design provides better avalanche effect over the conventional integrity algorithms.

A novel riboregulator switch system of gene expression for enhanced microbial production of succinic acid.

PubMed

Wang, Jing; Wang, Haoyuan; Yang, Le; Lv, Liping; Zhang, Zhe; Ren, Bin; Dong, Lichun; Li, Ning

2018-04-01

In this paper, a novel riboregulator Switch System of Gene Expression including an OFF-TO-ON switch and an ON-TO-OFF switch was designed to regulate the expression state of target genes between "ON" and "OFF" by switching the identifiability of ribosome recognition site (RBS) based on the thermodynamic stability of different RNA-RNA hybridizations between RBS and small noncoding RNAs. The proposed riboregulator switch system was employed for the fermentative production of succinic acid using an engineered strain of E. coli JW1021, during which the expression of mgtC gene was controlled at "ON" state and that of pepc and ecaA genes were controlled at the "OFF" state in the lag phase and switched to the "OFF" and "ON" state once the strain enters the logarithmic phase. The results showed that using the strain of JW1021, the yield and productivity of succinic acid can reach 0.91 g g -1 and 3.25 g L -1  h -1 , respectively, much higher than those using the strains without harboring the riboregulator switch system.

47 CFR 68.201 - Connection to the public switched telephone network.

Code of Federal Regulations, 2010 CFR

2010-10-01

... network. 68.201 Section 68.201 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES (CONTINUED) CONNECTION OF TERMINAL EQUIPMENT TO THE TELEPHONE NETWORK Terminal Equipment Approval Procedures § 68.201 Connection to the public switched telephone network. Terminal equipment may...

47 CFR 68.201 - Connection to the public switched telephone network.

Code of Federal Regulations, 2011 CFR

2011-10-01

... network. 68.201 Section 68.201 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES (CONTINUED) CONNECTION OF TERMINAL EQUIPMENT TO THE TELEPHONE NETWORK Terminal Equipment Approval Procedures § 68.201 Connection to the public switched telephone network. Terminal equipment may...

Discrete-time systems with random switches: From systems stability to networks synchronization.

PubMed

Guo, Yao; Lin, Wei; Ho, Daniel W C

2016-03-01

In this article, we develop some approaches, which enable us to more accurately and analytically identify the essential patterns that guarantee the almost sure stability of discrete-time systems with random switches. We allow for the case that the elements in the switching connection matrix even obey some unbounded and continuous-valued distributions. In addition to the almost sure stability, we further investigate the almost sure synchronization in complex dynamical networks consisting of randomly connected nodes. Numerical examples illustrate that a chaotic dynamics in the synchronization manifold is preserved when statistical parameters enter some almost sure synchronization region established by the developed approach. Moreover, some delicate configurations are considered on probability space for ensuring synchronization in networks whose nodes are described by nonlinear maps. Both theoretical and numerical results on synchronization are presented by setting only a few random connections in each switch duration. More interestingly, we analytically find it possible to achieve almost sure synchronization in the randomly switching complex networks even with very large population sizes, which cannot be easily realized in non-switching but deterministically connected networks.

Discrete-time systems with random switches: From systems stability to networks synchronization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Yao; Lin, Wei, E-mail: wlin@fudan.edu.cn; Shanghai Key Laboratory of Contemporary Applied Mathematics, LMNS, and Shanghai Center for Mathematical Sciences, Shanghai 200433

2016-03-15

In this article, we develop some approaches, which enable us to more accurately and analytically identify the essential patterns that guarantee the almost sure stability of discrete-time systems with random switches. We allow for the case that the elements in the switching connection matrix even obey some unbounded and continuous-valued distributions. In addition to the almost sure stability, we further investigate the almost sure synchronization in complex dynamical networks consisting of randomly connected nodes. Numerical examples illustrate that a chaotic dynamics in the synchronization manifold is preserved when statistical parameters enter some almost sure synchronization region established by the developedmore » approach. Moreover, some delicate configurations are considered on probability space for ensuring synchronization in networks whose nodes are described by nonlinear maps. Both theoretical and numerical results on synchronization are presented by setting only a few random connections in each switch duration. More interestingly, we analytically find it possible to achieve almost sure synchronization in the randomly switching complex networks even with very large population sizes, which cannot be easily realized in non-switching but deterministically connected networks.« less

Tensegrity II. How structural networks influence cellular information processing networks

NASA Technical Reports Server (NTRS)

Ingber, Donald E.

2003-01-01

The major challenge in biology today is biocomplexity: the need to explain how cell and tissue behaviors emerge from collective interactions within complex molecular networks. Part I of this two-part article, described a mechanical model of cell structure based on tensegrity architecture that explains how the mechanical behavior of the cell emerges from physical interactions among the different molecular filament systems that form the cytoskeleton. Recent work shows that the cytoskeleton also orients much of the cell's metabolic and signal transduction machinery and that mechanical distortion of cells and the cytoskeleton through cell surface integrin receptors can profoundly affect cell behavior. In particular, gradual variations in this single physical control parameter (cell shape distortion) can switch cells between distinct gene programs (e.g. growth, differentiation and apoptosis), and this process can be viewed as a biological phase transition. Part II of this article covers how combined use of tensegrity and solid-state mechanochemistry by cells may mediate mechanotransduction and facilitate integration of chemical and physical signals that are responsible for control of cell behavior. In addition, it examines how cell structural networks affect gene and protein signaling networks to produce characteristic phenotypes and cell fate transitions during tissue development.

Hypoxia induces a HIF-1α dependent signaling cascade to make a complex metabolic switch in SGBS-adipocytes.

PubMed

Leiherer, Andreas; Geiger, Kathrin; Muendlein, Axel; Drexel, Heinz

2014-03-05

To elucidate the complex impact of hypoxia on adipose tissue, resulting in biased metabolism, insulin resistance and finally diabetes we used mature adipocytes derived from a Simpson-Golabi-Behmel syndrome patient for microarray analysis. We found a significantly increased transcription rate of genes involved in glycolysis and a striking association between the pattern of upregulated genes and disease biomarkers for diabetes mellitus and insulin resistance. Although their upregulation turned out to be HIF-1α-dependent, we identified further transcription factors mainly AP-1 components to play also an important role in hypoxia response. Analyzing the regulatory network of mentioned transcription factors and glycolysis targets we revealed a clear hint for directing glycolysis to glutathione and glycogen synthesis. This metabolic switch in adipocytes enables the cell to prevent oxidative damage in the short term but might induce lipogenesis and establish systemic metabolic disorders in the long run. Copyright © 2013 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Advanced optical components for next-generation photonic networks

NASA Astrophysics Data System (ADS)

Yoo, S. J. B.

2003-08-01

Future networks will require very high throughput, carrying dominantly data-centric traffic. The role of Photonic Networks employing all-optical systems will become increasingly important in providing scalable bandwidth, agile reconfigurability, and low-power consumptions in the future. In particular, the self-similar nature of data traffic indicates that packet switching and burst switching will be beneficial in the Next Generation Photonic Networks. While the natural conclusion is to pursue Photonic Packet Switching and Photonic Burst Switching systems, there are significant challenges in realizing such a system due to practical limitations in optical component technologies. Lack of a viable all-optical memory technology will continue to drive us towards exploring rapid reconfigurability in the wavelength domain. We will introduce and discuss the advanced optical component technologies behind the Photonic Packet Routing system designed and demonstrated at UC Davis. The system is capable of packet switching and burst switching, as well as circuit switching with 600 psec switching speed and scalability to 42 petabit/sec aggregated switching capacity. By utilizing a combination of rapidly tunable wavelength conversion and a uniform-loss cyclic frequency (ULCF) arrayed waveguide grating router (AWGR), the system is capable of rapidly switching the packets in wavelength, time, and space domains. The label swapping module inside the Photonic Packet Routing system containing a Mach-Zehnder wavelength converter and a narrow-band fiber Bragg-grating achieves all-optical label swapping with optical 2R (potentially 3R) regeneration while maintaining optical transparency for the data payload. By utilizing the advanced optical component technologies, the Photonic Packet Routing system successfully demonstrated error-free, cascaded, multi-hop photonic packet switching and routing with optical-label swapping. This paper will review the advanced optical component technologies and their role in the Next Generation Photonic Networks.

Crossbar Switches For Optical Data-Communication Networks

NASA Technical Reports Server (NTRS)

Monacos, Steve P.

1994-01-01

Optoelectronic and electro-optical crossbar switches called "permutation engines" (PE's) developed to route packets of data through fiber-optic communication networks. Basic network concept described in "High-Speed Optical Wide-Area Data-Communication Network" (NPO-18983). Nonblocking operation achieved by decentralized switching and control scheme. Each packet routed up or down in each column of this 5-input/5-output permutation engine. Routing algorithm ensures each packet arrives at its designated output port without blocking any other packet that does not contend for same output port.

Analysis of adaptive algorithms for an integrated communication network

NASA Technical Reports Server (NTRS)

Reed, Daniel A.; Barr, Matthew; Chong-Kwon, Kim

1985-01-01

Techniques were examined that trade communication bandwidth for decreased transmission delays. When the network is lightly used, these schemes attempt to use additional network resources to decrease communication delays. As the network utilization rises, the schemes degrade gracefully, still providing service but with minimal use of the network. Because the schemes use a combination of circuit and packet switching, they should respond to variations in the types and amounts of network traffic. Also, a combination of circuit and packet switching to support the widely varying traffic demands imposed on an integrated network was investigated. The packet switched component is best suited to bursty traffic where some delays in delivery are acceptable. The circuit switched component is reserved for traffic that must meet real time constraints. Selected packet routing algorithms that might be used in an integrated network were simulated. An integrated traffic places widely varying workload demands on a network. Adaptive algorithms were identified, ones that respond to both the transient and evolutionary changes that arise in integrated networks. A new algorithm was developed, hybrid weighted routing, that adapts to workload changes.

Principle and verification of novel optical virtual private networks over multiprotocol label switching/optical packet switching networks

NASA Astrophysics Data System (ADS)

Zhang, Chongfu; Wang, Zhengsuan; Jin, Wei; Qiu, Kun

2012-11-01

A novel realization method of the optical virtual private networks (OVPN) over multiprotocol label switching/optical packet switching (MPLS/OPS) networks is proposed. In this scheme, the introduction of MPLS control plane makes OVPN over OPS networks more reliable and easier; OVPN makes use of the concept of high reconfiguration of light-paths offered by MPLS, to set up secure tunnels of high bandwidth across intelligent OPS networks. Through resource management, the signal mechanism, connection control, and the architecture of the creation and maintenance of OVPN are efficiently realized. We also present an OVPN architecture with two traffic priorities, which is used to analyze the capacity, throughput, delay time of the proposed networks, and the packet loss rate performance of the OVPN over MPLS/OPS networks based on full mesh topology. The results validate the applicability of such reliable connectivity to high quality services in the OVPN over MPLS/OPS networks. Along with the results, the feasibility of the approach as the basis for the next generation networks is demonstrated and discussed.

A model of gene expression based on random dynamical systems reveals modularity properties of gene regulatory networks.

PubMed

Antoneli, Fernando; Ferreira, Renata C; Briones, Marcelo R S

2016-06-01

Here we propose a new approach to modeling gene expression based on the theory of random dynamical systems (RDS) that provides a general coupling prescription between the nodes of any given regulatory network given the dynamics of each node is modeled by a RDS. The main virtues of this approach are the following: (i) it provides a natural way to obtain arbitrarily large networks by coupling together simple basic pieces, thus revealing the modularity of regulatory networks; (ii) the assumptions about the stochastic processes used in the modeling are fairly general, in the sense that the only requirement is stationarity; (iii) there is a well developed mathematical theory, which is a blend of smooth dynamical systems theory, ergodic theory and stochastic analysis that allows one to extract relevant dynamical and statistical information without solving the system; (iv) one may obtain the classical rate equations form the corresponding stochastic version by averaging the dynamic random variables (small noise limit). It is important to emphasize that unlike the deterministic case, where coupling two equations is a trivial matter, coupling two RDS is non-trivial, specially in our case, where the coupling is performed between a state variable of one gene and the switching stochastic process of another gene and, hence, it is not a priori true that the resulting coupled system will satisfy the definition of a random dynamical system. We shall provide the necessary arguments that ensure that our coupling prescription does indeed furnish a coupled regulatory network of random dynamical systems. Finally, the fact that classical rate equations are the small noise limit of our stochastic model ensures that any validation or prediction made on the basis of the classical theory is also a validation or prediction of our model. We illustrate our framework with some simple examples of single-gene system and network motifs. Copyright © 2016 Elsevier Inc. All rights reserved.

Tcf7 Is an Important Regulator of the Switch of Self-Renewal and Differentiation in a Multipotential Hematopoietic Cell Line

PubMed Central

Schulz, Vincent P.; Hariharan, Manoj; Tuck, David; Lian, Jin; Du, Jiang; Shi, Minyi; Ye, Zhijia; Gerstein, Mark; Snyder, Michael P.; Weissman, Sherman

2012-01-01

A critical problem in biology is understanding how cells choose between self-renewal and differentiation. To generate a comprehensive view of the mechanisms controlling early hematopoietic precursor self-renewal and differentiation, we used systems-based approaches and murine EML multipotential hematopoietic precursor cells as a primary model. EML cells give rise to a mixture of self-renewing Lin-SCA+CD34+ cells and partially differentiated non-renewing Lin-SCA-CD34− cells in a cell autonomous fashion. We identified and validated the HMG box protein TCF7 as a regulator in this self-renewal/differentiation switch that operates in the absence of autocrine Wnt signaling. We found that Tcf7 is the most down-regulated transcription factor when CD34+ cells switch into CD34− cells, using RNA–Seq. We subsequently identified the target genes bound by TCF7, using ChIP–Seq. We show that TCF7 and RUNX1 (AML1) bind to each other's promoter regions and that TCF7 is necessary for the production of the short isoforms, but not the long isoforms of RUNX1, suggesting that TCF7 and the short isoforms of RUNX1 function coordinately in regulation. Tcf7 knock-down experiments and Gene Set Enrichment Analyses suggest that TCF7 plays a dual role in promoting the expression of genes characteristic of self-renewing CD34+ cells while repressing genes activated in partially differentiated CD34− state. Finally a network of up-regulated transcription factors of CD34+ cells was constructed. Factors that control hematopoietic stem cell (HSC) establishment and development, cell growth, and multipotency were identified. These studies in EML cells demonstrate fundamental cell-intrinsic properties of the switch between self-renewal and differentiation, and yield valuable insights for manipulating HSCs and other differentiating systems. PMID:22412390

Method and apparatus for determining and utilizing a time-expanded decision network

NASA Technical Reports Server (NTRS)

de Weck, Olivier (Inventor); Silver, Matthew (Inventor)

2012-01-01

A method, apparatus and computer program for determining and utilizing a time-expanded decision network is presented. A set of potential system configurations is defined. Next, switching costs are quantified to create a "static network" that captures the difficulty of switching among these configurations. A time-expanded decision network is provided by expanding the static network in time, including chance and decision nodes. Minimum cost paths through the network are evaluated under plausible operating scenarios. The set of initial design configurations are iteratively modified to exploit high-leverage switches and the process is repeated to convergence. Time-expanded decision networks are applicable, but not limited to, the design of systems, products, services and contracts.

Architecture for on-die interconnect

DOEpatents

Khare, Surhud; More, Ankit; Somasekhar, Dinesh; Dunning, David S.

2016-03-15

In an embodiment, an apparatus includes: a plurality of islands configured on a semiconductor die, each of the plurality of islands having a plurality of cores; and a plurality of network switches configured on the semiconductor die and each associated with one of the plurality of islands, where each network switch includes a plurality of output ports, a first set of the output ports are each to couple to the associated network switch of an island via a point-to-point interconnect and a second set of the output ports are each to couple to the associated network switches of a plurality of islands via a point-to-multipoint interconnect. Other embodiments are described and claimed.

On-board B-ISDN fast packet switching architectures. Phase 2: Development. Proof-of-concept architecture definition report

NASA Technical Reports Server (NTRS)

Shyy, Dong-Jye; Redman, Wayne

1993-01-01

For the next-generation packet switched communications satellite system with onboard processing and spot-beam operation, a reliable onboard fast packet switch is essential to route packets from different uplink beams to different downlink beams. The rapid emergence of point-to-point services such as video distribution, and the large demand for video conference, distributed data processing, and network management makes the multicast function essential to a fast packet switch (FPS). The satellite's inherent broadcast features gives the satellite network an advantage over the terrestrial network in providing multicast services. This report evaluates alternate multicast FPS architectures for onboard baseband switching applications and selects a candidate for subsequent breadboard development. Architecture evaluation and selection will be based on the study performed in phase 1, 'Onboard B-ISDN Fast Packet Switching Architectures', and other switch architectures which have become commercially available as large scale integration (LSI) devices.

Effects of fundamentals acquisition and strategy switch on stock price dynamics

NASA Astrophysics Data System (ADS)

Wu, Songtao; He, Jianmin; Li, Shouwei

2018-02-01

An agent-based artificial stock market is developed to simulate trading behavior of investors. In the market, acquisition and employment of information about fundamentals and strategy switch are investigated to explain stock price dynamics. Investors could obtain the information from both market and neighbors resided on their social networks. Depending on information status and performances of different strategies, an informed investor may switch to the strategy of fundamentalist. This in turn affects the information acquisition process, since fundamentalists are more inclined to search and spread the information than chartists. Further investigation into price dynamics generated from three typical networks, i.e. regular lattice, small-world network and random graph, are conducted after general relation between network structures and price dynamics is revealed. In each network, integrated effects of different combinations of information efficiency and switch intensity are investigated. Results have shown that, along with increasing switch intensity, market and social information efficiency play different roles in the formation of price distortion, standard deviation and kurtosis of returns.

Intelligent optical networking with photonic cross connections

NASA Astrophysics Data System (ADS)

Ceuppens, L.; Jerphagnon, Olivier L.; Lang, Jonathan; Banerjee, Ayan; Blumenthal, Daniel J.

2002-09-01

Optical amplification and dense wavelength division multiplexing (DWDM) have fundamentally changed optical transport networks. Now that these technologies are widely adopted, the bottleneck has moved from the outside line plant to nodal central offices, where electrical switching equipment has not kept pace. While OEO technology was (and still is) necessary for grooming and traffic aggregation, the transport network has dramatically changed, requiring a dramatic rethinking of how networks need to be designed and operated. While todays transport networks carry remarkable amounts of bandwidth, their optical layer is fundamentally static and provides for only simple point-to-point transport. Efficiently managing the growing number of wavelengths can only be achieved through a new breed of networking element. Photonic switching systems (PSS) can efficiently execute these functions because they are bit rate, wavelength, and protocol transparent. With their all-optical switch cores and interfaces, PSS can switch optical signals at various levels of granularity wavelength, sub band, and composite DWDM fiber levels. Though cross-connect systems with electrical switch cores are available, they perform these functions at very high capital costs and operational inefficiencies. This paper examines enabling technologies for deployment of intelligent optical transport networks (OTN), and takes a practical perspective on survivability architecture migration and implementation issues.

Multistage switching hardware and software implementations for student experiment purpose

NASA Astrophysics Data System (ADS)

Sani, A.; Suherman

2018-02-01

Current communication and internet networks are underpinned by the switching technologies that interconnect one network to the others. Students’ understanding on networks rely on how they conver the theories. However, understanding theories without touching the reality may exert spots in the overall knowledge. This paper reports the progress of the multistage switching design and implementation for student laboratory activities. The hardware and software designs are based on three stages clos switching architecture with modular 2x2 switches, controlled by an arduino microcontroller. The designed modules can also be extended for batcher and bayan switch, and working on circuit and packet switching systems. The circuit analysis and simulation show that the blocking probability for each switch combinations can be obtained by generating random or patterned traffics. The mathematic model and simulation analysis shows 16.4% blocking probability differences as the traffic generation is uniform. The circuits design components and interfacing solution have been identified to allow next step implementation.

An approach to efficient mobility management in intelligent networks

NASA Technical Reports Server (NTRS)

Murthy, K. M. S.

1995-01-01

Providing personal communication systems supporting full mobility require intelligent networks for tracking mobile users and facilitating outgoing and incoming calls over different physical and network environments. In realizing the intelligent network functionalities, databases play a major role. Currently proposed network architectures envision using the SS7-based signaling network for linking these DB's and also for interconnecting DB's with switches. If the network has to support ubiquitous, seamless mobile services, then it has to support additionally mobile application parts, viz., mobile origination calls, mobile destination calls, mobile location updates and inter-switch handovers. These functions will generate significant amount of data and require them to be transferred between databases (HLR, VLR) and switches (MSC's) very efficiently. In the future, the users (fixed or mobile) may use and communicate with sophisticated CPE's (e.g. multimedia, multipoint and multisession calls) which may require complex signaling functions. This will generate volumness service handling data and require efficient transfer of these message between databases and switches. Consequently, the network providers would be able to add new services and capabilities to their networks incrementally, quickly and cost-effectively.

47 CFR 68.110 - Compatibility of the public switched telephone network and terminal equipment.

Code of Federal Regulations, 2011 CFR

2011-10-01

... network and terminal equipment. 68.110 Section 68.110 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES (CONTINUED) CONNECTION OF TERMINAL EQUIPMENT TO THE TELEPHONE NETWORK Conditions on Use of Terminal Equipment § 68.110 Compatibility of the public switched telephone network and...

47 CFR 68.110 - Compatibility of the public switched telephone network and terminal equipment.

Code of Federal Regulations, 2010 CFR

2010-10-01

... network and terminal equipment. 68.110 Section 68.110 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES (CONTINUED) CONNECTION OF TERMINAL EQUIPMENT TO THE TELEPHONE NETWORK Conditions on Use of Terminal Equipment § 68.110 Compatibility of the public switched telephone network and...

Thermally Driven Transport and Relaxation Switching Self-Powered Electromagnetic Energy Conversion.

PubMed

Cao, Maosheng; Wang, Xixi; Cao, Wenqiang; Fang, Xiaoyong; Wen, Bo; Yuan, Jie

2018-06-07

Electromagnetic energy radiation is becoming a "health-killer" of living bodies, especially around industrial transformer substation and electricity pylon. Harvesting, converting, and storing waste energy for recycling are considered the ideal ways to control electromagnetic radiation. However, heat-generation and temperature-rising with performance degradation remain big problems. Herein, graphene-silica xerogel is dissected hierarchically from functions to "genes," thermally driven relaxation and charge transport, experimentally and theoretically, demonstrating a competitive synergy on energy conversion. A generic approach of "material genes sequencing" is proposed, tactfully transforming the negative effects of heat energy to superiority for switching self-powered and self-circulated electromagnetic devices, beneficial for waste energy harvesting, conversion, and storage. Graphene networks with "well-sequencing genes" (w = P c /P p > 0.2) can serve as nanogenerators, thermally promoting electromagnetic wave absorption by 250%, with broadened bandwidth covering the whole investigated frequency. This finding of nonionic energy conversion opens up an unexpected horizon for converting, storing, and reusing waste electromagnetic energy, providing the most promising way for governing electromagnetic pollution with self-powered and self-circulated electromagnetic devices. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multi-Domain SDN Survivability for Agricultural Wireless Sensor Networks.

PubMed

Huang, Tao; Yan, Siyu; Yang, Fan; Liu, Jiang

2016-11-06

Wireless sensor networks (WSNs) have been widely applied in agriculture field; meanwhile, the advent of multi-domain software-defined networks (SDNs) have improved the wireless resource utilization rate and strengthened network management. In recent times, multi-domain SDNs have been applied to agricultural sensor networks, namely multi-domain software-defined wireless sensor networks (SDWSNs). However, when the SDNs controlling agriculture networks suddenly become unavailable, whether intra-domain or inter-domain, sensor network communication is abnormal because of the loss of control. Moreover, there are controller and switch info-updating problems even if the controller becomes available again. To resolve these problems, this paper proposes a new approach based on an Open vSwitch extension for multi-domain SDWSNs, which can enhance agriculture network survivability and stability. We achieved this by designing a connection-state mechanism, a communication mechanism on both L2 and L3, and an info-updating mechanism based on Open vSwitch. The experimental results show that, whether it is agricultural inter-domain or intra-domain during the controller failure period, the sensor switches can enter failure recovery mode as soon as possible so that the sensor network keeps a stable throughput, a short failure recovery time below 300 ms, and low packet loss. Further, the domain can smoothly control the domain network again once the controller becomes available. This approach based on an Open vSwitch extension can enhance the survivability and stability of multi-domain SDWSNs in precision agriculture.

Multi-Domain SDN Survivability for Agricultural Wireless Sensor Networks

PubMed Central

Huang, Tao; Yan, Siyu; Yang, Fan; Liu, Jiang

2016-01-01

Wireless sensor networks (WSNs) have been widely applied in agriculture field; meanwhile, the advent of multi-domain software-defined networks (SDNs) have improved the wireless resource utilization rate and strengthened network management. In recent times, multi-domain SDNs have been applied to agricultural sensor networks, namely multi-domain software-defined wireless sensor networks (SDWSNs). However, when the SDNs controlling agriculture networks suddenly become unavailable, whether intra-domain or inter-domain, sensor network communication is abnormal because of the loss of control. Moreover, there are controller and switch info-updating problems even if the controller becomes available again. To resolve these problems, this paper proposes a new approach based on an Open vSwitch extension for multi-domain SDWSNs, which can enhance agriculture network survivability and stability. We achieved this by designing a connection-state mechanism, a communication mechanism on both L2 and L3, and an info-updating mechanism based on Open vSwitch. The experimental results show that, whether it is agricultural inter-domain or intra-domain during the controller failure period, the sensor switches can enter failure recovery mode as soon as possible so that the sensor network keeps a stable throughput, a short failure recovery time below 300 ms, and low packet loss. Further, the domain can smoothly control the domain network again once the controller becomes available. This approach based on an Open vSwitch extension can enhance the survivability and stability of multi-domain SDWSNs in precision agriculture. PMID:27827971

MEMS for optical switching: technologies, applications, and perspectives

NASA Astrophysics Data System (ADS)

Lin, Lih-Y.; Goldstein, Evan L.

1999-09-01

Micro-electro-mechanical-systems (MEMS), due to their unique ability to integrate electrical, mechanical, and optical elements on a single chip, have recently begun to exhibit great potential for realizing optical components and subsystems in compact, lowcost form. Recently, this technology has been applied to wavelength-division-multiplexed (WDM) networks, and resulted in advances in several network elements, including switches, filters, modulators, and wavelength-add/drop multiplexers. Due largely to the exploding capacity demand arising from data traffic, the transmission capacity demanded of and available from WDM networks is anticipated to increase rapidly. For managing such networks, optical switching is of particular interest due to the fact that its complexity is essentially immune to steady advances in the per-channel bit-rate. We will review various micromachined optical-switching technologies, emphasizing studies of their reliability. We then summarizing recent progress in the free-space MEMS optical switch we have demonstrated.

MEMS for optical switching: technologies, applications, and perspectives

NASA Astrophysics Data System (ADS)

Lin, Lih-Yuan; Goldstein, Evan L.

1999-09-01

Micro-electro-mechanical-systems (MEMS), due to their unique ability to integrate electrical, mechanical, and optical elements on a single chip, have recently begun to exhibit great potential for realizing optical components and subsystems in compact, low-cost form. Recently, this technology has been applied to wavelength-division-multiplexed (WDM) networks, and resulted in advances in several network elements, including switches, filters, modulators, and wavelength-add/drop multiplexers. Due largely to the exploding capacity demand arising from data traffic, the transmission capacity demanded of and available from WDM networks is anticipated to increase rapidly. For managing such networks, optical switching is of particular interest due to the fact that its complexity is essentially immune to steady advances in the per-channel bit-rate. We will review various micromachined optical-switching technologies, emphasizing studies of their reliability. We then summarizing recent progress in the free-space MEMS optical switch we have demonstrated.

Performance of circuit switching in the Internet

NASA Astrophysics Data System (ADS)

Molinero-Fernández, Pablo; McKeown, Nick

2003-04-01

We study the performance of an Internet that uses circuit switching (CS) instead of, or in addition to, packet switching (PS). On the face of it, this would seem a pointless exercise; the Internet is packet switched, and it was deliberately built that way to enable the efficiencies afforded by statistical multiplexing and the robustness of fast rerouting around failures. But link utilization is low particularly at the core of the Internet, which makes statistical multiplexing less important than it once was. Moreover, circuit switches today are capable of rapid reconfiguration around failures. There is also renewed interest in CS because of the ease of building very-high-capacity optical circuit switches. Although several proposals have suggested ways in which CS may be introduced into the Internet, the research presented here is based on Transmission Control Protocol (TCP) switching, in which a new circuit is created for each application flow. Here we explore the performance of a network that uses TCP switching, with particular emphasis on the response time experienced by users. We use simple M/GI/1 and M/GI/N queues to model application flows in both packet-switched and circuit-switched networks, as well as ns-2 simulations. We conclude that because of high-bandwidth long-lived flows, it does not make sense to use CS in shared-access or local area networks. But our results suggest that in the core of the network, where high capacity is needed most, and where peak flow rate is limited by the access link, there is little or no difference in performance between CS and PS. Given that circuit switches can be built to be much faster than packet switches, this suggests that a circuit-switched core warrants further investigation.

From Understanding the Development Landscape of the Canonical Fate-Switch Pair to Constructing a Dynamic Landscape for Two-Step Neural Differentiation

PubMed Central

2012-01-01

Abstract Recent progress in stem cell biology, notably cell fate conversion, calls for novel theoretical understanding for cell differentiation. The existing qualitative concept of Waddington’s “epigenetic landscape” has attracted particular attention because it captures subsequent fate decision points, thus manifesting the hierarchical (“tree-like”) nature of cell fate diversification. Here, we generalized a recent work and explored such a developmental landscape for a two-gene fate decision circuit by integrating the underlying probability landscapes with different parameters (corresponding to distinct developmental stages). The change of entropy production rate along the parameter changes indicates which parameter changes can represent a normal developmental process while other parameters’ change can not. The transdifferentiation paths over the landscape under certain conditions reveal the possibility of a direct and reversible phenotypic conversion. As the intensity of noise increases, we found that the landscape becomes flatter and the dominant paths more straight, implying the importance of biological noise processing mechanism in development and reprogramming. We further extended the landscape of the one-step fate decision to that for two-step decisions in central nervous system (CNS) differentiation. A minimal network and dynamic model for CNS differentiation was firstly constructed where two three-gene motifs are coupled. We then implemented the SDEs (Stochastic Differentiation Equations) simulation for the validity of the network and model. By integrating the two landscapes for the two switch gene pairs, we constructed the two-step development landscape for CNS differentiation. Our work provides new insights into cellular differentiation and important clues for better reprogramming strategies. PMID:23300518

Optical network scaling: roles of spectral and spatial aggregation.

PubMed

Arık, Sercan Ö; Ho, Keang-Po; Kahn, Joseph M

2014-12-01

As the bit rates of routed data streams exceed the throughput of single wavelength-division multiplexing channels, spectral and spatial traffic aggregation become essential for optical network scaling. These aggregation techniques reduce network routing complexity by increasing spectral efficiency to decrease the number of fibers, and by increasing switching granularity to decrease the number of switching components. Spectral aggregation yields a modest decrease in the number of fibers but a substantial decrease in the number of switching components. Spatial aggregation yields a substantial decrease in both the number of fibers and the number of switching components. To quantify routing complexity reduction, we analyze the number of multi-cast and wavelength-selective switches required in a colorless, directionless and contentionless reconfigurable optical add-drop multiplexer architecture. Traffic aggregation has two potential drawbacks: reduced routing power and increased switching component size.

Cooperative Adaptive Output Regulation for Second-Order Nonlinear Multiagent Systems With Jointly Connected Switching Networks.

PubMed

Liu, Wei; Huang, Jie

2018-03-01

This paper studies the cooperative global robust output regulation problem for a class of heterogeneous second-order nonlinear uncertain multiagent systems with jointly connected switching networks. The main contributions consist of the following three aspects. First, we generalize the result of the adaptive distributed observer from undirected jointly connected switching networks to directed jointly connected switching networks. Second, by performing a new coordinate and input transformation, we convert our problem into the cooperative global robust stabilization problem of a more complex augmented system via the distributed internal model principle. Third, we solve the stabilization problem by a distributed state feedback control law. Our result is illustrated by the leader-following consensus problem for a group of Van der Pol oscillators.

GLOBECOM '89 - IEEE Global Telecommunications Conference and Exhibition, Dallas, TX, Nov. 27-30, 1989, Conference Record. Volumes 1, 2, & 3

NASA Astrophysics Data System (ADS)

The present conference discusses topics in multiwavelength network technology and its applications, advanced digital radio systems in their propagation environment, mobile radio communications, switching programmability, advancements in computer communications, integrated-network management and security, HDTV and image processing in communications, basic exchange communications radio advancements in digital switching, intelligent network evolution, speech coding for telecommunications, and multiple access communications. Also discussed are network designs for quality assurance, recent progress in coherent optical systems, digital radio applications, advanced communications technologies for mobile users, communication software for switching systems, AI and expert systems in network management, intelligent multiplexing nodes, video and image coding, network protocols and performance, system methods in quality and reliability, the design and simulation of lightwave systems, local radio networks, mobile satellite communications systems, fiber networks restoration, packet video networks, human interfaces for future networks, and lightwave networking.

A theoretical and experimental study of neuromorphic atomic switch networks for reservoir computing.

PubMed

Sillin, Henry O; Aguilera, Renato; Shieh, Hsien-Hang; Avizienis, Audrius V; Aono, Masakazu; Stieg, Adam Z; Gimzewski, James K

2013-09-27

Atomic switch networks (ASNs) have been shown to generate network level dynamics that resemble those observed in biological neural networks. To facilitate understanding and control of these behaviors, we developed a numerical model based on the synapse-like properties of individual atomic switches and the random nature of the network wiring. We validated the model against various experimental results highlighting the possibility to functionalize the network plasticity and the differences between an atomic switch in isolation and its behaviors in a network. The effects of changing connectivity density on the nonlinear dynamics were examined as characterized by higher harmonic generation in response to AC inputs. To demonstrate their utility for computation, we subjected the simulated network to training within the framework of reservoir computing and showed initial evidence of the ASN acting as a reservoir which may be optimized for specific tasks by adjusting the input gain. The work presented represents steps in a unified approach to experimentation and theory of complex systems to make ASNs a uniquely scalable platform for neuromorphic computing.

A theoretical and experimental study of neuromorphic atomic switch networks for reservoir computing

NASA Astrophysics Data System (ADS)

Sillin, Henry O.; Aguilera, Renato; Shieh, Hsien-Hang; Avizienis, Audrius V.; Aono, Masakazu; Stieg, Adam Z.; Gimzewski, James K.

2013-09-01

Atomic switch networks (ASNs) have been shown to generate network level dynamics that resemble those observed in biological neural networks. To facilitate understanding and control of these behaviors, we developed a numerical model based on the synapse-like properties of individual atomic switches and the random nature of the network wiring. We validated the model against various experimental results highlighting the possibility to functionalize the network plasticity and the differences between an atomic switch in isolation and its behaviors in a network. The effects of changing connectivity density on the nonlinear dynamics were examined as characterized by higher harmonic generation in response to AC inputs. To demonstrate their utility for computation, we subjected the simulated network to training within the framework of reservoir computing and showed initial evidence of the ASN acting as a reservoir which may be optimized for specific tasks by adjusting the input gain. The work presented represents steps in a unified approach to experimentation and theory of complex systems to make ASNs a uniquely scalable platform for neuromorphic computing.

A physical mechanism of cancer heterogeneity

NASA Astrophysics Data System (ADS)

Chen, Cong; Wang, Jin

2016-02-01

We studied a core cancer gene regulatory network motif to uncover possible source of cancer heterogeneity from epigenetic sources. When the time scale of the protein regulation to the gene is faster compared to the protein synthesis and degradation (adiabatic regime), normal state, cancer state and an intermediate premalignant state emerge. Due to the epigenetics such as DNA methylation and histone remodification, the time scale of the protein regulation to the gene can be slower or comparable to the protein synthesis and degradation (non-adiabatic regime). In this case, many more states emerge as possible phenotype alternations. This gives the origin of the heterogeneity. The cancer heterogeneity is reflected from the emergence of more phenotypic states, larger protein concentration fluctuations, wider kinetic distributions and multiplicity of kinetic paths from normal to cancer state, higher energy cost per gene switching, and weaker stability.

Integrated DoD Voice and Data Networks and Ground Packet Radio Technology

DTIC Science & Technology

1976-08-01

as the traffic requirement level increases. Moreover, the satellite switch selection problem is only meaningful over a limited traffic range. When...5: CPU TIMES VS. NUMBER OF SWITCHES SATELLITE SWITCH SELECTION ALGORITHM Computer Used: PDP-10 ♦O’S" means 0 minutes and 5 seconds. 5.30...Saturation Algorithm for Topo\\ogical Design of Parket-Switched Communications Networks," National Te3 ecommunications Conference Proceed- ings, San

Interconnecting network for switching data packets and method for switching data packets

DOEpatents

Benner, Alan Frederic; Minkenberg, Cyriel Johan Agnes; Stunkel, Craig Brian

2010-05-25

The interconnecting network for switching data packets, having data and flow control information, comprises a local packet switch element (S1) with local input buffers (I(1,1) . . . I(1,y)) for buffering the incoming data packets, a remote packet switch element (S2) with remote input buffers (I(2,1) . . . I(2,y)) for buffering the incoming data packets, and data lines (L) for interconnecting the local and the remote packet switch elements (S1, S2). The interconnecting network further comprises a local and a remote arbiter (A1, A2) which are connected via control lines (CL) to the input buffers (I(1,1) . . . I(1,y), I(2,1) . . . I(2,y)), and which are formed such that they can provide that the flow control information is transmitted via the data lines (L) and the control lines (CL).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Dong; Heidelberger, Philip; Sugawara, Yutaka

An apparatus and method for extending the scalability and improving the partitionability of networks that contain all-to-all links for transporting packet traffic from a source endpoint to a destination endpoint with low per-endpoint (per-server) cost and a small number of hops. An all-to-all wiring in the baseline topology is decomposed into smaller all-to-all components in which each smaller all-to-all connection is replaced with star topology by using global switches. Stacking multiple copies of the star topology baseline network creates a multi-planed switching topology for transporting packet traffic. Point-to-point unified stacking method using global switch wiring methods connects multiple planes ofmore » a baseline topology by using the global switches to create a large network size with a low number of hops, i.e., low network latency. Grouped unified stacking method increases the scalability (network size) of a stacked topology.« less

Temperature dependence of the multistability of lactose utilization network of Escherichia coli

NASA Astrophysics Data System (ADS)

Nepal, Sudip; Kumar, Pradeep

Biological systems are capable of producing multiple states out of a single set of inputs. Multistability acts like a biological switch that allows organisms to respond differently to different environmental conditions and hence plays an important role in adaptation to changing environment. One of the widely studied gene regulatory networks underlying the metabolism of bacteria is the lactose utilization network, which exhibits a multistable behavior as a function of lactose concentration. We have studied the effect of temperature on multistability of the lactose utilization network at various concentrations of thio-methylgalactoside (TMG), a synthetic lactose. We find that while the lactose utilization network exhibits a bistable behavior for temperature T >20° C , a graded response arises for temperature T <=20° C. Furthermore, we construct a phase diagram of the graded and bistable response of lactose utilization network as a function of temperature and TMG concentration. Our results suggest that environmental conditions, in this case temperature, can alter the nature of cellular regulation of metabolism.

Burst switching without guard interval in all-optical software-define star intra-data center network

NASA Astrophysics Data System (ADS)

Ji, Philip N.; Wang, Ting

2014-02-01

Optical switching has been introduced in intra-data center networks (DCNs) to increase capacity and to reduce power consumption. Recently we proposed a star MIMO OFDM-based all-optical DCN with burst switching and software-defined networking. Here, we introduce the control procedure for the star DCN in detail for the first time. The timing, signaling, and operation are described for each step to achieve efficient bandwidth resource utilization. Furthermore, the guidelines for the burst assembling period selection that allows burst switching without guard interval are discussed. The star all-optical DCN offers flexible and efficient control for next-generation data center application.

Experience with PACS in an ATM/Ethernet switched network environment.

PubMed

Pelikan, E; Ganser, A; Kotter, E; Schrader, U; Timmermann, U

1998-03-01

Legacy local area network (LAN) technologies based on shared media concepts are not adequate for the growth of a large-scale picture archiving and communication system (PACS) in a client-server architecture. First, an asymmetric network load, due to the requests of a large number of PACS clients for only a few main servers, should be compensated by communication links to the servers with a higher bandwidth compared to the clients. Secondly, as the number of PACS nodes increases, the network throughout should not measurably cut production. These requirements can easily be fulfilled using switching technologies. Here asynchronous transfer mode (ATM) is clearly one of the hottest topics in networking because the ATM architecture provides integrated support for a variety of communication services, and it supports virtual networking. On the other hand, most of the imaging modalities are not yet ready for integration into a native ATM network. For a lot of nodes already joining an Ethernet, a cost-effective and pragmatic way to benefit from the switching concept would be a combined ATM/Ethernet switching environment. This incorporates an incremental migration strategy with the immediate benefits of high-speed, high-capacity ATM (for servers and high-sophisticated display workstations), while preserving elements of the existing network technologies. In addition, Ethernet switching instead of shared media Ethernet improves the performance considerably. The LAN emulation (LANE) specification by the ATM forum defines mechanisms that allow ATM networks to coexist with legacy systems using any data networking protocol. This paper points out the suitability of this network architecture in accordance with an appropriate system design.

Analysis of 100Mb/s Ethernet for the Whitney Commodity Computing Testbed

NASA Technical Reports Server (NTRS)

Fineberg, Samuel A.; Pedretti, Kevin T.; Kutler, Paul (Technical Monitor)

1997-01-01

We evaluate the performance of a Fast Ethernet network configured with a single large switch, a single hub, and a 4x4 2D torus topology in a testbed cluster of "commodity" Pentium Pro PCs. We also evaluated a mixed network composed of ethernet hubs and switches. An MPI collective communication benchmark, and the NAS Parallel Benchmarks version 2.2 (NPB2) show that the torus network performs best for all sizes that we were able to test (up to 16 nodes). For larger networks the ethernet switch outperforms the hub, though its performance is far less than peak. The hub/switch combination tests indicate that the NAS parallel benchmarks are relatively insensitive to hub densities of less than 7 nodes per hub.

Fault-Tolerant Local-Area Network

NASA Technical Reports Server (NTRS)

Morales, Sergio; Friedman, Gary L.

1988-01-01

Local-area network (LAN) for computers prevents single-point failure from interrupting communication between nodes of network. Includes two complete cables, LAN 1 and LAN 2. Microprocessor-based slave switches link cables to network-node devices as work stations, print servers, and file servers. Slave switches respond to commands from master switch, connecting nodes to two cable networks or disconnecting them so they are completely isolated. System monitor and control computer (SMC) acts as gateway, allowing nodes on either cable to communicate with each other and ensuring that LAN 1 and LAN 2 are fully used when functioning properly. Network monitors and controls itself, automatically routes traffic for efficient use of resources, and isolates and corrects its own faults, with potential dramatic reduction in time out of service.

Deep learning based state recognition of substation switches

NASA Astrophysics Data System (ADS)

Wang, Jin

2018-06-01

Different from the traditional method which recognize the state of substation switches based on the running rules of electrical power system, this work proposes a novel convolutional neuron network-based state recognition approach of substation switches. Inspired by the theory of transfer learning, we first establish a convolutional neuron network model trained on the large-scale image set ILSVRC2012, then the restricted Boltzmann machine is employed to replace the full connected layer of the convolutional neuron network and trained on our small image dataset of 110kV substation switches to get a stronger model. Experiments conducted on our image dataset of 110kV substation switches show that, the proposed approach can be applicable to the substation to reduce the running cost and implement the real unattended operation.

Multilevel-Dc-Bus Inverter For Providing Sinusoidal And Pwm Electrical Machine Voltages

DOEpatents

Su, Gui-Jia [Knoxville, TN

2005-11-29

A circuit for controlling an ac machine comprises a full bridge network of commutation switches which are connected to supply current for a corresponding voltage phase to the stator windings, a plurality of diodes, each in parallel connection to a respective one of the commutation switches, a plurality of dc source connections providing a multi-level dc bus for the full bridge network of commutation switches to produce sinusoidal voltages or PWM signals, and a controller connected for control of said dc source connections and said full bridge network of commutation switches to output substantially sinusoidal voltages to the stator windings. With the invention, the number of semiconductor switches is reduced to m+3 for a multi-level dc bus having m levels. A method of machine control is also disclosed.

Design of a digital, ultra-broadband electro-optic switch for reconfigurable optical networks-on-chip.

PubMed

Van Campenhout, Joris; Green, William M J; Vlasov, Yurii A

2009-12-21

We present a novel design for a noise-tolerant, ultra-broadband electro-optic switch, based on a Mach-Zehnder lattice (MZL) interferometer. We analyze the switch performance through rigorous optical simulations, for devices implemented in silicon-on-insulator with carrier-injection-based phase shifters. We show that such a MZL switch can be designed to have a step-like switching response, resulting in improved tolerance to drive-voltage noise and temperature variations as compared to a single-stage Mach-Zehnder switch. Furthermore, we show that degradation in switching crosstalk and insertion loss due to free-carrier absorption can be largely overcome by a MZL switch design. Finally, MZL switches can be designed for having an ultra-wide, temperature-insensitive optical bandwidth of more than 250 nm. The proposed device shows good potential as a broadband optical switch in reconfigurable optical networks-on-chip.

DOE Office of Scientific and Technical Information (OSTI.GOV)

D'Huys, Otti, E-mail: otti.dhuys@phy.duke.edu; Haynes, Nicholas D.; Lohmann, Johannes

Autonomous Boolean networks are commonly used to model the dynamics of gene regulatory networks and allow for the prediction of stable dynamical attractors. However, most models do not account for time delays along the network links and noise, which are crucial features of real biological systems. Concentrating on two paradigmatic motifs, the toggle switch and the repressilator, we develop an experimental testbed that explicitly includes both inter-node time delays and noise using digital logic elements on field-programmable gate arrays. We observe transients that last millions to billions of characteristic time scales and scale exponentially with the amount of time delaysmore » between nodes, a phenomenon known as super-transient scaling. We develop a hybrid model that includes time delays along network links and allows for stochastic variation in the delays. Using this model, we explain the observed super-transient scaling of both motifs and recreate the experimentally measured transient distributions.« less

Hyperswitch Network For Hypercube Computer

NASA Technical Reports Server (NTRS)

Chow, Edward; Madan, Herbert; Peterson, John

1989-01-01

Data-driven dynamic switching enables high speed data transfer. Proposed hyperswitch network based on mixed static and dynamic topologies. Routing header modified in response to congestion or faults encountered as path established. Static topology meets requirement if nodes have switching elements that perform necessary routing header revisions dynamically. Hypercube topology now being implemented with switching element in each computer node aimed at designing very-richly-interconnected multicomputer system. Interconnection network connects great number of small computer nodes, using fixed hypercube topology, characterized by point-to-point links between nodes.

Proton Single Event Effects (SEE) Testing of the Myrinet Crossbar Switch and Network Interface Card

NASA Technical Reports Server (NTRS)

Howard, James W., Jr.; LaBel, Kenneth A.; Carts, Martin A.; Stattel, Ronald; Irwin, Timothy L.; Day, John H. (Technical Monitor)

2002-01-01

As part of the Remote Exploration and Experimentation Project (REE), work was performed to do a proton SEE (Single Event Effect) evaluation of the Myricom network protocol system (Myrinet). This testing included the evaluation of the Myrinet crossbar switch and the Network Interface Card (NIC). To this end, two crossbar switch devices and five components in the NIC were exposed to the proton beam at the University of California at Davis Crocker Nuclear Laboratory (CNL).

High-performance flat data center network architecture based on scalable and flow-controlled optical switching system

NASA Astrophysics Data System (ADS)

Calabretta, Nicola; Miao, Wang; Dorren, Harm

2016-03-01

Traffic in data centers networks (DCNs) is steadily growing to support various applications and virtualization technologies. Multi-tenancy enabling efficient resource utilization is considered as a key requirement for the next generation DCs resulting from the growing demands for services and applications. Virtualization mechanisms and technologies can leverage statistical multiplexing and fast switch reconfiguration to further extend the DC efficiency and agility. We present a novel high performance flat DCN employing bufferless and distributed fast (sub-microsecond) optical switches with wavelength, space, and time switching operation. The fast optical switches can enhance the performance of the DCNs by providing large-capacity switching capability and efficiently sharing the data plane resources by exploiting statistical multiplexing. Benefiting from the Software-Defined Networking (SDN) control of the optical switches, virtual DCNs can be flexibly created and reconfigured by the DCN provider. Numerical and experimental investigations of the DCN based on the fast optical switches show the successful setup of virtual network slices for intra-data center interconnections. Experimental results to assess the DCN performance in terms of latency and packet loss show less than 10^-5 packet loss and 640ns end-to-end latency with 0.4 load and 16- packet size buffer. Numerical investigation on the performance of the systems when the port number of the optical switch is scaled to 32x32 system indicate that more than 1000 ToRs each with Terabit/s interface can be interconnected providing a Petabit/s capacity. The roadmap to photonic integration of large port optical switches will be also presented.

Universal method for constructing N-port non-blocking optical router based on 2 × 2 optical switch for photonic networks-on-chip.

PubMed

Chen, Qiaoshan; Zhang, Fanfan; Ji, Ruiqiang; Zhang, Lei; Yang, Lin

2014-05-19

We propose a universal method for constructing N-port non-blocking optical router for photonic networks-on-chip, in which all microring (MR) optical switches or Mach-Zehnder (M-Z) optical switches behave as 2 × 2 optical switches. The optical router constructed by the proposed method has minimum optical switches, in which the number of the optical switches is reduced about 50% compared to the reported optical routers based on MR optical switches and more than 30% compared to the reported optical routers based on M-Z optical switches, and therefore is more compact in footprint and more power-efficient. We also present a strict mathematical proof of the non-blocking routing of the proposed N-port optical router.

Apparatus and method for fusion of compute and switching functions of exascale system into a single component by using configurable network-on-chip fabric with distributed dual mode input-output ports and programmable network interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khare, Surhud; Somasekhar, Dinesh; More, Ankit

Described is an apparatus which comprises: a Network-On-Chip fabric using crossbar switches, having distributed ingress and egress ports; and a dual-mode network interface coupled to at least one crossbar switch, the dual-mode network interface is to include: a dual-mode circuitry; a controller operable to: configure the dual-mode circuitry to transmit and receive differential signals via the egress and ingress ports, respectively, and configure the dual-mode circuitry to transmit and receive signal-ended signals via the egress and ingress ports, respectively.

Packet Switching Networks: An Introduction with Some Attention to Selected Vendors.

ERIC Educational Resources Information Center

Sanchez, James Joseph

The purpose of this paper is to provide an overview of the history, development, and services of the packet switching network services that currently exist in the United States. The character of packet switching, a computerized method of transmitting data, is used as the basis for tracing the development of the industry itself. Contending that the…

Antigenic variation in malaria: in situ switching, relaxed and mutually exclusive transcription of var genes during intra-erythrocytic development in Plasmodium falciparum.

PubMed Central

Scherf, A; Hernandez-Rivas, R; Buffet, P; Bottius, E; Benatar, C; Pouvelle, B; Gysin, J; Lanzer, M

1998-01-01

Members of the Plasmodium falciparum var gene family encode clonally variant adhesins, which play an important role in the pathogenicity of tropical malaria. Here we employ a selective panning protocol to generate isogenic P.falciparum populations with defined adhesive phenotypes for CD36, ICAM-1 and CSA, expressing single and distinct var gene variants. This technique has established the framework for examining var gene expression, its regulation and switching. It was found that var gene switching occurs in situ. Ubiquitous transcription of all var gene variants appears to occur in early ring stages. However, var gene expression is tightly regulated in trophozoites and is exerted through a silencing mechanism. Transcriptional control is mutually exclusive in parasites that express defined adhesive phenotypes. In situ var gene switching is apparently mediated at the level of transcriptional initiation, as demonstrated by nuclear run-on analyses. Our results suggest that an epigenetic mechanism(s) is involved in var gene regulation. PMID:9736619

Free-space optics technology employed in an UMTS release 4 bearer independent core network access part

NASA Astrophysics Data System (ADS)

Bibac, Ionut

2005-08-01

The UMTS Bearer Independent Core Network program introduced the 3rd Generation Partnership Program Release 4 BICN architecture into the legacy UMTS TDM-switched network. BICN is the application of calI server archltecture for voice and circuit switched data, enabling the provisioning of traditional circuit-switched services using a packet-switched transport network. Today"s business climate has made it essential for service providers to develop a comprehensive networking strategy that means introduction of RCBICN networks. The R4-BICN solution to the evolution of the Core Network in UMTS will enable operators to significantly reduce the capital and operational costs of delivering both traditional voice sewices and new multimedia services. To build the optical backbone, which can support the third generation (3G) packetized infrastructure, the operators could choose a fibre connection, or they could retain the benefits of a wireless connectivity by using a FSO - Free Space Optical lmk, the only wireless technology available that is capable of achieving data rates up to 2.4 Gbit/s. FSO offers viable alternatives for both core transmission networks and for replacing microwaves links in NodeB - RNC access networks. The paper and presentation aim to demonstrate the manner in which FSO products and networks are employed into R4-BICN design solutions.

Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach

PubMed Central

Ishii, Shun’ichi; Suzuki, Shino; Tenney, Aaron; Norden-Krichmar, Trina M.; Nealson, Kenneth H.; Bretschger, Orianna

2015-01-01

Microorganisms almost always exist as mixed communities in nature. While the significance of microbial community activities is well appreciated, a thorough understanding about how microbial communities respond to environmental perturbations has not yet been achieved. Here we have used a combination of metagenomic, genome binning, and stimulus-induced metatranscriptomic approaches to estimate the metabolic network and stimuli-induced metabolic switches existing in a complex microbial biofilm that was producing electrical current via extracellular electron transfer (EET) to a solid electrode surface. Two stimuli were employed: to increase EET and to stop EET. An analysis of cell activity marker genes after stimuli exposure revealed that only two strains within eleven binned genomes had strong transcriptional responses to increased EET rates, with one responding positively and the other responding negatively. Potential metabolic switches between eleven dominant members were mainly observed for acetate, hydrogen, and ethanol metabolisms. These results have enabled the estimation of a multi-species metabolic network and the associated short-term responses to EET stimuli that induce changes to metabolic flow and cooperative or competitive microbial interactions. This systematic meta-omics approach represents a next step towards understanding complex microbial roles within a community and how community members respond to specific environmental stimuli. PMID:26443302

Exploring adolescent cognitive control in a combined interference switching task.

PubMed

Mennigen, Eva; Rodehacke, Sarah; Müller, Kathrin U; Ripke, Stephan; Goschke, Thomas; Smolka, Michael N

2014-08-01

Cognitive control enables individuals to flexibly adapt to environmental challenges. In the present functional magnetic resonance imaging (fMRI) study, we investigated 185 adolescents at the age of 14 with a combined response interference switching task measuring behavioral responses (reaction time, RT and error rate, ER) and brain activity during the task. This task comprises two types of conflict which are co-occurring, namely, task switching and stimulus-response incongruence. Data indicated that already in adolescents an overlapping cognitive control network comprising the dorsal anterior cingulate cortex (dACC), dorsolateral prefrontal cortex (DLPFC), pre-supplementary motor area (preSMA) and posterior parietal cortex (PPC) is recruited by conflicts arising from task switching and response incongruence. Furthermore our study revealed higher blood oxygenation level dependent (BOLD) responses elicited by incongruent stimuli in participants with a pronounced incongruence effect, calculated as the RT difference between incongruent and congruent trials. No such correlation was observed for switch costs. Furthermore, increased activation of the default mode network (DMN) was only observed in congruent trials compared to incongruent trials, but not in task repetition relative to task switch trials. These findings suggest that even though the two processes of task switching and response incongruence share a common cognitive control network they might be processed differentially within the cognitive control network. Results are discussed in the context of a novel hypothesis concerning antagonistic relations between the DMN and the cognitive control network. Copyright © 2014 Elsevier Ltd. All rights reserved.

Selective randomized load balancing and mesh networks with changing demands

NASA Astrophysics Data System (ADS)

Shepherd, F. B.; Winzer, P. J.

2006-05-01

We consider the problem of building cost-effective networks that are robust to dynamic changes in demand patterns. We compare several architectures using demand-oblivious routing strategies. Traditional approaches include single-hop architectures based on a (static or dynamic) circuit-switched core infrastructure and multihop (packet-switched) architectures based on point-to-point circuits in the core. To address demand uncertainty, we seek minimum cost networks that can carry the class of hose demand matrices. Apart from shortest-path routing, Valiant's randomized load balancing (RLB), and virtual private network (VPN) tree routing, we propose a third, highly attractive approach: selective randomized load balancing (SRLB). This is a blend of dual-hop hub routing and randomized load balancing that combines the advantages of both architectures in terms of network cost, delay, and delay jitter. In particular, we give empirical analyses for the cost (in terms of transport and switching equipment) for the discussed architectures, based on three representative carrier networks. Of these three networks, SRLB maintains the resilience properties of RLB while achieving significant cost reduction over all other architectures, including RLB and multihop Internet protocol/multiprotocol label switching (IP/MPLS) networks using VPN-tree routing.

Biomolecular engineering of intracellular switches in eukaryotes

PubMed Central

Pastuszka, M.K.; Mackay, J.A.

2010-01-01

Tools to selectively and reversibly control gene expression are useful to study and model cellular functions. When optimized, these cellular switches can turn a protein's function “on” and “off” based on cues designated by the researcher. These cues include small molecules, drugs, hormones, and even temperature variations. Here we review three distinct areas in gene expression that are commonly targeted when designing cellular switches. Transcriptional switches target gene expression at the level of mRNA polymerization, with examples including the tetracycline gene induction system as well as nuclear receptors. Translational switches target the process of turning the mRNA signal into protein, with examples including riboswitches and RNA interference. Post-translational switches control how proteins interact with one another to attenuate or relay signals. Examples of post-translational modification include dimerization and intein splicing. In general, the delay times between switch and effect decreases from transcription to translation to post-translation; furthermore, the fastest switches may offer the most elegant opportunities to influence and study cell behavior. We discuss the pros and cons of these strategies, which directly influence their usefulness to study and implement drug targeting at the tissue and cellular level. PMID:21209849

Modular protein switches derived from antibody mimetic proteins.

PubMed

Nicholes, N; Date, A; Beaujean, P; Hauk, P; Kanwar, M; Ostermeier, M

2016-02-01

Protein switches have potential applications as biosensors and selective protein therapeutics. Protein switches built by fusion of proteins with the prerequisite input and output functions are currently developed using an ad hoc process. A modular switch platform in which existing switches could be readily adapted to respond to any ligand would be advantageous. We investigated the feasibility of a modular protein switch platform based on fusions of the enzyme TEM-1 β-lactamase (BLA) with two different antibody mimetic proteins: designed ankyrin repeat proteins (DARPins) and monobodies. We created libraries of random insertions of the gene encoding BLA into genes encoding a DARPin or a monobody designed to bind maltose-binding protein (MBP). From these libraries, we used a genetic selection system for β-lactamase activity to identify genes that conferred MBP-dependent ampicillin resistance to Escherichia coli. Some of these selected genes encoded switch proteins whose enzymatic activity increased up to 14-fold in the presence of MBP. We next introduced mutations into the antibody mimetic domain of these switches that were known to cause binding to different ligands. To different degrees, introduction of the mutations resulted in switches with the desired specificity, illustrating the potential modularity of these platforms. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Dopamine and cognitive control: sex-by-genotype interactions influence the capacity to switch attention.

PubMed

Gurvich, C; Rossell, S L

2015-03-15

Cognitive performance in healthy persons varies widely between individuals. Sex differences in cognition are well reported, and there is an emerging body of evidence suggesting that the relationship between dopaminergic neurotransmission, implicated in many cognitive functions, is modulated by sex. Here, we examine the influence of sex and genetic variations along the dopaminergic pathway on aspects of cognitive control. A total of 415 healthy individuals, selected from an international consortium linked to Brain Research and Integrative Neuroscience Network (BRAINnet), were genotyped for two common and functional genetic variations of dopamine regulating genes: the catechol-O-methyltransferase [COMT] gene (rs4680) and the dopamine receptor D2 [DRD2] gene (rs6277). Cognitive measures were selected to explore sustained attention (using a continuous performance task), switching of attention (using a Trails B adaptation) and working memory (a visual computerised adaptation of digit span). While there were no main effects for genotype across any tasks, analyses revealed significant sex by genotype interactions for the capacity to switch attention. In relation to COMT, superior performance was noted in females with the Val/Val genotype and for DRD2, superior performance was seen for TT females and CC males. These findings highlight the importance of considering genetic variation in baseline dopamine levels in addition to sex, when considering the impact of dopamine on cognition in healthy populations. These findings also have important implications for the many neuropsychiatric disorders that implicate dopamine, cognitive changes and sex differences. Copyright © 2014 Elsevier B.V. All rights reserved.

Modelling switching-time effects in high-frequency power conditioning networks

NASA Technical Reports Server (NTRS)

Owen, H. A.; Sloane, T. H.; Rimer, B. H.; Wilson, T. G.

1979-01-01

Power transistor networks which switch large currents in highly inductive environments are beginning to find application in the hundred kilohertz switching frequency range. Recent developments in the fabrication of metal-oxide-semiconductor field-effect transistors in the power device category have enhanced the movement toward higher switching frequencies. Models for switching devices and of the circuits in which they are imbedded are required to properly characterize the mechanisms responsible for turning on and turning off effects. Easily interpreted results in the form of oscilloscope-like plots assist in understanding the effects of parametric studies using topology oriented computer-aided analysis methods.

Optimizing the switching time for 400 kV SF6 circuit breakers

NASA Astrophysics Data System (ADS)

Ciulica, D.

2018-01-01

This paper presents real-time voltage and current analysis for optimizing the wave switching point of the circuit breaker SF6. Circuit Breaker plays an important role in power systems. It provides protection for equipment in embedded stations in transport networks. SF6 Circuit Breaker is very important equipment in Power Systems, which is used for up to 400 kV due to its excellent performance. The controlled switching is used to eliminate transient modes and electrodynamic and dielectric charges in the network at manual switching of capacitor, shunt reactors and power transformers. These effects reduce the reliability and lifetime of the equipment installed on the network, or may lead to erroneous protection.

Radial Basis Function Neural Network Application to Power System Restoration Studies

PubMed Central

Sadeghkhani, Iman; Ketabi, Abbas; Feuillet, Rene

2012-01-01

One of the most important issues in power system restoration is overvoltages caused by transformer switching. These overvoltages might damage some equipment and delay power system restoration. This paper presents a radial basis function neural network (RBFNN) to study transformer switching overvoltages. To achieve good generalization capability for developed RBFNN, equivalent parameters of the network are added to RBFNN inputs. The developed RBFNN is trained with the worst-case scenario of switching angle and remanent flux and tested for typical cases. The simulated results for a partial of 39-bus New England test system show that the proposed technique can estimate the peak values and duration of switching overvoltages with good accuracy. PMID:22792093

Pluripotency, Differentiation, and Reprogramming: A Gene Expression Dynamics Model with Epigenetic Feedback Regulation

PubMed Central

Miyamoto, Tadashi; Furusawa, Chikara; Kaneko, Kunihiko

2015-01-01

Embryonic stem cells exhibit pluripotency: they can differentiate into all types of somatic cells. Pluripotent genes such as Oct4 and Nanog are activated in the pluripotent state, and their expression decreases during cell differentiation. Inversely, expression of differentiation genes such as Gata6 and Gata4 is promoted during differentiation. The gene regulatory network controlling the expression of these genes has been described, and slower-scale epigenetic modifications have been uncovered. Although the differentiation of pluripotent stem cells is normally irreversible, reprogramming of cells can be experimentally manipulated to regain pluripotency via overexpression of certain genes. Despite these experimental advances, the dynamics and mechanisms of differentiation and reprogramming are not yet fully understood. Based on recent experimental findings, we constructed a simple gene regulatory network including pluripotent and differentiation genes, and we demonstrated the existence of pluripotent and differentiated states from the resultant dynamical-systems model. Two differentiation mechanisms, interaction-induced switching from an expression oscillatory state and noise-assisted transition between bistable stationary states, were tested in the model. The former was found to be relevant to the differentiation process. We also introduced variables representing epigenetic modifications, which controlled the threshold for gene expression. By assuming positive feedback between expression levels and the epigenetic variables, we observed differentiation in expression dynamics. Additionally, with numerical reprogramming experiments for differentiated cells, we showed that pluripotency was recovered in cells by imposing overexpression of two pluripotent genes and external factors to control expression of differentiation genes. Interestingly, these factors were consistent with the four Yamanaka factors, Oct4, Sox2, Klf4, and Myc, which were necessary for the establishment of induced pluripotent stem cells. These results, based on a gene regulatory network and expression dynamics, contribute to our wider understanding of pluripotency, differentiation, and reprogramming of cells, and they provide a fresh viewpoint on robustness and control during development. PMID:26308610

Design and evaluation of a DAMQ multiprocessor network with self-compacting buffers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, J.; O`Krafka, B.W.O.; Vassiliadis, S.

1994-12-31

This paper describes a new approach to implement Dynamically Allocated Multi-Queue (DAMQ) switching elements using a technique called ``self-compacting buffers``. This technique is efficient in that the amount of hardware required to manage the buffers is relatively small; it offers high performance since it is an implementation of a DAMQ. The first part of this paper describes the self-compacting buffer architecture in detail, and compares it against a competing DAMQ switch design. The second part presents extensive simulation results comparing the performance of a self compacting buffer switch against an ideal switch including several examples of k-ary n-cubes and deltamore » networks. In addition, simulation results show how the performance of an entire network can be quickly and accurately approximated by simulating just a single switching element.« less

20 kA PFN capacitor bank with solid-state switching. [pulse forming network for plasma studies

NASA Technical Reports Server (NTRS)

Posta, S. J.; Michels, C. J.

1973-01-01

A compact high-current pulse-forming network capacitor bank using paralleled silicon controlled rectifiers as switches is described. The maximum charging voltage of the bank is 1kV and maximum load current is 20 kA. The necessary switch equalization criteria and performance with dummy load and an arc plasma generator are described.

Functional brain and age-related changes associated with congruency in task switching

PubMed Central

Eich, Teal S.; Parker, David; Liu, Dan; Oh, Hwamee; Razlighi, Qolamreza; Gazes, Yunglin; Habeck, Christian; Stern, Yaakov

2016-01-01

Alternating between completing two simple tasks, as opposed to completing only one task, has been shown to produce costs to performance and changes to neural patterns of activity, effects which are augmented in old age. Cognitive conflict may arise from factors other than switching tasks, however. Sensorimotor congruency (whether stimulus-response mappings are the same or different for the two tasks) has been shown to behaviorally moderate switch costs in older, but not younger adults. In the current study, we used fMRI to investigate the neurobiological mechanisms of response-conflict congruency effects within a task switching paradigm in older (N=75) and younger (N=62) adults. Behaviorally, incongruency moderated age-related differences in switch costs. Neurally, switch costs were associated with greater activation in the dorsal attention network for older relative to younger adults. We also found that older adults recruited an additional set of brain areas in the ventral attention network to a greater extent than did younger adults to resolve congruency-related response-conflict. These results suggest both a network and an age-based dissociation between congruency and switch costs in task switching. PMID:27520472

Large optical 3D MEMS switches in access networks

NASA Astrophysics Data System (ADS)

Madamopoulos, Nicholas; Kaman, Volkan; Yuan, Shifu; Jerphagnon, Olivier; Helkey, Roger; Bowers, John E.

2007-09-01

Interest is high among residential customers and businesses for advanced, broadband services such as fast Internet access, electronic commerce, video-on-demand, digital broadcasting, teleconferencing and telemedicine. In order to satisfy such growing demand of end-customers, access technologies such as fiber-to-the-home/building (FTTH/B) are increasingly being deployed. Carriers can reduce maintenance costs, minimize technology obsolescence and introduce new services easily by reducing active elements in the fiber access network. However, having a passive optical network (PON) also introduces operational and maintenance challenges. Increased diagnostic monitoring capability of the network becomes a necessity as more and more fibers are provisioned to deliver services to the end-customers. This paper demonstrates the clear advantages that large 3D optical MEMS switches offer in solving these access network problems. The advantages in preventative maintenance, remote monitoring, test and diagnostic capability are highlighted. The low optical insertion loss for all switch optical connections of the switch enables the monitoring, grooming and serving of a large number of PON lines and customers. Furthermore, the 3D MEMS switch is transparent to optical wavelengths and data formats, thus making it easy to incorporate future upgrades, such higher bit rates or DWDM overlay to a PON.

Dynamic switching enables efficient bacterial colonization in flow.

PubMed

Kannan, Anerudh; Yang, Zhenbin; Kim, Minyoung Kevin; Stone, Howard A; Siryaporn, Albert

2018-05-22

Bacteria colonize environments that contain networks of moving fluids, including digestive pathways, blood vasculature in animals, and the xylem and phloem networks in plants. In these flow networks, bacteria form distinct biofilm structures that have an important role in pathogenesis. The physical mechanisms that determine the spatial organization of bacteria in flow are not understood. Here, we show that the bacterium P. aeruginosa colonizes flow networks using a cyclical process that consists of surface attachment, upstream movement, detachment, movement with the bulk flow, and surface reattachment. This process, which we have termed dynamic switching, distributes bacterial subpopulations upstream and downstream in flow through two phases: movement on surfaces and cellular movement via the bulk. The model equations that describe dynamic switching are identical to those that describe dynamic instability, a process that enables microtubules in eukaryotic cells to search space efficiently to capture chromosomes. Our results show that dynamic switching enables bacteria to explore flow networks efficiently, which maximizes dispersal and colonization and establishes the organizational structure of biofilms. A number of eukaryotic and mammalian cells also exhibit movement in two phases in flow, which suggests that dynamic switching is a modality that enables efficient dispersal for a broad range of cell types.

A genetic switch controls the production of flagella and toxins in Clostridium difficile.

PubMed

Anjuwon-Foster, Brandon R; Tamayo, Rita

2017-03-01

In the human intestinal pathogen Clostridium difficile, flagella promote adherence to intestinal epithelial cells. Flagellar gene expression also indirectly impacts production of the glucosylating toxins, which are essential to diarrheal disease development. Thus, factors that regulate the expression of the flgB operon will likely impact toxin production in addition to flagellar motility. Here, we report the identification a "flagellar switch" that controls the phase variable production of flagella and glucosylating toxins. The flagellar switch, located upstream of the flgB operon containing the early stage flagellar genes, is a 154 bp invertible sequence flanked by 21 bp inverted repeats. Bacteria with the sequence in one orientation expressed flagellum and toxin genes, produced flagella, and secreted the toxins ("flg phase ON"). Bacteria with the sequence in the inverse orientation were attenuated for flagellar and toxin gene expression, were aflagellate, and showed decreased toxin secretion ("flg phase OFF"). The orientation of the flagellar switch is reversible during growth in vitro. We provide evidence that gene regulation via the flagellar switch occurs post-transcription initiation and requires a C. difficile-specific regulatory factor to destabilize or degrade the early flagellar gene mRNA when the flagellar switch is in the OFF orientation. Lastly, through mutagenesis and characterization of flagellar phase locked isolates, we determined that the tyrosine recombinase RecV, which catalyzes inversion at the cwpV switch, is also responsible for inversion at the flagellar switch in both directions. Phase variable flagellar motility and toxin production suggests that these important virulence factors have both advantageous and detrimental effects during the course of infection.

3-DIMENSIONAL Optoelectronic

NASA Astrophysics Data System (ADS)

Krishnamoorthy, Ashok Venketaraman

This thesis covers the design, analysis, optimization, and implementation of optoelectronic (N,M,F) networks. (N,M,F) networks are generic space-division networks that are well suited to implementation using optoelectronic integrated circuits and free-space optical interconnects. An (N,M,F) networks consists of N input channels each having a fanout F_{rm o}, M output channels each having a fanin F_{rm i}, and Log_{rm K}(N/F) stages of K x K switches. The functionality of the fanout, switching, and fanin stages depends on the specific application. Three applications of optoelectronic (N,M,F) networks are considered. The first is an optoelectronic (N,1,1) content -addressable memory system that achieves associative recall on two-dimensional images retrieved from a parallel-access optical memory. The design and simulation of the associative memory are discussed, and an experimental emulation of a prototype system using images from a parallel-readout optical disk is presented. The system design provides superior performance to existing electronic content-addressable memory chips in terms of capacity and search rate, and uses readily available optical disk and VLSI technologies. Next, a scalable optoelectronic (N,M,F) neural network that uses free-space holographic optical interconnects is presented. The neural architecture minimizes the number of optical transmitters needed, and provides accurate electronic fanin with low signal skew, and dendritic-type fan-in processing capability in a compact layout. Optimal data-encoding methods and circuit techniques are discussed. The implementation of an prototype optoelectronic neural system, and its application to a simple recognition task is demonstrated. Finally, the design, analysis, and optimization of a (N,N,F) self-routing, packet-switched multistage interconnection network is described. The network is suitable for parallel computing and broadband switching applications. The tradeoff between optical and electronic interconnects is examined quantitatively by varying the electronic switch size K. The performance of the (N,N,F) network versus the fanning parameter F, is also analyzed. It is shown that the optoelectronic (N,N,F) networks provide a range of performance-cost alternatives, and offer superior performance-per-cost to fully electronic switching networks and to previous networks designs.

MPNACK: an optical switching scheme enabling the buffer-less reliable transmission

NASA Astrophysics Data System (ADS)

Yu, Xiaoshan; Gu, Huaxi; Wang, Kun; Xu, Meng; Guo, Yantao

2016-01-01

Optical data center networks are becoming an increasingly promising solution to solve the bottlenecks faced by electrical networks, such as low transmission bandwidth, high wiring complexity, and unaffordable power consumption. However, the optical circuit switching (OCS) network is not flexible enough to carry the traffic burst while the optical packet switching (OPS) network cannot solve the packet contention in an efficient way. To this end, an improved switching strategy named OPS with multi-hop Negative Acknowledgement (MPNACK) is proposed. This scheme uses a feedback mechanism, rather than the buffering structure, to handle the optical packet contention. The collided packet is treated as a NACK packet and sent back to the source server. When the sender receives this NACK packet, it knows a collision happens in the transmission path and a retransmission procedure is triggered. Overall, the OPS-NACK scheme enables a reliable transmission in the buffer-less optical network. Furthermore, with this scheme, the expensive and energy-hungry elements, optical or electrical buffers, can be removed from the optical interconnects, thus a more scalable and cost-efficient network can be constructed for cloud computing data centers.

All-optical OXC transition strategy from WDM optical network to elastic optical network.

PubMed

Chen, Xin; Li, Juhao; Guo, Bingli; Zhu, Paikun; Tang, Ruizhi; Chen, Zhangyuan; He, Yongqi

2016-02-22

Elastic optical network (EON) has been proposed recently as a spectrum-efficient optical layer to adapt to rapidly-increasing traffic demands instead of current deployed wavelength-division-multiplexing (WDM) optical network. In contrast with conventional WDM optical cross-connect (OXCs) based on wavelength selective switches (WSSs), the EON OXCs are based on spectrum selective switches (SSSs) which are much more expensive than WSSs, especially for large-scale switching architectures. So the transition cost from WDM OXCs to EON OXCs is a major obstacle to realizing EON. In this paper, we propose and experimentally demonstrate a transition OXC (TOXC) structure based on 2-stage cascading switching architectures, which make full use of available WSSs in current deployed WDM OXCs to reduce number and port count of required SSSs. Moreover, we propose a contention-aware spectrum allocation (CASA) scheme for EON built with the proposed TOXCs. We show by simulation that the TOXCs reduce the network capital expenditure transiting from WDM optical network to EON about 50%, with a minor traffic blocking performance degradation and about 10% accommodated traffic number detriment compared with all-SSS EON OXC architectures.

High-density, fail-in-place switches for computer and data networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coteus, Paul W.; Doany, Fuad E.; Hall, Shawn A.

A structure for a network switch. The network switch may include a plurality of spine chips arranged on a plurality of spine cards, where one or more spine chips are located on each spine card; and a plurality of leaf chips arranged on a plurality of leaf cards, wherein one or more leaf chips are located on each leaf card, where each spine card is connected to every leaf chip and the plurality of spine chips are surrounded on at least two sides by leaf cards.

A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.

PubMed

Haus, Sylvia; Jabbari, Sara; Millat, Thomas; Janssen, Holger; Fischer, Ralf-Jörg; Bahl, Hubert; King, John R; Wolkenhauer, Olaf

2011-01-19

Clostridium acetobutylicum is an anaerobic bacterium which is known for its solvent-producing capabilities, namely regarding the bulk chemicals acetone and butanol, the latter being a highly efficient biofuel. For butanol production by C. acetobutylicum to be optimized and exploited on an industrial scale, the effect of pH-induced gene regulation on solvent production by C. acetobutylicum in continuous culture must be understood as fully as possible. We present an ordinary differential equation model combining the metabolic network governing solvent production with regulation at the genetic level of the enzymes required for this process. Parameterizing the model with experimental data from continuous culture, we demonstrate the influence of pH upon fermentation products: at high pH (pH 5.7) acids are the dominant product while at low pH (pH 4.5) this switches to solvents. Through steady-state analyses of the model we focus our investigations on how alteration in gene expression of C. acetobutylicum could be exploited to increase butanol yield in a continuous culture fermentation. Incorporating gene regulation into the model of solvent production by C. acetobutylicum enables an accurate representation of the pH-induced switch to solvent production to be obtained and theoretical investigations of possible synthetic-biology approaches to be pursued. Steady-state analyses suggest that, to increase butanol yield, alterations in the expression of single solvent-associated genes are insufficient; a more complex approach targeting two or more genes is required.

A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture

PubMed Central

2011-01-01

Background Clostridium acetobutylicum is an anaerobic bacterium which is known for its solvent-producing capabilities, namely regarding the bulk chemicals acetone and butanol, the latter being a highly efficient biofuel. For butanol production by C. acetobutylicum to be optimized and exploited on an industrial scale, the effect of pH-induced gene regulation on solvent production by C. acetobutylicum in continuous culture must be understood as fully as possible. Results We present an ordinary differential equation model combining the metabolic network governing solvent production with regulation at the genetic level of the enzymes required for this process. Parameterizing the model with experimental data from continuous culture, we demonstrate the influence of pH upon fermentation products: at high pH (pH 5.7) acids are the dominant product while at low pH (pH 4.5) this switches to solvents. Through steady-state analyses of the model we focus our investigations on how alteration in gene expression of C. acetobutylicum could be exploited to increase butanol yield in a continuous culture fermentation. Conclusions Incorporating gene regulation into the model of solvent production by C. acetobutylicum enables an accurate representation of the pH-induced switch to solvent production to be obtained and theoretical investigations of possible synthetic-biology approaches to be pursued. Steady-state analyses suggest that, to increase butanol yield, alterations in the expression of single solvent-associated genes are insufficient; a more complex approach targeting two or more genes is required. PMID:21247470

Framework for waveband switching in multigranular optical networks: part I-multigranular cross-connect architectures [Invited

NASA Astrophysics Data System (ADS)

Cao, Xiaojun; Anand, Vishal; Qiao, Chunming

2006-12-01

Optical networks using wavelength-division multiplexing (WDM) are the foremost solution to the ever-increasing traffic in the Internet backbone. Rapid advances in WDM technology will enable each fiber to carry hundreds or even a thousand wavelengths (using dense-WDM, or DWDM, and ultra-DWDM) of traffic. This, coupled with worldwide fiber deployment, will bring about a tremendous increase in the size of the optical cross-connects, i.e., the number of ports of the wavelength switching elements. Waveband switching (WBS), wherein wavelengths are grouped into bands and switched as a single entity, can reduce the cost and control complexity of switching nodes by minimizing the port count. This paper presents a detailed study on recent advances and open research issues in WBS networks. In this study, we investigate in detail the architecture for various WBS cross-connects and compare them in terms of the number of ports and complexity and also in terms of how flexible they are in adjusting to dynamic traffic. We outline various techniques for grouping wavelengths into bands for the purpose of WBS and show how traditional wavelength routing is different from waveband routing and why techniques developed for wavelength-routed networks (WRNs) cannot be simply applied to WBS networks. We also outline how traffic grooming of subwavelength traffic can be done in WBS networks. In part II of this study [Cao , submitted to J. Opt. Netw.], we study the effect of wavelength conversion on the performance of WBS networks with reconfigurable MG-OXCs. We present an algorithm for waveband grouping in wavelength-convertible networks and evaluate its performance. We also investigate issues related to survivability in WBS networks and show how waveband and wavelength conversion can be used to recover from failures in WBS networks.

Solid-state switch increases switching speed

NASA Technical Reports Server (NTRS)

Mcgowan, G. F.

1966-01-01

Solid state switch for commutating capacitors in an RC commutated network increases switching speed and extends the filtering or commutating frequency spectrum well into the kilocycle region. The switch is equivalent to the standard double- pole double-throw /DPDT/ relay and is driven from digital micrologic circuits.

Synchrony in Metapopulations with Sporadic Dispersal

NASA Astrophysics Data System (ADS)

Jeter, Russell; Belykh, Igor

2015-06-01

We study synchronization in ecological networks under the realistic assumption that the coupling among the patches is sporadic/stochastic and due to rare and short-term meteorological conditions. Each patch is described by a tritrophic food chain model, representing the producer, consumer, and predator. If all three species can migrate, we rigorously prove that the network can synchronize as long as the migration occurs frequently, i.e. fast compared to the period of the ecological cycle, even though the network is disconnected most of the time. In the case where only the top trophic level (i.e. the predator) can migrate, we reveal an unexpected range of intermediate switching frequencies where synchronization becomes stable in a network which switches between two nonsynchronous dynamics. As spatial synchrony increases the danger of extinction, this counterintuitive effect of synchrony emerging from slower switching dispersal can be destructive for overall metapopulation persistence, presumably expected from switching between two dynamics which are unfavorable to extinction.

Moving the boundary between wavelength resources in optical packet and circuit integrated ring network.

PubMed

Furukawa, Hideaki; Miyazawa, Takaya; Wada, Naoya; Harai, Hiroaki

2014-01-13

Optical packet and circuit integrated (OPCI) networks provide both optical packet switching (OPS) and optical circuit switching (OCS) links on the same physical infrastructure using a wavelength multiplexing technique in order to deal with best-effort services and quality-guaranteed services. To immediately respond to changes in user demand for OPS and OCS links, OPCI networks should dynamically adjust the amount of wavelength resources for each link. We propose a resource-adjustable hybrid optical packet/circuit switch and transponder. We also verify that distributed control of resource adjustments can be applied to the OPCI ring network testbed we developed. In cooperation with the resource adjustment mechanism and the hybrid switch and transponder, we demonstrate that automatically allocating a shared resource and moving the wavelength resource boundary between OPS and OCS links can be successfully executed, depending on the number of optical paths in use.

TWC and AWG based optical switching structure for OVPN in WDM-PON

NASA Astrophysics Data System (ADS)

Bai, Hui-feng; Chen, Yu-xin; Wang, Qin

2015-03-01

With the rapid development of optical elements with large capacity and high speed, the network architecture is of great importance in determing the performance of wavelength division multiplexing passive optical network (WDM-PON). This paper proposes a switching structure based on the tunable wavelength converter (TWC) and the arrayed-waveguide grating (AWG) for WDM-PON, in order to provide the function of opitcal virtual private network (OVPN). Using the tunable wavelength converter technology, this switch structure is designed and works between the optical line terminal (OLT) and optical network units (ONUs) in the WDM-PON system. Moreover, the wavelength assignment of upstream/downstream can be realized and direct communication between ONUs is also allowed by privite wavelength channel. Simulation results show that the proposed TWC and AWG based switching structure is able to achieve OVPN function and to gain better performances in terms of bite error rate (BER) and time delay.

MOBS - A modular on-board switching system

NASA Astrophysics Data System (ADS)

Berner, W.; Grassmann, W.; Piontek, M.

The authors describe a multibeam satellite system that is designed for business services and for communications at a high bit rate. The repeater is regenerative with a modular onboard switching system. It acts not only as baseband switch but also as the central node of the network, performing network control and protocol evaluation. The hardware is based on a modular bus/memory architecture with associated processors.

Development of optical packet and circuit integrated ring network testbed.

PubMed

Furukawa, Hideaki; Harai, Hiroaki; Miyazawa, Takaya; Shinada, Satoshi; Kawasaki, Wataru; Wada, Naoya

2011-12-12

We developed novel integrated optical packet and circuit switch-node equipment. Compared with our previous equipment, a polarization-independent 4 × 4 semiconductor optical amplifier switch subsystem, gain-controlled optical amplifiers, and one 100 Gbps optical packet transponder and seven 10 Gbps optical path transponders with 10 Gigabit Ethernet (10GbE) client-interfaces were newly installed in the present system. The switch and amplifiers can provide more stable operation without equipment adjustments for the frequent polarization-rotations and dynamic packet-rate changes of optical packets. We constructed an optical packet and circuit integrated ring network testbed consisting of two switch nodes for accelerating network development, and we demonstrated 66 km fiber transmission and switching operation of multiplexed 14-wavelength 10 Gbps optical paths and 100 Gbps optical packets encapsulating 10GbE frames. Error-free (frame error rate < 1×10(-4)) operation was achieved with optical packets of various packet lengths and packet rates, and stable operation of the network testbed was confirmed. In addition, 4K uncompressed video streaming over OPS links was successfully demonstrated. © 2011 Optical Society of America

Gene regulatory network architecture in different developmental contexts influences the genetic basis of morphological evolution.

PubMed

Kittelmann, Sebastian; Buffry, Alexandra D; Franke, Franziska A; Almudi, Isabel; Yoth, Marianne; Sabaris, Gonzalo; Couso, Juan Pablo; Nunes, Maria D S; Frankel, Nicolás; Gómez-Skarmeta, José Luis; Pueyo-Marques, Jose; Arif, Saad; McGregor, Alistair P

2018-05-01

Convergent phenotypic evolution is often caused by recurrent changes at particular nodes in the underlying gene regulatory networks (GRNs). The genes at such evolutionary 'hotspots' are thought to maximally affect the phenotype with minimal pleiotropic consequences. This has led to the suggestion that if a GRN is understood in sufficient detail, the path of evolution may be predictable. The repeated evolutionary loss of larval trichomes among Drosophila species is caused by the loss of shavenbaby (svb) expression. svb is also required for development of leg trichomes, but the evolutionary gain of trichomes in the 'naked valley' on T2 femurs in Drosophila melanogaster is caused by reduced microRNA-92a (miR-92a) expression rather than changes in svb. We compared the expression and function of components between the larval and leg trichome GRNs to investigate why the genetic basis of trichome pattern evolution differs in these developmental contexts. We found key differences between the two networks in both the genes employed, and in the regulation and function of common genes. These differences in the GRNs reveal why mutations in svb are unlikely to contribute to leg trichome evolution and how instead miR-92a represents the key evolutionary switch in this context. Our work shows that variability in GRNs across different developmental contexts, as well as whether a morphological feature is lost versus gained, influence the nodes at which a GRN evolves to cause morphological change. Therefore, our findings have important implications for understanding the pathways and predictability of evolution.

Nonvolatile Ionic Two-Terminal Memory Device

NASA Technical Reports Server (NTRS)

Williams, Roger M.

1990-01-01

Conceptual solid-state memory device nonvolatile and erasable and has only two terminals. Proposed device based on two effects: thermal phase transition and reversible intercalation of ions. Transfer of sodium ions between source of ions and electrical switching element increases or decreases electrical conductance of element, turning switch "on" or "off". Used in digital computers and neural-network computers. In neural networks, many small, densely packed switches function as erasable, nonvolatile synaptic elements.

Space Communications Technology Conference: Onboard Processing and Switching

NASA Technical Reports Server (NTRS)

1991-01-01

Papers and presentations from the conference are presented. The topics covered include the following: satellite network architecture, network control and protocols, fault tolerance and autonomy, multichanned demultiplexing and demodulation, information switching and routing, modulation and coding, and planned satellite communications systems.

75 FR 76426 - Privacy Act of 1974; System of Records

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-08

..., access control lists, file system permissions, intrusion detection and prevention systems and log..., address, mailing address, country, organization, phone, fax, mobile, pager, Defense Switched Network (DSN..., address, mailing address, country, organization, phone, fax, mobile, pager, Defense Switched Network (DSN...

Overcoming residual interference in mental set switching: Neural correlates and developmental trajectory

PubMed Central

Witt, Suzanne T.; Stevens, Michael C.

2012-01-01

Mental set switching is a key facet of executive control measured behaviorally through reaction time or accuracy (i.e., ‘switch costs’) when shifting among task types. One of several experimentally-dissociable influences on switch costs is ‘task set inertia’, conceptualized as the residual interference conferred when a previous stimulus-response tendency interferes with subsequent stimulus processing on a new task. Task set inertia is thought to represent the passive decay of the previous stimulus-response set from working memory, and its effects decrease with increased interstimulus interval. Closely spaced trials confer high task set inertia, while sparsely spaced trials confer low task set inertia. This functional magnetic resonance imaging (fMRI) study characterized, for the first time, two opposing brain systems engaged to resolve task set inertia: 1) a frontoparietal ‘cortical control’ network for overcoming high task set inertia interference and 2) a subcortical-motor network more active during trials with low task set inertia. These networks were distinct from brain regions showing general switching effects (i.e., switch > non-switch) and from other previously-characterized interference effects. Moreover, there were ongoing maturational effects throughout adolescence for the brain regions engaged to overcome high task set inertia not seen for generalized switching effects. These novel findings represent a new avenue of exploration of cognitive set switching neural function. PMID:22584223

High speed all-optical networks

NASA Technical Reports Server (NTRS)

Chlamtac, Imrich

1993-01-01

An inherent problem of conventional point-to-point WAN architectures is that they cannot translate optical transmission bandwidth into comparable user available throughput due to the limiting electronic processing speed of the switching nodes. This report presents the first solution to WDM based WAN networks that overcomes this limitation. The proposed Lightnet architecture takes into account the idiosyncrasies of WDM switching/transmission leading to an efficient and pragmatic solution. The Lightnet architecture trades the ample WDM bandwidth for a reduction in the number of processing stages and a simplification of each switching stage, leading to drastically increased effective network throughputs.

High-speed on-chip windowed centroiding using photodiode-based CMOS imager

NASA Technical Reports Server (NTRS)

Pain, Bedabrata (Inventor); Sun, Chao (Inventor); Yang, Guang (Inventor); Cunningham, Thomas J. (Inventor); Hancock, Bruce (Inventor)

2003-01-01

A centroid computation system is disclosed. The system has an imager array, a switching network, computation elements, and a divider circuit. The imager array has columns and rows of pixels. The switching network is adapted to receive pixel signals from the image array. The plurality of computation elements operates to compute inner products for at least x and y centroids. The plurality of computation elements has only passive elements to provide inner products of pixel signals the switching network. The divider circuit is adapted to receive the inner products and compute the x and y centroids.

High-speed on-chip windowed centroiding using photodiode-based CMOS imager

NASA Technical Reports Server (NTRS)

Pain, Bedabrata (Inventor); Sun, Chao (Inventor); Yang, Guang (Inventor); Cunningham, Thomas J. (Inventor); Hancock, Bruce (Inventor)

2004-01-01

A centroid computation system is disclosed. The system has an imager array, a switching network, computation elements, and a divider circuit. The imager array has columns and rows of pixels. The switching network is adapted to receive pixel signals from the image array. The plurality of computation elements operates to compute inner products for at least x and y centroids. The plurality of computation elements has only passive elements to provide inner products of pixel signals the switching network. The divider circuit is adapted to receive the inner products and compute the x and y centroids.

Evolutionary prisoner's dilemma games on the network with punishment and opportunistic partner switching

NASA Astrophysics Data System (ADS)

Takesue, H.

2018-02-01

Punishment and partner switching are two well-studied mechanisms that support the evolution of cooperation. Observation of human behaviour suggests that the extent to which punishment is adopted depends on the usage of alternative mechanisms, including partner switching. In this study, we investigate the combined effect of punishment and partner switching in evolutionary prisoner's dilemma games conducted on a network. In the model, agents are located on the network and participate in the prisoner's dilemma games with punishment. In addition, they can opportunistically switch interaction partners to improve their payoff. Our Monte Carlo simulation showed that a large frequency of punishers is required to suppress defectors when the frequency of partner switching is low. In contrast, cooperation is the most abundant strategy when the frequency of partner switching is high regardless of the strength of punishment. Interestingly, cooperators become abundant not because they avoid the cost of inflicting punishment and earn a larger average payoff per game but rather because they have more numerous opportunities to be referred to as a role agent by defectors. Our results imply that the fluidity of social relationships has a profound effect on the adopted strategy in maintaining cooperation.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mlynarczyk, Paul J.; Pullen, Robert H.; Abel, Steven M., E-mail: abel@utk.edu

2016-01-07

Positive feedback is a common feature in signal transduction networks and can lead to phenomena such as bistability and signal propagation by domain growth. Physical features of the cellular environment, such as spatial confinement and the mobility of proteins, play important but inadequately understood roles in shaping the behavior of signaling networks. Here, we use stochastic, spatially resolved kinetic Monte Carlo simulations to explore a positive feedback network as a function of system size, system shape, and mobility of molecules. We show that these physical properties can markedly alter characteristics of bistability and stochastic switching when compared with well-mixed simulations.more » Notably, systems of equal volume but different shapes can exhibit qualitatively different behaviors under otherwise identical conditions. We show that stochastic switching to a state maintained by positive feedback occurs by cluster formation and growth. Additionally, the frequency at which switching occurs depends nontrivially on the diffusion coefficient, which can promote or suppress switching relative to the well-mixed limit. Taken together, the results provide a framework for understanding how confinement and protein mobility influence emergent features of the positive feedback network by modulating molecular concentrations, diffusion-influenced rate parameters, and spatiotemporal correlations between molecules.« less

Observability of Automata Networks: Fixed and Switching Cases.

PubMed

Li, Rui; Hong, Yiguang; Wang, Xingyuan

2018-04-01

Automata networks are a class of fully discrete dynamical systems, which have received considerable interest in various different areas. This brief addresses the observability of automata networks and switched automata networks in a unified framework, and proposes simple necessary and sufficient conditions for observability. The results are achieved by employing methods from symbolic computation, and are suited for implementation using computer algebra systems. Several examples are presented to demonstrate the application of the results.

The developing brain in a multitasking world

PubMed Central

Rothbart, Mary K.; Posner, Michael I.

2015-01-01

To understand the problem of multitasking, it is necessary to examine the brain’s attention networks that underlie the ability to switch attention between stimuli and tasks and to maintain a single focus among distractors. In this paper we discuss the development of brain networks related to the functions of achieving the alert state, orienting to sensory events, and developing self-control. These brain networks are common to everyone, but their efficiency varies among individuals and reflects both genes and experience. Training can alter brain networks. We consider two forms of training: (1) practice in tasks that involve particular networks, and (2) changes in brain state through such practices as meditation that may influence many networks. Playing action video games and multitasking are themselves methods of training the brain that can lead to improved performance but also to overdependence on media activity. We consider both of these outcomes and ideas about how to resist overdependence on media. Overall, our paper seeks to inform the reader about what has been learned about attention that can influence multitasking over the course of development. PMID:25821335

The developing brain in a multitasking world.

PubMed

Rothbart, Mary K; Posner, Michael I

2015-03-01

To understand the problem of multitasking, it is necessary to examine the brain's attention networks that underlie the ability to switch attention between stimuli and tasks and to maintain a single focus among distractors. In this paper we discuss the development of brain networks related to the functions of achieving the alert state, orienting to sensory events, and developing self-control. These brain networks are common to everyone, but their efficiency varies among individuals and reflects both genes and experience. Training can alter brain networks. We consider two forms of training: (1) practice in tasks that involve particular networks, and (2) changes in brain state through such practices as meditation that may influence many networks. Playing action video games and multitasking are themselves methods of training the brain that can lead to improved performance but also to overdependence on media activity. We consider both of these outcomes and ideas about how to resist overdependence on media. Overall, our paper seeks to inform the reader about what has been learned about attention that can influence multitasking over the course of development.

Controllability of switched singular mix-valued logical control networks with constraints

NASA Astrophysics Data System (ADS)

Deng, Lei; Gong, Mengmeng; Zhu, Peiyong

2018-03-01

The present paper investigates the controllability problem of switched singular mix-valued logical control networks (SSMLCNs) with constraints on states and controls. First, using the semi-tenser product (STP) of matrices, the SSMLCN is expressed in an algebraic form, based on which a necessary and sufficient condition is given for the uniqueness of solution of SSMLCNs. Second, a necessary and sufficient criteria is derived for the controllability of constrained SSMLCNs, by converting a constrained SSMLCN into a parallel constrained switched mix-valued logical control network. Third, an algorithm is presented to design a proper switching sequence and a control scheme which force a state to a reachable state. Finally, a numerical example is given to demonstrate the efficiency of the results obtained in this paper.

A Scheme to Optimize Flow Routing and Polling Switch Selection of Software Defined Networks.

PubMed

Chen, Huan; Li, Lemin; Ren, Jing; Wang, Yang; Zhao, Yangming; Wang, Xiong; Wang, Sheng; Xu, Shizhong

2015-01-01

This paper aims at minimizing the communication cost for collecting flow information in Software Defined Networks (SDN). Since flow-based information collecting method requires too much communication cost, and switch-based method proposed recently cannot benefit from controlling flow routing, jointly optimize flow routing and polling switch selection is proposed to reduce the communication cost. To this end, joint optimization problem is formulated as an Integer Linear Programming (ILP) model firstly. Since the ILP model is intractable in large size network, we also design an optimal algorithm for the multi-rooted tree topology and an efficient heuristic algorithm for general topology. According to extensive simulations, it is found that our method can save up to 55.76% communication cost compared with the state-of-the-art switch-based scheme.

On-board processing satellite network architecture and control study

NASA Technical Reports Server (NTRS)

Campanella, S. Joseph; Pontano, Benjamin A.; Chalmers, Harvey

1987-01-01

The market for telecommunications services needs to be segmented into user classes having similar transmission requirements and hence similar network architectures. Use of the following transmission architecture was considered: satellite switched TDMA; TDMA up, TDM down; scanning (hopping) beam TDMA; FDMA up, TDM down; satellite switched MF/TDMA; and switching Hub earth stations with double hop transmission. A candidate network architecture will be selected that: comprises multiple access subnetworks optimized for each user; interconnects the subnetworks by means of a baseband processor; and optimizes the marriage of interconnection and access techniques. An overall network control architecture will be provided that will serve the needs of the baseband and satellite switched RF interconnected subnetworks. The results of the studies shall be used to identify elements of network architecture and control that require the greatest degree of technology development to realize an operational system. This will be specified in terms of: requirements of the enabling technology; difference from the current available technology; and estimate of the development requirements needed to achieve an operational system. The results obtained for each of these tasks are presented.

Advances in integrated photonic circuits for packet-switched interconnection

NASA Astrophysics Data System (ADS)

Williams, Kevin A.; Stabile, Ripalta

2014-03-01

Sustained increases in capacity and connectivity are needed to overcome congestion in a range of broadband communication network nodes. Packet routing and switching in the electronic domain are leading to unsustainable energy- and bandwidth-densities, motivating research into hybrid solutions: optical switching engines are introduced for massive-bandwidth data transport while the electronic domain is clocked at more modest GHz rates to manage routing. Commercially-deployed optical switching engines using MEMS technologies are unwieldy and too slow to reconfigure for future packet-based networking. Optoelectronic packet-compliant switch technologies have been demonstrated as laboratory prototypes, but they have so far mostly used discretely pigtailed components, which are impractical for control plane development and product assembly. Integrated photonics has long held the promise of reduced hardware complexity and may be the critical step towards packet-compliant optical switching engines. Recently a number of laboratories world-wide have prototyped optical switching circuits using monolithic integration technology with up to several hundreds of integrated optical components per chip. Our own work has focused on multi-input to multi-output switching matrices. Recently we have demonstrated 8×8×8λ space and wavelength selective switches using gated cyclic routers and 16×16 broadband switching chips using monolithic multi-stage networks. We now operate these advanced circuits with custom control planes implemented with FPGAs to explore real time packet routing in multi-wavelength, multi-port test-beds. We review our contributions in the context of state of the art photonic integrated circuit technology and packet optical switching hardware demonstrations.

Population Dynamics of Genetic Regulatory Networks

NASA Astrophysics Data System (ADS)

Braun, Erez

2005-03-01

Unlike common objects in physics, a biological cell processes information. The cell interprets its genome and transforms the genomic information content, through the action of genetic regulatory networks, into proteins which in turn dictate its metabolism, functionality and morphology. Understanding the dynamics of a population of biological cells presents a unique challenge. It requires to link the intracellular dynamics of gene regulation, through the mechanism of cell division, to the level of the population. We present experiments studying adaptive dynamics of populations of genetically homogeneous microorganisms (yeast), grown for long durations under steady conditions. We focus on population dynamics that do not involve random genetic mutations. Our experiments follow the long-term dynamics of the population distributions and allow to quantify the correlations among generations. We focus on three interconnected issues: adaptation of genetically homogeneous populations following environmental changes, selection processes on the population and population variability and expression distributions. We show that while the population exhibits specific short-term responses to environmental inputs, it eventually adapts to a robust steady-state, largely independent of external conditions. Cycles of medium-switch show that the adapted state is imprinted in the population and that this memory is maintained for many generations. To further study population adaptation, we utilize the process of gene recruitment whereby a gene naturally regulated by a specific promoter is placed under a different regulatory system. This naturally occurring process has been recognized as a major driving force in evolution. We have recruited an essential gene to a foreign regulatory network and followed the population long-term dynamics. Rewiring of the regulatory network allows us to expose their complex dynamics and phase space structure.

Formation of Polymer Networks for Fast In-Plane Switching of Liquid Crystals at Low Temperatures

NASA Astrophysics Data System (ADS)

Yu, Byeong-Hun; Song, Dong Han; Kim, Ki-Han; Wok Park, Byung; Choi, Sun-Wook; Park, Sung Il; Kang, Sung Gu; Yoon, Jeong Hwan; Kim, Byeong Koo; Yoon, Tae-Hoon

2013-09-01

We formed a polymer structure to enable fast in-plane switching of liquid crystals at low temperatures. The problem of the inevitable slow response at low temperatures was reduced by the formation of in-cell polymer networks in in-plane switching (IPS) cells. The electro-optic characteristics of polymer-networked IPS cells were measured at temperatures ranging from -10 to 20 °C. The turn-on and turn-off times of an IPS cell were reduced by 44.5 and 47.2% at -10 °C by the formation of polymer networks. We believe that the proposed technology can be applied to emerging display devices such as mobile phones and automotive displays that may be used at low temperatures.

Research and development of a NYNEX switched multi-megabit data service prototype system

NASA Astrophysics Data System (ADS)

Maman, K. H.; Haines, Robert; Chatterjee, Samir

1991-02-01

Switched Multi-megabit Data Service (SMDS) is a proposed high-speed packet-switched service which will support broadband applications such as Local Area Network (LAN) interconnections across a metropolitan area and beyond. This service is designed to take advantage of evolving Metropolitan Area Network (MAN) standards and technology which will provide customers with 45-mbps and 1 . 5-mbps access to high-speed public data communications networks. This paper will briefly discuss SMDS and review its architecture including the Subscriber Network Interface (SNI) and the SMDS Interface Protocol (SIP). It will review the fundamental features of SMDS such as address screening addressing scheme and access classes. Then it will describe the SMDS prototype system developed in-house by NYNEX Science Technology.

Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach.

PubMed

Steggles, L Jason; Banks, Richard; Shaw, Oliver; Wipat, Anil

2007-02-01

New developments in post-genomic technology now provide researchers with the data necessary to study regulatory processes in a holistic fashion at multiple levels of biological organization. One of the major challenges for the biologist is to integrate and interpret these vast data resources to gain a greater understanding of the structure and function of the molecular processes that mediate adaptive and cell cycle driven changes in gene expression. In order to achieve this biologists require new tools and techniques to allow pathway related data to be modelled and analysed as network structures, providing valuable insights which can then be validated and investigated in the laboratory. We propose a new technique for constructing and analysing qualitative models of genetic regulatory networks based on the Petri net formalism. We take as our starting point the Boolean network approach of treating genes as binary switches and develop a new Petri net model which uses logic minimization to automate the construction of compact qualitative models. Our approach addresses the shortcomings of Boolean networks by providing access to the wide range of existing Petri net analysis techniques and by using non-determinism to cope with incomplete and inconsistent data. The ideas we present are illustrated by a case study in which the genetic regulatory network controlling sporulation in the bacterium Bacillus subtilis is modelled and analysed. The Petri net model construction tool and the data files for the B. subtilis sporulation case study are available at http://bioinf.ncl.ac.uk/gnapn.

Identification of a Transcriptionally Forward α Gene and Two υ Genes within the Pigeon (Columba livia) IgH Gene Locus.

PubMed

Huang, Tian; Wang, Xifeng; Si, Run; Chi, Hao; Han, Binyue; Han, Haitang; Cao, Gengsheng; Zhao, Yaofeng

2018-06-01

Compared with mammals, the bird Ig genetic system relies on gene conversion to create an Ab repertoire, with inversion of the IgA-encoding gene and very few cases of Ig subclass diversification. Although gene conversion has been studied intensively, class-switch recombination, a mechanism by which the IgH C region is exchanged, has rarely been investigated in birds. In this study, based on the published genome of pigeon ( Columba livia ) and high-throughput transcriptome sequencing of immune-related tissues, we identified a transcriptionally forward α gene and found that the pigeon IgH gene locus is arranged as μ-α-υ1-υ2. In this article, we show that both DNA deletion and inversion may result from IgA and IgY class switching, and similar junction patterns were observed for both types of class-switch recombination. We also identified two subclasses of υ genes in pigeon, which share low sequence identity. Phylogenetic analysis suggests that divergence of the two pigeon υ genes occurred during the early stage of bird evolution. The data obtained in this study provide new insight into class-switch recombination and Ig gene evolution in birds. Copyright © 2018 by The American Association of Immunologists, Inc.

A cross-stacked plasmonic nanowire network for high-contrast femtosecond optical switching.

PubMed

Lin, Yuanhai; Zhang, Xinping; Fang, Xiaohui; Liang, Shuyan

2016-01-21

We report an ultrafast optical switching device constructed by stacking two layers of gold nanowires into a perpendicularly crossed network, which works at a speed faster than 280 fs with an on/off modulation depth of about 22.4%. The two stacks play different roles in enhancing consistently the optical switching performance due to their different dependence on the polarization of optical electric fields. The cross-plasmon resonance based on the interaction between the perpendicularly stacked gold nanowires and its Fano-coupling with Rayleigh anomaly is the dominant mechanism for such a high-contrast optical switching device.

Nonuniform traffic spots (NUTS) in multistage interconnection networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lang, T.; Kurisaki, L.

1990-09-01

The performance of multistage interconnection networks for multiprocessors is degraded when the traffic pattern produces nonuniform congestion in the blocking switches, that is, when there exist nonuniform traffic spots. For some specific patterns the authors evaluate this degradation in performance and propose modifications to the network organization and operation to reduce the degradation. Successful modifications are the use of diverting switches and the extension of the network with additional links. The use of these modifications makes the network more effective for a larger variety of traffic patterns. The authors also consider the case in which the network carries the superpositionmore » of two types of traffic. One type is the high throughput data and instruction traffic, while the other consists of control and I/O packets which are of low throughput but have severe real-time constraints. The authors conclude that diverting switches and networks with additional links are also suitable for assuring low latency for the real-time traffic, especially when using the displacing mode.« less

DISCRETE EVENT SIMULATION OF OPTICAL SWITCH MATRIX PERFORMANCE IN COMPUTER NETWORKS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Imam, Neena; Poole, Stephen W

2013-01-01

In this paper, we present application of a Discrete Event Simulator (DES) for performance modeling of optical switching devices in computer networks. Network simulators are valuable tools in situations where one cannot investigate the system directly. This situation may arise if the system under study does not exist yet or the cost of studying the system directly is prohibitive. Most available network simulators are based on the paradigm of discrete-event-based simulation. As computer networks become increasingly larger and more complex, sophisticated DES tool chains have become available for both commercial and academic research. Some well-known simulators are NS2, NS3, OPNET,more » and OMNEST. For this research, we have applied OMNEST for the purpose of simulating multi-wavelength performance of optical switch matrices in computer interconnection networks. Our results suggest that the application of DES to computer interconnection networks provides valuable insight in device performance and aids in topology and system optimization.« less

Programmability of nanowire networks

NASA Astrophysics Data System (ADS)

Bellew, A. T.; Bell, A. P.; McCarthy, E. K.; Fairfield, J. A.; Boland, J. J.

2014-07-01

Electrical connectivity in networks of nanoscale junctions must be better understood if nanowire devices are to be scaled up from single wires to functional material systems. We show that the natural connectivity behaviour found in random nanowire networks presents a new paradigm for creating multi-functional, programmable materials. In devices made from networks of Ni/NiO core-shell nanowires at different length scales, we discover the emergence of distinct behavioural regimes when networks are electrically stressed. We show that a small network, with few nanowire-nanowire junctions, acts as a unipolar resistive switch, demonstrating very high ON/OFF current ratios (>105). However, large networks of nanowires distribute an applied bias across a large number of junctions, and thus respond not by switching but instead by evolving connectivity. We demonstrate that these emergent properties lead to fault-tolerant materials whose resistance may be tuned, and which are capable of adaptively reconfiguring under stress. By combining these two behavioural regimes, we demonstrate that the same nanowire network may be programmed to act both as a metallic interconnect, and a resistive switch device with high ON/OFF ratio. These results enable the fabrication of programmable, multi-functional materials from random nanowire networks.Electrical connectivity in networks of nanoscale junctions must be better understood if nanowire devices are to be scaled up from single wires to functional material systems. We show that the natural connectivity behaviour found in random nanowire networks presents a new paradigm for creating multi-functional, programmable materials. In devices made from networks of Ni/NiO core-shell nanowires at different length scales, we discover the emergence of distinct behavioural regimes when networks are electrically stressed. We show that a small network, with few nanowire-nanowire junctions, acts as a unipolar resistive switch, demonstrating very high ON/OFF current ratios (>105). However, large networks of nanowires distribute an applied bias across a large number of junctions, and thus respond not by switching but instead by evolving connectivity. We demonstrate that these emergent properties lead to fault-tolerant materials whose resistance may be tuned, and which are capable of adaptively reconfiguring under stress. By combining these two behavioural regimes, we demonstrate that the same nanowire network may be programmed to act both as a metallic interconnect, and a resistive switch device with high ON/OFF ratio. These results enable the fabrication of programmable, multi-functional materials from random nanowire networks. Electronic supplementary information (ESI) available: Nanowire statistics (length, diameter statistics, and oxide thickness) are provided. Forming curves for single junctions and networks. Passive voltage contrast image demonstrating selectivity of conductive pathways in 100 μm network. See DOI: 10.1039/c4nr02338b

Cellular Dichotomy Between Anchorage-Independent Growth Responses to bFGF and TA Reflects Molecular Switch in Commitment to Carcinogenesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Waters, Katrina M.; Tan, Ruimin; Opresko, Lee K.

2009-11-01

We have investigated gene expression patterns underlying reversible and irreversible anchorage-independent growth (AIG) phenotypes to identify more sensitive markers of cell transformation for studies directed at interrogating carcinogenesis responses. In JB6 mouse epidermal cells, basic fibroblast growth factor (bFGF) induces an unusually efficient and reversible AIG response, relative to 12-O-tetradecanoyl phorbol-13-acetate (TPA)-induced AIG which is irreversible. The reversible and irreversible AIG phenotypes are characterized by largely non-overlapping global gene expression profiles. However, a subset of differentially expressed genes were identified as common to reversible and irreversible AIG phenotypes, including genes regulated in a reciprocal fashion. Hepatic leukemia factor (HLF) andmore » D-site albumin promoter-binding protein (DBP) were increased in both bFGF and TPA soft agar colonies and selected for functional validation. Ectopic expression of human HLF and DBP in JB6 cells resulted in a marked increase in TPA- and bFGF-regulated AIG responses. HLF and DBP expression were increased in soft agar colonies arising from JB6 cells exposed to gamma radiation and in a human basal cell carcinoma tumor tissue, relative to paired non-tumor tissue. Subsequent biological network analysis suggests that many of the differentially expressed genes that are common to bFGF- and TPA-dependent AIG are regulated by c-Myc, SP-1 and HNF-4 transcription factors. Collectively, we have identified a potential molecular switch that mediates the transition from reversible to irreversible AIG.« less

Adaptive Topological Configuration of an Integrated Circuit/Packet-Switched Computer Network.

DTIC Science & Technology

1984-01-01

Gitman et al. [45] state that there are basically two approaches to the integrated network design problem: (1) solve the link/capacity problem for...1972), 1385-1397. 33. Frank, H., and Gitman , I. Economic analysis of integrated voice and data networks: a case study. Proc. of IEEE 66 , 11 (Nov. 1978...1974), 1074-1079. 45. Gitman , I., Hsieh, W., and Occhiogrosso, B. J. Analysis and design of hybrid switching networks. IEEE Trans. on Comm. Com-29

An iteration algorithm for optimal network flows

NASA Astrophysics Data System (ADS)

Woong, C. J.

1983-09-01

A packet switching network has the desirable feature of rapidly handling short (bursty) messages of the type often found in computer communication systems. In evaluating packet switching networks, the average time delay per packet is one of the most important measures of performance. The problem of message routing to minimize time delay is analyzed here using two approaches, called "successive saturation' and "max-slack', for various traffic requirement matrices and networks with fixed topology and link capacities.

A Change in the Ion Selectivity of Ligand-Gated Ion Channels Provides a Mechanism to Switch Behavior.

PubMed

Pirri, Jennifer K; Rayes, Diego; Alkema, Mark J

2015-01-01

Behavioral output of neural networks depends on a delicate balance between excitatory and inhibitory synaptic connections. However, it is not known whether network formation and stability is constrained by the sign of synaptic connections between neurons within the network. Here we show that switching the sign of a synapse within a neural circuit can reverse the behavioral output. The inhibitory tyramine-gated chloride channel, LGC-55, induces head relaxation and inhibits forward locomotion during the Caenorhabditis elegans escape response. We switched the ion selectivity of an inhibitory LGC-55 anion channel to an excitatory LGC-55 cation channel. The engineered cation channel is properly trafficked in the native neural circuit and results in behavioral responses that are opposite to those produced by activation of the LGC-55 anion channel. Our findings indicate that switches in ion selectivity of ligand-gated ion channels (LGICs) do not affect network connectivity or stability and may provide an evolutionary and a synthetic mechanism to change behavior.

Reliable WDM multicast in optical burst-switched networks

NASA Astrophysics Data System (ADS)

Jeong, Myoungki; Qiao, Chunming; Xiong, Yijun

2000-09-01

IN this paper,l we present a reliable WDM (Wavelength-Division Multiplexing) multicast protocol in optical burst-switched (OBS) networks. Since the burst dropping (loss) probability may be potentially high in a heavily loaded OBS backbone network, reliable multicast protocols that have developed for IP networks at the transport (or application) layer may incur heavy overheads such as a large number of duplicate retransmissions. In addition, it may take a longer time for an end host to detect and then recover from burst dropping (loss) occurred at the WDM layer. For efficiency reasons, we propose burst loss recovery within the OBS backbone (i.e., at the WDM link layer). The proposed protocol requires two additional functions to be performed by the WDM switch controller: subcasting and maintaining burst states, when the WDM switch has more than one downstream on the WDM multicast tree. We show that these additional functions are simple to implement and the overhead associated with them is manageable.

NETWORK SYNTHESIS OF CASCADED THRESHOLD ELEMENTS.

DTIC Science & Technology

A threshold function is a switching function which can be stimulated by a single, simplified, idealized neuron, or threshold element. In this report... threshold functions are examined in the context of abstract set theory and linear algebra for the purpose of obtaining practical synthesis procedures...for networks of threshold elements. A procedure is described by which, for any given switching function, a cascade network of these elements can be

Combined guaranteed throughput and best effort network-on-chip

DOEpatents

Chen, Gregory K.; Anders, Mark A.; Kaul, Himanshu; Krishnamurthy, Ram K.; Stillmaker, Aaron T.

2018-05-22

A first packet-switched reservation request is received. Data associated with the first packet-switched reservation request is communicated through a first circuit-switched channel according to a best effort communication scheme. A second packet-switched reservation request is received. Data associated with the second packet-switched reservation request is communicated through a second circuit-switched channel according to a guaranteed throughput communication scheme.

A Fully Implemented 12 × 12 Data Vortex Optical Packet Switching Interconnection Network

NASA Astrophysics Data System (ADS)

Shacham, Assaf; Small, Benjamin A.; Liboiron-Ladouceur, Odile; Bergman, Keren

2005-10-01

A fully functional optical packet switching (OPS) interconnection network based on the data vortex architecture is presented. The photonic switching fabric uniquely capitalizes on the enormous bandwidth advantage of wavelength division multiplexing (WDM) wavelength parallelism while delivering minimal packet transit latency. Utilizing semiconductor optical amplifier (SOA)-based switching nodes and conventional fiber-optic technology, the 12-port system exhibits a capacity of nearly 1 Tb/s. Optical packets containing an eight-wavelength WDM payload with 10 Gb/s per wavelength are routed successfully to all 12 ports while maintaining a bit error rate (BER) of 10-12 or better. Median port-to-port latencies of 110 ns are achieved with a distributed deflection routing network that resolves packet contention on-the-fly without the use of optical buffers and maintains the entire payload path in the optical domain.

Traffic shaping and scheduling for OBS-based IP/WDM backbones

NASA Astrophysics Data System (ADS)

Elhaddad, Mahmoud S.; Melhem, Rami G.; Znati, Taieb; Basak, Debashis

2003-10-01

We introduce Proactive Reservation-based Switching (PRS) -- a switching architecture for IP/WDM networks based on Labeled Optical Burst Switching. PRS achieves packet delay and loss performance comparable to that of packet-switched networks, without requiring large buffering capacity, or burst scheduling across a large number of wavelengths at the core routers. PRS combines proactive channel reservation with periodic shaping of ingress-egress traffic aggregates to hide the offset latency and approximate the utilization/buffering characteristics of discrete-time queues with periodic arrival streams. A channel scheduling algorithm imposes constraints on burst departure times to ensure efficient utilization of wavelength channels and to maintain the distance between consecutive bursts through the network. Results obtained from simulation using TCP traffic over carefully designed topologies indicate that PRS consistently achieves channel utilization above 90% with modest buffering requirements.

A Scheme to Optimize Flow Routing and Polling Switch Selection of Software Defined Networks

PubMed Central

Chen, Huan; Li, Lemin; Ren, Jing; Wang, Yang; Zhao, Yangming; Wang, Xiong; Wang, Sheng; Xu, Shizhong

2015-01-01

This paper aims at minimizing the communication cost for collecting flow information in Software Defined Networks (SDN). Since flow-based information collecting method requires too much communication cost, and switch-based method proposed recently cannot benefit from controlling flow routing, jointly optimize flow routing and polling switch selection is proposed to reduce the communication cost. To this end, joint optimization problem is formulated as an Integer Linear Programming (ILP) model firstly. Since the ILP model is intractable in large size network, we also design an optimal algorithm for the multi-rooted tree topology and an efficient heuristic algorithm for general topology. According to extensive simulations, it is found that our method can save up to 55.76% communication cost compared with the state-of-the-art switch-based scheme. PMID:26690571

A programmable Si-photonic node for SDN-enabled Bloom filter forwarding in disaggregated data centers

NASA Astrophysics Data System (ADS)

Moralis-Pegios, M.; Terzenidis, N.; Vagionas, C.; Pitris, S.; Chatzianagnostou, E.; Brimont, A.; Zanzi, A.; Sanchis, P.; Marti, J.; Kraft, J.; Rochracher, K.; Dorrestein, S.; Bogdan, M.; Tekin, T.; Syrivelis, D.; Tassiulas, L.; Miliou, A.; Pleros, N.; Vyrsokinos, K.

2017-02-01

Programmable switching nodes supporting Software-Defined Networking (SDN) over optical interconnecting technologies arise as a key enabling technology for future disaggregated Data Center (DC) environments. The SDNenabling roadmap of intra-DC optical solutions is already a reality for rack-to-rack interconnects, with recent research reporting on interesting applications of programmable silicon photonic switching fabrics addressing board-to-board and even on-board applications. In this perspective, simplified information addressing schemes like Bloom filter (BF)-based labels emerge as a highly promising solution for ensuring rapid switch reconfiguration, following quickly the changes enforced in network size, network topology or even in content location. The benefits of BF-based forwarding have been so far successfully demonstrated in the Information-Centric Network (ICN) paradigm, while theoretical studies have also revealed the energy consumption and speed advantages when applied in DCs. In this paper we present for the first time a programmable 4x4 Silicon Photonic switch that supports SDN through the use of BF-labeled router ports. Our scheme significantly simplifies packet forwarding as it negates the need for large forwarding tables, allowing for its remote control through modifications in the assigned BF labels. We demonstrate 1x4 switch operation controlling the Si-Pho switch by a Stratix V FPGA module, which is responsible for processing the packet ID and correlating its destination with the appropriate BF-labeled outgoing port. DAC- and amplifier-less control of the carrier-injection Si-Pho switches is demonstrated, revealing successful switching of 10Gb/s data packets with BF-based forwarding information changes taking place at a time-scale that equals the duration of four consecutive packets.

Optical implementation of polarization-independent, bidirectional, nonblocking Clos network using polarization control technique in free space

NASA Astrophysics Data System (ADS)

Yang, Junbo; Yang, Jiankun; Li, Xiujian; Chang, Shengli; Su, Xianyu; Ping, Xu

2011-04-01

The clos network is one of the earliest multistage interconnection networks. Recently, it has been widely studied in parallel optical information processing systems, and there have been many efforts to develop this network. In this paper, a smart and compact Clos network, including Clos(2,3,2) and Clos(2,4,2), is proposed by using polarizing beam-splitters (PBS), phase spatial light modulators (PSLM), and mirrors. PBS features that are s-component (perpendicular to the incident plane) of the incident light beam is reflected, and the p-component (parallel to the incident plane) passes through it. According to switching logic, under control of external electrical signals, PSLM functions to control routing paths of the signal beams, i.e., the polarization of each optical signal is rotated or not rotated 90° by a programmable PSLM. This new type of configuration grants the features of less optical components, compact in structure, efficient in performance, and insensitive to polarization of signal beam. In addition, the straight, the exchange, and the broadcast functions of the basic switch element are implemented bidirectionally in free-space. Furthermore, the new optical experimental module of 2×3 and 2×4 optical switch is also presented by a cascading polarization-independent bidirectional 2×2 optical switch. Simultaneously, the routing state-table of 2×3 and 2×4 optical switch to perform all permutation output and nonblocking switch for the input signal beam, is achieved. Since the proposed optical setup consists of only optical polarization elements, it is compact in structure, and possesses a low energy loss, a high signal-to-ratio, and an available large number of optical channels. Finally, the discussions and the experimental results show that the Clos network proposed here should be helpful in the design of large-scale network matrix, and may be used in optical communication and optical information processing.

Pattern Switchable Antenna System Using Inkjet-Printed Directional Bow-Tie for Bi-Direction Sensing Applications

PubMed Central

Eom, Seung-Hyun; Seo, Yunsik; Lim, Sungjoon

2015-01-01

In this paper, we propose a paper-based pattern switchable antenna system using inkjet-printing technology for bi-direction sensor applications. The proposed antenna system is composed of two directional bow-tie antennas and a switching network. The switching network consists of a single-pole-double-throw (SPDT) switch and a balun element. A double-sided parallel-strip line (DSPSL) is employed to convert the unbalanced microstrip mode to the balanced strip mode. Two directional bow-tie antennas have different radiation patterns because of the different orientation of the reflectors and antennas. It is demonstrated from electromagnetic (EM) simulation and measurement that the radiation patterns of the proposed antenna are successfully switched by the SPDT switch. PMID:26690443

Pattern Switchable Antenna System Using Inkjet-Printed Directional Bow-Tie for Bi-Direction Sensing Applications.

PubMed

Eom, Seung-Hyun; Seo, Yunsik; Lim, Sungjoon

2015-12-10

In this paper, we propose a paper-based pattern switchable antenna system using inkjet-printing technology for bi-direction sensor applications. The proposed antenna system is composed of two directional bow-tie antennas and a switching network. The switching network consists of a single-pole-double-throw (SPDT) switch and a balun element. A double-sided parallel-strip line (DSPSL) is employed to convert the unbalanced microstrip mode to the balanced strip mode. Two directional bow-tie antennas have different radiation patterns because of the different orientation of the reflectors and antennas. It is demonstrated from electromagnetic (EM) simulation and measurement that the radiation patterns of the proposed antenna are successfully switched by the SPDT switch.

Vibration reduction for smart periodic structures via periodic piezoelectric arrays with nonlinear interleaved-switched electronic networks

NASA Astrophysics Data System (ADS)

Bao, Bin; Guyomar, Daniel; Lallart, Mickaël

2017-01-01

Smart periodic structures covered by periodically distributed piezoelectric patches have drawn more and more attention in recent years for wave propagation attenuation and corresponding structural vibration suppression. Since piezoelectric materials are special type of energy conversion materials that link mechanical characteristics with electrical characteristics, shunt circuits coupled with such materials play a key role in the wave propagation and/or vibration control performance in smart periodic structures. Conventional shunt circuit designs utilize resistive shunt (R-shunt) and resonant shunt (RL-shunt). More recently, semi-passive nonlinear approaches have also been developed for efficiently controlling the vibrations of such structures. In this paper, an innovative smart periodic beam structure with nonlinear interleaved-switched electric networks based on synchronized switching damping on inductor (SSDI) is proposed and investigated for vibration reduction and wave propagation attenuation. Different from locally resonant band gap mechanism forming narrow band gaps around the desired resonant frequencies, the proposed interleaved electrical networks can induce new broadly low-frequency stop bands and broaden primitive Bragg stop bands by virtue of unique interleaved electrical configurations and the SSDI technique which has the unique feature of realizing automatic impedance adaptation with a small inductance. Finite element modeling of a Timoshenko electromechanical beam structure is also presented for validating dispersion properties of the structure. Both theoretical and experimental results demonstrate that the proposed beam structure not only shows better vibration and wave propagation attenuation than the smart beam structure with independent switched networks, but also has technical simplicity of requiring only half of the number of switches than the independent switched network needs.

Default mode network abnormalities during state switching in attention deficit hyperactivity disorder.

PubMed

Sidlauskaite, J; Sonuga-Barke, E; Roeyers, H; Wiersema, J R

2016-02-01

Individuals with attention deficit hyperactivity disorder (ADHD) display excess levels of default mode network (DMN) activity during goal-directed tasks, which are associated with attentional disturbances and performance decrements. One hypothesis is that this is due to attenuated down-regulation of this network during rest-to-task switching. A second related hypothesis is that it may be associated with right anterior insula (rAI) dysfunction - a region thought to control the actual state-switching process. These hypotheses were tested in the current fMRI study in which 19 adults with ADHD and 21 typically developing controls undertook a novel state-to-state switching paradigm. Advance cues signalled upcoming switches between rest and task periods and switch-related anticipatory modulation of DMN and rAI was measured. To examine whether rest-to-task switching impairments may be a specific example of a more general state regulation deficit, activity upon task-to-rest cues was also analysed. Against our hypotheses, we found that the process of down-regulating the DMN when preparing to switch from rest to task was unimpaired in ADHD and that there was no switch-specific deficit in rAI modulation. However, individuals with ADHD showed difficulties up-regulating the DMN when switching from task to rest. Rest-to-task DMN attenuation seems to be intact in adults with ADHD and thus appears unrelated to excess DMN activity observed during tasks. Instead, individuals with ADHD exhibit attenuated up-regulation of the DMN, hence suggesting disturbed re-initiation of a rest state.

A genetic switch controls the production of flagella and toxins in Clostridium difficile

PubMed Central

2017-01-01

In the human intestinal pathogen Clostridium difficile, flagella promote adherence to intestinal epithelial cells. Flagellar gene expression also indirectly impacts production of the glucosylating toxins, which are essential to diarrheal disease development. Thus, factors that regulate the expression of the flgB operon will likely impact toxin production in addition to flagellar motility. Here, we report the identification a “flagellar switch” that controls the phase variable production of flagella and glucosylating toxins. The flagellar switch, located upstream of the flgB operon containing the early stage flagellar genes, is a 154 bp invertible sequence flanked by 21 bp inverted repeats. Bacteria with the sequence in one orientation expressed flagellum and toxin genes, produced flagella, and secreted the toxins (“flg phase ON”). Bacteria with the sequence in the inverse orientation were attenuated for flagellar and toxin gene expression, were aflagellate, and showed decreased toxin secretion (“flg phase OFF”). The orientation of the flagellar switch is reversible during growth in vitro. We provide evidence that gene regulation via the flagellar switch occurs post-transcription initiation and requires a C. difficile-specific regulatory factor to destabilize or degrade the early flagellar gene mRNA when the flagellar switch is in the OFF orientation. Lastly, through mutagenesis and characterization of flagellar phase locked isolates, we determined that the tyrosine recombinase RecV, which catalyzes inversion at the cwpV switch, is also responsible for inversion at the flagellar switch in both directions. Phase variable flagellar motility and toxin production suggests that these important virulence factors have both advantageous and detrimental effects during the course of infection. PMID:28346491

On-board processing satellite network architectures for broadband ISDN

NASA Technical Reports Server (NTRS)

Inukai, Thomas; Faris, Faris; Shyy, Dong-Jye

1992-01-01

Onboard baseband processing architectures for future satellite broadband integrated services digital networks (B-ISDN's) are addressed. To assess the feasibility of implementing satellite B-ISDN services, critical design issues, such as B-ISDN traffic characteristics, transmission link design, and a trade-off between onboard circuit and fast packet switching, are analyzed. Examples of the two types of switching mechanisms and potential onboard network control functions are presented. A sample network architecture is also included to illustrate a potential onboard processing system.

Optical network democratization.

PubMed

Nejabati, Reza; Peng, Shuping; Simeonidou, Dimitra

2016-03-06

The current Internet infrastructure is not able to support independent evolution and innovation at physical and network layer functionalities, protocols and services, while at same time supporting the increasing bandwidth demands of evolving and heterogeneous applications. This paper addresses this problem by proposing a completely democratized optical network infrastructure. It introduces the novel concepts of the optical white box and bare metal optical switch as key technology enablers for democratizing optical networks. These are programmable optical switches whose hardware is loosely connected internally and is completely separated from their control software. To alleviate their complexity, a multi-dimensional abstraction mechanism using software-defined network technology is proposed. It creates a universal model of the proposed switches without exposing their technological details. It also enables a conventional network programmer to develop network applications for control of the optical network without specific technical knowledge of the physical layer. Furthermore, a novel optical network virtualization mechanism is proposed, enabling the composition and operation of multiple coexisting and application-specific virtual optical networks sharing the same physical infrastructure. Finally, the optical white box and the abstraction mechanism are experimentally evaluated, while the virtualization mechanism is evaluated with simulation. © 2016 The Author(s).

Satellite networks in the ISDN era

NASA Astrophysics Data System (ADS)

Amadesi, P.; Haines, P.; Patacchini, A.

1986-12-01

The development of an integrated service digital network (ISDN) capable of supporting a wide range of services using a small set of standard multipurpose user-network interfaces is examined. The ISDN environment is expected to consist of functional elements such as, circuit switching, packet switching, and common channel signaling. The use of satellites or fiber optics in the ISDN is evaluated. The relation between satellites and the ISDN in the short-, medium-, and long-terms is analyzed. The recommendations of the consultative committee, CCIR, concerning the definition of the hypothetical reference digital path and the required quality and availability for ISDN applications, and the proposed plans of Eutelsat and Intelsat for satellite systems compatible with an ISDN are discussed. The application of business satellite networks and packet satellite networks to an ISDN is studied. The long-term objectives for an ISDN is a wideband system that accommodates digital transmission on circuit and packet switched bases.

Method of optimum channel switching in equipment of infocommunication network in conditions of cyber attacks to their telecommunication infrastructure.

NASA Astrophysics Data System (ADS)

Kochedykov, S. S.; Noev, A. N.; Dushkin, A. V.; Gubin, I. A.

2018-05-01

On the basis of the mathematical graph theory, the method of optimum switching of infocommunication networks in the conditions of cyber attacks is developed. The idea of representation of a set of possible ways on the graph in the form of the multilevel tree ordered by rules of algebra of a logic theory is the cornerstone of a method. As a criterion of optimization, the maximum of network transmission capacity to which assessment Ford- Falkerson's theorem is applied is used. The method is realized in the form of a numerical algorithm, which can be used not only for design, but also for operational management of infocommunication networks in conditions of violation of the functioning of their switching centers.

TTEthernet for Integrated Spacecraft Networks

NASA Technical Reports Server (NTRS)

Loveless, Andrew

2015-01-01

Aerospace projects have traditionally employed federated avionics architectures, in which each computer system is designed to perform one specific function (e.g. navigation). There are obvious downsides to this approach, including excessive weight (from so much computing hardware), and inefficient processor utilization (since modern processors are capable of performing multiple tasks). There has therefore been a push for integrated modular avionics (IMA), in which common computing platforms can be leveraged for different purposes. This consolidation of multiple vehicle functions to shared computing platforms can significantly reduce spacecraft cost, weight, and design complexity. However, the application of IMA principles introduces significant challenges, as the data network must accommodate traffic of mixed criticality and performance levels - potentially all related to the same shared computer hardware. Because individual network technologies are rarely so competent, the development of truly integrated network architectures often proves unreasonable. Several different types of networks are utilized - each suited to support a specific vehicle function. Critical functions are typically driven by precise timing loops, requiring networks with strict guarantees regarding message latency (i.e. determinism) and fault-tolerance. Alternatively, non-critical systems generally employ data networks prioritizing flexibility and high performance over reliable operation. Switched Ethernet has seen widespread success filling this role in terrestrial applications. Its high speed, flexibility, and the availability of inexpensive commercial off-the-shelf (COTS) components make it desirable for inclusion in spacecraft platforms. Basic Ethernet configurations have been incorporated into several preexisting aerospace projects, including both the Space Shuttle and International Space Station (ISS). However, classical switched Ethernet cannot provide the high level of network determinism required by real-time spacecraft applications. Even with modern advancements, the uncoordinated (i.e. event-driven) nature of Ethernet communication unavoidably leads to message contention within network switches. The arbitration process used to resolve such conflicts introduces variation in the time it takes for messages to be forwarded. TTEthernet1 introduces decentralized clock synchronization to switched Ethernet, enabling message transmission according to a time-triggered (TT) paradigm. A network planning tool is used to allocate each device a finite amount of time in which it may transmit a frame. Each time slot is repeated sequentially to form a periodic communication schedule that is then loaded onto each TTEthernet device (e.g. switches and end systems). Each network participant references the synchronized time in order to dispatch messages at predetermined instances. This schedule guarantees that no contention exists between time-triggered Ethernet frames in the network switches, therefore eliminating the need for arbitration (and the timing variation it causes). Besides time-triggered messaging, TTEthernet networks may provide two additional traffic classes to support communication of different criticality levels. In the rate-constrained (RC) traffic class, the frame payload size and rate of transmission along each communication channel are limited to predetermined maximums. The network switches can therefore be configured to accommodate the known worst-case traffic pattern, and buffer overflows can be eliminated. The best-effort (BE) traffic class behaves akin to classical Ethernet. No guarantees are provided regarding transmission latency or successful message delivery. TTEthernet coordinates transmission of all three traffic classes over the same physical connections, therefore accommodating the full spectrum of traffic criticality levels required in IMA architectures. Common computing platforms (e.g. LRUs) can share networking resources in such a way that failures in non-critical systems (using BE or RC communication modes) cannot impact flight-critical functions (using TT communication). Furthermore, TTEthernet hardware (e.g. switches, cabling) can be shared by both TTEthernet and classical Ethernet traffic.

Diplexer switch

NASA Technical Reports Server (NTRS)

Grauling, C. H., Jr.; Parker, T. W.

1977-01-01

Switch achieves high isolation and continuous input/output matching by using resonant coupling structure of diplexer. Additionally, dc bias network used to control switch is decoupled from RF input and output lines. Voltage transients in external circuits are thus minimized.

ISDN Application in the Army Environment

DTIC Science & Technology

1992-02-01

Signalling System Number 7 ( SS7 ). SS7 is a packet switched signalling network operating in parallel with the traffic bearing network. The current, in...for example, require SS7 . Further into the future, broadband ISDN (B-ISDN) is expected to provide high-quality, full-motion video, High Definition...smaller business offices, ISDN could be a viable alternative to private networks, especially when switches are connected through SS7 . ISDN, in combination

Going End to End to Deliver High-Speed Data

NASA Technical Reports Server (NTRS)

2005-01-01

By the end of the 1990s, the optical fiber "backbone" of the telecommunication and data-communication networks had evolved from megabits-per-second transmission rates to gigabits-per-second transmission rates. Despite this boom in bandwidth, however, users at the end nodes were still not being reached on a consistent basis. (An end node is any device that does not behave like a router or a managed hub or switch. Examples of end node objects are computers, printers, serial interface processor phones, and unmanaged hubs and switches.) The primary reason that prevents bandwidth from reaching the end nodes is the complex local network topology that exists between the optical backbone and the end nodes. This complex network topology consists of several layers of routing and switch equipment which introduce potential congestion points and network latency. By breaking down the complex network topology, a true optical connection can be achieved. Access Optical Networks, Inc., is making this connection a reality with guidance from NASA s nondestructive evaluation experts.

Gene switching in Amoeba proteus caused by endosymbiotic bacteria.

PubMed

Jeon, Taeck J; Jeon, Kwang W

2004-02-01

The expression of genes for S-adenosylmethionine synthetase (SAMS), which catalyzes the synthesis of S-adenosylmethionine (AdoMet), a major methyl donor in cells, was studied in symbiont-free (D) and symbiont-bearing (xD) amoeba strains to determine the effect of bacterial endosymbionts. The symbionts suppressed the expression of the gene in host xD amoebae, but amoebae still exhibited about half the enzyme activity found in symbiont-free D amoebae. The study was aimed at elucidating mechanisms of the suppression of the amoeba's gene and determining the alternative source for the gene product. Unexpectedly, we found a second sams (sams2) gene in amoebae, which encoded 390 amino acids. Results of experiments measuring SAMS activities and amounts of AdoMet in D and xD amoebae showed that the half SAMS activity found in xD amoebae came from the amoeba's SAMS2 and not from their endosymbionts. The expression of amoeba sams genes was switched from sams1 to sams2 as a result of infection with X-bacteria, raising the possibility that the switch in the expression of sams genes by bacteria plays a role in the development of symbiosis and the host-pathogen interactions. This is the first report showing such a switch in the expression of host sams genes by infecting bacteria.

Fully programmable and scalable optical switching fabric for petabyte data center.

PubMed

Zhu, Zhonghua; Zhong, Shan; Chen, Li; Chen, Kai

2015-02-09

We present a converged EPS and OCS switching fabric for data center networks (DCNs) based on a distributed optical switching architecture leveraging both WDM & SDM technologies. The architecture is topology adaptive, well suited to dynamic and diverse *-cast traffic patterns. Compared to a typical folded-Clos network, the new architecture is more readily scalable to future multi-Petabyte data centers with 1000 + racks while providing a higher link bandwidth, reducing transceiver count by 50%, and improving cabling efficiency by more than 90%.

Ultrafast Laser Beam Switching and Pulse Train Generation by Using Coupled Vertical-Cavity, Surface-Emitting Lasers (VCSELS)

NASA Technical Reports Server (NTRS)

Goorjian, Peter M. (Inventor); Ning, Cun-Zheng (Inventor)

2005-01-01

Ultrafast directional beam switching is achieved using coupled VCSELs. This approach is demonstrated to achieve beam switching frequencies of 40 GHz and more and switching directions of about eight degrees. This switching scheme is likely to be useful for ultrafast optical networks at frequencies much higher than achievable with other approaches.

Optical switch based on thermocapillarity

NASA Astrophysics Data System (ADS)

Sakata, Tomomi; Makihara, Mitsuhiro; Togo, Hiroyoshi; Shimokawa, Fusao; Kaneko, Kazumasa

2001-11-01

Space-division optical switches are essential for the protection, optical cross-connects (OXCs), and optical add/drop multiplexers (OADMs) needed in future fiber-optic communication networks. For applications in these areas, we proposed a thermocapillarity switch called oil-latching interfacial-tension variation effect (OLIVE) switch. An OLIVE switch is a micro-mechanical optical switch fabricated on planar lightwave circuits (PLC) using micro-electro-mechanical systems (MEMS) technology. It consists of a crossing waveguide that has a groove at each crossing point and a pair of microheaters. The groove is partially filled with the refractive-index-matching liquid, and optical signals are switched according to the liquid's position in the groove, i.e., whether it is passing straight through the groove or reflecting at the sidewall of the groove. The liquid is driven by thermocapillarity and latched by capillarity. Using the total internal reflection to switch the optical path, the OLIVE switch exhibits excellent optical characteristics, such as high transparency (insertion loss: < 2 dB), high extinction ratio (> 50 dB), and low crosstalk (< -50 dB). Moreover, since this switch has a simple structure and bi-stability, it has wide variety of applications in wavelength division multiplexing (WDM) networks.

Molecular basis of wing coloration in a Batesian mimic butterfly, Papilio polytes

PubMed Central

Nishikawa, Hideki; Iga, Masatoshi; Yamaguchi, Junichi; Saito, Kazuki; Kataoka, Hiroshi; Suzuki, Yutaka; Sugano, Sumio; Fujiwara, Haruhiko

2013-01-01

Batesian mimicry protects animals from predators through resemblance with distasteful models in shape, color pattern, or behavior. To elucidate the wing coloration mechanisms involved in the mimicry, we investigated chemical composition and gene expression of the pale yellow and red pigments of a swallowtail butterfly, Papilio polytes, whose females mimic the unpalatable butterfly Pachliopta aristolochiae. Using LC/MS, we showed that the pale yellow wing regions in non-mimetic females consist of kynurenine and N-β-alanyldopamine (NBAD). Moreover, qRT-PCR showed that kynurenine/NBAD biosynthetic genes were upregulated in these regions in non-mimetic females. However, these pigments were absent in mimetic females. RNA-sequencing showed that kynurenine/NBAD synthesis and Toll signaling genes were upregulated in the red spots specific to mimetic female wings. These results demonstrated that drastic changes in gene networks in the red and pale yellow regions can switch wing color patterns between non-mimetic and mimetic females of P. polytes. PMID:24212474

Molecular basis of wing coloration in a Batesian mimic butterfly, Papilio polytes.

PubMed

Nishikawa, Hideki; Iga, Masatoshi; Yamaguchi, Junichi; Saito, Kazuki; Kataoka, Hiroshi; Suzuki, Yutaka; Sugano, Sumio; Fujiwara, Haruhiko

2013-11-11

Batesian mimicry protects animals from predators through resemblance with distasteful models in shape, color pattern, or behavior. To elucidate the wing coloration mechanisms involved in the mimicry, we investigated chemical composition and gene expression of the pale yellow and red pigments of a swallowtail butterfly, Papilio polytes, whose females mimic the unpalatable butterfly Pachliopta aristolochiae. Using LC/MS, we showed that the pale yellow wing regions in non-mimetic females consist of kynurenine and N-β-alanyldopamine (NBAD). Moreover, qRT-PCR showed that kynurenine/NBAD biosynthetic genes were upregulated in these regions in non-mimetic females. However, these pigments were absent in mimetic females. RNA-sequencing showed that kynurenine/NBAD synthesis and Toll signaling genes were upregulated in the red spots specific to mimetic female wings. These results demonstrated that drastic changes in gene networks in the red and pale yellow regions can switch wing color patterns between non-mimetic and mimetic females of P. polytes.

SDN-Enabled Dynamic Feedback Control and Sensing in Agile Optical Networks

NASA Astrophysics Data System (ADS)

Lin, Likun

Fiber optic networks are no longer just pipelines for transporting data in the long haul backbone. Exponential growth in traffic in metro-regional areas has pushed higher capacity fiber toward the edge of the network, and highly dynamic patterns of heterogeneous traffic have emerged that are often bursty, severely stressing the historical "fat and dumb pipe" static optical network, which would need to be massively over-provisioned to deal with these loads. What is required is a more intelligent network with a span of control over the optical as well as electrical transport mechanisms which enables handling of service requests in a fast and efficient way that guarantees quality of service (QoS) while optimizing capacity efficiency. An "agile" optical network is a reconfigurable optical network comprised of high speed intelligent control system fed by real-time in situ network sensing. It provides fast response in the control and switching of optical signals in response to changing traffic demands and network conditions. This agile control of optical signals is enabled by pushing switching decisions downward in the network stack to the physical layer. Implementing such agility is challenging due to the response dynamics and interactions of signals in the physical layer. Control schemes must deal with issues such as dynamic power equalization, EDFA transients and cascaded noise effects, impairments due to self-phase modulation and dispersion, and channel-to-channel cross talk. If these issues are not properly predicted and mitigated, attempts at dynamic control can drive the optical network into an unstable state. In order to enable high speed actuation of signal modulators and switches, the network controller must be able to make decisions based on predictive models. In this thesis, we consider how to take advantage of Software Defined Networking (SDN) capabilities for network reconfiguration, combined with embedded models that access updates from deployed network monitoring sensors. In order to maintain signal quality while optimizing network resources, we find that it is essential to model and update estimates of the physical link impairments in real-time. In this thesis, we consider the key elements required to enable an agile optical network, with contributions as follows: • Control Framework: extended the SDN concept to include the optical transport network through extensions to the OpenFlow (OF) protocol. A unified SDN control plane is built to facilitate control and management capability across the electrical/packet-switched and optical/circuit-switched portions of the network seamlessly. The SDN control plane serves as a platform to abstract the resources of multilayer/multivendor networks. Through this platform, applications can dynamically request the network resources to meet their service requirements. • Use of In-situ Monitors: enabled real-time physical impairment sensing in the control plane using in-situ Optical Performance Monitoring (OPM) and bit error rate (BER) analyzers. OPM and BER values are used as quantitative indicators of the link status and are fed to the control plane through a high-speed data collection interface to form a closed-loop feedback system to enable adaptive resource allocation. • Predictive Network Model: used a network model embedded in the control layer to study the link status. The estimated results of network status is fed into the control decisions to precompute the network resources. The performance of the network model can be enhanced by the sensing results. • Real-Time Control Algorithms: investigated various dynamic resource allocation mechanisms supporting an agile optical network. Intelligent routing and wavelength switching for recovering from traffic impairments is achieved experimentally in the agile optical network within one second. A distance-adaptive spectrum allocation scheme to address transmission impairments caused by cascaded Wavelength Selective Switches (WSS) is proposed and evaluated for improving network spectral efficiency.

System and Method for Network Bandwidth, Buffers and Timing Management Using Hybrid Scheduling of Traffic with Different Priorities and Guarantees

NASA Technical Reports Server (NTRS)

Bonk, Ted (Inventor); Hall, Brendan (Inventor); Smithgall, William Todd (Inventor); Varadarajan, Srivatsan (Inventor); DeLay, Benjamin F. (Inventor)

2017-01-01

Systems and methods for network bandwidth, buffers and timing management using hybrid scheduling of traffic with different priorities and guarantees are provided. In certain embodiments, a method of managing network scheduling and configuration comprises, for each transmitting end station, reserving one exclusive buffer for each virtual link to be transmitted from the transmitting end station; for each receiving end station, reserving exclusive buffers for each virtual link to be received at the receiving end station; and for each switch, reserving a exclusive buffer for each virtual link to be received at an input port of the switch. The method further comprises determining if each respective transmitting end station, receiving end station, and switch has sufficient capability to support the reserved buffers; and reporting buffer infeasibility if each respective transmitting end station, receiving end station, and switch does not have sufficient capability to support the reserved buffers.

On-board congestion control for satellite packet switching networks

NASA Technical Reports Server (NTRS)

Chu, Pong P.

1991-01-01

It is desirable to incorporate packet switching capability on-board for future communication satellites. Because of the statistical nature of packet communication, incoming traffic fluctuates and may cause congestion. Thus, it is necessary to incorporate a congestion control mechanism as part of the on-board processing to smooth and regulate the bursty traffic. Although there are extensive studies on congestion control for both baseband and broadband terrestrial networks, these schemes are not feasible for space based switching networks because of the unique characteristics of satellite link. Here, we propose a new congestion control method for on-board satellite packet switching. This scheme takes into consideration the long propagation delay in satellite link and takes advantage of the the satellite's broadcasting capability. It divides the control between the ground terminals and satellite, but distributes the primary responsibility to ground terminals and only requires minimal hardware resource on-board satellite.

Optimization of multicast optical networks with genetic algorithm

NASA Astrophysics Data System (ADS)

Lv, Bo; Mao, Xiangqiao; Zhang, Feng; Qin, Xi; Lu, Dan; Chen, Ming; Chen, Yong; Cao, Jihong; Jian, Shuisheng

2007-11-01

In this letter, aiming to obtain the best multicast performance of optical network in which the video conference information is carried by specified wavelength, we extend the solutions of matrix games with the network coding theory and devise a new method to solve the complex problems of multicast network switching. In addition, an experimental optical network has been testified with best switching strategies by employing the novel numerical solution designed with an effective way of genetic algorithm. The result shows that optimal solutions with genetic algorithm are accordance with the ones with the traditional fictitious play method.

Traffic protection in MPLS networks using an off-line flow optimization model

NASA Astrophysics Data System (ADS)

Krzesinski, Anthony E.; Muller, Karen E.

2002-07-01

MPLS-based recovery is intended to effect rapid and complete restoration of traffic affected by a fault in an MPLS network. Two MPLS-based recovery models have been proposed: IP re-routing which establishes recovery paths on demand, and protection switching which works with pre-established recovery paths. IP re-routing is robust and frugal since no resources are pre-committed but is inherently slower than protection switching which is intended to offer high reliability to premium services where fault recovery takes place at the 100 ms time scale. We present a model of protection switching in MPLS networks. A variant of the flow deviation method is used to find and capacitate a set of optimal label switched paths. The traffic is routed over a set of working LSPs. Global repair is implemented by reserving a set of pre-established recovery LSPs. An analytic model is used to evaluate the MPLS-based recovery mechanisms in response to bi-directional link failures. A simulation model is used to evaluate the MPLS recovery cycle in terms of the time needed to restore the traffic after a uni-directional link failure. The models are applied to evaluate the effectiveness of protection switching in networks consisting of between 20 and 100 nodes.

Optical slotted circuit switched network: a bandwidth efficient alternative to wavelength-routed network

NASA Astrophysics Data System (ADS)

Li, Yan; Collier, Martin

2007-11-01

Wavelength-routed networks have received enormous attention due to the fact that they are relatively simple to implement and implicitly offer Quality of Service (QoS) guarantees. However, they suffer from a bandwidth inefficiency problem and require complex Routing and Wavelength Assignment (RWA). Most attempts to address the above issues exploit the joint use of WDM and TDM technologies. The resultant TDM-based wavelength-routed networks partition the wavelength bandwidth into fixed-length time slots organized as a fixed-length frame. Multiple connections can thus time-share a wavelength and the grooming of their traffic leads to better bandwidth utilization. The capability of switching in both wavelength and time domains in such networks also mitigates the RWA problem. However, TMD-based wavelength-routed networks work in synchronous mode and strict synchronization among all network nodes is required. Global synchronization for all-optical networks which operate at extremely high speed is technically challenging, and deploying an optical synchronizer for each wavelength involves considerable cost. An Optical Slotted Circuit Switching (OSCS) architecture is proposed in this paper. In an OSCS network, slotted circuits are created to better utilize the wavelength bandwidth than in classic wavelength-routed networks. The operation of the protocol is such as to avoid the need for global synchronization required by TDM-based wavelength-routed networks.

Characterization of the transcriptome profiles related to globin gene switching during in vitro erythroid maturation

PubMed Central

2012-01-01

Background The fetal and adult globin genes in the human β-globin cluster on chromosome 11 are sequentially expressed to achieve normal hemoglobin switching during human development. The pharmacological induction of fetal γ-globin (HBG) to replace abnormal adult sickle βS-globin is a successful strategy to treat sickle cell disease; however the molecular mechanism of γ-gene silencing after birth is not fully understood. Therefore, we performed global gene expression profiling using primary erythroid progenitors grown from human peripheral blood mononuclear cells to characterize gene expression patterns during the γ-globin to β-globin (γ/β) switch observed throughout in vitro erythroid differentiation. Results We confirmed erythroid maturation in our culture system using cell morphologic features defined by Giemsa staining and the γ/β-globin switch by reverse transcription-quantitative PCR (RT-qPCR) analysis. We observed maximal γ-globin expression at day 7 with a switch to a predominance of β-globin expression by day 28 and the γ/β-globin switch occurred around day 21. Expression patterns for transcription factors including GATA1, GATA2, KLF1 and NFE2 confirmed our system produced the expected pattern of expression based on the known function of these factors in globin gene regulation. Subsequent gene expression profiling was performed with RNA isolated from progenitors harvested at day 7, 14, 21, and 28 in culture. Three major gene profiles were generated by Principal Component Analysis (PCA). For profile-1 genes, where expression decreased from day 7 to day 28, we identified 2,102 genes down-regulated > 1.5-fold. Ingenuity pathway analysis (IPA) for profile-1 genes demonstrated involvement of the Cdc42, phospholipase C, NF-Kβ, Interleukin-4, and p38 mitogen activated protein kinase (MAPK) signaling pathways. Transcription factors known to be involved in γ-and β-globin regulation were identified. The same approach was used to generate profile-2 genes where expression was up-regulated over 28 days in culture. IPA for the 2,437 genes with > 1.5-fold induction identified the mitotic roles of polo-like kinase, aryl hydrocarbon receptor, cell cycle control, and ATM (Ataxia Telangiectasia Mutated Protein) signaling pathways; transcription factors identified included KLF1, GATA1 and NFE2 among others. Finally, profile-3 was generated from 1,579 genes with maximal expression at day 21, around the time of the γ/β-globin switch. IPA identified associations with cell cycle control, ATM, and aryl hydrocarbon receptor signaling pathways. Conclusions The transcriptome analysis completed with erythroid progenitors grown in vitro identified groups of genes with distinct expression profiles, which function in metabolic pathways associated with cell survival, hematopoiesis, blood cells activation, and inflammatory responses. This study represents the first report of a transcriptome analysis in human primary erythroid progenitors to identify transcription factors involved in hemoglobin switching. Our results also demonstrate that the in vitro liquid culture system is an excellent model to define mechanisms of global gene expression and the DNA-binding protein and signaling pathways involved in globin gene regulation. PMID:22537182

A 10Gbps optical burst switching network incorporating ultra-fast (5ns) wavelength switched tunable laser sources

NASA Astrophysics Data System (ADS)

Ryan, Neil; Todd, Michael; Farrell, Tom; Lavin, Adrian; Rigole, Pierre-Jean; Corbett, Brian; Roycroft, Brendan; Engelstaedter, Jan-Peter

2017-11-01

This paper outlines the development of a prototype optical burst mode switching network based upon a star topology, the ultimate application of which could be as a transparent payload processor onboard satellite repeaters. The network architecture incorporates multiple tunable laser sources, burst mode receivers and a passive optical router (Arrayed Waveguide Grating). Each tunable optical signal should carry >=10Gbps and be capable of wavelength switching in c. 5ns timescales. Two monolithic tunable laser types, based upon different technologies, will be utilised: a Slotted Fabry Perot laser (a Fabry Perot laser with slots added in order to introduce controlled cavity perturbations); and a Modulated Grating Y-Branch Laser (MGY: a widely tunable, multi-section device similar to the DBR laser). While the Slotted Fabry Perot laser is expected to achieve the required switching times, it is an immature technology not yet capable of achieving tunability over 80 ITU channels from a single chip. The MGY device is a more mature technology and has full C-band ITU channel coverage, but is not capable of the required short switching times. Hence, in order to facilitate the integration of this more mature technology into the prototype breadboard with the requisite switching time capabilities, a system of `dual laser' transmitters is being developed to enable data transmission from one MGY laser while the other switches and vice-versa. This work is being performed under ESA contract AO 1-5025/06/NL/PM, Optical Technologies for Ultra - fast Processing.

Cognitive Control Signals in Posterior Cingulate Cortex

PubMed Central

Hayden, Benjamin Y.; Smith, David V.; Platt, Michael L.

2010-01-01

Efficiently shifting between tasks is a central function of cognitive control. The role of the default network – a constellation of areas with high baseline activity that declines during task performance – in cognitive control remains poorly understood. We hypothesized that task switching demands cognitive control to shift the balance of processing toward the external world, and therefore predicted that switching between the two tasks would require suppression of activity of neurons within the posterior cingulate cortex (CGp). To test this idea, we recorded the activity of single neurons in CGp, a central node in the default network, in monkeys performing two interleaved tasks. As predicted, we found that basal levels of neuronal activity were reduced following a switch from one task to another and gradually returned to pre-switch baseline on subsequent trials. We failed to observe these effects in lateral intraparietal cortex, part of the dorsal fronto-parietal cortical attention network directly connected to CGp. These findings indicate that suppression of neuronal activity in CGp facilitates cognitive control, and suggest that activity in the default network reflects processes that directly compete with control processes elsewhere in the brain. PMID:21160560

Quantum key based burst confidentiality in optical burst switched networks.

PubMed

Balamurugan, A M; Sivasubramanian, A

2014-01-01

The optical burst switching (OBS) is an emergent result to the technology concern that could achieve a feasible network in future. They are endowed with the ability to meet the bandwidth requirement of those applications that require intensive bandwidth. There are more domains opening up in the OBS that evidently shows their advantages and their capability to face the future network traffic. However, the concept of OBS is still far from perfection facing issues in case of security threat. The transfer of optical switching paradigm to optical burst switching faces serious downfall in the fields of burst aggregation, routing, authentication, dispute resolution, and quality of service (QoS). This paper deals with employing RC4 (stream cipher) to encrypt and decrypt bursts thereby ensuring the confidentiality of the burst. Although the use of AES algorithm has already been proposed for the same issue, by contrasting the two algorithms under the parameters of burst encryption and decryption time, end-to-end delay, it was found that RC4 provided better results. This paper looks to provide a better solution for the confidentiality of the burst in OBS networks.

Quantum Key Based Burst Confidentiality in Optical Burst Switched Networks

PubMed Central

Balamurugan, A. M.; Sivasubramanian, A.

2014-01-01

The optical burst switching (OBS) is an emergent result to the technology concern that could achieve a feasible network in future. They are endowed with the ability to meet the bandwidth requirement of those applications that require intensive bandwidth. There are more domains opening up in the OBS that evidently shows their advantages and their capability to face the future network traffic. However, the concept of OBS is still far from perfection facing issues in case of security threat. The transfer of optical switching paradigm to optical burst switching faces serious downfall in the fields of burst aggregation, routing, authentication, dispute resolution, and quality of service (QoS). This paper deals with employing RC4 (stream cipher) to encrypt and decrypt bursts thereby ensuring the confidentiality of the burst. Although the use of AES algorithm has already been proposed for the same issue, by contrasting the two algorithms under the parameters of burst encryption and decryption time, end-to-end delay, it was found that RC4 provided better results. This paper looks to provide a better solution for the confidentiality of the burst in OBS networks. PMID:24578663

Piezoelectric Diffraction-Based Optical Switches

NASA Technical Reports Server (NTRS)

Spremo, Stevan; Fuhr, Peter; Schipper, John

2003-01-01

Piezoelectric diffraction-based optoelectronic devices have been invented to satisfy requirements for switching signals quickly among alternative optical paths in optical communication networks. These devices are capable of operating with switching times as short as microseconds or even nanoseconds in some cases.

Novel flat datacenter network architecture based on scalable and flow-controlled optical switch system.

PubMed

Miao, Wang; Luo, Jun; Di Lucente, Stefano; Dorren, Harm; Calabretta, Nicola

2014-02-10

We propose and demonstrate an optical flat datacenter network based on scalable optical switch system with optical flow control. Modular structure with distributed control results in port-count independent optical switch reconfiguration time. RF tone in-band labeling technique allowing parallel processing of the label bits ensures the low latency operation regardless of the switch port-count. Hardware flow control is conducted at optical level by re-using the label wavelength without occupying extra bandwidth, space, and network resources which further improves the performance of latency within a simple structure. Dynamic switching including multicasting operation is validated for a 4 x 4 system. Error free operation of 40 Gb/s data packets has been achieved with only 1 dB penalty. The system could handle an input load up to 0.5 providing a packet loss lower that 10(-5) and an average latency less that 500 ns when a buffer size of 16 packets is employed. Investigation on scalability also indicates that the proposed system could potentially scale up to large port count with limited power penalty.

Phase-Change Thermoplastic Elastomer Blends for Tunable Shape Memory by Physical Design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mineart, Kenneth P.; Tallury, Syamal S.; Li, Tao

Shape-memory polymers (SMPs) change shape upon exposure to an environmental stimulus.1-3 They are of considerable importance in the ongoing development of stimuli-responsive biomedical4,5 and deployable6 devices, and their function depends on the presence of two components.7 The first provides mechanical rigidity to ensure retention of one or more temporary strain states and also serves as a switch capable of releasing a temporary strain state. The second, a network-forming component, is required to restore the polymer to a prior strain state upon stimulation. In thermally-activated SMPs, the switching element typically relies on a melting or glass transition temperature,1-3,7 and broad ormore » multiple switches permit several temporary strain states.8-10 Chemical integration of network-forming and switching species endows SMPs with specific properties.8,10,11 Here, we demonstrate that phase-change materials incorporated into network-forming macromolecules yield shape-memory polymer blends (SMPBs) with physically tunable switching temperatures and recovery kinetics for use in multi-responsive laminates and shape-change electronics.« less

A Novel QKD-based Secure Edge Router Architecture Design for Burst Confidentiality in Optical Burst Switched Networks

NASA Astrophysics Data System (ADS)

Balamurugan, A. M.; Sivasubramanian, A.

2014-06-01

The Optical Burst Switching (OBS) is an emergent result to the technology issue that could achieve a viable network in future. They have the ability to meet the bandwidth requisite of those applications that call for intensive bandwidth. The field of optical transmission has undergone numerous advancements and is still being researched mainly due to the fact that optical data transmission can be done at enormous speeds. The concept of OBS is still far from perfection facing issues in case of security threat. The transfer of optical switching paradigm to optical burst switching faces serious downfall in the fields of burst aggregation, routing, authentication, dispute resolution and quality of service (QoS). This paper proposes a framework based on QKD based secure edge router architecture design to provide burst confidentiality. The QKD protocol offers high level of confidentiality as it is indestructible. The design architecture was implemented in FPGA using diverse models and the results were taken. The results show that the proposed model is suitable for real time secure routing applications of the Optical burst switched networks.

Performance analysis of signaling protocols on OBS switches

NASA Astrophysics Data System (ADS)

Kirci, Pinar; Zaim, A. Halim

2005-10-01

In this paper, Just-In-Time (JIT), Just-Enough-Time (JET) and Horizon signalling schemes for Optical Burst Switched Networks (OBS) are presented. These signaling schemes run over a core dWDM network and a network architecture based on Optical Burst Switches (OBS) is proposed to support IP, ATM and Burst traffic. In IP and ATM traffic several packets are assembled in a single packet called burst and the burst contention is handled by burst dropping. The burst length distribution in IP traffic is arbitrary between 0 and 1, and is fixed in ATM traffic at 0,5. Burst traffic on the other hand is arbitrary between 1 and 5. The Setup and Setup ack length distributions are arbitrary. We apply the Poisson model with rate λ and Self-Similar model with pareto distribution rate α to identify inter-arrival times in these protocols. We consider a communication between a source client node and a destination client node over an ingress and one or more multiple intermediate switches.We use buffering only in the ingress node. The communication is based on single burst connections in which, the connection is set up just before sending a burst and then closed as soon as the burst is sent. Our analysis accounts for several important parameters, including the burst setup, burst setup ack, keepalive messages and the optical switching protocol. We compare the performance of the three signalling schemes on the network under as burst dropping probability under a range of network scenarios.

Satellite ATM Networks: Architectures and Guidelines Developed

NASA Technical Reports Server (NTRS)

vonDeak, Thomas C.; Yegendu, Ferit

1999-01-01

An important element of satellite-supported asynchronous transfer mode (ATM) networking will involve support for the routing and rerouting of active connections. Work published under the auspices of the Telecommunications Industry Association (http://www.tiaonline.org), describes basic architectures and routing protocol issues for satellite ATM (SATATM) networks. The architectures and issues identified will serve as a basis for further development of technical specifications for these SATATM networks. Three ATM network architectures for bent pipe satellites and three ATM network architectures for satellites with onboard ATM switches were developed. The architectures differ from one another in terms of required level of mobility, supported data rates, supported terrestrial interfaces, and onboard processing and switching requirements. The documentation addresses low-, middle-, and geosynchronous-Earth-orbit satellite configurations. The satellite environment may require real-time routing to support the mobility of end devices and nodes of the ATM network itself. This requires the network to be able to reroute active circuits in real time. In addition to supporting mobility, rerouting can also be used to (1) optimize network routing, (2) respond to changing quality-of-service requirements, and (3) provide a fault tolerance mechanism. Traffic management and control functions are necessary in ATM to ensure that the quality-of-service requirements associated with each connection are not violated and also to provide flow and congestion control functions. Functions related to traffic management were identified and described. Most of these traffic management functions will be supported by on-ground ATM switches, but in a hybrid terrestrial-satellite ATM network, some of the traffic management functions may have to be supported by the onboard satellite ATM switch. Future work is planned to examine the tradeoffs of placing traffic management functions onboard a satellite as opposed to implementing those functions at the Earth station components.

Enhanced Thermo-Optical Switching of Paraffin-Wax Composite Spots under Laser Heating

PubMed Central

Said, Asmaa; Salah, Abeer; Abdel Fattah, Gamal

2017-01-01

Thermo-optical switches are of particular significance in communications networks where increasingly high switching speeds are required. Phase change materials (PCMs), in particular those based on paraffin wax, provide wealth of exciting applications with unusual thermally-induced switching properties, only limited by paraffin’s rather low thermal conductivity. In this paper, the use of different carbon fillers as thermal conductivity enhancers for paraffin has been investigated, and a novel structure based on spot of paraffin wax as a thermo-optic switch is presented. Thermo-optical switching parameters are enhanced with the addition of graphite and graphene, due to the extreme thermal conductivity of the carbon fillers. Differential Scanning Calorimetry (DSC) and Scanning electron microscope (SEM) are performed on paraffin wax composites, and specific heat capacities are calculated based on DSC measurements. Thermo-optical switching based on transmission is measured as a function of the host concentration under conventional electric heating and laser heating of paraffin-carbon fillers composites. Further enhancements in thermo-optical switching parameters are studied under Nd:YAG laser heating. This novel structure can be used in future networks with huge bandwidth requirements and electric noise free remote aerial laser switching applications. PMID:28772884

Enhanced Thermo-Optical Switching of Paraffin-Wax Composite Spots under Laser Heating.

PubMed

Said, Asmaa; Salah, Abeer; Fattah, Gamal Abdel

2017-05-12

Thermo-optical switches are of particular significance in communications networks where increasingly high switching speeds are required. Phase change materials (PCMs), in particular those based on paraffin wax, provide wealth of exciting applications with unusual thermally-induced switching properties, only limited by paraffin's rather low thermal conductivity. In this paper, the use of different carbon fillers as thermal conductivity enhancers for paraffin has been investigated, and a novel structure based on spot of paraffin wax as a thermo-optic switch is presented. Thermo-optical switching parameters are enhanced with the addition of graphite and graphene, due to the extreme thermal conductivity of the carbon fillers. Differential Scanning Calorimetry (DSC) and Scanning electron microscope (SEM) are performed on paraffin wax composites, and specific heat capacities are calculated based on DSC measurements. Thermo-optical switching based on transmission is measured as a function of the host concentration under conventional electric heating and laser heating of paraffin-carbon fillers composites. Further enhancements in thermo-optical switching parameters are studied under Nd:YAG laser heating. This novel structure can be used in future networks with huge bandwidth requirements and electric noise free remote aerial laser switching applications.

Discovery of nitrate-CPK-NLP signalling in central nutrient-growth networks

PubMed Central

Liu, Kun-hsiang; Niu, Yajie; Konishi, Mineko; Wu, Yue; Du, Hao; Sun Chung, Hoo; Li, Lei; Boudsocq, Marie; McCormack, Matthew; Maekawa, Shugo; Ishida, Tetsuya; Zhang, Chao; Shokat, Kevan; Yanagisawa, Shuichi; Sheen, Jen

2018-01-01

Nutrient signalling integrates and coordinates gene expression, metabolism and growth. However, its primary molecular mechanisms remain incompletely understood in plants and animals. Here we report novel Ca2+ signalling triggered by nitrate with live imaging of an ultrasensitive biosensor in Arabidopsis leaves and roots. A nitrate-sensitized and targeted functional genomic screen identifies subgroup III Ca2+-sensor protein kinases (CPKs) as master regulators orchestrating primary nitrate responses. A chemical switch with the engineered CPK10(M141G) kinase enables conditional analyses of cpk10,30,32 to define comprehensive nitrate-associated regulatory and developmental programs, circumventing embryo lethality. Nitrate-CPK signalling phosphorylates conserved NIN-LIKE PROTEIN (NLP) transcription factors (TFs) to specify reprogramming of gene sets for downstream TFs, transporters, N-assimilation, C/N-metabolism, redox, signalling, hormones, and proliferation. Conditional cpk10,30,32 and nlp7 similarly impair nitrate-stimulated system-wide shoot growth and root establishment. The nutrient-coupled Ca2+ signalling network integrates transcriptome and cellular metabolism with shoot-root coordination and developmental plasticity in shaping organ biomass and architecture. PMID:28489820

Discovery of nitrate-CPK-NLP signalling in central nutrient-growth networks.

PubMed

Liu, Kun-Hsiang; Niu, Yajie; Konishi, Mineko; Wu, Yue; Du, Hao; Sun Chung, Hoo; Li, Lei; Boudsocq, Marie; McCormack, Matthew; Maekawa, Shugo; Ishida, Tetsuya; Zhang, Chao; Shokat, Kevan; Yanagisawa, Shuichi; Sheen, Jen

2017-05-18

Nutrient signalling integrates and coordinates gene expression, metabolism and growth. However, its primary molecular mechanisms remain incompletely understood in plants and animals. Here we report unique Ca 2+ signalling triggered by nitrate with live imaging of an ultrasensitive biosensor in Arabidopsis leaves and roots. A nitrate-sensitized and targeted functional genomic screen identifies subgroup III Ca 2+ -sensor protein kinases (CPKs) as master regulators that orchestrate primary nitrate responses. A chemical switch with the engineered mutant CPK10(M141G) circumvents embryo lethality and enables conditional analyses of cpk10 cpk30 cpk32 triple mutants to define comprehensive nitrate-associated regulatory and developmental programs. Nitrate-coupled CPK signalling phosphorylates conserved NIN-LIKE PROTEIN (NLP) transcription factors to specify the reprogramming of gene sets for downstream transcription factors, transporters, nitrogen assimilation, carbon/nitrogen metabolism, redox, signalling, hormones and proliferation. Conditional cpk10 cpk30 cpk32 and nlp7 mutants similarly impair nitrate-stimulated system-wide shoot growth and root establishment. The nutrient-coupled Ca 2+ signalling network integrates transcriptome and cellular metabolism with shoot-root coordination and developmental plasticity in shaping organ biomass and architecture.

Optical burst switching for the next generation Optical Internet

NASA Astrophysics Data System (ADS)

Yoo, Myungsik

2000-11-01

In recent years, Internet Protocol (IP) over Wavelength Division Multiplexing (WDM) networks for the next generation Internet (or the so-called Optical Internet) have received enormous attention. There are two main drivers for an Optical Internet. One is the explosion of Internet traffic, which seems to keep growing exponentially. The other driver is the rapid advance in the WDM optical networking technology. In this study, key issues in the optical (WDM) layer will be investigated. As a novel switching paradigm for Optical Internet, Optical Burst Switching (OBS) is discussed. By leveraging the attractive properties of optical communications and at the same time, taking into account its limitations, OBS can combine the best of optical circuit-switching and packet/cell switching. The general concept of JET-based OBS protocol is described, including offset time and delayed reservation. In the next generation Optical Internet, one must address how to support Quality of Service (QoS) at the WDM layer since current IP provides only best effort services. The offset-time- based QoS scheme is proposed as a way of supporting QoS at the WDM layer. Unlike existing QoS schemes, offset- time-based QoS scheme does not mandate the use of buffer to differentiate services. For the bufferless WDM switch, the performance of offset- time-based QoS scheme is evaluated in term of blocking probability. In addition, the extra offset time required for class isolation is quantified and the theoretical bounds on blocking probability are analyzed. The offset-time-based scheme is applied to WDM switch with limited fiber delay line (FDL) buffer. We evaluate the effect of having a FDL buffer on the QoS performance of the offset-time-based scheme in terms of the loss probability and queuing delay of bursts. Finally, in order to dimension the network resources in Optical Internet backbone networks, the performance of the offset-time-based QoS scheme is evaluated for the multi-hop case. In particular, we consider very high performance Backbone Network Service (vBNS) backbone network. Various policies such as drop, retransmission, deflection routing and buffering are considered for performance evaluation. The performance results obtained under these policies are compared to decide the most efficient policy for the WDM backbone network.

Building SDN-Based Agricultural Vehicular Sensor Networks Based on Extended Open vSwitch.

PubMed

Huang, Tao; Yan, Siyu; Yang, Fan; Pan, Tian; Liu, Jiang

2016-01-19

Software-defined vehicular sensor networks in agriculture, such as autonomous vehicle navigation based on wireless multi-sensor networks, can lead to more efficient precision agriculture. In SDN-based vehicle sensor networks, the data plane is simplified and becomes more efficient by introducing a centralized controller. However, in a wireless environment, the main controller node may leave the sensor network due to the dynamic topology change or the unstable wireless signal, leaving the rest of network devices without control, e.g., a sensor node as a switch may forward packets according to stale rules until the controller updates the flow table entries. To solve this problem, this paper proposes a novel SDN-based vehicular sensor networks architecture which can minimize the performance penalty of controller connection loss. We achieve this by designing a connection state detection and self-learning mechanism. We build prototypes based on extended Open vSwitch and Ryu. The experimental results show that the recovery time from controller connection loss is under 100 ms and it keeps rule updating in real time with a stable throughput. This architecture enhances the survivability and stability of SDN-based vehicular sensor networks in precision agriculture.

Building SDN-Based Agricultural Vehicular Sensor Networks Based on Extended Open vSwitch

PubMed Central

Huang, Tao; Yan, Siyu; Yang, Fan; Pan, Tian; Liu, Jiang

2016-01-01

Software-defined vehicular sensor networks in agriculture, such as autonomous vehicle navigation based on wireless multi-sensor networks, can lead to more efficient precision agriculture. In SDN-based vehicle sensor networks, the data plane is simplified and becomes more efficient by introducing a centralized controller. However, in a wireless environment, the main controller node may leave the sensor network due to the dynamic topology change or the unstable wireless signal, leaving the rest of network devices without control, e.g., a sensor node as a switch may forward packets according to stale rules until the controller updates the flow table entries. To solve this problem, this paper proposes a novel SDN-based vehicular sensor networks architecture which can minimize the performance penalty of controller connection loss. We achieve this by designing a connection state detection and self-learning mechanism. We build prototypes based on extended Open vSwitch and Ryu. The experimental results show that the recovery time from controller connection loss is under 100 ms and it keeps rule updating in real time with a stable throughput. This architecture enhances the survivability and stability of SDN-based vehicular sensor networks in precision agriculture. PMID:26797616

FPGA Based Reconfigurable ATM Switch Test Bed

NASA Technical Reports Server (NTRS)

Chu, Pong P.; Jones, Robert E.

1998-01-01

Various issues associated with "FPGA Based Reconfigurable ATM Switch Test Bed" are presented in viewgraph form. Specific topics include: 1) Network performance evaluation; 2) traditional approaches; 3) software simulation; 4) hardware emulation; 5) test bed highlights; 6) design environment; 7) test bed architecture; 8) abstract sheared-memory switch; 9) detailed switch diagram; 10) traffic generator; 11) data collection circuit and user interface; 12) initial results; and 13) the following conclusions: Advances in FPGA make hardware emulation feasible for performance evaluation, hardware emulation can provide several orders of magnitude speed-up over software simulation; due to the complexity of hardware synthesis process, development in emulation is much more difficult than simulation and requires knowledge in both networks and digital design.

Engineering dynamical control of cell fate switching using synthetic phospho-regulons

PubMed Central

Gordley, Russell M.; Williams, Reid E.; Bashor, Caleb J.; Toettcher, Jared E.; Yan, Shude; Lim, Wendell A.

2016-01-01

Many cells can sense and respond to time-varying stimuli, selectively triggering changes in cell fate only in response to inputs of a particular duration or frequency. A common motif in dynamically controlled cells is a dual-timescale regulatory network: although long-term fate decisions are ultimately controlled by a slow-timescale switch (e.g., gene expression), input signals are first processed by a fast-timescale signaling layer, which is hypothesized to filter what dynamic information is efficiently relayed downstream. Directly testing the design principles of how dual-timescale circuits control dynamic sensing, however, has been challenging, because most synthetic biology methods have focused solely on rewiring transcriptional circuits, which operate at a single slow timescale. Here, we report the development of a modular approach for flexibly engineering phosphorylation circuits using designed phospho-regulon motifs. By then linking rapid phospho-feedback with slower downstream transcription-based bistable switches, we can construct synthetic dual-timescale circuits in yeast in which the triggering dynamics and the end-state properties of the ON state can be selectively tuned. These phospho-regulon tools thus open up the possibility to engineer cells with customized dynamical control. PMID:27821768

Detection of thiol-based redox switch processes in parasites - facts and future.

PubMed

Rahbari, Mahsa; Diederich, Kathrin; Becker, Katja; Krauth-Siegel, R Luise; Jortzik, Esther

2015-05-01

Malaria and African trypanosomiasis are tropical diseases caused by the protozoa Plasmodium and Trypanosoma, respectively. The parasites undergo complex life cycles in the mammalian host and insect vector, during which they are exposed to oxidative and nitrosative challenges induced by the host immune system and endogenous processes. Attacking the parasite's redox metabolism is a target mechanism of several known antiparasitic drugs and a promising approach to novel drug development. Apart from this aspect, oxidation of cysteine residues plays a key role in protein-protein interaction, metabolic responses to redox events, and signaling. Understanding the role and dynamics of reactive oxygen species and thiol switches in regulating cellular redox homeostasis is crucial for both basic and applied biomedical approaches. Numerous techniques have therefore been established to detect redox changes in parasites including biochemical methods, fluorescent dyes, and genetically encoded probes. In this review, we aim to give an insight into the characteristics of redox networks in the pathogens Plasmodium and Trypanosoma, including a comprehensive overview of the consequences of specific deletions of redox-associated genes. Furthermore, we summarize mechanisms and detection methods of thiol switches in both parasites and discuss their specificity and sensitivity.

Evidence for rare capsular switching in Streptococcus agalactiae.

PubMed

Martins, Elisabete Raquel; Melo-Cristino, José; Ramirez, Mário

2010-03-01

The polysaccharide capsule is a major antigenic factor in Streptococcus agalactiae (Lancefield group B streptococcus [GBS]). Previous observations suggest that exchange of capsular loci is likely to occur rather frequently in GBS, even though GBS is not known to be naturally transformable. We sought to identify and characterize putative capsular switching events, by means of a combination of phenotypic and genotypic methods, including pulsed-field gel electrophoretic profiling, multilocus sequence typing, and surface protein and pilus gene profiling. We show that capsular switching by horizontal gene transfer is not as frequent as previously suggested. Serotyping errors may be the main reason behind the overestimation of capsule switching, since phenotypic techniques are prone to errors of interpretation. The identified putative capsular transformants involved the acquisition of the entire capsular locus and were not restricted to the serotype-specific central genes, the previously suggested main mechanism underlying capsular switching. Our data, while questioning the frequency of capsular switching, provide clear evidence for in vivo capsular transformation in S. agalactiae, which may be of critical importance in planning future vaccination strategies against this pathogen.

Evidence for Rare Capsular Switching in Streptococcus agalactiae▿

PubMed Central

Martins, Elisabete Raquel; Melo-Cristino, José; Ramirez, Mário

2010-01-01

The polysaccharide capsule is a major antigenic factor in Streptococcus agalactiae (Lancefield group B streptococcus [GBS]). Previous observations suggest that exchange of capsular loci is likely to occur rather frequently in GBS, even though GBS is not known to be naturally transformable. We sought to identify and characterize putative capsular switching events, by means of a combination of phenotypic and genotypic methods, including pulsed-field gel electrophoretic profiling, multilocus sequence typing, and surface protein and pilus gene profiling. We show that capsular switching by horizontal gene transfer is not as frequent as previously suggested. Serotyping errors may be the main reason behind the overestimation of capsule switching, since phenotypic techniques are prone to errors of interpretation. The identified putative capsular transformants involved the acquisition of the entire capsular locus and were not restricted to the serotype-specific central genes, the previously suggested main mechanism underlying capsular switching. Our data, while questioning the frequency of capsular switching, provide clear evidence for in vivo capsular transformation in S. agalactiae, which may be of critical importance in planning future vaccination strategies against this pathogen. PMID:20023016

Sex-lethal enables germline stem cell differentiation by down-regulating Nanos protein levels during Drosophila oogenesis

PubMed Central

Chau, Johnnie; Kulnane, Laura Shapiro; Salz, Helen K.

2012-01-01

Drosophila ovarian germ cells require Sex-lethal (Sxl) to exit from the stem cell state and to enter the differentiation pathway. Sxl encodes a female-specific RNA binding protein and in somatic cells serves as the developmental switch gene for somatic sex determination and X-chromosome dosage compensation. None of the known Sxl target genes are required for germline differentiation, leaving open the question of how Sxl promotes the transition from stem cell to committed daughter cell. We address the mechanism by which Sxl regulates this transition through the identification of nanos as one of its target genes. Previous studies have shown that Nanos protein is necessary for GSC self-renewal and is rapidly down-regulated in the daughter cells fated to differentiate in the adult ovary. We find that this dynamic expression pattern is limited to female germ cells and is under Sxl control. In the absence of Sxl, or in male germ cells, Nanos protein is continuously expressed. Furthermore, this female-specific expression pattern is dependent on the presence of canonical Sxl binding sites located in the nanos 3′ untranslated region. These results, combined with the observation that nanos RNA associates with the Sxl protein in ovarian extracts and loss and gain of function studies, suggest that Sxl enables the switch from germline stem cell to committed daughter cell by posttranscriptional down-regulation of nanos expression. These findings connect sexual identity to the stem cell self-renewal/differentiation decision and highlight the importance of posttranscriptional gene regulatory networks in controlling stem cell behavior. PMID:22645327

Sex-lethal enables germline stem cell differentiation by down-regulating Nanos protein levels during Drosophila oogenesis.

PubMed

Chau, Johnnie; Kulnane, Laura Shapiro; Salz, Helen K

2012-06-12

Drosophila ovarian germ cells require Sex-lethal (Sxl) to exit from the stem cell state and to enter the differentiation pathway. Sxl encodes a female-specific RNA binding protein and in somatic cells serves as the developmental switch gene for somatic sex determination and X-chromosome dosage compensation. None of the known Sxl target genes are required for germline differentiation, leaving open the question of how Sxl promotes the transition from stem cell to committed daughter cell. We address the mechanism by which Sxl regulates this transition through the identification of nanos as one of its target genes. Previous studies have shown that Nanos protein is necessary for GSC self-renewal and is rapidly down-regulated in the daughter cells fated to differentiate in the adult ovary. We find that this dynamic expression pattern is limited to female germ cells and is under Sxl control. In the absence of Sxl, or in male germ cells, Nanos protein is continuously expressed. Furthermore, this female-specific expression pattern is dependent on the presence of canonical Sxl binding sites located in the nanos 3' untranslated region. These results, combined with the observation that nanos RNA associates with the Sxl protein in ovarian extracts and loss and gain of function studies, suggest that Sxl enables the switch from germline stem cell to committed daughter cell by posttranscriptional down-regulation of nanos expression. These findings connect sexual identity to the stem cell self-renewal/differentiation decision and highlight the importance of posttranscriptional gene regulatory networks in controlling stem cell behavior.

Report of the Defense Science Board Task Force on Defensive Information Operations. 2000 Summer Study. Volume II

DTIC Science & Technology

2001-03-01

distinguishing between attacks and other events such as accidents, system failures, or hacking by thrill-seekers. This challenge is exacerbated by the...and is referred to as Signaling System # 7 ( SS7 ). Commercial Intelligent Network Architecture Switching Signal Point (SSP) Service - Originates...Wireless access point to fixed infrastructure Ut c Signaling Transfer Point (STP) - Packet switch in CCITT#7 Network SP SW SS7 System Data Bases Network

Optical multicast system for data center networks.

PubMed

Samadi, Payman; Gupta, Varun; Xu, Junjie; Wang, Howard; Zussman, Gil; Bergman, Keren

2015-08-24

We present the design and experimental evaluation of an Optical Multicast System for Data Center Networks, a hardware-software system architecture that uniquely integrates passive optical splitters in a hybrid network architecture for faster and simpler delivery of multicast traffic flows. An application-driven control plane manages the integrated optical and electronic switched traffic routing in the data plane layer. The control plane includes a resource allocation algorithm to optimally assign optical splitters to the flows. The hardware architecture is built on a hybrid network with both Electronic Packet Switching (EPS) and Optical Circuit Switching (OCS) networks to aggregate Top-of-Rack switches. The OCS is also the connectivity substrate of splitters to the optical network. The optical multicast system implementation requires only commodity optical components. We built a prototype and developed a simulation environment to evaluate the performance of the system for bulk multicasting. Experimental and numerical results show simultaneous delivery of multicast flows to all receivers with steady throughput. Compared to IP multicast that is the electronic counterpart, optical multicast performs with less protocol complexity and reduced energy consumption. Compared to peer-to-peer multicast methods, it achieves at minimum an order of magnitude higher throughput for flows under 250 MB with significantly less connection overheads. Furthermore, for delivering 20 TB of data containing only 15% multicast flows, it reduces the total delivery energy consumption by 50% and improves latency by 55% compared to a data center with a sole non-blocking EPS network.

Distributed fault detection over sensor networks with Markovian switching topologies

NASA Astrophysics Data System (ADS)

Ge, Xiaohua; Han, Qing-Long

2014-05-01

This paper deals with the distributed fault detection for discrete-time Markov jump linear systems over sensor networks with Markovian switching topologies. The sensors are scatteredly deployed in the sensor field and the fault detectors are physically distributed via a communication network. The system dynamics changes and sensing topology variations are modeled by a discrete-time Markov chain with incomplete mode transition probabilities. Each of these sensor nodes firstly collects measurement outputs from its all underlying neighboring nodes, processes these data in accordance with the Markovian switching topologies, and then transmits the processed data to the remote fault detector node. Network-induced delays and accumulated data packet dropouts are incorporated in the data transmission between the sensor nodes and the distributed fault detector nodes through the communication network. To generate localized residual signals, mode-independent distributed fault detection filters are proposed. By means of the stochastic Lyapunov functional approach, the residual system performance analysis is carried out such that the overall residual system is stochastically stable and the error between each residual signal and the fault signal is made as small as possible. Furthermore, a sufficient condition on the existence of the mode-independent distributed fault detection filters is derived in the simultaneous presence of incomplete mode transition probabilities, Markovian switching topologies, network-induced delays, and accumulated data packed dropouts. Finally, a stirred-tank reactor system is given to show the effectiveness of the developed theoretical results.

Information Switching Processor (ISP) contention analysis and control

NASA Technical Reports Server (NTRS)

Shyy, D.; Inukai, T.

1993-01-01

Future satellite communications, as a viable means of communications and an alternative to terrestrial networks, demand flexibility and low end-user cost. On-board switching/processing satellites potentially provide these features, allowing flexible interconnection among multiple spot beams, direct to the user communications services using very small aperture terminals (VSAT's), independent uplink and downlink access/transmission system designs optimized to user's traffic requirements, efficient TDM downlink transmission, and better link performance. A flexible switching system on the satellite in conjunction with low-cost user terminals will likely benefit future satellite network users.

Microsecond reconfigurable NxN data-communication switch using DMD

NASA Astrophysics Data System (ADS)

Blanche, Pierre-Alexandre; Miles, Alexander; Lynn, Brittany; Wissinger, John; Carothers, Daniel; Norwood, Robert A.; Peyghambarian, Nasser

2014-03-01

We present here the use the DMD as a diffraction-based optical switch, where Fourier diffraction patterns are used to steer the incoming beams to any output configuration. We have implemented a single-mode fiber coupled N X N switch and demonstrated its ability to operate over the entire telecommunication C-band centered at 1550 nm. The all-optical switch was built primarily with off-the-shelf components and a Texas Instruments DLP7000™with an array of 1024 X 768 micromirrors. This DMD is capable of switching 100 times faster than currently available technology (3D MOEMS). The switch is robust to typical failure modes, protocol and bit-rate agnostic, and permits full reconfigurable optical add drop multiplexing (ROADM). The switch demonstrator was inserted into a networking testbed for the majority of the measurements. The testbed assembled under the Center for Integrated Access Networks (ClAN), a National Science Foundation (NSF) Engineering Research Center (ERC), provided an environment in which to simulate and test the data routing functionality of the switch. A Fujitsu Flashwave 9500 PS was used to provide the data signal, which was sent through the switch and received by a second Flashwave node. We successfully transmitted an HD video stream through a switched channel without any measurable data loss.

Next generation satellite communications networks

NASA Astrophysics Data System (ADS)

Garland, P. J.; Osborne, F. J.; Streibl, I.

The paper introduces two potential uses for new space hardware to permit enhanced levels of signal handling and switching in satellite communication service for Canada. One application involves increased private-sector services in the Ku band; the second supports new personal/mobile services by employing higher levels of handling and switching in the Ka band. First-generation satellite regeneration and switching experiments involving the NASA/ACTS spacecraft are described, where the Ka band and switching satellite network problems are emphasized. Second-generation satellite development is outlined based on demand trends for more packet-based switching, low-cost earth stations, and closed user groups. A demonstration mission for new Ka- and Ku-band technologies is proposed, including the payload configuration. The half ANIK E payload is shown to meet the demonstration objectives, and projected to maintain a fully operational payload for at least 10 years.

Demonstration of 720×720 optical fast circuit switch for intra-datacenter networks

NASA Astrophysics Data System (ADS)

Ueda, Koh; Mori, Yojiro; Hasegawa, Hiroshi; Matsuura, Hiroyuki; Ishii, Kiyo; Kuwatsuka, Haruhiko; Namiki, Shu; Sato, Ken-ichi

2016-03-01

Intra-datacenter traffic is growing more than 20% a year. In typical datacenters, many racks/pods including servers are interconnected via multi-tier electrical switches. The electrical switches necessitate power-consuming optical-to- electrical (OE) and electrical-to-optical (EO) conversion, the power consumption of which increases with traffic. To overcome this problem, optical switches that eliminate costly OE and EO conversion and enable low power consumption switching are being investigated. There are two major requirements for the optical switch. First, it must have a high port count to construct reduced tier intra-datacenter networks. Second, switching speed must be short enough that most of the traffic load can be offloaded from electrical switches. Among various optical switches, we focus on those based on arrayed-waveguide gratings (AWGs), since the AWG is a passive device with minimal power consumption. We previously proposed a high-port-count optical switch architecture that utilizes tunable lasers, route-and-combine switches, and wavelength-routing switches comprised of couplers, erbium-doped fiber amplifiers (EDFAs), and AWGs. We employed conventional external cavity lasers whose wavelength-tuning speed was slower than 100 ms. In this paper, we demonstrate a large-scale optical switch that offers fast wavelength routing. We construct a 720×720 optical switch using recently developed lasers whose wavelength-tuning period is below 460 μs. We evaluate the switching time via bit-error-ratio measurements and achieve 470-μs switching time (includes 10-μs guard time to handle EDFA surge). To best of our knowledge, this is the first demonstration of such a large-scale optical switch with practical switching time.

Optical datacenter network employing slotted (TDMA) operation for dynamic resource allocation

NASA Astrophysics Data System (ADS)

Bakopoulos, P.; Tokas, K.; Spatharakis, C.; Patronas, I.; Landi, G.; Christodoulopoulos, K.; Capitani, M.; Kyriakos, A.; Aziz, M.; Reisis, D.; Varvarigos, E.; Zahavi, E.; Avramopoulos, H.

2018-02-01

The soaring traffic demands in datacenter networks (DCNs) are outpacing progresses in CMOS technology, challenging the bandwidth and energy scalability of currently established technologies. Optical switching is gaining traction as a promising path for sustaining the explosive growth of DCNs; however, its practical deployment necessitates extensive modifications to the network architecture and operation, tailored to the technological particularities of optical switches (i.e. no buffering, limitations in radix size and speed). European project NEPHELE is developing an optical network infrastructure that leverages optical switching within a software-defined networking (SDN) framework to overcome the bandwidth and energy scaling challenges of datacenter networks. An experimental validation of the NEPHELE data plane is reported based on commercial off-the-shelf optical components controlled by FPGA boards. To facilitate dynamic allocation of the network resources and perform collision-free routing in a lossless network environment, slotted operation is employed (i.e. using time-division multiple-access - TDMA). Error-free operation of the NEPHELE data plane is verified for 200 μs slots in various scenarios that involve communication between Ethernet hosts connected to custom-designed top-of-rack (ToR) switches, located in the same or in different datacenter pods. Control of the slotted data plane is obtained through an SDN framework comprising an OpenDaylight controller with appropriate add-ons. Communication between servers in the optical-ToR is demonstrated with various routing scenarios, concerning communication between hosts located in the same rack or in different racks, within the same or different datacenter pods. Error-free operation is confirmed for all evaluated scenarios, underpinning the feasibility of the NEPHELE architecture.

Toward next-generation optical networks: a network operator perspective based on experimental tests and economic analysis

NASA Astrophysics Data System (ADS)

Xiao, Xiaojun; Du, Chunsheng; Zhou, Rongsheng

2004-04-01

As a result of data traffic"s exponential growth, network is currently evolving from fixed circuit switched services to dynamic packet switched services, which has brought unprecedented changes to the existing transport infrastructure. It is generally agreed that automatic switched optical network (ASON) is one of the promising solutions for the next generation optical networks. In this paper, we present the results of our experimental tests and economic analysis on ASON. The intention of this paper is to present our perspective, in terms of evolution strategy toward ASON, on next generation optical networks. It is shown through experimental tests that the performance of current Pre-standard ASON enabled equipments satisfies the basic requirements of network operators and is ready for initial deployment. The results of the economic analysis show that network operators can be benefit from the deployment of ASON from three sides. Firstly, ASON can reduce the CAPEX for network expanding by integrating multiple ADM & DCS into one box. Secondly, ASON can reduce the OPEX for network operation by introducing automatic resource control scheme. Finally, ASON can increase margin revenue by providing new optical network services such as Bandwidth on Demand, optical VPN etc. Finally, the evolution strategy is proposed as our perspective toward next generation optical networks. We hope the evolution strategy introduced may be helpful for the network operators to gracefully migrate their fixed ring based legacy networks to next generation dynamic mesh based network.

Ikaros controls isotype selection during immunoglobulin class switch recombination.

PubMed

Sellars, MacLean; Reina-San-Martin, Bernardo; Kastner, Philippe; Chan, Susan

2009-05-11

Class switch recombination (CSR) allows the humoral immune response to exploit different effector pathways through specific secondary antibody isotypes. However, the molecular mechanisms and factors that control immunoglobulin (Ig) isotype choice for CSR are unclear. We report that deficiency for the Ikaros transcription factor results in increased and ectopic CSR to IgG(2b) and IgG(2a), and reduced CSR to all other isotypes, regardless of stimulation. Ikaros suppresses active chromatin marks, transcription, and activation-induced cytidine deaminase (AID) accessibility at the gamma2b and gamma2a genes to inhibit class switching to these isotypes. Further, Ikaros directly regulates isotype gene transcription as it directly binds the Igh 3' enhancer and interacts with isotype gene promoters. Finally, Ikaros-mediated repression of gamma2b and gamma2a transcription promotes switching to other isotype genes by allowing them to compete for AID-mediated recombination at the single-cell level. Thus, our results reveal transcriptional competition between constant region genes in individual cells to be a critical and general mechanism for isotype specification during CSR. We show that Ikaros is a master regulator of this competition.

Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stabilizing the uninduced phenotypic state.

PubMed

Ge, Hao; Wu, Pingping; Qian, Hong; Xie, Xiaoliang Sunney

2018-03-01

Within an isogenic population, even in the same extracellular environment, individual cells can exhibit various phenotypic states. The exact role of stochastic gene-state switching regulating the transition among these phenotypic states in a single cell is not fully understood, especially in the presence of positive feedback. Recent high-precision single-cell measurements showed that, at least in bacteria, switching in gene states is slow relative to the typical rates of active transcription and translation. Hence using the lac operon as an archetype, in such a region of operon-state switching, we present a fluctuating-rate model for this classical gene regulation module, incorporating the more realistic operon-state switching mechanism that was recently elucidated. We found that the positive feedback mechanism induces bistability (referred to as deterministic bistability), and that the parameter range for its occurrence is significantly broadened by stochastic operon-state switching. We further show that in the absence of positive feedback, operon-state switching must be extremely slow to trigger bistability by itself. However, in the presence of positive feedback, which stabilizes the induced state, the relatively slow operon-state switching kinetics within the physiological region are sufficient to stabilize the uninduced state, together generating a broadened parameter region of bistability (referred to as stochastic bistability). We illustrate the opposite phenotype-transition rate dependence upon the operon-state switching rates in the two types of bistability, with the aid of a recently proposed rate formula for fluctuating-rate models. The rate formula also predicts a maximal transition rate in the intermediate region of operon-state switching, which is validated by numerical simulations in our model. Overall, our findings suggest a biological function of transcriptional "variations" among genetically identical cells, for the emergence of bistability and transition between phenotypic states.

Atomic switch networks as complex adaptive systems

NASA Astrophysics Data System (ADS)

Scharnhorst, Kelsey S.; Carbajal, Juan P.; Aguilera, Renato C.; Sandouk, Eric J.; Aono, Masakazu; Stieg, Adam Z.; Gimzewski, James K.

2018-03-01

Complexity is an increasingly crucial aspect of societal, environmental and biological phenomena. Using a dense unorganized network of synthetic synapses it is shown that a complex adaptive system can be physically created on a microchip built especially for complex problems. These neuro-inspired atomic switch networks (ASNs) are a dynamic system with inherent and distributed memory, recurrent pathways, and up to a billion interacting elements. We demonstrate key parameters describing self-organized behavior such as non-linearity, power law dynamics, and multistate switching regimes. Device dynamics are then investigated using a feedback loop which provides control over current and voltage power-law behavior. Wide ranging prospective applications include understanding and eventually predicting future events that display complex emergent behavior in the critical regime.

Stability analysis for uncertain switched neural networks with time-varying delay.

PubMed

Shen, Wenwen; Zeng, Zhigang; Wang, Leimin

2016-11-01

In this paper, stability for a class of uncertain switched neural networks with time-varying delay is investigated. By exploring the mode-dependent properties of each subsystem, all the subsystems are categorized into stable and unstable ones. Based on Lyapunov-like function method and average dwell time technique, some delay-dependent sufficient conditions are derived to guarantee the exponential stability of considered uncertain switched neural networks. Compared with general results, our proposed approach distinguishes the stable and unstable subsystems rather than viewing all subsystems as being stable, thus getting less conservative criteria. Finally, two numerical examples are provided to show the validity and the advantages of the obtained results. Copyright © 2016 Elsevier Ltd. All rights reserved.

Silicon Modulators, Switches and Sub-systems for Optical Interconnect

NASA Astrophysics Data System (ADS)

Li, Qi

Silicon photonics is emerging as a promising platform for manufacturing and integrating photonic devices for light generation, modulation, switching and detection. The compatibility with existing CMOS microelectronic foundries and high index contrast in silicon could enable low cost and high performance photonic systems, which find many applications in optical communication, data center networking and photonic network-on-chip. This thesis first develops and demonstrates several experimental work on high speed silicon modulators and switches with record performance and novel functionality. A 8x40 Gb/s transmitter based on silicon microrings is first presented. Then an end-to-end link using microrings for Binary Phase Shift Keying (BPSK) modulation and demodulation is shown, and its performance with conventional BPSK modulation/ demodulation techniques is compared. Next, a silicon traveling-wave Mach- Zehnder modulator is demonstrated at data rate up to 56 Gb/s for OOK modulation and 48 Gb/s for BPSK modulation, showing its capability at high speed communication systems. Then a single silicon microring is shown with 2x2 full crossbar switching functionality, enabling optical interconnects with ultra small footprint. Then several other experiments in the silicon platform are presented, including a fully integrated in-band Optical Signal to Noise Ratio (OSNR) monitor, characterization of optical power upper bound in a silicon microring modulator, and wavelength conversion in a dispersion-engineered waveguide. The last part of this thesis is on network-level application of photonics, specically a broadcast-and-select network based on star coupler is introduced, and its scalability performance is studied. Finally a novel switch architecture for data center networks is discussed, and its benefits as a disaggregated network are presented.

Near-optimality of special periodic protocols for fluid models of single server switched networks with switchover times

NASA Astrophysics Data System (ADS)

Matveev, A. S.; Ishchenko, R.

2017-11-01

We consider a generic deterministic time-invariant fluid model of a single server switched network, which consists of finitely many infinite size buffers (queues) and receives constant rate inflows of jobs from the outside. Any flow undergoes a multi-phase service, entering a specific buffer after every phase, and ultimately leaves the network; the route of the flow over the buffers is pre-specified, and flows may merge inside the network. They share a common source of service, which can serve at most one buffer at a time and has to switch among buffers from time to time; any switch consumes a nonzero switchover period. With respect to the long-run maximal scaled wip (work in progress) performance metric, near-optimality of periodic scheduling and service protocols is established: the deepest optimum (that is over all feasible processes in the network, irrespective of the initial state) is furnished by such a protocol up to as small error as desired. Moreover, this can be achieved with a special periodic protocol introduced in the paper. It is also shown that the exhaustive policy is optimal for any buffer whose service at the maximal rate does not cause growth of the scaled wip.

Output synchronization of discrete-time dynamical networks based on geometrically incremental dissipativity.

PubMed

Li, Chensong; Zhao, Jun

2017-01-01

In this work, we investigate the output synchronization problem for discrete-time dynamical networks with identical nodes. Firstly, if each node of a network is geometrically incrementally dissipative, the entire network can be viewed as a geometrically dissipative nonlinear system by choosing a particular input-output pair. Then, based on the geometrical dissipativity property, we consider two cases: output synchronization under arbitrary topology and switching topology, respectively. For the first case, we establish several criteria of output synchronization under arbitrary switching between a set of connection topologies by employing a common Lyapunov function. For the other case, we give the design method of a switching signal to achieve output synchronization even if all subnetworks are not synchronous. Finally, an example is provided to illustrate the effectiveness of the main results. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

A multi-ring optical packet and circuit integrated network with optical buffering.

PubMed

Furukawa, Hideaki; Shinada, Satoshi; Miyazawa, Takaya; Harai, Hiroaki; Kawasaki, Wataru; Saito, Tatsuhiko; Matsunaga, Koji; Toyozumi, Tatuya; Wada, Naoya

2012-12-17

We newly developed a 3 × 3 integrated optical packet and circuit switch-node. Optical buffers and burst-mode erbium-doped fiber amplifiers with the gain flatness are installed in the 3 × 3 switch-node. The optical buffer can prevent packet collisions and decrease packet loss. We constructed a multi-ring optical packet and circuit integrated network testbed connecting two single-ring networks and a client network by the 3 × 3 switch-node. For the first time, we demonstrated 244 km fiber transmission and 5-node hopping of multiplexed 14-wavelength 10 Gbps optical paths and 100 Gbps optical packets encapsulating 10 Gigabit Ethernet frames on the testbed. Error-free (frame error rate < 1 × 10(-4)) operation was achieved with optical packets of various packet lengths. In addition, successful avoidance of packet collisions by optical buffers was confirmed.

Optical switching using IP protocol

NASA Astrophysics Data System (ADS)

Utreras, Andres J.; Gusqui, Luis; Reyes, Andres; Mena, Ricardo I.; Licenko, Gennady L.; Amirgaliyev, Yedilkhan; Komada, Paweł; Luganskaya, Saule; Kashaganova, Gulzhan

2017-08-01

To understand and evaluate the Optical Layer, and how it will affect the IP protocols over WDM (Switching), the present analyse is proposed. Optical communications have attractive proprieties, but also have some disadvantages, so the challenge is to combine the best of both branches. In this paper, general concepts for different options of switching are reviewed as: optical burst switching (OBS) and automatically switching optical network (ASON). Specific details such as their architectures are also discussed. In addition, the relevant characteristics of each variation for switching are reviewed.

Magneto-optic garnet and liquid crystal optical switches

NASA Technical Reports Server (NTRS)

Krawczak, J. A.; Torok, E. J.; Harvey, W. A.; Hewitt, F. G.; Nelson, G. L.

1984-01-01

Magnetic stripe domain and liquid crystal devices are being developed and evaluated as fiber optic switches that can be utilized for nonblocking type nxm optical matrix switches in networking and optical processing. Liquid crystal switches are characterized by very low insertion loss and crosstalk, while stripe domain switches commutate in less than one microsecond. Both switches operate on multimode, randomly polarized fiber light with potentially large values for (n,m). The applications of these magnetic stripe domain and liquid crystal devices are discussed.

Sequential Logic Model Deciphers Dynamic Transcriptional Control of Gene Expressions

PubMed Central

Yeo, Zhen Xuan; Wong, Sum Thai; Arjunan, Satya Nanda Vel; Piras, Vincent; Tomita, Masaru; Selvarajoo, Kumar; Giuliani, Alessandro; Tsuchiya, Masa

2007-01-01

Background Cellular signaling involves a sequence of events from ligand binding to membrane receptors through transcription factors activation and the induction of mRNA expression. The transcriptional-regulatory system plays a pivotal role in the control of gene expression. A novel computational approach to the study of gene regulation circuits is presented here. Methodology Based on the concept of finite state machine, which provides a discrete view of gene regulation, a novel sequential logic model (SLM) is developed to decipher control mechanisms of dynamic transcriptional regulation of gene expressions. The SLM technique is also used to systematically analyze the dynamic function of transcriptional inputs, the dependency and cooperativity, such as synergy effect, among the binding sites with respect to when, how much and how fast the gene of interest is expressed. Principal Findings SLM is verified by a set of well studied expression data on endo16 of Strongylocentrotus purpuratus (sea urchin) during the embryonic midgut development. A dynamic regulatory mechanism for endo16 expression controlled by three binding sites, UI, R and Otx is identified and demonstrated to be consistent with experimental findings. Furthermore, we show that during transition from specification to differentiation in wild type endo16 expression profile, SLM reveals three binary activities are not sufficient to explain the transcriptional regulation of endo16 expression and additional activities of binding sites are required. Further analyses suggest detailed mechanism of R switch activity where indirect dependency occurs in between UI activity and R switch during specification to differentiation stage. Conclusions/Significance The sequential logic formalism allows for a simplification of regulation network dynamics going from a continuous to a discrete representation of gene activation in time. In effect our SLM is non-parametric and model-independent, yet providing rich biological insight. The demonstration of the efficacy of this approach in endo16 is a promising step for further application of the proposed method. PMID:17712424

HLS7, a hemopoietic lineage switch gene homologous to the leukemia-inducing gene MLF1.

PubMed Central

Williams, J H; Daly, L N; Ingley, E; Beaumont, J G; Tilbrook, P A; Lalonde, J P; Stillitano, J P; Klinken, S P

1999-01-01

Hemopoietic lineage switching occurs when leukemic cells, apparently committed to one lineage, change and display the phenotype of another pathway. cDNA representational difference analysis was used to identify myeloid-specific genes that may be associated with an erythroid to myeloid lineage switch involving the murine J2E erythroleukemic cell line. One of the genes isolated (HLS7) is homologous to the novel human oncogene myeloid leukemia factor 1 (MLF1) involved in the t(3;5)(q25.1;q34) translocation associated with acute myeloid leukemia. Enforced expression of HLS7 in J2E cells induced a monoblastoid phenotype, thereby recapitulating the spontaneous erythroid to myeloid lineage switch. HLS7 also inhibited erythropoietin- or chemically-induced differentiation of erythroleukemic cell lines and suppressed development of erythropoietin-responsive colonies in semi-solid culture. However, intracellular signaling activated by erythropoietin was not impeded by ectopic expression of HLS7. In contrast, HLS7 promoted maturation of M1 monoblastoid cells and increased myeloid colony formation in vitro. These data show that HLS7 can influence erythroid/myeloid lineage switching and the development of normal hemopoietic cells. PMID:10523300

HLS7, a hemopoietic lineage switch gene homologous to the leukemia-inducing gene MLF1.

PubMed

Williams, J H; Daly, L N; Ingley, E; Beaumont, J G; Tilbrook, P A; Lalonde, J P; Stillitano, J P; Klinken, S P

1999-10-15

Hemopoietic lineage switching occurs when leukemic cells, apparently committed to one lineage, change and display the phenotype of another pathway. cDNA representational difference analysis was used to identify myeloid-specific genes that may be associated with an erythroid to myeloid lineage switch involving the murine J2E erythroleukemic cell line. One of the genes isolated (HLS7) is homologous to the novel human oncogene myeloid leukemia factor 1 (MLF1) involved in the t(3;5)(q25.1;q34) translocation associated with acute myeloid leukemia. Enforced expression of HLS7 in J2E cells induced a monoblastoid phenotype, thereby recapitulating the spontaneous erythroid to myeloid lineage switch. HLS7 also inhibited erythropoietin- or chemically-induced differentiation of erythroleukemic cell lines and suppressed development of erythropoietin-responsive colonies in semi-solid culture. However, intracellular signaling activated by erythropoietin was not impeded by ectopic expression of HLS7. In contrast, HLS7 promoted maturation of M1 monoblastoid cells and increased myeloid colony formation in vitro. These data show that HLS7 can influence erythroid/myeloid lineage switching and the development of normal hemopoietic cells.

Roles of factorial noise in inducing bimodal gene expression

NASA Astrophysics Data System (ADS)

Liu, Peijiang; Yuan, Zhanjiang; Huang, Lifang; Zhou, Tianshou

2015-06-01

Some gene regulatory systems can exhibit bimodal distributions of mRNA or protein although the deterministic counterparts are monostable. This noise-induced bimodality is an interesting phenomenon and has important biological implications, but it is unclear how different sources of expression noise (each source creates so-called factorial noise that is defined as a component of the total noise) contribute separately to this stochastic bimodality. Here we consider a minimal model of gene regulation, which is monostable in the deterministic case. Although simple, this system contains factorial noise of two main kinds: promoter noise due to switching between gene states and transcriptional (or translational) noise due to synthesis and degradation of mRNA (or protein). To better trace the roles of factorial noise in inducing bimodality, we also analyze two limit models, continuous and adiabatic approximations, apart from the exact model. We show that in the case of slow gene switching, the continuous model where only promoter noise is considered can exhibit bimodality; in the case of fast switching, the adiabatic model where only transcriptional or translational noise is considered can also exhibit bimodality but the exact model cannot; and in other cases, both promoter noise and transcriptional or translational noise can cooperatively induce bimodality. Since slow gene switching and large protein copy numbers are characteristics of eukaryotic cells, whereas fast gene switching and small protein copy numbers are characteristics of prokaryotic cells, we infer that eukaryotic stochastic bimodality is induced mainly by promoter noise, whereas prokaryotic stochastic bimodality is induced primarily by transcriptional or translational noise.

Network Solutions.

ERIC Educational Resources Information Center

Vietzke, Robert; And Others

1996-01-01

This special section explains the latest developments in networking technologies, profiles school districts benefiting from successful implementations, and reviews new products for building networks. Highlights include ATM (asynchronous transfer mode), cable modems, networking switches, Internet screening software, file servers, network management…

On-board processing architectures for satellite B-ISDN services

NASA Technical Reports Server (NTRS)

Inukai, Thomas; Shyy, Dong-Jye; Faris, Faris

1991-01-01

Onboard baseband processing architectures for future satellite broadband integrated services digital networks (B-ISDN's) are addressed. To assess the feasibility of implementing satellite B-ISDN services, critical design issues, such as B-ISDN traffic characteristics, transmission link design, and a trade-off between onboard circuit and fast packet switching, are analyzed. Examples of the two types of switching mechanisms and potential onboard network control functions are presented. A sample network architecture is also included to illustrate a potential onboard processing system.

Investigation of the Genes Involved in Antigenic Switching at the vlsE Locus in Borrelia burgdorferi: An Essential Role for the RuvAB Branch Migrase

PubMed Central

Dresser, Ashley R.; Hardy, Pierre-Olivier; Chaconas, George

2009-01-01

Persistent infection by pathogenic organisms requires effective strategies for the defense of these organisms against the host immune response. A common strategy employed by many pathogens to escape immune recognition and clearance is to continually vary surface epitopes through recombinational shuffling of genetic information. Borrelia burgdorferi, a causative agent of Lyme borreliosis, encodes a surface-bound lipoprotein, VlsE. This protein is encoded by the vlsE locus carried at the right end of the linear plasmid lp28-1. Adjacent to the expression locus are 15 silent cassettes carrying information that is moved into the vlsE locus through segmental gene conversion events. The protein players and molecular mechanism of recombinational switching at vlsE have not been characterized. In this study, we analyzed the effect of the independent disruption of 17 genes that encode factors involved in DNA recombination, repair or replication on recombinational switching at the vlsE locus during murine infection. In Neisseria gonorrhoeae, 10 such genes have been implicated in recombinational switching at the pilE locus. Eight of these genes, including recA, are either absent from B. burgdorferi, or do not show an obvious requirement for switching at vlsE. The only genes that are required in both organisms are ruvA and ruvB, which encode subunits of a Holliday junction branch migrase. Disruption of these genes results in a dramatic decrease in vlsE recombination with a phenotype similar to that observed for lp28-1 or vls-minus spirochetes: productive infection at week 1 with clearance by day 21. In SCID mice, the persistence defect observed with ruvA and ruvB mutants was fully rescued as previously observed for vlsE-deficient B. burgdorferi. We report the requirement of the RuvAB branch migrase in recombinational switching at vlsE, the first essential factor to be identified in this process. These findings are supported by the independent work of Lin et al. in the accompanying article, who also found a requirement for the RuvAB branch migrase. Our results also indicate that the mechanism of switching at vlsE in B. burgdorferi is distinct from switching at pilE in N. gonorrhoeae, which is the only other organism analyzed genetically in detail. Finally, our findings suggest a unique mechanism for switching at vlsE and a role for currently unidentified B. burgdorferi proteins in this process. PMID:19997508

Demonstration of reconfigurable joint orbital angular momentum mode and space switching

PubMed Central

Liu, Jun; Wang, Jian

2016-01-01

We propose and demonstrate space-selective switch functions employing orbital angular momentum (OAM) modes in the space domain for switching network. One is the switching among different OAM modes having different spatial phase structures, called OAM mode switching. The other is the switching among different space locations, called space switching. The switching operation mechanism relies on linear optics. Reconfigurable 4 × 4 OAM mode switching, space switching, and joint OAM mode and space switching fabric using a single spatial light modulator (SLM) are all demonstrated in the experiment. In addition, the presented OAM-incorporated space-selective switch might be further extended to N × N joint OAM mode and space switching with fast response, scalability, cascading ability and compability to facilitate robust switching applications. PMID:27869133

Demonstration of reconfigurable joint orbital angular momentum mode and space switching

NASA Astrophysics Data System (ADS)

Liu, Jun; Wang, Jian

2016-11-01

We propose and demonstrate space-selective switch functions employing orbital angular momentum (OAM) modes in the space domain for switching network. One is the switching among different OAM modes having different spatial phase structures, called OAM mode switching. The other is the switching among different space locations, called space switching. The switching operation mechanism relies on linear optics. Reconfigurable 4 × 4 OAM mode switching, space switching, and joint OAM mode and space switching fabric using a single spatial light modulator (SLM) are all demonstrated in the experiment. In addition, the presented OAM-incorporated space-selective switch might be further extended to N × N joint OAM mode and space switching with fast response, scalability, cascading ability and compability to facilitate robust switching applications.

Demonstration of reconfigurable joint orbital angular momentum mode and space switching.

PubMed

Liu, Jun; Wang, Jian

2016-11-21

We propose and demonstrate space-selective switch functions employing orbital angular momentum (OAM) modes in the space domain for switching network. One is the switching among different OAM modes having different spatial phase structures, called OAM mode switching. The other is the switching among different space locations, called space switching. The switching operation mechanism relies on linear optics. Reconfigurable 4 × 4 OAM mode switching, space switching, and joint OAM mode and space switching fabric using a single spatial light modulator (SLM) are all demonstrated in the experiment. In addition, the presented OAM-incorporated space-selective switch might be further extended to N × N joint OAM mode and space switching with fast response, scalability, cascading ability and compability to facilitate robust switching applications.

Overload protection for switching regulators

NASA Technical Reports Server (NTRS)

Lachochi, E.

1980-01-01

Circuit protects all output lines of switching regulator against overloads without requiring current sensors on every line. If overload is sensed, device short circuits bias on switching transistor so that power is rapidly cut off from loads. Circuit also includes delay network to inhibit erroneous operation during startup.

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

Testing Single Phase IGBT H-Bridge Switch Plates for the High Voltage Converter Modulator at the Spallation Neutron Source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peplov, Vladimir V; Anderson, David E; Solley, Dennis J

2014-01-01

Three IGBT H-bridge switching networks are used in each High Voltage Converter Modulator (HVCM) system at the Spallation Neutron Source (SNS) to generate drive currents to three boost transformer primaries switching between positive and negative bus voltages at 20 kHz. Every switch plate assembly is tested before installing it into an operational HVCM. A Single Phase Test Stand has been built for this purpose, and it is used for adjustment, measurement and testing of different configurations of switch plates. This paper will present a description of the Test Stand configuration and discuss the results of testing switch plates with twomore » different types of IGBT gate drivers currently in use on the HVCM systems. Comparison of timing characteristics of the original and new drivers and the resulting performance reinforces the necessity to replace the original H-bridge network drivers with the upgraded units.« less

A Physical Mechanism and Global Quantification of Breast Cancer

PubMed Central

Yu, Chong; Wang, Jin

2016-01-01

Initiation and progression of cancer depend on many factors. Those on the genetic level are often considered crucial. To gain insight into the physical mechanisms of breast cancer, we construct a gene regulatory network (GRN) which reflects both genetic and environmental aspects of breast cancer. The construction of the GRN is based on available experimental data. Three basins of attraction, representing the normal, premalignant and cancer states respectively, were found on the phenotypic landscape. The progression of breast cancer can be seen as switching transitions between different state basins. We quantified the stabilities and kinetic paths of the three state basins to uncover the biological process of breast cancer formation. The gene expression levels at each state were obtained, which can be tested directly in experiments. Furthermore, by performing global sensitivity analysis on the landscape topography, six key genes (HER2, MDM2, TP53, BRCA1, ATM, CDK2) and four regulations (HER2⊣TP53, CDK2⊣BRCA1, ATM→MDM2, TP53→ATM) were identified as being critical for breast cancer. Interestingly, HER2 and MDM2 are the most popular targets for treating breast cancer. BRCA1 and TP53 are the most important oncogene of breast cancer and tumor suppressor gene, respectively. This further validates the feasibility of our model and the reliability of our prediction results. The regulation ATM→MDM2 has been extensive studied on DNA damage but not on breast cancer. We notice the importance of ATM→MDM2 on breast cancer. Previous studies of breast cancer have often focused on individual genes and the anti-cancer drugs are mainly used to target the individual genes. Our results show that the network-based strategy is more effective on treating breast cancer. The landscape approach serves as a new strategy for analyzing breast cancer on both the genetic and epigenetic levels and can help on designing network based medicine for breast cancer. PMID:27410227

Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process

PubMed Central

Boullu, Loïs; Morin, Valérie; Vallin, Elodie; Guillemin, Anissa; Papili Gao, Nan; Cosette, Jérémie; Arnaud, Ophélie; Kupiec, Jean-Jacques; Espinasse, Thibault

2016-01-01

In some recent studies, a view emerged that stochastic dynamics governing the switching of cells from one differentiation state to another could be characterized by a peak in gene expression variability at the point of fate commitment. We have tested this hypothesis at the single-cell level by analyzing primary chicken erythroid progenitors through their differentiation process and measuring the expression of selected genes at six sequential time-points after induction of differentiation. In contrast to population-based expression data, single-cell gene expression data revealed a high cell-to-cell variability, which was masked by averaging. We were able to show that the correlation network was a very dynamical entity and that a subgroup of genes tend to follow the predictions from the dynamical network biomarker (DNB) theory. In addition, we also identified a small group of functionally related genes encoding proteins involved in sterol synthesis that could act as the initial drivers of the differentiation. In order to assess quantitatively the cell-to-cell variability in gene expression and its evolution in time, we used Shannon entropy as a measure of the heterogeneity. Entropy values showed a significant increase in the first 8 h of the differentiation process, reaching a peak between 8 and 24 h, before decreasing to significantly lower values. Moreover, we observed that the previous point of maximum entropy precedes two paramount key points: an irreversible commitment to differentiation between 24 and 48 h followed by a significant increase in cell size variability at 48 h. In conclusion, when analyzed at the single cell level, the differentiation process looks very different from its classical population average view. New observables (like entropy) can be computed, the behavior of which is fully compatible with the idea that differentiation is not a “simple” program that all cells execute identically but results from the dynamical behavior of the underlying molecular network. PMID:28027290

Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process.

PubMed

Richard, Angélique; Boullu, Loïs; Herbach, Ulysse; Bonnafoux, Arnaud; Morin, Valérie; Vallin, Elodie; Guillemin, Anissa; Papili Gao, Nan; Gunawan, Rudiyanto; Cosette, Jérémie; Arnaud, Ophélie; Kupiec, Jean-Jacques; Espinasse, Thibault; Gonin-Giraud, Sandrine; Gandrillon, Olivier

2016-12-01

In some recent studies, a view emerged that stochastic dynamics governing the switching of cells from one differentiation state to another could be characterized by a peak in gene expression variability at the point of fate commitment. We have tested this hypothesis at the single-cell level by analyzing primary chicken erythroid progenitors through their differentiation process and measuring the expression of selected genes at six sequential time-points after induction of differentiation. In contrast to population-based expression data, single-cell gene expression data revealed a high cell-to-cell variability, which was masked by averaging. We were able to show that the correlation network was a very dynamical entity and that a subgroup of genes tend to follow the predictions from the dynamical network biomarker (DNB) theory. In addition, we also identified a small group of functionally related genes encoding proteins involved in sterol synthesis that could act as the initial drivers of the differentiation. In order to assess quantitatively the cell-to-cell variability in gene expression and its evolution in time, we used Shannon entropy as a measure of the heterogeneity. Entropy values showed a significant increase in the first 8 h of the differentiation process, reaching a peak between 8 and 24 h, before decreasing to significantly lower values. Moreover, we observed that the previous point of maximum entropy precedes two paramount key points: an irreversible commitment to differentiation between 24 and 48 h followed by a significant increase in cell size variability at 48 h. In conclusion, when analyzed at the single cell level, the differentiation process looks very different from its classical population average view. New observables (like entropy) can be computed, the behavior of which is fully compatible with the idea that differentiation is not a "simple" program that all cells execute identically but results from the dynamical behavior of the underlying molecular network.

Improved Electro-Optical Switches

NASA Technical Reports Server (NTRS)

Nelson, Bruce N.; Cooper, Ronald F.

1994-01-01

Improved single-pole, double-throw electro-optical switches operate in switching times less than microsecond developed for applications as optical communication systems and networks of optical sensors. Contain no moving parts. In comparison with some prior electro-optical switches, these are simpler and operate with smaller optical losses. Beam of light switched from one output path to other by applying, to electro-optical crystal, voltage causing polarization of beam of light to change from vertical to horizontal.

Distributed parallel messaging for multiprocessor systems

DOEpatents

Chen, Dong; Heidelberger, Philip; Salapura, Valentina; Senger, Robert M; Steinmacher-Burrow, Burhard; Sugawara, Yutaka

2013-06-04

A method and apparatus for distributed parallel messaging in a parallel computing system. The apparatus includes, at each node of a multiprocessor network, multiple injection messaging engine units and reception messaging engine units, each implementing a DMA engine and each supporting both multiple packet injection into and multiple reception from a network, in parallel. The reception side of the messaging unit (MU) includes a switch interface enabling writing of data of a packet received from the network to the memory system. The transmission side of the messaging unit, includes switch interface for reading from the memory system when injecting packets into the network.

Study on spin filtering and switching action in a double-triangular network chain

NASA Astrophysics Data System (ADS)

Zhang, Yongmei

2018-04-01

Spin transport properties of a double-triangular quantum network with local magnetic moment on backbones and magnetic flux penetrating the network plane are studied. Numerical simulation results show that such a quantum network will be a good candidate for spin filter and spin switch. Local dispersion and density of states are considered in the framework of tight-binding approximation. Transmission coefficients are calculated by the method of transfer matrix. Spin transmission is regulated by substrate magnetic moment and magnetic flux piercing those triangles. Experimental realization of such theoretical research will be conducive to designing of new spintronic devices.

An incoherent regulatory network architecture that orchestrates B cell diversification in response to antigen signaling

PubMed Central

Sciammas, Roger; Li, Ying; Warmflash, Aryeh; Song, Yiqiang; Dinner, Aaron R; Singh, Harinder

2011-01-01

The B-lymphocyte lineage is a leading system for analyzing gene regulatory networks (GRNs) that orchestrate distinct cell fate transitions. Upon antigen recognition, B cells can diversify their immunoglobulin (Ig) repertoire via somatic hypermutation (SHM) and/or class switch DNA recombination (CSR) before differentiating into antibody-secreting plasma cells. We construct a mathematical model for a GRN underlying this developmental dynamic. The intensity of signaling through the Ig receptor is shown to control the bimodal expression of a pivotal transcription factor, IRF-4, which dictates B cell fate outcomes. Computational modeling coupled with experimental analysis supports a model of ‘kinetic control', in which B cell developmental trajectories pass through an obligate transient state of variable duration that promotes diversification of the antibody repertoire by SHM/CSR in direct response to antigens. More generally, this network motif could be used to translate a morphogen gradient into developmental inductive events of varying time, thereby enabling the specification of distinct cell fates. PMID:21613984

Flexible-rate optical packet generation/detection and label swapping for optical label switching networks

NASA Astrophysics Data System (ADS)

Wu, Zhongying; Li, Juhao; Tian, Yu; Ge, Dawei; Zhu, Paikun; Chen, Yuanxiang; Chen, Zhangyuan; He, Yongqi

2017-03-01

In recent years, optical label switching (OLS) gains lots of attentions due to its intrinsic advantages to implement protocol, bit-rate, granularity and data format transparency packet switching. In this paper, we propose a novel scheme to realize flexible-rate optical packet switching for OLS networks. At the transmitter node, flexible-rate packet is generated by parallel modulating different combinations of optical carriers generated from the optical multi-carrier generator (OMCG), among which the low-speed optical label occupies one carrier. At the switching node, label is extracted and re-generated in label processing unit (LPU). The payloads are switched based on routing information and new label is added after switching. At the receiver node, another OMCG serves as local oscillators (LOs) for optical payloads coherent detection. The proposed scheme offers good flexibility for dynamic optical packet switching by adjusting the payload bandwidth and could also effectively reduce the number of lasers, modulators and receivers for packet generation/detection. We present proof-of-concept demonstrations of flexible-rate packet generation/detection and label swapping in 12.5 GHz grid. The influence of crosstalk for cascaded label swapping is also investigated.

Noise-induced polarization switching in complex networks

NASA Astrophysics Data System (ADS)

Haerter, Jan O.; Díaz-Guilera, Albert; Serrano, M. Ángeles

2017-04-01

The combination of bistability and noise is ubiquitous in complex systems, from biology to social interactions, and has important implications for their functioning and resilience. Here we use a simple three-state dynamical process, in which nodes go from one pole to another through an intermediate state, to show that noise can induce polarization switching in bistable systems if dynamical correlations are significant. In large, fully connected networks, where dynamical correlations can be neglected, increasing noise yields a collapse of bistability to an unpolarized configuration where the three possible states of the nodes are equally likely. In contrast, increased noise induces abrupt and irreversible polarization switching in sparsely connected networks. In multiplexes, where each layer can have a different polarization tendency, one layer is dominant and progressively imposes its polarization state on the other, offsetting or promoting the ability of noise to switch its polarization. Overall, we show that the interplay of noise and dynamical correlations can yield discontinuous transitions between extremes, which cannot be explained by a simple mean-field description.

Future optical communication networks beyond 160 Gbit/s based on OTDM

NASA Astrophysics Data System (ADS)

Prati, Giancarlo; Bogoni, Antonella; Poti, Luca

2005-01-01

The virtually unlimited bandwidth of optical fibers has caused a great increase in data transmission speed over the past decade and, hence, stimulated high-demand multimedia services such as distance learning, video-conferencing and peer to peer applications. For this reason data traffic is exceeding telephony traffic, and this trend is driving the convergence of telecommunications and computer communications. In this scenario Internet Protocol (IP) is becoming the dominant protocol for any traffic, shifting the attention of the network designers from a circuit switching approach to a packet switching approach. A role of paramount importance in packet switching networks is played by the router that must implement the functionalities to set up and maintain the inter-nodal communications. The main functionalities a router must implement are routing, forwarding, switching, synchronization, contention resolution, and buffering. Nowadays, opto-electronic conversion is still required at each network node to process the incoming signal before routing that to the right output port. However, when the single channel bit rate increases beyond electronic speed limit, Optical Time Division Multiplexing (OTDM) becomes a forced choice, and all-optical processing must be performed to extract the information from the incoming packet. In this paper enabling techniques for ultra-fast all-optical network will be addressed. First a 160 Gbit/s complete transmission system will be considered. As enabling technique, an overview for all-optical logics will be discussed and experimental results will be presented using a particular reconfigurable NOLM based on Self-Phase-Modulation (SPM) or Cross-Phase-Modulation (XPM). Finally, a rough experiment on label extraction, all-optical switching and packet forwarding is shown.

Transcriptional reprogramming and phenotypic switching associated with the adaptation of Lactobacillus plantarum C2 to plant niches

PubMed Central

Filannino, Pasquale; Di Cagno, Raffaella; Crecchio, Carmine; De Virgilio, Caterina; De Angelis, Maria; Gobbetti, Marco

2016-01-01

Lactobacillus plantarum has been isolated from a large variety of ecological niches, thus highlighting its remarkable environmental adaptability as a generalist. Plant fermentation conditions markedly affect the functional features of L. plantarum strains. We investigated the plant niche-specific traits of L. plantarum through whole-transcriptome and phenotypic microarray profiles. Carrot (CJ) and pineapple (PJ) juices were chosen as model systems, and MRS broth was used as a control. A set of 3,122 genes was expressed, and 21 to 31% of genes were differentially expressed depending on the plant niche and cell physiological state. L. plantarum C2 seemed to specifically respond to plant media conditions. When L. plantarum was cultured in CJ, useful pathways were activated, which were aimed to sense the environment, save energy and adopt alternative routes for NAD+ regeneration. In PJ the acidic environment caused a transcriptional switching, which was network-linked to an acid tolerance response involving carbohydrate flow, amino acid and protein metabolism, pH homeostasis and membrane fluidity. The most prominent phenotypic dissimilarities observed in cells grown in CJ and PJ were related to carbon and nitrogen metabolism, respectively. Summarising, a snapshot of a carrot and pineapple sensing and adaptive regulation model for L. plantarum C2 was proposed. PMID:27273017

Three layers multi-granularity OCDM switching system based on learning-stateful PCE

NASA Astrophysics Data System (ADS)

Wang, Yubao; Liu, Yanfei; Sun, Hao

2017-10-01

In the existing three layers multi-granularity OCDM switching system (TLMG-OCDMSS), F-LSP, L-LSP and OC-LSP can be bundled as switching granularity. For CPU-intensive network, the node not only needs to compute the path but also needs to bundle the switching granularity so that the load of single node is heavy. The node will paralyze when the traffic of the node is too heavy, which will impact the performance of the whole network seriously. The introduction of stateful PCE(S-PCE) will effectively solve these problems. PCE is composed of two parts, namely, the path computation element and the database (TED and LSPDB), and returns the result of path computation to PCC (path computation clients) after PCC sends the path computation request to it. In this way, the pressure of the distributed path computation in each node is reduced. In this paper, we propose the concept of Learning PCE (L-PCE), which uses the existing LSPDB as the data source of PCE's learning. By this means, we can simplify the path computation and reduce the network delay, as a result, improving the performance of network.

A scalable silicon photonic chip-scale optical switch for high performance computing systems.

PubMed

Yu, Runxiang; Cheung, Stanley; Li, Yuliang; Okamoto, Katsunari; Proietti, Roberto; Yin, Yawei; Yoo, S J B

2013-12-30

This paper discusses the architecture and provides performance studies of a silicon photonic chip-scale optical switch for scalable interconnect network in high performance computing systems. The proposed switch exploits optical wavelength parallelism and wavelength routing characteristics of an Arrayed Waveguide Grating Router (AWGR) to allow contention resolution in the wavelength domain. Simulation results from a cycle-accurate network simulator indicate that, even with only two transmitter/receiver pairs per node, the switch exhibits lower end-to-end latency and higher throughput at high (>90%) input loads compared with electronic switches. On the device integration level, we propose to integrate all the components (ring modulators, photodetectors and AWGR) on a CMOS-compatible silicon photonic platform to ensure a compact, energy efficient and cost-effective device. We successfully demonstrate proof-of-concept routing functions on an 8 × 8 prototype fabricated using foundry services provided by OpSIS-IME.

Association of ADRA2A and MTHFR gene polymorphisms with weight loss following antipsychotic switching to aripiprazole or ziprasidone.

PubMed

Roffeei, Siti Norsyuhada; Reynolds, Gavin P; Zainal, Nor Zuraida; Said, Mas Ayu; Hatim, Ahmad; Aida, Syarinaz Ahmad; Mohamed, Zahurin

2014-01-01

Various genetic polymorphisms have been reported to be associated with antipsychotic-induced weight gain. In this study, we aimed to determine whether risk polymorphisms in 12 candidate genes are associated with reduction in body mass index (BMI) of patients following switching of antipsychotics to aripiprazole or ziprasidone. We recruited 115 schizophrenia patients with metabolic abnormalities and who have been on at least 1 year treatment with other antipsychotics; they were then switched to either aripiprazole or ziprasidone. They were genotyped, and their BMI monitored for 6 months. Significant associations with reduction in BMI at 6 months following switching were found in two of these genes: with rs1800544 of the ADRA2A gene (CC + CG [-0.32 ± 1.41 kg/m²] vs GG [-1.04 ± 1.63 kg/m²], p = 0.013) and with rs1801131 of the MTHFR gene (AA [-0.36 ± 1.53] vs AC + CC [-1.07 ± 1.53], p = 0.015). The study data indicated that carriage of the ADRA2A rs1800544 GG genotype and the MTHFR rs1801131 C allele are associated with BMI reduction in this population following switching of antipsychotics to aripiprazole and ziprasidone. Copyright © 2013 John Wiley & Sons, Ltd.

Congestion control and routing over satellite networks

NASA Astrophysics Data System (ADS)

Cao, Jinhua

Satellite networks and transmissions find their application in fields of computer communications, telephone communications, television broadcasting, transportation, space situational awareness systems and so on. This thesis mainly focuses on two networking issues affecting satellite networking: network congestion control and network routing optimization. Congestion, which leads to long queueing delays, packet losses or both, is a networking problem that has drawn the attention of many researchers. The goal of congestion control mechanisms is to ensure high bandwidth utilization while avoiding network congestion by regulating the rate at which traffic sources inject packets into a network. In this thesis, we propose a stable congestion controller using data-driven, safe switching control theory to improve the dynamic performance of satellite Transmission Control Protocol/Active Queue Management (TCP/AQM) networks. First, the stable region of the Proportional-Integral (PI) parameters for a nominal model is explored. Then, a PI controller, whose parameters are adaptively tuned by switching among members of a given candidate set, using observed plant data, is presented and compared with some classical AQM policy examples, such as Random Early Detection (RED) and fixed PI control. A new cost detectable switching law with an interval cost function switching algorithm, which improves the performance and also saves the computational cost, is developed and compared with a law commonly used in the switching control literature. Finite-gain stability of the system is proved. A fuzzy logic PI controller is incorporated as a special candidate to achieve good performance at all nominal points with the available set of candidate controllers. Simulations are presented to validate the theory. An effocient routing algorithm plays a key role in optimizing network resources. In this thesis, we briefly analyze Low Earth Orbit (LEO) satellite networks, review the Cross Entropy (CE) method and then develop a novel on-demand routing system named Cross Entropy Accelerated Ant Routing System (CEAARS) for regular constellation LEO satellite networks. By implementing simulations on an Iridium-like satellite network, we compare the proposed CEAARS algorithm with the two approaches to adaptive routing protocols on the Internet: distance-vector (DV) and link-state (LS), as well as with the original Cross Entropy Ant Routing System (CEARS). DV algorithms are based on distributed Bellman Ford algorithm, and LS algorithms are implementation of Dijkstras single source shortest path. The results show that CEAARS not only remarkably improves the convergence speed of achieving optimal or suboptimal paths, but also reduces the number of overhead ants (management packets).

Ribozyme-based aminoglycoside switches of gene expression engineered by genetic selection in S. cerevisiae.

PubMed

Klauser, Benedikt; Atanasov, Janina; Siewert, Lena K; Hartig, Jörg S

2015-05-15

Systems for conditional gene expression are powerful tools in basic research as well as in biotechnology. For future applications, it is of great importance to engineer orthogonal genetic switches that function reliably in diverse contexts. RNA-based switches have the advantage that effector molecules interact immediately with regulatory modules inserted into the target RNAs, getting rid of the need of transcription factors usually mediating genetic control. Artificial riboswitches are characterized by their simplicity and small size accompanied by a high degree of modularity. We have recently reported a series of hammerhead ribozyme-based artificial riboswitches that allow for post-transcriptional regulation of gene expression via switching mRNA, tRNA, or rRNA functions. A more widespread application was so far hampered by moderate switching performances and a limited set of effector molecules available. Here, we report the re-engineering of hammerhead ribozymes in order to respond efficiently to aminoglycoside antibiotics. We first established an in vivo selection protocol in Saccharomyces cerevisiae that enabled us to search large sequence spaces for optimized switches. We then envisioned and characterized a novel strategy of attaching the aptamer to the ribozyme catalytic core, increasing the design options for rendering the ribozyme ligand-dependent. These innovations enabled the development of neomycin-dependent RNA modules that switch gene expression up to 25-fold. The presented aminoglycoside-responsive riboswitches belong to the best-performing RNA-based genetic regulators reported so far. The developed in vivo selection protocol should allow for sampling of large sequence spaces for engineering of further optimized riboswitches.

Interleukin-like EMT inducer regulates partial phenotype switching in MITF-low melanoma cell lines

PubMed Central

Noguchi, Ken; Dalton, Annamarie C.; Howley, Breege V.; McCall, Buckley J.; Yoshida, Akihiro; Diehl, J. Alan

2017-01-01

ILEI (FAM3C) is a secreted factor that contributes to the epithelial-to-mesenchymal transition (EMT), a cell biological process that confers metastatic properties to a tumor cell. Initially, we found that ILEI mRNA is highly expressed in melanoma metastases but not in primary tumors, suggesting that ILEI contributes to the malignant properties of melanoma. While melanoma is not an epithelial cell-derived tumor and does not undergo a traditional EMT, melanoma undergoes a similar process known as phenotype switching in which high (micropthalmia-related transcription factor) MITF expressing (MITF-high) proliferative cells switch to a low expressing (MITF-low) invasive state. We observed that MITF-high proliferative cells express low levels of ILEI (ILEI-low) and MITF-low invasive cells express high levels of ILEI (ILEI-high). We found that inducing phenotype switching towards the MITF-low invasive state increases ILEI mRNA expression, whereas phenotype switching towards the MITF-high proliferative state decreases ILEI mRNA expression. Next, we used in vitro assays to show that knockdown of ILEI attenuates invasive potential but not MITF expression or chemoresistance. Finally, we used gene expression analysis to show that ILEI regulates several genes involved in the MITF-low invasive phenotype including JARID1B, HIF-2α, and BDNF. Gene set enrichment analysis suggested that ILEI-regulated genes are enriched for JUN signaling, a known regulator of the MITF-low invasive phenotype. In conclusion, we demonstrate that phenotype switching regulates ILEI expression, and that ILEI regulates partial phenotype switching in MITF-low melanoma cell lines. PMID:28545079

The Fragility of Interdependency: Coupled Networks Switching Phenomena

NASA Astrophysics Data System (ADS)

Stanley, H. Eugene

2013-03-01

Recent disasters ranging from abrupt financial ``flash crashes'' and large-scale power outages to sudden death among the elderly dramatically exemplify the fact that the most dangerous vulnerability is hiding in the many interdependencies among different networks. In the past year, we have quantified failures in model of interconnected networks, and demonstrated the need to consider mutually dependent network properties in designing resilient systems. Specifically, we have uncovered new laws governing the nature of switching phenomena in coupled networks, and found that phenomena that are continuous ``second order'' phase transitions in isolated networks become discontinuous abrupt ``first order'' transitions in interdependent networks [S. V. Buldyrev, R. Parshani, G. Paul, H. E. Stanley, and S. Havlin, ``Catastrophic Cascade of Failures in Interdependent Networks,'' Nature 464, 1025 (2010); J. Gao, S. V. Buldyrev, H. E. Stanley, and S. Havlin, ``Novel Behavior of Networks Formed from Interdependent Networks,'' Nature Physics 8, 40 (2012). We conclude by discussing the network basis for understanding sudden death in the elderly, and the possibility that financial ``flash crashes'' are not unlike the catastrophic first-order failure incidents occurring in coupled networks. Specifically, we study the coupled networks that are responsible for financial fluctuations. It appears that ``trend switching phenomena'' that we uncover are remarkably independent of the scale over which they are analyzed. For example, we find that the same laws governing the formation and bursting of the largest financial bubbles also govern the tiniest finance bubbles, over a factor of 1,000,000,000 in time scale [T. Preis, J. Schneider, and H. E. Stanley, ``Switching Processes in Financial Markets,'' Proc. Natl. Acad. Sci. USA 108, 7674 (2011); T. Preis and H. E. Stanley, ``Bubble Trouble: Can a Law Describe Bubbles and Crashes in Financial Markets?'' Physics World 24, No. 5, 29 (May 2011)]. This work was carried out in collaboration with a number of colleagues, including T. Preis, J. J. Schneider, S. Havlin, R. Parshani, S. V. Buldyrev, J. Gao, and G. Paul-see ``When Networks Network,'' Science News, 22 Sept. 2012.

In Vivo magnetic resonance imaging of xenografted tumors using FTH1 reporter gene expression controlled by a tet-on switch.

PubMed

He, Xiaoya; Cai, Jinhua; Li, Hao; Liu, Bo; Qin, Yong; Zhong, Yi; Wang, Longlun; Liao, Yifan

2016-11-29

As a promising magnetic resonance imaging (MRI) reporter, ferritin has been used to track cells in vivo; however, its continuous overexpression can be cytotoxic, which restricts its application. In this study, we aimed to develop a switch to turn this genetic reporter "on" or "off" while monitoring cell grafts via MRI. To accomplish this, we genetically modified the ferritin heavy chain (FTH1) with a Tet-On switch and assessed the expression of FTH1 in transduced neuroblastoma cells (SK-N-SH) in vitro and in xenografted tumors in vivo. We found that FTH1 expression induced by doxycycline (Dox) in SK-N-SH-FTH1 cells depended on treatment dose and duration. We successfully detected T2-weighted MRI contrast in cell grafts after switching "on" the reporter gene using Dox, and this contrast disappeared when we switched it "off". The genetic reporter FTH1 can thus be switched "on" or "off" throughout longitudinal monitoring of cell grafts, limiting expression to when MRI contrast is needed. The controllable imaging system we have developed minimizes risks from constitutive reporter gene overexpression and facilitates tumor cell monitoring in vitro and in vivo.

Future large broadband switched satellite communications networks

NASA Technical Reports Server (NTRS)

Staelin, D. H.; Harvey, R. R.

1979-01-01

Critical technical, market, and policy issues relevant to future large broadband switched satellite networks are summarized. Our market projections for the period 1980 to 2000 are compared. Clusters of switched satellites, in lieu of large platforms, etc., are shown to have significant advantages. Analysis of an optimum terrestrial network architecture suggests the proper densities of ground stations and that link reliabilities 99.99% may entail less than a 10% cost premium for diversity protection at 20/30 GHz. These analyses suggest that system costs increase as the 0.6 power of traffic. Cost estimates for nominal 20/30 GHz satellite and ground facilities suggest optimum system configurations might employ satellites with 285 beams, multiple TDMA bands each carrying 256 Mbps, and 16 ft ground station antennas. A nominal development program is outlined.

The Influence of Vacuum Circuit Breakers and Different Motor Models on Switching Overvoltages in Motor Circuits

NASA Astrophysics Data System (ADS)

Wong, Cat S. M.; Snider, L. A.; Lo, Edward W. C.; Chung, T. S.

Switching of induction motors with vacuum circuit breakers continues to be a concern. In this paper the influence on statistical overvoltages of the stochastic characteristics of vacuum circuit breakers, high frequency models of motors and transformers, and network characteristics, including cable lengths and network topology are evaluated and a general view of the overvoltages phenomena is presented. Finally, a real case study on the statistical voltage levels and risk-of-failure resulting from switching of a vacuum circuit breaker in an industrial installation in Hong Kong is presented.

Tlx acts as a proangiogenic switch by regulating extracellular assembly of fibronectin matrices in retinal astrocytes.

PubMed

Uemura, Akiyoshi; Kusuhara, Sentaro; Wiegand, Stanley J; Yu, Ruth T; Nishikawa, Shin-ichi

2006-02-01

In response to hypoxia, hypoxia-inducible factors act as the primary proangiogenic triggers by regulating transcription levels of target genes, including VEGF. However, little is known about the specific factors that control other components of the angiogenic process, particularly formation of matrix scaffolds that promote adhesion and migration of endothelial cells. We show that in the postnatal mouse retina, the orphan nuclear receptor tailless (Tlx) is strongly expressed in the proangiogenic astrocytes, which secrete VEGF and fibronectin. Tlx expression by retinal astrocytes is controlled by oxygen concentration and rapidly downregulated upon contact with blood vessels. In mice null for Tlx, retinal astrocytes maintain VEGF expression; however, the extracellular assembly of fibronectin matrices by astrocytes is severely impaired, leading to defective scaffold formation and a complete failure of normal retinal vascular development. This work identifies Tlx as an essential component of the molecular network involved in the hypoxia-inducible proangiogenic switch in retinal astrocytes.

Tlx acts as a proangiogenic switch by regulating extracellular assembly of fibronectin matrices in retinal astrocytes

PubMed Central

Uemura, Akiyoshi; Kusuhara, Sentaro; Wiegand, Stanley J.; Yu, Ruth T.; Nishikawa, Shin-Ichi

2006-01-01

In response to hypoxia, hypoxia-inducible factors act as the primary proangiogenic triggers by regulating transcription levels of target genes, including VEGF. However, little is known about the specific factors that control other components of the angiogenic process, particularly formation of matrix scaffolds that promote adhesion and migration of endothelial cells. We show that in the postnatal mouse retina, the orphan nuclear receptor tailless (Tlx) is strongly expressed in the proangiogenic astrocytes, which secrete VEGF and fibronectin. Tlx expression by retinal astrocytes is controlled by oxygen concentration and rapidly downregulated upon contact with blood vessels. In mice null for Tlx, retinal astrocytes maintain VEGF expression; however, the extracellular assembly of fibronectin matrices by astrocytes is severely impaired, leading to defective scaffold formation and a complete failure of normal retinal vascular development. This work identifies Tlx as an essential component of the molecular network involved in the hypoxia-inducible proangiogenic switch in retinal astrocytes. PMID:16424942

An Acetylation Switch Regulates SUMO-Dependent Protein Interaction Networks

PubMed Central

Ullmann, Rebecca; Chien, Christopher D.; Avantaggiati, Maria Laura; Muller, Stefan

2013-01-01

SUMMARY The attachment of the SUMO modifier to proteins controls cellular signaling pathways through noncovalent binding to SUMO-interaction motifs (SIMs). Canonical SIMs contain a core of hydrophobic residues that bind to a hydrophobic pocket on SUMO. Negatively charged residues of SIMs frequently contribute to binding by interacting with a basic surface on SUMO. Here we define acetylation within this basic interface as a central mechanism for the control of SUMO-mediated interactions. The acetyl-mediated neutralization of basic charges on SUMO prevents binding to SIMs in PML, Daxx, and PIAS family members but does not affect the interaction between RanBP2 and SUMO. Acetylation is controlled by HDACs and attenuates SUMO- and PIAS-mediated gene silencing. Moreover, it affects the assembly of PML nuclear bodies and restrains the recruitment of the corepressor Daxx to these structures. This acetyl-dependent switch thus expands the regulatory repertoire of SUMO signaling and determines the selectivity and dynamics of SUMO-SIM interactions. PMID:22578841

Network Speech Systems Technology Program

NASA Astrophysics Data System (ADS)

Weinstein, C. J.

1980-09-01

This report documents work performed during FY 1980 on the DCA-sponsored Network Speech Systems Technology Program. The areas of work reported are: (1) communication systems studies in Demand-Assignment Multiple Access (DAMA), voice/data integration, and adaptive routing, in support of the evolving Defense Communications System (DCS) and Defense Switched Network (DSN); (2) a satellite/terrestrial integration design study including the functional design of voice and data interfaces to interconnect terrestrial and satellite network subsystems; and (3) voice-conferencing efforts dealing with support of the Secure Voice and Graphics Conferencing (SVGC) Test and Evaluation Program. Progress in definition and planning of experiments for the Experimental Integrated Switched Network (EISN) is detailed separately in an FY 80 Experiment Plan Supplement.

Low power digitally controlled oscillator designs with a novel 3-transistor XNOR gate

NASA Astrophysics Data System (ADS)

Kumar, Manoj; Arya, Sandeep K.; Pandey, Sujata

2012-03-01

Digital controlled oscillators (DCOs) are the core of all digital phase locked loop (ADPLL) circuits. Here, DCO structures with reduced hardware and power consumption having full digital control have been proposed. Three different DCO architectures have been proposed based on ring based topology. Three, four and five bit controlled DCO with NMOS, PMOS and NMOS & PMOS transistor switching networks are presented. A three-transistor XNOR gate has been used as the inverter which is used as the delay cell. Delay has been controlled digitally with a switch network of NMOS and PMOS transistors. The three bit DCO with one NMOS network shows frequency variations of 1.6141-1.8790 GHz with power consumption variations 251.9224-276.8591 μW. The four bit DCO with one NMOS network shows frequency variation of 1.6229-1.8868 GHz with varying power consumption of 251.9225-278.0740 μW. A six bit DCO with one NMOS switching network gave an output frequency of 1.7237-1.8962 GHz with power consumption of 251.928-278.998 μW. Output frequency and power consumption results for 4 & 6 bit DCO circuits with one PMOS and NMOS & PMOS switching network have also been presented. The phase noise parameter with an offset frequency of 1 MHz has also been reported for the proposed circuits. Comparisons with earlier reported circuits have been made and the present approach shows advantages over previous circuits.

Stochastic models for regulatory networks of the genetic toggle switch.

PubMed

Tian, Tianhai; Burrage, Kevin

2006-05-30

Bistability arises within a wide range of biological systems from the lambda phage switch in bacteria to cellular signal transduction pathways in mammalian cells. Changes in regulatory mechanisms may result in genetic switching in a bistable system. Recently, more and more experimental evidence in the form of bimodal population distributions indicates that noise plays a very important role in the switching of bistable systems. Although deterministic models have been used for studying the existence of bistability properties under various system conditions, these models cannot realize cell-to-cell fluctuations in genetic switching. However, there is a lag in the development of stochastic models for studying the impact of noise in bistable systems because of the lack of detailed knowledge of biochemical reactions, kinetic rates, and molecular numbers. In this work, we develop a previously undescribed general technique for developing quantitative stochastic models for large-scale genetic regulatory networks by introducing Poisson random variables into deterministic models described by ordinary differential equations. Two stochastic models have been proposed for the genetic toggle switch interfaced with either the SOS signaling pathway or a quorum-sensing signaling pathway, and we have successfully realized experimental results showing bimodal population distributions. Because the introduced stochastic models are based on widely used ordinary differential equation models, the success of this work suggests that this approach is a very promising one for studying noise in large-scale genetic regulatory networks.

Stochastic models for regulatory networks of the genetic toggle switch

PubMed Central

Tian, Tianhai; Burrage, Kevin

2006-01-01

Bistability arises within a wide range of biological systems from the λ phage switch in bacteria to cellular signal transduction pathways in mammalian cells. Changes in regulatory mechanisms may result in genetic switching in a bistable system. Recently, more and more experimental evidence in the form of bimodal population distributions indicates that noise plays a very important role in the switching of bistable systems. Although deterministic models have been used for studying the existence of bistability properties under various system conditions, these models cannot realize cell-to-cell fluctuations in genetic switching. However, there is a lag in the development of stochastic models for studying the impact of noise in bistable systems because of the lack of detailed knowledge of biochemical reactions, kinetic rates, and molecular numbers. In this work, we develop a previously undescribed general technique for developing quantitative stochastic models for large-scale genetic regulatory networks by introducing Poisson random variables into deterministic models described by ordinary differential equations. Two stochastic models have been proposed for the genetic toggle switch interfaced with either the SOS signaling pathway or a quorum-sensing signaling pathway, and we have successfully realized experimental results showing bimodal population distributions. Because the introduced stochastic models are based on widely used ordinary differential equation models, the success of this work suggests that this approach is a very promising one for studying noise in large-scale genetic regulatory networks. PMID:16714385

Cost-effective optical switch matrix for microwave phased-array

NASA Technical Reports Server (NTRS)

Pan, J. J.; Chia, S. L.; Li, W. Z.; Grove, C. H.

1991-01-01

An all-fiber (6x6) optical shutter switch matrix with the control system for microwave phased array has been demonstrated. The device offers the advantages of integrated configuration, low cost, low power consumption, small size, and light weight. The maximum extinction ratio (among 36 individual pixel) of this switch matrix at 840 nm is 24.2 dB, and the switching time is less than 120 microsec. In addition to phased array application, this low cost switch matrix is extremely attractive for fiber optic switching networks.

New MPLS network management techniques based on adaptive learning.

PubMed

Anjali, Tricha; Scoglio, Caterina; de Oliveira, Jaudelice Cavalcante

2005-09-01

The combined use of the differentiated services (DiffServ) and multiprotocol label switching (MPLS) technologies is envisioned to provide guaranteed quality of service (QoS) for multimedia traffic in IP networks, while effectively using network resources. These networks need to be managed adaptively to cope with the changing network conditions and provide satisfactory QoS. An efficient strategy is to map the traffic from different DiffServ classes of service on separate label switched paths (LSPs), which leads to distinct layers of MPLS networks corresponding to each DiffServ class. In this paper, three aspects of the management of such a layered MPLS network are discussed. In particular, an optimal technique for the setup of LSPs, capacity allocation of the LSPs and LSP routing are presented. The presented techniques are based on measurement of the network state to adapt the network configuration to changing traffic conditions.

SELECTED ANNOTATED BIBLIOGRAPHY ON SYSTEMS OF THEORETICAL DEVICES,

DTIC Science & Technology

BIONICS, BIBLIOGRAPHIES), (*BIBLIOGRAPHIES, BIONICS), (*CYBERNETICS, BIBLIOGRAPHIES), MATHEMATICS, COMPUTER LOGIC, NETWORKS, NERVOUS SYSTEM , THEORY , SEQUENCE SWITCHES, SWITCHING CIRCUITS, REDUNDANT COMPONENTS, LEARNING, MATHEMATICAL MODELS, BEHAVIOR, NERVES, SIMULATION, NERVE CELLS

Identification of microRNAs controlling hepatic mRNA levels for metabolic genes during the metabolic transition from embryonic to posthatch development in the chicken.

PubMed

Hicks, Julie A; Porter, Tom E; Liu, Hsiao-Ching

2017-09-05

The transition from embryonic to posthatch development in the chicken represents a massive metabolic switch from primarily lipolytic to primarily lipogenic metabolism. This metabolic switch is essential for the chick to successfully transition from the metabolism of stored egg yolk to the utilization of carbohydrate-based feed. However, regulation of this metabolic switch is not well understood. We hypothesized that microRNAs (miRNAs) play an important role in the metabolic switch that is essential to efficient growth of chickens. We used high-throughput RNA sequencing to characterize expression profiles of mRNA and miRNA in liver during late embryonic and early posthatch development of the chicken. This extensive data set was used to define the contributions of microRNAs to the metabolic switch during development that is critical to growth and nutrient utilization in chickens. We found that expression of over 800 mRNAs and 30 miRNAs was altered in the embryonic liver between embryonic day 18 and posthatch day 3, and many of these differentially expressed mRNAs and miRNAs are associated with metabolic processes. We confirmed the regulation of some of these mRNAs by miRNAs expressed in a reciprocal pattern using luciferase reporter assays. Finally, through the use of yeast one-hybrid screens, we identified several proteins that likely regulate expression of one of these important miRNAs. Integration of the upstream regulatory mechanisms governing miRNA expression along with monitoring the downstream effects of this expression will ultimately allow for the construction of complete miRNA regulatory networks associated with the hepatic metabolic switch in chickens. Our findings support a key role for miRNAs in controlling the metabolic switch that occurs between embryonic and posthatch development in the chicken.

Alternative Splicing of Four Trafficking Genes Regulates Myofiber Structure and Skeletal Muscle Physiology.

PubMed

Giudice, Jimena; Loehr, James A; Rodney, George G; Cooper, Thomas A

2016-11-15

During development, transcriptional and post-transcriptional networks are coordinately regulated to drive organ maturation. Alternative splicing contributes by producing temporal-specific protein isoforms. We previously found that genes undergoing splicing transitions during mouse postnatal heart development are enriched for vesicular trafficking and membrane dynamics functions. Here, we show that adult trafficking isoforms are also expressed in adult skeletal muscle and hypothesize that striated muscle utilizes alternative splicing to generate specific isoforms required for function of adult tissue. We deliver morpholinos into flexor digitorum brevis muscles in adult mice to redirect splicing of four trafficking genes to the fetal isoforms. The splicing switch results in multiple structural and functional defects, including transverse tubule (T-tubule) disruption and dihydropyridine receptor alpha (DHPR) and Ryr1 mislocalization, impairing excitation-contraction coupling, calcium handling, and force generation. The results demonstrate a previously unrecognized role for trafficking functions in adult muscle tissue homeostasis and a specific requirement for the adult splice variants. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Proposed Construction of Boulder Seismic Station Monitoring Sites, Boulder, Wyoming. Environmental Assessment

DTIC Science & Technology

2009-02-01

power battery box and controllers, WiFi radio, network switch, vault seismometers, infrasonic digitizers, and excess cabling. In addition to the...installed around the boreholes. Immediately upon completion, each site will be cleared of all unused equipment, debris, materials, and trash . All...controllers, WiFi radio, network switch, vault seismometers, infrasonic digitizers, and excess cabling. In addition to the permanent infrastructure listed

Destination directed packet switch architecture for a 30/20 GHz FDMA/TDM geostationary communication satellite network

NASA Technical Reports Server (NTRS)

Ivancic, William D.; Shalkhauser, Mary JO

1991-01-01

Emphasis is on a destination directed packet switching architecture for a 30/20 GHz frequency division multiplex access/time division multiplex (FDMA/TDM) geostationary satellite communication network. Critical subsystems and problem areas are identified and addressed. Efforts have concentrated heavily on the space segment; however, the ground segment was considered concurrently to ensure cost efficiency and realistic operational constraints.

Network Speech Systems Technology Program.

DTIC Science & Technology

1980-09-30

ognized that the lumped-speaker approximation could be extended even more generally to include cases of combined circuit-switched speech and packet...based on these tables. The first function is an im- portant element of the more general task of system control for a switched network, which in...programs are in preparation, as described below, for both steady-state evaluation and dynamic performance simulation of the algorithm in general

Communications Management at the Parks Reserve Forces Training Area, Camp Parks, California

DTIC Science & Technology

1994-10-31

The overall objective of the audit was to evaluate DoD management of circuit configurations for Defense Switched Network access requirements. The specific objective for this segment of the audit was to determine whether the Army used the most cost effective configuration of base and long haul telecommunications equipment and services at Camp Parks to access the Defense Switched Network.

Circuit-switch architecture for a 30/20-GHz FDMA/TDM geostationary satellite communications network

NASA Technical Reports Server (NTRS)

Ivancic, William D.

1992-01-01

A circuit switching architecture is described for a 30/20 GHz frequency division, multiple access uplink/time division multiplexed downlink (FDMA/TDM) geostationary satellite communications network. Critical subsystems and problem areas are identified and addressed. Work was concentrated primarily on the space segment; however, the ground segment was considered concurrently to ensure cost efficiency and realistic operational constraints.

Destination-directed, packet-switching architecture for 30/20-GHz FDMA/TDM geostationary communications satellite network

NASA Technical Reports Server (NTRS)

Ivancic, William D.; Shalkhauser, Mary JO

1992-01-01

A destination-directed packet switching architecture for a 30/20-GHz frequency division multiple access/time division multiplexed (FDMA/TDM) geostationary satellite communications network is discussed. Critical subsystems and problem areas are identified and addressed. Efforts have concentrated heavily on the space segment; however, the ground segment has been considered concurrently to ensure cost efficiency and realistic operational constraints.

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)

Switching performance of OBS network model under prefetched real traffic

NASA Astrophysics Data System (ADS)

Huang, Zhenhua; Xu, Du; Lei, Wen

2005-11-01

Optical Burst Switching (OBS) [1] is now widely considered as an efficient switching technique in building the next generation optical Internet .So it's very important to precisely evaluate the performance of the OBS network model. The performance of the OBS network model is variable in different condition, but the most important thing is that how it works under real traffic load. In the traditional simulation models, uniform traffics are usually generated by simulation software to imitate the data source of the edge node in the OBS network model, and through which the performance of the OBS network is evaluated. Unfortunately, without being simulated by real traffic, the traditional simulation models have several problems and their results are doubtable. To deal with this problem, we present a new simulation model for analysis and performance evaluation of the OBS network, which uses prefetched IP traffic to be data source of the OBS network model. The prefetched IP traffic can be considered as real IP source of the OBS edge node and the OBS network model has the same clock rate with a real OBS system. So it's easy to conclude that this model is closer to the real OBS system than the traditional ones. The simulation results also indicate that this model is more accurate to evaluate the performance of the OBS network system and the results of this model are closer to the actual situation.

A network of genetic repression and derepression specifies projection fates in the developing neocortex.

PubMed

Srinivasan, Karpagam; Leone, Dino P; Bateson, Rosalie K; Dobreva, Gergana; Kohwi, Yoshinori; Kohwi-Shigematsu, Terumi; Grosschedl, Rudolf; McConnell, Susan K

2012-11-20

Neurons within each layer in the mammalian cortex have stereotypic projections. Four genes-Fezf2, Ctip2, Tbr1, and Satb2-regulate these projection identities. These genes also interact with each other, and it is unclear how these interactions shape the final projection identity. Here we show, by generating double mutants of Fezf2, Ctip2, and Satb2, that cortical neurons deploy a complex genetic switch that uses mutual repression to produce subcortical or callosal projections. We discovered that Tbr1, EphA4, and Unc5H3 are critical downstream targets of Satb2 in callosal fate specification. This represents a unique role for Tbr1, implicated previously in specifying corticothalamic projections. We further show that Tbr1 expression is dually regulated by Satb2 and Ctip2 in layers 2-5. Finally, we show that Satb2 and Fezf2 regulate two disease-related genes, Auts2 (Autistic Susceptibility Gene2) and Bhlhb5 (mutated in Hereditary Spastic Paraplegia), providing a molecular handle to investigate circuit disorders in neurodevelopmental diseases.

SDN architecture for optical packet and circuit integrated networks

NASA Astrophysics Data System (ADS)

Furukawa, Hideaki; Miyazawa, Takaya

2016-02-01

We have been developing an optical packet and circuit integrated (OPCI) network, which realizes dynamic optical path, high-density packet multiplexing, and flexible wavelength resource allocation. In the OPCI networks, a best-effort service and a QoS-guaranteed service are provided by employing optical packet switching (OPS) and optical circuit switching (OCS) respectively, and users can select these services. Different wavelength resources are assigned for OPS and OCS links, and the amount of their wavelength resources are dynamically changed in accordance with the service usage conditions. To apply OPCI networks into wide-area (core/metro) networks, we have developed an OPCI node with a distributed control mechanism. Moreover, our OPCI node works with a centralized control mechanism as well as a distributed one. It is therefore possible to realize SDN-based OPCI networks, where resource requests and a centralized configuration are carried out. In this paper, we show our SDN architecture for an OPS system that configures mapping tables between IP addresses and optical packet addresses and switching tables according to the requests from multiple users via a web interface. While OpenFlow-based centralized control protocol is coming into widespread use especially for single-administrative, small-area (LAN/data-center) networks. Here, we also show an interworking mechanism between OpenFlow-based networks (OFNs) and the OPCI network for constructing a wide-area network, and a control method of wavelength resource selection to automatically transfer diversified flows from OFNs to the OPCI network.

Neural network-based sliding mode control for atmospheric-actuated spacecraft formation using switching strategy

NASA Astrophysics Data System (ADS)

Sun, Ran; Wang, Jihe; Zhang, Dexin; Shao, Xiaowei

2018-02-01

This paper presents an adaptive neural networks-based control method for spacecraft formation with coupled translational and rotational dynamics using only aerodynamic forces. It is assumed that each spacecraft is equipped with several large flat plates. A coupled orbit-attitude dynamic model is considered based on the specific configuration of atmospheric-based actuators. For this model, a neural network-based adaptive sliding mode controller is implemented, accounting for system uncertainties and external perturbations. To avoid invalidation of the neural networks destroying stability of the system, a switching control strategy is proposed which combines an adaptive neural networks controller dominating in its active region and an adaptive sliding mode controller outside the neural active region. An optimal process is developed to determine the control commands for the plates system. The stability of the closed-loop system is proved by a Lyapunov-based method. Comparative results through numerical simulations illustrate the effectiveness of executing attitude control while maintaining the relative motion, and higher control accuracy can be achieved by using the proposed neural-based switching control scheme than using only adaptive sliding mode controller.

Multistability in the lactose utilization network of Escherichia coli

NASA Astrophysics Data System (ADS)

Ozbudak, Ertugrul M.; Thattai, Mukund; Lim, Han N.; Shraiman, Boris I.; van Oudenaarden, Alexander

2004-02-01

Multistability, the capacity to achieve multiple internal states in response to a single set of external inputs, is the defining characteristic of a switch. Biological switches are essential for the determination of cell fate in multicellular organisms, the regulation of cell-cycle oscillations during mitosis and the maintenance of epigenetic traits in microbes. The multistability of several natural and synthetic systems has been attributed to positive feedback loops in their regulatory networks. However, feedback alone does not guarantee multistability. The phase diagram of a multistable system, a concise description of internal states as key parameters are varied, reveals the conditions required to produce a functional switch. Here we present the phase diagram of the bistable lactose utilization network of Escherichia coli. We use this phase diagram, coupled with a mathematical model of the network, to quantitatively investigate processes such as sugar uptake and transcriptional regulation in vivo. We then show how the hysteretic response of the wild-type system can be converted to an ultrasensitive graded response. The phase diagram thus serves as a sensitive probe of molecular interactions and as a powerful tool for rational network design.

Power converter

NASA Technical Reports Server (NTRS)

Black, J. M. (Inventor)

1981-01-01

A dc-to-dc converter employs four transistor switches in a bridge to chop dc power from a source, and a voltage multiplying diode rectifying ladder network to rectify and filter the chopped dc power for delivery to a load. The bridge switches are cross coupled in order for diagonally opposite pairs to turn on and off together using RC networks for the cross coupling to achieve the mode of operation of a free running multivibrator, and the diode rectifying ladder is configured to operate in a push-pull mode driven from opposite sides of the multivibrator outputs of the ridge switches. The four transistor switches provide a square-wave output voltage which as a peak-to-peak amplitude that is twice the input dc voltage, and is thus useful as a dc-to-ac inverter.

On-chip switch for reconfigurable mode-multiplexing optical network.

PubMed

Sun, Chunlei; Yu, Yu; Chen, Guanyu; Zhang, Xinliang

2016-09-19

The switching and routing is essential for an advanced and reconfigurable optical network, and great efforts have been done for traditional single-mode system. We propose and demonstrate an on-chip switch compatible with mode-division multiplexing system. By controlling the induced phase difference, the functionalities of dynamically routing data channels can be achieved. The proposed switch is experimentally demonstrated with low insertion loss of ~1 dB and high extinction ratio of ~20 dB over the C-band for OFF-ON switchover. For further demonstration, the non-return-to-zero on-off keying signals at 10 Gb/s carried on the two spatial modes are successfully processed. Open and clear eye diagrams can be observed and the bit error rate measurements indicate a good data routing performance.

Cell-Type–Specific Transcriptional Profiles of the Dimorphic Pathogen Penicillium marneffei Reflect Distinct Reproductive, Morphological, and Environmental Demands

PubMed Central

Pasricha, Shivani; Payne, Michael; Canovas, David; Pase, Luke; Ngaosuwankul, Nathamon; Beard, Sally; Oshlack, Alicia; Smyth, Gordon K.; Chaiyaroj, Sansanee C.; Boyce, Kylie J.; Andrianopoulos, Alex

2013-01-01

Penicillium marneffei is an opportunistic human pathogen endemic to Southeast Asia. At 25° P. marneffei grows in a filamentous hyphal form and can undergo asexual development (conidiation) to produce spores (conidia), the infectious agent. At 37° P. marneffei grows in the pathogenic yeast cell form that replicates by fission. Switching between these growth forms, known as dimorphic switching, is dependent on temperature. To understand the process of dimorphic switching and the physiological capacity of the different cell types, two microarray-based profiling experiments covering approximately 42% of the genome were performed. The first experiment compared cells from the hyphal, yeast, and conidiation phases to identify “phase or cell-state–specific” gene expression. The second experiment examined gene expression during the dimorphic switch from one morphological state to another. The data identified a variety of differentially expressed genes that have been organized into metabolic clusters based on predicted function and expression patterns. In particular, C-14 sterol reductase–encoding gene ergM of the ergosterol biosynthesis pathway showed high-level expression throughout yeast morphogenesis compared to hyphal. Deletion of ergM resulted in severe growth defects with increased sensitivity to azole-type antifungal agents but not amphotericin B. The data defined gene classes based on spatio-temporal expression such as those expressed early in the dimorphic switch but not in the terminal cell types and those expressed late. Such classifications have been helpful in linking a given gene of interest to its expression pattern throughout the P. marneffei dimorphic life cycle and its likely role in pathogenicity. PMID:24062530

47 CFR 51.5 - Terms and definitions.

Code of Federal Regulations, 2014 CFR

2014-10-01

.... The Communications Act of 1934, as amended. Advanced intelligent network. Advanced intelligent network is a telecommunications network architecture in which call processing, call routing, and network... carrier's network. Advanced services. The term “advanced services” is defined as high speed, switched...

Switched-beam radiometer front-end network analysis

NASA Technical Reports Server (NTRS)

Trew, R. J.; Bilbro, G. L.

1994-01-01

The noise figure performance of various delay-line networks fabricated from microstrip lines with varying number of elements was investigated using a computer simulation. The effects of resistive losses in both the transmission lines and power combiners were considered. In general, it is found that an optimum number of elements exists, depending upon the resistive losses present in the network. Small resistive losses are found to have a significant degrading effect upon the noise figure performance of the array. Extreme stability in switching characteristics is necessary to minimize the nondeterministic noise of the array. For example, it is found that a 6 percent tolerance on the delay-line lengths will produce a 0.2 db uncertainty in the noise figure which translates into a 13.67 K temperature uncertainty generated by the network. If the tolerance can be held to 2 percent, the uncertainty in noise figure and noise temperature will be 0.025 db and 1.67 K, respectively. Three phase shift networks fabricated using a commercially available PIN diode switch were investigated. Loaded-line phase shifters are found to have desirable RF and noise characteristics and are attractive components for use in phased-array networks.

Ordinary differential equations and Boolean networks in application to modelling of 6-mercaptopurine metabolism.

PubMed

Lavrova, Anastasia I; Postnikov, Eugene B; Zyubin, Andrey Yu; Babak, Svetlana V

2017-04-01

We consider two approaches to modelling the cell metabolism of 6-mercaptopurine, one of the important chemotherapy drugs used for treating acute lymphocytic leukaemia: kinetic ordinary differential equations, and Boolean networks supplied with one controlling node, which takes continual values. We analyse their interplay with respect to taking into account ATP concentration as a key parameter of switching between different pathways. It is shown that the Boolean networks, which allow avoiding the complexity of general kinetic modelling, preserve the possibility of reproducing the principal switching mechanism.

Energy Efficient, Cross-Layer Enabled, Dynamic Aggregation Networks for Next Generation Internet

NASA Astrophysics Data System (ADS)

Wang, Michael S.

Today, the Internet traffic is growing at a near exponential rate, driven predominately by data center-based applications and Internet-of-Things services. This fast-paced growth in Internet traffic calls into question the ability of the existing optical network infrastructure to support this continued growth. The overall optical networking equipment efficiency has not been able to keep up with the traffic growth, creating a energy gap that makes energy and cost expenditures scale linearly with the traffic growth. The implication of this energy gap is that it is infeasible to continue using existing networking equipment to meet the growing bandwidth demand. A redesign of the optical networking platform is needed. The focus of this dissertation is on the design and implementation of energy efficient, cross-layer enabled, dynamic optical networking platforms, which is a promising approach to address the exponentially growing Internet bandwidth demand. Chapter 1 explains the motivation for this work by detailing the huge Internet traffic growth and the unsustainable energy growth of today's networking equipment. Chapter 2 describes the challenges and objectives of enabling agile, dynamic optical networking platforms and the vision of the Center for Integrated Access Networks (CIAN) to realize these objectives; the research objectives of this dissertation and the large body of related work in this field is also summarized. Chapter 3 details the design and implementation of dynamic networking platforms that support wavelength switching granularity. The main contribution of this work involves the experimental validation of deep cross-layer communication across the optical performance monitoring (OPM), data, and control planes. The first experiment shows QoS-aware video streaming over a metro-scale test-bed through optical power monitoring of the transmission wavelength and cross-layer feedback control of the power level. The second experiment extends the performance monitoring capabilities to include real-time monitoring of OSNR and polarization mode dispersion (PMD) to enable dynamic wavelength switching and selective restoration. Chapter 4 explains the author?s contributions in designing dynamic networking at the sub-wavelength switching granularity, which can provide greater network efficiency due to its finer granularity. To support dynamic switching, regeneration, adding/dropping, and control decisions on each individual packet, the cross-layer enabled node architecture is enhanced with a FPGA controller that brings much more precise timing and control to the switching, OPM, and control planes. Furthermore, QoS-aware packet protection and dynamic switching, dropping, and regeneration functionalities were experimentally demonstrated in a multi-node network. Chapter 5 describes a technique to perform optical grooming, a process of optically combining multiple incoming data streams into a single data stream, which can simultaneously achieve greater bandwidth utilization and increased spectral efficiency. In addition, an experimental demonstration highlighting a fully functioning multi-node, agile optical networking platform is detailed. Finally, a summary and discussion of future work is provided in Chapter 6. The future of the Internet is very exciting, filled with not-yet-invented applications and services driven by cloud computing and Internet-of-Things. The author is cautiously optimistic that agile, dynamically reconfigurable optical networking is the solution to realizing this future.

Experimental demonstration of software defined data center optical networks with Tbps end-to-end tunability

NASA Astrophysics Data System (ADS)

Zhao, Yongli; Zhang, Jie; Ji, Yuefeng; Li, Hui; Wang, Huitao; Ge, Chao

2015-10-01

The end-to-end tunability is important to provision elastic channel for the burst traffic of data center optical networks. Then, how to complete the end-to-end tunability based on elastic optical networks? Software defined networking (SDN) based end-to-end tunability solution is proposed for software defined data center optical networks, and the protocol extension and implementation procedure are designed accordingly. For the first time, the flexible grid all optical networks with Tbps end-to-end tunable transport and switch system have been online demonstrated for data center interconnection, which are controlled by OpenDayLight (ODL) based controller. The performance of the end-to-end tunable transport and switch system has been evaluated with wavelength number tuning, bit rate tuning, and transmit power tuning procedure.

A robust low-rate coding scheme for packet video

NASA Technical Reports Server (NTRS)

Chen, Y. C.; Sayood, Khalid; Nelson, D. J.; Arikan, E. (Editor)

1991-01-01

Due to the rapidly evolving field of image processing and networking, video information promises to be an important part of telecommunication systems. Although up to now video transmission has been transported mainly over circuit-switched networks, it is likely that packet-switched networks will dominate the communication world in the near future. Asynchronous transfer mode (ATM) techniques in broadband-ISDN can provide a flexible, independent and high performance environment for video communication. For this paper, the network simulator was used only as a channel in this simulation. Mixture blocking coding with progressive transmission (MBCPT) has been investigated for use over packet networks and has been found to provide high compression rate with good visual performance, robustness to packet loss, tractable integration with network mechanics and simplicity in parallel implementation.

Age-associated Cognitive Decline: Insights into Molecular Switches and Recovery Avenues.

PubMed

Konar, Arpita; Singh, Padmanabh; Thakur, Mahendra K

2016-03-01

Age-associated cognitive decline is an inevitable phenomenon that predisposes individuals for neurological and psychiatric disorders eventually affecting the quality of life. Scientists have endeavored to identify the key molecular switches that drive cognitive decline with advancing age. These newly identified molecules are then targeted as recovery of cognitive aging and related disorders. Cognitive decline during aging is multi-factorial and amongst several factors influencing this trajectory, gene expression changes are pivotal. Identifying these genes would elucidate the neurobiological underpinnings as well as offer clues that make certain individuals resilient to withstand the inevitable age-related deteriorations. Our laboratory has focused on this aspect and investigated a wide spectrum of genes involved in crucial brain functions that attribute to senescence induced cognitive deficits. We have recently identified master switches in the epigenome regulating gene expression alteration during brain aging. Interestingly, these factors when manipulated by chemical or genetic strategies successfully reverse the age-related cognitive impairments. In the present article, we review findings from our laboratory and others combined with supporting literary evidences on molecular switches of brain aging and their potential as recovery targets.

When global rule reversal meets local task switching: The neural mechanisms of coordinated behavioral adaptation to instructed multi-level demand changes.

PubMed

Shi, Yiquan; Wolfensteller, Uta; Schubert, Torsten; Ruge, Hannes

2018-02-01

Cognitive flexibility is essential to cope with changing task demands and often it is necessary to adapt to combined changes in a coordinated manner. The present fMRI study examined how the brain implements such multi-level adaptation processes. Specifically, on a "local," hierarchically lower level, switching between two tasks was required across trials while the rules of each task remained unchanged for blocks of trials. On a "global" level regarding blocks of twelve trials, the task rules could reverse or remain the same. The current task was cued at the start of each trial while the current task rules were instructed before the start of a new block. We found that partly overlapping and partly segregated neural networks play different roles when coping with the combination of global rule reversal and local task switching. The fronto-parietal control network (FPN) supported the encoding of reversed rules at the time of explicit rule instruction. The same regions subsequently supported local task switching processes during actual implementation trials, irrespective of rule reversal condition. By contrast, a cortico-striatal network (CSN) including supplementary motor area and putamen was increasingly engaged across implementation trials and more so for rule reversal than for nonreversal blocks, irrespective of task switching condition. Together, these findings suggest that the brain accomplishes the coordinated adaptation to multi-level demand changes by distributing processing resources either across time (FPN for reversed rule encoding and later for task switching) or across regions (CSN for reversed rule implementation and FPN for concurrent task switching). © 2017 Wiley Periodicals, Inc.

Single molecules can operate as primitive biological sensors, switches and oscillators.

PubMed

Hernansaiz-Ballesteros, Rosa D; Cardelli, Luca; Csikász-Nagy, Attila

2018-06-18

Switch-like and oscillatory dynamical systems are widely observed in biology. We investigate the simplest biological switch that is composed of a single molecule that can be autocatalytically converted between two opposing activity forms. We test how this simple network can keep its switching behaviour under perturbations in the system. We show that this molecule can work as a robust bistable system, even for alterations in the reactions that drive the switching between various conformations. We propose that this single molecule system could work as a primitive biological sensor and show by steady state analysis of a mathematical model of the system that it could switch between possible states for changes in environmental signals. Particularly, we show that a single molecule phosphorylation-dephosphorylation switch could work as a nucleotide or energy sensor. We also notice that a given set of reductions in the reaction network can lead to the emergence of oscillatory behaviour. We propose that evolution could have converted this switch into a single molecule oscillator, which could have been used as a primitive timekeeper. We discuss how the structure of the simplest known circadian clock regulatory system, found in cyanobacteria, resembles the proposed single molecule oscillator. Besides, we speculate if such minimal systems could have existed in an RNA world.

Layer-switching cost and optimality in information spreading on multiplex networks

PubMed Central

Min, Byungjoon; Gwak, Sang-Hwan; Lee, Nanoom; Goh, K. -I.

2016-01-01

We study a model of information spreading on multiplex networks, in which agents interact through multiple interaction channels (layers), say online vs. offline communication layers, subject to layer-switching cost for transmissions across different interaction layers. The model is characterized by the layer-wise path-dependent transmissibility over a contact, that is dynamically determined dependently on both incoming and outgoing transmission layers. We formulate an analytical framework to deal with such path-dependent transmissibility and demonstrate the nontrivial interplay between the multiplexity and spreading dynamics, including optimality. It is shown that the epidemic threshold and prevalence respond to the layer-switching cost non-monotonically and that the optimal conditions can change in abrupt non-analytic ways, depending also on the densities of network layers and the type of seed infections. Our results elucidate the essential role of multiplexity that its explicit consideration should be crucial for realistic modeling and prediction of spreading phenomena on multiplex social networks in an era of ever-diversifying social interaction layers. PMID:26887527

Time-varying multiplex network: Intralayer and interlayer synchronization

NASA Astrophysics Data System (ADS)

Rakshit, Sarbendu; Majhi, Soumen; Bera, Bidesh K.; Sinha, Sudeshna; Ghosh, Dibakar

2017-12-01

A large class of engineered and natural systems, ranging from transportation networks to neuronal networks, are best represented by multiplex network architectures, namely a network composed of two or more different layers where the mutual interaction in each layer may differ from other layers. Here we consider a multiplex network where the intralayer coupling interactions are switched stochastically with a characteristic frequency. We explore the intralayer and interlayer synchronization of such a time-varying multiplex network. We find that the analytically derived necessary condition for intralayer and interlayer synchronization, obtained by the master stability function approach, is in excellent agreement with our numerical results. Interestingly, we clearly find that the higher frequency of switching links in the layers enhances both intralayer and interlayer synchrony, yielding larger windows of synchronization. Further, we quantify the resilience of synchronous states against random perturbations, using a global stability measure based on the concept of basin stability, and this reveals that intralayer coupling strength is most crucial for determining both intralayer and interlayer synchrony. Lastly, we investigate the robustness of interlayer synchronization against a progressive demultiplexing of the multiplex structure, and we find that for rapid switching of intralayer links, the interlayer synchronization persists even when a large number of interlayer nodes are disconnected.

Time-varying multiplex network: Intralayer and interlayer synchronization.

PubMed

Rakshit, Sarbendu; Majhi, Soumen; Bera, Bidesh K; Sinha, Sudeshna; Ghosh, Dibakar

2017-12-01

A large class of engineered and natural systems, ranging from transportation networks to neuronal networks, are best represented by multiplex network architectures, namely a network composed of two or more different layers where the mutual interaction in each layer may differ from other layers. Here we consider a multiplex network where the intralayer coupling interactions are switched stochastically with a characteristic frequency. We explore the intralayer and interlayer synchronization of such a time-varying multiplex network. We find that the analytically derived necessary condition for intralayer and interlayer synchronization, obtained by the master stability function approach, is in excellent agreement with our numerical results. Interestingly, we clearly find that the higher frequency of switching links in the layers enhances both intralayer and interlayer synchrony, yielding larger windows of synchronization. Further, we quantify the resilience of synchronous states against random perturbations, using a global stability measure based on the concept of basin stability, and this reveals that intralayer coupling strength is most crucial for determining both intralayer and interlayer synchrony. Lastly, we investigate the robustness of interlayer synchronization against a progressive demultiplexing of the multiplex structure, and we find that for rapid switching of intralayer links, the interlayer synchronization persists even when a large number of interlayer nodes are disconnected.

A fast, robust and tunable synthetic gene oscillator.

PubMed

Stricker, Jesse; Cookson, Scott; Bennett, Matthew R; Mather, William H; Tsimring, Lev S; Hasty, Jeff

2008-11-27

One defining goal of synthetic biology is the development of engineering-based approaches that enable the construction of gene-regulatory networks according to 'design specifications' generated from computational modelling. This approach provides a systematic framework for exploring how a given regulatory network generates a particular phenotypic behaviour. Several fundamental gene circuits have been developed using this approach, including toggle switches and oscillators, and these have been applied in new contexts such as triggered biofilm development and cellular population control. Here we describe an engineered genetic oscillator in Escherichia coli that is fast, robust and persistent, with tunable oscillatory periods as fast as 13 min. The oscillator was designed using a previously modelled network architecture comprising linked positive and negative feedback loops. Using a microfluidic platform tailored for single-cell microscopy, we precisely control environmental conditions and monitor oscillations in individual cells through multiple cycles. Experiments reveal remarkable robustness and persistence of oscillations in the designed circuit; almost every cell exhibited large-amplitude fluorescence oscillations throughout observation runs. The oscillatory period can be tuned by altering inducer levels, temperature and the media source. Computational modelling demonstrates that the key design principle for constructing a robust oscillator is a time delay in the negative feedback loop, which can mechanistically arise from the cascade of cellular processes involved in forming a functional transcription factor. The positive feedback loop increases the robustness of the oscillations and allows for greater tunability. Examination of our refined model suggested the existence of a simplified oscillator design without positive feedback, and we construct an oscillator strain confirming this computational prediction.

76 FR 62431 - Notice of Issuance of Final Determination Concerning Certain Ethernet Switches

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-07

... importing 7 Series Ethernet switches assembled in China. The switches are designed to interconnect servers... country of origin of Arista's 7048, 7050, 7100, 7124, and 7500 series (``7 Series'') local area network..., packaged, and prepared for shipping. Arista's EOS TM (Extensible Operating System) software is designed to...

High-resolution mapping of bifurcations in nonlinear biochemical circuits

NASA Astrophysics Data System (ADS)

Genot, A. J.; Baccouche, A.; Sieskind, R.; Aubert-Kato, N.; Bredeche, N.; Bartolo, J. F.; Taly, V.; Fujii, T.; Rondelez, Y.

2016-08-01

Analog molecular circuits can exploit the nonlinear nature of biochemical reaction networks to compute low-precision outputs with fewer resources than digital circuits. This analog computation is similar to that employed by gene-regulation networks. Although digital systems have a tractable link between structure and function, the nonlinear and continuous nature of analog circuits yields an intricate functional landscape, which makes their design counter-intuitive, their characterization laborious and their analysis delicate. Here, using droplet-based microfluidics, we map with high resolution and dimensionality the bifurcation diagrams of two synthetic, out-of-equilibrium and nonlinear programs: a bistable DNA switch and a predator-prey DNA oscillator. The diagrams delineate where function is optimal, dynamics bifurcates and models fail. Inverse problem solving on these large-scale data sets indicates interference from enzymatic coupling. Additionally, data mining exposes the presence of rare, stochastically bursting oscillators near deterministic bifurcations.

Designing Secure Library Networks.

ERIC Educational Resources Information Center

Breeding, Michael

1997-01-01

Focuses on designing a library network to maximize security. Discusses UNIX and file servers; connectivity to campus, corporate networks and the Internet; separation of staff from public servers; controlling traffic; the threat of network sniffers; hubs that eliminate eavesdropping; dividing the network into subnets; Switched Ethernet;…

Circulating current battery heater

DOEpatents

Ashtiani, Cyrus N.; Stuart, Thomas A.

2001-01-01

A circuit for heating energy storage devices such as batteries is provided. The circuit includes a pair of switches connected in a half-bridge configuration. Unidirectional current conduction devices are connected in parallel with each switch. A series resonant element for storing energy is connected from the energy storage device to the pair of switches. An energy storage device for intermediate storage of energy is connected in a loop with the series resonant element and one of the switches. The energy storage device which is being heated is connected in a loop with the series resonant element and the other switch. Energy from the heated energy storage device is transferred to the switched network and then recirculated back to the battery. The flow of energy through the battery causes internal power dissipation due to electrical to chemical conversion inefficiencies. The dissipated power causes the internal temperature of the battery to increase. Higher internal temperatures expand the cold temperature operating range and energy capacity utilization of the battery. As disclosed, either fixed frequency or variable frequency modulation schemes may be used to control the network.

All-optical switch consisting of two-stage interferometers controlled by using saturable absorption of monolayer graphene.

PubMed

Oya, Masayuki; Kishikawa, Hiroki; Goto, Nobuo; Yanagiya, Shin-ichiro

2012-11-19

At routing nodes in future photonic networks, pico-second switching will be a key function. We propose an all-optical switch consisting of two-stage Mach-Zehnder interferometers, whose arms contain graphene saturable absorption films. Optical amplitudes along the interferometers are controlled to perform switching between two output ports instead of phase control used in conventional switches. Since only absorption is used for realizing complete switching, insertion loss of 10.2 dB is accompanied in switching. Picosecond response can be expected because of the fast response of saturable absorption of graphene. The switching characteristics are theoretically analyzed and numerically simulated by the finite-difference beam propagation method (FD-BPM).

Study on multiple-hops performance of MOOC sequences-based optical labels for OPS networks

NASA Astrophysics Data System (ADS)

Zhang, Chongfu; Qiu, Kun; Ma, Chunli

2009-11-01

In this paper, we utilize a new study method that is under independent case of multiple optical orthogonal codes to derive the probability function of MOOCS-OPS networks, discuss the performance characteristics for a variety of parameters, and compare some characteristics of the system employed by single optical orthogonal code or multiple optical orthogonal codes sequences-based optical labels. The performance of the system is also calculated, and our results verify that the method is effective. Additionally it is found that performance of MOOCS-OPS networks would, negatively, be worsened, compared with single optical orthogonal code-based optical label for optical packet switching (SOOC-OPS); however, MOOCS-OPS networks can greatly enlarge the scalability of optical packet switching networks.

Turning the gene tap off; implications of regulating gene expression for cancer therapeutics

PubMed Central

Curtin, James F.; Candolfi, Marianela; Xiong, Weidong; Lowenstein, Pedro R.; Castro, Maria G.

2008-01-01

Cancer poses a tremendous therapeutic challenge worldwide, highlighting the critical need for developing novel therapeutics. A promising cancer treatment modality is gene therapy, which is a form of molecular medicine designed to introduce into target cells genetic material with therapeutic intent. Anticancer gene therapy strategies currently used in preclinical models, and in some cases in the clinic, include proapoptotic genes, oncolytic/replicative vectors, conditional cytotoxic approaches, inhibition of angiogenesis, inhibition of growth factor signaling, inactivation of oncogenes, inhibition of tumor invasion and stimulation of the immune system. The translation of these novel therapeutic modalities from the preclinical setting to the clinic has been driven by encouraging preclinical efficacy data and advances in gene delivery technologies. One area of intense research involves the ability to accurately regulate the levels of therapeutic gene expression to achieve enhanced efficacy and provide the capability to switch gene expression off completely if adverse side effects should arise. This feature could also be implemented to switch gene expression off when a successful therapeutic outcome ensues. Here, we will review recent developments related to the engineering of transcriptional switches within gene delivery systems, which could be implemented in clinical gene therapy applications directed at the treatment of cancer. PMID:18347132

Uncovering the mechanisms of Caenorhabditis elegans ageing from global quantification of the underlying landscape.

PubMed

Zhao, Lei; Wang, Jin

2016-11-01

Recent studies on Caenorhabditis elegans reveal that gene manipulations can extend its lifespan several fold. However, how the genes work together to determine longevity is still an open question. Here we construct a gene regulatory network for worm ageing and quantify its underlying potential and flux landscape. We found ageing and rejuvenation states can emerge as basins of attraction at certain gene expression levels. The system state can switch from one attractor to another driven by the intrinsic or external perturbations through genetics or the environment. Furthermore, we simulated gene silencing experiments and found that the silencing of longevity-promoting or lifespan-limiting genes leads to ageing or rejuvenation domination, respectively. This indicates that the difference in depths between ageing and the rejuvenation attractor is highly correlated with worm longevity. We further uncovered some key genes and regulations which have a strong influence on landscape basin stability. A dynamic landscape model is proposed to describe the whole process of ageing: the ageing attractor dominates when senescence progresses. We also uncovered the oscillation dynamics, and a similar behaviour was observed in the long-lived creature Turritopsis dohrnii Our landscape theory provides a global and physical approach to explore the underlying mechanisms of ageing. © 2016 The Author(s).

Reconfigurable radio-over-fiber system based on optical switch and tunable filter

NASA Astrophysics Data System (ADS)

Li, Xiao; Yin, Rui; Ji, Wei; Sun, Kai; Zhang, Shicheng

2017-09-01

As the best candidate for wireless-access networks, radio-over-fiber (RoF) technology can carry a variety of business. It is necessary to provide differentiated services for different users, so the network needs to produce signals with different modulation formats and different frequencies. A reconfigurable RoF system based on a switch and tunable optical filter that can realize modulation format conversion and multiple frequency signal switching functions is designed. It has a good performance in terms of bit error rate and an eye diagram. The design can help to use radio frequency resources efficiently and make dynamic bandwidth resources controllable.

Binary synaptic connections based on memory switching in a-Si:H for artificial neural networks

NASA Technical Reports Server (NTRS)

Thakoor, A. P.; Lamb, J. L.; Moopenn, A.; Khanna, S. K.

1987-01-01

A scheme for nonvolatile associative electronic memory storage with high information storage density is proposed which is based on neural network models and which uses a matrix of two-terminal passive interconnections (synapses). It is noted that the massive parallelism in the architecture would require the ON state of a synaptic connection to be unusually weak (highly resistive). Memory switching using a-Si:H along with ballast resistors patterned from amorphous Ge-metal alloys is investigated for a binary programmable read only memory matrix. The fabrication of a 1600 synapse test array of uniform connection strengths and a-Si:H switching elements is discussed.

An agile high-capacity FDMA digital satellite network

NASA Astrophysics Data System (ADS)

Hawkins, R. B.; Johannes, V. I.; Lowell, R.

A centrally controlled digital transmission satellite network has been designed for High Speed Switched Digital Service (HSSDS), which uses both satellite and earth transmission facilities to provide point-to-point digital trunks on a reservation basis. HSSDS customers connect via 1.544 Mb/s loops to the nodes where switches are located, and the FDMA system employed offers 24 one-way 1.544 Mb/s trunks per satellite transponder.

Multigranular integrated services optical network

NASA Astrophysics Data System (ADS)

Yu, Oliver; Yin, Leping; Xu, Huan; Liao, Ming

2006-12-01

Based on all-optical switches without requiring fiber delay lines and optical-electrical-optical interfaces, the multigranular optical switching (MGOS) network integrates three transport services via unified core control to efficiently support bursty and stream traffic of subwavelength to multiwavelength bandwidth. Adaptive robust optical burst switching (AR-OBS) aggregates subwavelength burst traffic into asynchronous light-rate bursts, transported via slotted-time light paths established by fast two-way reservation with robust blocking recovery control. Multiwavelength optical switching (MW-OS) decomposes multiwavelength stream traffic into a group of timing-related light-rate streams, transported via a light-path group to meet end-to-end delay-variation requirements. Optical circuit switching (OCS) simply converts wavelength stream traffic from an electrical-rate into a light-rate stream. The MGOS network employs decoupled routing, wavelength, and time-slot assignment (RWTA) and novel group routing and wavelength assignment (GRWA) to select slotted-time light paths and light-path groups, respectively. The selected resources are reserved by the unified multigranular robust fast optical reservation protocol (MG-RFORP). Simulation results show that elastic traffic is efficiently supported via AR-OBS in terms of loss rate and wavelength utilization, while connection-oriented wavelength traffic is efficiently supported via wavelength-routed OCS in terms of connection blocking and wavelength utilization. The GRWA-tuning result for MW-OS is also shown.

Instant provisioning of wavelength service using quasi-circuit optical burst switching

NASA Astrophysics Data System (ADS)

Xie, Hongyi; Li, Yanhe; Zheng, Xiaoping; Zhang, Hanyi

2006-09-01

Due to the recent outstanding advancement of optical networking technology, pervasive Grid computing will be a feasible option in the near future. As Grid infrastructure, optical networks must be able to handle different Grid traffic patterns with various traffic characteristics as well as different QoS requirements. With current optical switching technology, optical circuit switching is suitable for data-intensive Grid applications while optical burst switching is suitable to submit small Grid jobs. However, there would be high bandwidth short-lived traffic in some emerging Grid applications such as multimedia editing. This kind of traffic couldn't be well supported by both OCS and conventional OBS because of considerable path setup delay and bandwidth waste in OCS and inherent loss in OBS. Quasi-Circuit OBS (QCOBS) is proposed in this paper to address this challenge, providing one-way reserved, nearly lossless, instant provisioned wavelength service in OBS networks. Simulation results show that QCOBS achieves lossless transmission at low and moderate loads, and very low loss probability at high loads with proper guard time configuration.

BTG interacts with retinoblastoma to control cell fate in Dictyostelium.

PubMed

Conte, Daniele; MacWilliams, Harry K; Ceccarelli, Adriano

2010-03-12

In the genesis of many tissues, a phase of cell proliferation is followed by cell cycle exit and terminal differentiation. The latter two processes overlap: genes involved in the cessation of growth may also be important in triggering differentiation. Though conceptually distinct, they are often causally related and functional interactions between the cell cycle machinery and cell fate control networks are fundamental to coordinate growth and differentiation. A switch from proliferation to differentiation may also be important in the life cycle of single-celled organisms, and genes which arose as regulators of microbial differentiation may be conserved in higher organisms. Studies in microorganisms may thus contribute to understanding the molecular links between cell cycle machinery and the determination of cell fate choice networks. Here we show that in the amoebozoan D. discoideum, an ortholog of the metazoan antiproliferative gene btg controls cell fate, and that this function is dependent on the presence of a second tumor suppressor ortholog, the retinoblastoma-like gene product. Specifically, we find that btg-overexpressing cells preferentially adopt a stalk cell (and, more particularly, an Anterior-Like Cell) fate. No btg-dependent preference for ALC fate is observed in cells in which the retinoblastoma-like gene has been genetically inactivated. Dictyostelium btg is the only example of non-metazoan member of the BTG family characterized so far, suggesting that a genetic interaction between btg and Rb predated the divergence between dictyostelids and metazoa. While the requirement for retinoblastoma function for BTG antiproliferative activity in metazoans is known, an interaction of these genes in the control of cell fate has not been previously documented. Involvement of a single pathway in the control of mutually exclusive processes may have relevant implication in the evolution of multicellularity.

Thiol-Based Redox Switches and Gene Regulation

PubMed Central

2011-01-01

Abstract Cysteine is notable among the universal, proteinogenic amino acids for its facile redox chemistry. Cysteine thiolates are readily modified by reactive oxygen species (ROS), reactive electrophilic species (RES), and reactive nitrogen species (RNS). Although thiol switches are commonly triggered by disulfide bond formation, they can also be controlled by S-thiolation, S-alkylation, or modification by RNS. Thiol-based switches are common in both prokaryotic and eukaryotic organisms and activate functions that detoxify reactive species and restore thiol homeostasis while repressing functions that would be deleterious if expressed under oxidizing conditions. Here, we provide an overview of the best-understood examples of thiol-based redox switches that affect gene expression. Intra- or intermolecular disulfide bond formation serves as a direct regulatory switch for several bacterial transcription factors (OxyR, OhrR/2-Cys, Spx, YodB, CrtJ, and CprK) and indirectly regulates others (the RsrA anti-σ factor and RegB sensory histidine kinase). In eukaryotes, thiol-based switches control the yeast Yap1p transcription factor, the Nrf2/Keap1 electrophile and oxidative stress response, and the Chlamydomonas NAB1 translational repressor. Collectively, these regulators reveal a remarkable range of chemical modifications exploited by Cys residues to effect changes in gene expression. Antioxid. Redox Signal. 14, 1049—1063. PMID:20626317

Optical implementation of (3, 3, 2) regular rectangular CC-Banyan optical network

NASA Astrophysics Data System (ADS)

Yang, Junbo; Su, Xianyu

2007-07-01

CC-Banyan network plays an important role in the optical interconnection network. Based on previous reports of (2, 2, 3) the CC-Banyan network, another rectangular-Banyan network, i.e. (3, 3, 2) rectangular CC-Banyan network, has been discussed. First, according to its construction principle, the topological graph and the routing rule of (3, 3, 2) rectangular CC-Banyan network have been proposed. Then, the optically experimental setup of (3, 3, 2) rectangular CC-Banyan network has been designed and achieved. Each stage of node switch consists of phase spatial light modulator (PSLM) and polarizing beam-splitter (PBS), and fiber has been used to perform connection between adjacent stages. PBS features that s-component (perpendicular to the incident plane) of the incident light beam is reflected, and p-component (parallel to the incident plane) passes through it. According to switching logic, under the control of external electrical signals, PSLM functions to control routing paths of the signal beams, i.e. the polarization of each optical signal is rotated or not rotated 90° by a programmable PSLM. Finally, the discussion and analysis show that the experimental setup designed here can realize many functions such as optical signal switch and permutation. It has advantages of large number of input/output-ports, compact in structure, and low energy loss. Hence, the experimental setup can be used in optical communication and optical information processing.

GMPLS-based control plane for optical networks: early implementation experience

NASA Astrophysics Data System (ADS)

Liu, Hang; Pendarakis, Dimitrios; Komaee, Nooshin; Saha, Debanjan

2002-07-01

Generalized Multi-Protocol Label Switching (GMPLS) extends MPLS signaling and Internet routing protocols to provide a scalable, interoperable, distributed control plane, which is applicable to multiple network technologies such as optical cross connects (OXCs), photonic switches, IP routers, ATM switches, SONET and DWDM systems. It is intended to facilitate automatic service provisioning and dynamic neighbor and topology discovery across multi-vendor intelligent transport networks, as well as their clients. Efforts to standardize such a distributed common control plane have reached various stages in several bodies such as the IETF, ITU and OIF. This paper describes the design considerations and architecture of a GMPLS-based control plane that we have prototyped for core optical networks. Functional components of GMPLS signaling and routing are integrated in this architecture with an application layer controller module. Various requirements including bandwidth, network protection and survivability, traffic engineering, optimal utilization of network resources, and etc. are taken into consideration during path computation and provisioning. Initial experiments with our prototype demonstrate the feasibility and main benefits of GMPLS as a distributed control plane for core optical networks. In addition to such feasibility results, actual adoption and deployment of GMPLS as a common control plane for intelligent transport networks will depend on the successful completion of relevant standardization activities, extensive interoperability testing as well as the strengthening of appropriate business drivers.

Adaptive Neural Networks Prescribed Performance Control Design for Switched Interconnected Uncertain Nonlinear Systems.

PubMed

Li, Yongming; Tong, Shaocheng

2017-06-28

In this paper, an adaptive neural networks (NNs)-based decentralized control scheme with the prescribed performance is proposed for uncertain switched nonstrict-feedback interconnected nonlinear systems. It is assumed that nonlinear interconnected terms and nonlinear functions of the concerned systems are unknown, and also the switching signals are unknown and arbitrary. A linear state estimator is constructed to solve the problem of unmeasured states. The NNs are employed to approximate unknown interconnected terms and nonlinear functions. A new output feedback decentralized control scheme is developed by using the adaptive backstepping design technique. The control design problem of nonlinear interconnected switched systems with unknown switching signals can be solved by the proposed scheme, and only a tuning parameter is needed for each subsystem. The proposed scheme can ensure that all variables of the control systems are semi-globally uniformly ultimately bounded and the tracking errors converge to a small residual set with the prescribed performance bound. The effectiveness of the proposed control approach is verified by some simulation results.

Switching-type regulator circuit has increased efficiency

NASA Technical Reports Server (NTRS)

Clapp, W. M.

1967-01-01

Switching series regulator circuit uses an inductive network to feed most of the current applied to the control circuit to the load. This circuit eliminates resistive losses and the need for heat sinks.

Compound semiconductor optical waveguide switch

DOEpatents

Spahn, Olga B.; Sullivan, Charles T.; Garcia, Ernest J.

2003-06-10

An optical waveguide switch is disclosed which is formed from III-V compound semiconductors and which has a moveable optical waveguide with a cantilevered portion that can be bent laterally by an integral electrostatic actuator to route an optical signal (i.e. light) between the moveable optical waveguide and one of a plurality of fixed optical waveguides. A plurality of optical waveguide switches can be formed on a common substrate and interconnected to form an optical switching network.

Solid state switch

DOEpatents

Merritt, Bernard T.; Dreifuerst, Gary R.

1994-01-01

A solid state switch, with reverse conducting thyristors, is designed to operate at 20 kV hold-off voltage, 1500 A peak, 1.0 .mu.s pulsewidth, and 4500 pps, to replace thyratrons. The solid state switch is more reliable, more economical, and more easily repaired. The switch includes a stack of circuit card assemblies, a magnetic assist and a trigger chassis. Each circuit card assembly contains a reverse conducting thyristor, a resistor capacitor network, and triggering circuitry.

Patent Abstract Digest. Volume II.

DTIC Science & Technology

1981-03-01

THE AIR FORCE SYSTEMS COMMAND United States Patent 191 [J 4,190,815 Albanese [45] Feb. 26, 1980 [541 HIGH POWER HYBRID SWITCH 3,659.227 4/1972...R.F. power are controlled and switched [22] Filed: Mar. 9, 1978 by means of a hybrid switching network that employs [511 nt. C. 2...broadband quadrature 3dB hybrid . Switching is accomplished by selectively inserting a [561 Referenees Cited 180 phase shift means into the lower power

A Forward Genetic Approach in Chlamydomonas reinhardtii as a Strategy for Exploring Starch Catabolism

PubMed Central

Duchêne, Thierry; Cogez, Virginie; Cousin, Charlotte; Peltier, Gilles; Ball, Steven G.; Dauvillée, David

2013-01-01

A screen was recently developed to study the mobilization of starch in the unicellular green alga Chlamydomonas reinhardtii. This screen relies on starch synthesis accumulation during nitrogen starvation followed by the supply of nitrogen and the switch to darkness. Hence multiple regulatory networks including those of nutrient starvation, cell cycle control and light to dark transitions are likely to impact the recovery of mutant candidates. In this paper we monitor the specificity of this mutant screen by characterizing the nature of the genes disrupted in the selected mutants. We show that one third of the mutants consisted of strains mutated in genes previously reported to be of paramount importance in starch catabolism such as those encoding β-amylases, the maltose export protein, and branching enzyme I. The other mutants were defective for previously uncharacterized functions some of which are likely to define novel proteins affecting starch mobilization in green algae. PMID:24019981

Combinatorial Control of Light Induced Chromatin Remodeling and Gene Activation in Neurospora

PubMed Central

Sancar, Cigdem; Ha, Nati; Yilmaz, Rüstem; Tesorero, Rafael; Fisher, Tamas; Brunner, Michael; Sancar, Gencer

2015-01-01

Light is an important environmental cue that affects physiology and development of Neurospora crassa. The light-sensing transcription factor (TF) WCC, which consists of the GATA-family TFs WC1 and WC2, is required for light-dependent transcription. SUB1, another GATA-family TF, is not a photoreceptor but has also been implicated in light-inducible gene expression. To assess regulation and organization of the network of light-inducible genes, we analyzed the roles of WCC and SUB1 in light-induced transcription and nucleosome remodeling. We show that SUB1 co-regulates a fraction of light-inducible genes together with the WCC. WCC induces nucleosome eviction at its binding sites. Chromatin remodeling is facilitated by SUB1 but SUB1 cannot activate light-inducible genes in the absence of WCC. We identified FF7, a TF with a putative O-acetyl transferase domain, as an interaction partner of SUB1 and show their cooperation in regulation of a fraction of light-inducible and a much larger number of non light-inducible genes. Our data suggest that WCC acts as a general switch for light-induced chromatin remodeling and gene expression. SUB1 and FF7 synergistically determine the extent of light-induction of target genes in common with WCC but have in addition a role in transcription regulation beyond light-induced gene expression. PMID:25822411

Evaluation of Two Statistical Methods Provides Insights into the Complex Patterns of Alternative Polyadenylation Site Switching

PubMed Central

Li, Jie; Li, Rui; You, Leiming; Xu, Anlong; Fu, Yonggui; Huang, Shengfeng

2015-01-01

Switching between different alternative polyadenylation (APA) sites plays an important role in the fine tuning of gene expression. New technologies for the execution of 3’-end enriched RNA-seq allow genome-wide detection of the genes that exhibit significant APA site switching between different samples. Here, we show that the independence test gives better results than the linear trend test in detecting APA site-switching events. Further examination suggests that the discrepancy between these two statistical methods arises from complex APA site-switching events that cannot be represented by a simple change of average 3’-UTR length. In theory, the linear trend test is only effective in detecting these simple changes. We classify the switching events into four switching patterns: two simple patterns (3’-UTR shortening and lengthening) and two complex patterns. By comparing the results of the two statistical methods, we show that complex patterns account for 1/4 of all observed switching events that happen between normal and cancerous human breast cell lines. Because simple and complex switching patterns may convey different biological meanings, they merit separate study. We therefore propose to combine both the independence test and the linear trend test in practice. First, the independence test should be used to detect APA site switching; second, the linear trend test should be invoked to identify simple switching events; and third, those complex switching events that pass independence testing but fail linear trend testing can be identified. PMID:25875641

ICC '86; Proceedings of the International Conference on Communications, Toronto, Canada, June 22-25, 1986, Conference Record. Volumes 1, 2, & 3

NASA Astrophysics Data System (ADS)

Papers are presented on ISDN, mobile radio systems and techniques for digital connectivity, centralized and distributed algorithms in computer networks, communications networks, quality assurance and impact on cost, adaptive filters in communications, the spread spectrum, signal processing, video communication techniques, and digital satellite services. Topics discussed include performance evaluation issues for integrated protocols, packet network operations, the computer network theory and multiple-access, microwave single sideband systems, switching architectures, fiber optic systems, wireless local communications, modulation, coding, and synchronization, remote switching, software quality, transmission, and expert systems in network operations. Consideration is given to wide area networks, image and speech processing, office communications application protocols, multimedia systems, customer-controlled network operations, digital radio systems, channel modeling and signal processing in digital communications, earth station/on-board modems, computer communications system performance evaluation, source encoding, compression, and quantization, and adaptive communications systems.

Negative regulatory loci coupling flagellin synthesis to flagellar assembly in Salmonella typhimurium.

PubMed Central

Gillen, K L; Hughes, K T

1991-01-01

The complex regulation of flagellin gene expression in Salmonella typhimurium was characterized in vivo by using lac transcriptional fusions to the two flagellin structural genes (fliC [H1] and fljB [H2]). Phase variation was measured as the rate of switching of flagellin gene expression. Switching frequencies varied from 1/500 per cell per generation to 1/10,000 per cell per generation depending on the particular insertion and the direction of switching. There is a 4- to 20-fold bias in favor of switching from the fljB(On) to the fljB(Off) orientation. Random Tn10dTc insertions were isolated which failed to express flagellin. While most of these insertions mapped to loci known to be required for flagellin expression, several new loci were identified. The presence of functional copies of all of the genes responsible for complete flagellar assembly, except the hook-associated proteins (flgK, flgL, and fliD gene products), were required for expression of the fliC or fljB flagellin genes. Two novel loci involved in negative regulation of fliC and fljB in fla mutant backgrounds were identified. One of these loci, designated the flgR locus, mapped to the flg operon at 23 min on the Salmonella linkage map. An flgR insertion mutation resulted in relief of repression of the fliC and fljB genes in all fla mutant backgrounds except for mutants in the positive regulatory loci (flhC, flhD, and fliA genes). PMID:1848842

A chemotactic signaling surface on CheY defined by suppressors of flagellar switch mutations.

PubMed Central

Roman, S J; Meyers, M; Volz, K; Matsumura, P

1992-01-01

CheY is the response regulator protein that interacts with the flagellar switch apparatus to modulate flagellar rotation during chemotactic signaling. CheY can be phosphorylated and dephosphorylated in vitro, and evidence indicates that CheY-P is the activated form that induces clockwise flagellar rotation, resulting in a tumble in the cell's swimming pattern. The flagellar switch apparatus is a complex macromolecular structure composed of at least three gene products, FliG, FliM, and FliN. Genetic analysis of Escherichia coli has identified fliG and fliM as genes in which mutations occur that allele specifically suppress cheY mutations, indicating interactions among these gene products. We have generated a class of cheY mutations selected for dominant suppression of fliG mutations. Interestingly, these cheY mutations dominantly suppressed both fliG and fliM mutations; this is consistent with the idea that the CheY protein interacts with both switch gene products during signaling. Biochemical characterization of wild-type and suppressor CheY proteins did not reveal altered phosphorylation properties or evidence for phosphorylation-dependent CheY multimerization. These data indicate that suppressor CheY proteins are specifically altered in the ability to transduce chemotactic signals to the switch at some point subsequent to phosphorylation. Physical mapping of suppressor amino acid substitutions on the crystal structure of CheY revealed a high degree of spatial clustering, suggesting that this region of CheY is a signaling surface that transduces chemotactic signals to the switch. Images PMID:1400175

A new scheduling algorithm to provide proportional QoS in optical burst switching networks

NASA Astrophysics Data System (ADS)

Tan, Wei; Luo, Yunhan; Wang, Sheng; Xu, Du; Pan, Yonghong; Li, Lemin

2005-02-01

A new scheduling algorithm, which aims to provide proportional and controllable QoS in terms of burst loss probability for OBS (optical burst switching) networks, is proposed on the basis of a summary of current QoS schemes in OBS. With simulations, performance analyses and comparisons are studied in detail. The results show that, in the proposed scheme, burst loss probabilities are proportional to the given factors and the control of QoS performance can be achieved with better performance. This scheme will be beneficial to the OBS network management and the tariff policy making.

Fully-elastic multi-granular network with space/frequency/time switching using multi-core fibres and programmable optical nodes.

PubMed

Amaya, N; Irfan, M; Zervas, G; Nejabati, R; Simeonidou, D; Sakaguchi, J; Klaus, W; Puttnam, B J; Miyazawa, T; Awaji, Y; Wada, N; Henning, I

2013-04-08

We present the first elastic, space division multiplexing, and multi-granular network based on two 7-core MCF links and four programmable optical nodes able to switch traffic utilising the space, frequency and time dimensions with over 6000-fold bandwidth granularity. Results show good end-to-end performance on all channels with power penalties between 0.75 dB and 3.7 dB.

Routing and wavelength assignment based on normalized resource and constraints for all-optical network

NASA Astrophysics Data System (ADS)

Joo, Seong-Soon; Nam, Hyun-Soon; Lim, Chang-Kyu

2003-08-01

With the rapid growth of the Optical Internet, high capacity pipes is finally destined to support end-to-end IP on the WDM optical network. Newly launched 2D MEMS optical switching module in the market supports that expectations of upcoming a transparent optical cross-connect in the network have encouraged the field applicable research on establishing real all-optical transparent network. To open up a customer-driven bandwidth services, design of the optical transport network becomes more challenging task in terms of optimal network resource usage. This paper presents a practical approach to finding a route and wavelength assignment for wavelength routed all-optical network, which has λ-plane OXC switches and wavelength converters, and supports that optical paths are randomly set up and released by dynamic wavelength provisioning to create bandwidth between end users with timescales on the order of seconds or milliseconds. We suggest three constraints to make the RWA problem become more practical one on deployment for wavelength routed all-optical network in network view: limitation on maximum hop of a route within bearable optical network impairments, limitation on minimum hops to travel before converting a wavelength, and limitation on calculation time to find all routes for connections requested at once. We design the NRCD (Normalized Resource and Constraints for All-Optical Network RWA Design) algorithm for the Tera OXC: network resource for a route is calculated by the number of internal switching paths established in each OXC nodes on the route, and is normalized by ratio of number of paths established and number of paths equipped in a node. We show that it fits for the RWA algorithm of the wavelength routed all-optical network through real experiments on the distributed objects platform.

All-optical routing and switching for three-dimensional photonic circuitry

PubMed Central

Keil, Robert; Heinrich, Matthias; Dreisow, Felix; Pertsch, Thomas; Tünnermann, Andreas; Nolte, Stefan; Christodoulides, Demetrios N.; Szameit, Alexander

2011-01-01

The ability to efficiently transmit and rapidly process huge amounts of data has become almost indispensable to our daily lives. It turned out that all-optical networks provide a very promising platform to deal with this task. Within such networks opto-optical switches, where light is directed by light, are a crucial building block for an effective operation. In this article, we present an experimental analysis of the routing and switching behaviour of light in two-dimensional evanescently coupled waveguide arrays of Y- and T-junction geometries directly inscribed into fused silica using ultrashort laser pulses. These systems have the fundamental advantage of supporting three-dimensional network topologies, thereby breaking the limitations on complexity associated with planar structures while maintaining a high dirigibility of the light. Our results show how such arrays can be used to control the flow of optical signals within integrated photonic circuits. PMID:22355612

Fault-tolerant onboard digital information switching and routing for communications satellites

NASA Technical Reports Server (NTRS)

Shalkhauser, Mary JO; Quintana, Jorge A.; Soni, Nitin J.; Kim, Heechul

1993-01-01

The NASA Lewis Research Center is developing an information-switching processor for future meshed very-small-aperture terminal (VSAT) communications satellites. The information-switching processor will switch and route baseband user data onboard the VSAT satellite to connect thousands of Earth terminals. Fault tolerance is a critical issue in developing information-switching processor circuitry that will provide and maintain reliable communications services. In parallel with the conceptual development of the meshed VSAT satellite network architecture, NASA designed and built a simple test bed for developing and demonstrating baseband switch architectures and fault-tolerance techniques. The meshed VSAT architecture and the switching demonstration test bed are described, and the initial switching architecture and the fault-tolerance techniques that were developed and tested are discussed.

Final Report for the project titled "Enabling Supernova Computations by Integrated Transport and Provisioning Methods Optimized for Dedicated Channels"

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malathi Veeraraghavan

2007-10-31

A high-speed optical circuit network is one that offers users rate-guaranteed connectivity between two endpoints, unlike today’s IP-routed Internet in which the rate available to a pair of users fluctuates based on the volume of competing traffic. This particular research project advanced our understanding of circuit networks in two ways. First, transport protocols were developed for circuit networks. In a circuit network, since bandwidth resources are reserved for each circuit on an end-to-end basis (much like how a person reserves a seat on every leg of a multi-segment flight), and the sender is limited to send at the rate ofmore » the circuit, there is no possibility of congestion during data transfer. Therefore, no congestion control functions are necessary in a transport protocol designed for circuits. However, error control and flow control are still required because bits can become errored due to noise and interference even on highly reliable optical links, and receivers can, due to multitasking or other reasons, not deplete the receive buffer fast enough to keep up with the sending rate (e.g., if the receiving host is multitasking between receiving a file transfer and some other computation). In this work, we developed two transport protocols for circuits, both of which are described below. Second, this project developed techniques for internetworking different types of connection-oriented networks, which are of two types: circuit-switched or packet-switched. In circuit-switched networks, multiplexing on links is “position based,” where “position” refers to the frequency, time slot, and port (fiber), while connection-oriented packet-switched networks use packet header information to demultiplex packets and switch them from node to node. The latter are commonly referred to as virtual circuit networks. Examples of circuit networks are time-division multiplexed Synchronous Optical Network/Synchronous Digital Hierarchy (SONET/SDH) and Wavelength Division Multiplexing (WDM) networks, while examples of virtual-circuit networks are MultiProtocol Label Switched (MPLS) networks and Ethernet Virtual Local Area Network (VLAN) networks. A series of new technologies have been developed to carry Ethernet VLAN tagged frames on SONET/SDH and WDM networks, such as Generic Framing Procedure (GFP) and ITU G.709, respectively. These technologies form the basis of our solution for connection-oriented internetworking. The benefit of developing such an architecture is that it allows different providers to choose different connection-oriented networking technologies for their networks, and yet be able to allow their customers to connect to those of other providers. As Metcalfe, the inventor of Ethernet, noted, the value of a network service grows exponentially with the number of endpoints to which any single endpoint can connect. Therefore internetworking solutions are key to commercial success. The technical effectiveness of our solutions was measured with proof-of-concept prototypes and experiments. These solutions were shown to be highly effective. Economic feasibility requires business case analyses that were beyond the scope of this project. The project results are beneficial to the public as they demonstrate the viability of simultaneously supporting different types of networks and data communication services much like the variety of services available for the transportation of people and goods. For example, Fedex service offers a deadline based delivery while the USPS offers basic package delivery service. Similarly, a circuit network can offer a deadline based delivery of a data file while the IP-routed network offers only basic delivery service with no guarantees. Two project Web sites, 13 publications, 7 software programs, 21 presentations resulted from this work. This report provides the complete list of publications, software programs and presentations. As for student education and training (human resources), this DOE project, along with an NSF project, jointly supported two postdoctoral fellowships, three PhDs, three Masters, and two undergraduate students. Specifically, two of the Masters students were directly funded on this DOE project.« less

Switch Transcripts in Immunoglobulin Class Switching

NASA Astrophysics Data System (ADS)

Lorenz, Matthias; Jung, Steffen; Radbruch, Andreas

1995-03-01

B cells can exchange gene segments for the constant region of the immunoglobulin heavy chain, altering the class and effector function of the antibodies that they produce. Class switching is directed to distinct classes by cytokines, which induce transcription of the targeted DNA sequences. These transcripts are processed, resulting in spliced "switch" transcripts. Switch recombination can be directed to immunoglobulin G1 (IgG1) by the heterologous human metallothionein II_A promoter in mutant mice. Induction of the structurally conserved, spliced switch transcripts is sufficient to target switch recombination to IgG1, whereas transcription alone is not.

Wavelength-tunable filter utilizing non-cyclic arrayed waveguide grating to create colorless, directionless, contentionless ROADMs

NASA Astrophysics Data System (ADS)

Niwa, Masaki; Takashina, Shoichi; Mori, Yojiro; Hasegawa, Hiroshi; Sato, Ken-ichi; Watanabe, Toshio

2015-01-01

With the continuous increase in Internet traffic, reconfigurable optical add-drop multiplexers (ROADMs) have been widely adopted in the core and metro core networks. Current ROADMs, however, allow only static operation. To realize future dynamic optical-network services, and to minimize any human intervention in network operation, the optical signal add/drop part should have colorless/directionless/contentionless (C/D/C) capabilities. This is possible with matrix switches or a combination of splitter-switches and optical tunable filters. The scale of the matrix switch increases with the square of the number of supported channels, and hence, the matrix-switch-based architecture is not suitable for creating future large-scale ROADMs. In contrast, the numbers of splitter ports, switches, and tunable filters increase linearly with the number of supported channels, and hence the tunable-filter-based architecture will support all future traffic. So far, we have succeeded in fabricating a compact tunable filter that consists of multi-stage cyclic arrayed-waveguide gratings (AWGs) and switches by using planar-lightwave-circuit (PLC) technologies. However, this multistage configuration suffers from large insertion loss and filter narrowing. Moreover, power-consuming temperature control is necessary since it is difficult to make cyclic AWGs athermal. We propose here novel tunable-filter architecture that sandwiches a single-stage non-cyclic athermal AWG having flatter-topped passbands between small-scale switches. With this configuration, the optical tunable filter attains low insertion loss, large passband bandwidths, low power consumption, compactness, and high cost-effectiveness. A prototype is monolithically fabricated with PLC technologies and its excellent performance is experimentally confirmed utilizing 80-channel 30-GBaud dual-polarization quadrature phase-shift-keying (QPSK) signals.

Implementation of remote monitoring and managing switches

NASA Astrophysics Data System (ADS)

Leng, Junmin; Fu, Guo

2010-12-01

In order to strengthen the safety performance of the network and provide the big convenience and efficiency for the operator and the manager, the system of remote monitoring and managing switches has been designed and achieved using the advanced network technology and present network resources. The fast speed Internet Protocol Cameras (FS IP Camera) is selected, which has 32-bit RSIC embedded processor and can support a number of protocols. An Optimal image compress algorithm Motion-JPEG is adopted so that high resolution images can be transmitted by narrow network bandwidth. The architecture of the whole monitoring and managing system is designed and implemented according to the current infrastructure of the network and switches. The control and administrative software is projected. The dynamical webpage Java Server Pages (JSP) development platform is utilized in the system. SQL (Structured Query Language) Server database is applied to save and access images information, network messages and users' data. The reliability and security of the system is further strengthened by the access control. The software in the system is made to be cross-platform so that multiple operating systems (UNIX, Linux and Windows operating systems) are supported. The application of the system can greatly reduce manpower cost, and can quickly find and solve problems.

IP voice over ATM satellite: experimental results over satellite channels

NASA Astrophysics Data System (ADS)

Saraf, Koroush A.; Butts, Norman P.

1999-01-01

IP telephony, a new technology to provide voice communication over traditional data networks, has the potential to revolutionize telephone communication within the modern enterprise. This innovation uses packetization techniques to carry voice conversations over IP networks. This packet switched technology promises new integrated services, and lower cost long-distance communication compared to traditional circuit switched telephone networks. Future satellites will need to carry IP traffic efficiently in order to stay competitive in servicing the global data- networking and global telephony infrastructure. However, the effects of Voice over IP over switched satellite channels have not been investigated in detail. To fully understand the effects of satellite channels on Voice over IP quality; several experiments were conducted at Lockheed Martin Telecommunications' Satellite Integration Lab. The result of those experiments along with suggested improvements for voice communication over satellite are presented in this document. First, a detailed introduction of IP telephony as a suitable technology for voice communication over future satellites is presented. This is followed by procedures for the experiments, along with results and strategies. In conclusion we hope that these capability demonstrations will alleviate any uncertainty regarding the applicability of this technology to satellite networks.

Impairments Computation for Routing Purposes in a Transparent-Access Optical Network Based on Optical CDMA and WDM

NASA Astrophysics Data System (ADS)

Musa, Ahmed

2016-06-01

Optical access networks are becoming more widespread and the use of multiple services might require a transparent optical network (TON). Multiplexing and privacy could benefit from the combination of wavelength division multiplexing (WDM) and optical coding (OC) and wavelength conversion in optical switches. The routing process needs to be cognizant of different resource types and characteristics such as fiber types, fiber linear impairments such as attenuation, dispersion, etc. as well as fiber nonlinear impairments such as four-wave mixing, cross-phase modulation, etc. Other types of impairments, generated by optical nodes or photonic switches, also affect the signal quality (Q) or the optical signal to noise ratio (OSNR), which is related to the bit error rate (BER). Therefore, both link and switch impairments must be addressed and somehow incorporated into the routing algorithm. However, it is not practical to fully integrate all photonic-specific attributes in the routing process. In this study, new routing parameters and constraints are defined that reflect the distinct characteristics of photonic networking. These constraints are applied to the design phase of TON and expressed as a cost or metric form that will be used in the network routing algorithm.

Chip-set for quality of service support in passive optical networks

NASA Astrophysics Data System (ADS)

Ringoot, Edwin; Hoebeke, Rudy; Slabbinck, B. Hans; Verhaert, Michel

1998-10-01

In this paper the design of a chip-set for QoS provisioning in ATM-based Passive Optical Networks is discussed. The implementation of a general-purpose switch chip on the Optical Network Unit is presented, with focus on the design of the cell scheduling and buffer management logic. The cell scheduling logic supports `colored' grants, priority jumping and weighted round-robin scheduling. The switch chip offers powerful buffer management capabilities enabling the efficient support of GFR and UBR services. Multicast forwarding is also supported. In addition, the architecture of a MAC controller chip developed for a SuperPON access network is introduced. In particular, the permit scheduling logic and its implementation on the Optical Line Termination will be discussed. The chip-set enables the efficient support of services with different service requirements on the SuperPON. The permit scheduling logic built into the MAC controller chip in combination with the cell scheduling and buffer management capabilities of the switch chip can be used by network operators to offer guaranteed service performance to delay sensitive services, and to efficiently and fairly distribute any spare capacity to delay insensitive services.

Simultaneous and coordinated rotational switching of all molecular rotors in a network

DOE PAGES

Zhang, Y.; Kersell, H.; Stefak, R.; ...

2016-05-09

A range of artificial molecular systems have been created that can exhibit controlled linear and rotational motion. In the development of such systems, a key step is the addition of communication between molecules in a network. Here, we show that a two-dimensional array of dipolar molecular rotors can undergo simultaneous rotational switching by applying an electric field from the tip of a scanning tunnelling microscope. Several hundred rotors made from porphyrin-based double-decker complexes can be simultaneously rotated when in a hexagonal rotor network on a Cu(111) surface by applying biases above ±1 V at 80 K. The phenomenon is observedmore » only in a hexagonal rotor network due to the degeneracy of the ground state dipole rotational energy barrier of the system. Defects are essential to increase electric torque on the rotor network and to stabilize the switched rotor domains. At low biases and low initial rotator angles, slight reorientations of individual rotors can occur resulting in the rotator arms pointing in different directions. In conclusion, analysis reveals that the rotator arm directions here are not random, but are coordinated to minimize energy via cross talk among the rotors through dipolar interactions.« less

Molecular pathways to parallel evolution: I. Gene nexuses and their morphological correlates.

PubMed

Zuckerkandl, E

1994-12-01

Aspects of the regulatory interactions among genes are probably as old as most genes are themselves. Correspondingly, similar predispositions to changes in such interactions must have existed for long evolutionary periods. Features of the structure and the evolution of the system of gene regulation furnish the background necessary for a molecular understanding of parallel evolution. Patently "unrelated" organs, such as the fat body of a fly and the liver of a mammal, can exhibit fractional homology, a fraction expected to become subject to quantitation. This also seems to hold for different organs in the same organism, such as wings and legs of a fly. In informational macromolecules, on the other hand, homology is indeed all or none. In the quite different case of organs, analogy is expected usually to represent attenuated homology. Many instances of putative convergence are likely to turn out to be predominantly parallel evolution, presumably including the case of the vertebrate and cephalopod eyes. Homology in morphological features reflects a similarity in networks of active genes. Similar nexuses of active genes can be established in cells of different embryological origins. Thus, parallel development can be considered a counterpart to parallel evolution. Specific macromolecular interactions leading to the regulation of the c-fos gene are given as an example of a "controller node" defined as a regulatory unit. Quantitative changes in gene control are distinguished from relational changes, and frequent parallelism in quantitative changes is noted in Drosophila enzymes. Evolutionary reversions in quantitative gene expression are also expected. The evolution of relational patterns is attributed to several distinct mechanisms, notably the shuffling of protein domains. The growth of such patterns may in part be brought about by a particular process of compensation for "controller gene diseases," a process that would spontaneously tend to lead to increased regulatory and organismal complexity. Despite the inferred increase in gene interaction complexity, whose course over evolutionary time is unknown, the number of homology groups for the functional and structural protein units designated as domains has probably remained rather constant, even as, in some of its branches, evolution moved toward "higher" organisms. In connection with this process, the question is raised of parallel evolution within the purview of activating and repressing master switches and in regard to the number of levels into which the hierarchies of genic master switches will eventually be resolved.

Solid state switch

DOEpatents

Merritt, B.T.; Dreifuerst, G.R.

1994-07-19

A solid state switch, with reverse conducting thyristors, is designed to operate at 20 kV hold-off voltage, 1,500 A peak, 1.0 [mu]s pulsewidth, and 4,500 pps, to replace thyratrons. The solid state switch is more reliable, more economical, and more easily repaired. The switch includes a stack of circuit card assemblies, a magnetic assist and a trigger chassis. Each circuit card assembly contains a reverse conducting thyristor, a resistor capacitor network, and triggering circuitry. 6 figs.

Dynamic optimization of metabolic networks coupled with gene expression.

PubMed

Waldherr, Steffen; Oyarzún, Diego A; Bockmayr, Alexander

2015-01-21

The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization techniques. However, metabolic adaptations driven by changes in gene expression cannot be analyzed by steady state models, as these do not account for temporal changes in biomass composition. Here we present a dynamic optimization framework that integrates the metabolic network with the dynamics of biomass production and composition. An approximation by a timescale separation leads to a coupled model of quasi-steady state constraints on the metabolic reactions, and differential equations for the substrate concentrations and biomass composition. We propose a dynamic optimization approach to determine reaction fluxes for this model, explicitly taking into account enzyme production costs and enzymatic capacity. In contrast to the established dynamic flux balance analysis, our approach allows predicting dynamic changes in both the metabolic fluxes and the biomass composition during metabolic adaptations. Discretization of the optimization problems leads to a linear program that can be efficiently solved. We applied our algorithm in two case studies: a minimal nutrient uptake network, and an abstraction of core metabolic processes in bacteria. In the minimal model, we show that the optimized uptake rates reproduce the empirical Monod growth for bacterial cultures. For the network of core metabolic processes, the dynamic optimization algorithm predicted commonly observed metabolic adaptations, such as a diauxic switch with a preference ranking for different nutrients, re-utilization of waste products after depletion of the original substrate, and metabolic adaptation to an impending nutrient depletion. These examples illustrate how dynamic adaptations of enzyme expression can be predicted solely from an optimization principle. Copyright © 2014 Elsevier Ltd. All rights reserved.

Optical switch compatible with wavelength division multiplexing and mode division multiplexing for photonic networks-on-chip.

PubMed

Jia, Hao; Zhou, Ting; Zhang, Lei; Ding, Jianfeng; Fu, Xin; Yang, Lin

2017-08-21

We propose a 2 × 2 multimode optical switch, which is composed of two mode de-multiplexers, n 2 × 2 single-mode optical switches where n is the number of the supported spatial modes, and two mode multiplexers. As a proof of concept, asymmetric directional couplers are employed to construct the mode multiplexers and de-multiplexers, balanced Mach-Zehnder interferometer is utilized to construct the 2 × 2 single-mode optical switches. The fabricated silicon 2 × 2 multimode optical switch has a broad optical bandwidth and can support four spatial modes. The link-crosstalk for all four modes is smaller than -18.8 dB. The inter-mode crosstalk for the same optical link is less than -22.1 dB. 40 Gbps data transmission is performed for all spatial modes and all optical links. The power penalties for the error-free switching (BER<10 -9 ) at 25 Gbps are less than 1.8 dB for all channels at the wavelength of 1550 nm. The power consumption of the device is 117.9 mW in the "cross" state and 116.2 mW in the "bar" state. The switching time is about 21 μs. This work enables large-capacity multimode photonic networks-on-chip.

Temperature control of fimbriation circuit switch in uropathogenic Escherichia coli: quantitative analysis via automated model abstraction.

PubMed

Kuwahara, Hiroyuki; Myers, Chris J; Samoilov, Michael S

2010-03-26

Uropathogenic Escherichia coli (UPEC) represent the predominant cause of urinary tract infections (UTIs). A key UPEC molecular virulence mechanism is type 1 fimbriae, whose expression is controlled by the orientation of an invertible chromosomal DNA element-the fim switch. Temperature has been shown to act as a major regulator of fim switching behavior and is overall an important indicator as well as functional feature of many urologic diseases, including UPEC host-pathogen interaction dynamics. Given this panoptic physiological role of temperature during UTI progression and notable empirical challenges to its direct in vivo studies, in silico modeling of corresponding biochemical and biophysical mechanisms essential to UPEC pathogenicity may significantly aid our understanding of the underlying disease processes. However, rigorous computational analysis of biological systems, such as fim switch temperature control circuit, has hereto presented a notoriously demanding problem due to both the substantial complexity of the gene regulatory networks involved as well as their often characteristically discrete and stochastic dynamics. To address these issues, we have developed an approach that enables automated multiscale abstraction of biological system descriptions based on reaction kinetics. Implemented as a computational tool, this method has allowed us to efficiently analyze the modular organization and behavior of the E. coli fimbriation switch circuit at different temperature settings, thus facilitating new insights into this mode of UPEC molecular virulence regulation. In particular, our results suggest that, with respect to its role in shutting down fimbriae expression, the primary function of FimB recombinase may be to effect a controlled down-regulation (rather than increase) of the ON-to-OFF fim switching rate via temperature-dependent suppression of competing dynamics mediated by recombinase FimE. Our computational analysis further implies that this down-regulation mechanism could be particularly significant inside the host environment, thus potentially contributing further understanding toward the development of novel therapeutic approaches to UPEC-caused UTIs.

The genetic network controlling plasma cell differentiation.

PubMed

Nutt, Stephen L; Taubenheim, Nadine; Hasbold, Jhagvaral; Corcoran, Lynn M; Hodgkin, Philip D

2011-10-01

Upon activation by antigen, mature B cells undergo immunoglobulin class switch recombination and differentiate into antibody-secreting plasma cells, the endpoint of the B cell developmental lineage. Careful quantitation of these processes, which are stochastic, independent and strongly linked to the division history of the cell, has revealed that populations of B cells behave in a highly predictable manner. Considerable progress has also been made in the last few years in understanding the gene regulatory network that controls the B cell to plasma cell transition. The mutually exclusive transcriptomes of B cells and plasma cells are maintained by the antagonistic influences of two groups of transcription factors, those that maintain the B cell program, including Pax5, Bach2 and Bcl6, and those that promote and facilitate plasma cell differentiation, notably Irf4, Blimp1 and Xbp1. In this review, we discuss progress in the definition of both the transcriptional and cellular events occurring during late B cell differentiation, as integrating these two approaches is crucial to defining a regulatory network that faithfully reflects the stochastic features and complexity of the humoral immune response. 2011 Elsevier Ltd. All rights reserved.

Genetic regulation of mammalian gonad development.

PubMed

Eggers, Stefanie; Ohnesorg, Thomas; Sinclair, Andrew

2014-11-01

Sex-specific gonadal development starts with formation of the bipotential gonad, which then differentiates into either a mature testis or an ovary. This process is dependent on activation of either the testis-specific or the ovary-specific pathway while the opposite pathway is continuously repressed. A network of transcription factors tightly regulates initiation and maintenance of these distinct pathways; disruption of these networks can lead to disorders of sex development in humans and male-to-female or female-to-male sex reversal in mice. Sry is the Y-linked master switch that is both required and sufficient to drive the testis-determining pathway. Another key component of the testis pathway is Sox9, which acts immediately downstream of Sry. In contrast to the testis pathway, no single sex-determining factor has been identified in the ovary pathway; however, multiple genes, such as Foxl2, Rspo1, Ctnnb1, and Wnt4, seem to work synergistically and in parallel to ensure proper ovary development. Our understanding of the regulatory networks that underpin testis and ovary development has grown substantially over the past two decades.

Modeling and visualizing cell type switching.

PubMed

Ghaffarizadeh, Ahmadreza; Podgorski, Gregory J; Flann, Nicholas S

2014-01-01

Understanding cellular differentiation is critical in explaining development and for taming diseases such as cancer. Differentiation is conventionally represented using bifurcating lineage trees. However, these lineage trees cannot readily capture or quantify all the types of transitions now known to occur between cell types, including transdifferentiation or differentiation off standard paths. This work introduces a new analysis and visualization technique that is capable of representing all possible transitions between cell states compactly, quantitatively, and intuitively. This method considers the regulatory network of transcription factors that control cell type determination and then performs an analysis of network dynamics to identify stable expression profiles and the potential cell types that they represent. A visualization tool called CellDiff3D creates an intuitive three-dimensional graph that shows the overall direction and probability of transitions between all pairs of cell types within a lineage. In this study, the influence of gene expression noise and mutational changes during myeloid cell differentiation are presented as a demonstration of the CellDiff3D technique, a new approach to quantify and envision all possible cell state transitions in any lineage network.

A hybrid optical switch architecture to integrate IP into optical networks to provide flexible and intelligent bandwidth on demand for cloud computing

NASA Astrophysics Data System (ADS)

Yang, Wei; Hall, Trevor J.

2013-12-01

The Internet is entering an era of cloud computing to provide more cost effective, eco-friendly and reliable services to consumer and business users. As a consequence, the nature of the Internet traffic has been fundamentally transformed from a pure packet-based pattern to today's predominantly flow-based pattern. Cloud computing has also brought about an unprecedented growth in the Internet traffic. In this paper, a hybrid optical switch architecture is presented to deal with the flow-based Internet traffic, aiming to offer flexible and intelligent bandwidth on demand to improve fiber capacity utilization. The hybrid optical switch is capable of integrating IP into optical networks for cloud-based traffic with predictable performance, for which the delay performance of the electronic module in the hybrid optical switch architecture is evaluated through simulation.

Data distribution satellite

NASA Technical Reports Server (NTRS)

Stevens, Grady H.

1992-01-01

The Data Distribution Satellite (DDS), operating in conjunction with the planned space network, the National Research and Education Network and its commercial derivatives, would play a key role in networking the emerging supercomputing facilities, national archives, academic, industrial, and government institutions. Centrally located over the United States in geostationary orbit, DDS would carry sophisticated on-board switching and make use of advanced antennas to provide an array of special services. Institutions needing continuous high data rate service would be networked together by use of a microwave switching matrix and electronically steered hopping beams. Simultaneously, DDS would use other beams and on board processing to interconnect other institutions with lesser, low rate, intermittent needs. Dedicated links to White Sands and other facilities would enable direct access to space payloads and sensor data. Intersatellite links to a second generation ATDRS, called Advanced Space Data Acquisition and Communications System (ASDACS), would eliminate one satellite hop and enhance controllability of experimental payloads by reducing path delay. Similarly, direct access would be available to the supercomputing facilities and national data archives. Economies with DDS would be derived from its ability to switch high rate facilities amongst users needed. At the same time, having a CONUS view, DDS would interconnect with any institution regardless of how remote. Whether one needed high rate service or low rate service would be immaterial. With the capability to assign resources on demand, DDS will need only carry a portion of the resources needed if dedicated facilities were used. Efficiently switching resources to users as needed, DDS would become a very feasible spacecraft, even though it would tie together the space network, the terrestrial network, remote sites, 1000's of small users, and those few who need very large data links intermittently.

The DDN (Defense Data Network) Course,

DTIC Science & Technology

1986-04-01

devices will share the same node-to-node channels. * Simultaneous availability of source and destination is not required. * Speed and code conversion can...address multiple addresses simultaneously 3) Disadvantages of Message Switching Systems Not suited to real time or interactive use * Long and highly...transmission b) Unlike message switching, packet switching requires the -. simultaneous availability of source and destination. 64 -4 ) ..xa...e s

Shape-Memory Hydrogels: Evolution of Structural Principles To Enable Shape Switching of Hydrophilic Polymer Networks.

PubMed

Löwenberg, Candy; Balk, Maria; Wischke, Christian; Behl, Marc; Lendlein, Andreas

2017-04-18

The ability of hydrophilic chain segments in polymer networks to strongly interact with water allows the volumetric expansion of the material and formation of a hydrogel. When polymer chain segments undergo reversible hydration depending on environmental conditions, smart hydrogels can be realized, which are able to shrink/swell and thus alter their volume on demand. In contrast, implementing the capacity of hydrogels to switch their shape rather than volume demands more sophisticated chemical approaches and structural concepts. In this Account, the principles of hydrogel network design, incorporation of molecular switches, and hydrogel microstructures are summarized that enable a spatially directed actuation of hydrogels by a shape-memory effect (SME) without major volume alteration. The SME involves an elastic deformation (programming) of samples, which are temporarily fixed by reversible covalent or physical cross-links resulting in a temporary shape. The material can reverse to the original shape when these molecular switches are affected by application of a suitable stimulus. Hydrophobic shape-memory polymers (SMPs), which are established with complex functions including multiple or reversible shape-switching, may provide inspiration for the molecular architecture of shape-memory hydrogels (SMHs), but cannot be identically copied in the world of hydrophilic soft materials. For instance, fixation of the temporary shape requires cross-links to be formed also in an aqueous environment, which may not be realized, for example, by crystalline domains from the hydrophilic main chains as these may dissolve in presence of water. Accordingly, dual-shape hydrogels have evolved, where, for example, hydrophobic crystallizable side chains have been linked into hydrophilic polymer networks to act as temperature-sensitive temporary cross-links. By incorporating a second type of such side chains, triple-shape hydrogels can be realized. Considering the typically given light permeability of hydrogels and the fully hydrated state with easy permeation by small molecules, other types of stimuli like light, pH, or ions can be employed that may not be easily used in hydrophobic SMPs. In some cases, those molecular switches can respond to more than one stimulus, thus increasing the number of opportunities to induce actuation of these synthetic hydrogels. Beyond this, biopolymer-based hydrogels can be equipped with a shape switching function when facilitating, for example, triple helix formation in proteins or ionic interactions in polysaccharides. Eventually, microstructured SMHs such as hybrid or porous structures can combine the shape-switching function with an improved performance by helping to overcome frequent shortcomings of hydrogels such as low mechanical strength or volume change upon temporary cross-link cleavage. Specifically, shape switching without major volume alteration is possible in porous SMHs by decoupling small volume changes of pore walls on the microscale and the macroscopic sample size. Furthermore, oligomeric rather than short aliphatic side chains as molecular switches allow stabilization of the sample volumes. Based on those structural principles and switching functionalities, SMHs have already entered into applications as soft actuators and are considered, for example, for cell manipulation in biomedicine. In the context of those applications, switching kinetics, switching forces, and reversibility of switching are aspects to be further explored.

Partner switching promotes cooperation among myopic agents on a geographical plane

NASA Astrophysics Data System (ADS)

Li, Yixiao; Min, Yong; Zhu, Xiaodong; Cao, Jie

2013-02-01

We study the coupling dynamics between the evolution of cooperation and the evolution of partnership network on a geographical plane. While agents play networked prisoner’s dilemma games, they can dynamically adjust their partnerships based on local information about reputation. We incorporate geographical features into the process of the agent’s partner switching and investigate the corresponding effects. At each time step of the coevolution, a random agent can either update his strategy by imitation or adjust his partnership by switching from the lowest reputation partner to the highest reputation one among his neighbors. We differentiate two types of neighbors: geographical neighbors (i.e., the set of agents who are close to the focal agent in terms of geographical distance) and connectivity neighbors (i.e., the set of agents who are close to the focal agent in the partnership network in terms of geodesic distance). We find that switching to either geographical neighbors or connectivity neighbors enhances cooperation greatly in a wide parameter range. Cooperation can be favored in a much stricter condition when agents switch to connectivity neighbors more frequently. However, an increasing tendency of reconnecting to geographical neighbors shortens the geographical distance between a pair of partners on average. When agents consider the cost of geographical distance in adjusting the partnership, they are prone to reconnect to geographical neighbors.

State space truncation with quantified errors for accurate solutions to discrete Chemical Master Equation

PubMed Central

Cao, Youfang; Terebus, Anna; Liang, Jie

2016-01-01

The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEG), we truncate the state space by limiting the total molecular copy numbers in each MEG. We further describe a theoretical framework for analysis of the truncation error in the steady state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of 1) the birth and death model, 2) the single gene expression model, 3) the genetic toggle switch model, and 4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate out theories. Overall, the novel state space truncation and error analysis methods developed here can be used to ensure accurate direct solutions to the dCME for a large number of stochastic networks. PMID:27105653

State Space Truncation with Quantified Errors for Accurate Solutions to Discrete Chemical Master Equation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Youfang; Terebus, Anna; Liang, Jie

The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEGs), we truncate the state space by limiting the total molecular copy numbers in each MEG. Wemore » further describe a theoretical framework for analysis of the truncation error in the steady-state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of (1) the birth and death model, (2) the single gene expression model, (3) the genetic toggle switch model, and (4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady-state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate our theories. Overall, the novel state space truncation and error analysis methods developed here can be used to ensure accurate direct solutions to the dCME for a large number of stochastic networks.« less

State Space Truncation with Quantified Errors for Accurate Solutions to Discrete Chemical Master Equation

DOE PAGES

Cao, Youfang; Terebus, Anna; Liang, Jie

2016-04-22

The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEGs), we truncate the state space by limiting the total molecular copy numbers in each MEG. Wemore » further describe a theoretical framework for analysis of the truncation error in the steady-state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of (1) the birth and death model, (2) the single gene expression model, (3) the genetic toggle switch model, and (4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady-state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate our theories. Overall, the novel state space truncation and error analysis methods developed here can be used to ensure accurate direct solutions to the dCME for a large number of stochastic networks.« less

Designing Predictive Diagnose Method for Insulation Resistance Degradation of the Electrical Power Cables from Neutral Insulated Power Networks

NASA Astrophysics Data System (ADS)

Dobra, R.; Pasculescu, D.; Risteiu, M.; Buica, G.; Jevremović, V.

2017-06-01

This paper describe some possibilities to minimize voltages switching-off risks from the mining power networks, in case of insulated resistance faults by using a predictive diagnose method. The cables from the neutral insulated power networks (underground mining) are designed to provide a flexible electrical connection between portable or mobile equipment and a point of supply, including main feeder cable for continuous miners, pump cable, and power supply cable. An electronic protection for insulated resistance of mining power cables can be made using this predictive strategy. The main role of electronic relays for insulation resistance degradation of the electrical power cables, from neutral insulated power networks, is to provide a permanent measurement of the insulated resistance between phases and ground, in order to switch-off voltage when the resistance value is below a standard value. The automat system of protection is able to signalize the failure and the human operator will be early informed about the switch-off power and will have time to take proper measures to fix the failure. This logic for fast and automat switch-off voltage without aprioristic announcement is suitable for the electrical installations, realizing so a protection against fires and explosion. It is presented an algorithm and an anticipative relay for insulated resistance control from three-phase low voltage installations with insulated neutral connection.

Enhanced just-in-time plus protocol for optical burst switching networks

NASA Astrophysics Data System (ADS)

Rodrigues, Joel J. P. C.; Gregório, José M. B.; Vasilakos, Athanasios V.

2010-07-01

We propose a new one-way resource reservation protocol for optical burst switching (OBS) networks, called Enhanced Just-in-Time Plus (E-JIT+). The protocol is described in detail, and its formal specification is presented, following an extended finite state machine approach. The performance evaluation of E-JIT+ is analyzed in comparison with other proposed OBS protocols (JIT+ and E-JIT) for the following network topologies: rings; degree-two, degree-three, and degree-four chordal rings; mesh-torus; NSFNET; ARPANET; FCCN-NET; and the European Optical Network. We evaluate and compare the performance of the different protocols in terms of burst loss probability, taking into account the most important OBS network parameters. It was shown that E-JIT+ performs better than available one-way resource reservation protocols for all the evaluated network topologies. Moreover, the scalability of E-JIT+ was observed, and when the network traffic increases, the burst loss probability also increases, leading to a worse network performance.

Noise-constrained switching times for heteroclinic computing

NASA Astrophysics Data System (ADS)

Neves, Fabio Schittler; Voit, Maximilian; Timme, Marc

2017-03-01

Heteroclinic computing offers a novel paradigm for universal computation by collective system dynamics. In such a paradigm, input signals are encoded as complex periodic orbits approaching specific sequences of saddle states. Without inputs, the relevant states together with the heteroclinic connections between them form a network of states—the heteroclinic network. Systems of pulse-coupled oscillators or spiking neurons naturally exhibit such heteroclinic networks of saddles, thereby providing a substrate for general analog computations. Several challenges need to be resolved before it becomes possible to effectively realize heteroclinic computing in hardware. The time scales on which computations are performed crucially depend on the switching times between saddles, which in turn are jointly controlled by the system's intrinsic dynamics and the level of external and measurement noise. The nonlinear dynamics of pulse-coupled systems often strongly deviate from that of time-continuously coupled (e.g., phase-coupled) systems. The factors impacting switching times in pulse-coupled systems are still not well understood. Here we systematically investigate switching times in dependence of the levels of noise and intrinsic dissipation in the system. We specifically reveal how local responses to pulses coact with external noise. Our findings confirm that, like in time-continuous phase-coupled systems, piecewise-continuous pulse-coupled systems exhibit switching times that transiently increase exponentially with the number of switches up to some order of magnitude set by the noise level. Complementarily, we show that switching times may constitute a good predictor for the computation reliability, indicating how often an input signal must be reiterated. By characterizing switching times between two saddles in conjunction with the reliability of a computation, our results provide a first step beyond the coding of input signal identities toward a complementary coding for the intensity of those signals. The results offer insights on how future heteroclinic computing systems may operate under natural, and thus noisy, conditions.

GLOBECOM '85 - Global Telecommunications Conference, New Orleans, LA, December 2-5, 1985, Conference Record. Volumes 1, 2, & 3

NASA Astrophysics Data System (ADS)

Various papers on global telecommunications are presented. The general topics addressed include: multiservice integration with optical fibers, multicompany owned telecommunication networks, softworks quality and reliability, advanced on-board processing, impact of new services and systems on operations and maintenance, analytical studies of protocols for data communication networks, topics in packet radio networking, CCITT No. 7 to support new services, document processing and communication, antenna technology and system aspects in satellite communications. Also considered are: communication systems modelling methodology, experimental integrated local area voice/data nets, spread spectrum communications, motion video at the DS-0 rate, optical and data communications, intelligent work stations, switch performance analysis, novel radio communication systems, wireless local networks, ISDN services, LAN communication protocols, user-system interface, radio propagation and performance, mobile satellite system, software for computer networks, VLSI for ISDN terminals, quality management, man-machine interfaces in switching, and local area network performance.

Effect of TNF{alpha} on activities of different promoters of human apolipoprotein A-I gene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orlov, Sergey V., E-mail: serge@iem.sp.ru; Department of Embryology, St. Petersburg State University, 199034 St. Petersburg; Mogilenko, Denis A.

2010-07-23

Research highlights: {yields} TNF{alpha} stimulates the distal alternative promoter of human apoA-I gene. {yields} TNF{alpha} acts by weakening of promoter competition within apoA-I gene (promoter switching). {yields} MEK1/2 and nuclear receptors PPAR{alpha} and LXRs take part in apoA-I promoter switching. -- Abstract: Human apolipoprotein A-I (ApoA-I) is a major structural and functional protein component of high-density lipoproteins. The expression of the apolipoprotein A-I gene (apoA-I) in hepatocytes is repressed by pro-inflammatory cytokines such as IL-1{beta} and TNF{alpha}. Recently, two novel additional (alternative) promoters for human apoA-I gene have been identified. Nothing is known about the role of alternative promoters inmore » TNF{alpha}-mediated downregulation of apoA-I gene. In this article we report for the first time about the different effects of TNF{alpha} on two alternative promoters of human apoA-I gene. Stimulation of HepG2 cells by TNF{alpha} leads to activation of the distal alternative apoA-I promoter and downregulation of the proximal alternative and the canonical apoA-I promoters. This effect is mediated by weakening of the promoter competition within human apoA-I 5'-regulatory region (apoA-I promoter switching) in the cells treated by TNF{alpha}. The MEK1/2-ERK1/2 cascade and nuclear receptors PPAR{alpha} and LXRs are important for TNF{alpha}-mediated apoA-I promoter switching.« less

Method to optimize optical switch topology for photonic network-on-chip

NASA Astrophysics Data System (ADS)

Zhou, Ting; Jia, Hao

2018-04-01

In this paper, we propose a method to optimize the optical switch by substituting optical waveguide crossings for optical switching units and an optimizing algorithm to complete the optimization automatically. The functionality of the optical switch remains constant under optimization. With this method, we simplify the topology of optical switch, which means the insertion loss and power consumption of the whole optical switch can be effectively minimized. Simulation result shows that the number of switching units of the optical switch based on Spanke-Benes can be reduced by 16.7%, 20%, 20%, 19% and 17.9% for the scale from 4 × 4 to 8 × 8 respectively. As a proof of concept, the experimental demonstration of an optimized six-port optical switch based on Spanke-Benes structure by means of silicon photonics chip is reported.

Construction of large scale switch matrix by interconnecting integrated optical switch chips with EDFAs

NASA Astrophysics Data System (ADS)

Liao, Mingle; Wu, Baojian; Hou, Jianhong; Qiu, Kun

2018-03-01

Large scale optical switches are essential components in optical communication network. We aim to build up a large scale optical switch matrix by the interconnection of silicon-based optical switch chips using 3-stage CLOS structure, where EDFAs are needed to compensate for the insertion loss of the chips. The optical signal-to-noise ratio (OSNR) performance of the resulting large scale optical switch matrix is investigated for TE-mode light and the experimental results are in agreement with the theoretical analysis. We build up a 64 ×64 switch matrix by use of 16 ×16 optical switch chips and the OSNR and receiver sensibility can respectively be improved by 0.6 dB and 0.2 dB by optimizing the gain configuration of the EDFAs.

Using of explosive technologies for development of a compact current-limiting device for operation on 110 kV class systems

NASA Astrophysics Data System (ADS)

Shurupov, A. V.; Shurupov, M. A.; Kozlov, A. A.; Kotov, A. V.

2016-11-01

This paper considers the possibility of creating on new physical principles a highspeed current-limiting device (CLD) for the networks with voltage of 110 kV, namely, on the basis of the explosive switching elements. The device is designed to limit the steady short-circuit current to acceptable values for the time does not exceed 3 ms at electric power facilities. The paper presents an analysis of the electrical circuit of CLD. The main features of the scheme are: a new high-speed switching element with high regenerating voltage; fusible switching element that enables to limit the overvoltage after sudden breakage of network of the explosive switch; non-inductive resistor with a high heat capacity and a special reactor with operating time less than 1 s. We analyzed the work of the CLD with help of special software PSPICE, which is based on the equivalent circuit of single-phase short circuit to ground in 110 kV network. Analysis of the equivalent circuit operation CLD shows its efficiency and determines the CLD as a perspective direction of the current-limiting devices of new generation.

Multiple coupled landscapes and non-adiabatic dynamics with applications to self-activating genes.

PubMed

Chen, Cong; Zhang, Kun; Feng, Haidong; Sasai, Masaki; Wang, Jin

2015-11-21

Many physical, chemical and biochemical systems (e.g. electronic dynamics and gene regulatory networks) are governed by continuous stochastic processes (e.g. electron dynamics on a particular electronic energy surface and protein (gene product) synthesis) coupled with discrete processes (e.g. hopping among different electronic energy surfaces and on and off switching of genes). One can also think of the underlying dynamics as the continuous motion on a particular landscape and discrete hoppings among different landscapes. The main difference of such systems from the intra-landscape dynamics alone is the emergence of the timescale involved in transitions among different landscapes in addition to the timescale involved in a particular landscape. The adiabatic limit when inter-landscape hoppings are fast compared to continuous intra-landscape dynamics has been studied both analytically and numerically, but the analytical treatment of the non-adiabatic regime where the inter-landscape hoppings are slow or comparable to continuous intra-landscape dynamics remains challenging. In this study, we show that there exists mathematical mapping of the dynamics on 2(N) discretely coupled N continuous dimensional landscapes onto one single landscape in 2N dimensional extended continuous space. On this 2N dimensional landscape, eddy current emerges as a sign of non-equilibrium non-adiabatic dynamics and plays an important role in system evolution. Many interesting physical effects such as the enhancement of fluctuations, irreversibility, dissipation and optimal kinetics emerge due to non-adiabaticity manifested by the eddy current illustrated for an N = 1 self-activator. We further generalize our theory to the N-gene network with multiple binding sites and multiple synthesis rates for discretely coupled non-equilibrium stochastic physical and biological systems.

Efficient randomization of biological networks while preserving functional characterization of individual nodes.

PubMed

Iorio, Francesco; Bernardo-Faura, Marti; Gobbi, Andrea; Cokelaer, Thomas; Jurman, Giuseppe; Saez-Rodriguez, Julio

2016-12-20

Networks are popular and powerful tools to describe and model biological processes. Many computational methods have been developed to infer biological networks from literature, high-throughput experiments, and combinations of both. Additionally, a wide range of tools has been developed to map experimental data onto reference biological networks, in order to extract meaningful modules. Many of these methods assess results' significance against null distributions of randomized networks. However, these standard unconstrained randomizations do not preserve the functional characterization of the nodes in the reference networks (i.e. their degrees and connection signs), hence including potential biases in the assessment. Building on our previous work about rewiring bipartite networks, we propose a method for rewiring any type of unweighted networks. In particular we formally demonstrate that the problem of rewiring a signed and directed network preserving its functional connectivity (F-rewiring) reduces to the problem of rewiring two induced bipartite networks. Additionally, we reformulate the lower bound to the iterations' number of the switching-algorithm to make it suitable for the F-rewiring of networks of any size. Finally, we present BiRewire3, an open-source Bioconductor package enabling the F-rewiring of any type of unweighted network. We illustrate its application to a case study about the identification of modules from gene expression data mapped on protein interaction networks, and a second one focused on building logic models from more complex signed-directed reference signaling networks and phosphoproteomic data. BiRewire3 it is freely available at https://www.bioconductor.org/packages/BiRewire/ , and it should have a broad application as it allows an efficient and analytically derived statistical assessment of results from any network biology tool.

Alpha3, a transposable element that promotes host sexual reproduction.

PubMed

Barsoum, Emad; Martinez, Paula; Aström, Stefan U

2010-01-01

Theoretical models predict that selfish DNA elements require host sex to persist in a population. Therefore, a transposon that induces sex would strongly favor its own spread. We demonstrate that a protein homologous to transposases, called alpha3, was essential for mating type switch in Kluyveromyces lactis. Mutational analysis showed that amino acids conserved among transposases were essential for its function. During switching, sequences in the 5' and 3' flanking regions of the alpha3 gene were joined, forming a DNA circle, showing that alpha3 mobilized from the genome. The sequences encompassing the alpha3 gene circle junctions in the mating type alpha (MATalpha) locus were essential for switching from MATalpha to MATa, suggesting that alpha3 mobilization was a coupled event. Switching also required a DNA-binding protein, Mating type switch 1 (Mts1), whose binding sites in MATalpha were important. Expression of Mts1 was repressed in MATa/MATalpha diploids and by nutrients, limiting switching to haploids in low-nutrient conditions. A hairpin-capped DNA double-strand break (DSB) was observed in the MATa locus in mre11 mutant strains, indicating that mating type switch was induced by MAT-specific DSBs. This study provides empirical evidence for selfish DNA promoting host sexual reproduction by mediating mating type switch.

Modelling Feedback Excitation, Pacemaker Properties and Sensory Switching of Electrically Coupled Brainstem Neurons Controlling Rhythmic Activity

PubMed Central

Hull, Michael J.; Soffe, Stephen R.; Willshaw, David J.; Roberts, Alan

2016-01-01

What cellular and network properties allow reliable neuronal rhythm generation or firing that can be started and stopped by brief synaptic inputs? We investigate rhythmic activity in an electrically-coupled population of brainstem neurons driving swimming locomotion in young frog tadpoles, and how activity is switched on and off by brief sensory stimulation. We build a computational model of 30 electrically-coupled conditional pacemaker neurons on one side of the tadpole hindbrain and spinal cord. Based on experimental estimates for neuron properties, population sizes, synapse strengths and connections, we show that: long-lasting, mutual, glutamatergic excitation between the neurons allows the network to sustain rhythmic pacemaker firing at swimming frequencies following brief synaptic excitation; activity persists but rhythm breaks down without electrical coupling; NMDA voltage-dependency doubles the range of synaptic feedback strengths generating sustained rhythm. The network can be switched on and off at short latency by brief synaptic excitation and inhibition. We demonstrate that a population of generic Hodgkin-Huxley type neurons coupled by glutamatergic excitatory feedback can generate sustained asynchronous firing switched on and off synaptically. We conclude that networks of neurons with NMDAR mediated feedback excitation can generate self-sustained activity following brief synaptic excitation. The frequency of activity is limited by the kinetics of the neuron membrane channels and can be stopped by brief inhibitory input. Network activity can be rhythmic at lower frequencies if the neurons are electrically coupled. Our key finding is that excitatory synaptic feedback within a population of neurons can produce switchable, stable, sustained firing without synaptic inhibition. PMID:26824331

The ETS-5 transcription factor regulates activity states in Caenorhabditis elegans by controlling satiety

PubMed Central

Juozaityte, Vaida; Pladevall-Morera, David; Podolska, Agnieszka; Nørgaard, Steffen; Pocock, Roger

2017-01-01

Animal behavior is shaped through interplay among genes, the environment, and previous experience. As in mammals, satiety signals induce quiescence in Caenorhabditis elegans. Here we report that the C. elegans transcription factor ETS-5, an ortholog of mammalian FEV/Pet1, controls satiety-induced quiescence. Nutritional status has a major influence on C. elegans behavior. When foraging, food availability controls behavioral state switching between active (roaming) and sedentary (dwelling) states; however, when provided with high-quality food, C. elegans become sated and enter quiescence. We show that ETS-5 acts to promote roaming and inhibit quiescence by setting the internal “satiety quotient” through fat regulation. Acting from the ASG and BAG sensory neurons, we show that ETS-5 functions in a complex network with serotonergic and neuropeptide signaling pathways to control food-regulated behavioral state switching. Taken together, our results identify a neuronal mechanism for controlling intestinal fat stores and organismal behavioral states in C. elegans, and establish a paradigm for the elucidation of obesity-relevant mechanisms. PMID:28193866

Pacific Educational Computer Network Study. Final Report.

ERIC Educational Resources Information Center

Hawaii Univ., Honolulu. ALOHA System.

The Pacific Educational Computer Network Feasibility Study examined technical and non-technical aspects of the formation of an international Pacific Area computer network for higher education. The technical study covered the assessment of the feasibility of a packet-switched satellite and radio ground distribution network for data transmission…

Nonsmooth Finite-Time Synchronization of Switched Coupled Neural Networks.

PubMed

Liu, Xiaoyang; Cao, Jinde; Yu, Wenwu; Song, Qiang

2016-10-01

This paper is concerned with the finite-time synchronization (FTS) issue of switched coupled neural networks with discontinuous or continuous activations. Based on the framework of nonsmooth analysis, some discontinuous or continuous controllers are designed to force the coupled networks to synchronize to an isolated neural network. Some sufficient conditions are derived to ensure the FTS by utilizing the well-known finite-time stability theorem for nonlinear systems. Compared with the previous literatures, such synchronization objective will be realized when the activations and the controllers are both discontinuous. The obtained results in this paper include and extend the earlier works on the synchronization issue of coupled networks with Lipschitz continuous conditions. Moreover, an upper bound of the settling time for synchronization is estimated. Finally, numerical simulations are given to demonstrate the effectiveness of the theoretical results.

Engineering of ribozyme-based aminoglycoside switches of gene expression by in vivo genetic selection in Saccharomyces cerevisiae.

PubMed

Klauser, Benedikt; Rehm, Charlotte; Summerer, Daniel; Hartig, Jörg S

2015-01-01

Synthetic RNA-based switches are a growing class of genetic controllers applied in synthetic biology to engineer cellular functions. In this chapter, we detail a protocol for the selection of posttranscriptional controllers of gene expression in yeast using the Schistosoma mansoni hammerhead ribozyme as a central catalytic unit. Incorporation of a small molecule-sensing aptamer domain into the ribozyme renders its activity ligand-dependent. Aptazymes display numerous advantages over conventional protein-based transcriptional controllers, namely, the use of little genomic space for encryption, their modular architecture allowing for easy reprogramming to new inputs, the physical linkage to the message to be controlled, and the ability to function without protein cofactors. Herein, we describe the method to select ribozyme-based switches of gene expression in Saccharomyces cerevisiae that we successfully implemented to engineer neomycin- and theophylline-responsive switches. We also highlight how to adapt the protocol to screen for switches responsive to other ligands. Reprogramming of the sensor unit and incorporation into any RNA of interest enables the fulfillment of a variety of regulatory functions. However, proper functioning of the aptazyme is largely dependent on optimal connection between the aptamer and the catalytic core. We obtained functional switches from a pool of variants carrying randomized connection sequences by an in vivo selection in MaV203 yeast cells that allows screening of a large sequence space of up to 1×10(9) variants. The protocol given explains how to construct aptazyme libraries, carry out the in vivo selection and characterize novel ON- and OFF-switches. © 2015 Elsevier Inc. All rights reserved.

Telecommunications network optimization

NASA Technical Reports Server (NTRS)

Lee, J.

1979-01-01

Analysis discusses STACOM (state criminal justic communication) network topology program used to design and evaluate digital telecommunications networks STACOM employs ESAU-WILLIAMS technique to search for direct links between system terminations and regional switching center. Inputs include traffic data, terminal locations, and functional requirements.

CMPF: class-switching minimized pathfinding in metabolic networks.

PubMed

Lim, Kevin; Wong, Limsoon

2012-01-01

The metabolic network is an aggregation of enzyme catalyzed reactions that converts one compound to another. Paths in a metabolic network are a sequence of enzymes that describe how a chemical compound of interest can be produced in a biological system. As the number of such paths is quite large, many methods have been developed to score paths so that the k-shortest paths represent the set of paths that are biologically meaningful or efficient. However, these approaches do not consider whether the sequence of enzymes can be manufactured in the same pathway/species/localization. As a result, a predicted sequence might consist of groups of enzymes that operate in distinct pathway/species/localization and may not truly reflect the events occurring within cell. We propose a path weighting method CMPF (Class-switching Minimized Pathfinder) to search for routes in a metabolic network which minimizes pathway switching. In biological terms, a pathway is a series of chemical reactions which define a specific function (e.g. glycolysis). We conjecture that routes that cross many pathways are inefficient since different pathways define different metabolic functions. In addition, native routes are also well characterized within pathways, suggesting that reasonable paths should not involve too many pathway switches. Our method can be generalized when reactions participate in a class set (e.g., pathways, species or cellular localization) so that the paths predicted have minimal class crossings. We show that our method generates k-paths that involve the least number of class switching. In addition, we also show that native paths are recoverable and alternative paths deviates less from native paths compared to other methods. This suggests that paths ranked by our method could be a way to predict paths that are likely to occur in biological systems.

Dendritic Slow Dynamics Enables Localized Cortical Activity to Switch between Mobile and Immobile Modes with Noisy Background Input

PubMed Central

Kurashige, Hiroki; Câteau, Hideyuki

2011-01-01

Mounting lines of evidence suggest the significant computational ability of a single neuron empowered by active dendritic dynamics. This motivates us to study what functionality can be acquired by a network of such neurons. The present paper studies how such rich single-neuron dendritic dynamics affects the network dynamics, a question which has scarcely been specifically studied to date. We simulate neurons with active dendrites networked locally like cortical pyramidal neurons, and find that naturally arising localized activity – called a bump – can be in two distinct modes, mobile or immobile. The mode can be switched back and forth by transient input to the cortical network. Interestingly, this functionality arises only if each neuron is equipped with the observed slow dendritic dynamics and with in vivo-like noisy background input. If the bump activity is considered to indicate a point of attention in the sensory areas or to indicate a representation of memory in the storage areas of the cortex, this would imply that the flexible mode switching would be of great potential use for the brain as an information processing device. We derive these conclusions using a natural extension of the conventional field model, which is defined by combining two distinct fields, one representing the somatic population and the other representing the dendritic population. With this tool, we analyze the spatial distribution of the degree of after-spike adaptation and explain how we can understand the presence of the two distinct modes and switching between the modes. We also discuss the possible functional impact of this mode-switching ability. PMID:21931635

Ping-pong auto-zero amplifier with glitch reduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larson, Mark R

A ping-pong amplifier with reduced glitching is described. The ping-pong amplifier includes a nulling amplifier coupled to a switching network. The switching network is used to auto-zero a ping amplifier within a ping-pong amplifier. The nulling amplifier drives the output of a ping amplifier to a proper output voltage level during auto-zeroing of the ping amplifier. By being at a proper output voltage level, glitches associated with transitioning between a ping amplifier and a pong amplifier are reduced or eliminated.

Automatic transducer switching provides accurate wide range measurement of pressure differential

NASA Technical Reports Server (NTRS)

Yoder, S. K.

1967-01-01

Automatic pressure transducer switching network sequentially selects any one of a number of limited-range transducers as gas pressure rises or falls, extending the range of measurement and lessening the chances of damage due to high pressure.

Jimena: efficient computing and system state identification for genetic regulatory networks.

PubMed

Karl, Stefan; Dandekar, Thomas

2013-10-11

Boolean networks capture switching behavior of many naturally occurring regulatory networks. For semi-quantitative modeling, interpolation between ON and OFF states is necessary. The high degree polynomial interpolation of Boolean genetic regulatory networks (GRNs) in cellular processes such as apoptosis or proliferation allows for the modeling of a wider range of node interactions than continuous activator-inhibitor models, but suffers from scaling problems for networks which contain nodes with more than ~10 inputs. Many GRNs from literature or new gene expression experiments exceed those limitations and a new approach was developed. (i) As a part of our new GRN simulation framework Jimena we introduce and setup Boolean-tree-based data structures; (ii) corresponding algorithms greatly expedite the calculation of the polynomial interpolation in almost all cases, thereby expanding the range of networks which can be simulated by this model in reasonable time. (iii) Stable states for discrete models are efficiently counted and identified using binary decision diagrams. As application example, we show how system states can now be sampled efficiently in small up to large scale hormone disease networks (Arabidopsis thaliana development and immunity, pathogen Pseudomonas syringae and modulation by cytokinins and plant hormones). Jimena simulates currently available GRNs about 10-100 times faster than the previous implementation of the polynomial interpolation model and even greater gains are achieved for large scale-free networks. This speed-up also facilitates a much more thorough sampling of continuous state spaces which may lead to the identification of new stable states. Mutants of large networks can be constructed and analyzed very quickly enabling new insights into network robustness and behavior.

Optical MEMS platform for low-cost on-chip integration of planar light circuits and optical switching

NASA Astrophysics Data System (ADS)

German, Kristine A.; Kubby, Joel; Chen, Jingkuang; Diehl, James; Feinberg, Kathleen; Gulvin, Peter; Herko, Larry; Jia, Nancy; Lin, Pinyen; Liu, Xueyuan; Ma, Jun; Meyers, John; Nystrom, Peter; Wang, Yao Rong

2004-07-01

Xerox Corporation has developed a technology platform for on-chip integration of latching MEMS optical waveguide switches and Planar Light Circuit (PLC) components using a Silicon On Insulator (SOI) based process. To illustrate the current state of this new technology platform, working prototypes of a Reconfigurable Optical Add/Drop Multiplexer (ROADM) and a l-router will be presented along with details of the integrated latching MEMS optical switches. On-chip integration of optical switches and PLCs can greatly reduce the size, manufacturing cost and operating cost of multi-component optical equipment. It is anticipated that low-cost, low-overhead optical network products will accelerate the migration of functions and services from high-cost long-haul markets to price sensitive markets, including networks for metropolitan areas and fiber to the home. Compared to the more common silica-on-silicon PLC technology, the high index of refraction of silicon waveguides created in the SOI device layer enables miniaturization of optical components, thereby increasing yield and decreasing cost projections. The latching SOI MEMS switches feature moving waveguides, and are advantaged across multiple attributes relative to alternative switching technologies, such as thermal optical switches and polymer switches. The SOI process employed was jointly developed under the auspice of the NIST APT program in partnership with Coventor, Corning IntelliSense Corp., and MicroScan Systems to enable fabrication of a broad range of free space and guided wave MicroOptoElectroMechanical Systems (MOEMS).

Recovery Act: Energy Efficiency of Data Networks through Rate Adaptation (EEDNRA) - Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matthew Andrews; Spyridon Antonakopoulos; Steve Fortune

2011-07-12

This Concept Definition Study focused on developing a scientific understanding of methods to reduce energy consumption in data networks using rate adaptation. Rate adaptation is a collection of techniques that reduce energy consumption when traffic is light, and only require full energy when traffic is at full provisioned capacity. Rate adaptation is a very promising technique for saving energy: modern data networks are typically operated at average rates well below capacity, but network equipment has not yet been designed to incorporate rate adaptation. The Study concerns packet-switching equipment, routers and switches; such equipment forms the backbone of the modern Internet.more » The focus of the study is on algorithms and protocols that can be implemented in software or firmware to exploit hardware power-control mechanisms. Hardware power-control mechanisms are widely used in the computer industry, and are beginning to be available for networking equipment as well. Network equipment has different performance requirements than computer equipment because of the very fast rate of packet arrival; hence novel power-control algorithms are required for networking. This study resulted in five published papers, one internal report, and two patent applications, documented below. The specific technical accomplishments are the following: • A model for the power consumption of switching equipment used in service-provider telecommunication networks as a function of operating state, and measured power-consumption values for typical current equipment. • An algorithm for use in a router that adapts packet processing rate and hence power consumption to traffic load while maintaining performance guarantees on delay and throughput. • An algorithm that performs network-wide traffic routing with the objective of minimizing energy consumption, assuming that routers have less-than-ideal rate adaptivity. • An estimate of the potential energy savings in service-provider networks using feasibly-implementable rate adaptivity. • A buffer-management algorithm that is designed to reduce the size of router buffers, and hence energy consumed. • A packet-scheduling algorithm designed to minimize packet-processing energy requirements. Additional research is recommended in at least two areas: further exploration of rate-adaptation in network switching equipment, including incorporation of rate-adaptation in actual hardware, allowing experimentation in operational networks; and development of control protocols that allow parts of networks to be shut down while minimizing disruption to traffic flow in the network. The research is an integral part of a large effort within Bell Laboratories, Alcatel-Lucent, aimed at dramatic improvements in the energy efficiency of telecommunication networks. This Study did not explicitly consider any commercialization opportunities.« less

PPARδ activation in human myotubes increases mitochondrial fatty acid oxidative capacity and reduces glucose utilization by a switch in substrate preference.

PubMed

Feng, Yuan Z; Nikolić, Nataša; Bakke, Siril S; Boekschoten, Mark V; Kersten, Sander; Kase, Eili T; Rustan, Arild C; Thoresen, G Hege

2014-02-01

The role of peroxisome proliferator-activated receptor δ (PPARδ) activation on global gene expression and mitochondrial fuel utilization were investigated in human myotubes. Only 21 genes were up-regulated and 3 genes were down-regulated after activation by the PPARδ agonist GW501516. Pathway analysis showed up-regulated mitochondrial fatty acid oxidation, TCA cycle and cholesterol biosynthesis. GW501516 increased oleic acid oxidation and mitochondrial oxidative capacity by 2-fold. Glucose uptake and oxidation were reduced, but total substrate oxidation was not affected, indicating a fuel switch from glucose to fatty acid. Cholesterol biosynthesis was increased, but lipid biosynthesis and mitochondrial content were not affected. This study confirmed that the principal effect of PPARδ activation was to increase mitochondrial fatty acid oxidative capacity. Our results further suggest that PPARδ activation reduced glucose utilization through a switch in mitochondrial substrate preference by up-regulating pyruvate dehydrogenase kinase isozyme 4 and genes involved in lipid metabolism and fatty acid oxidation.

Genomic identification of direct target genes of LEAFY

PubMed Central

William, Dilusha A.; Su, Yanhui; Smith, Michael R.; Lu, Meina; Baldwin, Don A.; Wagner, Doris

2004-01-01

The switch from vegetative to reproductive development in plants necessitates a switch in the developmental program of the descendents of the stem cells in the shoot apical meristem. Genetic and molecular investigations have demonstrated that the plant-specific transcription factor and meristem identity regulator LEAFY (LFY) controls this developmental transition by inducing expression of a second transcription factor, APETALA1, and by regulating the expression of additional, as yet unknown, genes. Here we show that the additional LFY targets include the APETALA1-related factor, CAULI-FLOWER, as well as three transcription factors and two putative signal transduction pathway components. These genes are up-regulated by LFY even when protein synthesis is inhibited and, hence, appear to be direct targets of LFY. Supporting this conclusion, cis-regulatory regions upstream of these genes are bound by LFY in vivo. The newly identified LFY targets likely initiate the transcriptional changes that are required for the switch from vegetative to reproductive development in Arabidopsis. PMID:14736918

Migration of optical core network to next generation networks - Carrier Grade Ethernet Optical Transport Network

NASA Astrophysics Data System (ADS)

Glamočanin, D.

2017-05-01

In order to maintain the continuity of the telecom operators’ network construction, while monitoring development needs, increasing customers’ demands and application of technological improvements, it is necessary to migrate optical transport core network to the next generation networks - Carrier Grade Ethernet Optical Transport Network (OTN CE). The primary objective of OTN CE is to realize an environment that is based solely on the switching in the optical domain, i.e. the realization of transparent optical networks and optical switching to the second layer of ISO / OSI model. The realization of such a network provides opportunities for further development of existing, but also technologically more demanding, new services. It is also a prerequisite to provide higher scalability, reliability, security and quality of QoS service, as well as prerequisites for the establishment of SLA (Service Level Agreement) for existing services, especially traffic in real time. This study aims to clarify the proposed model, which has the potential to be eventually adjusted in accordance with new scientific knowledge in this field as well as market requirements.

Cost-effective method of manufacturing a 3D MEMS optical switch

NASA Astrophysics Data System (ADS)

Carr, Emily; Zhang, Ping; Keebaugh, Doug; Chau, Kelvin

2009-02-01

growth of data and video transport networks. All-optical switching eliminates the need for optical-electrical conversion offering the ability to switch optical signals transparently: independent of data rates, formats and wavelength. It also provides network operators much needed automation capabilities to create, monitor and protect optical light paths. To further accelerate the market penetration, it is necessary to identify a path to reduce the manufacturing cost significantly as well as enhance the overall system performance, uniformity and reliability. Currently, most MEMS optical switches are assembled through die level flip-chip bonding with either epoxies or solder bumps. This is due to the alignment accuracy requirements of the switch assembly, defect matching of individual die, and cost of the individual components. In this paper, a wafer level assembly approach is reported based on silicon fusion bonding which aims to reduce the packaging time, defect count and cost through volume production. This approach is successfully demonstrated by the integration of two 6-inch wafers: a mirror array wafer and a "snap-guard" wafer, which provides a mechanical structure on top of the micromirror to prevent electrostatic snap-down. The direct silicon-to-silicon bond eliminates the CTEmismatch and stress issues caused by non-silicon bonding agents. Results from a completed integrated switch assembly will be presented, which demonstrates the reliability and uniformity of some key parameters of this MEMS optical switch.