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Sample records for underlying biochemical network

  1. A systematic molecular circuit design method for gene networks under biochemical time delays and molecular noises

    Directory of Open Access Journals (Sweden)

    Chang Yu-Te

    2008-11-01

    Full Text Available Abstract Background Gene networks in nanoscale are of nonlinear stochastic process. Time delays are common and substantial in these biochemical processes due to gene transcription, translation, posttranslation protein modification and diffusion. Molecular noises in gene networks come from intrinsic fluctuations, transmitted noise from upstream genes, and the global noise affecting all genes. Knowledge of molecular noise filtering and biochemical process delay compensation in gene networks is crucial to understand the signal processing in gene networks and the design of noise-tolerant and delay-robust gene circuits for synthetic biology. Results A nonlinear stochastic dynamic model with multiple time delays is proposed for describing a gene network under process delays, intrinsic molecular fluctuations, and extrinsic molecular noises. Then, the stochastic biochemical processing scheme of gene regulatory networks for attenuating these molecular noises and compensating process delays is investigated from the nonlinear signal processing perspective. In order to improve the robust stability for delay toleration and noise filtering, a robust gene circuit for nonlinear stochastic time-delay gene networks is engineered based on the nonlinear robust H∞ stochastic filtering scheme. Further, in order to avoid solving these complicated noise-tolerant and delay-robust design problems, based on Takagi-Sugeno (T-S fuzzy time-delay model and linear matrix inequalities (LMIs technique, a systematic gene circuit design method is proposed to simplify the design procedure. Conclusion The proposed gene circuit design method has much potential for application to systems biology, synthetic biology and drug design when a gene regulatory network has to be designed for improving its robust stability and filtering ability of disease-perturbed gene network or when a synthetic gene network needs to perform robustly under process delays and molecular noises.

  2. Characterizing multistationarity regimes in biochemical reaction networks.

    Directory of Open Access Journals (Sweden)

    Irene Otero-Muras

    Full Text Available Switch like responses appear as common strategies in the regulation of cellular systems. Here we present a method to characterize bistable regimes in biochemical reaction networks that can be of use to both direct and reverse engineering of biological switches. In the design of a synthetic biological switch, it is important to study the capability for bistability of the underlying biochemical network structure. Chemical Reaction Network Theory (CRNT may help at this level to decide whether a given network has the capacity for multiple positive equilibria, based on their structural properties. However, in order to build a working switch, we also need to ensure that the bistability property is robust, by studying the conditions leading to the existence of two different steady states. In the reverse engineering of biological switches, knowledge collected about the bistable regimes of the underlying potential model structures can contribute at the model identification stage to a drastic reduction of the feasible region in the parameter space of search. In this work, we make use and extend previous results of the CRNT, aiming not only to discriminate whether a biochemical reaction network can exhibit multiple steady states, but also to determine the regions within the whole space of parameters capable of producing multistationarity. To that purpose we present and justify a condition on the parameters of biochemical networks for the appearance of multistationarity, and propose an efficient and reliable computational method to check its satisfaction through the parameter space.

  3. BioNessie - a grid enabled biochemical networks simulation environment

    OpenAIRE

    Liu, X.; Jiang, J.; Ajayi, O.; Gu, X.; Gilbert, D.; Sinnott, R.O.

    2008-01-01

    The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations.

  4. Dynamic analysis of biochemical network using complex network method

    Directory of Open Access Journals (Sweden)

    Wang Shuqiang

    2015-01-01

    Full Text Available In this study, the stochastic biochemical reaction model is proposed based on the law of mass action and complex network theory. The dynamics of biochemical reaction system is presented as a set of non-linear differential equations and analyzed at the molecular-scale. Given the initial state and the evolution rules of the biochemical reaction system, the system can achieve homeostasis. Compared with random graph, the biochemical reaction network has larger information capacity and is more efficient in information transmission. This is consistent with theory of evolution.

  5. Conservation Laws in Biochemical Reaction Networks

    DEFF Research Database (Denmark)

    Mahdi, Adam; Ferragut, Antoni; Valls, Claudia

    2017-01-01

    We study the existence of linear and nonlinear conservation laws in biochemical reaction networks with mass-action kinetics. It is straightforward to compute the linear conservation laws as they are related to the left null-space of the stoichiometry matrix. The nonlinear conservation laws...... are difficult to identify and have rarely been considered in the context of mass-action reaction networks. Here, using the Darboux theory of integrability, we provide necessary structural (i.e., parameterindependent) conditions on a reaction network to guarantee the existence of nonlinear conservation laws...

  6. Biochemical Network Stochastic Simulator (BioNetS: software for stochastic modeling of biochemical networks

    Directory of Open Access Journals (Sweden)

    Elston Timothy C

    2004-03-01

    Full Text Available Abstract Background Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. Results We have developed the software package Biochemical Network Stochastic Simulator (BioNetS for efficientlyand accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solvesthe appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from http://www.biospice.org. BioNetS also can be run as a stand alone package. All the required files are accessible from http://x.amath.unc.edu/BioNetS. Conclusions We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.

  7. Fitness effects of fluctuations in biochemical networks

    Science.gov (United States)

    Tanase-Nicola, Sorin

    2009-03-01

    The concentration of many cellular components fluctuates not only as a response to external and internal inputs but also due to random birth and death events of individual molecules. This biochemical noise affects the capacity of every individual cell in a population to respond and adapt to the environment. While the sources and effects of biochemical fluctuations on individual cells have been intensively studied, the effects of noise on the growth rate of a population of cells are much less understood. We present a model of the cell cycle in which the growth and division of individual cells are coupled with the noisy dynamics of their internal components. The model allows us to compute the contribution of the biochemical noise to the average growth rate of a population of cells as a function of the noise strength and the correlation time of the fluctuations. We show that, due to fluctuations, the growth rate of a population of cells is always larger than the average growth rate of a individual cell and can be larger even than a corresponding deterministic model. In most relevant cases it is assumed that the average concentration of a cellular component is close to a value that maximizes the population growth as given by the external, environmental, conditions and the internal cellular regulation. In such cases we show that contribution of fluctuations to the growth rate is negative and increases with the sensitivity of the biochemical networks to the noise sources and the noise correlation time. We also discuss how the selection pressure due to fluctuations affects the structure and parameters of genetic regulatory networks.

  8. On the Adaptive Design Rules of Biochemical Networks in Evolution

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    Bor-Sen Chen

    2007-01-01

    Full Text Available Biochemical networks are the backbones of physiological systems of organisms. Therefore, a biochemical network should be sufficiently robust (not sensitive to tolerate genetic mutations and environmental changes in the evolutionary process. In this study, based on the robustness and sensitivity criteria of biochemical networks, the adaptive design rules are developed for natural selection in the evolutionary process. This will provide insights into the robust adaptive mechanism of biochemical networks in the evolutionary process. We find that if a mutated biochemical network satisfies the robustness and sensitivity criteria of natural selection, there is a high probability for the biochemical network to prevail during natural selection in the evolutionary process. Since there are various mutated biochemical networks that can satisfy these criteria but have some differences in phenotype, the biochemical networks increase their diversities in the evolutionary process. The robustness of a biochemical network enables co-option so that new phenotypes can be generated in evolution. The proposed robust adaptive design rules of natural selection gain much insight into the evolutionary mechanism and provide a systematic robust biochemical circuit design method of biochemical networks for biotechnological and therapeutic purposes in the future.

  9. Structuring evolution: biochemical networks and metabolic diversification in birds.

    Science.gov (United States)

    Morrison, Erin S; Badyaev, Alexander V

    2016-08-25

    Recurrence and predictability of evolution are thought to reflect the correspondence between genomic and phenotypic dimensions of organisms, and the connectivity in deterministic networks within these dimensions. Direct examination of the correspondence between opportunities for diversification imbedded in such networks and realized diversity is illuminating, but is empirically challenging because both the deterministic networks and phenotypic diversity are modified in the course of evolution. Here we overcome this problem by directly comparing the structure of a "global" carotenoid network - comprising of all known enzymatic reactions among naturally occurring carotenoids - with the patterns of evolutionary diversification in carotenoid-producing metabolic networks utilized by birds. We found that phenotypic diversification in carotenoid networks across 250 species was closely associated with enzymatic connectivity of the underlying biochemical network - compounds with greater connectivity occurred the most frequently across species and were the hotspots of metabolic pathway diversification. In contrast, we found no evidence for diversification along the metabolic pathways, corroborating findings that the utilization of the global carotenoid network was not strongly influenced by history in avian evolution. The finding that the diversification in species-specific carotenoid networks is qualitatively predictable from the connectivity of the underlying enzymatic network points to significant structural determinism in phenotypic evolution.

  10. 'BioNessie(G) - a grid enabled biochemical networks simulation environment

    OpenAIRE

    Liu, X; Jiang, J; Ajayi, O; Gu, X; Gilbert, D; Sinnott, R

    2008-01-01

    The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scal...

  11. Robust simplifications of multiscale biochemical networks

    Directory of Open Access Journals (Sweden)

    Zinovyev Andrei

    2008-10-01

    Full Text Available Abstract Background Cellular processes such as metabolism, decision making in development and differentiation, signalling, etc., can be modeled as large networks of biochemical reactions. In order to understand the functioning of these systems, there is a strong need for general model reduction techniques allowing to simplify models without loosing their main properties. In systems biology we also need to compare models or to couple them as parts of larger models. In these situations reduction to a common level of complexity is needed. Results We propose a systematic treatment of model reduction of multiscale biochemical networks. First, we consider linear kinetic models, which appear as "pseudo-monomolecular" subsystems of multiscale nonlinear reaction networks. For such linear models, we propose a reduction algorithm which is based on a generalized theory of the limiting step that we have developed in 1. Second, for non-linear systems we develop an algorithm based on dominant solutions of quasi-stationarity equations. For oscillating systems, quasi-stationarity and averaging are combined to eliminate time scales much faster and much slower than the period of the oscillations. In all cases, we obtain robust simplifications and also identify the critical parameters of the model. The methods are demonstrated for simple examples and for a more complex model of NF-κB pathway. Conclusion Our approach allows critical parameter identification and produces hierarchies of models. Hierarchical modeling is important in "middle-out" approaches when there is need to zoom in and out several levels of complexity. Critical parameter identification is an important issue in systems biology with potential applications to biological control and therapeutics. Our approach also deals naturally with the presence of multiple time scales, which is a general property of systems biology models.

  12. Network planning under uncertainties

    Science.gov (United States)

    Ho, Kwok Shing; Cheung, Kwok Wai

    2008-11-01

    One of the main focuses for network planning is on the optimization of network resources required to build a network under certain traffic demand projection. Traditionally, the inputs to this type of network planning problems are treated as deterministic. In reality, the varying traffic requirements and fluctuations in network resources can cause uncertainties in the decision models. The failure to include the uncertainties in the network design process can severely affect the feasibility and economics of the network. Therefore, it is essential to find a solution that can be insensitive to the uncertain conditions during the network planning process. As early as in the 1960's, a network planning problem with varying traffic requirements over time had been studied. Up to now, this kind of network planning problems is still being active researched, especially for the VPN network design. Another kind of network planning problems under uncertainties that has been studied actively in the past decade addresses the fluctuations in network resources. One such hotly pursued research topic is survivable network planning. It considers the design of a network under uncertainties brought by the fluctuations in topology to meet the requirement that the network remains intact up to a certain number of faults occurring anywhere in the network. Recently, the authors proposed a new planning methodology called Generalized Survivable Network that tackles the network design problem under both varying traffic requirements and fluctuations of topology. Although all the above network planning problems handle various kinds of uncertainties, it is hard to find a generic framework under more general uncertainty conditions that allows a more systematic way to solve the problems. With a unified framework, the seemingly diverse models and algorithms can be intimately related and possibly more insights and improvements can be brought out for solving the problem. This motivates us to seek a

  13. A new dynamical layout algorithm for complex biochemical reaction networks

    OpenAIRE

    Kummer Ursula; Wegner Katja

    2005-01-01

    Abstract Background To study complex biochemical reaction networks in living cells researchers more and more rely on databases and computational methods. In order to facilitate computational approaches, visualisation techniques are highly important. Biochemical reaction networks, e.g. metabolic pathways are often depicted as graphs and these graphs should be drawn dynamically to provide flexibility in the context of different data. Conventional layout algorithms are not sufficient for every k...

  14. Biochemical and secondary metabolites changes under moisture ...

    African Journals Online (AJOL)

    The study showed the importance of carbohydrate and nitrogen cycle related metabolites in mediating tolerance in cassava by affecting their phenotypic expression in the plant. Keywords: Hydrothermal stress, bio-chemicals, pigments, secondary metabolites, cassava. African Journal of Biotechnology, Vol 13(31) 3173-3186 ...

  15. Chemical reaction network approaches to Biochemical Systems Theory.

    Science.gov (United States)

    Arceo, Carlene Perpetua P; Jose, Editha C; Marin-Sanguino, Alberto; Mendoza, Eduardo R

    2015-11-01

    This paper provides a framework to represent a Biochemical Systems Theory (BST) model (in either GMA or S-system form) as a chemical reaction network with power law kinetics. Using this representation, some basic properties and the application of recent results of Chemical Reaction Network Theory regarding steady states of such systems are shown. In particular, Injectivity Theory, including network concordance [36] and the Jacobian Determinant Criterion [43], a "Lifting Theorem" for steady states [26] and the comprehensive results of Müller and Regensburger [31] on complex balanced equilibria are discussed. A partial extension of a recent Emulation Theorem of Cardelli for mass action systems [3] is derived for a subclass of power law kinetic systems. However, it is also shown that the GMA and S-system models of human purine metabolism [10] do not display the reactant-determined kinetics assumed by Müller and Regensburger and hence only a subset of BST models can be handled with their approach. Moreover, since the reaction networks underlying many BST models are not weakly reversible, results for non-complex balanced equilibria are also needed. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks

    Directory of Open Access Journals (Sweden)

    Luca Marchetti

    2017-01-01

    Full Text Available HSimulator is a multithread simulator for mass-action biochemical reaction systems placed in a well-mixed environment. HSimulator provides optimized implementation of a set of widespread state-of-the-art stochastic, deterministic, and hybrid simulation strategies including the first publicly available implementation of the Hybrid Rejection-based Stochastic Simulation Algorithm (HRSSA. HRSSA, the fastest hybrid algorithm to date, allows for an efficient simulation of the models while ensuring the exact simulation of a subset of the reaction network modeling slow reactions. Benchmarks show that HSimulator is often considerably faster than the other considered simulators. The software, running on Java v6.0 or higher, offers a simulation GUI for modeling and visually exploring biological processes and a Javadoc-documented Java library to support the development of custom applications. HSimulator is released under the COSBI Shared Source license agreement (COSBI-SSLA.

  17. Mean field interaction in biochemical reaction networks

    KAUST Repository

    Tembine, Hamidou

    2011-09-01

    In this paper we establish a relationship between chemical dynamics and mean field game dynamics. We show that chemical reaction networks can be studied using noisy mean field limits. We provide deterministic, noisy and switching mean field limits and illustrate them with numerical examples. © 2011 IEEE.

  18. anthropometric and biochemical assessment among under five

    African Journals Online (AJOL)

    DR. AMIN

    Micronutrient deficiencies, especially iron and iodine cause delayed psychomotor development and impaired cognitive function (Leo,. 2011). There are many under nourished children in. Katsina State (Doctors without Border, 2009). Consequently, this study was designed to estimate the prevalence of malnutrition among ...

  19. Autocatalytic sets in a partitioned biochemical network.

    Science.gov (United States)

    Smith, Joshua I; Steel, Mike; Hordijk, Wim

    2014-01-01

    In previous work, RAF theory has been developed as a tool for making theoretical progress on the origin of life question, providing insight into the structure and occurrence of self-sustaining and collectively autocatalytic sets within catalytic polymer networks. We present here an extension in which there are two "independent" polymer sets, where catalysis occurs within and between the sets, but there are no reactions combining polymers from both sets. Such an extension reflects the interaction between nucleic acids and peptides observed in modern cells and proposed forms of early life. We present theoretical work and simulations which suggest that the occurrence of autocatalytic sets is robust to the partitioned structure of the network. We also show that autocatalytic sets remain likely even when the molecules in the system are not polymers, and a low level of inhibition is present. Finally, we present a kinetic extension which assigns a rate to each reaction in the system, and show that identifying autocatalytic sets within such a system is an NP-complete problem. Recent experimental work has challenged the necessity of an RNA world by suggesting that peptide-nucleic acid interactions occurred early in chemical evolution. The present work indicates that such a peptide-RNA world could support the spontaneous development of autocatalytic sets and is thus a feasible alternative worthy of investigation.

  20. Silicon mediated biochemical changes in wheat under salinized and ...

    African Journals Online (AJOL)

    We report on the effects of silicon (150 mg L-1) on the morphological, physiological and biochemical traits in wheat (Triticum aestivum L.) cultivars (salt sensitive; Auqab-2000 and salt tolerant; SARC-5) differing in salt tolerance under saline (10 dS m-1) and non-saline (2 dS m-1) hydroponic culture. Silicon supplementation ...

  1. Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

    Science.gov (United States)

    Kaltenbacher, Barbara; Hasenauer, Jan

    2017-01-01

    Mechanistic mathematical modeling of biochemical reaction networks using ordinary differential equation (ODE) models has improved our understanding of small- and medium-scale biological processes. While the same should in principle hold for large- and genome-scale processes, the computational methods for the analysis of ODE models which describe hundreds or thousands of biochemical species and reactions are missing so far. While individual simulations are feasible, the inference of the model parameters from experimental data is computationally too intensive. In this manuscript, we evaluate adjoint sensitivity analysis for parameter estimation in large scale biochemical reaction networks. We present the approach for time-discrete measurement and compare it to state-of-the-art methods used in systems and computational biology. Our comparison reveals a significantly improved computational efficiency and a superior scalability of adjoint sensitivity analysis. The computational complexity is effectively independent of the number of parameters, enabling the analysis of large- and genome-scale models. Our study of a comprehensive kinetic model of ErbB signaling shows that parameter estimation using adjoint sensitivity analysis requires a fraction of the computation time of established methods. The proposed method will facilitate mechanistic modeling of genome-scale cellular processes, as required in the age of omics. PMID:28114351

  2. A new dynamical layout algorithm for complex biochemical reaction networks.

    Science.gov (United States)

    Wegner, Katja; Kummer, Ursula

    2005-08-26

    To study complex biochemical reaction networks in living cells researchers more and more rely on databases and computational methods. In order to facilitate computational approaches, visualisation techniques are highly important. Biochemical reaction networks, e.g. metabolic pathways are often depicted as graphs and these graphs should be drawn dynamically to provide flexibility in the context of different data. Conventional layout algorithms are not sufficient for every kind of pathway in biochemical research. This is mainly due to certain conventions to which biochemists/biologists are used to and which are not in accordance to conventional layout algorithms. A number of approaches has been developed to improve this situation. Some of these are used in the context of biochemical databases and make more or less use of the information in these databases to aid the layout process. However, visualisation becomes also more and more important in modelling and simulation tools which mostly do not offer additional connections to databases. Therefore, layout algorithms used in these tools have to work independently of any databases. In addition, all of the existing algorithms face some limitations with respect to the number of edge crossings when it comes to larger biochemical systems due to the interconnectivity of these. Last but not least, in some cases, biochemical conventions are not met properly. Out of these reasons we have developed a new algorithm which tackles these problems by reducing the number of edge crossings in complex systems, taking further biological conventions into account to identify and visualise cycles. Furthermore the algorithm is independent from database information in order to be easily adopted in any application. It can also be tested as part of the SimWiz package (free to download for academic users at 1). The new algorithm reduces the complexity of pathways, as well as edge crossings and edge length in the resulting graphical representation

  3. A new dynamical layout algorithm for complex biochemical reaction networks

    Directory of Open Access Journals (Sweden)

    Kummer Ursula

    2005-08-01

    Full Text Available Abstract Background To study complex biochemical reaction networks in living cells researchers more and more rely on databases and computational methods. In order to facilitate computational approaches, visualisation techniques are highly important. Biochemical reaction networks, e.g. metabolic pathways are often depicted as graphs and these graphs should be drawn dynamically to provide flexibility in the context of different data. Conventional layout algorithms are not sufficient for every kind of pathway in biochemical research. This is mainly due to certain conventions to which biochemists/biologists are used to and which are not in accordance to conventional layout algorithms. A number of approaches has been developed to improve this situation. Some of these are used in the context of biochemical databases and make more or less use of the information in these databases to aid the layout process. However, visualisation becomes also more and more important in modelling and simulation tools which mostly do not offer additional connections to databases. Therefore, layout algorithms used in these tools have to work independently of any databases. In addition, all of the existing algorithms face some limitations with respect to the number of edge crossings when it comes to larger biochemical systems due to the interconnectivity of these. Last but not least, in some cases, biochemical conventions are not met properly. Results Out of these reasons we have developed a new algorithm which tackles these problems by reducing the number of edge crossings in complex systems, taking further biological conventions into account to identify and visualise cycles. Furthermore the algorithm is independent from database information in order to be easily adopted in any application. It can also be tested as part of the SimWiz package (free to download for academic users at 1. Conclusion The new algorithm reduces the complexity of pathways, as well as edge crossings

  4. Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices

    DEFF Research Database (Denmark)

    Schmidt, Karsten; Carlsen, Morten; Nielsen, Jens Bredal

    1997-01-01

    has been implemented that describes label distribution in primary carbon metabolism, i.e., in a metabolic network including the Embden-Meyerhof-Parnas and pentose phosphate pathway, the tricarboxylic acid cycle, and selected anaplerotic reaction sequences. The model calculates the steady state label......Within the last decades NMR spectroscopy has undergone tremendous development and has become a powerful analytical tool for the investigation of intracellular flux distributions in biochemical networks using C-13-labeled substrates. Not only are the experiments much easier to conduct than...... experiments employing radioactive tracer elements, but NMR spectroscopy also provides additional information on the labeling pattern of the metabolites. Whereas the maximum amount of information obtainable with C-14-labeled substrates is the fractional enrichment in the individual carbon atom positions, NMR...

  5. Efficient Parallel Statistical Model Checking of Biochemical Networks

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    Paolo Ballarini

    2009-12-01

    Full Text Available We consider the problem of verifying stochastic models of biochemical networks against behavioral properties expressed in temporal logic terms. Exact probabilistic verification approaches such as, for example, CSL/PCTL model checking, are undermined by a huge computational demand which rule them out for most real case studies. Less demanding approaches, such as statistical model checking, estimate the likelihood that a property is satisfied by sampling executions out of the stochastic model. We propose a methodology for efficiently estimating the likelihood that a LTL property P holds of a stochastic model of a biochemical network. As with other statistical verification techniques, the methodology we propose uses a stochastic simulation algorithm for generating execution samples, however there are three key aspects that improve the efficiency: first, the sample generation is driven by on-the-fly verification of P which results in optimal overall simulation time. Second, the confidence interval estimation for the probability of P to hold is based on an efficient variant of the Wilson method which ensures a faster convergence. Third, the whole methodology is designed according to a parallel fashion and a prototype software tool has been implemented that performs the sampling/verification process in parallel over an HPC architecture.

  6. Coarse-graining stochastic biochemical networks: adiabaticity and fast simulations

    Energy Technology Data Exchange (ETDEWEB)

    Nemenman, Ilya [Los Alamos National Laboratory; Sinitsyn, Nikolai [Los Alamos National Laboratory; Hengartner, Nick [Los Alamos National Laboratory

    2008-01-01

    We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscoplc, non-Poissonian fluctuations of the slow ones. Our approach, which is similar to the Born-Oppenhelmer approximation in quantum mechanics, follows from the stochastic path Integral representation of the cumulant generating function of reaction events. In applications with a small number of chemIcal reactions, It produces analytical expressions for cumulants of chemical fluxes between the slow variables. This allows for a low-dimensional, Interpretable representation and can be used for coarse-grained numerical simulation schemes with a small computational complexity and yet high accuracy. As an example, we derive the coarse-grained description for a chain of biochemical reactions, and show that the coarse-grained and the microscopic simulations are in an agreement, but the coarse-gralned simulations are three orders of magnitude faster.

  7. Least-squares methods for identifying biochemical regulatory networks from noisy measurements

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    Heslop-Harrison Pat

    2007-01-01

    Full Text Available Abstract Background We consider the problem of identifying the dynamic interactions in biochemical networks from noisy experimental data. Typically, approaches for solving this problem make use of an estimation algorithm such as the well-known linear Least-Squares (LS estimation technique. We demonstrate that when time-series measurements are corrupted by white noise and/or drift noise, more accurate and reliable identification of network interactions can be achieved by employing an estimation algorithm known as Constrained Total Least Squares (CTLS. The Total Least Squares (TLS technique is a generalised least squares method to solve an overdetermined set of equations whose coefficients are noisy. The CTLS is a natural extension of TLS to the case where the noise components of the coefficients are correlated, as is usually the case with time-series measurements of concentrations and expression profiles in gene networks. Results The superior performance of the CTLS method in identifying network interactions is demonstrated on three examples: a genetic network containing four genes, a network describing p53 activity and mdm2 messenger RNA interactions, and a recently proposed kinetic model for interleukin (IL-6 and (IL-12b messenger RNA expression as a function of ATF3 and NF-κB promoter binding. For the first example, the CTLS significantly reduces the errors in the estimation of the Jacobian for the gene network. For the second, the CTLS reduces the errors from the measurements that are corrupted by white noise and the effect of neglected kinetics. For the third, it allows the correct identification, from noisy data, of the negative regulation of (IL-6 and (IL-12b by ATF3. Conclusion The significant improvements in performance demonstrated by the CTLS method under the wide range of conditions tested here, including different levels and types of measurement noise and different numbers of data points, suggests that its application will enable

  8. Optimal experiment design for model selection in biochemical networks.

    Science.gov (United States)

    Vanlier, Joep; Tiemann, Christian A; Hilbers, Peter A J; van Riel, Natal A W

    2014-02-20

    Mathematical modeling is often used to formalize hypotheses on how a biochemical network operates by discriminating between competing models. Bayesian model selection offers a way to determine the amount of evidence that data provides to support one model over the other while favoring simple models. In practice, the amount of experimental data is often insufficient to make a clear distinction between competing models. Often one would like to perform a new experiment which would discriminate between competing hypotheses. We developed a novel method to perform Optimal Experiment Design to predict which experiments would most effectively allow model selection. A Bayesian approach is applied to infer model parameter distributions. These distributions are sampled and used to simulate from multivariate predictive densities. The method is based on a k-Nearest Neighbor estimate of the Jensen Shannon divergence between the multivariate predictive densities of competing models. We show that the method successfully uses predictive differences to enable model selection by applying it to several test cases. Because the design criterion is based on predictive distributions, which can be computed for a wide range of model quantities, the approach is very flexible. The method reveals specific combinations of experiments which improve discriminability even in cases where data is scarce. The proposed approach can be used in conjunction with existing Bayesian methodologies where (approximate) posteriors have been determined, making use of relations that exist within the inferred posteriors.

  9. Modelling biochemical networks with intrinsic time delays: a hybrid semi-parametric approach

    Directory of Open Access Journals (Sweden)

    Oliveira Rui

    2010-09-01

    Full Text Available Abstract Background This paper presents a method for modelling dynamical biochemical networks with intrinsic time delays. Since the fundamental mechanisms leading to such delays are many times unknown, non conventional modelling approaches become necessary. Herein, a hybrid semi-parametric identification methodology is proposed in which discrete time series are incorporated into fundamental material balance models. This integration results in hybrid delay differential equations which can be applied to identify unknown cellular dynamics. Results The proposed hybrid modelling methodology was evaluated using two case studies. The first of these deals with dynamic modelling of transcriptional factor A in mammalian cells. The protein transport from the cytosol to the nucleus introduced a delay that was accounted for by discrete time series formulation. The second case study focused on a simple network with distributed time delays that demonstrated that the discrete time delay formalism has broad applicability to both discrete and distributed delay problems. Conclusions Significantly better prediction qualities of the novel hybrid model were obtained when compared to dynamical structures without time delays, being the more distinctive the more significant the underlying system delay is. The identification of the system delays by studies of different discrete modelling delays was enabled by the proposed structure. Further, it was shown that the hybrid discrete delay methodology is not limited to discrete delay systems. The proposed method is a powerful tool to identify time delays in ill-defined biochemical networks.

  10. BIOCHEMICAL PROCESSES IN CHERNOZEM SOIL UNDER DIFFERENT FERTILIZATION SYSTEMS

    Directory of Open Access Journals (Sweden)

    Ecaterina Emnova

    2012-06-01

    Full Text Available The paper deals with the evaluation of the intensity of certain soil biochemical processes (e.g. soil organic C mineralization at Organic and mixed Mineral+Organic fertilization of typical chernozem in crop rotation dynamics (for 6 years by use of eco-physiological indicators of biological soil quality: microbial biomass carbon, basal soil respiration, as well as, microbial and metabolic quotients. Soil sampling was performed from a long-term field crop experiment, which has been established in 1971 at the Balti steppe (Northern Moldova. The crop types had a more considerable impact on the soil microbial biomass accumulation and community biochemical activity compared to long-term Organic or mixed Mineral + Organic fertilizers amendments. The Org fertilization system doesn’t make it possible to avoid the loss of organic C in arable typical chernozem. The organic fertilizer (cattle manure is able to mitigate the negative consequences of long-term mineral fertilization.

  11. Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

    LENUS (Irish Health Repository)

    Casey, Fergal

    2011-08-22

    Abstract Background Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. Results We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. Conclusion We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.

  12. Discriminating between rival biochemical network models: three approaches to optimal experiment design.

    Science.gov (United States)

    Mélykúti, Bence; August, Elias; Papachristodoulou, Antonis; El-Samad, Hana

    2010-04-01

    The success of molecular systems biology hinges on the ability to use computational models to design predictive experiments, and ultimately unravel underlying biological mechanisms. A problem commonly encountered in the computational modelling of biological networks is that alternative, structurally different models of similar complexity fit a set of experimental data equally well. In this case, more than one molecular mechanism can explain available data. In order to rule out the incorrect mechanisms, one needs to invalidate incorrect models. At this point, new experiments maximizing the difference between the measured values of alternative models should be proposed and conducted. Such experiments should be optimally designed to produce data that are most likely to invalidate incorrect model structures. In this paper we develop methodologies for the optimal design of experiments with the aim of discriminating between different mathematical models of the same biological system. The first approach determines the 'best' initial condition that maximizes the L2 (energy) distance between the outputs of the rival models. In the second approach, we maximize the L2-distance of the outputs by designing the optimal external stimulus (input) profile of unit L2-norm. Our third method uses optimized structural changes (corresponding, for example, to parameter value changes reflecting gene knock-outs) to achieve the same goal. The numerical implementation of each method is considered in an example, signal processing in starving Dictyostelium amoebae. Model-based design of experiments improves both the reliability and the efficiency of biochemical network model discrimination. This opens the way to model invalidation, which can be used to perfect our understanding of biochemical networks. Our general problem formulation together with the three proposed experiment design methods give the practitioner new tools for a systems biology approach to experiment design.

  13. Discriminating between rival biochemical network models: three approaches to optimal experiment design

    Directory of Open Access Journals (Sweden)

    August Elias

    2010-04-01

    Full Text Available Abstract Background The success of molecular systems biology hinges on the ability to use computational models to design predictive experiments, and ultimately unravel underlying biological mechanisms. A problem commonly encountered in the computational modelling of biological networks is that alternative, structurally different models of similar complexity fit a set of experimental data equally well. In this case, more than one molecular mechanism can explain available data. In order to rule out the incorrect mechanisms, one needs to invalidate incorrect models. At this point, new experiments maximizing the difference between the measured values of alternative models should be proposed and conducted. Such experiments should be optimally designed to produce data that are most likely to invalidate incorrect model structures. Results In this paper we develop methodologies for the optimal design of experiments with the aim of discriminating between different mathematical models of the same biological system. The first approach determines the 'best' initial condition that maximizes the L2 (energy distance between the outputs of the rival models. In the second approach, we maximize the L2-distance of the outputs by designing the optimal external stimulus (input profile of unit L2-norm. Our third method uses optimized structural changes (corresponding, for example, to parameter value changes reflecting gene knock-outs to achieve the same goal. The numerical implementation of each method is considered in an example, signal processing in starving Dictyostelium amœbæ. Conclusions Model-based design of experiments improves both the reliability and the efficiency of biochemical network model discrimination. This opens the way to model invalidation, which can be used to perfect our understanding of biochemical networks. Our general problem formulation together with the three proposed experiment design methods give the practitioner new tools for a systems

  14. Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology.

    Science.gov (United States)

    Santra, Tapesh; Kolch, Walter; Kholodenko, Boris N

    2013-07-06

    Recent advancements in genetics and proteomics have led to the acquisition of large quantitative data sets. However, the use of these data to reverse engineer biochemical networks has remained a challenging problem. Many methods have been proposed to infer biochemical network topologies from different types of biological data. Here, we focus on unraveling network topologies from steady state responses of biochemical networks to successive experimental perturbations. We propose a computational algorithm which combines a deterministic network inference method termed Modular Response Analysis (MRA) and a statistical model selection algorithm called Bayesian Variable Selection, to infer functional interactions in cellular signaling pathways and gene regulatory networks. It can be used to identify interactions among individual molecules involved in a biochemical pathway or reveal how different functional modules of a biological network interact with each other to exchange information. In cases where not all network components are known, our method reveals functional interactions which are not direct but correspond to the interaction routes through unknown elements. Using computer simulated perturbation responses of signaling pathways and gene regulatory networks from the DREAM challenge, we demonstrate that the proposed method is robust against noise and scalable to large networks. We also show that our method can infer network topologies using incomplete perturbation datasets. Consequently, we have used this algorithm to explore the ERBB regulated G1/S transition pathway in certain breast cancer cells to understand the molecular mechanisms which cause these cells to become drug resistant. The algorithm successfully inferred many well characterized interactions of this pathway by analyzing experimentally obtained perturbation data. Additionally, it identified some molecular interactions which promote drug resistance in breast cancer cells. The proposed algorithm

  15. Validation of artificial neural network models for predicting biochemical markers associated with male infertility.

    Science.gov (United States)

    Vickram, A S; Kamini, A Rao; Das, Raja; Pathy, M Ramesh; Parameswari, R; Archana, K; Sridharan, T B

    2016-08-01

    Seminal fluid is the secretion from many glands comprised of several organic and inorganic compounds including free amino acids, proteins, fructose, glucosidase, zinc, and other scavenging elements like Mg(2+), Ca(2+), K(+), and Na(+). Therefore, in the view of development of novel approaches and proper diagnosis to male infertility, overall understanding of the biochemical and molecular composition and its role in regulation of sperm quality is highly desirable. Perhaps this can be achieved through artificial intelligence. This study was aimed to elucidate and predict various biochemical markers present in human seminal plasma with three different neural network models. A total of 177 semen samples were collected for this research (both fertile and infertile samples) and immediately processed to prepare a semen analysis report, based on the protocol of the World Health Organization (WHO [2010]). The semen samples were then categorized into oligoasthenospermia (n=35), asthenospermia (n=35), azoospermia (n=22), normospermia (n=34), oligospermia (n=34), and control (n=17). The major biochemical parameters like total protein content, fructose, glucosidase, and zinc content were elucidated by standard protocols. All the biochemical markers were predicted by using three different artificial neural network (ANN) models with semen parameters as inputs. Of the three models, the back propagation neural network model (BPNN) yielded the best results with mean absolute error 0.025, -0.080, 0.166, and -0.057 for protein, fructose, glucosidase, and zinc, respectively. This suggests that BPNN can be used to predict biochemical parameters for the proper diagnosis of male infertility in assisted reproductive technology (ART) centres. AAS: absorption spectroscopy; AI: artificial intelligence; ANN: artificial neural networks; ART: assisted reproductive technology; BPNN: back propagation neural network model; DT: decision tress; MLP: multilayer perceptron; PESA: percutaneous

  16. Synchronization analysis of coloured delayed networks under ...

    Indian Academy of Sciences (India)

    This paper investigates synchronization of coloured delayed networks under decentralized pinning intermittent control. To begin with, the time delays are taken into account in the coloured networks. In addition, we propose a decentralized pinning intermittent control for coloured delayed networks, which is different from that ...

  17. Identification of neutral biochemical network models from time series data

    Directory of Open Access Journals (Sweden)

    Maia Marco

    2009-05-01

    Full Text Available Abstract Background The major difficulty in modeling biological systems from multivariate time series is the identification of parameter sets that endow a model with dynamical behaviors sufficiently similar to the experimental data. Directly related to this parameter estimation issue is the task of identifying the structure and regulation of ill-characterized systems. Both tasks are simplified if the mathematical model is canonical, i.e., if it is constructed according to strict guidelines. Results In this report, we propose a method for the identification of admissible parameter sets of canonical S-systems from biological time series. The method is based on a Monte Carlo process that is combined with an improved version of our previous parameter optimization algorithm. The method maps the parameter space into the network space, which characterizes the connectivity among components, by creating an ensemble of decoupled S-system models that imitate the dynamical behavior of the time series with sufficient accuracy. The concept of sloppiness is revisited in the context of these S-system models with an exploration not only of different parameter sets that produce similar dynamical behaviors but also different network topologies that yield dynamical similarity. Conclusion The proposed parameter estimation methodology was applied to actual time series data from the glycolytic pathway of the bacterium Lactococcus lactis and led to ensembles of models with different network topologies. In parallel, the parameter optimization algorithm was applied to the same dynamical data upon imposing a pre-specified network topology derived from prior biological knowledge, and the results from both strategies were compared. The results suggest that the proposed method may serve as a powerful exploration tool for testing hypotheses and the design of new experiments.

  18. Identification of neutral biochemical network models from time series data.

    Science.gov (United States)

    Vilela, Marco; Vinga, Susana; Maia, Marco A Grivet Mattoso; Voit, Eberhard O; Almeida, Jonas S

    2009-05-05

    The major difficulty in modeling biological systems from multivariate time series is the identification of parameter sets that endow a model with dynamical behaviors sufficiently similar to the experimental data. Directly related to this parameter estimation issue is the task of identifying the structure and regulation of ill-characterized systems. Both tasks are simplified if the mathematical model is canonical, i.e., if it is constructed according to strict guidelines. In this report, we propose a method for the identification of admissible parameter sets of canonical S-systems from biological time series. The method is based on a Monte Carlo process that is combined with an improved version of our previous parameter optimization algorithm. The method maps the parameter space into the network space, which characterizes the connectivity among components, by creating an ensemble of decoupled S-system models that imitate the dynamical behavior of the time series with sufficient accuracy. The concept of sloppiness is revisited in the context of these S-system models with an exploration not only of different parameter sets that produce similar dynamical behaviors but also different network topologies that yield dynamical similarity. The proposed parameter estimation methodology was applied to actual time series data from the glycolytic pathway of the bacterium Lactococcus lactis and led to ensembles of models with different network topologies. In parallel, the parameter optimization algorithm was applied to the same dynamical data upon imposing a pre-specified network topology derived from prior biological knowledge, and the results from both strategies were compared. The results suggest that the proposed method may serve as a powerful exploration tool for testing hypotheses and the design of new experiments.

  19. Deterministic and stochastic simulation and analysis of biochemical reaction networks the lactose operon example.

    Science.gov (United States)

    Yildirim, Necmettin; Kazanci, Caner

    2011-01-01

    A brief introduction to mathematical modeling of biochemical regulatory reaction networks is presented. Both deterministic and stochastic modeling techniques are covered with examples from enzyme kinetics, coupled reaction networks with oscillatory dynamics and bistability. The Yildirim-Mackey model for lactose operon is used as an example to discuss and show how deterministic and stochastic methods can be used to investigate various aspects of this bacterial circuit. © 2011 Elsevier Inc. All rights reserved.

  20. Physiological and biochemical relationship under drought stress in ...

    African Journals Online (AJOL)

    Some statistical procedures like correlation, stepwise regression, factor analysis and cluster analysis were used to study the relationship between wheat grain yield and some physiological parameters under drought conditions. Results reveal that the ratio fv/fm of chlorophyll fluorescence is the most effective parameter to ...

  1. Engineering interpenetrating network hydrogels as biomimetic cell niche with independently tunable biochemical and mechanical properties.

    Science.gov (United States)

    Tong, Xinming; Yang, Fan

    2014-02-01

    Hydrogels have been widely used as artificial cell niche to mimic extracellular matrix with tunable properties. However, changing biochemical cues in hydrogels developed-to-date would often induce simultaneous changes in mechanical properties, which do not support mechanistic studies on stem cell-niche interactions. Here we report the development of a PEG-based interpenetrating network (IPN), which is composed of two polymer networks that can independently and simultaneously crosslink to form hydrogels in a cell-friendly manner. The resulting IPN hydrogel allows independently tunable biochemical and mechanical properties, as well as stable and more homogeneous presentation of biochemical ligands in 3D than currently available methods. We demonstrate the potential of our IPN platform for elucidating stem cell-niche interactions by modulating osteogenic differentiation of human adipose-derived stem cells. The versatility of such IPN hydrogels is further demonstrated using three distinct and widely used polymers to form the mechanical network while keeping the biochemical network constant. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. A structured approach for the engineering of biochemical network models, illustrated for signalling pathways

    NARCIS (Netherlands)

    Breitling, Rainer; Gilbert, David; Heiner, Monika; Orton, Richard

    Quantitative models of biochemical networks (signal transduction cascades, metabolic pathways, gene regulatory circuits) are a central component of modern systems biology. Building and managing these complex models is a major challenge that can benefit from the application of formal methods adopted

  3. Efficient Characterization of Parametric Uncertainty of Complex (Biochemical Networks.

    Directory of Open Access Journals (Sweden)

    Claudia Schillings

    2015-08-01

    Full Text Available Parametric uncertainty is a particularly challenging and relevant aspect of systems analysis in domains such as systems biology where, both for inference and for assessing prediction uncertainties, it is essential to characterize the system behavior globally in the parameter space. However, current methods based on local approximations or on Monte-Carlo sampling cope only insufficiently with high-dimensional parameter spaces associated with complex network models. Here, we propose an alternative deterministic methodology that relies on sparse polynomial approximations. We propose a deterministic computational interpolation scheme which identifies most significant expansion coefficients adaptively. We present its performance in kinetic model equations from computational systems biology with several hundred parameters and state variables, leading to numerical approximations of the parametric solution on the entire parameter space. The scheme is based on adaptive Smolyak interpolation of the parametric solution at judiciously and adaptively chosen points in parameter space. As Monte-Carlo sampling, it is "non-intrusive" and well-suited for massively parallel implementation, but affords higher convergence rates. This opens up new avenues for large-scale dynamic network analysis by enabling scaling for many applications, including parameter estimation, uncertainty quantification, and systems design.

  4. Thermodynamically based constraints for rate coefficients of large biochemical networks.

    Science.gov (United States)

    Vlad, Marcel O; Ross, John

    2009-01-01

    Wegscheider cyclicity conditions are relationships among the rate coefficients of a complex reaction network, which ensure the compatibility of kinetic equations with the conditions for thermodynamic equilibrium. The detailed balance at equilibrium, that is the equilibration of forward and backward rates for each elementary reaction, leads to compatibility between the conditions of kinetic and thermodynamic equilibrium. Therefore, Wegscheider cyclicity conditions can be derived by eliminating the equilibrium concentrations from the conditions of detailed balance. We develop matrix algebra tools needed to carry out this elimination, reexamine an old derivation of the general form of Wegscheider cyclicity condition, and develop new derivations which lead to more compact and easier-to-use formulas. We derive scaling laws for the nonequilibrium rates of a complex reaction network, which include Wegscheider conditions as a particular case. The scaling laws for the rates are used for clarifying the kinetic and thermodynamic meaning of Wegscheider cyclicity conditions. Finally, we discuss different ways of using Wegscheider cyclicity conditions for kinetic computations in systems biology.

  5. Recursively constructing analytic expressions for equilibrium distributions of stochastic biochemical reaction networks.

    Science.gov (United States)

    Meng, X Flora; Baetica, Ania-Ariadna; Singhal, Vipul; Murray, Richard M

    2017-05-01

    Noise is often indispensable to key cellular activities, such as gene expression, necessitating the use of stochastic models to capture its dynamics. The chemical master equation (CME) is a commonly used stochastic model of Kolmogorov forward equations that describe how the probability distribution of a chemically reacting system varies with time. Finding analytic solutions to the CME can have benefits, such as expediting simulations of multiscale biochemical reaction networks and aiding the design of distributional responses. However, analytic solutions are rarely known. A recent method of computing analytic stationary solutions relies on gluing simple state spaces together recursively at one or two states. We explore the capabilities of this method and introduce algorithms to derive analytic stationary solutions to the CME. We first formally characterize state spaces that can be constructed by performing single-state gluing of paths, cycles or both sequentially. We then study stochastic biochemical reaction networks that consist of reversible, elementary reactions with two-dimensional state spaces. We also discuss extending the method to infinite state spaces and designing the stationary behaviour of stochastic biochemical reaction networks. Finally, we illustrate the aforementioned ideas using examples that include two interconnected transcriptional components and biochemical reactions with two-dimensional state spaces. © 2017 The Author(s).

  6. Identification of alterations in the Jacobian of biochemical reaction networks from steady state covariance data at two conditions.

    Science.gov (United States)

    Kügler, Philipp; Yang, Wei

    2014-06-01

    Model building of biochemical reaction networks typically involves experiments in which changes in the behavior due to natural or experimental perturbations are observed. Computational models of reaction networks are also used in a systems biology approach to study how transitions from a healthy to a diseased state result from changes in genetic or environmental conditions. In this paper we consider the nonlinear inverse problem of inferring information about the Jacobian of a Langevin type network model from covariance data of steady state concentrations associated to two different experimental conditions. Under idealized assumptions on the Langevin fluctuation matrices we prove that relative alterations in the network Jacobian can be uniquely identified when comparing the two data sets. Based on this result and the premise that alteration is locally confined to separable parts due to network modularity we suggest a computational approach using hybrid stochastic-deterministic optimization for the detection of perturbations in the network Jacobian using the sparsity promoting effect of [Formula: see text]-penalization. Our approach is illustrated by means of published metabolomic and signaling reaction networks.

  7. METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks

    Directory of Open Access Journals (Sweden)

    Holzhütter Hermann-Georg

    2007-01-01

    Full Text Available Abstract Background One central goal of computational systems biology is the mathematical modelling of complex metabolic reaction networks. The first and most time-consuming step in the development of such models consists in the stoichiometric reconstruction of the network, i. e. compilation of all metabolites, reactions and transport processes relevant to the considered network and their assignment to the various cellular compartments. Therefore an information system is required to collect and manage data from different databases and scientific literature in order to generate a metabolic network of biochemical reactions that can be subjected to further computational analyses. Results The computer program METANNOGEN facilitates the reconstruction of metabolic networks. It uses the well-known database of biochemical reactions KEGG of biochemical reactions as primary information source from which biochemical reactions relevant to the considered network can be selected, edited and stored in a separate, user-defined database. Reactions not contained in KEGG can be entered manually into the system. To aid the decision whether or not a reaction selected from KEGG belongs to the considered network METANNOGEN contains information of SWISSPROT and ENSEMBL and provides Web links to a number of important information sources like METACYC, BRENDA, NIST, and REACTOME. If a reaction is reported to occur in more than one cellular compartment, a corresponding number of reactions is generated each referring to one specific compartment. Transport processes of metabolites are entered like chemical reactions where reactants and products have different compartment attributes. The list of compartmentalized biochemical reactions and membrane transport processes compiled by means of METANNOGEN can be exported as an SBML file for further computational analysis. METANNOGEN is highly customizable with respect to the content of the SBML output file, additional data

  8. CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis.

    Science.gov (United States)

    Inoue, Kentaro; Maeda, Kazuhiro; Miyabe, Takaaki; Matsuoka, Yu; Kurata, Hiroyuki

    2014-09-01

    Mathematical modeling has become a standard technique to understand the dynamics of complex biochemical systems. To promote the modeling, we had developed the CADLIVE dynamic simulator that automatically converted a biochemical map into its associated mathematical model, simulated its dynamic behaviors and analyzed its robustness. To enhance the feasibility by CADLIVE and extend its functions, we propose the CADLIVE toolbox available for MATLAB, which implements not only the existing functions of the CADLIVE dynamic simulator, but also the latest tools including global parameter search methods with robustness analysis. The seamless, bottom-up processes consisting of biochemical network construction, automatic construction of its dynamic model, simulation, optimization, and S-system analysis greatly facilitate dynamic modeling, contributing to the research of systems biology and synthetic biology. This application can be freely downloaded from http://www.cadlive.jp/CADLIVE_MATLAB/ together with an instruction.

  9. Condor-COPASI: high-throughput computing for biochemical networks

    Directory of Open Access Journals (Sweden)

    Kent Edward

    2012-07-01

    Full Text Available Abstract Background Mathematical modelling has become a standard technique to improve our understanding of complex biological systems. As models become larger and more complex, simulations and analyses require increasing amounts of computational power. Clusters of computers in a high-throughput computing environment can help to provide the resources required for computationally expensive model analysis. However, exploiting such a system can be difficult for users without the necessary expertise. Results We present Condor-COPASI, a server-based software tool that integrates COPASI, a biological pathway simulation tool, with Condor, a high-throughput computing environment. Condor-COPASI provides a web-based interface, which makes it extremely easy for a user to run a number of model simulation and analysis tasks in parallel. Tasks are transparently split into smaller parts, and submitted for execution on a Condor pool. Result output is presented to the user in a number of formats, including tables and interactive graphical displays. Conclusions Condor-COPASI can effectively use a Condor high-throughput computing environment to provide significant gains in performance for a number of model simulation and analysis tasks. Condor-COPASI is free, open source software, released under the Artistic License 2.0, and is suitable for use by any institution with access to a Condor pool. Source code is freely available for download at http://code.google.com/p/condor-copasi/, along with full instructions on deployment and usage.

  10. Emergence of switch-like behavior in a large family of simple biochemical networks.

    Directory of Open Access Journals (Sweden)

    Dan Siegal-Gaskins

    2011-05-01

    Full Text Available Bistability plays a central role in the gene regulatory networks (GRNs controlling many essential biological functions, including cellular differentiation and cell cycle control. However, establishing the network topologies that can exhibit bistability remains a challenge, in part due to the exceedingly large variety of GRNs that exist for even a small number of components. We begin to address this problem by employing chemical reaction network theory in a comprehensive in silico survey to determine the capacity for bistability of more than 40,000 simple networks that can be formed by two transcription factor-coding genes and their associated proteins (assuming only the most elementary biochemical processes. We find that there exist reaction rate constants leading to bistability in ∼90% of these GRN models, including several circuits that do not contain any of the TF cooperativity commonly associated with bistable systems, and the majority of which could only be identified as bistable through an original subnetwork-based analysis. A topological sorting of the two-gene family of networks based on the presence or absence of biochemical reactions reveals eleven minimal bistable networks (i.e., bistable networks that do not contain within them a smaller bistable subnetwork. The large number of previously unknown bistable network topologies suggests that the capacity for switch-like behavior in GRNs arises with relative ease and is not easily lost through network evolution. To highlight the relevance of the systematic application of CRNT to bistable network identification in real biological systems, we integrated publicly available protein-protein interaction, protein-DNA interaction, and gene expression data from Saccharomyces cerevisiae, and identified several GRNs predicted to behave in a bistable fashion.

  11. Dramatic reduction of dimensionality in large biochemical networks owing to strong pair correlations

    Science.gov (United States)

    Dworkin, Michael; Mukherjee, Sayak; Jayaprakash, Ciriyam; Das, Jayajit

    2012-01-01

    Large multi-dimensionality of high-throughput datasets pertaining to cell signalling and gene regulation renders it difficult to extract mechanisms underlying the complex kinetics involving various biochemical compounds (e.g. proteins and lipids). Data-driven models often circumvent this difficulty by using pair correlations of the protein expression levels to produce a small number (fewer than 10) of principal components, each a linear combination of the concentrations, to successfully model how cells respond to different stimuli. However, it is not understood if this reduction is specific to a particular biological system or to nature of the stimuli used in these experiments. We study temporal changes in pair correlations, described by the covariance matrix, between concentrations of different molecular species that evolve following deterministic mass-action kinetics in large biologically relevant reaction networks and show that this dramatic reduction of dimensions (from hundreds to less than five) arises from the strong correlations between different species at any time and is insensitive to the form of the nonlinear interactions, network architecture, and to a wide range of values of rate constants and concentrations. We relate temporal changes in the eigenvalue spectrum of the covariance matrix to low-dimensional, local changes in directions of the system trajectory embedded in much larger dimensions using elementary differential geometry. We illustrate how to extract biologically relevant insights such as identifying significant timescales and groups of correlated chemical species from our analysis. Our work provides for the first time, to our knowledge, a theoretical underpinning for the successful experimental analysis and points to a way to extract mechanisms from large-scale high-throughput datasets. PMID:22378749

  12. Dramatic reduction of dimensionality in large biochemical networks owing to strong pair correlations.

    Science.gov (United States)

    Dworkin, Michael; Mukherjee, Sayak; Jayaprakash, Ciriyam; Das, Jayajit

    2012-08-07

    Large multi-dimensionality of high-throughput datasets pertaining to cell signalling and gene regulation renders it difficult to extract mechanisms underlying the complex kinetics involving various biochemical compounds (e.g. proteins and lipids). Data-driven models often circumvent this difficulty by using pair correlations of the protein expression levels to produce a small number (fewer than 10) of principal components, each a linear combination of the concentrations, to successfully model how cells respond to different stimuli. However, it is not understood if this reduction is specific to a particular biological system or to nature of the stimuli used in these experiments. We study temporal changes in pair correlations, described by the covariance matrix, between concentrations of different molecular species that evolve following deterministic mass-action kinetics in large biologically relevant reaction networks and show that this dramatic reduction of dimensions (from hundreds to less than five) arises from the strong correlations between different species at any time and is insensitive to the form of the nonlinear interactions, network architecture, and to a wide range of values of rate constants and concentrations. We relate temporal changes in the eigenvalue spectrum of the covariance matrix to low-dimensional, local changes in directions of the system trajectory embedded in much larger dimensions using elementary differential geometry. We illustrate how to extract biologically relevant insights such as identifying significant timescales and groups of correlated chemical species from our analysis. Our work provides for the first time, to our knowledge, a theoretical underpinning for the successful experimental analysis and points to a way to extract mechanisms from large-scale high-throughput datasets.

  13. A structured approach for the engineering of biochemical network models, illustrated for signalling pathways.

    Science.gov (United States)

    Breitling, Rainer; Gilbert, David; Heiner, Monika; Orton, Richard

    2008-09-01

    Quantitative models of biochemical networks (signal transduction cascades, metabolic pathways, gene regulatory circuits) are a central component of modern systems biology. Building and managing these complex models is a major challenge that can benefit from the application of formal methods adopted from theoretical computing science. Here we provide a general introduction to the field of formal modelling, which emphasizes the intuitive biochemical basis of the modelling process, but is also accessible for an audience with a background in computing science and/or model engineering. We show how signal transduction cascades can be modelled in a modular fashion, using both a qualitative approach--qualitative Petri nets, and quantitative approaches--continuous Petri nets and ordinary differential equations (ODEs). We review the major elementary building blocks of a cellular signalling model, discuss which critical design decisions have to be made during model building, and present a number of novel computational tools that can help to explore alternative modular models in an easy and intuitive manner. These tools, which are based on Petri net theory, offer convenient ways of composing hierarchical ODE models, and permit a qualitative analysis of their behaviour. We illustrate the central concepts using signal transduction as our main example. The ultimate aim is to introduce a general approach that provides the foundations for a structured formal engineering of large-scale models of biochemical networks.

  14. Flows in networks under fuzzy conditions

    CERN Document Server

    Bozhenyuk, Alexander Vitalievich; Kacprzyk, Janusz; Rozenberg, Igor Naymovich

    2017-01-01

    This book offers a comprehensive introduction to fuzzy methods for solving flow tasks in both transportation and networks. It analyzes the problems of minimum cost and maximum flow finding with fuzzy nonzero lower flow bounds, and describes solutions to minimum cost flow finding in a network with fuzzy arc capacities and transmission costs. After a concise introduction to flow theory and tasks, the book analyzes two important problems. The first is related to determining the maximum volume for cargo transportation in the presence of uncertain network parameters, such as environmental changes, measurement errors and repair work on the roads. These parameters are represented here as fuzzy triangular, trapezoidal numbers and intervals. The second problem concerns static and dynamic flow finding in networks under fuzzy conditions, and an effective method that takes into account the network’s transit parameters is presented here. All in all, the book provides readers with a practical reference guide to state-of-...

  15. Yield, quality and biochemical properties of various strawberry cultivars under water stress.

    Science.gov (United States)

    Adak, Nafiye; Gubbuk, Hamide; Tetik, Nedim

    2018-01-01

    Although strawberry (Fragaria x ananassa Duch.) species are sensitive to abiotic stress conditions, some cultivars are known to be tolerant to different environmental conditions. We examined the response of different strawberry cultivars to water stress conditions in terms of yield, quality and biochemical features. The trial was conducted under two different irrigation regimes: in grow bags containing cocopeat (control, 30%; water stress, 15% drainage) with four different cultivars (Camarosa, Albion, Amiga and Rubygem). Fruit weight declined by 59.72% and the yield per unit area by 63.62% under water stress conditions as compared to control. Albion and Rubygem were found to be more tolerant and Amiga the most sensitive in terms of yield under stress conditions. Water stress increased all biochemical features in fruits such as total phenol, total anthocyanin, antioxidant activity and sugar contents. Among the cultivars, glucose and fructose was higher in Albion. Considering the rise in global warming, identification of resistant and tolerant cultivars to stress conditions are crucial for future breeding programmes. Our results showed that some of the fruit's physical features were affected negatively by stress conditions whereas many of the biochemical features such as total anthocyanin content, total phenolic content and antioxidant activity were positively modulated. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  16. A microfluidic platform for controlled biochemical stimulation of twin neuronal networks.

    Science.gov (United States)

    Biffi, Emilia; Piraino, Francesco; Pedrocchi, Alessandra; Fiore, Gianfranco B; Ferrigno, Giancarlo; Redaelli, Alberto; Menegon, Andrea; Rasponi, Marco

    2012-06-01

    Spatially and temporally resolved delivery of soluble factors is a key feature for pharmacological applications. In this framework, microfluidics coupled to multisite electrophysiology offers great advantages in neuropharmacology and toxicology. In this work, a microfluidic device for biochemical stimulation of neuronal networks was developed. A micro-chamber for cell culturing, previously developed and tested for long term neuronal growth by our group, was provided with a thin wall, which partially divided the cell culture region in two sub-compartments. The device was reversibly coupled to a flat micro electrode array and used to culture primary neurons in the same microenvironment. We demonstrated that the two fluidically connected compartments were able to originate two parallel neuronal networks with similar electrophysiological activity but functionally independent. Furthermore, the device allowed to connect the outlet port to a syringe pump and to transform the static culture chamber in a perfused one. At 14 days invitro, sub-networks were independently stimulated with a test molecule, tetrodotoxin, a neurotoxin known to block action potentials, by means of continuous delivery. Electrical activity recordings proved the ability of the device configuration to selectively stimulate each neuronal network individually. The proposed microfluidic approach represents an innovative methodology to perform biological, pharmacological, and electrophysiological experiments on neuronal networks. Indeed, it allows for controlled delivery of substances to cells, and it overcomes the limitations due to standard drug stimulation techniques. Finally, the twin network configuration reduces biological variability, which has important outcomes on pharmacological and drug screening.

  17. Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks.

    Science.gov (United States)

    Jol, Stefan J; Kümmel, Anne; Hatzimanikatis, Vassily; Beard, Daniel A; Heinemann, Matthias

    2010-11-17

    Thermodynamic analysis of metabolic networks has recently generated increasing interest for its ability to add constraints on metabolic network operation, and to combine metabolic fluxes and metabolite measurements in a mechanistic manner. Concepts for the calculation of the change in Gibbs energy of biochemical reactions have long been established. However, a concept for incorporation of cross-membrane transport in these calculations is still missing, although the theory for calculating thermodynamic properties of transport processes is long known. Here, we have developed two equivalent equations to calculate the change in Gibbs energy of combined transport and reaction processes based on two different ways of treating biochemical thermodynamics. We illustrate the need for these equations by showing that in some cases there is a significant difference between the proposed correct calculation and using an approximative method. With the developed equations, thermodynamic analysis of metabolic networks spanning over multiple physical compartments can now be correctly described. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  18. Complex networks under dynamic repair model

    Science.gov (United States)

    Chaoqi, Fu; Ying, Wang; Kun, Zhao; Yangjun, Gao

    2018-01-01

    Invulnerability is not the only factor of importance when considering complex networks' security. It is also critical to have an effective and reasonable repair strategy. Existing research on network repair is confined to the static model. The dynamic model makes better use of the redundant capacity of repaired nodes and repairs the damaged network more efficiently than the static model; however, the dynamic repair model is complex and polytropic. In this paper, we construct a dynamic repair model and systematically describe the energy-transfer relationships between nodes in the repair process of the failure network. Nodes are divided into three types, corresponding to three structures. We find that the strong coupling structure is responsible for secondary failure of the repaired nodes and propose an algorithm that can select the most suitable targets (nodes or links) to repair the failure network with minimal cost. Two types of repair strategies are identified, with different effects under the two energy-transfer rules. The research results enable a more flexible approach to network repair.

  19. Strategies for optical transport network recovery under epidemic network failures

    DEFF Research Database (Denmark)

    Ruepp, Sarah Renée; Fagertun, Anna Manolova; Kosteas, Vasileios

    2015-01-01

    are evaluated under multiple correlated large-scale failures. We employ the Susceptible–Infected– Disabled epidemic failure spreading model and look into possible trade-offs between resiliency and resource effi- ciency. Via extensive simulations, we show that source rerouting outperforms on-site rerouting......The current trend in deploying automatic control plane solutions for increased flexibility in the optical transport layer leads to numerous advantages for both the operators and the customers, but also pose challenges related to the stability of the network and its ability to operate in a robust......, and that there exist a clear trade-off between policy performance and network resource consumption, which must be addressed by network operators for improved robustness of their transport infrastructures. Applying proactive methods for avoiding areas where epidemic failures spread results in 50% less connections...

  20. Parametric sensitivity analysis for biochemical reaction networks based on pathwise information theory.

    Science.gov (United States)

    Pantazis, Yannis; Katsoulakis, Markos A; Vlachos, Dionisios G

    2013-10-22

    Stochastic modeling and simulation provide powerful predictive methods for the intrinsic understanding of fundamental mechanisms in complex biochemical networks. Typically, such mathematical models involve networks of coupled jump stochastic processes with a large number of parameters that need to be suitably calibrated against experimental data. In this direction, the parameter sensitivity analysis of reaction networks is an essential mathematical and computational tool, yielding information regarding the robustness and the identifiability of model parameters. However, existing sensitivity analysis approaches such as variants of the finite difference method can have an overwhelming computational cost in models with a high-dimensional parameter space. We develop a sensitivity analysis methodology suitable for complex stochastic reaction networks with a large number of parameters. The proposed approach is based on Information Theory methods and relies on the quantification of information loss due to parameter perturbations between time-series distributions. For this reason, we need to work on path-space, i.e., the set consisting of all stochastic trajectories, hence the proposed approach is referred to as "pathwise". The pathwise sensitivity analysis method is realized by employing the rigorously-derived Relative Entropy Rate, which is directly computable from the propensity functions. A key aspect of the method is that an associated pathwise Fisher Information Matrix (FIM) is defined, which in turn constitutes a gradient-free approach to quantifying parameter sensitivities. The structure of the FIM turns out to be block-diagonal, revealing hidden parameter dependencies and sensitivities in reaction networks. As a gradient-free method, the proposed sensitivity analysis provides a significant advantage when dealing with complex stochastic systems with a large number of parameters. In addition, the knowledge of the structure of the FIM can allow to efficiently address

  1. Biochemical components and dry matter of lemon and mandarin hybrids under salt stress

    Directory of Open Access Journals (Sweden)

    Francisco V. da S. Sá

    Full Text Available ABSTRACT The objective was to study the biochemical changes and dry matter content in lemon and mandarin hybrids under salt stress during rootstock formation. For this, a study was conducted in randomized complete block, using a 2 x 5 factorial scheme, with two salinity levels (0.3 and 4.0 dS m-1 applied in five citrus rootstock genotypes (1. TSKC x CTARG - 019; 2. LRF; 3. TSKC x (LCR x TR - 040; 4. LCRSTC and 5. LVK, with three replicates and four plants per plot. At 90 days after sowing, saline treatments started to be applied and continued until 120 days after sowing, the moment in which the plants were collected for evaluation of biochemical characteristics and phytomass accumulation. The increase in water salinity negatively affected the biochemical components and dry matter accumulation of citrus genotypes. The genotypes TSKC x (LCR x TR - 040, LCRSTC and LVK were the least affected by salt stress, standing out as the materials most tolerant to salinity.

  2. Arbuscular mycorrhizal colonization improves growth and biochemical profile in Acacia arabica under salt stress

    Directory of Open Access Journals (Sweden)

    Promita Datta

    2014-12-01

    Full Text Available This study elucidated the individual and mixed mycorrhizal effects of two arbuscular mycorrhizal (AM isolates on growth and biochemical status of Acacia arabica under salinity stress gradients. Salt treatment provided in soil hampered legume growth and its biochemical status. But, mycorrhizal colonizations in plant root system reduced the extent of deleterious salt effect and also helped in plant growth enhancement. Additionally, mixed mycorrhizal association (Glomus mosseae + Glomus fasciculatum responded better towards osmolyte accumulation and in salt stress alleviation. Due to individual and mixed mycorrhizal colonizations in A. arabica; protein, carbohydrate and reducing sugar acquisitions were found maximum at soil salinity of 5.94 dS/m over corresponding non-mycorrhizal plant. However, mixed AM inoculation accumulated proline content and improved dry biomass to a higher magnitude at the highest soil salinity level. Mixed AM (G. mosseae + G. fasciculatum colonization improved maximum amount of total chlorophyll (20.94%, protein (19.72%, carbohydrate (23.83%, reducing sugar (17.60% at soil salinity of 5.94 dS/m and dry biomass (20.35%, proline content (10.99% at salinity level of 8.26 dS/m when compared with non-mycorrhizal counterpart. Greater magnitude of AM root colonization was found in mixed AM treated plant and may be responsible for more improvement in growth and biochemical status and consequently mitigated adverse salt effect better.

  3. Propagation of kinetic uncertainties through a canonical topology of the TLR4 signaling network in different regions of biochemical reaction space

    Directory of Open Access Journals (Sweden)

    St Laurent Georges

    2010-03-01

    Full Text Available Abstract Background Signal transduction networks represent the information processing systems that dictate which dynamical regimes of biochemical activity can be accessible to a cell under certain circumstances. One of the major concerns in molecular systems biology is centered on the elucidation of the robustness properties and information processing capabilities of signal transduction networks. Achieving this goal requires the establishment of causal relations between the design principle of biochemical reaction systems and their emergent dynamical behaviors. Methods In this study, efforts were focused in the construction of a relatively well informed, deterministic, non-linear dynamic model, accounting for reaction mechanisms grounded on standard mass action and Hill saturation kinetics, of the canonical reaction topology underlying Toll-like receptor 4 (TLR4-mediated signaling events. This signaling mechanism has been shown to be deployed in macrophages during a relatively short time window in response to lypopolysaccharyde (LPS stimulation, which leads to a rapidly mounted innate immune response. An extensive computational exploration of the biochemical reaction space inhabited by this signal transduction network was performed via local and global perturbation strategies. Importantly, a broad spectrum of biologically plausible dynamical regimes accessible to the network in widely scattered regions of parameter space was reconstructed computationally. Additionally, experimentally reported transcriptional readouts of target pro-inflammatory genes, which are actively modulated by the network in response to LPS stimulation, were also simulated. This was done with the main goal of carrying out an unbiased statistical assessment of the intrinsic robustness properties of this canonical reaction topology. Results Our simulation results provide convincing numerical evidence supporting the idea that a canonical reaction mechanism of the TLR4

  4. Modeling and Robustness Analysis of Biochemical Networks of Glycerol Metabolism by Klebsiella Pneumoniae

    Science.gov (United States)

    Ye, Jianxiong; Feng, Enmin; Wang, Lei; Xiu, Zhilong; Sun, Yaqin

    Glycerol bioconversion to 1,3-propanediol (1,3-PD) by Klebsiella pneumoniae (K. pneumoniae) can be characterized by an intricate network of interactions among biochemical fluxes, metabolic compounds, key enzymes and genetic regulatory. To date, there still exist some uncertain factors in this complex network because of the limitation in bio-techniques, especially in measuring techniques for intracellular substances. In this paper, among these uncertain factors, we aim to infer the transport mechanisms of glycerol and 1,3-PD across the cell membrane, which have received intensive interest in recent years. On the basis of different inferences of the transport mechanisms, we reconstruct various metabolic networks correspondingly and subsequently develop their dynamical systems (S-systems). To determine the most reasonable metabolic network from all possible ones, we establish a quantitative definition of biological robustness and undertake parameter identification and robustness analysis for each system. Numerical results show that it is most possible that both glycerol and 1,3-PD pass the cell membrane by active transport and passive diffusion.

  5. Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory

    Directory of Open Access Journals (Sweden)

    Qian Hong

    2008-05-01

    Full Text Available Abstract Background: Several approaches, including metabolic control analysis (MCA, flux balance analysis (FBA, correlation metric construction (CMC, and biochemical circuit theory (BCT, have been developed for the quantitative analysis of complex biochemical networks. Here, we present a comprehensive theory of linear analysis for nonequilibrium steady-state (NESS biochemical reaction networks that unites these disparate approaches in a common mathematical framework and thermodynamic basis. Results: In this theory a number of relationships between key matrices are introduced: the matrix A obtained in the standard, linear-dynamic-stability analysis of the steady-state can be decomposed as A = SRT where R and S are directly related to the elasticity-coefficient matrix for the fluxes and chemical potentials in MCA, respectively; the control-coefficients for the fluxes and chemical potentials can be written in terms of RT BS and ST BS respectively where matrix B is the inverse of A; the matrix S is precisely the stoichiometric matrix in FBA; and the matrix eAt plays a central role in CMC. Conclusion: One key finding that emerges from this analysis is that the well-known summation theorems in MCA take different forms depending on whether metabolic steady-state is maintained by flux injection or concentration clamping. We demonstrate that if rate-limiting steps exist in a biochemical pathway, they are the steps with smallest biochemical conductances and largest flux control-coefficients. We hypothesize that biochemical networks for cellular signaling have a different strategy for minimizing energy waste and being efficient than do biochemical networks for biosynthesis. We also discuss the intimate relationship between MCA and biochemical systems analysis (BSA.

  6. Reduction of multiscale stochastic biochemical reaction networks using exact moment derivation.

    Directory of Open Access Journals (Sweden)

    Jae Kyoung Kim

    2017-06-01

    Full Text Available Biochemical reaction networks (BRNs in a cell frequently consist of reactions with disparate timescales. The stochastic simulations of such multiscale BRNs are prohibitively slow due to high computational cost for the simulations of fast reactions. One way to resolve this problem uses the fact that fast species regulated by fast reactions quickly equilibrate to their stationary distribution while slow species are unlikely to be changed. Thus, on a slow timescale, fast species can be replaced by their quasi-steady state (QSS: their stationary conditional expectation values for given slow species. As the QSS are determined solely by the state of slow species, such replacement leads to a reduced model, where fast species are eliminated. However, it is challenging to derive the QSS in the presence of nonlinear reactions. While various approximation schemes for the QSS have been developed, they often lead to considerable errors. Here, we propose two classes of multiscale BRNs which can be reduced by deriving an exact QSS rather than approximations. Specifically, if fast species constitute either a feedforward network or a complex balanced network, the reduced model based on the exact QSS can be derived. Such BRNs are frequently observed in a cell as the feedforward network is one of fundamental motifs of gene or protein regulatory networks. Furthermore, complex balanced networks also include various types of fast reversible bindings such as bindings between transcriptional factors and gene regulatory sites. The reduced models based on exact QSS, which can be calculated by the computational packages provided in this work, accurately approximate the slow scale dynamics of the original full model with much lower computational cost.

  7. A new computational method to split large biochemical networks into coherent subnets

    Directory of Open Access Journals (Sweden)

    Verwoerd Wynand S

    2011-02-01

    Full Text Available Abstract Background Compared to more general networks, biochemical networks have some special features: while generally sparse, there are a small number of highly connected metabolite nodes; and metabolite nodes can also be divided into two classes: internal nodes with associated mass balance constraints and external ones without. Based on these features, reclassifying selected internal nodes (separators to external ones can be used to divide a large complex metabolic network into simpler subnetworks. Selection of separators based on node connectivity is commonly used but affords little detailed control and tends to produce excessive fragmentation. The method proposed here (Netsplitter allows the user to control separator selection. It combines local connection degree partitioning with global connectivity derived from random walks on the network, to produce a more even distribution of subnetwork sizes. Partitioning is performed progressively and the interactive visual matrix presentation used allows the user considerable control over the process, while incorporating special strategies to maintain the network integrity and minimise the information loss due to partitioning. Results Partitioning of a genome scale network of 1348 metabolites and 1468 reactions for Arabidopsis thaliana encapsulates 66% of the network into 10 medium sized subnets. Applied to the flavonoid subnetwork extracted in this way, it is shown that Netsplitter separates this naturally into four subnets with recognisable functionality, namely synthesis of lignin precursors, flavonoids, coumarin and benzenoids. A quantitative quality measure called efficacy is constructed and shows that the new method gives improved partitioning for several metabolic networks, including bacterial, plant and mammal species. Conclusions For the examples studied the Netsplitter method is a considerable improvement on the performance of connection degree partitioning, giving a better balance of

  8. Supply chain network design under uncertainty

    DEFF Research Database (Denmark)

    Govindan, Kannan; Fattahi, Mohammad; Keyvanshokooh, Esmaeil

    2017-01-01

    Supply chain network design (SCND) is one of the most crucial planning problems in supply chain management (SCM). Nowadays, design decisions should be viable enough to function well under complex and uncertain business environments for many years or decades. Therefore, it is essential to make...... programming, risk-averse stochastic programming, robust optimization, and fuzzy mathematical programming are explored in terms of mathematical modeling and solution approaches. Finally, the drawbacks and missing aspects of the related literature are highlighted and a list of potential issues for future...

  9. Biochemical basis of drought tolerance in hybrid Populus grown under field production conditions. CRADA final report

    Energy Technology Data Exchange (ETDEWEB)

    Tschaplinski, T.J.; Tuskan, G.A. [Oak Ridge National Lab., TN (United States); Wierman, C. [Boise Cascade Corp., Wallula, WA (United States)

    1997-04-01

    The purpose of this cooperative effort was to assess the use of osmotically active compounds as molecular selection criteria for drought tolerance in Populus in a large-scale field trial. It is known that some plant species, and individuals within a plant species, can tolerate increasing stress associated with reduced moisture availability by accumulating solutes. The biochemical matrix of such metabolites varies among species and among individuals. The ability of Populus clones to tolerate drought has equal value to other fiber producers, i.e., the wood products industry, where irrigation is used in combination with other cultural treatments to obtain high dry weight yields. The research initially involved an assessment of drought stress under field conditions and characterization of changes in osmotic constitution among the seven clones across the six moisture levels. The near-term goal was to provide a mechanistic basis for clonal differences in productivity under various irrigation treatments over time.

  10. Application of approximate pattern matching in two dimensional spaces to grid layout for biochemical network maps.

    Science.gov (United States)

    Inoue, Kentaro; Shimozono, Shinichi; Yoshida, Hideaki; Kurata, Hiroyuki

    2012-01-01

    For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process. We propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor) algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts. Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html.

  11. Application of approximate pattern matching in two dimensional spaces to grid layout for biochemical network maps.

    Directory of Open Access Journals (Sweden)

    Kentaro Inoue

    Full Text Available BACKGROUND: For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process. RESULTS: We propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts. CONCLUSIONS: Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html.

  12. Network Performance Improvement under Epidemic Failures in Optical Transport Networks

    DEFF Research Database (Denmark)

    Fagertun, Anna Manolova; Ruepp, Sarah Renée

    2013-01-01

    In this paper we investigate epidemic failure spreading in large- scale GMPLS-controlled transport networks. By evaluating the effect of the epidemic failure spreading on the network, we design several strategies for cost-effective network performance improvement via differentiated repair times....... First we identify the most vulnerable and the most strategic nodes in the network. Then, via extensive simulations we show that strategic placement of resources for improved failure recovery has better performance than randomly assigning lower repair times among the network nodes. Our OPNET simulation...... model can be used during the network planning process for facilitating cost- effective network survivability design....

  13. Biochemical adaptations of four submerged macrophytes under combined exposure to hypoxia and hydrogen sulphide.

    Science.gov (United States)

    Parveen, Mahfuza; Asaeda, Takashi; Rashid, Md H

    2017-01-01

    A hydroponic experiment was performed to investigate the stress responses and biochemical adaptations of four submerged macrophytes, Potamogeton crispus, Myriophyllum spicatum, Egeria densa, and Potamogeton oxyphyllus, to the combined exposure of hypoxia and hydrogen sulfide (H2S, provided by NaHS). The investigated plants were subjected to a control, hypoxia, 0.1mM NaHS, 0.5 mM NaHS, 0.1 mM NaHS+hypoxia and 0.5 mM NaHS+hypoxia conditions. All experimental plants grew optimally under control, hypoxic and NaHS conditions in comparison to that grown in the combined exposure of hypoxia and hydrogen sulfide. For P. crispus and M. spicatum, significant decreases of total chlorophyll and increases in oxidative stress (measured by hydrogen peroxide, H2O2, and malondialdehyde, MDA) were observed with exposure to both sulfide concentrations. However, the decrease in catalase (CAT) and ascorbate peroxidase (APX) from exposure to 0.5 mM NaHS suggests that the function of the protective enzymes reached their limit under these conditions. In contrast, for E. densa and P. oxyphyllus, the higher activities of the three antioxidative enzymes and their anaerobic respiration abilities (ADH activity) resulted in higher tolerance and susceptibility under high sulfide concentrations.

  14. Biochemical adaptations of four submerged macrophytes under combined exposure to hypoxia and hydrogen sulphide.

    Directory of Open Access Journals (Sweden)

    Mahfuza Parveen

    Full Text Available A hydroponic experiment was performed to investigate the stress responses and biochemical adaptations of four submerged macrophytes, Potamogeton crispus, Myriophyllum spicatum, Egeria densa, and Potamogeton oxyphyllus, to the combined exposure of hypoxia and hydrogen sulfide (H2S, provided by NaHS. The investigated plants were subjected to a control, hypoxia, 0.1mM NaHS, 0.5 mM NaHS, 0.1 mM NaHS+hypoxia and 0.5 mM NaHS+hypoxia conditions. All experimental plants grew optimally under control, hypoxic and NaHS conditions in comparison to that grown in the combined exposure of hypoxia and hydrogen sulfide. For P. crispus and M. spicatum, significant decreases of total chlorophyll and increases in oxidative stress (measured by hydrogen peroxide, H2O2, and malondialdehyde, MDA were observed with exposure to both sulfide concentrations. However, the decrease in catalase (CAT and ascorbate peroxidase (APX from exposure to 0.5 mM NaHS suggests that the function of the protective enzymes reached their limit under these conditions. In contrast, for E. densa and P. oxyphyllus, the higher activities of the three antioxidative enzymes and their anaerobic respiration abilities (ADH activity resulted in higher tolerance and susceptibility under high sulfide concentrations.

  15. Network Performance Improvement under Epidemic Failures in Optical Transport Networks

    DEFF Research Database (Denmark)

    Fagertun, Anna Manolova; Ruepp, Sarah Renée

    2013-01-01

    In this paper we investigate epidemic failure spreading in large- scale GMPLS-controlled transport networks. By evaluating the effect of the epidemic failure spreading on the network, we design several strategies for cost-effective network performance improvement via differentiated repair times....... First we identify the most vulnerable and the most strategic nodes in the network. Then, via extensive simulations we show that strategic placement of resources for improved failure recovery has better performance than randomly assigning lower repair times among the network nodes. Our OPNET simulation...

  16. Synchronization analysis of coloured delayed networks under ...

    Indian Academy of Sciences (India)

    But, the inner interaction is always overlooked. Afterwards, the coloured network model has been brought in this scope by Wu et al [8]. A brief introduction of coloured network is reviewed as fol- lows: In social networks, there are many relationships between individuals, e.g., between schoolmates, relatives and collaborators.

  17. Escherichia coli under Ionic Silver Stress: An Integrative Approach to Explore Transcriptional, Physiological and Biochemical Responses.

    Science.gov (United States)

    Saulou-Bérion, Claire; Gonzalez, Ignacio; Enjalbert, Brice; Audinot, Jean-Nicolas; Fourquaux, Isabelle; Jamme, Frédéric; Cocaign-Bousquet, Muriel; Mercier-Bonin, Muriel; Girbal, Laurence

    2015-01-01

    For a better understanding of the systemic effect of sub-lethal micromolar concentrations of ionic silver on Escherichia coli, we performed a multi-level characterization of cells under Ag+-mediated stress using an integrative biology approach combining physiological, biochemical and transcriptomic data. Physiological parameters, namely bacterial growth and survival after Ag+ exposure, were first quantified and related to the accumulation of intracellular silver, probed for the first time by nano secondary ion mass spectroscopy at sub-micrometer lateral resolution. Modifications in E. coli biochemical composition were evaluated under Ag+-mediated stress by in situ synchrotron Fourier-transform infrared microspectroscopy and a comprehensive transcriptome response was also determined. Using multivariate statistics, correlations between the physiological parameters, the extracellular concentration of AgNO3 and the intracellular silver content, gene expression profiles and micro-spectroscopic data were investigated. We identified Ag+-dependent regulation of gene expression required for growth (e.g. transporter genes, transcriptional regulators, ribosomal proteins), for ionic silver transport and detoxification (e.g. copA, cueO, mgtA, nhaR) and for coping with various types of stress (dnaK, pspA, metA,R, oxidoreductase genes). The silver-induced shortening of the acyl chain of fatty acids, mostly encountered in cell membrane, was highlighted by microspectroscopy and correlated with the down-regulated expression of genes involved in fatty acid transport (fadL) and synthesis/modification of lipid A (lpxA and arnA). The increase in the disordered secondary structure of proteins in the presence of Ag+ was assessed through the conformational shift shown for amides I and II, and further correlated with the up-regulated expression of peptidase (hfq) and chaperone (dnaJ), and regulation of transpeptidase expression (ycfS and ycbB). Interestingly, as these transpeptidases act on

  18. Escherichia coli under Ionic Silver Stress: An Integrative Approach to Explore Transcriptional, Physiological and Biochemical Responses.

    Directory of Open Access Journals (Sweden)

    Claire Saulou-Bérion

    Full Text Available For a better understanding of the systemic effect of sub-lethal micromolar concentrations of ionic silver on Escherichia coli, we performed a multi-level characterization of cells under Ag+-mediated stress using an integrative biology approach combining physiological, biochemical and transcriptomic data. Physiological parameters, namely bacterial growth and survival after Ag+ exposure, were first quantified and related to the accumulation of intracellular silver, probed for the first time by nano secondary ion mass spectroscopy at sub-micrometer lateral resolution. Modifications in E. coli biochemical composition were evaluated under Ag+-mediated stress by in situ synchrotron Fourier-transform infrared microspectroscopy and a comprehensive transcriptome response was also determined. Using multivariate statistics, correlations between the physiological parameters, the extracellular concentration of AgNO3 and the intracellular silver content, gene expression profiles and micro-spectroscopic data were investigated. We identified Ag+-dependent regulation of gene expression required for growth (e.g. transporter genes, transcriptional regulators, ribosomal proteins, for ionic silver transport and detoxification (e.g. copA, cueO, mgtA, nhaR and for coping with various types of stress (dnaK, pspA, metA,R, oxidoreductase genes. The silver-induced shortening of the acyl chain of fatty acids, mostly encountered in cell membrane, was highlighted by microspectroscopy and correlated with the down-regulated expression of genes involved in fatty acid transport (fadL and synthesis/modification of lipid A (lpxA and arnA. The increase in the disordered secondary structure of proteins in the presence of Ag+ was assessed through the conformational shift shown for amides I and II, and further correlated with the up-regulated expression of peptidase (hfq and chaperone (dnaJ, and regulation of transpeptidase expression (ycfS and ycbB. Interestingly, as these

  19. Biochemical and Anatomical Changes and Yield Reduction in Rice (Oryza sativa L. under Varied Salinity Regimes

    Directory of Open Access Journals (Sweden)

    M. A. Hakim

    2014-01-01

    Full Text Available Five Malaysian rice (Oryza sativa L. varieties, MR33, MR52, MR211, MR219, and MR232, were tested in pot culture under different salinity regimes for biochemical response, physiological activity, and grain yield. Three different levels of salt stresses, namely, 4, 8, and 12 dS m−1, were used in a randomized complete block design with four replications under glass house conditions. The results revealed that the chlorophyll content, proline, sugar content, soluble protein, free amino acid, and yield per plant of all the genotypes were influenced by different salinity levels. The chlorophyll content was observed to decrease with salinity level but the proline increased with salinity levels in all varieties. Reducing sugar and total sugar increased up to 8 dS m−1 and decreased up to 12 dS m−1. Nonreducing sugar decreased with increasing the salinity levels in all varieties. Soluble protein and free amino acid also decreased with increasing salinity levels. Cortical cells of MR211 and MR232 did not show cell collapse up to 8 dS m−1 salinity levels compared to susceptible checks (IR20 and BRRI dhan29. Therefore, considering all parameters, MR211 and MR232 showed better salinity tolerance among the tested varieties. Both cluster and principal component analyses depict the similar results.

  20. Biochemical and anatomical changes and yield reduction in rice (Oryza sativa L.) under varied salinity regimes.

    Science.gov (United States)

    Hakim, M A; Juraimi, Abdul Shukor; Hanafi, M M; Ismail, Mohd Razi; Selamat, Ahmad; Rafii, M Y; Latif, M A

    2014-01-01

    Five Malaysian rice (Oryza sativa L.) varieties, MR33, MR52, MR211, MR219, and MR232, were tested in pot culture under different salinity regimes for biochemical response, physiological activity, and grain yield. Three different levels of salt stresses, namely, 4, 8, and 12 dS m(-1), were used in a randomized complete block design with four replications under glass house conditions. The results revealed that the chlorophyll content, proline, sugar content, soluble protein, free amino acid, and yield per plant of all the genotypes were influenced by different salinity levels. The chlorophyll content was observed to decrease with salinity level but the proline increased with salinity levels in all varieties. Reducing sugar and total sugar increased up to 8 dS m(-1) and decreased up to 12 dS m(-1). Nonreducing sugar decreased with increasing the salinity levels in all varieties. Soluble protein and free amino acid also decreased with increasing salinity levels. Cortical cells of MR211 and MR232 did not show cell collapse up to 8 dS m(-1) salinity levels compared to susceptible checks (IR20 and BRRI dhan29). Therefore, considering all parameters, MR211 and MR232 showed better salinity tolerance among the tested varieties. Both cluster and principal component analyses depict the similar results.

  1. The stochastic network dynamics underlying perceptual discrimination

    Directory of Open Access Journals (Sweden)

    Genis Prat-Ortega

    2015-04-01

    Full Text Available The brain is able to interpret streams of high-dimensional ambiguous information and yield coherent percepts. The mechanisms governing sensory integration have been extensively characterized using time-varying visual stimuli (Britten et al. 1996; Roitman and Shadlen 2002, but some of the basic principles regarding the network dynamics underlying this process remain largely unknown. We captured the basic features of a neural integrator using three canonical one-dimensional models: (1 the Drift Diffusion Model (DDM, (2 the Perfect Integrator (PI which is a particular case of the DDM where the bounds are set to infinity and (3 the double-well potential (DW which captures the dynamics of the attractor networks (Wang 2002; Roxin and Ledberg 2008. Although these models has been widely studied (Bogacz et al. 2006; Roxin and Ledberg 2008; Gold and Shadlen 2002, it has been difficult to experimentally discriminate among them because most of the observables measured are only quantitatively different among these models (e.g. psychometric curves. Here we aim to find experimentally measurable quantities that can yield qualitatively different behaviors depending on the nature of the underlying network dynamics. We examined the categorization dynamics of these models in response to fluctuating stimuli of different duration (T. On each time step, stimuli are drawn from a Gaussian distribution N(μ, σ and the two stimulus categories are defined by μ > 0 and μ < 0. Psychometric curves can therefore be obtained by quantifying the probability of the integrator to yield one category versus μ . We find however that varying σ can reveal more clearly the differences among the different integrators. In the small σ regime, both the DW and the DDM perform transient integration and exhibit a decaying stimulus reverse correlation kernel revealing a primacy effect (Nienborg and Cumming 2009; Wimmer et al. 2015 . In the large σ regime, the integration in the DDM

  2. The influence of Metisevit on biochemical and morphological indicators of blood of piglets under nitrate loading

    Directory of Open Access Journals (Sweden)

    B. Gutyj

    2017-07-01

    Full Text Available The article presents the results of research on the influence of the developed complex preparation Metisevit on the dynamics of morphological and biochemical blood indicators of piglets under nitrate loading. The research established that sodium nitrate intoxication causes disbalance of the physiological level of hematological indicators of the tested animals’ organisms. This was indicated by the manifestations of subclinical chronic nitrate-nitrite toxicosis: the increase in the level of nitrates, nitrites and methemoglobin in the blood. After prolonged feeding of the piglets with sodium nitrate at a dose of 0.3 g nitrate ion/kg, the concentration of nitrates and nitrites in the blood serum reached its maximum on the 60th day of the experiment. Also, the number of leukocytes and erythrocytes in the blood increased, and the activity of aspartate- and alanineaminotransferase in the blood serum increased. We rank the extent of liver intoxication with nitrates according to intensity of aminotransferase in the blood serum of the tested piglets. The normalization of morphological and biochemical blood indicators of piglets under nitrate-nitrite intoxication requires usage of a preparation which contains vitamins, zeolites and antioxidants. If the fodder contains high doses of nitrates, 1.0 mg/kg dose of Metisevit is added to the fodder for preventing subclinical nitrate-nitrite toxicosis. Metisevit contains the following agents: phenozan acid, methionine, zeolite, selenium, vitamins E and C. The research conducted proved the feasibility of using Metisevit for preventing chronic nitrate-nitrite toxicosis in piglets. This preparation caused a decrease in the concentration of nitrates, nitrites and in the level of methemoglobin in the blood of piglets. Usage of Metisevit on piglets showed normalization of the number of erythrocytes and hemoglobin in the blood on the 10th day, and normalization of ASAT and ALAT on 30th and 90th days. The mechanism of

  3. Optimization of temporal networks under uncertainty

    CERN Document Server

    Wiesemann, Wolfram

    2012-01-01

    Many decision problems in Operations Research are defined on temporal networks, that is, workflows of time-consuming tasks whose processing order is constrained by precedence relations. For example, temporal networks are used to model projects, computer applications, digital circuits and production processes. Optimization problems arise in temporal networks when a decision maker wishes to determine a temporal arrangement of the tasks and/or a resource assignment that optimizes some network characteristic (e.g. the time required to complete all tasks). The parameters of these optimization probl

  4. Morphogenic and biochemical variations under different spectral lights in callus cultures of Artemisia absinthium L.

    Science.gov (United States)

    Tariq, Umayya; Ali, Mohammad; Abbasi, Bilal Haider

    2014-01-05

    Through its impact on morphogenesis, light is the key environmental factor that alters plant architectural development; however, the understanding that how light controls plant growth and developmental processes is still poor and needs further research. In this study, we monitored the effect of various monochromatic lights and plant growth regulators (PGRs) combinations on morphogenic and biochemical variation in wild grown-leaf derived callus cultures of Artemisia absinthium L. Combination of α-naphthalene acetic acid (NAA 1.0mg/l) and Thidiazuron (TDZ 2.0mg/l) resulted in optimum callogenic frequency (90%) when kept under fluorescent light for 4weeks (16/8h). In contrast to the control (white spectrum), red spectrum enhanced peroxidase activity, protease activity, total protein content and chlorophyll a/b ratio. Green spectrum was found to be more supportive for total phenolics, total flavonoids and antioxidant activity. Yellow light enhanced MDA content while white and green light improved total chlorophyll content and carotenoid content. A positive correlation among callogenic response, antioxidant activities and set of antioxidative enzyme activities was also observed in the current report. This study will help in understanding the influence of light on production of commercially important secondary metabolites and their optimization in the in vitro cultures of A. absinthium L. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. Biochemical impacts of Hg in Mytilus galloprovincialis under present and predicted warming scenarios.

    Science.gov (United States)

    Coppola, Francesca; Almeida, Ângela; Henriques, Bruno; Soares, Amadeu M V M; Figueira, Etelvina; Pereira, Eduarda; Freitas, Rosa

    2017-12-01

    The interest in the consequences of climate change on the physiological and biochemical functioning of marine organisms is increasing, but the indirect and interactive effects resulting from warming on bioconcentration and responsiveness to pollutants are still poorly explored, particularly in terms of cellular responses. The present study investigated the impacts of Hg in Mytilus galloprovincialis under control (17°C) and warming (21°C) conditions, assessing mussels Hg bioconcentration capacity, metabolic and oxidative status after 14 and 28days of exposure. Results obtained showed greater impacts in mussels exposed for 28days in comparison to 14days of exposure. Furthermore, our findings revealed that the increase in temperature from 17 to 21°C reduced the bioconcentration of Hg by M. galloprovincialis, which may explain higher mortality rates at 17°C in comparison to 21°C. Lower Hg concentration at 21°C in mussels tissue may result from valves closure for longer periods, identified by reduced energy reserves consumption at higher temperature, which in turn might also contributed to higher oxidative stress in organisms exposed to this condition. The highest LPO levels observed in mussels exposed to higher temperatures alone indicate that warming conditions will greatly affect M. galloprovincialis. Furthermore, the present study showed that the impacts induced by the combination of Hg and warming were similar to the ones caused by increased temperature acting alone, mainly due to increased antioxidant defenses in organisms under combined effects of Hg and warming, suggesting that warming was the factor that mostly contributed to oxidative stress in mussels. Although higher mortality was observed in individuals exposed to 17°C and Hg compared to organisms exposed to Hg at 21°C, the oxidative stress induced at higher temperature may generate negative consequences on mussels reproductive and feeding capacity, growth and, consequently, on population

  6. Robustness Analysis of Real Network Topologies Under Multiple Failure Scenarios

    DEFF Research Database (Denmark)

    Manzano, M.; Marzo, J. L.; Calle, E.

    2012-01-01

    on topological characteristics. Recently approaches also consider the services supported by such networks. In this paper we carry out a robustness analysis of five real backbone telecommunication networks under defined multiple failure scenarios, taking into account the consequences of the loss of established......Nowadays the ubiquity of telecommunication networks, which underpin and fulfill key aspects of modern day living, is taken for granted. Significant large-scale failures have occurred in the last years affecting telecommunication networks. Traditionally, network robustness analysis has been focused...... connections. Results show which networks are more robust in response to a specific type of failure....

  7. Stochastic Online Learning in Dynamic Networks under Unknown Models

    Science.gov (United States)

    2016-08-02

    Stochastic Online Learning in Dynamic Networks under Unknown Models This research aims to develop fundamental theories and practical algorithms for...12211 Research Triangle Park, NC 27709-2211 Online learning , multi-armed bandit, dynamic networks REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S... Online Learning in Dynamic Networks under Unknown Models Report Title This research aims to develop fundamental theories and practical algorithms for

  8. Video interpretability rating scale under network impairments

    Science.gov (United States)

    Kreitmair, Thomas; Coman, Cristian

    2014-01-01

    This paper presents the results of a study of the impact of network transmission channel parameters on the quality of streaming video data. A common practice for estimating the interpretability of video information is to use the Motion Imagery Quality Equation (MIQE). MIQE combines a few technical features of video images (such as: ground sampling distance, relative edge response, modulation transfer function, gain and signal-to-noise ratio) to estimate the interpretability level. One observation of this study is that the MIQE does not fully account for video-specific parameters such as spatial and temporal encoding, which are relevant to appreciating degradations caused by the streaming process. In streaming applications the main artifacts impacting the interpretability level are related to distortions in the image caused by lossy decompression of video data (due to loss of information and in some cases lossy re-encoding by the streaming server). One parameter in MIQE that is influenced by network transmission errors is the Relative Edge Response (RER). The automated calculation of RER includes the selection of the best edge in the frame, which in case of network errors may be incorrectly associated with a blocked region (e.g. low resolution areas caused by loss of information). A solution is discussed in this document to address this inconsistency by removing corrupted regions from the image analysis process. Furthermore, a recommendation is made on how to account for network impairments in the MIQE, such that a more realistic interpretability level is estimated in case of streaming applications.

  9. Modeling protein network evolution under genome duplication and domain shuffling

    Directory of Open Access Journals (Sweden)

    Isambert Hervé

    2007-11-01

    Full Text Available Abstract Background Successive whole genome duplications have recently been firmly established in all major eukaryote kingdoms. Such exponential evolutionary processes must have largely contributed to shape the topology of protein-protein interaction (PPI networks by outweighing, in particular, all time-linear network growths modeled so far. Results We propose and solve a mathematical model of PPI network evolution under successive genome duplications. This demonstrates, from first principles, that evolutionary conservation and scale-free topology are intrinsically linked properties of PPI networks and emerge from i prevailing exponential network dynamics under duplication and ii asymmetric divergence of gene duplicates. While required, we argue that this asymmetric divergence arises, in fact, spontaneously at the level of protein-binding sites. This supports a refined model of PPI network evolution in terms of protein domains under exponential and asymmetric duplication/divergence dynamics, with multidomain proteins underlying the combinatorial formation of protein complexes. Genome duplication then provides a powerful source of PPI network innovation by promoting local rearrangements of multidomain proteins on a genome wide scale. Yet, we show that the overall conservation and topology of PPI networks are robust to extensive domain shuffling of multidomain proteins as well as to finer details of protein interaction and evolution. Finally, large scale features of direct and indirect PPI networks of S. cerevisiae are well reproduced numerically with only two adjusted parameters of clear biological significance (i.e. network effective growth rate and average number of protein-binding domains per protein. Conclusion This study demonstrates the statistical consequences of genome duplication and domain shuffling on the conservation and topology of PPI networks over a broad evolutionary scale across eukaryote kingdoms. In particular, scale

  10. Antagonistic neural networks underlying differentiated leadership roles

    Science.gov (United States)

    Boyatzis, Richard E.; Rochford, Kylie; Jack, Anthony I.

    2014-01-01

    The emergence of two distinct leadership roles, the task leader and the socio-emotional leader, has been documented in the leadership literature since the 1950s. Recent research in neuroscience suggests that the division between task-oriented and socio-emotional-oriented roles derives from a fundamental feature of our neurobiology: an antagonistic relationship between two large-scale cortical networks – the task-positive network (TPN) and the default mode network (DMN). Neural activity in TPN tends to inhibit activity in the DMN, and vice versa. The TPN is important for problem solving, focusing of attention, making decisions, and control of action. The DMN plays a central role in emotional self-awareness, social cognition, and ethical decision making. It is also strongly linked to creativity and openness to new ideas. Because activation of the TPN tends to suppress activity in the DMN, an over-emphasis on task-oriented leadership may prove deleterious to social and emotional aspects of leadership. Similarly, an overemphasis on the DMN would result in difficulty focusing attention, making decisions, and solving known problems. In this paper, we will review major streams of theory and research on leadership roles in the context of recent findings from neuroscience and psychology. We conclude by suggesting that emerging research challenges the assumption that role differentiation is both natural and necessary, in particular when openness to new ideas, people, emotions, and ethical concerns are important to success. PMID:24624074

  11. Antagonistic Neural Networks Underlying Differentiated Leadership Roles

    Directory of Open Access Journals (Sweden)

    Richard Eleftherios Boyatzis

    2014-03-01

    Full Text Available The emergence of two distinct leadership roles, the task leader and the socio-emotional leader, has been documented in the leadership literature since the 1950’s. Recent research in neuroscience suggests that the division between task oriented and socio-emotional oriented roles derives from a fundamental feature of our neurobiology: an antagonistic relationship between two large-scale cortical networks -- the Task Positive Network (TPN and the Default Mode Network (DMN. Neural activity in TPN tends to inhibit activity in the DMN, and vice versa. The TPN is important for problem solving, focusing of attention, making decisions, and control of action. The DMN plays a central role in emotional self-awareness, social cognition, and ethical decision making. It is also strongly linked to creativity and openness to new ideas. Because activation of the TPN tends to suppress activity in the DMN, an over-emphasis on task oriented leadership may prove deleterious to social and emotional aspects of leadership. Similarly, an overemphasis on the DMN would result in difficulty focusing attention, making decisions and solving known problems. In this paper, we will review major streams of theory and research on leadership roles in the context of recent findings from neuroscience and psychology. We conclude by suggesting that emerging research challenges the assumption that role differentiation is both natural and necessary, in particular when openness to new ideas, people, emotions, and ethical concerns are important to success.

  12. Antagonistic neural networks underlying differentiated leadership roles.

    Science.gov (United States)

    Boyatzis, Richard E; Rochford, Kylie; Jack, Anthony I

    2014-01-01

    The emergence of two distinct leadership roles, the task leader and the socio-emotional leader, has been documented in the leadership literature since the 1950s. Recent research in neuroscience suggests that the division between task-oriented and socio-emotional-oriented roles derives from a fundamental feature of our neurobiology: an antagonistic relationship between two large-scale cortical networks - the task-positive network (TPN) and the default mode network (DMN). Neural activity in TPN tends to inhibit activity in the DMN, and vice versa. The TPN is important for problem solving, focusing of attention, making decisions, and control of action. The DMN plays a central role in emotional self-awareness, social cognition, and ethical decision making. It is also strongly linked to creativity and openness to new ideas. Because activation of the TPN tends to suppress activity in the DMN, an over-emphasis on task-oriented leadership may prove deleterious to social and emotional aspects of leadership. Similarly, an overemphasis on the DMN would result in difficulty focusing attention, making decisions, and solving known problems. In this paper, we will review major streams of theory and research on leadership roles in the context of recent findings from neuroscience and psychology. We conclude by suggesting that emerging research challenges the assumption that role differentiation is both natural and necessary, in particular when openness to new ideas, people, emotions, and ethical concerns are important to success.

  13. A potential biochemical mechanism underlying the influence of sterol deprivation stress on Caenorhabditis elegans longevity

    Science.gov (United States)

    To investigate the biochemical mechanism for sterol-mediated alteration in aging in Caenorhabditis elegans, we established sterol depletion conditions by treating worms with azacoprostane, which reduced mean lifespan of adult C. elegans by 35%. Proteomic analyses of egg proteins from treated and un...

  14. Effect of nitrogen fertilization on morphological and biochemical traits of some Apiaceae crops under arid region conditions in Egypt

    Directory of Open Access Journals (Sweden)

    KHALID ALI KHALID

    2013-05-01

    Full Text Available Khalid KA. 2013. Effect of nitrogen fertilization on morphological and biochemical traits of some Apiaceae crops under arid region conditions in Egypt. Nusantara Bioscience 5: 15-20. Arid regions in Egypt are characterized by poor nutrients content and unfavorable environmental conditions which negatively affect growth and productivity of medicinal and aromatic plants including anise, coriander and sweet fennel. So the main objective of the present investigation was to study the effect of different levels of N, namely 0 (control, 100, 150 and 200 kg ha-1 used as ammonium sulphate [(NH42SO4] (20% N, on selected morphological and biochemical characteristics of anise, coriander and sweet fennel plants cultivated under arid regions conditions during two successive seasons. The most effective dose of nitrogen was 200 kg ha-1 of N, resulting in a positive increase in vegetative growth characters and content of essential oil, fixed oil, total carbohydrates, soluble sugars, protein and nutrients (NPK.

  15. [The biochemical markers of hepatobiliary function in children under environmental pollution].

    Science.gov (United States)

    Lukach, M V; Hnateĭko, O Z; Kosmynina, N S

    2014-01-01

    It has been carred out an analysis of biochemical parameters of the hepatobiliary system in 119 children who have been living in ecologically unfavourable districts in order to improve early diagnosis of environmentally triggered hepatobiliary disease. Our results found that 57.2% of patients from polluted region had early signs of liver dysfunction the most frequently of which was elevation of biochemical markers of cholestasis. Among the investigated enzymes the high frequency of abnormal levels of gamma-glutamyltransferase (54.6%) alkaline phosphatase (36.1%), sorbitol dehydrogenase (28.6%) were detected in children from ecologically unfavorable districts which may indicate that these markers were helpful for the early diagnosis of environmentally triggered hepatobiliary disease. It was revealed that almost every third child (41.1% examined children) from the ecologically unfavourable districts had decrease of liver detoxification enzyme activity (arginase).

  16. Blood biochemical parameters of Brazilian sport horses under training in tropical climate

    Directory of Open Access Journals (Sweden)

    Felipe Gomes Ferreira Padilha

    Full Text Available ABSTRACT This study aimed to provide baseline data for the serum biochemical parameters of Brazilian sport horses undergoing physical training for eventing to be used as a practical guide. A total of 139 blood samples were collected by vacuum venipuncture of the jugular vein from healthy horses in training. Tubes without anticoagulant were used for biochemical analysis. Means and standard deviations were determined for aspartate aminotransferase (AST (306.27±84.66 U/L, creatine kinase (CK (181.06±80.38 U/L, urea (29.51±5.82 mg/dL, creatinine (1.44±0.20 mg/dL, gamma glutamyl transferase (GGT (14.58±6.55 U/L, calcium (13.22±0.59 mg/dL, and albumin (2.86±0.16 g/dL. The specific reference ranges were: AST, 197-454 U/L; CK, 116-290 U/L; urea, 22-42 mg/dL; creatinine, 1.2-1.8 mg/dL; GGT, 9-26 U/L; calcium, 12.2-14.2 mg/dL; and albumin, 2.6-3.1 g/dL. Beneficial effects of the training program on the horses were observed and these effects did not lead to any changes in the biochemical parameters studied. The environment may influence the serum biochemical parameters, particularly AST and CK, of Brazilian sport horses.

  17. Intruder Activity Analysis under Unreliable Sensor Networks

    Energy Technology Data Exchange (ETDEWEB)

    Tae-Sic Yoo; Humberto E. Garcia

    2007-09-01

    This paper addresses the problem of counting intruder activities within a monitored domain by a sensor network. The deployed sensors are unreliable. We characterize imperfect sensors with misdetection and false-alarm probabilities. We model intruder activities with Markov Chains. A set of Hidden Markov Models (HMM) models the imperfect sensors and intruder activities to be monitored. A novel sequential change detection/isolation algorithm is developed to detect and isolate a change from an HMM representing no intruder activity to another HMM representing some intruder activities. Procedures for estimating the entry time and the trace of intruder activities are developed. A domain monitoring example is given to illustrate the presented concepts and computational procedures.

  18. Analysis of Network Topologies Underlying Ethylene Growth Response Kinetics.

    Science.gov (United States)

    Prescott, Aaron M; McCollough, Forest W; Eldreth, Bryan L; Binder, Brad M; Abel, Steven M

    2016-01-01

    Most models for ethylene signaling involve a linear pathway. However, measurements of seedling growth kinetics when ethylene is applied and removed have resulted in more complex network models that include coherent feedforward, negative feedback, and positive feedback motifs. The dynamical responses of the proposed networks have not been explored in a quantitative manner. Here, we explore (i) whether any of the proposed models are capable of producing growth-response behaviors consistent with experimental observations and (ii) what mechanistic roles various parts of the network topologies play in ethylene signaling. To address this, we used computational methods to explore two general network topologies: The first contains a coherent feedforward loop that inhibits growth and a negative feedback from growth onto itself (CFF/NFB). In the second, ethylene promotes the cleavage of EIN2, with the product of the cleavage inhibiting growth and promoting the production of EIN2 through a positive feedback loop (PFB). Since few network parameters for ethylene signaling are known in detail, we used an evolutionary algorithm to explore sets of parameters that produce behaviors similar to experimental growth response kinetics of both wildtype and mutant seedlings. We generated a library of parameter sets by independently running the evolutionary algorithm many times. Both network topologies produce behavior consistent with experimental observations, and analysis of the parameter sets allows us to identify important network interactions and parameter constraints. We additionally screened these parameter sets for growth recovery in the presence of sub-saturating ethylene doses, which is an experimentally-observed property that emerges in some of the evolved parameter sets. Finally, we probed simplified networks maintaining key features of the CFF/NFB and PFB topologies. From this, we verified observations drawn from the larger networks about mechanisms underlying ethylene

  19. Analysis of Network Topologies Underlying Ethylene Growth Response Kinetics

    Directory of Open Access Journals (Sweden)

    Aaron M. Prescott

    2016-08-01

    underlying ethylene signaling. Analysis of each network topology results in predictions about changes that occur in network components that can be experimentally tested to give insights into which, if either, network underlies ethylene responses.

  20. Prediction of dissolved oxygen in Surma River by biochemical oxygen demand and chemical oxygen demand using the artificial neural networks (ANNs)

    OpenAIRE

    A.A. Masrur Ahmed

    2017-01-01

    The objective of this study is to develop a feed forward neural network (FFNN) model and a radial basis function neural network (RBFNN) model to predict the dissolved oxygen from biochemical oxygen demand (BOD) and chemical oxygen demand (COD) in the Surma River, Bangladesh. The neural network model was developed using experimental data which were collected during a three year long study. The input combinations were prepared based on the correlation coefficient with dissolved oxygen. Performa...

  1. Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks

    NARCIS (Netherlands)

    Jol, Stefan J; Kümmel, Anne; Hatzimanikatis, Vassily; Beard, Daniel A; Heinemann, Matthias

    2010-01-01

    Thermodynamic analysis of metabolic networks has recently generated increasing interest for its ability to add constraints on metabolic network operation, and to combine metabolic fluxes and metabolite measurements in a mechanistic manner. Concepts for the calculation of the change in Gibbs energy

  2. Extracting vascular networks under physiological constraints via integer programming.

    Science.gov (United States)

    Rempfler, Markus; Schneider, Matthias; Ielacqua, Giovanna D; Xiao, Xianghui; Stock, Stuart R; Klohs, Jan; Székely, Gábor; Andres, Bjoern; Menze, Bjoern H

    2014-01-01

    We introduce an integer programming-based approach to vessel network extraction that enforces global physiological constraints on the vessel structure and learn this prior from a high-resolution reference network. The method accounts for both image evidence and geometric relationships between vessels by formulating and solving an integer programming problem. Starting from an over-connected network, it is pruning vessel stumps and spurious connections by evaluating bifurcation angle and connectivity of the graph. We utilize a high-resolution micro computed tomography (μCT) dataset of a cerebrovascular corrosion cast to obtain a reference network, perform experiments on micro magnetic resonance angiography (μMRA) images of mouse brains and discuss properties of the networks obtained under different tracking and pruning approaches.

  3. Research On The Assessment Of Biochemical Parameters Of Poultry Meat Under A Constant Level Of Energy And Protein

    Directory of Open Access Journals (Sweden)

    Mihai Neacsu

    2016-05-01

    Full Text Available Biochemical parameters for poultry meat, in constant level of energy and protein, in terms of dry matter, raw fat content, and raw ash content were estimated in two poultry genetic type Cobb 500 and Ross 308. A total 16 records, belonging to 60 individuals (male and female which coming random from these two hybrids were analyzed. There was a little variability in all analyzed traits. According to values of traits and t test, between two genetic types there are some statistically significant differences, under identical conditions of feeding and housing.

  4. Biochemical, microbiological and physiological changes in Jamun (Syzyium cumini L.) kept for long term storage under modified atmosphere packaging.

    Science.gov (United States)

    Rai, Deepak Raj; Chadha, Sonia; Kaur, Maninder P; Jaiswal, Pranita; Patil, Ramabhau T

    2011-06-01

    Jamun or Indian blackberry (Syzygium cumini L.) is a minor and highly perishable fruit enriched with flavonoids, essential oils, anthocyanins phenolic compounds and other antioxidants. The quantitative and qualitative losses in this seasonal fruit are tremendous and can be reduced by appropriate packaging and storage techniques which have not been applied hitherto. This study was undertaken to extend the shelf-life as well as to assess the biochemical, microbiological and physiological changes in jamun fruit under perforated and non-perforated modified atmosphere (MA) conditions. Fruits were stored under differential MA in macro-perforated (1 and 2 perforations, 0.3 mm dia. each) and non-perforated polypropylene (PP) film packages (Thickness: 35 μm, bag area: 0.036 m(2)) at 5 °C and 75% relative humidity (RH) for 23 days. Sachets containing white silica gel beads were placed inside all the packages to check water accumulation, if any. Different physiological, biochemical and microbiological characteristics which generally affect the post-harvest life of the produce were monitored during the storage period. Results of the study suggested most of the subjectively and objectively determined qualitative parameters to be retained satisfactorily under macro-perforated packaging treatments. Further, the microbiological analysis, surmised that the fruits could be stored for long term using packages with 1 macro-perforation.

  5. Physiological and biochemical responses of two maize cultivars (Corralejo and Tlaltizapon under salt stress

    Directory of Open Access Journals (Sweden)

    T. Amdouni

    2014-08-01

    Full Text Available The aim of the present work was to study the effect of different concentrations of NaCl (0, 50 and 100mM in two cultivars of maize (Corralejo and Tlaltizapan, on their nutritional and photosynthetic comportment. The measures focused on the physiological parameters (growth weight, hydration and nutritional status of plants and biochemical (chlorophyll, PEPC activity, activity of some anti-oxidant enzymes and lipid peroxidation. Analysis of morphological parameters showed a yellowing of the extremity of leaves, at 100 mM of NaCl. These visual symptoms are associated with a decrease of chlorophyll. A decrease in potential growth was found in two cultivars, but less significant in Corralejo. The best salt tolerance of the latter was due to a better hydration of the leaves, to a lesser accumulation of Na+ and Cl- in its leaves and a better selectivity K/Na. To identify the biochemical characteristics associated with the physiological behavior, we conducted measures activity of PEPC, the protein, catalase and peroxidase on the fourth leaf from the bottom. A negative correlation between the activity of PEPC and Na+ amount was found at 50 mM in the sensitive cultivar and at 100 mM of NaCl in tolerant cultivar Corralejo. Furthermore, the antioxidant response was marked by a greater accumulation of malondialdehyde, in Tlaltizapan at 100 mM of NaCl. At the same concentration, catalase peroxidase and SOD activities weren't decreased in this cultivar. This suggests that salt has created a stress oxidative state only in Tlaltizapan leaves. These results showed a better performance of Corralejo cultivar compared to Tlaltizapan cultivar, at 50 and 100 mM of NaCl.

  6. Trade networks evolution under the conditions of stock market globalization

    Directory of Open Access Journals (Sweden)

    Kopylova Olga Volodymyrivna

    2016-12-01

    Full Text Available The modern perception of the stock market in terms of information technologies rapid development and under the institutionalists influence has been significantly modified and becomes multifaceted. It was detected that the main function of the market is activated, information asymmetry is minimized and more advanced financial architecture space is formed through trade networks. Formation of the modern trade networks has started on the basis of the old infrastructure, that had the highest tendency to self-organization and adaptation. The proposed architecture of trade networks of the stock market has a very clear vector of subordination – from top to bottom and has a number of positive points.

  7. Robust Optimization of Fourth Party Logistics Network Design under Disruptions

    Directory of Open Access Journals (Sweden)

    Jia Li

    2015-01-01

    Full Text Available The Fourth Party Logistics (4PL network faces disruptions of various sorts under the dynamic and complex environment. In order to explore the robustness of the network, the 4PL network design with consideration of random disruptions is studied. The purpose of the research is to construct a 4PL network that can provide satisfactory service to customers at a lower cost when disruptions strike. Based on the definition of β-robustness, a robust optimization model of 4PL network design under disruptions is established. Based on the NP-hard characteristic of the problem, the artificial fish swarm algorithm (AFSA and the genetic algorithm (GA are developed. The effectiveness of the algorithms is tested and compared by simulation examples. By comparing the optimal solutions of the 4PL network for different robustness level, it is indicated that the robust optimization model can evade the market risks effectively and save the cost in the maximum limit when it is applied to 4PL network design.

  8. An Integrated Framework to Model Cellular Phenotype as a Component of Biochemical Networks

    Directory of Open Access Journals (Sweden)

    Michael Gormley

    2011-01-01

    Full Text Available Identification of regulatory molecules in signaling pathways is critical for understanding cellular behavior. Given the complexity of the transcriptional gene network, the relationship between molecular expression and phenotype is difficult to determine using reductionist experimental methods. Computational models provide the means to characterize regulatory mechanisms and predict phenotype in the context of gene networks. Integrating gene expression data with phenotypic data in transcriptional network models enables systematic identification of critical molecules in a biological network. We developed an approach based on fuzzy logic to model cell budding in Saccharomyces cerevisiae using time series expression microarray data of the cell cycle. Cell budding is a phenotype of viable cells undergoing division. Predicted interactions between gene expression and phenotype reflected known biological relationships. Dynamic simulation analysis reproduced the behavior of the yeast cell cycle and accurately identified genes and interactions which are essential for cell viability.

  9. Analysis and Reduction of Complex Networks Under Uncertainty.

    Energy Technology Data Exchange (ETDEWEB)

    Ghanem, Roger G [University of Southern California

    2014-07-31

    This effort was a collaboration with Youssef Marzouk of MIT, Omar Knio of Duke University (at the time at Johns Hopkins University) and Habib Najm of Sandia National Laboratories. The objective of this effort was to develop the mathematical and algorithmic capacity to analyze complex networks under uncertainty. Of interest were chemical reaction networks and smart grid networks. The statements of work for USC focused on the development of stochastic reduced models for uncertain networks. The USC team was led by Professor Roger Ghanem and consisted of one graduate student and a postdoc. The contributions completed by the USC team consisted of 1) methodology and algorithms to address the eigenvalue problem, a problem of significance in the stability of networks under stochastic perturbations, 2) methodology and algorithms to characterize probability measures on graph structures with random flows. This is an important problem in characterizing random demand (encountered in smart grid) and random degradation (encountered in infrastructure systems), as well as modeling errors in Markov Chains (with ubiquitous relevance !). 3) methodology and algorithms for treating inequalities in uncertain systems. This is an important problem in the context of models for material failure and network flows under uncertainty where conditions of failure or flow are described in the form of inequalities between the state variables.

  10. Dynamic Modeling of Cell-Free Biochemical Networks Using Effective Kinetic Models

    Science.gov (United States)

    2015-03-03

    influenza hemagglutinin stem domain for potentially broadly protective influenza vaccines . Proc. Natl. Acad. Sci. USA 2014, 111, 125–130. 27. Hodgman...integrated into network models, these rules captured classic regulatory patterns such as product- induced feedback inhibition. Lastly, we showed, at...captured classic regulatory patterns such as product- induced feedback inhibition. Lastly, we showed, at least for the network architectures considered here

  11. Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network.

    Directory of Open Access Journals (Sweden)

    Jinyuan Yan

    2017-08-01

    Full Text Available Bacteria of many species rely on a simple molecule, the intracellular secondary messenger c-di-GMP (Bis-(3'-5'-cyclic dimeric guanosine monophosphate, to make a vital choice: whether to stay in one place and form a biofilm, or to leave it in search of better conditions. The c-di-GMP network has a bow-tie shaped architecture that integrates many signals from the outside world-the input stimuli-into intracellular c-di-GMP levels that then regulate genes for biofilm formation or for swarming motility-the output phenotypes. How does the 'uninformed' process of evolution produce a network with the right input/output association and enable bacteria to make the right choice? Inspired by new data from 28 clinical isolates of Pseudomonas aeruginosa and strains evolved in laboratory experiments we propose a mathematical model where the c-di-GMP network is analogous to a machine learning classifier. The analogy immediately suggests a mechanism for learning through evolution: adaptation though incremental changes in c-di-GMP network proteins acquires knowledge from past experiences and enables bacteria to use it to direct future behaviors. Our model clarifies the elusive function of the ubiquitous c-di-GMP network, a key regulator of bacterial social traits associated with virulence. More broadly, the link between evolution and machine learning can help explain how natural selection across fluctuating environments produces networks that enable living organisms to make sophisticated decisions.

  12. Dispersal governs the reorganization of ecological networks under environmental change.

    Science.gov (United States)

    Thompson, Patrick L; Gonzalez, Andrew

    2017-05-08

    Ecological networks, such as food webs, mutualist webs and host-parasite webs, are reorganizing as species abundances and spatial distributions shift in response to environmental change. Current theoretical expectations for how this reorganization will occur are available for competition or for parts of interaction networks, but these may not extend to more complex networks. Here we use metacommunity theory to develop new expectations for how complex networks will reorganize under environmental change, and show that dispersal is crucial for determining the degree to which networks will retain their composition and structure. When dispersal between habitat patches is low, all types of species interactions act as a strong determinant for whether species can colonize suitable habitats. This colonization resistance drives species turnover, which breaks apart current networks and leads to the formation of new networks. However, when dispersal rates are increased, colonists arrive in high abundance in habitats where they are well adapted, so interactions with resident species contribute less to colonization success. Dispersal ensures that species associations are maintained as they shift in space, so networks retain similar composition and structure. The crucial role of dispersal reinforces the need to manage habitat connectivity to sustain species and interaction diversity into the future.

  13. Robustness of Dengue Complex Network under Targeted versus Random Attack

    Directory of Open Access Journals (Sweden)

    Hafiz Abid Mahmood Malik

    2017-01-01

    Full Text Available Dengue virus infection is one of those epidemic diseases that require much consideration in order to save the humankind from its unsafe impacts. According to the World Health Organization (WHO, 3.6 billion individuals are at risk because of the dengue virus sickness. Researchers are striving to comprehend the dengue threat. This study is a little commitment to those endeavors. To observe the robustness of the dengue network, we uprooted the links between nodes randomly and targeted by utilizing different centrality measures. The outcomes demonstrated that 5% targeted attack is equivalent to the result of 65% random assault, which showed the topology of this complex network validated a scale-free network instead of random network. Four centrality measures (Degree, Closeness, Betweenness, and Eigenvector have been ascertained to look for focal hubs. It has been observed through the results in this study that robustness of a node and links depends on topology of the network. The dengue epidemic network presented robust behaviour under random attack, and this network turned out to be more vulnerable when the hubs of higher degree have higher probability to fail. Moreover, representation of this network has been projected, and hub removal impact has been shown on the real map of Gombak (Malaysia.

  14. Conceptual and Experimental Tools to Understand Spatial Effects and Transport Phenomena in Nonlinear Biochemical Networks Illustrated with Patchy Switching.

    Science.gov (United States)

    Pompano, Rebecca R; Chiang, Andrew H; Kastrup, Christian J; Ismagilov, Rustem F

    2017-06-20

    Many biochemical systems are spatially heterogeneous and exhibit nonlinear behaviors, such as state switching in response to small changes in the local concentration of diffusible molecules. Systems as varied as blood clotting, intracellular calcium signaling, and tissue inflammation are all heavily influenced by the balance of rates of reaction and mass transport phenomena including flow and diffusion. Transport of signaling molecules is also affected by geometry and chemoselective confinement via matrix binding. In this review, we use a phenomenon referred to as patchy switching to illustrate the interplay of nonlinearities, transport phenomena, and spatial effects. Patchy switching describes a change in the state of a network when the local concentration of a diffusible molecule surpasses a critical threshold. Using patchy switching as an example, we describe conceptual tools from nonlinear dynamics and chemical engineering that make testable predictions and provide a unifying description of the myriad possible experimental observations. We describe experimental microfluidic and biochemical tools emerging to test conceptual predictions by controlling transport phenomena and spatial distribution of diffusible signals, and we highlight the unmet need for in vivo tools.

  15. Some biochemical and hematological changes in female rats under protein malnutrition

    International Nuclear Information System (INIS)

    EL-Sherbiny, E.M.; El-Mahdy, A.A.; Bayoumi, M.M.

    2006-01-01

    The aim of this study was to clarify the effect of low and high dietary protein on some biochemical and hematological parameters in blood of female albino rats. A total number of 75 albino female rats were equally divided into 3 groups, the first group was fed 20% protein diet and served as control and the second and third groups were fed 5% and 65% protein for 5 weeks and served as low and high protein dietary groups, respectively. The results showed high significant decreases in serum growth hormone, ferritin levels and iron concentration in group II and there was significant increase in unsaturated iron binding capacity (UIBC) in group III, compared to control group. Studies of total protein and its fractions revealed high significant decreases in total protein, albumin, alpha-1-globulin, beta-globulin as well as gamma globulin in group II and significant increases in total protein, alpha-1- globulin, beta-globulin and gamma-globulin in group III, compared to normal control group. The hematological investigations in group II revealed significant decreases in hemoglobin value, total leukocyte count, platelets, mean corpuscular hemoglobin concentration (MCHC), erythrocytic count and mean corpuscular volume (MCV). On the other hand, there was significant increase in total leukocyte count in group III if compared to control group

  16. Biochemical peculiarity of in vitro morphogenesis under conservation strategy of Ruscus aculeatus L.

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    Cristian Banciu

    2009-12-01

    Full Text Available The present study is part of the actual concerns in biodiversity conservation of endangered angyosperm species from the Comana Natural Park. Ruscus aculeatus L. species is protected both at national and European level (trough Habitats Directive of EU and Bern Convention. The aspects of in vitro morphogenesis through all the stages from inoculation, multiplication to rooting and acclimatization have been studied. In order to long term conservation and multiplication or to exploit somaclonal variation induced by in vitro technique is required the identification of some biochemical or molecular markers for fast evaluation of regenerants. In this respect, genetic stability or variability of Ruscus aculeatus plants collected from three populations and regenerants obtained in vitro culture was estimated by electrophoretical methods. Therefore, zymograms of different enzymes as esterase, acid and alkaline phosphatase, glutamate-oxaloacetate transferase, malate dehydrogenase and peroxidase were analyzed. The expression of esterases, phosphatases, malate dehydrogenases displayed changes in correlation with growth condition, while the peroxidases pattern was more stabile in natural population as well as in vitro regenerated plantlet.

  17. Renal biochemical and histopathological alterations of diabetic rats under treatment with hydro alcoholic Morus nigra extrac

    Science.gov (United States)

    Rahimi-Madiseh, Mohammad; Naimi, Azar; Heydarian, Esfandiar; Rafieian-Kopaei, Mahmoud

    2017-01-01

    Introduction: Morus nigra fruit is known to have antioxidant effects and used to control the blood sugar level in traditional medicine. Objectives: This study was conducted to investigate the biochemical and histopathological changes in the serum and kidneys of diabetic rats treated with hydroalcoholic M. nigra extract. Materials and Methods: In this study, 60 male Wistar rats were divided into five groups of 12 each. After induction of diabetes with alloxan, the diabetic rats were treated with hydroalcoholic extract of M. nigra at different concentrations. Then, the animals were anesthetized and the serum levels of glucose, creatinine, and urea as well as kidney tissue catalase level measured. The kidney tissue was also histopathologically examined. Results: Milder glomerular damage was seen in the group treated with 800 mg/kg of the M. nigra extract compared with diabetic and positive controls, and no difference in the expansion of mesenchymal tissue into renal glomerular vessels observed between the group treated with 800 mg/kg of M. nigra extract and diabetic and positive controls. Furthermore, creatinine levels were significantly higher and urea levels significantly lower in the group treated with 800 mg/kg of M. nigra extract than healthy and positive control groups (Pnigra extract at 800 mg/kg can prevent kidney tissue damage in diabetic rats and this fruit seems to be beneficial to patients with diabetes. PMID:28487873

  18. Soil biochemical properties of grassland ecosystems under anthropogenic emission of nitrogen compounds

    Science.gov (United States)

    Kudrevatykh, Irina; Ivashchenko, Kristina; Ananyeva, Nadezhda

    2016-04-01

    Inflow of pollutants in terrestrial ecosystems nowadays increases dramatically, that might be led to disturbance of natural biogeochemical cycles and landscapes structure. Production of nitrogen fertilizers is one of the air pollution sources, namely by nitrogen compounds (NH4+, NO3-, NO2-). Air pollution by nitrogen compounds of terrestrial ecosystems might be affected on soil biochemical properties, which results increasing mineral nitrogen content in soil, changing soil P/N and Al/Ca ratios, and, finally, the deterioration of soil microbial community functioning. The research is focused on the assessment of anthropogenic emission of nitrogen compounds on soil properties of grassland ecosystems in European Russia. Soil samples (Voronic Chernozem Pachic, upper 10 cm mineral layer, totally 10) were taken from grassland ecosystem: near (5-10 m) nitrogen fertilizer factory (NFF), and far from it (20-30 km, served as a control) in Tula region. In soil samples the NH4+ and NO3- (Kudeyarov's photocolorimetric method), P, Ca, Al (X-ray fluorescence method) contents were measured. Soil microbial biomass carbon (Cmic) was analyzed by substrate-induced respiration method. Soil microbial respiration (MR) was assessed by CO2 rate production. Soil microbial metabolic quotient (qCO2) was calculated as MR/Cmic ratio. Near NFF the soil ammonium and nitrate nitrogen contents were a strongly varied, variation coefficient (CV) was 42 and 86This study was supported by Russian Foundation of Basic Research Grant No. 14-04-00098, 15-44-03220, 15-04-00915.

  19. Biochemical and Hematological Profiles of Common Carp (Cyprinus Carpio under Sublethal Effects of Trivalent Chromium

    Directory of Open Access Journals (Sweden)

    Zeynab Abedi

    2016-07-01

    Full Text Available Background: In natural waters and/or aquaculture facilities, fish are often exposed to chromium waste and demonstrate cumulative deleterious effects. To our knowledge, there are no studies concerning the effects of trivalent Cr on C. carpio hematology. This study presents hematological and some biochemical parameters of common carp, Cyprinus carpio, affected by sublethal concentration of trivalent chromium. Methods: The fish in the experimental aquaria (three replicates each were exposed to a sublethal chromium chloride concentration of 2 mg L−1, which was prepared as stock solution and added depending on the volume of the aquaria to obtain the required concentration. After a period of 28 days, parameters such as hematocrit (Hct, hemoglobin (Hb, lymphocytes (Lym, neutrophils (Neu, total protein (TP, albumin, immunoglobulin M (IgM, glucose, red and white blood cells (RBC and WBC, mean corpuscular volume (MCV, mean corpuscular hemoglobin (MCH, and mean corpuscular hemoglobin concentration (MCHC were examined. Results: Chromium exposure for 28 days significantly (P0.05 between the Cr-exposed fish and the control. Conclusion: Hematological indices of fish, caused by chromium toxicity to C. carpio, can be secondary responses to toxicants, including exposure to low concentrations of heavy metals, which reflect the launch of stress reaction in the affected fish.

  20. Inferring the gene network underlying the branching of tomato inflorescence.

    Directory of Open Access Journals (Sweden)

    Laura Astola

    Full Text Available The architecture of tomato inflorescence strongly affects flower production and subsequent crop yield. To understand the genetic activities involved, insight into the underlying network of genes that initiate and control the sympodial growth in the tomato is essential. In this paper, we show how the structure of this network can be derived from available data of the expressions of the involved genes. Our approach starts from employing biological expert knowledge to select the most probable gene candidates behind branching behavior. To find how these genes interact, we develop a stepwise procedure for computational inference of the network structure. Our data consists of expression levels from primary shoot meristems, measured at different developmental stages on three different genotypes of tomato. With the network inferred by our algorithm, we can explain the dynamics corresponding to all three genotypes simultaneously, despite their apparent dissimilarities. We also correctly predict the chronological order of expression peaks for the main hubs in the network. Based on the inferred network, using optimal experimental design criteria, we are able to suggest an informative set of experiments for further investigation of the mechanisms underlying branching behavior.

  1. Reconstructing cerebrovascular networks under local physiological constraints by integer programming.

    Science.gov (United States)

    Rempfler, Markus; Schneider, Matthias; Ielacqua, Giovanna D; Xiao, Xianghui; Stock, Stuart R; Klohs, Jan; Székely, Gábor; Andres, Bjoern; Menze, Bjoern H

    2015-10-01

    We introduce a probabilistic approach to vessel network extraction that enforces physiological constraints on the vessel structure. The method accounts for both image evidence and geometric relationships between vessels by solving an integer program, which is shown to yield the maximum a posteriori (MAP) estimate to a probabilistic model. Starting from an overconnected network, it is pruning vessel stumps and spurious connections by evaluating the local geometry and the global connectivity of the graph. We utilize a high-resolution micro computed tomography (μCT) dataset of a cerebrovascular corrosion cast to obtain a reference network and learn the prior distributions of our probabilistic model and we perform experiments on in-vivo magnetic resonance microangiography (μMRA) images of mouse brains. We finally discuss properties of the networks obtained under different tracking and pruning approaches. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Library User Education under the Circumstance of Network

    Science.gov (United States)

    Zhu, Tian-hui

    2009-01-01

    Based on the concept of user education, this paper discusses the necessity of user education in library under the circumstance of network, describes the contents and forms of user education and puts forward the problems that should be paid attention to during education. [This paper was supported by scientific research project of Qufu Normal…

  3. Security Evaluation of the Cyber Networks under Advanced Persistent Threats

    NARCIS (Netherlands)

    Yang, L.; Li, Pengdeng; Yang, Xiaofan; Tang, Yuan Yan

    2017-01-01

    Advanced persistent threats (APTs) pose a grave threat to cyberspace, because they deactivate all the conventional cyber defense mechanisms. This paper addresses the issue of evaluating the security of the cyber networks under APTs. For this purpose, a dynamic model capturing the APT-based

  4. Biochemical parameters in the blood of grass snakes (Natrix natrix in ecosystems under varying degrees of anthropogenic influence

    Directory of Open Access Journals (Sweden)

    V. Y. Gasso

    2016-09-01

    Full Text Available The grass snake Natrix natrix (Linnaeus, 1758 is a partly hygrophilous species, distributed throughoutUkraine. This snake may be considered as a test object for environmental biomonitoring. Modern biochemical methods make it possible to obtain new scientific data on the effects of anthropogenic pressure on reptiles. Blood is a sensitive and informative indicator of the condition of an organism as it responds quickly to most changes in exogenous and endogenous factors, and reflects negative influences on both individual and, indirectly, populations. Changes in biochemical parameters may be used as biomarkers of the state of health of reptiles in ecosystems under varying degrees of anthropogenic pressure. Due the increase in anthropogenic influence the development and introduction of new methods of perceptual research, collection of up-to-date information and development of a database of reptile biochemical parameters have become an urgent priority. We collected mature individuals of the grass snake in floodplain ecosystems on the right bank of the Dnieper River in Dnipropetrovsk city. Grass snakes from floodplain habitats on the left bank of theSamaraRiver (O.L. Belgard Prysamarskii International Biosphere Station, Novomoskovsk district, Dnipropetrovsk province were studied as the control specimens. Our study demonstrated statistically significant differences between snakes from the study sites in the amount of albumin, urea and urea nitrogen, and inorganic phosphorus, as well as in alanine aminotransferase (ALT and alkaline phosphatise (AP activity. The amount of albumin in the blood serum of specimens from the anthropogenically transformed areas was significantly lower (by 25% than in that of the snakes caught in the control habitats. Decrease of the albumin concentration usually indicates abnormal processes in the kidneys and liver. According to the changes observed in the concentration of albumin, a corresponding increase in the albumin to

  5. Different Biochemical Mechanisms Ensure Network-Wide Balancing of Reducing Equivalents in Microbial Metabolism▿ †

    OpenAIRE

    Fuhrer, Tobias; Sauer, Uwe

    2009-01-01

    To sustain growth, the catabolic formation of the redox equivalent NADPH must be balanced with the anabolic demand. The mechanisms that ensure such network-wide balancing, however, are presently not understood. Based on 13C-detected intracellular fluxes, metabolite concentrations, and cofactor specificities for all relevant central metabolic enzymes, we have quantified catabolic NADPH production in Agrobacterium tumefaciens, Bacillus subtilis, Escherichia coli, Paracoccus versutus, Pseudomona...

  6. The impacts of As accumulation under different pH levels: Comparing Ruditapes decussatus and Ruditapes philippinarum biochemical performance.

    Science.gov (United States)

    Velez, Catia; Figueira, Etelvina; Soares, Amadeu M V M; Freitas, Rosa

    2016-11-01

    Marine bivalves have been used to assess environmental As contamination and the effects of seawater acidification when both factors are acting alone, but limited information is available regarding the impacts of both factors acting in combination. The aim of this study was to compare physiological (glycogen) and biochemical (lipid peroxidation, superoxide dismutase, catalase, glutathione-S-transferase and alkaline phosphatase) responses in both native (Ruditapes decussatus) and introduced (R. philippinarum) clams, when exposed to the combined effects of pH (7.8, control; 7.3) and As concentrations (0 and 4mg/L). The combined effect of As and pH on the health risks associated with clam consumption was also analyzed. Results revealed that both species were able to accumulate As under both pH levels, although higher As concentrations where observed under low pH. Thus, predicted pH decrease will potentiate health risks associated with the consumption of such species, since less amount of clams exposed to As is needed for an adult to exceed the provisional tolerable weekly intake (PTWI). Low pH, As exposure and the combination of both factors did not negatively affect the native species, since clams were able to maintain their physiological and biochemical performance among all conditions. On the other hand, R. philippinarum was negatively affected by As exposure at control pH (7.8), inducing biotransformation and antioxidant defense mechanisms against As toxicity. R. philippinarum exposed and non-exposed to As presented similar responses under low pH although at this condition the introduced species accumulated twice the amount of As than R. decussatus. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Inferring dynamic gene networks under varying conditions for transcriptomic network comparison.

    Science.gov (United States)

    Shimamura, Teppei; Imoto, Seiya; Yamaguchi, Rui; Nagasaki, Masao; Miyano, Satoru

    2010-04-15

    Elucidating the differences between cellular responses to various biological conditions or external stimuli is an important challenge in systems biology. Many approaches have been developed to reverse engineer a cellular system, called gene network, from time series microarray data in order to understand a transcriptomic response under a condition of interest. Comparative topological analysis has also been applied based on the gene networks inferred independently from each of the multiple time series datasets under varying conditions to find critical differences between these networks. However, these comparisons often lead to misleading results, because each network contains considerable noise due to the limited length of the time series. We propose an integrated approach for inferring multiple gene networks from time series expression data under varying conditions. To the best of our knowledge, our approach is the first reverse-engineering method that is intended for transcriptomic network comparison between varying conditions. Furthermore, we propose a state-of-the-art parameter estimation method, relevance-weighted recursive elastic net, for providing higher precision and recall than existing reverse-engineering methods. We analyze experimental data of MCF-7 human breast cancer cells stimulated by epidermal growth factor or heregulin with several doses and provide novel biological hypotheses through network comparison. The software NETCOMP is available at http://bonsai.ims.u-tokyo.ac.jp/ approximately shima/NETCOMP/.

  8. Common and distinct brain networks underlying verbal and visual creativity.

    Science.gov (United States)

    Zhu, Wenfeng; Chen, Qunlin; Xia, Lingxiang; Beaty, Roger E; Yang, Wenjing; Tian, Fang; Sun, Jiangzhou; Cao, Guikang; Zhang, Qinglin; Chen, Xu; Qiu, Jiang

    2017-04-01

    Creativity is imperative to the progression of human civilization, prosperity, and well-being. Past creative researches tends to emphasize the default mode network (DMN) or the frontoparietal network (FPN) somewhat exclusively. However, little is known about how these networks interact to contribute to creativity and whether common or distinct brain networks are responsible for visual and verbal creativity. Here, we use functional connectivity analysis of resting-state functional magnetic resonance imaging data to investigate visual and verbal creativity-related regions and networks in 282 healthy subjects. We found that functional connectivity within the bilateral superior parietal cortex of the FPN was negatively associated with visual and verbal creativity. The strength of connectivity between the DMN and FPN was positively related to both creative domains. Visual creativity was negatively correlated with functional connectivity within the precuneus of the pDMN and right middle frontal gyrus of the FPN, and verbal creativity was negatively correlated with functional connectivity within the medial prefrontal cortex of the aDMN. Critically, the FPN mediated the relationship between the aDMN and verbal creativity, and it also mediated the relationship between the pDMN and visual creativity. Taken together, decreased within-network connectivity of the FPN and DMN may allow for flexible between-network coupling in the highly creative brain. These findings provide indirect evidence for the cooperative role of the default and executive control networks in creativity, extending past research by revealing common and distinct brain systems underlying verbal and visual creative cognition. Hum Brain Mapp 38:2094-2111, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  9. Biochemical analysis of ‘kerosene tree’ Hymenaea courbaril L. under heat stress

    Science.gov (United States)

    Gupta, Dinesh; Eldakak, Moustafa; Rohila, Jai S; Basu, Chhandak

    2014-01-01

    Hymenaea courbaril or jatoba is a tropical tree known for its medically important secondary metabolites production. Considering climate change, the goal of this study was to investigate differential expression of proteins and lipids produced by this tree under heat stress conditions. Total lipid was extracted from heat stressed plant leaves and various sesquiterpenes produced by the tree under heat stress were identified. Gas chromatographic and mass spectrometric analysis were used to study lipid and volatile compounds produced by the plant. Several volatiles, isoprene, 2-methyl butanenitrile, β ocimene and a numbers of sesquiterpenes differentially produced by the plant under heat stress were identified. We propose these compounds were produced by the tree to cope up with heat stress. A protein gel electrophoresis (2-D DIGE) was performed to study differential expression of proteins in heat stressed plants. Several proteins were found to be expressed many folds different in heat stressed plants compared to the control. These proteins included heat shock proteins, histone proteins, oxygen evolving complex, and photosynthetic proteins, which, we believe, played key roles in imparting thermotolerance in Hymenaea tree. To the best of our knowledge, this is the first report of extensive molecular physiological study of Hymenaea trees under heat stress. This work will open avenues of further research on effects of heat stress in Hymenaea and the findings can be applied to understand how global warming can affect physiology of other plants. PMID:25482765

  10. Biochemical analysis of 'kerosene tree' Hymenaea courbaril L. under heat stress.

    Science.gov (United States)

    Gupta, Dinesh; Eldakak, Moustafa; Rohila, Jai S; Basu, Chhandak

    2014-01-01

    Hymenaea courbaril or jatoba is a tropical tree known for its medically important secondary metabolites production. Considering climate change, the goal of this study was to investigate differential expression of proteins and lipids produced by this tree under heat stress conditions. Total lipid was extracted from heat stressed plant leaves and various sesquiterpenes produced by the tree under heat stress were identified. Gas chromatographic and mass spectrometric analysis were used to study lipid and volatile compounds produced by the plant. Several volatiles, isoprene, 2-methyl butanenitrile, β ocimene and a numbers of sesquiterpenes differentially produced by the plant under heat stress were identified. We propose these compounds were produced by the tree to cope up with heat stress. A protein gel electrophoresis (2-D DIGE) was performed to study differential expression of proteins in heat stressed plants. Several proteins were found to be expressed many folds different in heat stressed plants compared to the control. These proteins included heat shock proteins, histone proteins, oxygen evolving complex, and photosynthetic proteins, which, we believe, played key roles in imparting thermotolerance in Hymenaea tree. To the best of our knowledge, this is the first report of extensive molecular physiological study of Hymenaea trees under heat stress. This work will open avenues of further research on effects of heat stress in Hymenaea and the findings can be applied to understand how global warming can affect physiology of other plants.

  11. Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks.

    Science.gov (United States)

    Schillings, Claudia; Sunnåker, Mikael; Stelling, Jörg; Schwab, Christoph

    2015-08-01

    Parametric uncertainty is a particularly challenging and relevant aspect of systems analysis in domains such as systems biology where, both for inference and for assessing prediction uncertainties, it is essential to characterize the system behavior globally in the parameter space. However, current methods based on local approximations or on Monte-Carlo sampling cope only insufficiently with high-dimensional parameter spaces associated with complex network models. Here, we propose an alternative deterministic methodology that relies on sparse polynomial approximations. We propose a deterministic computational interpolation scheme which identifies most significant expansion coefficients adaptively. We present its performance in kinetic model equations from computational systems biology with several hundred parameters and state variables, leading to numerical approximations of the parametric solution on the entire parameter space. The scheme is based on adaptive Smolyak interpolation of the parametric solution at judiciously and adaptively chosen points in parameter space. As Monte-Carlo sampling, it is "non-intrusive" and well-suited for massively parallel implementation, but affords higher convergence rates. This opens up new avenues for large-scale dynamic network analysis by enabling scaling for many applications, including parameter estimation, uncertainty quantification, and systems design.

  12. Time course of physiological, biochemical, and gene expression changes under short-term salt stress in Brassica juncea L.

    Directory of Open Access Journals (Sweden)

    Manish Pandey

    2017-06-01

    Full Text Available Salinity-imposed limitations on plant growth are manifested through osmotic and ionic imbalances. However, because salinity-induced responses vary considerably among crop plants, monitoring of such responses at an early stage has relevance. In this study, physiological (seed germination, seed vigor index, root length, shoot length, fresh weight, dry weight and biochemical attributes (osmoprotectants, K+/Na+ ratio were analyzed for a time-course assessment of salt responses in Indian mustard (Brassica juncea L. with an emphasis on early monitoring. The results showed strong correlations for total soluble sugars at germination phase (24 h, proline content in the seedling establishment phase (48 h and various physiological parameters including seed vigor index (R2 = 0.901, shoot length (R2 = 0.982, and fresh weight (R2 = 0.980 at 72 h (adaptation under stress. In addition, transcriptional changes were observed under NaCl treatment for key genes belonging to the family of selective ion transporters (NHX, HKT and abscisic acid synthesis (AAO-3. The status of mitochondrial respiration was also examined as a probe for salinity tolerance at an early stage. The results suggested that although all the analyzed parameters showed correlations (negative or positive with salt stress magnitude, their critical response times differed, with most of the studied biochemical, physiological, or molecular markers providing valuable information only after radicle emergence, whereas mitochondrial respiration via alternative oxidase was useful for the early detection of salt responses.

  13. Microbiological and biochemical changes in pearl spot (Etroplus suratensis Bloch) stored under modified atmospheres.

    Science.gov (United States)

    Lalitha, K V; Sonaji, E R; Manju, S; Jose, L; Gopal, T K S; Ravisankar, C N

    2005-01-01

    This study aimed to determine the effect of packaging [air, modified atmosphere (MA)] on microbial growth, sensory and chemical parameters and also on shelf life of fresh pearl spot (Etroplus suratensis Bloch) and on the selection of microbial association. Fresh pearl spot (whole, gutted) were packaged under both 100% air and MAs (40%CO(2)/60% O(2), 50%CO(2)/50%O(2), 60% CO(2)/40%O(2), 70% CO(2)/30% O(2) and 40% CO(2)/30% O(2)/30% N(2)) and stored at 0 degrees C. Microbial growth (counts of total aerobic bacteria, H(2)S-producing bacteria, Lactic acid bacteria, Brochothrix thermosphacta, yeast and mould), chemical spoilage indicators (pH, total volatile basic nitrogen) and sensory characteristics were monitored. Microbial changes in Pearl spot packed under 100% air and 40% CO(2)/30%O(2)/30% N(2) were similar. The total volatile basic nitrogen values increased, but the values never exceeded the acceptability limit of 25 mg 100 g(-1). MA 60% CO(2) : 40%O(2) was found to be better with a shelf life of 21 days whereas air stored samples had a shelf-life of 12-14 days only. Storage of pearl spot under MAs 60% CO(2) : 40%O(2) is a promising method to extend shelf-life. Longer shelf life expands the market potential of pearl spot and reduces waste during distribution and retail display.

  14. Mixed Transportation Network Design under a Sustainable Development Perspective

    Directory of Open Access Journals (Sweden)

    Jin Qin

    2013-01-01

    Full Text Available A mixed transportation network design problem considering sustainable development was studied in this paper. Based on the discretization of continuous link-grade decision variables, a bilevel programming model was proposed to describe the problem, in which sustainability factors, including vehicle exhaust emissions, land-use scale, link load, and financial budget, are considered. The objective of the model is to minimize the total amount of resources exploited under the premise of meeting all the construction goals. A heuristic algorithm, which combined the simulated annealing and path-based gradient projection algorithm, was developed to solve the model. The numerical example shows that the transportation network optimized with the method above not only significantly alleviates the congestion on the link, but also reduces vehicle exhaust emissions within the network by up to 41.56%.

  15. Node vulnerability of water distribution networks under cascading failures

    International Nuclear Information System (INIS)

    Shuang, Qing; Zhang, Mingyuan; Yuan, Yongbo

    2014-01-01

    Water distribution networks (WDNs) are important in modern lifeline system. Its stability and reliability are critical for guaranteeing high living quality and continuous operation of urban functions. The aim of this paper is to evaluate the nodal vulnerability of WDNs under cascading failures. Vulnerability is defined to analyze the effects of the consequent failures. A cascading failure is a step-by-step process which is quantitatively investigated by numerical simulation with intentional attack. Monitored pressures in different nodes and flows in different pipes have been used to estimate the network topological structure and the consequences of nodal failure. Based on the connectivity loss of topological structure, the nodal vulnerability has been evaluated. A load variation function is established to record the nodal failure reason and describe the relative differences between the load and the capacity. The proposed method is validated by an illustrative example. The results revealed that the network vulnerability should be evaluated with the consideration of hydraulic analysis and network topology. In the case study, 70.59% of the node failures trigger the cascading failures with different failure processes. It is shown that the cascading failures result in severe consequences in WDNs. - Highlights: • The aim of this paper is to evaluate the nodal vulnerability of water distribution networks under cascading failures. • Monitored pressures and flows have been used to estimate the network topological structure and the consequences of nodal failure. • Based on the connectivity loss of topological structure, the nodal vulnerability has been evaluated. • A load variation function is established to record the failure reason and describe the relative differences between load and capacity. • The results show that 70.59% of the node failures trigger the cascading failures with different failure processes

  16. Analytic Treatment of Deep Neural Networks Under Additive Gaussian Noise

    KAUST Repository

    Alfadly, Modar M.

    2018-04-12

    Despite the impressive performance of deep neural networks (DNNs) on numerous vision tasks, they still exhibit yet-to-understand uncouth behaviours. One puzzling behaviour is the reaction of DNNs to various noise attacks, where it has been shown that there exist small adversarial noise that can result in a severe degradation in the performance of DNNs. To rigorously treat this, we derive exact analytic expressions for the first and second moments (mean and variance) of a small piecewise linear (PL) network with a single rectified linear unit (ReLU) layer subject to general Gaussian input. We experimentally show that these expressions are tight under simple linearizations of deeper PL-DNNs, especially popular architectures in the literature (e.g. LeNet and AlexNet). Extensive experiments on image classification show that these expressions can be used to study the behaviour of the output mean of the logits for each class, the inter-class confusion and the pixel-level spatial noise sensitivity of the network. Moreover, we show how these expressions can be used to systematically construct targeted and non-targeted adversarial attacks. Then, we proposed a special estimator DNN, named mixture of linearizations (MoL), and derived the analytic expressions for its output mean and variance, as well. We employed these expressions to train the model to be particularly robust against Gaussian attacks without the need for data augmentation. Upon training this network on a loss that is consolidated with the derived output probabilistic moments, the network is not only robust under very high variance Gaussian attacks but is also as robust as networks that are trained with 20 fold data augmentation.

  17. Physiological and biochemical assisted screening of wheat varieties under partial rhizosphere drying.

    Science.gov (United States)

    Raza, Muhammad Aown Sammar; Ahmad, Salman; Saleem, Muhammad Farrukh; Khan, Imran Haider; Iqbal, Rashid; Zaheer, Muhammad Saqlain; Haider, Imran; Ali, Muhammad

    2017-07-01

    Wheat is one of the major staple food of the world, which is badly affected by water deficit stress. To fulfill the dietary needs of increasing population with depleting water resources there is need to adopt technologies which result in sufficient crop yield with less water consumption. One of them is partial root zone drying (PRD). Keeping in view these conditions, a wire house experiment was conducted at University College of Agriculture and Environmental Sciences, The Islamia University Bahawalpur during 2015, to screen out the different wheat genotypes for PRD. Five approved local wheat cultivars (V 1 = Galaxy-2013, V 2 = Punjab-2011, V 3  = Faisalabad-2008, V 4  = Lasani-2008 and V 5  = V.8200) and two irrigation levels (I 1  = control irrigation and I 2  = PRD irrigation) with completely randomized design having four replications were used in the experiment. Among the varieties Galaxy-2013 performed the best and attained maximum plant height, leaf area, stomatal conductance, photosynthesis, total sugars, proline contents and antioxidant enzymes activities and minimum values of all growth and physiological parameters were recorded in variety V.8200. For irrigation levels, higher values of growth, physiological and water related parameters were recorded in control treatment (I 1 ) except leaf water potential, osmotic potential, total sugars and proline contents. However enzymes activities were higher under PRD treatment for all varieties. It was concluded that Galaxy-2013 was the most compatible and V.8200 was the most susceptible variety under PRD condition, respectively and more quality traits and enzymatic activities were recorded under PRD condition as compared to control treatment. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  18. Noise transmission and delay-induced stochastic oscillations in biochemical network motifs

    International Nuclear Information System (INIS)

    Liu Sheng-Jun; Wang Qi; Liu Bo; Yan Shi-Wei; Sakata Fumihiko

    2011-01-01

    With the aid of stochastic delayed-feedback differential equations, we derive an analytic expression for the power spectra of reacting molecules included in a generic biological network motif that is incorporated with a feedback mechanism and time delays in gene regulation. We systematically analyse the effects of time delays, the feedback mechanism, and biological stochasticity on the power spectra. It has been clarified that the time delays together with the feedback mechanism can induce stochastic oscillations at the molecular level and invalidate the noise addition rule for a modular description of the noise propagator. Delay-induced stochastic resonance can be expected, which is related to the stability loss of the reaction systems and Hopf bifurcation occurring for solutions of the corresponding deterministic reaction equations. Through the analysis of the power spectrum, a new approach is proposed to estimate the oscillation period. (interdisciplinary physics and related areas of science and technology)

  19. Flow Analysis of Physiological and Biochemical Networks in Human Body—A Holistic View

    Science.gov (United States)

    Aoki, Ichiro

    1990-09-01

    A system-theoretical approach, the input-output flow analysis, is applied to the study of water flow, protein metabolism and energy flow in human body: indices characterizing patterns of flow, that is, throughflow, total system throughflow, path length, cycling index and trophic position are calculated and discussed for flow-networks within human body. Cycling indices for energy-flow are zero and those for mass-flow are large; this tendency is also the case for ecosystems as systems-ecology shows. In this respect, a human body can be regarded as a “mini-ecosystem”. Trophic positions for mass-flow are larger than the numberings of compartment, showing also quantitatively the existence of intense cycling in mass-flow in human body.

  20. Landauer in the Age of Synthetic Biology: Energy Consumption and Information Processing in Biochemical Networks

    Science.gov (United States)

    Mehta, Pankaj; Lang, Alex H.; Schwab, David J.

    2016-03-01

    A central goal of synthetic biology is to design sophisticated synthetic cellular circuits that can perform complex computations and information processing tasks in response to specific inputs. The tremendous advances in our ability to understand and manipulate cellular information processing networks raises several fundamental physics questions: How do the molecular components of cellular circuits exploit energy consumption to improve information processing? Can one utilize ideas from thermodynamics to improve the design of synthetic cellular circuits and modules? Here, we summarize recent theoretical work addressing these questions. Energy consumption in cellular circuits serves five basic purposes: (1) increasing specificity, (2) manipulating dynamics, (3) reducing variability, (4) amplifying signal, and (5) erasing memory. We demonstrate these ideas using several simple examples and discuss the implications of these theoretical ideas for the emerging field of synthetic biology. We conclude by discussing how it may be possible to overcome these limitations using "post-translational" synthetic biology that exploits reversible protein modification.

  1. SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks

    DEFF Research Database (Denmark)

    Draeger, Andreas; Zielinski, Daniel C.; Keller, Roland

    2015-01-01

    simplified the network reconstruction process, but building kinetic models for these systems is still a manually intensive task. Appropriate kinetic equations, based upon reaction rate laws, must be constructed and parameterized for each reaction. The complex test-and-evaluation cycles that can be involved...... during kinetic model construction would thus benefit from automated methods for rate law assignment. Results: We present a high-throughput algorithm to automatically suggest and create suitable rate laws based upon reaction type according to several criteria. The criteria for choices made...... by the algorithm can be influenced in order to assign the desired type of rate law to each reaction. This algorithm is implemented in the software package SBMLsqueezer 2. In addition, this program contains an integrated connection to the kinetics database SABIO-RK to obtain experimentally-derived rate laws when...

  2. The Network Structure Underlying the Earth Observation Assessment

    Science.gov (United States)

    Vitkin, S.; Doane, W. E. J.; Mary, J. C.

    2017-12-01

    The Earth Observations Assessment (EOA 2016) is a multiyear project designed to assess the effectiveness of civil earth observation data sources (instruments, sensors, models, etc.) on societal benefit areas (SBAs) for the United States. Subject matter experts (SMEs) provided input and scored how data sources inform products, product groups, key objectives, SBA sub-areas, and SBAs in an attempt to quantify the relationships between data sources and SBAs. The resulting data were processed by Integrated Applications Incorporated (IAI) using MITRE's PALMA software to create normalized relative impact scores for each of these relationships. However, PALMA processing obscures the natural network representation of the data. Any network analysis that might identify patterns of interaction among data sources, products, and SBAs is therefore impossible. Collaborating with IAI, we cleaned and recreated a network from the original dataset. Using R and Python we explore the underlying structure of the network and apply frequent itemset mining algorithms to identify groups of data sources and products that interact. We reveal interesting patterns and relationships in the EOA dataset that were not immediately observable from the EOA 2016 report and provide a basis for further exploration of the EOA network dataset.

  3. Network attributes underlying intellectual giftedness in the developing brain.

    Science.gov (United States)

    Ma, Jiyoung; Kang, Hee Jin; Kim, Jung Yoon; Jeong, Hyeonseok S; Im, Jooyeon Jamie; Namgung, Eun; Kim, Myeong Ju; Lee, Suji; Kim, Tammy D; Oh, Jin Kyoung; Chung, Yong-An; Lyoo, In Kyoon; Lim, Soo Mee; Yoon, Sujung

    2017-09-12

    Brain network is organized to maximize the efficiency of both segregated and integrated information processing that may be related to human intelligence. However, there have been surprisingly few studies that focus on the topological characteristics of brain network underlying extremely high intelligence that is intellectual giftedness, particularly in adolescents. Here, we examined the network topology in 25 adolescents with superior intelligence (SI-Adol), 25 adolescents with average intelligence (AI-Adol), and 27 young adults with AI (AI-Adult). We found that SI-Adol had network topological properties of high global efficiency as well as high clustering with a low wiring cost, relative to AI-Adol. However, contrary to the suggested role that brain hub regions play in general intelligence, the network efficiency of rich club connection matrix, which represents connections among brain hubs, was low in SI-Adol in comparison to AI-Adol. Rather, a higher level of local connection density was observed in SI-Adol than in AI-Adol. The highly intelligent brain may not follow this efficient yet somewhat stereotypical process of information integration entirely. Taken together, our results suggest that a highly intelligent brain may communicate more extensively, while being less dependent on rich club communications during adolescence.

  4. Sustainable and Resilient Supply Chain Network Design under Disruption Risks

    Directory of Open Access Journals (Sweden)

    Sonia Irshad Mari

    2014-09-01

    Full Text Available Sustainable supply chain network design is a rich area for academic research that is still in its infancy and has potential to affect supply chain performance. Increasing regulations for carbon and waste management are forcing firms to consider their supply chains from ecological and social objectives, but in reality, however, facilities and the links connecting them are disrupted from time to time, due to poor weather, natural or manmade disasters or a combination of any other factors. Supply chain systems drop their sustainability objectives while coping with these unexpected disruptions. Hence, the new challenges for supply chain managers are to design an efficient and effective supply chain network that will be resilient enough to bounce back from any disruption and that also should have sufficient vigilance to offer same sustainability under a disruption state. This paper focuses on ecological sustainability, because an environmental focus in a supply chain system is more important and also links with other pillars of sustainability, as the products need to be produced, packed and transported in an ethical way, which should not harm social balance and the environment. Owing to importance of the considered issue, this paper attempts to introduce a network optimization model for a sustainable and resilient supply chain network by incorporating (1 sustainability via carbon emissions and embodied carbon footprints and (2 resilience by incorporating location-specific risks. The proposed goal programming (GP model optimizes the total cost, while considering the resilience and sustainability of the supply chain network.

  5. Physio-biochemical and morphological characters of halophyte legume shrub, Acacia ampliceps seedlings in response to salt stress under greenhouse.

    Science.gov (United States)

    Theerawitaya, Cattarin; Tisarum, Rujira; Samphumphuang, Thapanee; Singh, Harminder P; Suriyan Cha-Um; Kirdmanee, Chalermpol; Takabe, Teruhiro

    2015-01-01

    Acacia ampliceps (salt wattle), a leguminous shrub, has been introduced in salt-affected areas in the northeast of Thailand for the remediation of saline soils. However, the defense mechanisms underlying salt tolerance A. ampliceps are unknown. We investigated various physio-biochemical and morphological attributes of A. ampliceps in response to varying levels of salt treatment (200-600 mM NaCl). Seedlings of A. ampliceps (25 ± 2 cm in plant height) raised from seeds were treated with 200 mM (mild stress), 400 and 600 mM (extreme stress) of salt treatment (NaCl) under greenhouse conditions. Na(+) and Ca(2+) contents in the leaf tissues increased significantly under salt treatment, whereas K(+) content declined in salt-stressed plants. Free proline and soluble sugar contents in plants grown under extreme salt stress (600 mM NaCl) for 9 days significantly increased by 28.7 (53.33 μmol g(-1) FW) and 3.2 (42.11 mg g(-1) DW) folds, respectively over the control, thereby playing a major role as osmotic adjustment. Na(+) enrichment in the phyllode tissues of salt-stressed seedlings positively related to total chlorophyll (TC) degradation (R (2) = 0.72). Photosynthetic pigments and chlorophyll fluorescence in salt-stressed plants increased under mild salt stress (200 mM NaCl). However, these declined under high levels of salinity (400-600 mM NaCl), consequently resulting in a reduced net photosynthetic rate (R (2) = 0.81) and plant dry weight (R (2) = 0.91). The study concludes that A. ampliceps has an osmotic adjustment and Na(+) compartmentation as effective salt defense mechanisms, and thus it could be an excellent species to grow in salt-affected soils.

  6. Physio-biochemical and morphological characters of halophyte legume shrub, Acacia ampliceps seedlings in response to salt stress under greenhouse

    Directory of Open Access Journals (Sweden)

    Cattarin eTheerawitaya

    2015-08-01

    Full Text Available Acacia ampliceps (salt wattle, a leguminous shrub, has been introduced in salt-affected areas in northeast of Thailand for remediation of saline soils. However, the defense mechanisms underlying salt tolerance A. ampliceps are unknown. We investigated various physio-biochemical and morphological attributes of A. ampliceps in response to varying levels of salt treatment (200 to 600 mM NaCl. Seedlings of A. ampliceps (252 cm in plant height raised from seeds were treated with 200 mM (mild stress, 400 and 600 mM (extreme stress of salt treatment (NaCl under greenhouse conditions. Na+ and Ca2+ contents in the leaf tissues increased significantly under salt treatment, whereas K+ content declined in salt-stressed plants. Free proline and soluble sugar contents in plant grown under extreme salt stress (600 mM NaCl for 9 days significantly increased by 28.7 (53.33 mol g1 FW and 3.2 (42.11 mg g1 DW folds, respectively over the control, thereby playing a major role as osmotic adjustment. Na+ enrichment in the phyllode tissues of salt-stressed seedlings positively related to total chlorophyll degradation (R2=0.72. Photosynthetic pigments and chlorophyll fluorescence in salt-stressed plants increased under mild salt stress (200 mM NaCl. However, these declined under high level of salinity (400-600 mM NaCl, consequently resulting in reduced net photosynthetic rate (R2=0.81 and plant dry weight (R2= 0.91. The study concludes that A. ampliceps has an osmotic adjustment and Na+ compartmentation as effective salt defense mechanisms, and thus it could be an excellent species to grow in salt-affected soils.

  7. Mineral Content and Biochemical Variables of Aloe vera L. under Salt Stress

    Science.gov (United States)

    Murillo-Amador, Bernardo; Córdoba-Matson, Miguel Víctor; Villegas-Espinoza, Jorge Arnoldo; Hernández-Montiel, Luis Guillermo; Troyo-Diéguez, Enrique; García-Hernández, José Luis

    2014-01-01

    Despite the proven economic importance of Aloe vera, studies of saline stress and its effects on the biochemistry and mineral content in tissues of this plant are scarce. The objective of this study was to grow Aloe under NaCl stress of 0, 30, 60, 90 and 120 mM and compare: (1) proline, total protein, and enzyme phosphoenolpyruvate carboxylase (PEP-case) in chlorenchyma and parenchyma tissues, and (2) ion content (Na, K, Ca, Mg, Cl, Fe, P. N, Zn, B, Mn, and Cu) in roots, stems, leaves and sprouts. Proline and PEP-case increased as salinity increased in both parenchyma and chlorenchyma, while total protein increased in parenchyma and decreased in chlorenchyma, although at similar salt concentrations total protein was always higher in chlorenchyma. As salinity increased Na and Cl ions increased in roots, stems, leaves, while K decreased only significantly in sprouts. Salinity increases typically caused mineral content in tissue to decrease, or not change significantly. In roots, as salinity increased Mg decreased, while all other minerals failed to show a specific trend. In stems, the mineral concentrations that changed were Fe and P which increased with salinity while Cu decreased. In leaves, Mg, Mn, N, and B decreased with salinity, while Cu increased. In sprouts, the minerals that decreased with increasing salinity were Mg, Mn, and Cu. Zinc did not exhibit a trend in any of the tissues. The increase in protein, proline and PEP-case activity, as well as the absorption and accumulation of cations under moderate NaCl stress caused osmotic adjustment which kept the plant healthy. These results suggest that Aloe may be a viable crop for soil irrigated with hard water or affected by salinity at least at concentrations used in the present study. PMID:24736276

  8. Mineral content and biochemical variables of Aloe vera L. under salt stress.

    Science.gov (United States)

    Murillo-Amador, Bernardo; Córdoba-Matson, Miguel Víctor; Villegas-Espinoza, Jorge Arnoldo; Hernández-Montiel, Luis Guillermo; Troyo-Diéguez, Enrique; García-Hernández, José Luis

    2014-01-01

    Despite the proven economic importance of Aloe vera, studies of saline stress and its effects on the biochemistry and mineral content in tissues of this plant are scarce. The objective of this study was to grow Aloe under NaCl stress of 0, 30, 60, 90 and 120 mM and compare: (1) proline, total protein, and enzyme phosphoenolpyruvate carboxylase (PEP-case) in chlorenchyma and parenchyma tissues, and (2) ion content (Na, K, Ca, Mg, Cl, Fe, P. N, Zn, B, Mn, and Cu) in roots, stems, leaves and sprouts. Proline and PEP-case increased as salinity increased in both parenchyma and chlorenchyma, while total protein increased in parenchyma and decreased in chlorenchyma, although at similar salt concentrations total protein was always higher in chlorenchyma. As salinity increased Na and Cl ions increased in roots, stems, leaves, while K decreased only significantly in sprouts. Salinity increases typically caused mineral content in tissue to decrease, or not change significantly. In roots, as salinity increased Mg decreased, while all other minerals failed to show a specific trend. In stems, the mineral concentrations that changed were Fe and P which increased with salinity while Cu decreased. In leaves, Mg, Mn, N, and B decreased with salinity, while Cu increased. In sprouts, the minerals that decreased with increasing salinity were Mg, Mn, and Cu. Zinc did not exhibit a trend in any of the tissues. The increase in protein, proline and PEP-case activity, as well as the absorption and accumulation of cations under moderate NaCl stress caused osmotic adjustment which kept the plant healthy. These results suggest that Aloe may be a viable crop for soil irrigated with hard water or affected by salinity at least at concentrations used in the present study.

  9. Mineral content and biochemical variables of Aloe vera L. under salt stress.

    Directory of Open Access Journals (Sweden)

    Bernardo Murillo-Amador

    Full Text Available Despite the proven economic importance of Aloe vera, studies of saline stress and its effects on the biochemistry and mineral content in tissues of this plant are scarce. The objective of this study was to grow Aloe under NaCl stress of 0, 30, 60, 90 and 120 mM and compare: (1 proline, total protein, and enzyme phosphoenolpyruvate carboxylase (PEP-case in chlorenchyma and parenchyma tissues, and (2 ion content (Na, K, Ca, Mg, Cl, Fe, P. N, Zn, B, Mn, and Cu in roots, stems, leaves and sprouts. Proline and PEP-case increased as salinity increased in both parenchyma and chlorenchyma, while total protein increased in parenchyma and decreased in chlorenchyma, although at similar salt concentrations total protein was always higher in chlorenchyma. As salinity increased Na and Cl ions increased in roots, stems, leaves, while K decreased only significantly in sprouts. Salinity increases typically caused mineral content in tissue to decrease, or not change significantly. In roots, as salinity increased Mg decreased, while all other minerals failed to show a specific trend. In stems, the mineral concentrations that changed were Fe and P which increased with salinity while Cu decreased. In leaves, Mg, Mn, N, and B decreased with salinity, while Cu increased. In sprouts, the minerals that decreased with increasing salinity were Mg, Mn, and Cu. Zinc did not exhibit a trend in any of the tissues. The increase in protein, proline and PEP-case activity, as well as the absorption and accumulation of cations under moderate NaCl stress caused osmotic adjustment which kept the plant healthy. These results suggest that Aloe may be a viable crop for soil irrigated with hard water or affected by salinity at least at concentrations used in the present study.

  10. Modeling the Propagation of Mobile Phone Virus under Complex Network

    OpenAIRE

    Yang, Wei; Wei, Xi-liang; Guo, Hao; An, Gang; Guo, Lei; Yao, Yu

    2014-01-01

    Mobile phone virus is a rogue program written to propagate from one phone to another, which can take control of a mobile device by exploiting its vulnerabilities. In this paper the propagation model of mobile phone virus is tackled to understand how particular factors can affect its propagation and design effective containment strategies to suppress mobile phone virus. Two different propagation models of mobile phone viruses under the complex network are proposed in this paper. One is intende...

  11. Biochemical alterations in inflammatory reactive chondrocytes: evidence for intercellular network communication

    Directory of Open Access Journals (Sweden)

    Eva Skiöldebrand

    2018-01-01

    Full Text Available Chondrocytes are effectively involved in the pathophysiological processes of inflammation in joints. They form cellular processes in the superficial layer of the articular cartilage and form gap junction coupled syncytium to facilitate cell-to-cell communication. However, very little is known about their physiological cellular identity and communication. The aim with the present work is to evaluate the physiological behavior after stimulation with the inflammatory inducers interleukin-1β and lipopolysaccharide. The cytoskeleton integrity and intracellular Ca2+ release were assessed as indicators of inflammatory state. Cytoskeleton integrity was analyzed through cartilage oligomeric matrix protein and actin labeling with an Alexa 488-conjugated phalloidin probe. Ca2+ responses were assessed through the Ca2+ sensitive fluorophore Fura-2/AM. Western blot analyses of several inflammatory markers were performed. The results show reorganization of the actin filaments. Glutamate, 5-hydoxytryptamine, and ATP evoked intracellular Ca2+ release changed from single peaks to oscillations after inflammatory induction in the chondrocytes. The expression of toll-like receptor 4, the glutamate transporters GLAST and GLT-1, and the matrix metalloproteinase-13 increased. This work demonstrates that chondrocytes are a key part in conditions that lead to inflammation in the cartilage. The inflammatory inducers modulate the cytoskeleton, the Ca2+ signaling, and several inflammatory parameters. In conclusion, our data show that the cellular responses to inflammatory insults from healthy and inflammatory chondrocytes resemble those previously observed in astrocyte and cardiac fibroblasts networks.

  12. Different biochemical mechanisms ensure network-wide balancing of reducing equivalents in microbial metabolism.

    Science.gov (United States)

    Fuhrer, Tobias; Sauer, Uwe

    2009-04-01

    To sustain growth, the catabolic formation of the redox equivalent NADPH must be balanced with the anabolic demand. The mechanisms that ensure such network-wide balancing, however, are presently not understood. Based on 13C-detected intracellular fluxes, metabolite concentrations, and cofactor specificities for all relevant central metabolic enzymes, we have quantified catabolic NADPH production in Agrobacterium tumefaciens, Bacillus subtilis, Escherichia coli, Paracoccus versutus, Pseudomonas fluorescens, Rhodobacter sphaeroides, Sinorhizobium meliloti, and Zymomonas mobilis. For six species, the estimated NADPH production from glucose catabolism exceeded the requirements for biomass synthesis. Exceptions were P. fluorescens, with balanced rates, and E. coli, with insufficient catabolic production, in which about one-third of the NADPH is supplied via the membrane-bound transhydrogenase PntAB. P. versutus and B. subtilis were the only species that appear to rely on transhydrogenases for balancing NADPH overproduction during growth on glucose. In the other four species, the main but not exclusive redox-balancing mechanism appears to be the dual cofactor specificities of several catabolic enzymes and/or the existence of isoenzymes with distinct cofactor specificities, in particular glucose 6-phosphate dehydrogenase. An unexpected key finding for all species, except E. coli and B. subtilis, was the lack of cofactor specificity in the oxidative pentose phosphate pathway, which contrasts with the textbook view of the pentose phosphate pathway dehydrogenases as being NADP+ dependent.

  13. Enzymatic activity of granulations tissues under low doses of radiation. Biochemical analysis in rats

    International Nuclear Information System (INIS)

    Tosoni, Guilherme Monteiro; Boscolo, Frab Norberto; Cury, Jaime Aparecido; Watanabe, Plauto Christopher Aranha

    1994-01-01

    This paper was designed to investigate in the rat subcutaneous sponge-induced granulation tissue under low doses of X-ray, the activity of alkaline phosphatase, 5'nucleotide phosphodiesterase and adenosine triphosphatase (ATPase) enzymes. One hundred and fourteen Wistar rats were divided into three groups, as follows: Group I as control, Group II that received single 7,14 R in split-dosis immediately after sponge-implantation at the third and fifth days postoperatively. Biopsies were taken after 7, 11, 14, 21 and 28 days and the activity of the three enzymes was determined. The results have shown that in Group II alkaline phosphatase had higher activity in the 14th day of tissue evolution when compared to Groups I and III . The 5'nucleotide phosphodiesterase activity in Group I was similar in all days checked, although in Group II the enzyme showed higher activity in 7th day and lower in 21st. In Group III the activity was higher after 14 and 7 days and lower after 28 and 21 days. There was no observation of changing in adenosine triphosphatase (ATPase) activity when the three groups were compared. (author)

  14. Evolution of cooperation under social pressure in multiplex networks

    Science.gov (United States)

    Pereda, María

    2016-09-01

    In this work, we aim to contribute to the understanding of human prosocial behavior by studying the influence that a particular form of social pressure, "being watched," has on the evolution of cooperative behavior. We study how cooperation emerges in multiplex complex topologies by analyzing a particular bidirectionally coupled dynamics on top of a two-layer multiplex network (duplex). The coupled dynamics appears between the prisoner's dilemma game in a network and a threshold cascade model in the other. The threshold model is intended to abstract the behavior of a network of vigilant nodes that impose the pressure of being observed altering hence the temptation to defect of the dilemma. Cooperation or defection in the game also affects the state of a node of being vigilant. We analyze these processes on different duplex networks structures and assess the influence of the topology, average degree and correlated multiplexity, on the outcome of cooperation. Interestingly, we find that the social pressure of vigilance may impact cooperation positively or negatively, depending on the duplex structure, specifically the degree correlations between layers is determinant. Our results give further quantitative insights in the promotion of cooperation under social pressure.

  15. Analysis and Reduction of Complex Networks Under Uncertainty

    Energy Technology Data Exchange (ETDEWEB)

    Knio, Omar M

    2014-04-09

    This is a collaborative proposal that aims at developing new methods for the analysis and reduction of complex multiscale networks under uncertainty. The approach is based on combining methods of computational singular perturbation (CSP) and probabilistic uncertainty quantification. In deterministic settings, CSP yields asymptotic approximations of reduced-dimensionality “slow manifolds” on which a multiscale dynamical system evolves. Introducing uncertainty raises fundamentally new issues, particularly concerning its impact on the topology of slow manifolds, and means to represent and quantify associated variability. To address these challenges, this project uses polynomial chaos (PC) methods to reformulate uncertain network models, and to analyze them using CSP in probabilistic terms. Specific objectives include (1) developing effective algorithms that can be used to illuminate fundamental and unexplored connections among model reduction, multiscale behavior, and uncertainty, and (2) demonstrating the performance of these algorithms through applications to model problems.

  16. Development of Shale Gas Supply Chain Network under Market Uncertainties

    Directory of Open Access Journals (Sweden)

    Jorge Chebeir

    2017-02-01

    Full Text Available The increasing demand of energy has turned the shale gas and shale oil into one of the most promising sources of energy in the United States. In this article, a model is proposed to address the long-term planning problem of the shale gas supply chain under uncertain conditions. A two-stage stochastic programming model is proposed to describe and optimize the shale gas supply chain network. Inherent uncertainty in final products’ prices, such as natural gas and natural gas liquids (NGL, is treated through the utilization of a scenario-based method. A binomial option pricing model is utilized to approximate the stochastic process through the generation of scenario trees. The aim of the proposed model is to generate an appropriate and realistic supply chain network configuration as well as scheduling of different operations throughout the planning horizon of a shale gas development project.

  17. Final Report. Analysis and Reduction of Complex Networks Under Uncertainty

    Energy Technology Data Exchange (ETDEWEB)

    Marzouk, Youssef M. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Coles, T. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Spantini, A. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Tosatto, L. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

    2013-09-30

    The project was a collaborative effort among MIT, Sandia National Laboratories (local PI Dr. Habib Najm), the University of Southern California (local PI Prof. Roger Ghanem), and The Johns Hopkins University (local PI Prof. Omar Knio, now at Duke University). Our focus was the analysis and reduction of large-scale dynamical systems emerging from networks of interacting components. Such networks underlie myriad natural and engineered systems. Examples important to DOE include chemical models of energy conversion processes, and elements of national infrastructure—e.g., electric power grids. Time scales in chemical systems span orders of magnitude, while infrastructure networks feature both local and long-distance connectivity, with associated clusters of time scales. These systems also blend continuous and discrete behavior; examples include saturation phenomena in surface chemistry and catalysis, and switching in electrical networks. Reducing size and stiffness is essential to tractable and predictive simulation of these systems. Computational singular perturbation (CSP) has been effectively used to identify and decouple dynamics at disparate time scales in chemical systems, allowing reduction of model complexity and stiffness. In realistic settings, however, model reduction must contend with uncertainties, which are often greatest in large-scale systems most in need of reduction. Uncertainty is not limited to parameters; one must also address structural uncertainties—e.g., whether a link is present in a network—and the impact of random perturbations, e.g., fluctuating loads or sources. Research under this project developed new methods for the analysis and reduction of complex multiscale networks under uncertainty, by combining computational singular perturbation (CSP) with probabilistic uncertainty quantification. CSP yields asymptotic approximations of reduceddimensionality “slow manifolds” on which a multiscale dynamical system evolves. Introducing

  18. Connection Management and Recovery Strategies under Epidemic Network Failures in Optical Transport Networks

    DEFF Research Database (Denmark)

    Fagertun, Anna Manolova; Ruepp, Sarah Renée

    2014-01-01

    The current trend in deploying automatic control plane solutions for increased flexibility in the optical transport layer leads to numerous advantages for both the operators and the customers, but also pose challenges related to the stability of the network and its ability to operate in a robust ...... of their transport infrastructures. Applying proactive methods for avoiding areas where epidemic failures spread results in 50% less connections requiring recovery, which translates in improved quality of service to customers....... manner under attacks. This work proposes four policies for failure handling in a connection-oriented optical transport network, under Generalized MultiProtocol Label Switching control plane, and evaluates their performance under multiple correlated large-scale failures. We employ the Susceptible......-Infected-Disabled epidemic failure spreading model and look into possible tradeoffs between resiliency and resource efficiency. Via extensive simulations we show that there exist a clear tradeoff between policy performance and network resource consumption, which must be addressed by network operators for improved robustness...

  19. The dtudy of physiological and biochemical responses of Agrostis stolonifera and Festuca arundinacea Schreb. under drought stress

    Directory of Open Access Journals (Sweden)

    Mohammad Hassan Alibiglouei

    2014-12-01

    Full Text Available Drought stress is a main limiting factor of turfgrass growth in arid and semi-arid regions. Therefore, in this study, the physiological and biochemical changes in two turfgrass species Agrostis stolonifera and Festuca arundinacea schreb during drought stress (70-75 centibar in a 40-day period and recovery were investigated. Control plants during drought stress were regularly irrigated at soil field capacity (20-25 centibar. The results showed that leaf relative water content and leaf chlorophyll content with long-term stress decreased. Electrolyte leakage and proline during drought stress significantly increased and in recovery stage, the level of electrolyte leakage and proline reached to the control. The activity of peroxidase and superoxide dismutase in two turfgrass significantly increased after 30 days and then significantly reduced. In F. arundinacea schreb the activity of ascorbat peroxidase after 20 days significantly increased and then significantly reduced. Also, in F. arundinacea schreb species the activity of catalase increased during drought stress and in recovery stage the activity of catalase reduced. In studied species during drought stress and recovery stage, the activity of ascorbat peroxidase and catalase significantly increased compared to the control. These results suggested that the resistant species F. arundinacea schreb, under drought stress had a low level of electrolyte leakage, higher level of relative water content and chlorophyll destruction was less than A. stolonifera.

  20. Soil restoration under pasture after lignite mining - management effects on soil biochemical properties and their relationships with herbage yields

    Energy Technology Data Exchange (ETDEWEB)

    Ross, D.J.; Speir, T.W.; Cowling, J.C.; Feltham, C.W. (DSIR, Lower Hutt (New Zealand))

    1992-01-01

    The recovery of soil biochemical properties under grazed, grass-clover pasture after simulated lignite mining was studied over a 5-year period in a mesic Typic Dystrochrept soil at Waimumu, Southland, New Zealand. Restoration procedures involved four replacement treatments, after A,B and C horizon materials had been separately removed, from all except the control, and stockpiled for 2-3 weeks. Replacement treatment markedly influenced the recovery of herbage production and soil organic C and total N contents, N mineralization, microbial biomass (as indicated by mineral-N flush) and invertase and sulphatase activities. The effectiveness of replacement treatments decreased in the order: 1. control (no stripping or replacement). 2. A,B and C horizon materials replaced in the same order. 3. A,B and C horizon materials each mixed with an equal amount of siltstone overburden and replaced in order, 4. A and B horizon materials mixed before replacing over C horizon materials. Ripping increased herbage production, net N mineralization and microbial biomass. Fertilizer N also stimulated herbage production but depressed clover growth. Increases in soil invertase and, to a lesser extent, sulphatase activity were closely related to changes in herbage production. Microbial biomass increased more rapidly than soil organic C in early stages in the trial. Rates of net N mineralization suggest that N availability would have limited pasture growth.

  1. Optimal Retrofit Scheme for Highway Network under Seismic Hazards

    Directory of Open Access Journals (Sweden)

    Yongxi Huang

    2014-06-01

    Full Text Available Many older highway bridges in the United States (US are inadequate for seismic loads and could be severely damaged or collapsed in a relatively small earthquake. According to the most recent American Society of Civil Engineers’ infrastructure report card, one-third of the bridges in the US are rated as structurally deficient and many of these structurally deficient bridges are located in seismic zones. To improve this situation, at-risk bridges must be identified and evaluated and effective retrofitting programs should be in place to reduce their seismic vulnerabilities. In this study, a new retrofit strategy decision scheme for highway bridges under seismic hazards is developed and seamlessly integrate the scenario-based seismic analysis of bridges and the traffic network into the proposed optimization modeling framework. A full spectrum of bridge retrofit strategies is considered based on explicit structural assessment for each seismic damage state. As an empirical case study, the proposed retrofit strategy decision scheme is utilized to evaluate the bridge network in one of the active seismic zones in the US, Charleston, South Carolina. The developed modeling framework, on average, will help increase network throughput traffic capacity by 45% with a cost increase of only $15million for the Mw 5.5 event and increase the capacity fourfold with a cost of only $32m for the Mw 7.0 event.

  2. Modeling the Propagation of Mobile Phone Virus under Complex Network

    Directory of Open Access Journals (Sweden)

    Wei Yang

    2014-01-01

    Full Text Available Mobile phone virus is a rogue program written to propagate from one phone to another, which can take control of a mobile device by exploiting its vulnerabilities. In this paper the propagation model of mobile phone virus is tackled to understand how particular factors can affect its propagation and design effective containment strategies to suppress mobile phone virus. Two different propagation models of mobile phone viruses under the complex network are proposed in this paper. One is intended to describe the propagation of user-tricking virus, and the other is to describe the propagation of the vulnerability-exploiting virus. Based on the traditional epidemic models, the characteristics of mobile phone viruses and the network topology structure are incorporated into our models. A detailed analysis is conducted to analyze the propagation models. Through analysis, the stable infection-free equilibrium point and the stability condition are derived. Finally, considering the network topology, the numerical and simulation experiments are carried out. Results indicate that both models are correct and suitable for describing the spread of two different mobile phone viruses, respectively.

  3. Modeling the propagation of mobile phone virus under complex network.

    Science.gov (United States)

    Yang, Wei; Wei, Xi-liang; Guo, Hao; An, Gang; Guo, Lei; Yao, Yu

    2014-01-01

    Mobile phone virus is a rogue program written to propagate from one phone to another, which can take control of a mobile device by exploiting its vulnerabilities. In this paper the propagation model of mobile phone virus is tackled to understand how particular factors can affect its propagation and design effective containment strategies to suppress mobile phone virus. Two different propagation models of mobile phone viruses under the complex network are proposed in this paper. One is intended to describe the propagation of user-tricking virus, and the other is to describe the propagation of the vulnerability-exploiting virus. Based on the traditional epidemic models, the characteristics of mobile phone viruses and the network topology structure are incorporated into our models. A detailed analysis is conducted to analyze the propagation models. Through analysis, the stable infection-free equilibrium point and the stability condition are derived. Finally, considering the network topology, the numerical and simulation experiments are carried out. Results indicate that both models are correct and suitable for describing the spread of two different mobile phone viruses, respectively.

  4. Spread of Epidemic on Complex Networks Under Voluntary Vaccination Mechanism

    Science.gov (United States)

    Xue, Shengjun; Ruan, Feng; Yin, Chuanyang; Zhang, Haifeng; Wang, Binghong

    Under the assumption that the decision of vaccination is a voluntary behavior, in this paper, we use two forms of risk functions to characterize how susceptible individuals estimate the perceived risk of infection. One is uniform case, where each susceptible individual estimates the perceived risk of infection only based on the density of infection at each time step, so the risk function is only a function of the density of infection; another is preferential case, where each susceptible individual estimates the perceived risk of infection not only based on the density of infection but only related to its own activities/immediate neighbors (in network terminology, the activity or the number of immediate neighbors is the degree of node), so the risk function is a function of the density of infection and the degree of individuals. By investigating two different ways of estimating the risk of infection for susceptible individuals on complex network, we find that, for the preferential case, the spread of epidemic can be effectively controlled; yet, for the uniform case, voluntary vaccination mechanism is almost invalid in controlling the spread of epidemic on networks. Furthermore, given the temporality of some vaccines, the waves of epidemic for two cases are also different. Therefore, our work insight that the way of estimating the perceived risk of infection determines the decision on vaccination options, and then determines the success or failure of control strategy.

  5. Modeling the Propagation of Mobile Phone Virus under Complex Network

    Science.gov (United States)

    Yang, Wei; Wei, Xi-liang; Guo, Hao; An, Gang; Guo, Lei

    2014-01-01

    Mobile phone virus is a rogue program written to propagate from one phone to another, which can take control of a mobile device by exploiting its vulnerabilities. In this paper the propagation model of mobile phone virus is tackled to understand how particular factors can affect its propagation and design effective containment strategies to suppress mobile phone virus. Two different propagation models of mobile phone viruses under the complex network are proposed in this paper. One is intended to describe the propagation of user-tricking virus, and the other is to describe the propagation of the vulnerability-exploiting virus. Based on the traditional epidemic models, the characteristics of mobile phone viruses and the network topology structure are incorporated into our models. A detailed analysis is conducted to analyze the propagation models. Through analysis, the stable infection-free equilibrium point and the stability condition are derived. Finally, considering the network topology, the numerical and simulation experiments are carried out. Results indicate that both models are correct and suitable for describing the spread of two different mobile phone viruses, respectively. PMID:25133209

  6. Impact of seasonal thermal stress on physiological and blood biochemical parameters in pigs under different dietary energy levels.

    Science.gov (United States)

    Pathak, P K; Roychoudhury, R; Saharia, J; Borah, M C; Dutta, D J; Bhuyan, R; Kalita, D

    2018-02-13

    The present study was formulated to find out the status of important season related thermal stress biomarkers of pure-bred (Hampshire) and crossbred (50% Hampshire × 50% local) pigs under the agro-climatic condition of Assam State, India. The experiment was also aimed to study the role of different level of energy ration (110, 100, and 90% energy of NRC feeding standard for pig) in variation of physiological and biochemical parameters in two genetic groups of pigs in different seasons. The metabolizable energy value were 3260, 2936.5, and 3585.8 kcal/kg in grower ration and 3260.2, 2936.6, and 3587 kcal/kg in finisher ration for normal energy (NE), low energy (LE) and high energy (HE), respectively. Both the genetic group of animals were housed separately under intensive system of management. Each pen was measuring 10' × 12' along with an outer enclosure. Six weaned piglets (almost similar body weight of average 10.55 kg) of each group were kept in a separate pen. However, after attainment of 35 kg body weight, the animals of a group were divided in two pens of three animals each. The present experiment indicated that average ambient temperature during summer months (27.33-29.51 °C) was above the comfort zone for pigs (22 °C). The significantly (P energy (HE) ration during summer season. Serum triiodothyronine (T 3 ) and thyroxine (T 4 ) concentrations were significantly (P energy level of the ration might be helpful to minimize the effects of thermal stress during summer.

  7. Adaptive neural network motion control for aircraft under uncertainty conditions

    Science.gov (United States)

    Efremov, A. V.; Tiaglik, M. S.; Tiumentsev, Yu V.

    2018-02-01

    We need to provide motion control of modern and advanced aircraft under diverse uncertainty conditions. This problem can be solved by using adaptive control laws. We carry out an analysis of the capabilities of these laws for such adaptive systems as MRAC (Model Reference Adaptive Control) and MPC (Model Predictive Control). In the case of a nonlinear control object, the most efficient solution to the adaptive control problem is the use of neural network technologies. These technologies are suitable for the development of both a control object model and a control law for the object. The approximate nature of the ANN model was taken into account by introducing additional compensating feedback into the control system. The capabilities of adaptive control laws under uncertainty in the source data are considered. We also conduct simulations to assess the contribution of adaptivity to the behavior of the system.

  8. Performance of a Rain Barrel Sharing Network under Climate Change

    Directory of Open Access Journals (Sweden)

    Seong Jin Noh

    2015-07-01

    Full Text Available Rain barrels can be technically shared through social practices or mutual agreement between individual households. This study proposes the evaluation system for a rain barrel sharing network (RBSN considering three performance criteria of reliability, resiliency, and vulnerability, under plausible climate change scenarios. First, this study shows how the system can be improved in terms of the performance criteria using historical daily rainfall data based on the storage-reliability-yield relationship. This study then examined how the benefits from RBSN are affected by climate change after 100 years. Three climate change scenarios (A1B, A2 and B2 and three global circulation models were used for this purpose. The results showed that the reliability and vulnerability are improved due to sharing and their improvements become larger under climate change conditions. In contrast, the resiliency reduces slightly due to sharing and its reduction is attenuated under climate change conditions. In particular, vulnerability will be reduced significantly under climate change. These results suggest that the sharing of various water resources systems can be an effective climate change adaptation strategy that reduces vulnerability and increases the reliability of the system.

  9. Jasmonic Acid Modulates the Physio-Biochemical Attributes, Antioxidant Enzyme Activity, and Gene Expression in Glycine max under Nickel Toxicity.

    Science.gov (United States)

    Sirhindi, Geetika; Mir, Mudaser Ahmad; Abd-Allah, Elsayed Fathi; Ahmad, Parvaiz; Gucel, Salih

    2016-01-01

    In present study, we evaluated the effects of Jasmonic acid (JA) on physio-biochemical attributes, antioxidant enzyme activity, and gene expression in soybean (Glycine max L.) plants subjected to nickel (Ni) stress. Ni stress decreases the shoot and root length and chlorophyll content by 37.23, 38.31, and 39.21%, respectively, over the control. However, application of JA was found to improve the chlorophyll content and length of shoot and root of Ni-fed seedlings. Plants supplemented with JA restores the chlorophyll fluorescence, which was disturbed by Ni stress. The present study demonstrated increase in proline, glycinebetaine, total protein, and total soluble sugar (TSS) by 33.09, 51.26, 22.58, and 49.15%, respectively, under Ni toxicity over the control. Addition of JA to Ni stressed plants further enhanced the above parameters. Ni stress increases hydrogen peroxide (H2O2) by 68.49%, lipid peroxidation (MDA) by 50.57% and NADPH oxidase by 50.92% over the control. Supplementation of JA minimizes the accumulation of H2O2, MDA, and NADPH oxidase, which helps in stabilization of biomolecules. The activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) increases by 40.04, 28.22, 48.53, and 56.79%, respectively, over the control in Ni treated seedlings and further enhancement in the antioxidant activity was observed by the application of JA. Ni treated soybean seedlings showed increase in expression of Fe-SOD by 77.62, CAT by 15.25, POD by 58.33, and APX by 80.58% over the control. Nevertheless, application of JA further enhanced the expression of the above genes in the present study. Our results signified that Ni stress caused negative impacts on soybean seedlings, but, co-application of JA facilitate the seedlings to combat the detrimental effects of Ni through enhanced osmolytes, activity of antioxidant enzymes and gene expression.

  10. Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions.

    Science.gov (United States)

    Bellesia, Giovanni; Bales, Benjamin B

    2016-10-01

    We investigate, via Brownian dynamics simulations, the reaction dynamics of a generic, nonlinear chemical network under spatial confinement and crowding conditions. In detail, the Willamowski-Rossler chemical reaction system has been "extended" and considered as a prototype reaction-diffusion system. Our results are potentially relevant to a number of open problems in biophysics and biochemistry, such as the synthesis of primitive cellular units (protocells) and the definition of their role in the chemical origin of life and the characterization of vesicle-mediated drug delivery processes. More generally, the computational approach presented in this work makes the case for the use of spatial stochastic simulation methods for the study of biochemical networks in vivo where the "well-mixed" approximation is invalid and both thermal and intrinsic fluctuations linked to the possible presence of molecular species in low number copies cannot be averaged out.

  11. Joint Secrecy for D2D Communications Underlying Cellular Networks

    KAUST Repository

    Hyadi, Amal

    2018-01-15

    In this work, we investigate the ergodic secrecy rate region of a block-fading spectrum-sharing system, where a D2D communication is underlying a cellular channel. We consider that both the primary and the secondary transmissions require their respective transmitted messages to be kept secret from a common eavesdropper under a joint secrecy constraint. The presented results are for three different scenarios, each corresponding to a particular requirement of the cellular system. First, we consider the case of a fair cellular system, and we show that the impact of jointly securing the transmissions can be balanced between the primary and the secondary systems. The second scenario examines the case when the primary network is demanding and requires the secondary transmission to be at a rate that is decodable by the primary receiver, while the last scenario assumes a joint transmission of artificial noise by the primary and the secondary transmitters. For each scenario, we present an achievable ergodic secrecy rate region that can be used as an indicator for the cellular and the D2D systems to agree under which terms the spectrum will be shared.

  12. Work of scientific and technological information under network environment

    International Nuclear Information System (INIS)

    Chen Yingxi; Huang Daifu; Yang Lifeng

    2010-01-01

    With the development of internet and information technology, the work of scientific and technological information is faced with great challenge. This article expounds the new changes of scientific and technological information in enterprise under network environment by giving a minute description on the situation the work faced and characteristic of the work. Not only does it carry out enthusiastic discussion upon problems which are present in the work of scientific and technological information in the company, but puts forward proposals and specific measures as well. Service theory is also offered by adjusting and reforming the resources construction, service ways and the job of providing contents. We should take vigorous action to the research work of scientific and technological information, changing the information directional service into knowledge providing service. (authors)

  13. The effect of triazole induced photosynthetic pigments and biochemical constituents of Zea mays L. (Maize) under drought stress

    Science.gov (United States)

    Rajasekar, Mahalingam; Rabert, Gabriel Amalan; Manivannan, Paramasivam

    2016-06-01

    In this investigation, pot culture experiment was carried out to estimate the ameliorating effect of triazole compounds, namely Triadimefon (TDM), Tebuconazole (TBZ), and Propiconazole (PCZ) on drought stress, photosynthetic pigments, and biochemical constituents of Zea mays L. (Maize). From 30 days after sowing (DAS), the plants were subjected to 4 days interval drought (DID) stress and drought with TDM at 15 mg l-1, TBZ at 10 mg l-1, and PCZ at 15 mg l-1. Irrigation at 1-day interval was kept as control. Irrigation performed on alternative day. The plant samples were collected on 40, 50, and 60 DAS and separated into root, stem, and leaf for estimating the photosynthetic pigments and biochemical constituents. Drought and drought with triazole compounds treatment increased the biochemical glycine betaine content, whereas the protein and the pigments contents chlorophyll-a, chlorophyll-b, total chlorophyll, carotenoid, and anthocyanin decreased when compared to control. The triazole treatment mitigated the adverse effects of drought stress by increasing the biochemical potentials and paved the way to overcome drought stress in corn plant.

  14. Jasmonic acid Modulates the Physio-Biochemical Attributes, Antioxidant Enzyme Activity and Gene Expression in Glycine max under Nickel Toxicity

    Directory of Open Access Journals (Sweden)

    Geetika eSirhindi

    2016-05-01

    Full Text Available In present study, we evaluated the effects of Jasmonic acid (JA on physio-biochemical attributes, antioxidant enzyme activity and gene expression in soybean (Glycine max L. plants subjected to nickel (Ni stress. Ni stress decreases the shoot and root length and chlorophyll content by 37.23%, 38.31% and 39.21% respectively over the control. However, application of JA was found to improve the chlorophyll content and growth of Ni-stressed seedlings in terms of root and shoot length. Plants supplemented with Jasmonate restores the chlorophyll fluorescence, which was disturbed by Ni stress. The present study demonstrated increase in proline, glycinebetaine, total protein and total soluble sugar (TSS by 33.09%, 51.26%, 22.58% and 49.15% respectively under Ni toxicity as compared to control. Supplementation of JA to Ni stressed plants further enhanced the above parameters. Ni stress increases hydrogen peroxide (H2O2 by 68.49%, lipid peroxidation (MDA by 50.57% and NADPH oxidase by 50.92% over the control. Supplementation of JA minimizes the accumulation of H2O2, MDA and NADPH oxidase, which helps in stabilization of biomolecules. The activities of superoxide dismutase (SOD, peroxidase (POD, catalase (CAT and ascorbate peroxidase (APX increases by 40.04%, 28.22%, 48.53% and 56.79% respectively over the control in Ni treated seedlings and further enhancement in the antioxidant activity was observed by the application of JA. Ni treated soybean seedlings showed increase in expression of Fe-SOD by 77.62%, CAT by 15.25%, POD by 58.33% and APX by 80.58% over the control. Nevertheless, application of JA further enhanced the expression of the above genes in the present study. Our results signified that Ni stress caused negative impacts on soybean seedlings, but, co-application of JA facilitate the seedlings to combat the detrimental effects of Ni through enhanced osmolytes and osmoprotectants, antioxidant enzyme activity and gene expression.

  15. Gaussian process regression for sensor networks under localization uncertainty

    Science.gov (United States)

    Jadaliha, M.; Xu, Yunfei; Choi, Jongeun; Johnson, N.S.; Li, Weiming

    2013-01-01

    In this paper, we formulate Gaussian process regression with observations under the localization uncertainty due to the resource-constrained sensor networks. In our formulation, effects of observations, measurement noise, localization uncertainty, and prior distributions are all correctly incorporated in the posterior predictive statistics. The analytically intractable posterior predictive statistics are proposed to be approximated by two techniques, viz., Monte Carlo sampling and Laplace's method. Such approximation techniques have been carefully tailored to our problems and their approximation error and complexity are analyzed. Simulation study demonstrates that the proposed approaches perform much better than approaches without considering the localization uncertainty properly. Finally, we have applied the proposed approaches on the experimentally collected real data from a dye concentration field over a section of a river and a temperature field of an outdoor swimming pool to provide proof of concept tests and evaluate the proposed schemes in real situations. In both simulation and experimental results, the proposed methods outperform the quick-and-dirty solutions often used in practice.

  16. Transcriptional regulatory networks underlying gene expression changes in Huntington's disease.

    Science.gov (United States)

    Ament, Seth A; Pearl, Jocelynn R; Cantle, Jeffrey P; Bragg, Robert M; Skene, Peter J; Coffey, Sydney R; Bergey, Dani E; Wheeler, Vanessa C; MacDonald, Marcy E; Baliga, Nitin S; Rosinski, Jim; Hood, Leroy E; Carroll, Jeffrey B; Price, Nathan D

    2018-03-26

    Transcriptional changes occur presymptomatically and throughout Huntington's disease (HD), motivating the study of transcriptional regulatory networks (TRNs) in HD We reconstructed a genome-scale model for the target genes of 718 transcription factors (TFs) in the mouse striatum by integrating a model of genomic binding sites with transcriptome profiling of striatal tissue from HD mouse models. We identified 48 differentially expressed TF-target gene modules associated with age- and CAG repeat length-dependent gene expression changes in Htt CAG knock-in mouse striatum and replicated many of these associations in independent transcriptomic and proteomic datasets. Thirteen of 48 of these predicted TF-target gene modules were also differentially expressed in striatal tissue from human disease. We experimentally validated a specific model prediction that SMAD3 regulates HD-related gene expression changes using chromatin immunoprecipitation and deep sequencing (ChIP-seq) of mouse striatum. We found CAG repeat length-dependent changes in the genomic occupancy of SMAD3 and confirmed our model's prediction that many SMAD3 target genes are downregulated early in HD. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

  17. A bilateral frontoparietal network underlies visuospatial analogical reasoning.

    Science.gov (United States)

    Watson, Christine E; Chatterjee, Anjan

    2012-02-01

    Our ability to reason by analogy facilitates problem solving and allows us to communicate ideas efficiently. In this study, we examined the neural correlates of analogical reasoning and, more specifically, the contribution of rostrolateral prefrontal cortex (RLPFC) to reasoning. This area of the brain has been hypothesized to integrate relational information, as in analogy, or the outcomes of subgoals, as in multi-tasking and complex problem solving. Using fMRI, we compared visuospatial analogical reasoning to a control task that was as complex and difficult as the analogies and required the coordination of subgoals but not the integration of relations. We found that analogical reasoning more strongly activated bilateral RLPFC, suggesting that anterior prefrontal cortex is preferentially recruited by the integration of relational knowledge. Consistent with the need for inhibition during analogy, bilateral, and particularly right, inferior frontal gyri were also more active during analogy. Finally, greater activity in bilateral inferior parietal cortex during the analogy task is consistent with recent evidence for the neural basis of spatial relation knowledge. Together, these findings indicate that a network of frontoparietal areas underlies analogical reasoning; we also suggest that hemispheric differences may emerge depending on the visuospatial or verbal/semantic nature of the analogies. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. Modeling the Differences in Biochemical Capabilities of Pseudomonas Species by Flux Balance Analysis: How Good Are Genome-Scale Metabolic Networks at Predicting the Differences?

    Directory of Open Access Journals (Sweden)

    Parizad Babaei

    2014-01-01

    Full Text Available To date, several genome-scale metabolic networks have been reconstructed. These models cover a wide range of organisms, from bacteria to human. Such models have provided us with a framework for systematic analysis of metabolism. However, little effort has been put towards comparing biochemical capabilities of closely related species using their metabolic models. The accuracy of a model is highly dependent on the reconstruction process, as some errors may be included in the model during reconstruction. In this study, we investigated the ability of three Pseudomonas metabolic models to predict the biochemical differences, namely, iMO1086, iJP962, and iSB1139, which are related to P. aeruginosa PAO1, P. putida KT2440, and P. fluorescens SBW25, respectively. We did a comprehensive literature search for previous works containing biochemically distinguishable traits over these species. Amongst more than 1700 articles, we chose a subset of them which included experimental results suitable for in silico simulation. By simulating the conditions provided in the actual biological experiment, we performed case-dependent tests to compare the in silico results to the biological ones. We found out that iMO1086 and iJP962 were able to predict the experimental data and were much more accurate than iSB1139.

  19. Modeling the differences in biochemical capabilities of pseudomonas species by flux balance analysis: how good are genome-scale metabolic networks at predicting the differences?

    Science.gov (United States)

    Babaei, Parizad; Ghasemi-Kahrizsangi, Tahereh; Marashi, Sayed-Amir

    2014-01-01

    To date, several genome-scale metabolic networks have been reconstructed. These models cover a wide range of organisms, from bacteria to human. Such models have provided us with a framework for systematic analysis of metabolism. However, little effort has been put towards comparing biochemical capabilities of closely related species using their metabolic models. The accuracy of a model is highly dependent on the reconstruction process, as some errors may be included in the model during reconstruction. In this study, we investigated the ability of three Pseudomonas metabolic models to predict the biochemical differences, namely, iMO1086, iJP962, and iSB1139, which are related to P. aeruginosa PAO1, P. putida KT2440, and P. fluorescens SBW25, respectively. We did a comprehensive literature search for previous works containing biochemically distinguishable traits over these species. Amongst more than 1700 articles, we chose a subset of them which included experimental results suitable for in silico simulation. By simulating the conditions provided in the actual biological experiment, we performed case-dependent tests to compare the in silico results to the biological ones. We found out that iMO1086 and iJP962 were able to predict the experimental data and were much more accurate than iSB1139.

  20. Analyzing Bullwhip Effect in Supply Networks under Exogenous Uncertainty

    Directory of Open Access Journals (Sweden)

    Mitra Darvish

    2014-05-01

    Full Text Available This paper explains a model for analyzing and measuring the propagation of order amplifications (i.e. bullwhip effect for a single-product supply network topology considering exogenous uncertainty and linear and time-invariant inventory management policies for network entities. The stream of orders placed by each entity of the network is characterized assuming customer demand is ergodic. In fact, we propose an exact formula in order to measure the bullwhip effect in the addressed supply network topology considering the system in Markovian chain framework and presenting a matrix of network member relationships and relevant order sequences. The formula turns out using a mathematical method called frequency domain analysis. The major contribution of this paper is analyzing the bullwhip effect considering exogenous uncertainty in supply networks and using the Fourier transform in order to simplify the relevant calculations. We present a number of numerical examples to assess the analytical results accuracy in quantifying the bullwhip effect.

  1. Effects of dietary chromium picolinate and peppermint essential oil on growth performance and blood biochemical parameters of broiler chicks reared under heat stress conditions

    Science.gov (United States)

    Akbari, Mohsen; Torki, Mehran

    2014-08-01

    A study was conducted using 240 female day-old broiler chicks to evaluate the effects of dietary chromium picolinate (CrPic), peppermint essential oil (P.mint), or their combination on growth performance and blood biochemical parameters of female broiler chicks raised under heat stress conditions (HS, 23.9 to 38 °C cycling). Average daily gain (ADG), average daily feed intake (ADFI), and feed conversion ratio (FCR) were obtained from 1 to 42 days of age. Furthermore, at the end of the experiment (day 42), birds were bled to determine some blood biochemical parameters and weighed for final body weight (BW). ADFI, ADG, and BW were not influenced significantly by dietary CrPic and P.mint ( P > 0.05). A significant interaction between dietary CrPic and P.mint on FCR ( P = 0.012) was detected. FCR significantly decreased in chicks fed the diet including both CrPic and P.mint compared with the CrPic group. Significant interaction between dietary P.mint and CrPic on serum concentrations of triglycerides, glucose, and albumin were observed ( P dietary treatments ( P > 0.05). The serum concentrations of glucose, triglycerides were decreased ( P dietary supplementation with combined P.mint and CrPic could have beneficial effects on some blood biochemical parameters of female chicks reared under heat stress conditions.

  2. Physio-biochemical and molecular mechanism underlying the enhanced heavy metal tolerance in highland barley seedlings pre-treated with low-dose gamma irradiation.

    Science.gov (United States)

    Wang, Xiaojie; Ma, Ruonan; Cui, Dongjie; Cao, Qing; Shan, Zhe; Jiao, Zhen

    2017-10-27

    Heavy metal pollution, as a consequence of rapid industrialization and urbanization, poses a threat to highland barley grown in Tibet. This study investigates the effect of different doses of gamma irradiation (50-300 Gy) on the physio-biochemical and molecular mechanism of highland barley under heavy metal stress. Growth data showed that 50-Gy gamma irradiation had the maximal beneficial effects on the highland barley seedlings under lead/cadmium stress. The results of oxidative parameters demonstrated that 50-Gy gamma-irradiated seedlings had lower hydrogen peroxide and malondialdehyde contents under lead/cadmium stress compared to non-irradiated seedlings. Moreover, the activities of antioxidant enzyme and proline levels in 50-Gy gamma-irradiated seedlings were drastically higher than those in non-irradiated seedlings under lead/cadmium stress. Additionally, transmission electron microscopy results revealed that the 50-Gy gamma-irradiated seedlings exhibited improved chloroplasts ultrastructure compared with non-irradiated seedlings exposed to lead/cadmium stress. Notably, transcriptional expression analysis showed that 50-Gy gamma irradiation could significantly affect the expression of genes related to heavy metal transport and abscisic acid metabolism under lead/cadmium stress. Collectively, these results provide insights into the physio-biochemical and molecular mechanisms of low-dose-gamma-irradiation-enhanced heavy metal tolerance in highland barley seedlings, thus proposing gamma irradiation as a potential technology to mitigate heavy metal toxicity in crops.

  3. Robustness of networks against propagating attacks under vaccination strategies

    International Nuclear Information System (INIS)

    Hasegawa, Takehisa; Masuda, Naoki

    2011-01-01

    We study the effect of vaccination on the robustness of networks against propagating attacks that obey the susceptible–infected–removed model. By extending the generating function formalism developed by Newman (2005 Phys. Rev. Lett. 95 108701), we analytically determine the robustness of networks that depends on the vaccination parameters. We consider the random defense where nodes are vaccinated randomly and the degree-based defense where hubs are preferentially vaccinated. We show that, when vaccines are inefficient, the random graph is more robust against propagating attacks than the scale-free network. When vaccines are relatively efficient, the scale-free network with the degree-based defense is more robust than the random graph with the random defense and the scale-free network with the random defense

  4. Social contact networks and disease eradicability under voluntary vaccination.

    Directory of Open Access Journals (Sweden)

    Ana Perisic

    2009-02-01

    Full Text Available Certain theories suggest that it should be difficult or impossible to eradicate a vaccine-preventable disease under voluntary vaccination: Herd immunity implies that the individual incentive to vaccinate disappears at high coverage levels. Historically, there have been examples of declining coverage for vaccines, such as MMR vaccine and whole-cell pertussis vaccine, that are consistent with this theory. On the other hand, smallpox was globally eradicated by 1980 despite voluntary vaccination policies in many jurisdictions. Previous modeling studies of the interplay between disease dynamics and individual vaccinating behavior have assumed that infection is transmitted in a homogeneously mixing population. By comparison, here we simulate transmission of a vaccine-preventable SEIR infection through a random, static contact network. Individuals choose whether to vaccinate based on infection risks from neighbors, and based on vaccine risks. When neighborhood size is small, rational vaccinating behavior results in rapid containment of the infection through voluntary ring vaccination. As neighborhood size increases (while the average force of infection is held constant, a threshold is reached beyond which the infection can break through partially vaccinated rings, percolating through the whole population and resulting in considerable epidemic final sizes and a large number vaccinated. The former outcome represents convergence between individually and socially optimal outcomes, whereas the latter represents their divergence, as observed in most models of individual vaccinating behavior that assume homogeneous mixing. Similar effects are observed in an extended model using smallpox-specific natural history and transmissibility assumptions. This work illustrates the significant qualitative differences between behavior-infection dynamics in discrete contact-structured populations versus continuous unstructured populations. This work also shows how disease

  5. Analysis of Network Vulnerability Under Joint Node and Link Attacks

    Science.gov (United States)

    Li, Yongcheng; Liu, Shumei; Yu, Yao; Cao, Ting

    2018-03-01

    The security problem of computer network system is becoming more and more serious. The fundamental reason is that there are security vulnerabilities in the network system. Therefore, it’s very important to identify and reduce or eliminate these vulnerabilities before they are attacked. In this paper, we are interested in joint node and link attacks and propose a vulnerability evaluation method based on the overall connectivity of the network to defense this attack. Especially, we analyze the attack cost problem from the attackers’ perspective. The purpose is to find the set of least costs for joint links and nodes, and their deletion will lead to serious network connection damage. The simulation results show that the vulnerable elements obtained from the proposed method are more suitable for the attacking idea of the malicious persons in joint node and link attack. It is easy to find that the proposed method has more realistic protection significance.

  6. Brain networks underlying mental imagery of auditory and visual information.

    Science.gov (United States)

    Zvyagintsev, Mikhail; Clemens, Benjamin; Chechko, Natalya; Mathiak, Krystyna A; Sack, Alexander T; Mathiak, Klaus

    2013-05-01

    Mental imagery is a complex cognitive process that resembles the experience of perceiving an object when this object is not physically present to the senses. It has been shown that, depending on the sensory nature of the object, mental imagery also involves correspondent sensory neural mechanisms. However, it remains unclear which areas of the brain subserve supramodal imagery processes that are independent of the object modality, and which brain areas are involved in modality-specific imagery processes. Here, we conducted a functional magnetic resonance imaging study to reveal supramodal and modality-specific networks of mental imagery for auditory and visual information. A common supramodal brain network independent of imagery modality, two separate modality-specific networks for imagery of auditory and visual information, and a common deactivation network were identified. The supramodal network included brain areas related to attention, memory retrieval, motor preparation and semantic processing, as well as areas considered to be part of the default-mode network and multisensory integration areas. The modality-specific networks comprised brain areas involved in processing of respective modality-specific sensory information. Interestingly, we found that imagery of auditory information led to a relative deactivation within the modality-specific areas for visual imagery, and vice versa. In addition, mental imagery of both auditory and visual information widely suppressed the activity of primary sensory and motor areas, for example deactivation network. These findings have important implications for understanding the mechanisms that are involved in generation of mental imagery. © 2013 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

  7. BIOCHEMICAL STATUS OF BLOOD SERUM OF RAINBOW TROUT Oncorhynchus mykiss (Walbaum, 1792 UNDER DIFFERENT KEEPING AND FEEDING CONDITIONS

    Directory of Open Access Journals (Sweden)

    Edhem Hasković

    2013-01-01

    Full Text Available We analyzed the blood serum of the rainbow trout in relation to various physico-chemical properties of water and diet composition. Fish were reared in two ponds that were supplied by water from different sources. The identified differences in the biochemical parameters are caused by different environmental factors in ponds and different feed composition. Low oxygen values caused by different temperatures is a key stress factor of the noted differences. Statistically significant differences are noted for AST (aspartate aminotransferase, ALT (alanine aminotransferase, triglycerides, urea and iron (0.00. Evident were also different mineral concentrations of Ca and P (0.05 as well as glucose and cholesterol (0.05.

  8. Molecular and elemental effects underlying the biochemical action of transcranial direct current stimulation (tDCS) in appetite control

    Science.gov (United States)

    Surowka, Artur D.; Ziomber, Agata; Czyzycki, Mateusz; Migliori, Alessandro; Kasper, Kaja; Szczerbowska-Boruchowska, Magdalena

    2018-04-01

    Recent studies highlight that obesity may alter the electric activity in brain areas triggering appetite and craving. Transcranial direct current brain stimulation (tDCS) has recently emerged as a safe alternative for treating food addiction via modulating cortical excitability without any high-risk surgical procedure to be utilized. As for anodal-type tDCS (atDCS), we observe increased excitability and spontaneous firing of the cortical neurons, whilst for the cathodal-type tDCS (ctDCS) a significant decrease is induced. Unfortunately, for the method to be fully used in a clinical setting, its biochemical action mechanism must be precisely defined, although it is proposed that molecular remodelling processes play in concert with brain activity changes involving the ions of: Na, Cl, K and Ca. Herein, we proposed for the first time Fourier transform infrared (FTIR) and synchrotron X-ray fluorescence (SRXRF) microprobes for a combined molecular and elemental analysis in the brain areas implicated appetite control, upon experimental treatment by either atDCS or ctDCS. The study, although preliminary, shows that by stimulating the prefrontal cortex in the rats fed high-caloric nutrients, the feeding behavior can be significantly changed, resulting in significantly inhibited appetite. Both, atDCS and ctDCS produced significant molecular changes involving qualitative and structural properties of lipids, whereas atDCS was found with a somewhat more significant effect on protein secondary structure in all the brain areas investigated. Also, tDCS was reported to reduce surface masses of Na, Cl, K, and Ca in almost all brain areas investigated, although the atDCS deemed to have a stronger neuro-modulating effect. Taken together, one can report that tDCS is an effective treatment technique, and its action mechanism in the appetite control seems to involve a variety of lipid-, protein- and metal/non-metal-ion-driven biochemical changes, regardless the current polarization.

  9. Effect of maltose and trehalose on growth, yield and some biochemical components of wheat plant under water stress

    Directory of Open Access Journals (Sweden)

    Hemmat A. Ibrahim

    2016-12-01

    Full Text Available In the greenhouse experiment, wheat plants (Triticum aestivum L. cv. Giza 168 were treated with 10 mM of maltose and trehalose as foliar spray using Tween 20 as wetting agent at 15, 30 and 45 days post sowing with two times of irrigation at 10 and 20 days intervals. Two samples were taken after 45 and 120 days from planting. At the first sample date, plant height, shoot fresh and dry weights and leaf area were recorded. At harvesting time (the second sample no. of spikes/plant, no. of spikelets/plant and weight of 1000 grains were taken. Chemical analyses were conducted in leaves at the first sample date for determination of phenolic compounds, flavonoids, amino acids, reducing sugars, total soluble sugars, protein, proline, PAL, POD, ascorbate peroxidase, catalase, PPO and MDA. The obtained results indicated that maltose and trehalose had significant and positive effect on most growth parameters. Opposite trend was found in plant height, no. of spike/plant and weight of 1000 grains by drought treatment. Maltose and trehalose treatments enhanced in the most biochemical components whereas they decreased PAL and catalase activity. Variable trends in amino acids and ascorbate peroxidase were observed by drought. However, the drought has more stimulative effect in most cases than the first time period of irrigation. The results concluded that foliar applications with maltose or trehalose induced water stress tolerance in wheat plants. Maltose treatment gave the best results in most morphological parameters, grains yield and biochemical components than trehalose treatment.

  10. Dynamical Response of Networks Under External Perturbations: Exact Results

    Science.gov (United States)

    Chinellato, David D.; Epstein, Irving R.; Braha, Dan; Bar-Yam, Yaneer; de Aguiar, Marcus A. M.

    2015-04-01

    We give exact statistical distributions for the dynamic response of influence networks subjected to external perturbations. We consider networks whose nodes have two internal states labeled 0 and 1. We let nodes be frozen in state 0, in state 1, and the remaining nodes change by adopting the state of a connected node with a fixed probability per time step. The frozen nodes can be interpreted as external perturbations to the subnetwork of free nodes. Analytically extending and to be smaller than 1 enables modeling the case of weak coupling. We solve the dynamical equations exactly for fully connected networks, obtaining the equilibrium distribution, transition probabilities between any two states and the characteristic time to equilibration. Our exact results are excellent approximations for other topologies, including random, regular lattice, scale-free and small world networks, when the numbers of fixed nodes are adjusted to take account of the effect of topology on coupling to the environment. This model can describe a variety of complex systems, from magnetic spins to social networks to population genetics, and was recently applied as a framework for early warning signals for real-world self-organized economic market crises.

  11. Robust Evaluation for Transportation Network Capacity under Demand Uncertainty

    Directory of Open Access Journals (Sweden)

    Muqing Du

    2017-01-01

    Full Text Available As more and more cities in worldwide are facing the problems of traffic jam, governments have been concerned about how to design transportation networks with adequate capacity to accommodate travel demands. To evaluate the capacity of a transportation system, the prescribed origin and destination (O-D matrix for existing travel demand has been noticed to have a significant effect on the results of network capacity models. However, the exact data of the existing O-D demand are usually hard to be obtained in practice. Considering the fluctuation of the real travel demand in transportation networks, the existing travel demand is represented as uncertain parameters which are defined within a bounded set. Thus, a robust reserve network capacity (RRNC model using min–max optimization is formulated based on the demand uncertainty. An effective heuristic approach utilizing cutting plane method and sensitivity analysis is proposed for the solution of the RRNC problem. Computational experiments and simulations are implemented to demonstrate the validity and performance of the proposed robust model. According to simulation experiments, it is showed that the link flow pattern from the robust solutions to network capacity problems can reveal the probability of high congestion for each link.

  12. A dynamically coupled allosteric network underlies binding cooperativity in Src kinase

    Science.gov (United States)

    Foda, Zachariah H.; Shan, Yibing; Kim, Eric T.; Shaw, David E.; Seeliger, Markus A.

    2015-01-01

    Protein tyrosine kinases are attractive drug targets because many human diseases are associated with the deregulation of kinase activity. However, how the catalytic kinase domain integrates different signals and switches from an active to an inactive conformation remains incompletely understood. Here we identify an allosteric network of dynamically coupled amino acids in Src kinase that connects regulatory sites to the ATP- and substrate-binding sites. Surprisingly, reactants (ATP and peptide substrates) bind with negative cooperativity to Src kinase while products (ADP and phosphopeptide) bind with positive cooperativity. We confirm the molecular details of the signal relay through the allosteric network by biochemical studies. Experiments on two additional protein tyrosine kinases indicate that the allosteric network may be largely conserved among these enzymes. Our work provides new insights into the regulation of protein tyrosine kinases and establishes a potential conduit by which resistance mutations to ATP-competitive kinase inhibitors can affect their activity.

  13. A dynamically coupled allosteric network underlies binding cooperativity in Src kinase.

    Science.gov (United States)

    Foda, Zachariah H; Shan, Yibing; Kim, Eric T; Shaw, David E; Seeliger, Markus A

    2015-01-20

    Protein tyrosine kinases are attractive drug targets because many human diseases are associated with the deregulation of kinase activity. However, how the catalytic kinase domain integrates different signals and switches from an active to an inactive conformation remains incompletely understood. Here we identify an allosteric network of dynamically coupled amino acids in Src kinase that connects regulatory sites to the ATP- and substrate-binding sites. Surprisingly, reactants (ATP and peptide substrates) bind with negative cooperativity to Src kinase while products (ADP and phosphopeptide) bind with positive cooperativity. We confirm the molecular details of the signal relay through the allosteric network by biochemical studies. Experiments on two additional protein tyrosine kinases indicate that the allosteric network may be largely conserved among these enzymes. Our work provides new insights into the regulation of protein tyrosine kinases and establishes a potential conduit by which resistance mutations to ATP-competitive kinase inhibitors can affect their activity.

  14. Similarity between community structures of different online social networks and its impact on underlying community detection

    Science.gov (United States)

    Fan, W.; Yeung, K. H.

    2015-03-01

    As social networking services are popular, many people may register in more than one online social network. In this paper we study a set of users who have accounts of three online social networks: namely Foursquare, Facebook and Twitter. Community structure of this set of users may be reflected in these three online social networks. Therefore, high correlation between these reflections and the underlying community structure may be observed. In this work, community structures are detected in all three online social networks. Also, we investigate the similarity level of community structures across different networks. It is found that they show strong correlation with each other. The similarity between different networks may be helpful to find a community structure close to the underlying one. To verify this, we propose a method to increase the weights of some connections in networks. With this method, new networks are generated to assist community detection. By doing this, value of modularity can be improved and the new community structure match network's natural structure better. In this paper we also show that the detected community structures of online social networks are correlated with users' locations which are identified on Foursquare. This information may also be useful for underlying community detection.

  15. Factors Underlying Farmers’ Decisions to Participate in Networks

    Directory of Open Access Journals (Sweden)

    Bianka Kühne

    2013-11-01

    Full Text Available 800x600 The objective of this elicitation study is to provide insights into farmers’ beliefs which influence their participation in knowledge exchange and innovation networks to enable the enhancement of network participation. A set of facilitating and impeding factors was obtained. Participants identified (a 13 categories of behavioural beliefs (e.g. ‘You learn something’ and ‘Low perceived return on investment’, (b 4 groups of normative beliefs (influence of colleagues, spouses, network coordinators and chain partners and (c 11 control beliefs (facilitators or barriers related to, for example, ‘Network skills’, ‘No time’ and ‘Perceived restraint by farmers in communicating openly and honestly’. Normal 0 21 false false false DE X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0pt 5.4pt 0pt 5.4pt; mso-para-margin:0pt; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman","serif";}

  16. Genetic Algorithm for Multiuser Discrete Network Design Problem under Demand Uncertainty

    Directory of Open Access Journals (Sweden)

    Wu Juan

    2012-01-01

    Full Text Available Discrete network design is an important part of urban transportation planning. The purpose of this paper is to present a bilevel model for discrete network design. The upper-level model aims to minimize the total travel time under a stochastic demand to design a discrete network. In the lower-level model, demands are assigned to the network through a multiuser traffic equilibrium assignment. Generally, discrete network could affect path selections of demands, while the results of the multiuser traffic equilibrium assignment need to reconstruct a new discrete network. An iterative approach including an improved genetic algorithm and Frank-Wolfe algorithm is used to solve the bi-level model. The numerical results on Nguyen Dupuis network show that the model and the related algorithms were effective for discrete network design.

  17. Bistability in biochemical signaling models.

    Science.gov (United States)

    Sobie, Eric A

    2011-09-20

    This Teaching Resource provides lecture notes, slides, and a student assignment for a two-part lecture on the principles underlying bistability in biochemical signaling networks, which are illustrated with examples from the literature. The lectures cover analog, or graded, versus digital, all-or-none, responses in cells, with examples from different types of biological processes requiring each. Rate-balance plots are introduced as a method for determining whether generic one-variable systems exhibit one or several stable steady states. Bifurcation diagrams are presented as a more general method for detecting the presence of bistability in biochemical signaling networks. The examples include an artificial toggle switch, the lac operon in bacteria, and the mitogen-activated protein kinase cascade in both Xenopus oocytes and mammalian cells. The second part of the lecture links the concepts of bistability more closely to the mathematical tools provided by dynamical systems analysis. The examples from the first part of the lecture are analyzed with phase-plane techniques and bifurcation analysis, using the scientific programming language MATLAB. Using these programs as a template, the assignment requires the students to implement a model from the literature and analyze the stability of this model's steady states.

  18. Defense strategies for asymmetric networked systems under composite utilities

    Energy Technology Data Exchange (ETDEWEB)

    Rao, Nageswara S. [ORNL; Ma, Chris Y. T. [Hang Seng Management College, Hon Kong; Hausken, Kjell [University of Stavanger, Norway; He, Fei [Texas A& M University, Kingsville, TX, USA; Yau, David K. Y. [Singapore University of Technology and Design; Zhuang, Jun [University at Buffalo (SUNY)

    2017-11-01

    We consider an infrastructure of networked systems with discrete components that can be reinforced at certain costs to guard against attacks. The communications network plays a critical, asymmetric role of providing the vital connectivity between the systems. We characterize the correlations within this infrastructure at two levels using (a) aggregate failure correlation function that specifies the infrastructure failure probability giventhe failure of an individual system or network, and (b) first order differential conditions on system survival probabilities that characterize component-level correlations. We formulate an infrastructure survival game between an attacker and a provider, who attacks and reinforces individual components, respectively. They use the composite utility functions composed of a survival probability term and a cost term, and the previously studiedsum-form and product-form utility functions are their special cases. At Nash Equilibrium, we derive expressions for individual system survival probabilities and the expected total number of operational components. We apply and discuss these estimates for a simplified model of distributed cloud computing infrastructure

  19. Assessing mechanical vulnerability in water distribution networks under multiple failures

    Science.gov (United States)

    Berardi, Luigi; Ugarelli, Rita; Røstum, Jon; Giustolisi, Orazio

    2014-03-01

    Understanding mechanical vulnerability of water distribution networks (WDN) is of direct relevance for water utilities since it entails two different purposes. On the one hand, it might support the identification of severe failure scenarios due to external causes (e.g., natural or intentional events) which result into the most critical consequences on WDN supply capacity. On the other hand, it aims at figure out the WDN portions which are more prone to be affected by asset disruptions. The complexity of such analysis stems from the number of possible scenarios with single and multiple simultaneous shutdowns of asset elements leading to modifications of network topology and insufficient water supply to customers. In this work, the search for the most disruptive combinations of multiple asset failure events is formulated and solved as a multiobjective optimization problem. The higher vulnerability failure scenarios are detected as those causing the lower supplied demand due to the lower number of simultaneous failures. The automatic detection of WDN topology, subsequent to the detachments of failed elements, is combined with pressure-driven analysis. The methodology is demonstrated on a real water distribution network. Results show that, besides the failures causing the detachment of reservoirs, tanks, or pumps, there are other different topological modifications which may cause severe WDN service disruptions. Such information is of direct relevance to support planning asset enhancement works and improve the preparedness to extreme events.

  20. Network architecture underlying maximal separation of neuronal representations

    Directory of Open Access Journals (Sweden)

    Ron A Jortner

    2013-01-01

    Full Text Available One of the most basic and general tasks faced by all nervous systems is extracting relevant information from the organism’s surrounding world. While physical signals available to sensory systems are often continuous, variable, overlapping and noisy, high-level neuronal representations used for decision-making tend to be discrete, specific, invariant, and highly separable. This study addresses the question of how neuronal specificity is generated. Inspired by experimental findings on network architecture in the olfactory system of the locust, I construct a highly simplified theoretical framework which allows for analytic solution of its key properties. For generalized feed-forward systems, I show that an intermediate range of connectivity values between source- and target-populations leads to a combinatorial explosion of wiring possibilities, resulting in input spaces which are, by their very nature, exquisitely sparsely populated. In particular, connection probability ½, as found in the locust antennal-lobe–mushroom-body circuit, serves to maximize separation of neuronal representations across the target Kenyon-cells, and explains their specific and reliable responses. This analysis yields a function expressing response specificity in terms of lower network-parameters; together with appropriate gain control this leads to a simple neuronal algorithm for generating arbitrarily sparse and selective codes and linking network architecture and neural coding. I suggest a way to easily construct ecologically meaningful representations from this code.

  1. Invulnerability of grown Peer-to-Peer networks under progressive targeted attacks

    Science.gov (United States)

    Peng, Hao; Zhao, Dandan; Han, Jianmin; Lu, Jianfeng

    2015-06-01

    Security issues of Peer-to-Peer (P2P) networks have attracted more and more research in recent years. In this paper, using complex features of P2P networks, we shift the focus to the study of invulnerability of grown P2P networks under progressive targeted attacks. Based on dynamic process and reverse percolation theory, we present several mechanisms that attacked P2P networks can adopt to minimize the disasters aftermath progressive targeted attacks. In this process, we proposed: (i) the dynamics of grown P2P networks under targeted attacks can make sure an attacked P2P network restore a power-law (PL) characteristic to a normal level; (ii) a global degree restoring process from the aftermath of progressive targeted attacks can restore the status of set of high degree peers to normal; (iii) a reverse percolation process glues the fragmented small connected component of a destroyed grown P2P network into a giant connected component (GCC). Experimental results show that an attacked grown P2P network can restore the key characteristics, such as power-law characteristic of original P2P network, the set of high degree peers and the giant connected component, to a regular status. In this way, we can illustrate the invulnerability of progressive targeted attacks on grown P2P networks which is particularly useful in designing complex P2P networks.

  2. Confocal Raman spectroscopy: In vivo biochemical changes in the human skin by topical formulations under UV radiation.

    Science.gov (United States)

    Tosato, M G; Orallo, D E; Ali, S M; Churio, M S; Martin, A A; Dicelio, L

    2015-12-01

    A new approach to the study of the effects on human skin of mycosporine-like amino acids (MAAs) and gadusol (Gad) incorporated in polymer gel is proposed in this work. The depth profile and photoprotector effects of Pluronic F127® gels containing each of the natural actives were evaluated by in vivo confocal Raman spectroscopy aiming at the analysis of the biochemical changes on human skin. Hierarchical cluster analysis (HCA) showed that the data corresponding to different depths of the skin, from surface to 4 μm, and from 6 to 16 μm, remained in the same cluster. In vivo Raman spectra, classified into five different layers of epidermis according to their similarities, indicated that the amount of Gad gel increased by about 26% in the outermost layer of the stratum corneum (SC) and that MAAs gel at 2 μm depth was 103.4% higher than in the outermost layer of the SC. Variations in the SC of urocanic acid at 1490-1515 cm(-1) and 1652 cm(-1) and histidine at 1318 cm(-1) were calculated, before and after UV exposure with or without gels. With the application of gels the vibrational modes that correspond to lipids in trans conformation (1063 and 1128 cm(-1)) increased with respect to normal skin, whereas gauche conformation (1085 cm(-1)) disappeared. Our studies suggest that gels protected the skin against the stress of the natural defense mechanism caused by high levels of UV exposure. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Electromechanical properties of carbon nanotube networks under compression

    Czech Academy of Sciences Publication Activity Database

    Slobodian, P.; Říha, Pavel; Olejník, R.; Sáha, P.

    2011-01-01

    Roč. 22, č. 12 (2011), s. 124006 ISSN 0957-0233 R&D Projects: GA AV ČR IAA200600803 Grant - others:Interní grantová agentura UTB(CZ) IGA/12/FT/10/D; OP VaVpI(XE) CZ.1.05/2.1.00/03.0111 Institutional research plan: CEZ:AV0Z20600510 Keywords : carbon nanotube network * compression * electrical conductivity * stress sensor Subject RIV: JB - Sensor s, Measurment, Regulation Impact factor: 1.494, year: 2011

  4. Effect of foliar application of α-tocopherol on vegetative growth and some biochemical constituents of two soybean genotypes under salt stress

    Science.gov (United States)

    Rahmawati, N.; Damanik, R. I. M.

    2018-02-01

    Foliar spray of plant growth regulating compounds including antioxidants is an effective strategy to overcome the adverse effects of environmental constraints on different plants. A field experiment was conducted on May - July 2017 at the experimental farm in Paluh Merbau Village Deli Serdang (EC 6 - 7 dS/m). The aim was to study the effects of foliar spray of α-tocopherol (0, 250, 500, 500 ppm) on vegetative growth and some chemical constituents of 2 soybean genotypes (Grobogan x Grobogan and Grobogan x Anjasmoro) under salt stress (EC 6 - 7 dS/m). Most of morphological and biochemical parameters were significantly affected by application of α-tocopherol. The α-tocopherol at 500 ppm recorded the best value of root fresh weight, shoot and root dry weight, number of leaves, chlorophyll b, and soluble protein content. There was significant difference found between plants treated with α-tocopherol in terms of number of branch, shoot fresh weight, and chlorophyll a. Soybean genotypes showed diverse morphology and physiological responses to salt stress. Grobogan x Anjasmoro genotype was salt-sensitive based on all variable, while Grobogan x Grobogan genotype was more tolerant based on morphological and biochemical characters.

  5. Gene network inference and biochemical assessment delineates GPCR pathways and CREB targets in small intestinal neuroendocrine neoplasia.

    Directory of Open Access Journals (Sweden)

    Ignat Drozdov

    Full Text Available Small intestinal (SI neuroendocrine tumors (NET are increasing in incidence, however little is known about their biology. High throughput techniques such as inference of gene regulatory networks from microarray experiments can objectively define signaling machinery in this disease. Genome-wide co-expression analysis was used to infer gene relevance network in SI-NETs. The network was confirmed to be non-random, scale-free, and highly modular. Functional analysis of gene co-expression modules revealed processes including 'Nervous system development', 'Immune response', and 'Cell-cycle'. Importantly, gene network topology and differential expression analysis identified over-expression of the GPCR signaling regulators, the cAMP synthetase, ADCY2, and the protein kinase A, PRKAR1A. Seven CREB response element (CRE transcripts associated with proliferation and secretion: BEX1, BICD1, CHGB, CPE, GABRB3, SCG2 and SCG3 as well as ADCY2 and PRKAR1A were measured in an independent SI dataset (n = 10 NETs; n = 8 normal preparations. All were up-regulated (p<0.035 with the exception of SCG3 which was not differently expressed. Forskolin (a direct cAMP activator, 10(-5 M significantly stimulated transcription of pCREB and 3/7 CREB targets, isoproterenol (a selective ß-adrenergic receptor agonist and cAMP activator, 10(-5 M stimulated pCREB and 4/7 targets while BIM-53061 (a dopamine D(2 and Serotonin [5-HT(2] receptor agonist, 10(-6 M stimulated 100% of targets as well as pCREB; CRE transcription correlated with the levels of cAMP accumulation and PKA activity; BIM-53061 stimulated the highest levels of cAMP and PKA (2.8-fold and 2.5-fold vs. 1.8-2-fold for isoproterenol and forskolin. Gene network inference and graph topology analysis in SI NETs suggests that SI NETs express neural GPCRs that activate different CRE targets associated with proliferation and secretion. In vitro studies, in a model NET cell system, confirmed that transcriptional

  6. Crystal structure and biochemical characterization of the recombinant ThBgl, a GH1 β-glucosidase overexpressed in Trichoderma harzianum under biomass degradation conditions.

    Science.gov (United States)

    Santos, Clelton A; Zanphorlin, Letícia M; Crucello, Aline; Tonoli, Celisa C C; Ruller, Roberto; Horta, Maria A C; Murakami, Mario T; de Souza, Anete Pereira

    2016-01-01

    The conversion of biomass-derived sugars via enzymatic hydrolysis for biofuel production is a challenge. Therefore, the search for microorganisms and key enzymes that increase the efficiency of the saccharification of cellulosic substrates remains an important and high-priority area of study. Trichoderma harzianum is an important fungus known for producing high levels of cellulolytic enzymes that can be used for cellulosic ethanol production. In this context, β-glucosidases, which act synergistically with cellobiohydrolases and endo-β-1,4-glucanases in the saccharification process, are potential biocatalysts for the conversion of plant biomass to free glucose residues. In the present study, we used RNA-Seq and genomic data to identify the major β-glucosidase expressed by T. harzianum under biomass degradation conditions. We mapped and quantified the expression of all of the β-glucosidases from glycoside hydrolase families 1 and 3, and we identified the enzyme with the highest expression under these conditions. The target gene was cloned and heterologously expressed in Escherichia coli, and the recombinant protein (rThBgl) was purified with high yields. rThBgl was characterized using a comprehensive set of biochemical, spectroscopic, and hydrodynamic techniques. Finally, we determined the crystallographic structure of the recombinant protein at a resolution of 2.6 Å. Using a rational approach, we investigated the biochemical characteristics and determined the three-dimensional protein structure of a β-glucosidase that is highly expressed by T. harzianum under biomass degradation conditions. The methodology described in this manuscript will be useful for the bio-prospection of key enzymes, including cellulases and other accessory enzymes, for the development and/or improvement of enzymatic cocktails designed to produce ethanol from plant biomass.

  7. A systematic framework for enterprise-wide optimization: Synthesis and design of processing network under uncertainty

    DEFF Research Database (Denmark)

    Quaglia, Alberto; Sarup, Bent; Sin, Gürkan

    2013-01-01

    In this paper, a systematic framework for synthesis and design of processing networks under uncertaintyis presented. Through the framework, an enterprise-wide optimization problem is formulated and solvedunder uncertain conditions, to identify the network (composed of raw materials, process techn...

  8. Real-time relationship between PKA biochemical signal network dynamics and increased action potential firing rate in heart pacemaker cells

    Science.gov (United States)

    Yaniv, Yael; Ganesan, Ambhighainath; Yang, Dongmei; Ziman, Bruce D.; Lyashkov, Alexey E.; Levchenko, Andre; Zhang, Jin; Lakatta, Edward G.

    2015-01-01

    cAMP-PKA protein kinase is a key nodal signaling pathway that regulates a wide range of heart pacemaker cell functions. These functions are predicted to be involved in regulation of spontaneous action potential (AP) generation of these cells. Here we investigate if the kinetics and stoichiometry of increase in PKA activity match the increase in AP firing rate in response to β-adrenergic receptor (β-AR) stimulation or phosphodiesterase (PDE) inhibition, that alter the AP firing rate of heart sinoatrial pacemaker cells. In cultured adult rabbit pacemaker cells infected with an adenovirous expressing the FRET sensor AKAR3, the EC50 in response to graded increases in the intensity of β-AR stimulation (by Isoproterenol) the magnitude of the increases in PKA activity and the spontaneous AP firing rate were similar (0.4±0.1nM vs. 0.6±0.15nM, respectively). Moreover, the kinetics (t1/2) of the increases in PKA activity and spontaneous AP firing rate in response to β-AR stimulation or PDE inhibition were tightly linked. We characterized the system rate-limiting biochemical reactions by integrating these experimentally derived data into mechanistic-computational model. Model simulations predicted that phospholamban phosphorylation is a potent target of the increase in PKA activity that links to increase in spontaneous AP firing rate. In summary, the kinetics and stoichiometry of increases in PKA activity in response to a physiological (β-AR stimulation) or pharmacological (PDE inhibitor) stimuli match those of changes in the AP firing rate. Thus Ca2+-cAMP/PKA-dependent phosphorylation limits the rate and magnitude of increase in spontaneous AP firing rate. PMID:26241846

  9. Shelf-life of chilled fresh Mediterranean swordfish (Xiphias gladius) stored under various packaging conditions: microbiological, biochemical and sensory attributes.

    Science.gov (United States)

    Pantazi, D; Papavergou, A; Pournis, N; Kontominas, M G; Savvaidis, I N

    2008-02-01

    The present work evaluated the effect of air, vacuum and modified atmosphere packaging (MAP) on the shelf-life of chilled Mediterranean swordfish (Xiphias gladius). Fresh swordfish slices were stored in air, under vacuum and MAP (40%/30%/30%, CO(2)/N(2)/O(2)) under refrigeration (4 degrees C) for a period of 16 days. Of the three treatments used (vacuum, MAP and air), both MAP and vacuum packaging (VP) were the most effective for inhibiting growth of aerobic microflora in swordfish samples until days 9-10 of refrigerated storage. Of the microbial species determined, both Pseudomonas spp. and H(2)S-producing bacteria (including Shewanella putrefaciens) were dominant in swordfish samples stored in air, whereas growth of these species was partly inhibited under VP and MAP conditions. Lactic acid bacteria (LAB) and Enterobacteriaceae were also found to be members of the final swordfish microbial flora, irrespective of packaging conditions throughout the entire storage period. Of the chemical freshness indices determined, thiobarbituric acid (TBA) values were variable in swordfish samples, indicative of no specific oxidative rancidity trend. Trimethylamine nitrogen (TMA-N) values of swordfish samples stored in air, under VP and MAP exceeded the limit value of 5mgN/100g fish muscle after days 7, 8-9 and 11 days of storage, respectively. In a similar trend, total volatile basic nitrogen (TVB-N) for swordfish samples stored in air, under VP and MAP exceeded the limit value of 25mgN/100g fish muscle after 7-8, 10 and 12 days of storage, respectively. Sensory analyses (odor and taste attributes) indicated a shelf-life of ca. 7 days for air, 9 days for VP and 11-12 days for the MA-packaged swordfish samples.

  10. Physiological and biochemical characterization of the assai palm (Euterpe oleracea Mart. during seed germination and seedling growth under aerobic and anaerobic conditions

    Directory of Open Access Journals (Sweden)

    José Francisco de Carvalho Gonçalves

    2010-12-01

    Full Text Available Physiological and biochemical aspects of assai palm during seed germination and early seedling growth were investigated. Seeds collected from plants growing in flooded and upland forests were used to determine the influence of normoxic (aerobic and anoxic (anaerobic conditions in germination and the initial and average time of development in the roots and shoots. After 75 days, seedlings germinated under normoxia were transferred to trays and submitted to flooding. Seed reserves (lipids, proteins, soluble sugars and starch were monitored for quiescent and germinated seeds maintained under normoxic and anoxic conditions, as well as after 5, 10 and 20 days of seedling growth. Alcohol dehydrogenase (ADH activity was quantified in roots and leaves of seedlings without or with flooding (partial and total. Seeds were not able to germinate under anoxia. Different strategies of storage mobilization of lipids, proteins, soluble sugars and starch were observed in seeds of each environment. ADH activity was induced by anoxia, with the highest level observed in the leaves. This study showed that, under normoxic conditions, the best developmental performance of assai palm seeds, from flooded or upland forest areas, during germination was associated with primary metabolites mobilization and seedling flooding tolerance with increased ADH activity. We conclude that the assai palm is well adapted to the anoxic conditions provoked by flooding.

  11. Timing of product introduction in network economies under heterogeneous demand

    DEFF Research Database (Denmark)

    Winther, Christian Dahl

    as a function of time and the scope for private rents. First, the paper derives a function showing the intertemporal evolution in market shares as a function of the choices made by the newcomer. Second, under incompatibility of standards each level of research is associated with both a minimum and a maximum...

  12. Supplemental selenium improves wheat grain yield and quality through alterations in biochemical processes under normal and water deficit conditions.

    Science.gov (United States)

    Nawaz, Fahim; Ashraf, M Y; Ahmad, R; Waraich, E A; Shabbir, R N; Bukhari, M A

    2015-05-15

    The paper mainly reported the effects of exogenous selenium (Se) supply (Se seed priming, Se fertigation and Se foliar spray) on physiological and antioxidant system of wheat aiming to clarify its effect on yield and nutritional quality of wheat under both normal and water deficit conditions. Water stress markedly decreased the grain Se, iron (Fe), phosphorous (P), zinc (Zn) and magnesium (Mg) contents. Supplemental Se (Na2SeO4) improved the yield and quality of water stressed plants due to enhancement in the production of osmoprotectants and increased activity of antioxidant enzymes. The foliar spray of Se was more effective than Se fertigation and Se seed treatment. To the best of our knowledge, this is the first elaborate study that involved various Se application methods to evaluate the efficiency of Se supply to plants that would be crucial to develop better understanding of Se translocation and accumulation within crop plants under drought stress. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Epidemic Survivability: Characterizing Networks Under Epidemic-like Failure Propagation Scenarios

    DEFF Research Database (Denmark)

    Manzano, Marc; Calle, Eusebi; Ripoll, Jordi

    2013-01-01

    in telecommunication networks has not been extensively considered, nowadays, with the increasing computation capacity and complexity of operating systems of modern network devices (routers, switches, etc.), the study of possible epidemic-like failure scenarios must be taken into account. When epidemics occur......, such as in other multiple failure scenarios, identifying the level of vulnerability offered by a network is one of the main challenges. In this paper, we present epidemic survivability, a new network measure that describes the vulnerability of each node of a network under a specific epidemic intensity. Moreover......, this metric is able to identify the set of nodes which are more vulnerable under an epidemic attack. In addition, two applications of epidemic survivability are provided. First, we introduce epidemic criticality, a novel robustness metric for epidemic failure scenarios. A case study shows the utility...

  14. Information Diffusion in Facebook-Like Social Networks Under Information Overload

    Science.gov (United States)

    Li, Pei; Xing, Kai; Wang, Dapeng; Zhang, Xin; Wang, Hui

    2013-07-01

    Research on social networks has received remarkable attention, since many people use social networks to broadcast information and stay connected with their friends. However, due to the information overload in social networks, it becomes increasingly difficult for users to find useful information. This paper takes Facebook-like social networks into account, and models the process of information diffusion under information overload. The term view scope is introduced to model the user information-processing capability under information overload, and the average number of times a message appears in view scopes after it is generated is proposed to characterize the information diffusion efficiency. Through theoretical analysis, we find that factors such as network structure and view scope number have no impact on the information diffusion efficiency, which is a surprising result. To verify the results, we conduct simulations and provide the simulation results, which are consistent with the theoretical analysis results perfectly.

  15. Bistable responses in bacterial genetic networks: Designs and dynamical consequences

    Science.gov (United States)

    Tiwari, Abhinav; Ray, J. Christian J.; Narula, Jatin; Igoshin, Oleg A.

    2011-01-01

    A key property of living cells is their ability to react to stimuli with specific biochemical responses. These responses can be understood through the dynamics of underlying biochemical and genetic networks. Evolutionary design principles have been well studied in networks that display graded responses, with a continuous relationship between input signal and system output. Alternatively, biochemical networks can exhibit bistable responses so that over a range of signals the network possesses two stable steady states. In this review, we discuss several conceptual examples illustrating network designs that can result in a bistable response of the biochemical network. Next, we examine manifestations of these designs in bacterial master-regulatory genetic circuits. In particular, we discuss mechanisms and dynamic consequences of bistability in three circuits: two-component systems, sigma-factor networks, and a multistep phosphorelay. Analyzing these examples allows us to expand our knowledge of evolutionary design principles for networks with bistable responses. PMID:21385588

  16. Memory under stress: from single systems to network changes.

    Science.gov (United States)

    Schwabe, Lars

    2017-02-01

    Stressful events have profound effects on learning and memory. These effects are mainly mediated by catecholamines and glucocorticoid hormones released from the adrenals during stressful encounters. It has been known for long that both catecholamines and glucocorticoids influence the functioning of the hippocampus, a critical hub for episodic memory. However, areas implicated in other forms of memory, such as the insula or the dorsal striatum, can be affected by stress as well. Beyond changes in single memory systems, acute stress triggers the reconfiguration of large scale neural networks which sets the stage for a shift from thoughtful, 'cognitive' control of learning and memory toward more reflexive, 'habitual' processes. Stress-related alterations in amygdala connectivity with the hippocampus, dorsal striatum, and prefrontal cortex seem to play a key role in this shift. The bias toward systems proficient in threat processing and the implementation of well-established routines may facilitate coping with an acute stressor. Overreliance on these reflexive systems or the inability to shift flexibly between them, however, may represent a risk factor for psychopathology in the long-run. © 2016 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

  17. On the underlying assumptions of threshold Boolean networks as a model for genetic regulatory network behavior.

    Science.gov (United States)

    Tran, Van; McCall, Matthew N; McMurray, Helene R; Almudevar, Anthony

    2013-01-01

    Boolean networks (BoN) are relatively simple and interpretable models of gene regulatory networks. Specifying these models with fewer parameters while retaining their ability to describe complex regulatory relationships is an ongoing methodological challenge. Additionally, extending these models to incorporate variable gene decay rates, asynchronous gene response, and synergistic regulation while maintaining their Markovian nature increases the applicability of these models to genetic regulatory networks (GRN). We explore a previously-proposed class of BoNs characterized by linear threshold functions, which we refer to as threshold Boolean networks (TBN). Compared to traditional BoNs with unconstrained transition functions, these models require far fewer parameters and offer a more direct interpretation. However, the functional form of a TBN does result in a reduction in the regulatory relationships which can be modeled. We show that TBNs can be readily extended to permit self-degradation, with explicitly modeled degradation rates. We note that the introduction of variable degradation compromises the Markovian property fundamental to BoN models but show that a simple state augmentation procedure restores their Markovian nature. Next, we study the effect of assumptions regarding self-degradation on the set of possible steady states. Our findings are captured in two theorems relating self-degradation and regulatory feedback to the steady state behavior of a TBN. Finally, we explore assumptions of synchronous gene response and asynergistic regulation and show that TBNs can be easily extended to relax these assumptions. Applying our methods to the budding yeast cell-cycle network revealed that although the network is complex, its steady state is simplified by the presence of self-degradation and lack of purely positive regulatory cycles.

  18. An effective method to improve the robustness of small-world networks under attack

    International Nuclear Information System (INIS)

    Zhang Zheng-Zhen; Xu Wen-Jun; Lin Jia-Ru; Zeng Shang-You

    2014-01-01

    In this study, the robustness of small-world networks to three types of attack is investigated. Global efficiency is introduced as the network coefficient to measure the robustness of a small-world network. The simulation results prove that an increase in rewiring probability or average degree can enhance the robustness of the small-world network under all three types of attack. The effectiveness of simultaneously increasing both rewiring probability and average degree is also studied, and the combined increase is found to significantly improve the robustness of the small-world network. Furthermore, the combined effect of rewiring probability and average degree on network robustness is shown to be several times greater than that of rewiring probability or average degree individually. This means that small-world networks with a relatively high rewiring probability and average degree have advantages both in network communications and in good robustness to attacks. Therefore, simultaneously increasing rewiring probability and average degree is an effective method of constructing realistic networks. Consequently, the proposed method is useful to construct efficient and robust networks in a realistic scenario. (interdisciplinary physics and related areas of science and technology)

  19. Systems biology and the origins of life? part II. Are biochemical networks possible ancestors of living systems? networks of catalysed chemical reactions: non-equilibrium, self-organization and evolution.

    Science.gov (United States)

    Ricard, Jacques

    2010-01-01

    The present article discusses the possibility that catalysed chemical networks can evolve. Even simple enzyme-catalysed chemical reactions can display this property. The example studied is that of a two-substrate proteinoid, or enzyme, reaction displaying random binding of its substrates A and B. The fundamental property of such a system is to display either emergence or integration depending on the respective values of the probabilities that the enzyme has bound one of its substrate regardless it has bound the other substrate, or, specifically, after it has bound the other substrate. There is emergence of information if p(A)>p(AB) and p(B)>p(BA). Conversely, if p(A)equilibrium. Moreover, in such systems, emergence results in an increase of the energy level of the ternary EAB complex that becomes closer to the transition state of the reaction, thus leading to the enhancement of catalysis. Hence a drift from quasi-equilibrium is, to a large extent, responsible for the production of information and enhancement of catalysis. Non-equilibrium of these simple systems must be an important aspect that leads to both self-organization and evolutionary processes. These conclusions can be extended to networks of catalysed chemical reactions. Such networks are, in fact, networks of networks, viz. meta-networks. In this formal representation, nodes are chemical reactions catalysed by poorly specific proteinoids, and links can be identified to the transport of metabolites from proteinoid to proteinoid. The concepts of integration and emergence can be applied to such situations and can be used to define the identity of these networks and therefore their evolution. Defined as open non-equilibrium structures, such biochemical networks possess two remarkable properties: (1) the probability of occurrence of their nodes is dependant upon the input and output of matter in, and from, the system and (2) the probability of occurrence of the nodes is strictly linked to their degree of

  20. Network of vascular diseases, death and biochemical characteristics in a set of 4,197 patients with type 1 diabetes (The FinnDiane Study

    Directory of Open Access Journals (Sweden)

    Wadén Johan

    2009-10-01

    Full Text Available Background Cardiovascular disease is the main cause of premature death in patients with type 1 diabetes. Patients with diabetic kidney disease have an increased risk of heart attack or stroke. Accurate knowledge of the complex inter-dependencies between the risk factors is critical for pinpointing the best targets for research and treatment. Therefore, the aim of this study was to describe the association patterns between clinical and biochemical features of diabetic complications. Methods Medical records and serum and urine samples of 4,197 patients with type 1 diabetes were collected from health care centers in Finland. At baseline, the mean diabetes duration was 22 years, 52% were male, 23% had kidney disease (urine albumin excretion over 300 mg/24 h or end-stage renal disease and 8% had a history of macrovascular events. All-cause mortality was evaluated after an average of 6.5 years of follow-up (25,714 patient years. The dataset comprised 28 clinical and 25 biochemical variables that were regarded as the nodes of a network to assess their mutual relationships. Results The networks contained cliques that were densely inter-connected (r > 0.6, including cliques for high-density lipoprotein (HDL markers, for triglycerides and cholesterol, for urinary excretion and for indices of body mass. The links between the cliques showed biologically relevant interactions: an inverse relationship between HDL cholesterol and the triglyceride clique (r P -16, a connection between triglycerides and body mass via C-reactive protein (r > 0.3, P -16 and intermediate-density cholesterol as the connector between lipoprotein metabolism and albuminuria (r > 0.3, P -16. Aging and macrovascular disease were linked to death via working ability and retinopathy. Diabetic kidney disease, serum creatinine and potassium, retinopathy and blood pressure were inter-connected. Blood pressure correlations indicated accelerated vascular aging in individuals with kidney disease

  1. Utilization of extended bayesian networks in decision making under uncertainty

    Energy Technology Data Exchange (ETDEWEB)

    Van Eeckhout, Edward M [Los Alamos National Laboratory; Leishman, Deborah A [Los Alamos National Laboratory; Gibson, William L [Los Alamos National Laboratory

    2009-01-01

    Bayesian network tool (called IKE for Integrated Knowledge Engine) has been developed to assess the probability of undesirable events. The tool allows indications and observables from sensors and/or intelligence to feed directly into hypotheses of interest, thus allowing one to quantify the probability and uncertainty of these events resulting from very disparate evidence. For example, the probability that a facility is processing nuclear fuel or assembling a weapon can be assessed by examining the processes required, establishing the observables that should be present, then assembling information from intelligence, sensors and other information sources related to the observables. IKE also has the capability to determine tasking plans, that is, prioritize which observable should be collected next to most quickly ascertain the 'true' state and drive the probability toward 'zero' or 'one.' This optimization capability is called 'evidence marshaling.' One example to be discussed is a denied facility monitoring situation; there is concern that certain process(es) are being executed at the site (due to some intelligence or other data). We will show how additional pieces of evidence will then ascertain with some degree of certainty the likelihood of this process(es) as each piece of evidence is obtained. This example shows how both intelligence and sensor data can be incorporated into the analysis. A second example involves real-time perimeter security. For this demonstration we used seismic, acoustic, and optical sensors linked back to IKE. We show how these sensors identified and assessed the likelihood of 'intruder' versus friendly vehicles.

  2. Measurement of antioxidant activity and antioxidant compounds under versatile extraction conditions: I. the immuno-biochemical antioxidant properties of sweet cherry (Prunus avium) extracts.

    Science.gov (United States)

    Hanbali, Lama B; Ghadieh, Rana M; Hasan, Hiba A; K Nakhal, Yasmine; Haddad, John J

    2013-01-01

    Previously, we have meticulously examined the efficacy of the measurable antimicrobial activity of sweet cherry (Prunus avium) extracts on a wide spectrum of gram-positive and gram-negative bacteria, in addition to the fungus, Candida albicans, a priori. In order to further understand the biochemical constituents and antioxidant activities of a variety of extracts of sweet cherries, antioxidant compounds of immunological significance, including L-ascorbic acid (vitamin C), phenols, flavonoids, and anthocyanins, and the total antioxidant (free radical scavenging) activity were simultaneously measured under varying and versatile extraction conditions (mild heating [5, 10 and 20 min.], and brief microwave exposure [1, 2 and 5 min.]) for a variety of extracts: i) whole juice extracts (WJE), ii) methanol-extracted juice (MEJ), iii) ddH2O-extracted pomace (dPOM), and iv) methanol-extracted pomace (mPOM). The antioxidant activity under the versatile extraction conditions adopted in this study was conspicuously reduced, such that the % inhibition against 2,2- diphenyl-1-picrylhydrazyl (DPPH) followed an inverse, negative correlational trendline. Moreover, ascorbic acid content was not affected with mild to prolonged heating or microwave exposure, except tangibly with dPOM and mPOM. The total phenols content assessed showed no significant variations, as compared with control extracts. In a manner similar to ascorbic acid, total flavonoids were mildly reduced under varying conditions, an effect mimicked to a certain extent with anthocyanins. Assessment of extraction means as compared with WJE revealed sharp decrease in the antioxidant activity for dPOM and mPOM, significant increase in L-ascorbic acid, total phenol, and flavonoid contents for MEJ, dPOM, and mPOM, and mild decrease in anthocyanin contents for dPOM and mPOM. These results confirm the measurable antioxidant activities and contents of P. avium extracts under versatile conditions of mild exposure, an effect

  3. Lipid droplets accumulation and other biochemical changes induced in the fungal pathogen Ustilago maydis under nitrogen-starvation.

    Science.gov (United States)

    Aguilar, Lucero Romero; Pardo, Juan Pablo; Lomelí, Mónica Montero; Bocardo, Oscar Ivan Luqueño; Juárez Oropeza, Marco A; Guerra Sánchez, Guadalupe

    2017-10-01

    In many organisms, the growth under nitrogen-deprivation or a poor nitrogen source impacts on the carbon flow distribution and causes accumulation of neutral lipids, which are stored as lipid droplets (LDs). Efforts are in progress to find the mechanism of LDs synthesis and degradation, and new organisms capable of accumulating large amounts of lipids for biotechnological applications. In this context, when Ustilago maydis was cultured in the absence of a nitrogen source, there was a large accumulation of lipid bodies containing mainly triacylglycerols. The most abundant fatty acids in lipid bodies at the stationary phase were palmitic, linoleic, and oleic acids, and they were synthesized de novo by the fatty-acid synthase. In regard to the production of NADPH for the synthesis of fatty acids, the cytosolic NADP + -dependent isocitrate dehydrogenase and the glucose-6-phosphate and 6-phosphogluconate dehydrogenases couple showed the highest specific activities, with a lower activity of the malic enzyme. The ATP-citrate lyase activity was not detected in any of the culture conditions, which points to a different mechanism for the transfer of acetyl-CoA into the cytosol. Protein and RNA contents decreased when U. maydis was grown without a nitrogen source. Due to the significant accumulation of triacylglycerols and the particular composition of fatty acids, U. maydis can be considered an alternative model for biotechnological applications.

  4. Evaluation of Chlorophyll Fluorescence and Biochemical Traits of Lettuce under Drought Stress and Super Absorbent or Bentonite Application

    Directory of Open Access Journals (Sweden)

    Akram Valizadeh Ghale Beig

    2014-03-01

    Full Text Available The effects of two superabsorbents (natural-bentonite and (synthetic-A 200 on the chlorophyll fluorescence index, proline accumulation, phenolic compounds, antioxidant activity and total carbohydrate in lettuce (Lactuca sativa L. was evaluated. For this purpose, a factorial experiment using completely randomized design with superabsorbents at 3 levels (0, 0.15, 0.30 w/w%, drought stress at 2 levels (60 and 100% of field capacity and 4 replicates was conducted. Results showed that photosystem photochemical efficiency (Fv/Fm II under drought stress (60% FC as well as lower levels of bentonite superabsorbent polymer reduced. The minimum and maximum proline content were obtained in 0.3% bentonite, 100% FC and 0 benetonite, 60% FC, respectively. The lowest and highest phenolic compounds was corresponded to the highest levels in both super absorbents and control respectively, so that the super absorbent and bentonite, reduced phenolic compounds by 62.65 and 66.21% compared to control. 0 and 0.15 wt % bentonite in high drought stress (60% FC showed the highest and 0.3 wt % bentonite and 100% FC attained the lowest level of antioxidant activity. Control bentonite treatment beds at 60% FC and beds containing 0.3 wt. % bentonite in 100% FC, showed the lowest and the highest total carbohydrate content respectively. Results of this study indicate that bentonite can reduce the negative effects of drought stress similar to artificial super absorbent.

  5. Luteinizing hormone-releasing hormone (LHRH) receptors in the neuroendocrine-immune network. Biochemical bases and implications for reproductive physiopathology.

    Science.gov (United States)

    Marchetti, B; Gallo, F; Farinella, Z; Romeo, C; Morale, M C

    1996-04-30

    It seems apparent that the brain-pituitary-reproductive axis and the brain-thymus-lymphoid axis are linked by an array of internal mechanisms of communication that use similar signals (neurotransmitters, peptides, growth factors, hormones) acting on similar recognition targets. Moreover, such communication networks form the basis and control of each step and every level of reproductive physiology. This work has focused on the LHRH system, a primary central and peripheral clock of both neuroendocrine and immune functions. From the initiation of a sexually organized response, the detection of sexual odors, and the induction of mating behavior, extrahypothalamic and hypothalamic LHRH orchestrates the neuroendocrine modulation of gonadotropin secretion, while its expression within the ovary directly controls specific events such as follicular atresia. The presence of LHRH receptors in oocytes clearly anticipates a potential action of the decapeptide during the process of fertilization and/or implantation. Within the thymus and other peripheral immune organs, LHRH plays a unique role of immunomodulator, contributing to the sex-dependent changes in immune responsiveness during the estrous-menstrual cycle as well as pregnancy. The reciprocity of the neuroendocrine-immune signaling systems is further supported by the ability of sex steroids to modulate thymus-dependent immune functions via direct effects on specific target genes involved in the development of sex dimorphism and sex-dimorphic immune responses, including the downregulation of immune response observed during pregnancy. Such cyclic changes in immune responsiveness could have a physiological implication, such as the decrease or suppression in cell-mediated immunity observed in the postovulatory phase of the cycle and in pregnancy, respectively, and might play a role during the implantation process and the establishment of pregnancy. In this context, the ability of corticosterone to directly inhibit both GR

  6. Network optimization including gas lift and network parameters under subsurface uncertainty

    Energy Technology Data Exchange (ETDEWEB)

    Schulze-Riegert, R.; Baffoe, J.; Pajonk, O. [SPT Group GmbH, Hamburg (Germany); Badalov, H.; Huseynov, S. [Technische Univ. Clausthal, Clausthal-Zellerfeld (Germany). ITE; Trick, M. [SPT Group, Calgary, AB (Canada)

    2013-08-01

    Optimization of oil and gas field production systems poses a great challenge to field development due to complex and multiple interactions between various operational design parameters and subsurface uncertainties. Conventional analytical methods are capable of finding local optima based on single deterministic models. They are less applicable for efficiently generating alternative design scenarios in a multi-objective context. Practical implementations of robust optimization workflows integrate the evaluation of alternative design scenarios and multiple realizations of subsurface uncertainty descriptions. Production or economic performance indicators such as NPV (Net Present Value) are linked to a risk-weighted objective function definition to guide the optimization processes. This work focuses on an integrated workflow using a reservoir-network simulator coupled to an optimization framework. The work will investigate the impact of design parameters while considering the physics of the reservoir, wells, and surface facilities. Subsurface uncertainties are described by well parameters such as inflow performance. Experimental design methods are used to investigate parameter sensitivities and interactions. Optimization methods are used to find optimal design parameter combinations which improve key performance indicators of the production network system. The proposed workflow will be applied to a representative oil reservoir coupled to a network which is modelled by an integrated reservoir-network simulator. Gas-lift will be included as an explicit measure to improve production. An objective function will be formulated for the net present value of the integrated system including production revenue and facility costs. Facility and gas lift design parameters are tuned to maximize NPV. Well inflow performance uncertainties are introduced with an impact on gas lift performance. Resulting variances on NPV are identified as a risk measure for the optimized system design. A

  7. Physiological And Blood Biochemical Responses To Dried Live Yeast Plus Vitamin E As A Dietary Supplement To Bovine Baladi Calves Under Hot Summer Conditions

    International Nuclear Information System (INIS)

    ABDALLA, E.B.; EL-MASRY, K.A.; TEAMA, F.E.; EMARA, S.S.

    2009-01-01

    The experiment was designed to study the effect of supplemented dried live yeast (DLY) + vitamin E to the diet of growing calves under hot summer conditions in Egypt. Six bovine Baladi calves with 115 kg initial body weight and 8-10 months old were used during two periods. In the first period, the calves were offered the concentrated basal diet only for one month and considered as a control period. In the second period, the calves were fed the same basal diet which supplemented with 15 g dried live yeast (Saccharomyces cerevisiae) + 600 IU vitamin E (alpha- tocopherol) per calf daily for one month and considered as a treated period. Body weight was recorded at the beginning and the end of each period, and daily gain was calculated for each animal. Blood samples were collected from each animal at the end of each period to determine some blood biochemical parameters and T 3 and T 4 concentrations as well as some immunological indices.The results showed that supplementation of DLY + 600 IU vitamin E to the diet of calves reduced significantly (P 3 and T 4 levels and improved feed efficiency and daily gain. It is concluded that supplementation of growing calves with 15 g DLY + 600 IU vitamin E / calf / day under Egyptian hot summer conditions reduced the effect of heat stress as shown by a decline in RT and modified most blood constituents and thyroid function which leads to an improvement in growing calves

  8. The research on optimization of auto supply chain network robust model under macroeconomic fluctuations

    International Nuclear Information System (INIS)

    Guo, Chunxiang; Liu, Xiaoli; Jin, Maozhu; Lv, Zhihan

    2016-01-01

    Considering the uncertainty of the macroeconomic environment, the robust optimization method is studied for constructing and designing the automotive supply chain network, and based on the definition of robust solution a robust optimization model is built for integrated supply chain network design that consists of supplier selection problem and facility location–distribution problem. The tabu search algorithm is proposed for supply chain node configuration, analyzing the influence of the level of uncertainty on robust results, and by comparing the performance of supply chain network design through the stochastic programming model and robustness optimize model, on this basis, determining the rational layout of supply chain network under macroeconomic fluctuations. At last the contrastive test result validates that the performance of tabu search algorithm is outstanding on convergence and computational time. Meanwhile it is indicated that the robust optimization model can reduce investment risks effectively when it is applied to supply chain network design.

  9. Uranium mining and metallurgy library information service under the network environment

    International Nuclear Information System (INIS)

    Tang Lilei

    2012-01-01

    This paper analyzes the effect of the network environment on the uranium mining and metallurgy of the information service. Introduces some measures such as strengthening professional characteristic literature resources construction, changing the service mode, building up information navigation, deepening service, meet the individual needs of users, raising librarian's quality, promoting the co-construction and sharing of library information resources, and puts forward the development idea of uranium mining and metallurgy library information service under the network environment. (author)

  10. Power Flow Calculation for Traction Networks under Regenerative Braking Condition Based on Locomotive-Traction Network Coupling

    OpenAIRE

    Han Xudong; Gao Shibin; Hu Haitao; Wang Bin

    2013-01-01

    The regenerative braking technology is widely applied in high-speed electric multiple units (EMUs). And the voltage rise problem at end of the traction network would be caused by regenerative braking attracts more and more attention. The arm of this paper is to analyze the power flow calculation for EMUs under regenerative braking condition. Power flow calculation was done for two different EMU operation conditions by using a “locomotive-traction network” coupling model. In this model, a cons...

  11. Performance Evaluation of Survivability Strategies for Elastic Optical Networks under Physical Layer Impairments

    Directory of Open Access Journals (Sweden)

    Jurandir Lacerda Jr

    2017-08-01

    Full Text Available This paper carried out a performance evaluation study that compares two survivability strategies (DPP and SM-RSA for elastic optical networks with and without physical layer impairments. The evaluated scenarios include three representative topologies for elastic optical network, NSFNET, EON and USA. It also analyzes the increase of blocking probability when the survivability strategies are evaluated under the realistic scenario that assumes physical layer impairments. For all studied topologies under physical layer impairments, the survivability strategies achieved blocking probability above 80%.

  12. Methylglyoxal produces more changes in biochemical and biophysical properties of human IgG under high glucose compared to normal glucose level

    Science.gov (United States)

    Khan, Mohd Adnan; Arif, Zarina; Khan, Mohd Asad; Moinuddin

    2018-01-01

    Hyperglycaemia triggers increased production of methylglyoxal which can cause gross modification in proteins’ structure vis-a-vis function though advanced glycation end products (AGEs). The AGEs may initiate vascular and nonvascular pathologies. In this study, we have examined the biochemical and biophysical changes in human IgG under normal and high glucose after introducing methylglyoxal into the assay mixture. This non-enzymatic reaction mainly engaged lysine residues as indicated by TNBS results. The UV results showed hyperchromicity in modified-IgG samples while fluorescence data supported AGEs formation during the course of reaction. Shift in amide I and amide II band position indicated perturbations in secondary structure. Increase carbonyl content and decrease in sulfhydryl suggests that the modification is accompanied by oxidative stress. All modified-IgG samples showed more thermostability than native IgG; the highest Tm was shown by IgG-high glucose-MGO variant. Results of ANS, Congo red and Thioflavin T dyes clearly suggest increase in hydrophobic patches and aggregation, respectively. SEM and TEM images support aggregates generation in modified-IgG samples. PMID:29351321

  13. Global stability analysis and robust design of multi-time-scale biological networks under parametric uncertainties.

    Science.gov (United States)

    Meyer-Baese, Anke; Koshkouei, Ali J; Emmett, Mark R; Goodall, David P

    2009-01-01

    Biological networks are prone to internal parametric fluctuations and external noises. Robustness represents a crucial property of these networks, which militates the effects of internal fluctuations and external noises. In this paper biological networks are formulated as coupled nonlinear differential systems operating at different time-scales under vanishing perturbations. In contrast to previous work viewing biological parametric uncertain systems as perturbations to a known nominal linear system, the perturbed biological system is modeled as nonlinear perturbations to a known nonlinear idealized system and is represented by two time-scales (subsystems). In addition, conditions for the existence of a global uniform attractor of the perturbed biological system are presented. By using an appropriate Lyapunov function for the coupled system, a maximal upper bound for the fast time-scale associated with the fast state is derived. The proposed robust system design principles are potentially applicable to robust biosynthetic network design. Finally, two examples of two important biological networks, a neural network and a gene regulatory network, are presented to illustrate the applicability of the developed theoretical framework.

  14. Coverage probability of cellular networks using interference alignment under imperfect CSI

    Directory of Open Access Journals (Sweden)

    Raoul F. Guiazon

    2016-11-01

    Full Text Available Interference alignment (IA is well understood to approach the capacity of interference channels, and believed to be crucial in cellular networks in which the ability to control and exploit interference is key. However, the achievable performance of IA in cellular networks depends on the quality of channel state information (CSI and how effective IA is in practical settings is not known. This paper studies the use of IA to mitigate inter-cell interference of cellular networks under imperfect CSI conditions. Our analysis is based on stochastic geometry where the structure of the base station (BS locations is considered by a Poisson point process (PPP. Our main contribution is the coverage probability of the network and simulation results confirm the accuracy.

  15. Securing ad hoc wireless sensor networks under Byzantine attacks by implementing non-cryptographic method

    Directory of Open Access Journals (Sweden)

    Shabir Ahmad Sofi

    2017-05-01

    Full Text Available Ad Hoc wireless sensor network (WSN is a collection of nodes that do not need to rely on predefined infrastructure to keep the network connected. The level of security and performance are always somehow related to each other, therefore due to limited resources in WSN, cryptographic methods for securing the network against attacks is not feasible. Byzantine attacks disrupt the communication between nodes in the network without regard to its own resource consumption. This paper discusses the performance of cluster based WSN comparing LEACH with Advanced node based clusters under byzantine attacks. This paper also proposes an algorithm for detection and isolation of the compromised nodes to mitigate the attacks by non-cryptographic means. The throughput increases after using the algorithm for isolation of the malicious nodes, 33% in case of Gray Hole attack and 62% in case of Black Hole attack.

  16. Dynamic Network Design Problem under Demand Uncertainty: An Adjustable Robust Optimization Approach

    Directory of Open Access Journals (Sweden)

    Hua Sun

    2014-01-01

    Full Text Available This paper develops an adjustable robust optimization approach for a network design problem explicitly incorporating traffic dynamics and demand uncertainty. In particular, a cell transmission model based network design problem of linear programming type is considered to describe dynamic traffic flows, and a polyhedral uncertainty set is used to characterize the demand uncertainty. The major contribution of this paper is to formulate such an adjustable robust network design problem as a tractable linear programming model and justify the model which is less conservative by comparing its solution performance with the robust solution from the usual robust model. The numerical results using one network from the literature demonstrate the modeling advantage of the adjustable robust optimization and provided strategic managerial insights for enacting capacity expansion policies under demand uncertainty.

  17. Assessment of biological and biochemical indicators in soil under transgenic Bt and non-Bt cotton crop in a sub-tropical environment.

    Science.gov (United States)

    Sarkar, Binoy; Patra, Ashok K; Purakayastha, T J; Megharaj, Mallavarapu

    2009-09-01

    There is concern that transgenic Bt-crops carry genes that could have undesirable effects on natural and agro-ecosystem functions. We investigated the effect of Bt-cotton (expressing the Cry 1Ac protein) on several microbial and biochemical indicators in a sandy loam soil. Bt-cotton (MRC-6301Bt) and its non-transgenic near-isoline (MRC-6301) were grown in a net-house on a sandy clay loam soil. Soil and root samples were collected 60, 90, and 120 days after sowing. Soil from a control (no-crop) treatment was also included. Samples were analysed for microbial biomass C, N and P (MBC, MBN, MBP), total organic carbon (TOC), and several soil enzyme activities. The microbial quotient (MQ) was calculated as the ratio of MBC-to-TOC. The average of the three sampling events revealed a significant increase in MBC, MBN, MBP and MQ in the soil under Bt-cotton over the non-Bt isoline. The TOC was similar in Bt and non-Bt systems. Potential N mineralization, nitrification, nitrate reductase, and acid and alkaline phosphatase activities were all higher in the soil under Bt-cotton. Root dry weights were not different (P > 0.05), but root volume of Bt-cotton was higher on 90 and 120 days than that of non-Bt cotton. The time of sampling strongly affected the above parameters, with most being highest on 90 days after sowing. We concluded from the data that there were some positive or no negative effects of Bt-cotton on the studied indicators, and therefore cultivation of Bt-cotton appears to be no risk to soil ecosystem functions.

  18. Phyto-management of Cr-contaminated soils by sunflower hybrids: physiological and biochemical response and metal extractability under Cr stress.

    Science.gov (United States)

    Farid, Mujahid; Ali, Shafaqat; Akram, Nudrat Aisha; Rizwan, Muhammad; Abbas, Farhat; Bukhari, Syed Asad Hussain; Saeed, Rashid

    2017-07-01

    Chromium (Cr) is a biologically non-essential, carcinogenic and toxic heavy metal. The cultivation of Cr-tolerant genotypes seems the most favorable and environment friendly strategy for rehabilitation and remediation of Cr-contaminated soils. To prove this hypothesis and identify the Cr tolerance, the present study was performed to assess the physiological and biochemical response of sunflower genotypes to Cr stress. The seeds of six sunflower hybrids, namely FH-425, FH-600, FH-612, FH-614, FH-619, and FH-620, were grown in spiked soil for 12 weeks under increasing concentrations of Cr (0, 5, 10, and 20 mg kg -1 ). A seed germination test was also run under different concentrations of Cr (0, 5, 10, 200 mM) in petri dishes. Plants were harvested after 12 weeks of germination. Different plant attributes such as growth; biomass; photosynthesis; gas exchange; activity of antioxidant enzymes, i.e., superoxide dismutase (SOD), guaiacol peroxidase (POD), ascorbate (APX), and catalases (CAT); reactive oxygen species (ROS); lipid peroxidation; electrolyte leakage; and Cr concentration as well as accumulations in all plant parts were studied for the selection of the most Cr-tolerant genotype. Increasing concentration of Cr in soil triggered the reduction of all plant parameters in sunflower. Cr stress increased electrolyte leakage and production of reactive oxygen species which stimulated the activities of antioxidant enzymes and gas exchange attributes of sunflower. Chromium accumulation in the root and shoot increased gradually with increasing Cr treatments and caused reduction in overall plant growth. The accumulation of Cr was recorded in the order of FH-614 > FH-620 > FH-600 > FH-619 > FH-612 > FH-425. The differential uptake and accumulation of Cr by sunflower hybrids may be useful in selection and breeding for Cr-tolerant genotypes.

  19. Enhancing network performance under single link failure with AS-disjoint BGP extension

    DEFF Research Database (Denmark)

    Manolova, Anna Vasileva; Romeral, S.; Ruepp, Sarah Renée

    2009-01-01

    In this paper we propose an enhancement of the BGP protocol for obtaining AS-disjoint paths in GMPLS multi-domain networks. We evaluate the benefits of having AS-disjoint paths under single inter-domain link failure for two main applications: routing of future connection requests during routing...... protocol re-convergence and applying multi-domain restoration as survivability mechanism in case of a single link failure. The proposed BGP modification is a simple and effective solution for disjoint path selection in connection-oriented multi-domain networks. Our results show that applying the proper...... failure notification method combined with our proposal reduces the blocking of new connection requests under protocol re-convergence. Furthermore. we show that our proposal is a valuable complementary process for increasing the network resilience....

  20. The evaluation of the activity of glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase under different patho-physiological conditions : a combined enzyme histochemical and biochemical approach

    NARCIS (Netherlands)

    E.A. Elias (Ezzat); R.O. van der Heul

    1988-01-01

    textabstractThis thesis is based on a series of metabolic studies conducted on material obtained from human and experimental animal tissues and cells. The studies are essentially enzyme histochemical complemented when thought necessary with biochemical investigations performed on tissue

  1. Modelling the Cost Performance of a Given Logistics Network Operating Under Regular and Irregular Conditions

    NARCIS (Netherlands)

    Janic, M.

    2009-01-01

    This paper develops an analytical model for the assessment of the cost performance of a given logistics network operating under regular and irregular (disruptive) conditions. In addition, the paper aims to carry out a sensitivity analysis of this cost with respect to changes of the most influencing

  2. Robustness of the Drinking Water Distribution Network under Changing Future Demand

    NARCIS (Netherlands)

    Agudelo-Vera, C.; Blokker, M.; Vreeburg, J.; Bongard, T.; Hillegers, S.; Van der Hoek, J.P.

    2014-01-01

    A methodology to determine the robustness of the drinking water distribution system is proposed. The performance of three networks under ten future demand scenarios was tested, using head loss and residence time as indicators. The scenarios consider technological and demographic changes. Daily

  3. Creating and Using a Computer Networking and Systems Administration Laboratory Built under Relaxed Financial Constraints

    Science.gov (United States)

    Conlon, Michael P.; Mullins, Paul

    2011-01-01

    The Computer Science Department at Slippery Rock University created a laboratory for its Computer Networks and System Administration and Security courses under relaxed financial constraints. This paper describes the department's experience designing and using this laboratory, including lessons learned and descriptions of some student projects…

  4. Bayesian networks for clinical decision support: A rational approach to dynamic decision-making under uncertainty

    NARCIS (Netherlands)

    Gerven, M.A.J. van

    2007-01-01

    This dissertation deals with decision support in the context of clinical oncology. (Dynamic) Bayesian networks are used as a framework for (dynamic) decision-making under uncertainty and applied to a variety of diagnostic, prognostic, and treatment problems in medicine. It is shown that the proposed

  5. Bayesian networks for clinical decision support: A rational approach to dynamic decision-making under uncertainty

    OpenAIRE

    Gerven, M.A.J. van

    2007-01-01

    This dissertation deals with decision support in the context of clinical oncology. (Dynamic) Bayesian networks are used as a framework for (dynamic) decision-making under uncertainty and applied to a variety of diagnostic, prognostic, and treatment problems in medicine. It is shown that the proposed models perform well in realistic settings

  6. Thermo-economic optimization of secondary distribution network of low temperature district heating network under local conditions of South Korea

    DEFF Research Database (Denmark)

    Park, Byung Sik; Imran, Muhammad; Hoon, Im-Yong

    2017-01-01

    A secondary distribution network of a low temperature district heating system is designed and optimized for a residential apartment complex under the local conditions of South Korea in the TRNSYS simulation environment. The residential apartment complex is a typical example of Korean residential...... °C, area of heat exchanger is increased by 68.2%, pumping power is also increased by 9.8% and heat loss is reduced by 15.6%. These results correspond to a temperature difference of 20 °C, the standard temperature difference in South Korea residential heating system. Economic assessment...

  7. Suppression of anomalous synchronization and nonstationary behavior of neural network under small-world topology

    Science.gov (United States)

    Boaretto, B. R. R.; Budzinski, R. C.; Prado, T. L.; Kurths, J.; Lopes, S. R.

    2018-05-01

    It is known that neural networks under small-world topology can present anomalous synchronization and nonstationary behavior for weak coupling regimes. Here, we propose methods to suppress the anomalous synchronization and also to diminish the nonstationary behavior occurring in weakly coupled neural network under small-world topology. We consider a network of 2000 thermally sensitive identical neurons, based on the model of Hodgkin-Huxley in a small-world topology, with the probability of adding non local connection equal to p = 0 . 001. Based on experimental protocols to suppress anomalous synchronization, as well as nonstationary behavior of the neural network dynamics, we make use of (i) external stimulus (pulsed current); (ii) biologic parameters changing (neuron membrane conductance changes); and (iii) body temperature changes. Quantification analysis to evaluate phase synchronization makes use of the Kuramoto's order parameter, while recurrence quantification analysis, particularly the determinism, computed over the easily accessible mean field of network, the local field potential (LFP), is used to evaluate nonstationary states. We show that the methods proposed can control the anomalous synchronization and nonstationarity occurring for weak coupling parameter without any effect on the individual neuron dynamics, neither in the expected asymptotic synchronized states occurring for large values of the coupling parameter.

  8. Adaptive Sensing with Reliable Guarantee under White Gaussian Noise Channels of Sensor Networks

    Directory of Open Access Journals (Sweden)

    Jun Long

    2015-01-01

    Full Text Available Quality of sensing is a fundamental research topic in sensor networks. In this paper, we propose an adaptive sensing technique to guarantee the end-to-end reliability while maximizing the lifetime of sensor networks under additive white Gaussian noise channels. First, we conduct theoretical analysis to obtain optimal node number N∗, node placement d∗, and node transmission structure P∗ under minimum total energy consumption and minimum unit data transmission energy consumption. Then, because sensor nodes closer to the sink consume more energy, nodes far from the sink have more residual energy. Based on this observation, we propose an adaptive sensing technique to achieve balanced network energy consumption. It adopts lower reliability requirement and shorter transmission distance for nodes near the sink and adopts higher reliability requirement and farther transmission distance for nodes far from the sink. Theoretical analysis and experimental results show that our design can improve the network lifetime by several times (1–5 times and network utility by 20% and the desired reliability level is also guaranteed.

  9. COST-EFFECTIVE BANDWIDTH PROVISIONING IN MICROWAVE WIRELESS NETWORKS UNDER UNRELIABLE CHANNEL CONDITIONS

    Directory of Open Access Journals (Sweden)

    Brigitte Jaumard

    Full Text Available ABSTRACT Cost-effective planning and dimensioning of backhaul microwave networks under unreliable channel conditions remains a relatively underexplored area in the literature. In particular, bandwidth assignment requires special attention as the transport capacity of microwave links is prone to variations due to, e.g., weather conditions. In this paper, we formulate an optimization model that determines the minimum cost bandwidth assignment of the links in the network for which traffic requirements can be fulfilled with high probability. This model also aims to increase network reliability by adjusting dynamically traffic routes in response to variations of link capacities induced by channel conditions. Experimental results show that 45% of the bandwidth cost can be saved compared to the case where a bandwidth over-provisioning policy is uniformly applied to all links in the network planning. Comparisons with previous work also show that our solution approach, based on column generation technique, is able to solve much larger instances in significantly shorter computing times (i.e., few minutes for medium-size networks, and up to 2 hours for very large networks, unsolved so far by previous models/algorithms, with a comparable level of reliability.

  10. A model of social network formation under the impact of structural balance

    Science.gov (United States)

    Li, Pei; Cheng, Jiajun; Chen, Yingwen; Wang, Hui

    2016-03-01

    Social networks have attracted remarkable attention from both academic and industrial societies and it is of great importance to understand the formation of social networks. However, most existing research cannot be applied directly to investigate social networks, where relationships are heterogeneous and structural balance is a common phenomenon. In this paper, we take both positive and negative relationships into consideration and propose a model to characterize the process of social network formation under the impact of structural balance. In this model, a new node first establishes a link with an existing node and then tries to connect to each of the newly connected node’s neighbors. If a new link is established, the type of this link is determined by structural balance. Then we analyze the degree distribution of the generated network theoretically, and estimate the fractions of positive and negative links. All analysis results are verified by simulations. These results are of importance to understand the formation of social networks, and the model can be easily extended to consider more realistic situations.

  11. Formal Models of the Network Co-occurrence Underlying Mental Operations.

    Directory of Open Access Journals (Sweden)

    Danilo Bzdok

    2016-06-01

    Full Text Available Systems neuroscience has identified a set of canonical large-scale networks in humans. These have predominantly been characterized by resting-state analyses of the task-unconstrained, mind-wandering brain. Their explicit relationship to defined task performance is largely unknown and remains challenging. The present work contributes a multivariate statistical learning approach that can extract the major brain networks and quantify their configuration during various psychological tasks. The method is validated in two extensive datasets (n = 500 and n = 81 by model-based generation of synthetic activity maps from recombination of shared network topographies. To study a use case, we formally revisited the poorly understood difference between neural activity underlying idling versus goal-directed behavior. We demonstrate that task-specific neural activity patterns can be explained by plausible combinations of resting-state networks. The possibility of decomposing a mental task into the relative contributions of major brain networks, the "network co-occurrence architecture" of a given task, opens an alternative access to the neural substrates of human cognition.

  12. Selenium Supplementation Affects Physiological and Biochemical Processes to Improve Fodder Yield and Quality of Maize (Zea mays L.) under Water Deficit Conditions

    Science.gov (United States)

    Nawaz, Fahim; Naeem, Muhammad; Ashraf, Muhammad Y.; Tahir, Muhammad N.; Zulfiqar, Bilal; Salahuddin, Muhammad; Shabbir, Rana N.; Aslam, Muhammad

    2016-01-01

    Climate change is one of the most complex challenges that pose serious threats to livelihoods of poor people who rely heavily on agriculture and livestock particularly in climate-sensitive developing countries of the world. The negative effects of water scarcity, due to climate change, are not limited to productivity food crops but have far-reaching consequences on livestock feed production systems. Selenium (Se) is considered essential for animal health and has also been reported to counteract various abiotic stresses in plants, however, understanding of Se regulated mechanisms for improving nutritional status of fodder crops remains elusive. We report the effects of exogenous selenium supply on physiological and biochemical processes that may influence green fodder yield and quality of maize (Zea mays L.) under drought stress conditions. The plants were grown in lysimeter tanks under natural conditions and were subjected to normal (100% field capacity) and water stress (60% field capacity) conditions. Foliar spray of Se was carried out before the start of tasseling stage (65 days after sowing) and was repeated after 1 week, whereas, water spray was used as a control. Drought stress markedly reduced the water status, pigments and green fodder yield and resulted in low forage quality in water stressed maize plants. Nevertheless, exogenous Se application at 40 mg L-1 resulted in less negative leaf water potential (41%) and enhanced relative water contents (30%), total chlorophyll (53%), carotenoid contents (60%), accumulation of total free amino acids (40%) and activities of superoxide dismutase (53%), catalase (30%), peroxidase (27%), and ascorbate peroxidase (27%) with respect to control under water deficit conditions. Consequently, Se regulated processes improved fodder yield (15%) and increased crude protein (47%), fiber (10%), nitrogen free extract (10%) and Se content (36%) but did not affect crude ash content in water stressed maize plants. We propose that Se

  13. Selenium Supplementation Affects Physiological and Biochemical Processes to Improve Fodder Yield and Quality of Maize (Zea mays L.) under Water Deficit Conditions.

    Science.gov (United States)

    Nawaz, Fahim; Naeem, Muhammad; Ashraf, Muhammad Y; Tahir, Muhammad N; Zulfiqar, Bilal; Salahuddin, Muhammad; Shabbir, Rana N; Aslam, Muhammad

    2016-01-01

    Climate change is one of the most complex challenges that pose serious threats to livelihoods of poor people who rely heavily on agriculture and livestock particularly in climate-sensitive developing countries of the world. The negative effects of water scarcity, due to climate change, are not limited to productivity food crops but have far-reaching consequences on livestock feed production systems. Selenium (Se) is considered essential for animal health and has also been reported to counteract various abiotic stresses in plants, however, understanding of Se regulated mechanisms for improving nutritional status of fodder crops remains elusive. We report the effects of exogenous selenium supply on physiological and biochemical processes that may influence green fodder yield and quality of maize ( Zea mays L.) under drought stress conditions. The plants were grown in lysimeter tanks under natural conditions and were subjected to normal (100% field capacity) and water stress (60% field capacity) conditions. Foliar spray of Se was carried out before the start of tasseling stage (65 days after sowing) and was repeated after 1 week, whereas, water spray was used as a control. Drought stress markedly reduced the water status, pigments and green fodder yield and resulted in low forage quality in water stressed maize plants. Nevertheless, exogenous Se application at 40 mg L -1 resulted in less negative leaf water potential (41%) and enhanced relative water contents (30%), total chlorophyll (53%), carotenoid contents (60%), accumulation of total free amino acids (40%) and activities of superoxide dismutase (53%), catalase (30%), peroxidase (27%), and ascorbate peroxidase (27%) with respect to control under water deficit conditions. Consequently, Se regulated processes improved fodder yield (15%) and increased crude protein (47%), fiber (10%), nitrogen free extract (10%) and Se content (36%) but did not affect crude ash content in water stressed maize plants. We propose that

  14. Selenium Supplementation Affects Physiological and Biochemical Processes to Improve Fodder Yield and Quality of Maize (Zea mays L. under Water Deficit Conditions

    Directory of Open Access Journals (Sweden)

    Fahim Nawaz

    2016-09-01

    Full Text Available Climate change is one of the most complex challenges that pose serious threats to livelihoods of poor people who rely heavily on agriculture and livestock particularly in climate-sensitive developing countries of the world. The negative effects of water scarcity, due to climate change, are not limited to productivity food crops but have far-reaching consequences on livestock feed production systems. Selenium (Se is considered essential for animal health and has also been reported to counteract various abiotic stresses in plants however, understanding of Se regulated mechanisms for improving nutritional status of fodder crops remains elusive. We report the effects of exogenous selenium (Se supply on physiological and biochemical processes that may influence green fodder yield and quality of maize (Zea mays L. under drought stress conditions. The plants were grown in lysimeter tanks under natural conditions and were subjected to normal (100% field capacity and water stress (60% field capacity conditions. Foliar spray of Se was carried out before the start of tasseling stage (65 days after sowing and was repeated after one week, whereas water spray was used as a control. Drought stress markedly reduced the water status, pigments and green fodder yield and resulted in low forage quality in water stressed maize plants. Nevertheless, exogenous Se application at 40 mg L-1 resulted in less negative leaf water potential (41% and enhanced relative water contents (30%, total chlorophyll (53%, carotenoid contents (60%, accumulation of total free amino acids (40% and activities of superoxide dismutase (53%, catalase (30%, peroxidase (27% and ascorbate peroxidase (27% with respect to control under water deficit conditions. Consequently, Se regulated processes improved fodder yield (15% and increased crude protein (47%, fibre (10%, nitrogen free extract (10% and Se content (36% but did not affect crude ash content in water stressed maize plants. We propose

  15. An attempt to interpret a biochemical mechanism of C4 photosynthetic thermo-tolerance under sudden heat shock on detached leaf in elevated CO2 grown maize.

    Directory of Open Access Journals (Sweden)

    Mingnan Qu

    Full Text Available Detached leaves at top canopy structures always experience higher solar irradiance and leaf temperature under natural conditions. The ability of tolerance to high temperature represents thermotolerance potential of whole-plants, but was less of concern. In this study, we used a heat-tolerant (B76 and a heat-susceptible (B106 maize inbred line to assess the possible mitigation of sudden heat shock (SHS effects on photosynthesis (PN and C4 assimilation pathway by elevated [CO2]. Two maize lines were grown in field-based open top chambers (OTCs at ambient and elevated (+180 ppm [CO2]. Top-expanded leaves for 30 days after emergence were suddenly exposed to a 45°C SHS for 2 hours in midday during measurements. Analysis on thermostability of cellular membrane showed there was 20% greater electrolyte leakage in response to the SHS in B106 compared to B76, in agreement with prior studies. Elevated [CO2] protected PN from SHS in B76 but not B106. The responses of PN to SHS among the two lines and grown CO2 treatments were closely correlated with measured decreases of NADP-ME enzyme activity and also to its reduced transcript abundance. The SHS treatments induced starch depletion, the accumulation of hexoses and also disrupted the TCA cycle as well as the C4 assimilation pathway in the both lines. Elevated [CO2] reversed SHS effects on citrate and related TCA cycle metabolites in B106 but the effects of elevated [CO2] were small in B76. These findings suggested that heat stress tolerance is a complex trait, and it is difficult to identify biochemical, physiological or molecular markers that accurately and consistently predict heat stress tolerance.

  16. Cooperative integration and representation underlying bilateral network of fly motion-sensitive neurons.

    Directory of Open Access Journals (Sweden)

    Yoshinori Suzuki

    Full Text Available How is binocular motion information integrated in the bilateral network of wide-field motion-sensitive neurons, called lobula plate tangential cells (LPTCs, in the visual system of flies? It is possible to construct an accurate model of this network because a complete picture of synaptic interactions has been experimentally identified. We investigated the cooperative behavior of the network of horizontal LPTCs underlying the integration of binocular motion information and the information representation in the bilateral LPTC network through numerical simulations on the network model. First, we qualitatively reproduced rotational motion-sensitive response of the H2 cell previously reported in vivo experiments and ascertained that it could be accounted for by the cooperative behavior of the bilateral network mainly via interhemispheric electrical coupling. We demonstrated that the response properties of single H1 and Hu cells, unlike H2 cells, are not influenced by motion stimuli in the contralateral visual hemi-field, but that the correlations between these cell activities are enhanced by the rotational motion stimulus. We next examined the whole population activity by performing principal component analysis (PCA on the population activities of simulated LPTCs. We showed that the two orthogonal patterns of correlated population activities given by the first two principal components represent the rotational and translational motions, respectively, and similar to the H2 cell, rotational motion produces a stronger response in the network than does translational motion. Furthermore, we found that these population-coding properties are strongly influenced by the interhemispheric electrical coupling. Finally, to test the generality of our conclusions, we used a more simplified model and verified that the numerical results are not specific to the network model we constructed.

  17. Functional Ecological Gene Networks to Reveal the Changes Among Microbial Interactions Under Elevated Carbon Dioxide Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Ye; Zhou, Jizhong; Luo, Feng; He, Zhili; Tu, Qichao; Zhi, Xiaoyang

    2010-05-17

    Biodiversity and its responses to environmental changes is a central issue in ecology, and for society. Almost all microbial biodiversity researches focus on species richness and abundance but ignore the interactions among different microbial species/populations. However, determining the interactions and their relationships to environmental changes in microbial communities is a grand challenge, primarily due to the lack of information on the network structure among different microbial species/populations. Here, a novel random matrix theory (RMT)-based conceptual framework for identifying functional ecological gene networks (fEGNs) is developed with the high throughput functional gene array hybridization data from the grassland microbial communities in a long-term FACE (Free Air CO2 Enrichment) experiment. Both fEGNs under elevated CO2 (eCO2) and ambient CO2 (aCO2) possessed general characteristics of many complex systems such as scale-free, small-world, modular and hierarchical. However, the topological structure of the fEGNs is distinctly different between eCO2 and aCO2, suggesting that eCO2 dramatically altered the interactions among different microbial functional groups/populations. In addition, the changes in network structure were significantly correlated with soil carbon and nitrogen dynamics, and plant productivity, indicating the potential importance of network interactions in ecosystem functioning. Elucidating network interactions in microbial communities and their responses to environmental changes are fundamentally important for research in microbial ecology, systems microbiology, and global change.

  18. Stochastic noncooperative and cooperative evolutionary game strategies of a population of biological networks under natural selection.

    Science.gov (United States)

    Chen, Bor-Sen; Yeh, Chin-Hsun

    2017-12-01

    We review current static and dynamic evolutionary game strategies of biological networks and discuss the lack of random genetic variations and stochastic environmental disturbances in these models. To include these factors, a population of evolving biological networks is modeled as a nonlinear stochastic biological system with Poisson-driven genetic variations and random environmental fluctuations (stimuli). To gain insight into the evolutionary game theory of stochastic biological networks under natural selection, the phenotypic robustness and network evolvability of noncooperative and cooperative evolutionary game strategies are discussed from a stochastic Nash game perspective. The noncooperative strategy can be transformed into an equivalent multi-objective optimization problem and is shown to display significantly improved network robustness to tolerate genetic variations and buffer environmental disturbances, maintaining phenotypic traits for longer than the cooperative strategy. However, the noncooperative case requires greater effort and more compromises between partly conflicting players. Global linearization is used to simplify the problem of solving nonlinear stochastic evolutionary games. Finally, a simple stochastic evolutionary model of a metabolic pathway is simulated to illustrate the procedure of solving for two evolutionary game strategies and to confirm and compare their respective characteristics in the evolutionary process. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Automatic Matching of Multi-scale Road Networks under the Constraints of Smaller Scale Road Meshes

    Directory of Open Access Journals (Sweden)

    PEI Hongxing

    2017-06-01

    Full Text Available A new method is proposed to achieve automatic matching for multi-scale roads under the constraints of the smaller scale data. Firstly, meshes should be extracted from the two different scales road data. Secondly, several basic meshes in the larger scale road network will be merged as a composite one, which will be matched with one mesh from the smaller scale road network, so that the meshes with many-to-one and one-to-one matching relationships will be matched. Thirdly, meshes from the two different scale road data with many-to-many matching relationships will be matched. Finally, road will be classified into two categories under the constraints of meshes: mesh border roads and mesh internal roads, and then matching will be done in their own categories according to the matching relationships between the two scales meshes. The results showed that roads from different scale will be more precisely matched.

  20. Experimental study and artificial neural network modeling of tartrazine removal by photocatalytic process under solar light.

    Science.gov (United States)

    Sebti, Aicha; Souahi, Fatiha; Mohellebi, Faroudja; Igoud, Sadek

    2017-07-01

    This research focuses on the application of an artificial neural network (ANN) to predict the removal efficiency of tartrazine from simulated wastewater using a photocatalytic process under solar illumination. A program is developed in Matlab software to optimize the neural network architecture and select the suitable combination of training algorithm, activation function and hidden neurons number. The experimental results of a batch reactor operated under different conditions of pH, TiO 2 concentration, initial organic pollutant concentration and solar radiation intensity are used to train, validate and test the networks. While negligible mineralization is demonstrated, the experimental results show that under sunlight irradiation, 85% of tartrazine is removed after 300 min using only 0.3 g/L of TiO 2 powder. Therefore, irradiation time is prolonged and almost 66% of total organic carbon is reduced after 15 hours. ANN 5-8-1 with Bayesian regulation back-propagation algorithm and hyperbolic tangent sigmoid transfer function is found to be able to predict the response with high accuracy. In addition, the connection weights approach is used to assess the importance contribution of each input variable on the ANN model response. Among the five experimental parameters, the irradiation time has the greatest effect on the removal efficiency of tartrazine.

  1. Effects of Dietary L-carnitine Supplementation on Growth Performance, Organ Weight, Biochemical Parameters and Ascites Susceptibility in Broilers Reared Under Low-temperature Environment

    Directory of Open Access Journals (Sweden)

    Y. W. Wang

    2013-02-01

    Full Text Available The objective of this study was to investigate the effects of L-carnitine on growth performance, organ weight, biochemical parameters of blood, heart and liver, and ascites susceptibility of broilers at different ages reared under a low-temperature environment. A total of 420 1-d-old male Ross 308 broilers were randomly assigned to two dietary treatments with fifteen replicates of fourteen broilers each. Treatment diets consisted of L-carnitine supplementation at levels of 0 and 100 mg/kg. At 11-d of age, low temperature stress was used to increase ascites susceptibility. Blood, heart and liver samples were collected at different ages for analysis of boichemical parameters. The results showed that, there was no significant difference in growth performance with L-carnitine supplementation, but the mortality due to ascites was significantly decreased. Dietary L-carnitine supplementation significantly reduced heart index (HI and ascites heart index (AHI on d 21, lung index (LUI on d 35 and liver index (LI on d 42. The broilers fed diets containing L-carnitine had significantly lower red blood cell counts (RBC, hemoglobin (HGB concentration and hematocrit (HCT on d 42. Dietary L-carnitine supplementation significantly reduced malondialdehyde (MDA content of heart tissue on d 21 and 35, and significantly increased total superoxide dismutase (T-SOD and Glutathione peroxidase (GSH-Px activity of the heart on d 21 and 42. L-carnitine supplementation significantly reduced serum triglyceride (TG content on d 28 and 35 and serum glucose (GLU on d 35 and 42, and significantly increased serum total protein (TP and globulin (GLO content on d 42. L-carnitine supplementation significantly enhanced liver succinodehydrogenase (SDH, malic dehydrogenase (MDH and Na+-K+-ATPase activity on d 28, and tended to reduce the lactic acid (LD level of liver on d 35 (p = 0.06. L-carnitine supplementation significantly reduced serum uric acid (UA content on d 28, 35 and 42

  2. Strategies for a better performance of RPL under mobility in wireless sensor networks

    Science.gov (United States)

    Latib, Z. A.; Jamil, A.; Alduais, N. A. M.; Abdullah, J.; Audah, L. H. M.; Alias, R.

    2017-09-01

    A Wireless Sensor Network (WSN) is usually stationary, which the network comprises of static nodes. The increase demand for mobility in various applications such as environmental monitoring, medical, home automation, and military, raises the question how IPv6 Routing Protocol for Low-Power and Lossy Networks (RPL) would perform under these mobility applications. This paper aims to understand performance of RPL and come out with strategies for a better performance of RPL in mobility scenarios. Because of this, this paper evaluates the performance of the RPL protocol under three different scenarios: sink and sensor nodes are static, static sink and mobile sensor nodes, and sink and sensor nodes are mobile. The network scenarios are implemented in Cooja simulator. A WSN consists of 25 sensor nodes and one sink node is configured in the simulation environment. The simulation is varied over different packet rates and ContikiMAC's Clear Channel Assessment (CCA) rate. As the performance metric, RPL is evaluated in term of packet delivery ratio (PDR), power consumption and packet rates. The simulation results show RPL provides a poor PDR in the mobility scenarios when compared to the static scenario. In addition, RPL consumes more power and increases duty-cycle rate to support mobility when compared to the static scenario. Based on the findings, we suggest three strategies for a better performance of RPL in mobility scenarios. First, RPL should operates at a lower packet rates when implemented in the mobility scenarios. Second, RPL should be implemented with a higher duty-cycle rate. Lastly, the sink node should be positioned as much as possible in the center of the mobile network.

  3. Neural network model for evaluation of seedling vigour under clinostated conditions

    Science.gov (United States)

    Zaidi, M.; Murase, H.

    A hierarchical neural net can be applied to simulate nonlinear phenomena found in biological systems. The learning process of the hierarchical neural net can be used as an algorithm for nonlinear multivariate analysis. The non- invasive technique for monitoring the plant's growth stage is one part of the required technology of the bio-response feedback control system. The stage of a plant's growth can be identified or quantified by measuring physical indices. Automated monitoring is also necessary in the clinostat experiment and neural networks are used for the calibration of lettuce plant growth. A back propagation neural network was trained to evaluate the plant growth in terms of plant growth characteristics, with a network consisting of 4, 8 and 1 processing units in the input, hidden and output layers, respectively. Sixteen sets of training data were used. The training was terminated after 800 times of iterative calculations at the RMS error value equal to 3.35x10-3 . Four sets of validation data were used to calculate the prediction error. The ability of the neural network models to predict the required information is very accurate. As a result, there is potential for the present technique to be applied to seedling vigour evaluating system under the clinostated conditions.

  4. Determinants of investment under incentive regulation: The case of the Norwegian electricity distribution networks

    International Nuclear Information System (INIS)

    Poudineh, Rahmatallah; Jamasb, Tooraj

    2016-01-01

    Investment in electricity networks, as regulated natural monopolies, is among the highest regulatory and energy policy priorities. The electricity sector regulators adopt different incentive mechanisms to ensure that the firms undertake sufficient investment to maintain and modernise the grid. Thus, an effective regulatory treatment of investment requires understanding the response of companies to the regulatory incentives. This study analyses the determinants of investment in electricity distribution networks using a panel dataset of 129 Norwegian companies observed from 2004 to 2010. A Bayesian Model Averaging approach is used to provide a robust statistical inference by taking into account the uncertainties around model selection and estimation. The results show that three factors drive nearly all network investments: investment rate in previous period, socio-economic costs of energy not supplied and finally useful life of assets. The results indicate that Norwegian companies have, to some degree, responded to the investment incentives provided by the regulatory framework. However, some of the incentives do not appear to be effective in driving the investments. - Highlights: • This paper investigates determinants of investment under incentive regulation. • We apply a Bayesian model averaging technique to deal with model uncertainty. • Dataset comprises 129 Norwegian electricity network companies from 2004 to 2010. • The results show that firms have generally responded to investment incentives. • However, some of the incentives do not appear to have been effective.

  5. A multi-period distribution network design model under demand uncertainty

    Science.gov (United States)

    Tabrizi, Babak H.; Razmi, Jafar

    2013-05-01

    Supply chain management is taken into account as an inseparable component in satisfying customers' requirements. This paper deals with the distribution network design (DND) problem which is a critical issue in achieving supply chain accomplishments. A capable DND can guarantee the success of the entire network performance. However, there are many factors that can cause fluctuations in input data determining market treatment, with respect to short-term planning, on the one hand. On the other hand, network performance may be threatened by the changes that take place within practicing periods, with respect to long-term planning. Thus, in order to bring both kinds of changes under control, we considered a new multi-period, multi-commodity, multi-source DND problem in circumstances where the network encounters uncertain demands. The fuzzy logic is applied here as an efficient tool for controlling the potential customers' demand risk. The defuzzifying framework leads the practitioners and decision-makers to interact with the solution procedure continuously. The fuzzy model is then validated by a sensitivity analysis test, and a typical problem is solved in order to illustrate the implementation steps. Finally, the formulation is tested by some different-sized problems to show its total performance.

  6. Core regulatory network motif underlies the ocellar complex patterning in Drosophila melanogaster

    Science.gov (United States)

    Aguilar-Hidalgo, D.; Lemos, M. C.; Córdoba, A.

    2015-03-01

    During organogenesis, developmental programs governed by Gene Regulatory Networks (GRN) define the functionality, size and shape of the different constituents of living organisms. Robustness, thus, is an essential characteristic that GRNs need to fulfill in order to maintain viability and reproducibility in a species. In the present work we analyze the robustness of the patterning for the ocellar complex formation in Drosophila melanogaster fly. We have systematically pruned the GRN that drives the development of this visual system to obtain the minimum pathway able to satisfy this pattern. We found that the mechanism underlying the patterning obeys to the dynamics of a 3-nodes network motif with a double negative feedback loop fed by a morphogenetic gradient that triggers the inhibition in a French flag problem fashion. A Boolean modeling of the GRN confirms robustness in the patterning mechanism showing the same result for different network complexity levels. Interestingly, the network provides a steady state solution in the interocellar part of the patterning and an oscillatory regime in the ocelli. This theoretical result predicts that the ocellar pattern may underlie oscillatory dynamics in its genetic regulation.

  7. Biochemical characterization of human gluconokinase and the proposed metabolic impact of gluconic Acid as determined by constraint based metabolic network analysis

    DEFF Research Database (Denmark)

    Rohatgi, Neha; Nielsen, Tine Kragh; Bjørn, Sara Petersen

    2014-01-01

    to the hexose monophosphate shunt (HMS) are induced through a small increase in gluconate concentration. We argue that the enzyme takes part in a context specific carbon flux route into the HMS that, in humans, remains incompletely explored. Apart from the biochemical description of human gluconokinase...

  8. Gene Profiling of Aortic Valve Interstitial Cells under Elevated Pressure Conditions: Modulation of Inflammatory Gene Networks

    Directory of Open Access Journals (Sweden)

    James N. Warnock

    2011-01-01

    Full Text Available The study aimed to identify mechanosensitive pathways and gene networks that are stimulated by elevated cyclic pressure in aortic valve interstitial cells (VICs and lead to detrimental tissue remodeling and/or pathogenesis. Porcine aortic valve leaflets were exposed to cyclic pressures of 80 or 120 mmHg, corresponding to diastolic transvalvular pressure in normal and hypertensive conditions, respectively. Linear, two-cycle amplification of total RNA, followed by microarray was performed for transcriptome analysis (with qRT-PCR validation. A combination of systems biology modeling and pathway analysis identified novel genes and molecular mechanisms underlying the biological response of VICs to elevated pressure. 56 gene transcripts related to inflammatory response mechanisms were differentially expressed. TNF-α, IL-1α, and IL-1β were key cytokines identified from the gene network model. Also of interest was the discovery that pentraxin 3 (PTX3 was significantly upregulated under elevated pressure conditions (41-fold change. In conclusion, a gene network model showing differentially expressed inflammatory genes and their interactions in VICs exposed to elevated pressure has been developed. This system overview has detected key molecules that could be targeted for pharmacotherapy of aortic stenosis in hypertensive patients.

  9. Complex network analysis of phase dynamics underlying oil-water two-phase flows

    Science.gov (United States)

    Gao, Zhong-Ke; Zhang, Shan-Shan; Cai, Qing; Yang, Yu-Xuan; Jin, Ning-De

    2016-01-01

    Characterizing the complicated flow behaviors arising from high water cut and low velocity oil-water flows is an important problem of significant challenge. We design a high-speed cycle motivation conductance sensor and carry out experiments for measuring the local flow information from different oil-in-water flow patterns. We first use multivariate time-frequency analysis to probe the typical features of three flow patterns from the perspective of energy and frequency. Then we infer complex networks from multi-channel measurements in terms of phase lag index, aiming to uncovering the phase dynamics governing the transition and evolution of different oil-in-water flow patterns. In particular, we employ spectral radius and weighted clustering coefficient entropy to characterize the derived unweighted and weighted networks and the results indicate that our approach yields quantitative insights into the phase dynamics underlying the high water cut and low velocity oil-water flows. PMID:27306101

  10. Topological Control on the Structural Relaxation of Atomic Networks under Stress

    Science.gov (United States)

    Bauchy, Mathieu; Wang, Mengyi; Yu, Yingtian; Wang, Bu; Krishnan, N. M. Anoop; Masoero, Enrico; Ulm, Franz-Joseph; Pellenq, Roland

    2017-07-01

    Upon loading, atomic networks can feature delayed irreversible relaxation. However, the effect of composition and structure on relaxation remains poorly understood. Herein, relying on accelerated molecular dynamics simulations and topological constraint theory, we investigate the relationship between atomic topology and stress-induced structural relaxation, by taking the example of creep deformations in calcium silicate hydrates (C - S - H ), the binding phase of concrete. Under constant shear stress, C - S - H is found to feature delayed logarithmic shear deformations. We demonstrate that the propensity for relaxation is minimum for isostatic atomic networks, which are characterized by the simultaneous absence of floppy internal modes of relaxation and eigenstress. This suggests that topological nanoengineering could lead to the discovery of nonaging materials.

  11. Under-Frequency Load Shedding Technique Considering Event-Based for an Islanded Distribution Network

    Directory of Open Access Journals (Sweden)

    Hasmaini Mohamad

    2016-06-01

    Full Text Available One of the biggest challenge for an islanding operation is to sustain the frequency stability. A large power imbalance following islanding would cause under-frequency, hence an appropriate control is required to shed certain amount of load. The main objective of this research is to develop an adaptive under-frequency load shedding (UFLS technique for an islanding system. The technique is designed considering an event-based which includes the moment system is islanded and a tripping of any DG unit during islanding operation. A disturbance magnitude is calculated to determine the amount of load to be shed. The technique is modeled by using PSCAD simulation tool. A simulation studies on a distribution network with mini hydro generation is carried out to evaluate the UFLS model. It is performed under different load condition: peak and base load. Results show that the load shedding technique have successfully shed certain amount of load and stabilized the system frequency.

  12. Network structure underlying resolution of conflicting non-verbal and verbal social information.

    Science.gov (United States)

    Watanabe, Takamitsu; Yahata, Noriaki; Kawakubo, Yuki; Inoue, Hideyuki; Takano, Yosuke; Iwashiro, Norichika; Natsubori, Tatsunobu; Takao, Hidemasa; Sasaki, Hiroki; Gonoi, Wataru; Murakami, Mizuho; Katsura, Masaki; Kunimatsu, Akira; Abe, Osamu; Kasai, Kiyoto; Yamasue, Hidenori

    2014-06-01

    Social judgments often require resolution of incongruity in communication contents. Although previous studies revealed that such conflict resolution recruits brain regions including the medial prefrontal cortex (mPFC) and posterior inferior frontal gyrus (pIFG), functional relationships and networks among these regions remain unclear. In this functional magnetic resonance imaging study, we investigated the functional dissociation and networks by measuring human brain activity during resolving incongruity between verbal and non-verbal emotional contents. First, we found that the conflict resolutions biased by the non-verbal contents activated the posterior dorsal mPFC (post-dmPFC), bilateral anterior insula (AI) and right dorsal pIFG, whereas the resolutions biased by the verbal contents activated the bilateral ventral pIFG. In contrast, the anterior dmPFC (ant-dmPFC), bilateral superior temporal sulcus and fusiform gyrus were commonly involved in both of the resolutions. Second, we found that the post-dmPFC and right ventral pIFG were hub regions in networks underlying the non-verbal- and verbal-content-biased resolutions, respectively. Finally, we revealed that these resolution-type-specific networks were bridged by the ant-dmPFC, which was recruited for the conflict resolutions earlier than the two hub regions. These findings suggest that, in social conflict resolutions, the ant-dmPFC selectively recruits one of the resolution-type-specific networks through its interaction with resolution-type-specific hub regions. © The Author (2013). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

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

    Science.gov (United States)

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

    2016-11-01

    Music is a powerful means for communicating emotions among individuals. Here we reveal that this continuous stream of affective information is commonly represented in the brains of different listeners and that particular musical attributes mediate this link. We examined participants' brain responses to two naturalistic musical pieces using functional Magnetic Resonance imaging (fMRI). Following scanning, as participants listened to the musical pieces for a second time, they continuously indicated their emotional experience on scales of valence and arousal. These continuous reports were used along with a detailed annotation of the musical features, to predict a novel index of Dynamic Common Activation (DCA) derived from ten large-scale data-driven functional networks. We found an association between the unfolding music-induced emotionality and the DCA modulation within a vast network of limbic regions. The limbic-DCA modulation further corresponded with continuous changes in two temporal musical features: beat-strength and tempo. Remarkably, this "collective limbic sensitivity" to temporal features was found to mediate the link between limbic-DCA and the reported emotionality. An additional association with the emotional experience was found in a left fronto-parietal network, but only among a sub-group of participants with a high level of musical experience (>5years). These findings may indicate two processing-levels underlying the unfolding of common music emotionality; (1) a widely shared core-affective process that is confined to a limbic network and mediated by temporal regularities in music and (2) an experience based process that is rooted in a left fronto-parietal network that may involve functioning of the 'mirror-neuron system'. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Network interactions underlying mirror feedback in stroke: A dynamic causal modeling study

    Directory of Open Access Journals (Sweden)

    Soha Saleh

    2017-01-01

    Full Text Available Mirror visual feedback (MVF is potentially a powerful tool to facilitate recovery of disordered movement and stimulate activation of under-active brain areas due to stroke. The neural mechanisms underlying MVF have therefore been a focus of recent inquiry. Although it is known that sensorimotor areas can be activated via mirror feedback, the network interactions driving this effect remain unknown. The aim of the current study was to fill this gap by using dynamic causal modeling to test the interactions between regions in the frontal and parietal lobes that may be important for modulating the activation of the ipsilesional motor cortex during mirror visual feedback of unaffected hand movement in stroke patients. Our intent was to distinguish between two theoretical neural mechanisms that might mediate ipsilateral activation in response to mirror-feedback: transfer of information between bilateral motor cortices versus recruitment of regions comprising an action observation network which in turn modulate the motor cortex. In an event-related fMRI design, fourteen chronic stroke subjects performed goal-directed finger flexion movements with their unaffected hand while observing real-time visual feedback of the corresponding (veridical or opposite (mirror hand in virtual reality. Among 30 plausible network models that were tested, the winning model revealed significant mirror feedback-based modulation of the ipsilesional motor cortex arising from the contralesional parietal cortex, in a region along the rostral extent of the intraparietal sulcus. No winning model was identified for the veridical feedback condition. We discuss our findings in the context of supporting the latter hypothesis, that mirror feedback-based activation of motor cortex may be attributed to engagement of a contralateral (contralesional action observation network. These findings may have important implications for identifying putative cortical areas, which may be targeted with

  15. Serviceability Assessment for Cascading Failures in Water Distribution Network under Seismic Scenario

    Directory of Open Access Journals (Sweden)

    Qing Shuang

    2016-01-01

    Full Text Available The stability of water service is a hot point in industrial production, public safety, and academic research. The paper establishes a service evaluation model for the water distribution network (WDN. The serviceability is measured in three aspects: (1 the functionality of structural components under disaster environment; (2 the recognition of cascading failure process; and (3 the calculation of system reliability. The node and edge failures in WDN are interrelated under seismic excitations. The cascading failure process is provided with the balance of water supply and demand. The matrix-based system reliability (MSR method is used to represent the system events and calculate the nonfailure probability. An example is used to illustrate the proposed method. The cascading failure processes with different node failures are simulated. The serviceability is analyzed. The critical node can be identified. The result shows that the aged network has a greater influence on the system service under seismic scenario. The maintenance could improve the antidisaster ability of WDN. Priority should be given to controlling the time between the initial failure and the first secondary failure, for taking postdisaster emergency measures within this time period can largely cut down the spread of cascade effect in the whole WDN.

  16. COMPONENT SUPPLY MODEL FOR REPAIR ACTIVITIES NETWORK UNDER CONDITIONS OF PROBABILISTIC INDEFINITENESS.

    Directory of Open Access Journals (Sweden)

    Victor Yurievich Stroganov

    2017-02-01

    Full Text Available This article contains the systematization of the major production functions of repair activities network and the list of planning and control functions, which are described in the form of business processes (BP. Simulation model for analysis of the delivery effectiveness of components under conditions of probabilistic uncertainty was proposed. It has been shown that a significant portion of the total number of business processes is represented by the management and planning of the parts and components movement. Questions of construction of experimental design techniques on the simulation model in the conditions of non-stationarity were considered.

  17. Investigating risk and robustness measures for supply chain network design under demand uncertainty

    DEFF Research Database (Denmark)

    Govindan, Kannan; Fattahi, Mohammad

    2017-01-01

    This paper addresses a multi-stage and multi-period supply chain network design problem in which multiple commodities should be produced through different subsequent levels of manufacturing processes. The problem is formulated as a two-stage stochastic program under stochastic and highly time......-variable demands. To deal with the stochastic demands, a Latin Hypercube Sampling method is applied to generate a fan of scenarios and then, a backward scenario reduction technique reduces the number of scenarios. Weighted mean-risk objectives by using different risk measures and minimax objective are examined...

  18. Identifying gene coexpression networks underlying the dynamic regulation of wood-forming tissues in Populus under diverse environmental conditions.

    Science.gov (United States)

    Zinkgraf, Matthew; Liu, Lijun; Groover, Andrew; Filkov, Vladimir

    2017-06-01

    Trees modify wood formation through integration of environmental and developmental signals in complex but poorly defined transcriptional networks, allowing trees to produce woody tissues appropriate to diverse environmental conditions. In order to identify relationships among genes expressed during wood formation, we integrated data from new and publically available datasets in Populus. These datasets were generated from woody tissue and include transcriptome profiling, transcription factor binding, DNA accessibility and genome-wide association mapping experiments. Coexpression modules were calculated, each of which contains genes showing similar expression patterns across experimental conditions, genotypes and treatments. Conserved gene coexpression modules (four modules totaling 8398 genes) were identified that were highly preserved across diverse environmental conditions and genetic backgrounds. Functional annotations as well as correlations with specific experimental treatments associated individual conserved modules with distinct biological processes underlying wood formation, such as cell-wall biosynthesis, meristem development and epigenetic pathways. Module genes were also enriched for DNase I hypersensitivity footprints and binding from four transcription factors associated with wood formation. The conserved modules are excellent candidates for modeling core developmental pathways common to wood formation in diverse environments and genotypes, and serve as testbeds for hypothesis generation and testing for future studies. No claim to original US government works. New Phytologist © 2017 New Phytologist Trust.

  19. Hypothalamus-Related Resting Brain Network Underlying Short-Term Acupuncture Treatment in Primary Hypertension

    Directory of Open Access Journals (Sweden)

    Hongyan Chen

    2013-01-01

    Full Text Available The present study attempted to explore modulated hypothalamus-seeded resting brain network underlying the cardiovascular system in primary hypertensive patients after short-term acupuncture treatment. Thirty right-handed patients (14 male were divided randomly into acupuncture and control groups. The acupuncture group received a continuous five-day acupuncture treatment and undertook three resting-state fMRI scans and 24-hour ambulatory blood pressure monitoring (ABPM as well as SF-36 questionnaires before, after, and one month after acupuncture treatment. The control group undertook fMRI scans and 24-hour ABPM. For verum acupuncture, average blood pressure (BP and heart rate (HR decreased after treatment but showed no statistical differences. There were no significant differences in BP and HR between the acupuncture and control groups. Notably, SF-36 indicated that bodily pain (P = 0.005 decreased and vitality (P = 0.036 increased after acupuncture compared to the baseline. The hypothalamus-related brain network showed increased functional connectivity with the medulla, brainstem, cerebellum, limbic system, thalamus, and frontal lobes. In conclusion, short-term acupuncture did not decrease BP significantly but appeared to improve body pain and vitality. Acupuncture may regulate the cardiovascular system through a complicated brain network from the cortical level, the hypothalamus, and the brainstem.

  20. Converging models of schizophrenia - Network alterations of prefrontal cortex underlying cognitive impairments

    Science.gov (United States)

    Sakurai, Takeshi; Gamo, Nao J; Hikida, Takatoshi; Kim, Sun-Hong; Murai, Toshiya; Tomoda, Toshifumi; Sawa, Akira

    2015-01-01

    The prefrontal cortex (PFC) and its connections with other brain areas are crucial for cognitive function. Cognitive impairments are one of the core symptoms associated with schizophrenia, and manifest even before the onset of the disorder. Altered neural networks involving PFC contribute to cognitive impairments in schizophrenia. Both genetic and environmental risk factors affect the development of the local circuitry within PFC as well as development of broader brain networks, and make the system vulnerable to further insults during adolescence, leading to the onset of the disorder in young adulthood. Since spared cognitive functions correlate with functional outcome and prognosis, a better understanding of the mechanisms underlying cognitive impairments will have important implications for novel therapeutics for schizophrenia focusing on cognitive functions. Multidisciplinary approaches, from basic neuroscience to clinical studies, are required to link molecules, circuitry, networks, and behavioral phenotypes. Close interactions among such fields by sharing a common language on connectomes, behavioral readouts, and other concepts are crucial for this goal. PMID:26408506

  1. Spatially Nonlinear Interdependence of Alpha-Oscillatory Neural Networks under Chan Meditation

    Directory of Open Access Journals (Sweden)

    Pei-Chen Lo

    2013-01-01

    Full Text Available This paper reports the results of our investigation of the effects of Chan meditation on brain electrophysiological behaviors from the viewpoint of spatially nonlinear interdependence among regional neural networks. Particular emphasis is laid on the alpha-dominated EEG (electroencephalograph. Continuous-time wavelet transform was adopted to detect the epochs containing substantial alpha activities. Nonlinear interdependence quantified by similarity index S(X∣Y, the influence of source signal Y on sink signal X, was applied to the nonlinear dynamical model in phase space reconstructed from multichannel EEG. Experimental group involved ten experienced Chan-Meditation practitioners, while control group included ten healthy subjects within the same age range, yet, without any meditation experience. Nonlinear interdependence among various cortical regions was explored for five local neural-network regions, frontal, posterior, right-temporal, left-temporal, and central regions. In the experimental group, the inter-regional interaction was evaluated for the brain dynamics under three different stages, at rest (stage R, pre-meditation background recording, in Chan meditation (stage M, and the unique Chakra-focusing practice (stage C. Experimental group exhibits stronger interactions among various local neural networks at stages M and C compared with those at stage R. The intergroup comparison demonstrates that Chan-meditation brain possesses better cortical inter-regional interactions than the resting brain of control group.

  2. Estimation of biochemical variables using quantumbehaved particle ...

    African Journals Online (AJOL)

    Due to the difficulties in the measurement of biochemical variables in fermentation process, softsensing model based on radius basis function neural network had been established for estimating the variables. To generate a more efficient neural network estimator, we employed the previously proposed quantum-behaved ...

  3. Retrospective analysis of "new" flame retardants in the global atmosphere under the GAPS Network.

    Science.gov (United States)

    Lee, Sum Chi; Sverko, Ed; Harner, Tom; Pozo, Karla; Barresi, Enzo; Schachtschneider, JoAnne; Zaruk, Donna; DeJong, Maryl; Narayan, Julie

    2016-10-01

    A retrospective analysis was conducted on air samples that were collected in 2005 under the Global Atmospheric Passive Sampling (GAPS) Network around the time period when the Stockholm Convention on Persistent Organic Pollutants came into force. Results are presented for several new flame retardants, including hexabromocyclododecane (HBCD), which was recently listed under the Convention (2013). These results represent the first global-scale distributions in air for these compounds. The targeted compounds are shown to have unique global distributions in air, which highlights the challenges in understanding the sources and environmental fate of each chemical, and ultimately in their assessments as persistent organic pollutants. The study also demonstrates the feasibility of using the PUF disk passive air sampler to study these new flame retardants in air, many of which exist entirely in the particle-phase as demonstrated in this study using a KOA-based partitioning model. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

  4. Memory networks supporting retrieval effort and retrieval success under conditions of full and divided attention.

    Science.gov (United States)

    Skinner, Erin I; Fernandes, Myra A; Grady, Cheryl L

    2009-01-01

    We used a multivariate analysis technique, partial least squares (PLS), to identify distributed patterns of brain activity associated with retrieval effort and retrieval success. Participants performed a recognition memory task under full attention (FA) or two different divided attention (DA) conditions during retrieval. Behaviorally, recognition was disrupted when a word, but not digit-based distracting task, was performed concurrently with retrieval. PLS was used to identify patterns of brain activation that together covaried with the three memory conditions and which were functionally connected with activity in the right hippocampus to produce successful memory performance. Results indicate that activity in the right dorsolateral frontal cortex increases during conditions of DA at retrieval, and that successful memory performance in the DA-digit condition is associated with activation of the same network of brain regions functionally connected to the right hippocampus, as under FA, which increases with increasing memory performance. Finally, DA conditions that disrupt successful memory performance (DA-word) interfere with recruitment of both retrieval-effort and retrieval-success networks.

  5. Carboxylated multi-walled carbon nanotubes aggravated biochemical and subcellular damages in leaves of broad bean (Vicia faba L.) seedlings under combined stress of lead and cadmium

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Chengrun, E-mail: chengrunwang@163.com [School of Life Science, Huainan Normal University, Huainan 232001 (China); Liu, Haitao; Chen, Jinyun [School of Life Science, Huainan Normal University, Huainan 232001 (China); Tian, Yuan [Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 (United States); Shi, Jian; Li, Dongdong; Guo, Chen; Ma, Qingping [School of Life Science, Huainan Normal University, Huainan 232001 (China)

    2014-06-01

    Highlights: • MWCNTs-COOH disturb mineral elements and cause oxidative damages in the leaves. • Cd and Pb combination result in reduction of mineral elements and enrichment of Na, involving in toxicity mechanisms. • MWCNTs-COOH facilitate Cd and Pb uptake, and aggravate biochemical and subcellular damages. - Abstract: Increasing industrialization of multi-walled carbon nanotubes (MWCNTs) would inevitably lead to their release into the environment and combination with heavy metals. However, studies concerning the combined effects of MWCNTs and heavy metals on agricultural crops are limited. Herein, effects and mechanisms of carboxylated MWCNTs (MWCNTs-COOH) (2.5, 5 and 10 mg/L) and their combination with 20 μM Pb and 5 μM Cd (shortened as Pb + Cd) on Vicia faba L. seedlings were investigated. The results showed that the MWCNTs-COOH disturbed the imbalance of nutrient elements, and caused oxidative stress and damages in the leaves. Additionally, the combination of MWCNTs-COOH with Pb + Cd resulted in enrichment of Pb and Cd, and deterioration of oxidative damages compared with the treatments of MWCNTs-COOH or Pb + Cd alone in the leaves. As the results, the concentrations of MWCNTs-COOH not only caused oxidative stress, but also exacerbated the biochemical and subcellular damages due to the treatment of Pb + Cd in the leaves. It also suggests that persistent release of MWCNTs-COOH into the environment may cause phytotoxicity and aggravate ecological risks due to combination of heavy metals.

  6. Biochemical acclimation, stomatal limitation and precipitation patterns underlie decreases in photosynthetic stimulation of soybean (Glycine max) at elevated [CO₂] and temperatures under fully open air field conditions.

    Science.gov (United States)

    Rosenthal, David M; Ruiz-Vera, Ursula M; Siebers, Matthew H; Gray, Sharon B; Bernacchi, Carl J; Ort, Donald R

    2014-09-01

    The net effect of elevated [CO2] and temperature on photosynthetic acclimation and plant productivity is poorly resolved. We assessed the effects of canopy warming and fully open air [CO2] enrichment on (1) the acclimation of two biochemical parameters that frequently limit photosynthesis (A), the maximum carboxylation capacity of Rubisco (Vc,max) and the maximum potential linear electron flux through photosystem II (Jmax), (2) the associated responses of leaf structural and chemical properties related to A, as well as (3) the stomatal limitation (l) imposed on A, for soybean over two growing seasons in a conventionally managed agricultural field in Illinois, USA. Acclimation to elevated [CO2] was consistent over two growing seasons with respect to Vc,max and Jmax. However, elevated temperature significantly decreased Jmax contributing to lower photosynthetic stimulation by elevated CO2. Large seasonal differences in precipitation altered soil moisture availability modulating the complex effects of elevated temperature and CO2 on biochemical and structural properties related to A. Elevated temperature also reduced the benefit of elevated [CO2] by eliminating decreases in stomatal limitation at elevated [CO2]. These results highlight the critical importance of considering multiple environmental factors (i.e. temperature, moisture, [CO2]) when trying to predict plant productivity in the context of climate change. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  7. Secure Distributed Detection under Energy Constraint in IoT-Oriented Sensor Networks.

    Science.gov (United States)

    Zhang, Guomei; Sun, Hao

    2016-12-16

    We study the secure distributed detection problems under energy constraint for IoT-oriented sensor networks. The conventional channel-aware encryption (CAE) is an efficient physical-layer secure distributed detection scheme in light of its energy efficiency, good scalability and robustness over diverse eavesdropping scenarios. However, in the CAE scheme, it remains an open problem of how to optimize the key thresholds for the estimated channel gain, which are used to determine the sensor's reporting action. Moreover, the CAE scheme does not jointly consider the accuracy of local detection results in determining whether to stay dormant for a sensor. To solve these problems, we first analyze the error probability and derive the optimal thresholds in the CAE scheme under a specified energy constraint. These results build a convenient mathematic framework for our further innovative design. Under this framework, we propose a hybrid secure distributed detection scheme. Our proposal can satisfy the energy constraint by keeping some sensors inactive according to the local detection confidence level, which is characterized by likelihood ratio. In the meanwhile, the security is guaranteed through randomly flipping the local decisions forwarded to the fusion center based on the channel amplitude. We further optimize the key parameters of our hybrid scheme, including two local decision thresholds and one channel comparison threshold. Performance evaluation results demonstrate that our hybrid scheme outperforms the CAE under stringent energy constraints, especially in the high signal-to-noise ratio scenario, while the security is still assured.

  8. How does the quality of life and the underlying biochemical indicators correlate with the performance in academic examinations in a group of medical students of Sri Lanka?

    Science.gov (United States)

    Hettiarachchi, Manjula; Fonseka, Chathuranga Lakmal; Gunasekara, Priyanka; Jayasinghe, Prasanjanie; Maduranga, Dasun

    2014-01-01

    Individual variation of examination performance depends on many modifiable and non-modifiable factors, including pre-examination anxiety. Medical students' quality of life (QoL) and certain biochemical changes occurring while they are preparing for examinations has not been explored. We hypothesize that these parameters would determine the examination performance among medical students. Fourth-year medical students (n=78) from the University of Ruhuna, Sri Lanka, were invited. Their pre- and post-exam status of QoL, using the World Health Organization Quality of Life (WHOQOL-BREF) questionnaire, and the level of biochemical marker levels (i.e., serum levels of thyroid profile including thyroglobulin, cortisol and ferritin) were assessed. Differences between the scores of QoL and serum parameters were compared with their performance at the examination. The mean QoL score was significantly lower at pre-exam (56.19±8.1) when compared with post-exam (61.7±7.1) levels (pexam (0.9 mIU/L; interquartile range 0.74-1.4 mIU/L) was significantly lower (p=0.001) when compared with the level after the exam (median of 2.7 mIU/L; IQR 1.90-3.60). The mean±SD fT4 level was significantly higher before the exam (19.48±0.4 pmol/L at study entry vs. 17.43±0.3 pmol/L after the exam; pexam (43.15 (23.5-63.3) µg/L) was significantly lower (p≤0.001) when compared with after-exam status (72.36 (49.9-94.9) µg/L). However, there was no difference in mean serum cortisol levels (16.51±0.7 at pre-exam and 15.88±0.7 at post-exam, respectively; p=0.41). Students had higher fT4 and low ferritin levels on pre-exam biochemical assessment. It was evident that students who perform better at the examination had significantly higher QoL scores at each domain tested through the questionnaire (Physical health, Psychological, Social interaction and Environment). The higher the QoL scores, the better the grades were. It was also found that students who failed exhibited profound differences in the

  9. How does the quality of life and the underlying biochemical indicators correlate with the performance in academic examinations in a group of medical students of Sri Lanka?

    Directory of Open Access Journals (Sweden)

    Manjula Hettiarachchi

    2014-02-01

    Full Text Available Background: Individual variation of examination performance depends on many modifiable and non-modifiable factors, including pre-examination anxiety. Medical students’ quality of life (QoL and certain biochemical changes occurring while they are preparing for examinations has not been explored. Purpose: We hypothesize that these parameters would determine the examination performance among medical students. Methods: Fourth-year medical students (n=78 from the University of Ruhuna, Sri Lanka, were invited. Their pre- and post-exam status of QoL, using the World Health Organization Quality of Life (WHOQOL-BREF questionnaire, and the level of biochemical marker levels (i.e., serum levels of thyroid profile including thyroglobulin, cortisol and ferritin were assessed. Differences between the scores of QoL and serum parameters were compared with their performance at the examination. Results: The mean QoL score was significantly lower at pre-exam (56.19±8.1 when compared with post-exam (61.7±7.1 levels (p<0.001. The median serum TSH level prior to the exam (0.9 mIU/L; interquartile range 0.74–1.4 mIU/L was significantly lower (p=0.001 when compared with the level after the exam (median of 2.7 mIU/L; IQR 1.90–3.60. The mean±SD fT4 level was significantly higher before the exam (19.48±0.4 pmol/L at study entry vs. 17.43±0.3 pmol/L after the exam; p<0.001. Median serum ferritin (SF level prior to the exam (43.15 (23.5–63.3 µg/L was significantly lower (p≤0.001 when compared with after-exam status (72.36 (49.9–94.9 µg/L. However, there was no difference in mean serum cortisol levels (16.51±0.7 at pre-exam and 15.88±0.7 at post-exam, respectively; p=0.41. Conclusions: Students had higher fT4 and low ferritin levels on pre-exam biochemical assessment. It was evident that students who perform better at the examination had significantly higher QoL scores at each domain tested through the questionnaire (Physical health, Psychological

  10. Short-term incorporation of organic manures and biofertilizers influences biochemical and microbial characteristics of soils under an annual crop [Turmeric (Curcuma longa L.)].

    Science.gov (United States)

    Dinesh, R; Srinivasan, V; Hamza, S; Manjusha, A

    2010-06-01

    The study was conducted to determine whether short-term incorporation of organic manures and biofertilizers influence biochemical and microbial variables reflecting soil quality. For the study, soils were collected from a field experiment conducted on turmeric (Curcuma longa L.) involving organic nutrient management (ONM), chemical nutrient management (CNM) and integrated nutrient management (INM). The findings revealed that application of organic manures and biofertilizers (ONM and INM) positively influenced microbial biomass C, N mineralization, soil respiration and enzymes activities. Contrarily, greater metabolic quotient levels in CNM indicated a stressed soil microbial community. Principal component analysis indicated the strong relationship between microbial activity and the availability of labile and easily mineralizable organic matter. The findings imply that even short-term incorporation of organic manures and biofertilizers promoted soil microbial and enzyme activities and these parameters are sensitive enough to detect changes in soil quality due to short-term incorporation of biological fertilizers. (c) 2010 Elsevier Ltd. All rights reserved.

  11. Evaluating the connectivity of a protected areas' network under the prism of global change: the efficiency of the European Natura 2000 network for four birds of prey.

    Science.gov (United States)

    Mazaris, Antonios D; Papanikolaou, Alexandra D; Barbet-Massin, Morgane; Kallimanis, Athanasios S; Jiguet, Frédéric; Schmeller, Dirk S; Pantis, John D

    2013-01-01

    Climate and land use changes are major threats to biodiversity. To preserve biodiversity, networks of protected areas have been established worldwide, like the Natura 2000 network across the European Union (EU). Currently, this reserve network consists of more than 26000 sites covering more than 17% of EU terrestrial territory. Its efficiency to mitigate the detrimental effects of land use and climate change remains an open research question. Here, we examined the potential current and future geographical ranges of four birds of prey under scenarios of both land use and climate changes. By using graph theory, we examined how the current Natura 2000 network will perform in regard to the conservation of these species. This approach determines the importance of a site in regard to the total network and its connectivity. We found that sites becoming unsuitable due to climate change are not a random sample of the network, but are less connected and contribute less to the overall connectivity than the average site and thus their loss does not disrupt the full network. Hence, the connectivity of the remaining network changed only slightly from present day conditions. Our findings highlight the need to establish species-specific management plans with flexible conservation strategies ensuring protection under potential future range expansions. Aquila pomarina is predicted to disappear from the southern part of its range and to become restricted to northeastern Europe. Gyps fulvus, Aquila chrysaetos, and Neophron percnopterus are predicted to locally lose some suitable sites; hence, some isolated small populations may become extinct. However, their geographical range and metapopulation structure will remain relatively unaffected throughout Europe. These species would benefit more from an improved habitat quality and management of the existing network of protected areas than from increased connectivity or assisted migration.

  12. Priority Queue Based Reactive Buffer Management Policy for Delay Tolerant Network under City Based Environments

    Science.gov (United States)

    Ngadi, Asri; Rashid, Sulma; Habib, Hafiz Adnan

    2018-01-01

    Delay Tolerant Network (DTN) multi-copy routing protocols are privileged to create and transmit multiple copies of each message that causes congestion and some messages are dropped. This process is known as reactive drop because messages were dropped re-actively to overcome buffer overflows. The existing reactive buffer management policies apply a single metric to drop source, relay and destine messages. Hereby, selection to drop a message is dubious because each message as source, relay or destine may have consumed dissimilar magnitude of network resources. Similarly, DTN has included time to live (ttl) parameter which defines lifetime of message. Hence, when ttl expires then message is automatically destroyed from relay nodes. However, time-to-live (ttl) is not applicable on messages reached at their destinations. Moreover, nodes keep replicating messages till ttl expires even-though large number of messages has already been dispersed. In this paper, we have proposed Priority Queue Based Reactive Buffer Management Policy (PQB-R) for DTN under City Based Environments. The PQB-R classifies buffered messages into source, relay and destine queues. Moreover, separate drop metric has been applied on individual queue. The experiment results prove that proposed PQB-R has reduced number of messages transmissions, message drop and increases delivery ratio. PMID:29438438

  13. Time-Series Analyses of Transcriptomes and Proteomes Reveal Molecular Networks Underlying Oil Accumulation in Canola.

    Science.gov (United States)

    Wan, Huafang; Cui, Yixin; Ding, Yijuan; Mei, Jiaqin; Dong, Hongli; Zhang, Wenxin; Wu, Shiqi; Liang, Ying; Zhang, Chunyu; Li, Jiana; Xiong, Qing; Qian, Wei

    2016-01-01

    Understanding the regulation of lipid metabolism is vital for genetic engineering of canola ( Brassica napus L.) to increase oil yield or modify oil composition. We conducted time-series analyses of transcriptomes and proteomes to uncover the molecular networks associated with oil accumulation and dynamic changes in these networks in canola. The expression levels of genes and proteins were measured at 2, 4, 6, and 8 weeks after pollination (WAP). Our results show that the biosynthesis of fatty acids is a dominant cellular process from 2 to 6 WAP, while the degradation mainly happens after 6 WAP. We found that genes in almost every node of fatty acid synthesis pathway were significantly up-regulated during oil accumulation. Moreover, significant expression changes of two genes, acetyl-CoA carboxylase and acyl-ACP desaturase, were detected on both transcriptomic and proteomic levels. We confirmed the temporal expression patterns revealed by the transcriptomic analyses using quantitative real-time PCR experiments. The gene set association analysis show that the biosynthesis of fatty acids and unsaturated fatty acids are the most significant biological processes from 2-4 WAP and 4-6 WAP, respectively, which is consistent with the results of time-series analyses. These results not only provide insight into the mechanisms underlying lipid metabolism, but also reveal novel candidate genes that are worth further investigation for their values in the genetic engineering of canola.

  14. Priority Queue Based Reactive Buffer Management Policy for Delay Tolerant Network under City Based Environments.

    Directory of Open Access Journals (Sweden)

    Qaisar Ayub

    Full Text Available Delay Tolerant Network (DTN multi-copy routing protocols are privileged to create and transmit multiple copies of each message that causes congestion and some messages are dropped. This process is known as reactive drop because messages were dropped re-actively to overcome buffer overflows. The existing reactive buffer management policies apply a single metric to drop source, relay and destine messages. Hereby, selection to drop a message is dubious because each message as source, relay or destine may have consumed dissimilar magnitude of network resources. Similarly, DTN has included time to live (ttl parameter which defines lifetime of message. Hence, when ttl expires then message is automatically destroyed from relay nodes. However, time-to-live (ttl is not applicable on messages reached at their destinations. Moreover, nodes keep replicating messages till ttl expires even-though large number of messages has already been dispersed. In this paper, we have proposed Priority Queue Based Reactive Buffer Management Policy (PQB-R for DTN under City Based Environments. The PQB-R classifies buffered messages into source, relay and destine queues. Moreover, separate drop metric has been applied on individual queue. The experiment results prove that proposed PQB-R has reduced number of messages transmissions, message drop and increases delivery ratio.

  15. Intraspecific evolution of the intercellular signaling network underlying a robust developmental system.

    Science.gov (United States)

    Milloz, Josselin; Duveau, Fabien; Nuez, Isabelle; Félix, Marie-Anne

    2008-11-01

    Many biological systems produce an invariant output when faced with stochastic or environmental variation. This robustness of system output to variation affecting the underlying process may allow for "cryptic" genetic evolution within the system without change in output. We studied variation of cell fate patterning of Caenorhabditis elegans vulva precursors, a developmental system that relies on a simple intercellular signaling network and yields an invariant output of cell fates and lineages among C. elegans wild isolates. We first investigated the system's genetic variation in C. elegans by means of genetic tools and cell ablation to break down its buffering mechanisms. We uncovered distinct architectures of quantitative variation along the Ras signaling cascade, including compensatory variation, and differences in cell sensitivity to induction along the anteroposterior axis. In the unperturbed system, we further found variation between isolates in spatio-temporal dynamics of Ras pathway activity, which can explain the phenotypic differences revealed upon perturbation. Finally, the variation mostly affects the signaling pathways in a tissue-specific manner. We thus demonstrate and characterize microevolution of a developmental signaling network. In addition, our results suggest that the vulva genetic screens would have yielded a different mutation spectrum, especially for Wnt pathway mutations, had they been performed in another C. elegans genetic background.

  16. Network-constrained AC unit commitment under uncertainty: A Benders' decomposition approach

    DEFF Research Database (Denmark)

    Nasri, Amin; Kazempour, Seyyedjalal; Conejo, Antonio J.

    2015-01-01

    This paper proposes an efficient solution approach based on Benders’ decomposition to solve a network-constrained ac unit commitment problem under uncertainty. The wind power production is the only source of uncertainty considered in this paper, which is modeled through a suitable set of scenarios...... intractable, into a mixed-integer linear master problem and a set of nonlinear, but continuous subproblems, one per scenario. In addition, to temporally decompose the proposed ac unit commitment problem, a heuristic technique is used to relax the inter-temporal ramping constraints of the generating units....... Numerical results from a case study based on the IEEE one-area reliability test system (RTS) demonstrate the usefulness of the proposed approach...

  17. Exploring the genetics underlying autoimmune diseases with network analysis and link prediction

    KAUST Repository

    Alanis Lobato, Gregorio

    2014-02-01

    Ever since the first Genome Wide Association Study (GWAS) was carried out we have seen an important number of discoveries of biological and clinical relevance. However, there are some scientists that consider that these research outcomes and their utility are far from what was expected from this experimental design. We instead believe that the thousands of genetic variants associated with complex disorders by means of GWASs are an extremely valuable source of information that needs to be mined in a different way. Based on this philosophy, we followed a holistic perspective to analyze GWAS data and explored the structural properties of the network representation of one of these datasets with the aim to advance our understanding of the genetic intricacies underlying autoimmune human diseases. The simplicity, computational efficiency and precision of the tools proposed in this paper represent a new means to address GWAS data and contribute to the better exploitation of these rich sources of information. © 2014 IEEE.

  18. PREDICTION OF SITE RESPONSE SPECTRUM UNDER EARTHQUAKE VIBRATION USING AN OPTIMIZED DEVELOPED ARTIFICIAL NEURAL NETWORK MODEL

    Directory of Open Access Journals (Sweden)

    Reza Esmaeilabadi

    2016-06-01

    Full Text Available Site response spectrum is one of the key factors to determine the maximum acceleration and displacement, as well as structure behavior analysis during earthquake vibrations. The main objective of this paper is to develop an optimized model based on artificial neural network (ANN using five different training algorithms to predict nonlinear site response spectrum subjected to Silakhor earthquake vibrations is. The model output was tested for a specified area in west of Iran. The performance and quality of optimized model under all training algorithms have been examined by various statistical, analytical and graph analyses criteria as well as a comparison with numerical methods. The observed adaptabilities in results indicate a feasible and satisfactory engineering alternative method for predicting the analysis of nonlinear site response.

  19. The Performance Evaluation of an IEEE 802.11 Network Containing Misbehavior Nodes under Different Backoff Algorithms

    Directory of Open Access Journals (Sweden)

    Trong-Minh Hoang

    2017-01-01

    Full Text Available Security of any wireless network is always an important issue due to its serious impacts on network performance. Practically, the IEEE 802.11 medium access control can be violated by several native or smart attacks that result in downgrading network performance. In recent years, there are several studies using analytical model to analyze medium access control (MAC layer misbehavior issue to explore this problem but they have focused on binary exponential backoff only. Moreover, a practical condition such as the freezing backoff issue is not included in the previous models. Hence, this paper presents a novel analytical model of the IEEE 802.11 MAC to thoroughly understand impacts of misbehaving node on network throughput and delay parameters. Particularly, the model can express detailed backoff algorithms so that the evaluation of the network performance under some typical attacks through numerical simulation results would be easy.

  20. Biochemical and bioactive phytonutrients changes in tissues of two cultivars of fresh-cut cassava in stick form under refrigerated storage

    Directory of Open Access Journals (Sweden)

    Mateus da Silva Junqueira

    2014-07-01

    Full Text Available The aim of this study was to evaluate the effects of fresh-cut in stick form of two cassava cultivars on their biochemical and antioxidant characteristics, at two harvest times. The fresh cut cassava sticks were packaged in polypropylene, maintained at 5±1ºC, with 90±5% relative humidity for 12 days. The concentration of carotenoids, total soluble phenolic compounds and the activity of phenylalanine ammonia lyase and antioxidant capacity were significantly higher for the sticks of cultivar 'Amarela' cassava than for the sticks of cultivar 'Cacau'. The concentrations of carotenoids, total soluble phenolic compounds, and the activity of phenylalanine ammonia lyase and antioxidant capacity were all significantly greater when harvested at 14-month of age. There was a significant increase in the activity of phenylalanine ammonia lyase during the 12 days of storage at 5ºC. However, there was a decrease in total carotenoids, soluble phenolic compounds, and in the antioxidant capacity of the two cultivars.

  1. Radiation effect on pregnant rats receiving progesterone and Biochemical changes during pregnancy in rats under effect of gamma rays. Vol. 4

    International Nuclear Information System (INIS)

    Abdel-Wahab, M.F.; Abdel-Aziz, S.M.; Abdel-Gawad, I.I.

    1996-01-01

    The following terms were carried out to provide a comprehensive picture of the radiation induced biochemical changes in pregnant rats with and without progesterone injections. 1- serum total proteins. Animals irradiated on the third day and sacrificed on day 8, 14, 18, and 21 showed non-significant increase in serum total proteins on the day 8 of gestation in irradiated animals as compared to control animals, while on the other days serum total proteins increased significantly in irradiated animals compared to control animals. 2- serum total lipids. Animals irradiated on the third day of gestation and 8 th day all showed significant increase in serum total lipids with exception of those on the 14 th which showed nonsignificant change. Those on the 21 st showed a reverse effect of decrease. 3- serum progesterone. It is evident that animals irradiated on third day sacrificed on day 8, 14, 18, and 21 showed non-significant change in serum progesterone on the day 8, but on the other days it is significantly decreased compared to control levels. 4-Calcium. Animals irradiated on the third day and sacrificed on the 8 th day change in calcium level, others showed a significant decrease compared to control level. 8 figs., 2 tabs

  2. Genetic polymorphisms of antioxidant enzymes CAT and SOD affect the outcome of clinical, biochemical, and anthropometric variables in people with obesity under a dietary intervention.

    Science.gov (United States)

    Hernández-Guerrero, César; Parra-Carriedo, Alicia; Ruiz-de-Santiago, Diana; Galicia-Castillo, Oscar; Buenrostro-Jáuregui, Mario; Díaz-Gutiérrez, Carmen

    2018-01-01

    Genetic polymorphisms of antioxidant enzymes CAT, GPX, and SOD are involved in the etiology of obesity and its principal comorbidities. The aim of the present study was to analyze the effect of aforementioned SNPs over the output of several variables in people with obesity after a nutritional intervention. The study included 92 Mexican women, which received a dietary intervention by 3 months. Participants were genotyped and stratified into two groups: (1) carriers; mutated homozygous plus heterozygous (CR) and (2) homozygous wild type (WT). A comparison between CR and WT was done in clinical (CV), biochemical (BV), and anthropometric variables (AV), at the beginning and at the end of the intervention. Participants ( n  = 92) showed statistically significant differences ( p  T GPX1 (rs1050450), - 251A>G SOD1 (rs2070424), and - 262C>T CAT (rs1001179). (B) Only CR showed statistically changes ( p  T CAT (rs7943316) and 47C>T SOD2 (rs4880). The dietary intervention effect was statistically significantly between the polymorphisms of 47C>T SOD2 and BMI, SBP, TBARS, total cholesterol, and C-LCL ( p  T CAT (rs7943316) and SBP, DBP, total cholesterol, and atherogenic index ( p  CAT enzymes.

  3. Performance of a Cognitive Relay Network under AF Relay Selection Scheme with Imperfect Channel Estimation

    Directory of Open Access Journals (Sweden)

    B. Prasad

    2016-06-01

    Full Text Available In this paper outage performance of a secondary user (SU is evaluated under amplify and forward (AF relay selection scheme with an imperfect channel state information (CSIwhile sharing spectrum in an underlay cognitive radio network (CRN. In underlay, the SU coexists with primary user (PU in the same band provided the interference produced by SU at the PU receiver is below the interference threshold of PU which limits the transmission power of SU and coverage area. Relays help to improve the performance of SU in underlay. However relays are also constrained in transmit power due to interference constraint imposed by PU. Closed form expression of the outage probability of SU with maximum transmit power constraint of relay under imperfect CSI is derived. A scaling factor based power control is used for the SU transmitter and the relay in order to maintain the interference constraint at PU receiver due to imperfect CSI. The impact of different parameters viz. correlation coefficient, channel estimation error, tolerable interference threshold, number of relays and the maximum transmit power constraint of relay on SU performance is investigated. A MATLAB based test bed has also been developed to carry out simulation in order to validate the theoretical result.

  4. Design of real-time voice over internet protocol system under bandwidth network

    Science.gov (United States)

    Zhang, Li; Gong, Lina

    2017-04-01

    With the increasing bandwidth of the network and network convergence accelerating, VoIP means of communication across the network is becoming increasingly popular phenomenon. The real-time identification and analysis for VOIP flow over backbone network become the urgent needs and research hotspot of network operations management. Based on this, the paper proposes a VoIP business management system over backbone network. The system first filters VoIP data stream over backbone network and further resolves the call signaling information and media voice. The system can also be able to design appropriate rules to complete real-time reduction and presentation of specific categories of calls. Experimental results show that the system can parse and process real-time backbone of the VoIP call, and the results are presented accurately in the management interface, VoIP-based network traffic management and maintenance provide the necessary technical support.

  5. Coarse-grained simulation of a real-time process control network under peak load

    International Nuclear Information System (INIS)

    George, A.D.; Clapp, N.E. Jr.

    1992-01-01

    This paper presents a simulation study on the real-time process control network proposed for the new ANS reactor system at ORNL. A background discussion is provided on networks, modeling, and simulation, followed by an overview of the ANS process control network, its three peak-load models, and the results of a series of coarse-grained simulation studies carried out on these models using implementations of 802.3, 802.4, and 802.5 standard local area networks

  6. Networking Island Societies under Globalization The Case of the Pacific Islands

    OpenAIRE

    Kakazu, Hiroshi; 嘉数, 啓

    2006-01-01

    Network activities are particularly important in the context of small, remote island societies where the benefits from network externalities are greater than one might think. The intensity of networking depends on several factors including: geographical location, culture, socio-economic interdependence, political affiliations and information and communication technology (ICT), all which are examined in this paper. This paper has focused on external and internal networking of Okinawa's islands...

  7. Take it of leave it : Mechanisms underlying bacterial bistable regulatory networks

    NARCIS (Netherlands)

    Siebring, Jeroen; Sorg, Robin; Herber, Martijn; Kuipers, Oscar; Filloux, Alain A.M.

    2012-01-01

    Bistable switches occur in regulatory networks that can exist in two distinct stable states. Such networks allow distinct switching of individual cells. In bacteria these switches coexist with regulatory networks that respond gradually to environmental input. Bistable switches play key roles in high

  8. Hybrid optical CDMA-FSO communications network under spatially correlated gamma-gamma scintillation

    DEFF Research Database (Denmark)

    Jurado-Navas, Antonio; Raddo, Thiago R.; Garrido-Balsells, José María

    2016-01-01

    In this paper, we propose a new hybrid network solution based on asynchronous optical code-division multiple-access (OCDMA) and free-space optical (FSO) technologies for last-mile access networks, where fiber deployment is impractical. The architecture of the proposed hybrid OCDMA-FSO network is ...

  9. Functional MRI as a tool for investigating networks underlying the orienting reflex

    International Nuclear Information System (INIS)

    Lagopoulos, J.; Ward, P.B.; Rennie, C.; University of Sydney,; Williams, L.; Gordon, E.

    2001-01-01

    Full text: The 'Orienting Reflex' (OR) indexed by skin conductance response (SCR) is a physiological response to novel stimuli, orienting the organism to examine the stimulus in detail. The OR is also associated with lowering of thresholds in sensory-motor networks and preparation for action. The specific anatomical origins of the OR have long been speculated upon, and have primarily been derived from lesion studies on animals. Our group have developed a system to simultaneously acquire a measure of electrodermal orienting (SCR) with fMRI whilst the subject is undertaking an auditory oddball paradigm. The spatial and temporal resolution achievable with fMRI allows elucidation of the networks underlying the generation of ORs and their consequent inhibition with stimulus repetition. We tested five right handed healthy volunteers on an event related FMR paradigm using echoplanar MR images acquired on a 1.5T MRI scanner retrofitted with advanced NMR hardware using a standard head coil. The auditory oddball paradigm was delivered to the volunteers using a Silent Scan system with a button press response for target detection. SCR data was acquired simultaneously using an SCR device specifically designed for use in an MR environment. The significance (p<0.001)activation maps for the targets associated with an OR vs targets which did not elicit an OR, indicate a unilateral activation in the anterior thalamus, anterior cingulate gyrus and lateral orbitofrontal cortex. Target stimuli with no OR (versus background stimuli) revealed activations bilaterally in the supramarginal gyrus, the right thalamus and the anterior cingulate gyrus. Copyright (2001) Australian Neuroscience Society

  10. Transcriptional regulatory networks underlying the reprogramming of spermatogonial stem cells to multipotent stem cells.

    Science.gov (United States)

    Jeong, Hoe-Su; Bhin, Jinhyuk; Joon Kim, Hyung; Hwang, Daehee; Ryul Lee, Dong; Kim, Kye-Seong

    2017-04-14

    Spermatogonial stem cells (SSCs) are germline stem cells located along the basement membrane of seminiferous tubules in testes. Recently, SSCs were shown to be reprogrammed into multipotent SSCs (mSSCs). However, both the key factors and biological networks underlying this reprogramming remain elusive. Here, we present transcriptional regulatory networks (TRNs) that control cellular processes related to the SSC-to-mSSC reprogramming. Previously, we established intermediate SSCs (iSSCs) undergoing the transition to mSSCs and generated gene expression profiles of SSCs, iSSCs and mSSCs. By comparing these profiles, we identified 2643 genes that were up-regulated during the reprogramming process and 15 key transcription factors (TFs) that regulate these genes. Using the TF-target relationships, we developed TRNs describing how these TFs regulate three pluripotency-related processes (cell proliferation, stem cell maintenance and epigenetic regulation) during the reprogramming. The TRNs showed that 4 of the 15 TFs (Oct4/Pou5f1, Cux1, Zfp143 and E2f4) regulated cell proliferation during the early stages of reprogramming, whereas 11 TFs (Oct4/Pou5f1, Foxm1, Cux1, Zfp143, Trp53, E2f4, Esrrb, Nfyb, Nanog, Sox2 and Klf4) regulated the three pluripotency-related processes during the late stages of reprogramming. Our TRNs provide a model for the temporally coordinated transcriptional regulation of pluripotency-related processes during the SSC-to-mSSC reprogramming, which can be further tested in detailed functional studies.

  11. A risk analysis for gas transport network planning expansion under regulatory uncertainty in Western Europe

    International Nuclear Information System (INIS)

    Pelletier, C.; Wortmann, J.C.

    2009-01-01

    The natural gas industry in Western Europe went through drastic changes induced by the unbundling of the national companies, followed by the liberalization of gas trade and the regulation of gas transmission. Natural gas transmission is operated through a network of interconnected grids, and is capacity constrained. Each of the grids is locally regulated in terms of price limits on transportation services. Local tariff differences may induce unnatural gas routing within a network, creating congestion in some part of it. This phenomena is referred to as the Jepma effect. Following Jepma [2001. Gaslevering onder druk. Stichting JIN. Available at: (www.jiqweb.org) (52pp) (in Dutch)] this may lead to misguided investment decisions. In this paper a multi-stage linear program is used to simulate the repartition of the natural gas flow in an interconnected grid system on a succession of contracting periods. By this simulation, the risk linked to infrastructure investment is assessed. The risk measured can be seen as the probability of a negative present net value for the investment. The model is applied on an example of two grids that are on alternative routes serving same destinations. When applied to a specific situation of North-West Europe (Germany and The Netherlands), the model clearly demonstrates that the risks turn out to be too high to invest: there are hardly any scenarios under which an acceptable ROI will be realized. Given the current tariff policy and current publicly available forecasts of demand and supply, it is unlikely that market forces will attract additional investments in transportation capacity. This reluctance to invest can be prohibitive for further growth of supply if the demand would increase significantly

  12. Neural networks underlying language and social cognition during self-other processing in Autism spectrum disorders.

    Science.gov (United States)

    Kana, Rajesh K; Sartin, Emma B; Stevens, Carl; Deshpande, Hrishikesh D; Klein, Christopher; Klinger, Mark R; Klinger, Laura Grofer

    2017-07-28

    The social communication impairments defining autism spectrum disorders (ASD) may be built upon core deficits in perspective-taking, language processing, and self-other representation. Self-referential processing entails the ability to incorporate self-awareness, self-judgment, and self-memory in information processing. Very few studies have examined the neural bases of integrating self-other representation and semantic processing in individuals with ASD. The main objective of this functional MRI study is to examine the role of language and social brain networks in self-other processing in young adults with ASD. Nineteen high-functioning male adults with ASD and 19 age-sex-and-IQ-matched typically developing (TD) control participants made "yes" or "no" judgments of whether an adjective, presented visually, described them (self) or their favorite teacher (other). Both ASD and TD participants showed significantly increased activity in the medial prefrontal cortex (MPFC) during self and other processing relative to letter search. Analyses of group differences revealed significantly reduced activity in left inferior frontal gyrus (LIFG), and left inferior parietal lobule (LIPL) in ASD participants, relative to TD controls. ASD participants also showed significantly weaker functional connectivity of the anterior cingulate cortex (ACC) with several brain areas while processing self-related words. The LIFG and IPL are important regions functionally at the intersection of language and social roles; reduced recruitment of these regions in ASD participants may suggest poor level of semantic and social processing. In addition, poor connectivity of the ACC may suggest the difficulty in meeting the linguistic and social demands of this task in ASD. Overall, this study provides new evidence of the altered recruitment of the neural networks underlying language and social cognition in ASD. Published by Elsevier Ltd.

  13. Study Under AC Stimulation on Excitement Properties of Weighted Small-World Biological Neural Networks with Side-Restrain Mechanism

    International Nuclear Information System (INIS)

    Yuan Wujie; Luo Xiaoshu; Jiang Pinqun

    2007-01-01

    In this paper, we propose a new model of weighted small-world biological neural networks based on biophysical Hodgkin-Huxley neurons with side-restrain mechanism. Then we study excitement properties of the model under alternating current (AC) stimulation. The study shows that the excitement properties in the networks are preferably consistent with the behavior properties of a brain nervous system under different AC stimuli, such as refractory period and the brain neural excitement response induced by different intensities of noise and coupling. The results of the study have reference worthiness for the brain nerve electrophysiology and epistemological science.

  14. BIOCHEMICAL ATTRIBUTES OF TWO SAVANNAH SOILS UNDER DIFFERENT MANAGEMENT SYSTEMS AND USE ATRIBUTOS BIOQUÍMICOS EM DOIS SOLOS DE CERRADO SOB DIFERENTES SISTEMAS DE MANEJO E USO

    Directory of Open Access Journals (Sweden)

    Américo Nunes da Silveira Neto

    2008-11-01

    Full Text Available

    Soil biochemical attributes can be used as sensitive indicators of alterations promoted by the agricultural use, being a tool to guide tillage practices planning and evaluation to maintain soil sustainability. The objective of this study was to evaluate alterations in the soil organic carbon, biomass and microbial activity, urease and acid phosphatase activity, in two savannah soils, as affected by soil management systems. The study consisted of five soil management systems in a Typic Quartzipsamment, four in an Oxisol, and reference areas without alterations in the two soil types. The management systems changed the biochemical attributes of both soils. The Typic Quartzipsamment area under the soybean/Brachiaria decumbens sequence decreased the soil organic carbon and the microbial biomass carbon, and increased the respiration and qCO2, while the Oxisol, in all the areas, except for pasture, promoted reductions in the biochemical attributes. Among the management systems studied,  the pasture provided improvements in the evaluated attributes, in both soils.

    KEY-WORDS: Soil quality; microbial biomass; soil enzymatic activity.

  1. Ear Detection under Uncontrolled Conditions with Multiple Scale Faster Region-Based Convolutional Neural Networks

    Directory of Open Access Journals (Sweden)

    Yi Zhang

    2017-04-01

    Full Text Available Ear detection is an important step in ear recognition approaches. Most existing ear detection techniques are based on manually designing features or shallow learning algorithms. However, researchers found that the pose variation, occlusion, and imaging conditions provide a great challenge to the traditional ear detection methods under uncontrolled conditions. This paper proposes an efficient technique involving Multiple Scale Faster Region-based Convolutional Neural Networks (Faster R-CNN to detect ears from 2D profile images in natural images automatically. Firstly, three regions of different scales are detected to infer the information about the ear location context within the image. Then an ear region filtering approach is proposed to extract the correct ear region and eliminate the false positives automatically. In an experiment with a test set of 200 web images (with variable photographic conditions, 98% of ears were accurately detected. Experiments were likewise conducted on the Collection J2 of University of Notre Dame Biometrics Database (UND-J2 and University of Beira Interior Ear dataset (UBEAR, which contain large occlusion, scale, and pose variations. Detection rates of 100% and 98.22%, respectively, demonstrate the effectiveness of the proposed approach.

  2. Exome sequencing and network analysis identifies shared mechanisms underlying spinocerebellar ataxia.

    Science.gov (United States)

    Nibbeling, Esther A R; Duarri, Anna; Verschuuren-Bemelmans, Corien C; Fokkens, Michiel R; Karjalainen, Juha M; Smeets, Cleo J L M; de Boer-Bergsma, Jelkje J; van der Vries, Gerben; Dooijes, Dennis; Bampi, Giovana B; van Diemen, Cleo; Brunt, Ewout; Ippel, Elly; Kremer, Berry; Vlak, Monique; Adir, Noam; Wijmenga, Cisca; van de Warrenburg, Bart P C; Franke, Lude; Sinke, Richard J; Verbeek, Dineke S

    2017-11-01

    The autosomal dominant cerebellar ataxias, referred to as spinocerebellar ataxias in genetic nomenclature, are a rare group of progressive neurodegenerative disorders characterized by loss of balance and coordination. Despite the identification of numerous disease genes, a substantial number of cases still remain without a genetic diagnosis. Here, we report five novel spinocerebellar ataxia genes, FAT2, PLD3, KIF26B, EP300, and FAT1, identified through a combination of exome sequencing in genetically undiagnosed families and targeted resequencing of exome candidates in a cohort of singletons. We validated almost all genes genetically, assessed damaging effects of the gene variants in cell models and further consolidated a role for several of these genes in the aetiology of spinocerebellar ataxia through network analysis. Our work links spinocerebellar ataxia to alterations in synaptic transmission and transcription regulation, and identifies these as the main shared mechanisms underlying the genetically diverse spinocerebellar ataxia types. © The Author (2017). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  3. A neural network underlying intentional emotional facial expression in neurodegenerative disease.

    Science.gov (United States)

    Gola, Kelly A; Shany-Ur, Tal; Pressman, Peter; Sulman, Isa; Galeana, Eduardo; Paulsen, Hillary; Nguyen, Lauren; Wu, Teresa; Adhimoolam, Babu; Poorzand, Pardis; Miller, Bruce L; Rankin, Katherine P

    2017-01-01

    Intentional facial expression of emotion is critical to healthy social interactions. Patients with neurodegenerative disease, particularly those with right temporal or prefrontal atrophy, show dramatic socioemotional impairment. This was an exploratory study examining the neural and behavioral correlates of intentional facial expression of emotion in neurodegenerative disease patients and healthy controls. One hundred and thirty three participants (45 Alzheimer's disease, 16 behavioral variant frontotemporal dementia, 8 non-fluent primary progressive aphasia, 10 progressive supranuclear palsy, 11 right-temporal frontotemporal dementia, 9 semantic variant primary progressive aphasia patients and 34 healthy controls) were video recorded while imitating static images of emotional faces and producing emotional expressions based on verbal command; the accuracy of their expression was rated by blinded raters. Participants also underwent face-to-face socioemotional testing and informants described participants' typical socioemotional behavior. Patients' performance on emotion expression tasks was correlated with gray matter volume using voxel-based morphometry (VBM) across the entire sample. We found that intentional emotional imitation scores were related to fundamental socioemotional deficits; patients with known socioemotional deficits performed worse than controls on intentional emotion imitation; and intentional emotional expression predicted caregiver ratings of empathy and interpersonal warmth. Whole brain VBMs revealed a rightward cortical atrophy pattern homologous to the left lateralized speech production network was associated with intentional emotional imitation deficits. Results point to a possible neural mechanisms underlying complex socioemotional communication deficits in neurodegenerative disease patients.

  4. K Coverage Probability of 5G Wireless Cognitive Radio Network under Shadow Fading Effects

    Directory of Open Access Journals (Sweden)

    Ankur S. Kang

    2016-09-01

    Full Text Available Land mobile communication is burdened with typical propagation constraints due to the channel characteristics in radio systems.Also,the propagation characteristics vary form place to place and also as the mobile unit moves,from time to time.Hence,the tramsmission path between transmitter and receiver varies from simple direct LOS to the one which is severely obstructed by buildings,foliage and terrain.Multipath propagation and shadow fading effects affect the signal strength of an arbitrary Transmitter-Receiver due to the rapid fluctuations in the phase and amplitude of signal which also determines the average power over an area of tens or hundreds of meters.Shadowing introduces additional fluctuations,so the received local mean power varies around the area –mean.The present section deals with the performance analysis of fifth generation wireless cognitive radio network on the basis of signal and interference level based k coverage probability under the shadow fading effects.

  5. A hybrid solution approach for a multi-objective closed-loop logistics network under uncertainty

    Science.gov (United States)

    Mehrbod, Mehrdad; Tu, Nan; Miao, Lixin

    2015-06-01

    The design of closed-loop logistics (forward and reverse logistics) has attracted growing attention with the stringent pressures of customer expectations, environmental concerns and economic factors. This paper considers a multi-product, multi-period and multi-objective closed-loop logistics network model with regard to facility expansion as a facility location-allocation problem, which more closely approximates real-world conditions. A multi-objective mixed integer nonlinear programming formulation is linearized by defining new variables and adding new constraints to the model. By considering the aforementioned model under uncertainty, this paper develops a hybrid solution approach by combining an interactive fuzzy goal programming approach and robust counterpart optimization based on three well-known robust counterpart optimization formulations. Finally, this paper compares the results of the three formulations using different test scenarios and parameter-sensitive analysis in terms of the quality of the final solution, CPU time, the level of conservatism, the degree of closeness to the ideal solution, the degree of balance involved in developing a compromise solution, and satisfaction degree.

  6. The study of diffusion in network-forming liquids under pressure and temperature

    Energy Technology Data Exchange (ETDEWEB)

    Hung, P.K. [Department of Computational Physics, Hanoi University of Technology, 1Dai Co Viet, Hanoi (Viet Nam); Kien, P.H., E-mail: phkien80@gmail.com [Department of Physics, Thainguyen University of Education, 20 Luong Ngoc Quyen, Thainguyen (Viet Nam); San, L.T.; Hong, N.V. [Department of Computational Physics, Hanoi University of Technology, 1Dai Co Viet, Hanoi (Viet Nam)

    2016-11-15

    In this paper, the molecular dynamics simulation is applied to investigate the diffusion in silica liquids under different temperature and pressure. We show that the diffusion is controlled by the rate of effective SiO{sub x}→SiO{sub x±1} and OSi{sub y}→OSi{sub y±1} reaction. With increasing the pressure, the rate of reaction increases and the Si–O bond is weaker. Moreover, the reactions are not uniformly distributed in the space, but instead they happen frequently or rarely in separate regions. We also reveal two motion types: free and correlation motion. The correlation motion concerns the moving of a group of atoms which is similar to that of the diffusion of a super-molecule in the liquid. A detailed analysis of the movement of atoms from specified set shows the clustering of them which indicates structure and dynamics heterogeneity. Further, we find that the correlation motion is very important for the diffusion in network-forming liquid. The observed phenomena such as diffusion anomaly, dynamics heterogeneity and dynamical slowdown are originated from the correlation motion of atom.

  7. The study of diffusion in network-forming liquids under pressure and temperature

    International Nuclear Information System (INIS)

    Hung, P.K.; Kien, P.H.; San, L.T.; Hong, N.V.

    2016-01-01

    In this paper, the molecular dynamics simulation is applied to investigate the diffusion in silica liquids under different temperature and pressure. We show that the diffusion is controlled by the rate of effective SiO x →SiO x±1 and OSi y →OSi y±1 reaction. With increasing the pressure, the rate of reaction increases and the Si–O bond is weaker. Moreover, the reactions are not uniformly distributed in the space, but instead they happen frequently or rarely in separate regions. We also reveal two motion types: free and correlation motion. The correlation motion concerns the moving of a group of atoms which is similar to that of the diffusion of a super-molecule in the liquid. A detailed analysis of the movement of atoms from specified set shows the clustering of them which indicates structure and dynamics heterogeneity. Further, we find that the correlation motion is very important for the diffusion in network-forming liquid. The observed phenomena such as diffusion anomaly, dynamics heterogeneity and dynamical slowdown are originated from the correlation motion of atom.

  8. Macroporous Double-Network Hydrogel for High-Efficiency Solar Steam Generation Under 1 sun Illumination.

    Science.gov (United States)

    Yin, Xiangyu; Zhang, Yue; Guo, Qiuquan; Cai, Xiaobing; Xiao, Junfeng; Ding, Zhifeng; Yang, Jun

    2018-04-04

    Solar steam generation is one of the most promising solar-energy-harvesting technologies to address the issue of water shortage. Despite intensive efforts to develop high-efficiency solar steam generation devices, challenges remain in terms of the relatively low solar thermal efficiency, complicated fabrications, high cost, and difficulty in scaling up. Herein, a double-network hydrogel with a porous structure (p-PEGDA-PANi) is demonstrated for the first time as a flexible, recyclable, and efficient photothermal platform for low-cost and scalable solar steam generation. As a novel photothermal platform, the p-PEGDA-PANi involves all necessary properties of efficient broadband solar absorption, exceptional hydrophilicity, low heat conductivity, and porous structure for high-efficiency solar steam generation. As a result, the hydrogel-based solar steam generator exhibits a maximum solar thermal efficiency of 91.5% with an evaporation rate of 1.40 kg m -2 h -1 under 1 sun illumination, which is comparable to state-of-the-art solar steam generation devices. Furthermore, the good durability and environmental stability of the p-PEGDA-PANi hydrogel enables a convenient recycling and reusing process toward real-life applications. The present research not only provides a novel photothermal platform for solar energy harvest but also opens a new avenue for the application of the hydrogel materials in solar steam generation.

  9. Mesoporous Three-Dimensional Graphene Networks for Highly Efficient Solar Desalination under 1 sun Illumination.

    Science.gov (United States)

    Kim, Kwanghyun; Yu, Sunyoung; An, Cheolwon; Kim, Sung-Wook; Jang, Ji-Hyun

    2018-04-26

    Solar desalination via thermal evaporation of seawater is one of the most promising technologies for addressing the serious problem of global water scarcity because it does not require additional supporting energy other than infinite solar energy for generating clean water. However, low efficiency and a large amount of heat loss are considered critical limitations of solar desalination technology. The combination of mesoporous three-dimensional graphene networks (3DGNs) with a high solar absorption property and water-transporting wood pieces with a thermal insulation property has exhibited greatly enhanced solar-to-vapor conversion efficiency. 3DGN deposited on a wood piece provides an outstanding value of solar-to-vapor conversion efficiency, about 91.8%, under 1 sun illumination and excellent desalination efficiency of 5 orders salinity decrement. The mass-producible 3DGN enriched with many mesopores efficiently releases the vapors from an enormous area of the surface by heat localization on the top surface of the wood piece. Because the efficient solar desalination device made by 3DGN on the wood piece is highly scalable and inexpensive, it could serve as one of the main sources for the worldwide supply of purified water achieved via earth-abundant materials without an extra supporting energy source.

  10. Spontaneous default mode network phase-locking moderates performance perceptions under stereotype threat.

    Science.gov (United States)

    Forbes, Chad E; Leitner, Jordan B; Duran-Jordan, Kelly; Magerman, Adam B; Schmader, Toni; Allen, John J B

    2015-07-01

    This study assessed whether individual differences in self-oriented neural processing were associated with performance perceptions of minority students under stereotype threat. Resting electroencephalographic activity recorded in white and minority participants was used to predict later estimates of task errors and self-doubt on a presumed measure of intelligence. We assessed spontaneous phase-locking between dipole sources in left lateral parietal cortex (LPC), precuneus/posterior cingulate cortex (P/PCC), and medial prefrontal cortex (MPFC); three regions of the default mode network (DMN) that are integral for self-oriented processing. Results revealed that minorities with greater LPC-P/PCC phase-locking in the theta band reported more accurate error estimations. All individuals experienced less self-doubt to the extent they exhibited greater LPC-MPFC phase-locking in the alpha band but this effect was driven by minorities. Minorities also reported more self-doubt to the extent they overestimated errors. Findings reveal novel neural moderators of stereotype threat effects on subjective experience. Spontaneous synchronization between DMN regions may play a role in anticipatory coping mechanisms that buffer individuals from stereotype threat. © The Author (2014). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  11. Restorability on 3-connected WDM Networks Under Single and Dual Physical Link Failures

    DEFF Research Database (Denmark)

    Gutierrez Lopez, Jose Manuel; Jensen, Michael; Riaz, Tahir

    2013-01-01

    This work studies the influence the network interconnection has over restoration techniques. The way physical links are distributed to interconnect network nodes has a great impact on parameters such as path distances when failures occur and restoration is applied. The work focuses on single and ...... to network planning, the trade-off network length vs. performance of the different topological options is studied. The results show how 3-connected graphs could provide a reasonable trade-off between costs, link failure rates, and restored path parameters....

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

    Science.gov (United States)

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

    2016-03-01

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

  13. Book Review - V Pogoretskyy, Freedom of Transit and Access to Gas Pipeline Networks Under WTO Law (Cambridge University Press, 2017)

    NARCIS (Netherlands)

    Marhold, Anna

    2017-01-01

    In Freedom of Transit and Access to Pipeline Networks under WTO Law, the author appropriately introduces the topic by stating that energy is featuring increasingly prominently as a topic in international trade law. Indeed, while being a dormant issue in the World Trade Organization (“WTO” forum for

  14. Transformações bioquímicas de abacaxi minimamente processado armazenado sob atmosfera modificada Biochemical modifications of pineapple minimally processed under modified atmosphere

    Directory of Open Access Journals (Sweden)

    Mônica Elisabeth Torres Prado

    2004-12-01

    Full Text Available Realizou-se estudo sobre a influência da atmosfera modificada com diferentes concentrações de gases durante o armazenamento de abacaxi cv. Smooth cayennne minimamente processado, por oito dias, à temperatura de 5ºC e 85% de UR. Foram realizadas análises de açúcares neutros, celulose, hemicelulose e poliuronídeos totais na parede celular. O abacaxi minimamente processado foi acondicionado sob duas Atmosferas Modificadas Ativas, uma com 5% de O2 e 5% de CO2 (AM1,outra com 2% de O2 e 10% de CO2 (AM2,e uma Atmosfera Modificada Passiva (Controle durante 8 dias de armazenamento. O uso de atmosferas modificadas ativas permitiu que o abacaxi minimamente processado sofresse menor degradação da parede celular com menor solubilização das hemiceluloses. Abacaxis minimamente processados e armazenados sob atmosfera modificada obtiveram uma vida de prateleira média de 6 dias, a 5º C.Pineapples minimally processed were, stored eight days (5ºC and 85% RH under passive and active atmosphere (MA. Neutral sugars, cellulose, hemicellulose, and total polyuronide analysis in cell wall were done. Two different active MA were tested: 5% of O2 + 5% of CO2 (MA1 and 2% of O2 + 10% of CO2 (MA2 and one passive MA (Control; during eight days of storage. Pineapples minimally processed stored under active modified atmosphere showed degradation of cell wall and less solubilization of hemicelluloses, besides being more effective in control of ethanol production and formation of off flavours. Pineapples minimally processed stored under modified atmosphere, showed life average of 6 days under refrigeration at 5ºC.

  15. The Stochastic Evolutionary Game for a Population of Biological Networks Under Natural Selection

    Science.gov (United States)

    Chen, Bor-Sen; Ho, Shih-Ju

    2014-01-01

    In this study, a population of evolutionary biological networks is described by a stochastic dynamic system with intrinsic random parameter fluctuations due to genetic variations and external disturbances caused by environmental changes in the evolutionary process. Since information on environmental changes is unavailable and their occurrence is unpredictable, they can be considered as a game player with the potential to destroy phenotypic stability. The biological network needs to develop an evolutionary strategy to improve phenotypic stability as much as possible, so it can be considered as another game player in the evolutionary process, ie, a stochastic Nash game of minimizing the maximum network evolution level caused by the worst environmental disturbances. Based on the nonlinear stochastic evolutionary game strategy, we find that some genetic variations can be used in natural selection to construct negative feedback loops, efficiently improving network robustness. This provides larger genetic robustness as a buffer against neutral genetic variations, as well as larger environmental robustness to resist environmental disturbances and maintain a network phenotypic traits in the evolutionary process. In this situation, the robust phenotypic traits of stochastic biological networks can be more frequently selected by natural selection in evolution. However, if the harbored neutral genetic variations are accumulated to a sufficiently large degree, and environmental disturbances are strong enough that the network robustness can no longer confer enough genetic robustness and environmental robustness, then the phenotype robustness might break down. In this case, a network phenotypic trait may be pushed from one equilibrium point to another, changing the phenotypic trait and starting a new phase of network evolution through the hidden neutral genetic variations harbored in network robustness by adaptive evolution. Further, the proposed evolutionary game is extended to

  16. Model of Learning Organizational Development of Primary School Network under the Office of Basic Education Commission

    Science.gov (United States)

    Sai-rat, Wipa; Tesaputa, Kowat; Sriampai, Anan

    2015-01-01

    The objectives of this study were 1) to study the current state of and problems with the Learning Organization of the Primary School Network, 2) to develop a Learning Organization Model for the Primary School Network, and 3) to study the findings of analyses conducted using the developed Learning Organization Model to determine how to develop the…

  17. IMPROVED VIRTUAL CIRCUIT ROUTING ALGORITHM FOR WIRELESS SENSOR NETWORKS UNDER THE ASPECT OF POWER AWARENESS

    Directory of Open Access Journals (Sweden)

    Abid Ali Minhas

    2006-06-01

    Full Text Available Routing algorithms have shown their importance in the power aware wireless micro-sensor networks. In this paper first we present virtual circuit algorithm (VCRA, a routing algorithm for wireless sensor networks. We analyze the power utilized by nodes to lengthen the battery life and thus improving the lifetime of wireless sensor network. We discuss VCRA in comparison with the Multihoprouter, an algorithm developed by UC Berkeley. Then we present Improved Virtual Circuit Routing Algorithm (IVCRA which is an improved form of VCRA. In IVCRA node failure detection and path repairing scheme has been implemented. We also present the energy analysis of IVCRA and prove that IVCRA is the best choice. We first implement our routing algorithms in simulator TOSSIM and then on real hardware of mica2 mote-sensor network platform and prove the reliable routing of the data packets from different nodes to the base station. The motes used as nodes in our mote-sensor network are from Berkeley USA. By using simulator POWERTOSSIM, we estimate and present the energy utilized by different nodes of the network. At the end we present a comparison of our work with the network layer of Zigbee/IEEE 802.15.4, which is an emerging standard for wireless sensor networks and then compare its energy efficiency with the packet size chosen for our algorithm.

  18. Transgenic Peanut (Arachis hypogaeaL.) OverexpressingmtlDGene Showed Improved Photosynthetic, Physio-Biochemical, and Yield-Parameters under Soil-Moisture Deficit Stress in Lysimeter System.

    Science.gov (United States)

    Patel, Kirankumar G; Thankappan, Radhakrishnan; Mishra, Gyan P; Mandaliya, Viralkumar B; Kumar, Abhay; Dobaria, Jentibhai R

    2017-01-01

    Peanut, an important oilseed crop, frequently encounters drought stress (DS) during its life cycle. In this study, four previously developed mtlD transgenic (T) peanut lines were used for detailed characterization under DS, at the reproductive stage using lysimeter system under controlled greenhouse conditions. In dry-down experiments, T lines maintained better photosynthetic machinery, such as, photosynthesis rate, stomatal conductance, transpiration rate, and SPAD (Soil-Plant Analyses Development) values, and had lower oxidative damage, including lipid membrane peroxidation and hydrogen peroxide and superoxide radical accumulation than WT, when exposed to 24 days of DS. WT plants had a more negative water potential (WP; up to -3.22 MPa) than T lines did (-2.56 to -2.71 MPa) at day 24 of DS treatment. During recovery, T lines recovered easily whereas 67% of WT plants failed to recover. In T lines, the rate of photosynthesis strongly and positively correlated with the transpiration rate ( r = 0.92), RWC ( r = 0.90), WP ( r = 0.86), and total chlorophyll content ( r = 0.75), suggesting its strong correlation with water retention-related parameters. Furthermore, yield parameters such as, pod weight and harvest index of T lines were up to 2.19 and 1.38 times more than those of WT plants, respectively. Thus, the significantly better performance of mtlD T peanut lines than of WT plants under DS could be attributed to the accumulation of mannitol, which in turn helped in maintaining the osmoregulation and ROS scavenging activity of mannitol and ultimately conferred water-economizing capacity and higher yield in T lines than in WT plants.

  19. Modelling the public opinion transmission on social networks under opinion leaders

    Science.gov (United States)

    Li, Zuozhi; Li, Meng; Ji, Wanwan

    2017-06-01

    In this paper, based on Social Network Analysis (SNA), the social network model of opinion leaders influencing the public opinion transmission is explored. The hot event, A Female Driver Was Beaten Due To Lane Change, has characteristics of individual short-term and non-government intervention, which is used to data extraction, and formed of the network structure on opinion leaders influencing the public opinion transmission. And the evolution mechanism are analyzed in the three evolutionary situations. Opinion leaders influence micro-blogging public opinion on social network evolution model shows that this type of network public opinion transmission is largely constrained by opinion leaders, so the opinion leaders behavior supervising on the spread of this public opinion is pivotal, and which has a guiding significance.

  20. A Regularizer Approach for RBF Networks Under the Concurrent Weight Failure Situation.

    Science.gov (United States)

    Leung, Chi-Sing; Wan, Wai Yan; Feng, Ruibin

    2017-06-01

    Many existing results on fault-tolerant algorithms focus on the single fault source situation, where a trained network is affected by one kind of weight failure. In fact, a trained network may be affected by multiple kinds of weight failure. This paper first studies how the open weight fault and the multiplicative weight noise degrade the performance of radial basis function (RBF) networks. Afterward, we define the objective function for training fault-tolerant RBF networks. Based on the objective function, we then develop two learning algorithms, one batch mode and one online mode. Besides, the convergent conditions of our online algorithm are investigated. Finally, we develop a formula to estimate the test set error of faulty networks trained from our approach. This formula helps us to optimize some tuning parameters, such as RBF width.

  1. Overview of DFIG-based Wind Power System Resonances under Weak Networks

    DEFF Research Database (Denmark)

    Song, Yipeng; Blaabjerg, Frede

    2017-01-01

    The wind power generation techniques are continuing to develop and increasing numbers of Doubly Fed Induction Generator (DFIG)-based wind power systems are connecting to the on-shore and off-shore grids, local standalone weak networks, and also micro grid applications. The impedances of the weak...... weak network respectively. This paper will discuss the SSR and the HFR phenomena based on the impedance modeling of the DFIG system and the weak networks, and the cause of these two resonances will be explained in details. The following factors including 1) transformer configuration; 2) different power...... networks are too large to be neglected and require careful attention. Due to the impedance interaction between the weak network and the DFIG system, both Sub- Synchronous Resonance (SSR) and High Frequency Resonance (HFR) may occur when the DFIG system is connected to the series or parallel compensated...

  2. Sustained enhancement of photosynthesis in coffee trees grown under free-air CO2 enrichment conditions: disentangling the contributions of stomatal, mesophyll, and biochemical limitations

    Science.gov (United States)

    DaMatta, Fábio M.; Godoy, Alice G.; Menezes-Silva, Paulo E.; Martins, Samuel C.V.; Sanglard, Lílian M.V.P.; Morais, Leandro E.; Torre-Neto, André; Ghini, Raquel

    2016-01-01

    Coffee (Coffea spp.), a globally traded commodity, is a slow-growing tropical tree species that displays an improved photosynthetic performance when grown under elevated atmospheric CO2 concentrations ([CO2]). To investigate the mechanisms underlying this response, two commercial coffee cultivars (Catuaí and Obatã) were grown using the first free-air CO2 enrichment (FACE) facility in Latin America. Measurements were conducted in two contrasting growth seasons, which were characterized by the high (February) and low (August) sink demand. Elevated [CO2] led to increases in net photosynthetic rates (A) in parallel with decreased photorespiration rates, with no photochemical limitations to A. The stimulation of A by elevated CO2 supply was more prominent in August (56% on average) than in February (40% on average). Overall, the stomatal and mesophyll conductances, as well as the leaf nitrogen and phosphorus concentrations, were unresponsive to the treatments. Photosynthesis was strongly limited by diffusional constraints, particularly at the stomata level, and this pattern was little, if at all, affected by elevated [CO2]. Relative to February, starch pools (but not soluble sugars) increased remarkably (>500%) in August, with no detectable alteration in the maximum carboxylation capacity estimated on a chloroplast [CO2] basis. Upregulation of A by elevated [CO2] took place with no signs of photosynthetic downregulation, even during the period of low sink demand, when acclimation would be expected to be greatest. PMID:26503540

  3. Neural network underlying ictal pouting ("chapeau de gendarme") in frontal lobe epilepsy.

    Science.gov (United States)

    Souirti, Zouhayr; Landré, Elisabeth; Mellerio, Charles; Devaux, Bertrand; Chassoux, Francine

    2014-08-01

    In order to determine the anatomical neural network underlying ictal pouting (IP), with the mouth turned down like a "chapeau de gendarme", in frontal lobe epilepsy (FLE), we reviewed the video-EEG recordings of 36 patients with FLE who became seizure-free after surgery. We selected the cases presenting IP, defined as a symmetrical and sustained (>5s) lowering of labial commissures with contraction of chin, mimicking an expression of fear, disgust, or menace. Ictal pouting was identified in 11 patients (8 males; 16-48 years old). We analyzed the clinical semiology, imaging, and electrophysiological data associated with IP, including FDG-PET in 10 and SEEG in 9 cases. In 37 analyzed seizures (2-7/patient), IP was an early symptom, occurring during the first 10s in 9 cases. The main associated features consisted of fear, anguish, vegetative disturbances, behavioral disorders (sudden agitation, insults, and fighting), tonic posturing, and complex motor activities. The epileptogenic zone assessed by SEEG involved the mesial frontal areas, especially the anterior cingulate cortex (ACC) in 8 patients, whereas lateral frontal onset with an early spread to the ACC was seen in the other patient. Ictal pouting associated with emotional changes and hypermotor behavior had high localizing value for rostroventral "affective" ACC, whereas less intense facial expressions were related to the dorsal "cognitive" ACC. Fluorodeoxyglucose positron emission tomography demonstrated the involvement of both the ACC and lateral cortex including the anterior insula in all cases. We propose that IP is sustained by reciprocal mesial and lateral frontal interactions involved in emotional and cognitive processes, in which the ACC plays a pivotal role. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Learning Physics-based Models in Hydrology under the Framework of Generative Adversarial Networks

    Science.gov (United States)

    Karpatne, A.; Kumar, V.

    2017-12-01

    Generative adversarial networks (GANs), that have been highly successful in a number of applications involving large volumes of labeled and unlabeled data such as computer vision, offer huge potential for modeling the dynamics of physical processes that have been traditionally studied using simulations of physics-based models. While conventional physics-based models use labeled samples of input/output variables for model calibration (estimating the right parametric forms of relationships between variables) or data assimilation (identifying the most likely sequence of system states in dynamical systems), there is a greater opportunity to explore the full power of machine learning (ML) methods (e.g, GANs) for studying physical processes currently suffering from large knowledge gaps, e.g. ground-water flow. However, success in this endeavor requires a principled way of combining the strengths of ML methods with physics-based numerical models that are founded on a wealth of scientific knowledge. This is especially important in scientific domains like hydrology where the number of data samples is small (relative to Internet-scale applications such as image recognition where machine learning methods has found great success), and the physical relationships are complex (high-dimensional) and non-stationary. We will present a series of methods for guiding the learning of GANs using physics-based models, e.g., by using the outputs of physics-based models as input data to the generator-learner framework, and by using physics-based models as generators trained using validation data in the adversarial learning framework. These methods are being developed under the broad paradigm of theory-guided data science that we are developing to integrate scientific knowledge with data science methods for accelerating scientific discovery.

  5. Neural network remodeling underlying motor map reorganization induced by rehabilitative training after ischemic stroke.

    Science.gov (United States)

    Okabe, Naohiko; Shiromoto, Takashi; Himi, Naoyuki; Lu, Feng; Maruyama-Nakamura, Emi; Narita, Kazuhiko; Iwachidou, Nobuhisa; Yagita, Yoshiki; Miyamoto, Osamu

    2016-12-17

    Motor map reorganization is believed to be one mechanism underlying rehabilitation-induced functional recovery. Although the ipsilesional secondary motor area has been known to reorganize motor maps and contribute to rehabilitation-induced functional recovery, it is unknown how the secondary motor area is reorganized by rehabilitative training. In the present study, using skilled forelimb reaching tasks, we investigated neural network remodeling in the rat rostral forelimb area (RFA) of the secondary motor area during 4weeks of rehabilitative training. Following photothrombotic stroke in the caudal forelimb area (CFA), rehabilitative training led to task-specific recovery and motor map reorganization in the RFA. A second injury to the RFA resulted in reappearance of motor deficits. Further, when both the CFA and RFA were destroyed simultaneously, rehabilitative training no longer improved task-specific recovery. In neural tracer studies, although rehabilitative training did not alter neural projection to the RFA from other brain areas, rehabilitative training increased neural projection from the RFA to the lower spinal cord, which innervates the muscles in the forelimb. Double retrograde tracer studies revealed that rehabilitative training increased the neurons projecting from the RFA to both the upper cervical cord, which innervates the muscles in the neck, trunk, and part of the proximal forelimb, and the lower cervical cord. These results suggest that neurons projecting to the upper cervical cord provide new connections to the denervated forelimb area of the spinal cord, and these new connections may contribute to rehabilitation-induced task-specific recovery and motor map reorganization in the secondary motor area. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

  6. Insights into the mechanisms underlying mercury-induced oxidative stress in gills of wild fish (Liza aurata) combining {sup 1}H NMR metabolomics and conventional biochemical assays

    Energy Technology Data Exchange (ETDEWEB)

    Cappello, Tiziana, E-mail: tcappello@unime.it [Department of Biological and Environmental Sciences, University of Messina, 98166 Messina (Italy); Brandão, Fátima, E-mail: fatimabrandao@ua.pt [Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro (Portugal); Guilherme, Sofia; Santos, Maria Ana [Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro (Portugal); Maisano, Maria; Mauceri, Angela [Department of Biological and Environmental Sciences, University of Messina, 98166 Messina (Italy); Canário, João [Centro de Química Estrutural, Instítuto Superíor Técnico, Universidade de Lisboa, 1049-001 Lisbon (Portugal); Pacheco, Mário; Pereira, Patrícia [Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro (Portugal)

    2016-04-01

    Oxidative stress has been described as a key pathway to initiate mercury (Hg) toxicity in fish. However, the mechanisms underlying Hg-induced oxidative stress in fish still need to be clarified. To this aim, environmental metabolomics in combination with a battery of conventional oxidative stress biomarkers were applied to the gills of golden grey mullet (Liza aurata) collected from Largo do Laranjo (LAR), a confined Hg contaminated area, and São Jacinto (SJ), selected as reference site (Aveiro Lagoon, Portugal). Higher accumulation of inorganic Hg and methylmercury was found in gills of fish from LAR relative to SJ. Nuclear magnetic resonance (NMR)-based metabolomics revealed changes in metabolites related to antioxidant protection, namely depletion of reduced glutathione (GSH) and its constituent amino acids, glutamate and glycine. The interference of Hg with the antioxidant protection of gills was corroborated through oxidative stress endpoints, namely the depletion of glutathione peroxidase and superoxide dismutase activities at LAR. The increase of total glutathione content (reduced glutathione + oxidized glutathione) at LAR, in parallel with GSH depletion aforementioned, indicates the occurrence of massive GSH oxidation under Hg stress, and an inability to carry out its regeneration (glutathione reductase activity was unaltered) or de novo synthesis. Nevertheless, the results suggest the occurrence of alternative mechanisms for preventing lipid peroxidative damage, which may be associated with the enhancement of membrane stabilization/repair processes resulting from depletion in the precursors of phosphatidylcholine (phosphocholine and glycerophosphocholine), as highlighted by NMR spectroscopy. However, the observed decrease in taurine may be attributable to alterations in the structure of cell membranes or interference in osmoregulatory processes. Overall, the novel concurrent use of metabolomics and conventional oxidative stress endpoints demonstrated to

  7. The effects of different levels of Chlorella microalgae on blood biochemical parameters and trace mineral concentrations of laying hens reared under heat stress condition

    Science.gov (United States)

    Moradi kor, Nasroallah; Akbari, Mohsen; Olfati, Ali

    2016-05-01

    This study was conducted to investigate the effect of different supplementation levels of Chlorella microalgae on serum metabolites and the plasma content of minerals in laying hens reared under heat stress condition (27.5-36.7 °C, variable). A total number of 378 (40 weeks of age, with mean body weight of 1390 ± 120 g) were randomly allocated to six treatments with seven replicates. The birds were randomly assigned to 6 treatments (C, T1, T2, T3, T4, and T5) with 7 replicate cages of 9 birds. C. microalgae at the rates of 100, 200, 300, 400, and 500 ppm with water were offered to groups T1, T2, T3, T4, and T5, respectively, while group C served as a control. At 71 days of trial, blood samples (14 samples per treatment) were taken for measuring serum metabolites and at 72 days for plasma mineral analysis. The results of this experiment showed that the supplementation of 200-500 ppm C. microalgae decreased the serum content of cholesterol, triglycerides, and LDL ( P < 0.05) whereas HDL content increased ( P < 0.05) in the hens supplemented with C. microalgae (300 or 400 and 500 ppm). C. microalgae at rates of 300-500 ppm caused a marked ( P < 0.05) increase in the plasma content of manganese or iodine and selenium but other minerals were not statistically different among treatments. Overall, from the results of the present experiment, it can be concluded that supplementation of C. microalgae at high rates was beneficial on blood parameters of laying hens reared under heat stress.

  8. Signal or noise: brain network interactions underlying the experience and training of mindfulness.

    Science.gov (United States)

    Mooneyham, Benjamin W; Mrazek, Michael D; Mrazek, Alissa J; Schooler, Jonathan W

    2016-04-01

    A broad set of brain regions has been associated with the experience and training of mindfulness. Many of these regions lie within key intrinsic brain networks, including the executive control, salience, and default networks. In this paper, we review the existing literature on the cognitive neuroscience of mindfulness through the lens of network science. We describe the characteristics of the intrinsic brain networks implicated in mindfulness and summarize the relevant findings pertaining to changes in functional connectivity (FC) within and between these networks. Convergence across these findings suggests that mindfulness may be associated with increased FC between two regions within the default network: the posterior cingulate cortex and the ventromedial prefrontal cortex. Additionally, extensive meditation experience may be associated with increased FC between the insula and the dorsolateral prefrontal cortex. However, little consensus has emerged within the existing literature owing to the diversity of operational definitions of mindfulness, neuroimaging methods, and network characterizations. We describe several challenges to develop a coherent cognitive neuroscience of mindfulness and to provide detailed recommendations for future research. © 2016 New York Academy of Sciences.

  9. A Simple Approach to Study Designs in Complex Biochemical ...

    Indian Academy of Sciences (India)

    Somdatta Sinha

    Protein sequences. • Biochemical & Genetic information. REVERSE ENGINEERING. LARGE NETWORKS. FORWARD ENGINEERING. All designs that are not physically forbidden are realizable, but not all realizable designs are functionally effective. (in relation to context and constraints of the system and environment).

  10. Near-optimal Downlink precoding of a MISO system for a secondary network under the SINR constraints of a primary network

    KAUST Repository

    Park, Kihong

    2013-04-01

    In this paper, we study a multiple-input single-output cognitive radio (CR) system where only the primary base station (BS) has multiple antennas. We consider a rate maximization problem of the secondary network under signal-to-interference-plus-noise-ratio constraints on the primary network in order to guarantee the quality-of-service for the latter network. While the interference due to the secondary transmission in the conventional underlay CR approach may severely degrade the performance of the primary network, we propose a primary BS-aided approach in which the primary BS helps relay the secondary users\\' signals instead of allowing them to communicate with each other via a direct path between them. In addition, an algorithm to find a near-optimal beamforming solution at the primary BS is proposed. Finally, based on some selected numerical results, we show that the proposed scheme outperforms the conventional underlay CR configuration over a wide transmit power range. © 2013 IEEE.

  11. Using Nonlinear Stochastic Evolutionary Game Strategy to Model an Evolutionary Biological Network of Organ Carcinogenesis Under a Natural Selection Scheme.

    Science.gov (United States)

    Chen, Bor-Sen; Tsai, Kun-Wei; Li, Cheng-Wei

    2015-01-01

    -associated cell network takes 54.5 years from a normal state to stage I cancer, 1.5 years from stage I to stage II cancer, and 2.5 years from stage II to stage III cancer, with a reasonable match for the statistical result of the average age of lung cancer. These results suggest that a robust negative feedback scheme, based on a stochastic evolutionary game strategy, plays a critical role in an evolutionary biological network of carcinogenesis under a natural selection scheme.

  12. Effect of priming on growth, biochemical parameters and mineral composition of different cultivars of coriander (Coriandrum sativum L. under salt stress

    Directory of Open Access Journals (Sweden)

    Ben Fredj Meriem

    2014-08-01

    Full Text Available At Higher Institute of Agriculture of Chott Mariem, Sousse, Tunisia, this study was conducted to evaluate the interactive effect of salinity and seed priming on coriander. The experiment was carried out in completely randomized design with three replications consisting of four coriander genotypes (Tunisian cv, Algerian cv, Syrian cv and Egyptian cv at two seed conditions (seed priming with 4 g/l NaCl for 12h or no seed priming. Results revealed that seed priming and salinity had significantly (p≤0.05 affected all the parameters under study. On the first hand, salinity stress had adversely affected growth, chlorophyll content, mineral composition (K+ and Ca2+ of coriander in all genotypes. Also, it activated Na+ accumulation and synthesis of proline, soluble sugars and proteins. However, seed priming with NaCl had diminished the negative impact of salt stress in all cultivars and primed plants showed better response to salinity compared to unprimed plants. Maximum values were recorded in tolerant cultivar which is Tunisian one whereas minimum values were noted in sensitive cultivar (Algerian cv.

  13. Multi-operator collaboration for green cellular networks under roaming price consideration

    KAUST Repository

    Ghazzai, Hakim

    2014-09-01

    This paper investigates the collaboration between multiple mobile operators to optimize the energy efficiency of cellular networks. Our framework studies the case of LTE-Advanced networks deployed in the same area and owning renewable energy generators. The objective is to reduce the CO2 emissions of cellular networks via collaborative techniques and using base station sleeping strategy while respecting the network quality of service. Low complexity and practical algorithm is employed to achieve green goals during low traffic periods. Cooperation decision criteria are also established basing on derived roaming prices and profit gains of competitive mobile operators. Our numerical results show a significant save in terms of CO2 compared to the non-collaboration case and that cooperative mobile operator exploiting renewables are more awarded than traditional operators.

  14. Hybrid optical CDMA-FSO communications network under spatially correlated gamma-gamma scintillation.

    Science.gov (United States)

    Jurado-Navas, Antonio; Raddo, Thiago R; Garrido-Balsells, José María; Borges, Ben-Hur V; Olmos, Juan José Vegas; Monroy, Idelfonso Tafur

    2016-07-25

    In this paper, we propose a new hybrid network solution based on asynchronous optical code-division multiple-access (OCDMA) and free-space optical (FSO) technologies for last-mile access networks, where fiber deployment is impractical. The architecture of the proposed hybrid OCDMA-FSO network is thoroughly described. The users access the network in a fully asynchronous manner by means of assigned fast frequency hopping (FFH)-based codes. In the FSO receiver, an equal gain-combining technique is employed along with intensity modulation and direct detection. New analytical formalisms for evaluating the average bit error rate (ABER) performance are also proposed. These formalisms, based on the spatially correlated gamma-gamma statistical model, are derived considering three distinct scenarios, namely, uncorrelated, totally correlated, and partially correlated channels. Numerical results show that users can successfully achieve error-free ABER levels for the three scenarios considered as long as forward error correction (FEC) algorithms are employed. Therefore, OCDMA-FSO networks can be a prospective alternative to deliver high-speed communication services to access networks with deficient fiber infrastructure.

  15. Task-related changes in functional properties of the human brain network underlying attentional control.

    Directory of Open Access Journals (Sweden)

    Tetsuo Kida

    Full Text Available Previous studies have demonstrated task-related changes in brain activation and inter-regional connectivity but the temporal dynamics of functional properties of the brain during task execution is still unclear. In the present study, we investigated task-related changes in functional properties of the human brain network by applying graph-theoretical analysis to magnetoencephalography (MEG. Subjects performed a cue-target attention task in which a visual cue informed them of the direction of focus for incoming auditory or tactile target stimuli, but not the sensory modality. We analyzed the MEG signal in the cue-target interval to examine network properties during attentional control. Cluster-based non-parametric permutation tests with the Monte-Carlo method showed that in the cue-target interval, beta activity was desynchronized in the sensori-motor region including premotor and posterior parietal regions in the hemisphere contralateral to the attended side. Graph-theoretical analysis revealed that, in beta frequency, global hubs were found around the sensori-motor and prefrontal regions, and functional segregation over the entire network was decreased during attentional control compared to the baseline. Thus, network measures revealed task-related temporal changes in functional properties of the human brain network, leading to the understanding of how the brain dynamically responds to task execution as a network.

  16. Flexible investment under uncertainty in smart distribution networks with demand side response: Assessment framework and practical implementation

    International Nuclear Information System (INIS)

    Schachter, Jonathan A.; Mancarella, Pierluigi; Moriarty, John; Shaw, Rita

    2016-01-01

    Classical deterministic models applied to investment valuation in distribution networks may not be adequate for a range of real-world decision-making scenarios as they effectively ignore the uncertainty found in the most important variables driving network planning (e.g., load growth). As greater uncertainty is expected from growing distributed energy resources in distribution networks, there is an increasing risk of investing in too much or too little network capacity and hence causing the stranding and inefficient use of network assets; these costs are then passed on to the end-user. An alternative emerging solution in the context of smart grid development is to release untapped network capacity through Demand-Side Response (DSR). However, to date there is no approach able to quantify the value of ‘smart’ DSR solutions against ‘conventional’ asset-heavy investments. On these premises, this paper presents a general real options framework and a novel probabilistic tool for the economic assessment of DSR for smart distribution network planning under uncertainty, which allows the modeling and comparison of multiple investment strategies, including DSR and capacity reinforcements, based on different cost and risk metrics. In particular the model provides an explicit quantification of the economic value of DSR against alternative investment strategies. Through sensitivity analysis it is able to indicate the maximum price payable for DSR service such that DSR remains economically optimal against these alternatives. The proposed model thus provides Regulators with clear insights for overseeing DSR contractual arrangements. Further it highlights that differences exist in the economic perspective of the regulated DNO business and of customers. Our proposed model is therefore capable of highlighting instances where a particular investment strategy is favorable to the DNO but not to its customers, or vice-versa, and thus aspects of the regulatory framework which may

  17. Long-term evolution of hillslopes and drainage networks under repeated impact of glacial erosion

    Science.gov (United States)

    Salcher, Bernhard; Baumann, Sebastian; Kober, Florian; Robl, Jörg

    2015-04-01

    The morphology of hillslopes is an important indicator of landscape change and erosion. In nonglacial catchments, its characteristics depend to a large extent on channel processes and are a function of climate, tectonic and underlying bedrock. These factors may however become secondary when affected by glacial erosion as it is the case in many mid- to high-latitude mountain belts. The perturbation of the initial steady state hillslope morphology (where uplift is balanced by surface lowering rates) will tend to become successively larger if the repeated action of glacial processes exceeds the potential of fluvial readjustment during deglaciated periods. In the limiting case that fluvial or colluvial readjustments to the topography are smaller than modifications by glacial action, the history of glacial erosion rate may be faithfully archived in the form of hillslopes and the channel network (Salcher et al., 2014). This relation is furthermore important as significant mass is generally mobilized and eroded in the hillslope domain delivering material to the channel system. Here we analyzed the glacially modified topography of the European Central Alps, a region which has been multiply glaciated during the Quaternary and were tectonic processes have largely ceased. The higher elevated catchments suffered a more intense impact of glacial erosion than lower elevated catchments whereas fluvial (steady state) processes dominate the alpine foothills or regions outside the former ice sheets. To investigate variations to the hillslope domain we utilized digital elevation models to define hillslope parameters (area, length relief) as function of channel head locations. Channel heads are then calculated as a function of minimum channel plan curvature. Our results show that hillslope area, relief and length increases with the cumulative impact of glacial action. This relation is however only valid were individual tributary glaciers and associated headward erosion could evolve

  18. Estimating the Theoretical Value for LAN Network Throughput Based Power Line Communications Technology Under the Homeplug 1.0 Standard

    Directory of Open Access Journals (Sweden)

    Martha Fabiola Contreras Higuera

    2013-06-01

    Full Text Available Power Line Communications (PLC refers to a group of technologies that allow to establish communication processes under the use of the grid as a physical means of transmission. The use of the grid as a physical means of transmission of information is not a new idea. Until a few years ago, the use of PLC had been limited to the implementation of solutions of control, automation and monitoring of sensors; which did not require a high bandwidth for its operation.During the late 1990s due to the new technological developments and the need to implement new alternatives for transfer of information, it was possible to reach speeds on the order of the Mbps, establishing the possibility of making use of the electricity network as a network of access. The current state of technology PLC allows to reach speeds of up to 200Mbps, which has enabled the transformation of the grid in a true network of band wide, capable of supporting data, voice and video provided by a telecommunications operator. The use of PLC-based network adapters allow easily design LANs and broadband communications through the electrical network, making any outlet in a point of connection for the user, without the need for wiring additional to existing ones.  The electrical network is a structure which so far has been exclusively used for the transport of electrical energy. However, it is possible to make use of this network in processes of communication and transmission of information such as: voice, data and video; Bearing in mind that grid had not been designed for this purpose. The performance is without doubt one of the aspects of greatest interest in the global analysis in networks LAN, due to the effect it produces on the end user. Basically, the most common parameters for evaluating the performance of a network are: Throughput, use of the canal and various measures of retardation. In this article is presented a simple analysis of the HomePlug 1.0 standard applied to the

  19. Wireless Powered Relaying Networks Under Imperfect Channel State Information: System Performance and Optimal Policy for Instantaneous Rate

    Directory of Open Access Journals (Sweden)

    D. T. Do

    2017-09-01

    Full Text Available In this investigation, we consider wireless powered relaying systems, where energy is scavenged by a relay via radio frequency (RF signals. We explore hybrid time switching-based and power splitting-based relaying protocol (HTPSR and compare performance of Amplify-and-Forward (AF with Decode-and-Forward (DF scheme under imperfect channel state information (CSI. Most importantly, the instantaneous rate, achievable bit error rate (BER are determined in the closed-form expressions under the impact of imperfect CSI. Through numerical analysis, we evaluate system insights via different parameters such as power splitting (PS and time switching (TS ratio of the considered HTPSR which affect outage performance and BER. It is noted that DF relaying networks outperform AF relaying networks. Besides that, the numerical results are given to prove the optimization problems of PS and TS ratio to obtain optimal instantaneous rate.

  20. A Markov random walk under constraint for discovering overlapping communities in complex networks

    International Nuclear Information System (INIS)

    Jin, Di; Yang, Bo; Liu, Dayou; He, Dongxiao; Liu, Jie; Baquero, Carlos

    2011-01-01

    The detection of overlapping communities in complex networks has motivated recent research in relevant fields. Aiming to address this problem, we propose a Markov-dynamics-based algorithm, called UEOC, which means 'unfold and extract overlapping communities'. In UEOC, when identifying each natural community that overlaps, a Markov random walk method combined with a constraint strategy, which is based on the corresponding annealed network (degree conserving random network), is performed to unfold the community. Then, a cutoff criterion with the aid of a local community function, called conductance, which can be thought of as the ratio between the number of edges inside the community and those leaving it, is presented to extract this emerged community from the entire network. The UEOC algorithm depends on only one parameter whose value can be easily set, and it requires no prior knowledge of the hidden community structures. The proposed UEOC has been evaluated both on synthetic benchmarks and on some real-world networks, and has been compared with a set of competing algorithms. The experimental result has shown that UEOC is highly effective and efficient for discovering overlapping communities

  1. Common and distinct brain networks underlying panic and social anxiety disorders.

    Science.gov (United States)

    Kim, Yong-Ku; Yoon, Ho-Kyoung

    2018-01-03

    Although panic disorder (PD) and phobic disorders are independent anxiety disorders with distinct sets of diagnostic criteria, there is a high level of overlap between them in terms of pathogenesis and neural underpinnings. Functional connectivity research using resting-state functional magnetic resonance imaging (rsfMRI) shows great potential in identifying the similarities and differences between PD and phobias. Understanding common and distinct networks between PD and phobic disorders is critical for identifying both specific and general neural characteristics of these disorders. We review recent rsfMRI studies and explore the clinical relevance of resting-state functional connectivity (rsFC) in PD and phobias. Although findings differ between studies, there are some meaningful, consistent findings. Social anxiety disorder (SAD) and PD share common default mode network alterations. Alterations within the sensorimotor network are observed primarily in PD. Increased connectivity in the salience network is consistently reported in SAD. This review supports hypotheses that PD and phobic disorders share common rsFC abnormalities and that the different clinical phenotypes between the disorders come from distinct brain functional network alterations. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Optimal design of supply chain network under uncertainty environment using hybrid analytical and simulation modeling approach

    Science.gov (United States)

    Chiadamrong, N.; Piyathanavong, V.

    2017-12-01

    Models that aim to optimize the design of supply chain networks have gained more interest in the supply chain literature. Mixed-integer linear programming and discrete-event simulation are widely used for such an optimization problem. We present a hybrid approach to support decisions for supply chain network design using a combination of analytical and discrete-event simulation models. The proposed approach is based on iterative procedures until the difference between subsequent solutions satisfies the pre-determined termination criteria. The effectiveness of proposed approach is illustrated by an example, which shows closer to optimal results with much faster solving time than the results obtained from the conventional simulation-based optimization model. The efficacy of this proposed hybrid approach is promising and can be applied as a powerful tool in designing a real supply chain network. It also provides the possibility to model and solve more realistic problems, which incorporate dynamism and uncertainty.

  3. Sustainable and Resilient Garment Supply Chain Network Design with Fuzzy Multi-Objectives under Uncertainty

    Directory of Open Access Journals (Sweden)

    Sonia Irshad Mari

    2016-10-01

    Full Text Available Researchers and practitioners are taking more interest in developing sustainable garment supply chains in recent times. On the other hand, the supply chain manager drops sustainability objectives while coping with unexpected natural and man-made disruption risks. Hence, supply chain managers are now trying to develop sustainable supply chains that are simultaneously resilient enough to cope with disruption risks. Owing to the importance of the considered issue, this study proposed a network optimization model for a sustainable and resilient supply chain network by considering sustainability via embodied carbon footprints and carbon emissions and resilience by considering resilience index. In this paper, initially, a possibilistic fuzzy multi-objective sustainable and resilient supply chain network model is developed for the garment industry considering economic, sustainable, and resilience objectives. Secondly, a possibilistic fuzzy linguistic weight-based interactive solution method is proposed. Finally, a numerical case example is presented to show the applicability of the proposed model and solution methodology.

  4. Decentralized supply chain network design: monopoly, duopoly and oligopoly competitions under uncertainty

    Science.gov (United States)

    Seyedhosseini, Seyed Mohammad; Fahimi, Kaveh; Makui, Ahmad

    2017-12-01

    This paper presents the competitive supply chain network design problem in which n decentralized supply chains simultaneously enter the market with no existing rival chain, shape their networks and set wholesale and retail prices in competitive mode. The customer demand is elastic and price dependent, customer utility function is based on the Hoteling model and the chains produce identical or highly substitutable products. We construct a solution algorithm based on bi-level programming and possibility theory. In the proposed bi-level model, the inner part sets the prices based on simultaneous extra- and Stackleberg intra- chains competitions, and the outer part shapes the networks in cooperative competitions. Finally, we use a real-word study to discuss the effect of the different structures of the competitors on the equilibrium solution. Moreover, sensitivity analyses are conducted and managerial insights are offered.

  5. Multivoxel Patterns Reveal Functionally Differentiated Networks Underlying Auditory Feedback Processing of Speech

    DEFF Research Database (Denmark)

    Zheng, Zane Z.; Vicente-Grabovetsky, Alejandro; MacDonald, Ewen N.

    2013-01-01

    within a multivoxel pattern analysis framework, that this sensorimotor process is supported by functionally differentiated brain networks. During scanning, a real-time speech-tracking system was used to deliver two acoustically different types of distorted auditory feedback or unaltered feedback while...... human participants were vocalizing monosyllabic words, and to present the same auditory stimuli while participants were passively listening. Whole-brain analysis of neural-pattern similarity revealed three functional networks that were differentially sensitive to distorted auditory feedback during...... acoustically different, distorted feedback types, only during articulation (not during passive listening). In contrast, a frontotemporal network appears sensitive to the speech features of auditory stimuli during passive listening; this preference for speech features was diminished when the same stimuli were...

  6. Thermo-Mechanical Properties of Semi-Degradable Poly(β-amino ester)-co-Methyl Methacrylate Networks under Simulated Physiological Conditions

    Science.gov (United States)

    Safranski, David L.; Crabtree, Jacob C.; Huq, Yameen R.; Gall, Ken

    2011-01-01

    Poly(β-amino ester) networks are being explored for biomedical applications, but they may lack the mechanical properties necessary for long term implantation. The objective of this study is to evaluate the effect of adding methyl methacrylate on networks' mechanical properties under simulated physiological conditions. The networks were synthesized in two parts: (1) a biodegradable crosslinker was formed from a diacrylate and amine, (2) and then varying concentrations of methyl methacrylate were added prior to photopolymerizing the network. Degradation rate, mechanical properties, and glass transition temperature were studied as a function of methyl methacrylate composition. The crosslinking density played a limited role on mechanical properties for these networks, but increasing methyl methacrylate concentration improved the toughness by several orders of magnitude. Under simulated physiological conditions, networks showed increasing toughness or sustained toughness as degradation occurred. This work establishes a method of creating degradable networks with tailorable toughness while undergoing partial degradation. PMID:21966028

  7. Networking

    OpenAIRE

    Rauno Lindholm, Daniel; Boisen Devantier, Lykke; Nyborg, Karoline Lykke; Høgsbro, Andreas; Fries, de; Skovlund, Louise

    2016-01-01

    The purpose of this project was to examine what influencing factor that has had an impact on the presumed increasement of the use of networking among academics on the labour market and how it is expressed. On the basis of the influence from globalization on the labour market it can be concluded that the globalization has transformed the labour market into a market based on the organization of networks. In this new organization there is a greater emphasis on employees having social qualificati...

  8. Understanding the Validity of Data: A Knowledge-Based Network Underlying Research Expertise in Scientific Disciplines

    Science.gov (United States)

    Roberts, Ros

    2016-01-01

    This article considers what might be taught to meet a widely held curriculum aim of students being able to understand research in a discipline. Expertise, which may appear as a "chain of practice," is widely held to be underpinned by networks of understanding. Scientific research expertise is considered from this perspective. Within…

  9. A risk analysis for gas transport network planning expansion under regulatory uncertainty in Western Europe

    NARCIS (Netherlands)

    Pelletier, 27736; Wortmann, J.C.; Noteboom, H.J.

    The natural gas industry in Western Europe went through drastic changes induced by the unbundling of the national companies, followed by the liberalization of gas trade and the regulation of gas transmission. Natural gas transmission is operated through a network of interconnected grids, and is

  10. Deficiency of brain structural sub-network underlying post-ischaemic stroke apathy.

    Science.gov (United States)

    Yang, S; Hua, P; Shang, X; Cui, Z; Zhong, S; Gong, G; William Humphreys, G

    2015-02-01

    This study aimed to reveal the structural basis of post-ischaemic stroke apathy, especially in relation to disruptions in structural connectivity. Eighty-eight participants were included. The Apathy Evaluation Scale, clinician version, was used to characterize the severity of apathy. Diffusion tensor imaging tractography was used to examine white matter integrity and to reconstruct white matter networks using 90 nodes based on the automated anatomical labeling atlas. The degree for each node was extracted to determine the relationship to the severity of apathy. Apathy was not significantly associated with damage to any single brain region. The degrees of 24 nodes (limbic system, three nodes; frontal lobe, six; basal ganglia, two; temporal lobe, three; parietal lobe, three; insula, two; occipital lobe, five) were significantly correlated to the Apathy Evaluation Scale scores. These 24 nodes constituted an apathy-related sub-network and its global and local efficiencies were negatively correlated with apathy levels (global, r = -0.54, P apathy (odds ratio 0.03, 95% confidence interval 0.01-0.04, P = 0.007). Efficiencies of the non-apathy-related sub-network (the remaining 66 nodes) did not correlate or predict the presence of apathy. Post-stroke apathy is not due to the dysfunction of a single region or circuit. Rather, it results from disconnection of a complex sub-network of brain regions. This provides new insights into the neuroanatomical basis of post-stroke apathy. © 2014 EAN.

  11. Exploring Mechanisms Underlying Impaired Brain Function in Gulf War Illness through Advanced Network Analysis

    Science.gov (United States)

    2017-10-01

    networks of the brain responsible for visual processing, mood regulation, motor coordination, sensory processing, and language command, but increased...GWI Syndromes 1, 2, and 3; neurologic symptoms, neurocognitive; affective; pain; sensory ; resting state functional MRI; independent components analysis...neuropathic pain, memory and concentration deficits, vestibular disturbances, and depression. The objective/goal of this project titled, “Exploring

  12. Radiant heat transfer network in the simulated protective clothing ; System under high heat flux

    NARCIS (Netherlands)

    Fukazawa, T.; Hartog, E.A. den; Daanen, H.A.M.; Penders-van Elk, N.; Tochihara, Y.; Havenith, G.

    2005-01-01

    A radiant network model was developed for design of the protective clothing system against solar and infrared radiative heat flux. A one-dimensional model was employed in the present study, because the aim of this study was to obtain precise temperature distribution through the system with use of a

  13. Integrative network analysis highlights biological processes underlying GLP-1 stimulated insulin secretion: A DIRECT study

    DEFF Research Database (Denmark)

    Gudmundsdottir, Valborg; Pedersen, Helle Krogh; Allebrandt, Karla Viviani

    2018-01-01

    cohorts. The network contains both known and novel genes in the context of insulin secretion and is enriched for members of the focal adhesion, extracellular-matrix receptor interaction, actin cytoskeleton regulation, Rap1 and PI3K-Akt signaling pathways. Adipose tissue is, like the beta-cell, one...

  14. Evaluating the effectiveness of conservation site networks under climate change: accounting for uncertainty.

    Science.gov (United States)

    Bagchi, Robert; Crosby, Mike; Huntley, Brian; Hole, David G; Butchart, Stuart H M; Collingham, Yvonne; Kalra, Mohit; Rajkumar, Jagadish; Rahmani, Asad; Pandey, Mitra; Gurung, Hum; Trai, Le Trong; Van Quang, Nguyen; Willis, Stephen G

    2013-04-01

    We forecasted potential impacts of climate change on the ability of a network of key sites for bird conservation (Important Bird Areas; IBAs) to provide suitable climate for 370 bird species of current conservation concern in two Asian biodiversity hotspots: the Eastern Himalaya and Lower Mekong. Comparable studies have largely not accounted for uncertainty, which may lead to inappropriate conclusions. We quantified the contribution of four sources of variation (choice of general circulation models, emission scenarios and species distribution modelling methods and variation in species distribution data) to uncertainty in forecasts and tested if our projections were robust to these uncertainties. Declines in the availability of suitable climate within the IBA network by 2100 were forecast as 'extremely likely' for 45% of species, whereas increases were projected for only 2%. Thus, we predict almost 24 times as many 'losers' as 'winners'. However, for no species was suitable climate 'extremely likely' to be completely lost from the network. Considerable turnover (median = 43%, 95% CI = 35-69%) in species compositions of most IBAs were projected by 2100. Climatic conditions in 47% of IBAs were projected as 'extremely likely' to become suitable for fewer priority species. However, no IBA was forecast to become suitable for more species. Variation among General Circulation Models and Species Distribution Models contributed most to uncertainty among forecasts. This uncertainty precluded firm conclusions for 53% of species and IBAs because 95% confidence intervals included projections of no change. Considering this uncertainty, however, allows robust recommendations concerning the remaining species and IBAs. Overall, while the IBA network will continue to sustain bird conservation, climate change will modify which species each site will be suitable for. Thus, adaptive management of the network, including modified site conservation strategies and facilitating species

  15. Dynamic behavior of dual cross-linked nanoparticle networks under oscillatory shear

    International Nuclear Information System (INIS)

    Iyer, Balaji V S; Yashin, Victor V; Balazs, Anna C

    2014-01-01

    Via computer simulations, we investigate the linear and nonlinear viscoelastic response of polymer grafted nanoparticle networks subject to oscillatory shear at different amplitudes and frequencies. The individual nanoparticles are composed of a rigid spherical core and a corona of grafted polymers that encompass reactive end groups. With the overlap of the coronas on adjacent particles, the reactive end groups form permanent or labile bonds, and thus form a ‘dual cross-linked’ network. The existing labile bonds between particles can break and reform depending on the bond rupture rate, extent of deformation and the frequency of oscillation. We study how the viscoelastic behavior of the material depends on the energy of the labile bonds and identify the network characteristics that give rise to the observed viscoelastic response. We observe that with an increase in labile bond energy, the storage modulus increases while the loss modulus shows a more complex response depending on the labile bond energy. Specifically, in the case of the samples with the weaker labile bonds, the loss modulus increases monotonically, while for the samples with the stronger labile bonds, the loss modulus exhibits a minimum with an increase in frequency. We show that an increase in the storage modulus corresponds to an enhancement in the average number of bonds in the samples and the characteristics of the loss modulus depend on both the bond kinetics and the mobility of the particles in the network. Furthermore, we determine that the effective contribution of the bonds to the storage modulus decreases with increase in strain amplitude. In particular, while bond formation at small amplitude drives an increase in storage modulus, at large amplitudes it promotes clustering and formation of voids leading to strain softening. Our simulations provide a mesoscopic picture of how the nature of labile bonds affects the performance of cross-linked polymer-grafted nanoparticle networks. (paper)

  16. Spike Pattern Structure Influences Synaptic Efficacy Variability under STDP and Synaptic Homeostasis. II: Spike Shuffling Methods on LIF Networks

    Science.gov (United States)

    Bi, Zedong; Zhou, Changsong

    2016-01-01

    Synapses may undergo variable changes during plasticity because of the variability of spike patterns such as temporal stochasticity and spatial randomness. Here, we call the variability of synaptic weight changes during plasticity to be efficacy variability. In this paper, we investigate how four aspects of spike pattern statistics (i.e., synchronous firing, burstiness/regularity, heterogeneity of rates and heterogeneity of cross-correlations) influence the efficacy variability under pair-wise additive spike-timing dependent plasticity (STDP) and synaptic homeostasis (the mean strength of plastic synapses into a neuron is bounded), by implementing spike shuffling methods onto spike patterns self-organized by a network of excitatory and inhibitory leaky integrate-and-fire (LIF) neurons. With the increase of the decay time scale of the inhibitory synaptic currents, the LIF network undergoes a transition from asynchronous state to weak synchronous state and then to synchronous bursting state. We first shuffle these spike patterns using a variety of methods, each designed to evidently change a specific pattern statistics; and then investigate the change of efficacy variability of the synapses under STDP and synaptic homeostasis, when the neurons in the network fire according to the spike patterns before and after being treated by a shuffling method. In this way, we can understand how the change of pattern statistics may cause the change of efficacy variability. Our results are consistent with those of our previous study which implements spike-generating models on converging motifs. We also find that burstiness/regularity is important to determine the efficacy variability under asynchronous states, while heterogeneity of cross-correlations is the main factor to cause efficacy variability when the network moves into synchronous bursting states (the states observed in epilepsy). PMID:27555816

  17. Spike Pattern Structure Influences Synaptic Efficacy Variability Under STDP and Synaptic Homeostasis. II: Spike Shuffling Methods on LIF Networks

    Directory of Open Access Journals (Sweden)

    Zedong Bi

    2016-08-01

    Full Text Available Synapses may undergo variable changes during plasticity because of the variability of spike patterns such as temporal stochasticity and spatial randomness. Here, we call the variability of synaptic weight changes during plasticity to be efficacy variability. In this paper, we investigate how four aspects of spike pattern statistics (i.e., synchronous firing, burstiness/regularity, heterogeneity of rates and heterogeneity of cross-correlations influence the efficacy variability under pair-wise additive spike-timing dependent plasticity (STDP and synaptic homeostasis (the mean strength of plastic synapses into a neuron is bounded, by implementing spike shuffling methods onto spike patterns self-organized by a network of excitatory and inhibitory leaky integrate-and-fire (LIF neurons. With the increase of the decay time scale of the inhibitory synaptic currents, the LIF network undergoes a transition from asynchronous state to weak synchronous state and then to synchronous bursting state. We first shuffle these spike patterns using a variety of methods, each designed to evidently change a specific pattern statistics; and then investigate the change of efficacy variability of the synapses under STDP and synaptic homeostasis, when the neurons in the network fire according to the spike patterns before and after being treated by a shuffling method. In this way, we can understand how the change of pattern statistics may cause the change of efficacy variability. Our results are consistent with those of our previous study which implements spike-generating models on converging motifs. We also find that burstiness/regularity is important to determine the efficacy variability under asynchronous states, while heterogeneity of cross-correlations is the main factor to cause efficacy variability when the network moves into synchronous bursting states (the states observed in epilepsy.

  18. Computational Analysis of Molecular Interaction Networks Underlying Change of HIV-1 Resistance to Selected Reverse Transcriptase Inhibitors.

    Science.gov (United States)

    Kierczak, Marcin; Dramiński, Michał; Koronacki, Jacek; Komorowski, Jan

    2010-12-12

    Despite more than two decades of research, HIV resistance to drugs remains a serious obstacle in developing efficient AIDS treatments. Several computational methods have been developed to predict resistance level from the sequence of viral proteins such as reverse transcriptase (RT) or protease. These methods, while powerful and accurate, give very little insight into the molecular interactions that underly acquisition of drug resistance/hypersusceptibility. Here, we attempt at filling this gap by using our Monte Carlo feature selection and interdependency discovery method (MCFS-ID) to elucidate molecular interaction networks that characterize viral strains with altered drug resistance levels. We analyzed a number of HIV-1 RT sequences annotated with drug resistance level using the MCFS-ID method. This let us expound interdependency networks that characterize change of drug resistance to six selected RT inhibitors: Abacavir, Lamivudine, Stavudine, Zidovudine, Tenofovir and Nevirapine. The networks consider interdependencies at the level of physicochemical properties of mutating amino acids, eg,: polarity. We mapped each network on the 3D structure of RT in attempt to understand the molecular meaning of interacting pairs. The discovered interactions describe several known drug resistance mechanisms and, importantly, some previously unidentified ones. Our approach can be easily applied to a whole range of problems from the domain of protein engineering. A portable Java implementation of our MCFS-ID method is freely available for academic users and can be obtained at: http://www.ipipan.eu/staff/m.draminski/software.htm.

  19. Performance of Overlaid MIMO Cellular Networks with TAS/MRC under Hybrid-Access Small Cells and Poisson Field Interference

    KAUST Repository

    AbdelNabi, Amr A.

    2018-02-12

    This paper presents new approaches to characterize the achieved performance of hybrid control-access small cells in the context of two-tier multi-input multi-output (MIMO) cellular networks with random interference distributions. The hybrid scheme at small cells (such as femtocells) allows for sharing radio resources between the two network tiers according to the densities of small cells and their associated users, as well as the observed interference power levels in the two network tiers. The analysis considers MIMO transceivers at all nodes, for which antenna arrays can be utilized to implement transmit antenna selection (TAS) and receive maximal ratio combining (MRC) under MIMO point-to-point channels. Moreover, it tar-gets network-level models of interference sources inside each tier and between the two tiers, which are assumed to follow Poisson field processes. To fully capture the occasions for Poisson field distribution on MIMO spatial domain. Two practical scenarios of interference sources are addressed including highly-correlated or uncorrelated transmit antenna arrays of the serving macrocell base station. The analysis presents new analytical approaches that can characterize the downlink outage probability performance in any tier. Furthermore, the outage performance in high signal-to-noise (SNR) regime is also obtained, which can be useful to deduce diversity and/or coding gains.

  20. Integrative network analysis highlights biological processes underlying GLP-1 stimulated insulin secretion: A DIRECT study.

    Directory of Open Access Journals (Sweden)

    Valborg Gudmundsdottir

    Full Text Available Glucagon-like peptide 1 (GLP-1 stimulated insulin secretion has a considerable heritable component as estimated from twin studies, yet few genetic variants influencing this phenotype have been identified. We performed the first genome-wide association study (GWAS of GLP-1 stimulated insulin secretion in non-diabetic individuals from the Netherlands Twin register (n = 126. This GWAS was enhanced using a tissue-specific protein-protein interaction network approach. We identified a beta-cell protein-protein interaction module that was significantly enriched for low gene scores based on the GWAS P-values and found support at the network level in an independent cohort from Tübingen, Germany (n = 100. Additionally, a polygenic risk score based on SNPs prioritized from the network was associated (P < 0.05 with glucose-stimulated insulin secretion phenotypes in up to 5,318 individuals in MAGIC cohorts. The network contains both known and novel genes in the context of insulin secretion and is enriched for members of the focal adhesion, extracellular-matrix receptor interaction, actin cytoskeleton regulation, Rap1 and PI3K-Akt signaling pathways. Adipose tissue is, like the beta-cell, one of the target tissues of GLP-1 and we thus hypothesized that similar networks might be functional in both tissues. In order to verify peripheral effects of GLP-1 stimulation, we compared the transcriptome profiling of ob/ob mice treated with liraglutide, a clinically used GLP-1 receptor agonist, versus baseline controls. Some of the upstream regulators of differentially expressed genes in the white adipose tissue of ob/ob mice were also detected in the human beta-cell network of genes associated with GLP-1 stimulated insulin secretion. The findings provide biological insight into the mechanisms through which the effects of GLP-1 may be modulated and highlight a potential role of the beta-cell expressed genes RYR2, GDI2, KIAA0232, COL4A1 and COL4A2 in GLP-1 stimulated

  1. Application of LMS-Based NN Structure for Power Quality Enhancement in a Distribution Network Under Abnormal Conditions.

    Science.gov (United States)

    Agarwal, Rahul Kumar; Hussain, Ikhlaq; Singh, Bhim

    2017-03-16

    This paper proposes an application of a least mean-square (LMS)-based neural network (NN) structure for the power quality improvement of a three-phase power distribution network under abnormal conditions. It uses a single-layer neuron structure for the control in a distribution static compensator (DSTATCOM) to attenuate the harmonics such as noise, bias, notches, dc offset, and distortion, injected in the grid current due to connection of several nonlinear loads. This admittance LMS-based NN structure has a simple architecture which reduces the computational complexity and burden which makes it easy to implement. A DSTATCOM is a custom power device which performs various functionalities such as harmonics attenuation, reactive power compensation, load balancing, zero voltage regulation, and power factor correction. Other main contribution of this paper involves operation of the system under abnormal conditions of distribution network which means noise and distortion in voltage and imbalance in three-phase voltages at the point of interconnection. For substantiating and demonstrating the performance of proposed control approach, simulations are carried on MATLAB/Simulink software and corresponding experimental tests are conducted on a developed prototype in the laboratory.

  2. The effect of dietary folic acid on biochemical parameters and gene expression of three heat shock proteins (HSPs) of blunt snout bream (Megalobrama amblycephala) fingerling under acute high temperature stress.

    Science.gov (United States)

    Sesay, Daniella Fatmata; Habte-Tsion, Habte-Michael; Zhou, Qunlan; Ren, Mingchun; Xie, Jun; Liu, Bo; Chen, Ruli; Pan, Liangkun

    2017-08-01

    The effects of dietary folic acid on biochemical parameters and gene expression of three heat shock proteins (HSPs) of blunt snout bream (Megalobrama amblycephala) fingerling under acute high temperature stress. Six dietary folic acid groups (0.0, 0.5, 1.0, 2.0, 5.0, and 10.0) mg/kg diets were designed and assigned into 18 tanks in three replicates each (300 l/tank) and were administered for 10 weeks in a re-circulated water system. The fingerlings with an initial weight of 27.0 ± 0.03 g were fed with their respective diets four times daily. At the end of the experiment, samples were collected before challenge, 0, 24, 72 h, and 7 days. Serum total protein (TP), alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), cortisol, glucose, complement C3 (C3), complement C4 (C4, immunoglobulin M (IgM) hepatic superoxide dismutase (SOD), catalase (CAT), malondialdehyde (MDA), and the expression of heat shock protein 60 (HSP60), 70 (HSP70), and 90 (HSP90) were studied. The results showed that fish fed with dietary folic acid between 1.0, 2.0, and 5.0 mg/kg significantly (P dietary folic acid level 1.0, 2.0, and 5.0 mg/kg before and after the same temperature challenge of 32 °C. Before stress, 0, 24, 72 h, and 7 days significantly (P dietary folic acid inclusion level and temperature duration have significant interactive effect on serum biochemical parameters, antioxidant parameters, and gene expression level (P > 0.05) of the three HSPs. However, there were statistical significant interactive effect between dietary folic acid inclusion level and temperature duration on serum C3 and C4 (P  0.05). The present results indicate that supplementation of basal diet from 1.0 mg/kg; 2.0 and 5.0 mg/kg can enhance acute high temperature resistance ability in M. amblycephala fingerling to some degree and improve physiological response, immune and antioxidant capacities, and expression level of three HSPs.

  3. Epidemic Survivability: Characterizing Networks Under Epidemic-like Failure Propagation Scenarios

    DEFF Research Database (Denmark)

    Manzano, Marc; Calle, Eusebi; Ripoll, Jordi

    2013-01-01

    Epidemics theory has been used in different contexts in order to describe the propagation of diseases, human interactions or natural phenomena. In computer science, virus spreading has been also characterized using epidemic models. Although in the past the use of epidemic models in telecommunicat......Epidemics theory has been used in different contexts in order to describe the propagation of diseases, human interactions or natural phenomena. In computer science, virus spreading has been also characterized using epidemic models. Although in the past the use of epidemic models...... in telecommunication networks has not been extensively considered, nowadays, with the increasing computation capacity and complexity of operating systems of modern network devices (routers, switches, etc.), the study of possible epidemic-like failure scenarios must be taken into account. When epidemics occur...

  4. Adaptive Chemical Networks under Non-Equilibrium Conditions: The Evaporating Droplet.

    Science.gov (United States)

    Armao, Joseph J; Lehn, Jean-Marie

    2016-10-17

    Non-volatile solutes in an evaporating drop experience an out-of-equilibrium state due to non-linear concentration effects and complex flow patterns. Here, we demonstrate a small molecule chemical reaction network that undergoes a rapid adaptation response to the out-of-equilibrium conditions inside the droplet leading to control over the molecular constitution and spatial arrangement of the deposition pattern. Adaptation results in a pronounced coffee stain effect and coupling to chemical concentration gradients within the drop is demonstrated. Amplification and suppression of network species are readily identifiable with confocal fluorescence microscopy. We anticipate that these observations will contribute to the design and exploration of out-of-equilibrium chemical systems, as well as be useful towards the development of point-of-care medical diagnostics and controlled deposition of small molecules through inkjet printing. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. High Frequency Resonance Damping of DFIG based Wind Power System under Weak Network

    DEFF Research Database (Denmark)

    Song, Yipeng; Wang, Xiongfei; Blaabjerg, Frede

    2017-01-01

    When operating in a micro or weak grid which has a relatively large network impedance, the Doubly Fed Induction Generator (DFIG) based wind power generation system is prone to suffer high frequency resonance due to the impedance interaction between DFIG system and the parallel compensated network...... (series RL + shunt C). In order to improve the performance of the DFIG system as well as other units and loads connected to the weak grid, the high frequency resonance needs to be effectively damped. In this paper, the proposed active damping control strategy is able to implement effective damping either...... in the Rotor Side Converter (RSC) or in the Grid Side Converter (GSC), through the introduction of virtual positive capacitor or virtual negative inductor to reshape the DFIG system impedance and mitigate the high frequency resonance. A detailed theoretical explanation on the virtual positive capacitor...

  6. Dynamics of random Boolean networks under fully asynchronous stochastic update based on linear representation.

    Directory of Open Access Journals (Sweden)

    Chao Luo

    Full Text Available A novel algebraic approach is proposed to study dynamics of asynchronous random Boolean networks where a random number of nodes can be updated at each time step (ARBNs. In this article, the logical equations of ARBNs are converted into the discrete-time linear representation and dynamical behaviors of systems are investigated. We provide a general formula of network transition matrices of ARBNs as well as a necessary and sufficient algebraic criterion to determine whether a group of given states compose an attractor of length[Formula: see text] in ARBNs. Consequently, algorithms are achieved to find all of the attractors and basins in ARBNs. Examples are showed to demonstrate the feasibility of the proposed scheme.

  7. A new multi objective optimization model for designing a green supply chain network under uncertainty

    Directory of Open Access Journals (Sweden)

    Mohammad Mahdi Saffar

    2015-01-01

    Full Text Available Recently, researchers have focused on how to minimize the negative effects of industrial activities on environment. Consequently, they work on mathematical models, which minimize the environmental issues as well as optimizing the costs. In the field of supply chain network design, most managers consider economic and environmental issues, simultaneously. This paper introduces a bi-objective supply chain network design, which uses fuzzy programming to obtain the capability of resisting uncertain conditions. The design considers production, recovery, and distribution centers. The advantage of using this model includes the optimal facilities, locating them and assigning the optimal facilities to them. It also chooses the type and the number of technologies, which must be bought. The fuzzy programming converts the multi objective model to an auxiliary crisp model by Jimenez approach and solves it with ε-constraint. For solving large size problems, the Multi Objective Differential Evolutionary algorithm (MODE is applied.

  8. Validation of Tilt Gain under Realistic Path Loss Model and Network Scenario

    DEFF Research Database (Denmark)

    Nguyen, Huan Cong; Rodriguez, Ignacio; Sørensen, Troels Bundgaard

    2013-01-01

    Despite being a simple and commonly-applied radio optimization technique, the impact on practical network performance from base station antenna downtilt is not well understood. Most published studies based on empirical path loss models report tilt angles and performance gains that are far higher...... than practical experience suggests. We motivate in this paper, based on a practical LTE scenario, that the discrepancy partly lies in the path loss model, and shows that a more detailed semi-deterministic model leads to both lower gains in terms of SINR, outage probability and downlink throughput...... and lower optimum tilt settings. Furthermore, we show that a simple geometrically based tilt optimization algorithm can outperform other tilt profiles, including the setting applied by the cellular operator in the specific case. In general, the network performance is not highly sensitive to the tilt...

  9. Radio/Antenna Mounting System for Wireless Networking under Row-Crop Agriculture Conditions

    OpenAIRE

    Daniel K. Fisher

    2015-01-01

    Interest in and deployment of wireless monitoring systems is increasing in many diverse environments, including row-crop agricultural fields. While many studies have been undertaken to evaluate various aspects of wireless monitoring and networking, such as electronic hardware components, data-collection procedures, power management, and communication protocols, little information related to physical deployment issues has been reported. To achieve acceptable wireless transmission capability, t...

  10. Large-scale brain networks underlying language acquisition in early infancy

    Directory of Open Access Journals (Sweden)

    Fumitaka eHomae

    2011-05-01

    Full Text Available A critical issue in human development is that of whether the language-related areas in the left frontal and temporal regions work as a functional network in preverbal infants. Here, we used 94-channel near-infrared spectroscopy (NIRS to reveal the functional networks in the brains of sleeping 3-month-old infants with and without presenting speech sounds. During the first 3 min, we measured spontaneous brain activation (period 1. After period 1, we provided stimuli by playing Japanese sentences for 3 min (period 2. Finally, we measured brain activation for 3 min without providing the stimulus (period 3, as in period 1. We found that not only the bilateral temporal and temporoparietal regions but also the prefrontal and occipital regions showed oxygenated hemoglobin (oxy-Hb signal increases and deoxygenated hemoglobin (deoxy-Hb signal decreases when speech sounds were presented to infants. By calculating time-lagged cross-correlations and coherences of oxy-Hb signals between channels, we tested the functional connectivity for the 3 periods. The oxy-Hb signals in neighboring channels, as well as their homologous channels in the contralateral hemisphere, showed high correlation coefficients in period 1. Similar correlations were observed in period 2; however, the number of channels showing high correlations was higher in the ipsilateral hemisphere, especially in the anterior-posterior direction. The functional connectivity in period 3 showed a close relationship between the frontal and temporal regions, which was less prominent in period 1, indicating that these regions form the functional networks and work as a hysteresis system that has memory of the previous inputs. We propose a hypothesis that the spatiotemporally large-scale brain networks, including the frontal and temporal regions, underlie speech processing in infants and they might play important roles in language acquisition during infancy.

  11. Strong geomagnetic activity forecast by neural networks under dominant southern orientation of the interplanetary magnetic field

    Czech Academy of Sciences Publication Activity Database

    Valach, F.; Bochníček, Josef; Hejda, Pavel; Revallo, M.

    2014-01-01

    Roč. 53, č. 4 (2014), s. 589-598 ISSN 0273-1177 R&D Projects: GA AV ČR(CZ) IAA300120608; GA MŠk OC09070 Institutional support: RVO:67985530 Keywords : geomagnetic activity * interplanetary magnetic field * artificial neural network * ejection of coronal mass * X-ray flares Subject RIV: DE - Earth Magnetism, Geodesy, Geography Impact factor: 1.358, year: 2014

  12. Resistance and resistance fluctuations in random resistor networks under biased percolation.

    Science.gov (United States)

    Pennetta, Cecilia; Reggiani, L; Trefán, Gy; Alfinito, E

    2002-06-01

    We consider a two-dimensional random resistor network (RRN) in the presence of two competing biased processes consisting of the breaking and recovering of elementary resistors. These two processes are driven by the joint effects of an electrical bias and of the heat exchange with a thermal bath. The electrical bias is set up by applying a constant voltage or, alternatively, a constant current. Monte Carlo simulations are performed to analyze the network evolution in the full range of bias values. Depending on the bias strength, electrical failure or steady state are achieved. Here we investigate the steady state of the RRN focusing on the properties of the non-Ohmic regime. In constant-voltage conditions, a scaling relation is found between /(0) and V/V(0), where is the average network resistance, (0) the linear regime resistance, and V0 the threshold value for the onset of nonlinearity. A similar relation is found in constant-current conditions. The relative variance of resistance fluctuations also exhibits a strong nonlinearity whose properties are investigated. The power spectral density of resistance fluctuations presents a Lorentzian spectrum and the amplitude of fluctuations shows a significant non-Gaussian behavior in the prebreakdown region. These results compare well with electrical breakdown measurements in thin films of composites and of other conducting materials.

  13. Probabilistic Optimal Power Dispatch in Multi-Carrier Networked Microgrids under Uncertainties

    Directory of Open Access Journals (Sweden)

    Vahid Amir

    2017-11-01

    Full Text Available A microgrid (MG is a small-scale version of the power system which makes possible the integration of renewable resources as well as achieving maximum demand side management (DSM utilization. The future power system will be faced with severe uncertainties owing to penetration of renewable resources. Consequently, the uncertainty assessment of system performance is essential. The conventional energy scheduling in an MG may not be suitable for active distribution networks. Hence, this study focuses on the probabilistic analysis of optimal power dispatch considering economic aspects in a multi-carrier networked microgrid. The aim is to study the impact of uncertain behavior of loads, renewable resources, and electricity market on the optimal management of a multi-carrier networked microgrid. Furthermore, a novel time-based demand side management is proposed in order to reshape the load curve, as well as preventing the excessive use of energy in peak hours. The optimization model is formulated as a mixed integer nonlinear program (MINLP and is solved using MATLAB and GAMS software. Results show that the energy sharing capability between MCMGs and MCMGs and the main grids as well as utilization of demand side management can decrease operating costs for smart distribution grids.

  14. Distributed Fault-Tolerant Control of Networked Uncertain Euler-Lagrange Systems Under Actuator Faults.

    Science.gov (United States)

    Chen, Gang; Song, Yongduan; Lewis, Frank L

    2016-05-03

    This paper investigates the distributed fault-tolerant control problem of networked Euler-Lagrange systems with actuator and communication link faults. An adaptive fault-tolerant cooperative control scheme is proposed to achieve the coordinated tracking control of networked uncertain Lagrange systems on a general directed communication topology, which contains a spanning tree with the root node being the active target system. The proposed algorithm is capable of compensating for the actuator bias fault, the partial loss of effectiveness actuation fault, the communication link fault, the model uncertainty, and the external disturbance simultaneously. The control scheme does not use any fault detection and isolation mechanism to detect, separate, and identify the actuator faults online, which largely reduces the online computation and expedites the responsiveness of the controller. To validate the effectiveness of the proposed method, a test-bed of multiple robot-arm cooperative control system is developed for real-time verification. Experiments on the networked robot-arms are conduced and the results confirm the benefits and the effectiveness of the proposed distributed fault-tolerant control algorithms.

  15. Achievable Outage Rates In Cognitive Radio Networks under Imperfect Spectrum Sensing

    Directory of Open Access Journals (Sweden)

    N. Tafaghodi Khajavi

    2012-06-01

    Full Text Available In this paper, we aim at deriving the outage rates achieved by the primary user due spectrum sensing in a cognitive radio network, that we call sensing-induced primary outage rates. To reach this goal, in the first step, instead of classical spectrum sensing techniques that evaluate sensing performance only based on correct detection of the presence of the primary user’s signal, we propose a modified framework that also takes into account the correct detection of the absence of primary user’s signal for spectrum sensing performance evaluation. In a second step, we derive the information rates achieved by the coexistence of a primary and a cognitive network. In the last step, assuming slow fading sensing channels, we derive the sensing-induced primary outage rates, i.e., outage rates achieved by the primary network in the presence of a CR with imperfect spectrum sensing, characterized by a given miss-detection probability. Numerical results show that the proposed spectrum sensing outperforms conventional spectrum sensing techniques in terms of primary signal outage rates and total achievable throughputs, without any increase in the cognitive radio complexity.

  16. Hybrid Access Femtocells in Overlaid MIMO Cellular Networks with Transmit Selection under Poisson Field Interference

    KAUST Repository

    Abdel Nabi, Amr A

    2017-09-21

    This paper analyzes the performance of hybrid control-access schemes for small cells (such as femtocells) in the context of two-tier overlaid cellular networks. The proposed hybrid access schemes allow for sharing the same downlink resources between the small-cell network and the original macrocell network, and their mode of operations are characterized considering post-processed signal-to-interference-plus-noise ratios (SINRs) or pre-processed interference-aware operation. The work presents a detailed treatment of achieved performance of a desired user that benefits from MIMO arrays configuration through the use of transmit antenna selection (TAS) and maximal ratio combining (MRC) in the presence of Poisson field interference processes on spatial links. Furthermore, based on the interference awareness at the desired user, two TAS approaches are treated, which are the signal-to-noise (SNR)-based selection and SINR-based selection. The analysis is generalized to address the cases of highly-correlated and un-correlated aggregated interference on different transmit channels. In addition, the effect of delayed TAS due to imperfect feedback and the impact of arbitrary TAS processing are investigated. The analytical results are validated by simulations, to clarify some of the main outcomes herein.

  17. Optimizing Bus Frequencies under Uncertain Demand: Case Study of the Transit Network in a Developing City

    Directory of Open Access Journals (Sweden)

    Zhengfeng Huang

    2013-01-01

    Full Text Available Various factors can make predicting bus passenger demand uncertain. In this study, a bilevel programming model for optimizing bus frequencies based on uncertain bus passenger demand is formulated. There are two terms constituting the upper-level objective. The first is transit network cost, consisting of the passengers’ expected travel time and operating costs, and the second is transit network robustness performance, indicated by the variance in passenger travel time. The second term reflects the risk aversion of decision maker, and it can make the most uncertain demand be met by the bus operation with the optimal transit frequency. With transit link’s proportional flow eigenvalues (mean and covariance obtained from the lower-level model, the upper-level objective is formulated by the analytical method. In the lower-level model, the above two eigenvalues are calculated by analyzing the propagation of mean transit trips and their variation in the optimal strategy transit assignment process. The genetic algorithm (GA used to solve the model is tested in an example network. Finally, the model is applied to determining optimal bus frequencies in the city of Liupanshui, China. The total cost of the transit system in Liupanshui can be reduced by about 6% via this method.

  18. Energy consumption analysis for various memristive networks under different learning strategies

    International Nuclear Information System (INIS)

    Deng, Lei; Wang, Dong; Zhang, Ziyang; Tang, Pei; Li, Guoqi; Pei, Jing

    2016-01-01

    Highlights: • Estimation methodology for energy consumed by memristor is established. • Energy comparisons for different learning strategies in various networks are touched. • Less-pulses and low-power-first modulation methods are energy efficient. • Proper decreasing the memristor modulation precision reduces the energy consumption. • Helpful solutions for power improving in memristive systems are proposed. - Abstract: Recently, various memristive systems emerge to emulate the efficient computing paradigm of the brain cortex; whereas, how to make them energy efficient still remains unclear, especially from an overall perspective. Here, a systematical and bottom-up energy consumption analysis is demonstrated, including the memristor device level and the network learning level. We propose an energy estimating methodology when modulating the memristive synapses, which is simulated in three typical neural networks with different synaptic structures and learning strategies for both offline and online learning. These results provide an in-depth insight to create energy efficient brain-inspired neuromorphic devices in the future.

  19. Enhancing Radio Access Network Performance over LTE-A for Machine-to-Machine Communications under Massive Access

    Directory of Open Access Journals (Sweden)

    Fatemah Alsewaidi

    2016-01-01

    Full Text Available The expected tremendous growth of machine-to-machine (M2M devices will require solutions to improve random access channel (RACH performance. Recent studies have shown that radio access network (RAN performance is degraded under the high density of devices. In this paper, we propose three methods to enhance RAN performance for M2M communications over the LTE-A standard. The first method employs a different value for the physical RACH configuration index to increase random access opportunities. The second method addresses a heterogeneous network by using a number of picocells to increase resources and offload control traffic from the macro base station. The third method involves aggregation points and addresses their effect on RAN performance. Based on evaluation results, our methods improved RACH performance in terms of the access success probability and average access delay.

  20. Biochemical adaptation to ocean acidification.

    Science.gov (United States)

    Stillman, Jonathon H; Paganini, Adam W

    2015-06-01

    The change in oceanic carbonate chemistry due to increased atmospheric PCO2  has caused pH to decline in marine surface waters, a phenomenon known as ocean acidification (OA). The effects of OA on organisms have been shown to be widespread among diverse taxa from a wide range of habitats. The majority of studies of organismal response to OA are in short-term exposures to future levels of PCO2 . From such studies, much information has been gathered on plastic responses organisms may make in the future that are beneficial or harmful to fitness. Relatively few studies have examined whether organisms can adapt to negative-fitness consequences of plastic responses to OA. We outline major approaches that have been used to study the adaptive potential for organisms to OA, which include comparative studies and experimental evolution. Organisms that inhabit a range of pH environments (e.g. pH gradients at volcanic CO2 seeps or in upwelling zones) have great potential for studies that identify adaptive shifts that have occurred through evolution. Comparative studies have advanced our understanding of adaptation to OA by linking whole-organism responses with cellular mechanisms. Such optimization of function provides a link between genetic variation and adaptive evolution in tuning optimal function of rate-limiting cellular processes in different pH conditions. For example, in experimental evolution studies of organisms with short generation times (e.g. phytoplankton), hundreds of generations of growth under future conditions has resulted in fixed differences in gene expression related to acid-base regulation. However, biochemical mechanisms for adaptive responses to OA have yet to be fully characterized, and are likely to be more complex than simply changes in gene expression or protein modification. Finally, we present a hypothesis regarding an unexplored area for biochemical adaptation to ocean acidification. In this hypothesis, proteins and membranes exposed to the

  1. Neural network modeling to evaluate the dynamic flow stress of high strength armor steels under high strain rate compression

    Directory of Open Access Journals (Sweden)

    Ravindranadh Bobbili

    2014-12-01

    Full Text Available An artificial neural network (ANN constitutive model is developed for high strength armor steel tempered at 500 °C, 600 °C and 650 °C based on high strain rate data generated from split Hopkinson pressure bar (SHPB experiments. A new neural network configuration consisting of both training and validation is effectively employed to predict flow stress. Tempering temperature, strain rate and strain are considered as inputs, whereas flow stress is taken as output of the neural network. A comparative study on Johnson–Cook (J–C model and neural network model is performed. It was observed that the developed neural network model could predict flow stress under various strain rates and tempering temperatures. The experimental stress–strain data obtained from high strain rate compression tests using SHPB, over a range of tempering temperatures (500–650 °C, strains (0.05–0.2 and strain rates (1000–5500/s are employed to formulate J–C model to predict the high strain rate deformation behavior of high strength armor steels. The J-C model and the back-propagation ANN model were developed to predict the high strain rate deformation behavior of high strength armor steel and their predictability is evaluated in terms of correlation coefficient (R and average absolute relative error (AARE. R and AARE for the J–C model are found to be 0.7461 and 27.624%, respectively, while R and AARE for the ANN model are 0.9995 and 2.58%, respectively. It was observed that the predictions by ANN model are in consistence with the experimental data for all tempering temperatures.

  2. A network model of genomic hormone interactions underlying dementia and its translational validation through serendipitous off-target effect

    Science.gov (United States)

    2013-01-01

    Background While the majority of studies have focused on the association between sex hormones and dementia, emerging evidence supports the role of other hormone signals in increasing dementia risk. However, due to the lack of an integrated view on mechanistic interactions of hormone signaling pathways associated with dementia, molecular mechanisms through which hormones contribute to the increased risk of dementia has remained unclear and capacity of translating hormone signals to potential therapeutic and diagnostic applications in relation to dementia has been undervalued. Methods Using an integrative knowledge- and data-driven approach, a global hormone interaction network in the context of dementia was constructed, which was further filtered down to a model of convergent hormone signaling pathways. This model was evaluated for its biological and clinical relevance through pathway recovery test, evidence-based analysis, and biomarker-guided analysis. Translational validation of the model was performed using the proposed novel mechanism discovery approach based on ‘serendipitous off-target effects’. Results Our results reveal the existence of a well-connected hormone interaction network underlying dementia. Seven hormone signaling pathways converge at the core of the hormone interaction network, which are shown to be mechanistically linked to the risk of dementia. Amongst these pathways, estrogen signaling pathway takes the major part in the model and insulin signaling pathway is analyzed for its association to learning and memory functions. Validation of the model through serendipitous off-target effects suggests that hormone signaling pathways substantially contribute to the pathogenesis of dementia. Conclusions The integrated network model of hormone interactions underlying dementia may serve as an initial translational platform for identifying potential therapeutic targets and candidate biomarkers for dementia-spectrum disorders such as Alzheimer

  3. Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories.

    Science.gov (United States)

    Guthrie, Violeta Beleva; Allen, Jennifer; Camps, Manel; Karchin, Rachel

    2011-09-01

    Understanding how novel functions evolve (genetic adaptation) is a critical goal of evolutionary biology. Among asexual organisms, genetic adaptation involves multiple mutations that frequently interact in a non-linear fashion (epistasis). Non-linear interactions pose a formidable challenge for the computational prediction of mutation effects. Here we use the recent evolution of β-lactamase under antibiotic selection as a model for genetic adaptation. We build a network of coevolving residues (possible functional interactions), in which nodes are mutant residue positions and links represent two positions found mutated together in the same sequence. Most often these pairs occur in the setting of more complex mutants. Focusing on extended-spectrum resistant sequences, we use network-theoretical tools to identify triple mutant trajectories of likely special significance for adaptation. We extrapolate evolutionary paths (n = 3) that increase resistance and that are longer than the units used to build the network (n = 2). These paths consist of a limited number of residue positions and are enriched for known triple mutant combinations that increase cefotaxime resistance. We find that the pairs of residues used to build the network frequently decrease resistance compared to their corresponding singlets. This is a surprising result, given that their coevolution suggests a selective advantage. Thus, β-lactamase adaptation is highly epistatic. Our method can identify triplets that increase resistance despite the underlying rugged fitness landscape and has the unique ability to make predictions by placing each mutant residue position in its functional context. Our approach requires only sequence information, sufficient genetic diversity, and discrete selective pressures. Thus, it can be used to analyze recent evolutionary events, where coevolution analysis methods that use phylogeny or statistical coupling are not possible. Improving our ability to assess

  4. Temporal entrainment of cognitive functions: musical mnemonics induce brain plasticity and oscillatory synchrony in neural networks underlying memory.

    Science.gov (United States)

    Thaut, Michael H; Peterson, David A; McIntosh, Gerald C

    2005-12-01

    In a series of experiments, we have begun to investigate the effect of music as a mnemonic device on learning and memory and the underlying plasticity of oscillatory neural networks. We used verbal learning and memory tests (standardized word lists, AVLT) in conjunction with electroencephalographic analysis to determine differences between verbal learning in either a spoken or musical (verbal materials as song lyrics) modality. In healthy adults, learning in both the spoken and music condition was associated with significant increases in oscillatory synchrony across all frequency bands. A significant difference between the spoken and music condition emerged in the cortical topography of the learning-related synchronization. When using EEG measures as predictors during learning for subsequent successful memory recall, significantly increased coherence (phase-locked synchronization) within and between oscillatory brain networks emerged for music in alpha and gamma bands. In a similar study with multiple sclerosis patients, superior learning and memory was shown in the music condition when controlled for word order recall, and subjects were instructed to sing back the word lists. Also, the music condition was associated with a significant power increase in the low-alpha band in bilateral frontal networks, indicating increased neuronal synchronization. Musical learning may access compensatory pathways for memory functions during compromised PFC functions associated with learning and recall. Music learning may also confer a neurophysiological advantage through the stronger synchronization of the neuronal cell assemblies underlying verbal learning and memory. Collectively our data provide evidence that melodic-rhythmic templates as temporal structures in music may drive internal rhythm formation in recurrent cortical networks involved in learning and memory.

  5. The risk assessment of sudden water pollution for river network system under multi-source random emission

    Science.gov (United States)

    Li, D.

    2016-12-01

    Sudden water pollution accidents are unavoidable risk events that we must learn to co-exist with. In China's Taihu River Basin, the river flow conditions are complicated with frequently artificial interference. Sudden water pollution accident occurs mainly in the form of a large number of abnormal discharge of wastewater, and has the characteristics with the sudden occurrence, the uncontrollable scope, the uncertainty object and the concentrated distribution of many risk sources. Effective prevention of pollution accidents that may occur is of great significance for the water quality safety management. Bayesian networks can be applied to represent the relationship between pollution sources and river water quality intuitively. Using the time sequential Monte Carlo algorithm, the pollution sources state switching model, water quality model for river network and Bayesian reasoning is integrated together, and the sudden water pollution risk assessment model for river network is developed to quantify the water quality risk under the collective influence of multiple pollution sources. Based on the isotope water transport mechanism, a dynamic tracing model of multiple pollution sources is established, which can describe the relationship between the excessive risk of the system and the multiple risk sources. Finally, the diagnostic reasoning algorithm based on Bayesian network is coupled with the multi-source tracing model, which can identify the contribution of each risk source to the system risk under the complex flow conditions. Taking Taihu Lake water system as the research object, the model is applied to obtain the reasonable results under the three typical years. Studies have shown that the water quality risk at critical sections are influenced by the pollution risk source, the boundary water quality, the hydrological conditions and self -purification capacity, and the multiple pollution sources have obvious effect on water quality risk of the receiving water body

  6. Transcriptome analysis reveals regulatory networks underlying differential susceptibility to Botrytis cinerea in response to nitrogen availability in Solanum lycopersicum.

    Directory of Open Access Journals (Sweden)

    Andrea eVega

    2015-11-01

    Full Text Available Nitrogen (N is one of the main limiting nutrients for plant growth and crop yield. It is well documented that changes in nitrate availability, the main N source found in agricultural soils, influences a myriad of developmental programs and processes including the plant defense response. Indeed, many agronomical reports indicate that the plant N nutritional status influences their ability to respond effectively when challenged by different pathogens. However, the molecular mechanisms involved in N-modulation of plant susceptibility to pathogens are poorly characterized. In this work, we show that Solanum lycopersicum defense response to the necrotrophic fungus Botrytis cinerea is affected by plant N availability, with higher susceptibility in nitrate-limiting conditions. Global gene expression responses of tomato against B. cinerea under contrasting nitrate conditions reveals that plant primary metabolism is affected by the fungal infection regardless of N regimes. This result suggests that differential susceptibility to pathogen attack under contrasting N conditions is not only explained by a metabolic alteration. We used a systems biology approach to identify the transcriptional regulatory network implicated in plant response to the fungus infection under contrasting nitrate conditions. Interestingly, hub genes in this network are known key transcription factors involved in ethylene and jasmonic acid signaling. This result positions these hormones as key integrators of nitrate and defense against B. cinerea in tomato plants. Our results provide insights into potential crosstalk mechanisms between necrotrophic defense response and N status in plants.

  7. Robust Finite-Time Stabilization of Fractional-Order Neural Networks With Discontinuous and Continuous Activation Functions Under Uncertainty.

    Science.gov (United States)

    Ding, Zhixia; Zeng, Zhigang; Wang, Leimin

    2017-03-10

    This paper is concerned with robust finite-time stabilization for a class of fractional-order neural networks (FNNs) with two types of activation functions (i.e., discontinuous and continuous activation function) under uncertainty. It is worth noting that there exist few results about FNNs with discontinuous activation functions, which is mainly because classical solutions and theories of differential equations cannot be applied in this case. Especially, there is no relevant finite-time stabilization research for such system, and this paper makes up for the gap. The existence of global solution under the framework of Filippov for such system is guaranteed by limiting discontinuous activation functions. According to set-valued analysis and Kakutani's fixed point theorem, we obtain the existence of equilibrium point. In particular, based on differential inclusion theory and fractional Lyapunov stability theory, several new sufficient conditions are given to ensure finite-time stabilization via a novel discontinuous controller, and the upper bound of the settling time for stabilization is estimated. In addition, we analyze the finite-time stabilization of FNNs with Lipschitz-continuous activation functions under uncertainty. The results of this paper improve corresponding ones of integer-order neural networks with discontinuous and continuous activation functions. Finally, three numerical examples are given to show the effectiveness of the theoretical results.

  8. Measures of Biochemical Sociology

    Science.gov (United States)

    Snell, Joel; Marsh, Mitchell

    2008-01-01

    In a previous article, the authors introduced a new sub field in sociology that we labeled "biochemical sociology." We introduced the definition of a sociology that encompasses sociological measures, psychological measures, and biological indicators Snell & Marsh (2003). In this article, we want to demonstrate a research strategy that would assess…

  9. Biochemical Education in Brazil.

    Science.gov (United States)

    Vella, F.

    1988-01-01

    Described are discussions held concerning the problems of biochemical education in Brazil at a meeting of the Sociedade Brazileira de Bioquimica in April 1988. Also discussed are other visits that were made to universities in Brazil. Three major recommendations to improve the state of biochemistry education in Brazil are presented. (CW)

  10. CMOS-based Stochastically Spiking Neural Network for Optimization under Uncertainties

    Science.gov (United States)

    2017-03-01

    the digital representation of xin are updated in each clock cycle for F(xin) = u in Fig. 6(b). Thereby, with a random uniform distribution of u...network, and enables power-performance trade-off. Circuit in Fig. 8(a) is triggered by a spike, and produces a pulse controlled by a digital weight-bits...sign(dx/dt) for input variable x. Circuit schematic in Fig. 9(b) computes sign of derivative of its input. Based on clock signals CLK/CLKB

  11. Advanced modelling of doubly fed induction generator wind turbine under network disturbance

    DEFF Research Database (Denmark)

    Seman, S.; Iov, Florin; Niiranen, J.

    This paper presents a variable speed wind turbine simulator. The simulator is used for a 2 MW wind turbine transient behavior study during a short-term symmetrical network disturbance. The mechanical part of wind turbine model consists of the rotor aerodynamic model, the wind turbine control...... and the drive train model. The Doubly Fed Induction Generator (DFIG) is represented by an analytical two-axis model with constant lumped parameters and by Finite Element Method (FEM) based model. The model of the DFIG is coupled with the model of the passive crowbar protected and DTC controlled frequency...

  12. Multidimensional biochemical information processing of dynamical patterns.

    Science.gov (United States)

    Hasegawa, Yoshihiko

    2018-02-01

    Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multidimensional information from dynamical concentration patterns of signaling molecules. We herein study how biochemical systems can process multidimensional information embedded in dynamical patterns. We model the decoding networks by linear response functions, and optimize the functions with the calculus of variations to maximize the mutual information between patterns and output. We find that, when the noise intensity is lower, decoders with different linear response functions, i.e., distinct decoders, can extract much information. However, when the noise intensity is higher, distinct decoders do not provide the maximum amount of information. This indicates that, when transmitting information by dynamical patterns, embedding information in multiple patterns is not optimal when the noise intensity is very large. Furthermore, we explore the biochemical implementations of these decoders using control theory and demonstrate that these decoders can be implemented biochemically through the modification of cascade-type networks, which are prevalent in actual signaling pathways.

  13. Multidimensional biochemical information processing of dynamical patterns

    Science.gov (United States)

    Hasegawa, Yoshihiko

    2018-02-01

    Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multidimensional information from dynamical concentration patterns of signaling molecules. We herein study how biochemical systems can process multidimensional information embedded in dynamical patterns. We model the decoding networks by linear response functions, and optimize the functions with the calculus of variations to maximize the mutual information between patterns and output. We find that, when the noise intensity is lower, decoders with different linear response functions, i.e., distinct decoders, can extract much information. However, when the noise intensity is higher, distinct decoders do not provide the maximum amount of information. This indicates that, when transmitting information by dynamical patterns, embedding information in multiple patterns is not optimal when the noise intensity is very large. Furthermore, we explore the biochemical implementations of these decoders using control theory and demonstrate that these decoders can be implemented biochemically through the modification of cascade-type networks, which are prevalent in actual signaling pathways.

  14. A flood-based information flow analysis and network minimization method for gene regulatory networks.

    Science.gov (United States)

    Pavlogiannis, Andreas; Mozhayskiy, Vadim; Tagkopoulos, Ilias

    2013-04-24

    Biological networks tend to have high interconnectivity, complex topologies and multiple types of interactions. This renders difficult the identification of sub-networks that are involved in condition- specific responses. In addition, we generally lack scalable methods that can reveal the information flow in gene regulatory and biochemical pathways. Doing so will help us to identify key participants and paths under specific environmental and cellular context. This paper introduces the theory of network flooding, which aims to address the problem of network minimization and regulatory information flow in gene regulatory networks. Given a regulatory biological network, a set of source (input) nodes and optionally a set of sink (output) nodes, our task is to find (a) the minimal sub-network that encodes the regulatory program involving all input and output nodes and (b) the information flow from the source to the sink nodes of the network. Here, we describe a novel, scalable, network traversal algorithm and we assess its potential to achieve significant network size reduction in both synthetic and E. coli networks. Scalability and sensitivity analysis show that the proposed method scales well with the size of the network, and is robust to noise and missing data. The method of network flooding proves to be a useful, practical approach towards information flow analysis in gene regulatory networks. Further extension of the proposed theory has the potential to lead in a unifying framework for the simultaneous network minimization and information flow analysis across various "omics" levels.

  15. Exponential synchronization of delayed neutral-type neural networks with Lévy noise under non-Lipschitz condition

    Science.gov (United States)

    Ma, Shuo; Kang, Yanmei

    2018-04-01

    In this paper, the exponential synchronization of stochastic neutral-type neural networks with time-varying delay and Lévy noise under non-Lipschitz condition is investigated for the first time. Using the general Itô's formula and the nonnegative semi-martingale convergence theorem, we derive general sufficient conditions of two kinds of exponential synchronization for the drive system and the response system with adaptive control. Numerical examples are presented to verify the effectiveness of the proposed criteria.

  16. An investigation into the authorship of scientific data webs of a network under construction

    Directory of Open Access Journals (Sweden)

    Jackson da Silva Medeiros

    2016-05-01

    Full Text Available This work aims to analyze the scientific authorship from the data sharing. For this purpose, it uses the Actor-Network Theory (ANT, which seeks, from an idea of symmetry between human and non-human, do not assume a division between those entities, allowing to view the establishment and dissolution of a network from the relationships that are created at different levels. The data collected, which were the basis for description and analysis from the literature that also emerged from what ware collected by observation, interviews and bibliographic materials. The study was carried out by the Repositório de Dados de Estudos Ecológicos do Programa de Pesquisa em Biodiversidade (PPBio. Concludes that conceptual and pragmatic objects can not be seen in isolate way, but like actors directly affected by the technology, should be considered important actants in the process of production, sharing and use of digital research data. The construction of scientific and social fact authorship is coordinated by a number of elements, such as data collection, curation, scientific data and its metadata, funding sources, data policy, repository and its management software for data and metadata, licensing, ownership and responsibility, acting like a kind of exploitation of a phenomena arrangement.

  17. Altered effective connectivity of default model brain network underlying amnestic MCI

    Science.gov (United States)

    Yan, Hao; Wang, Yonghui; Tian, Jie

    2012-02-01

    Mild cognitive impairment (MCI) is the transitional, heterogeneous continuum from healthy elderly to Alzheimer's disease (AD). Previous studies have shown that brain functional activity in the default mode network (DMN) is impaired in MCI patients. However, the altered effective connectivity of the DMN in MCI patients remains largely unknown. The present study combined an independent component analysis (ICA) approach with Granger causality analysis (mGCA) to investigate the effective connectivity within the DMN in 12 amnestic MCI patients and 12 age-matched healthy elderly. Compared to the healthy control, the MCI exhibited decreased functional activity in the posterior DMN regions, as well as a trend towards activity increases in anterior DMN regions. Results from mGCA further supported this conclusion that the causal influence projecting to the precuneus/PCC became much weaker in MCI, while stronger interregional interactions emerged within the frontal-parietal cortices. These findings suggested that abnormal effective connectivity within the DMN may elucidate the dysfunctional and compensatory processes in MCI brain networks.

  18. Using a Novel Wireless-Networked Decentralized Control Scheme under Unpredictable Environmental Conditions.

    Science.gov (United States)

    Chang, Chung-Liang; Huang, Yi-Ming; Hong, Guo-Fong

    2015-11-12

    The direction of sunshine or the installation sites of environmental control facilities in the greenhouse result in different temperature and humidity levels in the various zones of the greenhouse, and thus, the production quality of crop is inconsistent. This study proposed a wireless-networked decentralized fuzzy control scheme to regulate the environmental parameters of various culture zones within a greenhouse. The proposed scheme can create different environmental conditions for cultivating different crops in various zones and achieve diversification or standardization of crop production. A star-type wireless sensor network is utilized to communicate with each sensing node, actuator node, and control node in various zones within the greenhouse. The fuzzy rule-based inference system is used to regulate the environmental parameters for temperature and humidity based on real-time data of plant growth response provided by a growth stage selector. The growth stage selector defines the control ranges of temperature and humidity of the various culture zones according to the leaf area of the plant, the number of leaves, and the cumulative amount of light. The experimental results show that the proposed scheme is stable and robust and provides basis for future greenhouse applications.

  19. Using a Novel Wireless-Networked Decentralized Control Scheme under Unpredictable Environmental Conditions

    Directory of Open Access Journals (Sweden)

    Chung-Liang Chang

    2015-11-01

    Full Text Available The direction of sunshine or the installation sites of environmental control facilities in the greenhouse result in different temperature and humidity levels in the various zones of the greenhouse, and thus, the production quality of crop is inconsistent. This study proposed a wireless-networked decentralized fuzzy control scheme to regulate the environmental parameters of various culture zones within a greenhouse. The proposed scheme can create different environmental conditions for cultivating different crops in various zones and achieve diversification or standardization of crop production. A star-type wireless sensor network is utilized to communicate with each sensing node, actuator node, and control node in various zones within the greenhouse. The fuzzy rule-based inference system is used to regulate the environmental parameters for temperature and humidity based on real-time data of plant growth response provided by a growth stage selector. The growth stage selector defines the control ranges of temperature and humidity of the various culture zones according to the leaf area of the plant, the number of leaves, and the cumulative amount of light. The experimental results show that the proposed scheme is stable and robust and provides basis for future greenhouse applications.

  20. Influence maximization in social networks under an independent cascade-based model

    Science.gov (United States)

    Wang, Qiyao; Jin, Yuehui; Lin, Zhen; Cheng, Shiduan; Yang, Tan

    2016-02-01

    The rapid growth of online social networks is important for viral marketing. Influence maximization refers to the process of finding influential users who make the most of information or product adoption. An independent cascade-based model for influence maximization, called IMIC-OC, was proposed to calculate positive influence. We assumed that influential users spread positive opinions. At the beginning, users held positive or negative opinions as their initial opinions. When more users became involved in the discussions, users balanced their own opinions and those of their neighbors. The number of users who did not change positive opinions was used to determine positive influence. Corresponding influential users who had maximum positive influence were then obtained. Experiments were conducted on three real networks, namely, Facebook, HEP-PH and Epinions, to calculate maximum positive influence based on the IMIC-OC model and two other baseline methods. The proposed model resulted in larger positive influence, thus indicating better performance compared with the baseline methods.

  1. Characterization of dynamical systems under noise using recurrence networks: Application to simulated and EEG data

    Energy Technology Data Exchange (ETDEWEB)

    Puthanmadam Subramaniyam, Narayan, E-mail: npsubramaniyam@gmail.com [Department of Electronics and Communications, Tampere University of Technology, Tampere (Finland); BioMediTech, Tampere (Finland); Hyttinen, Jari [Department of Electronics and Communications, Tampere University of Technology, Tampere (Finland); BioMediTech, Tampere (Finland)

    2014-10-24

    In this letter, we study the influence of observational noise on recurrence network (RN) measures, the global clustering coefficient (C) and average path length (L) using the Rössler system and propose the application of RN measures to analyze the structural properties of electroencephalographic (EEG) data. We find that for an appropriate recurrence rate (RR>0.02) the influence of noise on C can be minimized while L is independent of RR for increasing levels of noise. Indications of structural complexity were found for healthy EEG, but to a lesser extent than epileptic EEG. Furthermore, C performed better than L in case of epileptic EEG. Our results show that RN measures can provide insights into the structural properties of EEG in normal and pathological states. - Highlights: • We study the influence of noise on the recurrence network measures C and L. • We propose the application of C and L to healthy and epileptic EEG data. • The influence of noise can be minimized by increasing the recurrence rate. • Measures C and L can describe the structural complexity of EEG data. • In case of epileptic EEG, C performs better than L.

  2. Energy Management Optimization for Cellular Networks under Renewable Energy Generation Uncertainty

    KAUST Repository

    Rached, Nadhir B.

    2017-03-28

    The integration of renewable energy (RE) as an alternative power source for cellular networks has been deeply investigated in literature. However, RE generation is often assumed to be deterministic; an impractical assumption for realistic scenarios. In this paper, an efficient energy procurement strategy for cellular networks powered simultaneously by the smart grid (SG) and locally deployed RE sources characterized by uncertain processes is proposed. For a one-day operation cycle, the mobile operator aims to reduce its total energy cost by optimizing the amounts of energy to be procured from the local RE sources and SG at each time period. Additionally, it aims to determine the amount of extra generated RE to be sold back to SG. A chance constrained optimization is first proposed to deal with the RE generation uncertainty. Then, two convex approximation approaches: Chernoff and Chebyshev methods, characterized by different levels of knowledge about the RE generation, are developed to determine the energy procurement strategy for different risk levels. In addition, their performances are analyzed for various daily scenarios through selected simulation results. It is shown that the higher complex Chernoff method outperforms the Chebyshev one for different risk levels set by the operator.

  3. Stochastic almost output synchronization for time-varying networks of non-identical and non-introspective agents under external stochastic disturbances and disturbances with known frequencies

    NARCIS (Netherlands)

    Zhang, Meirong; Stoorvogel, Antonie Arij; Saberi, Ali; Belur, Madhu N.; Camlibel, M. Kanat; Rapisarda, Paolo; Scherpen, Jacquelien M.A.

    2015-01-01

    We consider stochastic almost output synchronization for time-varying directed networks of nonidentical and non-introspective (i.e., agents have no access to their own states or outputs) agents under external stochastic disturbances. The network experiences switches at unknown moments in time

  4. Experimental Evaluation of Novel Master-Slave Configurations for Position Control under Random Network Delay and Variable Load for Teleoperation

    Directory of Open Access Journals (Sweden)

    Ahmet Kuzu

    2014-01-01

    Full Text Available This paper proposes two novel master-slave configurations that provide improvements in both control and communication aspects of teleoperation systems to achieve an overall improved performance in position control. The proposed novel master-slave configurations integrate modular control and communication approaches, consisting of a delay regulator to address problems related to variable network delay common to such systems, and a model tracking control that runs on the slave side for the compensation of uncertainties and model mismatch on the slave side. One of the configurations uses a sliding mode observer and the other one uses a modified Smith predictor scheme on the master side to ensure position transparency between the master and slave, while reference tracking of the slave is ensured by a proportional-differentiator type controller in both configurations. Experiments conducted for the networked position control of a single-link arm under system uncertainties and randomly varying network delays demonstrate significant performance improvements with both configurations over the past literature.

  5. Interactive network configuration maintains bacterioplankton community structure under elevated CO2 in a eutrophic coastal mesocosm experiment

    Science.gov (United States)

    Lin, Xin; Huang, Ruiping; Li, Yan; Li, Futian; Wu, Yaping; Hutchins, David A.; Dai, Minhan; Gao, Kunshan

    2018-01-01

    There is increasing concern about the effects of ocean acidification on marine biogeochemical and ecological processes and the organisms that drive them, including marine bacteria. Here, we examine the effects of elevated CO2 on the bacterioplankton community during a mesocosm experiment using an artificial phytoplankton community in subtropical, eutrophic coastal waters of Xiamen, southern China. Through sequencing the bacterial 16S rRNA gene V3-V4 region, we found that the bacterioplankton community in this high-nutrient coastal environment was relatively resilient to changes in seawater carbonate chemistry. Based on comparative ecological network analysis, we found that elevated CO2 hardly altered the network structure of high-abundance bacterioplankton taxa but appeared to reassemble the community network of low abundance taxa. This led to relatively high resilience of the whole bacterioplankton community to the elevated CO2 level and associated chemical changes. We also observed that the Flavobacteria group, which plays an important role in the microbial carbon pump, showed higher relative abundance under the elevated CO2 condition during the early stage of the phytoplankton bloom in the mesocosms. Our results provide new insights into how elevated CO2 may influence bacterioplankton community structure.

  6. Interactive network configuration maintains bacterioplankton community structure under elevated CO2 in a eutrophic coastal mesocosm experiment

    Directory of Open Access Journals (Sweden)

    X. Lin

    2018-01-01

    Full Text Available There is increasing concern about the effects of ocean acidification on marine biogeochemical and ecological processes and the organisms that drive them, including marine bacteria. Here, we examine the effects of elevated CO2 on the bacterioplankton community during a mesocosm experiment using an artificial phytoplankton community in subtropical, eutrophic coastal waters of Xiamen, southern China. Through sequencing the bacterial 16S rRNA gene V3-V4 region, we found that the bacterioplankton community in this high-nutrient coastal environment was relatively resilient to changes in seawater carbonate chemistry. Based on comparative ecological network analysis, we found that elevated CO2 hardly altered the network structure of high-abundance bacterioplankton taxa but appeared to reassemble the community network of low abundance taxa. This led to relatively high resilience of the whole bacterioplankton community to the elevated CO2 level and associated chemical changes. We also observed that the Flavobacteria group, which plays an important role in the microbial carbon pump, showed higher relative abundance under the elevated CO2 condition during the early stage of the phytoplankton bloom in the mesocosms. Our results provide new insights into how elevated CO2 may influence bacterioplankton community structure.

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

    DEFF Research Database (Denmark)

    Herz, Damian M.; Haagensen, Brian N.; Christensen, Mark S.

    2015-01-01

    Dopaminergic signalling in the striatum contributes to reinforcement of actions and motivational enhancement of motor vigour. Parkinson's disease leads to progressive dopaminergic denervation of the striatum, impairing the function of cortico-basal ganglia networks. While levodopa therapy...... alleviates basal ganglia dysfunction in Parkinson's disease, it often elicits involuntary movements, referred to as levodopa-induced peak-of-dose dyskinesias. Here, we used a novel pharmacodynamic neuroimaging approach to identify the changes in cortico-basal ganglia connectivity that herald the emergence...... of levodopa-induced dyskinesias. Twenty-six patients with Parkinson's disease (age range: 51–84 years; 11 females) received a single dose of levodopa and then performed a task in which they had to produce or suppress a movement in response to visual cues. Task-related activity was continuously mapped...

  8. Distributed detection in UWB sensor networks under non-orthogonal Nakagami-m fading

    KAUST Repository

    Mehbodniya, Abolfazl

    2011-09-01

    Several attractive features of ultra wideband (UWB) communications make it a good candidate for physical-layer of wireless sensor networks (WSN). These features include low power consumption, low complexity and low cost of implementation. In this paper, we present an opportunistic power assignment strategy for distributed detection in parallel fusion WSNs, considering a Nakagami-m fading model for the communication channel and time-hopping (TH) UWB for the transmitter circuit of the sensor nodes. In a parallel fusion WSN, local decisions are made by local sensors and transmitted through wireless channels to a fusion center. The fusion center processes the information and makes the final decision. Simulation results are provided for the global probability of detection error and relative performance gain to evaluate the efficiency of the proposed power assignment strategy in different fading environments. © 2011 IEEE.

  9. Developing a cross-docking network design model under uncertain environment

    Science.gov (United States)

    Seyedhoseini, S. M.; Rashid, Reza; Teimoury, E.

    2014-09-01

    Cross-docking is a logistic concept, which plays an important role in supply chain management by decreasing inventory holding, order packing, transportation costs and delivery time. Paying attention to these concerns, and importance of the congestion in cross docks, we present a mixed-integer model to optimize the location and design of cross docks at the same time to minimize the total transportation and operating costs. The model combines queuing theory for design aspects, for that matter, we consider a network of cross docks and customers where two M/M/c queues have been represented to describe operations of indoor trucks and outdoor trucks in each cross dock. To prepare a perfect illustration for performance of the model, a real case also has been examined that indicated effectiveness of the proposed model.

  10. Developing a cross-docking network design model under uncertain environment

    Science.gov (United States)

    Seyedhoseini, S. M.; Rashid, Reza; Teimoury, E.

    2015-06-01

    Cross-docking is a logistic concept, which plays an important role in supply chain management by decreasing inventory holding, order packing, transportation costs and delivery time. Paying attention to these concerns, and importance of the congestion in cross docks, we present a mixed-integer model to optimize the location and design of cross docks at the same time to minimize the total transportation and operating costs. The model combines queuing theory for design aspects, for that matter, we consider a network of cross docks and customers where two M/M/c queues have been represented to describe operations of indoor trucks and outdoor trucks in each cross dock. To prepare a perfect illustration for performance of the model, a real case also has been examined that indicated effectiveness of the proposed model.

  11. Spectral network based on component cells under the SOPHIA European project

    Energy Technology Data Exchange (ETDEWEB)

    Núñez, Rubén, E-mail: ruben.nunez@ies-def.upm.es; Antón, Ignacio; Askins, Steve; Sala, Gabriel [Instituto de Energía Solar - Universidad Politécnica de Madrid, Ciudad Universitaria, 28040 Madrid (Spain); Domínguez, César; Voarino, Philippe [CEA-INES, 50 avenue du Lac Léman, 73375 Le Bourget-du-Lac (France); Steiner, Marc; Siefer, Gerald [Fraunhofer ISE, Heidenhofstr. 2, 79110 Freiburg (Germany); Fucci, Rafaelle; Roca, Franco [ENEA, P.le E.Fermi 1, Località Granatello, 80055 Portici (Italy); Minuto, Alessandro; Morabito, Paolo [RSE, Via Rubattino 54, 20134 Milan (Italy)

    2015-09-28

    In the frame of the European project SOPHIA, a spectral network based on component (also called isotypes) cells has been created. Among the members of this project, several spectral sensors based on component cells and collimating tubes, so-called spectroheliometers, were installed in the last years, allowing the collection of minute-resolution spectral data useful for CPV systems characterization across Europe. The use of spectroheliometers has been proved useful to establish the necessary spectral conditions to perform power rating of CPV modules and systems. If enough data in a given period of time is collected, ideally a year, it is possible to characterize spectrally the place where measurements are taken, in the same way that hours of annual irradiation can be estimated using a pyrheliometer.

  12. Discussion on the nuclear information resources co-constructing and sharing under network information

    International Nuclear Information System (INIS)

    Wu Yang

    2010-01-01

    During the tenth five-year plan, along with the digitization of information, and the development of information transmission network, the co-construction and sharing of China's nuclear industry information is facing a new development opportunities and challenges. This paper is based on the analysis of the nuclear library status and characteristics, combined of the development process of nuclear information resources over the past 20 years. For the characteristic of information sharing and services in the net environment, the problem in the current co-construction and sharing of nuclear information, and the needs of the future nuclear research and development of nuclear production, this paper forecast the work trends of nuclear information, and gives some countermeasure to strength the development of the co-construction and sharing of nuclear information. (author)

  13. Hybrid Electromagnetism-Like Algorithm for Dynamic Supply Chain Network Design under Traffic Congestion and Uncertainty

    Directory of Open Access Journals (Sweden)

    Javid Jouzdani

    2016-01-01

    Full Text Available With the constantly increasing pressure of the competitive environment, supply chain (SC decision makers are forced to consider several aspects of business climate. More specifically, they should take into account the endogenous features (e.g., available means of transportation, and the variety of products and exogenous criteria (e.g., the environmental uncertainty, and transportation system conditions. In this paper, a mixed integer nonlinear programming (MINLP model for dynamic design of a supply chain network is proposed. In this model, multiple products and multiple transportation modes, the time value of money, traffic congestion, and both supply-side and demand-side uncertainties are considered. Due to the complexity of such models, conventional solution methods are not applicable; therefore, two hybrid Electromagnetism-Like Algorithms (EMA are designed and discussed for tackling the problem. The numerical results show the applicability of the proposed model and the capabilities of the solution approaches to the MINLP problem.

  14. Global dysrhythmia of cerebro-basal ganglia-cerebellar networks underlies motor tics following striatal disinhibition.

    Science.gov (United States)

    McCairn, Kevin W; Iriki, Atsushi; Isoda, Masaki

    2013-01-09

    Motor tics, a cardinal symptom of Tourette syndrome (TS), are hypothesized to arise from abnormalities within cerebro-basal ganglia circuits. Yet noninvasive neuroimaging of TS has previously identified robust activation in the cerebellum. To date, electrophysiological properties of cerebellar activation and its role in basal ganglia-mediated tic expression remain unknown. We performed multisite, multielectrode recordings of single-unit activity and local field potentials from the cerebellum, basal ganglia, and primary motor cortex using a pharmacologic monkey model of motor tics/TS. Following microinjections of bicuculline into the sensorimotor putamen, periodic tics occurred predominantly in the orofacial region, and a sizable number of cerebellar neurons showed phasic changes in activity associated with tic episodes. Specifically, 64% of the recorded cerebellar cortex neurons exhibited increases in activity, and 85% of the dentate nucleus neurons displayed excitatory, inhibitory, or multiphasic responses. Critically, abnormal discharges of cerebellar cortex neurons and excitatory-type dentate neurons mostly preceded behavioral tic onset, indicating their central origins. Latencies of pathological activity in the cerebellum and primary motor cortex substantially overlapped, suggesting that aberrant signals may be traveling along divergent pathways to these structures from the basal ganglia. Furthermore, the occurrence of tic movement was most closely associated with local field potential spikes in the cerebellum and primary motor cortex, implying that these structures may function as a gate to release overt tic movements. These findings indicate that tic-generating networks in basal ganglia mediated tic disorders extend beyond classical cerebro-basal ganglia circuits, leading to global network dysrhythmia including cerebellar circuits.

  15. Metapopulation modelling of riparian tree species persistence in river networks under climate change.

    Science.gov (United States)

    Van Looy, Kris; Piffady, Jérémy

    2017-11-01

    Floodplain landscapes are highly fragmented by river regulation resulting in habitat degradation and flood regime perturbation, posing risks to population persistence. Climate change is expected to pose supplementary risks in this context of fragmented landscapes, and especially for river systems adaptation management programs are developed. The association of habitat quality and quantity with the landscape dynamics and resilience to human-induced disturbances is still poorly understood in the context of species survival and colonization processes, but essential to prioritize conservation and restoration actions. We present a modelling approach that elucidates network connectivity and landscape dynamics in spatial and temporal context to identify vital corridors and conservation priorities in the Loire river and its tributaries. Alteration of flooding and flow regimes is believed to be critical to population dynamics in river ecosystems. Still, little is known of critical levels of alteration both spatially and temporally. We applied metapopulation modelling approaches for a dispersal-limited tree species, white elm; and a recruitment-limited tree species, black poplar. In different model steps the connectivity and natural dynamics of the river landscape are confronted with physical alterations (dams/dykes) to species survival and then future scenarios for climatic changes and potential adaptation measures are entered in the model and translated in population persistence over the river basin. For the two tree species we highlighted crucial network zones in relation to habitat quality and connectivity. Where the human impact model already shows currently restricted metapopulation development, climate change is projected to aggravate this persistence perspective substantially. For both species a significant drawback to the basin population is observed, with 1/3 for elm and ¼ for poplar after 25 years already. But proposed adaptation measures prove effective to even

  16. Estimation of lost circulation amount occurs during under balanced drilling using drilling data and neural network

    Directory of Open Access Journals (Sweden)

    Pouria Behnoud far

    2017-09-01

    Full Text Available Lost circulation can cause an increase in time and cost of operation. Pipe sticking, formation damage and uncontrolled flow of oil and gas may be consequences of lost circulation. Dealing with this problem is a key factor to conduct a successful drilling operation. Estimation of lost circulation amount is necessary to find a solution. Lost circulation is influenced by different parameters such as mud weight, pump pressure, depth etc. Mud weight, pump pressure and flow rate of mud should be designed to prevent induced fractures and have the least amount of lost circulation. Artificial neural network is useful to find the relations of parameters with lost circulation. Genetic algorithm is applied on the achieved relations to determine the optimum mud weight, pump pressure, and flow rate. In an Iranian oil field, daily drilling reports of wells which are drilled using UBD technique are studied. Asmari formation is the most important oil reservoir of the studied field and UBD is used only in this interval. Three wells with the most, moderate and without lost circulation are chosen. In this article, the effect of mud weight, depth, pump pressure and flow rate of pump on lost circulation in UBD of Asmari formation in one of the Southwest Iranian fields is studied using drilling data and artificial neural network. In addition, the amount of lost circulation is predicted precisely with respect to two of the studied parameters using the presented correlations and the optimum mud weight, pump pressure and flow rate are calculated to minimize the lost circulation amount.

  17. An Interference Mitigation Scheme of Device-to-Device Communications for Sensor Networks Underlying LTE-A.

    Science.gov (United States)

    Kim, Jeehyeong; Karim, Nzabanita Abdoul; Cho, Sunghyun

    2017-05-10

    Device-to-Device (D2D) communication technology has become a key factor in wireless sensor networks to form autonomous communication links among sensor nodes. Many research results for D2D have been presented to resolve different technical issues of D2D. Nevertheless, the previous works have not resolved the shortage of data rate and limited coverage of wireless sensor networks. Due to bandwidth shortages and limited communication coverage, 3rd Generation Partnership Project (3GPP) has introduced a new Device-to-Device (D2D) communication technique underlying cellular networks, which can improve spectral efficiencies by enabling the direct communication of devices in proximity without passing through enhanced-NodeB (eNB). However, to enable D2D communication in a cellular network presents a challenge with regard to radio resource management since D2D links reuse the uplink radio resources of cellular users and it can cause interference to the receiving channels of D2D user equipment (DUE). In this paper, a hybrid mechanism is proposed that uses Fractional Frequency Reuse (FFR) and Almost Blank Sub-frame (ABS) schemes to handle inter-cell interference caused by cellular user equipments (CUEs) to D2D receivers (DUE-Rxs), reusing the same resources at the cell edge area. In our case, DUE-Rxs are considered as victim nodes and CUEs as aggressor nodes, since our primary target is to minimize inter-cell interference in order to increase the signal to interference and noise ratio (SINR) of the target DUE-Rx at the cell edge area. The numerical results show that the interference level of the target D2D receiver (DUE-Rx) decreases significantly compared to the conventional FFR at the cell edge. In addition, the system throughput of the proposed scheme can be increased up to 60% compared to the conventional FFR.

  18. Characterization of biochemical behavior of sorghum ( Sorghum ...

    African Journals Online (AJOL)

    The aim of this research was to characterize the biochemical behavior of sorghum plants under saline stress using multivariate statistical analysis methods for efficient management of Sorghum bicolor [Moench.]). The experimental design was completely randomized design composed of three saline concentrations (0, 1.5 ...

  19. Prediction of composite fatigue life under variable amplitude loading using artificial neural network trained by genetic algorithm

    Science.gov (United States)

    Rohman, Muhamad Nur; Hidayat, Mas Irfan P.; Purniawan, Agung

    2018-04-01

    Neural networks (NN) have been widely used in application of fatigue life prediction. In the use of fatigue life prediction for polymeric-base composite, development of NN model is necessary with respect to the limited fatigue data and applicable to be used to predict the fatigue life under varying stress amplitudes in the different stress ratios. In the present paper, Multilayer-Perceptrons (MLP) model of neural network is developed, and Genetic Algorithm was employed to optimize the respective weights of NN for prediction of polymeric-base composite materials under variable amplitude loading. From the simulation result obtained with two different composite systems, named E-glass fabrics/epoxy (layups [(±45)/(0)2]S), and E-glass/polyester (layups [90/0/±45/0]S), NN model were trained with fatigue data from two different stress ratios, which represent limited fatigue data, can be used to predict another four and seven stress ratios respectively, with high accuracy of fatigue life prediction. The accuracy of NN prediction were quantified with the small value of mean square error (MSE). When using 33% from the total fatigue data for training, the NN model able to produce high accuracy for all stress ratios. When using less fatigue data during training (22% from the total fatigue data), the NN model still able to produce high coefficient of determination between the prediction result compared with obtained by experiment.

  20. Performance analysis of multi-radio routing protocol in cognitive radio ad hoc networks under different path failure rate

    International Nuclear Information System (INIS)

    Che-Aron, Z; Abdalla, A H; Abdullah, K; Hassan, W H

    2013-01-01

    In recent years, Cognitive Radio (CR) technology has largely attracted significant studies and research. Cognitive Radio Ad Hoc Network (CRAHN) is an emerging self-organized, multi-hop, wireless network which allows unlicensed users to opportunistically access available licensed spectrum bands for data communication under an intelligent and cautious manner. However, in CRAHNs, a lot of failures can easily occur during data transmission caused by PU (Primary User) activity, topology change, node fault, or link degradation. In this paper, an attempt has been made to evaluate the performance of the Multi-Radio Link-Quality Source Routing (MR-LQSR) protocol in CRAHNs under different path failure rate. In the MR-LQSR protocol, the Weighted Cumulative Expected Transmission Time (WCETT) is used as the routing metric. The simulations are carried out using the NS-2 simulator. The protocol performance is evaluated with respect to performance metrics like average throughput, packet loss, average end-to-end delay and average jitter. From the simulation results, it is observed that the number of path failures depends on the PUs number and mobility rate of SUs (Secondary Users). Moreover, the protocol performance is greatly affected when the path failure rate is high, leading to major service outages

  1. Monitoring of biofilm formation and activity in drinking water distribution networks under oligotrophic conditions

    DEFF Research Database (Denmark)

    Boe-Hansen, Rasmus; Martiny, Adam Camillo; Arvin, Erik

    2003-01-01

    In this study, the construction a model distribution system suitable for studies of attached and suspended microbial activity in drinking water under controlled circumstances is outlined. The model system consisted of two loops connected in series with a total of 140 biofilm sampling points...

  2. Local biochemical and morphological differences in human Achilles tendinopathy

    DEFF Research Database (Denmark)

    Pingel, Jessica; Fredberg, U.; Qvortrup, Klaus

    2012-01-01

    The incidence of Achilles tendinopathy is high and underlying etiology as well as biochemical and morphological pathology associated with the disease is largely unknown. The aim of the present study was to describe biochemical and morphological differences in chronic Achilles tendinopathy....... The expressions of growth factors, inflammatory mediators and tendon morphology were determined in both chronically diseased and healthy tendon parts....

  3. The role of the default mode network in component processes underlying the wandering mind.

    Science.gov (United States)

    Poerio, Giulia L; Sormaz, Mladen; Wang, Hao-Ting; Margulies, Daniel; Jefferies, Elizabeth; Smallwood, Jonathan

    2017-07-01

    Experiences such as mind-wandering illustrate that cognition is not always tethered to events in the here-and-now. Although converging evidence emphasises the default mode network (DMN) in mind-wandering, its precise contribution remains unclear. The DMN comprises cortical regions that are maximally distant from primary sensory and motor cortex, a topological location that may support the stimulus-independence of mind-wandering. The DMN is functionally heterogeneous, comprising regions engaged by memory, social cognition and planning; processes relevant to mind-wandering content. Our study examined the relationships between: (i) individual differences in resting-state DMN connectivity, (ii) performance on memory, social and planning tasks and (iii) variability in spontaneous thought, to investigate whether the DMN is critical to mind-wandering because it supports stimulus-independent cognition, memory retrieval, or both. Individual variation in task performance modulated the functional organization of the DMN: poor external engagement was linked to stronger coupling between medial and dorsal subsystems, while decoupling of the core from the cerebellum predicted reports of detailed memory retrieval. Both patterns predicted off-task future thoughts. Consistent with predictions from component process accounts of mind-wandering, our study suggests a 2-fold involvement of the DMN: (i) it supports experiences that are unrelated to the environment through strong coupling between its sub-systems; (ii) it allows memory representations to form the basis of conscious experience. © The Author (2017). Published by Oxford University Press.

  4. Artificial neural networks based estimation of optical parameters by diffuse reflectance imaging under in vitro conditions

    Directory of Open Access Journals (Sweden)

    Mahmut Ozan Gökkan

    2017-01-01

    Full Text Available Optical parameters (properties of tissue-mimicking phantoms are determined through noninvasive optical imaging. Objective of this study is to decompose obtained diffuse reflectance into these optical properties such as absorption and scattering coefficients. To do so, transmission spectroscopy is firstly used to measure the coefficients via an experimental setup. Next, the optical properties of each characterized phantom are input for Monte Carlo (MC simulations to get diffuse reflectance. Also, a surface image for each single phantom with its known optical properties is obliquely captured due to reflectance-based geometrical setup using CMOS camera that is positioned at 5∘ angle to the phantoms. For the illumination of light, a laser light source at 633nm wavelength is preferred, because optical properties of different components in a biological tissue on that wavelength are nonoverlapped. During in vitro measurements, we prepared 30 different mixture samples adding clinoleic intravenous lipid emulsion (CILE and evans blue (EB dye into a distilled water. Finally, all obtained diffuse reflectance values are used to estimate the optical coefficients by artificial neural networks (ANNs in inverse modeling. For a biological tissue it is found that the simulated and measured values in our results are in good agreement.

  5. Flow and pressures networks simulation under VisSim trademark graphic interphase

    International Nuclear Information System (INIS)

    Roldan-Villasana, E.J.; Porras-Loaiza, G.L.; Jimenez-Sauma, B.; Berdon-Alarcon, R.

    1996-01-01

    In this work, a graphic interphase to facilitate the interaction between the user and a flow and pressure network (FPN) model is presented. The graphic interphase was designed using the VisSim trademark commercial software (VisSim, 1994) which is a visual programming mathematical tool that allows direct simulation from graphics constructed using block diagrams. VisSim trademark was not used to solve the FPN but an external program (solver) was designed ex professo. The reason for this is that VisSim trademark is not able to work with a model whose structure may vary in size and topology. Thus, VisSim trademark was used as a graphic interphase exclusively. The main problem was to interpret the flow diagram (which shows the topology of the system) to feed the solver. This interpretation was made with a preprocessor which reads the VisSim trademark data file (·VSM file) containing the information of all the VisSim trademark configuration, extracts the information of the topology, and feeds the solver

  6. Radio/Antenna Mounting System for Wireless Networking under Row-Crop Agriculture Conditions

    Directory of Open Access Journals (Sweden)

    Daniel K. Fisher

    2015-07-01

    Full Text Available Interest in and deployment of wireless monitoring systems is increasing in many diverse environments, including row-crop agricultural fields. While many studies have been undertaken to evaluate various aspects of wireless monitoring and networking, such as electronic hardware components, data-collection procedures, power management, and communication protocols, little information related to physical deployment issues has been reported. To achieve acceptable wireless transmission capability, the radio/antenna must be positioned properly relative to the ground surface or crop canopy to minimize degradation of the radio signal, usually requiring the mounting of the radio/antenna above the canopy. This results in the presence of obstacles to normal agricultural equipment traffic and production operations and potential damage to the wireless monitoring system. A simple and rugged radio/antenna mounting system was designed which could be subjected to encounters with agricultural equipment without suffering physical damage. The mounting system was deployed and tested, and operated successfully following repeated encounters with various agricultural machines and implements. The radio/antenna mount is simple and inexpensive to fabricate using locally available components.

  7. The influence of age and mild cognitive impairment on associative memory performance and underlying brain networks.

    Science.gov (United States)

    Oedekoven, Christiane S H; Jansen, Andreas; Keidel, James L; Kircher, Tilo; Leube, Dirk

    2015-12-01

    Associative memory is essential to everyday activities, such as the binding of faces and corresponding names to form single bits of information. However, this ability often becomes impaired with increasing age. The most important neural substrate of associative memory is the hippocampus, a structure crucially implicated in the pathogenesis of Alzheimer's disease (AD). The main aim of this study was to compare neural correlates of associative memory in healthy aging and mild cognitive impairment (MCI), an at-risk state for AD. We used fMRI to investigate differences in brain activation and connectivity between young controls (n = 20), elderly controls (n = 32) and MCI patients (n = 21) during associative memory retrieval. We observed lower hippocampal activation in MCI patients than control groups during a face-name recognition task, and the magnitude of this decrement was correlated with lower associative memory performance. Further, increased activation in precentral regions in all older adults indicated a stronger involvement of the task positive network (TPN) with age. Finally, functional connectivity analysis revealed a stronger link of hippocampal and striatal components in older adults in comparison to young controls, regardless of memory impairment. In elderly controls, this went hand-in-hand with a stronger activation of striatal areas. Increased TPN activation may be linked to greater reliance on cognitive control in both older groups, while increased functional connectivity between the hippocampus and the striatum may suggest dedifferentiation, especially in elderly controls.

  8. Intelligent Management System of Power Network Information Collection Under Big Data Storage

    Directory of Open Access Journals (Sweden)

    Qin Yingying

    2017-01-01

    Full Text Available With the development of economy and society, big data storage in enterprise management has become a problem that can’t be ignored. How to manage and optimize the allocation of tasks better is an important factor in the sustainable development of an enterprise. Now the enterprise information intelligent management has become a hot spot of management mode and concept in the information age. It presents information to the business managers in a more efficient, lower cost, and global form. The system uses the SG-UAP development tools, which is based on Eclipse development environment, and suits for Windows operating system, with Oracle as database development platform, Tomcat network information service for application server. The system uses SOA service-oriented architecture, provides RESTful style service, and HTTP(S as the communication protocol, and JSON as the data format. The system is divided into two parts, the front-end and the backs-end, achieved functions like user login, registration, password retrieving, enterprise internal personnel information management and internal data display and other functions.

  9. Modeling of agent-based complex network under cyber-violence

    Science.gov (United States)

    Huang, Chuanchao; Hu, Bin; Jiang, Guoyin; Yang, Ruixian

    2016-09-01

    Public opinion reversal arises frequently in modern society, due to the continual interactions between individuals and their surroundings. To explore the underlying mechanism of the interesting social phenomenon, we introduce here a new model which takes the relationship between the individual cognitive bias and their corresponding choice behavior into account. Experimental results show that the proposed model can provide an accurate description of the entire process of public opinion reversal under the internet environment and the distribution of cognitive bias plays the role of a measure for the reversal probability. In particular, the application to cyber violence, a typical example of public opinion reversal, suggests that public opinion is prone to be seriously affected by the spread of misleading and harmful information. Furthermore, our model is very robust and thus can be employed to other empirical studies that concern the sudden change of public and personal opinion on internet.

  10. Valuing Expansions of the Electricity Transmission Network under Uncertainty: The Binodal Case

    Directory of Open Access Journals (Sweden)

    José M. Chamorro

    2011-10-01

    Full Text Available Transmission investments are currently needed to meet an increasing electricity demand, to address security of supply concerns, and to reach carbon-emissions targets. A key issue when assessing the benefits from an expanded grid concerns the valuation of the uncertain cash flows that result from the expansion. We propose a valuation model that accommodates both physical and economic uncertainties following the Real Options approach. It combines optimization techniques with Monte Carlo simulation. We illustrate the use of our model in a simplified, two-node grid and assess the decision whether to invest or not in a particular upgrade. The generation mix includes coal- and natural gas-fired stations that operate under carbon constraints. The underlying parameters are estimated from observed market data.

  11. Improved methods for the mathematically controlled comparison of biochemical systems

    Directory of Open Access Journals (Sweden)

    Schwacke John H

    2004-06-01

    Full Text Available Abstract The method of mathematically controlled comparison provides a structured approach for the comparison of alternative biochemical pathways with respect to selected functional effectiveness measures. Under this approach, alternative implementations of a biochemical pathway are modeled mathematically, forced to be equivalent through the application of selected constraints, and compared with respect to selected functional effectiveness measures. While the method has been applied successfully in a variety of studies, we offer recommendations for improvements to the method that (1 relax requirements for definition of constraints sufficient to remove all degrees of freedom in forming the equivalent alternative, (2 facilitate generalization of the results thus avoiding the need to condition those findings on the selected constraints, and (3 provide additional insights into the effect of selected constraints on the functional effectiveness measures. We present improvements to the method and related statistical models, apply the method to a previously conducted comparison of network regulation in the immune system, and compare our results to those previously reported.

  12. Dynamic modeling and control of DFIG-based wind turbines under balanced network conditions

    DEFF Research Database (Denmark)

    Mehdipour, Cyrous; Hajizadeh, Amin; Mehdipour, Iman

    2016-01-01

    The performance of wind power station is researched by utilizing a detailed model which includes a wind turbine (WT), doubly fed induction generator (DFIG) and power electronic devices. In the initial stage, a comprehensive review and definition of each part of this system are presented....... Then dynamic modeling and simulation of a sample power system are carried out. The operation of a DFIG coupled with WT under balanced condition of a power grid is investigated and stationary reference frame is utilized for analysis of a wind energy conversion system. At the second step, a wind power station...

  13. Decision making under uncertainty in a spiking neural network model of the basal ganglia.

    Science.gov (United States)

    Héricé, Charlotte; Khalil, Radwa; Moftah, Marie; Boraud, Thomas; Guthrie, Martin; Garenne, André

    2016-12-01

    The mechanisms of decision-making and action selection are generally thought to be under the control of parallel cortico-subcortical loops connecting back to distinct areas of cortex through the basal ganglia and processing motor, cognitive and limbic modalities of decision-making. We have used these properties to develop and extend a connectionist model at a spiking neuron level based on a previous rate model approach. This model is demonstrated on decision-making tasks that have been studied in primates and the electrophysiology interpreted to show that the decision is made in two steps. To model this, we have used two parallel loops, each of which performs decision-making based on interactions between positive and negative feedback pathways. This model is able to perform two-level decision-making as in primates. We show here that, before learning, synaptic noise is sufficient to drive the decision-making process and that, after learning, the decision is based on the choice that has proven most likely to be rewarded. The model is then submitted to lesion tests, reversal learning and extinction protocols. We show that, under these conditions, it behaves in a consistent manner and provides predictions in accordance with observed experimental data.

  14. Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops--A Proteomic Perspective.

    Science.gov (United States)

    Kosová, Klára; Vítámvás, Pavel; Urban, Milan Oldřich; Klíma, Miroslav; Roy, Amitava; Prášil, Ilja Tom

    2015-09-01

    Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum), durum wheat (Triticum durum), barley (Hordeum vulgare), maize (Zea mays); leguminous plants: alfalfa (Medicago sativa), soybean (Glycine max), common bean (Phaseolus vulgaris), pea (Pisum sativum); oilseed rape (Brassica napus); potato (Solanum tuberosum); tobacco (Nicotiana tabaccum); tomato (Lycopersicon esculentum); and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals) are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton) are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed.

  15. Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops—A Proteomic Perspective

    Science.gov (United States)

    Kosová, Klára; Vítámvás, Pavel; Urban, Milan Oldřich; Klíma, Miroslav; Roy, Amitava; Prášil, Ilja Tom

    2015-01-01

    Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum), durum wheat (Triticum durum), barley (Hordeum vulgare), maize (Zea mays); leguminous plants: alfalfa (Medicago sativa), soybean (Glycine max), common bean (Phaseolus vulgaris), pea (Pisum sativum); oilseed rape (Brassica napus); potato (Solanum tuberosum); tobacco (Nicotiana tabaccum); tomato (Lycopersicon esculentum); and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals) are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton) are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed. PMID:26340626

  16. Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops—A Proteomic Perspective

    Directory of Open Access Journals (Sweden)

    Klára Kosová

    2015-09-01

    Full Text Available Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum, durum wheat (Triticum durum, barley (Hordeum vulgare, maize (Zea mays; leguminous plants: alfalfa (Medicago sativa, soybean (Glycine max, common bean (Phaseolus vulgaris, pea (Pisum sativum; oilseed rape (Brassica napus; potato (Solanum tuberosum; tobacco (Nicotiana tabaccum; tomato (Lycopersicon esculentum; and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed.

  17. Loss of variation of state detected in soybean metabolic and human myelomonocytic leukaemia cell transcriptional networks under external stimuli

    KAUST Repository

    Sakata, Katsumi

    2016-10-24

    Soybean (Glycine max) is sensitive to flooding stress, and flood damage at the seedling stage is a barrier to growth. We constructed two mathematical models of the soybean metabolic network, a control model and a flooded model, from metabolic profiles in soybean plants. We simulated the metabolic profiles with perturbations before and after the flooding stimulus using the two models. We measured the variation of state that the system could maintain from a state–space description of the simulated profiles. The results showed a loss of variation of state during the flooding response in the soybean plants. Loss of variation of state was also observed in a human myelomonocytic leukaemia cell transcriptional network in response to a phorbol-ester stimulus. Thus, we detected a loss of variation of state under external stimuli in two biological systems, regardless of the regulation and stimulus types. Our results suggest that a loss of robustness may occur concurrently with the loss of variation of state in biological systems. We describe the possible applications of the quantity of variation of state in plant genetic engineering and cell biology. Finally, we present a hypothetical “external stimulus-induced information loss” model of biological systems.

  18. [Calculation of soil water erosion modulus based on RUSLE and its assessment under support of artificial neural network].

    Science.gov (United States)

    Li, Yuhuan; Wang, Jing; Zhang, Jixian

    2006-06-01

    With Hengshan County of Shanxi Province in the North Loess Plateau as an example, and by using ETM + and remote sensing data and RUSLE module, this paper quantitatively derived the soil and water loss in loess hilly region based on "3S" technology, and assessed the derivation results under the support of artificial neural network. The results showed that the annual average erosion modulus of Hengshan County was 103.23 t x hm(-2), and the gross erosion loss per year was 4. 38 x 10(7) t. The erosion was increased from northwest to southeast, and varied significantly with topographic position. A slight erosion or no erosion happened in walled basin, flat-headed mountain ridges and sandy area, which always suffered from dropping erosion, while strip erosion often happened on the upslope of mountain ridge and mountaintop flat. Moderate rill erosion always occurred on the middle and down slope of mountain ridge and mountaintop flat, and weighty rushing erosion occurred on the steep ravine and brink. The RUSLE model and artificial neural network technique were feasible and could be propagandized for drainage areas control and preserved practice.

  19. A multi-objective optimization model for hub network design under uncertainty: An inexact rough-interval fuzzy approach

    Science.gov (United States)

    Niakan, F.; Vahdani, B.; Mohammadi, M.

    2015-12-01

    This article proposes a multi-objective mixed-integer model to optimize the location of hubs within a hub network design problem under uncertainty. The considered objectives include minimizing the maximum accumulated travel time, minimizing the total costs including transportation, fuel consumption and greenhouse emissions costs, and finally maximizing the minimum service reliability. In the proposed model, it is assumed that for connecting two nodes, there are several types of arc in which their capacity, transportation mode, travel time, and transportation and construction costs are different. Moreover, in this model, determining the capacity of the hubs is part of the decision-making procedure and balancing requirements are imposed on the network. To solve the model, a hybrid solution approach is utilized based on inexact programming, interval-valued fuzzy programming and rough interval programming. Furthermore, a hybrid multi-objective metaheuristic algorithm, namely multi-objective invasive weed optimization (MOIWO), is developed for the given problem. Finally, various computational experiments are carried out to assess the proposed model and solution approaches.

  20. Distribution network design under demand uncertainty using genetic algorithm and Monte Carlo simulation approach: a case study in pharmaceutical industry

    Science.gov (United States)

    Izadi, Arman; Kimiagari, Ali Mohammad

    2014-05-01

    Distribution network design as a strategic decision has long-term effect on tactical and operational supply chain management. In this research, the location-allocation problem is studied under demand uncertainty. The purposes of this study were to specify the optimal number and location of distribution centers and to determine the allocation of customer demands to distribution centers. The main feature of this research is solving the model with unknown demand function which is suitable with the real-world problems. To consider the uncertainty, a set of possible scenarios for customer demands is created based on the Monte Carlo simulation. The coefficient of variation of costs is mentioned as a measure of risk and the most stable structure for firm's distribution network is defined based on the concept of robust optimization. The best structure is identified using genetic algorithms and 14 % reduction in total supply chain costs is the outcome. Moreover, it imposes the least cost variation created by fluctuation in customer demands (such as epidemic diseases outbreak in some areas of the country) to the logistical system. It is noteworthy that this research is done in one of the largest pharmaceutical distribution firms in Iran.

  1. Bearing Fault Diagnosis under Variable Speed Using Convolutional Neural Networks and the Stochastic Diagonal Levenberg-Marquardt Algorithm

    Directory of Open Access Journals (Sweden)

    Viet Tra

    2017-12-01

    Full Text Available This paper presents a novel method for diagnosing incipient bearing defects under variable operating speeds using convolutional neural networks (CNNs trained via the stochastic diagonal Levenberg-Marquardt (S-DLM algorithm. The CNNs utilize the spectral energy maps (SEMs of the acoustic emission (AE signals as inputs and automatically learn the optimal features, which yield the best discriminative models for diagnosing incipient bearing defects under variable operating speeds. The SEMs are two-dimensional maps that show the distribution of energy across different bands of the AE spectrum. It is hypothesized that the variation of a bearing’s speed would not alter the overall shape of the AE spectrum rather, it may only scale and translate it. Thus, at different speeds, the same defect would yield SEMs that are scaled and shifted versions of each other. This hypothesis is confirmed by the experimental results, where CNNs trained using the S-DLM algorithm yield significantly better diagnostic performance under variable operating speeds compared to existing methods. In this work, the performance of different training algorithms is also evaluated to select the best training algorithm for the CNNs. The proposed method is used to diagnose both single and compound defects at six different operating speeds.

  2. Distributed Adaptive Finite-Time Approach for Formation-Containment Control of Networked Nonlinear Systems Under Directed Topology.

    Science.gov (United States)

    Wang, Yujuan; Song, Yongduan; Ren, Wei

    2017-07-06

    This paper presents a distributed adaptive finite-time control solution to the formation-containment problem for multiple networked systems with uncertain nonlinear dynamics and directed communication constraints. By integrating the special topology feature of the new constructed symmetrical matrix, the technical difficulty in finite-time formation-containment control arising from the asymmetrical Laplacian matrix under single-way directed communication is circumvented. Based upon fractional power feedback of the local error, an adaptive distributed control scheme is established to drive the leaders into the prespecified formation configuration in finite time. Meanwhile, a distributed adaptive control scheme, independent of the unavailable inputs of the leaders, is designed to keep the followers within a bounded distance from the moving leaders and then to make the followers enter the convex hull shaped by the formation of the leaders in finite time. The effectiveness of the proposed control scheme is confirmed by the simulation.

  3. Modeling root length density of field grown potatoes under different irrigation strategies and soil textures using artificial neural networks

    DEFF Research Database (Denmark)

    Ahmadi, Seyed Hamid; Sepaskhah, Ali Reza; Andersen, Mathias Neumann

    2014-01-01

    Root length density (RLD) is a highly wanted parameter for use in crop growth modeling but difficult to measure under field conditions. Therefore, artificial neural networks (ANNs) were implemented to predict the RLD of field grown potatoes that were subject to three irrigation strategies and three...... soil textures with different soil water status and soil densities. The objectives of the study were to test whether soil textural information, soil water status, and soil density might be used by ANN to simulate RLD at harvest. In the study 63 data pairs were divided into data sets of training (80......) of the eight input variables: soil layer intervals (D), percentages of sand (Sa), silt (Si), and clay (Cl), bulk density of soil layers (Bd), weighted soil moisture deficit during the irrigation strategies period (SMD), geometric mean particle size diameter (dg), and geometric standard deviation (σg...

  4. An integrated location inventory routing model in supply chain network designing under uncertainty

    Directory of Open Access Journals (Sweden)

    Hojat Angazi

    2016-09-01

    Full Text Available In this study an integrated model is proposed for the location inventory routing problem under uncertainty. This problem involves determining the location of distribution centers (DCs in a three echelon supply chain. The DCs receive orders from the customer and according to a continuous review inventory replenishment policy place orders to the supplier. The products are directly shipped from the supplier to the DCs. The vehicles start from the DCs to fulfill the demands of the customers. Determining the routing of the vehicles is one of the decisions involved in this problem. The demands of customers are stochastically distributed and the capacity of DCs are limited. If one of the DCs undergo a disruption and is unable to fulfill the demands of the customers, shortage may occur. Moreover in the proposed model the shortage is considered as partial backlogging. This means that if shortage occurs, some of the orders result in lost sales and other orders are fulfilled in the next period. In order to optimally solve the proposed model a nonlinear integer programming (INLP model is developed. However, since the problem is NP-hard, the mathematical formulation cannot be efficiently solved for large sized instances of the problem. Therefore an outer approximation method is developed to solve the problem more efficiently. The computational results show the efficiency of the proposed method.

  5. Large scale functional brain networks underlying temporal integration of audio-visual speech perception: An EEG study

    Directory of Open Access Journals (Sweden)

    G. Vinodh Kumar

    2016-10-01

    Full Text Available Observable lip movements of the speaker influence perception of auditory speech. A classical example of this influence is reported by listeners who perceive an illusory (cross-modal speech sound (McGurk-effect when presented with incongruent audio-visual (AV speech stimuli. Recent neuroimaging studies of AV speech perception accentuate the role of frontal, parietal and the integrative brain sites in the vicinity of the superior temporal sulcus (STS for multisensory speech perception. However, if and how does the network across the whole brain participates during multisensory perception processing remains an open question. We posit that a large-scale functional connectivity among the neural population situated in distributed brain sites may provide valuable insights involved in processing and fusing of AV speech. Varying the psychophysical parameters in tandem with electroencephalogram (EEG recordings, we exploited the trial-by-trial perceptual variability of incongruent audio-visual (AV speech stimuli to identify the characteristics of the large-scale cortical network that facilitates multisensory perception during synchronous and asynchronous AV speech. We evaluated the spectral landscape of EEG signals during multisensory speech perception at varying AV lags. Functional connectivity dynamics for all sensor pairs was computed using the time-frequency global coherence, the vector sum of pairwise coherence changes over time. During synchronous AV speech, we observed enhanced global gamma-band coherence and decreased alpha and beta-band coherence underlying cross-modal (illusory perception compared to unisensory perception around a temporal window of 300-600 ms following onset of stimuli. During asynchronous speech stimuli, a global broadband coherence was observed during cross-modal perception at earlier times along with pre-stimulus decreases of lower frequency power, e.g., alpha rhythms for positive AV lags and theta rhythms for negative AV

  6. Biochemical Hypermedia: Galactose Metabolism.

    Directory of Open Access Journals (Sweden)

    J.K. Sugai

    2013-05-01

    Full Text Available Introduction: Animations of biochemical processes and virtual laboratory environments lead to true molecular simulations. The use of interactive software’s in education can improve cognitive capacity, better learning and, mainly, it makes information acquisition easier. Material and Methods: This work presents the development of a biochemical hypermedia to understanding of the galactose metabolism. It was developed with the help of concept maps, ISIS Draw, ADOBE Photoshop and FLASH MX Program. Results and Discussion: A step by step animation process shows the enzymatic reactions of galactose conversion to glucose-1-phosphate (to glycogen synthesis, glucose-6-phosphate (glycolysis intermediary, UDP-galactose (substrate to mucopolysaccharides synthesis and collagen’s glycosylation. There are navigation guide that allow scrolling the mouse over the names of the components of enzymatic reactions of via the metabolism of galactose. Thus, explanatory text box, chemical structures and animation of the actions of enzymes appear to navigator. Upon completion of the module, the user’s response to the proposed exercise can be checked immediately through text box with interactive content of the answer. Conclusion: This hypermedia was presented for undergraduate students (UFSC who revealed that it was extremely effective in promoting the understanding of the theme.

  7. Biochemical and hematological profile of different breeds of goat ...

    African Journals Online (AJOL)

    Biochemical and hematological profile of different breeds of goat maintained under intensive production system. Samira Ahmed Mohammed, Mohammed Abdur Razzaque, Anaam E. Omar, Sheeba Albert, Waleed M. Al-Gallaf ...

  8. Gene networks underlying convergent and pleiotropic phenotypes in a large and systematically-phenotyped cohort with heterogeneous developmental disorders.

    Directory of Open Access Journals (Sweden)

    Tallulah Andrews

    2015-03-01

    Full Text Available Readily-accessible and standardised capture of genotypic variation has revolutionised our understanding of the genetic contribution to disease. Unfortunately, the corresponding systematic capture of patient phenotypic variation needed to fully interpret the impact of genetic variation has lagged far behind. Exploiting deep and systematic phenotyping of a cohort of 197 patients presenting with heterogeneous developmental disorders and whose genomes harbour de novo CNVs, we systematically applied a range of commonly-used functional genomics approaches to identify the underlying molecular perturbations and their phenotypic impact. Grouping patients into 408 non-exclusive patient-phenotype groups, we identified a functional association amongst the genes disrupted in 209 (51% groups. We find evidence for a significant number of molecular interactions amongst the association-contributing genes, including a single highly-interconnected network disrupted in 20% of patients with intellectual disability, and show using microcephaly how these molecular networks can be used as baits to identify additional members whose genes are variant in other patients with the same phenotype. Exploiting the systematic phenotyping of this cohort, we observe phenotypic concordance amongst patients whose variant genes contribute to the same functional association but note that (i this relationship shows significant variation across the different approaches used to infer a commonly perturbed molecular pathway, and (ii that the phenotypic similarities detected amongst patients who share the same inferred pathway perturbation result from these patients sharing many distinct phenotypes, rather than sharing a more specific phenotype, inferring that these pathways are best characterized by their pleiotropic effects.

  9. Stability from Structure : Metabolic Networks Are Unlike Other Biological Networks

    NARCIS (Netherlands)

    Van Nes, P.; Bellomo, D.; Reinders, M.J.T.; De Ridder, D.

    2009-01-01

    In recent work, attempts have been made to link the structure of biochemical networks to their complex dynamics. It was shown that structurally stable network motifs are enriched in such networks. In this work, we investigate to what extent these findings apply to metabolic networks. To this end, we

  10. Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution

    Science.gov (United States)

    Tse, Amanda; Verkhivker, Gennady M.

    2015-01-01

    Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib) and promiscuous (Bosutinib, Dasatinib) kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations of key mediating

  11. Implementation of Integrated Service Networks under the Quebec Mental Health Reform: Facilitators and Barriers associated with Different Territorial Profiles

    Directory of Open Access Journals (Sweden)

    Marie-Josée Fleury

    2017-03-01

    Full Text Available Introduction: This study evaluates implementation of the Quebec Mental Health Reform (2005–2015, which promoted the development of integrated service networks, in 11 local service networks organized into four territorial groups according to socio-demographic characteristics and mental health services offered. Methods: Data were collected from documents concerning networks; structured questionnaires completed by 90 managers and by 16 respondent-psychiatrists; and semi-structured interviews with 102 network stakeholders. Factors associated with implementation and integration were organized according to: 1 reform characteristics; 2 implementation context; 3 organizational characteristics; and 4 integration strategies. Results: While local networks were in a process of development and expansion, none were fully integrated at the time of the study. Facilitators and barriers to implementation and integration were primarily associated with organizational characteristics. Integration was best achieved in larger networks including a general hospital with a psychiatric department, followed by networks with a psychiatric hospital. Formalized integration strategies such as service agreements, liaison officers, and joint training reduced some barriers to implementation in networks experiencing less favourable conditions. Conclusion: Strategies for the implementation of healthcare reform and integrated service networks should include sustained support and training in best-practices, adequate performance indicators and resources, formalized integration strategies to improve network coordination and suitable initiatives to promote staff retention.

  12. Finding Risk Groups by Optimizing Artificial Neural Networks on the Area under the Survival Curve Using Genetic Algorithms.

    Directory of Open Access Journals (Sweden)

    Jonas Kalderstam

    Full Text Available We investigate a new method to place patients into risk groups in censored survival data. Properties such as median survival time, and end survival rate, are implicitly improved by optimizing the area under the survival curve. Artificial neural networks (ANN are trained to either maximize or minimize this area using a genetic algorithm, and combined into an ensemble to predict one of low, intermediate, or high risk groups. Estimated patient risk can influence treatment choices, and is important for study stratification. A common approach is to sort the patients according to a prognostic index and then group them along the quartile limits. The Cox proportional hazards model (Cox is one example of this approach. Another method of doing risk grouping is recursive partitioning (Rpart, which constructs a decision tree where each branch point maximizes the statistical separation between the groups. ANN, Cox, and Rpart are compared on five publicly available data sets with varying properties. Cross-validation, as well as separate test sets, are used to validate the models. Results on the test sets show comparable performance, except for the smallest data set where Rpart's predicted risk groups turn out to be inverted, an example of crossing survival curves. Cross-validation shows that all three models exhibit crossing of some survival curves on this small data set but that the ANN model manages the best separation of groups in terms of median survival time before such crossings. The conclusion is that optimizing the area under the survival curve is a viable approach to identify risk groups. Training ANNs to optimize this area combines two key strengths from both prognostic indices and Rpart. First, a desired minimum group size can be specified, as for a prognostic index. Second, the ability to utilize non-linear effects among the covariates, which Rpart is also able to do.

  13. Neural correlates and network connectivity underlying narrative production and comprehension: a combined fMRI and PET study.

    Science.gov (United States)

    AbdulSabur, Nuria Y; Xu, Yisheng; Liu, Siyuan; Chow, Ho Ming; Baxter, Miranda; Carson, Jessica; Braun, Allen R

    2014-08-01

    The neural correlates of narrative production and comprehension remain poorly understood. Here, using positron emission tomography (PET), functional magnetic resonance imaging (fMRI), contrast and functional network connectivity analyses we comprehensively characterize the neural mechanisms underlying these complex behaviors. Eighteen healthy subjects told and listened to fictional stories during scanning. In addition to traditional language areas (e.g., left inferior frontal and posterior middle temporal gyri), both narrative production and comprehension engaged regions associated with mentalizing and situation model construction (e.g., dorsomedial prefrontal cortex, precuneus and inferior parietal lobules) as well as neocortical premotor areas, such as the pre-supplementary motor area and left dorsal premotor cortex. Narrative comprehension alone showed marked bilaterality, activating right hemisphere homologs of perisylvian language areas. Narrative production remained predominantly left lateralized, uniquely activating executive and motor-related regions essential to language formulation and articulation. Connectivity analyses revealed strong associations between language areas and the superior and middle temporal gyri during both tasks. However, only during storytelling were these same language-related regions connected to cortical and subcortical motor regions. In contrast, during story comprehension alone, they were strongly linked to regions supporting mentalizing. Thus, when employed in a more complex, ecologically-valid context, language production and comprehension show both overlapping and idiosyncratic patterns of activation and functional connectivity. Importantly, in each case the language system is integrated with regions that support other cognitive and sensorimotor domains. Copyright © 2014. Published by Elsevier Ltd.

  14. Age-related changes in sleep and circadian rhythms: impact on cognitive performance and underlying neuroanatomical networks

    Directory of Open Access Journals (Sweden)

    Christina eSchmidt

    2012-07-01

    Full Text Available Circadian and homeostatic sleep-wake regulatory processes interact in a fine tuned manner to modulate human cognitive performance. Dampening of the circadian alertness signal and attenuated deterioration of psychomotor vigilance in response to elevated sleep pressure with aging change this interaction pattern. As evidenced by neuroimaging studies, both homeostatic sleep pressure and circadian sleep-wake promotion impact on cognition-related cortical and arousal-promoting subcortical brain regions including the thalamus, the anterior hypothalamus and the brainstem locus coeruleus (LC. However, how age- related changes in circadian and homeostatic processes impact on the cerebral activity subtending waking performance remains largely unexplored. Post-mortem studies point to neuronal degeneration in the SCN and age-related modifications to aging in the arousal-promoting LC. Alongside, cortical frontal brain areas are particularly susceptible both to aging and misalignment between circadian and homeostatic processes. In this perspective, we summarise and discuss here the potential neuroanatomical networks underlying age-related changes in circadian and homeostatic modulation of waking performance, ranging from basic arousal to higher order cognitive behaviours.

  15. Modelling the release of volatile fission product cesium from CANDU fuel under severe accident conditions using artificial neural networks

    International Nuclear Information System (INIS)

    Andrews, W.S.; Lewis, B.J.; Cox, D.S.

    1997-01-01

    An artificial neural network (ANN) model has been developed to predict the release of volatile fission products from CANDU fuel under severe accident conditions. The model was based on data for the release Of 134 Cs measured during three annealing experiments (Hot Cell Experiments 1 and 2, or HCE- 1, HCE-2 and Metallurgical Cell Experiment 1, or MCE- 1) at Chalk River Laboratories. These experiments were comprised of a total of 30 separate tests. The ANN established a correlation among 14 separate input variables and predicted the cumulative fractional release for a set of 386 data points drawn from 29 tests to a normalized error, E n , of 0.104 and an average absolute error, E abs , of 0.064. Predictions for a blind validation set (test HCE2-CM6) had an E n of 0.064 and an E abs of 0.054. A methodology is presented for deploying the ANN model by providing the connection weights. Finally, the performance of an ANN model was compared to a fuel oxidation model developed by Lewis et al. and to the U.S. Nuclear Regulatory Commission's CORSOR-M. (author)

  16. Quality Changes of N-3 PUFAs Enriched and Conventional Eggs under Different Home Storage Conditions with Wireless Sensor Network

    Directory of Open Access Journals (Sweden)

    Wenkang Li

    2017-11-01

    Full Text Available Omega-3 polyunsaturated fatty acids (n-3 PUFAs enriched eggs are popular for their enrichment of PUFAs, but their freshness and quality are prone to decline with time, particularly if storage conditions are not well maintained. Home storage is the last but a neglected important tach in eggs supply chain, but few studies are available on the egg storage in the home stage. This study aimed to evaluate the internal quality change of both n-3 PUFAs enriched and conventional eggs by simulating eggs stored at consumers’ home in refrigeration and under room temperature. The egg quality indices (Haugh unit, yolk index, weight, and albumen pH were adopted and analyzed for both storage conditions. Wireless sensor network (WSN was used for real-time monitoring of the temperature and humidity during storage. The results showed that temperature, humidity and time of storage all have an influence on the freshness of both n-3 PUFAs enriched and conventional eggs and there is no significant difference happened to n-3 PUFAs enriched eggs and conventional eggs. Refrigeration can decelerate the quality deterioration of both n-3 PUFAs enriched and conventional eggs and consumers should be educated about how to maintain the internal quality of eggs during home storage.

  17. Elimination of intermediate species in multiscale stochastic reaction networks

    DEFF Research Database (Denmark)

    Cappelletti, Daniele; Wiuf, Carsten

    2016-01-01

    We study networks of biochemical reactions modelled by continuoustime Markov processes. Such networks typically contain many molecular species and reactions and are hard to study analytically as well as by simulation. Particularly, we are interested in reaction networks with intermediate species...... such as the substrate-enzyme complex in the Michaelis-Menten mechanism. Such species are virtually in all real-world networks, they are typically short-lived, degraded at a fast rate and hard to observe experimentally. We provide conditions under which the Markov process of a multiscale reaction network...... with intermediate species is approximated by the Markov process of a simpler reduced reaction network without intermediate species. We do so by embedding the Markov processes into a one-parameter family of processes, where reaction rates and species abundances are scaled in the parameter. Further, we show...

  18. Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems.

    Science.gov (United States)

    Pischel, Dennis; Sundmacher, Kai; Flassig, Robert J

    2017-07-15

    Biological cells operate in a noisy regime influenced by intrinsic, extrinsic and external noise, which leads to large differences of individual cell states. Stochastic effects must be taken into account to characterize biochemical kinetics accurately. Since the exact solution of the chemical master equation, which governs the underlying stochastic process, cannot be derived for most biochemical systems, approximate methods are used to obtain a solution. In this study, a method to efficiently simulate the various sources of noise simultaneously is proposed and benchmarked on several examples. The method relies on the combination of the sigma point approach to describe extrinsic and external variability and the τ -leaping algorithm to account for the stochasticity due to probabilistic reactions. The comparison of our method to extensive Monte Carlo calculations demonstrates an immense computational advantage while losing an acceptable amount of accuracy. Additionally, the application to parameter optimization problems in stochastic biochemical reaction networks is shown, which is rarely applied due to its huge computational burden. To give further insight, a MATLAB script is provided including the proposed method applied to a simple toy example of gene expression. MATLAB code is available at Bioinformatics online. flassig@mpi-magdeburg.mpg.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  19. Systemwide Reform in Districts under Pressure: The Role of Social Networks in Defining, Acquiring, Using, and Diffusing Research Evidence

    Science.gov (United States)

    Finnigan, Kara S.; Daly, Alan J.; Che, Jing

    2013-01-01

    Purpose: The purpose of this paper is to examine the way in which low-performing schools and their district define, acquire, use, and diffuse research-based evidence. Design/methodology/approach: The mixed methods case study builds upon the prior research on research evidence and social networks, drawing on social network analyses, survey data and…

  20. Social connections and the persuasiveness of viral campaigns in social network sites: persuasive intent as the underlying mechanism

    NARCIS (Netherlands)

    van Noort, G.; Antheunis, M.L.; van Reijmersdal, E.A.

    2012-01-01

    Social media are increasingly popular. Consequently, marketers more and more recognize social network sites as a platform for commercial campaigns. Social network users forward these campaigns to their online connections. However, our understanding of the persuasiveness of these campaigns is scarce.