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Sample records for biochemical networks due

  1. Associative learning in biochemical networks

    OpenAIRE

    Ghandi, Nikhil; Ashkenasy, Gonen; Tannenbaum, Emmanuel

    2007-01-01

    We develop a simple, chemostat-based model illustrating how a process analogous to associative learning can occur in a biochemical network. Associative learning is a form of learning whereby a system "learns" to associate two stimuli with one another. In our model, two types of replicating molecules, denoted A and B, are present in some initial concentration in the chemostat. Molecules A and B are stimulated to replicate by some growth factors, denoted GA and GB, respectively. It is also assu...

  2. Vector Encoding in Biochemical Networks

    Science.gov (United States)

    Potter, Garrett; Sun, Bo

    Encoding of environmental cues via biochemical signaling pathways is of vital importance in the transmission of information for cells in a network. The current literature assumes a single cell state is used to encode information, however, recent research suggests the optimal strategy utilizes a vector of cell states sampled at various time points. To elucidate the optimal sampling strategy for vector encoding, we take an information theoretic approach and determine the mutual information of the calcium signaling dynamics obtained from fibroblast cells perturbed with different concentrations of ATP. Specifically, we analyze the sampling strategies under the cases of fixed and non-fixed vector dimension as well as the efficiency of these strategies. Our results show that sampling with greater frequency is optimal in the case of non-fixed vector dimension but that, in general, a lower sampling frequency is best from both a fixed vector dimension and efficiency standpoint. Further, we find the use of a simple modified Ornstein-Uhlenbeck process as a model qualitatively captures many of our experimental results suggesting that sampling in biochemical networks is based on a few basic components.

  3. Associative learning in biochemical networks.

    Science.gov (United States)

    Gandhi, Nikhil; Ashkenasy, Gonen; Tannenbaum, Emmanuel

    2007-11-07

    It has been recently suggested that there are likely generic features characterizing the emergence of systems constructed from the self-organization of self-replicating agents acting under one or more selection pressures. Therefore, structures and behaviors at one length scale may be used to infer analogous structures and behaviors at other length scales. Motivated by this suggestion, we seek to characterize various "animate" behaviors in biochemical networks, and the influence that these behaviors have on genomic evolution. Specifically, in this paper, we develop a simple, chemostat-based model illustrating how a process analogous to associative learning can occur in a biochemical network. Associative learning is a form of learning whereby a system "learns" to associate two stimuli with one another. Associative learning, also known as conditioning, is believed to be a powerful learning process at work in the brain (associative learning is essentially "learning by analogy"). In our model, two types of replicating molecules, denoted as A and B, are present in some initial concentration in the chemostat. Molecules A and B are stimulated to replicate by some growth factors, denoted as G(A) and G(B), respectively. It is also assumed that A and B can covalently link, and that the conjugated molecule can be stimulated by either the G(A) or G(B) growth factors (and can be degraded). We show that, if the chemostat is stimulated by both growth factors for a certain time, followed by a time gap during which the chemostat is not stimulated at all, and if the chemostat is then stimulated again by only one of the growth factors, then there will be a transient increase in the number of molecules activated by the other growth factor. Therefore, the chemostat bears the imprint of earlier, simultaneous stimulation with both growth factors, which is indicative of associative learning. It is interesting to note that the dynamics of our model is consistent with certain aspects of

  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. Characterizing multistationarity regimes in biochemical reaction networks.

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    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.

  6. LucidDraw: Efficiently visualizing complex biochemical networks within MATLAB

    Directory of Open Access Journals (Sweden)

    Shi Guiyang

    2010-01-01

    Full Text Available Abstract Background Biochemical networks play an essential role in systems biology. Rapidly growing network data and versatile research activities call for convenient visualization tools to aid intuitively perceiving abstract structures of networks and gaining insights into the functional implications of networks. There are various kinds of network visualization software, but they are usually not adequate for visual analysis of complex biological networks mainly because of the two reasons: 1 most existing drawing methods suitable for biochemical networks have high computation loads and can hardly achieve near real-time visualization; 2 available network visualization tools are designed for working in certain network modeling platforms, so they are not convenient for general analyses due to lack of broader range of readily accessible numerical utilities. Results We present LucidDraw as a visual analysis tool, which features (a speed: typical biological networks with several hundreds of nodes can be drawn in a few seconds through a new layout algorithm; (b ease of use: working within MATLAB makes it convenient to manipulate and analyze the network data using a broad spectrum of sophisticated numerical functions; (c flexibility: layout styles and incorporation of other available information about functional modules can be controlled by users with little effort, and the output drawings are interactively modifiable. Conclusions Equipped with a new grid layout algorithm proposed here, LucidDraw serves as an auxiliary network analysis tool capable of visualizing complex biological networks in near real-time with controllable layout styles and drawing details. The framework of the algorithm enables easy incorporation of extra biological information, if available, to influence the output layouts with predefined node grouping features.

  7. BNDB – The Biochemical Network Database

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    Kaufmann Michael

    2007-10-01

    Full Text Available Abstract Background Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been established over the last decades and are essential resources for scientists nowadays. However, the diversity of the databases and the underlying data models make it difficult to combine this information for solving complex problems in systems biology. Currently, researchers typically have to browse several, often highly focused, databases to obtain the required information. Hence, there is a pressing need for more efficient systems for integrating, analyzing, and interpreting these data. The standardization and virtual consolidation of the databases is a major challenge resulting in a unified access to a variety of data sources. Description We present the Biochemical Network Database (BNDB, a powerful relational database platform, allowing a complete semantic integration of an extensive collection of external databases. BNDB is built upon a comprehensive and extensible object model called BioCore, which is powerful enough to model most known biochemical processes and at the same time easily extensible to be adapted to new biological concepts. Besides a web interface for the search and curation of the data, a Java-based viewer (BiNA provides a powerful platform-independent visualization and navigation of the data. BiNA uses sophisticated graph layout algorithms for an interactive visualization and navigation of BNDB. Conclusion BNDB allows a simple, unified access to a variety of external data sources. Its tight integration with the biochemical network library BN++ offers the possibility for import, integration, analysis, and visualization of the data. BNDB is freely accessible at http://www.bndb.org.

  8. Identification of biochemical network modules based on shortest retroactive distances.

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    Gautham Vivek Sridharan

    2011-11-01

    Full Text Available Modularity analysis offers a route to better understand the organization of cellular biochemical networks as well as to derive practically useful, simplified models of these complex systems. While there is general agreement regarding the qualitative properties of a biochemical module, there is no clear consensus on the quantitative criteria that may be used to systematically derive these modules. In this work, we investigate cyclical interactions as the defining characteristic of a biochemical module. We utilize a round trip distance metric, termed Shortest Retroactive Distance (ShReD, to characterize the retroactive connectivity between any two reactions in a biochemical network and to group together network components that mutually influence each other. We evaluate the metric on two types of networks that feature feedback interactions: (i epidermal growth factor receptor (EGFR signaling and (ii liver metabolism supporting drug transformation. For both networks, the ShReD partitions found hierarchically arranged modules that confirm biological intuition. In addition, the partitions also revealed modules that are less intuitive. In particular, ShReD-based partition of the metabolic network identified a 'redox' module that couples reactions of glucose, pyruvate, lipid and drug metabolism through shared production and consumption of NADPH. Our results suggest that retroactive interactions arising from feedback loops and metabolic cycles significantly contribute to the modularity of biochemical networks. For metabolic networks, cofactors play an important role as allosteric effectors that mediate the retroactive interactions.

  9. SABRE: A Tool for Stochastic Analysis of Biochemical Reaction Networks

    CERN Document Server

    Didier, Frederic; Mateescu, Maria; Wolf, Verena

    2010-01-01

    The importance of stochasticity within biological systems has been shown repeatedly during the last years and has raised the need for efficient stochastic tools. We present SABRE, a tool for stochastic analysis of biochemical reaction networks. SABRE implements fast adaptive uniformization (FAU), a direct numerical approximation algorithm for computing transient solutions of biochemical reaction networks. Biochemical reactions networks represent biological systems studied at a molecular level and these reactions can be modeled as transitions of a Markov chain. SABRE accepts as input the formalism of guarded commands, which it interprets either as continuous-time or as discrete-time Markov chains. Besides operating in a stochastic mode, SABRE may also perform a deterministic analysis by directly computing a mean-field approximation of the system under study. We illustrate the different functionalities of SABRE by means of biological case studies.

  10. 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.

  11. Programming the dynamics of biochemical reaction networks.

    Science.gov (United States)

    Simmel, Friedrich C

    2013-01-22

    The development of complex self-organizing molecular systems for future nanotechnology requires not only robust formation of molecular structures by self-assembly but also precise control over their temporal dynamics. As an exquisite example of such control, in this issue of ACS Nano, Fujii and Rondelez demonstrate a particularly compact realization of a molecular "predator-prey" ecosystem consisting of only three DNA species and three enzymes. The system displays pronounced oscillatory dynamics, in good agreement with the predictions of a simple theoretical model. Moreover, its considerable modularity also allows for ecological studies of competition and cooperation within molecular networks.

  12. Modeling stochasticity in biochemical reaction networks

    Science.gov (United States)

    Constantino, P. H.; Vlysidis, M.; Smadbeck, P.; Kaznessis, Y. N.

    2016-03-01

    Small biomolecular systems are inherently stochastic. Indeed, fluctuations of molecular species are substantial in living organisms and may result in significant variation in cellular phenotypes. The chemical master equation (CME) is the most detailed mathematical model that can describe stochastic behaviors. However, because of its complexity the CME has been solved for only few, very small reaction networks. As a result, the contribution of CME-based approaches to biology has been very limited. In this review we discuss the approach of solving CME by a set of differential equations of probability moments, called moment equations. We present different approaches to produce and to solve these equations, emphasizing the use of factorial moments and the zero information entropy closure scheme. We also provide information on the stability analysis of stochastic systems. Finally, we speculate on the utility of CME-based modeling formalisms, especially in the context of synthetic biology efforts.

  13. Information processing by biochemical networks: a dynamic approach.

    Science.gov (United States)

    Bowsher, Clive G

    2011-02-06

    Understanding how information is encoded and transferred by biochemical networks is of fundamental importance in cellular and systems biology. This requires analysis of the relationships between the stochastic trajectories of the constituent molecular (or submolecular) species that comprise the network. We describe how to identify conditional independences between the trajectories or time courses of groups of species. These are robust network properties that provide important insight into how information is processed. An entire network can then be decomposed exactly into modules on informational grounds. In the context of signalling networks with multiple inputs, the approach identifies the routes and species involved in sequential information processing between input and output modules. An algorithm is developed which allows automated identification of decompositions for large networks and visualization using a tree that encodes the conditional independences. Only stoichiometric information is used and neither simulations nor knowledge of rate parameters are required. A bespoke version of the algorithm for signalling networks identifies the routes of sequential encoding between inputs and outputs, visualized as paths in the tree. Application to the toll-like receptor signalling network reveals that inputs can be informative in ways unanticipated by steady-state analyses, that the information processing structure is not well described as a bow tie, and that encoding for the interferon response is unusually sparse compared with other outputs of this innate immune system.

  14. 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.

  15. Efficient Parallel Statistical Model Checking of Biochemical Networks

    Directory of Open Access Journals (Sweden)

    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.

  16. 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.

  17. 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.

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

    DEFF Research Database (Denmark)

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

    1997-01-01

    must be estimated by nonlinear least squares analysis, in which experimental labeling data is compared with simulated steady state isotopomer distributions. Hence, mathematical models are required to compute the steady state isotopomer distribution as a function of a given set of steady state fluxes......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...... of the isotopomer distribution in metabolite pools can be obtained. The isotopomer distribution is the maximum amount of information that in theory can be obtained from C-13-tracer studies. The wealth of information contained in NMR spectra frequently leads to overdetermined algebraic systems. Consequently, fluxes...

  19. Trade-Offs in Delayed Information Transmission in Biochemical Networks

    Science.gov (United States)

    Mancini, F.; Marsili, M.; Walczak, A. M.

    2016-03-01

    In order to transmit biochemical signals, biological regulatory systems dissipate energy with concomitant entropy production. Additionally, signaling often takes place in challenging environmental conditions. In a simple model regulatory circuit given by an input and a delayed output, we explore the trade-offs between information transmission and the system's energetic efficiency. We determine the maximally informative network, given a fixed amount of entropy production and a delayed response, exploring both the case with and without feedback. We find that feedback allows the circuit to overcome energy constraints and transmit close to the maximum available information even in the dissipationless limit. Negative feedback loops, characteristic of shock responses, are optimal at high dissipation. Close to equilibrium positive feedback loops, known for their stability, become more informative. Asking how the signaling network should be constructed to best function in the worst possible environment, rather than an optimally tuned one or in steady state, we discover that at large dissipation the same universal motif is optimal in all of these conditions.

  20. CHANGES IN THE BIOCHEMICAL CONSTITUENTS OF CARROT ROOTS DUE TO BACTERIAL SOFT ROT

    Directory of Open Access Journals (Sweden)

    V. K. Parthiban

    2013-03-01

    Full Text Available Carrot is a rich source of nutrients. The carrot contains carotene and lycopene, which gives bright color to the roots. The quality of the carrots was assessed based on the carotene, lycopene and other biochemical constituents like sugars, starch and protein. To study the effect of various isolates of the Erwinia carotovora var. carotovora on the above biochemical constituents, the pathogens were inoculated and the contents were analyzed separately at 1, 2, 3, 4, 5 days after inoculation. The contents of β-carotene increased significantly due to all the three isolates of the pathogen and the Coimbatore isolate recorded highest of 36.03 per cent. A same trend was also observed in the lycopene content with 93.55 per cent increase over control. The contents of total and reducing sugars were found to significantly increase due to inoculation with the pathogen. The starch content showed a decreasing trend in all the isolates tested. The maximum reduction of 62.98 per cent was observed in the roots inoculated with Coimbatore isolate.

  1. 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.

  2. The alterations in biochemical signaling of hippocampal network activity in the autism brain The alterations in biochemical signaling of hippocampal network activity in the autism brain The alterations in biochemical signaling of hippocampal network activity in the autism brain

    Institute of Scientific and Technical Information of China (English)

    田允; 黄继云; 王锐; 陶蓉蓉; 卢应梅; 廖美华; 陆楠楠; 李静; 芦博; 韩峰

    2012-01-01

    Autism is a highly heritable neurodevelopmental condition characterized by impaired social interaction and communication. However, the role of synaptic dysfunction during development of autism remains unclear. In the present study, we address the alterations of biochemical signaling in hippocampal network following induction of the autism in experimental animals. Here, the an- imal disease model and DNA array being used to investigate the differences in transcriptome or- ganization between autistic and normal brain by gene co--expression network analysis.

  3. Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple 'Omic' Layers.

    Science.gov (United States)

    Yugi, Katsuyuki; Kubota, Hiroyuki; Hatano, Atsushi; Kuroda, Shinya

    2016-04-01

    We propose 'trans-omic' analysis for reconstructing global biochemical networks across multiple omic layers by use of both multi-omic measurements and computational data integration. We introduce technologies for connecting multi-omic data based on prior knowledge of biochemical interactions and characterize a biochemical trans-omic network by concepts of a static and dynamic nature. We introduce case studies of metabolism-centric trans-omic studies to show how to reconstruct a biochemical trans-omic network by connecting multi-omic data and how to analyze it in terms of the static and dynamic nature. We propose a trans-ome-wide association study (trans-OWAS) connecting phenotypes with trans-omic networks that reflect both genetic and environmental factors, which can characterize several complex lifestyle diseases as breakdowns in the trans-omic system.

  4. 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.

  5. A moment-convergence method for stochastic analysis of biochemical reaction networks

    Science.gov (United States)

    Zhang, Jiajun; Nie, Qing; Zhou, Tianshou

    2016-05-01

    Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in terms of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.

  6. A moment-convergence method for stochastic analysis of biochemical reaction networks.

    Science.gov (United States)

    Zhang, Jiajun; Nie, Qing; Zhou, Tianshou

    2016-05-21

    Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in terms of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.

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

    Science.gov (United States)

    2013-01-01

    Background 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. Results 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. Conclusions 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

  8. Insights into the organization of biochemical regulatory networks using graph theory analyses.

    Science.gov (United States)

    Ma'ayan, Avi

    2009-02-27

    Graph theory has been a valuable mathematical modeling tool to gain insights into the topological organization of biochemical networks. There are two types of insights that may be obtained by graph theory analyses. The first provides an overview of the global organization of biochemical networks; the second uses prior knowledge to place results from multivariate experiments, such as microarray data sets, in the context of known pathways and networks to infer regulation. Using graph analyses, biochemical networks are found to be scale-free and small-world, indicating that these networks contain hubs, which are proteins that interact with many other molecules. These hubs may interact with many different types of proteins at the same time and location or at different times and locations, resulting in diverse biological responses. Groups of components in networks are organized in recurring patterns termed network motifs such as feedback and feed-forward loops. Graph analysis revealed that negative feedback loops are less common and are present mostly in proximity to the membrane, whereas positive feedback loops are highly nested in an architecture that promotes dynamical stability. Cell signaling networks have multiple pathways from some input receptors and few from others. Such topology is reminiscent of a classification system. Signaling networks display a bow-tie structure indicative of funneling information from extracellular signals and then dispatching information from a few specific central intracellular signaling nexuses. These insights show that graph theory is a valuable tool for gaining an understanding of global regulatory features of biochemical networks.

  9. 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

    Background: The size and complexity of published biochemical network reconstructions are steadily increasing, expanding the potential scale of derived computational models. However, the construction of large biochemical network models is a laborious and error-prone task. Automated methods have...... desired. Conclusions: The described approach fills a heretofore absent niche in workflows for large-scale biochemical kinetic model construction. In several applications the algorithm has already been demonstrated to be useful and scalable. SBMLsqueezer is platform independent and can be used as a stand...

  10. Biochemical and biomolecular aspects of oxidative stress due to acute and severe hypoxia in human muscle tissue.

    Science.gov (United States)

    Corbucci, G G; Sessego, R; Velluti, C; Salvi, M

    1995-01-01

    Mitochondrial oxidative stress was investigated in severe and acute hypoxia and in reperfusion applied to human muscle tissues. The biochemical and biomolecular relationship between the response of the respiratory-chain enzymic complexes and the metabolism of specific hypoxia stress proteins (HSP) suggest an adaptive mechanism which antagonizes the oxidative damage due to acute and severe tissue hypoxia.

  11. 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

  12. A Geometric Method for Model Reduction of Biochemical Networks with Polynomial Rate Functions.

    Science.gov (United States)

    Samal, Satya Swarup; Grigoriev, Dima; Fröhlich, Holger; Weber, Andreas; Radulescu, Ovidiu

    2015-12-01

    Model reduction of biochemical networks relies on the knowledge of slow and fast variables. We provide a geometric method, based on the Newton polytope, to identify slow variables of a biochemical network with polynomial rate functions. The gist of the method is the notion of tropical equilibration that provides approximate descriptions of slow invariant manifolds. Compared to extant numerical algorithms such as the intrinsic low-dimensional manifold method, our approach is symbolic and utilizes orders of magnitude instead of precise values of the model parameters. Application of this method to a large collection of biochemical network models supports the idea that the number of dynamical variables in minimal models of cell physiology can be small, in spite of the large number of molecular regulatory actors.

  13. [Changes in platelet concentrates from dogs due to storage. II. Biochemical changes in concentrate plasma].

    Science.gov (United States)

    Klein, A; Adamik, A; Mischke, R

    1999-08-01

    Platelet concentrate (PC) obtained from dogs with an automatic cell separator was stored in C4-cell separation sets with low gasdiffusionable Polyvinylchlorid (PVC) storage containers or in C4L-sets developed for storage with high gasdiffusionable Polyolefin(PO) containers, respectively. PC were stored for 10 days under permanent agitation at 22 degrees C (C4/22 degrees C, n = 10; C4L/22 degrees C, n = 11) or at 4 degrees C (C4L/4 degrees C, n = 6), respectively. Measurements were carried out directly after production of the PC, after 6 hours and then daily during the 10-day storage period. In the second part of this paper the results of pH, the concentration of bicarbonate, glucose, lactate and potassium ions as well as the activity of lactate dehydrogenase (LDH) are presented. The varying duration and intensity of the energy metabolism of the platelets and different part of glycolysis became obvious by the consumption of glucose and production of lactate, which differed significantly between the different storage conditions. Resulting from this, the mean pH decreased under the limit prescribed for human PC (pH = 6.3) already after a storage period of 3 days due to the slight capacity of gas diffusion in PVC-containers (C4/22 degrees C). In the PO-containers the pH fell below this limit at 22 degrees C (C4L/22 degrees C) after a storage period of 5 days and at 4 degrees C (C4L/4 degrees C) after 10 days. The latter reflects the high gas diffusion capacity of the PO-containers and the decreased metabolism activity at 4 degrees C. The increase of activity of LDH and of the concentration of potassium ions, which are localized in the cytosol of platelets, depended also on the different storage conditions and, thereby, reflected the different rapidity of increasing membrane permeability or the destruction of the cell membrane, respectively. The results of this study nearly are in agreement with the changes of platelet function shown in part I. Biochemical changes occur

  14. 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.

  15. Model-order reduction of biochemical reaction networks

    NARCIS (Netherlands)

    Rao, Shodhan; Schaft, Arjan van der; Eunen, Karen van; Bakker, Barbara M.; Jayawardhana, Bayu

    2013-01-01

    In this paper we propose a model-order reduction method for chemical reaction networks governed by general enzyme kinetics, including the mass-action and Michaelis-Menten kinetics. The model-order reduction method is based on the Kron reduction of the weighted Laplacian matrix which describes the gr

  16. Algebraic Statistical Model for Biochemical Network Dynamics Inference.

    Science.gov (United States)

    Linder, Daniel F; Rempala, Grzegorz A

    2013-12-01

    With modern molecular quantification methods, like, for instance, high throughput sequencing, biologists may perform multiple complex experiments and collect longitudinal data on RNA and DNA concentrations. Such data may be then used to infer cellular level interactions between the molecular entities of interest. One method which formalizes such inference is the stoichiometric algebraic statistical model (SASM) of [2] which allows to analyze the so-called conic (or single source) networks. Despite its intuitive appeal, up until now the SASM has been only heuristically studied on few simple examples. The current paper provides a more formal mathematical treatment of the SASM, expanding the original model to a wider class of reaction systems decomposable into multiple conic subnetworks. In particular, it is proved here that on such networks the SASM enjoys the so-called sparsistency property, that is, it asymptotically (with the number of observed network trajectories) discards the false interactions by setting their reaction rates to zero. For illustration, we apply the extended SASM to in silico data from a generic decomposable network as well as to biological data from an experimental search for a possible transcription factor for the heat shock protein 70 (Hsp70) in the zebrafish retina.

  17. On Projection-Based Model Reduction of Biochemical Networks Part I: The Deterministic Case

    OpenAIRE

    Sootla, Aivar; Anderson, James

    2014-01-01

    This paper addresses the problem of model reduction for dynamical system models that describe biochemical reaction networks. Inherent in such models are properties such as stability, positivity and network structure. Ideally these properties should be preserved by model reduction procedures, although traditional projection based approaches struggle to do this. We propose a projection based model reduction algorithm which uses generalised block diagonal Gramians to preserve structure and posit...

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

    NARCIS (Netherlands)

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

    2008-01-01

    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

  19. 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.

  20. 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.

  1. 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.

  2. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space.

    Science.gov (United States)

    Ruess, Jakob

    2015-12-28

    Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space.

  3. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space

    Science.gov (United States)

    Ruess, Jakob

    2015-12-01

    Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space.

  4. Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments.

    Science.gov (United States)

    van Riel, Natal A W

    2006-12-01

    Systems biology applies quantitative, mechanistic modelling to study genetic networks, signal transduction pathways and metabolic networks. Mathematical models of biochemical networks can look very different. An important reason is that the purpose and application of a model are essential for the selection of the best mathematical framework. Fundamental aspects of selecting an appropriate modelling framework and a strategy for model building are discussed. Concepts and methods from system and control theory provide a sound basis for the further development of improved and dedicated computational tools for systems biology. Identification of the network components and rate constants that are most critical to the output behaviour of the system is one of the major problems raised in systems biology. Current approaches and methods of parameter sensitivity analysis and parameter estimation are reviewed. It is shown how these methods can be applied in the design of model-based experiments which iteratively yield models that are decreasingly wrong and increasingly gain predictive power.

  5. Massive pleural effusion due to paragonimiasis: Biochemical, cytological, and parasitological findings

    Directory of Open Access Journals (Sweden)

    Takhellambam Shantikumar Singh

    2014-01-01

    Full Text Available Paragonimiasis is an important food-borne parasitic zoonosis caused by trematode species of the genus, Paragonimus occurring in many parts of the world except in Australia and Antarctica. In India, it is an emerging parasitic disease, which is endemic in the northeast states where people have a common practice of eating raw or inadequately cooked freshwater crabs. In these states, Paragonimus heterotremus has been identified as the major causative agent of the human paragonimiasis. The most common clinical form of the disease is pulmonary paragonimiasis; however, extra-pulmonary manifestations are not uncommon. Here, we report a case of primary massive unilateral pleural effusion due to paragonimiasis. The diagnosis was confirmed by finding Paragonimus ova in the pleural fluid. The patient was successfully treated with repeated thoracocentesis and a course of praziquantel.

  6. ConvAn: a convergence analyzing tool for optimization of biochemical networks.

    Science.gov (United States)

    Kostromins, Andrejs; Mozga, Ivars; Stalidzans, Egils

    2012-01-01

    Dynamic models of biochemical networks usually are described as a system of nonlinear differential equations. In case of optimization of models for purpose of parameter estimation or design of new properties mainly numerical methods are used. That causes problems of optimization predictability as most of numerical optimization methods have stochastic properties and the convergence of the objective function to the global optimum is hardly predictable. Determination of suitable optimization method and necessary duration of optimization becomes critical in case of evaluation of high number of combinations of adjustable parameters or in case of large dynamic models. This task is complex due to variety of optimization methods, software tools and nonlinearity features of models in different parameter spaces. A software tool ConvAn is developed to analyze statistical properties of convergence dynamics for optimization runs with particular optimization method, model, software tool, set of optimization method parameters and number of adjustable parameters of the model. The convergence curves can be normalized automatically to enable comparison of different methods and models in the same scale. By the help of the biochemistry adapted graphical user interface of ConvAn it is possible to compare different optimization methods in terms of ability to find the global optima or values close to that as well as the necessary computational time to reach them. It is possible to estimate the optimization performance for different number of adjustable parameters. The functionality of ConvAn enables statistical assessment of necessary optimization time depending on the necessary optimization accuracy. Optimization methods, which are not suitable for a particular optimization task, can be rejected if they have poor repeatability or convergence properties. The software ConvAn is freely available on www.biosystems.lv/convan.

  7. Combining Flux Balance and Energy Balance Analysis for Large-Scale Metabolic Network: Biochemical Circuit Theory for Analysis of Large-Scale Metabolic Networks

    Science.gov (United States)

    Beard, Daniel A.; Liang, Shou-Dan; Qian, Hong; Biegel, Bryan (Technical Monitor)

    2001-01-01

    Predicting behavior of large-scale biochemical metabolic networks represents one of the greatest challenges of bioinformatics and computational biology. Approaches, such as flux balance analysis (FBA), that account for the known stoichiometry of the reaction network while avoiding implementation of detailed reaction kinetics are perhaps the most promising tools for the analysis of large complex networks. As a step towards building a complete theory of biochemical circuit analysis, we introduce energy balance analysis (EBA), which compliments the FBA approach by introducing fundamental constraints based on the first and second laws of thermodynamics. Fluxes obtained with EBA are thermodynamically feasible and provide valuable insight into the activation and suppression of biochemical pathways.

  8. Fast Evaluation of Fluctuations in Biochemical Networks With the Linear Noise Approximation

    Science.gov (United States)

    Elf, Johan; Ehrenberg, Måns

    2003-01-01

    Biochemical networks in single cells can display large fluctuations in molecule numbers, making mesoscopic approaches necessary for correct system descriptions. We present a general method that allows rapid characterization of the stochastic properties of intracellular networks. The starting point is a macroscopic description that identifies the system's elementary reactions in terms of rate laws and stoichiometries. From this formulation follows directly the stationary solution of the linear noise approximation (LNA) of the Master equation for all the components in the network. The method complements bifurcation studies of the system's parameter dependence by providing estimates of sizes, correlations, and time scales of stochastic fluctuations. We describe how the LNA can give precise system descriptions also near macroscopic instabilities by suitable variable changes and elimination of fast variables. PMID:14597656

  9. Functional brain network changes associated with clinical and biochemical measures of the severity of hepatic encephalopathy.

    Science.gov (United States)

    Jao, Tun; Schröter, Manuel; Chen, Chao-Long; Cheng, Yu-Fan; Lo, Chun-Yi Zac; Chou, Kun-Hsien; Patel, Ameera X; Lin, Wei-Che; Lin, Ching-Po; Bullmore, Edward T

    2015-11-15

    Functional properties of the brain may be associated with changes in complex brain networks. However, little is known about how properties of large-scale functional brain networks may be altered stepwise in patients with disturbance of consciousness, e.g., an encephalopathy. We used resting-state fMRI data on patients suffering from various degrees of hepatic encephalopathy (HE) to explore how topological and spatial network properties of functional brain networks changed at different cognitive and consciousness states. Severity of HE was measured clinically and by neuropsychological tests. Fifty-eight non-alcoholic liver cirrhosis patients and 62 normal controls were studied. Patients were subdivided into liver cirrhosis with no outstanding HE (NoHE, n=23), minimal HE with cognitive impairment only detectable by neuropsychological tests (MHE, n=28), and clinically overt HE (OHE, n=7). From the earliest stage, the NoHE, functional brain networks were progressively more random, less clustered, and less modular. Since the intermediate stage (MHE), increased ammonia level was accompanied by concomitant exponential decay of mean connectivity strength, especially in the primary cortical areas and midline brain structures. Finally, at the OHE stage, there were radical reorganization of the topological centrality-i.e., the relative importance-of the hubs and reorientation of functional connections between nodes. In summary, this study illustrated progressively greater abnormalities in functional brain network organization in patients with clinical and biochemical evidence of more severe hepatic encephalopathy. The early-than-expected brain network dysfunction in cirrhotic patients suggests that brain functional connectivity and network analysis may provide useful and complementary biomarkers for more aggressive and earlier intervention of hepatic encephalopathy. Moreover, the stepwise deterioration of functional brain networks in HE patients may suggest that hierarchical

  10. 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.

  11. Scalable rule-based modelling of allosteric proteins and biochemical networks.

    Directory of Open Access Journals (Sweden)

    Julien F Ollivier

    Full Text Available Much of the complexity of biochemical networks comes from the information-processing abilities of allosteric proteins, be they receptors, ion-channels, signalling molecules or transcription factors. An allosteric protein can be uniquely regulated by each combination of input molecules that it binds. This "regulatory complexity" causes a combinatorial increase in the number of parameters required to fit experimental data as the number of protein interactions increases. It therefore challenges the creation, updating, and re-use of biochemical models. Here, we propose a rule-based modelling framework that exploits the intrinsic modularity of protein structure to address regulatory complexity. Rather than treating proteins as "black boxes", we model their hierarchical structure and, as conformational changes, internal dynamics. By modelling the regulation of allosteric proteins through these conformational changes, we often decrease the number of parameters required to fit data, and so reduce over-fitting and improve the predictive power of a model. Our method is thermodynamically grounded, imposes detailed balance, and also includes molecular cross-talk and the background activity of enzymes. We use our Allosteric Network Compiler to examine how allostery can facilitate macromolecular assembly and how competitive ligands can change the observed cooperativity of an allosteric protein. We also develop a parsimonious model of G protein-coupled receptors that explains functional selectivity and can predict the rank order of potency of agonists acting through a receptor. Our methodology should provide a basis for scalable, modular and executable modelling of biochemical networks in systems and synthetic biology.

  12. Linear systems approach to analysis of complex dynamic behaviours in biochemical networks.

    Science.gov (United States)

    Schmidt, H; Jacobsen, E W

    2004-06-01

    Central functions in the cell are often linked to complex dynamic behaviours, such as sustained oscillations and multistability, in a biochemical reaction network. Determination of the specific mechanisms underlying such behaviours is important, e.g. to determine sensitivity, robustness, and modelling requirements of given cell functions. In this work we adopt a systems approach to the analysis of complex behaviours in intracellular reaction networks, described by ordinary differential equations with known kinetic parameters. We propose to decompose the overall system into a number of low complexity subsystems, and consider the importance of interactions between these in generating specific behaviours. Rather than analysing the network in a state corresponding to the complex non-linear behaviour, we move the system to the underlying unstable steady state, and focus on the mechanisms causing destabilisation of this steady state. This is motivated by the fact that all complex behaviours in unforced systems can be traced to destabilisation (bifurcation) of some steady state, and hence enables us to use tools from linear system theory to qualitatively analyse the sources of given network behaviours. One important objective of the present study is to see how far one can come with a relatively simple approach to the analysis of highly complex biochemical networks. The proposed method is demonstrated by application to a model of mitotic control in Xenopus frog eggs, and to a model of circadian oscillations in Drosophila. In both examples we are able to identify the subsystems, and the related interactions, which are instrumental in generating the observed complex non-linear behaviours.

  13. An efficient algorithm for computing fixed length attractors based on bounded model checking in synchronous Boolean networks with biochemical applications.

    Science.gov (United States)

    Li, X Y; Yang, G W; Zheng, D S; Guo, W S; Hung, W N N

    2015-01-01

    Genetic regulatory networks are the key to understanding biochemical systems. One condition of the genetic regulatory network under different living environments can be modeled as a synchronous Boolean network. The attractors of these Boolean networks will help biologists to identify determinant and stable factors. Existing methods identify attractors based on a random initial state or the entire state simultaneously. They cannot identify the fixed length attractors directly. The complexity of including time increases exponentially with respect to the attractor number and length of attractors. This study used the bounded model checking to quickly locate fixed length attractors. Based on the SAT solver, we propose a new algorithm for efficiently computing the fixed length attractors, which is more suitable for large Boolean networks and numerous attractors' networks. After comparison using the tool BooleNet, empirical experiments involving biochemical systems demonstrated the feasibility and efficiency of our approach.

  14. Criticalities in crosslinked actin networks due to myosin activity

    Science.gov (United States)

    Sheinman, Michael

    2013-03-01

    Many essential processes in cells and tissues, like motility and morphogenesis, are orchestrated by molecular motors applying internal, active stresses on crosslinked networks of actin filaments. Using scaling analysis, mean-field calculation, numerical modelling and in vitro experiments of such active networks we predict and observe different mechanical regimes exhibiting interesting critical behaviours with non-trivial power-law dependencies. Firstly, we find that the presence of active stresses can dramatically increase the stiffness of a floppy network, as was observed in reconstituted intracellular F-actin networks with myosin motors and extracellular gels with contractile cells. Uniform internal stress results in an anomalous, critical mechanical regime only in the vicinity of the rigidity percolation points of the network. However, taking into account heterogeneity of motors, we demonstrate that the motors, stiffening any floppy network, induce large non-affine fluctuations, giving rise to a critical mechanical regime. Secondly, upon increasing motor concentration, the resulting large internal stress is able to significantly enhance unbinding of the network's crosslinks and, therefore, disconnect the initially well-connected network to isolated clusters. However, during this process, when the network approaches marginal connectivity the internal stresses are expected to drop drastically such that the connectivity stabilizes. This general argument and detailed numerical simulations show that motors should drive a well connected network to a close vicinity of a critical point of marginal connectivity. Experiments clearly confirm this conclusion and demonstrate robust critical connectivity of initially well-connected networks, ruptured by the motor activity for a wide range of parameters. M. Sheinman, C.P. Broedersz and F.C. MacKintosh, Phys. Rev. Lett, in press. J. Alvarado, M. Sheinman, A. Sharma, F.C. MacKintosh and G. Koenderink, in preparation.

  15. 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.

  16. 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.

  17. Bistability in a simple fluid network due to viscosity contrast

    CERN Document Server

    Geddes, John B; Gardner, David; Carr, Russell T

    2009-01-01

    We study the existence of multiple equilibrium states in a simple fluid network using Newtonian fluids and laminar flow. We demonstrate theoretically the presence of hysteresis and bistability, and we confirm these predictions in an experiment using two miscible fluids of different viscosity--sucrose solution and water. Possible applications include bloodflow, microfluidics, and other network flows governed by similar principles.

  18. 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

  19. 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.

  20. HRSSA – Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks

    Energy Technology Data Exchange (ETDEWEB)

    Marchetti, Luca, E-mail: marchetti@cosbi.eu [The Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, 1, 38068 Rovereto (Italy); Priami, Corrado, E-mail: priami@cosbi.eu [The Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, 1, 38068 Rovereto (Italy); University of Trento, Department of Mathematics (Italy); Thanh, Vo Hong, E-mail: vo@cosbi.eu [The Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, 1, 38068 Rovereto (Italy)

    2016-07-15

    This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance and accuracy of HRSSA against other state of the art algorithms.

  1. HRSSA - Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks

    Science.gov (United States)

    Marchetti, Luca; Priami, Corrado; Thanh, Vo Hong

    2016-07-01

    This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance and accuracy of HRSSA against other state of the art algorithms.

  2. 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.

  3. Nonlinear Biochemical Signal Processing via Noise Propagation

    OpenAIRE

    Kim, Kyung Hyuk; Qian, Hong; Sauro, Herbert M.

    2013-01-01

    Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance, fluctuations in biochemical activities become significant and such "noise" can propagate through regulatory cascades in terms of biochemical reaction networks. Here we develop an intuitive, yet fully quantitative method for analyzing how noise affects cell...

  4. 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

  5. Constrictor: Flux Balance Analysis Constraint Modification Provides Insight for Design of Biochemical Networks

    Science.gov (United States)

    Erickson, Keesha; Chatterjee, Anushree

    2014-03-01

    The use of in silico methods has become standard practice to correlate the structure of a biochemical network to the expression of a desired phenotype. Flux balance analysis (FBA) is one of the most prevalent techniques for modeling metabolism. FBA models have been successfully applied to obtain growth predictions, theoretical product yields from heterologous pathways, and genome engineering targets. We take inspiration from high-throughput recombineering techniques, which show that combinatorial exploration can reveal optimal mutants, and apply the advantages of computational techniques to analyze these combinations. We introduce Constrictor, an in silico tool for FBA that allows gene mutations to be analyzed in a combinatorial fashion, by applying simulated constraints accounting for regulation of gene expression. We apply this algorithm to study ethylene production in E. coli through the addition of the heterologous ethylene-forming enzyme from P. syringae. Targeting individual reactions as well as sets of reactions results in theoretical ethylene yields that are as much 65% greater than yields calculated using typical FBA. Constrictor is an adaptable technique that can be used to generate and analyze disparate populations of in silico mutants & select gene expression levels.

  6. Patterns of Stochastic Behavior in Dynamically Unstable High-Dimensional Biochemical Networks

    Directory of Open Access Journals (Sweden)

    Simon Rosenfeld

    2009-01-01

    Full Text Available The question of dynamical stability and stochastic behavior of large biochemical networks is discussed. It is argued that stringent conditions of asymptotic stability have very little chance to materialize in a multidimensional system described by the differential equations of chemical kinetics. The reason is that the criteria of asymptotic stability (Routh- Hurwitz, Lyapunov criteria, Feinberg’s Deficiency Zero theorem would impose the limitations of very high algebraic order on the kinetic rates and stoichiometric coefficients, and there are no natural laws that would guarantee their unconditional validity. Highly nonlinear, dynamically unstable systems, however, are not necessarily doomed to collapse, as a simple Jacobian analysis would suggest. It is possible that their dynamics may assume the form of pseudo-random fluctuations quite similar to a shot noise, and, therefore, their behavior may be described in terms of Langevin and Fokker-Plank equations. We have shown by simulation that the resulting pseudo-stochastic processes obey the heavy-tailed Generalized Pareto Distribution with temporal sequence of pulses forming the set of constituent-specific Poisson processes. Being applied to intracellular dynamics, these properties are naturally associated with burstiness, a well documented phenomenon in the biology of gene expression.

  7. Patterns of stochastic behavior in dynamically unstable high-dimensional biochemical networks.

    Science.gov (United States)

    Rosenfeld, Simon

    2009-01-29

    The question of dynamical stability and stochastic behavior of large biochemical networks is discussed. It is argued that stringent conditions of asymptotic stability have very little chance to materialize in a multidimensional system described by the differential equations of chemical kinetics. The reason is that the criteria of asymptotic stability (Routh-Hurwitz, Lyapunov criteria, Feinberg's Deficiency Zero theorem) would impose the limitations of very high algebraic order on the kinetic rates and stoichiometric coefficients, and there are no natural laws that would guarantee their unconditional validity. Highly nonlinear, dynamically unstable systems, however, are not necessarily doomed to collapse, as a simple Jacobian analysis would suggest. It is possible that their dynamics may assume the form of pseudo-random fluctuations quite similar to a shot noise, and, therefore, their behavior may be described in terms of Langevin and Fokker-Plank equations. We have shown by simulation that the resulting pseudo-stochastic processes obey the heavy-tailed Generalized Pareto Distribution with temporal sequence of pulses forming the set of constituent-specific Poisson processes. Being applied to intracellular dynamics, these properties are naturally associated with burstiness, a well documented phenomenon in the biology of gene expression.

  8. Combining Genomics, Metabolome Analysis, and Biochemical Modelling to Understand Metabolic Networks

    Directory of Open Access Journals (Sweden)

    Oliver Fiehn

    2006-04-01

    Full Text Available Now that complete genome sequences are available for a variety of organisms, the elucidation of gene functions involved in metabolism necessarily includes a better understanding of cellular responses upon mutations on all levels of gene products, mRNA, proteins, and metabolites. Such progress is essential since the observable properties of organisms – the phenotypes – are produced by the genotype in juxtaposition with the environment. Whereas much has been done to make mRNA and protein profiling possible, considerably less effort has been put into profiling the end products of gene expression, metabolites. To date, analytical approaches have been aimed primarily at the accurate quantification of a number of pre-defined target metabolites, or at producing fingerprints of metabolic changes without individually determining metabolite identities. Neither of these approaches allows the formation of an in-depth understanding of the biochemical behaviour within metabolic networks. Yet, by carefully choosing protocols for sample preparation and analytical techniques, a number of chemically different classes of compounds can be quantified simultaneously to enable such understanding. In this review, the terms describing various metabolite-oriented approaches are given, and the differences among these approaches are outlined. Metabolite target analysis, metabolite profiling, metabolomics, and metabolic fingerprinting are considered. For each approach, a number of examples are given, and potential applications are discussed.

  9. Conditional robustness analysis for fragility discovery and target identification in biochemical networks and in cancer systems biology

    OpenAIRE

    Bianconi, Fortunato; Baldelli, Elisa; Luovini, Vienna; Petricoin, Emanuel F.; Crinò, Lucio; Valigi, Paolo

    2015-01-01

    Background The study of cancer therapy is a key issue in the field of oncology research and the development of target therapies is one of the main problems currently under investigation. This is particularly relevant in different types of tumor where traditional chemotherapy approaches often fail, such as lung cancer. Results We started from the general definition of robustness introduced by Kitano and applied it to the analysis of dynamical biochemical networks, proposing a new algorithm bas...

  10. Cooperativity and saturation in biochemical networks: a saturable formalism using Taylor series approximations.

    Science.gov (United States)

    Sorribas, Albert; Hernández-Bermejo, Benito; Vilaprinyo, Ester; Alves, Rui

    2007-08-01

    Cooperative and saturable systems are common in molecular biology. Nevertheless, common canonical formalisms for kinetic modeling that are theoretically well justified do not have a saturable form. Modeling and fitting data from saturable systems are widely done using Hill-like equations. In practice, there is no theoretical justification for the generalized use of these equations, other than their ability to fit experimental data. Thus it is important to find a canonical formalism that is (a) theoretically well supported, (b) has a saturable functional form, and (c) can be justifiably applicable to any biochemical network. Here we derive such a formalism using Taylor approximations in a special transformation space defined by power-inverses and logarithms of power-inverses. This formalism is generalized for processes with n-variables, leading to a useful mathematical representation for molecular biology: the Saturable and Cooperative Formalism (SC formalism). This formalism provides an appropriate representation that can be used for modeling processes with cooperativity and saturation. We also show that the Hill equation can be seen as a special case within this formalism. Parameter estimation for the SC formalism requires information that is also necessary to build Power-Law models, Metabolic Control Analysis descriptions or (log)linear and Lin-log models. In addition, the saturation fraction of the relevant processes at the operating point needs to be considered. The practical use of the SC formalism for modeling is illustrated with a few examples. Similar models are built using different formalisms and compared to emphasize advantages and limitations of the different approaches.

  11. SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks

    Directory of Open Access Journals (Sweden)

    Schröder Adrian

    2008-04-01

    Full Text Available Abstract Background The development of complex biochemical models has been facilitated through the standardization of machine-readable representations like SBML (Systems Biology Markup Language. This effort is accompanied by the ongoing development of the human-readable diagrammatic representation SBGN (Systems Biology Graphical Notation. The graphical SBML editor CellDesigner allows direct translation of SBGN into SBML, and vice versa. For the assignment of kinetic rate laws, however, this process is not straightforward, as it often requires manual assembly and specific knowledge of kinetic equations. Results SBMLsqueezer facilitates exactly this modeling step via automated equation generation, overcoming the highly error-prone and cumbersome process of manually assigning kinetic equations. For each reaction the kinetic equation is derived from the stoichiometry, the participating species (e.g., proteins, mRNA or simple molecules as well as the regulatory relations (activation, inhibition or other modulations of the SBGN diagram. Such information allows distinctions between, for example, translation, phosphorylation or state transitions. The types of kinetics considered are numerous, for instance generalized mass-action, Hill, convenience and several Michaelis-Menten-based kinetics, each including activation and inhibition. These kinetics allow SBMLsqueezer to cover metabolic, gene regulatory, signal transduction and mixed networks. Whenever multiple kinetics are applicable to one reaction, parameter settings allow for user-defined specifications. After invoking SBMLsqueezer, the kinetic formulas are generated and assigned to the model, which can then be simulated in CellDesigner or with external ODE solvers. Furthermore, the equations can be exported to SBML, LaTeX or plain text format. Conclusion SBMLsqueezer considers the annotation of all participating reactants, products and regulators when generating rate laws for reactions. Thus, for

  12. Network analysis of biochemical logic for noise reduction and stability: a system of three coupled enzymatic and gates.

    Science.gov (United States)

    Privman, Vladimir; Arugula, Mary A; Halámek, Jan; Pita, Marcos; Katz, Evgeny

    2009-04-16

    We develop an approach aimed at optimizing the parameters of a network of biochemical logic gates for reduction of the "analog" noise buildup. Experiments for three coupled enzymatic AND gates are reported, illustrating our procedure. Specifically, starch, one of the controlled network inputs, is converted to maltose by beta-amylase. With the use of phosphate (another controlled input), maltose phosphorylase then produces glucose. Finally, nicotinamide adenine dinucleotide (NAD(+)), the third controlled input, is reduced under the action of glucose dehydrogenase to yield the optically detected signal. Network functioning is analyzed by varying selective inputs and fitting standardized few-parameters "response-surface" functions assumed for each gate. This allows a certain probe of the individual gate quality, but primarily yields information on the relative contribution of the gates to noise amplification. The derived information is then used to modify our experimental system to put it in a regime of a less noisy operation.

  13. 77 FR 27381 - Financial Crimes Enforcement Network: Customer Due Diligence Requirements for Financial...

    Science.gov (United States)

    2012-05-10

    ...; ] DEPARTMENT OF THE TREASURY 31 CFR Chapter X RIN 1506-AB15 Financial Crimes Enforcement Network: Customer Due Diligence Requirements for Financial Institutions; Extension of Comment Period AGENCY: Financial Crimes... Rulemaking (ANPRM) it published concerning customer due diligence requirements for financial...

  14. Chronic stress due to high stocking density in open sea cage farming induces variation in biochemical and immunological functions in Asian seabass (Lates calcarifer, Bloch).

    Science.gov (United States)

    Sadhu, Narasimhulu; Sharma, S R Krupesha; Joseph, Shoji; Dube, Praveen; Philipose, K K

    2014-08-01

    Stocking density is an important factor in cage aquaculture of finfish. Effects of high stocking density (35 fish cubic m(-1)) on a range of biochemical and immunological parameters in Asian seabass reared in open sea floating net cages were compared to fish held in relatively low density (15 fish cubic m(-1)). The results revealed that chronic stress due to high stocking density induced variations in most of the parameters studied as evidenced by increased cortisol and glucose levels and decreased activity of lysozyme, myeloperoxidase and complement. Production of reactive oxygen species, total leucocyte count and total serum protein were also decreased, whereas anti-protease, alkaline phosphatase and acid phosphatase activities were increased in high stocking-density group when compared to low stocking-density group. Effects of chronic stress due to high stocking density were discussed in relation to variations in these parameters.

  15. The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions

    Directory of Open Access Journals (Sweden)

    Thomas Philipp

    2012-05-01

    Full Text Available Abstract Background It is well known that the deterministic dynamics of biochemical reaction networks can be more easily studied if timescale separation conditions are invoked (the quasi-steady-state assumption. In this case the deterministic dynamics of a large network of elementary reactions are well described by the dynamics of a smaller network of effective reactions. Each of the latter represents a group of elementary reactions in the large network and has associated with it an effective macroscopic rate law. A popular method to achieve model reduction in the presence of intrinsic noise consists of using the effective macroscopic rate laws to heuristically deduce effective probabilities for the effective reactions which then enables simulation via the stochastic simulation algorithm (SSA. The validity of this heuristic SSA method is a priori doubtful because the reaction probabilities for the SSA have only been rigorously derived from microscopic physics arguments for elementary reactions. Results We here obtain, by rigorous means and in closed-form, a reduced linear Langevin equation description of the stochastic dynamics of monostable biochemical networks in conditions characterized by small intrinsic noise and timescale separation. The slow-scale linear noise approximation (ssLNA, as the new method is called, is used to calculate the intrinsic noise statistics of enzyme and gene networks. The results agree very well with SSA simulations of the non-reduced network of elementary reactions. In contrast the conventional heuristic SSA is shown to overestimate the size of noise for Michaelis-Menten kinetics, considerably under-estimate the size of noise for Hill-type kinetics and in some cases even miss the prediction of noise-induced oscillations. Conclusions A new general method, the ssLNA, is derived and shown to correctly describe the statistics of intrinsic noise about the macroscopic concentrations under timescale separation conditions

  16. Prediction of concrete compressive strength due to long term sulfate attack using neural network

    Directory of Open Access Journals (Sweden)

    Ahmed M. Diab

    2014-09-01

    Full Text Available This work was divided into two phases. Phase one included the validation of neural network to predict mortar and concrete properties due to sulfate attack. These properties were expansion, weight loss, and compressive strength loss. Assessment of concrete compressive strength up to 200 years due to sulfate attack was considered in phase two. The neural network model showed high validity on predicting compressive strength, expansion and weight loss due to sulfate attack. Design charts were constructed to predict concrete compressive strength loss. The inputs of these charts were cement content, water cement ratio, C3A content, and sulfate concentration. These charts can be used easily to predict the compressive strength loss after any certain age and sulfate concentration for different concrete compositions.

  17. 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.

  18. A biochemical network can control formation of a synthetic material by sensing numerous specific stimuli

    Science.gov (United States)

    Hun Yeon, Ju; Chan, Karen Y. T.; Wong, Ting-Chia; Chan, Kelvin; Sutherland, Michael R.; Ismagilov, Rustem F.; Pryzdial, Edward L. G.; Kastrup, Christian J.

    2015-05-01

    Developing bio-compatible smart materials that assemble in response to environmental cues requires strategies that can discriminate multiple specific stimuli in a complex milieu. Synthetic materials have yet to achieve this level of sensitivity, which would emulate the highly evolved and tailored reaction networks of complex biological systems. Here we show that the output of a naturally occurring network can be replaced with a synthetic material. Exploiting the blood coagulation system as an exquisite biological sensor, the fibrin clot end-product was replaced with a synthetic material under the biological control of a precisely regulated cross-linking enzyme. The functions of the coagulation network remained intact when the material was incorporated. Clot-like polymerization was induced in indirect response to distinct small molecules, phospholipids, enzymes, cells, viruses, an inorganic solid, a polyphenol, a polysaccharide, and a membrane protein. This strategy demonstrates for the first time that an existing stimulus-responsive biological network can be used to control the formation of a synthetic material by diverse classes of physiological triggers.

  19. Deformation of an Elastic Beam due to Viscous Flow in an Embedded Parallel Channel Network

    CERN Document Server

    Matia, Yoav

    2015-01-01

    Elastic deformation due to embedded fluidic networks is currently studied in the context of soft-actuators and soft-robotic applications. In this work, we analyze interaction between the elastic deflection of a slender beam and viscous flow within a long serpentine channel, embedded in the elastic beam. The channel is positioned asymmetrically with regard to the midplane of the beam, and thus pressure within the channel creates a local moment deforming the beam. We focus on creeping flows and small deflections of the elastic beam and obtain, in leading order, a fourth-order partial integro-differential equation governing the time-dependent deflection field. This relation enables the design of complex time-dependent deformation patterns of beams with embedded channel networks, including inertia-like standing and moving wave solutions in configurations with negligible inertia.

  20. 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.

  1. Noise transmission and delay-induced stochasticoscillations in biochemical network motifs

    Institute of Scientific and Technical Information of China (English)

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

    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.

  2. Model reduction and parameter estimation of non-linear dynamical biochemical reaction networks.

    Science.gov (United States)

    Sun, Xiaodian; Medvedovic, Mario

    2016-02-01

    Parameter estimation for high dimension complex dynamic system is a hot topic. However, the current statistical model and inference approach is known as a large p small n problem. How to reduce the dimension of the dynamic model and improve the accuracy of estimation is more important. To address this question, the authors take some known parameters and structure of system as priori knowledge and incorporate it into dynamic model. At the same time, they decompose the whole dynamic model into subset network modules, based on different modules, and then they apply different estimation approaches. This technique is called Rao-Blackwellised particle filters decomposition methods. To evaluate the performance of this method, the authors apply it to synthetic data generated from repressilator model and experimental data of the JAK-STAT pathway, but this method can be easily extended to large-scale cases.

  3. Probability of islanding in utility networks due to grid connected photovoltaic power systems

    Energy Technology Data Exchange (ETDEWEB)

    Verhoeven, B.

    2002-09-15

    This report for the International Energy Agency (IEA) made by Task 5 of the Photovoltaic Power Systems (PVPS) programme takes a look at the probability of islanding in utility networks due to grid-connected photovoltaic power systems. The mission of the Photovoltaic Power Systems Programme is to enhance the international collaboration efforts which accelerate the development and deployment of photovoltaic solar energy. Task 5 deals with issues concerning grid-interconnection and distributed PV power systems. This report summarises the results on a study on the probability of islanding in power networks with a high penetration level of grid connected PV-systems. The results are based on measurements performed during one year in a Dutch utility network. The measurements of active and reactive power were taken every second for two years and stored in a computer for off-line analysis. The area examined and its characteristics are described, as are the test set-up and the equipment used. The ratios between load and PV-power are discussed. The general conclusion is that the probability of islanding is virtually zero for low, medium and high penetration levels of PV-systems.

  4. Unscheduled load flow effect due to large variation in the distributed generation in a subtransmission network

    Science.gov (United States)

    Islam, Mujahidul

    A sustainable energy delivery infrastructure implies the safe and reliable accommodation of large scale penetration of renewable sources in the power grid. In this dissertation it is assumed there will be no significant change in the power transmission and distribution structure currently in place; except in the operating strategy and regulatory policy. That is to say, with the same old structure, the path towards unveiling a high penetration of switching power converters in the power system will be challenging. Some of the dimensions of this challenge are power quality degradation, frequent false trips due to power system imbalance, and losses due to a large neutral current. The ultimate result is the reduced life of many power distribution components - transformers, switches and sophisticated loads. Numerous ancillary services are being developed and offered by the utility operators to mitigate these problems. These services will likely raise the system's operational cost, not only from the utility operators' end, but also reflected on the Independent System Operators and by the Regional Transmission Operators (RTO) due to an unforeseen backlash of frequent variation in the load-side generation or distributed generation. The North American transmission grid is an interconnected system similar to a large electrical circuit. This circuit was not planned but designed over 100 years. The natural laws of physics govern the power flow among loads and generators except where control mechanisms are installed. The control mechanism has not matured enough to withstand the high penetration of variable generators at uncontrolled distribution ends. Unlike a radial distribution system, mesh or loop networks can alleviate complex channels for real and reactive power flow. Significant variation in real power injection and absorption on the distribution side can emerge as a bias signal on the routing reactive power in some physical links or channels that are not distinguishable

  5. 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.

  6. 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

  7. Automatic Verification of Biochemical Network Using Model Checking Method%基于模型校核的生化网络自动辨别方法

    Institute of Scientific and Technical Information of China (English)

    Jinkyung Kim; Younghee Lee; Il Moon

    2008-01-01

    This study focuses on automatic searching and verifying methods for the reachability, transition logics and hierarchical structure in all possible paths of biological processes using model checking. The automatic search and verification for alternative paths within complex and large networks in biological process can provide a consid-erable amount of solutions, which is difficult to handle manually. Model checking is an automatic method for veri-fying if a circuit or a condition, expressed as a concurrent transition system, satisfies a set of properties expressed ina temporal logic, such as computational tree logic (CTL). This article represents that model checking is feasible in biochemical network verification and it shows certain advantages over simulation for querying and searching of special behavioral properties in biochemical processes.

  8. Ictal singing due to right mesial temporal lobe epilepsy involving a bihemispheric network.

    Science.gov (United States)

    Lee, Eun Mi; Kang, Joong Koo; Park, Ga Young; Oh, Jung Su; Kim, Jae Seung

    2013-01-01

    Singing is a rare ictal symptom of focal epilepsy. Here, we report a case of a right-handed patient who demonstrated ictal singing due to right mesial temporal lobe epilepsy. Subtraction ictal SPECT coregistered to MRI (SISCOM) performed during ictal singing demonstrated areas of hyperperfusion in the bilateral frontal regions (more prominent in the left frontal lobe), bilateral subcortical regions, insular cortices, and bilateral cerebellum in addition to the right temporal area. An intracranial EEG revealed that an ictal singing episode commenced after an ictal rhythm from the right temporal area was propagated to the contralateral side of the left hemisphere. These findings suggest that the symptomatogenic zone for ictal singing includes neural networks from the frontal and temporal regions of both hemispheres rather than specific cortical areas even when the epileptogenic zone is located in the right mesial temporal area, as evidenced in this patient.

  9. Using artificial neural network approach for modelling rainfall–runoff due to typhoon

    Indian Academy of Sciences (India)

    S M Chen; Y M Wang; I Tsou

    2013-04-01

    In Taiwan, owing to the nonuniform temporal and spatial distribution of rainfall and high mountains all over the country, hydrologic systems are very complex. Therefore, preventing and controlling flood disasters is imperative. Nevertheless, water level and flow records are essential in hydrological analysis for designing related water works of flood management. Due to the complexity of the hydrological process, reliable runoff is hardly predicted by applying linear and non-linear regression methods. Therefore, in this study, a model for estimating runoff by using rainfall data from a river basin is developed and a neural network technique is employed to recover missing data. For achieving the objectives, hourly rainfall and flow data from Nanhe, Taiwu, and Laii rainfall stations and Sinpi flow station in the Linbien basin are used. The data records were of 27 typhoons between the years 2005 and 2009. The feed forward back propagation network (FFBP) and conventional regression analysis (CRA) were employed to study their performances. From the statistical evaluation, it has been found that the performance of FFBP exceeded that of regression analysis as reflected by the determination coefficients 2, which were 0.969 and 0.284 for FFBP and CRA, respectively.

  10. Nonlinear biochemical signal processing via noise propagation.

    Science.gov (United States)

    Kim, Kyung Hyuk; Qian, Hong; Sauro, Herbert M

    2013-10-14

    Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance, fluctuations in biochemical activities become significant and such "noise" can propagate through regulatory cascades in terms of biochemical reaction networks. Here we develop an intuitive, yet fully quantitative method for analyzing how noise affects cellular phenotypes based on identifying a system's nonlinearities and noise propagations. We observe that such noise can simultaneously enhance sensitivities in one behavioral region while reducing sensitivities in another. Employing this novel phenomenon we designed three biochemical signal processing modules: (a) A gene regulatory network that acts as a concentration detector with both enhanced amplitude and sensitivity. (b) A non-cooperative positive feedback system, with a graded dose-response in the deterministic case, that serves as a bistable switch due to noise-induced ultra-sensitivity. (c) A noise-induced linear amplifier for gene regulation that requires no feedback. The methods developed in the present work allow one to understand and engineer nonlinear biochemical signal processors based on fluctuation-induced phenotypes.

  11. Cascading failures in interdependent networks due to insufficient received support capability

    Science.gov (United States)

    Cui, Pengshuai; Zhu, Peidong; Shao, Chengcheng; Xun, Peng

    2017-03-01

    We propose a capability based dependency model of interdependent network that takes two node dependency properties into account. One is support capability and the other is required capability. The redundancy degree of an interdependent network is also defined, whose value is the ratio of its total support capability and total required capability. Through the numerical simulations, we found that: (1) Interdependent networks without redundant support-dependence links are extremely vulnerable, even the failure of one node could cause the collapse of whole network; (2) Increasing support-dependence links and redistributing the nodes' dependency properties can enhance the robustness of network without changing its redundancy degree; (3) Improving the redundancy degree could enhance network robustness without adding support-dependence links. These conclusions enlighten the design of interdependent networks: when network's redundancy degree is fixed, we can take strategy from results (2), and when network structure is settled, we can apply strategy from results (3).

  12. 生化网络的随机Petri网建模与分析%Modeling and analyzing biochemical networks using stochastic Petri nets

    Institute of Scientific and Technical Information of China (English)

    丁德武; 李文泽

    2012-01-01

    细胞的行为是随机性的,学习细胞中的随机性有助于理解细胞的组织,设计和进化.建立、确认和分析随机的生化网络模型是当前计算系统生物学领域的一个重要研究主题.当前,标准的Petri网模型已经成为生化网络模拟和定性分析的有力工具.尝试使用随机Petri网对生化网络进行建模与分析,简单描述了随机Petri网理论对标准Petri网的扩充,通过对二聚作用和肌动蛋白这两个典型例子的建模与演化模拟,介绍、论证了随机Petri网理论的新应用.%Cellular behavior is stochastic, and studying stochastic in the cell can help to understand the organization, design and evolution of the cell. Establishment, identification and analysis of stochastic biochemical network models is an important research topic in the field of computational systems biology. At present, the standard Petri net model has become a powerful tool for biochemical network modeling and qualitative analysis. This paper attempts to apply stochastic Petri nets to modeling and analyzing biochemical network, it briefly describes the expansion of the stochastic Petri net theory to standard Petri nets, then by modeling and evolution simulating two classic examples (dimerization and actin), it demonstrates new applications of stochastic Petri nets theory.

  13. 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.

  14. Self-management of hybrid networks – hidden costs due to TCP performance problems

    NARCIS (Netherlands)

    Moura, Giovane C.M.; Pras, Aiko; Fioreze, Tiago; Boer, de Pieter-Tjerk; Bauschert, Thomas

    2013-01-01

    Self-management is one of the most popular research topics in network and systems management. Little is known, however, regarding the costs, in particular with respect to performance, of self-management solutions. The goal of this paper is therefore to analyze such hidden per- formance costs. Our an

  15. Effect Attack on Scale-Free Networks due to Cascading Failures

    Institute of Scientific and Technical Information of China (English)

    WANG Jian-Wei; RONG Li-Li

    2008-01-01

    Adopting the initial load era node j to be Lj = [kj(Σm∈Γjkm )]α with kj and Γj being the degree of the node j and the set of its neighbouring nodes respectively, we propose a cascading model based on a local preferential redistribution rule of the load after removing a node. Assuming that a failed node leads only to a redistribution of the load passing through it to its neighbouring nodes, we explore the response of scale-free networks subject to two different attack strategies on nodes and find some interesting and counterintuitive results in our cascading model. On the one hand, unexpectedly, the attack on the nodes with the lowest degree is more harmful than the attack on the highest degree nodes when α< 1/2. On the other hand, when α = 1/2, the effects of two attacks for the robustness against cascading failures are almost identical. In addition, the numerical simulations are also verified by the theoretical analysis. These results may be very helpful for real-life networks to protect the key nodes selected effectively and to avoid cascading-failure-induced disasters.

  16. An Analysis of the Privacy Threat in Vehicular Ad Hoc Networks due to Radio Frequency Fingerprinting

    Directory of Open Access Journals (Sweden)

    Gianmarco Baldini

    2017-01-01

    Full Text Available In Vehicular Ad Hoc Networks (VANETs used in the road transportation sector, privacy risks may arise because vehicles could be tracked on the basis of the information transmitted by the Vehicle to Vehicle (V2V and Vehicle to Infrastructure (V2I communications implemented with the Dedicated Short Range Communications (DSRC standards operating at 5.9 GHz. Various techniques have been proposed in the literature to mitigate these privacy risks including the use of pseudonym schemes, but they are mostly focused on data anonymization at the network and application layer. At the physical layer, the capability to accurately identify and fingerprint wireless devices through their radio frequency (RF emissions has been demonstrated in the literature. This capability may generate a privacy threat because vehicles can be tracked using the RF emissions of their DSRC devices. This paper investigates the privacy risks related to RF fingerprinting to determine if privacy breaches are feasible in practice. In particular, this paper analyzes the tracking accuracy in challenging RF environments with high attenuation and fading.

  17. Synchronization transitions on scale-free neuronal networks due to finite information transmission delays

    Science.gov (United States)

    Wang, Qingyun; Perc, Matjaž; Duan, Zhisheng; Chen, Guanrong

    2009-08-01

    We investigate front propagation and synchronization transitions in dependence on the information transmission delay and coupling strength over scale-free neuronal networks with different average degrees and scaling exponents. As the underlying model of neuronal dynamics, we use the efficient Rulkov map with additive noise. We show that increasing the coupling strength enhances synchronization monotonously, whereas delay plays a more subtle role. In particular, we found that depending on the inherent oscillation frequency of individual neurons, regions of irregular and regular propagating excitatory fronts appear intermittently as the delay increases. These delay-induced synchronization transitions manifest as well-expressed minima in the measure for spatial synchrony, appearing at every multiple of the oscillation frequency. Larger coupling strengths or average degrees can broaden the region of regular propagating fronts by a given information transmission delay and further improve synchronization. These results are robust against variations in system size, intensity of additive noise, and the scaling exponent of the underlying scale-free topology. We argue that fine-tuned information transmission delays are vital for assuring optimally synchronized excitatory fronts on complex neuronal networks and, indeed, they should be seen as important as the coupling strength or the overall density of interneuronal connections. We finally discuss some biological implications of the presented results.

  18. Reliability of water distribution networks due to pumps failure: comparison of VSP and SSP application

    Directory of Open Access Journals (Sweden)

    N. Mehzad

    2012-07-01

    Full Text Available Reliability is an important indicator to ensure the operation of Water Distribution Networks (WDNs. To optimize the operation of WDN, it is necessary to incorporate the reliability of active components (such as pumps and tanks besides the reliability of pipes. In this research, a concept is suggested to calculate the reliability of WDNs' pumping stations. A computer code is provided in Visual Basic and is linked to EPANET2.0. To evaluate the proposed methodology a real WDN near the city of Tehran is considered. According to the obtained results, it is concluded that by increasing the demand of the WDN during a day, the reliability of pumps decrease. Therefore, it seems that decision-making is necessary if high demand hours are considered, in order to increase the reliability of the system. On the other hand, it is observed in this research that using variable speed pumps not only reduces the energy cost of the network, but also the reliability of the pumping stations with variable speed pumps is higher than single speed pumps. Therefore, using VSP is highly recommended in WDNs.

  19. Identification of Enterobacter sakazakii from closely related species: The use of Artificial Neural Networks in the analysis of biochemical and 16S rDNA data

    Directory of Open Access Journals (Sweden)

    Waddington Michael

    2006-03-01

    Full Text Available Abstract Background Enterobacter sakazakii is an emergent pathogen associated with ingestion of infant formula and accurate identification is important in both industrial and clinical settings. Bacterial species can be difficult to accurately characterise from complex biochemical datasets and computer algorithms can potentially simplify the process. Results Artificial Neural Networks were applied to biochemical and 16S rDNA data derived from 282 strains of Enterobacteriaceae, including 189 E. sakazakii isolates, in order to identify key characteristics which could improve the identification of E. sakazakii. The models developed resulted in a predictive performance for blind (validation data of 99.3 % correct discrimination between E. sakazakii and closely related species for both phenotypic and genotypic data. Three main regions of the partial rDNA sequence were found to be key in discriminating the species. Comparison between E. sakazakii and other strains also constitutively positive for expression of the enzyme α-glucosidase resulted in a predictive performance of 98.7 % for 16S rDNA sequence data and 100% for phenotypic data. Conclusion The computationally based methods developed here show a remarkable ability in reducing data dimensionality and complexity, in order to eliminate noise from the system in order to facilitate the speed and reliability of a potential strain identification system. Furthermore, the approaches described are also able to provide valuable information regarding the population structure and distribution of individual species thus providing the foundations for novel assays and diagnostic tests for rapid identification of pathogens.

  20. 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

    and strict specificity towards gluconate out of 122 substrates tested. In order to evaluate the metabolic impact of gluconate in humans we modeled gluconate metabolism using steady state metabolic network analysis. The results indicate that significant metabolic flux changes in anabolic pathways linked......The metabolism of gluconate is well characterized in prokaryotes where it is known to be degraded following phosphorylation by gluconokinase. Less is known of gluconate metabolism in humans. Human gluconokinase activity was recently identified proposing questions about the metabolic role...... 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...

  1. Height biases and scale variations in VLBI networks due to antenna gravitational deformations

    Science.gov (United States)

    Abbondanza, Claudio; Sarti, Pierguido; Petrov, Leonid; Negusini, Monia

    2010-05-01

    The impact of signal path variations (SPVs) caused by antenna gravity deformations on geodetic VLBI results is evaluated for the first time. Elevation-dependent models of SPV for Medicina and Noto (Italy) telescopes were derived from a combination of terrestrial surveying methods to account for gravitational deformations. After applying these models, estimates of the antenna reference point (ARP) positions are shifted upward by 8.9 mm and 6.7 mm, respectively. The impact on other parameters is negligible. To infer the impact of antenna gravity deformations on the entire VLBI network, lacking measurements for other telescopes, we rescaled the SPV models of Medicina and Noto for other antennas according to their size. The effects are changes in VLBI heights in the range [-3,73] mm and a significant net scale increase of 0.3 - 0.8 ppb. This demonstrates the need to include SPV models in routine VLBI data analysis.

  2. Quantitative assessment of energy conservation due to public awareness campaigns using neural networks

    Energy Technology Data Exchange (ETDEWEB)

    Mahmoud, Mohamed A.; Alajmi, Ali F. [Department of Mechanical Engineering, College of Technological Studies, P.O. Box 33145, Rumaithya (Kuwait)

    2010-01-15

    This case study aims to quantitatively assess the impact of an energy conservation campaign that was launched under the name ''Trsheed'' in Kuwait in the summer of 2007. Most electric energy (EE) consumption in the summer in the country is used in air conditioning and past trends indicate a strong correlation between ambient weather conditions and energy demand. The size and attitude of the population is an important factor in this regard; Kuwait has an expatriate population that is larger than the indigent population, and whose size is closely linked to economic activities that are largely dependent on oil revenues and varies with fluctuations of oil prices. Three neural network architectures (NNs) were evaluated in terms of their ability to estimate future EE demand based on previous trends. Backpropagation neural networks were found to be most suitable for this purpose in comparison to General Regression and Polynomial NNs. The inputs to the NNs investigated included hourly weather condition indicators; specifically the dry-bulb temperature and relative humidity. The output of the NNs was the hourly energy demand. An analysis based on actual weather data from 2004 to 2007 was performed to gauge the impact of the energy conservation campaign in the summer of 2007. Results of a second NN analysis show that round-the-clock mean weather conditions may be used to predict total future energy demand over a period of time (daily, weekly or monthly), but future peak loads should be estimated separately using mean weather conditions during peak hours only. Savings in national energy demand, as a result of future conservation campaigns, are estimated to be more than 5% and 4% in total and peak demands, respectively. (author)

  3. Characterizing waveform uncertainty due to ambient noise for the Global Seismic Network

    Science.gov (United States)

    Guandique, J. A.; Burdick, S.; Lekic, V.

    2015-12-01

    Ambient seismic noise is the vibration present on seismograms not due by any earthquake or discrete source. It can be caused by trees swaying in the wind or trucks rumbling on the freeway, but the main source of noise is the microseism caused by ocean waves. The frequency content and amplitude of seismic noise varies due to weather, season, and the location of a station, among other factors. Because noise affects recordings of earthquake waveforms, better understanding it could improve the detection of small earthquakes, reduce false positives in earthquake early warning, and quantify uncertainty in waveform-based studies In this study, we used two years of 3-component accelerograms from stations in the GSN. We eliminate days with major earthquakes, aggregate analysis by month, and calculate the mean power spectrum for each component and the transfer function between components. For each power spectrum, we determine the dominant frequency and amplitude of the primary (PM) and secondary (SM) microseisms which appear at periods of ~14s and ~7s, as well as any other prominent peaks. The cross-component terms show that noise recorded on different components cannot be treated as independent. Trends in coherence and phase delay suggest directionality in the noise and information about in which modes it propagates. Preliminary results show that the noise on island stations exhibits less monthly variability, and its PM peaks tend to be much weaker than the SM peaks. The continental stations show much less consistent behavior, with higher variability in the PM peaks between stations and higher frequency content during winter months. Stations that are further inland have smaller SM peaks compared to coastal stations, which are more similar to island stations. Using these spectra and cross-component results, we develop a method for generating realistic 3-component seismic noise and covariance matrices, which can be used across various seismic applications.

  4. 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

  5. Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways.

    Science.gov (United States)

    Lo, Chien-Chi; Bonner, Carol A; Xie, Gary; D'Souza, Mark; Jensen, Roy A

    2009-12-01

    Aspartokinase (Ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. Lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ASK network or from alternative pathways. Ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. Two subhomology divisions, ASK(alpha) and ASK(beta), have been recognized. The ASK(alpha) subhomology division is the most ancient, being widely distributed throughout the Archaea and Eukarya and in some Bacteria. Within an indel region of about 75 amino acids near the N terminus, ASK(beta) sequences differ from ASK(alpha) sequences by the possession of a proposed ancient deletion. ASK(beta) sequences are present in most Bacteria and usually exhibit an in-frame internal translational start site that can generate a small Ask subunit that is identical to the C-terminal portion of the larger subunit of a heterodimeric unit. Particularly novel are ask genes embedded in gene contexts that imply specialization for ectoine (osmotic agent) or aromatic amino acids. The cohesion group approach is well suited for the easy recognition of relatively recent lateral gene transfer (LGT) events, and many examples of these are described. Given the current density of genome representation for Proteobacteria, it is possible to reconstruct more ancient landmark LGT events. Thus, a plausible scenario in which the three well-studied and iconic Ask homologs of Escherichia coli are not within the vertical genealogy of Gammaproteobacteria, but rather originated via LGT from a Bacteroidetes donor, is supported.

  6. 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

  7. The application of information theory to biochemical signaling systems.

    Science.gov (United States)

    Rhee, Alex; Cheong, Raymond; Levchenko, Andre

    2012-08-01

    Cell signaling can be thought of fundamentally as an information transmission problem in which chemical messengers relay information about the external environment to the decision centers within a cell. Due to the biochemical nature of cellular signal transduction networks, molecular noise will inevitably limit the fidelity of any messages received and processed by a cell's signal transduction networks, leaving it with an imperfect impression of its environment. Fortunately, Shannon's information theory provides a mathematical framework independent of network complexity that can quantify the amount of information that can be transmitted despite biochemical noise. In particular, the channel capacity can be used to measure the maximum number of stimuli a cell can distinguish based upon the noisy responses of its signaling systems. Here, we provide a primer for quantitative biologists that covers fundamental concepts of information theory, highlights several key considerations when experimentally measuring channel capacity, and describes successful examples of the application of information theoretic analysis to biological signaling.

  8. Identification of efflux proteins using efficient radial basis function networks with position-specific scoring matrices and biochemical properties.

    Science.gov (United States)

    Ou, Yu-Yen; Chen, Shu-An; Chang, Yun-Min; Velmurugan, Devadasan; Fukui, Kazuhiko; Michael Gromiha, M

    2013-09-01

    Efflux proteins are membrane proteins, which are involved in the transportation of multidrugs. The annotation of efflux proteins in genomic sequences would aid to understand the function. Although the percentage of membrane proteins in genomes is estimated to be 25-30%, there is no information about the content of efflux proteins. For annotating such class of proteins it is necessary to develop a reliable method to identify efflux proteins from amino acid sequence information. In this work, we have developed a method based on radial basis function networks using position specific scoring matrices (PSSM) and amino acid properties. We noticed that the C-terminal domain of efflux proteins contain vital information for discrimination. Our method showed an accuracy of 78 and 92% in discriminating efflux proteins from transporters and membrane proteins, respectively using fivefold cross-validation. We utilized our method for annotating the genomes E. coli and P. aeruginosa and it predicted 8.7 and 9.2% of proteins as efflux proteins in these genomes, respectively. The predicted efflux proteins have been compared with available experimental data and we observed a very good agreement between them. Further, we developed a web server for classifying efflux proteins and it is freely available at http://rbf.bioinfo.tw/∼sachen/EFFLUXpredict/Efflux-RBF.php. We suggest that our method could be an effective tool for annotating efflux proteins in genomic sequences.

  9. Classification of transporters using efficient radial basis function networks with position-specific scoring matrices and biochemical properties.

    Science.gov (United States)

    Ou, Yu-Yen; Chen, Shu-An; Gromiha, M Michael

    2010-05-15

    Transporters are proteins that are involved in the movement of ions or molecules across biological membranes. Transporters are generally classified into channels/pores, electrochemical transporters, and active transporters. Discriminating the specific class of transporters and their subfamilies are essential tasks in computational biology for the advancement of structural and functional genomics. We have systematically analyzed the amino acid composition, residue pair preference and amino acid properties in six different families of transporters. Utilizing the information, we have developed a radial basis function (RBF) network method based on profiles obtained with position specific scoring matrices for discriminating transporters belonging to three different classes and six families. Our method showed a fivefold cross validation accuracy of 76%, 73%, and 69% for discriminating transporters and nontransporters, three different classes and six different families of transporters, respectively. Further, the method was tested with independent datasets, which showed similar level of accuracy. A web server has been developed for discriminating transporters based on three classes and six families, and it is available at http://rbf.bioinfo.tw/ approximately sachen/tcrbf.html. We suggest that our method could be effectively used to identify transporters and discriminating them into different classes and families.

  10. Post-crystallization increases in the mechanical strength of self-assembled fibrillar networks is due to an increase in network supramolecular ordering

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, Michael A; Marangoni, Alejandro G [Department of Food Science, University of Guelph, Guelph, ON, N1G2W1 (Canada); Wright, Amanda J [Department of Human Health and Nutritional Science, University of Guelph, Guelph, ON, N1G2W1 (Canada)], E-mail: amarango@uoguelph.ca

    2008-11-07

    Fibre-fibre interactions strongly influence the elastic properties of an organogel and are of critical importance to the ability of the network to entrain liquid oil. At 30 deg. C, there was a significant decrease in the storage modulus in time due to a decrease in the amount of crystalline material (i.e. a decrease in the free induction decay (FID) amplitude) and order of crystalline material (i.e. an increase in the FID T{sub 2} relaxation time (i.e. a measure of proton mobility)). Conversely, at 5 deg. C, there was an increase in G' in time but no changes were observed in both the amount of crystalline material and its order. This increase in G' was accompanied by a significant increase in the enthalpy of melt and the melting temperature, which translated to a significant increase in the entropy of melt of the system. This decrease in the absolute entropy of the system in time probably arose due to an increase in the number of van der Waals interactions between 12-hydroxystearic acid fibres. Hence the increased order of the system is due to the fibre-fibre interactions which results in a significant increase in G' in time at 5 deg. C.

  11. Post-crystallization increases in the mechanical strength of self-assembled fibrillar networks is due to an increase in network supramolecular ordering

    Science.gov (United States)

    Rogers, Michael A.; Wright, Amanda J.; Marangoni, Alejandro G.

    2008-11-01

    Fibre-fibre interactions strongly influence the elastic properties of an organogel and are of critical importance to the ability of the network to entrain liquid oil. At 30 °C, there was a significant decrease in the storage modulus in time due to a decrease in the amount of crystalline material (i.e. a decrease in the free induction decay (FID) amplitude) and order of crystalline material (i.e. an increase in the FID T2 relaxation time (i.e. a measure of proton mobility)). Conversely, at 5 °C, there was an increase in G' in time but no changes were observed in both the amount of crystalline material and its order. This increase in G' was accompanied by a significant increase in the enthalpy of melt and the melting temperature, which translated to a significant increase in the entropy of melt of the system. This decrease in the absolute entropy of the system in time probably arose due to an increase in the number of van der Waals interactions between 12-hydroxystearic acid fibres. Hence the increased order of the system is due to the fibre-fibre interactions which results in a significant increase in G' in time at 5 °C.

  12. Multiplexing oscillatory biochemical signals.

    Science.gov (United States)

    de Ronde, Wiet; ten Wolde, Pieter Rein

    2014-04-01

    In recent years it has been increasingly recognized that biochemical signals are not necessarily constant in time and that the temporal dynamics of a signal can be the information carrier. Moreover, it is now well established that the protein signaling network of living cells has a bow-tie structure and that components are often shared between different signaling pathways. Here we show by mathematical modeling that living cells can multiplex a constant and an oscillatory signal: they can transmit these two signals simultaneously through a common signaling pathway, and yet respond to them specifically and reliably. We find that information transmission is reduced not only by noise arising from the intrinsic stochasticity of biochemical reactions, but also by crosstalk between the different channels. Yet, under biologically relevant conditions more than 2 bits of information can be transmitted per channel, even when the two signals are transmitted simultaneously. These observations suggest that oscillatory signals are ideal for multiplexing signals.

  13. Service network design for an intermodal container network with flexible due dates/times and the possibility of using subcontracted transport

    NARCIS (Netherlands)

    B. van Riessen (Bart); R.R. Negenborn (Rudy); R. Dekker (Rommert); G. Lodewijks (Gabriel)

    2013-01-01

    textabstractAn intermodal container transportation network is being developed between Rotterdam and several inland terminals in North West Europe: the EUROPEAN GATEWAY SERVICES (EGS) network. This network is developed and operated by the seaports of EUROPE CONTAINER TERMINALS (ECT). To use this netw

  14. Assessment of the structural brain network reveals altered connectivity in children with unilateral cerebral palsy due to periventricular white matter lesions

    Directory of Open Access Journals (Sweden)

    Kerstin Pannek

    2014-01-01

    Conclusion: This study shows that network-based analysis of structural connectivity can identify alterations in FA in unilateral CP, and that these alterations in FA are related to clinical function. Application of this connectome-based analysis to investigate alterations in connectivity following treatment may elucidate the neurological correlates of improved functioning due to intervention.

  15. Stochastic bifurcation, slow fluctuations, and bistability as an origin of biochemical complexity.

    Science.gov (United States)

    Qian, Hong; Shi, Pei-Zhe; Xing, Jianhua

    2009-06-28

    We present a simple, unifying theory for stochastic biochemical systems with multiple time-scale dynamics that exhibit noise-induced bistability in an open-chemical environment, while the corresponding macroscopic reaction is unistable. Nonlinear stochastic biochemical systems like these are fundamentally different from classical systems in equilibrium or near-equilibrium steady state whose fluctuations are unimodal following Einstein-Onsager-Lax-Keizer theory. We show that noise-induced bistability in general arises from slow fluctuations, and a pitchfork bifurcation occurs as the rate of fluctuations decreases. Since an equilibrium distribution, due to detailed balance, has to be independent of changes in time-scale, the bifurcation is necessarily a driven phenomenon. As examples, we analyze three biochemical networks of currently interest: self-regulating gene, stochastic binary decision, and phosphorylation-dephosphorylation cycle with fluctuating kinase. The implications of bistability to biochemical complexity are discussed.

  16. Alterações bioquímicas e fisiológicas em sementes de milho causadas pelo ao envelhecimento acelerado Biochemical and physiological alterations in corn seeds due to accelerated aging

    Directory of Open Access Journals (Sweden)

    Maria Cristina Mingues Spinola

    2000-06-01

    Full Text Available Para avaliar possíveis alterações bioquímicas (análises eletroforéticas de proteínas totais e das isoenzimas peroxidase, fosfatase ácida e malato desidrogenase e fisiológicas (germinação e vigor que ocorrem nas sementes de milho durante a permanência das mesmas nas condições recomendadas na metodologia do teste de envelhecimento acelerado (41ºC e 100% UR, foi realizada a presente pesquisa. Utilizaram-se sementes de milho, híbrido AG122, provenientes de quatro lotes. Os períodos 0, 24, 48, 72, 96 e 120 horas de permanência das sementes na incubadora (envelhecimento acelerado definiram os tratamentos. As alterações nos perfís isoenzimáticos (fosfatase ácida e peroxidase detectadas nas sementes, a partir do período 72h de envelhecimento acelerado, revelaram o provável efeito deteriorativo provocado pela exposição das sementes às condições do teste, independentemente da qualidade do lote, apesar de a maioria dos testes determinantes da qualidade fisiológica das sementes não terem sido sensíveis para detectar tal efeito.In order to evaluate biochemical (total protein, acid phosphatase, peroxidase and malate dehydrogenase electrophoresis and physiological (germination and seed vigor alterations occurring during corn seed accelerated aging (41°C and 100%UR, four corn seed lots of the double hybrid (AG122 were submitted to zero, 24, 48, 72, 96 and 120 hours of accelerated aging. The biochemical assays carried out (isozyme electrophoretical patterns of acid phosphatase e peroxidase are more sensitive than the physiological test used to monitorate corn seed physiological quality deterioration during corn seed accelerated aging.

  17. Adaptative biochemical pathways and regulatory networks in Klebsiella oxytoca BAS-10 producing a biotechnologically relevant exopolysaccharide during Fe(III-citrate fermentation

    Directory of Open Access Journals (Sweden)

    Gallo Giuseppe

    2012-11-01

    Full Text Available Abstract Background A bacterial strain previously isolated from pyrite mine drainage and named BAS-10 was tentatively identified as Klebsiella oxytoca. Unlikely other enterobacteria, BAS-10 is able to grow on Fe(III-citrate as sole carbon and energy source, yielding acetic acid and CO2 coupled with Fe(III reduction to Fe(II and showing unusual physiological characteristics. In fact, under this growth condition, BAS-10 produces an exopolysaccharide (EPS having a high rhamnose content and metal-binding properties, whose biotechnological applications were proven as very relevant. Results Further phylogenetic analysis, based on 16S rDNA sequence, definitively confirmed that BAS-10 belongs to K. oxytoca species. In order to rationalize the biochemical peculiarities of this unusual enterobacteriun, combined 2D-Differential Gel Electrophoresis (2D-DIGE analysis and mass spectrometry procedures were used to investigate its proteomic changes: i under aerobic or anaerobic cultivation with Fe(III-citrate as sole carbon source; ii under anaerobic cultivations using Na(I-citrate or Fe(III-citrate as sole carbon source. Combining data from these differential studies peculiar levels of outer membrane proteins, key regulatory factors of carbon and nitrogen metabolism and enzymes involved in TCA cycle and sugar biosynthesis or required for citrate fermentation and stress response during anaerobic growth on Fe(III-citrate were revealed. The protein differential regulation seems to ensure efficient cell growth coupled with EPS production by adapting metabolic and biochemical processes in order to face iron toxicity and to optimize energy production. Conclusion Differential proteomics provided insights on the molecular mechanisms necessary for anaeorobic utilization of Fe(III-citrate in a biotechnologically promising enterobacteriun, also revealing genes that can be targeted for the rational design of high-yielding EPS producer strains.

  18. The application of information theory to biochemical signaling systems

    Science.gov (United States)

    Rhee, Alex; Cheong, Raymond; Levchenko, Andre

    2012-01-01

    Cell signaling can be thought of fundamentally as an information transmission problem in which chemical messengers relay information about the external environment to the decision centers within a cell. Due to the biochemical nature of cellular signal transduction networks, molecular noise will inevitably limit the fidelity of any messages received and processed by a cell’s signal transduction networks, leaving it with an imperfect impression of its environment. Fortunately, Shannon’s information theory provides a mathematical framework independent of network complexity that can quantify the amount of information that can be transmitted despite biochemical noise. In particular, the channel capacity can be used to measure the maximum number of stimuli a cell can distinguish based upon the noisy responses of its signaling systems. Here, we provide a primer for quantitative biologists that covers fundamental concepts of information theory, highlights several key considerations when experimentally measuring channel capacity, and describes successful examples of the application of information theoretic analysis to biological signaling. PMID:22872091

  19. Selected hematologic and biochemical measurements in African HIV-infected and uninfected pregnant women and their infants: the HIV Prevention Trials Network 024 protocol

    Directory of Open Access Journals (Sweden)

    Urassa Willy

    2009-08-01

    Full Text Available Abstract Background Reference values for hematological and biochemical assays in pregnant women and in newborn infants are based primarily on Caucasian populations. Normative data are limited for populations in sub-Saharan Africa, especially comparing women with and without HIV infection, and comparing infants with and without HIV infection or HIV exposure. Methods We determined HIV status and selected hematological and biochemical measurements in women at 20–24 weeks and at 36 weeks gestation, and in infants at birth and 4–6 weeks of age. All were recruited within a randomized clinical trial of antibiotics to prevent chorioamnionitis-associated mother-to-child transmission of HIV (HPTN024. We report nearly complete laboratory data on 2,292 HIV-infected and 367 HIV-uninfected pregnant African women who were representative of the public clinics from which the women were recruited. Nearly all the HIV-infected mothers received nevirapine prophylaxis at the time of labor, as did their infants after birth (always within 72 hours of birth, but typically within just a few hours at the four study sites in Malawi (2 sites, Tanzania, and Zambia. Results HIV-infected pregnant women had lower red blood cell counts, hemoglobin, hematocrit, and white blood cell counts than HIV-uninfected women. Platelet and monocyte counts were higher among HIV-infected women at both time points. At the 4–6-week visit, HIV-infected infants had lower hemoglobin, hematocrit and white blood cell counts than uninfected infants. Platelet counts were lower in HIV-infected infants than HIV-uninfected infants, both at birth and at 4–6 weeks of age. At 4–6 weeks, HIV-infected infants had higher alanine aminotransferase measures than uninfected infants. Conclusion Normative data in pregnant African women and their newborn infants are needed to guide the large-scale HIV care and treatment programs being scaled up throughout the continent. These laboratory measures will help

  20. ESA DUE Permafrost: Evaluation of remote sensing derived products using ground data from the Global Terrestrial Network of Permafrost (GTN-P)

    Science.gov (United States)

    Elger, K. K.; Heim, B.; Lantuit, H.; Boike, J.; Bartsch, A.; Paulik, C.; Duguay, C. R.; Hachem, S.; Soliman, A. S.

    2011-12-01

    The task of the ESA DUE Permafrost project is to build up an Earth observation service for high-latitudinal permafrost applications with extensive involvement of the permafrost research community. The DUE Permafrost products derived from remote sensing are land surface temperature (LST), surface soil moisture (SSM), surface frozen and thawed state (freeze/ thaw), terrain, land cover, and surface waters. Weekly and monthly averages for most of the DUE Permafrost products will be made available for the years 2007-2010. The DUE Permafrost products are provided for the circumpolar permafrost area (north of 55°N) with 25 km spatial resolution. In addition, regional products with higher spatial resolution (300-1000 m/ pixel) were developed for five case study regions. These regions are: (1) the Laptev Sea and Eastern Siberian Sea Region (RU, continuous very cold permafrost/ tundra), (2) the Yakutsk Region (RU, continuous cold permafrost/ taiga), (3) the Western Siberian transect including Yamal Peninsula and Ob Region (RU, continuous to discontinuous/ taiga-tundra), (4) the Alaska Highway Transect (US, continuous to discontinuous/ taiga-tundra), and (5) the Mackenzie Delta and Valley Transect (CA, continuous to discontinuous/ taiga-tundra). The challenge of the programme is to adapt remote sensing products that are well established and tested in agricultural low and mid-latitudinal areas for highly heterogeneous taiga/ tundra permafrost landscapes in arctic regions. Ground data is essential for the evaluation of DUE Permafrost products and is provided by user groups and global networks. A major part of the DUE Permafrost core user group is contributing to GTN-P, the Global Terrestrial Network of Permafrost. Its main programmes, the Circumpolar Active Layer Monitoring (CALM) and the Thermal State of Permafrost (TSP) have been thoroughly overhauled during the last International Polar Year (2007-2008). Their spatial coverage has been extended to provide a true circumpolar

  1. A low cost network of spectrometer radiation detectors based on the ArduSiPM a compact transportable Software/Hardware Data Acquisition system with Arduino DUE

    Energy Technology Data Exchange (ETDEWEB)

    Bocci, Valerio; Chiodi, Giacomo; Iacoangeli, Francesco; Nuccetelli, Massimo; Recchia, Luigi [INFN Sezione di Roma, P.le Aldo moro 2, Rome, I-00185 (Italy)

    2015-07-01

    The necessity to use Photo Multipliers (PM) as light detector limited in the past the use of crystals in radiation handled device preferring the Geiger approach. The Silicon Photomultipliers (SiPMs) are very small and cheap, solid photon detectors with good dynamic range and single photon detection capability, they are usable to supersede cumbersome and difficult to use Photo Multipliers (PM). A SiPM can be coupled with a scintillator crystal to build efficient, small and solid radiation detector. A cost effective and easily replicable Hardware software module for SiPM detector readout is made using the ArduSiPM solution. The ArduSiPM is an easily battery operable handled device using an Arduino DUE (an open Software/Hardware board) as processor board and a piggy-back custom designed board (ArduSiPM Shield), the Shield contains all the blocks features to monitor, set and acquire the SiPM using internet network. (authors)

  2. Robustness analysis of stochastic biochemical systems.

    Science.gov (United States)

    Ceska, Milan; Safránek, David; Dražan, Sven; Brim, Luboš

    2014-01-01

    We propose a new framework for rigorous robustness analysis of stochastic biochemical systems that is based on probabilistic model checking techniques. We adapt the general definition of robustness introduced by Kitano to the class of stochastic systems modelled as continuous time Markov Chains in order to extensively analyse and compare robustness of biological models with uncertain parameters. The framework utilises novel computational methods that enable to effectively evaluate the robustness of models with respect to quantitative temporal properties and parameters such as reaction rate constants and initial conditions. We have applied the framework to gene regulation as an example of a central biological mechanism where intrinsic and extrinsic stochasticity plays crucial role due to low numbers of DNA and RNA molecules. Using our methods we have obtained a comprehensive and precise analysis of stochastic dynamics under parameter uncertainty. Furthermore, we apply our framework to compare several variants of two-component signalling networks from the perspective of robustness with respect to intrinsic noise caused by low populations of signalling components. We have successfully extended previous studies performed on deterministic models (ODE) and showed that stochasticity may significantly affect obtained predictions. Our case studies demonstrate that the framework can provide deeper insight into the role of key parameters in maintaining the system functionality and thus it significantly contributes to formal methods in computational systems biology.

  3. Using ground data of the Global Terrestrial Network of Permafrost (GTN-P) for the evaluation of ESA Data User Element (DUE) Permafrost remote sensing derived products

    Science.gov (United States)

    Elger, K.; Heim, B.; Bartsch, A.; Paulik, Ch.; Duguay, C.; Hachem, S.; Soliman, A.; Boike, J.; Langer, M.; Lantuit, H.

    2012-04-01

    Permafrost is one of the essential climate variables addressed by the Global Terrestrial Observing System (GCOS). Remote sensing data provide area-wide monitoring of e.g. surface temperatures or soil surface status (frozen or thawed state) in the Arctic and Subarctic, where ground data collection is difficult and restricted to local measurements at few monitoring sites. The task of the ESA Data User Element (DUE) Permafrost project is to build-up an Earth observation service for northern high-latitudinal permafrost applications with extensive involvement of the international permafrost research community (www.ipf.tuwien.ac.at/permafrost). The satellite-derived DUE Permafrost products are Land Surface Temperature, Surface Soil Moisture, Surface Frozen and Thawed State, Digital Elevation Model (locally as remote sensing product and circumpolar as non-remote sensing product) and Subsidence, and Land Cover. Land Surface Temperature, Surface Soil Moisture, and Surface Frozen and Thawed State will be provided for the circumpolar permafrost area north of 55° N with 25 km spatial resolution. In addition, regional products with higher spatial resolution were developed for five case study regions in different permafrost zones of the tundra and taiga (Laptev Sea [RU], Central Yakutia [RU], Western Siberia [RU], Alaska N-S transect, [US] Mackenzie River and Valley [CA]). This study shows the evaluation of two DUE Permafrost regional products, Land Surface Temperature and Surface Frozen and Thawed State, using freely available ground truth data from the Global Terrestrial Network of Permafrost (GTN-P) and monitoring data from the Russian-German Samoylov research station in the Lena River Delta (Central Siberia, RU). The GTN-P permafrost monitoring sites with their position in different permafrost zones are highly qualified for the validation of DUE Permafrost remote sensing products. Air and surface temperatures with high-temporal resolution from eleven GTN-P sites in Alaska

  4. A low cost network of spectrometer radiation detectors based on the ArduSiPM a compact transportable Software/Hardware Data Acquisition system with Arduino DUE

    CERN Document Server

    Bocci, Valerio; Iacoangeli, Francesco; Nuccetelli, Massimo; Recchia, Luigi

    2015-01-01

    The necessity to use Photo Multipliers (PM) as light detector limited in the past the use of crystals in radiation handled device preferring the Geiger approach. The Silicon Photomultipliers (SiPMs) are very small and cheap, solid photon detectors with good dynamic range and single photon detection capability, they are usable to supersede in some application cumbersome and difficult to use Photo Multipliers (PM). A SiPM can be coupled with a scintillator crystal to build efficient, small and solid radiation detector. A cost effective and easily replicable Hardware software module for SiPM detector readout is made using the ArduSiPM solution [1]. The ArduSiPM is an easily battery operable handled device using an Arduino DUE (an open Software/Hardware board) as processor board and a piggy-back custom designed board (ArduSiPM Shield), the Shield contains all the blocks features to monitor, set and acquire the SiPM using internet network.

  5. Biomechanical and Biochemical Cellular Response Due to Shock Waves

    Science.gov (United States)

    2008-12-01

    using shock- wave-induced cavitation . Ultrasound in Medicine and Biology, 29, 1769-1776. Lew, H. L., J. H. Poole, S. Alvarez, and W. Moore, 2005...sheets of adipose derived stem cells to shock waves. A key guideline in the experimental design was to suppress cavitation . To this end we...shock-exposed cells and controls. We attribute this to the absence of cavitation . Time-resolved gene expression revealed that a large

  6. 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

  7. Comparative effectiveness of oral drug therapies for lower urinary tract symptoms due to benign prostatic hyperplasia: a systematic review and network meta-analysis.

    Directory of Open Access Journals (Sweden)

    Xinghuan Wang

    Full Text Available Lower urinary tract symptoms (LUTS due to benign prostatic hyperplasia (BPH are common in elder men and a number of drugs alone or combined are clinically used for this disorder. But available studies investigating the comparative effects of different drug therapies are limited. This study was aimed to compare the efficacy of different drug therapies for LUTS/BPH with network meta-analysis.An electronic search of PubMed, Cochrane Library and Embase was performed to identify randomized controlled trials (RCTs comparing different drug therapies for LUTS/BPH within 24 weeks. Comparative effects were calculated using Aggregate Data Drug Information System. Consistency models of network meta-analysis were created and cumulative probability was used to rank different therapies.A total 66 RCTs covering seven different therapies with 29384 participants were included. We found that α-blockers (ABs plus phosphodiesterase 5 inhibitors (PDE5-Is ranked highest in the test of IPSS total score, storage subscore and voiding subscore. The combination therapy of ABs plus 5α-reductase inhibitors was the best for increasing maximum urinary flow rate (Qmax with a mean difference (MD of 1.98 (95% CI, 1.12 to 2.86 as compared to placebo. ABs plus muscarinic receptor antagonists (MRAs ranked secondly on the reduction of IPSS storage subscore, although monotherapies including MRAs showed no effect on this aspect. Additionally, PDE5-Is alone showed great effectiveness for LUTS/BPH except Qmax.Based on our novel findings, combination therapy, especially ABs plus PDE5-Is, is recommended for short-term treatment for LUTS/BPH. There was also evidence that PDE5-Is used alone was efficacious except on Qmax. Additionally, it should be cautious when using MRAs. However, further clinical studies are required for longer duration which considers more treatment outcomes such as disease progression, as well as basic research investigating mechanisms involving PDE5-Is and other

  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. Approaches to Chemical and Biochemical Information and Signal Processing

    Science.gov (United States)

    Privman, Vladimir

    2012-02-01

    We outline models and approaches for error control required to prevent buildup of noise when ``gates'' and other ``network elements'' based on (bio)chemical reaction processes are utilized to realize stable, scalable networks for information and signal processing. We also survey challenges and possible future research. [4pt] [1] Control of Noise in Chemical and Biochemical Information Processing, V. Privman, Israel J. Chem. 51, 118-131 (2010).[0pt] [2] Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic, V. Privman, J. Halamek, M. A. Arugula, D. Melnikov, V. Bocharova and E. Katz, J. Phys. Chem. B 114, 14103-14109 (2010).[0pt] [3] Towards Biosensing Strategies Based on Biochemical Logic Systems, E. Katz, V. Privman and J. Wang, in: Proc. Conf. ICQNM 2010 (IEEE Comp. Soc. Conf. Publ. Serv., Los Alamitos, California, 2010), pages 1-9.

  11. Technical and economic assessment of a network controller in comparison to the grid extension due to EEG; Technische und wirtschaftliche Betrachtung eines Netzregelgeraetes im Vergleich zu einem Netzausbau aufgrund EEG

    Energy Technology Data Exchange (ETDEWEB)

    Wanner, Ulrich; Aigner, Andreas [LEW Netzservice GmbH, Augsburg (Germany); Finkel, Michael [Hochschule Augsburg (Germany)

    2011-07-01

    overvoltages due to the behavior of the controller under severe voltage dips have to be evaluated critically. If the electrical load is reduced or to the end of a power failure voltage values, which amount to well over 110% of the nominal voltage are caused by over-compensating of the controller. This can cause damage to equipment in customer installations and thus lead to demands for regress. In order to minimize these overvoltages at least for a fault in the MV and HV power grid, the response time of the network controller must be matched to the settings of the network protection devices. Thus, in these cases the occurrence of the overvoltages can be reduced, but cannot be avoided. Therefore, in practice the network controller can be used only in very limited cases, but in certain cases it is technically a good solution and can be implemented very quickly. Here, the current and future demand of electrical energy of the customers is crucial. The follow-up costs are also low. Finally, it should be noted that there exists no universal approach due to the advantages and disadvantages of each network expansion option. Yet for every network situation the appropriate network expansion option can be selected by considering the environmental conditions. If a single customer is connected via a long supply line and with low short circuit power then the 950-V-line is a feasible solution. If the criteria are sufficiently short-circuit power and customer-cased flicker and harmonics are small, the network controller can be used without difficulty. The network controller can also be considered for small local networks, due to the different offered devices. Are very isolated estates to supply, often the only possibility is a connection to the medium-voltage grid. (orig.)

  12. 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.

  13. Extension of in-situ stress test analysis to rapid hole evacuation at Yucca Mountain due to a network of open conduits

    Energy Technology Data Exchange (ETDEWEB)

    Davies, J.B.

    1994-01-01

    Yucca Mountain is underlain by tuffaceous rocks that are highly fractured and jointed. During drilling of bore-holes at Yucca Mountain there were numerous occurrences of lost circulation when whole mud was taken by the formation. This evidence suggests that parts of Yucca Mountain are controlled hydrologicaly by a network of open conduits along the existing joints and fractures. Also at Yucca Mountain, stress tests have been performed in-situ by charging a small section along the boreholes with an excess pressure head of water. For many of these tests, the initial drop in water head was so rapid that within seconds up to hundreds of meters of fall had occurred. The opening of fractures as the excess head increases has previously been proposed as an important factor in explaining the shape of the stress test curves at lower pressures. We propose that such induced hydraulic fractures, under increasing water heads, can grow to a length sufficient to intersect the existing network of open joints and fractures. We extend our previous model to incorporate flow out along these open conduits and examine the initial rapid drop in terms of these extended models. We show that this rapid evacuation model fits the observed data from many slug tests in wells in the vicinity of Yucca Mountain. This result is confirmation of the drilling evidence that a network of open conduits exists at various depths below the water table and over a large geographic region around Yucca Mountain.

  14. Translated chemical reaction networks.

    Science.gov (United States)

    Johnston, Matthew D

    2014-05-01

    Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems of polynomial ordinary differential equations. The steady states of these mass action systems have been analyzed via a variety of techniques, including stoichiometric network analysis, deficiency theory, and algebraic techniques (e.g., Gröbner bases). In this paper, we present a novel method for characterizing the steady states of mass action systems. Our method explicitly links a network's capacity to permit a particular class of steady states, called toric steady states, to topological properties of a generalized network called a translated chemical reaction network. These networks share their reaction vectors with their source network but are permitted to have different complex stoichiometries and different network topologies. We apply the results to examples drawn from the biochemical literature.

  15. Markovian Dynamics on Complex Reaction Networks

    CERN Document Server

    Goutsias, John

    2012-01-01

    Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underling population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions, the computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating...

  16. Alteration of default mode network in high school football athletes due to repetitive subconcussive mild traumatic brain injury: a resting-state functional magnetic resonance imaging study.

    Science.gov (United States)

    Abbas, Kausar; Shenk, Trey E; Poole, Victoria N; Breedlove, Evan L; Leverenz, Larry J; Nauman, Eric A; Talavage, Thomas M; Robinson, Meghan E

    2015-03-01

    Long-term neurological damage as a result of head trauma while playing sports is a major concern for football athletes today. Repetitive concussions have been linked to many neurological disorders. Recently, it has been reported that repetitive subconcussive events can be a significant source of accrued damage. Since football athletes can experience hundreds of subconcussive hits during a single season, it is of utmost importance to understand their effect on brain health in the short and long term. In this study, resting-state functional magnetic resonance imaging (rs-fMRI) was used to study changes in the default mode network (DMN) after repetitive subconcussive mild traumatic brain injury. Twenty-two high school American football athletes, clinically asymptomatic, were scanned using the rs-fMRI for a single season. Baseline scans were acquired before the start of the season, and follow-up scans were obtained during and after the season to track the potential changes in the DMN as a result of experienced trauma. Ten noncollision-sport athletes were scanned over two sessions as controls. Overall, football athletes had significantly different functional connectivity measures than controls for most of the year. The presence of this deviation of football athletes from their healthy peers even before the start of the season suggests a neurological change that has accumulated over the years of playing the sport. Football athletes also demonstrate short-term changes relative to their own baseline at the start of the season. Football athletes exhibited hyperconnectivity in the DMN compared to controls for most of the sessions, which indicates that, despite the absence of symptoms typically associated with concussion, the repetitive trauma accrued produced long-term brain changes compared to their healthy peers.

  17. Weighting schemes in metabolic graphs for identifying biochemical routes.

    Science.gov (United States)

    Ghosh, S; Baloni, P; Vishveshwara, S; Chandra, N

    2014-03-01

    Metabolism forms an integral part of all cells and its study is important to understand the functioning of the system, to understand alterations that occur in disease state and hence for subsequent applications in drug discovery. Reconstruction of genome-scale metabolic graphs from genomics and other molecular or biochemical data is now feasible. Few methods have also been reported for inferring biochemical pathways from these networks. However, given the large scale and complex inter-connections in the networks, the problem of identifying biochemical routes is not trivial and some questions still remain open. In particular, how a given path is altered in perturbed conditions remains a difficult problem, warranting development of improved methods. Here we report a comparison of 6 different weighting schemes to derive node and edge weights for a metabolic graph, weights reflecting various kinetic, thermodynamic parameters as well as abundances inferred from transcriptome data. Using a network of 50 nodes and 107 edges of carbohydrate metabolism, we show that kinetic parameter derived weighting schemes [Formula: see text] fare best. However, these are limited by their extent of availability, highlighting the usefulness of omics data under such conditions. Interestingly, transcriptome derived weights yield paths with best scores, but are inadequate to discriminate the theoretical paths. The method is tested on a system of Escherichia coli stress response. The approach illustrated here is generic in nature and can be used in the analysis for metabolic network from any species and perhaps more importantly for comparing condition-specific networks.

  18. Avian mortalities due to transmission line collisions: a review of current estimates and field methods with an emphasis on applications to the Canadian electric network

    Directory of Open Access Journals (Sweden)

    Sébastien Rioux

    2013-12-01

    Full Text Available Birds are vulnerable to collisions with human-made fixed structures. Despite ongoing development and increases in infrastructure, we have few estimates of the magnitude of collision mortality. We reviewed the existing literature on avian mortality associated with transmission lines and derived an initial estimate for Canada. Estimating mortality from collisions with power lines is challenging due to the lack of studies, especially from sites within Canada, and due to uncertainty about the magnitude of detection biases. Detection of bird collisions with transmission lines varies due to habitat type, species size, and scavenging rates. In addition, birds can be crippled by the impact and subsequently die, although crippling rates are poorly known and rarely incorporated into estimates. We used existing data to derive a range of estimates of avian mortality associated with collisions with transmission lines in Canada by incorporating detection, scavenging, and crippling biases. There are 231,966 km of transmission lines across Canada, mostly in the boreal forest. Mortality estimates ranged from 1 million to 229.5 million birds per year, depending on the bias corrections applied. We consider our most realistic estimate, taking into account variation in risk across Canada, to range from 2.5 million to 25.6 million birds killed per year. Data from multiple studies across Canada and the northern U.S. indicate that the most vulnerable bird groups are (1 waterfowl, (2 grebes, (3 shorebirds, and (4 cranes, which is consistent with other studies. Populations of several groups that are vulnerable to collisions are increasing across Canada (e.g., waterfowl, raptors, which suggests that collision mortality, at current levels, is not limiting population growth. However, there may be impacts on other declining species, such as shorebirds and some species at risk, including Alberta's Trumpeter Swans (Cygnus buccinator and western Canada's endangered Whooping

  19. Ouroboros - Playing A Biochemical

    Directory of Open Access Journals (Sweden)

    D. T. Rodrigues

    2014-08-01

    Full Text Available Ouroboros: Playing A Biochemical RODRIGUES,D.T.1,2;GAYER, M.C.1,2; ESCOTO, D.F.1; DENARDIN, E.L.G.2, ROEHRS, R.1,2 1Interdisciplinary Research Group on Teaching Practice, Graduate Program in Biochemistry, Unipampa, RS, Brazil 2Laboratory of Physicochemical Studies and Natural Products, Post Graduate Program in Biochemistry, Unipampa, RS, Brazil Introduction: Currently, teachers seek different alternatives to enhance the teaching-learning process. Innovative teaching methodologies are increasingly common tools in educational routine. The use of games, electronic or conventional, is an effective tool to assist in learning and also to raise the social interaction between students. Objective: In this sense our work aims to evaluate the card game and "Ouroboros" board as a teaching and learning tool in biochemistry for a graduating class in Natural Sciences. Materials and methods: The class gathered 22 students of BSc in Natural Sciences. Each letter contained a question across the board that was drawn to a group to answer within the allotted time. The questions related concepts of metabolism, organic and inorganic chemical reactions, bioenergetics, etc.. Before the game application, students underwent a pre-test with four issues involving the content that was being developed. Soon after, the game was applied. Then again questions were asked. Data analysis was performed from the ratio of the number of correct pre-test and post-test answers. Results and discussion: In the pre-test 18.1% of the students knew all issues, 18.1% got 3 correct answers, 40.9% answered only 2 questions correctly and 22.7% did not hit any. In post-test 45.4% answered all the questions right, 31.8% got 3 questions and 22.7% got 2 correct answers. The results show a significant improvement of the students about the field of content taught through the game. Conclusion: Generally, traditional approaches of chemistry and biochemistry are abstract and complex. Thus, through games

  20. Enzyme and biochemical producing fungi

    DEFF Research Database (Denmark)

    Lübeck, Peter Stephensen; Lübeck, Mette; Nilsson, Lena

    2010-01-01

    factories for sustainable production of important molecules. For developing fungi into efficient cell factories, the project includes identification of important factors that control the flux through the pathways using metabolic flux analysis and metabolic engineering of biochemical pathways....

  1. Kombucha tea fermentation: Microbial and biochemical dynamics.

    Science.gov (United States)

    Chakravorty, Somnath; Bhattacharya, Semantee; Chatzinotas, Antonis; Chakraborty, Writachit; Bhattacharya, Debanjana; Gachhui, Ratan

    2016-03-02

    Kombucha tea, a non-alcoholic beverage, is acquiring significant interest due to its claimed beneficial properties. The microbial community of Kombucha tea consists of bacteria and yeast which thrive in two mutually non-exclusive compartments: the soup or the beverage and the biofilm floating on it. The microbial community and the biochemical properties of the beverage have so far mostly been described in separate studies. This, however, may prevent understanding the causal links between the microbial communities and the beneficial properties of Kombucha tea. Moreover, an extensive study into the microbial and biochemical dynamics has also been missing. In this study, we thus explored the structure and dynamics of the microbial community along with the biochemical properties of Kombucha tea at different time points up to 21 days of fermentation. We hypothesized that several biochemical properties will change during the course of fermentation along with the shifts in the yeast and bacterial communities. The yeast community of the biofilm did not show much variation over time and was dominated by Candida sp. (73.5-83%). The soup however, showed a significant shift in dominance from Candida sp. to Lachancea sp. on the 7th day of fermentation. This is the first report showing Candida as the most dominating yeast genus during Kombucha fermentation. Komagateibacter was identified as the single largest bacterial genus present in both the biofilm and the soup (~50%). The bacterial diversity was higher in the soup than in the biofilm with a peak on the seventh day of fermentation. The biochemical properties changed with the progression of the fermentation, i.e., beneficial properties of the beverage such as the radical scavenging ability increased significantly with a maximum increase at day 7. We further observed a significantly higher D-saccharic acid-1,4-lactone content and caffeine degradation property compared to previously described Kombucha tea fermentations. Our

  2. Mathematical Models of Biochemical Oscillations

    OpenAIRE

    Conrad, Emery David

    1999-01-01

    The goal of this paper is to explain the mathematics involved in modeling biochemical oscillations. We first discuss several important biochemical concepts fundamental to the construction of descriptive mathematical models. We review the basic theory of differential equations and stability analysis as it relates to two-variable models exhibiting oscillatory behavior. The importance of the Hopf Bifurcation will be discussed in detail for the central role it plays in limit cycle behavior and...

  3. [Basic biochemical processes in glaucoma progression].

    Science.gov (United States)

    von Thun und Hohenstein-Blaul, N; Kunst, S; Pfeiffer, N; Grus, F H

    2015-05-01

    The term glaucoma summarizes a group of eye diseases that are accompanied by impairments of the optic nerve and related visual field deficits. An early diagnosis of glaucoma is currently not possible due to a lack of diagnostic tests; therefore, in most cases the disease is diagnosed many years after onset, which prevents an early therapy. The known risk factors for the development and progression of glaucomatous optic neuropathy comprise elevated intraocular pressure and a broad range of pressure fluctuations as well as lipometabolic disorders, genetic factor and diabetes. The consequences include the induction of anti-inflammatory proteins, elevated levels of oxidative stress and the destruction of retinal ganglion cells. Changes in the autoantibody repertoire have also been observed in the course of the disease. Basic ophthalmological research therefore focuses on the investigation of basic biochemical processes in the course of the disease. A better understanding of physiological and biochemical events is sought in order to develop new and more sensitive diagnostic options and to allow more targeted therapeutic measures. The understanding of biochemical processes allows a better insight into glaucoma progression to be gained, which will lead to improvements in diagnosis and therapy.

  4. Efficacy of anti-VEGF and laser photocoagulation in the treatment of visual impairment due to diabetic macular edema: a systematic review and network meta-analysis.

    Directory of Open Access Journals (Sweden)

    Stephane Régnier

    Full Text Available Compare the efficacy of ranibizumab, aflibercept, laser, and sham in the first-line treatment of diabetic macular edema (DME to inform technology assessments such as those conducted by the UK National Institute for Health and Care Excellence (NICE.MEDLINE, Embase, Cochrane Library, congress abstracts, ClinicalTrials.gov registry and Novartis data on file.Studies reporting 6- or 12-month results of randomized controlled trials (RCTs evaluating at least two of ranibizumab 0.5 mg pro re nata, aflibercept 2.0 mg bi-monthly, laser photocoagulation or sham. Study quality was assessed based on likelihood of bias in selection, attrition, detection and performance.Improvement in best-corrected visual acuity (BCVA measured as the proportion of patients gaining ≥10 letters on the Early Treatment Diabetic Retinopathy Study scale. The outcome was chosen following acceptance by NICE of a Markov model with 10-letter health states in the assessment of ranibizumab for DME.Bayesian network meta-analyses with fixed and random effects adjusted for differences in baseline BCVA or central retinal thickness.The analysis included 1,978 patients from eight RCTs. The random effects model adjusting for baseline BCVA was the best model based on total residual. The efficacy of ranibizumab was numerically, but not statistically, superior to aflibercept (odds ratio [OR] 1.59; 95% credible interval [CrI], 0.61-5.37. Ranibizumab and aflibercept were statistically superior to laser monotherapy with ORs of 5.50 (2.73-13.16 and 3.45 (1.62-6.84 respectively. The probability that ranibizumab is the most efficacious treatment was 73% compared with 14% for aflibercept, 12% for ranibizumab plus laser, and 0% for laser.Three of the eight RCTs included are not yet published. The models did not adjust for all potential effect modifiers.Ranibizumab was non-significantly superior to aflibercept and both anti-VEGF therapies had statistically superior efficacy to laser.

  5. [Fifty years of cooperation--FEBS and Polish Biochemical Society].

    Science.gov (United States)

    Barańska, Jolanta

    2014-01-01

    This year, the Federation of European Biochemical Societies (FEBS) celebrates its 50th anniversary. The Polish Biochemical Society, represented by the Society's President, Kazimierz Zakrzewski, was a founding member of the organization. The text presents a history of collaboration between FEBS and Polish Biochemical Society, the participation of Polish Biochemical Society members in different FEBS activities, as well as the role they played in running the Federation. Author describes FEBS Congresses which taken place in Warsaw, the first 3rd FEBS Meeting in 1966 and then 29th Congress in 2004. The profiles of Jakub Karol Parnas, the founding father of the Polish biochemistry and some crucial Presidents of the Society, are also presented. The text describes Parnas Conferences, organized jointly by Polish and Ukrainian Biochemical Societies from 1996, and growing from 2011 into three-nation event with participation of Ukrainian, Israeli and Polish scientists, largely due to significant help from FEBS. Summarizing the last few years, author judge the cooperation between the Federation and the Polish Biochemical Society as optimal.

  6. BEST: Biochemical Engineering Simulation Technology

    Energy Technology Data Exchange (ETDEWEB)

    1996-01-01

    The idea of developing a process simulator that can describe biochemical engineering (a relatively new technology area) was formulated at the National Renewable Energy Laboratory (NREL) during the late 1980s. The initial plan was to build a consortium of industrial and U.S. Department of Energy (DOE) partners to enhance a commercial simulator with biochemical unit operations. DOE supported this effort; however, before the consortium was established, the process simulator industry changed considerably. Work on the first phase of implementing various fermentation reactors into the chemical process simulator, ASPEN/SP-BEST, is complete. This report will focus on those developments. Simulation Sciences, Inc. (SimSci) no longer supports ASPEN/SP, and Aspen Technology, Inc. (AspenTech) has developed an add-on to its ASPEN PLUS (also called BioProcess Simulator [BPS]). This report will also explain the similarities and differences between BEST and BPS. ASPEN, developed by the Massachusetts Institute of Technology for DOE in the late 1970s, is still the state-of-the-art chemical process simulator. It was selected as the only simulator with the potential to be easily expanded into the biochemical area. ASPEN/SP, commercially sold by SimSci, was selected for the BEST work. SimSci completed work on batch, fed-batch, and continuous fermentation reactors in 1993, just as it announced it would no longer commercially support the complete ASPEN/SP product. BEST was left without a basic support program. Luckily, during this same time frame, AspenTech was developing a biochemical simulator with its version of ASPEN (ASPEN PLUS), which incorporates most BEST concepts. The future of BEST will involve developing physical property data and models appropriate to biochemical systems that are necessary for good biochemical process design.

  7. Acrocyanosis due to imipramine.

    OpenAIRE

    Anderson, R P; Morris, B. A.

    1988-01-01

    An 11 year old girl who was being treated for enuresis with imipramine developed acrocyanosis of the hands and feet. All biochemical and haematological investigations gave normal results. When imipramine was stopped the girl recovered within three days.

  8. Transcription fluctuation effects on biochemical oscillations.

    Directory of Open Access Journals (Sweden)

    Ryota Nishino

    Full Text Available Some biochemical systems show oscillation. They often consist of feedback loops with repressive transcription regulation. Such biochemical systems have distinctive characteristics in comparison with ordinary chemical systems: i numbers of molecules involved are small, ii there are typically only a couple of genes in a cell with a finite regulation time. Due to the fluctuations caused by these features, the system behavior can be quite different from the one by deterministic rate equations, because the rate equations ignore molecular fluctuations and thus are exact only in the infinite molecular number limit. The molecular fluctuations on a free-running circadian system have been studied by Gonze et al. (2002 by introducing a scale parameter [Formula: see text] for the system size. They consider, however, only the first effect, assuming that the gene process is fast enough for the second effect to be ignored, but this has not been examined systematically yet. Here we study fluctuation effects due to the finite gene regulation time by introducing a new scale parameter [Formula: see text], which we take as the unbinding time of a nuclear protein from the gene. We focus on the case where the fluctuations due to small molecular numbers are negligible. In simulations on the same system studied by Gonze et al., we find the system is unexpectedly sensitive to the fluctuation in the transcription regulation; the period of oscillation fluctuates about 30 min even when the regulation time scale [Formula: see text] is around 30 s, that is even smaller than 1/1000 of its circadian period. We also demonstrate that the distribution width for the oscillation period and amplitude scales with [Formula: see text], and the correlation time scales with [Formula: see text] in the small [Formula: see text] regime. The relative fluctuations for the period are about half of that for the amplitude, namely, the periodicity is more stable than the amplitude.

  9. Functional network inference of the suprachiasmatic nucleus

    Energy Technology Data Exchange (ETDEWEB)

    Abel, John H.; Meeker, Kirsten; Granados-Fuentes, Daniel; St. John, Peter C.; Wang, Thomas J.; Bales, Benjamin B.; Doyle, Francis J.; Herzog, Erik D.; Petzold, Linda R.

    2016-04-04

    In the mammalian suprachiasmatic nucleus (SCN), noisy cellular oscillators communicate within a neuronal network to generate precise system-wide circadian rhythms. Although the intracellular genetic oscillator and intercellular biochemical coupling mechanisms have been examined previously, the network topology driving synchronization of the SCN has not been elucidated. This network has been particularly challenging to probe, due to its oscillatory components and slow coupling timescale. In this work, we investigated the SCN network at a single-cell resolution through a chemically induced desynchronization. We then inferred functional connections in the SCN by applying the maximal information coefficient statistic to bioluminescence reporter data from individual neurons while they resynchronized their circadian cycling. Our results demonstrate that the functional network of circadian cells associated with resynchronization has small-world characteristics, with a node degree distribution that is exponential. We show that hubs of this small-world network are preferentially located in the central SCN, with sparsely connected shells surrounding these cores. Finally, we used two computational models of circadian neurons to validate our predictions of network structure.

  10. Functional network inference of the suprachiasmatic nucleus.

    Science.gov (United States)

    Abel, John H; Meeker, Kirsten; Granados-Fuentes, Daniel; St John, Peter C; Wang, Thomas J; Bales, Benjamin B; Doyle, Francis J; Herzog, Erik D; Petzold, Linda R

    2016-04-19

    In the mammalian suprachiasmatic nucleus (SCN), noisy cellular oscillators communicate within a neuronal network to generate precise system-wide circadian rhythms. Although the intracellular genetic oscillator and intercellular biochemical coupling mechanisms have been examined previously, the network topology driving synchronization of the SCN has not been elucidated. This network has been particularly challenging to probe, due to its oscillatory components and slow coupling timescale. In this work, we investigated the SCN network at a single-cell resolution through a chemically induced desynchronization. We then inferred functional connections in the SCN by applying the maximal information coefficient statistic to bioluminescence reporter data from individual neurons while they resynchronized their circadian cycling. Our results demonstrate that the functional network of circadian cells associated with resynchronization has small-world characteristics, with a node degree distribution that is exponential. We show that hubs of this small-world network are preferentially located in the central SCN, with sparsely connected shells surrounding these cores. Finally, we used two computational models of circadian neurons to validate our predictions of network structure.

  11. Biochemical markers of bone turnover

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Deog Yoon [College of Medicine, Kyunghee Univ., Seoul (Korea, Republic of)

    1999-08-01

    Biochemical markers of bone turnover has received increasing attention over the past few years, because of the need for sensitivity and specific tool in the clinical investigation of osteoporosis. Bone markers should be unique to bone, reflect changes of bone less, and should be correlated with radiocalcium kinetics, histomorphometry, or changes in bone mass. The markers also should be useful in monitoring treatment efficacy. Although no bone marker has been established to meet all these criteria, currently osteocalcin and pyridinium crosslinks are the most efficient markers to assess the level of bone turnover in the menopausal and senile osteoporosis. Recently, N-terminal telopeptide (NTX), C-terminal telopeptide (CTX) and bone specific alkaline phosphatase are considered as new valid markers of bone turnover. Recent data suggest that CTX and free deoxypyridinoline could predict the subsequent risk of hip fracture of elderly women. Treatment of postmenopausal women with estrogen, calcitonin and bisphosphonates demonstrated rapid decrease of the levels of bone markers that correlated with the long-term increase of bone mass. Factors such as circadian rhythms, diet, age, sex, bone mass and renal function affect the results of biochemical markers and should be appropriately adjusted whenever possible. Each biochemical markers of bone turnover may have its own specific advantages and limitations. Recent advances in research will provide more sensitive and specific assays.

  12. Exact hybrid particle/population simulation of rule-based models of biochemical systems.

    Directory of Open Access Journals (Sweden)

    Justin S Hogg

    2014-04-01

    Full Text Available Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad protein-protein interactions and post-translational modifications. Rule-based modeling overcomes this problem by representing molecules as structured objects and encoding their interactions as pattern-based rules. This greatly simplifies the process of model specification, avoiding the tedious and error prone task of manually enumerating all species and reactions that can potentially exist in a system. From a simulation perspective, rule-based models can be expanded algorithmically into fully-enumerated reaction networks and simulated using a variety of network-based simulation methods, such as ordinary differential equations or Gillespie's algorithm, provided that the network is not exceedingly large. Alternatively, rule-based models can be simulated directly using particle-based kinetic Monte Carlo methods. This "network-free" approach produces exact stochastic trajectories with a computational cost that is independent of network size. However, memory and run time costs increase with the number of particles, limiting the size of system that can be feasibly simulated. Here, we present a hybrid particle/population simulation method that combines the best attributes of both the network-based and network-free approaches. The method takes as input a rule-based model and a user-specified subset of species to treat as population variables rather than as particles. The model is then transformed by a process of "partial network expansion" into a dynamically equivalent form that can be simulated using a population-adapted network-free simulator. The transformation method has been implemented within the open-source rule-based modeling platform BioNetGen, and resulting hybrid models can be simulated using the particle-based simulator NFsim. Performance tests show that

  13. An efficient finite-difference strategy for sensitivity analysis of stochastic models of biochemical systems.

    Science.gov (United States)

    Morshed, Monjur; Ingalls, Brian; Ilie, Silvana

    2017-01-01

    Sensitivity analysis characterizes the dependence of a model's behaviour on system parameters. It is a critical tool in the formulation, characterization, and verification of models of biochemical reaction networks, for which confident estimates of parameter values are often lacking. In this paper, we propose a novel method for sensitivity analysis of discrete stochastic models of biochemical reaction systems whose dynamics occur over a range of timescales. This method combines finite-difference approximations and adaptive tau-leaping strategies to efficiently estimate parametric sensitivities for stiff stochastic biochemical kinetics models, with negligible loss in accuracy compared with previously published approaches. We analyze several models of interest to illustrate the advantages of our method.

  14. INVESTIGATIONS ON BIOCHEMICAL PURIFICATION OF GROUND WATER FROM HYDROGEN SULFIDE

    Directory of Open Access Journals (Sweden)

    Yu. P. Sedlukho

    2015-01-01

    Full Text Available The paper considers problems and features of biochemical removal of hydrogen sulfide from ground water. The analysis of existing methods for purification of ground water from hydrogen sulfide has been given in the paper. The paper has established shortcomings of physical and chemical purification of ground water. While using aeration methods for removal of hydrogen sulfide formation of colloidal sulfur that gives muddiness and opalescence to water occurs due to partial chemical air oxidation. In addition to this violation of sulfide-carbonate equilibrium taking place in the process of aeration due to desorption of H2S and CO2, often leads to clogging of degasifier nozzles with formed CaCO3 that causes serious operational problems. Chemical methods require relatively large flow of complex reagent facilities, storage facilities and transportation costs.In terms of hydrogen sulfide ground water purification the greatest interest is given to the biochemical method. Factors deterring widespread application of the biochemical method is its insufficient previous investigation and necessity to execute special research in order to determine optimal process parameters while purifying groundwater of a particular water supply source. Biochemical methods for oxidation of sulfur compounds are based on natural biological processes that ensure natural sulfur cycle. S. Vinogradsky has established a two-stage mechanism for oxidation of hydrogen sulfide with sulfur bacteria (Beggiatoa. The first stage presupposes oxidation of hydrogen sulphide to elemental sulfur which is accumulating in the cytoplasm in the form of globules. During the second stage sulfur bacteria begin to oxidize intracellular sulfur to sulfuric acid due to shortage of hydrogen sulfide.The paper provides the results of technological tests of large-scale pilot plants for biochemical purification of groundwater from hydrogen sulfide in semi-industrial conditions. Dependences of water quality

  15. Biochemical filter with sigmoidal response: increasing the complexity of biomolecular logic.

    Science.gov (United States)

    Privman, Vladimir; Halámek, Jan; Arugula, Mary A; Melnikov, Dmitriy; Bocharova, Vera; Katz, Evgeny

    2010-11-11

    The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs. Various logic gates have been realized, but a "toolbox" of analog elements for interconnectivity and signal processing has remained elusive. Filters are important as network elements that allow control of noise in signal transmission and conversion. We report a versatile biochemical filtering mechanism designed to have sigmoidal response in combination with signal-conversion process. Horseradish peroxidase-catalyzed oxidation of chromogenic electron donor by H(2)O(2) was altered by adding ascorbate, allowing to selectively suppress the output signal, modifying the response from convex to sigmoidal. A kinetic model was developed for evaluation of the quality of filtering. The results offer improved capabilities for design of scalable biomolecular information processing systems.

  16. Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic

    CERN Document Server

    Privman, Vladimir; Arugula, Mary A; Melnikov, Dmitriy; Bocharova, Vera; Katz, Evgeny

    2010-01-01

    The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs. Various logic gates have been realized, but a "toolbox" of analog elements for interconnectivity and signal processing has remained elusive. Filters are important as network elements that allow control of noise in signal transmission and conversion. We report a versatile biochemical filtering mechanism designed to have sigmoidal response in combination with signal-conversion process. Horseradish peroxidase-catalyzed oxidation of chromogenic electron donor by hydrogen peroxide, was altered by adding ascorbate, allowing to selectively suppress the output signal, modifying the response from convex to sigmoidal. A kinetic model was developed for evaluation of the quality of filtering. The results offer improved...

  17. Network Kriging

    OpenAIRE

    Chua, David B.; Kolaczyk, Eric D.; Crovella, Mark

    2005-01-01

    Network service providers and customers are often concerned with aggregate performance measures that span multiple network paths. Unfortunately, forming such network-wide measures can be difficult, due to the issues of scale involved. In particular, the number of paths grows too rapidly with the number of endpoints to make exhaustive measurement practical. As a result, it is of interest to explore the feasibility of methods that dramatically reduce the number of paths measured in such situati...

  18. Biochemical structure of Calendula officinalis.

    Science.gov (United States)

    Korakhashvili, A; Kacharava, T; Kiknavelidze, N

    2007-01-01

    Calendula officinalis is a well known medicinal herb. It is common knowledge that its medicinal properties are conditioned on biologically active complex substances of Carotin (Provitamin A), Stearin, Triterpiniod, Plavonoid, Kumarin, macro and micro compound elements. Because of constant need in raw material of Calendula officinalis, features of its ontogenetic development agro-biological qualities in various eco regions of Georgia were investigated. The data of biologically active compounds, biochemical structure and the maintenance both in flowers and in others parts of plant is presented; the pharmacological activity and importance in medicine was reviewed.

  19. Open innovation in networks

    DEFF Research Database (Denmark)

    Hu, Yimei

    Open innovation in networks has been a popular topic for long, this paper rethinks the concepts of innovation network and network organization, and clarifies the differences between them based on the network perspective. Network perspective means that: network is the context of firms; market...... and hierarchy can be analyzed from a network approach. Within a network perspective, there are different levels of network, and a firm may not always has the power to “manage” innovation networks due to different levels of power. Based on the strength of a firm’s power, its role may varies from manager...

  20. Biochemical aspects of Huntington's chorea.

    Science.gov (United States)

    Caraceni, T; Calderini, G; Consolazione, A; Riva, E; Algeri, S; Girotti, F; Spreafico, R; Branciforti, A; Dall'olio, A; Morselli, P L

    1977-01-01

    Fifteen patients affected by Huntington's chorea were divided into two groups, 'slow' and 'fast', according to IQ scores on the Wechsler-Bellevue scale, and scores on some motor performance tests. A possible correlation was looked for between some biochemical data (cerebrospinal fluid (CSF), homovanillic acid (HVA), and 5-hydroxyindolacetic acid (5HIAA) levels, plasma dopamine-beta-hydroxylase (DBH), dopamine (DA) uptake by platelets), and clinical data (duration of illness, severity of symptoms, age of patients, IQ scores, 'slow' and 'fast' groups). The CSF, HVA, and 5HIAA levels were found to be significantly lowered in comparison with normal controls. DBH activity and DA uptake by platelets did not differ significantly from normal subjects. Treatment with haloperidol in all patients and with dipropylacetic acid in three patients did not appear to modify the CSF, HVA, and 5HIAA concentrations, the plasma DBH activity, or the DA uptake. There were no significant differences in the CSF, HVA, and 5HIAA contents between the two groups of patients, and there was no correlation between biochemical data and clinical features. PMID:143508

  1. Biochemical abnormalities in Pearson syndrome.

    Science.gov (United States)

    Crippa, Beatrice Letizia; Leon, Eyby; Calhoun, Amy; Lowichik, Amy; Pasquali, Marzia; Longo, Nicola

    2015-03-01

    Pearson marrow-pancreas syndrome is a multisystem mitochondrial disorder characterized by bone marrow failure and pancreatic insufficiency. Children who survive the severe bone marrow dysfunction in childhood develop Kearns-Sayre syndrome later in life. Here we report on four new cases with this condition and define their biochemical abnormalities. Three out of four patients presented with failure to thrive, with most of them having normal development and head size. All patients had evidence of bone marrow involvement that spontaneously improved in three out of four patients. Unique findings in our patients were acute pancreatitis (one out of four), renal Fanconi syndrome (present in all patients, but symptomatic only in one), and an unusual organic aciduria with 3-hydroxyisobutyric aciduria in one patient. Biochemical analysis indicated low levels of plasma citrulline and arginine, despite low-normal ammonia levels. Regression analysis indicated a significant correlation between each intermediate of the urea cycle and the next, except between ornithine and citrulline. This suggested that the reaction catalyzed by ornithine transcarbamylase (that converts ornithine to citrulline) might not be very efficient in patients with Pearson syndrome. In view of low-normal ammonia levels, we hypothesize that ammonia and carbamylphosphate could be diverted from the urea cycle to the synthesis of nucleotides in patients with Pearson syndrome and possibly other mitochondrial disorders.

  2. Network Coded Software Defined Networking

    DEFF Research Database (Denmark)

    Hansen, Jonas; Roetter, Daniel Enrique Lucani; Krigslund, Jeppe

    2015-01-01

    Software defined networking has garnered large attention due to its potential to virtualize services in the Internet, introducing flexibility in the buffering, scheduling, processing, and routing of data in network routers. SDN breaks the deadlock that has kept Internet network protocols stagnant...... for decades, while applications and physical links have evolved. This article advocates for the use of SDN to bring about 5G network services by incorporating network coding (NC) functionalities. The latter constitutes a major leap forward compared to the state-of-the- art store and forward Internet paradigm....... The inherent flexibility of both SDN and NC provides fertile ground to envision more efficient, robust, and secure networking designs, which may also incorporate content caching and storage, all of which are key challenges of the upcoming 5G networks. This article not only proposes the fundamentals...

  3. Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics

    Directory of Open Access Journals (Sweden)

    Lecca Paola

    2012-05-01

    Full Text Available Abstract Background The representation of a biochemical system as a network is the precursor of any mathematical model of the processes driving the dynamics of that system. Pharmacokinetics uses mathematical models to describe the interactions between drug, and drug metabolites and targets and through the simulation of these models predicts drug levels and/or dynamic behaviors of drug entities in the body. Therefore, the development of computational techniques for inferring the interaction network of the drug entities and its kinetic parameters from observational data is raising great interest in the scientific community of pharmacologists. In fact, the network inference is a set of mathematical procedures deducing the structure of a model from the experimental data associated to the nodes of the network of interactions. In this paper, we deal with the inference of a pharmacokinetic network from the concentrations of the drug and its metabolites observed at discrete time points. Results The method of network inference presented in this paper is inspired by the theory of time-lagged correlation inference with regard to the deduction of the interaction network, and on a maximum likelihood approach with regard to the estimation of the kinetic parameters of the network. Both network inference and parameter estimation have been designed specifically to identify systems of biotransformations, at the biochemical level, from noisy time-resolved experimental data. We use our inference method to deduce the metabolic pathway of the gemcitabine. The inputs to our inference algorithm are the experimental time series of the concentration of gemcitabine and its metabolites. The output is the set of reactions of the metabolic network of the gemcitabine. Conclusions Time-lagged correlation based inference pairs up to a probabilistic model of parameter inference from metabolites time series allows the identification of the microscopic pharmacokinetics and

  4. Electroencephalography reveals lower regional blood perfusion and atrophy of the temporoparietal network associated with memory deficits and hippocampal volume reduction in mild cognitive impairment due to Alzheimer’s disease

    Directory of Open Access Journals (Sweden)

    Moretti DV

    2015-02-01

    Full Text Available Davide Vito MorettiNational Institute for the research and cure of Alzheimer’s disease, S. John of God, Fatebenefratelli, Brescia, Italy Background: An increased electroencephalographic (EEG upper/lower alpha power ratio has been associated with less regional blood perfusion, atrophy of the temporoparietal region of the brain, and reduction of hippocampal volume in subjects affected by mild cognitive impairment due to Alzheimer’s disease as compared with subjects who do not develop the disease. Moreover, EEG theta frequency activity is quite different in these groups. This study investigated the correlation between biomarkers and memory performance.Methods: EEG α3/α2 power ratio and cortical thickness were computed in 74 adult subjects with prodromal Alzheimer’s disease. Twenty of these subjects also underwent assessment of blood perfusion by single-photon emission computed tomography (SPECT. Pearson’s r was used to assess the correlation between cortical thinning, brain perfusion, and memory impairment.Results: In the higher α3/α2 frequency power ratio group, greater cortical atrophy and lower regional perfusion in the temporoparietal cortex was correlated with an increase in EEG theta frequency. Memory impairment was more pronounced in the magnetic resonance imaging group and SPECT groups.Conclusion: A high EEG upper/low alpha power ratio was associated with cortical thinning and less perfusion in the temporoparietal area. Moreover, atrophy and less regional perfusion were significantly correlated with memory impairment in subjects with prodromal Alzheimer’s disease. The EEG upper/lower alpha frequency power ratio could be useful for identifying individuals at risk for progression to Alzheimer’s dementia and may be of value in the clinical context.Keywords: electroencephalography, perfusion, atrophy, temporoparietal network, memory deficits, hippocampal volume, mild cognitive impairment, Alzheimer’s disease

  5. Organizational Networks

    DEFF Research Database (Denmark)

    Grande, Bård; Sørensen, Ole Henning

    1998-01-01

    The paper focuses on the concept of organizational networks. Four different uses of the concept of organizational network are identified and critically discussed. Special focus is placed on how information and communication technologies as communication mediators and cognitive pictures influence ...... the organizational forms discussed in the paper. It is asserted that the underlying organizational phenomena are not changing but that the manifestations and representations are shifting due to technological developments.......The paper focuses on the concept of organizational networks. Four different uses of the concept of organizational network are identified and critically discussed. Special focus is placed on how information and communication technologies as communication mediators and cognitive pictures influence...

  6. Biochemical Abnormalities in Batten's Syndrome

    DEFF Research Database (Denmark)

    Clausen, Jytte Lene; Nielsen, Gunnar Gissel; Jensen, Gunde Egeskov;

    1978-01-01

    The present data indicate that a group of ten patients with Batten's syndrome showed reduced activity of erythrocyte glutathione (GSH) peroxidase (Px) (glutathione: H2O2 oxidoreductase, EC 1.1.1.9.) using H2O2 as peroxide donor. Assay of erythrocyte GSHPx using H2O2, cumene hydroperoxide and t......-butyl hydroperoxide as donors also makes it possible biochemically to divide Batten's syndrome into two types: (1) one type with decreased values when H2O2 and cumene hydroperoxide are used, and (2) one type with increased values when t-butyl hydroperoxide is used. Furthermore an increased content of palmitic, oleic...... in whole blood. In normal human beings a connection was found between the erythrocyte selenium content and GSHPx activity assayed by cumene hydroperoxide as a peroxide donor....

  7. Biochemical nature of Russell Bodies.

    Science.gov (United States)

    Mossuto, Maria Francesca; Ami, Diletta; Anelli, Tiziana; Fagioli, Claudio; Doglia, Silvia Maria; Sitia, Roberto

    2015-07-30

    Professional secretory cells produce and release abundant proteins. Particularly in case of mutations and/or insufficient chaperoning, these can aggregate and become toxic within or amongst cells. Immunoglobulins (Ig) are no exception. In the extracellular space, certain Ig-L chains form fibrils causing systemic amyloidosis. On the other hand, Ig variants lacking the first constant domain condense in dilated cisternae of the early secretory compartment, called Russell Bodies (RB), frequently observed in plasma cell dyscrasias, autoimmune diseases and chronic infections. RB biogenesis can be recapitulated in lymphoid and non-lymphoid cells by expressing mutant Ig-μ, providing powerful models to investigate the pathophysiology of endoplasmic reticulum storage disorders. Here we analyze the aggregation propensity and the biochemical features of the intra- and extra-cellular Ig deposits in human cells, revealing β-aggregated features for RB.

  8. Biosensors and bioelectronics on smartphone for portable biochemical detection.

    Science.gov (United States)

    Zhang, Diming; Liu, Qingjun

    2016-01-15

    Smartphone has been widely integrated with sensors, such as test strips, sensor chips, and hand-held detectors, for biochemical detections due to its portability and ubiquitous availability. Utilizing built-in function modules, smartphone is often employed as controller, analyzer, and displayer for rapid, real-time, and point-of-care monitoring, which can significantly simplify design and reduce cost of the detecting systems. This paper presents a review of biosensors and bioelectronics on smartphone for portable biochemical detections. The biosensors and bioelectronics based on smartphone can mainly be classified into biosensors using optics, surface plasmon resonance, electrochemistry, and near-field communication. The developments of these biosensors and bioelectronics on smartphone are reviewed along with typical biochemical detecting cases. Sensor strategies, detector attachments, and coupling methods are highlighted to show designs of the compact, lightweight, and low-cost sensor systems. The performances and advantages of these designs are introduced with their applications in healthcare diagnosis, environment monitoring, and food evaluation. With advances in micro-manufacture, sensor technology, and miniaturized electronics, biosensor and bioelectronic devices on smartphone can be used to perform biochemical detections as common and convenient as electronic tag readout in foreseeable future.

  9. A stronger necessary condition for the multistationarity of chemical reaction networks.

    Science.gov (United States)

    Soliman, Sylvain

    2013-11-01

    Biochemical reaction networks grow bigger and bigger, fed by the high-throughput data provided by biologists and bred in open repositories of models allowing merging and evolution. Nevertheless, since the available data is still very far from permitting the identification of the increasing number of kinetic parameters of such models, the necessity of structural analyses for describing the dynamics of chemical networks appears stronger every day. Using the structural information, notably from the stoichiometric matrix, of a biochemical reaction system, we state a more strict version of the famous Thomas' necessary condition for multistationarity. In particular, the obvious cases where Thomas' condition was trivially satisfied, mutual inhibition due to a multimolecular reaction and mutual activation due to a reversible reaction, can now easily be ruled out. This more strict condition shall not be seen as some version of Thomas' circuit functionality for the continuous case but rather as related and complementary to the whole domain of the structural analysis of (bio)chemical reaction systems, as pioneered by the chemical reaction network theory.

  10. Identification and reconstitution of genetic regulatory networks for improved microbial tolerance to isooctane.

    Science.gov (United States)

    Kang, Aram; Chang, Matthew Wook

    2012-04-01

    Microbial tolerance to hydrocarbons has been studied in an effort to improve the productivity of biochemical processes and to enhance the efficiency of hydrocarbon bioremediation. Despite these studies, few attempts have been made to design rational strategies to improve microbial tolerance to hydrocarbons. Herein, we present an engineering framework that enables us to harness our understanding of genetic regulatory networks to improve hydrocarbon tolerance. In this study, isooctane was used as a representative hydrocarbon due to its use in petroleum refining and in biochemical processes. To increase isooctane tolerance, we first identified essential transcriptional determinants and genetic regulatory networks underlying cellular responses to isooctane in Escherichia coli using genome-wide microarray analysis. Based on functional transcriptome and bioinformatics analysis, a range of combinations of transcription factors whose activity was predictably perturbed by isooctane were knocked out and overexpressed to reconstitute the regulatory networks. We demonstrated that the reconstitution of the regulatory networks led to a significant improvement in isooctane tolerance, and especially, engineered E. coli strains lacking and overexpressing some of the perturbed transcription factors showed 3- to 5-fold improvement. This microbe with high tolerance to isooctane can be harnessed for biochemical processes, fuel oil bioremediation and metabolic engineering for biofuel production. Furthermore, we envision that the engineering framework employed to improve the tolerance in this study can be exploited for developing other microbes with desired phenotypes.

  11. Noise Filtering and Prediction in Biological Signaling Networks

    CERN Document Server

    Hathcock, David; Weisenberger, Casey; Ilker, Efe; Hinczewski, Michael

    2016-01-01

    Information transmission in biological signaling circuits has often been described using the metaphor of a noise filter. Cellular systems need accurate, real-time data about their environmental conditions, but the biochemical reaction networks that propagate, amplify, and process signals work with noisy representations of that data. Biology must implement strategies that not only filter the noise, but also predict the current state of the environment based on information delayed due to the finite speed of chemical signaling. The idea of a biochemical noise filter is actually more than just a metaphor: we describe recent work that has made an explicit mathematical connection between signaling fidelity in cellular circuits and the classic theories of optimal noise filtering and prediction that began with Wiener, Kolmogorov, Shannon, and Bode. This theoretical framework provides a versatile tool, allowing us to derive analytical bounds on the maximum mutual information between the environmental signal and the re...

  12. What Is the Potential Impact on the Department of Defense (DOD) Military Treatment Facility (MTF) Pharmacies due to the Increased Copays and the Disenrollment of a Retail Pharmacy from the TRICARE Network?

    Science.gov (United States)

    2012-12-14

    satisfied” 65% “very satisfied” (clinic satisfaction data) Independent, food, chain, and mass merchant tabulated to obtain retail ...THE DISENROLLMENT OF A RETAIL PHARMACY FROM THE TRICARE NETWORK? A thesis presented to the Faculty of the U.S. Army Command and General Staff...Disenrollment of a Retail Pharmacy from the TRICARE Network? 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S

  13. Topographical mapping of biochemical properties of articular cartilage in the equine fetlock joint

    NARCIS (Netherlands)

    Brama, P.A.J.; Tekoppele, J.M.; Bank, R.A.; Karssenberg, D.; Barneveld, A.; Weeren, P.R. van

    2000-01-01

    The aim of this study was to evaluate topographical differences in the biochemical composition of the extracellular matrix of articular cartilage of the normal equine fetlock joint. Water content, DNA content, glycosaminoglycan (GAG) content and a number of characteristics of the collagen network (t

  14. Human choline dehydrogenase: medical promises and biochemical challenges.

    Science.gov (United States)

    Salvi, Francesca; Gadda, Giovanni

    2013-09-15

    Human choline dehydrogenase (CHD) is located in the inner membrane of mitochondria primarily in liver and kidney and catalyzes the oxidation of choline to glycine betaine. Its physiological role is to regulate the concentrations of choline and glycine betaine in the blood and cells. Choline is important for regulation of gene expression, the biosynthesis of lipoproteins and membrane phospholipids and for the biosynthesis of the neurotransmitter acetylcholine; glycine betaine plays important roles as a primary intracellular osmoprotectant and as methyl donor for the biosynthesis of methionine from homocysteine, a required step for the synthesis of the ubiquitous methyl donor S-adenosyl methionine. Recently, CHD has generated considerable medical attention due to its association with various human pathologies, including male infertility, homocysteinuria, breast cancer and metabolic syndrome. Despite the renewed interest, the biochemical characterization of the enzyme has lagged behind due to difficulties in the obtainment of purified, active and stable enzyme. This review article summarizes the medical relevance and the physiological roles of human CHD, highlights the biochemical knowledge on the enzyme, and provides an analysis based on the comparison of the protein sequence with that of bacterial choline oxidase, for which structural and biochemical information is available.

  15. High-resolution mapping of bifurcations in nonlinear biochemical circuits

    Science.gov (United States)

    Genot, A. J.; Baccouche, A.; Sieskind, R.; Aubert-Kato, N.; Bredeche, N.; Bartolo, J. F.; Taly, V.; Fujii, T.; Rondelez, Y.

    2016-08-01

    Analog molecular circuits can exploit the nonlinear nature of biochemical reaction networks to compute low-precision outputs with fewer resources than digital circuits. This analog computation is similar to that employed by gene-regulation networks. Although digital systems have a tractable link between structure and function, the nonlinear and continuous nature of analog circuits yields an intricate functional landscape, which makes their design counter-intuitive, their characterization laborious and their analysis delicate. Here, using droplet-based microfluidics, we map with high resolution and dimensionality the bifurcation diagrams of two synthetic, out-of-equilibrium and nonlinear programs: a bistable DNA switch and a predator-prey DNA oscillator. The diagrams delineate where function is optimal, dynamics bifurcates and models fail. Inverse problem solving on these large-scale data sets indicates interference from enzymatic coupling. Additionally, data mining exposes the presence of rare, stochastically bursting oscillators near deterministic bifurcations.

  16. Statistical physics approaches to subnetwork dynamics in biochemical systems

    CERN Document Server

    Bravi, Barbara

    2016-01-01

    We apply a Gaussian variational approximation to model reduction in large biochemical networks of unary and binary reactions. We focus on a small subset of variables (subnetwork) of interest, e.g. because they are accessible experimentally, embedded in a larger network (bulk). The key goal is to write dynamical equations reduced to the subnetwork but still retaining the effects of the bulk. As a result, the subnetwork-reduced dynamics contains a memory term and an extrinsic noise term with non-trivial temporal correlations. We first derive expressions for this memory and noise in the linearized (Gaussian) dynamics and then use a perturbative power expansion to obtain first order nonlinear corrections. For the case of vanishing intrinsic noise, our description is explicitly shown to be equivalent to projection methods up to quadratic terms, but it is applicable also in the presence of stochastic fluctuations in the original dynamics. An example from the Epidermal Growth Factor Receptor (EGFR) signalling pathwa...

  17. High-resolution mapping of bifurcations in nonlinear biochemical circuits.

    Science.gov (United States)

    Genot, A J; Baccouche, A; Sieskind, R; Aubert-Kato, N; Bredeche, N; Bartolo, J F; Taly, V; Fujii, T; Rondelez, Y

    2016-08-01

    Analog molecular circuits can exploit the nonlinear nature of biochemical reaction networks to compute low-precision outputs with fewer resources than digital circuits. This analog computation is similar to that employed by gene-regulation networks. Although digital systems have a tractable link between structure and function, the nonlinear and continuous nature of analog circuits yields an intricate functional landscape, which makes their design counter-intuitive, their characterization laborious and their analysis delicate. Here, using droplet-based microfluidics, we map with high resolution and dimensionality the bifurcation diagrams of two synthetic, out-of-equilibrium and nonlinear programs: a bistable DNA switch and a predator-prey DNA oscillator. The diagrams delineate where function is optimal, dynamics bifurcates and models fail. Inverse problem solving on these large-scale data sets indicates interference from enzymatic coupling. Additionally, data mining exposes the presence of rare, stochastically bursting oscillators near deterministic bifurcations.

  18. Advanced Nanoporous Materials for Micro-Gravimetric Sensing to Trace-Level Bio/Chemical Molecules

    OpenAIRE

    Pengcheng Xu; Xinxin Li; Haitao Yu; Tiegang Xu

    2014-01-01

    Functionalized nanoporous materials have been developed recently as bio/chemical sensing materials. Due to the huge specific surface of the nano-materials for molecular adsorption, high hopes have been placed on gravimetric detection with micro/nano resonant cantilevers for ultra-sensitive sensing of low-concentration bio/chemical substances. In order to enhance selectivity of the gravimetric resonant sensors to the target molecules, it is crucial to modify specific groups onto the pore-surfa...

  19. Biochemical genetic markers in sugarcane.

    Science.gov (United States)

    Glaszmann, J C; Fautret, A; Noyer, J L; Feldmann, P; Lanaud, C

    1989-10-01

    Isozyme variation was used to identify biochemical markers of potential utility in sugarcane genetics and breeding. Electrophoretic polymorphism was surveyed for nine enzymes among 39 wild and noble sugarcane clones, belonging to the species most closely related to modern varieties. Up to 114 distinct bands showing presence versus absence type of variation were revealed and used for qualitative characterization of the materials. Multivariate analysis of the data isolated the Erianthus clone sampled and separated the Saccharum spontaneum clones from the S. robustum and S. officinarum clones; the latter two were not differentiated from one another. The analysis of self-progenies of a 2n=112 S. spontaneum and of a commercial variety showed examples of mono- and polyfactorial segregations. Within the progeny of the variety, co-segregation of two isozymes frequent in S. spontaneum led to them being assigned to a single chromosome initially contributed by a S. spontaneum donor. This illustrates how combined survey of ancestral species and segregation analysis in modern breeding materials should permit using the lack of interspecific cross-over to establish linkage groups in a sugarcane genome.

  20. Network Physiology: Mapping Interactions Between Networks of Physiologic Networks

    Science.gov (United States)

    Ivanov, Plamen Ch.; Bartsch, Ronny P.

    The human organism is an integrated network of interconnected and interacting organ systems, each representing a separate regulatory network. The behavior of one physiological system (network) may affect the dynamics of all other systems in the network of physiologic networks. Due to these interactions, failure of one system can trigger a cascade of failures throughout the entire network. We introduce a systematic method to identify a network of interactions between diverse physiologic organ systems, to quantify the hierarchical structure and dynamics of this network, and to track its evolution under different physiologic states. We find a robust relation between network structure and physiologic states: every state is characterized by specific network topology, node connectivity and links strength. Further, we find that transitions from one physiologic state to another trigger a markedly fast reorganization in the network of physiologic interactions on time scales of just a few minutes, indicating high network flexibility in response to perturbations. This reorganization in network topology occurs simultaneously and globally in the entire network as well as at the level of individual physiological systems, while preserving a hierarchical order in the strength of network links. Our findings highlight the need of an integrated network approach to understand physiologic function, since the framework we develop provides new information which can not be obtained by studying individual systems. The proposed system-wide integrative approach may facilitate the development of a new field, Network Physiology.

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

    OpenAIRE

    Kent Edward; Hoops Stefan; Mendes Pedro

    2012-01-01

    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 experti...

  2. 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.

  3. The free energy cost of accurate biochemical oscillations

    CERN Document Server

    Cao, Yuansheng; Ouyang, Qi; Tu, Yuhai

    2015-01-01

    Oscillation is an important cellular process that regulates timing of different vital life cycles. However, in the noisy cellular environment, oscillations can be highly inaccurate due to phase fluctuations. It remains poorly understood how biochemical circuits suppress phase fluctuations and what is the incurred thermodynamic cost. Here, we study four different types of biochemical oscillations representing three basic oscillation motifs shared by all known oscillatory systems. We find that the phase diffusion constant follows the same inverse dependence on the free energy dissipation per period for all systems studied. This relationship between the phase diffusion and energy dissipation is shown analytically in a model of noisy oscillation. Microscopically, we find that the oscillation is driven by multiple irreversible cycles that hydrolyze the fuel molecules such as ATP; the number of phase coherent periods is proportional to the free energy consumed per period. Experimental evidence in support of this un...

  4. Modeling cardiac β-adrenergic signaling with normalized-Hill differential equations: comparison with a biochemical model

    Directory of Open Access Journals (Sweden)

    Saucerman Jeffrey J

    2010-11-01

    Full Text Available Abstract Background New approaches are needed for large-scale predictive modeling of cellular signaling networks. While mass action and enzyme kinetic approaches require extensive biochemical data, current logic-based approaches are used primarily for qualitative predictions and have lacked direct quantitative comparison with biochemical models. Results We developed a logic-based differential equation modeling approach for cell signaling networks based on normalized Hill activation/inhibition functions controlled by logical AND and OR operators to characterize signaling crosstalk. Using this approach, we modeled the cardiac β1-adrenergic signaling network, including 36 reactions and 25 species. Direct comparison of this model to an extensively characterized and validated biochemical model of the same network revealed that the new model gave reasonably accurate predictions of key network properties, even with default parameters. Normalized Hill functions improved quantitative predictions of global functional relationships compared with prior logic-based approaches. Comprehensive sensitivity analysis revealed the significant role of PKA negative feedback on upstream signaling and the importance of phosphodiesterases as key negative regulators of the network. The model was then extended to incorporate recently identified protein interaction data involving integrin-mediated mechanotransduction. Conclusions The normalized-Hill differential equation modeling approach allows quantitative prediction of network functional relationships and dynamics, even in systems with limited biochemical data.

  5. BIOCHEMICAL SCREENING OF DIABETIC NEPHROPATHY

    Directory of Open Access Journals (Sweden)

    Vivek

    2016-01-01

    Full Text Available Diabetic nephropathy is a clinical syndrome characterized by the following- Persistent albuminuria (>300mg/d or >200μg/min, that is confirmed on at least 2 occasions 3-6 months apart diabetic, progressive decline in the Glomerular Filtration Rate (GFR, elevated arterial blood pressure. The earliest biochemical criteria for the diagnosis of diabetic nephropathy is the presence of micro-albumin in the urine, which if left untreated will eventually lead to End-Stage Renal Disease (ESRD. Micro-albuminuria refers to the excretion of albumin in the urine at a rate that exceeds normal limits. The current study was conducted to establish the prevalence of micro-albuminuria in a sequential sample of diabetic patients attending hospital and OPD Clinic to determine its relationship with known and putative risk factors to identify micro- and normo-albuminuric patients in their sample for subsequent comparison in different age, sex, weight and creatinine clearance of the micro- and normo-albuminuric patients. This cross-sectional analytical study was conducted in one hundred patients at Saraswathi Institute of Medical Sciences, Anwarpur, Hapur, U. P. Patients having diabetes mellitus in different age group ranging from 30 to 70 years were selected. Data was analysed by SPSS software. Micro-albuminuria was observed in 35% in patients with type 2 diabetes mellitus. It was observed that 65% patients were free from any type of albuminuria. Also micro-albuminuria was present in 10% of the patients less than 50 yrs. of age, while 15% of the patients more than 50 yrs. of age were having micro-albuminuria. There was a statistically significant correlation of micro-albuminuria with duration of diabetes. Incidence of micro-albuminuria increases with age as well as increased duration of diabetes mellitus. Our study shows that only 5% patients developed macro-albuminuria. Glycosylated haemoglobin and fasting plasma glucose was significantly raised among all these

  6. A Program on Biochemical and Biomedical Engineering.

    Science.gov (United States)

    San, Ka-Yiu; McIntire, Larry V.

    1989-01-01

    Presents an introduction to the Biochemical and Biomedical Engineering program at Rice University. Describes the development of the academic and enhancement programs, including organizational structure and research project titles. (YP)

  7. Causal correlation of foliar biochemical concentrations with AVIRIS spectra using forced entry linear regression

    Science.gov (United States)

    Dawson, Terence P.; Curran, Paul J.; Kupiec, John A.

    1995-01-01

    A major goal of airborne imaging spectrometry is to estimate the biochemical composition of vegetation canopies from reflectance spectra. Remotely-sensed estimates of foliar biochemical concentrations of forests would provide valuable indicators of ecosystem function at regional and eventually global scales. Empirical research has shown a relationship exists between the amount of radiation reflected from absorption features and the concentration of given biochemicals in leaves and canopies (Matson et al., 1994, Johnson et al., 1994). A technique commonly used to determine which wavelengths have the strongest correlation with the biochemical of interest is unguided (stepwise) multiple regression. Wavelengths are entered into a multivariate regression equation, in their order of importance, each contributing to the reduction of the variance in the measured biochemical concentration. A significant problem with the use of stepwise regression for determining the correlation between biochemical concentration and spectra is that of 'overfitting' as there are significantly more wavebands than biochemical measurements. This could result in the selection of wavebands which may be more accurately attributable to noise or canopy effects. In addition, there is a real problem of collinearity in that the individual biochemical concentrations may covary. A strong correlation between the reflectance at a given wavelength and the concentration of a biochemical of interest, therefore, may be due to the effect of another biochemical which is closely related. Furthermore, it is not always possible to account for potentially suitable waveband omissions in the stepwise selection procedure. This concern about the suitability of stepwise regression has been identified and acknowledged in a number of recent studies (Wessman et al., 1988, Curran, 1989, Curran et al., 1992, Peterson and Hubbard, 1992, Martine and Aber, 1994, Kupiec, 1994). These studies have pointed to the lack of a physical

  8. Towards biochemical filters with a sigmoidal response to pH changes: buffered biocatalytic signal transduction.

    Science.gov (United States)

    Pita, Marcos; Privman, Vladimir; Arugula, Mary A; Melnikov, Dmitriy; Bocharova, Vera; Katz, Evgeny

    2011-03-14

    We realize a biochemical filtering process by introducing a buffer in a biocatalytic signal-transduction logic system based on the function of an enzyme, esterase. The input, ethyl butyrate, is converted into butyric acid--the output signal, which in turn is measured by the drop in the pH value. The developed approach offers a versatile "network element" for increasing the complexity of biochemical information processing systems. Evaluation of an optimal regime for quality filtering is accomplished in the framework of a kinetic rate-equation model.

  9. Towards biochemical filters with a sigmoidal response to pH changes: buffered biocatalytic signal transduction

    Science.gov (United States)

    Pita, Marcos; Privman, Vladimir; Arugula, Mary A.; Melnikov, Dmitriy; Bocharova, Vera; Katz, Evgeny

    We realize a biochemical filtering process by introducing a buffer in a biocatalytic signal-transduction logic system based on the function of an enzyme, esterase. The input, ethyl butyrate, is converted into butyric acid-the output signal, which in turn is measured by the drop in the pH value. The developed approach offers a versatile "network element" for increasing the complexity of biochemical information processing systems. Evaluation of an optimal regime for quality filtering is accomplished in the framework of a kinetic rate-equation model.

  10. Microbial and biochemical alterations due to storage of deep-sea sediments under ambient tropical conditions

    Digital Repository Service at National Institute of Oceanography (India)

    Das, A.; Fernandes, C.E.G.; Naik, S.S.; Mourya, B.S.; Sujith, P.P.; Sharma, R.; LokaBharathi, P.A.

    Response of indigenous bacteria to incubation at normal pressure and tropical temperature (28 ± 2°C), were examined in four deep-sea sediments from polymetallic-nodule fields in Central Indian Basin (CIB). Sediments were stored in sterile air...

  11. Biochemical effects of Calotropis procera on hepatotoxicity

    Directory of Open Access Journals (Sweden)

    Ali Ismaiel Ali Abd Alrheam

    2015-12-01

    Full Text Available Introduction: Calotropis procera commonly known as Sodom apple is a 6-meter high shrub that belongs to the Aclepiadaceae plant family and is commonly found in West Africa and other tropical places. In Saudi Arabia the plant is commonly used in traditional medicine for the treatment of variety of diseases including fever, constipation, muscular spasm and joint pain. Aim: In the present study C. procera were investigated for the hepatoprotective activity. Material and Methods: Carbon tetrachloride is used to produce hepatotoxicity. Forty two male albino rats, weighting 150-200 gm divided into seven groups, each consisted of 6 rats. Carbon tetrachloride 2ml/kg was administered twice a week to all of the groups of animals except group I, which served as control and given the normal saline. Group II served as Carbon tetrachloirde control. Group III received Silymarin at 100 mg/kg/day dose, Group IV received aqueous leaves extracts C. procera 200mg/kg, Group V received chloroform leaves extracts C. procera 200mg/kg, Group VI received ethanol leaves extracts C. procera 200 mg/kg, Group VII received latex of C. procera 200mg/kg. The effect of aqueous, chloroform, ethanol leaves extract and latex C. procera on biochemical parameters of liver was measured. Results: The results showed that the aqueous, chloroform, ethanol leaves extract and latex C. procera produced significant decrease in Acid phosphatase, Alkaline phosphatase, Aspartate aminotransferase, Alanine aminotransferase, Total protein, Albumin and total bilirubin levels compared to the CCL4 treated group II. Conclusion: Calotropis procera appears to to have hepatoprotective activity and these may be due to enrich of the plant by phytoconstituents that activate and in hence a pharmacological response of different parts of the body and this study need further studies to shows the complete properties of the plant. [Biomed Res Ther 2015; 2(12.000: 446-453

  12. Stochastic analysis of biochemical systems

    CERN Document Server

    Anderson, David F

    2015-01-01

    This book focuses on counting processes and continuous-time Markov chains motivated by examples and applications drawn from chemical networks in systems biology.  The book should serve well as a supplement for courses in probability and stochastic processes.  While the material is presented in a manner most suitable for students who have studied stochastic processes up to and including martingales in continuous time, much of the necessary background material is summarized in the Appendix. Students and Researchers with a solid understanding of calculus, differential equations, and elementary probability and who are well-motivated by the applications will find this book of interest.    David F. Anderson is Associate Professor in the Department of Mathematics at the University of Wisconsin and Thomas G. Kurtz is Emeritus Professor in the Departments of Mathematics and Statistics at that university. Their research is focused on probability and stochastic processes with applications in biology and other ar...

  13. 40 CFR 158.2010 - Biochemical pesticides data requirements.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Biochemical pesticides data...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2010 Biochemical pesticides... required to support registration of biochemical pesticides. Sections 158.2080 through 158.2084 identify...

  14. Biochemical kinetics in changing volumes.

    Science.gov (United States)

    Pawłowski, Piotr H; Zielenkiewicz, Piotr

    2004-01-01

    The need of taking into account the change of compartment volume when developing chemical kinetics analysis inside the living cell is discussed. Literature models of a single enzymatic Michaelis-Menten process, glycolytic oscillations, and mitotic cyclin oscillations were tested with appropriate theoretical extension in the direction of volume modification allowance. Linear and exponential type of volume increase regimes were compared. Due to the above, in a growing cell damping of the amplitude, phase shift, and time pattern deformation of the metabolic rhythms considered were detected, depending on the volume change character. The performed computer simulations allow us to conclude that evolution of the cell volume can be an essential factor of the chemical kinetics in a growing cell. The phenomenon of additional metabolite oscillations caused by the periodic cell growth and division was theoretically predicted and mathematically described. Also, the hypothesis of the periodized state in the growing cell as the generalization of the steady-state was formulated.

  15. Due process traditionalism.

    Science.gov (United States)

    Sunstein, Cass R

    2008-06-01

    In important cases, the Supreme Court has limited the scope of "substantive due process" by reference to tradition, but it has yet to explain why it has done so. Due process traditionalism might be defended in several distinctive ways. The most ambitious defense draws on a set of ideas associated with Edmund Burke and Friedrich Hayek, who suggested that traditions have special credentials by virtue of their acceptance by many minds. But this defense runs into three problems. Those who have participated in a tradition may not have accepted any relevant proposition; they might suffer from a systematic bias; and they might have joined a cascade. An alternative defense sees due process traditionalism as a second-best substitute for two preferable alternatives: a purely procedural approach to the Due Process Clause, and an approach that gives legislatures the benefit of every reasonable doubt. But it is not clear that in these domains, the first-best approaches are especially attractive; and even if they are, the second-best may be an unacceptably crude substitute. The most plausible defense of due process traditionalism operates on rule-consequentialist grounds, with the suggestion that even if traditions are not great, they are often good, and judges do best if they defer to traditions rather than attempting to specify the content of "liberty" on their own. But the rule-consequentialist defense depends on controversial and probably false assumptions about the likely goodness of traditions and the institutional incapacities of judges.

  16. Model building and model checking for biochemical processes.

    Science.gov (United States)

    Antoniotti, Marco; Policriti, Alberto; Ugel, Nadia; Mishra, Bud

    2003-01-01

    A central claim of computational systems biology is that, by drawing on mathematical approaches developed in the context of dynamic systems, kinetic analysis, computational theory and logic, it is possible to create powerful simulation, analysis, and reasoning tools for working biologists to decipher existing data, devise new experiments, and ultimately to understand functional properties of genomes, proteomes, cells, organs, and organisms. In this article, a novel computational tool is described that achieves many of the goals of this new discipline. The novelty of this system involves an automaton-based semantics of the temporal evolution of complex biochemical reactions starting from the representation given as a set of differential equations. The related tools also provide ability to qualitatively reason about the systems using a propositional temporal logic that can express an ordered sequence of events succinctly and unambiguously. The implementation of mathematical and computational models in the Simpathica and XSSYS systems is described briefly. Several example applications of these systems to cellular and biochemical processes are presented: the two most prominent are Leibler et al.'s repressilator (an artificial synthesized oscillatory network), and Curto- Voit-Sorribas-Cascante's purine metabolism reaction model.

  17. Onycholysis due to trauma

    Directory of Open Access Journals (Sweden)

    Patricia Chang

    2014-04-01

    Full Text Available Female patient, 35 years old who came to the private office due to discoloration of her left thumbnail and little pain since 1 month ago. Clinical examination shows nail disease on her left thumbnail with onycholysis and dyschromia, dermatoscopy showed white-yellowish discoloration (Fig. 1A, B. The rest of the clinical examination was normal. Patient use to using acrylic nails since 2 years ago and denied some trauma at the nail. The diagnosis of onycholysis due to trauma was done and recommended her not to use acrylic nail, maintain the nail short and avoid wetness.

  18. eQuilibrator--the biochemical thermodynamics calculator.

    Science.gov (United States)

    Flamholz, Avi; Noor, Elad; Bar-Even, Arren; Milo, Ron

    2012-01-01

    The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like 'how much Gibbs energy is released by ATP hydrolysis at pH 5?' are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use.

  19. Advanced nanoporous materials for micro-gravimetric sensing to trace-level bio/chemical molecules.

    Science.gov (United States)

    Xu, Pengcheng; Li, Xinxin; Yu, Haitao; Xu, Tiegang

    2014-10-13

    Functionalized nanoporous materials have been developed recently as bio/chemical sensing materials. Due to the huge specific surface of the nano-materials for molecular adsorption, high hopes have been placed on gravimetric detection with micro/nano resonant cantilevers for ultra-sensitive sensing of low-concentration bio/chemical substances. In order to enhance selectivity of the gravimetric resonant sensors to the target molecules, it is crucial to modify specific groups onto the pore-surface of the nano-materials. By loading the nanoporous sensing material onto the desired region of the mass-type transducers like resonant cantilevers, the micro-gravimetric bio/chemical sensors can be formed. Recently, such micro-gravimetric bio/chemical sensors have been successfully applied for rapid or on-the-spot detection of various bio/chemical molecules at the trace-concentration level. The applicable nanoporous sensing materials include mesoporous silica, zeolite, nanoporous graphene oxide (GO) and so on. This review article focuses on the recent achievements in design, preparation, functionalization and characterization of advanced nanoporous sensing materials for micro-gravimetric bio/chemical sensing.

  20. Advances in Biochemical Indices of Zooplankton Production.

    Science.gov (United States)

    Yebra, L; Kobari, T; Sastri, A R; Gusmão, F; Hernández-León, S

    2017-01-01

    Several new approaches for measuring zooplankton growth and production rates have been developed since the publication of the ICES (International Council for the Exploration of the Sea) Zooplankton Methodology Manual (Harris et al., 2000). In this review, we summarize the advances in biochemical methods made in recent years. Our approach explores the rationale behind each method, the design of calibration experiments, the advantages and limitations of each method and their suitability as proxies for in situ rates of zooplankton community growth and production. We also provide detailed protocols for the existing methods and information relevant to scientists wanting to apply, calibrate or develop these biochemical indices for zooplankton production.

  1. Artificial neural networks in medicine

    Energy Technology Data Exchange (ETDEWEB)

    Keller, P.E.

    1994-07-01

    This Technology Brief provides an overview of artificial neural networks (ANN). A definition and explanation of an ANN is given and situations in which an ANN is used are described. ANN applications to medicine specifically are then explored and the areas in which it is currently being used are discussed. Included are medical diagnostic aides, biochemical analysis, medical image analysis and drug development.

  2. Managing Networks

    DEFF Research Database (Denmark)

    Jørgensen, Heidi; Vintergaard, Christian

    isprovided, that the relation between a company's strategy, structure and processesin fact have a considerable influence on its pattern of network behaviour. Threecase studies from the Danish biotech industry exemplify and illustrate how acompany's strategy is directly correlated with how it manages its...... of networkbehaviour, knowing how to manage this relation becomes essential, especiallyduring the development of new strategies.......Logically it seems that companies pursuing different business strategies wouldalso manage their relationships with other firms accordingly. Nevertheless, due tothe lack of research in the field of network strategies, this link still remainsinadequately examined. Based on the well-known framework...

  3. Complex Networks

    CERN Document Server

    Evsukoff, Alexandre; González, Marta

    2013-01-01

    In the last decade we have seen the emergence of a new inter-disciplinary field focusing on the understanding of networks which are dynamic, large, open, and have a structure sometimes called random-biased. The field of Complex Networks is helping us better understand many complex phenomena such as the spread of  deseases, protein interactions, social relationships, to name but a few. Studies in Complex Networks are gaining attention due to some major scientific breakthroughs proposed by network scientists helping us understand and model interactions contained in large datasets. In fact, if we could point to one event leading to the widespread use of complex network analysis is the availability of online databases. Theories of Random Graphs from Erdös and Rényi from the late 1950s led us to believe that most networks had random characteristics. The work on large online datasets told us otherwise. Starting with the work of Barabási and Albert as well as Watts and Strogatz in the late 1990s, we now know th...

  4. Social network data analytics

    CERN Document Server

    Aggarwal, Charu C

    2011-01-01

    Social network analysis applications have experienced tremendous advances within the last few years due in part to increasing trends towards users interacting with each other on the internet. Social networks are organized as graphs, and the data on social networks takes on the form of massive streams, which are mined for a variety of purposes. Social Network Data Analytics covers an important niche in the social network analytics field. This edited volume, contributed by prominent researchers in this field, presents a wide selection of topics on social network data mining such as Structural Pr

  5. 注入水中悬浮微粒导致储层伤害网络模拟研究%Network Simulation of Formation Damage Due to Suspended Particles in Injection Water

    Institute of Scientific and Technical Information of China (English)

    冯其红; 韩晓冬; 王守磊; 张欣; 周文胜

    2014-01-01

    注入流体中的悬浮固体微粒随流体进入储层后会对储层造成伤害,导致储层渗透率降低,明确不同因素对储层伤害的影响规律对现场储层伤害的预防和治理有十分重要的意义。因此应用网络模拟方法对不同条件下储层伤害变化规律及孔喉变化规律进行了研究。模拟结果表明:随驱替的不断进行,孔喉半径总体逐渐减小,且距离注入端面越近,孔喉半径减小幅度越大;注入流量越小、注入流体内微粒浓度越大、流体黏度越小、微粒粒径越大,越有利于微粒的沉积,造成的储层伤害越严重。%Particles suspended in injection water could damage the formation and decrease the permeability. And it’s of great importance to study the impact of various factors on the formation impairment for its prevention and treatment. In our study here,pore scale network modeling method is applied to the study of the formation damage patterns and the change of the pore-throat radius under various conditions. In network models,different microcosmic particle variation mechanisms are taken into consideration. The results indicate that the pore-throat radius will decrease with the process of waterflooding and pore-throats that are closer to the inlet face will have a much higher decrease of their radius. Besides,the lower the flow rate is,the higher the particle concentration in injection water is,the lower the fluid viscosity and bigger particle size,it will be beneficial for the formation damage.

  6. Biochemical Applications in the Analytical Chemistry Lab

    Science.gov (United States)

    Strong, Cynthia; Ruttencutter, Jeffrey

    2004-01-01

    An HPLC and a UV-visible spectrophotometer are identified as instruments that helps to incorporate more biologically-relevant experiments into the course, in order to increase the students understanding of selected biochemistry topics and enhances their ability to apply an analytical approach to biochemical problems. The experiment teaches…

  7. 2009 Biochemical Conversion Platform Review Report

    Energy Technology Data Exchange (ETDEWEB)

    Ferrell, John [Office of Energy Efficiency and Renewable Energy (EERE), Washington, DC (United States)

    2009-12-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the U.S. Department of Energy Biomass Program’s Biochemical Conversion platform review meeting, held on April 14-16, 2009, at the Sheraton Denver Downtown, Denver, Colorado.

  8. Biochemical and Anatomical Characteristics of Dolphin Muscles.

    Science.gov (United States)

    1984-01-01

    hexosamines. These data suggest a biochemical difference in dolphin and rat tendon, which may be of relevance to the unique myofascial design of the...glycosaminoglycan (GAG) chains . The GAG chain is a polymer of repeating disaccharides, each disaccharide containing a hexosamine and either a

  9. Biochemical Thermodynamics under near Physiological Conditions

    Science.gov (United States)

    Mendez, Eduardo

    2008-01-01

    The recommendations for nomenclature and tables in Biochemical Thermodynamics approved by IUBMB and IUPAC in 1994 can be easily introduced after the chemical thermodynamic formalism. Substitution of the usual standard thermodynamic properties by the transformed ones in the thermodynamic equations, and the use of appropriate thermodynamic tables…

  10. Homocystinuria due to cystathionine beta synthase deficiency

    Directory of Open Access Journals (Sweden)

    Rao T

    2008-01-01

    Full Text Available A two year-old male child presented with cutis marmorata congenita universalis, brittle hair, mild mental retardation, and finger spasms. Biochemical findings include increased levels of homocysteine in the blood-106.62 µmol/L (normal levels: 5.90-16µmol/L. Biochemical tests such as the silver nitroprusside and nitroprusside tests were positive suggesting homocystinuria. The patient was treated with oral pyridoxine therapy for three months. The child responded well to this therapy and the muscle spasms as well as skin manifestations such as cutis marmorata subsided. The treatment is being continued; the case is reported here because of its rarity. Homocysteinuria arising due to cystathionine beta-synthase (CBS deficiency is an autosomal recessive disorder of methionine metabolism that produces increased levels of urinary homocysteine and methionine It manifests itself in vascular, central nervous system, cutaneous, and connective tissue disturbances and phenotypically resembles Marfan′s syndrome. Skin manifestations include malar flush, thin hair, and cutis reticulata / marmorata.

  11. Credit where due.

    Science.gov (United States)

    Friedman, Steven G

    2016-08-01

    The history of medicine is filled with stories of tireless researchers who failed to get credit for their hard work. Examples of this include Rosalind Franklin, who helped to elucidate the structure of DNA; Frederick Banting, who helped to discover insulin; and Jay McLean, who discovered heparin. The founding of the field of vascular surgery provides one of the most vivid examples of uncredited work. Even though Alexis Carrel was an unpaid, untitled assistant in Charles Guthrie's laboratory, it was Carrel alone who received a Nobel Prize for their work. In an attempt to give credit where due, the reasons for this injustice are described.

  12. A computational model for the identification of biochemical pathways in the krebs cycle.

    Science.gov (United States)

    Oliveira, Joseph S; Bailey, Colin G; Jones-Oliveira, Janet B; Dixon, David A; Gull, Dean W; Chandler, Mary L

    2003-01-01

    We have applied an algorithmic methodology which provably decomposes any complex network into a complete family of principal subcircuits to study the minimal circuits that describe the Krebs cycle. Every operational behavior that the network is capable of exhibiting can be represented by some combination of these principal subcircuits and this computational decomposition is linearly efficient. We have developed a computational model that can be applied to biochemical reaction systems which accurately renders pathways of such reactions via directed hypergraphs (Petri nets). We have applied the model to the citric acid cycle (Krebs cycle). The Krebs cycle, which oxidizes the acetyl group of acetyl CoA to CO(2) and reduces NAD and FAD to NADH and FADH(2), is a complex interacting set of nine subreaction networks. The Krebs cycle was selected because of its familiarity to the biological community and because it exhibits enough complexity to be interesting in order to introduce this novel analytic approach. This study validates the algorithmic methodology for the identification of significant biochemical signaling subcircuits, based solely upon the mathematical model and not upon prior biological knowledge. The utility of the algebraic-combinatorial model for identifying the complete set of biochemical subcircuits as a data set is demonstrated for this important metabolic process.

  13. Non-transcriptional regulatory processes shape transcriptional network dynamics

    OpenAIRE

    Ray, J. Christian J; Tabor, Jeffrey J.; Igoshin, Oleg A.

    2011-01-01

    Information about the extra- or intracellular environment is often captured as biochemical signals propagating through regulatory networks. These signals eventually drive phenotypic changes, typically by altering gene expression programs in the cell. Reconstruction of transcriptional regulatory networks has given a compelling picture of bacterial physiology, but transcriptional network maps alone often fail to describe phenotypes. In many cases, the dynamical performance of transcriptional re...

  14. 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 ...

  15. Functional adaptation of equine articular cartilage: The formation of regional biochemical characteristics up to age one year

    NARCIS (Netherlands)

    Brama, P.A.J.; Tekoppele, J.M.; Bank, R.A.; Barneveld, A.; Weeren, P.R. van

    2000-01-01

    Biochemical heterogeneity of cartilage within a joint is well known in mature individuals. It has recently been reported that heterogeneity for proteoglycan content and chondrocyte metabolism in sheep develops postnatally under the influence of loading. No data exist on the collagen network in gener

  16. Dynamic biochemical reaction process analysis and pathway modification predictions.

    Science.gov (United States)

    Conejeros, R; Vassiliadis, V S

    2000-05-05

    Recently, the area of model predictive modification of biochemical pathways has received attention with the aim to increase the productivity of microbial systems. In this study, we present a generalization of previous work, where, using a sensitivity study over the fermentation as a dynamic system, the optimal selection of reaction steps for modification (amplification or attenuation) is determined. The influence of metabolites in the activity of enzymes has also been considered (through activation or inhibition). We further introduce a new concept in the dynamic modeling of biochemical reaction systems including a generalized continuous superstructure in which two artificial multiplicative terms are included to account for: (a) enzyme overexpression or underexpression (attenuation or amplification) for the whole enzyme pool; and (b) modification of the apparent order of a kinetic expression with respect to the concentration of a metabolite or any subset of metabolites participating in the pathway. This new formulation allows the prediction of the sensitivity of the pathway performance index (objective function) with respect to the concentration of the enzyme, as well as the interaction of the enzyme with other metabolites. Using this framework, a case study for the production of penicillin V is analyzed, obtaining the most sensitive reaction steps (or bottlenecks) and the most significant regulations of the system, due to the effect of concentration of intracellular metabolites on the activity of each enzyme.

  17. A micro-perfusion bioreactor for on line investigation of ECM remodeling under hydrodynamic and biochemical stimulation.

    Science.gov (United States)

    Garziano, A; Urciuolo, F; Imparato, G; Martorina, F; Corrado, B; Netti, P

    2016-03-07

    Tissue-on-chip (TOC) systems aim at replicating complex biological dynamics in vitro with the potential either to improve the understanding of human biology or to develop more accurate therapeutic strategies. To replicate faithfully the intricate interrelationships between cells and their surrounding microenvironment, the three-dimensional (3D) tissue model must possess a responsive extracellular matrix (ECM). ECM remodeling plays a pivotal role in guiding cells and tissues functions and such aspect is somewhat denied during in vitro studies. For this purpose, we fabricated a micro-perfusion bioreactor capable to sustain the viability of 3D engineered tissue models recapitulating the process of the native ECM deposition and assembly. Engineered human dermis micro-tissue precursors (HD-μTP) were used as building blocks to generate a final tissue. HD-μTP were loaded in the perfusion space of the micro-perfusion bioreactor and, under the superimposition of different fluid dynamic regimes and biochemical stimulation, they synthesized new collagen proteins that were, then, assembled in the perfusion space forming a continuum of cells embedded in their own ECM. The micro-perfusion bioreactor was fabricated to allow the on-line monitoring of the oxygen consumption and the assembly of the newly formed collagen network via real time acquisition of the second harmonic generation (SHG) signal. The possibility to detect the collagen reorganization due to both fluid dynamic and biochemical stimulation, let us to define the optimal perfusion configuration in order to obtain a TOC system based on an endogenous and responsive ECM.

  18. Achilles tendinosis: Changes in biochemical composition and collagen turnover rate

    NARCIS (Netherlands)

    Mos, M. de; El, B. van; Groot, J. de; Jahr, H.; Schie, H.T.M. van; Arkel, E.R. van; Tol, H.; Heijboer, R.; Osch, G.J.V.M. van; Verhaar, J.A.N.

    2007-01-01

    Background: Understanding biochemical and structural changes of the extracellular matrix in Achilles tendinosis might be important for developing mechanism-based therapies. Hypothesis: In Achilles tendinosis, changes occur in biochemical composition and collagen turnover rate. Study Design: Descript

  19. Achilles tendinosis - Changes in biochemical composition and collagen turnover rate

    NARCIS (Netherlands)

    de Mos, Marieke; van El, Benno; DeGroot, Jeroen; Jahr, Holger; van Schie, Hans T. M.; van Arkel, Ewoud R.; Tol, Hans; Heijboer, Rien; van Osch, Gerjo J. V. M.; Verhaar, Jan A. N.

    2007-01-01

    Background: Understanding biochemical and structural changes of the extracellular matrix in Achilles tendinosis might be important for developing mechanism-based therapies. Hypothesis: In Achilles tendinosis, changes occur in biochemical composition and collagen turnover rate. Study Design: Descript

  20. Advancement in biochemical assays in andrology

    Institute of Scientific and Technical Information of China (English)

    Wolf-BernhardSchill; RaftHenkel

    1999-01-01

    Determination of maikers of sperm function, accessory sex gland secretion and silent male genital tract inflammation is of considerable diagnostic value in the evaluation of male infertility. The introduction of biochemical tests into the analysis of male factor has the advantage that standardized assays with a coefficient of variafion characteristic of clinical chemistry are performed, in contrast to biological test systems with a large variability .Biochemical parameters may be used in clinical practice to evaluate the sperm fertitizing capacity (acrosin, aniline blue,ROS), to characterize male accessory sex gland secretinns (fructose, a-glucosidase, PSA), and to identify men with silent genital tract inflammation (elastase, C'3 complement component, coeruloplasmin, IgA, IgG, ROS). (As/an J Androl 1999 Jun; 1: 45-51)

  1. Optical Slot-Waveguide Based Biochemical Sensors

    Directory of Open Access Journals (Sweden)

    Carlos Angulo Barrios

    2009-06-01

    Full Text Available Slot-waveguides allow light to be guided and strongly confined inside a nanometer-scale region of low refractive index. Thus stronger light-analyte interaction can be obtained as compared to that achievable by a conventional waveguide, in which the propagating beam is confined to the high-refractive-index core of the waveguide. In addition, slot-waveguides can be fabricated by employing CMOS compatible materials and technology, enabling miniaturization, integration with electronic, photonic and fluidic components in a chip, and mass production. These advantages have made the use of slot-waveguides for highly sensitive biochemical optical integrated sensors an emerging field. In this paper, recent achievements in slot-waveguide based biochemical sensing will be reviewed. These include slot-waveguide ring resonator based refractometric label-free biosensors, label-based optical sensing, and nano-opto-mechanical sensors.

  2. Biochemical changes in blood under Cr6+

    OpenAIRE

    Kuzenko E.V.; Romaniuk A.M.; Butko H.Yu.; Logvinova H.V.

    2013-01-01

    Background. For the manufacture of dentures many different alloys containing chromium are used. Interaction with oral fluid, organic acids and food, results in formation of Cr3+, Cr6+ ions, but their influence on the whole organism is poorly investigated. Objective. To analyze the biochemical changes in blood plasma during the influence of Cr6+ ions. Methods. 15 animals of experimental group were receiving drinking water with potassium dichromate in a dose of 0,2 mol/l. Rats of control group ...

  3. Information thermodynamics on causal networks.

    Science.gov (United States)

    Ito, Sosuke; Sagawa, Takahiro

    2013-11-01

    We study nonequilibrium thermodynamics of complex information flows induced by interactions between multiple fluctuating systems. Characterizing nonequilibrium dynamics by causal networks (i.e., Bayesian networks), we obtain novel generalizations of the second law of thermodynamics and the fluctuation theorem, which include an informational quantity characterized by the topology of the causal network. Our result implies that the entropy production in a single system in the presence of multiple other systems is bounded by the information flow between these systems. We demonstrate our general result by a simple model of biochemical adaptation.

  4. Electronic modulation of biochemical signal generation

    Science.gov (United States)

    Gordonov, Tanya; Kim, Eunkyoung; Cheng, Yi; Ben-Yoav, Hadar; Ghodssi, Reza; Rubloff, Gary; Yin, Jun-Jie; Payne, Gregory F.; Bentley, William E.

    2014-08-01

    Microelectronic devices that contain biological components are typically used to interrogate biology rather than control biological function. Patterned assemblies of proteins and cells have, however, been used for in vitro metabolic engineering, where coordinated biochemical pathways allow cell metabolism to be characterized and potentially controlled on a chip. Such devices form part of technologies that attempt to recreate animal and human physiological functions on a chip and could be used to revolutionize drug development. These ambitious goals will, however, require new biofabrication methodologies that help connect microelectronics and biological systems and yield new approaches to device assembly and communication. Here, we report the electrically mediated assembly, interrogation and control of a multi-domain fusion protein that produces a bacterial signalling molecule. The biological system can be electrically tuned using a natural redox molecule, and its biochemical response is shown to provide the signalling cues to drive bacterial population behaviour. We show that the biochemical output of the system correlates with the electrical input charge, which suggests that electrical inputs could be used to control complex on-chip biological processes.

  5. Haematological and biochemical analysis in canine enteritis

    Directory of Open Access Journals (Sweden)

    Abid Ali Bhat

    Full Text Available Aim: The present investigation screened eighteen clinical cases of canine enteritis for haematological and biochemical analyses. Materials and Methods: Eighteen dogs suffering from enteritis were selected and detailed clinical manifestations were noted. Hematological and biochemical parameters were estimated by using various kits. Blood was also collected from twelve healthy dogs for establishing control values and data obtained were subjected to statistical analysis. Results: The affected dogs showed anorexia, diarrhoea, depression, varying degree of dehydration and tachycardia. There were significant changes in packed cell volume, neutrophils, lymphocytes and mean corpuscular haemoglobin concentration. Biochemical investigation revealed significant decrease in plasma glucose, total plasma protein, albumin and albumin:globulin ratio (A:G ratio. The level of potassium and chloride was markedly decreased. Significant increase in alanine aminotransferase (ALT and blood urea nitrogen (BUN was observed. Conclusion: Packed Cell Volume (PCV and Total Erythrocyte Count (TEC remained almost similar between healthy dogs and dogs affected with diarrhoea. Mean Total Leukocyte Count (TLC value was significantly higher as compared to the control group. Hypoglycemia, hypoproteinemia, hypokalemia, hypochloremia and increase in blood urea nitrogen was observed in dogs suffering from enteritis. [Vet World 2013; 6(7.000: 380-383

  6. Explorations into Chemical Reactions and Biochemical Pathways.

    Science.gov (United States)

    Gasteiger, Johann

    2016-12-01

    A brief overview of the work in the research group of the present author on extracting knowledge from chemical reaction data is presented. Methods have been developed to calculate physicochemical effects at the reaction site. It is shown that these physicochemical effects can quite favourably be used to derive equations for the calculation of data on gas phase reactions and on reactions in solution such as aqueous acidity of alcohols or carboxylic acids or the hydrolysis of amides. Furthermore, it is shown that these physicochemical effects are quite effective for assigning reactions into reaction classes that correspond to chemical knowledge. Biochemical reactions constitute a particularly interesting and challenging task for increasing our understanding of living species. The BioPath.Database is a rich source of information on biochemical reactions and has been used for a variety of applications of chemical, biological, or medicinal interests. Thus, it was shown that biochemical reactions can be assigned by the physicochemical effects into classes that correspond to the classification of enzymes by the EC numbers. Furthermore, 3D models of reaction intermediates can be used for searching for novel enzyme inhibitors. It was shown in a combined application of chemoinformatics and bioinformatics that essential pathways of diseases can be uncovered. Furthermore, a study showed that bacterial flavor-forming pathways can be discovered.

  7. Biochemical and haematological profile of pheasant hens during the laying period.

    Science.gov (United States)

    Schumann, J; Bedanova, I; Voslarova, E; Hrabcakova, P; Chloupek, J; Pistekova, V

    2014-01-01

    The present paper provides new experimental data on the biochemical and haematological profile of blood in pheasant hens, and points out the changes in both biochemical and haematological parameters that occur during the laying period. Significant effects of egg laying on both the biochemical and the haematological blood parameters of pheasant hens were found. Biochemical analyses revealed a significant increase in the metabolites cholesterol, uric acid, lactate, the enzyme aspartate aminotransferase (AST) and the minerals calcium and phosphorous, as well as a significant decrease in total protein, albumin and glucose in the course of the laying period. Haematological analyses revealed a significant increase in the count of leukocytes, lymphocytes, eosinophils, basophils and monocytes due to egg laying. In addition, the erythrocyte count and haemoglobin content significantly decreased in the middle of the laying period and then rebounded at the end of the laying period. The haematocrit content gradually decreased till the end of the laying period. All together, the results of this study underline the impact of the reproduction status of pheasant hens on basic blood parameters. The biochemical and haematological values presented in this study may be of help in assessing disease conditions in laying pheasant hens.

  8. The Use of Item Analysis for Improvement of Biochemical Teaching

    Science.gov (United States)

    Nagata, Ryoichi

    2004-01-01

    Item analysis was used to find out which biochemical explanations need to be improved in biochemical teaching, not which items are to be discarded, improved, or reusable in biochemical examinations. The analysis revealed the basic facts of which less able students had more misunderstanding than able students. Identifying these basic facts helps…

  9. Biochemical characteristics of four marine fish skins in Korea.

    Science.gov (United States)

    Cho, Jae-Kwon; Jin, Young-Guk; Rha, Sung-Ju; Kim, Seon-Jae; Hwang, Jae-Ho

    2014-09-15

    In this study, we investigated the biochemical characteristics of the fish skins of four industrial species: olive flounder (Paralichthys olivaceus), black rockfish (Sebastes schlegeli), sea bass (Lateolabrax maculatus) and red sea bream (Pagrus major). There is high domestic demand in Korea for farming of these fish for human consumption. Crude protein contents in the skin of these fish ranged from 73% to 94% by dry weight; this was in part due to a high content of the structural protein, collagen. Among the four species, olive flounder had the thickest dermal and epidermal layers in the dorsal skin. This species was also associated with the highest extraction ratio of acid-soluble collagen. We also examined whether fish skin could be a cost-effective alternative to current fish meal sources. Our analysis indicates that, when supplemented with additional fish oils and essential amino acids, fish skin is a viable alternative for fish meal formulations.

  10. Recommended Nordic paediatric reference intervals for 21 common biochemical properties

    DEFF Research Database (Denmark)

    Hilsted, Linda; Rustad, Pål; Aksglæde, Lise;

    2013-01-01

    Abstract Paediatric reference intervals based on samples from healthy children are difficult to establish and consequently data are often from hospitalized children. Furthermore, biases may present in published data due to differences in the analytical methods employed. Blood samples from 1429...... healthy Danish children were collected for establishing reference intervals for 21 common biochemical properties (Alanine transaminase, Albumin, Alkaline phosphatase, Aspartate transaminase, Bilirubin, Calcium, Cholesterol, Creatinine, Creatine kinase, HDL-Cholesterol, Iron, Lactate dehydrogenase, LDL...... values of X for the properties and statistical calculations carried out as performed in the NORIP study. Thus commutable (regarding analytical method) reference intervals for 20 properties were established and for LDL-Cholesterol reference intervals were reported for the specific analytical method...

  11. Methods for assessing biochemical oxygen demand (BOD): a review.

    Science.gov (United States)

    Jouanneau, S; Recoules, L; Durand, M J; Boukabache, A; Picot, V; Primault, Y; Lakel, A; Sengelin, M; Barillon, B; Thouand, G

    2014-02-01

    The Biochemical Oxygen Demand (BOD) is one of the most widely used criteria for water quality assessment. It provides information about the ready biodegradable fraction of the organic load in water. However, this analytical method is time-consuming (generally 5 days, BOD5), and the results may vary according to the laboratory (20%), primarily due to fluctuations in the microbial diversity of the inoculum used. Work performed during the two last decades has resulted in several technologies that are less time-consuming and more reliable. This review is devoted to the analysis of the technical features of the principal methods described in the literature in order to compare their performances (measuring window, reliability, robustness) and to identify the pros and the cons of each method.

  12. Computational study of noise in a large signal transduction network

    Directory of Open Access Journals (Sweden)

    Ruohonen Keijo

    2011-06-01

    Full Text Available Abstract Background Biochemical systems are inherently noisy due to the discrete reaction events that occur in a random manner. Although noise is often perceived as a disturbing factor, the system might actually benefit from it. In order to understand the role of noise better, its quality must be studied in a quantitative manner. Computational analysis and modeling play an essential role in this demanding endeavor. Results We implemented a large nonlinear signal transduction network combining protein kinase C, mitogen-activated protein kinase, phospholipase A2, and β isoform of phospholipase C networks. We simulated the network in 300 different cellular volumes using the exact Gillespie stochastic simulation algorithm and analyzed the results in both the time and frequency domain. In order to perform simulations in a reasonable time, we used modern parallel computing techniques. The analysis revealed that time and frequency domain characteristics depend on the system volume. The simulation results also indicated that there are several kinds of noise processes in the network, all of them representing different kinds of low-frequency fluctuations. In the simulations, the power of noise decreased on all frequencies when the system volume was increased. Conclusions We concluded that basic frequency domain techniques can be applied to the analysis of simulation results produced by the Gillespie stochastic simulation algorithm. This approach is suited not only to the study of fluctuations but also to the study of pure noise processes. Noise seems to have an important role in biochemical systems and its properties can be numerically studied by simulating the reacting system in different cellular volumes. Parallel computing techniques make it possible to run massive simulations in hundreds of volumes and, as a result, accurate statistics can be obtained from computational studies.

  13. Heterogeneous network architectures

    DEFF Research Database (Denmark)

    Christiansen, Henrik Lehrmann

    2006-01-01

    Future networks will be heterogeneous! Due to the sheer size of networks (e.g., the Internet) upgrades cannot be instantaneous and thus heterogeneity appears. This means that instead of trying to find the olution, networks hould be designed as being heterogeneous. One of the key equirements here...... is flexibility. This thesis investigates such heterogeneous network architectures and how to make them flexible. A survey of algorithms for network design is presented, and it is described how using heuristics can increase the speed. A hierarchical, MPLS based network architecture is described...... and it is discussed that it is advantageous to heterogeneous networks and illustrated by a number of examples. Modeling and simulation is a well-known way of doing performance evaluation. An approach to event-driven simulation of communication networks is presented and mixed complexity modeling, which can simplify...

  14. Effects of macromolecular crowding on genetic networks.

    Science.gov (United States)

    Morelli, Marco J; Allen, Rosalind J; Wolde, Pieter Rein ten

    2011-12-21

    The intracellular environment is crowded with proteins, DNA, and other macromolecules. Under physiological conditions, macromolecular crowding can alter both molecular diffusion and the equilibria of bimolecular reactions and therefore is likely to have a significant effect on the function of biochemical networks. We propose a simple way to model the effects of macromolecular crowding on biochemical networks via an appropriate scaling of bimolecular association and dissociation rates. We use this approach, in combination with kinetic Monte Carlo simulations, to analyze the effects of crowding on a constitutively expressed gene, a repressed gene, and a model for the bacteriophage λ genetic switch, in the presence and absence of nonspecific binding of transcription factors to genomic DNA. Our results show that the effects of crowding are mainly caused by the shift of association-dissociation equilibria rather than the slowing down of protein diffusion, and that macromolecular crowding can have relevant and counterintuitive effects on biochemical network performance.

  15. Learning Networks, Networked Learning

    NARCIS (Netherlands)

    Sloep, Peter

    2011-01-01

    Sloep, P. B. (2011). Learning Networks, Networked Learning. Presentation at Annual Assembly of the European Society for the Systemic Innovation of Education - ESSIE. May, 27, 2011, Leuven, Belgium: Open University in the Netherlands.

  16. Learning Networks, Networked Learning

    NARCIS (Netherlands)

    Sloep, Peter; Berlanga, Adriana

    2010-01-01

    Sloep, P. B., & Berlanga, A. J. (2011). Learning Networks, Networked Learning [Redes de Aprendizaje, Aprendizaje en Red]. Comunicar, XIX(37), 55-63. Retrieved from http://dx.doi.org/10.3916/C37-2011-02-05

  17. Innovation and network collaboration

    DEFF Research Database (Denmark)

    Kesting, Peter; Müller, Sabine; Jørgensen, Frances

    2011-01-01

    Research suggests that small and medium-sized enterprises (SMEs) can benefit from network collaboration by enhancing opportunities for innovation. Managing the necessary collaboration to benefit from network participation may however be particularly challenging for SMEs due to their size...... and their inherent shortage of resources. In this paper, we propose that human resource management (HRM) practices may provide a means by which SMEs can increase their innovation capacity through network collaboration. Following a brief presentation of the relevant literature on networks, and innovation in networks...

  18. Balanced biochemical reactions: a new approach to unify chemical and biochemical thermodynamics.

    Directory of Open Access Journals (Sweden)

    Antonio Sabatini

    Full Text Available A novel procedure is presented which, by balancing elements and electric charge of biochemical reactions which occur at constant pH and pMg, allows assessing the thermodynamics properties of reaction Δ(rG'⁰, Δ(rH'⁰, Δ(rS'⁰ and the change in binding of hydrogen and magnesium ions of these reactions. This procedure of general applicability avoids the complex calculations required by the use of the Legendre transformed thermodynamic properties of formation Δ(fG'⁰, Δ(fH'⁰ and Δ(fS'⁰ hitherto considered an obligatory prerequisite to deal with the thermodynamics of biochemical reactions. As a consequence, the term "conditional" is proposed in substitution of "Legendre transformed" to indicate these thermodynamics properties. It is also shown that the thermodynamic potential G is fully adequate to give a criterion of spontaneous chemical change for all biochemical reactions and then that the use of the Legendre transformed G' is unnecessary. The procedure proposed can be applied to any biochemical reaction, making possible to re-unify the two worlds of chemical and biochemical thermodynamics, which so far have been treated separately.

  19. Biochemical component identification by light scattering techniques in whispering gallery mode optical resonance based sensor

    Science.gov (United States)

    Saetchnikov, Vladimir A.; Tcherniavskaia, Elina A.; Saetchnikov, Anton V.; Schweiger, Gustav; Ostendorf, Andreas

    2014-03-01

    Experimental data on detection and identification of variety of biochemical agents, such as proteins (albumin, interferon, C reactive protein), microelements (Na+, Ca+), antibiotic of different generations, in both single and multi component solutions under varied in wide range concentration are represented. Analysis has been performed on the light scattering parameters of whispering gallery mode (WGM) optical resonance based sensor with dielectric microspheres from glass and PMMA as sensitive elements fixed by spin - coating techniques in adhesive layer on the surface of substrate or directly on the coupling element. Sensitive layer was integrated into developed fluidic cell with a digital syringe. Light from tuneable laser strict focusing on and scattered by the single microsphere was detected by a CMOS camera. The image was filtered for noise reduction and integrated on two coordinates for evaluation of integrated energy of a measured signal. As the entrance data following signal parameters were used: relative (to a free spectral range) spectral shift of frequency of WGM optical resonance in microsphere and relative efficiency of WGM excitation obtained within a free spectral range which depended on both type and concentration of investigated agents. Multiplexing on parameters and components has been realized using spatial and spectral parameters of scattered by microsphere light with developed data processing. Biochemical component classification and identification of agents under investigation has been performed by network analysis techniques based on probabilistic network and multilayer perceptron. Developed approach is demonstrated to be applicable both for single agent and for multi component biochemical analysis.

  20. Biochemical Markers for Assessing Aquatic Contamination

    Directory of Open Access Journals (Sweden)

    Zdeňka Svobodová

    2007-11-01

    Full Text Available Biochemical markers, specifically enzymes of the first phase of xenobiotic transformation - cytochrome P450 and ethoxyresorufin-O-deethylase (EROD - were used to determine the quantities of persistent organic pollutants (POPs in fish muscle (PCB, HCB, HCH, OCS, DDT. Eight rivers were monitored (Orlice, Chrudimka, Cidlina, Jizera, Vltava, Ohře and Bílina; and the River Blanice was used as a control. The indicator species selected was the chub (Leuciscus cephalus L.. There were no significant differences in cytochrome P450 content between the locations monitored. The highest concentration of cytochrome P450 in fish liver was in the Vltava (0.241 nmol mg-1 protein, and the lowest was in the Orlice (0.120 nmol mg-1 protein. Analysis of EROD activity showed a significant difference between the Blanice and the Vltava (P< 0.05, and also between the Orlice and the Vltava (P< 0.01, the Orlice and the Bílina (P< 0.01, and the Orlice and the Ohře (P< 0.05. The highest EROD activity in fish liver was in the Vltava (576.4 pmol min-1 mg-1 protein, and the lowest was in the Orlice (63.05 pmol min-1 mg-1 protein. In individual locations, results of chemical monitoring and values of biochemical markers were compared. A significant correlation (P< 0.05 was found between biochemical markers and OCS, and PCB. Among the tributaries studied those that contaminated the Elbe most were the Vltava and the Bílina. These tributaries should not be considered the main sources of industrial contamination of the River Elbe, because the most important contamination sources were along the river Elbe itself.

  1. [Chronic fatigue syndrome: biochemical examination of blood].

    Science.gov (United States)

    Hakariya, Yukiko; Kuratsune, Hirohiko

    2007-06-01

    Though patients with chronic fatigue syndrome (CFS) have lots of complaints, abnormal findings cannot be detected by biochemical screening tests. However, some specialized blood tests have revealed neuroendocrine immune axis abnormalities, which is closely associated with each other. Recent studies indicate that CFS can be understood as a special condition based on abnormality of the psycho-neuro-endocrino-immunological system, with the distinguishing feature of CFS seeming to be the secondary brain dysfunction caused by several cytokines and/or autoantibodies. In this paper, we summarize these abnormalities found in CFS and show the neuro-molecular mechanism leading to chronic fatigue.

  2. Azoospermia: clinical, hormonal, and biochemical investigation.

    Science.gov (United States)

    Papadimas, J; Papadopoulou, F; Ioannidis, S; Spanos, E; Tarlatzis, B; Bontis, J; Mantalenakis, S

    1996-01-01

    The aim of this study was to evaluate the clinical, hormonal and biochemical characteristics of infertile men with azoospermia. A total of 187 azoospermic out of 2610 infertile men (7.2%) were studied. Mean testicular volume and basal plasma levels of FSH were the most useful parameters concerning the evaluation of azoospermia. Basal plasma levels of LH and T were useful only in azoospermic men with hypogonadism, whereas plasma PRL levels, semen volume, and seminal plasma fructose levels were not found to be of common use except in selected cases.

  3. Biochemical Disincentives to Fertilizing Cellulosic Ethanol Crops

    Science.gov (United States)

    Gallagher, M. E.; Hockaday, W. C.; Snapp, S.; McSwiney, C.; Baldock, J.

    2010-12-01

    Corn grain biofuel crops produce the highest yields when the cropping ecosystem is not nitrogen (N)-limited, achieved by application of fertilizer. There are environmental consequences for excessive fertilizer application to crops, including greenhouse gas emissions, hypoxic “dead zones,” and health problems from N runoff into groundwater. The increase in corn acreage in response to demand for alternative fuels (i.e. ethanol) could exacerbate these problems, and divert food supplies to fuel production. A potential substitute for grain ethanol that could reduce some of these impacts is cellulosic ethanol. Cellulosic ethanol feedstocks include grasses (switchgrass), hardwoods, and crop residues (e.g. corn stover, wheat straw). It has been assumed that these feedstocks will require similar N fertilization rates to grain biofuel crops to maximize yields, but carbohydrate yield versus N application has not previously been monitored. We report the biochemical stocks (carbohydrate, protein, and lignin in Mg ha-1) of a corn ecosystem grown under varying N levels. We measured biochemical yield in Mg ha-1 within the grain, leaf and stem, and reproductive parts of corn plants grown at seven N fertilization rates (0-202 kg N ha-1), to evaluate the quantity and quality of these feedstocks across a N fertilization gradient. The N fertilization rate study was performed at the Kellogg Biological Station-Long Term Ecological Research Site (KBS-LTER) in Michigan. Biochemical stocks were measured using 13C nuclear magnetic resonance spectroscopy (NMR), combined with a molecular mixing model (Baldock et al. 2004). Carbohydrate and lignin are the main biochemicals of interest in ethanol production since carbohydrate is the ethanol feedstock, and lignin hinders the carbohydrate to ethanol conversion process. We show that corn residue carbohydrate yields respond only weakly to N fertilization compared to grain. Grain carbohydrate yields plateau in response to fertilization at

  4. Biochemical Markers of Joint Tissue Turnover

    DEFF Research Database (Denmark)

    Bay-Jensen, Anne-Christine; Sondergaard, Bodil Cecilie; Christiansen, Claus;

    2009-01-01

    Recent disappointments in late stage developments of anti-osteoarthritic drugs have reinforced efforts to develop better biomarkers for application in both the drug development process as well as in the routine management of these patients. Here we provide a brief review of biochemical tests...... available for the study of tissue turnover in each of the three compartments of the articular joint, that is the bone, the cartilage, and the synovium. Finally, we provide some perspective to future developments in biomarker discovery and discuss the potential impact such technologies could have on the drug...

  5. Biochemical composition of tangerine fruits under microfertilizers

    OpenAIRE

    Oksana Belous; Yuliya Abilfazova

    2016-01-01

    The paper presents the long-term research and its results in the field of biochemical composition and mechanical analysis of dwarf tangerine fruits ('Miagava-Vase') growing in the subtropical zone of the Black Sea coast, Krasnodar region. The given results have been obtained after treatments with the following micro fertilizers: H3BO3 (at a concentration of 0.06%), MnSO4 H2O (0.4%), ZnSO4 H2O (0.3%) and CuSO4 H2O (0.06%), an option with foliar water spraying served as a control. It is shown t...

  6. The Analysis of Social Networks.

    Science.gov (United States)

    O'Malley, A James; Marsden, Peter V

    2008-12-01

    Many questions about the social organization of medicine and health services involve interdependencies among social actors that may be depicted by networks of relationships. Social network studies have been pursued for some time in social science disciplines, where numerous descriptive methods for analyzing them have been proposed. More recently, interest in the analysis of social network data has grown among statisticians, who have developed more elaborate models and methods for fitting them to network data. This article reviews fundamentals of, and recent innovations in, social network analysis using a physician influence network as an example. After introducing forms of network data, basic network statistics, and common descriptive measures, it describes two distinct types of statistical models for network data: individual-outcome models in which networks enter the construction of explanatory variables, and relational models in which the network itself is a multivariate dependent variable. Complexities in estimating both types of models arise due to the complex correlation structures among outcome measures.

  7. Network Infrastructure Security

    CERN Document Server

    Wong, Angus

    2009-01-01

    Attacks to network infrastructure affect large portions of the Internet at a time and create large amounts of service disruption, due to breaches such as IP spoofing, routing table poisoning and routing loops. This book includes conceptual examples that show how network attacks can be run, along with appropriate countermeasures and solutions

  8. DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks.

    Science.gov (United States)

    Nguyen, Lan K; Degasperi, Andrea; Cotter, Philip; Kholodenko, Boris N

    2015-07-29

    Biochemical networks are dynamic and multi-dimensional systems, consisting of tens or hundreds of molecular components. Diseases such as cancer commonly arise due to changes in the dynamics of signalling and gene regulatory networks caused by genetic alternations. Elucidating the network dynamics in health and disease is crucial to better understand the disease mechanisms and derive effective therapeutic strategies. However, current approaches to analyse and visualise systems dynamics can often provide only low-dimensional projections of the network dynamics, which often does not present the multi-dimensional picture of the system behaviour. More efficient and reliable methods for multi-dimensional systems analysis and visualisation are thus required. To address this issue, we here present an integrated analysis and visualisation framework for high-dimensional network behaviour which exploits the advantages provided by parallel coordinates graphs. We demonstrate the applicability of the framework, named "Dynamics Visualisation based on Parallel Coordinates" (DYVIPAC), to a variety of signalling networks ranging in topological wirings and dynamic properties. The framework was proved useful in acquiring an integrated understanding of systems behaviour.

  9. Attractor metabolic networks.

    Directory of Open Access Journals (Sweden)

    Ildefonso M De la Fuente

    Full Text Available BACKGROUND: The experimental observations and numerical studies with dissipative metabolic networks have shown that cellular enzymatic activity self-organizes spontaneously leading to the emergence of a Systemic Metabolic Structure in the cell, characterized by a set of different enzymatic reactions always locked into active states (metabolic core while the rest of the catalytic processes are only intermittently active. This global metabolic structure was verified for Escherichia coli, Helicobacter pylori and Saccharomyces cerevisiae, and it seems to be a common key feature to all cellular organisms. In concordance with these observations, the cell can be considered a complex metabolic network which mainly integrates a large ensemble of self-organized multienzymatic complexes interconnected by substrate fluxes and regulatory signals, where multiple autonomous oscillatory and quasi-stationary catalytic patterns simultaneously emerge. The network adjusts the internal metabolic activities to the external change by means of flux plasticity and structural plasticity. METHODOLOGY/PRINCIPAL FINDINGS: In order to research the systemic mechanisms involved in the regulation of the cellular enzymatic activity we have studied different catalytic activities of a dissipative metabolic network under different external stimuli. The emergent biochemical data have been analysed using statistical mechanic tools, studying some macroscopic properties such as the global information and the energy of the system. We have also obtained an equivalent Hopfield network using a Boltzmann machine. Our main result shows that the dissipative metabolic network can behave as an attractor metabolic network. CONCLUSIONS/SIGNIFICANCE: We have found that the systemic enzymatic activities are governed by attractors with capacity to store functional metabolic patterns which can be correctly recovered from specific input stimuli. The network attractors regulate the catalytic patterns

  10. Pheochromocytoma-paraganglioma: Biochemical and genetic diagnosis.

    Science.gov (United States)

    Cano Megías, Marta; Rodriguez Puyol, Diego; Fernández Rodríguez, Loreto; Sención Martinez, Gloria Lisette; Martínez Miguel, Patricia

    Pheochromocytomas and paragangliomas are tumours derived from neural crest cells, which can be diagnosed by biochemical measurement of metanephrine and methoxytyramine. Advances in genetic research have identified many genes involved in the pathogenesis of these tumours, suggesting that up to 35-45% may have an underlying germline mutation. These genes have a singular transcriptional signature and can be grouped into 2 clusters (or groups): cluster 1 (VHL and SHDx), involved in angiogenesis and hypoxia pathways; and cluster 2 (MEN2 and NF1), linked to the kinase signalling pathway. In turn, these genes are associated with a characteristic biochemical phenotype (noradrenergic and adrenergic), and clinical features (location, biological behaviour, age of presentation, etc.) in a large number of cases. Early diagnosis of these tumours, accompanied by a correct genetic diagnosis, should eventually become a priority to enable better treatment, early detection of complications, proper screening of family members and related tumours, as well as an improvement in the overall prognosis of these patients.

  11. Biotin: biochemical, physiological and clinical aspects.

    Science.gov (United States)

    Said, Hamid M

    2012-01-01

    Significant progress has been made in our understanding of the biochemical, physiological and nutritional aspects of the water-soluble vitamin biotin (vitamin H). It is well know now that biotin plays important roles in a variety of critical metabolic reactions in the cell, and thus, is essential for normal human health, growth and development. This is underscored by the serious clinical abnormalities that occur in conditions of biotin deficiency, which include, among other things, growth retardation, neurological disorders, and dermatological abnormalities (reviewed in 1). Studies in animals have also shown that biotin deficiency during pregnancy leads to embryonic growth retardation, congenital malformation and death (Watanabe 1983; Cooper and Brown 1958; Mock et al. 2003; Zempleni and Mock 2000). The aim of this chapter is to provide coverage of current knowledge of the biochemical, physiological, and clinical aspects of biotin nutrition. Many sections of this chapter have been the subject of excellent recent reviews by others (Wolf 2001; McMahon 2002; Mock 2004; Rodriguez-Melendez and Zempleni 2003; Said 2004; Said et al. 2000; Said and Seetheram 2006), and thus, for more information the reader is advised to consider these additional sources.

  12. Biochemical research elucidating metabolic pathways in Pneumocystis*

    Directory of Open Access Journals (Sweden)

    Kaneshiro E.S.

    2010-12-01

    Full Text Available Advances in sequencing the Pneumocystis carinii genome have helped identify potential metabolic pathways operative in the organism. Also, data from characterizing the biochemical and physiological nature of these organisms now allow elucidation of metabolic pathways as well as pose new challenges and questions that require additional experiments. These experiments are being performed despite the difficulty in doing experiments directly on this pathogen that has yet to be subcultured indefinitely and produce mass numbers of cells in vitro. This article reviews biochemical approaches that have provided insights into several Pneumocystis metabolic pathways. It focuses on 1 S-adenosyl-L-methionine (AdoMet; SAM, which is a ubiquitous participant in numerous cellular reactions; 2 sterols: focusing on oxidosqualene cyclase that forms lanosterol in P. carinii; SAM:sterol C-24 methyltransferase that adds methyl groups at the C-24 position of the sterol side chain; and sterol 14α-demethylase that removes a methyl group at the C-14 position of the sterol nucleus; and 3 synthesis of ubiquinone homologs, which play a pivotal role in mitochondrial inner membrane and other cellular membrane electron transport.

  13. Biochemical Manifestation of HIV Lipodystrophy Syndrome

    Directory of Open Access Journals (Sweden)

    Kenneth Ihenetu, PhD

    2012-11-01

    Full Text Available Objectives:Highly active anti-retroviral therapy (HAART, including protease inhibitors (PI have led to dramatic improvements in the quality and quantity of life in patients with acquired immunodeficiency syndrome (AIDS. However, a significant number of AIDS patients on HAART develop characteristic changes in body fat redistribution referred to as lipodystrophy syndrome (LDS. Features of LDS include hypertrophy in the neck fat pad (buffalo hump, increased fat in the abdominal region (protease paunch, gynecomastia and loss of fat in the mid-face and extremities.Methods:The aim of this paper is to review the current knowledge regarding this syndrome. This article reviews the published investigations on biochemical manifestation of HIV lipodystrophy syndrome.Results:It is estimated that approximately 64% of patients treated with PI will experience this syndrome. Biochemically, these patients have increased triglycerides (Trig, total cholesterol (TC, low-density lipoprotein-cholesterol (LDL-C and extremely low high-density lipoprotein-cholesterol (HDL-C.Conclusions and Public Health Implications:It is hoped that awareness of this syndrome would aid in early diagnosis and better patient management, possibly leading to a lower incidence of cardiovascular complications among these patients.

  14. [Biochemical principles of early saturnism recognition].

    Science.gov (United States)

    Tsimakuridze, M P; Mansuradze, E A; Zurashvili, D G; Tsimakuridze, M P

    2009-03-01

    The aim of the work is to determine the major sensitive criteria of biochemical indicators that allow timely discovery of negative influence of lead on organism and assist in early diagnosis of primary stages of saturnism. The workers of Georgian typographies, performing technological processes of letterpress printing were observed. Professional groups having contact with lead aerosols (main group of 66 people) and the workers of the same typography not being in touch with the poison (control group of 24 people) were studied. It was distinguished that, protracted professional contact with lead causes moderate increase of lead, coproporphyrin and DALA in daily urine in most cases; it is more clearly evidenced in the professional groups of lead smelters and lino operators and less clearly among typesetter and printers. Upon the checkup of people, having a direct contact with lead, biochemical analysis of urine should be given a preference, especially the determination of quantitative content of lead and coproporphyrin in urine with the aim of revealing the lead carrier, which is one of the first signals for occupational lookout and medical monitoring of the similar contingent.

  15. Serum biochemical markers in carcinoma breast.

    Directory of Open Access Journals (Sweden)

    Seth R

    2003-08-01

    Full Text Available BACKGROUND: Despite the extensive research for many years throughout the world, the etiopathogenesis of cancer still remains obscure. For the early detection of carcinoma of various origins, a number of biochemical markers have been studied to evaluate the malignancy. AIM: To analyse serum gamma glutamyl transpeptidase (GGTP, lactate dehydrogenase (LDH and superoxide dismutase (SOD in carcinoma breast patients. SETTINGS & DESIGN: The serum biochemical markers were estimated in twenty five histopathologically confirmed patients with carcinoma breast and equal number of healthy age- matched individuals served as control. MATERIAL & METHODS: Serum gamma glutamyl transpeptidase (GGTP, lactate dehydrogenase (LDH and superoxide dismutase (SOD were estimated and their sensitivity determined. Statistics: Data was analysed with student′s ′t′-test and sensitivity score of these markers was determined. RESULTS & CONCLUSIONS: The mean serum GGTP, LDH and SOD activities in patients with carcinoma breast were tremendously increased as compared to controls, and a steady increase was observed in their activities from stage I through stage IV as well as following distant metastasis. Serum GGTP, LDH and SOD might prove to be most sensitive biomarkers in carcinoma breast in early detection of the disease.

  16. The biochemical content of articular cartilage: an original MRI approach.

    Science.gov (United States)

    Loeuille, Damien; Olivier, Pierre; Watrin, Astrid; Grossin, Laurent; Gonord, Patrick; Guillot, Geneviève; Etienne, Stéphanie; Blum, Alain; Netter, Patrick; Gillet, Pierre

    2002-01-01

    The MR aspect of articular cartilage, that reflects the interactions between protons and macromolecular constituents, is affected by the intrinsic tissue structure (water content, the content of matrix constituents, collagen network organization), imager characteristics, and acquisition parameters. On the T1-weighted sequences, the bovine articular cartilage appears as an homogeneous tissue in high signal intensity, whatever the age of animals considered, whereas on the T2-weighted sequences, the articular bovine cartilage presents variations of its imaging pattern (laminar appearance) well correlated to the variations of its histological and biochemical structure. The T2 relaxation time measurement (T2 mapping), which reflects quantitatively the signal intensity variations observed on T2 weighted sequences, is a way to evaluate more precisely the modifications of cartilage structure during the aging and maturation processes (rat's study). This technique so far confined to experimental micro-imagers is now developed on clinical imagers. Consequently, it may permit to depict the early stages of osteoarthritic disease (OA) or to evaluate the chondroprotective effect of drugs.

  17. Plant Glutathione Biosynthesis: Diversity in Biochemical Regulation and Reaction Products

    Directory of Open Access Journals (Sweden)

    Ashley eGalant

    2011-09-01

    Full Text Available In plants, exposure to temperature extremes, heavy metal-contaminated soils, drought, air pollutants, and pathogens results in the generation of reactive oxygen species that alter the intracellular redox environment, which in turn influences signaling pathways and cell fate. As part of their response to these stresses, plants produce glutathione. Glutathione acts as an antioxidant by quenching reactive oxygen species, and is involved in the ascorbate-glutathione cycle that eliminates damaging peroxides. Plants also use glutathione for the detoxification of xenobiotics, herbicides, air pollutants (sulfur dioxide and ozone, and toxic heavy metals. Two enzymes catalyze glutathione synthesis: glutamate-cysteine ligase (GCL, and glutathione synthetase (GS. Glutathione is a ubiquitous protective compound in plants, but the structural and functional details of the proteins that synthesize it, as well as the potential biochemical mechanisms of their regulation, have only begun to be explored. As discussed here, the core reactions of glutathione synthesis are conserved across various organisms, but plants have diversified both the regulatory mechanisms that control its synthesis and the range of products derived from this pathway. Understanding the molecular basis of glutathione biosynthesis and its regulation will expand our knowledge of this component in the plant stress response network.

  18. Plant glutathione biosynthesis: diversity in biochemical regulation and reaction products.

    Science.gov (United States)

    Galant, Ashley; Preuss, Mary L; Cameron, Jeffrey C; Jez, Joseph M

    2011-01-01

    In plants, exposure to temperature extremes, heavy metal-contaminated soils, drought, air pollutants, and pathogens results in the generation of reactive oxygen species that alter the intracellular redox environment, which in turn influences signaling pathways and cell fate. As part of their response to these stresses, plants produce glutathione. Glutathione acts as an anti-oxidant by quenching reactive oxygen species, and is involved in the ascorbate-glutathione cycle that eliminates damaging peroxides. Plants also use glutathione for the detoxification of xenobiotics, herbicides, air pollutants (sulfur dioxide and ozone), and toxic heavy metals. Two enzymes catalyze glutathione synthesis: glutamate-cysteine ligase, and glutathione synthetase. Glutathione is a ubiquitous protective compound in plants, but the structural and functional details of the proteins that synthesize it, as well as the potential biochemical mechanisms of their regulation, have only begun to be explored. As discussed here, the core reactions of glutathione synthesis are conserved across various organisms, but plants have diversified both the regulatory mechanisms that control its synthesis and the range of products derived from this pathway. Understanding the molecular basis of glutathione biosynthesis and its regulation will expand our knowledge of this component in the plant stress response network.

  19. Quality, microstructure, biochemical and immunochemical characteristics of hypoallergenic pasta.

    Science.gov (United States)

    Susanna, S; Prabhasankar, P

    2012-08-01

    Celiac disease is an immune-mediated enteropathy, characterized by lifelong intolerance to gluten in genetically susceptible individuals. This study aims to develop hypoallergenic pasta using blends of Triticum durum semolina, 40% of other non-wheat flours and additives. Formulated pasta samples were evaluated for product quality characteristics and also subjected to biochemical analysis. Results showed that cooking loss ranged from 6.9% to 7.4%, which were within the acceptable range of 8%. Color change was low and in vitro protein digestibility of the pasta was found to be insignificant. Pasting characteristics of the hypoallergenic flour showed the increased peak viscosity and decreased gelatinization temperature. The scanning electron microscopy results demonstrated less-affected microstructure of gluten network. Texture profile analysis and descriptive sensory analysis revealed that optimized hypoallergenic pasta with xanthan gum as additive was acceptable and comparable with control. SDS-PAGE pattern showed distinct protein profile and decreased intensity, which was supported by Dot-Blot. In conclusion, the hypoallergenic pasta prepared by replacing T durum flour by 40% of other non-gluten flours could be useful for celiac patients because of its low antigenic activity.

  20. Simulation methods with extended stability for stiff biochemical Kinetics

    Directory of Open Access Journals (Sweden)

    Rué Pau

    2010-08-01

    Full Text Available Abstract Background With increasing computer power, simulating the dynamics of complex systems in chemistry and biology is becoming increasingly routine. The modelling of individual reactions in (biochemical systems involves a large number of random events that can be simulated by the stochastic simulation algorithm (SSA. The key quantity is the step size, or waiting time, τ, whose value inversely depends on the size of the propensities of the different channel reactions and which needs to be re-evaluated after every firing event. Such a discrete event simulation may be extremely expensive, in particular for stiff systems where τ can be very short due to the fast kinetics of some of the channel reactions. Several alternative methods have been put forward to increase the integration step size. The so-called τ-leap approach takes a larger step size by allowing all the reactions to fire, from a Poisson or Binomial distribution, within that step. Although the expected value for the different species in the reactive system is maintained with respect to more precise methods, the variance at steady state can suffer from large errors as τ grows. Results In this paper we extend Poisson τ-leap methods to a general class of Runge-Kutta (RK τ-leap methods. We show that with the proper selection of the coefficients, the variance of the extended τ-leap can be well-behaved, leading to significantly larger step sizes. Conclusions The benefit of adapting the extended method to the use of RK frameworks is clear in terms of speed of calculation, as the number of evaluations of the Poisson distribution is still one set per time step, as in the original τ-leap method. The approach paves the way to explore new multiscale methods to simulate (biochemical systems.

  1. Biochemical and radiological predictors of malignant biliary strictures

    Institute of Scientific and Technical Information of China (English)

    Ibrahim A. Al-Mofleh; Abdulrahman M. Aljebreen; Saleh M. Al-Amri; Rashed S. Al-Rashed; Faleh Z. Al-Faleh; Hussein M. Al-Freihi; Ayman A. Abdo; Arthur C. Isnani

    2004-01-01

    AIM: Differentiation of benign biliary strictures (BBS) from malignant biliary strictures (MBS) remains difficult despite improvement in imaging and endoscopic techniques. The aim of this study was to identify the clinical, biochemical and or radiological predictors of malignant biliary strictures.METHODS: We retrospectively reviewed all charts of patients who had biliary strictures (BS) on endoscopic retrograde cholangiopancreatography (ERCP) or percutaneous cholangiography (PTC) in case of unsuccessful ERCP from March 1998 to August 2002. Patient characteristics, clinical features, biochemical, radiological and biopsy results were all recorded. Stricture etiology was determined based on cytology,biopsy or clinical follow-up. A receiver operator characteristic (ROC) curve was constructed to determine the optimal laboratory diagnostic criterion threshold in predicting MBS.RESULTS: One hundred twenty six patients with biliary strictures were enrolled, of which 72 were malignant. The mean age for BBS was 53 years compared to 62.4 years for MBS (P=0.0006). Distal bile duct stricture was mainly due to a malignant process 48.6% vs 9% (P=0.001). Alkaline phosphates and AST levels were more significantly elevated in MBS (P=0.0002). R OC curve showed that a bilirubin level of 84 pmol/L or more was the most predictive of MBS with a sensitivity of 98.6%, specificity of 59.3% and a positive likelihood ratio of 2.42 (95% CI=0.649-0.8L0). Proximal biliary dilatation was more frequently encountered in MBS compared to BBS, 73.8% vs39.5% (P=0.0001). Majority of BBS (87%) and MBS (78%) were managed endoscopically.CONCLUSION: A serum bilirubin level of 84 μmol/L or greater is the best predictor of MBS. Older age, proximal biliary dilatation, higher levels of bilirubin, alkaline phosphatase, ALT and AST are all associated with MBS. ERCP is necessary to diagnose and treat benign and malignant biliary strictures.

  2. Dietary intakes and some biochemical markers in hemodialysis patients

    Directory of Open Access Journals (Sweden)

    Emine Yassibas

    2016-03-01

    Full Text Available Purpose: Intake of energy and some nutrients is frequently inadequate in dialysis patients because of eating and appetite disorders due to uremic syndrome. Inadequate energy and protein intake cause to malnutrition. Anthropometric measurements, biochemical markers and dietary intake records have great importance in determining the nutritional status of hemodialysis (HD patients. Therefore this study was planned to determination of daily energy, nutrient intake and some biochemical markers of adult hemodialysis patients. Method and Material:  A hundred and thirty six (male = 73, female = 63 clinically stable HD patients were enrolled in this study. All patients were taken 24-hour dietary recall. The daily energy and nutrient intakes of patients were calculated by food consumption records and anthropometric measurements were taken. Results: The mean age was found 45.5±13.51 years. The ratio of patients with body mass index (BMI below 18.5 kg/m2 was 7.4% and 25 kg/m2 or upper was 16.9%. Blood hemoglobin, hematocrit, albumin and total protein levels were below the normal levels. The daily dietary energy and protein intakes were found under the recommended level in the study period. A significant positive correlation was found between daily protein intake and serum albumin levels (r=0.210, p=0.014, daily protein intake and serum total protein levels (r=0.201, p=0.019, daily energy intake and serum total protein levels (r=0.178, p=0.039. Conclusions: HD patients often have low protein and energy intakes and most of them suffer from malnutrition. Therefore nutritional status of patients should be evaluated and periodically nutrition education should be given for improving eating habits and increasing dietary compliance is recommended.

  3. Soil biochemical responses to nitrogen addition in a bamboo forest.

    Science.gov (United States)

    Tu, Li-hua; Chen, Gang; Peng, Yong; Hu, Hong-ling; Hu, Ting-xing; Zhang, Jian; Li, Xian-wei; Liu, Li; Tang, Yi

    2014-01-01

    Many vital ecosystem processes take place in the soils and are greatly affected by the increasing active nitrogen (N) deposition observed globally. Nitrogen deposition generally affects ecosystem processes through the changes in soil biochemical properties such as soil nutrient availability, microbial properties and enzyme activities. In order to evaluate the soil biochemical responses to elevated atmospheric N deposition in bamboo forest ecosystems, a two-year field N addition experiment in a hybrid bamboo (Bambusa pervariabilis × Dendrocalamopsis daii) plantation was conducted. Four levels of N treatment were applied: (1) control (CK, without N added), (2) low-nitrogen (LN, 50 kg N ha(-1) year(-1)), (3) medium-nitrogen (MN, 150 kg N ha(-1) year(-1)), and (4) high-nitrogen (HN, 300 kg N ha(-1) year(-1)). Results indicated that N addition significantly increased the concentrations of NH4(+), NO3(-), microbial biomass carbon, microbial biomass N, the rates of nitrification and denitrification; significantly decreased soil pH and the concentration of available phosphorus, and had no effect on the total organic carbon and total N concentration in the 0-20 cm soil depth. Nitrogen addition significantly stimulated activities of hydrolytic enzyme that acquiring N (urease) and phosphorus (acid phosphatase) and depressed the oxidative enzymes (phenol oxidase, peroxidase and catalase) activities. Results suggest that (1) this bamboo forest ecosystem is moving towards being limited by P or co-limited by P under elevated N deposition, (2) the expected progressive increases in N deposition may have a potential important effect on forest litter decomposition due to the interaction of inorganic N and oxidative enzyme activities, in such bamboo forests under high levels of ambient N deposition.

  4. Physical and Biochemical Characteristics of Sharhabiel Reservoir Water, NW Jordan

    Directory of Open Access Journals (Sweden)

    Nazem M. El-Radaideh

    2015-04-01

    Full Text Available Jordan relies heavily on rainwater stored in reservoirs because it has extremely limited alternative water resources. These reservoirs are essential for drinking water and irrigation, so monitoring their water quality is extremely important. Variations in physical and biochemical conditions were investigated at Sharhabiel Reservoir (Jordan. Water quality monitoring of Sharhabiel Dam, from January to December 2013 indicates that the dam is subject to agricultural runoff. It also revealed that mineral dissolution, sediment load, rainfall evaporation and pumping, are the major contributors to variations in water quality. The water chemistry of the impounded Sharnabiel Reservoir showed that Na, Ca, Mg, HCO3 , and Cl are the principal ions, reflecting the dominance of calcareous weathering, with some contribution of silicates. The pH values showed an irregular pattern with highest values observed in the spring months. Total dissolved solids (TDS, Ca, Mg, and HCO3 are primarily related to leaching and evaporation, with elevated levels that occurred in the winter months. In contrast, seasonal patterns in Na, K, Cl, and NH4–N contents showed decreased values in wet months. Peaks in NO3 –N observed in winter are strongly associated with agricultural runoff. Changes in chlorophyll-a level were coincided with low ratio of TN to TP. BOD5 and COD peaks in spring corresponding with high algal growth. No significant changes in most of physical and biochemical parameters with depth, probably due to shallow depth, high annual sedimentation rate and heavy pumping rate in dry months. No available recorded data for long-term monitoring of Sharhabiel reservoir water to emphasize the self-purification capacity of dam.

  5. Olmesartan Attenuates Tacrolimus-Induced Biochemical and Ultrastructural Changes in Rat Kidney Tissue

    OpenAIRE

    Al-Harbi, Naif O.; Faisal Imam; Al-Harbi, Mohammed M.; Muzaffar Iqbal; Ahmed Nadeem; Sayed-Ahmed, Mohammed M.; Alabidy, Ali D.; Almukhallafi, Ali F.

    2014-01-01

    Tacrolimus, a calcineurin inhibitor, is clinically used as an immunosuppressive agent in organ transplantation, but its use is limited due to its marked nephrotoxicity. The present study investigated the effect of olmesartan (angiotensin receptor blocker) on tacrolimus-induced nephrotoxicity in rats. A total of 24 rats were divided into four groups, which included control, tacrolimus, tacrolimus + olmesartan, and olmesartan groups. Tacrolimus-induced nephrotoxicity was assessed biochemically ...

  6. Evaluation of clinical signs, parasitemia, hematologic and biochemical changes in cattle experimentally infected with Trypanosoma vivax

    OpenAIRE

    Otavio Luiz Fidelis Junior; Paulo Henrique Sampaio; Rosangela Zacarias Machado; Marcos Rogério André; Luiz Carlos Marques; Fabiano Antonio Cadioli

    2016-01-01

    Abstract Infections by Trypanosoma vivax cause great losses to livestock in Africa and Central and South Americas. Outbreaks due this parasite have been occurred with increasing frequency in Brazil. Knowledge of changes caused byT. vivax during the course of this disease can be of great diagnostic value. Thus, clinical signs, parasitemia, hematologic and biochemical changes of cattle experimentally infected by this hemoparasite were evaluated. Two distinct phases were verified during the infe...

  7. Switching Dynamics in Reaction Networks Induced by Molecular Discreteness

    CERN Document Server

    Togashi, Y; Kaneko, Kunihiko; Togashi, Yuichi

    2006-01-01

    To study the fluctuations and dynamics in chemical reaction processes, stochastic differential equations based on the rate equation involving chemical concentrations are often adopted. When the number of molecules is very small, however, the discreteness in the number of molecules cannot be neglected since the number of molecules must be an integer. This discreteness can be important in biochemical reactions, where the total number of molecules is not significantly larger than the number of chemical species. To elucidate the effects of such discreteness, we study autocatalytic reaction systems comprising several chemical species through stochastic particle simulations. The generation of novel states is observed; it is caused by the extinction of some molecular species due to the discreteness in their number. We demonstrate that the reaction dynamics are switched by a single molecule, which leads to the reconstruction of the acting network structure. We also show the strong dependence of the chemical concentra...

  8. Parameters Obtained by Hepatobiliary Scintigraphy Have Significant Correlation with Biochemical Factors Early After Liver Transplantation

    Energy Technology Data Exchange (ETDEWEB)

    Kansoul, H.A.; Axelsson, R.; Yamamoto, S.; Savicheva, I.; Aspelin, P.; Ericzon, B.G.; Gjertsen, H. [Div. of Transplantation Surgery and Div. of Radiology, Dept. of Clinical Science, Intervention, and Technology, Karolinska Inst., Karolinska Univ. Hospital, Stockholm (Sweden)

    2007-08-15

    Background: Early postoperative hepatobiliary scintigraphy after liver transplantation is performed worldwide, but data on its significance for graft function are currently limited. Purpose: To examine the correlation between the result of early postoperative hepatobiliary scintigraphy and pre- and postoperative biochemical parameters in liver transplantation (LTx) patients. Material and Methods: Six parameters of hepatobiliary scintigraphy using {sup 99m}Tc mebrofenin were statistically analyzed in 108 LTx patients: 1) half-life of the activity of elimination of mebrofenin from the blood; 2) total clearance of mebrofenin from the blood due to all possible routes; 3) half-life of the activity due to liver uptake; 4) clearance of mebrofenin from the blood due to liver uptake; 5) time to maximal uptake in the liver; and 6) the hepatic extraction fraction (HEF) and biochemical data. Analysis between patients with preoperative normal liver function, familial amyloid polyneuropathy (FAP), and end-stage liver disease (non-FAP) was also performed. Results: Univariate and multivariate analysis revealed that total bilirubin postoperative day 3 correlated with all three scintigraphic parameters, and peak aspartate aminotransferase and alanine aminotransferase correlated with HEF. The analysis between patients with FAP and non-FAP revealed no significant difference of scintigraphic data between the two groups. Conclusion: A significant correlation between early postoperative scintigraphic results and biochemical parameters was demonstrated.

  9. Flow whitelisting in SCADA networks

    NARCIS (Netherlands)

    Barbosa, Rafael Ramos Regis; Sadre, Ramin; Pras, Aiko

    2013-01-01

    Supervisory control and data acquisition (SCADA) networks are commonly deployed in large industrial facilities. Modern SCADA networks are becoming more vulnerable to cyber attacks due to the common use of standard communications protocols and increased interconnections with corporate networks and th

  10. Scaling up Semi-Arid Grassland Biochemical Content from the Leaf to the Canopy Level: Challenges and Opportunities

    Directory of Open Access Journals (Sweden)

    Amy Mui

    2010-12-01

    Full Text Available Remote sensing imagery is being used intensively to estimate the biochemical content of vegetation (e.g., chlorophyll, nitrogen, and lignin at the leaf level. As a result of our need for vegetation biochemical information and our increasing ability to obtain canopy spectral data, a few techniques have been explored to scale leaf-level biochemical content to the canopy level for forests and crops. However, due to the contribution of non-green materials (i.e., standing dead litter, rock, and bare soil from canopy spectra in semi-arid grasslands, it is difficult to obtain information about grassland biochemical content from remote sensing data at the canopy level. This paper summarizes available methods used to scale biochemical information from the leaf level to the canopy level and groups these methods into three categories: direct extrapolation, canopy-integrated approach, and inversion of physical models. As for semi-arid heterogeneous grasslands, we conclude that all methods are useful, but none are ideal. It is recommended that future research should explore a systematic upscaling framework which combines spatial pattern analysis, canopy-integrated approach, and modeling methods to retrieve vegetation biochemical content at the canopy level.

  11. Hemoglobin variants: biochemical properties and clinical correlates.

    Science.gov (United States)

    Thom, Christopher S; Dickson, Claire F; Gell, David A; Weiss, Mitchell J

    2013-03-01

    Diseases affecting hemoglobin synthesis and function are extremely common worldwide. More than 1000 naturally occurring human hemoglobin variants with single amino acid substitutions throughout the molecule have been discovered, mainly through their clinical and/or laboratory manifestations. These variants alter hemoglobin structure and biochemical properties with physiological effects ranging from insignificant to severe. Studies of these mutations in patients and in the laboratory have produced a wealth of information on hemoglobin biochemistry and biology with significant implications for hematology practice. More generally, landmark studies of hemoglobin performed over the past 60 years have established important paradigms for the disciplines of structural biology, genetics, biochemistry, and medicine. Here we review the major classes of hemoglobin variants, emphasizing general concepts and illustrative examples.

  12. Simplifying biochemical models with intermediate species

    DEFF Research Database (Denmark)

    Feliu, Elisenda; Wiuf, Carsten

    2013-01-01

    canonical model that characterizes crucial dynamical properties, such as mono- and multistationarity and stability of steady states, of all models in the class. We show that if the core model does not have conservation laws, then the introduction of intermediates does not change the steady...... techniques, we study systematically the effects of intermediate, or transient, species in biochemical systems and provide a simple, yet rigorous mathematical classification of all models obtained from a core model by including intermediates. Main examples include enzymatic and post-translational modification...... systems, where intermediates often are considered insignificant and neglected in a model, or they are not included because we are unaware of their existence. All possible models obtained from the core model are classified into a finite number of classes. Each class is defined by a mathematically simple...

  13. On Biochemical Formation of Salt Deposits

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A water/salt system in an evaporative environment is both a physicochemical region and a biological one. All the parameters of the system, such as the salinity, temperature and CO2 partial pressure, are affected by halophilic bacteria. The system controls salt deposition but is modified by an accompanying ecological system; therefore it should be called a water/salt/biological system. Salt minerals result from accumulation of the remains of bacteria/algae, namely, bacteria/algae formation; whereas biological, biophysical and biochemical processes provide full evidence for organic involvement. Consequently, salt deposits should not be called purely chemical but biological/chemical ones. This new argument supplements and develops the traditional idea and helps perfect the mineralization theory of salts and even general deposits, thus giving guidance to prospecting for salt deposits.

  14. The biochemical basis of hereditary fructose intolerance.

    Science.gov (United States)

    Bouteldja, Nadia; Timson, David J

    2010-04-01

    Hereditary fructose intolerance is a rare, but potentially lethal, inherited disorder of fructose metabolism, caused by mutation of the aldolase B gene. Treatment currently relies solely on dietary restriction of problematic sugars. Biochemical study of defective aldolase B enzymes is key to revealing the molecular basis of the disease and providing a stronger basis for improved treatment and diagnosis. Such studies have revealed changes in enzyme activity, stability and oligomerisation. However, linking these changes to disease phenotypes has not always been straightforward. This review gives a general overview of the features of hereditary fructose intolerance, then concentrates on the biochemistry of the AP variant (Ala149Pro variant of aldolase B) and molecular pathological consequences of mutation of the aldolase B gene.

  15. Integrated label-free silicon nanowire sensor arrays for (bio)chemical analysis.

    Science.gov (United States)

    De, Arpita; van Nieuwkasteele, Jan; Carlen, Edwin T; van den Berg, Albert

    2013-06-07

    We present a label-free (bio)chemical analysis platform that uses all-electrical silicon nanowire sensor arrays integrated with a small volume microfluidic flow-cell for real-time (bio)chemical analysis and detection. The integrated sensing platform contains an automated multi-sample injection system that eliminates erroneous sensor responses from sample switching due to flow rate fluctuations and provides precise sample volumes down to 10 nl. Biochemical sensing is demonstrated with real-time 15-mer DNA-PNA (peptide nucleic acid) duplex hybridization measurements from different sample concentrations in a low ionic strength, and the equilibrium dissociation constant KD ≈ 140 nM has been extracted from the experimental data using the first order Langmuir binding model. Chemical sensing is demonstrated with pH measurements from different injected samples in flow that have sensitivities consistent with the gate-oxide materials. A differential sensor measurement configuration results in a 30× reduction in sensor drift. The integrated label-free analysis platform is suitable for a wide range of small volume chemical and biochemical analyses.

  16. Tissue microarrays compared with whole sections and biochemical analyses. A subgroup analysis of DBCG 82 b

    DEFF Research Database (Denmark)

    Kyndi, Marianne; Sørensen, Flemming Brandt; Knudsen, H;

    2008-01-01

    &c trials, were IHC stained for ER, PgR and HER2. In addition, ER and PgR were measured in the DBCG82 b&c trials by a biochemical analysis. Statistical analyses included Kappa statistics, Kaplan-Meier survival curves, Log-rank tests, and Cox regression hazards analyses. RESULTS AND CONCLUSION: IHC stainings...... stainings of TMA cores and biochemical analyses. Divergence between IHC and biochemical analyses was predominantly due to the chosen thresholds. IHC staining of one 1mm core from each tumor revealed a significant independent prognostic value of PgR and HER2 on overall survival. In conclusion, IHC stainings...... cores and biochemical analyses. PATIENTS AND METHODS: A central and a peripheral 1mm core and a whole section from each of 54 paraffin blocks from 27 breast cancers included in a one-institution cohort, and a single 1mm central TMA core, from each breast tumor from 1000 patients included in the DBCG82 b...

  17. Tissue microarrays compared with whole sections and biochemical analyses. A subgroup analysis of DBCG82 b

    DEFF Research Database (Denmark)

    Kyndi, M.; Sorensen, F.B.; Overgaard, M.;

    2008-01-01

    b&c trials, were IHC stained for ER, PgR and HER2. In addition, ER and PgR were measured in the DBCG82 b&c trials by a biochemical analysis. Statistical analyses included Kappa statistics, Kaplan-Meier survival curves, Log-rank tests, and Cox regression hazards analyses. Results and conclusion. IHC...... IHC stainings of TMA cores and biochemical analyses. Divergence between IHC and biochemical analyses was predominantly due to the chosen thresholds. IHC staining of one 1mm core from each tumor revealed a significant independent prognostic value of PgR and HER2 on overall survival. In conclusion, IHC...... cores and biochemical analyses. Patients and methods. A central and a peripheral 1mm core and a whole section from each of 54 paraffin blocks from 27 breast cancers included in a one-institution cohort, and a single 1 min central TMA core, from each breast tumor from 1000 patients included in the DBCG82...

  18. Physiological and biochemical responses of three Veneridae clams exposed to salinity changes.

    Science.gov (United States)

    Carregosa, Vanessa; Velez, Cátia; Soares, Amadeu M V M; Figueira, Etelvina; Freitas, Rosa

    2014-01-01

    Given their global importance, coastal marine environments are a major focus of concern regarding the potential impacts of climate change, namely due to alterations in seawater salinity. It is known that environmental characteristics, such as salinity, affect immune and physiological parameters of bivalves. Nevertheless, scarce information is available concerning the biochemical alterations associated with salinity changes. For this reason, the present work aimed to evaluate the biochemical responses of three venerid clam species (Venerupis decussata, Venerupis corrugata, Venerupis philippinarum) submitted to salinity changes. The effects on the native (V. decussata and V. corrugata) and invasive (V. philippinarum) species collected from the same sampling site and submitted to the same salinity gradient (0 to 42g/L) were compared. The results obtained demonstrated that V. corrugata is the most sensitive species to salinity changes and V. decussata is the species that can tolerate a wider range of salinities. Furthermore, our work showed that clams under salinity associated stress can alter their biochemical mechanisms, such as increasing their antioxidant defenses, to cope with the higher oxidative stress resulting from hypo and hypersaline conditions. Among the physiological and biochemical parameters analyzed (glycogen and protein content; lipid peroxidation levels, antioxidant enzymes activity; total, reduced and oxidized glutathione) Catalase (CAT) and especially superoxide dismutase (SOD) showed to be useful biomarkers to assess salinity impacts in clams.

  19. DETECTION OF TOPOLOGICAL PATTERNS IN PROTEIN NETWORKS.

    Energy Technology Data Exchange (ETDEWEB)

    MASLOV,S.SNEPPEN,K.

    2003-11-17

    Complex networks appear in biology on many different levels: (1) All biochemical reactions taking place in a single cell constitute its metabolic network, where nodes are individual metabolites, and edges are metabolic reactions converting them to each other. (2) Virtually every one of these reactions is catalyzed by an enzyme and the specificity of this catalytic function is ensured by the key and lock principle of its physical interaction with the substrate. Often the functional enzyme is formed by several mutually interacting proteins. Thus the structure of the metabolic network is shaped by the network of physical interactions of cell's proteins with their substrates and each other. (3) The abundance and the level of activity of each of the proteins in the physical interaction network in turn is controlled by the regulatory network of the cell. Such regulatory network includes all of the multiple mechanisms in which proteins in the cell control each other including transcriptional and translational regulation, regulation of mRNA editing and its transport out of the nucleus, specific targeting of individual proteins for degradation, modification of their activity e.g. by phosphorylation/dephosphorylation or allosteric regulation, etc. To get some idea about the complexity and interconnectedness of protein-protein regulations in baker's yeast Saccharomyces Cerevisiae in Fig. 1 we show a part of the regulatory network corresponding to positive or negative regulations that regulatory proteins exert on each other. (4) On yet higher level individual cells of a multicellular organism exchange signals with each other. This gives rise to several new networks such as e.g. nervous, hormonal, and immune systems of animals. The intercellular signaling network stages the development of a multicellular organism from the fertilized egg. (5) Finally, on the grandest scale, the interactions between individual species in ecosystems determine their food webs. An

  20. DETECTION OF TOPOLOGICAL PATTERNS IN PROTEIN NETWORKS.

    Energy Technology Data Exchange (ETDEWEB)

    MASLOV,S.SNEPPEN,K.

    2003-11-17

    Complex networks appear in biology on many different levels: (1) All biochemical reactions taking place in a single cell constitute its metabolic network, where nodes are individual metabolites, and edges are metabolic reactions converting them to each other. (2) Virtually every one of these reactions is catalyzed by an enzyme and the specificity of this catalytic function is ensured by the key and lock principle of its physical interaction with the substrate. Often the functional enzyme is formed by several mutually interacting proteins. Thus the structure of the metabolic network is shaped by the network of physical interactions of cell's proteins with their substrates and each other. (3) The abundance and the level of activity of each of the proteins in the physical interaction network in turn is controlled by the regulatory network of the cell. Such regulatory network includes all of the multiple mechanisms in which proteins in the cell control each other including transcriptional and translational regulation, regulation of mRNA editing and its transport out of the nucleus, specific targeting of individual proteins for degradation, modification of their activity e.g. by phosphorylation/dephosphorylation or allosteric regulation, etc. To get some idea about the complexity and interconnectedness of protein-protein regulations in baker's yeast Saccharomyces Cerevisiae in Fig. 1 we show a part of the regulatory network corresponding to positive or negative regulations that regulatory proteins exert on each other. (4) On yet higher level individual cells of a multicellular organism exchange signals with each other. This gives rise to several new networks such as e.g. nervous, hormonal, and immune systems of animals. The intercellular signaling network stages the development of a multicellular organism from the fertilized egg. (5) Finally, on the grandest scale, the interactions between individual species in ecosystems determine their food webs. An

  1. Biochemically enhanced methane production from coal

    Science.gov (United States)

    Opara, Aleksandra

    For many years, biogas was connected mostly with the organic matter decomposition in shallow sediments (e.g., wetlands, landfill gas, etc.). Recently, it has been realized that biogenic methane production is ongoing in many hydrocarbon reservoirs. This research examined microbial methane and carbon dioxide generation from coal. As original contributions methane production from various coal materials was examined in classical and electro-biochemical bench-scale reactors using unique, developed facultative microbial consortia that generate methane under anaerobic conditions. Facultative methanogenic populations are important as all known methanogens are strict anaerobes and their application outside laboratory would be problematic. Additional testing examined the influence of environmental conditions, such as pH, salinity, and nutrient amendments on methane and carbon dioxide generation. In 44-day ex-situ bench-scale batch bioreactor tests, up to 300,000 and 250,000 ppm methane was generated from bituminous coal and bituminous coal waste respectively, a significant improvement over 20-40 ppm methane generated from control samples. Chemical degradation of complex hydrocarbons using environmentally benign reagents, prior to microbial biodegradation and methanogenesis, resulted in dissolution of up to 5% bituminous coal and bituminous coal waste and up to 25% lignite in samples tested. Research results confirm that coal waste may be a significant underutilized resource that could be converted to useful fuel. Rapid acidification of lignite samples resulted in low pH (below 4.0), regardless of chemical pretreatment applied, and did not generate significant methane amounts. These results confirmed the importance of monitoring and adjusting in situ and ex situ environmental conditions during methane production. A patented Electro-Biochemical Reactor technology was used to supply electrons and electron acceptor environments, but appeared to influence methane generation in a

  2. Boolean network model predicts knockout mutant phenotypes of fission yeast.

    Directory of Open Access Journals (Sweden)

    Maria I Davidich

    Full Text Available BOOLEAN NETWORKS (OR: networks of switches are extremely simple mathematical models of biochemical signaling networks. Under certain circumstances, Boolean networks, despite their simplicity, are capable of predicting dynamical activation patterns of gene regulatory networks in living cells. For example, the temporal sequence of cell cycle activation patterns in yeasts S. pombe and S. cerevisiae are faithfully reproduced by Boolean network models. An interesting question is whether this simple model class could also predict a more complex cellular phenomenology as, for example, the cell cycle dynamics under various knockout mutants instead of the wild type dynamics, only. Here we show that a Boolean network model for the cell cycle control network of yeast S. pombe correctly predicts viability of a large number of known mutants. So far this had been left to the more detailed differential equation models of the biochemical kinetics of the yeast cell cycle network and was commonly thought to be out of reach for models as simplistic as Boolean networks. The new results support our vision that Boolean networks may complement other mathematical models in systems biology to a larger extent than expected so far, and may fill a gap where simplicity of the model and a preference for an overall dynamical blueprint of cellular regulation, instead of biochemical details, are in the focus.

  3. Boolean Network Model Predicts Knockout Mutant Phenotypes of Fission Yeast

    Science.gov (United States)

    Davidich, Maria I.; Bornholdt, Stefan

    2013-01-01

    Boolean networks (or: networks of switches) are extremely simple mathematical models of biochemical signaling networks. Under certain circumstances, Boolean networks, despite their simplicity, are capable of predicting dynamical activation patterns of gene regulatory networks in living cells. For example, the temporal sequence of cell cycle activation patterns in yeasts S. pombe and S. cerevisiae are faithfully reproduced by Boolean network models. An interesting question is whether this simple model class could also predict a more complex cellular phenomenology as, for example, the cell cycle dynamics under various knockout mutants instead of the wild type dynamics, only. Here we show that a Boolean network model for the cell cycle control network of yeast S. pombe correctly predicts viability of a large number of known mutants. So far this had been left to the more detailed differential equation models of the biochemical kinetics of the yeast cell cycle network and was commonly thought to be out of reach for models as simplistic as Boolean networks. The new results support our vision that Boolean networks may complement other mathematical models in systems biology to a larger extent than expected so far, and may fill a gap where simplicity of the model and a preference for an overall dynamical blueprint of cellular regulation, instead of biochemical details, are in the focus. PMID:24069138

  4. Soya bean Gα proteins with distinct biochemical properties exhibit differential ability to complement Saccharomyces cerevisiae gpa1 mutant.

    Science.gov (United States)

    Roy Choudhury, Swarup; Wang, Yuqi; Pandey, Sona

    2014-07-01

    Signalling pathways mediated by heterotrimeric G-proteins are common to all eukaryotes. Plants have a limited number of each of the G-protein subunits, with the most elaborate G-protein network discovered so far in soya bean (Glycine max, also known as soybean) which has four Gα, four Gβ and ten Gγ proteins. Biochemical characterization of Gα proteins from plants suggests significant variation in their properties compared with the well-characterized non-plant proteins. Furthermore, the four soya bean Gα (GmGα) proteins exhibit distinct biochemical activities among themselves, but the extent to which such biochemical differences contribute to their in vivo function is also not known. We used the yeast gpa1 mutant which displays constitutive signalling and growth arrest in the pheromone-response pathway as an in vivo model to evaluate the effect of distinct biochemical activities of GmGα proteins. We showed that specific GmGα proteins can be activated during pheromone-dependent receptor-mediated signalling in yeast and they display different strengths towards complementation of yeast gpa1 phenotypes. We also identified amino acids that are responsible for differential complementation abilities of specific Gα proteins. These data establish that specific plant Gα proteins are functional in the receptor-mediated pheromone-response pathway in yeast and that the subtle biochemical differences in their activity are physiologically relevant.

  5. Engineering stability in gene networks by autoregulation

    Science.gov (United States)

    Becskei, Attila; Serrano, Luis

    2000-06-01

    The genetic and biochemical networks which underlie such things as homeostasis in metabolism and the developmental programs of living cells, must withstand considerable variations and random perturbations of biochemical parameters. These occur as transient changes in, for example, transcription, translation, and RNA and protein degradation. The intensity and duration of these perturbations differ between cells in a population. The unique state of cells, and thus the diversity in a population, is owing to the different environmental stimuli the individual cells experience and the inherent stochastic nature of biochemical processes (for example, refs 5 and 6). It has been proposed, but not demonstrated, that autoregulatory, negative feedback loops in gene circuits provide stability, thereby limiting the range over which the concentrations of network components fluctuate. Here we have designed and constructed simple gene circuits consisting of a regulator and transcriptional repressor modules in Escherichia coli and we show the gain of stability produced by negative feedback.

  6. Network motifs provide signatures that characterize metabolism†

    OpenAIRE

    Shellman, Erin R.; Burant, Charles F.; Schnell, Santiago

    2013-01-01

    Motifs are repeating patterns that determine the local properties of networks. In this work, we characterized all 3-node motifs using enzyme commission numbers of the International Union of Biochemistry and Molecular Biology to show that motif abundance is related to biochemical function. Further, we present a comparative analysis of motif distributions in the metabolic networks of 21 species across six kingdoms of life. We found the distribution of motif abundances to be similar between spec...

  7. Catatonia due to systemic lupus erythematosus

    Directory of Open Access Journals (Sweden)

    Francisco de Assis Pinto Cabral Júnior Rabello

    2014-07-01

    Full Text Available Objectives Discuss neuropsychiatric aspects and differential diagnosis of catatonic syndrome secondary to systemic lupus erythematosus (SLE in a pediatric patient. Methods Single case report. Result A 13-year-old male, after two months diagnosed with SLE, started to present psychotic symptoms (behavioral changes, hallucinations and delusions that evolved into intense catatonia. During hospitalization, neuroimaging, biochemical and serological tests for differential diagnosis with metabolic encephalopathy, neurological tumors and neuroinfections, among other tests, were performed. The possibility of neuroleptic malignant syndrome, steroid-induced psychosis and catatonia was also evaluated. A complete reversal of catatonia was achieved after using benzodiazepines in high doses, associated with immunosuppressive therapy for lupus, which speaks in favor of catatonia secondary to autoimmune encephalitis due to lupus. Conclusion Although catatonia rarely is the initial clinical presentation of SLE, the delay in recognizing the syndrome can be risky, having a negative impact on prognosis. Benzodiazepines have an important role in the catatonia resolution, especially when associated with parallel specific organic base cause treatment. The use of neuroleptics should be avoided for the duration of the catatonic syndrome as it may cause clinical deterioration.

  8. Quantifying evolvability in small biological networks

    Energy Technology Data Exchange (ETDEWEB)

    Nemenman, Ilya [Los Alamos National Laboratory; Mugler, Andrew [COLUMBIA UNIV; Ziv, Etay [COLUMBIA UNIV; Wiggins, Chris H [COLUMBIA UNIV

    2008-01-01

    The authors introduce a quantitative measure of the capacity of a small biological network to evolve. The measure is applied to a stochastic description of the experimental setup of Guet et al. (Science 2002, 296, pp. 1466), treating chemical inducers as functional inputs to biochemical networks and the expression of a reporter gene as the functional output. The authors take an information-theoretic approach, allowing the system to set parameters that optimise signal processing ability, thus enumerating each network's highest-fidelity functions. All networks studied are highly evolvable by the measure, meaning that change in function has little dependence on change in parameters. Moreover, each network's functions are connected by paths in the parameter space along which information is not significantly lowered, meaning a network may continuously change its functionality without completely losing it along the way. This property further underscores the evolvability of the networks.

  9. DNA reaction networks: Providing a panoramic view

    Science.gov (United States)

    Wang, Fei; Fan, Chunhai

    2016-08-01

    A quantitative understanding of the functional landscape of a biochemical circuit can reveal the design rules required to optimize the circuit. Now, a high-throughput droplet-based microfluidic platform has been developed which enables high-resolution mapping of bifurcation diagrams for two nonlinear DNA networks.

  10. Green heterogeneous wireless networks

    CERN Document Server

    Ismail, Muhammad; Nee, Hans-Peter; Qaraqe, Khalid A; Serpedin, Erchin

    2016-01-01

    This book focuses on the emerging research topic "green (energy efficient) wireless networks" which has drawn huge attention recently from both academia and industry. This topic is highly motivated due to important environmental, financial, and quality-of-experience (QoE) considerations. Specifically, the high energy consumption of the wireless networks manifests in approximately 2% of all CO2 emissions worldwide. This book presents the authors’ visions and solutions for deployment of energy efficient (green) heterogeneous wireless communication networks. The book consists of three major parts. The first part provides an introduction to the "green networks" concept, the second part targets the green multi-homing resource allocation problem, and the third chapter presents a novel deployment of device-to-device (D2D) communications and its successful integration in Heterogeneous Networks (HetNets). The book is novel in that it specifically targets green networking in a heterogeneous wireless medium, which re...

  11. Persistent memories in transient networks

    OpenAIRE

    Babichev, Andrey; Dabaghian, Yuri

    2016-01-01

    Spatial awareness in mammals is based on an internalized representation of the environment, encoded by large networks of spiking neurons. While such representations can last for a long time, the underlying neuronal network is transient: neuronal cells die every day, synaptic connections appear and disappear, the networks constantly change their architecture due to various forms of synaptic and structural plasticity. How can a network with a dynamic architecture encode a stable map of space? W...

  12. Declarative Networking

    CERN Document Server

    Loo, Boon Thau

    2012-01-01

    Declarative Networking is a programming methodology that enables developers to concisely specify network protocols and services, which are directly compiled to a dataflow framework that executes the specifications. Declarative networking proposes the use of a declarative query language for specifying and implementing network protocols, and employs a dataflow framework at runtime for communication and maintenance of network state. The primary goal of declarative networking is to greatly simplify the process of specifying, implementing, deploying and evolving a network design. In addition, decla

  13. ESCHERICHIA COLI REDOX MUTANTS AS MICROBIAL CELL FACTORIES FOR THE SYNTHESIS OF REDUCED BIOCHEMICALS

    Directory of Open Access Journals (Sweden)

    Jimena A. Ruiz

    2012-10-01

    Full Text Available Bioprocesses conducted under conditions with restricted O2 supply are increasingly exploited for the synthesis of reduced biochemicals using different biocatalysts. The model facultative aerobe Escherichia coli, the microbial cell factory par excellence, has elaborate sensing and signal transduction mechanisms that respond to the availability of electron acceptors and alternative carbon sources in the surrounding environment. In particular, the ArcBA and CreBC two-component signal transduction systems are largely responsible for the metabolic regulation of redox control in response to O2 availability and carbon source utilization, respectively. Significant advances in the understanding of the biochemical, genetic, and physiological duties of these regulatory systems have been achieved in recent years. This situation allowed to rationally-design novel engineering approaches that ensure optimal carbon and energy flows within central metabolism, as well as to manipulate redox homeostasis, in order to optimize the production of industrially-relevant metabolites. In particular, metabolic flux analysis provided new clues to understand the metabolic regulation mediated by the ArcBA and CreBC systems. Genetic manipulation of these regulators proved useful for designing microbial cells factories tailored for the synthesis of reduced biochemicals with added value, such as poly(3-hydroxybutyrate, under conditions with restricted O2 supply. This network-wide strategy is in contrast with traditional metabolic engineering approaches, that entail direct modification of the pathway(s at stake, and opens new avenues for the targeted modulation of central catabolic pathways at the transcriptional level.

  14. Efficient, sparse biological network determination

    Directory of Open Access Journals (Sweden)

    Papachristodoulou Antonis

    2009-02-01

    Full Text Available Abstract Background Determining the interaction topology of biological systems is a topic that currently attracts significant research interest. Typical models for such systems take the form of differential equations that involve polynomial and rational functions. Such nonlinear models make the problem of determining the connectivity of biochemical networks from time-series experimental data much harder. The use of linear dynamics and linearization techniques that have been proposed in the past can circumvent this, but the general problem of developing efficient algorithms for models that provide more accurate system descriptions remains open. Results We present a network determination algorithm that can treat model descriptions with polynomial and rational functions and which does not make use of linearization. For this purpose, we make use of the observation that biochemical networks are in general 'sparse' and minimize the 1-norm of the decision variables (sum of weighted network connections while constraints keep the error between data and the network dynamics small. The emphasis of our methodology is on determining the interconnection topology rather than the specific reaction constants and it takes into account the necessary properties that a chemical reaction network should have – something that techniques based on linearization can not. The problem can be formulated as a Linear Program, a convex optimization problem, for which efficient algorithms are available that can treat large data sets efficiently and uncertainties in data or model parameters. Conclusion The presented methodology is able to predict with accuracy and efficiency the connectivity structure of a chemical reaction network with mass action kinetics and of a gene regulatory network from simulation data even if the dynamics of these systems are non-polynomial (rational and uncertainties in the data are taken into account. It also produces a network structure that can

  15. A Biochemical Approach to the Problem of Dyslexia.

    Science.gov (United States)

    Baker, Sidney McDonald

    1985-01-01

    The paper presents the case of a sixth-grade boy, labeled dyslexic, who responded positively to a biochemical approach. Remedy of iron, zinc, and Vitamin B-6 deficiencies as well as an imbalance of fatty acids resulted in improvements in hair and skin and also in reading. A biochemical approach to behavior problems is proposed. (Author/CL)

  16. Local biochemical and morphological differences in human Achilles tendinopathy

    DEFF Research Database (Denmark)

    J, Pingel; Fredberg, Ulrich; K, Qvortrup;

    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 ex...

  17. The physiological and biochemical bases of functional brain imaging

    OpenAIRE

    2007-01-01

    Functional brain imaging is based on the display of computer-derived images of changes in physiological and/or biochemical functions altered by activation or depression of local functional activities in the brain. This article reviews the physiological and biochemical mechanisms involved.

  18. Biochemical evaluation of phenylketonuria (PKU: from diagnosis to treatment

    Directory of Open Access Journals (Sweden)

    Leticia Belmont-Martínez

    2014-07-01

    Besides periodical Phe and Tyr testing, biochemical follow-up includes the measurement of necessary elements that guarantee normal physical and intellectual development such as selenium, zinc, B12 vitamin, folates, iron and long chain fatty acids. Clinical context is as important as biochemical status so periodic evaluation of nutritional, medical, social and psychological aspects should be included.

  19. Biochemical diagnosis of pheochromocytoma: which test is best?

    NARCIS (Netherlands)

    Lenders, J.W.M.; Pacak, K.; Walther, M.M.; Linehan, W.M.; Mannelli, M.; Friberg, P.; Keiser, H.R.; Goldstein, D.S.; Eisenhofer, G.

    2002-01-01

    CONTEXT: Diagnosis of pheochromocytoma depends on biochemical evidence of catecholamine production by the tumor. However, the best test to establish the diagnosis has not been determined. OBJECTIVE: To determine the biochemical test or combination of tests that provides the best method for diagnosis

  20. Editorial: ESBES - European Society of Biochemical Engineering Sciences.

    Science.gov (United States)

    Ferreira, Guilherme; Jungbauer, Alois

    2013-06-01

    The latest ESBES special issue on "Biochemical Engineering Sciences" is edited by Prof. Guilherme Ferreira (Chairman, ESBES) and Prof. Alois Jungbauer (co-Editor-in-Chief, Biotechnology Journal). This special issue comprises the latest research in biochemical engineering science presented at the 9(th) ESBES Conference held in Istanbul, Turkey in 2012.

  1. Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli

    Directory of Open Access Journals (Sweden)

    Eils Roland

    2007-05-01

    Full Text Available Abstract Background Biochemical investigations over the last decades have elucidated an increasingly complete image of the cellular metabolism. To derive a systems view for the regulation of the metabolism when cells adapt to environmental changes, whole genome gene expression profiles can be analysed. Moreover, utilising a network topology based on gene relationships may facilitate interpreting this vast amount of information, and extracting significant patterns within the networks. Results Interpreting expression levels as pixels with grey value intensities and network topology as relationships between pixels, allows for an image-like representation of cellular metabolism. While the topology of a regular image is a lattice grid, biological networks demonstrate scale-free architecture and thus advanced image processing methods such as wavelet transforms cannot directly be applied. In the study reported here, one-dimensional enzyme-enzyme pairs were tracked to reveal sub-graphs of a biological interaction network which showed significant adaptations to a changing environment. As a case study, the response of the hetero-fermentative bacterium E. coli to oxygen deprivation was investigated. With our novel method, we detected, as expected, an up-regulation in the pathways of hexose nutrients up-take and metabolism and formate fermentation. Furthermore, our approach revealed a down-regulation in iron processing as well as the up-regulation of the histidine biosynthesis pathway. The latter may reflect an adaptive response of E. coli against an increasingly acidic environment due to the excretion of acidic products during anaerobic growth in a batch culture. Conclusion Based on microarray expression profiling data of prokaryotic cells exposed to fundamental treatment changes, our novel technique proved to extract system changes for a rather broad spectrum of the biochemical network.

  2. Piecewise linear and Boolean models of chemical reaction networks.

    Science.gov (United States)

    Veliz-Cuba, Alan; Kumar, Ajit; Josić, Krešimir

    2014-12-01

    Models of biochemical networks are frequently complex and high-dimensional. Reduction methods that preserve important dynamical properties are therefore essential for their study. Interactions in biochemical networks are frequently modeled using Hill functions ([Formula: see text]). Reduced ODEs and Boolean approximations of such model networks have been studied extensively when the exponent [Formula: see text] is large. However, while the case of small constant [Formula: see text] appears in practice, it is not well understood. We provide a mathematical analysis of this limit and show that a reduction to a set of piecewise linear ODEs and Boolean networks can be mathematically justified. The piecewise linear systems have closed-form solutions that closely track those of the fully nonlinear model. The simpler, Boolean network can be used to study the qualitative behavior of the original system. We justify the reduction using geometric singular perturbation theory and compact convergence, and illustrate the results in network models of a toggle switch and an oscillator.

  3. Piecewise linear and Boolean models of chemical reaction networks

    Science.gov (United States)

    Veliz-Cuba, Alan; Kumar, Ajit; Josić, Krešimir

    2014-01-01

    Models of biochemical networks are frequently complex and high-dimensional. Reduction methods that preserve important dynamical properties are therefore essential for their study. Interactions in biochemical networks are frequently modeled using Hill functions (xn/(Jn + xn)). Reduced ODEs and Boolean approximations of such model networks have been studied extensively when the exponent n is large. However, while the case of small constant J appears in practice, it is not well understood. We provide a mathematical analysis of this limit, and show that a reduction to a set of piecewise linear ODEs and Boolean networks can be mathematically justified. The piecewise linear systems have closed form solutions that closely track those of the fully nonlinear model. The simpler, Boolean network can be used to study the qualitative behavior of the original system. We justify the reduction using geometric singular perturbation theory and compact convergence, and illustrate the results in network models of a toggle switch and an oscillator. PMID:25412739

  4. Fuzzy clustering of physicochemical and biochemical properties of amino acids.

    Science.gov (United States)

    Saha, Indrajit; Maulik, Ujjwal; Bandyopadhyay, Sanghamitra; Plewczynski, Dariusz

    2012-08-01

    In this article, we categorize presently available experimental and theoretical knowledge of various physicochemical and biochemical features of amino acids, as collected in the AAindex database of known 544 amino acid (AA) indices. Previously reported 402 indices were categorized into six groups using hierarchical clustering technique and 142 were left unclustered. However, due to the increasing diversity of the database these indices are overlapping, therefore crisp clustering method may not provide optimal results. Moreover, in various large-scale bioinformatics analyses of whole proteomes, the proper selection of amino acid indices representing their biological significance is crucial for efficient and error-prone encoding of the short functional sequence motifs. In most cases, researchers perform exhaustive manual selection of the most informative indices. These two facts motivated us to analyse the widely used AA indices. The main goal of this article is twofold. First, we present a novel method of partitioning the bioinformatics data using consensus fuzzy clustering, where the recently proposed fuzzy clustering techniques are exploited. Second, we prepare three high quality subsets of all available indices. Superiority of the consensus fuzzy clustering method is demonstrated quantitatively, visually and statistically by comparing it with the previously proposed hierarchical clustered results. The processed AAindex1 database, supplementary material and the software are available at http://sysbio.icm.edu.pl/aaindex/ .

  5. A biochemical/biophysical 3D FE intervertebral disc model.

    Science.gov (United States)

    Schroeder, Y; Huyghe, J M; van Donkelaar, C C; Ito, K

    2010-10-01

    Present research focuses on different strategies to preserve the degenerated disc. To assure long-term success of novel approaches, favorable mechanical conditions in the disc tissue are essential. To evaluate these, a model is required that can determine internal mechanical conditions which cannot be directly measured as a function of assessable biophysical characteristics. Therefore, the objective is to evaluate if constitutive and material laws acquired on isolated samples of nucleus and annulus tissue can be used directly in a whole-organ 3D FE model to describe intervertebral disc behavior. The 3D osmo-poro-visco-hyper-elastic disc (OVED) model describes disc behavior as a function of annulus and nucleus tissue biochemical composition, organization and specific constituent properties. The description of the 3D collagen network was enhanced to account for smaller fibril structures. Tissue mechanical behavior tests on isolated nucleus and annulus samples were simulated with models incorporating tissue composition to calculate the constituent parameter values. The obtained constitutive laws were incorporated into the whole-organ model. The overall behavior and disc properties of the model were corroborated against in vitro creep experiments of human L4/L5 discs. The OVED model simulated isolated tissue experiments on confined compression and uniaxial tensile test and whole-organ disc behavior. This was possible, provided that secondary fiber structures were accounted for. The fair agreement (radial bulge, axial creep deformation and intradiscal pressure) between model and experiment was obtained using constitutive properties that are the same for annulus and nucleus. Both tissue models differed in the 3D OVED model only by composition. The composition-based modeling presents the advantage of reducing the numbers of material parameters to a minimum and to use tissue composition directly as input. Hence, this approach provides the possibility to describe internal

  6. BALL - biochemical algorithms library 1.3

    Directory of Open Access Journals (Sweden)

    Stöckel Daniel

    2010-10-01

    Full Text Available Abstract Background The Biochemical Algorithms Library (BALL is a comprehensive rapid application development framework for structural bioinformatics. It provides an extensive C++ class library of data structures and algorithms for molecular modeling and structural bioinformatics. Using BALL as a programming toolbox does not only allow to greatly reduce application development times but also helps in ensuring stability and correctness by avoiding the error-prone reimplementation of complex algorithms and replacing them with calls into the library that has been well-tested by a large number of developers. In the ten years since its original publication, BALL has seen a substantial increase in functionality and numerous other improvements. Results Here, we discuss BALL's current functionality and highlight the key additions and improvements: support for additional file formats, molecular edit-functionality, new molecular mechanics force fields, novel energy minimization techniques, docking algorithms, and support for cheminformatics. Conclusions BALL is available for all major operating systems, including Linux, Windows, and MacOS X. It is available free of charge under the Lesser GNU Public License (LPGL. Parts of the code are distributed under the GNU Public License (GPL. BALL is available as source code and binary packages from the project web site at http://www.ball-project.org. Recently, it has been accepted into the debian project; integration into further distributions is currently pursued.

  7. Skin biochemical composition analysis by Raman spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Patricia Karen; Tosato, Maira Gaspar; Alves, Rani de Souza; Martin, Airton Abrahao; Favero, Priscila Pereira; Raniero, Leandro, E-mail: amartin@univap.br [Laboratorio de Espectroscopia Vibracional Biomedica, Instituto de Pesquisa e Desenvolvimento - IP e D, Universidade do Vale do Paraiba - UniVap, Sao Jose dos Campos, SP (Brazil)

    2012-09-15

    Skin aging is characterized by cellular and molecular alterations. In this context, Confocal Raman spectroscopy was used in vivo to measure these biochemical changes as function of the skin depth. In this study we have tried to correlate spectra from pure amino acids to in vivo spectra from volunteers with different ages. This study was performed on 32 volunteers: 11 from Group A (20-23 years), 11 from Group B (39-42 years) and 10 from Group C (59-62 years). For each group, the Raman spectra were measured on the surface (0 mm), 30 +- 3 mm and 60 +- 3 {mu}m below the surface. The results from intergroup comparisons showed that the oldest group had a prevalence of the tyrosine band, but it also presented a decrease in the band centered at 875 cm{sup -1} of pyrrolidone acid. The amide I band centered at 1637 cm{sup -1} that is attributed to collagen, as well as other proteins and lipid, showed a smaller amount of these biomolecules for Group C, which can be explained by the decrease in collagen concentration as a function of age. (author)

  8. PHA bioplastics, biochemicals, and energy from crops.

    Science.gov (United States)

    Somleva, Maria N; Peoples, Oliver P; Snell, Kristi D

    2013-02-01

    Large scale production of polyhydroxyalkanoates (PHAs) in plants can provide a sustainable supply of bioplastics, biochemicals, and energy from sunlight and atmospheric CO(2). PHAs are a class of polymers with various chain lengths that are naturally produced by some microorganisms as storage materials. The properties of these polyesters make them functionally equivalent to many of the petroleum-based plastics that are currently in the market place. However, unlike most petroleum-derived plastics, PHAs can be produced from renewable feedstocks and easily degrade in most biologically active environments. This review highlights research efforts over the last 20 years to engineer the production of PHAs in plants with a focus on polyhydroxybutryrate (PHB) production in bioenergy crops with C(4) photosynthesis. PHB has the potential to be a high volume commercial product with uses not only in the plastics and materials markets, but also in renewable chemicals and feed. The major challenges of improving product yield and plant fitness in high biomass yielding C(4) crops are discussed in detail.

  9. Virtual Interactomics of Proteins from Biochemical Standpoint

    Directory of Open Access Journals (Sweden)

    Jaroslav Kubrycht

    2012-01-01

    Full Text Available Virtual interactomics represents a rapidly developing scientific area on the boundary line of bioinformatics and interactomics. Protein-related virtual interactomics then comprises instrumental tools for prediction, simulation, and networking of the majority of interactions important for structural and individual reproduction, differentiation, recognition, signaling, regulation, and metabolic pathways of cells and organisms. Here, we describe the main areas of virtual protein interactomics, that is, structurally based comparative analysis and prediction of functionally important interacting sites, mimotope-assisted and combined epitope prediction, molecular (protein docking studies, and investigation of protein interaction networks. Detailed information about some interesting methodological approaches and online accessible programs or databases is displayed in our tables. Considerable part of the text deals with the searches for common conserved or functionally convergent protein regions and subgraphs of conserved interaction networks, new outstanding trends and clinically interesting results. In agreement with the presented data and relationships, virtual interactomic tools improve our scientific knowledge, help us to formulate working hypotheses, and they frequently also mediate variously important in silico simulations.

  10. Location-Based Services in Vehicular Networks

    Science.gov (United States)

    Wu, Di

    2013-01-01

    Location-based services have been identified as a promising communication paradigm in highly mobile and dynamic vehicular networks. However, existing mobile ad hoc networking cannot be directly applied to vehicular networking due to differences in traffic conditions, mobility models and network topologies. On the other hand, hybrid architectures…

  11. Multifractal analysis of complex networks

    Institute of Scientific and Technical Information of China (English)

    Wang Dan-Ling; Yu Zu-Guo; Anh V

    2012-01-01

    Complex networks have recently attracted much attention in diverse areas of science and technology.Many networks such as the WWW and biological networks are known to display spatial heterogeneity which can be characterized by their fractal dimensions.Multifractal analysis is a useful way to systematically describe the spatial heterogeneity of both theoretical and experimental fractal patterns.In this paper,we introduce a new box-covering algorithm for muttifractal analysis of complex networks.This algorithm is used to calculate the generalized fractal dimensions Dq of some theoretical networks,namely scale-free networks,small world networks,and random networks,and one kind of real network,namely protein-protein interaction networks of different species.Our numerical results indicate the existence of multifractality in scale-free networks and protein-protein interaction networks,while the multifractal behavior is not clear-cut for small world networks and random networks.The possible variation of Dq due to changes in the parameters of the theoretical network models is also discussed.

  12. Dye-linked D-amino acid dehydrogenases: biochemical characteristics and applications in biotechnology.

    Science.gov (United States)

    Satomura, Takenori; Sakuraba, Haruhiko; Suye, Shin-Ichiro; Ohshima, Toshihisa

    2015-11-01

    Dye-linked D-amino acid dehydrogenases (Dye-DADHs) catalyze the dehydrogenation of free D-amino acids in the presence of an artificial electron acceptor. Although Dye-DADHs functioning in catabolism of L-alanine and as primary enzymes in electron transport chains are widely distributed in mesophilic Gram-negative bacteria, biochemical and biotechnological information on these enzymes remains scanty. This is in large part due to their instability after isolation. On the other hand, in the last decade, several novel types of Dye-DADH have been found in thermophilic bacteria and hyperthermophilic archaea, where they contribute not only to L-alanine catabolism but also to the catabolism of other amino acids, including D-arginine and L-hydroxyproline. In this minireview, we summarize recent developments in our understanding of the biochemical characteristics of Dye-DADHs and their specific application to electrochemical biosensors.

  13. Biochemical mechanisms of insecticide resistance in field population of Dengue vector Aedes aegypti (Diptera: Culicidae.

    Directory of Open Access Journals (Sweden)

    R. Muthusamy

    2014-03-01

    Full Text Available Insecticide resistance has been known to be prevalent in several insect species including mosquito. It has become a major problem in vector control programme due to pesticide resistance through detoxification enzymes. The present study investigated the toxicity of Ae. aegypti to organophosphates and pyrethroid insecticide and biochemical mechanisms involved in insecticide resistance in larval population. Larval bioassay revealed an LC50 value of 0.734 ppm for dichlorvos and 1.140 ppm for λ-cyhalothrin exposure. Biochemical assay revealed increased activity of AChE (0.3 µmole/mg protein and GST in dichlorvos (1-1.5 µmole/mg protein treatment and esterase activity in λ-cyhalothrin treated compared to control activity. These studies suggest that AChE and GST is associated with organophosphate and esterase associated with pyrethroid resistance in Ae. aegypti.

  14. Biochemical studies in Ulva reticulata Forsskal

    Digital Repository Service at National Institute of Oceanography (India)

    Dhargalkar, V.K.

    Major metabolites like proteins, carbohydrates and lipids in the alga Ulva reticulata were estimated. Carbohydrate was found to decrease after December which may perhaps be due to the spore formation and extensive growth of the thallus. Protein...

  15. Risk of dyspepsia and anorexia due to glucagon-like peptide-1 receptor agonists in patients with type 2 diabetes mellitus:a Network Meta-analysis%胰高血糖素样肽1受体激动剂类降糖药致2型糖尿病患者消化不良和厌食发生风险的Network Meta分析

    Institute of Scientific and Technical Information of China (English)

    李志霞; 曾宪涛; 柴三葆; 全晓驰; 武珊珊; 杨智荣; 詹思延; 孙凤

    2015-01-01

    Objective To evaluate the risk of dyspepsia and anorexia due to glucagon-like peptide-1 receptor agonist(GLP-1 RA)in patients with type 2 diabetes mellitus(T2DM). Methods The electronic database of Chinese BioMedical Literature Database( CBMdisc ), Chinese Medical Current Contents( CMCC),Medline,EMbase,the Cochrane Library and web site of ClinicalTrials. gov were searched from inception to May 1st 2014. Those randomized controlled trials whose inclusion criteria including patients with T2DM as the research object,comparisons of GLP-1 RA and placebo or other conventional anti-diabetic drugs as the intervention measures,and dyspepsia and anorexia as the outcomes were collected. A traditional Meta-analysis and a Network Meta-analysis were used and relational graph and rank ordering figure of all the intervention measures were drawn. Results A total of 42 randomized controlled trials were enrolled into this study involving 20 916 patients with T2DM and 13 kinds of intervention measures comprised 7 kinds of GLP-1 RAs( exenatide,exenatide release agent,liraglutide, lixisenatide,taspoglutide, albiglutide, and dulaglutide ), 5 kinds of conventional anti-diabetic drugs ( insulin, metformin, sulfonylureas, sitagliptin, and thiazolidinediones ketones ), and placebo. The traditional Meta-analysis showed that,compared with placebo,the whole of GLP-1 RAs could increase the risks of dyspepsia[odds ratio(OR)=3. 04,95% confidence interval(CI):1. 79-5. 16]and anorexia (OR=2. 57,95%CI:1. 69-3. 91)and there were statistically significant differences(P 1. 00 except for lixisenatide versus sitagliptin )and,of them,dulaglutide was at the greatest risk,48. 91,16. 65,36. 24,and 4. 75 times as high as that of insulin,sulfonylureas,thiazolidinediones ketones,and sitagliptin,respectively. There was no statistically significant difference between two kinds of GLP-1 RAs for risks of dyspepsia and anorexia( all P>0. 05). The risks of dyspepsia and anorexia due to the 13 kinds of intervention

  16. Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.

    Directory of Open Access Journals (Sweden)

    Philipp Thomas

    Full Text Available The accepted stochastic descriptions of biochemical dynamics under well-mixed conditions are given by the Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter is a Monte-Carlo method, which, despite enjoying broad availability in a large number of existing software packages, is computationally expensive due to the huge amounts of ensemble averaging required for obtaining accurate statistical information. The former is a set of coupled differential-difference equations for the probability of the system being in any one of the possible mesoscopic states; these equations are typically computationally intractable because of the inherently large state space. Here we introduce the software package intrinsic Noise Analyzer (iNA, which allows for systematic analysis of stochastic biochemical kinetics by means of van Kampen's system size expansion of the Chemical Master Equation. iNA is platform independent and supports the popular SBML format natively. The present implementation is the first to adopt a complementary approach that combines state-of-the-art analysis tools using the computer algebra system Ginac with traditional methods of stochastic simulation. iNA integrates two approximation methods based on the system size expansion, the Linear Noise Approximation and effective mesoscopic rate equations, which to-date have not been available to non-expert users, into an easy-to-use graphical user interface. In particular, the present methods allow for quick approximate analysis of time-dependent mean concentrations, variances, covariances and correlations coefficients, which typically outperforms stochastic simulations. These analytical tools are complemented by automated multi-core stochastic simulations with direct statistical evaluation and visualization. We showcase iNA's performance by using it to explore the stochastic properties of cooperative and non-cooperative enzyme kinetics and a gene network

  17. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network

    DEFF Research Database (Denmark)

    Förster, Jochen; Famili, I.; Fu, P.;

    2003-01-01

    The metabolic network in the yeast Saccharomyces cerevisiae was reconstructed using currently available genomic, biochemical, and physiological information. The metabolic reactions were compartmentalized between the cytosol and the mitochondria, and transport steps between the compartments...... containing 1175 metabolic reactions and 584 metabolites. The number of gene functions included in the reconstructed network corresponds to similar to16% of all characterized ORFs in S. cerevisiae. Using the reconstructed network, the metabolic capabilities of S. cerevisiae were calculated and compared...

  18. Network Science

    Science.gov (United States)

    Barabási, Albert-László

    2016-07-01

    Preface; Personal introduction; 1. Introduction; 2. Graph theory; 3. Random networks; 4. The scale-free property; 5. The Barabási-Albert model; 6. Evolving networks; 7. Degree correlation; 8. Network robustness; 9. Communities; 10. Spreading phenomena; Index.

  19. Network fingerprint: a knowledge-based characterization of biomedical networks

    Science.gov (United States)

    Cui, Xiuliang; He, Haochen; He, Fuchu; Wang, Shengqi; Li, Fei; Bo, Xiaochen

    2015-01-01

    It can be difficult for biomedical researchers to understand complex molecular networks due to their unfamiliarity with the mathematical concepts employed. To represent molecular networks with clear meanings and familiar forms for biomedical researchers, we introduce a knowledge-based computational framework to decipher biomedical networks by making systematic comparisons to well-studied “basic networks”. A biomedical network is characterized as a spectrum-like vector called “network fingerprint”, which contains similarities to basic networks. This knowledge-based multidimensional characterization provides a more intuitive way to decipher molecular networks, especially for large-scale network comparisons and clustering analyses. As an example, we extracted network fingerprints of 44 disease networks in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The comparisons among the network fingerprints of disease networks revealed informative disease-disease and disease-signaling pathway associations, illustrating that the network fingerprinting framework will lead to new approaches for better understanding of biomedical networks. PMID:26307246

  20. The Biochemical Prognostic Factors of Subclinical Hypothyroidism

    Directory of Open Access Journals (Sweden)

    Myung Won Lee

    2014-06-01

    Full Text Available BackgroundPatients with subclinical hypothyroidism (SHT are common in clinical practice. However, the clinical significance of SHT, including prognosis, has not been established. Further clarifying SHT will be critical in devising a management plan and treatment guidelines for SHT patients. Thus, the aim of this study was to investigate the prognostic factors of SHT.MethodsWe reviewed the medical records of Korean patients who visited the endocrinology outpatient clinic of Severance Hospital from January 2008 to September 2012. Newly-diagnosed patients with SHT were selected and reviewed retrospectively. We compared two groups: the SHT maintenance group and the spontaneous improvement group.ResultsThe SHT maintenance group and the spontaneous improvement group had initial thyroid-stimulating hormone (TSH levels that were significantly different (P=0.035. In subanalysis for subjects with TSH levels between 5 to 10 µIU/mL, the spontaneous improvement group showed significantly lower antithyroid peroxidase antibody (anti-TPO-Ab titer than the SHT maintenance group (P=0.039. Regarding lipid profiles, only triglyceride level, unlike total cholesterol and low density lipoprotein cholesterol, was related to TSH level, which is correlated with the severity of SHT. Diffuse thyroiditis on ultrasonography only contributed to the severity of SHT, not to the prognosis. High sensitivity C-reactive protein and urine iodine excretion, generally regarded as possible prognostic factors, did not show any significant relation with the prognosis and severity of SHT.ConclusionOnly initial TSH level was a definite prognostic factor of SHT. TPO-Ab titer was also a helpful prognostic factor for SHT in cases with mildly elevated TSH. Other than TSH and TPO-Ab, we were unable to validate biochemical prognostic factors in this retrospective study for Korean SHT patients.

  1. Mitochondrial network energetics in the heart.

    Science.gov (United States)

    Aon, Miguel A; Cortassa, Sonia

    2012-01-01

    At the core of eukaryotic aerobic life, mitochondrial function like 'hubs' in the web of energetic and redox processes in cells. In the heart, these networks-extending beyond the complex connectivity of biochemical circuit diagrams and apparent morphology-exhibit collective dynamics spanning several spatiotemporal levels of organization, from the cell, to the tissue, and the organ. The network function of mitochondria, i.e., mitochondrial network energetics, represents an advantageous behavior. Its coordinated action, under normal physiology, provides robustness despite failure in a few nodes, and improves energy supply toward a swiftly changing demand. Extensive diffuse loops, encompassing mitochondrial-cytoplasmic reaction/transport networks, control and regulate energy supply and demand in the heart. Under severe energy crises, the network behavior of mitochondria and associated glycolytic and other metabolic networks collapse, thereby triggering fatal arrhythmias.

  2. From Offline Social Networks to Online Social Networks: Changes in Entrepreneurship

    Directory of Open Access Journals (Sweden)

    Yang SONG

    2015-01-01

    Full Text Available The paper reviewed studies of entrepreneurship based on the emergency of online social networks. Similar to offline social networks, entrepreneurs’ online social networks have their own unique characteristics. We first reviewed the offline network based research on entrepreneurship. Then we reviewed the studies of entrepreneurship in the context of online social networks including those focusing on topics of network structures and network ties. We highlighted online network communities based on the data collected from LinkedIn, Facebook and Twitter. Our research implies that both researcher and entrepreneurs are facing new opportunities due to the emergence of online social networks.

  3. Conducting Due Diligence in China

    Institute of Scientific and Technical Information of China (English)

    CHRIS; DEVONSHIRE-ELLIS

    2008-01-01

    Ninety percent of problems when set- ting up business in China can be avoided by the deployment of due diligence at the front end of the investment planning.Here we point out some of the areas that can hinder a sensible approach to due diligence,the hidden risks and basic checks.The process does not have to be expensive. Land use rights These relate to the status of the land on which your Chinese partner has his prem-

  4. Comparison of the nutritional, biochemical and physiological effects due to milk protein consumption by sedentary and trained rats

    OpenAIRE

    Giovana Ermetice de Almeida Costa

    2010-01-01

    Resumo: A atividade física (AF) de resistência provoca diversas respostas fisiológicas, dentre elas a alteração dos padrões de células sangüíneas e atividade enzimática. Recursos alimentares são freqüentemente utilizados para aumentar o rendimento esportivo e minimizar os danos causados pelo exercício. O tipo de proteína e sua forma são determinantes dos efeitos que estas podem proporcionar. As proteínas do soro do leite (PSL) são fontes de aminoácidos indispensáveis, dentre eles, os de cadei...

  5. 40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

    Science.gov (United States)

    2010-07-01

    ... requirements-biochemical pesticides. 158.2080 Section 158.2080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2080 Experimental use permit data requirements—biochemical pesticides. (a) Sections...

  6. Non-transcriptional regulatory processes shape transcriptional network dynamics.

    Science.gov (United States)

    Ray, J Christian J; Tabor, Jeffrey J; Igoshin, Oleg A

    2011-10-11

    Information about the extra- or intracellular environment is often captured as biochemical signals that propagate through regulatory networks. These signals eventually drive phenotypic changes, typically by altering gene expression programmes in the cell. Reconstruction of transcriptional regulatory networks has given a compelling picture of bacterial physiology, but transcriptional network maps alone often fail to describe phenotypes. Cellular response dynamics are ultimately determined by interactions between transcriptional and non-transcriptional networks, with dramatic implications for physiology and evolution. Here, we provide an overview of non-transcriptional interactions that can affect the performance of natural and synthetic bacterial regulatory networks.

  7. Prosthetic valve endocarditis due to Neisseria elongata subsp. elongata in a patient with Klinefelter's syndrome.

    Science.gov (United States)

    Evans, Morgan; Yazdani, Farah; Malnick, Henry; Shah, Jayesh J; Turner, David P J

    2007-06-01

    A case is reported of prosthetic valve endocarditis due to Neisseria elongata subsp. elongata in a patient with Klinefelter's syndrome. This is believed to be only the third case of endocarditis reported due to this subspecies. N. elongata is difficult to identify, and is morphologically and biochemically similar to Kingella spp. Sequencing of the 16S rRNA gene is useful for identification. The patient was successfully treated with amoxicillin and gentamicin, followed by ceftriaxone.

  8. Modeling Epidemic Network Failures

    DEFF Research Database (Denmark)

    Ruepp, Sarah Renée; Fagertun, Anna Manolova

    2013-01-01

    This paper presents the implementation of a failure propagation model for transport networks when multiple failures occur resulting in an epidemic. We model the Susceptible Infected Disabled (SID) epidemic model and validate it by comparing it to analytical solutions. Furthermore, we evaluate...... the SID model’s behavior and impact on the network performance, as well as the severity of the infection spreading. The simulations are carried out in OPNET Modeler. The model provides an important input to epidemic connection recovery mechanisms, and can due to its flexibility and versatility be used...... to evaluate multiple epidemic scenarios in various network types....

  9. Network susceptibilities: Theory and applications

    Science.gov (United States)

    Manik, Debsankha; Rohden, Martin; Ronellenfitsch, Henrik; Zhang, Xiaozhu; Hallerberg, Sarah; Witthaut, Dirk; Timme, Marc

    2017-01-01

    We introduce the concept of network susceptibilities quantifying the response of the collective dynamics of a network to small parameter changes. We distinguish two types of susceptibilities: vertex susceptibilities and edge susceptibilities, measuring the responses due to changes in the properties of units and their interactions, respectively. We derive explicit forms of network susceptibilities for oscillator networks close to steady states and offer example applications for Kuramoto-type phase-oscillator models, power grid models, and generic flow models. Focusing on the role of the network topology implies that these ideas can be easily generalized to other types of networks, in particular those characterizing flow, transport, or spreading phenomena. The concept of network susceptibilities is broadly applicable and may straightforwardly be transferred to all settings where networks responses of the collective dynamics to topological changes are essential.

  10. [Neurologic complications of subarachnoid hemorrhage due to intracranial aneurysm rupture].

    Science.gov (United States)

    Rama-Maceiras, P; Fàbregas Julià, N; Ingelmo Ingelmo, I; Hernández-Palazón, J

    2010-12-01

    The high rates of morbidity and mortality after subarachnoid hemorrhage due to spontaneous rupture of an intracranial aneurysm are mainly the result of neurologic complications. Sixty years after cerebral vasospasm was first described, this problem remains unsolved in spite of its highly adverse effect on prognosis after aneurysmatic rupture. Treatment is somewhat empirical, given that uncertainties remain in our understanding of the pathophysiology of this vascular complication, which involves structural and biochemical changes in the endothelium and smooth muscle of vessels. Vasospasm that is refractory to treatment leads to cerebral infarction. Prophylaxis, early diagnosis, and adequate treatment of neurologic complications are key elements in the management of vasospasm if neurologic damage, lengthy hospital stays, and increased use of health care resources are to be avoided. New approaches to early treatment of cerebral lesions and cortical ischemia in cases of subarachnoid hemorrhage due to aneurysm rupture should lead to more effective, specific management.

  11. 2011 Biomass Program Platform Peer Review: Biochemical Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Pezzullo, Leslie [Office of Energy Efficiency and Renewable Energy (EERE), Washington, DC (United States)

    2012-02-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the 2011 U.S. Department of Energy Biomass Program’s Biochemical Conversion Platform Review meeting.

  12. Biochemical methane potential (BMP) of solid organic materials

    DEFF Research Database (Denmark)

    Raposo, Francisco; Fernández-Cegrí, V.; De la Rubia, M.A.

    2010-01-01

    This paper describes the results obtained for different participating research groups in an interlaboratory study related to the biochemical methane potential (BMP). In this research work, the full experimental conditions influencing the test such as inoculum, substrate characteristics and experi...

  13. Assessment of biochemical concentrations of vegetation using remote sensing technology

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The main biochemicals (such as lignin, protein, cellulose, sugar, starch, chlorophyll and water) of vegetation are directly or indirectly involved in major ecological processes, such as the functions of terrestrial ecosystems (i.e., nutrient-cycling processes, primary production, and decomposition). Remote sensing techniques provide a very convenient way of data acquisition capable of covering a large area several times during one season, so it can play a unique and essential role provided that we can relate remote sensing measurements to the biochemical characteristics of the Earth surface in a reliable and operational way. The application of remote sensing techniques for the estimation of canopy biochemicals was reviewed. Three methods of estimating biochemical concentrations of vegetation were included in this paper: index, stepwise multiple linear regression, and stepwise multiple linear regression based on a model of the forest crown. In addition, the vitality and potential applying value are stressed.

  14. Serum biochemical parameters of farmed carp (Cyprinus carpio

    Directory of Open Access Journals (Sweden)

    Tanţi Patriche

    2011-04-01

    Full Text Available Despite advances in ichthyo-pathology of recent years, interpretation of fish serum biochemical parameters is often difficult by lack of reference values. That is why to know the value of the serum biochemical parameters can be a useful tool for monitoring health status, detecting illnesses and responses to therapy. This paper provides data concerning biochemical composition of carp serum (Cyprinus carpio bred at Brateş Farm of Institute of Research and Development for Aquatic Ecology, Fishing and Aquaculture from Galaţi and Pleaşa Farm from Ploieşti, Romania. In research conducted onCyprinus carpio were determined following serum biochemical parameters: glucose (GLU, total proteins (TP, blood urea nitrogen (BUN, cholesterol (CHOL, triglyceride (TRIG, sodium (Na, potassium (K, calcium (Ca, magnesium (Mg, phosphorus (P, iron (Fe.

  15. Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli.

    Science.gov (United States)

    Morris, Melody K; Saez-Rodriguez, Julio; Clarke, David C; Sorger, Peter K; Lauffenburger, Douglas A

    2011-03-01

    Predictive understanding of cell signaling network operation based on general prior knowledge but consistent with empirical data in a specific environmental context is a current challenge in computational biology. Recent work has demonstrated that Boolean logic can be used to create context-specific network models by training proteomic pathway maps to dedicated biochemical data; however, the Boolean formalism is restricted to characterizing protein species as either fully active or inactive. To advance beyond this limitation, we propose a novel form of fuzzy logic sufficiently flexible to model quantitative data but also sufficiently simple to efficiently construct models by training pathway maps on dedicated experimental measurements. Our new approach, termed constrained fuzzy logic (cFL), converts a prior knowledge network (obtained from literature or interactome databases) into a computable model that describes graded values of protein activation across multiple pathways. We train a cFL-converted network to experimental data describing hepatocytic protein activation by inflammatory cytokines and demonstrate the application of the resultant trained models for three important purposes: (a) generating experimentally testable biological hypotheses concerning pathway crosstalk, (b) establishing capability for quantitative prediction of protein activity, and (c) prediction and understanding of the cytokine release phenotypic response. Our methodology systematically and quantitatively trains a protein pathway map summarizing curated literature to context-specific biochemical data. This process generates a computable model yielding successful prediction of new test data and offering biological insight into complex datasets that are difficult to fully analyze by intuition alone.

  16. Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli.

    Directory of Open Access Journals (Sweden)

    Melody K Morris

    2011-03-01

    Full Text Available Predictive understanding of cell signaling network operation based on general prior knowledge but consistent with empirical data in a specific environmental context is a current challenge in computational biology. Recent work has demonstrated that Boolean logic can be used to create context-specific network models by training proteomic pathway maps to dedicated biochemical data; however, the Boolean formalism is restricted to characterizing protein species as either fully active or inactive. To advance beyond this limitation, we propose a novel form of fuzzy logic sufficiently flexible to model quantitative data but also sufficiently simple to efficiently construct models by training pathway maps on dedicated experimental measurements. Our new approach, termed constrained fuzzy logic (cFL, converts a prior knowledge network (obtained from literature or interactome databases into a computable model that describes graded values of protein activation across multiple pathways. We train a cFL-converted network to experimental data describing hepatocytic protein activation by inflammatory cytokines and demonstrate the application of the resultant trained models for three important purposes: (a generating experimentally testable biological hypotheses concerning pathway crosstalk, (b establishing capability for quantitative prediction of protein activity, and (c prediction and understanding of the cytokine release phenotypic response. Our methodology systematically and quantitatively trains a protein pathway map summarizing curated literature to context-specific biochemical data. This process generates a computable model yielding successful prediction of new test data and offering biological insight into complex datasets that are difficult to fully analyze by intuition alone.

  17. Green networking

    CERN Document Server

    Krief, Francine

    2012-01-01

    This book focuses on green networking, which is an important topic for the scientific community composed of engineers, academics, researchers and industrialists working in the networking field. Reducing the environmental impact of the communications infrastructure has become essential with the ever increasing cost of energy and the need for reducing global CO2 emissions to protect our environment.Recent advances and future directions in green networking are presented in this book, including energy efficient networks (wired networks, wireless networks, mobile networks), adaptive networ

  18. Anatomical and biochemical investigation of primary brain tumours

    Energy Technology Data Exchange (ETDEWEB)

    Del Sole, A. [Univ. di Milano (Italy); Falini, A. [Univ. Vita e Salute (Italy). IRCCS; Ravasi, L.; Ottobrini, L.; Lucignani, G. [Univ. di Milano (Italy). Ist. di Scienze Radiologiche; De Marchis, D. [Univ. di Milano-Bicocca (Italy); Bombardieri, E. [Istituto Nazionale dei Tumori, Milano (Italy)

    2001-12-01

    Cancerous transformation entails major biochemical changes including modifications of the energy metabolism of the cell, e.g. utilisation of glucose and other substrates, protein synthesis, and expression of receptors and antigens. Tumour growth also leads to heterogeneity in blood flow owing to focal necrosis, angiogenesis and metabolic demands, as well as disruption of transport mechanisms of substrates across cell membranes and other physiological boundaries such as the blood-brain barrier. All these biochemical, histological and anatomical changes can be assessed with emission tomography, X-ray computed tomography (CT), magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS). Whereas anatomical imaging is aimed at the diagnosis of brain tumours, biochemical imaging is better suited for tissue characterisation. The identification of a tumoural mass and the assessment of its size and vascularisation are best achieved with X-ray CT and MRI, while biochemical imaging can provide additional information that is crucial for tumour classification, differential diagnosis and follow-up. As the assessment of variables such as water content, appearance of cystic lesions and location of the tumour are largely irrelevant for tissue characterisation, a number of probes have been employed for the assessment of the biochemical features of tumours. Since biochemical changes may be related to the growth rate of cancer cells, they can be thought of as markers of tumour cell proliferation. Biochemical imaging with radionuclides of processes that occur at a cellular level provides information that complements findings obtained by anatomical imaging aimed at depicting structural, vascular and histological changes. This review focusses on the clinical application of anatomical brain imaging and biochemical assessment with positron emission tomography, single-photon emission tomography and MRS in the diagnosis of primary brain tumours, as well as in follow-up. (orig.)

  19. Diabetes, Biochemical Markers of Bone Turnover, Diabetes Control, and Bone

    OpenAIRE

    Starup-Linde, Jakob

    2013-01-01

    Diabetes mellitus is known to have late complications including micro vascular and macro vascular disease. This review focuses on another possible area of complication regarding diabetes; bone. Diabetes may affect bone via bone structure, bone density, and biochemical markers of bone turnover. The aim of the present review is to examine in vivo from humans on biochemical markers of bone turnover in diabetics compared to non-diabetics. Furthermore, the effect of glycemic control on bone marker...

  20. Stroke due to Hematologic Aspects

    Institute of Scientific and Technical Information of China (English)

    刘泽霖

    2004-01-01

    @@ Stroke due to ‘cerebral vein thrombosis' (CVT) is commonly used to refer to thrombosis of the cerebral venous system, including either dural venous sinuses, or deep and superficial (cortical) cerebral veins. CVT are frightening events due to the severity of their clinical manifestations and their high mortality rate (up to 30% in some casereports).The clinical signs and symptoms of CVT are relatively nonspecific: they include headache, papilledema, vomiting,seizures, focal neurological deficits (motor or sensory) and impaired consciousness. CVT has long been considered as rare and mostly infection-related event; moreover, due to its nonspecific clinical manifestations, the diagnosis has been difficult, delayed and could often be made only post mortem.

  1. The Thermotolerant Yeast Kluyveromyces marxianus Is a Useful Organism for Structural and Biochemical Studies of Autophagy.

    Science.gov (United States)

    Yamamoto, Hayashi; Shima, Takayuki; Yamaguchi, Masaya; Mochizuki, Yuh; Hoshida, Hisashi; Kakuta, Soichiro; Kondo-Kakuta, Chika; Noda, Nobuo N; Inagaki, Fuyuhiko; Itoh, Takehiko; Akada, Rinji; Ohsumi, Yoshinori

    2015-12-04

    Autophagy is a conserved degradation process in which autophagosomes are generated by cooperative actions of multiple autophagy-related (Atg) proteins. Previous studies using the model yeast Saccharomyces cerevisiae have provided various insights into the molecular basis of autophagy; however, because of the modest stability of several Atg proteins, structural and biochemical studies have been limited to a subset of Atg proteins, preventing us from understanding how multiple Atg proteins function cooperatively in autophagosome formation. With the goal of expanding the scope of autophagy research, we sought to identify a novel organism with stable Atg proteins that would be advantageous for in vitro analyses. Thus, we focused on a newly isolated thermotolerant yeast strain, Kluyveromyces marxianus DMKU3-1042, to utilize as a novel system elucidating autophagy. We developed experimental methods to monitor autophagy in K. marxianus cells, identified the complete set of K. marxianus Atg homologs, and confirmed that each Atg homolog is engaged in autophagosome formation. Biochemical and bioinformatic analyses revealed that recombinant K. marxianus Atg proteins have superior thermostability and solubility as compared with S. cerevisiae Atg proteins, probably due to the shorter primary sequences of KmAtg proteins. Furthermore, bioinformatic analyses showed that more than half of K. marxianus open reading frames are relatively short in length. These features make K. marxianus proteins broadly applicable as tools for structural and biochemical studies, not only in the autophagy field but also in other fields.

  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. Properties of herbage in relation to equine dysautonomia: biochemical composition and antioxidant and prooxidant actions.

    Science.gov (United States)

    McGorum, B C; Fry, S C; Wallace, G; Coenen, K; Robb, J; Williamson, G; Aruoma, O I

    2000-06-01

    To investigate the etiology of equine dysautonomia (ED), a degenerative polyneuropathy affecting grazing horses, the biochemical composition and antioxidant/prooxidant activities of aqueous extracts of plants collected from ED pastures were determined. Plants collected immediately after an outbreak of ED had reduced antioxidant and weak prooxidant activities when compared with control plants (plants collected from ED pastures out of ED season and control plants from ED pastures that were grown under favorable conditions). ED plants also had significantly increased concentrations of fructose and low molecular weight phenolic compounds, significantly more of one amino acid zone (probably valine), significantly less tartaric acid, and a nonsignificant decrease in ascorbic acid content when compared with control plants from ED pastures that were grown under favorable conditions. These findings suggest that ED plants may be under oxidative stress, possibly due to chilling, drought, or fungal colonization. However, experimental drought and chilling of plants did not reproduce the biochemical alterations identified in ED plants. It is possible that the altered biochemical content of ingested plants may contribute, directly or indirectly, to the development of ED in grazing horses.

  4. Activating and inhibiting connections in biological network dynamics

    Directory of Open Access Journals (Sweden)

    Knight Rob

    2008-12-01

    Full Text Available Abstract Background Many studies of biochemical networks have analyzed network topology. Such work has suggested that specific types of network wiring may increase network robustness and therefore confer a selective advantage. However, knowledge of network topology does not allow one to predict network dynamical behavior – for example, whether deleting a protein from a signaling network would maintain the network's dynamical behavior, or induce oscillations or chaos. Results Here we report that the balance between activating and inhibiting connections is important in determining whether network dynamics reach steady state or oscillate. We use a simple dynamical model of a network of interacting genes or proteins. Using the model, we study random networks, networks selected for robust dynamics, and examples of biological network topologies. The fraction of activating connections influences whether the network dynamics reach steady state or oscillate. Conclusion The activating fraction may predispose a network to oscillate or reach steady state, and neutral evolution or selection of this parameter may affect the behavior of biological networks. This principle may unify the dynamics of a wide range of cellular networks. Reviewers Reviewed by Sergei Maslov, Eugene Koonin, and Yu (Brandon Xia (nominated by Mark Gerstein. For the full reviews, please go to the Reviewers' comments section.

  5. Telecommunication networks

    CERN Document Server

    Iannone, Eugenio

    2011-01-01

    Many argue that telecommunications network infrastructure is the most impressive and important technology ever developed. Analyzing the telecom market's constantly evolving trends, research directions, infrastructure, and vital needs, Telecommunication Networks responds with revolutionized engineering strategies to optimize network construction. Omnipresent in society, telecom networks integrate a wide range of technologies. These include quantum field theory for the study of optical amplifiers, software architectures for network control, abstract algebra required to design error correction co

  6. KNOWLEDGE TRANSFER THROUGH NETWORKS

    Directory of Open Access Journals (Sweden)

    GYÖRGY ATTILA

    2012-06-01

    Full Text Available Knowledge is a vital intangible asset for any organization and cannot be valued exactly due its special form of materialization. Although we have this drawback, a scientifically established value should be used in order to measure the performance of knowledge holders. A correct valuation helps to know the worth of assets offered in exploitation. Exploitation of this resource could be done in several different ways, but integration in knowledge networks seems to generate best efficiency ratio. Networks offer the possibility to change information, to obtain new information, to build further ideas arose from network partners or to develop together new ideas. Thus, networks assure conditions to optimize the members’ knowledge portfolios. Optimization of knowledge usage creates benefits for network members. These benefits could be profits (if members are private companies or social welfare (if members are looking after collective purposes. Taxonomy of knowledge networks is diverse, permitting an adaptation to the needs of members. Networks permit a large scale of heterogeneity. Since an important part of new knowledge creating costs is covered from public budgetary resources, a special development is recorded at those networks which are exclusively or partly organized in the public sector or benefit by participation from the public sector.

  7. Biochemical and Immunological Modifications in Saliva of SFINCSS Experiment

    Science.gov (United States)

    Volozhin, A. I.; Kuznetsov, P. A.; Ilyin, V. K.; Kuzmina, E. M.; Sashkina, T. I.

    of Russian and foreign volunteers and was divided onto 3 parts, 4 persons per each depending on isolation time. All the individuals were isolated days in confined habitat.: 1st group - 240 days; 2nd and 3rd - 110 days each. 1 group members were individually orally instructed on perfect dental care, 2nd group members were given an instruction how to use means for mouth and dental care. 3rd group was only studied but was not given any instruction. Biochemical studies of non-stimulated mixed saliva were done before and after the experiment. protein concentration increased due to increasing of it's density. The urea concentration did not changed. The glucose concentration changes were flexible within norm values before experiment and sufficiently increased after the experiment only in two individuals. Natrium and potassium level was stable and did not differed from normal value before and after the experiment. There was a tendency of decreasing of calcium concentration in volunteers saliva as a result of their long-term isolation. Concentration of non-organic phosphor did not changed. Alanintranspherase (ALT) activity increased 2-3 times in 3 volunteers, aspartataminotranspherase (AST) activity increased in three people. No changes were revealed for alpha-amilase. Content of IgG increased which fact indirectly suggest bacterial overgrowth. No changes in IgA and SIgA were estimated. of urea and glucose didn't changed. The concentration of calcium had a tendency to decrease, no changes for non-organic phosphor, potassium and natrium. However ALT and AST values sufficiently increased as well as IgG concentration. isolation, despite of individual measures of mouth and dental care, and in group of 110-day isolation with no hygienic measures. Significant indices of mouth and dental state in long-term isolation are levels of: protein ALT, AST (cytoplasmatic enzymes), and IgG.

  8. Comparative Life Cycle Assessment of Lignocellulosic Ethanol Production: Biochemical Versus Thermochemical Conversion

    Science.gov (United States)

    Mu, Dongyan; Seager, Thomas; Rao, P. Suresh; Zhao, Fu

    2010-10-01

    Lignocellulosic biomass can be converted into ethanol through either biochemical or thermochemical conversion processes. Biochemical conversion involves hydrolysis and fermentation while thermochemical conversion involves gasification and catalytic synthesis. Even though these routes produce comparable amounts of ethanol and have similar energy efficiency at the plant level, little is known about their relative environmental performance from a life cycle perspective. Especially, the indirect impacts, i.e. emissions and resource consumption associated with the production of various process inputs, are largely neglected in previous studies. This article compiles material and energy flow data from process simulation models to develop life cycle inventory and compares the fossil fuel consumption, greenhouse gas emissions, and water consumption of both biomass-to-ethanol production processes. The results are presented in terms of contributions from feedstock, direct, indirect, and co-product credits for four representative biomass feedstocks i.e., wood chips, corn stover, waste paper, and wheat straw. To explore the potentials of the two conversion pathways, different technological scenarios are modeled, including current, 2012 and 2020 technology targets, as well as different production/co-production configurations. The modeling results suggest that biochemical conversion has slightly better performance on greenhouse gas emission and fossil fuel consumption, but that thermochemical conversion has significantly less direct, indirect, and life cycle water consumption. Also, if the thermochemical plant operates as a biorefinery with mixed alcohol co-products separated for chemicals, it has the potential to achieve better performance than biochemical pathway across all environmental impact categories considered due to higher co-product credits associated with chemicals being displaced. The results from this work serve as a starting point for developing full life cycle

  9. Endocarditis Due to Citrobacter Freundii

    OpenAIRE

    Reyes, Cesar V.; Folwarkiw, Oksana

    1984-01-01

    The etiologic association of acute bacterial endocarditis with the Citrobacter species has been rare, although it is one of the opportunistic organisms that afflicts the elderly, neonates, the debilitated and immunocompromised. We report a case of endocarditis due to Citrobacter freundii.

  10. Elephantine nose due to rhinoentomophthoromycosis.

    Science.gov (United States)

    Ghorpade, Ashok; Sarma, Podila S A; Iqbal, Syed Md

    2006-01-01

    Rhinoentomophthoromycosis in an immunocompetent Indian male due to Basidiobolus species resulting in a huge (elephantine) nasal deformity, is reported. The diagnosis was done by demonstration of hyphae in direct tissue smear examination in potassium hydroxide, histopathological examination and by cultural characteristics. He showed an excellent response to oral potassium iodide solution.

  11. Computation of steady-state probability distributions in stochastic models of cellular networks.

    Directory of Open Access Journals (Sweden)

    Mark Hallen

    2011-10-01

    Full Text Available Cellular processes are "noisy". In each cell, concentrations of molecules are subject to random fluctuations due to the small numbers of these molecules and to environmental perturbations. While noise varies with time, it is often measured at steady state, for example by flow cytometry. When interrogating aspects of a cellular network by such steady-state measurements of network components, a key need is to develop efficient methods to simulate and compute these distributions. We describe innovations in stochastic modeling coupled with approaches to this computational challenge: first, an approach to modeling intrinsic noise via solution of the chemical master equation, and second, a convolution technique to account for contributions of extrinsic noise. We show how these techniques can be combined in a streamlined procedure for evaluation of different sources of variability in a biochemical network. Evaluation and illustrations are given in analysis of two well-characterized synthetic gene circuits, as well as a signaling network underlying the mammalian cell cycle entry.

  12. Chemical and biochemical activities of sonochemically synthesized poly(N-isopropyl acrylamide)/silica nanocomposite

    Science.gov (United States)

    Chowdhury, Pranesh; Saha, Swadhin Kr; Guha, Arun; Saha, Samar Kr

    2012-11-01

    Poly(N-isopropyl acrylamide) (PNIPA) grafted mesoporous silica nanoparticles (MPSNP) leading to novel inorganic/organic core-shell nanocomposite has been synthesized sonochemically in an aqueous medium without additives like cross-linker, hydrophobic agent, organic solvent. The colloidal stability of MPSNP is enhanced significantly due to encapsulation of the polymer. The composites are characterized by TEM, FTIR and TGA. The chemical and biochemical activities of the sonochemically synthesized materials have been studied in the light of reaction with acid-base, protein adsorption, antimicrobial activity, biocompatibility and nonthrombogenic property. Advantages of sonochemical synthesis compared to other techniques have been evaluated.

  13. An efficient optical biochemical sensor based on a polyatomic photonic crystal ring resonator

    Science.gov (United States)

    Wang, Daobin; Liu, Yanjun; Yuan, Lihua; Lei, Jingli; Li, Xiaoxiao; wu, Gang; Hou, Shanglin

    2016-08-01

    In this paper, we introduce and investigate a design concept for a polyatomic photonic crystal ring resonator (PCRR). In contrast to conventional sensors, this PCRR comprises two different branching waveguides (WG), which are all oriented in the same lattice direction, but with different optical propagation properties due to the binary nature of the diatomic square lattice. Based on this new scheme, an on-chip biochemical sensor is proposed. Electromagnetic analysis, PWE and FDTD numerical techniques, were used to investigate the sensing performance. Our results show that such a sensor can efficiently detect small changes in the refractive index within the sensing area.

  14. Biochemical and histological characterization of tomato mutants

    Directory of Open Access Journals (Sweden)

    Carolina C. Monteiro

    2012-06-01

    Full Text Available Biochemical responses inherent to antioxidant systems as well morphological and anatomical properties of photomorphogenic, hormonal and developmental tomato mutants were investigated. Compared to the non-mutant Micro-Tom (MT, we observed that the malondialdehyde (MDA content was enhanced in the diageotropica (dgt and lutescent (l mutants, whilst the highest levels of hydrogen peroxide (H2O2 were observed in high pigment 1 (hp1 and aurea (au mutants. The analyses of antioxidant enzymes revealed that all mutants exhibited reduced catalase (CAT activity when compared to MT. Guaiacol peroxidase (GPOX was enhanced in both sitiens (sit and notabilis (not mutants, whereas in not mutant there was an increase in ascorbate peroxidase (APX. Based on PAGE analysis, the activities of glutathione reductase (GR isoforms III, IV, V and VI were increased in l leaves, while the activity of superoxide dismutase (SOD isoform III was reduced in leaves of sit, epi, Never ripe (Nr and green flesh (gf mutants. Microscopic analyses revealed that hp1 and au showed an increase in leaf intercellular spaces, whereas sit exhibited a decrease. The au and hp1 mutants also exhibited a decreased in the number of leaf trichomes. The characterization of these mutants is essential for their future use in plant development and ecophysiology studies, such as abiotic and biotic stresses on the oxidative metabolism.Neste trabalho, analisamos as respostas bioquímicas inerentes ao sistema antioxidante, assim como propriedades morfológicas e anatômicas de mutantes fotomorfogenéticos e hormonais de tomateiro. Comparados ao não mutante Micro-Tom (MT, observamos que o conteúdo de malondialdeído (MDA aumentou nos mutantes diageotropica (dgt e lutescent (l, enquanto os maiores níveis de H2O2 foram encontrados nos mutantes high pigment 1 (hp1 e aurea (au. Análises de enzimas antioxidantes mostraram que todos os mutantes reduziram a atividade de catalase (CAT quando comparado a MT. A

  15. BIOCHEMICAL STUDIES ON NIGERIAN MONODORA TENUIFOLIA SEED

    Directory of Open Access Journals (Sweden)

    Ekeanyanwu Raphael Chukwuma

    2013-01-01

    Full Text Available The nutritive constituents of the seeds of Monodora tenuifolia were analyzed to augment the available information on Monodora tenuifolia research. Blood glucose and lipid profile were investigated on the flavonoid rich fraction of M. tenuifolia in rats. The composition (gkg-1 of alkaloids, cyanogenic glycosides, tannins and flavonoids were 13.3±0.1, 21.2×10-2±0.6, 1.3±0.1, 1.7±0.1 and 11.7±1.1 respectively. The proximate composition (gkg-1 of M. tenuifolia seed were crude fibre (262.3±1.2, crude protein (82.6±1.0, crude fat (349.9±1.9, ash (49.9±0.6, moisture (190.0±0.00 and carbohydrate (65.5±4.7. Analysis of the minerals content (gkg-1 yielded calcium (864.0±29.38, sodium (2752.0±140.35, iron (3.34±0.06, zinc (5.26±0.08, potassium (326.4±13.06, magnesium (342.9±13.71 and phosphorus (9.52±0.17, while vitamin analysis yielded vitamin A (10.05±0.17 iu/100 g, C (56.40±0.14 gkg-1 and E (11.71±0.87 iu /100 g, thiamine (0.11±0.01 gkg-1, niacin (0.46±0.32 gkg-1 and riboflavin (0.04±0.01 gkg-1. The results of amino acid analysis showed the total amino acid of M. tenuifolia seed was 71.78 of crude protein. The total essential amino acid with Histidine was calculated to be 29.24 of the crude protein. The antinutrient analysis of M. tenuifolia shows it contained total phenol (0.8±0.0 gkg-1, oxalates (4.09±1.17 gkg-1, phytates (0.012±0.42 gkg-1 and trypsin inhibitor (0.230±0.42 iu/g. The main fatty acids of the seed oil are linoleic acid (401.7 g kg-1, oleic acid (346.1 g kg-1 and palmitic acid (122.61 g kg-1. The LD50 of the flavonoid-rich fraction was found to be above 5000 mg kg-1 b.w. After the day 14 study, biochemical markers such as triacylglycerol, very low density lipoprotein increased significantly (p0.05 effect was observed on the blood glucose and lipid profile of wistar albino rats compared with the control. The result shows that M. tenuifolia seed is rich

  16. Interconnected networks

    CERN Document Server

    2016-01-01

    This volume provides an introduction to and overview of the emerging field of interconnected networks which include multi layer or multiplex networks, as well as networks of networks. Such networks present structural and dynamical features quite different from those observed in isolated networks. The presence of links between different networks or layers of a network typically alters the way such interconnected networks behave – understanding the role of interconnecting links is therefore a crucial step towards a more accurate description of real-world systems. While examples of such dissimilar properties are becoming more abundant – for example regarding diffusion, robustness and competition – the root of such differences remains to be elucidated. Each chapter in this topical collection is self-contained and can be read on its own, thus making it also suitable as reference for experienced researchers wishing to focus on a particular topic.

  17. Handover Control for WCDMA Femtocell Networks

    CERN Document Server

    Chowdhury, Mostafa Zaman

    2010-01-01

    The ability to seamlessly switch between the macro networks and femtocell networks is a key driver for femtocell network deployment. The handover procedures for the integrated femtocell/macrocell networks differ from the existing handovers. Some modifications of existing network and protocol architecture for the integration of femtocell networks with the existing macrocell networks are also essential. These modifications change the signal flow for handover procedures due to different 2-tier cell (macrocell and femtocell) environment. The handover between two networks should be performed with minimum signaling. A frequent and unnecessary handover is another problem for hierarchical femtocell/macrocell network environment that must be minimized. This work studies the details mobility management schemes for small and medium scale femtocell network deployment. To do that, firstly we present two different network architectures for small scale and medium scale WCDMA femtocell deployment. The details handover call f...

  18. Discovering Network Structure Beyond Communities

    OpenAIRE

    Nishikawa, Takashi; Adilson E Motter

    2011-01-01

    To understand the formation, evolution, and function of complex systems, it is crucial to understand the internal organization of their interaction networks. Partly due to the impossibility of visualizing large complex networks, resolving network structure remains a challenging problem. Here we overcome this difficulty by combining the visual pattern recognition ability of humans with the high processing speed of computers to develop an exploratory method for discovering groups of nodes chara...

  19. Scalable and Practical Nonblocking Switching Networks

    Institute of Scientific and Technical Information of China (English)

    Si-Qing Zheng; Ashwin Gumaste

    2006-01-01

    Large-scale strictly nonblocking (SNB) and wide-sense nonblocking (WSNB) networks may be infeasible due to their high cost. In contrast, rearrangeable nonblocking (RNB) networks are more scalable because of their much lower cost. However, RNB networks are not suitable for circuit switching. In this paper, the concept of virtual nonblockingness is introduced. It is shown that a virtual nonblocking (VNB) network functions like an SNB or WSNB network, but it is constructed with the cost of an RNB network. The results indicate that for large-scale circuit switching applications, it is only needed to build VNB networks.

  20. Maternal mortality due to trauma.

    Science.gov (United States)

    Romero, Vivian Carolina; Pearlman, Mark

    2012-02-01

    Maternal mortality is an important indicator of adequacy of health care in our society. Improvements in the obstetric care system as well as advances in technology have contributed to reduction in maternal mortality rates. Trauma complicates up to 7% of all pregnancies and has emerged as the leading cause of maternal mortality, becoming a significant concern for the public health system. Maternal mortality secondary to trauma can often be prevented by coordinated medical care, but it is essential that caregivers recognize the unique situation of providing simultaneous care to 2 patients who have a complex physiologic relationship. Optimal management of the pregnant trauma victim requires a multidisciplinary team, where the obstetrician plays a central role. This review focuses on the incidence of maternal mortality due to trauma, the mechanisms involved in traumatic injury, the important anatomic and physiologic changes that may predispose to mortality due to trauma, and finally, preventive strategies that may decrease the incidence of traumatic maternal death.

  1. Network maintenance

    CERN Multimedia

    GS Department

    2009-01-01

    A site-wide network maintenance operation has been scheduled for Saturday 28 February. Most of the network devices of the general purpose network will be upgraded to a newer software version, in order to improve our network monitoring capabilities. This will result in a series of short (2-5 minutes) random interruptions everywhere on the CERN sites throughout the day. This upgrade will not affect the Computer Centre itself, Building 613, the Technical Network and the LHC experiments, dedicated networks at the pits. For further details of this intervention, please contact Netops by phone 74927 or e-mail mailto:Netops@cern.ch. IT/CS Group

  2. Network maintenance

    CERN Multimedia

    IT Department

    2009-01-01

    A site wide network maintenance has been scheduled for Saturday 28 February. Most of the network devices of the General Purpose network will be upgraded to a newer software version, in order to improve our network monitoring capabilities. This will result in a series of short (2-5 minutes) random interruptions everywhere on the CERN sites along this day. This upgrade will not affect: the Computer centre itself, building 613, the Technical Network and the LHC experiments dedicated networks at the pits. Should you need more details on this intervention, please contact Netops by phone 74927 or email mailto:Netops@cern.ch. IT/CS Group

  3. Autoerotic death due to electrocution

    Directory of Open Access Journals (Sweden)

    Piotr Arkuszewski

    2014-08-01

    Full Text Available Autoerotic death is a very rare case in forensic medicine. It is usually caused by asphyxia, but other reasons are also possible. Herein we present a case of autoerotic death due to electrocution caused by a self-made electrical device. The device was constructed to increase sexual feelings through stimulation of the scrotal area.

  4. Visual Impairment Due to Lissencephaly

    OpenAIRE

    Marqués-Fernández, V. E.; Sánchez-Tocino, H.; Escudero-Caro, M.T.; Cancho-Candela, R.; García-Zamora, M.

    2016-01-01

    Lissencephaly is a rare disorder due to abnormal neural migration, causing neurological impairment and clinically characterised by mental retardation and epilepsy. Any disturbance of the visual pathway can cause loss of vision. The authors describe a case of a 6-year-old boy referred to the ophthalmologist presenting poor bilateral vision. This child had no other known medical conditions, and neurological examination was completely normal. Only when a magnetic resonance imaging was made that ...

  5. The Biochemical Toxin Arsenal from Ant Venoms

    Directory of Open Access Journals (Sweden)

    Axel Touchard

    2016-01-01

    Full Text Available Ants (Formicidae represent a taxonomically diverse group of hymenopterans with over 13,000 extant species, the majority of which inject or spray secretions from a venom gland. The evolutionary success of ants is mostly due to their unique eusociality that has permitted them to develop complex collaborative strategies, partly involving their venom secretions, to defend their nest against predators, microbial pathogens, ant competitors, and to hunt prey. Activities of ant venom include paralytic, cytolytic, haemolytic, allergenic, pro-inflammatory, insecticidal, antimicrobial, and pain-producing pharmacologic activities, while non-toxic functions include roles in chemical communication involving trail and sex pheromones, deterrents, and aggregators. While these diverse activities in ant venoms have until now been largely understudied due to the small venom yield from ants, modern analytical and venomic techniques are beginning to reveal the diversity of toxin structure and function. As such, ant venoms are distinct from other venomous animals, not only rich in linear, dimeric and disulfide-bonded peptides and bioactive proteins, but also other volatile and non-volatile compounds such as alkaloids and hydrocarbons. The present review details the unique structures and pharmacologies of known ant venom proteinaceous and alkaloidal toxins and their potential as a source of novel bioinsecticides and therapeutic agents.

  6. The Biochemical Toxin Arsenal from Ant Venoms.

    Science.gov (United States)

    Touchard, Axel; Aili, Samira R; Fox, Eduardo Gonçalves Paterson; Escoubas, Pierre; Orivel, Jérôme; Nicholson, Graham M; Dejean, Alain

    2016-01-20

    Ants (Formicidae) represent a taxonomically diverse group of hymenopterans with over 13,000 extant species, the majority of which inject or spray secretions from a venom gland. The evolutionary success of ants is mostly due to their unique eusociality that has permitted them to develop complex collaborative strategies, partly involving their venom secretions, to defend their nest against predators, microbial pathogens, ant competitors, and to hunt prey. Activities of ant venom include paralytic, cytolytic, haemolytic, allergenic, pro-inflammatory, insecticidal, antimicrobial, and pain-producing pharmacologic activities, while non-toxic functions include roles in chemical communication involving trail and sex pheromones, deterrents, and aggregators. While these diverse activities in ant venoms have until now been largely understudied due to the small venom yield from ants, modern analytical and venomic techniques are beginning to reveal the diversity of toxin structure and function. As such, ant venoms are distinct from other venomous animals, not only rich in linear, dimeric and disulfide-bonded peptides and bioactive proteins, but also other volatile and non-volatile compounds such as alkaloids and hydrocarbons. The present review details the unique structures and pharmacologies of known ant venom proteinaceous and alkaloidal toxins and their potential as a source of novel bioinsecticides and therapeutic agents.

  7. Securing underwater wireless communication networks

    OpenAIRE

    Domingo Aladrén, Mari Carmen

    2011-01-01

    Underwater wireless communication networks are particularly vulnerable to malicious attacks due to the high bit error rates, large and variable propagation delays, and low bandwidth of acoustic channels. The unique characteristics of the underwater acoustic communication channel, and the differences between underwater sensor networks and their ground-based counterparts require the development of efficient and reliable security mechanisms. In this article, a compl...

  8. 4G Mobile Broadband Networks

    DEFF Research Database (Denmark)

    Kardaras, Georgios

    access radio networks becomes a necessity not only due to the high operation and maintenance cost but also because of the major trend of providing ecofriendly solutions across the industry. The benefits of incorporating remote radio modules in next-generation mobile networks were investigated...

  9. Network Ambivalence

    Directory of Open Access Journals (Sweden)

    Patrick Jagoda

    2015-08-01

    Full Text Available The language of networks now describes everything from the Internet to the economy to terrorist organizations. In distinction to a common view of networks as a universal, originary, or necessary form that promises to explain everything from neural structures to online traffic, this essay emphasizes the contingency of the network imaginary. Network form, in its role as our current cultural dominant, makes scarcely imaginable the possibility of an alternative or an outside uninflected by networks. If so many things and relationships are figured as networks, however, then what is not a network? If a network points towards particular logics and qualities of relation in our historical present, what others might we envision in the future? In  many ways, these questions are unanswerable from within the contemporary moment. Instead of seeking an avant-garde approach (to move beyond networks or opting out of networks (in some cases, to recover elements of pre-networked existence, this essay proposes a third orientation: one of ambivalence that operates as a mode of extreme presence. I propose the concept of "network aesthetics," which can be tracked across artistic media and cultural forms, as a model, style, and pedagogy for approaching interconnection in the twenty-first century. The following essay is excerpted from Network Ambivalence (Forthcoming from University of Chicago Press. 

  10. Network Coded Software Defined Networking

    DEFF Research Database (Denmark)

    Krigslund, Jeppe; Hansen, Jonas; Roetter, Daniel Enrique Lucani;

    2015-01-01

    Software Defined Networking (SDN) and Network Coding (NC) are two key concepts in networking that have garnered a large attention in recent years. On the one hand, SDN's potential to virtualize services in the Internet allows a large flexibility not only for routing data, but also to manage...... buffering, scheduling, and processing over the network. On the other hand, NC has shown great potential for increasing robustness and performance when deployed on intermediate nodes in the network. This new paradigm changes the dynamics of network protocols, requiring new designs that exploit its potential....... This paper advocates for the use of SDN to bring about future Internet and 5G network services by incorporating network coding (NC) functionalities. The inherent flexibility of both SDN and NC provides a fertile ground to envision more efficient, robust, and secure networking designs, that may also...

  11. The network researchers' network

    DEFF Research Database (Denmark)

    Henneberg, Stephan C.; Jiang, Zhizhong; Naudé, Peter;

    2009-01-01

    The Industrial Marketing and Purchasing (IMP) Group is a network of academic researchers working in the area of business-to-business marketing. The group meets every year to discuss and exchange ideas, with a conference having been held every year since 1984 (there was no meeting in 1987...... components in some detail. The egonets of three of the original 'founding fathers' are examined in detail, and we draw comparisons as to how their publishing strategies vary. Finally, the paper draws some more general conclusions as to the insights that SNA can bring to those working within business-to-business...... marketing....

  12. Autocatalysis in reaction networks.

    Science.gov (United States)

    Deshpande, Abhishek; Gopalkrishnan, Manoj

    2014-10-01

    The persistence conjecture is a long-standing open problem in chemical reaction network theory. It concerns the behavior of solutions to coupled ODE systems that arise from applying mass-action kinetics to a network of chemical reactions. The idea is that if all reactions are reversible in a weak sense, then no species can go extinct. A notion that has been found useful in thinking about persistence is that of "critical siphon." We explore the combinatorics of critical siphons, with a view toward the persistence conjecture. We introduce the notions of "drainable" and "self-replicable" (or autocatalytic) siphons. We show that: Every minimal critical siphon is either drainable or self-replicable; reaction networks without drainable siphons are persistent; and nonautocatalytic weakly reversible networks are persistent. Our results clarify that the difficulties in proving the persistence conjecture are essentially due to competition between drainable and self-replicable siphons.

  13. Biochemical characterisation during seed development of oil palm (Elaeis guineensis).

    Science.gov (United States)

    Kok, Sau-Yee; Namasivayam, Parameswari; Ee, Gwendoline Cheng-Lian; Ong-Abdullah, Meilina

    2013-07-01

    Developmental biochemical information is a vital base for the elucidation of seed physiology and metabolism. However, no data regarding the biochemical profile of oil palm (Elaeis guineensis Jacq.) seed development has been reported thus far. In this study, the biochemical changes in the developing oil palm seed were investigated to study their developmental pattern. The biochemical composition found in the seed differed significantly among the developmental stages. During early seed development, the water, hexose (glucose and fructose), calcium and manganese contents were present in significantly high levels compared to the late developmental stage. Remarkable changes in the biochemical composition were observed at 10 weeks after anthesis (WAA): the dry weight and sucrose content increased significantly, whereas the water content and hexose content declined. The switch from a high to low hexose/sucrose ratio could be used to identify the onset of the maturation phase. At the late stage, dramatic water loss occurred, whereas the content of storage reserves increased progressively. Lauric acid was the most abundant fatty acid found in oil palm seed starting from 10 WAA.

  14. Network workshop

    DEFF Research Database (Denmark)

    Bruun, Jesper; Evans, Robert Harry

    2014-01-01

    This paper describes the background for, realisation of and author reflections on a network workshop held at ESERA2013. As a new research area in science education, networks offer a unique opportunity to visualise and find patterns and relationships in complicated social or academic network data....... These include student relations and interactions and epistemic and linguistic networks of words, concepts and actions. Network methodology has already found use in science education research. However, while networks hold the potential for new insights, they have not yet found wide use in the science education...... research community. With this workshop, participants were offered a way into network science based on authentic educational research data. The workshop was constructed as an inquiry lesson with emphasis on user autonomy. Learning activities had participants choose to work with one of two cases of networks...

  15. Network workshop

    DEFF Research Database (Denmark)

    Bruun, Jesper; Evans, Robert Harry

    2014-01-01

    research community. With this workshop, participants were offered a way into network science based on authentic educational research data. The workshop was constructed as an inquiry lesson with emphasis on user autonomy. Learning activities had participants choose to work with one of two cases of networks......This paper describes the background for, realisation of and author reflections on a network workshop held at ESERA2013. As a new research area in science education, networks offer a unique opportunity to visualise and find patterns and relationships in complicated social or academic network data....... These include student relations and interactions and epistemic and linguistic networks of words, concepts and actions. Network methodology has already found use in science education research. However, while networks hold the potential for new insights, they have not yet found wide use in the science education...

  16. Petri Net Based Metabolic Network Parameters Fitting with GPU Acceleration%Petri Net Based Metabolic Network Parameters Fitting with GPU Acceleration

    Institute of Scientific and Technical Information of China (English)

    Gao, Jun; Zhu, Ruixin; Liu, Qi; Cao, Zhiwei

    2011-01-01

    Classical Petri net has been applied into biological analysis, especially as a qualitative model for biochemical pathways analysis, but lack of the ability for quantitative kinetic simulations. In our study, we presented an integra- tion work of the qualitative model--Petri nets with the quantitative approach-ordinary differential equations (ODEs) for the modeling and analysis of metabolic networks. As an application of our study, the computational modeling of arachidonic acid (AA) biochemical network was provided. A Petri net was set up to present the constraint-based dynamic simulations on AA metabolic network combined with the validated ODEs model. Furthermore, Graphics Processing Unit (GPU) was adopted to accelerate the calculation of kinetic parameters unavailable from experi- ments. Our results have indicated that the proposed simulation method was practicable and useful with GPU accel- eration, and provides new clues for the large-scale qualitative and quantitative models of biochemical networks.

  17. Endocarditis due to Kingella kingae.

    Science.gov (United States)

    Odum, L; Jensen, K T; Slotsbjerg, T D

    1984-06-01

    Four cases of endocarditis due to Kingella kingae are described in compromised patients. All had primary heart disease, and two had systemic lupus erythematosis and congenital heart defect respectively, in addition. Confirmation of Kingella kingae was made in one case at autopsy. The literature on 11 cases of endocarditis, 2 bacteremia, 4 osteomyelitis, 5 septic arthritis and 1 intervertebral disc infection, all caused by Kingella kingae, is reviewed. Our findings confirm that the organism is of low pathogenicity. Children may be predisposed to infection with Kingella kingae.

  18. Tardive akathisia due to sulpiride.

    Science.gov (United States)

    López de Munain, A; Poza, J J; Gorospe, A; Arce, A; Martí Massó, J F

    1994-10-01

    A 56 year-old woman who suffered from parkinsonism, oro-lingual dyskinesia (OLD) and tardive akathisia (TA) due to sulpiride is reported. OLD and TA appeared after sulpiride withdrawal. The patient was successfully treated with tetrabenazine even a mild parkinsonism was present. TA seems to be related with an apparent dopaminergic hyperactivity and it has to be differentiated of other neuroleptic-induced movement disorders such as restless legs syndrome in order of an appropriate treatment. Sulpiride has the same possible side effects than classic neuroleptics.

  19. Anaphylaxis Due to Head Injury

    Directory of Open Access Journals (Sweden)

    Bruner, Heather C.

    2015-05-01

    Full Text Available Both anaphylaxis and head injury are often seen in the emergency department, but they are rarely seen in combination. We present a case of a 30-year-old woman who presented with anaphylaxis with urticaria and angioedema following a minor head injury. The patient responded well to intramuscular epinephrine without further complications or airway compromise. Prior case reports have reported angioedema from hereditary angioedema during dental procedures and maxillofacial surgery, but there have not been any cases of first-time angioedema or anaphylaxis due to head injury. [West J Emerg Med. 2015;16(3:435–437.

  20. Interference due to coherence swapping

    Indian Academy of Sciences (India)

    Arun Kumar Pati; Marek Zukowski

    2001-02-01

    We propose a method called ‘coherence swapping’ which enables us to create superposition of a particle in two distinct paths, which is fed with initially incoherent, independent radiation. This phenomenon is also present for the charged particles, and can be used to swap the effect of flux line due to the Aharonov–Bohm effect. We propose an optical version of experimental set-up to test the coherence swapping. The phenomenon, which is simpler than entanglement swapping or teleportation, raises some fundamental questions about the true nature of wave-particle duality, and also opens up the possibility of studying the quantum erasure from a new angle.

  1. Network science.

    Science.gov (United States)

    Barabási, Albert-László

    2013-03-28

    Professor Barabási's talk described how the tools of network science can help understand the Web's structure, development and weaknesses. The Web is an information network, in which the nodes are documents (at the time of writing over one trillion of them), connected by links. Other well-known network structures include the Internet, a physical network where the nodes are routers and the links are physical connections, and organizations, where the nodes are people and the links represent communications.

  2. Networked Identities

    DEFF Research Database (Denmark)

    Ryberg, Thomas; Larsen, Malene Charlotte

    2008-01-01

    of CoPs we shall argue that the metaphor or theory of networked learning is itself confronted with some central tensions and challenges that need to be addressed. We then explore these theoretical and analytic challenges to the network metaphor, through an analysis of a Danish social networking site. We...

  3. Simulation of biochemical reactions with time-dependent rates by the rejection-based algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Thanh, Vo Hong, E-mail: vo@cosbi.eu [The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068 (Italy); Priami, Corrado, E-mail: priami@cosbi.eu [The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068 (Italy); Department of Mathematics, University of Trento, Trento (Italy)

    2015-08-07

    We address the problem of simulating biochemical reaction networks with time-dependent rates and propose a new algorithm based on our rejection-based stochastic simulation algorithm (RSSA) [Thanh et al., J. Chem. Phys. 141(13), 134116 (2014)]. The computation for selecting next reaction firings by our time-dependent RSSA (tRSSA) is computationally efficient. Furthermore, the generated trajectory is exact by exploiting the rejection-based mechanism. We benchmark tRSSA on different biological systems with varying forms of reaction rates to demonstrate its applicability and efficiency. We reveal that for nontrivial cases, the selection of reaction firings in existing algorithms introduces approximations because the integration of reaction rates is very computationally demanding and simplifying assumptions are introduced. The selection of the next reaction firing by our approach is easier while preserving the exactness.

  4. Lignin plays a negative role in the biochemical process for producing lignocellulosic biofuels.

    Science.gov (United States)

    Zeng, Yining; Zhao, Shuai; Yang, Shihui; Ding, Shi-You

    2014-06-01

    A biochemical platform holds the most promising route toward lignocellulosic biofuels, in which polysaccharides are hydrolyzed by cellulase enzymes into simple sugars and fermented to ethanol by microbes. However, these polysaccharides are cross-linked in the plant cell walls with the hydrophobic network of lignin that physically impedes enzymatic deconstruction. A thermochemical pretreatment process is often required to remove or delocalize lignin, which may also generate inhibitors that hamper enzymatic hydrolysis and fermentation. Here we review recent advances in understanding lignin structure in the plant cell walls and the negative roles of lignin in the processes of converting biomass to biofuels. Perspectives and future directions to improve the biomass conversion process are also discussed.

  5. Survey on Opportunistic Networks in Delay Tolerant Mobile Sensor Networks

    Directory of Open Access Journals (Sweden)

    Koushik.C.P

    2016-02-01

    Full Text Available Delay Tolerant Network is an emerging research field in Mobile sensor network. It use forwarding technique to transmit the message from source to destination, there is no complete path between sources to destination. Due to mobility of nodes there is frequent change in node paten and difficult to find the path, there is chance that message keep on forwarded inside the network. In this paper we made detail survey on Opportunistic Routing Protocol in mobile network, and in that node getting the message form neighbor node and moving away from Sink. We proposed a technique in Gradient based Routing Protocol to solve node moving away from sink with message.

  6. Click Chemistry-Mediated Nanosensors for Biochemical Assays.

    Science.gov (United States)

    Chen, Yiping; Xianyu, Yunlei; Wu, Jing; Yin, Binfeng; Jiang, Xingyu

    2016-01-01

    Click chemistry combined with functional nanoparticles have drawn increasing attention in biochemical assays because they are promising in developing biosensors with effective signal transformation/amplification and straightforward signal readout for clinical diagnostic assays. In this review, we focus on the latest advances of biochemical assays based on Cu (I)-catalyzed 1, 3-dipolar cycloaddition of azides and alkynes (CuAAC)-mediated nanosensors, as well as the functionalization of nanoprobes based on click chemistry. Nanoprobes including gold nanoparticles, quantum dots, magnetic nanoparticles and carbon nanomaterials are covered. We discuss the advantages of click chemistry-mediated nanosensors for biochemical assays, and give perspectives on the development of click chemistry-mediated approaches for clinical diagnosis and other biomedical applications.

  7. Click Chemistry-Mediated Nanosensors for Biochemical Assays

    Science.gov (United States)

    Chen, Yiping; Xianyu, Yunlei; Wu, Jing; Yin, Binfeng; Jiang, Xingyu

    2016-01-01

    Click chemistry combined with functional nanoparticles have drawn increasing attention in biochemical assays because they are promising in developing biosensors with effective signal transformation/amplification and straightforward signal readout for clinical diagnostic assays. In this review, we focus on the latest advances of biochemical assays based on Cu (I)-catalyzed 1, 3-dipolar cycloaddition of azides and alkynes (CuAAC)-mediated nanosensors, as well as the functionalization of nanoprobes based on click chemistry. Nanoprobes including gold nanoparticles, quantum dots, magnetic nanoparticles and carbon nanomaterials are covered. We discuss the advantages of click chemistry-mediated nanosensors for biochemical assays, and give perspectives on the development of click chemistry-mediated approaches for clinical diagnosis and other biomedical applications. PMID:27217831

  8. The Development of a Biochemical Profile of Acacia Honey by Identifying Biochemical Determinants of its Quality

    Directory of Open Access Journals (Sweden)

    Liviu Alexandru MARGHITAS

    2010-09-01

    Full Text Available Codex Alimentarius Standard, EU Legislation and National Standards state honey authenticity. Authenticity in respect of production (to prevent adulteration and authenticity in respect of geographical and botanical origin are the two main aspects of general honey authenticity. Quality of honey depends on the plant source, the chemical composition of these plants as well, as on the climatic conditions and soil mineral composition. Romanian acacia (Robinia pseudoacacia honey that came from the most important Transylvanian massif (Valea lui Mihai, Bihor County, Romania was evaluated for authenticity by pollen-analysis, several physico-chemical analyses, including sugar profile and mineral content. As polyphenolic content could be also an important factor for botanical authentification, HPLC-DAD-MS analyses were performed to assess the fingerprint of this important secondary plant metabolite. Statistical data were processed in order to develop a biochemical profile of this type of honey and the main quality categories identification. The results of physico-chemical analysis demonstrated that the tested honey samples could be framed into monofloral type of acacia honeys. The analysis of acacia honeys originating from Valea lui Mihai, Romania, showed that polyphenolic profile (phenolic acids and flavonoids could be used as a complementary method for authenticity determination together with pollen analysis and other physico-chemical analysis.

  9. Biochemical piezoresistive sensors based on pH- and glucose-sensitive hydrogels for medical applications

    Directory of Open Access Journals (Sweden)

    Schmidt Ulrike

    2016-09-01

    Full Text Available Many conventional analysis techniques to detect chemical or biological species are able to achieve a high detection sensitivity, however, they are equipment- or time-expensive due to a multi-step procedure. In this work we describe sensor concepts using piezoresistive pressure sensor chips with integrated analyte-sensitive hydrogels, that enable inexpensive and robust biochemical sensors which are miniaturizable and in-line capable. Biocompatible hydrogels were developed and tested for pH- and glucose-monitoring during the chemical and biochemical processes. For that, monomer mixtures based on hydroxypropyl methacrylate HPMA, 2-(dimethylaminoethyl methacrylate DMAEMA, tetraethylene glycol dimethacrylate TEGDMA and ethylene glycol EG were photo-polymerized. By means of carbodiimide chemistry, glucose oxidase was bound to the pH-sensitive HPMA/DMAEMA/TEGDMA/EG hydrogel squares causing the glucose-sensitivity. The crosslinked hydrogels were integrated in piezoresistive pressure sensors of different designs. pH- and glucose-depending reversible gel swelling processes were observed by means of the output voltage of dip sensors and of a novel implantable flexible sensor set-up. Due to its biocompatible components, the latter could be used inside the human body monitoring physiological blood values, for example glucose.

  10. Behavioural and biochemical alterations in Penaeus monodon post-larvae diet-exposed to inorganic mercury.

    Science.gov (United States)

    Harayashiki, Cyntia Ayumi Yokota; Reichelt-Brushett, Amanda J; Liu, Lei; Butcher, Paul

    2016-12-01

    Mercury is a metal naturally present in the environment with concentrations in aquatic systems increasing annually due to human activities. This represents a great concern mainly due to its high toxicity to organisms and consequences for human health. Most studies regarding the toxic effect of mercury have focussed on freshwater species using water as the exposure and uptake pathway. In contrast, the present study investigated the effects of dietary exposure of mercury to the marine crustacean Penaeus monodon post-larvae during 96 h to evaluate changes in behaviour (swimming activity and risk taken) and in biochemical biomarkers [acetylcholinesterase (AChE) and glutathione S-transferase (GST)]. Results showed a decrease in swimming activity with an increase in mercury exposure, but no changes were observed regarding the behavioural response 'risk taken'. Prawns from medium (0.56 μg g(-1)) and high (1.18 μg g(-1)) treatments had their GST activity reduced in relation to the beginning of experiment (time 0), while AChE activity was increased in the low (0.15 μg g(-1)) treatment in relation to time 0. In the present study, behaviour analysis were clearer than biochemical biomarkers and results might indicate P. monodon populations from a mercury contaminated environment might be at risk, since the behavioural alterations observed increases the risk of predation.

  11. Inference of Gene Regulatory Network Based on Local Bayesian Networks.

    Science.gov (United States)

    Liu, Fei; Zhang, Shao-Wu; Guo, Wei-Feng; Wei, Ze-Gang; Chen, Luonan

    2016-08-01

    The inference of gene regulatory networks (GRNs) from expression data can mine the direct regulations among genes and gain deep insights into biological processes at a network level. During past decades, numerous computational approaches have been introduced for inferring the GRNs. However, many of them still suffer from various problems, e.g., Bayesian network (BN) methods cannot handle large-scale networks due to their high computational complexity, while information theory-based methods cannot identify the directions of regulatory interactions and also suffer from false positive/negative problems. To overcome the limitations, in this work we present a novel algorithm, namely local Bayesian network (LBN), to infer GRNs from gene expression data by using the network decomposition strategy and false-positive edge elimination scheme. Specifically, LBN algorithm first uses conditional mutual information (CMI) to construct an initial network or GRN, which is decomposed into a number of local networks or GRNs. Then, BN method is employed to generate a series of local BNs by selecting the k-nearest neighbors of each gene as its candidate regulatory genes, which significantly reduces the exponential search space from all possible GRN structures. Integrating these local BNs forms a tentative network or GRN by performing CMI, which reduces redundant regulations in the GRN and thus alleviates the false positive problem. The final network or GRN can be obtained by iteratively performing CMI and local BN on the tentative network. In the iterative process, the false or redundant regulations are gradually removed. When tested on the benchmark GRN datasets from DREAM challenge as well as the SOS DNA repair network in E.coli, our results suggest that LBN outperforms other state-of-the-art methods (ARACNE, GENIE3 and NARROMI) significantly, with more accurate and robust performance. In particular, the decomposition strategy with local Bayesian networks not only effectively reduce

  12. A New Method for Computing Attention Network Scores and Relationships between Attention Networks

    OpenAIRE

    Yi-Feng Wang; Qian Cui; Feng Liu; Ya-Jun Huo; Feng-Mei Lu; Heng Chen; Hua-Fu Chen

    2014-01-01

    The attention network test (ANT) is a reliable tool to detect the efficiency of alerting, orienting, and executive control networks. However, studies using the ANT obtained inconsistent relationships between attention networks due to two reasons: on the one hand, the inter-network relationships of attention subsystems were far from clear; on the other hand, ANT scores in previous studies were disturbed by possible inter-network interactions. Here we proposed a new computing method by dissecti...

  13. Overall view of chemical and biochemical weapons.

    Science.gov (United States)

    Pitschmann, Vladimír

    2014-06-04

    This article describes a brief history of chemical warfare, which culminated in the signing of the Chemical Weapons Convention. It describes the current level of chemical weapons and the risk of using them. Furthermore, some traditional technology for the development of chemical weapons, such as increasing toxicity, methods of overcoming chemical protection, research on natural toxins or the introduction of binary technology, has been described. In accordance with many parameters, chemical weapons based on traditional technologies have achieved the limit of their development. There is, however, a big potential of their further development based on the most recent knowledge of modern scientific and technical disciplines, particularly at the boundary of chemistry and biology. The risk is even higher due to the fact that already, today, there is a general acceptance of the development of non-lethal chemical weapons at a technologically higher level. In the future, the chemical arsenal will be based on the accumulation of important information from the fields of chemical, biological and toxin weapons. Data banks obtained in this way will be hardly accessible and the risk of their materialization will persist.

  14. Aspects of biochemical effects by hyperthermia

    Energy Technology Data Exchange (ETDEWEB)

    Streffer, C.

    1982-06-01

    Hyperthermia caused an immediate decrease of DNA, RNA, and protein synthesis. The latter process was most sensitive. Initiation of DNA synthesis at the transition from G1-to S-phase and at the start of new replication units were inhibited. These effects were responsible for the growth delay of cells and were potentiated with irradiation. The immediate inhibition of protein synthesis was due mainly to a disaggregation of the synthesizing mechanisms. It led to a decrease of enzyme activities with a short biological half-life, e.g., ornithine decarboxylase. Lysosomal hydrolytic activities might be enhanced after hyperthermia and contribute to tissue damage. During hyperthermia, glycogen breakdown and glucose turnover through glycolysis and the citrate cycle were apparently increased, but after hyperthermia, respiration and glycolysis were reduced. No lactate accumulation occurred, but other acidic metabolites were enhanced and could induce a metabolic acidosis hours later. A glucose load potentiated the effects on respiration and glycolysis. Immediately after hyperthermia, a lactate accumulation was observed under these conditions. A formula is given by which the ratios of reduced to oxidized substrates might indicate the redox state in different cellular compartments, with oxygen pressure, and during other metabolic conditions. Such changes of the intracellular milieu are important for the thermosensitivity of cells.

  15. Overall View of Chemical and Biochemical Weapons

    Directory of Open Access Journals (Sweden)

    Vladimír Pitschmann

    2014-06-01

    Full Text Available This article describes a brief history of chemical warfare, which culminated in the signing of the Chemical Weapons Convention. It describes the current level of chemical weapons and the risk of using them. Furthermore, some traditional technology for the development of chemical weapons, such as increasing toxicity, methods of overcoming chemical protection, research on natural toxins or the introduction of binary technology, has been described. In accordance with many parameters, chemical weapons based on traditional technologies have achieved the limit of their development. There is, however, a big potential of their further development based on the most recent knowledge of modern scientific and technical disciplines, particularly at the boundary of chemistry and biology. The risk is even higher due to the fact that already, today, there is a general acceptance of the development of non-lethal chemical weapons at a technologically higher level. In the future, the chemical arsenal will be based on the accumulation of important information from the fields of chemical, biological and toxin weapons. Data banks obtained in this way will be hardly accessible and the risk of their materialization will persist.

  16. Information theoretical methods to deconvolute genetic regulatory networks applied to thyroid neoplasms

    Science.gov (United States)

    Hernández-Lemus, Enrique; Velázquez-Fernández, David; Estrada-Gil, Jesús K.; Silva-Zolezzi, Irma; Herrera-Hernández, Miguel F.; Jiménez-Sánchez, Gerardo

    2009-12-01

    Most common pathologies in humans are not caused by the mutation of a single gene, rather they are complex diseases that arise due to the dynamic interaction of many genes and environmental factors. This plethora of interacting genes generates a complexity landscape that masks the real effects associated with the disease. To construct dynamic maps of gene interactions (also called genetic regulatory networks) we need to understand the interplay between thousands of genes. Several issues arise in the analysis of experimental data related to gene function: on the one hand, the nature of measurement processes generates highly noisy signals; on the other hand, there are far more variables involved (number of genes and interactions among them) than experimental samples. Another source of complexity is the highly nonlinear character of the underlying biochemical dynamics. To overcome some of these limitations, we generated an optimized method based on the implementation of a Maximum Entropy Formalism (MaxEnt) to deconvolute a genetic regulatory network based on the most probable meta-distribution of gene-gene interactions. We tested the methodology using experimental data for Papillary Thyroid Cancer (PTC) and Thyroid Goiter tissue samples. The optimal MaxEnt regulatory network was obtained from a pool of 25,593,993 different probability distributions. The group of observed interactions was validated by several (mostly in silico) means and sources. For the associated Papillary Thyroid Cancer Gene Regulatory Network (PTC-GRN) the majority of the nodes (genes) have very few links (interactions) whereas a small number of nodes are highly connected. PTC-GRN is also characterized by high clustering coefficients and network heterogeneity. These properties have been recognized as characteristic of topological robustness, and they have been largely described in relation to biological networks. A number of biological validity outcomes are discussed with regard to both the

  17. Technical Network

    CERN Multimedia

    2007-01-01

    In order to optimise the management of the Technical Network (TN), to facilitate understanding of the purpose of devices connected to the TN and to improve security incident handling, the Technical Network Administrators and the CNIC WG have asked IT/CS to verify the "description" and "tag" fields of devices connected to the TN. Therefore, persons responsible for systems connected to the TN will receive e-mails from IT/CS asking them to add the corresponding information in the network database at "network-cern-ch". Thank you very much for your cooperation. The Technical Network Administrators & the CNIC WG

  18. Smart Business Networks Design and Business Genetics

    NARCIS (Netherlands)

    L-F. Pau (Louis-François)

    2006-01-01

    textabstractWith the emergence of smart business networks, agile networks, etc. as important research areas in management, for all the attractiveness of these concepts, a major issue remains around their design and the selection rules. While smart business networks should provide advantages due to t

  19. Modelling delay propagation within an airport network

    NARCIS (Netherlands)

    Pyrgiotis, N.; Malone, K.M.; Odoni, A.

    2013-01-01

    We describe an analytical queuing and network decomposition model developed to study the complex phenomenon of the propagation of delays within a large network of major airports. The Approximate Network Delays (AND) model computes the delays due to local congestion at individual airports and capture

  20. Open Home Networks: the TEAHA Approach

    NARCIS (Netherlands)

    Dijk, van Hylke W.; Scholten, Hans J.; Tobalina, Alvaro; García Muñoz, Victor; Milanini, Stephane; Kung, Antonio; Dini, C.; Smekal, Z.; Lochin, E.; Verma, P.

    2007-01-01

    The current trend for home appliances is networking. Although more and more of these appliances are networked, there is not a standard way of interaction, which restrains the development of services for in-home networks. The lack of standardisation is partly due to a legacy of business interests; wh

  1. Open home networks: the TEAHA approach

    NARCIS (Netherlands)

    Dijk, van Hylke; Scholten, Hans J.; Tobalina, Alvaro; García Muñoz, Victor; Milanini, Stephane; Kung, Antonio

    2006-01-01

    The current trend for home appliances is networking. Although more and more of these appliances are networked, there is not a standard way of interaction, which restrains the development of services for in-home networks. The lack of standardisation is partly due to a legacy of business interests; wh

  2. Field-effect-based multifunctional hybrid sensor module for the determination of both (bio-)chemical and physical parameters

    Science.gov (United States)

    Schoening, Michael J.; Poghossian, Arshak; Schultze, J. Walter; Lueth, Hans

    2002-02-01

    Sensor systems for multi-parameter detection in fluidics usually combine different sensors, which are designed to detect either a physical or (bio-)chemical parameter. Therefore, such systems include a more complicated fabrication technology and measuring set-up. In this work, an ISFET (ion-sensitive field-effect transistor), which is well known as a (bio-)chemical sensor, is utilized as transducer for the detection of both (bio-)chemical and physical parameters. A multifunctional hybrid module for the determination of two (bio-)chemical parameters (pH, penicillin concentration) and three physical parameters (temperature, flow velocity and flow direction) using only two sensor structures, an ion generator and a reference electrode, is realized and its performance has been investigated. Here, a multifunctionality of the sensor system is achieved by means of different sensor arrangements and/or different operation modes. A Ta2O5-gate ISFET was used as transducer for all sensors. A novel time-of-flight type ISFET-based flow-velocity (flow rate) and flow-direction sensor using in-situ electrochemical generation of chemical tracers is presented. Due to the fast response of the ISFET (usually in the millisecond range), an ISFET-based flow sensor is suitable for the measurement of the flow velocity in a wide range. With regard to practical applications, pH measurements with this ISFET were performed in rain droplets.

  3. Physiological and biochemical basis of salmon young ifshes migratory behavior

    Institute of Scientific and Technical Information of China (English)

    Vladimir Ivanovich Martemyanov

    2016-01-01

    The review presents data on structural changes, physiological and biochemical reactions occurring at salmon young fishes during smoltification. It is shown, that young salmon fishes located in fresh water, in the process of smoltification undergo a complex of structural, physiological and biochemical changes directed on preparation of the organism for living in the sea. These changes cause stress reaction which excites young fishes to migrate down the river towards the sea. Measures to improve reproduction of young salmon fishes at fish farms are offered.

  4. The Biochemical Properties of Antibodies and Their Fragments.

    Science.gov (United States)

    Hnasko, Robert M

    2015-01-01

    Immunoglobulins (Ig) or antibodies are powerful molecular recognition tools that can be used to identify minute quantities of a given target analyte. Their antigen-binding properties define both the sensitivity and selectivity of an immunoassay. Understanding the biochemical properties of this class of protein will provide users with the knowledge necessary to select the appropriate antibody composition to maximize immunoassay results. Here we define the general biochemical properties of antibodies and their similarities and differences, explain how these properties influence their functional relationship to an antigen target, and describe a method for the enzymatic fragmentation of antibodies into smaller functional parts.

  5. Collisional Aggregation due to Turbulence

    CERN Document Server

    Pumir, Alain

    2015-01-01

    Collisions between particles suspended in a fluid play an important role in many physical processes. As an example, collisions of microscopic water droplets in clouds are a necessary step in the production of macroscopic raindrops. Collisions of dust grains are also conjectured to be important for planet formation in the gas surrounding young stars, and also to play a role in the dynamics of sand storms. In these processes, collisions are favoured by fast turbulent motions. Here we review recent advances in the understanding of collisional aggregation due to turbulence. We discuss the role of fractal clustering of particles, and caustic singularities of their velocities. We also discuss limitations of the Smoluchowski equation for modelling these processes. These advances lead to a semi-quantitative understanding on the influence of turbulence on collision rates, and point to deficiencies in the current understanding of rainfall and planet formation.

  6. Teaching Biochemical Pathways Using Concept Maps

    Directory of Open Access Journals (Sweden)

    Simon Brown

    2013-08-01

    Full Text Available The interesting paper by Dinarvand and Vaisi-Raygan (1 makes valuable points about a particularly challenging aspect of biochemistry learning and teaching. Their work prompts me to ask two questions and make a comment. First, what do the authors mean by a concept map (CM? A pathway map could be considered a CM, but a CM could cover modes of regulation and kinetics in relation to particular reactions or pathways and there are many other possibilities. Irrespective of this, a CM can get extremely complex if more than a few concepts are involved (2, as can be seen in examples given by Novak (3. This is the fundamental problem of teaching and learning biochemistry (4, which combines the network of pathways, compartmentation, macromol¬ecular structure, regulation, kinetics and some fairly sophisticated chemical concepts.Second, how did the students go about preparing CMs? My experience is that students prefer to use a computer for most tasks, but standard CM software (5 may not be suitable. For example, they often struggle unnec¬essarily to use software to prepare a graphical summary of the structural features of a protein, its precursors and the gene encoding it. This distracts them from the material. My suggestions that pencil and paper might be sufficient are usually met with amazement. Third, as Dinarvand and Vaisi-Raygan (1 make clear, a coherent summary of the metabolism considered in a course in metabolic biochemistry is crucial if students are to appreciate the pathways and their interconn-ection and regulation. For many years I have used an approach in which students collaborate in tutorials to achieve this. The sessions are usually initiated by me drawing the plasma membrane and the mitochondrial membranes on a large board and inviting the students to fill in the blanks (I provide large sheets of paper so that students can make copies. With coaxing, someone volunteers and I explain that the volunteer is not alone because everyone is

  7. An unusual myopathy: speckled muscle fibers due to enlarged mitochondria.

    Science.gov (United States)

    Jeffree, Rosalind L; Wills, Edward J; Harper, Clive

    2007-07-01

    We report a 52-year-old woman who presented with a 6-month history of proximal muscle weakness, elevated serum creatine kinase, and myopathic pattern on electromyography (EMG). Histology of the muscle shows a speckled pattern due to clustering of enlarged mitochondria. The pathology resembles that of selenium deficiency. The patient was found to have borderline low serum selenium and also low vitamin D and thyroid-stimulating hormone. The cause of this unusual myopathy is probably multifactorial. This case is important because the unusual pathological picture represents a potentially treatable myopathy. In addition, we hope that publication of the complex clinical and biochemical abnormalities of this case, in conjunction with other case reports, may facilitate future elucidation of muscle mitochondrial function and dysfunction.

  8. [Meningoencephalitis due to Morganella morganii: a case report].

    Science.gov (United States)

    Ndiaye, M; Sène, M S; Sow, A D; Seck, L B; Coulibaly, T; Diagne, N S; Touré, K; Diop, A G; Ndiaye, M M

    2010-10-01

    A central nervous system infection due to Morganella morganii is uncommon. We report a case diagnosed at the neurological department of Fann teaching hospital in Dakar, Senegal. A 12-year-old boy was hospitalized for acute meningoencephalitis. The CT scan was normal and the study of cerebrospinal fluid (CSF) revealed cytological and biochemical abnormalities and M. morganii. HIV and syphilitic serologies were negative and blood CD4 lymphocyte count showed 354 per mm(3). The treatment with cefotaxime associated with gentamicin for 6 weeks was successful. The outcome of infection depends on many factors such as the onset and quality of treatment, the virulence of the germ and the status of immune system.

  9. Network science

    CERN Document Server

    Barabasi, Albert-Laszlo

    2016-01-01

    Networks are everywhere, from the Internet, to social networks, and the genetic networks that determine our biological existence. Illustrated throughout in full colour, this pioneering textbook, spanning a wide range of topics from physics to computer science, engineering, economics and the social sciences, introduces network science to an interdisciplinary audience. From the origins of the six degrees of separation to explaining why networks are robust to random failures, the author explores how viruses like Ebola and H1N1 spread, and why it is that our friends have more friends than we do. Using numerous real-world examples, this innovatively designed text includes clear delineation between undergraduate and graduate level material. The mathematical formulas and derivations are included within Advanced Topics sections, enabling use at a range of levels. Extensive online resources, including films and software for network analysis, make this a multifaceted companion for anyone with an interest in network sci...

  10. Networking with noise at the molecular, cellular, and population level

    Science.gov (United States)

    Vilar, Jose

    2002-03-01

    The intrinsic stochastic nature of biochemical reactions affects enzymatic and transcriptional networks at different levels. Yet, cells are able to function effectively and consistently amidst such random fluctuations. I will discuss some molecular mechanisms that are able to reduce the intrinsic noise of chemical reactions, how suitable designs can make networks resistant to noise, and what strategies can be used by populations to achieve precise functions.

  11. Gene regulatory networks governing pancreas development.

    Science.gov (United States)

    Arda, H Efsun; Benitez, Cecil M; Kim, Seung K

    2013-04-15

    Elucidation of cellular and gene regulatory networks (GRNs) governing organ development will accelerate progress toward tissue replacement. Here, we have compiled reference GRNs underlying pancreas development from data mining that integrates multiple approaches, including mutant analysis, lineage tracing, cell purification, gene expression and enhancer analysis, and biochemical studies of gene regulation. Using established computational tools, we integrated and represented these networks in frameworks that should enhance understanding of the surging output of genomic-scale genetic and epigenetic studies of pancreas development and diseases such as diabetes and pancreatic cancer. We envision similar approaches would be useful for understanding the development of other organs.

  12. Next generation network management technology

    Science.gov (United States)

    Baras, John S.; Atallah, George C.; Ball, Mike; Goli, Shravan; Karne, Ramesh K.; Kelley, Steve; Kumar, Harsha; Plaisant, Catherine; Roussopoulos, Nick; Schneiderman, Ben; Srinivasarao, Mulugu; Stathatos, Kosta; Teittinen, Marko; Whitefield, David

    1995-01-01

    Today's telecommunications networks are becoming increasingly large, complex, mission critical and heterogeneous in several dimensions. For example, the underlying physical transmission facilities of a given network may be ``mixed media'' (copper, fiber-optic, radio, and satellite); the subnetworks may be acquired from different vendors due to economic, performance, or general availability reasons; the information being transmitted over the network may be ``multimedia'' (video, data, voice, and images) and, finally, varying performance criteria may be imposed e.g., data transfer may require high throughput while the others, whose concern is voice communications, may require low call blocking probability. For these reasons, future telecommunications networks are expected to be highly complex in their services and operations. Due to this growing complexity and the disparity among management systems for individual sub-networks, efficient network management systems have become critical to the current and future success of telecommunications companies. This paper addresses a research and development effort which focuses on prototyping configuration management, since that is the central process of network management and all other network management functions must be built upon it. Our prototype incorporates ergonomically designed graphical user interfaces tailored to the network configuration management subsystem and to the proposed advanced object-oriented database structure. The resulting design concept follows open standards such as Open Systems Interconnection (OSI) and incorporates object oriented programming methodology to associate data with functions, permit customization, and provide an open architecture environment.

  13. Galactorrhea due to psychotropic drugs.

    Science.gov (United States)

    Kropp, S; Ziegenbein, M; Grohmann, R; Engel, R R; Degner, D

    2004-03-01

    Within the drug safety program in psychiatry AMSP ( Arzneimittelsicherheit in der Psychiatrie), severe adverse drug reactions (ADRs) are assessed. Currently 35 psychiatric hospitals and departments are participating in detecting severe ADRs. This paper focuses on prolactin-dependent ADRs such as gynecomastia and galactorrhea due to psychotropic medications. Related to the number of patients surveyed (122,562 from 1993 to 2000), these are rare events (0.03 % or 35 cases). Imputed drugs were mostly antipsychotics, but antidepressants were also imputed in single cases. In the group of antipsychotics, relative frequencies of galactorrhea were highest for amisulpride and risperidone and corresponded to the degree of D2 binding. Galactorrhea assessed as "severe" was accompanied by distressing symptoms such as pain, tension, enlargement of breasts, or soaked clothing. The AMSP data contribute to the knowledge on endocrine ADRs by the large number of patients examined and help clinicians select the appropriate drug if their patients have been prone to for these ADRs in the past.

  14. Rational design of functional and tunable oscillating enzymatic networks

    Science.gov (United States)

    Semenov, Sergey N.; Wong, Albert S. Y.; van der Made, R. Martijn; Postma, Sjoerd G. J.; Groen, Joost; van Roekel, Hendrik W. H.; de Greef, Tom F. A.; Huck, Wilhelm T. S.

    2015-02-01

    Life is sustained by complex systems operating far from equilibrium and consisting of a multitude of enzymatic reaction networks. The operating principles of biology's regulatory networks are known, but the in vitro assembly of out-of-equilibrium enzymatic reaction networks has proved challenging, limiting the development of synthetic systems showing autonomous behaviour. Here, we present a strategy for the rational design of programmable functional reaction networks that exhibit dynamic behaviour. We demonstrate that a network built around autoactivation and delayed negative feedback of the enzyme trypsin is capable of producing sustained oscillating concentrations of active trypsin for over 65 h. Other functions, such as amplification, analog-to-digital conversion and periodic control over equilibrium systems, are obtained by linking multiple network modules in microfluidic flow reactors. The methodology developed here provides a general framework to construct dissipative, tunable and robust (bio)chemical reaction networks.

  15. A network biology model of micronutrient related health

    NARCIS (Netherlands)

    Ommen, B. van; Fairweather-Tait, S.; Freidig, A.; Kardinaal, A.; Scalbert, A.; Wopereis, S.

    2008-01-01

    Micronutrients are involved in specific biochemical pathways and have dedicated functions in the body, but they are also interconnected in complex metabolic networks, such as oxidative-reductive and inflammatory pathways and hormonal regulation, in which the overarching function is to optimise healt

  16. Polynomial analysis of canopy spectra and biochemical component content inversion

    Institute of Scientific and Technical Information of China (English)

    YAN Chunyan; LIU Qiang; NIU Zheng; WANG Jihua; HUANG Wenjiang; LIU Liangyun

    2005-01-01

    A polynomial expression model was developed in this paper to describe directional canopy spectra, and the decomposition of the polynomial expression was used as a tool for retrieving biochemical component content from canopy multi-angle spectra. First, the basic formula of the polynomial expression was introduced and the physical meaning of its terms and coefficients was discussed. Based on this analysis, a complete polynomial expression model and its decomposition method were given. By decomposing the canopy spectra simulated with SAILH model, it shows that the polynomial expression can not only fit well the canopy spectra, but also show the contribution of every order scattering to the whole reflectance. Taking the first scattering coefficients a10 and a01 for example, the test results show that the polynomial coefficients reflect very well the hot spot phenomenon and the effects of viewing angles, LAI and leaf inclination angle on canopy spectra. By coupling the polynomial expression with leaf model PROSPECT, a canopy biochemical component content inversion model was given. In the simulated test, the canopy multi-angle spectra were simulated by two different models, SAILH and 4-SCALE respectively, then the biochemical component content was retrieved by inverting the coupled polynomial expression + PROSPECT model. Results of the simulated test are promising, and when applying the algorithm to measured corn canopy multi-angle spectra, we also get relatively accurate chlorophyll content. It shows that the polynomial analysis provides a new method to get biochemical component content independent of any specific canopy model.

  17. Saliva as research material: Biochemical, physicochemical and practical aspects

    NARCIS (Netherlands)

    Schipper, R.G.; Silletti, E.; Vingerhoeds, M.H.

    2007-01-01

    Whole saliva is a complex mixture of proteins and other molecules which originate from several sources. The biochemical and physicochemical properties of saliva contribute to the numerous functions of saliva in, e.g., speech, maintaining oral and general health, and food processing. Interest in sali

  18. MATLAB-Based Teaching Modules in Biochemical Engineering

    Science.gov (United States)

    Lee, Kilho; Comolli, Noelle K.; Kelly, William J.; Huang, Zuyi

    2015-01-01

    Mathematical models play an important role in biochemical engineering. For example, the models developed in the field of systems biology have been used to identify drug targets to treat pathogens such as Pseudomonas aeruginosa in biofilms. In addition, competitive binding models for chromatography processes have been developed to predict expanded…

  19. Biochemical aspects of pressure tolerance in marine mammals.

    Science.gov (United States)

    Castellini, Michael A; Rivera, Patricia M; Castellini, Judith M

    2002-11-01

    Some marine mammals can dive to depths approaching 2000 m. At these hydrostatic pressures (200 atm), some fish species show alterations in enzyme structure and function that make them pressure-tolerant. Do marine mammals also possess biochemical adaptations to withstand such pressures? In theory, biochemical alterations might occur at the control of enzymatic pathways, by impacting cell membrane fluidity changes or at a higher level, such as cellular metabolism. Studies of marine mammal tissues show evidence of all of these changes, but the results are not consistent across species or diving depth. This review discusses whether the elevated body temperature of marine mammals imparts pressure tolerance at the biochemical level, whether there are cell membrane structural differences in marine mammals and whether whole, living cells from marine mammals alter their metabolism when pressure stressed. We conclude that temperature alone is probably not protective against pressure and that cell membrane composition data are not conclusive. Whole cell studies suggest that marine mammals either respond positively to pressure or are not impacted by pressure. However, the range of tissue types and enzyme systems that have been studied is extremely limited and needs to be expanded before more general conclusions about how these mammals tolerate elevated pressures on a biochemical level can be drawn.

  20. The Stereochemistry of Biochemical Molecules: A Subject to Revisit

    Science.gov (United States)

    Centelles, Josep J.; Imperial, Santiago

    2005-01-01

    Although Fischer's convention for stereoisomers is useful for simple molecules, the stereochemistry of complex biochemical molecules is often poorly indicated in textbooks. This article reports on errors in stereochemistry of complex hydrosoluble vitamin B12 molecule. Twenty-five popular biochemistry textbooks were examined for their treatment of…

  1. [Experiments using rats on Kosmos biosatellites: morphologic and biochemical studies].

    Science.gov (United States)

    Il'in, E A; Kaplanskiĭ, A S; Savina, E A

    1989-01-01

    Results of morphological and biochemical investigations of rats flown on Cosmos biosatellites are discussed. It is emphasized that most changes occurring during exposure to microgravity are directly or indirectly related to lower musculoskeletal loads which in turn produce deconditioning of different physiological systems and organism as a whole. It is concluded that this deconditioning is associated with both metabolic and structural changes.

  2. Biochemical Parameters of Orienteers Competing in a Long Distance Race.

    Science.gov (United States)

    Mikan, Vladimir; And Others

    1992-01-01

    Measured important biochemical parameters in a group of orienteers two hours before beginning and immediately after an orienteering marathon. Found levels of dehydration. Suggests a drinking regimen which is designed for orienteering races. Concludes that no runner having kidney or liver abnormalities or changes in the urine should be allowed to…

  3. Model Based Monitoring and Control of Chemical and Biochemical Processes

    DEFF Research Database (Denmark)

    Huusom, Jakob Kjøbsted

    This presentation will give an overview of the work performed at the department of Chemical and Biochemical Engineering related to process control. A research vision is formulated and related to a number of active projects at the department. In more detail a project describing model estimation...

  4. Evaluation of biological and biochemical quality of whey protein.

    Science.gov (United States)

    Haraguchi, Fabiano Kenji; Pedrosa, Maria Lucia; Paula, Heberth de; Santos, Rinaldo Cardoso dos; Silva, Marcelo Eustáquio

    2010-12-01

    Nutritional and biochemical properties of noncommercial whey protein have been described since 1950. However, comparisons between commercial whey protein for human consumption and casein are rarely found. The aim of this study was to compare biological quality of a commercial whey protein with casein and its effect on biochemical parameters of rats. Thirty-two weanling Fisher rats were divided into three groups and given the following diets: casein group, standard diet (AOAC); whey protein group, modified AOAC diet with whey protein instead of casein; and casein:whey group, modified AOAC diet with 70%:30% casein:whey. A protein-free group was used for determination of endogenous nitrogen losses. Net protein ratio, protein efficiency ratio, and true digestibility were determined, and blood was collected for biochemical analysis. When compared with casein, whey protein showed significant differences for all biological parameters evaluated, as well as for albumin, total protein, total cholesterol, and glucose concentrations. Replacing 30% of casein with whey protein did not affect these parameters. A positive relation among whey protein, high-density lipoprotein-cholesterol, and paraoxonase activity was found. Hepatic or renal dysfunctions were not observed. In conclusion, in comparison with casein, commercial whey protein had higher values of biological parameters, and biochemical evaluation revealed it improved glycemic homeostasis, lipid status, and paraoxonase activity in rats.

  5. Development of a new first-aid biochemical detector

    Science.gov (United States)

    Hu, Jingfei; Liao, Haiyang; Su, Shilin; Ding, Hao; Liu, Suquan

    2016-10-01

    The traditional biochemical detector exhibits poor adaptability, inconvenient carrying and slow detection, which can't meet the needs of first-aid under field condition like natural or man-made disasters etc. Therefore a scheme of first-aid biochemical detector based on MOMES Micro Spectrometer, UV LED and Photodiode was proposed. An optical detection structure combined continuous spectrum sweep with fixed wavelength measurement was designed, which adopted mobile detection optical path consisting of Micro Spectrometer and Halogen Lamp to detect Chloride (Cl-), Creatinine (Cre), Glucose (Glu), Hemoglobin (Hb). The UV LED and Photodiode were designed to detect Potassium (K-), Carbon dioxide (CO2), Sodium (Na+). According to the field diagnosis and treatment requirements, we designed the embedded control hardware circuit and software system, the prototype of first-aid biochemical detector was developed and the clinical trials were conducted. Experimental results show that the sample's absorbance repeatability is less than 2%, the max coefficient of variation (CV) in the batch repeatability test of all 7 biochemical parameters in blood samples is 4.68%, less than the clinical requirements 10%, the correlation coefficient (R2) in the clinical contrast test with AU5800 is almost greater than 0.97. To sum up, the prototype meets the requirements of clinical application.

  6. Integrating Carbon Nanotubes into Microfluidic Chip for Separating Biochemical Compounds

    DEFF Research Database (Denmark)

    Chen, Miaoxiang Max; Mogensen, Klaus Bo; Bøggild, Peter

    2012-01-01

    We present a new type of device to separate biochemical compounds wherein carbon nanotubes (CNTs) are integrated as chromatographic stationary phase. The CNTs were directly grown on the bottom of microfluidic channels on Si/SiO2 substrates by chemical vapor deposition (CVD). Acetylene was used...

  7. Physicochemical and biochemical characterization of biosurfactants released by Lactobacillus strains

    NARCIS (Netherlands)

    Velraeds, MMC; vanderMei, HC; Reid, G; Busscher, HJ

    1996-01-01

    Biosurfactants from Lactobacillus casei subsp. rhamnosus 36 and ATCC 7469, Lactobacillus fermentum B54 and Lactobacillus acidophilus RC14 were isolated from bacteria in their mid-exponential (4-5 h) and stationary growth phases (18 h) and physicochemical and biochemical properties of the freeze-drie

  8. Metstoich--Teaching Quantitative Metabolism and Energetics in Biochemical Engineering

    Science.gov (United States)

    Wong, Kelvin W. W.; Barford, John P.

    2010-01-01

    Metstoich, a metabolic calculator developed for teaching, can provide a novel way to teach quantitative metabolism to biochemical engineering students. It can also introduce biochemistry/life science students to the quantitative aspects of life science subjects they have studied. Metstoich links traditional biochemistry-based metabolic approaches…

  9. Boolean network models of cellular regulation: prospects and limitations.

    Science.gov (United States)

    Bornholdt, Stefan

    2008-08-06

    Computer models are valuable tools towards an understanding of the cell's biochemical regulatory machinery. Possible levels of description of such models range from modelling the underlying biochemical details to top-down approaches, using tools from the theory of complex networks. The latter, coarse-grained approach is taken where regulatory circuits are classified in graph-theoretical terms, with the elements of the regulatory networks being reduced to simply nodes and links, in order to obtain architectural information about the network. Further, considering dynamics on networks at such an abstract level seems rather unlikely to match dynamical regulatory activity of biological cells. Therefore, it came as a surprise when recently examples of discrete dynamical network models based on very simplistic dynamical elements emerged which in fact do match sequences of regulatory patterns of their biological counterparts. Here I will review such discrete dynamical network models, or Boolean networks, of biological regulatory networks. Further, we will take a look at such models extended with stochastic noise, which allow studying the role of network topology in providing robustness against noise. In the end, we will discuss the interesting question of why at all such simple models can describe aspects of biology despite their simplicity. Finally, prospects of Boolean models in exploratory dynamical models for biological circuits and their mutants will be discussed.

  10. Discovering network structure beyond communities.

    Science.gov (United States)

    Nishikawa, Takashi; Motter, Adilson E

    2011-01-01

    To understand the formation, evolution, and function of complex systems, it is crucial to understand the internal organization of their interaction networks. Partly due to the impossibility of visualizing large complex networks, resolving network structure remains a challenging problem. Here we overcome this difficulty by combining the visual pattern recognition ability of humans with the high processing speed of computers to develop an exploratory method for discovering groups of nodes characterized by common network properties, including but not limited to communities of densely connected nodes. Without any prior information about the nature of the groups, the method simultaneously identifies the number of groups, the group assignment, and the properties that define these groups. The results of applying our method to real networks suggest the possibility that most group structures lurk undiscovered in the fast-growing inventory of social, biological, and technological networks of scientific interest.

  11. Discovering Network Structure Beyond Communities

    CERN Document Server

    Nishikawa, Takashi; 10.1038/srep00151

    2011-01-01

    To understand the formation, evolution, and function of complex systems, it is crucial to understand the internal organization of their interaction networks. Partly due to the impossibility of visualizing large complex networks, resolving network structure remains a challenging problem. Here we overcome this difficulty by combining the visual pattern recognition ability of humans with the high processing speed of computers to develop an exploratory method for discovering groups of nodes characterized by common network properties, including but not limited to communities of densely connected nodes. Without any prior information about the nature of the groups, the method simultaneously identifies the number of groups, the group assignment, and the properties that define these groups. The results of applying our method to real networks suggest the possibility that most group structures lurk undiscovered in the fast-growing inventory of social, biological, and technological networks of scientific interest.

  12. Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems

    Directory of Open Access Journals (Sweden)

    Goutsias John

    2010-11-01

    Full Text Available Abstract Background Estimating the rate constants of a biochemical reaction system with known stoichiometry from noisy time series measurements of molecular concentrations is an important step for building predictive models of cellular function. Inference techniques currently available in the literature may produce rate constant values that defy necessary constraints imposed by the fundamental laws of thermodynamics. As a result, these techniques may lead to biochemical reaction systems whose concentration dynamics could not possibly occur in nature. Therefore, development of a thermodynamically consistent approach for estimating the rate constants of a biochemical reaction system is highly desirable. Results We introduce a Bayesian analysis approach for computing thermodynamically consistent estimates of the rate constants of a closed biochemical reaction system with known stoichiometry given experimental data. Our method employs an appropriately designed prior probability density function that effectively integrates fundamental biophysical and thermodynamic knowledge into the inference problem. Moreover, it takes into account experimental strategies for collecting informative observations of molecular concentrations through perturbations. The proposed method employs a maximization-expectation-maximization algorithm that provides thermodynamically feasible estimates of the rate constant values and computes appropriate measures of estimation accuracy. We demonstrate various aspects of the proposed method on synthetic data obtained by simulating a subset of a well-known model of the EGF/ERK signaling pathway, and examine its robustness under conditions that violate key assumptions. Software, coded in MATLAB®, which implements all Bayesian analysis techniques discussed in this paper, is available free of charge at http://www.cis.jhu.edu/~goutsias/CSS%20lab/software.html. Conclusions Our approach provides an attractive statistical methodology for

  13. A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

    Science.gov (United States)

    Chevalier, Michael W.; El-Samad, Hana

    2014-12-01

    Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation times of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled.

  14. Pulmonary Complications due to Esophagectomy

    Directory of Open Access Journals (Sweden)

    Yashar Talebi

    2011-08-01

    Full Text Available Introduction: Esophageal carcinoma is the scourge of human beings. Pulmonary compli-cations in patients who have undergone operation are common (20-30% of cases and there are no suitable tools and ways to predict these complications. Methods: During a period of 10 years, from March 1998 to February 2007, 200 patients (150 male and 50 female underwent Esophagectomy due to esophageal carcinoma in thoracic surgery ward retrospectively. Complications include the length of hospitalization, mechanical ventilation, morbidity and mortality. Patients’ risk factors include age, preoperative chemo-radiotherapy, stage of the disease and preoperative spirometry condition. Results: We grouped our patients into three categories: Normal (FEV1 ≥ 80% predicted, mildly impaired (FEV1 65% to 79% predicted, more severely impaired (FEV1 < 65% predicted.Although almost all patients had radiographic pulmonary abnormalities, significant pulmonary complications occurred in 40 patients (20% which underwent Esophagectomy. Pleural effusion and atelectasia in 160 patients (80%. 24 patients needed chest-tube insertion. 20 patients (10% developed ARDS. 14 patients (7% developed chylothorax. 20 patients (10% of patients died during their postoperative hospital stay. 30 patients (15% required mechanical ventilation for greater than 48 hours. Conclusion: We reviewed a number of preoperative clinical variables to determine whether they contributed to postoperative pulmonary complications as well as other outcomes. In general, age, impaired pulmonary function especially in those patients with FEV1 less than 65% predicted was associated with prolonged hospital length of stay (LOS. In fact pulmonary complications rate after Esophagectomy are high and there was associated mortality and morbidity.

  15. Telomere attrition due to infection.

    Directory of Open Access Journals (Sweden)

    Petteri Ilmonen

    Full Text Available BACKGROUND: Telomeres--the terminal caps of chromosomes--become shorter as individuals age, and there is much interest in determining what causes telomere attrition since this process may play a role in biological aging. The leading hypothesis is that telomere attrition is due to inflammation, exposure to infectious agents, and other types of oxidative stress, which damage telomeres and impair their repair mechanisms. Several lines of evidence support this hypothesis, including observational findings that people exposed to infectious diseases have shorter telomeres. Experimental tests are still needed, however, to distinguish whether infectious diseases actually cause telomere attrition or whether telomere attrition increases susceptibility to infection. Experiments are also needed to determine whether telomere erosion reduces longevity. METHODOLOGY/PRINCIPAL FINDINGS: We experimentally tested whether repeated exposure to an infectious agent, Salmonella enterica, causes telomere attrition in wild-derived house mice (Mus musculus musculus. We repeatedly infected mice with a genetically diverse cocktail of five different S. enterica strains over seven months, and compared changes in telomere length with sham-infected sibling controls. We measured changes in telomere length of white blood cells (WBC after five infections using a real-time PCR method. Our results show that repeated Salmonella infections cause telomere attrition in WBCs, and particularly for males, which appeared less disease resistant than females. Interestingly, we also found that individuals having long WBC telomeres at early age were relatively disease resistant during later life. Finally, we found evidence that more rapid telomere attrition increases mortality risk, although this trend was not significant. CONCLUSIONS/SIGNIFICANCE: Our results indicate that infectious diseases can cause telomere attrition, and support the idea that telomere length could provide a molecular

  16. Analyzing negative ties in social networks

    OpenAIRE

    Mankirat Kaur; Sarbjeet Singh

    2016-01-01

    Online social networks are a source of sharing information and maintaining personal contacts with other people through social interactions and thus forming virtual communities online. Social networks are crowded with positive and negative relations. Positive relations are formed by support, endorsement and friendship and thus, create a network of well-connected users whereas negative relations are a result of opposition, distrust and avoidance creating disconnected networks. Due to increase i...

  17. Analysis of Municipal Pipe Network Franchise Institution

    Science.gov (United States)

    Yong, Sun; Haichuan, Tian; Feng, Xu; Huixia, Zhou

    Franchise institution of municipal pipe network has some particularity due to the characteristic of itself. According to the exposition of Chinese municipal pipe network industry franchise institution, the article investigates the necessity of implementing municipal pipe network franchise institution in China, the role of government in the process and so on. And this offers support for the successful implementation of municipal pipe network franchise institution in China.

  18. Impact of reduced scale free network on wireless sensor network

    Science.gov (United States)

    Keshri, Neha; Gupta, Anurag; Mishra, Bimal Kumar

    2016-12-01

    In heterogeneous wireless sensor network (WSN) each data-packet traverses through multiple hops over restricted communication range before it reaches the sink. The amount of energy required to transmit a data-packet is directly proportional to the number of hops. To balance the energy costs across the entire network and to enhance the robustness in order to improve the lifetime of WSN becomes a key issue of researchers. Due to high dimensionality of an epidemic model of WSN over a general scale free network, it is quite difficult to have close study of network dynamics. To overcome this complexity, we simplify a general scale free network by partitioning all of its motes into two classes: higher-degree motes and lower-degree motes, and equating the degrees of all higher-degree motes with lower-degree motes, yielding a reduced scale free network. We develop an epidemic model of WSN based on reduced scale free network. The existence of unique positive equilibrium is determined with some restrictions. Stability of the system is proved. Furthermore, simulation results show improvements made in this paper have made the entire network have a better robustness to the network failure and the balanced energy costs. This reduced model based on scale free network theory proves more applicable to the research of WSN.

  19. Molecular ecological network analyses

    Directory of Open Access Journals (Sweden)

    Deng Ye

    2012-05-01

    Full Text Available Abstract Background Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data. Results Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs through Random Matrix Theory (RMT-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with high-throughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological

  20. Multilayer Networks

    CERN Document Server

    Kivelä, Mikko; Barthelemy, Marc; Gleeson, James P; Moreno, Yamir; Porter, Mason A

    2013-01-01

    Most real and engineered systems include multiple subsystems and layers of connectivity, and it is important to take such features into account to try to obtain a complete understanding of these systems. It is thus necessary to generalize "traditional" network theory by developing (and validating) a framework and associated tools to study multilayer systems in a comprehensive fashion. The origins of such efforts occurred several decades ago, but now the study of multilayer networks has become one of the major directions in network science. In this paper, we discuss the history of multilayer networks (and related concepts) and then review the exploding body of work on such networks. To unify the disparate terminology in the large body of recent work, we discuss a general framework for multilayer networks, construct a dictionary of terminology to relate the numerous existing concepts to each other, and provide a thorough discussion that compares, contrasts, and translates between related notions such as multila...

  1. Cosmological networks

    CERN Document Server

    Boguna, Marian; Krioukov, Dmitri

    2013-01-01

    Networks often represent systems that do not have a long history of studies in traditional fields of physics, albeit there are some notable exceptions such as energy landscapes and quantum gravity. Here we consider networks that naturally arise in cosmology. Nodes in these networks are stationary observers uniformly distributed in an expanding open FLRW universe with any scale factor, and two observers are connected if one can causally influence the other. We show that these networks are growing Lorentz-invariant graphs with power-law distributions of node degrees. New links in these networks not only connect new nodes to existing ones, but also appear at a certain rate between existing nodes, as they do in many complex networks.

  2. Accurate atom-mapping computation for biochemical reactions.

    Science.gov (United States)

    Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D

    2012-11-26

    The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.

  3. Dynamics of simple gene-network motifs subject to extrinsic fluctuations

    Science.gov (United States)

    Roberts, Elijah; Be'er, Shay; Bohrer, Chris; Sharma, Rati; Assaf, Michael

    2015-12-01

    Cellular processes do not follow deterministic rules; even in identical environments genetically identical cells can make random choices leading to different phenotypes. This randomness originates from fluctuations present in the biomolecular interaction networks. Most previous work has been focused on the intrinsic noise (IN) of these networks. Yet, especially for high-copy-number biomolecules, extrinsic or environmental noise (EN) has been experimentally shown to dominate the variation. Here, we develop an analytical formalism that allows for calculation of the effect of EN on gene-expression motifs. We introduce a method for modeling bounded EN as an auxiliary species in the master equation. The method is fully generic and is not limited to systems with small EN magnitudes. We focus our study on motifs that can be viewed as the building blocks of genetic switches: a nonregulated gene, a self-inhibiting gene, and a self-promoting gene. The role of the EN properties (magnitude, correlation time, and distribution) on the statistics of interest are systematically investigated, and the effect of fluctuations in different reaction rates is compared. Due to its analytical nature, our formalism can be used to quantify the effect of EN on the dynamics of biochemical networks and can also be used to improve the interpretation of data from single-cell gene-expression experiments.

  4. Network medicine

    DEFF Research Database (Denmark)

    Pawson, Tony; Linding, Rune

    2008-01-01

    for new therapeutic intervention. We argue that by targeting the architecture of aberrant signaling networks associated with cancer and other diseases new therapeutic strategies can be implemented. Transforming medicine into a network driven endeavour will require quantitative measurements of cell...... signaling processes; we will describe how this may be performed and combined with new algorithms to predict the trajectories taken by a cellular system either in time or through disease states. We term this approach, network medicine....

  5. Secondary Circulating Prostate Cells Predict Biochemical Failure in Prostate Cancer Patients after Radical Prostatectomy and without Evidence of Disease

    Directory of Open Access Journals (Sweden)

    Nigel P. Murray

    2013-01-01

    Full Text Available Introduction. Although 90% of prostate cancer is considered to be localized, 20%–30% of patients will experience biochemical failure (BF, defined as serum PSA >0.2 ng/mL, after radical prostatectomy (RP. The presence of circulating prostate cells (CPCs in men without evidence of BF may be useful to predict patients at risk for BF. We describe the frequency of CPCs detected after RP, relation with clinicopathological parameters, and association with biochemical failure. Methods and Patients. Serial blood samples were taken during followup after RP, mononuclear cells were obtained by differential gel centrifugation, and CPCs identified using standard immunocytochemistry using anti-PSA monoclonal antibodies. Age, pathological stage (organ confined, nonorgan confined, pathological grade, margin status (positive, negative, extracapsular extension, perineural, vascular, and lymphatic infiltration (positive, negative were compared with the presence/absence of CPCs and with and without biochemical failure. Kaplan Meier methods were used to compare the unadjusted biochemical failure free survival of patients with and without CPCs. Results. 114 men participated, and secondary CPCs were detected more frequently in patients with positive margins, extracapsular extension, and vascular and lymphatic infiltration and were associated with biochemical failure independent of these clinicopathological variables, and with a shorter time to BF. Conclusions. Secondary CPCs are an independent risk factor associated with increased BF in men with a PSA <0.2 ng/mL after radical prostatectomy, but do not determine if the recurrence is due to local or systemic disease. These results warrant larger studies to confirm the findings.

  6. Melatonin and schistosomal antigens ameliorate the anti-oxidative and biochemical response to Schistosoma mansoni infection in hamster

    Institute of Scientific and Technical Information of China (English)

    Nahla S.El-SHENAWY; Maha F.M.SOLIMAN; Shimaa E.Abel-RAHMAN

    2009-01-01

    The present study was designed to investigate the potential protective effect of melatonin as an antioxidant separately or in combination with antigens (cercarial; CAP or soluble worm; SWAP) against Schistosoma mansoni infection in hamsters. Each hamster was sensitized with an initial immunization of 0.6 ml of the extracted antigen (30 μg protein/mL). After four days, a second injection of 0.4 mL was given (20 μg protein/mL). Then, each hamster was exposed to 260±20 S.mansoni cercariae followed with melatonin treatment (3.5 mg/kg) for thirty days from the 1st day of post infection. Levels of lipid peroxidation (LPO) products, catalase (CAT) activity, hepatic glutathione (GSH) and biochemical changes in the liver and kidneys functions were investigated. The results revealed a high significant increasing of LPO and decreasing of CAT and GSH in liver of infected hamsters. Biochemical observations showed severe damage in the liver enzyme activities and increasing cholesterol level in infected animals. Melatonin co-treatment with antigen to the infected-hamster attenuated the increase of LPO and restored the activity of CAT and levels of hepatic GSH. Also, the biochemical damages in the liver and kidneys functions were reduced. The present study suggests that melatonin may be useful in combating free radical-induced damage due to infection toxicity. The immunization with previous antigens resulted in a remarkable improvement on the liver enzyme activities, which were increased after infection. Thus, vaccination of hamsters with antigens (both CAP and SWAP) and melatonin treatment has more potent effect on the enhancement of antioxidant and biochemical of S.mansoni infected-hamster than each treatment separately. Immunization of the hamster with SWAP followed by melatonin was the best way among the other regime treatments to improve the biochemical and antioxidant parameters of the infected-hamsters[Current Zoology 55(2):165-172,2009].

  7. Complex networks: Dynamics and security

    Indian Academy of Sciences (India)

    Ying-Cheng Lai; Adilson Motter; Takashi Nishikawa; Kwangho Park; Liang Zhao

    2005-04-01

    This paper presents a perspective in the study of complex networks by focusing on how dynamics may affect network security under attacks. In particular, we review two related problems: attack-induced cascading breakdown and range-based attacks on links. A cascade in a network means the failure of a substantial fraction of the entire network in a cascading manner, which can be induced by the failure of or attacks on only a few nodes. These have been reported for the internet and for the power grid (e.g., the August 10, 1996 failure of the western United States power grid). We study a mechanism for cascades in complex networks by constructing a model incorporating the flows of information and physical quantities in the network. Using this model we can also show that the cascading phenomenon can be understood as a phase transition in terms of the key parameter characterizing the node capacity. For a parameter value below the phase-transition point, cascading failures can cause the network to disintegrate almost entirely. We will show how to obtain a theoretical estimate for the phase-transition point. The second problem is motivated by the fact that most existing works on the security of complex networks consider attacks on nodes rather than on links. We address attacks on links. Our investigation leads to the finding that many scale-free networks are more sensitive to attacks on short-range than on long-range links. Considering that the small-world phenomenon in complex networks has been identified as being due to the presence of long-range links, i.e., links connecting nodes that would otherwise be separated by a long node-to-node distance, our result, besides its importance concerning network efficiency and security, has the striking implication that the small-world property of scale-free networks is mainly due to short-range links.

  8. Nonoptimal component placement, but short processing paths, due to long-distance projections in neural systems.

    Directory of Open Access Journals (Sweden)

    Marcus Kaiser

    2006-07-01

    Full Text Available It has been suggested that neural systems across several scales of organization show optimal component placement, in which any spatial rearrangement of the components would lead to an increase of total wiring. Using extensive connectivity datasets for diverse neural networks combined with spatial coordinates for network nodes, we applied an optimization algorithm to the network layouts, in order to search for wire-saving component rearrangements. We found that optimized component rearrangements could substantially reduce total wiring length in all tested neural networks. Specifically, total wiring among 95 primate (Macaque cortical areas could be decreased by 32%, and wiring of neuronal networks in the nematode Caenorhabditis elegans could be reduced by 48% on the global level, and by 49% for neurons within frontal ganglia. Wiring length reductions were possible due to the existence of long-distance projections in neural networks. We explored the role of these projections by comparing the original networks with minimally rewired networks of the same size, which possessed only the shortest possible connections. In the minimally rewired networks, the number of processing steps along the shortest paths between components was significantly increased compared to the original networks. Additional benchmark comparisons also indicated that neural networks are more similar to network layouts that minimize the length of processing paths, rather than wiring length. These findings suggest that neural systems are not exclusively optimized for minimal global wiring, but for a variety of factors including the minimization of processing steps.

  9. Network security

    CERN Document Server

    Perez, André

    2014-01-01

    This book introduces the security mechanisms deployed in Ethernet, Wireless-Fidelity (Wi-Fi), Internet Protocol (IP) and MultiProtocol Label Switching (MPLS) networks. These mechanisms are grouped throughout the book according to the following four functions: data protection, access control, network isolation, and data monitoring. Data protection is supplied by data confidentiality and integrity control services. Access control is provided by a third-party authentication service. Network isolation is supplied by the Virtual Private Network (VPN) service. Data monitoring consists of applying

  10. Technical Network

    CERN Multimedia

    2007-01-01

    In order to optimize the management of the Technical Network (TN), to ease the understanding and purpose of devices connected to the TN, and to improve security incident handling, the Technical Network Administrators and the CNIC WG have asked IT/CS to verify the "description" and "tag" fields of devices connected to the TN. Therefore, persons responsible for systems connected to the TN will receive email notifications from IT/CS asking them to add the corresponding information in the network database. Thank you very much for your cooperation. The Technical Network Administrators & the CNIC WG

  11. OPTIMAL NETWORK TOPOLOGY DESIGN

    Science.gov (United States)

    Yuen, J. H.

    1994-01-01

    This program was developed as part of a research study on the topology design and performance analysis for the Space Station Information System (SSIS) network. It uses an efficient algorithm to generate candidate network designs (consisting of subsets of the set of all network components) in increasing order of their total costs, and checks each design to see if it forms an acceptable network. This technique gives the true cost-optimal network, and is particularly useful when the network has many constraints and not too many components. It is intended that this new design technique consider all important performance measures explicitly and take into account the constraints due to various technical feasibilities. In the current program, technical constraints are taken care of by the user properly forming the starting set of candidate components (e.g. nonfeasible links are not included). As subsets are generated, they are tested to see if they form an acceptable network by checking that all requirements are satisfied. Thus the first acceptable subset encountered gives the cost-optimal topology satisfying all given constraints. The user must sort the set of "feasible" link elements in increasing order of their costs. The program prompts the user for the following information for each link: 1) cost, 2) connectivity (number of stations connected by the link), and 3) the stations connected by that link. Unless instructed to stop, the program generates all possible acceptable networks in increasing order of their total costs. The program is written only to generate topologies that are simply connected. Tests on reliability, delay, and other performance measures are discussed in the documentation, but have not been incorporated into the program. This program is written in PASCAL for interactive execution and has been implemented on an IBM PC series computer operating under PC DOS. The disk contains source code only. This program was developed in 1985.

  12. PROGNOSTIC FACTORS OF BIOCHEMICAL RELAPSE FREE SURVIVAL FOLLOWING SALVAGE RADIOTHERAPY IN MEN WITH BIOCHEMICAL RECURRENCE AFTER RADICAL PROSTATECTOMY

    Directory of Open Access Journals (Sweden)

    P. D. Demeshko

    2014-07-01

    Full Text Available Purpose. To evaluate influence of clinical, biochemical and histological factors to biochemical relapse free survival (BRFS following salvage radiotherapy (RT in men with biochemical recurrence after radical prostatectomy.Material and methods. 77 patients with newly diagnosed biochemical recurrence (BR after RPE were included into retrospective study. All of them underwent local salvage RT. Сlinical variables (age, serum prostate-specific antigen [PSA] level and PSA kinetics, time RPE-BR, Gleason grade, stage after RPE and clinical findings were evaluated using Cox proportional hazards regression analysis.Results. The median, 1- and 3-year BRFS were 19,9 months, 63,8 ± 6,5 % and 24,7 ± 8,5 % respectively. Significant variables in the multivariable model were age, PSA level before RT, prostatectomy T3b stage, PSA doubling time and positive digital rectal examination findings (p < 0,05. Several clinical parameters help predict the outcomes of men with PSA elevation after radical prostatectomy. These data may be useful in counseling men regarding the timing of administration of adjuvant therapies.

  13. "Conjectural" links in complex networks

    Science.gov (United States)

    Snarskii, A. A.; Zorinets, D. I.; Lande, D. V.

    2016-11-01

    This paper introduces the concept of Conjectural Link for Complex Networks, in particular, social networks. Conjectural Link we understand as an implicit link, not available in the network, but supposed to be present, based on the characteristics of its topology. It is possible, for example, when in the formal description of the network some connections are skipped due to errors, deliberately hidden or withdrawn (e.g. in the case of partial destruction of the network). Introduced a parameter that allows ranking the Conjectural Link. The more this parameter - the more likely that this connection should be present in the network. This paper presents a method of recovery of partially destroyed Complex Networks using Conjectural Links finding. Presented two methods of finding the node pairs that are not linked directly to one another, but have a great possibility of Conjectural Link communication among themselves: a method based on the determination of the resistance between two nodes, and method based on the computation of the lengths of routes between two nodes. Several examples of real networks are reviewed and performed a comparison to know network links prediction methods, not intended to find the missing links in already formed networks.

  14. Google matrix analysis of directed networks

    CERN Document Server

    Ermann, Leonardo; Shepelyansky, Dima L

    2014-01-01

    In past ten years, modern societies developed enormous communication and social networks. Their classification and information retrieval processing become a formidable task for the society. Due to the rapid growth of World Wide Web, social and communication networks, new mathematical methods have been invented to characterize the properties of these networks on a more detailed and precise level. Various search engines are essentially using such methods. It is highly important to develop new tools to classify and rank enormous amount of network information in a way adapted to internal network structures and characteristics. This review describes the Google matrix analysis of directed complex networks demonstrating its efficiency on various examples including World Wide Web, Wikipedia, software architecture, world trade, social and citation networks, brain neural networks, DNA sequences and Ulam networks. The analytical and numerical matrix methods used in this analysis originate from the fields of Markov chain...

  15. Effects of Training Load on Some Hormonal, Hematological and Biochemical Profile of Male Cyclists

    Directory of Open Access Journals (Sweden)

    Pralay Majumdar

    2014-07-01

    Full Text Available Hematological profiles of cyclists fluctuates are based on the volume/frequency/intensity of training. The present study examined the effects of training load on the cyclist’s biochemical profile which may be associated with over training. Twelve male cyclists volunteered to participate in this study. The participants completed a systematic training program which was divided into four phases i.e. phase I (560 km, continuous aerobic training, II (680 km, continuous aerobic training, III (720 km, aerobic and anaerobic interval training and IV (560 km, continuous aerobic training. Blood samples were collected at the end of each phase. The hemoglobin level of the cyclists increased throughout the training cycle whereas iron level increased till the third phase and decreased in the fourth phase due to alteration in training. Hemoglobin level was high during the IV phase and this was due to the lowest volume/frequency of training given to the cyclists in final phase. Total Iron Binding Capacity (TIBC level was elevated during the competitive phase, due to the high volume / intensity during III phase. The depletion of ferritin was high during phase II which was associated with a 21% increase in training volume after the first phase. The highest intensity, volume and frequency of E2S training (phase III were associated with a large increase in Creatine Phosphokinase (CPK, Lactate Dehydrogenase (LDH and cortisol levels, demonstrating a significant decrease in testosterone that showed the over-trained state. Hence, these biochemical markers are important in monitoring athlete’s training load as these parameters are altered with the training intensity, frequency and volume of training given to the cyclist.

  16. Analytical, ultrastructural, autoradiographic and biochemical studies on [3H]dicarboxylic acid added to cultures of melanoma cells.

    Science.gov (United States)

    Ward, B J; Breathnach, A S; Robins, E J; Bhasin, Y; Ethridge, L; Passi, S; Nazzaro-Porro, M

    1984-07-01

    Lentigo maligna and malignant melanoma can be treated by dicarboxylic acids (C9 and C12), which are competitive inhibitors of tyrosinase. We therefore studied the intracellular location and possible sites of action of dodecanedioic acid (C12) in murine melanoma cells, using EM autoradiography and biochemical analysis of lipid extracts by HPLC. Significant levels of radioactivity were found in the mitochondria and in the nuclei but not in association with membranes of rough endoplasmic reticulum, Golgi-associated endoplasmic reticulum, or Golgi apparatus, and not in coated vesicles or melanosomes. Biochemical analysis revealed that the diacid underwent beta-oxidation, which occurs only in mitochondria. The results suggest that the toxicity of dicarboxylic acids in melanoma cells is not related to anti-tyrosinase activity but may be due to interference with oxidoreductase enzymes in the mitochondria and possibly to inhibition of DNA synthesis in the nucleus.

  17. Effects of network node consolidation in optical access and aggregation networks on costs and power consumption

    Science.gov (United States)

    Lange, Christoph; Hülsermann, Ralf; Kosiankowski, Dirk; Geilhardt, Frank; Gladisch, Andreas

    2010-01-01

    The increasing demand for higher bit rates in access networks requires fiber deployment closer to the subscriber resulting in fiber-to-the-home (FTTH) access networks. Besides higher access bit rates optical access network infrastructure and related technologies enable the network operator to establish larger service areas resulting in a simplified network structure with a lower number of network nodes. By changing the network structure network operators want to benefit from a changed network cost structure by decreasing in short and mid term the upfront investments for network equipment due to concentration effects as well as by reducing the energy costs due to a higher energy efficiency of large network sites housing a high amount of network equipment. In long term also savings in operational expenditures (OpEx) due to the closing of central office (CO) sites are expected. In this paper different architectures for optical access networks basing on state-of-the-art technology are analyzed with respect to network installation costs and power consumption in the context of access node consolidation. Network planning and dimensioning results are calculated for a realistic network scenario of Germany. All node consolidation scenarios are compared against a gigabit capable passive optical network (GPON) based FTTH access network operated from the conventional CO sites. The results show that a moderate reduction of the number of access nodes may be beneficial since in that case the capital expenditures (CapEx) do not rise extraordinarily and savings in OpEx related to the access nodes are expected. The total power consumption does not change significantly with decreasing number of access nodes but clustering effects enable a more energyefficient network operation and optimized power purchase order quantities leading to benefits in energy costs.

  18. Critical regions and region-disjoint paths in a network

    NARCIS (Netherlands)

    Trajanovski, S.; Kuipers, F. A.; Van Mieghem, P.; Ilić, A.; Crowcroft, J.

    2013-01-01

    Due to the importance of communication networks to society, it is pertinent that these networks can withstand failures. Improving the robustness of a network usually requires installing redundant resources, which is very costly. Network providers are consequently less inclined to take robustness mea

  19. Enlightened Multiscale Simulation of Biochemical Networks. Core Theory, Validating Experiments, and Implementation in Open Software

    Science.gov (United States)

    2006-10-01

    ohm” “steradian” “dimensionless” “item” “lumen” “pascal” “ tesla ” “farad” “joule” “lux” “radian” “volt”.) 20402. Redefinitions of the built-in unit...dc:contributor plus vCard), ”creator” (dc:creator plus vCard) and links to other resources (dc:relation, cf. proposal of Andrew Finney and Nicolas Le

  20. Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins

    Directory of Open Access Journals (Sweden)

    Tsoka Sophia

    2011-05-01

    Full Text Available Abstract Background Cellular ATP levels are generated by glucose-stimulated mitochondrial metabolism and determine metabolic responses, such as glucose-stimulated insulin secretion (GSIS from the β-cells of pancreatic islets. We describe an analysis of the evolutionary processes affecting the core enzymes involved in glucose-stimulated insulin secretion in mammals. The proteins involved in this system belong to ancient enzymatic pathways: glycolysis, the TCA cycle and oxidative phosphorylation. Results We identify two sets of proteins, or protein coalitions, in this group of 77 enzymes with distinct evolutionary patterns. Members of the glycolysis, TCA cycle, metabolite transport, pyruvate and NADH shuttles have low rates of protein sequence evolution, as inferred from a human-mouse comparison, and relatively high rates of evolutionary gene duplication. Respiratory chain and glutathione pathway proteins evolve faster, exhibiting lower rates of gene duplication. A small number of proteins in the system evolve significantly faster than co-pathway members and may serve as rapidly evolving adapters, linking groups of co-evolving genes. Conclusions Our results provide insights into the evolution of the involved proteins. We find evidence for two coalitions of proteins and the role of co-adaptation in protein evolution is identified and could be used in future research within a functional context.

  1. A Design Tool Utilizing Stoichiometric Structure for the Analysis of Biochemical Reaction Networks

    Science.gov (United States)

    1990-05-20

    Valine Pathway (adapted from Demain, 1966 and Lehninger , 1975) Key: 5. 1, Embden-Meyerhof pathway; 5.2, pyruvate dehydrogenase complex; 5.14...physiological systems, FASEB, 4fl, 2490-2493, (1987). Lehninger , A. L., Biochmista, 2nd edition, Worth Publishers, New York, 1975. Mavrovouniotis, M. L., Computer

  2. Overlay networks toward information networking

    CERN Document Server

    Tarkoma, Sasu

    2010-01-01

    With their ability to solve problems in massive information distribution and processing, while keeping scaling costs low, overlay systems represent a rapidly growing area of R&D with important implications for the evolution of Internet architecture. Inspired by the author's articles on content based routing, Overlay Networks: Toward Information Networking provides a complete introduction to overlay networks. Examining what they are and what kind of structures they require, the text covers the key structures, protocols, and algorithms used in overlay networks. It reviews the current state of th

  3. Capacity analysis of inhomogeneous hybrid wireless networks using directional antennas

    Institute of Scientific and Technical Information of China (English)

    WU Feng; ZHU Jiang; TIAN Yi-long; ZOU Jian-bin

    2016-01-01

    Most of studies on network capacity are based on the assumption that all the nodes are uniformly distributed, which means that the networks are characterized by homogeneity. However, many realistic networks exhibit inhomogeneity due to natural and man-made reasons. In this work, the capacity of inhomogeneous hybrid networks with directional antennas for the first time is studied. By setting different node distribution probabilities, the whole network can be devided into dense cells and sparse cells. On this basis, an inhomogeneous hybrid network model is proposed. The network can exhibit significant inhomogeneity due to the coexistence of two types of cells. Then, we derive the network capacity and maximize the capacity under different channel allocation schemes. Finally, how the network parameters influence the network capacity is analyzed. It is found that if there are plenty of base stations, the per-node throughput can achieve constant order, and if the beamwidth of directional antenna is small enough, the network capacity can scale.

  4. Olmesartan attenuates tacrolimus-induced biochemical and ultrastructural changes in rat kidney tissue.

    Science.gov (United States)

    Al-Harbi, Naif O; Imam, Faisal; Al-Harbi, Mohammed M; Iqbal, Muzaffar; Nadeem, Ahmed; Sayed-Ahmed, Mohammed M; Alabidy, Ali D; Almukhallafi, Ali F

    2014-01-01

    Tacrolimus, a calcineurin inhibitor, is clinically used as an immunosuppressive agent in organ transplantation, but its use is limited due to its marked nephrotoxicity. The present study investigated the effect of olmesartan (angiotensin receptor blocker) on tacrolimus-induced nephrotoxicity in rats. A total of 24 rats were divided into four groups, which included control, tacrolimus, tacrolimus + olmesartan, and olmesartan groups. Tacrolimus-induced nephrotoxicity was assessed biochemically and histopathologically. Tacrolimus significantly increased BUN and creatinine level. Treatment with olmesartan reversed tacrolimus-induced changes in the biochemical markers (BUN and creatinine) of nephrotoxicity. Tacrolimus significantly decreased GSH level and catalase activity while increasing MDA level. Olmesartan also attenuated the effects of tacrolimus on MDA, GSH, and catalase. In tacrolimus group histological examination showed marked changes in renal tubule, mitochondria, and podocyte processes. Histopathological and ultrastructural studies showed that treatment with olmesartan prevented tacrolimus-induced renal damage. These results suggest that olmesartan has protective effects on tacrolimus-induced nephrotoxicity, implying that RAS might be playing role in tacrolimus-induced nephrotoxicity.

  5. Sodium arsenite induced biochemical perturbations in rats: ameliorating effect of curcumin.

    Science.gov (United States)

    Yousef, Mokhtar I; El-Demerdash, Fatma M; Radwan, Fatma M E

    2008-11-01

    The present study was undertaken to evaluate the therapeutic efficacy of curcumin in terms of normalization of altered biochemical parameters following sodium arsenite treatment in rats. Animals were divided into four groups. The first group was used as control. While, groups 2, 3 and 4 were orally treated with curcumin (Cur, 15 mg/kg BW), sodium arsenite (Sa, 5 mg/kg BW) and sodium arsenite plus curcumin, respectively. Results showed that the activities of transaminases and phosphatases were significantly decreased in liver due to Sa administration, whereas increased in plasma. The activity of brain and plasma acetylcholinesterase (AChE) was decreased in rats treated with Sa. Also, Sa significantly decreased plasma total protein (TP), albumin (Alb) and high density lipoprotein-cholesterol (HDL-c), while increased glucose, urea, creatinine, bilirubin, total lipid (TL), cholesterol, triglyceride (TG) and low density lipoprotein-cholesterol (LDL-c). Curcumin alone decreased the levels of glucose, urea, creatinine, TL, cholesterol, TG and LDL-c. Curcumin reduced Sa-induced transaminases, phosphatases, glucose, urea, creatinine, bilirubin, TL, cholesterol and TG. Moreover, curcumin induced Sa-reduced liver transaminases and phosphatases, plasma and brain AChE, and the levels of TP and Alb. Experimental results, therefore suggested that curcumin protects arsenic induced biochemical alterations in rats.

  6. Soil Biochemical Changes Induced by Poultry Litter Application and Conservation Tillage under Cotton Production Systems

    Directory of Open Access Journals (Sweden)

    Seshadri Sajjala

    2012-07-01

    Full Text Available Problems arising from conventional tillage (CT systems (such as soil erosion, decrease of organic matter, environmental damage etc. have led many farmers to the adoption of no-till (NT systems that are more effective in improving soil physical, chemical and microbial properties. Results from this study clearly indicated that NT, mulch tillage (MT, and winter rye cover cropping systems increased the activity of phosphatase, β-glucosidase and arylsulfatase at a 0–10 cm soil depth but decreased the activity of these enzymes at 10–20 cm. The increase in enzyme activity was a good indicator of intensive soil microbial activity in different soil management practices. Poultry litter (PL application under NT, MT, and rye cropping system could be considered as effective management practices due to the improvement in carbon (C content and the biochemical quality at the soil surface. The activities of the studied enzymes were highly correlated with soil total nitrogen (STN soil organic carbon (SOC at the 0–10 cm soil depth, except for acid phosphatase where no correlation was observed. This study revealed that agricultural practices such as tillage, PL, and cover crop cropping system have a noticeable positive effect on soil biochemical activities under cotton production.

  7. Current Biochemical Monitoring and Risk Management of Immunosuppressive Therapy after Transplantation

    Directory of Open Access Journals (Sweden)

    Catić-Đorđević Aleksandra

    2017-01-01

    Full Text Available Immunosuppressive drugs play a crucial role in the inhibition of immune reaction and prevention of graft rejection as well as in the pharmacotherapy of autoimmune disorders. Effective immunosuppression should provide an adequate safety profile and improve treatment outcomes and the patients’ quality of life. High-risk transplant recipients may be identified, but a definitive prediction model has still not been recognized. Therapeutic drug monitoring (TDM for immunosuppressive drugs is an essential, but at the same time insufficient tool due to low predictability of drug exposition and marked pharmacokinetic variability. Parallel therapeutic, biochemical and clinical monitoring may successfully optimize and individualize therapy for transplanted recipients, providing optimal medical outcomes. Modern pharmacotherapy management should include new biomarkers with better sensitivity and specificity that can identify early cell damage. The aim of this study was to point out the importance of finding new biomarkers that would enable early detection of adverse drug events and cell damage in organ transplant recipients. We wanted to confirm the importance of routine biochemical monitoring in improving the safety of immunosuppressive treatment.

  8. Ultrastructural and Biochemical Evaluation of the Effect of Endosulfan on Mice Liver

    Directory of Open Access Journals (Sweden)

    Yildiz Caglar

    2013-04-01

    Full Text Available Purpose: The aim of this study is to examine the effect of endosulfan on mice liver as ultrastructural together with biochemical data, and also by light microscopy to evaluate. Materials and Methods: 12 male albino mice weighing between 26-30g were used. Mice were divided into two equal groups. For group receiving endosulfan, endosulfan (13 mg/kg/day, body weight dissolved in nut oil was administered orally to mice via intragastric-during 10 days. The control group received only nut oil. At the end of the 10th day, all the mice were sacrificed with cervical dislocation. Tissue samples were taken for histological examination and biochemical analysis (SOD; superoxide dismutase, GSH; glutathione peroxidase, CAT; catalase, G6PD; glucose-6-phosphate dehidrogenase, MDA; malondialdehyde. Results: Disruption of inner membrane of mitochondria, dilatation of endoplasmic reticulum, the presence of large lipid droplets and vacuolar structures were observed in some hepatocytes. Prominent vacuolization was seen in light microscopic observation. There was an increment in activities of G6PD, SOD, GSH and MDA. However, there was a decrease in CAT activity. Conclusion: It may be considered that the adverse effect of endosulfan on mice liver may be due to direct toxic effect of endosulfan and induction of oxidative stress. [Cukurova Med J 2013; 38(2.000: 274-284

  9. Physiological and biochemical responses of rice seeds to phosphine exposure during germination.

    Science.gov (United States)

    Niu, Xiaojun; Mi, Lina; Li, Yadong; Wei, Aishu; Yang, Zhiquan; Wu, Jiandong; Zhang, Di; Song, Xiaofei

    2013-11-01

    Rice seeds (Tianyou, 3618) were used to examine the physiological and biochemical responses to phosphine exposure during germination. A control (0 mg m(-3)) and four concentrations of phosphine (1.4 mg m(-3), 4.2 mg m(-3), 7.0 mg m(-3) and 13.9 mg m(-3)) were used to treat the rice seeds. Each treatment was applied for 90 min once per day for five days. The germination rate (GR); germination potential (GP); germination index (GI); antioxidant enzymes, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT); and lipid peroxidation measured through via malondialdehyde (MDA) were determined as indicators of the physiological and biochemical responses of the rice seeds to phosphine exposure. These indicators were determined once per day for five days. The results indicated that the GR, GP and GI of the rice seeds markedly decreased after phosphine exposure. The changes in the activities of the antioxidant enzymes due to the phosphine exposure were also significant. The exposure lowered the CAT and SOD activities and increased POD activity in the treated rice seeds compared with controls. The MDA content exhibited a slow increase trend with the increase of phosphine concentration. These results suggest that phosphine has inhibitory effects on seed germination. In addition, phosphine exposure caused oxidative stress in the seeds. The antioxidant enzymes could play a pivotal role against oxidative injury. Overall, the effect of phosphine on rice seeds is different from what has been reported previously for insects and mammals.

  10. Conceptual study proposal for the integration and management of biochemical markers of environmental contamination use

    Directory of Open Access Journals (Sweden)

    Vera Lúcia S. S. de Castro

    2012-03-01

    Full Text Available Sustainable agriculture prioritizes the rational use of land and biota. For this, there is a need for understanding the interaction between the agriculture inputs and the ecosystems. However, there is a lack of easy access methods for verifying environmental contamination due to many of these products, such as pesticides and their mixtures. The application of alternative methods for monitoring degraded areas can generate economic advantages when compared to the implementation of protocols for analysis using high cost methods which demand a longer analysis time. Since environmental health can be accessed through studies using biomarkers, the approach presented here aims to discuss some aspects on the environmental risk monitoring with sentinel non-target organisms, focusing on biochemical parameters. Such parameters showed that the pesticide penetrated into the body and caused a response according to the dose or time of exposition. These parameters shall be used as biochemical biomarkers in programs for environmental monitoring because of the early identification of changes. The results obtained through its use shall be used to support policies related to environmental risks management.

  11. Biochemical, mechanical, and spectroscopic analyses of genetically engineered flax fibers producing bioplastic (poly-beta-hydroxybutyrate).

    Science.gov (United States)

    Wróbel-Kwiatkowska, Magdalena; Skórkowska-Telichowska, Katarzyna; Dymińska, Lucyna; Maczka, Mirosław; Hanuza, Jerzy; Szopa, Jan

    2009-01-01

    The interest in biofibers has grown in recent years due to their expanding range of applications in fields as diverse as biomedical science and the automotive industry. Their low production costs, biodegradability, physical properties, and perceived eco-friendliness allow for their extensive use as composite components, a role in which they could replace petroleum-based synthetic polymers. We performed biochemical, mechanical, and structural analyses of flax stems and fibers derived from field-grown transgenic flax enriched with PHB (poly-beta-hydroxybutyrate). The analyses of the plant stems revealed an increase in the cellulose content and a decrease in the lignin and pectin contents relative to the control plants. However, the contents of the fibers' major components (cellulose, lignin, pectin) remain unchanged. An FT-IR study confirmed the results of the biochemical analyses of the flax fibers. However, the arrangement of the cellulose polymer in the transgenic fibers differed from that in the control, and a significant increase in the number of hydrogen bonds was detected. The mechanical properties of the transgenic flax stems were significantly improved, reflecting the cellulose content increase. However, the mechanical properties of the fibers did not change in comparison with the control, with the exception of the fibers from transgenic line M13. The generated transgenic flax plants, which produce both components of the flax/PHB composites (i.e., fibers and thermoplastic matrix in the same plant organ) are a source of an attractive and ecologically safe material for industry and medicine.

  12. A model of chlorpyrifos distribution and its biochemical effects on the liver and kidneys of rats.

    Science.gov (United States)

    Tanvir, E M; Afroz, R; Chowdhury, Maz; Gan, S H; Karim, N; Islam, M N; Khalil, M I

    2016-09-01

    This study investigated the main target sites of chlorpyrifos (CPF), its effect on biochemical indices, and the pathological changes observed in rat liver and kidney function using gas chromatography/mass spectrometry. Adult female Wistar rats (n = 12) were randomly assigned into two groups (one control and one test group; n = 6 each). The test group received CPF via oral gavage for 21 days at 5 mg/kg daily. The distribution of CPF was determined in various organs (liver, brain, heart, lung, kidney, ovary, adipose tissue, and skeletal muscle), urine and stool samples using GCMS. Approximately 6.18% of CPF was distributed in the body tissues, and the highest CPF concentration (3.80%) was found in adipose tissue. CPF also accumulated in the liver (0.29%), brain (0.22%), kidney (0.10%), and ovary (0.03%). Approximately 83.60% of CPF was detected in the urine. CPF exposure resulted in a significant increase in plasma transaminases, alkaline phosphatase, and total bilirubin levels, a significant reduction in total protein levels and an altered lipid profile. Oxidative stress due to CPF administration was also evidenced by a significant increase in liver malondialdehyde levels. The detrimental effects of CPF on kidney function consisted of a significant increase in plasma urea and creatinine levels. Liver and kidney histology confirmed the observed biochemical changes. In conclusion, CPF bioaccumulates over time and exerts toxic effects on animals.

  13. Olmesartan Attenuates Tacrolimus-Induced Biochemical and Ultrastructural Changes in Rat Kidney Tissue

    Directory of Open Access Journals (Sweden)

    Naif O. Al-Harbi

    2014-01-01

    Full Text Available Tacrolimus, a calcineurin inhibitor, is clinically used as an immunosuppressive agent in organ transplantation, but its use is limited due to its marked nephrotoxicity. The present study investigated the effect of olmesartan (angiotensin receptor blocker on tacrolimus-induced nephrotoxicity in rats. A total of 24 rats were divided into four groups, which included control, tacrolimus, tacrolimus + olmesartan, and olmesartan groups. Tacrolimus-induced nephrotoxicity was assessed biochemically and histopathologically. Tacrolimus significantly increased BUN and creatinine level. Treatment with olmesartan reversed tacrolimus-induced changes in the biochemical markers (BUN and creatinine of nephrotoxicity. Tacrolimus significantly decreased GSH level and catalase activity while increasing MDA level. Olmesartan also attenuated the effects of tacrolimus on MDA, GSH, and catalase. In tacrolimus group histological examination showed marked changes in renal tubule, mitochondria, and podocyte processes. Histopathological and ultrastructural studies showed that treatment with olmesartan prevented tacrolimus-induced renal damage. These results suggest that olmesartan has protective effects on tacrolimus-induced nephrotoxicity, implying that RAS might be playing role in tacrolimus-induced nephrotoxicity.

  14. Seasonal variation of serum biochemical values of Amazonian snakes (Boa constrictor constrictor kept in captivity

    Directory of Open Access Journals (Sweden)

    Dennis José da Silva Lima

    2012-11-01

    Full Text Available In northern Brazil, the seasons are not well defined compared to the South and Southeast regions, due to a hot and humid equatorial climate with a rainy season, known as the Amazonian winter, and a period with less rain, known as the Amazonian summer. The goal of this study was to evaluate the biochemical variation of serum from the Amazon Boa constrictor by correlating the values with the seasons of the region. A biochemical analysis of the serum was performed (AST, ALT, LDH, ALP, calcium, uric acid, phosphorus, total protein, albumin and globulin using 31 individuals of Boa constrictor constrictor, which were kept in captivity. It was observed that eight of the ten parameters were higher in the winter compared to the summer (total protein, albumin, globulin, ALT, AST, ALP, LDH and calcium. The ALT, AST and calcium values had statistically significant differences for the summer and winter, while the other parameters appear to be influenced by seasonality. This was the first study of snakes kept in captivity that analyzed the serum chemistry profile of Boa constrictor constrictor from the state of Pará, Brazil.

  15. Design of acoustic wave biochemical sensors using micro-electro-mechanical systems

    Science.gov (United States)

    Valentine, Jane E.; Przybycien, Todd M.; Hauan, Steinar

    2007-03-01

    Acoustic wave biochemical sensors work by detecting the frequency shifts resulting from the binding of target molecules to a functionalized resonator. Resonator types currently in use or under development include macroscopic quartz crystal microbalances (QCMs) as well as a number of different integrated Micro-electro-mechanical Systems (MEMS) structures. Due to an increased resonator surface area to mass ratio, we believe that membrane-based MEMS systems are particularly promising with regard to sensitivity. Prototypes have been developed [S. Hauan et al., U.S. Patent Application (filed 6 Nov. 2003)] and preliminary calculations [M. J. Bartkovsky et al., paper 385e presented at the AIChE Annual Meeting, Nov. 2003; J. E. Valentine et al., paper 197h presented at the AICHE Annual Meeting, Nov. 2003] indicate significant improvements over other methods, both macroscopic and MEMS based. In this article we describe our work on a MEMS-based acoustic wave biochemical sensor using a membrane resonator. We demonstrate the effects of spatial distributions of mass on the membrane on sensitivity and show how to use this spatial sensitivity to detect multiple targets simultaneously. To do so we derive a function approximating the membrane response surface to spatial mass loadings under the applicable range of conditions. We verify the agreement using finite element methods, and present our initial sensitivity calculations demonstrating the advantages of variable mass loadings.

  16. Network Flows

    Science.gov (United States)

    1988-12-01

    Researchers have suggested other solution strategies, using ideas from nonlinear progamming for solving this general separable convex cost flow problems. Some...plane methods and branch and bound procedures of integer programming, primal-dual methods of linear and nonlinear programming, and polyhedral methods...Combinatorial Optimization: Networks and Matroids), Bazaraa and Jarvis [1978] (Linear Programming and Network Flows), Minieka [1978] (Optimization Algorithms for

  17. Bibliometric Networks

    CERN Document Server

    Havemann, Frank

    2012-01-01

    This text is based on a translation of a chapter in a handbook about network analysis (published in German) where we tried to make beginners familiar with some basic notions and recent developments of network analysis applied to bibliometric issues (Havemann and Scharnhorst 2010). We have added some recent references.

  18. Networking Japan

    DEFF Research Database (Denmark)

    Hansen, Annette Skovsted

    HIDA). Many of these alumni have and will in the future exchange ideas and keep contact not only to Japan, but also to fellow alumni around the globe and, thereby, practice south-south exchanges, which are made possible and traceable by their established alumni network and the World Network of Friends...

  19. Robust Networking Architecture and Secure Communication Scheme for Heterogeneous Wireless Sensor Networks

    Science.gov (United States)

    McNeal, McKenzie, III.

    2012-01-01

    Current networking architectures and communication protocols used for Wireless Sensor Networks (WSNs) have been designed to be energy efficient, low latency, and long network lifetime. One major issue that must be addressed is the security in data communication. Due to the limited capabilities of low cost and small sized sensor nodes, designing…

  20. A variational approach to the growth dynamics of pre-stressed actin filament networks

    Science.gov (United States)

    John, Karin; Stöter, Thomas; Misbah, Chaouqi

    2016-09-01

    In order to model the growth dynamics of elastic bodies with residual stresses a thermodynamically consistent approach is needed such that the cross-coupling between growth and mechanics can be correctly described. In the present work we apply a variational principle to the formulation of the interfacial growth dynamics of dendritic actin filament networks growing from biomimetic beads, an experimentally well studied system, where the buildup of residual stresses governs the network growth. We first introduce the material model for the network via a strain energy density for an isotropic weakly nonlinear elastic material and then derive consistently from this model the dynamic equations for the interfaces, i.e. for a polymerizing internal interface in contact with the bead and a depolymerizing external interface directed towards the solvent. We show that (i) this approach automatically preserves thermodynamic symmetry-properties, which is not the case for the often cited ‘rubber-band-model’ (Sekimoto et al 2004 Eur. Phys. J. E 13 247-59, Plastino et al 2004 Eur. Biophys. J. 33 310-20) and (ii) leads to a robust morphological instability of the treadmilling network interfaces. The nature of the instability depends on the interplay of the two dynamic interfaces. Depending on the biochemical conditions the network envelope evolves into a comet-like shape (i.e. the actin envelope thins out at one side and thickens on the opposite side of the bead) via a varicose instability or it breaks the symmetry via higher order zigzag modes. We conclude that morphological instabilities due to mechano-chemical coupling mechanisms and the presences of mechancial pre-stresses can play a major role in locally organizing the cytoskeleton of living cells.

  1. Seasonal Variations in the Biochemical Fractionation of Hydrogen Isotopes by Spartina alterniflora.

    Science.gov (United States)

    Sessions, A. L.

    2005-12-01

    Hydrogen isotope ratios (D/H) of lipids are being intensively explored as a paleoenvironmental proxy, particularly for continental regimes where organic preservation in lakes is generally high. Several studies have already shown good correlations between δD values of lake water and sedimentary (core-top) lipids, but the fractionations indicated by those correlations do not agree well between studies. Moreover, the data cannot be adequately described by a single biochemical fractionation. These difficulties suggest that the relationship between environmental water and plant lipid δD is controlled by multiple environmental and biochemical factors. Understanding these factors will lead to a more robust interpretation of D/H as a paleoclimate proxy. Here we examine seasonal changes in biochemical H-isotopic fractionation by the salt marsh grass Spartina alterniflora. Because S. alterniflora grows partially submerged in a tidal estuary, it has an unlimited and isotopically unvarying source of water for growth. Thus environmental influences on fractionation should be negligible, allowing us to examine seasonal changes in biochemical fractionations. C27 and C29 n-alkanes, β-sitosterol, phytol, and C16 and C18 fatty acids were extracted and analyzed from 35 samples of S. alterniflora harvested from the same location over a period of 18 months. All lipids except β-sitosterol exhibit statistically significant depletions of D during summer months relative to the rest of the year. The magnitude of the isotopic shift is up to 36‰ in the fatty acids (δD values from -130 to -166‰), 31‰ in n-alkanes (-161 to -192‰), and 24‰ in phytol (-252 to -276‰). The shift in D/H ratio is in the opposite direction from that expected due to increased evapotranspiration during the summer months. The largest D-depletions coincide with periods of maximal growth. The observed pattern is interpreted as resulting from increased use of stored carbohydrates as substrates for lipid

  2. To Study the Clinical, Biochemical and Radiological Features of Acute Pancreatitis in HIV and AIDS

    Science.gov (United States)

    Raza, Shahzad; Chaudhry, Naueen A.; Brown, Jordan D.; Aghaie, Sina; Rezai, Damoun; Khan, Areej; Tan, Paul De Leon; Berger, Barbara J.

    2013-01-01

    Background Pancreatitis complicating HIV infection, even in the Highly Active Antiretroviral Therapy (HAART) era, remains a management challenge. We felt there is a need to discern patterns in the biochemical markers, radiological studies, co-infections, length of stay (LOS) in patients with HIV or AIDS AND pancreatitis. Methods This is a retrospective study conducted from June, 2008 to August, 2010 on patients admitted with acute pancreatitis to our hospital. We extracted and compared the following parameters: biochemical markers, HBV markers (surface antigen, core antibody and surface antibody), HCV antibody, radiological studies, and length of stay (LOS). The Balthazar Grade score was used to assess radiological severity of disease. We stratified the cohort into comparison subsets according to CD4 count. Results Ninety-four admissions met the criteria for HIV or AIDS AND pancreatitis; 67 unique patients comprised the cohort. Median age was 48 years (range, 23 to 60 years). Thirty seven (55%) were male, 30 (45%), female. Two third (n = 51) (76%) were African American. Known risk factors included a history of pancreatitis, 17 (25%); cholecystitis, 13 (19%); alcohol abuse, 25 (37%); Intravenous drug abuse, 18 (27%). Only 36 (38%) admissions were on HAART regimen. Biochemical features on admission were: WBC, 6,100/mm3 (900 - 25,700); amylase, 152 U/L (30 - 1,344); lipase, 702.5 U/L (30 - 5,766), triglyceride, 65 mg/dL (57 - 400); glucose, 94 mg/dL (60 - 1,670); lactate, 2.3 mmol/L (1.09 - 5.49); AST, 61.5 U/L (9 - 1,950); LDH, 762 U/L (394 - 5,500); bicarbonate 19.5 mEq/L (3.3 - 82.7). Interestingly, 62% patients had normal pancreas on CT scan on admission. Of 67 individuals, hepatitis profile was available in 43, 21 (49%) were positive for HCV, 11 (26%) had markers for HBV. Four of 11 patients (36) with CD4 200. P = 0.03 via t-test comparison. One patient with CD4 < 50 died due to acute pancreatitis. Conclusion Pancreatitis remains a major cause of morbidity in HIV

  3. Telecommunication Networks

    DEFF Research Database (Denmark)

    Olsen, Rasmus Løvenstein; Balachandran, Kartheepan; Hald, Sara Ligaard

    2014-01-01

    illustrates how protocols can be reconfigured to fulfil reliability requirements, as an important part of providing reliable data access to the critical applications running over the network. Thereafter, we take a look at the security of the network, by looking at a framework that describes the digital......In this chapter, we look into the role of telecommunication networks and their capability of supporting critical infrastructure systems and applications. The focus is on smart grids as the key driving example, bearing in mind that other such systems do exist, e.g., water management, traffic control......, etc. First, the role of basic communication is examined with a focus on critical infrastructures. We look at heterogenic networks and standards for smart grids, to give some insight into what has been done to ensure inter-operability in this direction. We then go to the physical network, and look...

  4. Network Affordances

    DEFF Research Database (Denmark)

    Samson, Audrey; Soon, Winnie

    2015-01-01

    This paper examines the notion of network affordance within the context of network art. Building on Gibson's theory (Gibson, 1979) we understand affordance as the perceived and actual parameters of a thing. We expand on Gaver's affordance of predictability (Gaver, 1996) to include ecological...... and computational parameters of unpredictability. We illustrate the notion of unpredictability by considering four specific works that were included in a network art exhibiton, SPEED SHOW [2.0] Hong Kong. The paper discusses how the artworks are contingent upon the parameteric relations (Parisi, 2013......), of the network. We introduce network affordance as a dynamic framework that could articulate the experienced tension arising from the (visible) symbolic representation of computational processes and its hidden occurrences. We base our proposal on the experience of both organising the SPEED SHOW and participating...

  5. What to Expect After Your Due Date

    Science.gov (United States)

    ... Management Education & Events Advocacy For Patients About ACOG What to Expect After Your Due Date Home For ... Your Due Date FAQ069, August 2011 PDF Format What to Expect After Your Due Date Pregnancy What ...

  6. Evaluation of Network Reliability for Computer Networks with Multiple Sources

    Directory of Open Access Journals (Sweden)

    Yi-Kuei Lin

    2012-01-01

    Full Text Available Evaluating the reliability of a network with multiple sources to multiple sinks is a critical issue from the perspective of quality management. Due to the unrealistic definition of paths of network models in previous literature, existing models are not appropriate for real-world computer networks such as the Taiwan Advanced Research and Education Network (TWAREN. This paper proposes a modified stochastic-flow network model to evaluate the network reliability of a practical computer network with multiple sources where data is transmitted through several light paths (LPs. Network reliability is defined as being the probability of delivering a specified amount of data from the sources to the sink. It is taken as a performance index to measure the service level of TWAREN. This paper studies the network reliability of the international portion of TWAREN from two sources (Taipei and Hsinchu to one sink (New York that goes through a submarine and land surface cable between Taiwan and the United States.

  7. A Network Coding Based Routing Protocol for Underwater Sensor Networks

    Directory of Open Access Journals (Sweden)

    Xin Guan

    2012-04-01

    Full Text Available Due to the particularities of the underwater environment, some negative factors will seriously interfere with data transmission rates, reliability of data communication, communication range, and network throughput and energy consumption of underwater sensor networks (UWSNs. Thus, full consideration of node energy savings, while maintaining a quick, correct and effective data transmission, extending the network life cycle are essential when routing protocols for underwater sensor networks are studied. In this paper, we have proposed a novel routing algorithm for UWSNs. To increase energy consumption efficiency and extend network lifetime, we propose a time-slot based routing algorithm (TSR.We designed a probability balanced mechanism and applied it to TSR. The theory of network coding is introduced to TSBR to meet the requirement of further reducing node energy consumption and extending network lifetime. Hence, time-slot based balanced network coding (TSBNC comes into being. We evaluated the proposed time-slot based balancing routing algorithm and compared it with other classical underwater routing protocols. The simulation results show that the proposed protocol can reduce the probability of node conflicts, shorten the process of routing construction, balance energy consumption of each node and effectively prolong the network lifetime.

  8. Pretreatment Endorectal Coil Magnetic Resonance Imaging Findings Predict Biochemical Tumor Control in Prostate Cancer Patients Treated With Combination Brachytherapy and External-Beam Radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Riaz, Nadeem [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Afaq, Asim; Akin, Oguz [Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Pei Xin; Kollmeier, Marisa A.; Cox, Brett [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Hricak, Hedvig [Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Zelefsky, Michael J., E-mail: zelefskm@mskcc.org [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States)

    2012-11-01

    Purpose: To investigate the utility of endorectal coil magenetic resonance imaging (eMRI) in predicting biochemical relapse in prostate cancer patients treated with combination brachytherapy and external-beam radiotherapy. Methods and Materials: Between 2000 and 2008, 279 men with intermediate- or high-risk prostate cancer underwent eMRI of their prostate before receiving brachytherapy and supplemental intensity-modulated radiotherapy. Endorectal coil MRI was performed before treatment and retrospectively reviewed by two radiologists experienced in genitourinary MRI. Image-based variables, including tumor diameter, location, number of sextants involved, and the presence of extracapsular extension (ECE), were incorporated with other established clinical variables to predict biochemical control outcomes. The median follow-up was 49 months (range, 1-13 years). Results: The 5-year biochemical relapse-free survival for the cohort was 92%. Clinical findings predicting recurrence on univariate analysis included Gleason score (hazard ratio [HR] 3.6, p = 0.001), PSA (HR 1.04, p = 0.005), and National Comprehensive Cancer Network risk group (HR 4.1, p = 0.002). Clinical T stage and the use of androgen deprivation therapy were not correlated with biochemical failure. Imaging findings on univariate analysis associated with relapse included ECE on MRI (HR 3.79, p = 0.003), tumor size (HR 2.58, p = 0.04), and T stage (HR 1.71, p = 0.004). On multivariate analysis incorporating both clinical and imaging findings, only ECE on MRI and Gleason score were independent predictors of recurrence. Conclusions: Pretreatment eMRI findings predict for biochemical recurrence in intermediate- and high-risk prostate cancer patients treated with combination brachytherapy and external-beam radiotherapy. Gleason score and the presence of ECE on MRI were the only significant predictors of biochemical relapse in this group of patients.

  9. 40 CFR 158.2084 - Experimental use permit biochemical pesticides nontarget organisms and environmental fate data...

    Science.gov (United States)

    2010-07-01

    ... pesticides nontarget organisms and environmental fate data requirements table. 158.2084 Section 158.2084 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2084 Experimental use permit biochemical...

  10. Polyamines as salinity biochemical marker in callus of eucalyptus urograndis

    Directory of Open Access Journals (Sweden)

    Giuseppina Lima Pace Pereira

    2003-01-01

    Full Text Available Biochemical markers have been used for the analysis of plant cells submitted to several types of stress, among them salinity. This work aimed at analyzing the effect of saline stress in callus of Eucalyptus urograndis on polyamine contents. Explants (hypocotyls obtained from seeds were inoculated in callus inductive medium, submitted to different levels of NaCl and analyzed at 10, 20 and 30 days after the inoculation. The free polyamines were extracted, isolated and quantified using TLC (Thin-Layer Chromatography. Putrescine content was higher and a fall in the spermidine content was observed in callus submitted to salinity condition. The results showed that polyamine accumulation is related to NaCl exposure in callus of Eucalyptus urograndis. The decrease in spermine content could be used as a biochemical marker for Eucalyptus callus subjected to salinity.

  11. Biochemical functionalization of peptide nanotubes with phage displayed peptides

    Science.gov (United States)

    Swaminathan, Swathi; Cui, Yue

    2016-09-01

    The development of a general approach for the biochemical functionalization of peptide nanotubes (PNTs) could open up existing opportunities in both fundamental studies as well as a variety of applications. PNTs are spontaneously assembled organic nanostructures made from peptides. Phage display has emerged as a powerful approach for identifying selective peptide binding motifs. Here, we demonstrate for the first time the biochemical functionalization of PNTs via peptides identified from a phage display peptide library. The phage-displayed peptides are shown to recognize PNTs. These advances further allow for the development of bifunctional peptides for the capture of bacteria and the self-assembly of silver particles onto PNTs. We anticipate that these results could provide significant opportunities for using PNTs in both fundamental studies and practical applications, including sensors and biosensors nanoelectronics, energy storage devices, drug delivery, and tissue engineering.

  12. 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.

  13. Electrolyte-Gated Graphene Ambipolar Frequency Multipliers for Biochemical Sensing.

    Science.gov (United States)

    Fu, Wangyang; Feng, Lingyan; Mayer, Dirk; Panaitov, Gregory; Kireev, Dmitry; Offenhäusser, Andreas; Krause, Hans-Joachim

    2016-04-13

    In this Letter, the ambipolar properties of an electrolyte-gated graphene field-effect transistor (GFET) have been explored to fabricate frequency-doubling biochemical sensor devices. By biasing the ambipolar GFETs in a common-source configuration, an input sinusoidal voltage at frequency f applied to the electrolyte gate can be rectified to a sinusoidal wave at frequency 2f at the drain electrode. The extraordinary high carrier mobility of graphene and the strong electrolyte gate coupling provide the graphene ambipolar frequency doubler an unprecedented unity gain, as well as a detection limit of ∼4 pM for 11-mer single strand DNA molecules in 1 mM PBS buffer solution. Combined with an improved drift characteristics and an enhanced low-frequency 1/f noise performance by sampling at doubled frequency, this good detection limit suggests the graphene ambipolar frequency doubler a highly promising biochemical sensing platform.

  14. Biomphalaria prona (Gastropoda: Planorbidae: a morphological and biochemical study

    Directory of Open Access Journals (Sweden)

    W. Lobato Paraense

    1992-06-01

    Full Text Available Two samples of Biomphalaria prona (Martens, 1873 from Lake Valencia (type locality and seven from other Venezuelan localities were studied morphologically (shell and reproductive system and biochemically (allozyme electrophoresis. In spite of marked differences in shell characters, all of them proved indistinguishable under the anatomic and biochemical criteria. So far B. prona has been considered an endemic species, restricted to Lake Valencia. It is now demonstrated that the extralacustrine populations refered to Biomphalaria havanensis (Pfeiffer, 1839 by several authors correspond in shell characters to an extreme variant of B. prona from the Lake and really belong to the last*mentioned species. They may be regarded as the result of a process of directional selection favoring a shell phenotype other than those making up the modal class in the Lake.

  15. The Metabolic Syndrome and Biochemical Recurrence following Radical Prostatectomy

    Directory of Open Access Journals (Sweden)

    Jennifer M. Post

    2011-01-01

    Full Text Available Metabolic syndrome refers to a set of conditions that increases the risk of cardiovascular disease and has been associated with an increased risk of prostate cancer, particularly among African American men. This study aimed to estimate the association of metabolic syndrome with biochemical recurrence (BCR in a racially diverse population. Among 383 radical prostatectomy patients, 67 patients had documented biochemical recurrence. Hypertension was significantly, positively associated with the rate of BCR (hazard ratio (HR = 2.1; 95%  CI = 1.1, 3.8. There were distinct racial differences in the prevalence of individual metabolic syndrome components; however, the observed associations with BCR did not differ appreciably by race. We conclude that hypertension may contribute to a poorer prognosis in surgically treated prostate cancer patients. Our findings suggest that targeting components of the metabolic syndrome which are potentially modifiable through lifestyle interventions may be a viable strategy to reduce risk of BCR in prostate cancer.

  16. THE SYNTHESIS OF HEMOPROTEIDS IN THE LIGHT OF BIOCHEMICAL EVOLUTION,

    Science.gov (United States)

    the light of biochemical evolution , hemoproteids - resp. the porphyrin compounds they are based upon - must have existed on earth as early as... the CO2-assimilation, which means that the porphyrin catalyse of oxydative metabolism consequently derived from the second period of the early atmosphere. This aspect is discussed. (Author)...biological organisms with oxydative metabolism occurred. Since the primitive early atmosphere was followed by a CO2-containing

  17. Biochemical recurrence of prostate cancer: the controversial recognition and management

    Institute of Scientific and Technical Information of China (English)

    XIA Shu-jie; JING Yi-feng

    2011-01-01

    @@ Over the past decaade, more and more patients diagnosed as prostate cancer have received radical management attributing to the advent of prostate-specific antigen (PSA) based medical screening.Radical prostatectomy (RP) and radiation therapy (RT) are the most commonly used forms of definitive therapy for clinically localized prostate cancer.However, despite these technique advances, biochemical recurrence (BCR),as determined by subsequent rises in the serum PSA level,is still a challenge that urologists face.

  18. Biochemical Changes During Seed Germination of Sterculia urens Roxb.

    OpenAIRE

    Botcha SATYANARAYANA; Prattipati Subhashini DEVI; Atluru ARUNDATHI

    2011-01-01

    The present study describes biochemical changes taking place during seed germination of Sterculia urens. The levels of proteins, total amino acids, reducing sugars, total soluble sugars and lipids were studied during various stages of seed germination (0-15 days). Total protein content was decreased in cotyledons during seed germination while free amino acid content increased to its maximum extent by 9th day of germination and reverse trend thereafter. The levels of reducing sugars and total ...

  19. Biological and biochemical properties in evaluation of forest soil quality

    OpenAIRE

    Błońska Ewa; Lasota Jarosław

    2014-01-01

    The aim of this study was to assess the possibility of using biological and biochemical parameters in the evaluation of forest soil quality and changes caused by land use. The study attempted to determine a relationship between the enzymatic activity of soil, the number of earthworms and soil physico-chemical properties. The study was carried out in central Poland in adjoining Forest Districts (Przedbórz and Smardzewice). In soil samples taken from 12 research plots, basic physico-chemical pr...

  20. Biological and biochemical properties in evaluation of forest soil quality

    OpenAIRE

    Błońska, Ewa; Lasota, Jarosław

    2014-01-01

    The aim of this study was to assess the possibility of using biological and biochemical parameters in the evaluation of forest soil quality and changes caused by land use. The study attempted to determine a relationship between the enzymatic activity of soil, the number of earthworms and soil physico-chemical properties. The study was carried out in central Poland in adjoining Forest Districts (Przedbórz and Smardzewice). In soil samples taken from 12 research plots, basic physico-chem...