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Sample records for gene circuit analysis

  1. Gene Circuit Analysis of the Terminal Gap Gene huckebein

    Science.gov (United States)

    Ashyraliyev, Maksat; Siggens, Ken; Janssens, Hilde; Blom, Joke; Akam, Michael; Jaeger, Johannes

    2009-01-01

    The early embryo of Drosophila melanogaster provides a powerful model system to study the role of genes in pattern formation. The gap gene network constitutes the first zygotic regulatory tier in the hierarchy of the segmentation genes involved in specifying the position of body segments. Here, we use an integrative, systems-level approach to investigate the regulatory effect of the terminal gap gene huckebein (hkb) on gap gene expression. We present quantitative expression data for the Hkb protein, which enable us to include hkb in gap gene circuit models. Gap gene circuits are mathematical models of gene networks used as computational tools to extract regulatory information from spatial expression data. This is achieved by fitting the model to gap gene expression patterns, in order to obtain estimates for regulatory parameters which predict a specific network topology. We show how considering variability in the data combined with analysis of parameter determinability significantly improves the biological relevance and consistency of the approach. Our models are in agreement with earlier results, which they extend in two important respects: First, we show that Hkb is involved in the regulation of the posterior hunchback (hb) domain, but does not have any other essential function. Specifically, Hkb is required for the anterior shift in the posterior border of this domain, which is now reproduced correctly in our models. Second, gap gene circuits presented here are able to reproduce mutants of terminal gap genes, while previously published models were unable to reproduce any null mutants correctly. As a consequence, our models now capture the expression dynamics of all posterior gap genes and some variational properties of the system correctly. This is an important step towards a better, quantitative understanding of the developmental and evolutionary dynamics of the gap gene network. PMID:19876378

  2. Circuit analysis for dummies

    CERN Document Server

    Santiago, John

    2013-01-01

    Circuits overloaded from electric circuit analysis? Many universities require that students pursuing a degree in electrical or computer engineering take an Electric Circuit Analysis course to determine who will ""make the cut"" and continue in the degree program. Circuit Analysis For Dummies will help these students to better understand electric circuit analysis by presenting the information in an effective and straightforward manner. Circuit Analysis For Dummies gives you clear-cut information about the topics covered in an electric circuit analysis courses to help

  3. Parameter estimation and determinability analysis applied to Drosophila gap gene circuits

    Directory of Open Access Journals (Sweden)

    Jaeger Johannes

    2008-09-01

    Full Text Available Abstract Background Mathematical modeling of real-life processes often requires the estimation of unknown parameters. Once the parameters are found by means of optimization, it is important to assess the quality of the parameter estimates, especially if parameter values are used to draw biological conclusions from the model. Results In this paper we describe how the quality of parameter estimates can be analyzed. We apply our methodology to assess parameter determinability for gene circuit models of the gap gene network in early Drosophila embryos. Conclusion Our analysis shows that none of the parameters of the considered model can be determined individually with reasonable accuracy due to correlations between parameters. Therefore, the model cannot be used as a tool to infer quantitative regulatory weights. On the other hand, our results show that it is still possible to draw reliable qualitative conclusions on the regulatory topology of the gene network. Moreover, it improves previous analyses of the same model by allowing us to identify those interactions for which qualitative conclusions are reliable, and those for which they are ambiguous.

  4. Circuit analysis with Multisim

    CERN Document Server

    Baez-Lopez, David

    2011-01-01

    This book is concerned with circuit simulation using National Instruments Multisim. It focuses on the use and comprehension of the working techniques for electrical and electronic circuit simulation. The first chapters are devoted to basic circuit analysis.It starts by describing in detail how to perform a DC analysis using only resistors and independent and controlled sources. Then, it introduces capacitors and inductors to make a transient analysis. In the case of transient analysis, it is possible to have an initial condition either in the capacitor voltage or in the inductor current, or bo

  5. Electronic Circuit Analysis Language (ECAL)

    Science.gov (United States)

    Chenghang, C.

    1983-03-01

    The computer aided design technique is an important development in computer applications and it is an important component of computer science. The special language for electronic circuit analysis is the foundation of computer aided design or computer aided circuit analysis (abbreviated as CACD and CACA) of simulated circuits. Electronic circuit analysis language (ECAL) is a comparatively simple and easy to use circuit analysis special language which uses the FORTRAN language to carry out the explanatory executions. It is capable of conducting dc analysis, ac analysis, and transient analysis of a circuit. Futhermore, the results of the dc analysis can be used directly as the initial conditions for the ac and transient analyses.

  6. Identification of a new gene regulatory circuit involving B cell receptor activated signaling using a combined analysis of experimental, clinical and global gene expression data

    Science.gov (United States)

    Schrader, Alexandra; Meyer, Katharina; Walther, Neele; Stolz, Ailine; Feist, Maren; Hand, Elisabeth; von Bonin, Frederike; Evers, Maurits; Kohler, Christian; Shirneshan, Katayoon; Vockerodt, Martina; Klapper, Wolfram; Szczepanowski, Monika; Murray, Paul G.; Bastians, Holger; Trümper, Lorenz; Spang, Rainer; Kube, Dieter

    2016-01-01

    To discover new regulatory pathways in B lymphoma cells, we performed a combined analysis of experimental, clinical and global gene expression data. We identified a specific cluster of genes that was coherently expressed in primary lymphoma samples and suppressed by activation of the B cell receptor (BCR) through αIgM treatment of lymphoma cells in vitro. This gene cluster, which we called BCR.1, includes numerous cell cycle regulators. A reduced expression of BCR.1 genes after BCR activation was observed in different cell lines and also in CD10+ germinal center B cells. We found that BCR activation led to a delayed entry to and progression of mitosis and defects in metaphase. Cytogenetic changes were detected upon long-term αIgM treatment. Furthermore, an inverse correlation of BCR.1 genes with c-Myc co-regulated genes in distinct groups of lymphoma patients was observed. Finally, we showed that the BCR.1 index discriminates activated B cell-like and germinal centre B cell-like diffuse large B cell lymphoma supporting the functional relevance of this new regulatory circuit and the power of guided clustering for biomarker discovery. PMID:27166259

  7. Color Coding of Circuit Quantities in Introductory Circuit Analysis Instruction

    Science.gov (United States)

    Reisslein, Jana; Johnson, Amy M.; Reisslein, Martin

    2015-01-01

    Learning the analysis of electrical circuits represented by circuit diagrams is often challenging for novice students. An open research question in electrical circuit analysis instruction is whether color coding of the mathematical symbols (variables) that denote electrical quantities can improve circuit analysis learning. The present study…

  8. Automatic design of digital synthetic gene circuits.

    Directory of Open Access Journals (Sweden)

    Mario A Marchisio

    2011-02-01

    Full Text Available De novo computational design of synthetic gene circuits that achieve well-defined target functions is a hard task. Existing, brute-force approaches run optimization algorithms on the structure and on the kinetic parameter values of the network. However, more direct rational methods for automatic circuit design are lacking. Focusing on digital synthetic gene circuits, we developed a methodology and a corresponding tool for in silico automatic design. For a given truth table that specifies a circuit's input-output relations, our algorithm generates and ranks several possible circuit schemes without the need for any optimization. Logic behavior is reproduced by the action of regulatory factors and chemicals on the promoters and on the ribosome binding sites of biological Boolean gates. Simulations of circuits with up to four inputs show a faithful and unequivocal truth table representation, even under parametric perturbations and stochastic noise. A comparison with already implemented circuits, in addition, reveals the potential for simpler designs with the same function. Therefore, we expect the method to help both in devising new circuits and in simplifying existing solutions.

  9. Automatic circuit analysis based on mask information

    International Nuclear Information System (INIS)

    Preas, B.T.; Lindsay, B.W.; Gwyn, C.W.

    1976-01-01

    The Circuit Mask Translator (CMAT) code has been developed which converts integrated circuit mask information into a circuit schematic. Logical operations, pattern recognition, and special functions are used to identify and interconnect diodes, transistors, capacitors, and resistances. The circuit topology provided by the translator is compatible with the input required for a circuit analysis program

  10. Ancestral regulatory circuits governing ectoderm patterning downstream of Nodal and BMP2/4 revealed by gene regulatory network analysis in an echinoderm.

    Directory of Open Access Journals (Sweden)

    Alexandra Saudemont

    2010-12-01

    Full Text Available Echinoderms, which are phylogenetically related to vertebrates and produce large numbers of transparent embryos that can be experimentally manipulated, offer many advantages for the analysis of the gene regulatory networks (GRN regulating germ layer formation. During development of the sea urchin embryo, the ectoderm is the source of signals that pattern all three germ layers along the dorsal-ventral axis. How this signaling center controls patterning and morphogenesis of the embryo is not understood. Here, we report a large-scale analysis of the GRN deployed in response to the activity of this signaling center in the embryos of the Mediterranean sea urchin Paracentrotus lividus, in which studies with high spatial resolution are possible. By using a combination of in situ hybridization screening, overexpression of mRNA, recombinant ligand treatments, and morpholino-based loss-of-function studies, we identified a cohort of transcription factors and signaling molecules expressed in the ventral ectoderm, dorsal ectoderm, and interposed neurogenic ("ciliary band" region in response to the known key signaling molecules Nodal and BMP2/4 and defined the epistatic relationships between the most important genes. The resultant GRN showed a number of striking features. First, Nodal was found to be essential for the expression of all ventral and dorsal marker genes, and BMP2/4 for all dorsal genes. Second, goosecoid was identified as a central player in a regulatory sub-circuit controlling mouth formation, while tbx2/3 emerged as a critical factor for differentiation of the dorsal ectoderm. Finally, and unexpectedly, a neurogenic ectoderm regulatory circuit characterized by expression of "ciliary band" genes was triggered in the absence of TGF beta signaling. We propose a novel model for ectoderm regionalization, in which neural ectoderm is the default fate in the absence of TGF beta signaling, and suggest that the stomodeal and neural subcircuits that we

  11. [Smart therapeutics based on synthetic gene circuits].

    Science.gov (United States)

    Peng, Shuguang; Xie, Zhen

    2017-03-25

    Synthetic biology has an important impact on biology research since its birth. Applying the thought and methods that reference from electrical engineering, synthetic biology uncovers many regulatory mechanisms of life systems, transforms and expands a series of biological components. Therefore, it brings a wide range of biomedical applications, including providing new ideas for disease diagnosis and treatment. This review describes the latest advances in the field of disease diagnosis and therapy based on mammalian cell or bacterial synthetic gene circuits, and provides new ideas for future smart therapy design.

  12. Drosophila olfactory memory: single genes to complex neural circuits.

    Science.gov (United States)

    Keene, Alex C; Waddell, Scott

    2007-05-01

    A central goal of neuroscience is to understand how neural circuits encode memory and guide behaviour. Studying simple, genetically tractable organisms, such as Drosophila melanogaster, can illuminate principles of neural circuit organization and function. Early genetic dissection of D. melanogaster olfactory memory focused on individual genes and molecules. These molecular tags subsequently revealed key neural circuits for memory. Recent advances in genetic technology have allowed us to manipulate and observe activity in these circuits, and even individual neurons, in live animals. The studies have transformed D. melanogaster from a useful organism for gene discovery to an ideal model to understand neural circuit function in memory.

  13. Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity--a large-scale system analysis of decoded bacterial genomes.

    Science.gov (United States)

    Shestov, Maksim; Ontañón, Santiago; Tozeren, Aydin

    2015-10-13

    Bacterial infections comprise a global health challenge as the incidences of antibiotic resistance increase. Pathogenic potential of bacteria has been shown to be context dependent, varying in response to environment and even within the strains of the same genus. We used the KEGG repository and extensive literature searches to identify among the 2527 bacterial genomes in the literature those implicated as pathogenic to the host, including those which show pathogenicity in a context dependent manner. Using data on the gene contents of these genomes, we identified sets of genes highly abundant in pathogenic but relatively absent in commensal strains and vice versa. In addition, we carried out genome comparison within a genus for the seventeen largest genera in our genome collection. We projected the resultant lists of ortholog genes onto KEGG bacterial pathways to identify clusters and circuits, which can be linked to either pathogenicity or synergy. Gene circuits relatively abundant in nonpathogenic bacteria often mediated biosynthesis of antibiotics. Other synergy-linked circuits reduced drug-induced toxicity. Pathogen-abundant gene circuits included modules in one-carbon folate, two-component system, type-3 secretion system, and peptidoglycan biosynthesis. Antibiotics-resistant bacterial strains possessed genes modulating phagocytosis, vesicle trafficking, cytoskeletal reorganization, and regulation of the inflammatory response. Our study also identified bacterial genera containing a circuit, elements of which were previously linked to Alzheimer's disease. Present study produces for the first time, a signature, in the form of a robust list of gene circuitry whose presence or absence could potentially define the pathogenicity of a microbiome. Extensive literature search substantiated a bulk majority of the commensal and pathogenic circuitry in our predicted list. Scanning microbiome libraries for these circuitry motifs will provide further insights into the complex

  14. Analysis of Bernstein's factorization circuit

    NARCIS (Netherlands)

    Lenstra, A.K.; Shamir, A.; Tomlinson, J.; Tromer, E.; Zheng, Y.

    2002-01-01

    In [1], Bernstein proposed a circuit-based implementation of the matrix step of the number field sieve factorization algorithm. These circuits offer an asymptotic cost reduction under the measure "construction cost x run time". We evaluate the cost of these circuits, in agreement with [1], but argue

  15. Interrogating the topological robustness of gene regulatory circuits by randomization.

    Directory of Open Access Journals (Sweden)

    Bin Huang

    2017-03-01

    Full Text Available One of the most important roles of cells is performing their cellular tasks properly for survival. Cells usually achieve robust functionality, for example, cell-fate decision-making and signal transduction, through multiple layers of regulation involving many genes. Despite the combinatorial complexity of gene regulation, its quantitative behavior has been typically studied on the basis of experimentally verified core gene regulatory circuitry, composed of a small set of important elements. It is still unclear how such a core circuit operates in the presence of many other regulatory molecules and in a crowded and noisy cellular environment. Here we report a new computational method, named random circuit perturbation (RACIPE, for interrogating the robust dynamical behavior of a gene regulatory circuit even without accurate measurements of circuit kinetic parameters. RACIPE generates an ensemble of random kinetic models corresponding to a fixed circuit topology, and utilizes statistical tools to identify generic properties of the circuit. By applying RACIPE to simple toggle-switch-like motifs, we observed that the stable states of all models converge to experimentally observed gene state clusters even when the parameters are strongly perturbed. RACIPE was further applied to a proposed 22-gene network of the Epithelial-to-Mesenchymal Transition (EMT, from which we identified four experimentally observed gene states, including the states that are associated with two different types of hybrid Epithelial/Mesenchymal phenotypes. Our results suggest that dynamics of a gene circuit is mainly determined by its topology, not by detailed circuit parameters. Our work provides a theoretical foundation for circuit-based systems biology modeling. We anticipate RACIPE to be a powerful tool to predict and decode circuit design principles in an unbiased manner, and to quantitatively evaluate the robustness and heterogeneity of gene expression.

  16. The analysis and design of linear circuits

    CERN Document Server

    Thomas, Roland E; Toussaint, Gregory J

    2009-01-01

    The Analysis and Design of Linear Circuits, 6e gives the reader the opportunity to not only analyze, but also design and evaluate linear circuits as early as possible. The text's abundance of problems, applications, pedagogical tools, and realistic examples helps engineers develop the skills needed to solve problems, design practical alternatives, and choose the best design from several competing solutions. Engineers searching for an accessible introduction to resistance circuits will benefit from this book that emphasizes the early development of engineering judgment.

  17. Digital Circuit Analysis Using an 8080 Processor.

    Science.gov (United States)

    Greco, John; Stern, Kenneth

    1983-01-01

    Presents the essentials of a program written in Intel 8080 assembly language for the steady state analysis of a combinatorial logic gate circuit. Program features and potential modifications are considered. For example, the program could also be extended to include clocked/unclocked sequential circuits. (JN)

  18. Equivalent circuit analysis of terahertz metamaterial filters

    KAUST Repository

    Zhang, Xueqian

    2011-01-01

    An equivalent circuit model for the analysis and design of terahertz (THz) metamaterial filters is presented. The proposed model, derived based on LMC equivalent circuits, takes into account the detailed geometrical parameters and the presence of a dielectric substrate with the existing analytic expressions for self-inductance, mutual inductance, and capacitance. The model is in good agreement with the experimental measurements and full-wave simulations. Exploiting the circuit model has made it possible to predict accurately the resonance frequency of the proposed structures and thus, quick and accurate process of designing THz device from artificial metamaterials is offered. ©2011 Chinese Optics Letters.

  19. Operational amplifier circuits analysis and design

    CERN Document Server

    Nelson, J C C

    1995-01-01

    This book, a revised and updated version of the author's Basic Operational Amplifiers (Butterworths 1986), enables the non-specialist to make effective use of readily available integrated circuit operational amplifiers for a range of applications, including instrumentation, signal generation and processing.It is assumed the reader has a background in the basic techniques of circuit analysis, particularly the use of j notation for reactive circuits, with a corresponding level of mathematical ability. The underlying theory is explained with sufficient but not excessive, detail. A range of compu

  20. Activity-regulated genes as mediators of neural circuit plasticity.

    Science.gov (United States)

    Leslie, Jennifer H; Nedivi, Elly

    2011-08-01

    Modifications of neuronal circuits allow the brain to adapt and change with experience. This plasticity manifests during development and throughout life, and can be remarkably long lasting. Evidence has linked activity-regulated gene expression to the long-term structural and electrophysiological adaptations that take place during developmental critical periods, learning and memory, and alterations to sensory map representations in the adult. In all these cases, the cellular response to neuronal activity integrates multiple tightly coordinated mechanisms to precisely orchestrate long-lasting, functional and structural changes in brain circuits. Experience-dependent plasticity is triggered when neuronal excitation activates cellular signaling pathways from the synapse to the nucleus that initiate new programs of gene expression. The protein products of activity-regulated genes then work via a diverse array of cellular mechanisms to modify neuronal functional properties. Synaptic strengthening or weakening can reweight existing circuit connections, while structural changes including synapse addition and elimination create new connections. Posttranscriptional regulatory mechanisms, often also dependent on activity, further modulate activity-regulated gene transcript and protein function. Thus, activity-regulated genes implement varied forms of structural and functional plasticity to fine-tune brain circuit wiring. Copyright © 2011 Elsevier Ltd. All rights reserved.

  1. State-Space Formulation for Circuit Analysis

    Science.gov (United States)

    Martinez-Marin, T.

    2010-01-01

    This paper presents a new state-space approach for temporal analysis of electrical circuits. The method systematically obtains the state-space formulation of nondegenerate linear networks without using concepts of topology. It employs nodal/mesh systematic analysis to reduce the number of undesired variables. This approach helps students to…

  2. Feedback analysis of transimpedance operational amplifier circuits

    DEFF Research Database (Denmark)

    Bruun, Erik

    1993-01-01

    The transimpedance or current feedback operational amplifier (CFB op-amp) is reviewed and compared to a conventional voltage mode op-amp using an analysis emphasizing the basic feedback characteristics of the circuit. With this approach the paradox of the constant bandwidth obtained from CFB op...

  3. Electromagnetic compatibility methods, analysis, circuits, and measurement

    CERN Document Server

    Weston, David A

    2016-01-01

    Revised, updated, and expanded, Electromagnetic Compatibility: Methods, Analysis, Circuits, and Measurement, Third Edition provides comprehensive practical coverage of the design, problem solving, and testing of electromagnetic compatibility (EMC) in electrical and electronic equipment and systems. This new edition provides novel information on theory, applications, evaluations, electromagnetic computational programs, and prediction techniques available. With sixty-nine schematics providing examples for circuit level electromagnetic interference (EMI) hardening and cost effective EMI problem solving, this book also includes 1130 illustrations and tables. Including extensive data on components and their correct implementation, the myths, misapplication, misconceptions, and fallacies that are common when discussing EMC/EMI will also be addressed and corrected.

  4. Modular thought in the circuit analysis

    Science.gov (United States)

    Wang, Feng

    2018-04-01

    Applied to solve the problem of modular thought, provides a whole for simplification's method, the complex problems have become of, and the study of circuit is similar to the above problems: the complex connection between components, make the whole circuit topic solution seems to be more complex, and actually components the connection between the have rules to follow, this article mainly tells the story of study on the application of the circuit modular thought. First of all, this paper introduces the definition of two-terminal network and the concept of two-terminal network equivalent conversion, then summarizes the common source resistance hybrid network modular approach, containing controlled source network modular processing method, lists the common module, typical examples analysis.

  5. Automatic Design of Synthetic Gene Circuits through Mixed Integer Non-linear Programming

    Science.gov (United States)

    Huynh, Linh; Kececioglu, John; Köppe, Matthias; Tagkopoulos, Ilias

    2012-01-01

    Automatic design of synthetic gene circuits poses a significant challenge to synthetic biology, primarily due to the complexity of biological systems, and the lack of rigorous optimization methods that can cope with the combinatorial explosion as the number of biological parts increases. Current optimization methods for synthetic gene design rely on heuristic algorithms that are usually not deterministic, deliver sub-optimal solutions, and provide no guaranties on convergence or error bounds. Here, we introduce an optimization framework for the problem of part selection in synthetic gene circuits that is based on mixed integer non-linear programming (MINLP), which is a deterministic method that finds the globally optimal solution and guarantees convergence in finite time. Given a synthetic gene circuit, a library of characterized parts, and user-defined constraints, our method can find the optimal selection of parts that satisfy the constraints and best approximates the objective function given by the user. We evaluated the proposed method in the design of three synthetic circuits (a toggle switch, a transcriptional cascade, and a band detector), with both experimentally constructed and synthetic promoter libraries. Scalability and robustness analysis shows that the proposed framework scales well with the library size and the solution space. The work described here is a step towards a unifying, realistic framework for the automated design of biological circuits. PMID:22536398

  6. Analysis of electronic circuits using digital computers

    International Nuclear Information System (INIS)

    Tapu, C.

    1968-01-01

    Various programmes have been proposed for studying electronic circuits with the help of computers. It is shown here how it possible to use the programme ECAP, developed by I.B.M., for studying the behaviour of an operational amplifier from different point of view: direct current, alternating current and transient state analysis, optimisation of the gain in open loop, study of the reliability. (author) [fr

  7. Genome engineering using a synthetic gene circuit in Bacillus subtilis.

    Science.gov (United States)

    Jeong, Da-Eun; Park, Seung-Hwan; Pan, Jae-Gu; Kim, Eui-Joong; Choi, Soo-Keun

    2015-03-31

    Genome engineering without leaving foreign DNA behind requires an efficient counter-selectable marker system. Here, we developed a genome engineering method in Bacillus subtilis using a synthetic gene circuit as a counter-selectable marker system. The system contained two repressible promoters (B. subtilis xylA (Pxyl) and spac (Pspac)) and two repressor genes (lacI and xylR). Pxyl-lacI was integrated into the B. subtilis genome with a target gene containing a desired mutation. The xylR and Pspac-chloramphenicol resistant genes (cat) were located on a helper plasmid. In the presence of xylose, repression of XylR by xylose induced LacI expression, the LacIs repressed the Pspac promoter and the cells become chloramphenicol sensitive. Thus, to survive in the presence of chloramphenicol, the cell must delete Pxyl-lacI by recombination between the wild-type and mutated target genes. The recombination leads to mutation of the target gene. The remaining helper plasmid was removed easily under the chloramphenicol absent condition. In this study, we showed base insertion, deletion and point mutation of the B. subtilis genome without leaving any foreign DNA behind. Additionally, we successfully deleted a 2-kb gene (amyE) and a 38-kb operon (ppsABCDE). This method will be useful to construct designer Bacillus strains for various industrial applications. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. A Simple Short Circuit Analysis for Power Networks

    Directory of Open Access Journals (Sweden)

    Koşalay İlhan

    2016-01-01

    Full Text Available This study investigates the transient behavior of short circuits in power circuits. The circuit consists of two part; input part and load part. These two parts are connected with a circuit breaker switch. The circuit works in two modes; first mode is when the switch is open and second mode is when the switch is closed. This study analyses the circuit when the switch is closed. The analysis is done with different types of closing angle. The analysis is done by forming state equations and those equations are solved numerically by using Matlab. The analysis and conclusion is performed by observing the behaviors of the graphs.

  9. Logic analysis and verification of n-input genetic logic circuits

    DEFF Research Database (Denmark)

    Baig, Hasan; Madsen, Jan

    2017-01-01

    . In this paper, we present an approach to analyze and verify the Boolean logic of a genetic circuit from the data obtained through stochastic analog circuit simulations. The usefulness of this analysis is demonstrated through different case studies illustrating how our approach can be used to verify the expected......Nature is using genetic logic circuits to regulate the fundamental processes of life. These genetic logic circuits are triggered by a combination of external signals, such as chemicals, proteins, light and temperature, to emit signals to control other gene expressions or metabolic pathways...... accordingly. As compared to electronic circuits, genetic circuits exhibit stochastic behavior and do not always behave as intended. Therefore, there is a growing interest in being able to analyze and verify the logical behavior of a genetic circuit model, prior to its physical implementation in a laboratory...

  10. A fast circuit analysis program based on microcomputer

    International Nuclear Information System (INIS)

    Hu Guoji

    1988-01-01

    A fast circuit analysis program (FCAP) is introduced. The program may be used to analyse DC operating point, frequency and transient response of fast circuit. The feature is that the model of active element is not specified. Users may choose one of many equivalent circuits. Written in FORTRAN 77, FCAP can be run on IBM PC and its compatible computers. It can be used as an assistant tool of analysis and design for fast circuits

  11. Design, Analysis and Test of Logic Circuits Under Uncertainty

    CERN Document Server

    Krishnaswamy, Smita; Hayes, John P

    2013-01-01

    Integrated circuits (ICs) increasingly exhibit uncertain characteristics due to soft errors, inherently probabilistic devices, and manufacturing variability. As device technologies scale, these effects can be detrimental to the reliability of logic circuits.  To improve future semiconductor designs, this book describes methods for analyzing, designing, and testing circuits subject to probabilistic effects. The authors first develop techniques to model inherently probabilistic methods in logic circuits and to test circuits for determining their reliability after they are manufactured. Then, they study error-masking mechanisms intrinsic to digital circuits and show how to leverage them to design more reliable circuits.  The book describes techniques for:   • Modeling and reasoning about probabilistic behavior in logic circuits, including a matrix-based reliability-analysis framework;   • Accurate analysis of soft-error rate (SER) based on functional-simulation, sufficiently scalable for use in gate-l...

  12. Timing Analysis of Genetic Logic Circuits using D-VASim

    DEFF Research Database (Denmark)

    Baig, Hasan; Madsen, Jan

    and propagation delay analysis of single as well as cascaded geneticlogic circuits can be performed. D-VASim allows user to change the circuit parameters during runtime simulation to observe its effectson circuit’s timing behavior. The results obtained from D-VASim can be used not only to characterize the timing...... delay analysis may play a very significant role in the designing of genetic logic circuits. In thisdemonstration, we present the capability of D-VASim (Dynamic Virtual Analyzer and Simulator) to perform the timing and propagationdelay analysis of genetic logic circuits. Using D-VASim, the timing...... behavior of geneticlogic circuits but also to analyze the timing constraints of cascaded genetic logic circuits....

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

    Science.gov (United States)

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

    2018-02-06

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

  14. Oscillator circuits frontiers in design, analysis and applications

    CERN Document Server

    2016-01-01

    This book surveys recent developments in the design, analysis and applications of oscillator circuit design. It highlights developments in the analysis of synchronization and wave phenomena, new analytical and design methods and their application, and novel engineering applications of oscillator circuits.

  15. Time series analysis in chaotic diode resonator circuit

    Energy Technology Data Exchange (ETDEWEB)

    Hanias, M.P. [TEI of Chalkis, GR 34400, Evia, Chalkis (Greece)] e-mail: mhanias@teihal.gr; Giannaris, G. [TEI of Chalkis, GR 34400, Evia, Chalkis (Greece); Spyridakis, A. [TEI of Chalkis, GR 34400, Evia, Chalkis (Greece); Rigas, A. [TEI of Chalkis, GR 34400, Evia, Chalkis (Greece)

    2006-01-01

    A diode resonator chaotic circuit is presented. Multisim is used to simulate the circuit and show the presence of chaos. Time series analysis performed by the method proposed by Grasberger and Procaccia. The correlation and minimum embedding dimension {nu} and m {sub min}, respectively, were calculated. Also the corresponding Kolmogorov entropy was calculated.

  16. Time series analysis in chaotic diode resonator circuit

    International Nuclear Information System (INIS)

    Hanias, M.P.; Giannaris, G.; Spyridakis, A.; Rigas, A.

    2006-01-01

    A diode resonator chaotic circuit is presented. Multisim is used to simulate the circuit and show the presence of chaos. Time series analysis performed by the method proposed by Grasberger and Procaccia. The correlation and minimum embedding dimension ν and m min , respectively, were calculated. Also the corresponding Kolmogorov entropy was calculated

  17. Nonlinear analysis of ring oscillator circuits

    KAUST Repository

    Ge, Xiaoqing

    2010-06-01

    Using nonlinear systems techniques, we analyze the stability properties and synchronization conditions for ring oscillator circuits, which are essential building blocks in digital systems. By making use of its cyclic structure, we investigate local and global stability properties of an n-stage ring oscillator. We present a sufficient condition for global asymptotic stability of the origin and obtain necessity if the ring oscillator consists of identical inverter elements. We then give a synchronization condition for identical interconnected ring oscillators.

  18. Nonlinear analysis of ring oscillator circuits

    KAUST Repository

    Ge, Xiaoqing; Arcak, Murat; Salama, Khaled N.

    2010-01-01

    Using nonlinear systems techniques, we analyze the stability properties and synchronization conditions for ring oscillator circuits, which are essential building blocks in digital systems. By making use of its cyclic structure, we investigate local and global stability properties of an n-stage ring oscillator. We present a sufficient condition for global asymptotic stability of the origin and obtain necessity if the ring oscillator consists of identical inverter elements. We then give a synchronization condition for identical interconnected ring oscillators.

  19. Synchronous long-term oscillations in a synthetic gene circuit.

    Science.gov (United States)

    Potvin-Trottier, Laurent; Lord, Nathan D; Vinnicombe, Glenn; Paulsson, Johan

    2016-10-27

    Synthetically engineered genetic circuits can perform a wide variety of tasks but are generally less accurate than natural systems. Here we revisit the first synthetic genetic oscillator, the repressilator, and modify it using principles from stochastic chemistry in single cells. Specifically, we sought to reduce error propagation and information losses, not by adding control loops, but by simply removing existing features. We show that this modification created highly regular and robust oscillations. Furthermore, some streamlined circuits kept 14 generation periods over a range of growth conditions and kept phase for hundreds of generations in single cells, allowing cells in flasks and colonies to oscillate synchronously without any coupling between them. Our results suggest that even the simplest synthetic genetic networks can achieve a precision that rivals natural systems, and emphasize the importance of noise analyses for circuit design in synthetic biology.

  20. Thermally-induced voltage alteration for integrated circuit analysis

    Energy Technology Data Exchange (ETDEWEB)

    Cole, E.I. Jr.

    2000-06-20

    A thermally-induced voltage alteration (TIVA) apparatus and method are disclosed for analyzing an integrated circuit (IC) either from a device side of the IC or through the IC substrate to locate any open-circuit or short-circuit defects therein. The TIVA apparatus uses constant-current biasing of the IC while scanning a focused laser beam over electrical conductors (i.e. a patterned metallization) in the IC to produce localized heating of the conductors. This localized heating produces a thermoelectric potential due to the Seebeck effect in any conductors with open-circuit defects and a resistance change in any conductors with short-circuit defects, both of which alter the power demand by the IC and thereby change the voltage of a source or power supply providing the constant-current biasing. By measuring the change in the supply voltage and the position of the focused and scanned laser beam over time, any open-circuit or short-circuit defects in the IC can be located and imaged. The TIVA apparatus can be formed in part from a scanning optical microscope, and has applications for qualification testing or failure analysis of ICs.

  1. Parts & Pools: A Framework for Modular Design of Synthetic Gene Circuits

    International Nuclear Information System (INIS)

    Marchisio, Mario Andrea

    2014-01-01

    Published in 2008, Parts & Pools represents one of the first attempts to conceptualize the modular design of bacterial synthetic gene circuits with Standard Biological Parts (DNA segments) and Pools of molecules referred to as common signal carriers (e.g., RNA polymerases and ribosomes). The original framework for modeling bacterial components and designing prokaryotic circuits evolved over the last years and brought, first, to the development of an algorithm for the automatic design of Boolean gene circuits. This is a remarkable achievement since gene digital circuits have a broad range of applications that goes from biosensors for health and environment care to computational devices. More recently, Parts & Pools was enabled to give a proper formal description of eukaryotic biological circuit components. This was possible by employing a rule-based modeling approach, a technique that permits a faithful calculation of all the species and reactions involved in complex systems such as eukaryotic cells and compartments. In this way, Parts & Pools is currently suitable for the visual and modular design of synthetic gene circuits in yeast and mammalian cells too.

  2. Parts & Pools: A Framework for Modular Design of Synthetic Gene Circuits

    Energy Technology Data Exchange (ETDEWEB)

    Marchisio, Mario Andrea, E-mail: marchisio@hit.edu.cn [School of Life Science and Technology, Harbin Institute of Technology, Harbin (China)

    2014-10-06

    Published in 2008, Parts & Pools represents one of the first attempts to conceptualize the modular design of bacterial synthetic gene circuits with Standard Biological Parts (DNA segments) and Pools of molecules referred to as common signal carriers (e.g., RNA polymerases and ribosomes). The original framework for modeling bacterial components and designing prokaryotic circuits evolved over the last years and brought, first, to the development of an algorithm for the automatic design of Boolean gene circuits. This is a remarkable achievement since gene digital circuits have a broad range of applications that goes from biosensors for health and environment care to computational devices. More recently, Parts & Pools was enabled to give a proper formal description of eukaryotic biological circuit components. This was possible by employing a rule-based modeling approach, a technique that permits a faithful calculation of all the species and reactions involved in complex systems such as eukaryotic cells and compartments. In this way, Parts & Pools is currently suitable for the visual and modular design of synthetic gene circuits in yeast and mammalian cells too.

  3. Cable Hot Shorts and Circuit Analysis in Fire Risk Assessment

    International Nuclear Information System (INIS)

    LaChance, Jeffrey; Nowlen, Steven P.; Wyant, Frank

    1999-01-01

    Under existing methods of probabilistic risk assessment (PRA), the analysis of fire-induced circuit faults has typically been conducted on a simplistic basis. In particular, those hot-short methodologies that have been applied remain controversial in regards to the scope of the assessments, the underlying methods, and the assumptions employed. To address weaknesses in fire PRA methodologies, the USNRC has initiated a fire risk analysis research program that includes a task for improving the tools for performing circuit analysis. The objective of this task is to obtain a better understanding of the mechanisms linking fire-induced cable damage to potentially risk-significant failure modes of power, control, and instrumentation cables. This paper discusses the current status of the circuit analysis task

  4. A framework for scalable parameter estimation of gene circuit models using structural information

    KAUST Repository

    Kuwahara, Hiroyuki

    2013-06-21

    Motivation: Systematic and scalable parameter estimation is a key to construct complex gene regulatory models and to ultimately facilitate an integrative systems biology approach to quantitatively understand the molecular mechanisms underpinning gene regulation. Results: Here, we report a novel framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits. Exploiting the structure commonly found in gene circuit models, this framework decomposes a system of coupled rate equations into individual ones and efficiently integrates them separately to reconstruct the mean time evolution of the gene products. The accuracy of the parameter estimates is refined by iteratively increasing the accuracy of numerical integration using the model structure. As a case study, we applied our framework to four gene circuit models with complex dynamics based on three synthetic datasets and one time series microarray data set. We compared our framework to three state-of-the-art parameter estimation methods and found that our approach consistently generated higher quality parameter solutions efficiently. Although many general-purpose parameter estimation methods have been applied for modeling of gene circuits, our results suggest that the use of more tailored approaches to use domain-specific information may be a key to reverse engineering of complex biological systems. The Author 2013.

  5. A framework for scalable parameter estimation of gene circuit models using structural information

    KAUST Repository

    Kuwahara, Hiroyuki; Fan, Ming; Wang, Suojin; Gao, Xin

    2013-01-01

    Motivation: Systematic and scalable parameter estimation is a key to construct complex gene regulatory models and to ultimately facilitate an integrative systems biology approach to quantitatively understand the molecular mechanisms underpinning gene regulation. Results: Here, we report a novel framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits. Exploiting the structure commonly found in gene circuit models, this framework decomposes a system of coupled rate equations into individual ones and efficiently integrates them separately to reconstruct the mean time evolution of the gene products. The accuracy of the parameter estimates is refined by iteratively increasing the accuracy of numerical integration using the model structure. As a case study, we applied our framework to four gene circuit models with complex dynamics based on three synthetic datasets and one time series microarray data set. We compared our framework to three state-of-the-art parameter estimation methods and found that our approach consistently generated higher quality parameter solutions efficiently. Although many general-purpose parameter estimation methods have been applied for modeling of gene circuits, our results suggest that the use of more tailored approaches to use domain-specific information may be a key to reverse engineering of complex biological systems. The Author 2013.

  6. A framework for scalable parameter estimation of gene circuit models using structural information.

    Science.gov (United States)

    Kuwahara, Hiroyuki; Fan, Ming; Wang, Suojin; Gao, Xin

    2013-07-01

    Systematic and scalable parameter estimation is a key to construct complex gene regulatory models and to ultimately facilitate an integrative systems biology approach to quantitatively understand the molecular mechanisms underpinning gene regulation. Here, we report a novel framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits. Exploiting the structure commonly found in gene circuit models, this framework decomposes a system of coupled rate equations into individual ones and efficiently integrates them separately to reconstruct the mean time evolution of the gene products. The accuracy of the parameter estimates is refined by iteratively increasing the accuracy of numerical integration using the model structure. As a case study, we applied our framework to four gene circuit models with complex dynamics based on three synthetic datasets and one time series microarray data set. We compared our framework to three state-of-the-art parameter estimation methods and found that our approach consistently generated higher quality parameter solutions efficiently. Although many general-purpose parameter estimation methods have been applied for modeling of gene circuits, our results suggest that the use of more tailored approaches to use domain-specific information may be a key to reverse engineering of complex biological systems. http://sfb.kaust.edu.sa/Pages/Software.aspx. Supplementary data are available at Bioinformatics online.

  7. Web-Based Trainer for Electrical Circuit Analysis

    Science.gov (United States)

    Weyten, L.; Rombouts, P.; De Maeyer, J.

    2009-01-01

    A Web-based system for training electric circuit analysis is presented in this paper. It is centered on symbolic analysis techniques and it not only verifies the student's final answer, but it also tracks and coaches him/her through all steps of his/her reasoning path. The system mimics homework assignments, enhanced by immediate personalized…

  8. Integrated genomic and gene expression profiling identifies two major genomic circuits in urothelial carcinoma.

    Directory of Open Access Journals (Sweden)

    David Lindgren

    Full Text Available Similar to other malignancies, urothelial carcinoma (UC is characterized by specific recurrent chromosomal aberrations and gene mutations. However, the interconnection between specific genomic alterations, and how patterns of chromosomal alterations adhere to different molecular subgroups of UC, is less clear. We applied tiling resolution array CGH to 146 cases of UC and identified a number of regions harboring recurrent focal genomic amplifications and deletions. Several potential oncogenes were included in the amplified regions, including known oncogenes like E2F3, CCND1, and CCNE1, as well as new candidate genes, such as SETDB1 (1q21, and BCL2L1 (20q11. We next combined genome profiling with global gene expression, gene mutation, and protein expression data and identified two major genomic circuits operating in urothelial carcinoma. The first circuit was characterized by FGFR3 alterations, overexpression of CCND1, and 9q and CDKN2A deletions. The second circuit was defined by E3F3 amplifications and RB1 deletions, as well as gains of 5p, deletions at PTEN and 2q36, 16q, 20q, and elevated CDKN2A levels. TP53/MDM2 alterations were common for advanced tumors within the two circuits. Our data also suggest a possible RAS/RAF circuit. The tumors with worst prognosis showed a gene expression profile that indicated a keratinized phenotype. Taken together, our integrative approach revealed at least two separate networks of genomic alterations linked to the molecular diversity seen in UC, and that these circuits may reflect distinct pathways of tumor development.

  9. A Computer Program for Short Circuit Analysis of Electric Power ...

    African Journals Online (AJOL)

    The Short Circuit Analysis Program (SCAP) is to be used to assess the composite effects of unbalanced and balanced faults on the overall reliability of electric power system. The program uses the symmetrical components method to compute all phase and sequence quantities for any bus or branch of a given power network ...

  10. Circuit analysis and computer simulations of ZT-40M

    International Nuclear Information System (INIS)

    Melton, J.G.

    1981-01-01

    The network analysis code SCEPTRE was extensively used to predict circuit performance under both normal and fault conditions. SCEPTRE's capabilities enabled us to include realistic nonlinear models for such components as the PF iron cores, the PCB transformers, the ignition switches, and even the complicated way in which the plasma couples the two circuits. Fault conditions for which protective measures were devised include; failure to achieve gas breakdown; disruption of the plasma current; saturation of the PF iron cores; prefire of a crowbar ignitron; overvoltage due to transients on the coax cables

  11. Modular design of synthetic gene circuits with biological parts and pools.

    Science.gov (United States)

    Marchisio, Mario Andrea

    2015-01-01

    Synthetic gene circuits can be designed in an electronic fashion by displaying their basic components-Standard Biological Parts and Pools of molecules-on the computer screen and connecting them with hypothetical wires. This procedure, achieved by our add-on for the software ProMoT, was successfully applied to bacterial circuits. Recently, we have extended this design-methodology to eukaryotic cells. Here, highly complex components such as promoters and Pools of mRNA contain hundreds of species and reactions whose calculation demands a rule-based modeling approach. We showed how to build such complex modules via the joint employment of the software BioNetGen (rule-based modeling) and ProMoT (modularization). In this chapter, we illustrate how to utilize our computational tool for synthetic biology with the in silico implementation of a simple eukaryotic gene circuit that performs the logic AND operation.

  12. A positive feedback-based gene circuit to increase the production of a membrane protein

    Directory of Open Access Journals (Sweden)

    Gennis Robert B

    2010-05-01

    Full Text Available Abstract Background Membrane proteins are an important class of proteins, playing a key role in many biological processes, and are a promising target in pharmaceutical development. However, membrane proteins are often difficult to produce in large quantities for the purpose of crystallographic or biochemical analyses. Results In this paper, we demonstrate that synthetic gene circuits designed specifically to overexpress certain genes can be applied to manipulate the expression kinetics of a model membrane protein, cytochrome bd quinol oxidase in E. coli, resulting in increased expression rates. The synthetic circuit involved is an engineered, autoinducer-independent variant of the lux operon activator LuxR from V. fischeri in an autoregulatory, positive feedback configuration. Conclusions Our proof-of-concept experiments indicate a statistically significant increase in the rate of production of the bd oxidase membrane protein. Synthetic gene networks provide a feasible solution for the problem of membrane protein production.

  13. Chaos in Electronic Circuits: Nonlinear Time Series Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Wheat, Jr., Robert M. [Kennedy Western Univ., Cheyenne, WY (United States)

    2003-07-01

    Chaos in electronic circuits is a phenomenon that has been largely ignored by engineers, manufacturers, and researchers until the early 1990’s and the work of Chua, Matsumoto, and others. As the world becomes more dependent on electronic devices, the detrimental effects of non-normal operation of these devices becomes more significant. Developing a better understanding of the mechanisms involved in the chaotic behavior of electronic circuits is a logical step toward the prediction and prevention of any potentially catastrophic occurrence of this phenomenon. Also, a better understanding of chaotic behavior, in a general sense, could potentially lead to better accuracy in the prediction of natural events such as weather, volcanic activity, and earthquakes. As a first step in this improvement of understanding, and as part of the research being reported here, methods of computer modeling, identifying and analyzing, and producing chaotic behavior in simple electronic circuits have been developed. The computer models were developed using both the Alternative Transient Program (ATP) and Spice, the analysis techniques have been implemented using the C and C++ programming languages, and the chaotically behaving circuits developed using “off the shelf” electronic components.

  14. Analysis of multiple spurions and associated circuits in Cofrentes

    International Nuclear Information System (INIS)

    Molina, J. J.; Celaya, M. A.

    2015-01-01

    The article describes the process followed by the Cofrentes Nuclear Power Plant (CNC) to conduct the analysis of multiple spurious in compliance with regulatory standards IS-30 rev 1 and CSN Safety Guide 1.19 based on the recommendations of the NEI-00-01 Guidance for Post-fire Safe Shutdown Circuit and NUREG/CR-6850. Fire PRA Methodology for Nuclear Power Facilities. (Author)

  15. Design and engineering of intracellular-metabolite-sensing/regulation gene circuits in Saccharomyces cerevisiae.

    Science.gov (United States)

    Wang, Meng; Li, Sijin; Zhao, Huimin

    2016-01-01

    The development of high-throughput phenotyping tools is lagging far behind the rapid advances of genotype generation methods. To bridge this gap, we report a new strategy for design, construction, and fine-tuning of intracellular-metabolite-sensing/regulation gene circuits by repurposing bacterial transcription factors and eukaryotic promoters. As proof of concept, we systematically investigated the design and engineering of bacterial repressor-based xylose-sensing/regulation gene circuits in Saccharomyces cerevisiae. We demonstrated that numerous properties, such as induction ratio and dose-response curve, can be fine-tuned at three different nodes, including repressor expression level, operator position, and operator sequence. By applying these gene circuits, we developed a cell sorting based, rapid and robust high-throughput screening method for xylose transporter engineering and obtained a sugar transporter HXT14 mutant with 6.5-fold improvement in xylose transportation capacity. This strategy should be generally applicable and highly useful for evolutionary engineering of proteins, pathways, and genomes in S. cerevisiae. © 2015 Wiley Periodicals, Inc.

  16. Genes co-regulated with LBD16 in nematode feeding sites inferred from in silico analysis show similarities to regulatory circuits mediated by the auxin/cytokinin balance in Arabidopsis.

    Science.gov (United States)

    Cabrera, Javier; Fenoll, Carmen; Escobar, Carolina

    2015-01-01

    Plant endoparasitic nematodes, root-knot and cyst nematodes (RKNs and CNs) induce within the root vascular cylinder transfer cells used for nourishing, termed giant cells (GCs) and syncytia. Understanding the molecular mechanisms behind this process is essential to develop tools for nematode control. Based on the crucial role in gall development of LBD16, also a key component of the auxin pathway leading to the divisions in the xylem pole pericycle during lateral root (LR) formation, we investigated genes co-regulated with LBD16 in different transcriptomes and analyzed their similarities and differences with those of RKNs and CNs feeding sites (FS). This analysis confirmed LBD16 and its co-regulated genes, integrated in signaling cascades mediated by auxins during LR and callus formation, as a particular feature of RKN-FS distinct to CNs. However, LBD16, and its positively co-regulated genes, were repressed in syncytia, suggesting a selective down- regulation of the LBD16 auxin mediated pathways in CNs-FS. Interestingly, cytokinin-induced genes are enriched in syncytia and we encountered similarities between the transcriptome of shoot regeneration from callus, modulated by cytokinins, and that of syncytia. These findings establish differences in the regulatory networks leading to both FS formation, probably modulated by the auxin/cytokinin balance.

  17. Optogenetic dissection of neuronal circuits in zebrafish using viral gene transfer and the Tet system

    Directory of Open Access Journals (Sweden)

    Peixin Zhu

    2009-12-01

    Full Text Available The conditional expression of transgenes at high levels in sparse and specific populations of neurons is important for high-resolution optogenetic analyses of neuronal circuits. We explored two complementary methods, viral gene delivery and the iTet-Off system, to express transgenes in the brain of zebrafish. High-level gene expression in neurons was achieved by Sindbis and Rabies viruses. The Tet system produced strong and specific gene expression that could be modulated conveniently by doxycycline. Moreover, transgenic lines showed expression in distinct, sparse and stable populations of neurons that appeared to be subsets of the neurons targeted by the promoter driving the Tet activator. The Tet system therefore provides the opportunity to generate libraries of diverse expression patterns similar to gene trap approaches or the thy-1 promoter in mice, but with the additional possibility to pre-select cell types of interest. In transgenic lines expressing channelrhodopsin-2, action potential firing could be precisely controlled by two-photon stimulation at low laser power, presumably because the expression levels of the Tet-controlled genes were high even in adults. In channelrhodopsin-2-expressing larvae, optical stimulation with a single blue LED evoked distinct swimming behaviors including backward swimming. These approaches provide new opportunities for the optogenetic dissection of neuronal circuit structure and function.

  18. ECAP-370/IFIN - A program for the analysis of electrical and electronic circuits

    International Nuclear Information System (INIS)

    Marinescu, C.D.

    1978-05-01

    A program to be used as a tool for electrical and electronic circuit design is presented. The program performs the DC, AC, and transient analysis for circuits with a given topological structure. (author)

  19. Analysis and application of analog electronic circuits to biomedical instrumentation

    CERN Document Server

    Northrop, Robert B

    2003-01-01

    This book introduces the basic mathematical tools used to describe noise and its propagation through linear systems and provides a basic description of the improvement of signal-to-noise ratio by signal averaging and linear filtering. The text also demonstrates how op amps are the keystone of modern analog signal conditioning systems design, and illustrates their use in isolation and instrumentation amplifiers, active filters, and numerous biomedical instrumentation systems and subsystems. It examines the properties of the ideal op amp and applies this model to the analysis of various circuits

  20. Eddy current analysis by the finite element circuit method

    International Nuclear Information System (INIS)

    Kameari, A.; Suzuki, Y.

    1977-01-01

    The analysis of the transient eddy current in the conductors by ''Finite Element Circuit Method'' is developed. This method can be easily applied to various geometrical shapes of thin conductors. The eddy currents on the vacuum vessel and the upper and lower support plates of JT-60 machine (which is now being constructed by Japan Atomic Energy Research Institute) are calculated by this method. The magnetic field induced by the eddy current is estimated in the domain occupied by the plasma. And the force exerted to the vacuum vessel is also estimated

  1. Reverse Engineering Integrated Circuits Using Finite State Machine Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Oler, Kiri J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Miller, Carl H. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-04-12

    In this paper, we present a methodology for reverse engineering integrated circuits, including a mathematical verification of a scalable algorithm used to generate minimal finite state machine representations of integrated circuits.

  2. Methods and Tools for the Analysis, Verification and Synthesis of Genetic Logic Circuits,

    DEFF Research Database (Denmark)

    Baig, Hasan

    2017-01-01

    . This usually requires simulating the mathematical models of these genetic circuits and perceive whether or not the circuit behaves appropriately. Furthermore, synthetic biology utilizes the concepts from electronic design automation (EDA) of abstraction and automated construction to generate genetic circuits...... that the proposed approach is effective to determine the variation in the behavior of genetic circuits when the circuit’s parameters are changed. In addition, the thesis also attempts to propose a synthesis and technology mapping tool, called GeneTech, for genetic circuits. It allows users to construct a genetic...... important design characteristics. This thesis also introduces an automated approach to analyze the behavior of genetic logic circuits from the simulation data. With this capability, the boolean logic of complex genetic circuits can be analyzed and/or verified automatically. It is also shown in this thesis...

  3. Simulation Approach for Timing Analysis of Genetic Logic Circuits

    DEFF Research Database (Denmark)

    Baig, Hasan; Madsen, Jan

    2017-01-01

    in a manner similar to electronic logic circuits, but they are much more stochastic and hence much harder to characterize. In this article, we introduce an approach to analyze the threshold value and timing of genetic logic circuits. We show how this approach can be used to analyze the timing behavior...... of single and cascaded genetic logic circuits. We further analyze the timing sensitivity of circuits by varying the degradation rates and concentrations. Our approach can be used not only to characterize the timing behavior but also to analyze the timing constraints of cascaded genetic logic circuits...

  4. Failure analysis of collector circuits associated with wind farms

    Directory of Open Access Journals (Sweden)

    Clifton Ashley P.

    2017-01-01

    Full Text Available Wind farm collector circuits generally comprise several wind turbine generators (WTG’s. WTG’s are connected in parallel to a substation. This connection acts as the point-of-connection to the national electricity grid. The electrical load in these circuits is close to component (power cables and accessories ratings. The objective of this paper is to identify cable joint failure paths; and, develop an understanding of specific contributing factors. All findings presented were established from literature review involving data analysis and discussion with industry experts working across the wind industry. Application of forces, inadequate workmanship, incorrect thermal resistance or other contributing factors, all contribute to high conductor operating temperatures. High conductor operating temperatures highlight issues including insufficient environmental heat transfer due to the use of inadequate cable trenching materials. This in turn results in the imbalanced application of force, experienced at the cable joint, as a direct result of frequent thermal expansion and contraction. For most cable joint failures, the root cause is insulation breakdown due to sustained deterioration of the cross-linked polyethylene insulation. This is a direct result from excessive operating temperatures.

  5. Analysis of High Power IGBT Short Circuit Failures

    Energy Technology Data Exchange (ETDEWEB)

    Pappas, G.

    2005-02-11

    The Next Linear Collider (NLC) accelerator proposal at SLAC requires a highly efficient and reliable, low cost, pulsed-power modulator to drive the klystrons. A solid-state induction modulator has been developed at SLAC to power the klystrons; this modulator uses commercial high voltage and high current Insulated Gate Bipolar Transistor (IGBT) modules. Testing of these IGBT modules under pulsed conditions was very successful; however, the IGBTs failed when tests were performed into a low inductance short circuit. The internal electrical connections of a commercial IGBT module have been analyzed to extract self and mutual partial inductances for the main current paths as well as for the gate structure. The IGBT module, together with the partial inductances, has been modeled using PSpice. Predictions for electrical paths that carry the highest current correlate with the sites of failed die under short circuit tests. A similar analysis has been carried out for a SLAC proposal for an IGBT module layout. This paper discusses the mathematical model of the IGBT module geometry and presents simulation results.

  6. Sub-circuits of a gene regulatory network control a developmental epithelial-mesenchymal transition.

    Science.gov (United States)

    Saunders, Lindsay R; McClay, David R

    2014-04-01

    Epithelial-mesenchymal transition (EMT) is a fundamental cell state change that transforms epithelial to mesenchymal cells during embryonic development, adult tissue repair and cancer metastasis. EMT includes a complex series of intermediate cell state changes including remodeling of the basement membrane, apical constriction, epithelial de-adhesion, directed motility, loss of apical-basal polarity, and acquisition of mesenchymal adhesion and polarity. Transcriptional regulatory state changes must ultimately coordinate the timing and execution of these cell biological processes. A well-characterized gene regulatory network (GRN) in the sea urchin embryo was used to identify the transcription factors that control five distinct cell changes during EMT. Single transcription factors were perturbed and the consequences followed with in vivo time-lapse imaging or immunostaining assays. The data show that five different sub-circuits of the GRN control five distinct cell biological activities, each part of the complex EMT process. Thirteen transcription factors (TFs) expressed specifically in pre-EMT cells were required for EMT. Three TFs highest in the GRN specified and activated EMT (alx1, ets1, tbr) and the 10 TFs downstream of those (tel, erg, hex, tgif, snail, twist, foxn2/3, dri, foxb, foxo) were also required for EMT. No single TF functioned in all five sub-circuits, indicating that there is no EMT master regulator. Instead, the resulting sub-circuit topologies suggest EMT requires multiple simultaneous regulatory mechanisms: forward cascades, parallel inputs and positive-feedback lock downs. The interconnected and overlapping nature of the sub-circuits provides one explanation for the seamless orchestration by the embryo of cell state changes leading to successful EMT.

  7. Rational design of modular circuits for gene transcription: A test of the bottom-up approach

    Directory of Open Access Journals (Sweden)

    Giordano Emanuele

    2010-11-01

    Full Text Available Abstract Background Most of synthetic circuits developed so far have been designed by an ad hoc approach, using a small number of components (i.e. LacI, TetR and a trial and error strategy. We are at the point where an increasing number of modular, inter-changeable and well-characterized components is needed to expand the construction of synthetic devices and to allow a rational approach to the design. Results We used interchangeable modular biological parts to create a set of novel synthetic devices for controlling gene transcription, and we developed a mathematical model of the modular circuits. Model parameters were identified by experimental measurements from a subset of modular combinations. The model revealed an unexpected feature of the lactose repressor system, i.e. a residual binding affinity for the operator site by induced lactose repressor molecules. Once this residual affinity was taken into account, the model properly reproduced the experimental data from the training set. The parameters identified in the training set allowed the prediction of the behavior of networks not included in the identification procedure. Conclusions This study provides new quantitative evidences that the use of independent and well-characterized biological parts and mathematical modeling, what is called a bottom-up approach to the construction of gene networks, can allow the design of new and different devices re-using the same modular parts.

  8. STICAP: A linear circuit analysis program with stiff systems capability. Volume 1: Theory manual. [network analysis

    Science.gov (United States)

    Cooke, C. H.

    1975-01-01

    STICAP (Stiff Circuit Analysis Program) is a FORTRAN 4 computer program written for the CDC-6400-6600 computer series and SCOPE 3.0 operating system. It provides the circuit analyst a tool for automatically computing the transient responses and frequency responses of large linear time invariant networks, both stiff and nonstiff (algorithms and numerical integration techniques are described). The circuit description and user's program input language is engineer-oriented, making simple the task of using the program. Engineering theories underlying STICAP are examined. A user's manual is included which explains user interaction with the program and gives results of typical circuit design applications. Also, the program structure from a systems programmer's viewpoint is depicted and flow charts and other software documentation are given.

  9. Circuit-wide Transcriptional Profiling Reveals Brain Region-Specific Gene Networks Regulating Depression Susceptibility.

    Science.gov (United States)

    Bagot, Rosemary C; Cates, Hannah M; Purushothaman, Immanuel; Lorsch, Zachary S; Walker, Deena M; Wang, Junshi; Huang, Xiaojie; Schlüter, Oliver M; Maze, Ian; Peña, Catherine J; Heller, Elizabeth A; Issler, Orna; Wang, Minghui; Song, Won-Min; Stein, Jason L; Liu, Xiaochuan; Doyle, Marie A; Scobie, Kimberly N; Sun, Hao Sheng; Neve, Rachael L; Geschwind, Daniel; Dong, Yan; Shen, Li; Zhang, Bin; Nestler, Eric J

    2016-06-01

    Depression is a complex, heterogeneous disorder and a leading contributor to the global burden of disease. Most previous research has focused on individual brain regions and genes contributing to depression. However, emerging evidence in humans and animal models suggests that dysregulated circuit function and gene expression across multiple brain regions drive depressive phenotypes. Here, we performed RNA sequencing on four brain regions from control animals and those susceptible or resilient to chronic social defeat stress at multiple time points. We employed an integrative network biology approach to identify transcriptional networks and key driver genes that regulate susceptibility to depressive-like symptoms. Further, we validated in vivo several key drivers and their associated transcriptional networks that regulate depression susceptibility and confirmed their functional significance at the levels of gene transcription, synaptic regulation, and behavior. Our study reveals novel transcriptional networks that control stress susceptibility and offers fundamentally new leads for antidepressant drug discovery. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. TCAD analysis of short-circuit oscillations in IGBTs

    DEFF Research Database (Denmark)

    Reigosa, Paula Diaz; Iannuzzo, Francesco; Rahimo, Munaf

    2017-01-01

    Insulated-Gate Bipolar Transistors (IGBTs) exhibit a gate-voltage oscillation phenomenon during short-circuit, which can result in a gate-oxide breakdown. The oscillations have been investigated through device simulations and experimental investigations of a 3.3-kV IGBT. It has been found...... during short circuit....

  11. Hopf bifurcation analysis of Chen circuit with direct time delay feedback

    International Nuclear Information System (INIS)

    Hai-Peng, Ren; Wen-Chao, Li; Ding, Liu

    2010-01-01

    Direct time delay feedback can make non-chaotic Chen circuit chaotic. The chaotic Chen circuit with direct time delay feedback possesses rich and complex dynamical behaviours. To reach a deep and clear understanding of the dynamics of such circuits described by delay differential equations, Hopf bifurcation in the circuit is analysed using the Hopf bifurcation theory and the central manifold theorem in this paper. Bifurcation points and bifurcation directions are derived in detail, which prove to be consistent with the previous bifurcation diagram. Numerical simulations and experimental results are given to verify the theoretical analysis. Hopf bifurcation analysis can explain and predict the periodical orbit (oscillation) in Chen circuit with direct time delay feedback. Bifurcation boundaries are derived using the Hopf bifurcation analysis, which will be helpful for determining the parameters in the stabilisation of the originally chaotic circuit

  12. Analysis and design of a genetic circuit for dynamic metabolic engineering.

    Science.gov (United States)

    Anesiadis, Nikolaos; Kobayashi, Hideki; Cluett, William R; Mahadevan, Radhakrishnan

    2013-08-16

    Recent advances in synthetic biology have equipped us with new tools for bioprocess optimization at the genetic level. Previously, we have presented an integrated in silico design for the dynamic control of gene expression based on a density-sensing unit and a genetic toggle switch. In the present paper, analysis of a serine-producing Escherichia coli mutant shows that an instantaneous ON-OFF switch leads to a maximum theoretical productivity improvement of 29.6% compared to the mutant. To further the design, global sensitivity analysis is applied here to a mathematical model of serine production in E. coli coupled with a genetic circuit. The model of the quorum sensing and the toggle switch involves 13 parameters of which 3 are identified as having a significant effect on serine concentration. Simulations conducted in this reduced parameter space further identified the optimal ranges for these 3 key parameters to achieve productivity values close to the maximum theoretical values. This analysis can now be used to guide the experimental implementation of a dynamic metabolic engineering strategy and reduce the time required to design the genetic circuit components.

  13. Analysis and synthesis of a logic control circuit by binary analysis methods

    International Nuclear Information System (INIS)

    Chicheportiche, Armand

    1974-06-01

    The analytical study of the logic circuits described in this report clearly shows the fruitful efficiency of the methods proposed by Binary Analysis. This study is a very new approach in logic and these mathematical methods are systematically precise in their applications. The detailed operations of an automatic system are to be studied in a way which cannot be reached by other methods. The definition and utilization of transition equations allow the determination of the different commutations in the auxiliary switch functions of a sequential system. This new way of analysis digital circuits will certainly develop in a very near future [fr

  14. A Two-Layer Gene Circuit for Decoupling Cell Growth from Metabolite Production.

    Science.gov (United States)

    Lo, Tat-Ming; Chng, Si Hui; Teo, Wei Suong; Cho, Han-Saem; Chang, Matthew Wook

    2016-08-01

    We present a synthetic gene circuit for decoupling cell growth from metabolite production through autonomous regulation of enzymatic pathways by integrated modules that sense nutrient and substrate. The two-layer circuit allows Escherichia coli to selectively utilize target substrates in a mixed pool; channel metabolic resources to growth by delaying enzymatic conversion until nutrient depletion; and activate, terminate, and re-activate conversion upon substrate availability. We developed two versions of controller, both of which have glucose nutrient sensors but differ in their substrate-sensing modules. One controller is specific for hydroxycinnamic acid and the other for oleic acid. Our hydroxycinnamic acid controller lowered metabolic stress 2-fold and increased the growth rate 2-fold and productivity 5-fold, whereas our oleic acid controller lowered metabolic stress 2-fold and increased the growth rate 1.3-fold and productivity 2.4-fold. These results demonstrate the potential for engineering strategies that decouple growth and production to make bio-based production more economical and sustainable. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  15. Application of reliability analysis methods to the comparison of two safety circuits

    International Nuclear Information System (INIS)

    Signoret, J.-P.

    1975-01-01

    Two circuits of different design, intended for assuming the ''Low Pressure Safety Injection'' function in PWR reactors are analyzed using reliability methods. The reliability analysis of these circuits allows the failure trees to be established and the failure probability derived. The dependence of these results on test use and maintenance is emphasized as well as critical paths. The great number of results obtained may allow a well-informed choice taking account of the reliability wanted for the type of circuits [fr

  16. A transition calculus for Boolean functions. [logic circuit analysis

    Science.gov (United States)

    Tucker, J. H.; Bennett, A. W.

    1974-01-01

    A transition calculus is presented for analyzing the effect of input changes on the output of logic circuits. The method is closely related to the Boolean difference, but it is more powerful. Both differentiation and integration are considered.

  17. Modelling, analysis, and acceleration of a printed circuit board ...

    Indian Academy of Sciences (India)

    Springer Verlag Heidelberg #4 2048 1996 Dec 15 10:16:45

    discuss lead time reduction in a qualitative way with illustrative case studies. Krishnan ... industry practices, and research questions that should drive new methods and computer ... There are three types of printed circuit boards available today.

  18. Analysis and synthesis of digital circuits for a computer of specific purposes

    International Nuclear Information System (INIS)

    Marchand Rosales, E.E.

    1975-01-01

    The circuits described in this paper are part of a computer system designed for the automation of plasma diagnostics using electrostatic probes. The automated system is designed to give: (a) The density of the plasma (state variable) every ten microseconds in binary digits; (b) Probe data, stored for subsequent diagnostics; (c) A graphic and digital display of results; (d) Presentation of numerical diagnostics results in floating point format and in the decimal system for convenience of interpretation. The project is aimed, furthermore, at the development of techniques for the design, construction and adjustment of digital circuits, and at the training of personnel who will apply these techniques in digital instrumentation. A block diagram of the system is discussed in general terms. Methods for analysis and synthesis of the sequential circuits applied to the circuit for aligning and normalizing the floating point format, the format circuit and the operational sequence circuit are also described. Recommendations are made and precautions suggested which it is thought advisable to follow at the stages of design, construction and adjustment of the digital circuits, and these apply also to the equipment and techniques (wire wrapping) used for building the circuits. The adjustment of the digital circuits proved to be satisfactory and a definition panel was thus obtained for the decimal point alignment circuit. It is concluded that the method of synthesis need not always be applied; the cases in which the method is recommended are mentioned, as are those in which the non-formal method of synthesis can be used. (author)

  19. Application of Fault Tree Analysis for Estimating Temperature Alarm Circuit Reliability

    International Nuclear Information System (INIS)

    El-Shanshoury, A.I.; El-Shanshoury, G.I.

    2011-01-01

    Fault Tree Analysis (FTA) is one of the most widely-used methods in system reliability analysis. It is a graphical technique that provides a systematic description of the combinations of possible occurrences in a system, which can result in an undesirable outcome. The presented paper deals with the application of FTA method in analyzing temperature alarm circuit. The criticality failure of this circuit comes from failing to alarm when temperature exceeds a certain limit. In order for a circuit to be safe, a detailed analysis of the faults causing circuit failure is performed by configuring fault tree diagram (qualitative analysis). Calculations of circuit quantitative reliability parameters such as Failure Rate (FR) and Mean Time between Failures (MTBF) are also done by using Relex 2009 computer program. Benefits of FTA are assessing system reliability or safety during operation, improving understanding of the system, and identifying root causes of equipment failures

  20. Analysis of electronic circuits using digital computers; L'analyse des circuits electroniques par les calculateurs numeriques

    Energy Technology Data Exchange (ETDEWEB)

    Tapu, C [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1968-07-01

    Various programmes have been proposed for studying electronic circuits with the help of computers. It is shown here how it possible to use the programme ECAP, developed by I.B.M., for studying the behaviour of an operational amplifier from different point of view: direct current, alternating current and transient state analysis, optimisation of the gain in open loop, study of the reliability. (author) [French] Differents programmes ont ete proposes pour l'etude des circuits electroniques a l'aide des calculateurs. On montre comment on peut utiliser le programme ECAP, mis au point par I. B. M., pour etudier le comportement d'un amplificateur operationnel, a differents points de vue: analyse en courant continu, courant alternatif et regime transitoire, optimalisation du gain en boucle ouverte, etude de la fiabilite. (auteur)

  1. Detailed Analysis of the Transient Voltage in a JT-60SA PF Coil Circuit

    International Nuclear Information System (INIS)

    Yamauchi, K.; Shimada, K.; Terakado, T.; Matsukawa, M.; Coletti, R.; Lampasi, A.; Gaio, E.; Coletti, A.; Novello, L.

    2013-01-01

    A superconducting coil system is actually complicated by the distributed parameters, e.g. the distributed mutual inductance among turns and the distributed capacitance between adjacent conductors. In this paper, such a complicated system was modeled with a reasonably simplified circuit network with lumped parameters. Then, a detailed circuit analysis was conducted to evaluate the possible voltage transient in the coil circuit. As a result, an appropriate (minimum) snubber capacitance for the Switching Network Unit, which is a fast high voltage generation circuit in JT-60SA, was obtained. (fusion engineering)

  2. Function analysis of unknown genes

    DEFF Research Database (Denmark)

    Rogowska-Wrzesinska, A.

    2002-01-01

      This thesis entitled "Function analysis of unknown genes" presents the use of proteome analysis for the characterisation of yeast (Saccharomyces cerevisiae) genes and their products (proteins especially those of unknown function). This study illustrates that proteome analysis can be used...... to describe different aspects of molecular biology of the cell, to study changes that occur in the cell due to overexpression or deletion of a gene and to identify various protein modifications. The biological questions and the results of the described studies show the diversity of the information that can...... genes and proteins. It reports the first global proteome database collecting 36 yeast single gene deletion mutants and selecting over 650 differences between analysed mutants and the wild type strain. The obtained results show that two-dimensional gel electrophoresis and mass spectrometry based proteome...

  3. Gene set analysis for GWAS

    DEFF Research Database (Denmark)

    Debrabant, Birgit; Soerensen, Mette

    2014-01-01

    Abstract We discuss the use of modified Kolmogorov-Smirnov (KS) statistics in the context of gene set analysis and review corresponding null and alternative hypotheses. Especially, we show that, when enhancing the impact of highly significant genes in the calculation of the test statistic, the co...

  4. Sociability Deficits and Altered Amygdala Circuits in Mice Lacking Pcdh10, an Autism Associated Gene.

    Science.gov (United States)

    Schoch, Hannah; Kreibich, Arati S; Ferri, Sarah L; White, Rachel S; Bohorquez, Dominique; Banerjee, Anamika; Port, Russell G; Dow, Holly C; Cordero, Lucero; Pallathra, Ashley A; Kim, Hyong; Li, Hongzhe; Bilker, Warren B; Hirano, Shinji; Schultz, Robert T; Borgmann-Winter, Karin; Hahn, Chang-Gyu; Feldmeyer, Dirk; Carlson, Gregory C; Abel, Ted; Brodkin, Edward S

    2017-02-01

    Behavioral symptoms in individuals with autism spectrum disorder (ASD) have been attributed to abnormal neuronal connectivity, but the molecular bases of these behavioral and brain phenotypes are largely unknown. Human genetic studies have implicated PCDH10, a member of the δ2 subfamily of nonclustered protocadherin genes, in ASD. PCDH10 expression is enriched in the basolateral amygdala, a brain region implicated in the social deficits of ASD. Previous reports indicate that Pcdh10 plays a role in axon outgrowth and glutamatergic synapse elimination, but its roles in social behaviors and amygdala neuronal connectivity are unknown. We hypothesized that haploinsufficiency of Pcdh10 would reduce social approach behavior and alter the structure and function of amygdala circuits. Mice lacking one copy of Pcdh10 (Pcdh10 +/- ) and wild-type littermates were assessed for social approach and other behaviors. The lateral/basolateral amygdala was assessed for dendritic spine number and morphology, and amygdala circuit function was studied using voltage-sensitive dye imaging. Expression of Pcdh10 and N-methyl-D-aspartate receptor (NMDAR) subunits was assessed in postsynaptic density fractions of the amygdala. Male Pcdh10 +/- mice have reduced social approach behavior, as well as impaired gamma synchronization, abnormal spine morphology, and reduced levels of NMDAR subunits in the amygdala. Social approach deficits in Pcdh10 +/- male mice were rescued with acute treatment with the NMDAR partial agonist d-cycloserine. Our studies reveal that male Pcdh10 +/- mice have synaptic and behavioral deficits, and establish Pcdh10 +/- mice as a novel genetic model for investigating neural circuitry and behavioral changes relevant to ASD. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  5. Power analysis dataset for QCA based multiplexer circuits

    Directory of Open Access Journals (Sweden)

    Md. Abdullah-Al-Shafi

    2017-04-01

    Full Text Available Power consumption in irreversible QCA logic circuits is a vital and a major issue; however in the practical cases, this focus is mostly omitted.The complete power depletion dataset of different QCA multiplexers have been worked out in this paper. At −271.15 °C temperature, the depletion is evaluated under three separate tunneling energy levels. All the circuits are designed with QCADesigner, a broadly used simulation engine and QCAPro tool has been applied for estimating the power dissipation.

  6. A PURE NODAL-ANALYSIS METHOD SUITABLE FOR ANALOG CIRCUITS USING NULLORS

    OpenAIRE

    E. Tlelo-Cuautle; L.A. Sarmiento-Reyes

    2003-01-01

    A novel technique suitable for computer-aided analysis of analog integrated circuits (ICs) is introduced. This technique uses the features of both nodal-analysis (NA) and symbolic analysis, at nullor level. First, the nullor is used to model the ideal behavior of several analog devices, namely: transistors, opamps, OTAs, and current conveyors. From this modeling approach, it is shown how to transform circuits working in voltage-mode to current-mode and vice-versa. Second, it is demonstrated t...

  7. Plasma Etching for Failure Analysis of Integrated Circuit Packages

    NARCIS (Netherlands)

    Tang, J.; Schelen, J.B.J.; Beenakker, C.I.M.

    2011-01-01

    Plastic integrated circuit packages with copper wire bonds are decapsulated by a Microwave Induced Plasma system. Improvements on microwave coupling of the system are achieved by frequency tuning and antenna modification. Plasmas with a mixture of O2 and CF4 showed a high etching rate around 2

  8. Inferring Drosophila gap gene regulatory network: Pattern analysis of simulated gene expression profiles and stability analysis

    OpenAIRE

    Fomekong-Nanfack, Y.; Postma, M.; Kaandorp, J.A.

    2009-01-01

    Abstract Background Inference of gene regulatory networks (GRNs) requires accurate data, a method to simulate the expression patterns and an efficient optimization algorithm to estimate the unknown parameters. Using this approach it is possible to obtain alternative circuits without making any a priori assumptions about the interactions, which all simulate the observed patterns. It is important to analyze the properties of the circuits. Findings We have analyzed the simulated gene expression ...

  9. A Small-Molecule Inducible Synthetic Circuit for Control of the SOS Gene Network without DNA Damage.

    Science.gov (United States)

    Kubiak, Jeffrey M; Culyba, Matthew J; Liu, Monica Yun; Mo, Charlie Y; Goulian, Mark; Kohli, Rahul M

    2017-11-17

    The bacterial SOS stress-response pathway is a pro-mutagenic DNA repair system that mediates bacterial survival and adaptation to genotoxic stressors, including antibiotics and UV light. The SOS pathway is composed of a network of genes under the control of the transcriptional repressor, LexA. Activation of the pathway involves linked but distinct events: an initial DNA damage event leads to activation of RecA, which promotes autoproteolysis of LexA, abrogating its repressor function and leading to induction of the SOS gene network. These linked events can each independently contribute to DNA repair and mutagenesis, making it difficult to separate the contributions of the different events to observed phenotypes. We therefore devised a novel synthetic circuit to unlink these events and permit induction of the SOS gene network in the absence of DNA damage or RecA activation via orthogonal cleavage of LexA. Strains engineered with the synthetic SOS circuit demonstrate small-molecule inducible expression of SOS genes as well as the associated resistance to UV light. Exploiting our ability to activate SOS genes independently of upstream events, we further demonstrate that the majority of SOS-mediated mutagenesis on the chromosome does not readily occur with orthogonal pathway induction alone, but instead requires DNA damage. More generally, our approach provides an exemplar for using synthetic circuit design to separate an environmental stressor from its associated stress-response pathway.

  10. Temperature control of fimbriation circuit switch in uropathogenic Escherichia coli: quantitative analysis via automated model abstraction.

    Science.gov (United States)

    Kuwahara, Hiroyuki; Myers, Chris J; Samoilov, Michael S

    2010-03-26

    Uropathogenic Escherichia coli (UPEC) represent the predominant cause of urinary tract infections (UTIs). A key UPEC molecular virulence mechanism is type 1 fimbriae, whose expression is controlled by the orientation of an invertible chromosomal DNA element-the fim switch. Temperature has been shown to act as a major regulator of fim switching behavior and is overall an important indicator as well as functional feature of many urologic diseases, including UPEC host-pathogen interaction dynamics. Given this panoptic physiological role of temperature during UTI progression and notable empirical challenges to its direct in vivo studies, in silico modeling of corresponding biochemical and biophysical mechanisms essential to UPEC pathogenicity may significantly aid our understanding of the underlying disease processes. However, rigorous computational analysis of biological systems, such as fim switch temperature control circuit, has hereto presented a notoriously demanding problem due to both the substantial complexity of the gene regulatory networks involved as well as their often characteristically discrete and stochastic dynamics. To address these issues, we have developed an approach that enables automated multiscale abstraction of biological system descriptions based on reaction kinetics. Implemented as a computational tool, this method has allowed us to efficiently analyze the modular organization and behavior of the E. coli fimbriation switch circuit at different temperature settings, thus facilitating new insights into this mode of UPEC molecular virulence regulation. In particular, our results suggest that, with respect to its role in shutting down fimbriae expression, the primary function of FimB recombinase may be to effect a controlled down-regulation (rather than increase) of the ON-to-OFF fim switching rate via temperature-dependent suppression of competing dynamics mediated by recombinase FimE. Our computational analysis further implies that this down

  11. Temperature control of fimbriation circuit switch in uropathogenic Escherichia coli: quantitative analysis via automated model abstraction.

    Directory of Open Access Journals (Sweden)

    Hiroyuki Kuwahara

    2010-03-01

    Full Text Available Uropathogenic Escherichia coli (UPEC represent the predominant cause of urinary tract infections (UTIs. A key UPEC molecular virulence mechanism is type 1 fimbriae, whose expression is controlled by the orientation of an invertible chromosomal DNA element-the fim switch. Temperature has been shown to act as a major regulator of fim switching behavior and is overall an important indicator as well as functional feature of many urologic diseases, including UPEC host-pathogen interaction dynamics. Given this panoptic physiological role of temperature during UTI progression and notable empirical challenges to its direct in vivo studies, in silico modeling of corresponding biochemical and biophysical mechanisms essential to UPEC pathogenicity may significantly aid our understanding of the underlying disease processes. However, rigorous computational analysis of biological systems, such as fim switch temperature control circuit, has hereto presented a notoriously demanding problem due to both the substantial complexity of the gene regulatory networks involved as well as their often characteristically discrete and stochastic dynamics. To address these issues, we have developed an approach that enables automated multiscale abstraction of biological system descriptions based on reaction kinetics. Implemented as a computational tool, this method has allowed us to efficiently analyze the modular organization and behavior of the E. coli fimbriation switch circuit at different temperature settings, thus facilitating new insights into this mode of UPEC molecular virulence regulation. In particular, our results suggest that, with respect to its role in shutting down fimbriae expression, the primary function of FimB recombinase may be to effect a controlled down-regulation (rather than increase of the ON-to-OFF fim switching rate via temperature-dependent suppression of competing dynamics mediated by recombinase FimE. Our computational analysis further implies

  12. A polynomial-chaos-expansion-based building block approach for stochastic analysis of photonic circuits

    Science.gov (United States)

    Waqas, Abi; Melati, Daniele; Manfredi, Paolo; Grassi, Flavia; Melloni, Andrea

    2018-02-01

    The Building Block (BB) approach has recently emerged in photonic as a suitable strategy for the analysis and design of complex circuits. Each BB can be foundry related and contains a mathematical macro-model of its functionality. As well known, statistical variations in fabrication processes can have a strong effect on their functionality and ultimately affect the yield. In order to predict the statistical behavior of the circuit, proper analysis of the uncertainties effects is crucial. This paper presents a method to build a novel class of Stochastic Process Design Kits for the analysis of photonic circuits. The proposed design kits directly store the information on the stochastic behavior of each building block in the form of a generalized-polynomial-chaos-based augmented macro-model obtained by properly exploiting stochastic collocation and Galerkin methods. Using this approach, we demonstrate that the augmented macro-models of the BBs can be calculated once and stored in a BB (foundry dependent) library and then used for the analysis of any desired circuit. The main advantage of this approach, shown here for the first time in photonics, is that the stochastic moments of an arbitrary photonic circuit can be evaluated by a single simulation only, without the need for repeated simulations. The accuracy and the significant speed-up with respect to the classical Monte Carlo analysis are verified by means of classical photonic circuit example with multiple uncertain variables.

  13. Two dimensional analysis of MHD generator by means of equivalent circuit

    International Nuclear Information System (INIS)

    Yoshida, Masaharu; Umoto, Juro

    1975-01-01

    The authors report on the method analyzing generally the MHD generator by means of the equivalent circuit including the negative resistance. At first, they divide the duct space into many space elements, and for each space element they derive the fundamental equivalent four-terminal circuit which satisfies the two-dimensional Ohm's law. Next, they make an attempt to apply the equivalent circuits to the typical MHD generators such as diagonal, Faraday and Hall generators considering the boundary layer in the duct and the wall leakage current. Using their analysis, the current density, Joul's heat, generated and output electrical powers, electrical efficiency etc. in the generator can be fairly easily calculated. (auth.)

  14. Analysis and Evaluation of Statistical Models for Integrated Circuits Design

    Directory of Open Access Journals (Sweden)

    Sáenz-Noval J.J.

    2011-10-01

    Full Text Available Statistical models for integrated circuits (IC allow us to estimate the percentage of acceptable devices in the batch before fabrication. Actually, Pelgrom is the statistical model most accepted in the industry; however it was derived from a micrometer technology, which does not guarantee reliability in nanometric manufacturing processes. This work considers three of the most relevant statistical models in the industry and evaluates their limitations and advantages in analog design, so that the designer has a better criterion to make a choice. Moreover, it shows how several statistical models can be used for each one of the stages and design purposes.

  15. Electrical circuit modeling and analysis of microwave acoustic interaction with biological tissues.

    Science.gov (United States)

    Gao, Fei; Zheng, Qian; Zheng, Yuanjin

    2014-05-01

    Numerical study of microwave imaging and microwave-induced thermoacoustic imaging utilizes finite difference time domain (FDTD) analysis for simulation of microwave and acoustic interaction with biological tissues, which is time consuming due to complex grid-segmentation and numerous calculations, not straightforward due to no analytical solution and physical explanation, and incompatible with hardware development requiring circuit simulator such as SPICE. In this paper, instead of conventional FDTD numerical simulation, an equivalent electrical circuit model is proposed to model the microwave acoustic interaction with biological tissues for fast simulation and quantitative analysis in both one and two dimensions (2D). The equivalent circuit of ideal point-like tissue for microwave-acoustic interaction is proposed including transmission line, voltage-controlled current source, envelop detector, and resistor-inductor-capacitor (RLC) network, to model the microwave scattering, thermal expansion, and acoustic generation. Based on which, two-port network of the point-like tissue is built and characterized using pseudo S-parameters and transducer gain. Two dimensional circuit network including acoustic scatterer and acoustic channel is also constructed to model the 2D spatial information and acoustic scattering effect in heterogeneous medium. Both FDTD simulation, circuit simulation, and experimental measurement are performed to compare the results in terms of time domain, frequency domain, and pseudo S-parameters characterization. 2D circuit network simulation is also performed under different scenarios including different sizes of tumors and the effect of acoustic scatterer. The proposed circuit model of microwave acoustic interaction with biological tissue could give good agreement with FDTD simulated and experimental measured results. The pseudo S-parameters and characteristic gain could globally evaluate the performance of tumor detection. The 2D circuit network

  16. Cell-to-Cell Communication Circuits: Quantitative Analysis of Synthetic Logic Gates

    Science.gov (United States)

    Hoffman-Sommer, Marta; Supady, Adriana; Klipp, Edda

    2012-01-01

    One of the goals in the field of synthetic biology is the construction of cellular computation devices that could function in a manner similar to electronic circuits. To this end, attempts are made to create biological systems that function as logic gates. In this work we present a theoretical quantitative analysis of a synthetic cellular logic-gates system, which has been implemented in cells of the yeast Saccharomyces cerevisiae (Regot et al., 2011). It exploits endogenous MAP kinase signaling pathways. The novelty of the system lies in the compartmentalization of the circuit where all basic logic gates are implemented in independent single cells that can then be cultured together to perform complex logic functions. We have constructed kinetic models of the multicellular IDENTITY, NOT, OR, and IMPLIES logic gates, using both deterministic and stochastic frameworks. All necessary model parameters are taken from literature or estimated based on published kinetic data, in such a way that the resulting models correctly capture important dynamic features of the included mitogen-activated protein kinase pathways. We analyze the models in terms of parameter sensitivity and we discuss possible ways of optimizing the system, e.g., by tuning the culture density. We apply a stochastic modeling approach, which simulates the behavior of whole populations of cells and allows us to investigate the noise generated in the system; we find that the gene expression units are the major sources of noise. Finally, the model is used for the design of system modifications: we show how the current system could be transformed to operate on three discrete values. PMID:22934039

  17. The Simulation Computer Based Learning (SCBL) for Short Circuit Multi Machine Power System Analysis

    Science.gov (United States)

    Rahmaniar; Putri, Maharani

    2018-03-01

    Strengthening Competitiveness of human resources become the reply of college as a conductor of high fomal education. Electrical Engineering Program UNPAB (Prodi TE UNPAB) as one of the department of electrical engineering that manages the field of electrical engineering expertise has a very important part in preparing human resources (HR), Which is required by where graduates are produced by DE UNPAB, Is expected to be able to compete globally, especially related to the implementation of Asean Economic Community (AEC) which requires the active participation of graduates with competence and quality of human resource competitiveness. Preparation of HR formation Competitive is done with the various strategies contained in the Seven (7) Higher Education Standard, one part of which is the implementation of teaching and learning process in Electrical system analysis with short circuit analysis (SCA) This course is a course The core of which is the basis for the competencies of other subjects in the advanced semester at Development of Computer Based Learning model (CBL) is done in the learning of interference analysis of multi-machine short circuit which includes: (a) Short-circuit One phase, (B) Two-phase Short Circuit Disruption, (c) Ground Short Circuit Disruption, (d) Short Circuit Disruption One Ground Floor Development of CBL learning model for Electrical System Analysis course provides space for students to be more active In learning in solving complex (complicated) problems, so it is thrilling Ilkan flexibility of student learning how to actively solve the problem of short-circuit analysis and to form the active participation of students in learning (Student Center Learning, in the course of electrical power system analysis.

  18. Simulation Analysis of DC and Switching Impulse Superposition Circuit

    Science.gov (United States)

    Zhang, Chenmeng; Xie, Shijun; Zhang, Yu; Mao, Yuxiang

    2018-03-01

    Surge capacitors running between the natural bus and the ground are affected by DC and impulse superposition voltage during operation in the converter station. This paper analyses the simulation aging circuit of surge capacitors by PSCAD electromagnetic transient simulation software. This paper also analyses the effect of the DC voltage to the waveform of the impulse voltage generation. The effect of coupling capacitor to the test voltage waveform is also studied. Testing results prove that the DC voltage has little effect on the waveform of the output of the surge voltage generator, and the value of the coupling capacitor has little effect on the voltage waveform of the sample. Simulation results show that surge capacitor DC and impulse superimposed aging test is feasible.

  19. Short circuit analysis of distribution system with integration of DG

    DEFF Research Database (Denmark)

    Su, Chi; Liu, Zhou; Chen, Zhe

    2014-01-01

    and as a result bring challenges to the network protection system. This problem has been frequently discussed in the literature, but mostly considering only the balanced fault situation. This paper presents an investigation on the influence of full converter based wind turbine (WT) integration on fault currents......Integration of distributed generation (DG) such as wind turbines into distribution system is increasing all around the world, because of the flexible and environmentally friendly characteristics. However, DG integration may change the pattern of the fault currents in the distribution system...... during both balanced and unbalanced faults. Major factors such as external grid short circuit power capacity, WT integration location, connection type of WT integration transformer are taken into account. In turn, the challenges brought to the protection system in the distribution network are presented...

  20. Circuit analysis method for thin-film solar cell modules

    Science.gov (United States)

    Burger, D. R.

    1985-01-01

    The design of a thin-film solar cell module is dependent on the probability of occurrence of pinhole shunt defects. Using known or assumed defect density data, dichotomous population statistics can be used to calculate the number of defects expected in a module. Probability theory is then used to assign the defective cells to individual strings in a selected series-parallel circuit design. Iterative numerical calculation is used to calcuate I-V curves using cell test values or assumed defective cell values as inputs. Good and shunted cell I-V curves are added to determine the module output power and I-V curve. Different levels of shunt resistance can be selected to model different defect levels.

  1. Application of damage function analysis to reactor coolant circuits

    International Nuclear Information System (INIS)

    MacDonald, D.D.

    2002-01-01

    The application of deterministic models for simulating stress corrosion cracking phenomena in Boiling Water Reactor primary coolant circuits is described. The first generation code, DAMAGE-PREDICTOR, has been used to model the radiolysis of the coolant, to estimate the electrochemical corrosion potential (ECP), and to calculate the crack growth rate (CGR) at fixed state points during reactor operation in about a dozen plants worldwide. This code has been validated in ''double-blind'' comparisons between the calculated and measured hydrogen concentration, oxygen concentration, and ECP in the recirculation system of the Leibstadt BWR in Switzerland, as well as through less formal comparisons with data from other plants. Second generation codes have now been developed, including REMAIN for simulating BWRs with internal coolant pumps and the ALERT series for modeling reactors with external pumps. One of this series, ALERT, yields the integrated damage function (IDF), which is the crack length versus time, on a component-by-component basis for a specified future operating scenario. This code therefore allows one to explore proposed future operating protocols, with the objective of identifying those that are most cost-effective and which minimizes the risk of failure of components in the coolant circuit by stress corrosion cracking. The application of this code is illustrated by exploring the benefits of partial hydrogen water chemistry (HWC) for an actual reactor, in which hydrogen is added to the feedwater over only limited periods during operation. The simulations show that the benefits, in terms of reduction in the IDFs for various components, are sensitive to when HWC was initiated in the plant life and to the length of time over which it is applied. (author)

  2. Application of damage function analysis to reactor coolant circuits

    Energy Technology Data Exchange (ETDEWEB)

    MacDonald, D.D. [Center for Electrochemical Science and Technology, Pennsylvania State Univ., University Park, PA (United States)

    2002-07-01

    The application of deterministic models for simulating stress corrosion cracking phenomena in Boiling Water Reactor primary coolant circuits is described. The first generation code, DAMAGE-PREDICTOR, has been used to model the radiolysis of the coolant, to estimate the electrochemical corrosion potential (ECP), and to calculate the crack growth rate (CGR) at fixed state points during reactor operation in about a dozen plants worldwide. This code has been validated in ''double-blind'' comparisons between the calculated and measured hydrogen concentration, oxygen concentration, and ECP in the recirculation system of the Leibstadt BWR in Switzerland, as well as through less formal comparisons with data from other plants. Second generation codes have now been developed, including REMAIN for simulating BWRs with internal coolant pumps and the ALERT series for modeling reactors with external pumps. One of this series, ALERT, yields the integrated damage function (IDF), which is the crack length versus time, on a component-by-component basis for a specified future operating scenario. This code therefore allows one to explore proposed future operating protocols, with the objective of identifying those that are most cost-effective and which minimizes the risk of failure of components in the coolant circuit by stress corrosion cracking. The application of this code is illustrated by exploring the benefits of partial hydrogen water chemistry (HWC) for an actual reactor, in which hydrogen is added to the feedwater over only limited periods during operation. The simulations show that the benefits, in terms of reduction in the IDFs for various components, are sensitive to when HWC was initiated in the plant life and to the length of time over which it is applied. (author)

  3. Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study.

    Science.gov (United States)

    Fan, Ming; Kuwahara, Hiroyuki; Wang, Xiaolei; Wang, Suojin; Gao, Xin

    2015-11-01

    Parameter estimation is a challenging computational problem in the reverse engineering of biological systems. Because advances in biotechnology have facilitated wide availability of time-series gene expression data, systematic parameter estimation of gene circuit models from such time-series mRNA data has become an important method for quantitatively dissecting the regulation of gene expression. By focusing on the modeling of gene circuits, we examine here the performance of three types of state-of-the-art parameter estimation methods: population-based methods, online methods and model-decomposition-based methods. Our results show that certain population-based methods are able to generate high-quality parameter solutions. The performance of these methods, however, is heavily dependent on the size of the parameter search space, and their computational requirements substantially increase as the size of the search space increases. In comparison, online methods and model decomposition-based methods are computationally faster alternatives and are less dependent on the size of the search space. Among other things, our results show that a hybrid approach that augments computationally fast methods with local search as a subsequent refinement procedure can substantially increase the quality of their parameter estimates to the level on par with the best solution obtained from the population-based methods while maintaining high computational speed. These suggest that such hybrid methods can be a promising alternative to the more commonly used population-based methods for parameter estimation of gene circuit models when limited prior knowledge about the underlying regulatory mechanisms makes the size of the parameter search space vastly large. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  4. Performance Analysis of Modified Drain Gating Techniques for Low Power and High Speed Arithmetic Circuits

    Directory of Open Access Journals (Sweden)

    Shikha Panwar

    2014-01-01

    Full Text Available This paper presents several high performance and low power techniques for CMOS circuits. In these design methodologies, drain gating technique and its variations are modified by adding an additional NMOS sleep transistor at the output node which helps in faster discharge and thereby providing higher speed. In order to achieve high performance, the proposed design techniques trade power for performance in the delay critical sections of the circuit. Intensive simulations are performed using Cadence Virtuoso in a 45 nm standard CMOS technology at room temperature with supply voltage of 1.2 V. Comparative analysis of the present circuits with standard CMOS circuits shows smaller propagation delay and lesser power consumption.

  5. Frequency analysis for the thermal hydraulic characterization of a natural circulation circuit

    International Nuclear Information System (INIS)

    Torres, Walmir M.; Macedo, Luiz A.; Sabundjian, Gaiane; Andrade, Delvonei A.; Umbehaun, Pedro E.; Conti, Thadeu N.; Mesquita, Roberto N.; Masotti, Paulo H.; Angelo, Gabriel

    2011-01-01

    This paper presents the frequency analysis studies of the pressure signals from an experimental natural circulation circuit during a heating process. The main objective is to identify the characteristic frequencies of this process using fast Fourier transform. Video images are used to associate these frequencies to the observed phenomenology in the circuit during the process. Sub-cooled and saturated flow boiling, heaters vibrations, overall circuit vibrations, chugging and geysering were observed. Each phenomenon has its specific frequency associated. Some phenomena and their frequencies must be avoided or attenuated since they can cause damages to the natural circulation circuit and its components. Special operation procedures and devices can be developed to avoid these undesirable frequencies. (author)

  6. Frequency analysis for the thermal hydraulic characterization of a natural circulation circuit

    Energy Technology Data Exchange (ETDEWEB)

    Torres, Walmir M.; Macedo, Luiz A.; Sabundjian, Gaiane; Andrade, Delvonei A.; Umbehaun, Pedro E.; Conti, Thadeu N.; Mesquita, Roberto N.; Masotti, Paulo H.; Angelo, Gabriel, E-mail: wmtorres@ipen.b, E-mail: lamacedo@ipen.b, E-mail: gdjian@ipen.b, E-mail: delvonei@ipen.b, E-mail: umbehaun@ipen.b, E-mail: tnconti@ipen.b, E-mail: , E-mail: rnavarro@ipen.b, E-mail: pmasotti@ipen.b, E-mail: gabriel.angelo@usp.b [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2011-07-01

    This paper presents the frequency analysis studies of the pressure signals from an experimental natural circulation circuit during a heating process. The main objective is to identify the characteristic frequencies of this process using fast Fourier transform. Video images are used to associate these frequencies to the observed phenomenology in the circuit during the process. Sub-cooled and saturated flow boiling, heaters vibrations, overall circuit vibrations, chugging and geysering were observed. Each phenomenon has its specific frequency associated. Some phenomena and their frequencies must be avoided or attenuated since they can cause damages to the natural circulation circuit and its components. Special operation procedures and devices can be developed to avoid these undesirable frequencies. (author)

  7. Short Circuit Ratio analysis of multi-infeed HVDC system with a VSC-HVDC link

    DEFF Research Database (Denmark)

    Liu, Yan; Chen, Zhe

    2011-01-01

    As an important indicator of system stability, Short Circuit Ratio (SCR) is commonly used in power system analysis. For systems include HVDC link connection, the Effective SCR (ESCR) is mostly applied to indicate the strength of HVDC infeed bus. The contribution of VSC-HVDC link to multi......-infeed HVDC system stability has been analyzed a lot but the study on ESCR of this kind of system is still insufficient. This paper presents a calculation method for ESCR of the hybrid multi infeed HVDC system based on a simple two-infeed HVDC system model. The equivalent circuit of this system under short...... circuit situation is firstly obtained based on the model. Then its Thevenin equivalent circuit is derived and system ESCR can be calculated. At last, simulation study verified that the calculated ESCR value under different cases can indicate the change of system stability....

  8. Short-Circuit Current Analysis for DFIG Wind Farm Considering the Action of a Crowbar

    Directory of Open Access Journals (Sweden)

    Yan Hong Yuan

    2018-02-01

    Full Text Available With the increasing capacity of wind farms integrated into the power grid, the short-circuit current analysis for wind farms becomes more and more important. Since the wind turbine is usually integrated into the power grid via power electronic devices, the “crowbar” is installed in the wind turbine to protect the power electronic devices and to improve the fault ride through capability. The impact of the crowbar has to be considered during the short-circuit current analysis for the wind farm. In order to fully analyze the short-circuit current characteristics of a wind farm, the short-circuit currents for a doubly-fed induction generator (DFIG wind turbine under symmetrical and asymmetrical faults considering the crowbar action characteristic are derived firstly. Then the action situation of the crowbar of a DFIG wind turbine is studied and the action area curve is obtained. Taking the crowbar action, or not, as the grouping criterion, wind turbines in the wind farm are divided into two groups, and the wind farm is aggregated into two equivalent wind turbines. Using the equivalent model, the short-circuit current of a wind farm can be calculated accurately. Finally, simulations are performed in MATLAB/Simulink which is the commercial math software produced by the MathWorks company in Natick, Massachusetts, the United States to verify the proposed short-circuit current calculation method for the DFIG wind farm.

  9. Analysis of Statistical Distributions Used for Modeling Reliability and Failure Rate of Temperature Alarm Circuit

    International Nuclear Information System (INIS)

    EI-Shanshoury, G.I.

    2011-01-01

    Several statistical distributions are used to model various reliability and maintainability parameters. The applied distribution depends on the' nature of the data being analyzed. The presented paper deals with analysis of some statistical distributions used in reliability to reach the best fit of distribution analysis. The calculations rely on circuit quantity parameters obtained by using Relex 2009 computer program. The statistical analysis of ten different distributions indicated that Weibull distribution gives the best fit distribution for modeling the reliability of the data set of Temperature Alarm Circuit (TAC). However, the Exponential distribution is found to be the best fit distribution for modeling the failure rate

  10. Measuring user similarity using electric circuit analysis: application to collaborative filtering.

    Science.gov (United States)

    Yang, Joonhyuk; Kim, Jinwook; Kim, Wonjoon; Kim, Young Hwan

    2012-01-01

    We propose a new technique of measuring user similarity in collaborative filtering using electric circuit analysis. Electric circuit analysis is used to measure the potential differences between nodes on an electric circuit. In this paper, by applying this method to transaction networks comprising users and items, i.e., user-item matrix, and by using the full information about the relationship structure of users in the perspective of item adoption, we overcome the limitations of one-to-one similarity calculation approach, such as the Pearson correlation, Tanimoto coefficient, and Hamming distance, in collaborative filtering. We found that electric circuit analysis can be successfully incorporated into recommender systems and has the potential to significantly enhance predictability, especially when combined with user-based collaborative filtering. We also propose four types of hybrid algorithms that combine the Pearson correlation method and electric circuit analysis. One of the algorithms exceeds the performance of the traditional collaborative filtering by 37.5% at most. This work opens new opportunities for interdisciplinary research between physics and computer science and the development of new recommendation systems.

  11. Measuring user similarity using electric circuit analysis: application to collaborative filtering.

    Directory of Open Access Journals (Sweden)

    Joonhyuk Yang

    Full Text Available We propose a new technique of measuring user similarity in collaborative filtering using electric circuit analysis. Electric circuit analysis is used to measure the potential differences between nodes on an electric circuit. In this paper, by applying this method to transaction networks comprising users and items, i.e., user-item matrix, and by using the full information about the relationship structure of users in the perspective of item adoption, we overcome the limitations of one-to-one similarity calculation approach, such as the Pearson correlation, Tanimoto coefficient, and Hamming distance, in collaborative filtering. We found that electric circuit analysis can be successfully incorporated into recommender systems and has the potential to significantly enhance predictability, especially when combined with user-based collaborative filtering. We also propose four types of hybrid algorithms that combine the Pearson correlation method and electric circuit analysis. One of the algorithms exceeds the performance of the traditional collaborative filtering by 37.5% at most. This work opens new opportunities for interdisciplinary research between physics and computer science and the development of new recommendation systems.

  12. E-learning platform for automated testing of electronic circuits using signature analysis method

    Science.gov (United States)

    Gherghina, Cǎtǎlina; Bacivarov, Angelica; Bacivarov, Ioan C.; Petricǎ, Gabriel

    2016-12-01

    Dependability of electronic circuits can be ensured only through testing of circuit modules. This is done by generating test vectors and their application to the circuit. Testability should be viewed as a concerted effort to ensure maximum efficiency throughout the product life cycle, from conception and design stage, through production to repairs during products operating. In this paper, is presented the platform developed by authors for training for testability in electronics, in general and in using signature analysis method, in particular. The platform allows highlighting the two approaches in the field namely analog and digital signature of circuits. As a part of this e-learning platform, it has been developed a database for signatures of different electronic components meant to put into the spotlight different techniques implying fault detection, and from this there were also self-repairing techniques of the systems with this kind of components. An approach for realizing self-testing circuits based on MATLAB environment and using signature analysis method is proposed. This paper analyses the benefits of signature analysis method and simulates signature analyzer performance based on the use of pseudo-random sequences, too.

  13. Short-Circuit Current Analysis for DFIG Wind Farm Considering the Action of a Crowbar

    OpenAIRE

    Yan Hong Yuan; Feng Wu

    2018-01-01

    With the increasing capacity of wind farms integrated into the power grid, the short-circuit current analysis for wind farms becomes more and more important. Since the wind turbine is usually integrated into the power grid via power electronic devices, the “crowbar” is installed in the wind turbine to protect the power electronic devices and to improve the fault ride through capability. The impact of the crowbar has to be considered during the short-circuit current analysis for the wind farm....

  14. A new nonlinear magnetic circuit model for dynamic analysis of interior permanent magnet synchronous motor

    International Nuclear Information System (INIS)

    Nakamura, Kenji; Saito, Kenichi; Watanabe, Tadaaki; Ichinokura, Osamu

    2005-01-01

    Interior permanent magnet synchronous motors (IPMSMs) have high efficiency and torque, since the motors can utilize reluctance torque in addition to magnet torque. The IPMSMs are widely used for electric household appliances and electric bicycles and vehicles. A quantitative analysis method of dynamic characteristics of the IPMSMs, however, has not been clarified fully. For optimum design, investigation of dynamic characteristics considering magnetic nonlinearity is needed. This paper presents a new nonlinear magnetic circuit model of an IPMSM, and suggests a dynamic analysis method using the proposed magnetic circuit model

  15. Epidemiological analysis of doping offences in the professional tennis circuit

    Directory of Open Access Journals (Sweden)

    Maquirriain Javier

    2010-12-01

    Full Text Available Abstract Introduction Tennis is a professional sport under a strict anti-doping control. However, since the first violation of the code, the positive cases have not been statistically studied. The objective of this study was to analyze doping offences in the international professional tennis circuit. Methods All offences to the Doping Code committed by tennis players during 2003-2009 were collected from the ITF official webpage, registered and analyzed. Results An average of 1905.7 (±174.5 samples was obtained per year. Fifty-two doping offences were reported and the overall incidence of positive doping samples accounted for 0.38% and 7.4 (±4.1 cases/year. Male players showed higher incidence doping offences than females (p = 0.0004. The incidence in wheelchair players was higher than in non-handicapped subjects (p = 0.0001 Banned substance distribution showed: stimulants 32.69%, cannabis 23.07%; anabolic 11.53%, diuretics and masking agents 11.53, β2-agonists 9.61%; corticosteroids 3.84%, others 3.84%. The overall incidence of 'social drugs' (cocaine, cannabis was 36.53%. All EPO and blood samples were normal, while the incidence of 'out-of-competition' offences was 0.12%. The lower incidence of doping was found in Grand Slams tournaments. Conclusions The incidence of positive doping samples among professional tennis players is quite low supporting the assumption that there is no evidence of systematic doping in Tennis. "Social drugs" misuse constitutes the main problem of doping in tennis. Male and wheelchair tennis players showed higher risk of infringing the doping code than their females and non-handicapped counterparts. Findings of this study should help to determine the direction of the ongoing strategy in the fight against doping in Tennis.

  16. Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study

    KAUST Repository

    Fan, M.

    2015-03-29

    Parameter estimation is a challenging computational problemin the reverse engineering of biological systems. Because advances in biotechnology have facilitated wide availability of time-series gene expression data, systematic parameter esti- mation of gene circuitmodels fromsuch time-series mRNA data has become an importantmethod for quantitatively dissecting the regulation of gene expression. By focusing on themodeling of gene circuits, we examine here the perform- ance of three types of state-of-the-art parameter estimation methods: population-basedmethods, onlinemethods and model-decomposition-basedmethods. Our results show that certain population-basedmethods are able to generate high- quality parameter solutions. The performance of thesemethods, however, is heavily dependent on the size of the param- eter search space, and their computational requirements substantially increase as the size of the search space increases. In comparison, onlinemethods andmodel decomposition-basedmethods are computationally faster alternatives and are less dependent on the size of the search space. Among other things, our results show that a hybrid approach that augments computationally fastmethods with local search as a subsequent refinement procedure can substantially increase the qual- ity of their parameter estimates to the level on par with the best solution obtained fromthe population-basedmethods whilemaintaining high computational speed. These suggest that such hybridmethods can be a promising alternative to themore commonly used population-basedmethods for parameter estimation of gene circuit models when limited prior knowledge about the underlying regulatorymechanismsmakes the size of the parameter search space vastly large. © The Author 2015. Published by Oxford University Press.

  17. An Analysis of Science Textbooks for Grade 6: The Electric Circuit Lesson

    Science.gov (United States)

    Sothayapetch, Pavinee; Lavonen, Jari; Juuti, Kalle

    2013-01-01

    Textbooks are a major tool in the teaching and learning process. This paper presents the results of an analysis of the Finnish and Thai 6th grade science textbooks: electric circuit lesson. Textual and pictorial information from the textbooks were analyzed under four main categories: 1) introduction of the concepts, 2) type of knowledge, 3)…

  18. An Exploratory Study Examining the Feasibility of Using Bayesian Networks to Predict Circuit Analysis Understanding

    Science.gov (United States)

    Chung, Gregory K. W. K.; Dionne, Gary B.; Kaiser, William J.

    2006-01-01

    Our research question was whether we could develop a feasible technique, using Bayesian networks, to diagnose gaps in student knowledge. Thirty-four college-age participants completed tasks designed to measure conceptual knowledge, procedural knowledge, and problem-solving skills related to circuit analysis. A Bayesian network was used to model…

  19. Encountering the Expertise Reversal Effect with a Computer-Based Environment on Electrical Circuit Analysis

    Science.gov (United States)

    Reisslein, Jana; Atkinson, Robert K.; Seeling, Patrick; Reisslein, Martin

    2006-01-01

    This study examined the effectiveness of a computer-based environment employing three example-based instructional procedures (example-problem, problem-example, and fading) to teach series and parallel electrical circuit analysis to learners classified by two levels of prior knowledge (low and high). Although no differences between the…

  20. Circuit Board Analysis for Lead by Atomic Absorption Spectroscopy in a Course for Nonscience Majors

    Science.gov (United States)

    Weidenhammer, Jeffrey D.

    2007-01-01

    A circuit board analysis of the atomic absorption spectroscopy, which is used to measure lead content in a course for nonscience majors, is being presented. The experiment can also be used to explain the potential environmental hazards of unsafe disposal of various used electronic equipments.

  1. Photonic circuit for high order USB and LSB separation for remote heterodyning: analysis and simulation.

    Science.gov (United States)

    Hasan, Mehedi; Hall, Trevor J

    2015-09-21

    A novel photonic integrated circuit is proposed that, using an RF source, generates at its output ports the same magnitude but opposite sign high order single optical side bands of a suppressed optical carrier. A single stage parallel Mach-Zehnder Modulator (MZM) and a two-stage series parallel MZM architecture are described and their relative merits discussed. A transfer matrix method is used to describe the operation of the circuits. The theoretical analysis is validated by computer simulation. As an illustration of a prospective application, it is shown how the circuit may be used as a key element of an optical transmission system to transport radio signals over fibre for wireless access; generating remotely a mm-wave carrier modulated by digital IQ data. A detailed calculation of symbol error rate is presented to characterise the system performance. The circuit may be fabricated in any integration platform offering a suitable phase modulator circuit element such as LiNbO(3), Silicon, and III-V or hybrid technology.

  2. Analysis of ringing effects due to magnetic core materials in pulsed nuclear magnetic resonance circuits

    International Nuclear Information System (INIS)

    Prabhu Gaunkar, N.; Bouda, N. R. Y.; Nlebedim, I. C.; Hadimani, R. L.; Mina, M.; Jiles, D. C.; Bulu, I.; Ganesan, K.; Song, Y. Q.

    2015-01-01

    This work presents investigations and detailed analysis of ringing in a non-resonant pulsed nuclear magnetic resonance (NMR) circuit. Ringing is a commonly observed phenomenon in high power switching circuits. The oscillations described as ringing impede measurements in pulsed NMR systems. It is therefore desirable that those oscillations decay fast. It is often assumed that one of the causes behind ringing is the role of the magnetic core used in the antenna (acting as an inductive load). We will demonstrate that an LRC subcircuit is also set-up due to the inductive load and needs to be considered due to its parasitic effects. It is observed that the parasitics associated with the inductive load become important at certain frequencies. The output response can be related to the response of an under-damped circuit and to the magnetic core material. This research work demonstrates and discusses ways of controlling ringing by considering interrelationships between different contributing factors

  3. Analysis of ringing effects due to magnetic core materials in pulsed nuclear magnetic resonance circuits

    Energy Technology Data Exchange (ETDEWEB)

    Prabhu Gaunkar, N., E-mail: neelampg@iastate.edu; Bouda, N. R. Y.; Nlebedim, I. C.; Hadimani, R. L.; Mina, M.; Jiles, D. C. [Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa 50011 (United States); Bulu, I.; Ganesan, K.; Song, Y. Q. [Schlumberger-Doll Research, Cambridge, Massachusetts 02139 (United States)

    2015-05-07

    This work presents investigations and detailed analysis of ringing in a non-resonant pulsed nuclear magnetic resonance (NMR) circuit. Ringing is a commonly observed phenomenon in high power switching circuits. The oscillations described as ringing impede measurements in pulsed NMR systems. It is therefore desirable that those oscillations decay fast. It is often assumed that one of the causes behind ringing is the role of the magnetic core used in the antenna (acting as an inductive load). We will demonstrate that an LRC subcircuit is also set-up due to the inductive load and needs to be considered due to its parasitic effects. It is observed that the parasitics associated with the inductive load become important at certain frequencies. The output response can be related to the response of an under-damped circuit and to the magnetic core material. This research work demonstrates and discusses ways of controlling ringing by considering interrelationships between different contributing factors.

  4. Analysis of Equivalent Circuits for Cells: A Fractional Calculus Approach

    Directory of Open Access Journals (Sweden)

    Bernal-Alvarado J.

    2012-07-01

    Full Text Available Fractional order systems are considered by many mathematicians the systems of the XXI century. The reason is that nature has proved to be best described in terms of systems composed of fractional order derivatives. This emerging area of research is slowly gaining more strength in engineering, biochemistry, medicine, biophysics, among others. This paper presents an analysis in the frequency domain equivalent of cellular systems described by equations of integer and fractional order; it also carries out an analysis in time domain in order to display the memory capacity of fractional systems. It presents the fractional differential equations equivalent models and simulations comparing integer and fractional order.

  5. Inferring Drosophila gap gene regulatory network: Pattern analysis of simulated gene expression profiles and stability analysis

    NARCIS (Netherlands)

    Fomekong-Nanfack, Y.; Postma, M.; Kaandorp, J.A.

    2009-01-01

    Background: Inference of gene regulatory networks (GRNs) requires accurate data, a method to simulate the expression patterns and an efficient optimization algorithm to estimate the unknown parameters. Using this approach it is possible to obtain alternative circuits without making any a priori

  6. Sensitive detection of proteasomal activation using the Deg-On mammalian synthetic gene circuit.

    Science.gov (United States)

    Zhao, Wenting; Bonem, Matthew; McWhite, Claire; Silberg, Jonathan J; Segatori, Laura

    2014-04-08

    The ubiquitin proteasome system (UPS) has emerged as a drug target for diverse diseases characterized by altered proteostasis, but pharmacological agents that enhance UPS activity have been challenging to establish. Here we report the Deg-On system, a genetic inverter that translates proteasomal degradation of the transcriptional regulator TetR into a fluorescent signal, thereby linking UPS activity to an easily detectable output, which can be tuned using tetracycline. We demonstrate that this circuit responds to modulation of UPS activity in cell culture arising from the inhibitor MG-132 and activator PA28γ. Guided by predictive modelling, we enhanced the circuit's signal sensitivity and dynamic range by introducing a feedback loop that enables self-amplification of TetR. By linking UPS activity to a simple and tunable fluorescence output, these genetic inverters will enable a variety of applications, including screening for UPS activating molecules and selecting for mammalian cells with different levels of proteasome activity.

  7. Monetary circuit and economy financing: a theoretical analysis.

    OpenAIRE

    Cavalieri, Duccio

    1999-01-01

    This is a theoretical analysis of the role of money and other less liquid financial assets in the financing of the private sector of a market economy. It is concerned, basically, with the functional relations between households, firms, banks and other financial institutions, and with those between certain financial instruments (money, deposits, credits and bonds). Attention is focused on the determinants of the money, credit and financial structure of the economy.

  8. Magnetic Circuit & Torque Analysis Of Brushless DC Motor

    Directory of Open Access Journals (Sweden)

    Arif J. Abbas

    2013-05-01

    Full Text Available       This work is concerned with magnetic and torque analysis of BLDCM and with development of a method of designing BLDCM that have symmetric winding on the rotor .make significant contribution to the rotor inductance position difficult. It is also show that the prediction detent torque can be extremely sensitive to the permanent magnet by altering magnet arc width. Finally, simple lumped models that allow one to predict motor performance and characteristics as a function of main dimension, magnet residual flux density and phase current are developed. These models are used as a basis for an approach to designing BLDCM

  9. Tumor Immunotherapy by Gene-circuit Recruited Immunomodulatory Systems (TIGRIS) for Prostate Cancer

    Science.gov (United States)

    2017-09-01

    Commercial Assays CytoTox 96 Non-Radioactive Cytotoxicity Assay Kit Promega Cat #G1780 Human IFN-g DuoSet ELISA R&D systems Cat #DY285 Human CCL21/6Ckine...DuoSet ELISA R&D systems Cat #DY366 Human IL-12 p70 DuoSet ELISA R&D systems Cat #DY1270 Cell Culture Reagents DMEM Life Technologies Cat #10569-044...after 24h and IFN-g concentration determined by Human IFN-g DuoSet ELISA (R&D systems, Min- neapolis, MN; catalog #DY285). Multiple-Output Circuit

  10. Single-Phase Full-Wave Rectifier as an Effective Example to Teach Normalization, Conduction Modes, and Circuit Analysis Methods

    Directory of Open Access Journals (Sweden)

    Predrag Pejovic

    2013-12-01

    Full Text Available Application of a single phase rectifier as an example in teaching circuit modeling, normalization, operating modes of nonlinear circuits, and circuit analysis methods is proposed.The rectifier supplied from a voltage source by an inductive impedance is analyzed in the discontinuous as well as in the continuous conduction mode. Completely analytical solution for the continuous conduction mode is derived. Appropriate numerical methods are proposed to obtain the circuit waveforms in both of the operating modes, and to compute the performance parameters. Source code of the program that performs such computation is provided.

  11. Transient Analysis of Lumped Circuit Networks Loaded Thin Wires By DGTD Method

    KAUST Repository

    Li, Ping

    2016-03-31

    With the purpose of avoiding very fine mesh cells in the proximity of a thin wire, the modified telegrapher’s equations (MTEs) are employed to describe the thin wire voltage and current distributions, which consequently results in reduced number of unknowns and augmented Courant-Friedrichs-Lewy (CFL) number. As hyperbolic systems, both the MTEs and the Maxwell’s equations are solved by the discontinuous Galerkin time-domain (DGTD) method. In realistic situations, the thin wires could be either driven or loaded by circuit networks. The thin wire-circuit interface performs as a boundary condition for the thin wire solver, where the thin wire voltage and current used for the incoming flux evaluation involved in the DGTD analyzed MTEs are not available. To obtain this voltage and current, an auxiliary current flowing through the thin wire-circuit interface is introduced at each interface. Corresponding auxiliary equations derived from the invariable property of characteristic variable for hyperbolic systems are developed and solved together with the circuit equations established by the modified nodal analysis (MNA) modality. Furthermore, in order to characterize the field and thin wire interactions, a weighted electric field and a volume current density are added into the MTEs and Maxwell-Ampere’s law equation, respectively. To validate the proposed algorithm, three representative examples are presented.

  12. Transient Analysis of Lumped Circuit Networks Loaded Thin Wires By DGTD Method

    KAUST Repository

    Li, Ping; Shi, Yifei; Jiang, Li Jun; Bagci, Hakan

    2016-01-01

    With the purpose of avoiding very fine mesh cells in the proximity of a thin wire, the modified telegrapher’s equations (MTEs) are employed to describe the thin wire voltage and current distributions, which consequently results in reduced number of unknowns and augmented Courant-Friedrichs-Lewy (CFL) number. As hyperbolic systems, both the MTEs and the Maxwell’s equations are solved by the discontinuous Galerkin time-domain (DGTD) method. In realistic situations, the thin wires could be either driven or loaded by circuit networks. The thin wire-circuit interface performs as a boundary condition for the thin wire solver, where the thin wire voltage and current used for the incoming flux evaluation involved in the DGTD analyzed MTEs are not available. To obtain this voltage and current, an auxiliary current flowing through the thin wire-circuit interface is introduced at each interface. Corresponding auxiliary equations derived from the invariable property of characteristic variable for hyperbolic systems are developed and solved together with the circuit equations established by the modified nodal analysis (MNA) modality. Furthermore, in order to characterize the field and thin wire interactions, a weighted electric field and a volume current density are added into the MTEs and Maxwell-Ampere’s law equation, respectively. To validate the proposed algorithm, three representative examples are presented.

  13. Transient and Steady-State Analysis of Nonlinear RF and Microwave Circuits

    Directory of Open Access Journals (Sweden)

    Zhu Lei(Lana

    2006-01-01

    Full Text Available This paper offers a review of simulation methods currently available for the transient and steady-state analysis of nonlinear RF and microwave circuits. The most general method continues to be the time-marching approach used in Spice, but more recent methods based on multiple time dimensions are particularly effective for RF and microwave circuits. We derive nodal formulations for the most widely used multiple time dimension methods. We put special emphasis on methods for the analysis of oscillators based in the warped multitime partial differential equations (WaMPDE approach. Case studies of a Colpitts oscillator and a voltage controlled Clapp-Gouriet oscillator are presented and discussed. The accuracy of the amplitude and phase of these methods is investigated. It is shown that the exploitation of frequency-domain latency reduces the computational effort.

  14. Spectral analysis to detection of short circuit fault of solar photovoltaic modules in strings

    International Nuclear Information System (INIS)

    Sevilla-Camacho, P.Y.; Robles-Ocampo, J.B.; Zuñiga-Reyes, Marco A.

    2017-01-01

    This research work presents a method to detect the number of short circuit faulted solar photovoltaic modules in strings of a photovoltaic system by taking into account speed, safety, and non-use of sensors and specialized and expensive equipment. The method consists on apply the spectral analysis and statistical techniques to the alternating current output voltage of a string and detect the number of failed modules through the changes in the amplitude of the component frequency of 12 kHz. For that, the analyzed string is disconnected of the array; and a small pulsed voltage signal of frequency of 12 kHz introduces him under dark condition and controlled temperature. Previous to the analysis, the signal is analogic filtered in order to reduce the direct current signal component. The spectral analysis technique used is the Fast Fourier Transform. The obtained experimental results were validated through simulation of the alternating current equivalent circuit of a solar cell. In all experimental and simulated test, the method allowed to identify correctly the number of photovoltaic modules with short circuit in the analyzed string. (author)

  15. System-Level Coupled Modeling of Piezoelectric Vibration Energy Harvesting Systems by Joint Finite Element and Circuit Analysis

    Directory of Open Access Journals (Sweden)

    Congcong Cheng

    2016-01-01

    Full Text Available A practical piezoelectric vibration energy harvesting (PVEH system is usually composed of two coupled parts: a harvesting structure and an interface circuit. Thus, it is much necessary to build system-level coupled models for analyzing PVEH systems, so that the whole PVEH system can be optimized to obtain a high overall efficiency. In this paper, two classes of coupled models are proposed by joint finite element and circuit analysis. The first one is to integrate the equivalent circuit model of the harvesting structure with the interface circuit and the second one is to integrate the equivalent electrical impedance of the interface circuit into the finite element model of the harvesting structure. Then equivalent circuit model parameters of the harvesting structure are estimated by finite element analysis and the equivalent electrical impedance of the interface circuit is derived by circuit analysis. In the end, simulations are done to validate and compare the proposed two classes of system-level coupled models. The results demonstrate that harvested powers from the two classes of coupled models approximate to theoretic values. Thus, the proposed coupled models can be used for system-level optimizations in engineering applications.

  16. Current, voltage and temperature distribution modeling of light-emitting diodes based on electrical and thermal circuit analysis

    International Nuclear Information System (INIS)

    Yun, J; Shim, J-I; Shin, D-S

    2013-01-01

    We demonstrate a modeling method based on the three-dimensional electrical and thermal circuit analysis to extract current, voltage and temperature distributions of light-emitting diodes (LEDs). In our model, the electrical circuit analysis is performed first to extract the current and voltage distributions in the LED. Utilizing the result obtained from the electrical circuit analysis as distributed heat sources, the thermal circuit is set up by using the duality between Fourier's law and Ohm's law. From the analysis of the thermal circuit, the temperature distribution at each epitaxial film is successfully obtained. Comparisons of experimental and simulation results are made by employing an InGaN/GaN multiple-quantum-well blue LED. Validity of the electrical circuit analysis is confirmed by comparing the light distribution at the surface. Since the temperature distribution at each epitaxial film cannot be obtained experimentally, the apparent temperature distribution is compared at the surface of the LED chip. Also, experimentally obtained average junction temperature is compared with the value calculated from the modeling, yielding a very good agreement. The analysis method based on the circuit modeling has an advantage of taking distributed heat sources as inputs, which is essential for high-power devices with significant self-heating. (paper)

  17. Gene set analysis using variance component tests.

    Science.gov (United States)

    Huang, Yen-Tsung; Lin, Xihong

    2013-06-28

    Gene set analyses have become increasingly important in genomic research, as many complex diseases are contributed jointly by alterations of numerous genes. Genes often coordinate together as a functional repertoire, e.g., a biological pathway/network and are highly correlated. However, most of the existing gene set analysis methods do not fully account for the correlation among the genes. Here we propose to tackle this important feature of a gene set to improve statistical power in gene set analyses. We propose to model the effects of an independent variable, e.g., exposure/biological status (yes/no), on multiple gene expression values in a gene set using a multivariate linear regression model, where the correlation among the genes is explicitly modeled using a working covariance matrix. We develop TEGS (Test for the Effect of a Gene Set), a variance component test for the gene set effects by assuming a common distribution for regression coefficients in multivariate linear regression models, and calculate the p-values using permutation and a scaled chi-square approximation. We show using simulations that type I error is protected under different choices of working covariance matrices and power is improved as the working covariance approaches the true covariance. The global test is a special case of TEGS when correlation among genes in a gene set is ignored. Using both simulation data and a published diabetes dataset, we show that our test outperforms the commonly used approaches, the global test and gene set enrichment analysis (GSEA). We develop a gene set analyses method (TEGS) under the multivariate regression framework, which directly models the interdependence of the expression values in a gene set using a working covariance. TEGS outperforms two widely used methods, GSEA and global test in both simulation and a diabetes microarray data.

  18. Simplified thermal-hydraulic analysis of single phase natural circulation circuit with two heat exchangers

    Energy Technology Data Exchange (ETDEWEB)

    Pinheiro, Larissa Cunha; Su, Jian, E-mail: larissa@lasme.coppe.ufrj.br, E-mail: sujian@lasme.coppe.ufrj.br [Coordenacao dos Programas de Pos-Graduacao em Engenharia (COPPE/UFRJ), Rio de Janeiro, RJ (Brazil). Programa de Engenhraria Nuclear; Cotta, Renato Machado, E-mail: cotta@mecanica.coppe.ufrj.br [Coordenacao dos Programas de Pos-Graduacao em Engenharia (POLI/COPPE/UFRJ), Rio de Janeiro, RJ (Brazil). Dept. de Engenharia Mecanica

    2015-07-01

    Single phase natural circulation circuits composed of two convective heat exchangers and connecting tubes are important for the passive heat removal from spent fuel pools (SFP). To keep the structural integrity of the stored spent fuel assemblies, continuously cooling has to be provided in order to avoid increase at the pool temperature and subsequent uncovering of the fuel and enhanced reaction between water and metal releasing hydrogen. Decay heat can achieve considerably high amounts of energy e.g. in the AP1000, considering the emergency fuel assemblies, the maximum heat decay will reach 13 MW in the 15th day (Westinghouse Electric Company, 2010). A highly efficient alternative to do so is by means of natural circulation, which is cost-effective compared to active cooling systems and is inherently safer since presents less associated devices and no external work is required. Many researchers have investigated safety and stability aspects of natural circulation loops (NCL). However, there is a lack of literature concerning the improvement of NCL through a standard unified methodology, especially for natural circulation circuits with two heat exchangers. In the present study, a simplified thermal-hydraulic analysis of single phase natural circulation circuit with two heat exchanges is presented. Relevant dimensionless key groups were proposed to for the design and safety analysis of a scaled NCL for the cooling of spent fuel storage pool with convective cooling and heating. (author)

  19. Measurement and Analysis of Multiple Output Transient Propagation in BJT Analog Circuits

    Science.gov (United States)

    Roche, Nicolas J.-H.; Khachatrian, A.; Warner, J. H.; Buchner, S. P.; McMorrow, D.; Clymer, D. A.

    2016-08-01

    The propagation of Analog Single Event Transients (ASETs) to multiple outputs of Bipolar Junction Transistor (BJTs) Integrated Circuits (ICs) is reported for the first time. The results demonstrate that ASETs can appear at several outputs of a BJT amplifier or comparator as a result of a single ion or single laser pulse strike at a single physical location on the chip of a large-scale integrated BJT analog circuit. This is independent of interconnect cross-talk or charge-sharing effects. Laser experiments, together with SPICE simulations and analysis of the ASET's propagation in the s-domain are used to explain how multiple-output transients (MOTs) are generated and propagate in the device. This study demonstrates that both the charge collection associated with an ASET and the ASET's shape, commonly used to characterize the propagation of SETs in devices and systems, are unable to explain quantitatively how MOTs propagate through an integrated analog circuit. The analysis methodology adopted here involves combining the Fourier transform of the propagating signal and the current-source transfer function in the s-domain. This approach reveals the mechanisms involved in the transient signal propagation from its point of generation to one or more outputs without the signal following a continuous interconnect path.

  20. Modeling and analysis of power extraction circuits for passive UHF RFID applications

    International Nuclear Information System (INIS)

    Fan Bo; Dai Yujie; Zhang Xiaoxing; Lue Yingjie

    2009-01-01

    Modeling and analysis of far field power extraction circuits for passive UHF RF identification (RFID) applications are presented. A mathematical model is derived to predict the complex nonlinear performance of UHF voltage multiplier using Schottky diodes. To reduce the complexity of the proposed model, a simple linear approximation for Schottky diode is introduced. Measurement results show considerable agreement with the values calculated by the proposed model. With the derived model, optimization on stage number for voltage multiplier to achieve maximum power conversion efficiency is discussed. Furthermore, according to the Bode-Fano criterion and the proposed model, a limitation on maximum power up range for passive UHF RFID power extraction circuits is also studied.

  1. Experiments and kinematics analysis of a hand rehabilitation exoskeleton with circuitous joints.

    Science.gov (United States)

    Zhang, Fuhai; Fu, Yili; Zhang, Qinchao; Wang, Shuguo

    2015-01-01

    Aiming at the hand rehabilitation of stroke patients, a wearable hand exoskeleton with circuitous joint is proposed. The circuitous joint adopts the symmetric pinion and rack mechanism (SPRM) with the parallel mechanism. The exoskeleton finger is a serial mechanism composed of three closed-chain SPRM joints in series. The kinematic equations of the open chain of the finger and the closed chains of the SPRM joints were built to analyze the kinematics of the hand rehabilitation exoskeleton. The experimental setup of the hand rehabilitation exoskeleton was built and the continuous passive motion (CPM) rehabilitation experiment and the test of human-robot interaction force measurement were conducted. Experiment results show that the mechanical design of the hand rehabilitation robot is reasonable and that the kinematic analysis is correct, thus the exoskeleton can be used for the hand rehabilitation of stroke patients.

  2. Analysis and modelling of GaN Schottky-based circuits at millimeter wavelengths

    International Nuclear Information System (INIS)

    Pardo, D; Grajal, J

    2015-01-01

    This work presents an analysis of the capabilities of GaN Schottky diodes for frequency multipliers and mixers at millimeter wavelengths. By using a Monte Carlo (MC) model of the diode coupled to a harmonic balance technique, the electrical and noise performances of these circuits are investigated. Despite the lower electron mobility of GaN compared to GaAs, multipliers based on GaN Schottky diodes can be competitive in the first stages of multiplier chains, due to the excellent power handling capabilities of this material. The performance of these circuits can be improved by taking advantage of the lateral Schottky diode structures based on AlGaN/GaN HEMT technology. (paper)

  3. Electronic devices and circuits

    CERN Document Server

    Pridham, Gordon John

    1972-01-01

    Electronic Devices and Circuits, Volume 3 provides a comprehensive account on electronic devices and circuits and includes introductory network theory and physics. The physics of semiconductor devices is described, along with field effect transistors, small-signal equivalent circuits of bipolar transistors, and integrated circuits. Linear and non-linear circuits as well as logic circuits are also considered. This volume is comprised of 12 chapters and begins with an analysis of the use of Laplace transforms for analysis of filter networks, followed by a discussion on the physical properties of

  4. Comparative Genomic Analysis of Soybean Flowering Genes

    Science.gov (United States)

    Jung, Chol-Hee; Wong, Chui E.; Singh, Mohan B.; Bhalla, Prem L.

    2012-01-01

    Flowering is an important agronomic trait that determines crop yield. Soybean is a major oilseed legume crop used for human and animal feed. Legumes have unique vegetative and floral complexities. Our understanding of the molecular basis of flower initiation and development in legumes is limited. Here, we address this by using a computational approach to examine flowering regulatory genes in the soybean genome in comparison to the most studied model plant, Arabidopsis. For this comparison, a genome-wide analysis of orthologue groups was performed, followed by an in silico gene expression analysis of the identified soybean flowering genes. Phylogenetic analyses of the gene families highlighted the evolutionary relationships among these candidates. Our study identified key flowering genes in soybean and indicates that the vernalisation and the ambient-temperature pathways seem to be the most variant in soybean. A comparison of the orthologue groups containing flowering genes indicated that, on average, each Arabidopsis flowering gene has 2-3 orthologous copies in soybean. Our analysis highlighted that the CDF3, VRN1, SVP, AP3 and PIF3 genes are paralogue-rich genes in soybean. Furthermore, the genome mapping of the soybean flowering genes showed that these genes are scattered randomly across the genome. A paralogue comparison indicated that the soybean genes comprising the largest orthologue group are clustered in a 1.4 Mb region on chromosome 16 of soybean. Furthermore, a comparison with the undomesticated soybean (Glycine soja) revealed that there are hundreds of SNPs that are associated with putative soybean flowering genes and that there are structural variants that may affect the genes of the light-signalling and ambient-temperature pathways in soybean. Our study provides a framework for the soybean flowering pathway and insights into the relationship and evolution of flowering genes between a short-day soybean and the long-day plant, Arabidopsis. PMID:22679494

  5. Npas4 regulates excitatory-inhibitory balance within neural circuits through cell-type-specific gene programs.

    Science.gov (United States)

    Spiegel, Ivo; Mardinly, Alan R; Gabel, Harrison W; Bazinet, Jeremy E; Couch, Cameron H; Tzeng, Christopher P; Harmin, David A; Greenberg, Michael E

    2014-05-22

    The nervous system adapts to experience by inducing a transcriptional program that controls important aspects of synaptic plasticity. Although the molecular mechanisms of experience-dependent plasticity are well characterized in excitatory neurons, the mechanisms that regulate this process in inhibitory neurons are only poorly understood. Here, we describe a transcriptional program that is induced by neuronal activity in inhibitory neurons. We find that, while neuronal activity induces expression of early-response transcription factors such as Npas4 in both excitatory and inhibitory neurons, Npas4 activates distinct programs of late-response genes in inhibitory and excitatory neurons. These late-response genes differentially regulate synaptic input to these two types of neurons, promoting inhibition onto excitatory neurons while inducing excitation onto inhibitory neurons. These findings suggest that the functional outcomes of activity-induced transcriptional responses are adapted in a cell-type-specific manner to achieve a circuit-wide homeostatic response. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. System Theoretic Dependability Analysis of the LHC Superconducting Magnet Circuit Protection

    CERN Document Server

    AUTHOR|(CDS)2254970

    Subject of the present work is the application of the methods STPA (System Theoretic Process Analysis) and CAST (Causal Analysis based on STAMP) to analyze the protection systems of the superconducting magnet circuit of the LHC at CERN, Geneva. The named methods are derived from the at MIT developed STAMP (System Theoretic Accident Model and Processes) accident model. The CAST method was applied to the analysis of the 2008 Incident during the Hardware Commissioning. An incorrect interconnection between two magnets damaged the accelerator severely. The analysis defines the control structure of the Commissioning and investigates every subsystem and the interaction between the components. The results were social and technical requirements. Among others, it shows the necessity for safety culture at CERN and a revision of the magnet interconnection process. The present analysis found the same root causes for the incident than a task force did in 2009. Further, the CAST analysis found more, socio-technica...

  7. Electric circuits essentials

    CERN Document Server

    REA, Editors of

    2012-01-01

    REA's Essentials provide quick and easy access to critical information in a variety of different fields, ranging from the most basic to the most advanced. As its name implies, these concise, comprehensive study guides summarize the essentials of the field covered. Essentials are helpful when preparing for exams, doing homework and will remain a lasting reference source for students, teachers, and professionals. Electric Circuits I includes units, notation, resistive circuits, experimental laws, transient circuits, network theorems, techniques of circuit analysis, sinusoidal analysis, polyph

  8. Optimization of the cooling circuit and thermo-mechanical analysis for the extraction grid of ELISE

    International Nuclear Information System (INIS)

    Nocentini, R.; Gutser, R.; Heinemann, B.; Froeschle, M.; Riedl, R.

    2011-01-01

    The NNBI test facility ELISE ('Extraction from a Large Ion Source Experiment'), presently under construction at IPP, will have an extraction area with the same width and half the height of the ITER source, acceleration up to 60 kV, for 10 s, every 180 s, and plasma generation up to 1 h. Electrons are co-extracted from the ion source. Suppression magnets in the extraction grid deflect the electrons onto the extraction grid surface. For 30 mA/cm 2 extracted electron current density and 10 kV extraction voltage, localized power density is in the order of 39 MW/m 2 near the grid apertures and a total heat load of 150 kW is deposited onto each extraction grid segment. Heat removal is provided by a water circuit inside the grid. For ELISE, a new cooling circuit has been developed to provide a more reliable operation. The optimization of the cooling circuit and the thermo-mechanical analysis of the extraction grid of ELISE, considering maximum grid temperature, mechanical stresses and grid deformation, has been performed using the codes KOBRA3, TrajAn, the ANSYS finite element package and the fluid dynamics code CFX.

  9. Equivalent Circuit Analysis of Photovoltaic-Thermoelectric Hybrid Device with Different TE Module Structure

    Directory of Open Access Journals (Sweden)

    Haijun Chen

    2014-01-01

    Full Text Available Combining two different types of solar cells with different absorption bands into a hybrid cell is a very useful method to improve the utilization efficiency of solar energy. The experimental data of dye-sensitized solar cells (DSSCs and thermoelectric generators (TEG was simulated by equivalent circuit method, and some parameters of DSSCs were obtained. Then, the equivalent circuit model with the obtained parameters was used to optimize the structure design of photovoltaic- (PV- thermoelectric (TE hybrid devices. The output power (Pout first increases to a maximum and then decreases by increasing the TE prism size, and a smaller spacing between p-type prism and n-type prism of a TE p-n junction causes a higher output power of TEG and hybrid device. When the spacing between TE prisms is 15 μm and the optimal base side length of TE prism is 40 μm, the maximum theoretical efficiency reaches 24.6% according to the equivalent circuit analysis. This work would give some enlightenment for the development of high-performance PV-TE hybrid devices.

  10. Modeling and Analysis of a Fractional-Order Generalized Memristor-Based Chaotic System and Circuit Implementation

    Science.gov (United States)

    Yang, Ningning; Xu, Cheng; Wu, Chaojun; Jia, Rong; Liu, Chongxin

    2017-12-01

    Memristor is a nonlinear “missing circuit element”, that can easily achieve chaotic oscillation. Memristor-based chaotic systems have received more and more attention. Research shows that fractional-order systems are more close to real systems. As an important parameter, the order can increase the flexibility and degree of freedom of the system. In this paper, a fractional-order generalized memristor, which consists of a diode bridge and a parallel circuit with an equivalent unit circuit and a linear resistance, is proposed. Frequency and electrical characteristics of the fractional-order memristor are analyzed. A chain structure circuit is used to implement the fractional-order unit circuit. Then replacing the conventional Chua’s diode by the fractional-order generalized memristor, a fractional-order memristor-based chaotic circuit is proposed. A large amount of research work has been done to investigate the influence of the order on the dynamical behaviors of the fractional-order memristor-based chaotic circuit. Varying with the order, the system enters the chaotic state from the periodic state through the Hopf bifurcation and period-doubling bifurcation. The chaotic state of the system has two types of attractors: single-scroll and double-scroll attractor. The stability theory of fractional-order systems is used to determine the minimum order occurring Hopf bifurcation. And the influence of the initial value on the system is analyzed. Circuit simulations are designed to verify the results of theoretical analysis and numerical simulation.

  11. Coupling a universal DNA circuit with graphene sheets/polyaniline/AuNPs nanocomposites for the detection of BCR/ABL fusion gene

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Xueping [Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 (China); Wang, Li [Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 (China); Department of Medical Laboratory, Chongqing Emergency Medical Center (Chongqing The Fourth Hospital), Chongqing, 400016 (China); Sheng, Shangchun [The No.2 Peoples' Hospital of Yibin, Sichuan, 644000 (China); Wang, Teng; Yang, Juan [Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 (China); Xie, Guoming, E-mail: guomingxie@cqmu.edu.cn [Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 (China); Feng, Wenli, E-mail: fengwlcqmu@sina.com [Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 (China)

    2015-08-19

    This article described a novel method by coupling a universal DNA circuit with graphene sheets/polyaniline/AuNPs nanocomposites (GS/PANI/AuNPs) for highly sensitive and specific detection of BCR/ABL fusion gene (bcr/abl) in chronic myeloid leukemia (CML). DNA circuit known as catalyzed hairpin assembly (CHA) is enzyme-free and can be simply operated to achieve exponential amplification, which has been widely employed in biosensing. However, application of CHA has been hindered by the need of specially redesigned sequences for each single-stranded DNA input. Herein, a transducer hairpin (HP) was designed to obtain a universal DNA circuit with favorable signal-to-background ratio. To further improve signal amplification, GS/PANI/AuNPs with excellent conductivity and enlarged effective area were introduced into this DNA circuit. Consequently, by combining the advantages of CHA and GS/PANI/AuNPs, bcr/abl could be detected in a linear range from 10 pM to 20 nM with a detection limit of 1.05 pM. Moreover, this protocol showed excellent specificity, good stability and was successfully applied for the detection of real sample, which demonstrated its great potential in clinical application. - Highlights: • A transducer hairpin was designed to improve the versatility of DNA circuit. • GS/PANI/AuNPs were introduced to the DNA circuit for further signal amplification. • The established biosensor displayed high sensitivity and good specificity.

  12. Serial analysis of gene expression (SAGE)

    NARCIS (Netherlands)

    van Ruissen, Fred; Baas, Frank

    2007-01-01

    In 1995, serial analysis of gene expression (SAGE) was developed as a versatile tool for gene expression studies. SAGE technology does not require pre-existing knowledge of the genome that is being examined and therefore SAGE can be applied to many different model systems. In this chapter, the SAGE

  13. Feedback in analog circuits

    CERN Document Server

    Ochoa, Agustin

    2016-01-01

    This book describes a consistent and direct methodology to the analysis and design of analog circuits with particular application to circuits containing feedback. The analysis and design of circuits containing feedback is generally presented by either following a series of examples where each circuit is simplified through the use of insight or experience (someone else’s), or a complete nodal-matrix analysis generating lots of algebra. Neither of these approaches leads to gaining insight into the design process easily. The author develops a systematic approach to circuit analysis, the Driving Point Impedance and Signal Flow Graphs (DPI/SFG) method that does not require a-priori insight to the circuit being considered and results in factored analysis supporting the design function. This approach enables designers to account fully for loading and the bi-directional nature of elements both in the feedback path and in the amplifier itself, properties many times assumed negligible and ignored. Feedback circuits a...

  14. A survey of SiC power MOSFETs short-circuit robustness and failure mode analysis

    DEFF Research Database (Denmark)

    Ceccarelli, L.; Reigosa, P. D.; Iannuzzo, F.

    2017-01-01

    The aim of this paper is to provide an extensive overview about the state-of-art commercially available SiC power MOSFET, focusing on their short-circuit ruggedness. A detailed literature investigation has been carried out, in order to collect and understand the latest research contribution within...... this topic and create a survey of the present scenario of SiC MOSFETs reliability evaluation and failure mode analysis, pointing out the evolution and improvements as well as the future challenges in this promising device technology....

  15. ANALYSIS OF INDUCTION MOTOR WITH BROKEN BARS AND CONSTANT SPEED USING CIRCUIT-FIELD COUPLED METHOD

    Directory of Open Access Journals (Sweden)

    N. Halem

    2015-07-01

    Full Text Available The paper presents the use of the two-dimensional finite element method for modeling the three-phase squirrel-cage induction motor by using circuit coupled method. In order to analyze the machine performances, the voltage source is considered. The Ansys magnetic analysis software is used for calculating the magnetic field of an induction motor having a cage fault. The experimental results prove that the proposed approach constitutes a useful tool for the study and diagnostics of induction motors.

  16. Web-based eTutor for learningn electrical circuit analysis

    OpenAIRE

    Debono, Jason; Muscat, Adrian; Porter, Chris; Connections

    2018-01-01

    This paper discusses a web-based eTutor for learning electrical circuit analysis. The eTutor system components, mainly the user-interface and the assessment model, are described. The system architecture developed provides a framework to support interactive sessions between the human and the machine for the case when the human is a student and the machine a tutor and also for the case when the roles of the human and the machine are swapped. To motivate the usefulness of the data...

  17. Transient analysis of unbalanced short circuits of the ERDA-NASA 100 kW wind turbine alternator

    Science.gov (United States)

    Hwang, H. H.; Gilbert, L. J.

    1976-01-01

    Unbalanced short-circuit faults on the alternator of the ERDA-NASA Mod-O100-kW experimental wind turbine are studied. For each case, complete solutions for armature, field, and damper-circuit currents; short-circuit torque; and open-phase voltage are derived directly by a mathematical analysis. Formulated results are tabulated. For the Mod-O wind turbine alternator, numerical calculations are given, and results are presented by graphs. Comparisons for significant points among the more important cases are summarized. For these cases the transients are found to be potentially severe. The effect of the alternator neutral-to-ground impedance is evaluated.

  18. Pluripotency gene network dynamics: System views from parametric analysis.

    Science.gov (United States)

    Akberdin, Ilya R; Omelyanchuk, Nadezda A; Fadeev, Stanislav I; Leskova, Natalya E; Oschepkova, Evgeniya A; Kazantsev, Fedor V; Matushkin, Yury G; Afonnikov, Dmitry A; Kolchanov, Nikolay A

    2018-01-01

    Multiple experimental data demonstrated that the core gene network orchestrating self-renewal and differentiation of mouse embryonic stem cells involves activity of Oct4, Sox2 and Nanog genes by means of a number of positive feedback loops among them. However, recent studies indicated that the architecture of the core gene network should also incorporate negative Nanog autoregulation and might not include positive feedbacks from Nanog to Oct4 and Sox2. Thorough parametric analysis of the mathematical model based on this revisited core regulatory circuit identified that there are substantial changes in model dynamics occurred depending on the strength of Oct4 and Sox2 activation and molecular complexity of Nanog autorepression. The analysis showed the existence of four dynamical domains with different numbers of stable and unstable steady states. We hypothesize that these domains can constitute the checkpoints in a developmental progression from naïve to primed pluripotency and vice versa. During this transition, parametric conditions exist, which generate an oscillatory behavior of the system explaining heterogeneity in expression of pluripotent and differentiation factors in serum ESC cultures. Eventually, simulations showed that addition of positive feedbacks from Nanog to Oct4 and Sox2 leads mainly to increase of the parametric space for the naïve ESC state, in which pluripotency factors are strongly expressed while differentiation ones are repressed.

  19. Reverse engineering validation using a benchmark synthetic gene circuit in human cells.

    Science.gov (United States)

    Kang, Taek; White, Jacob T; Xie, Zhen; Benenson, Yaakov; Sontag, Eduardo; Bleris, Leonidas

    2013-05-17

    Multicomponent biological networks are often understood incompletely, in large part due to the lack of reliable and robust methodologies for network reverse engineering and characterization. As a consequence, developing automated and rigorously validated methodologies for unraveling the complexity of biomolecular networks in human cells remains a central challenge to life scientists and engineers. Today, when it comes to experimental and analytical requirements, there exists a great deal of diversity in reverse engineering methods, which renders the independent validation and comparison of their predictive capabilities difficult. In this work we introduce an experimental platform customized for the development and verification of reverse engineering and pathway characterization algorithms in mammalian cells. Specifically, we stably integrate a synthetic gene network in human kidney cells and use it as a benchmark for validating reverse engineering methodologies. The network, which is orthogonal to endogenous cellular signaling, contains a small set of regulatory interactions that can be used to quantify the reconstruction performance. By performing successive perturbations to each modular component of the network and comparing protein and RNA measurements, we study the conditions under which we can reliably reconstruct the causal relationships of the integrated synthetic network.

  20. Automatic analysis at the commissioning of the LHC superconducting electrical circuits

    International Nuclear Information System (INIS)

    Reymond, H.; Andreassen, O.O.; Charrondiere, C.; Rijllart, A.; Zerlauth, M.

    2012-01-01

    Since the beginning of 2010 the LHC has been operating in a routinely manner, starting with a commissioning phase and then an operation for physics phase. The commissioning of the superconducting electrical circuits requires rigorous test procedures before entering into operation. To maximize the beam operation time of the LHC, these tests should be done as fast as procedures allow. A full commissioning need 12000 tests and is required after circuits have been warmed above liquid nitrogen temperature. Below this temperature, after an end of year break of two months, commissioning needs about 6000 tests. As the manual analysis of the tests takes a major part of the commissioning time, we automated existing analysis tools. We present here how these LabVIEW TM applications were automated, the evaluation of the gain in commissioning time and reduction of experts on night shift observed during the LHC hardware commissioning campaign of 2011 compared to 2010. We end with an outlook at what can be further optimized. (authors)

  1. Adhesion and failure analysis of metal-polymer interface in flexible printed circuits boards

    Science.gov (United States)

    Park, Sanghee; Kim, Ye Chan; Choi, Kisuk; Chae, Heeyop; Suhr, Jonghwan; Nam, Jae-Do

    2017-12-01

    As device miniaturization in microelectronics is currently requested in the development of high performance device, which usually include highly-integrated metal-polyimide multilayer structures. A redistribution layer (RDL) process is currently emerging as one of the most advance fabrication techniques for on-chip interconnect and packaging. One of the major issues in this process is the poor adhesion of the metal-polyimide interfaces particularly in flexible circuit boards due to the flexibility and bendability of devices. In this study, low pressure O2 plasma treatment was investigated to improve the adhesion of metal-polyimide interfaces, using inductively coupled plasma (ICP) treatment. We identified that the adhesion of metal-polyimide interfaces was greatly improved by the surface roughness control providing 46.1 MPa of shear force in the ball shear test after O2 plasma treatment, compared 14.2 MPa without O2 plasma treatment. It was seemingly due to the fact that the adhesion in metal-polyimide interfaces was improved by a chemical conversion of C=O to C-O bonds and by a ring opening reaction of imide groups, which was confirmed with FT-IR analysis. In the finite element numerical analysis of metal-polyimide interfaces, the O2 plasma treated interface showed that the in-plane stress distribution and the vertical directional deformation agreed well with real failure modes in flexible circuits manufacturing.

  2. Automatic Analysis at the Commissioning of the LHC Superconducting Electrical Circuits

    CERN Document Server

    Reymond, H; Charrondiere, C; Rijllart, A; Zerlauth, M

    2011-01-01

    Since the beginning of 2010 the LHC has been operating in a routinely manner, starting with a commissioning phase and then an operation for physics phase. The commissioning of the superconducting electrical circuits requires rigorous test procedures before entering into operation. To maximize the beam operation time of the LHC, these tests should be done as fast as procedures allow. A full commissioning need 12000 tests and is required after circuits have been warmed above liquid nitrogen temperature. Below this temperature, after an end of year break of two months, commissioning needs about 6000 tests. As the manual analysis of the tests takes a major part of the commissioning time, we automated existing analysis tools. We present here how these LabVIEW™ applications were automated, the evaluation of the gain in commissioning time and reduction of experts on night shift observed during the LHC hardware commissioning campaign of 2011 compared to 2010. We end with an outlook at what can be further optimized.

  3. Analysis and design of a charge pump circuit for high output current applications

    NARCIS (Netherlands)

    van Steenwijk, Gijs; van Steenwijk, Gijs; Hoen, Klaas; Hoen, Klaas; Wallinga, Hans

    1993-01-01

    A charge pump circuit has been developed that can deliver high currents even for a system supply voltage of 3 V. The circuit consists of capacitances, connected by MOS switches. The influence of the on-resistance of the switches on the circuit's output resistance has been analysed. The switches are

  4. Analysis of the main causes of failures in the Atucha I PWR moderator circuit branch piping

    International Nuclear Information System (INIS)

    Porto, J.; Sarmiento, G.S.

    1983-01-01

    From 1977 to 1979 four through cracks were detected in the auxiliary connection of the moderator piping with the coolant circuit in the PWR Atucha I Nuclear Plant. The failures were observed to occur systematically in the same place of the pipe, where mechanical stresses were detected experimentally and thermal stresses were calculated based on temperature values measured on the pipe. The temperature field in steady state conditions as well as during thermal shocks was modelled by finite element codes, and the corresponding thermal stresses were than numerically calculated. Considering those thermal and mechanical solicitations, a crack propagation analysis based on the elastoplastic fracture mechanics and the finite element method is now being developed. Among other causes such as fatigue corrosion and vibrations, the results of the analysis show that the most preponderant factors determining the cracking are mechanical stress, thermal stress and thermal fatigue

  5. Oscillator circuits

    CERN Document Server

    Graf, Rudolf F

    1996-01-01

    This series of circuits provides designers with a quick source for oscillator circuits. Why waste time paging through huge encyclopedias when you can choose the topic you need and select any of the specialized circuits sorted by application?This book in the series has 250-300 practical, ready-to-use circuit designs, with schematics and brief explanations of circuit operation. The original source for each circuit is listed in an appendix, making it easy to obtain additional information.Ready-to-use circuits.Grouped by application for easy look-up.Circuit source listing

  6. Measuring circuits

    CERN Document Server

    Graf, Rudolf F

    1996-01-01

    This series of circuits provides designers with a quick source for measuring circuits. Why waste time paging through huge encyclopedias when you can choose the topic you need and select any of the specialized circuits sorted by application?This book in the series has 250-300 practical, ready-to-use circuit designs, with schematics and brief explanations of circuit operation. The original source for each circuit is listed in an appendix, making it easy to obtain additional information.Ready-to-use circuits.Grouped by application for easy look-up.Circuit source listings

  7. Development of a computer code for dynamic analysis of the primary circuit of advanced reactors

    Energy Technology Data Exchange (ETDEWEB)

    Rocha, Jussie Soares da; Lira, Carlos A.B.O.; Magalhaes, Mardson A. de Sa, E-mail: cabol@ufpe.b [Universidade Federal de Pernambuco (DEN/UFPE), Recife, PE (Brazil). Dept. de Energia Nuclear

    2011-07-01

    Currently, advanced reactors are being developed, seeking for enhanced safety, better performance and low environmental impacts. Reactor designs must follow several steps and numerous tests before a conceptual project could be certified. In this sense, computational tools become indispensable in the preparation of such projects. Thus, this study aimed at the development of a computational tool for thermal-hydraulic analysis by coupling two computer codes to evaluate the influence of transients caused by pressure variations and flow surges in the region of the primary circuit of IRIS reactor between the core and the pressurizer. For the simulation, it was used a situation of 'insurge', characterized by the entry of water in the pressurizer, due to the expansion of the refrigerant in the primary circuit. This expansion was represented by a pressure disturbance in step form, through the block 'step' of SIMULINK, thus enabling the transient startup. The results showed that the dynamic tool, obtained through the coupling of the codes, generated very satisfactory responses within model limitations, preserving the most important phenomena in the process. (author)

  8. Development of a computer code for dynamic analysis of the primary circuit of advanced reactors

    International Nuclear Information System (INIS)

    Rocha, Jussie Soares da; Lira, Carlos A.B.O.; Magalhaes, Mardson A. de Sa

    2011-01-01

    Currently, advanced reactors are being developed, seeking for enhanced safety, better performance and low environmental impacts. Reactor designs must follow several steps and numerous tests before a conceptual project could be certified. In this sense, computational tools become indispensable in the preparation of such projects. Thus, this study aimed at the development of a computational tool for thermal-hydraulic analysis by coupling two computer codes to evaluate the influence of transients caused by pressure variations and flow surges in the region of the primary circuit of IRIS reactor between the core and the pressurizer. For the simulation, it was used a situation of 'insurge', characterized by the entry of water in the pressurizer, due to the expansion of the refrigerant in the primary circuit. This expansion was represented by a pressure disturbance in step form, through the block 'step' of SIMULINK, thus enabling the transient startup. The results showed that the dynamic tool, obtained through the coupling of the codes, generated very satisfactory responses within model limitations, preserving the most important phenomena in the process. (author)

  9. Principles of gene microarray data analysis.

    Science.gov (United States)

    Mocellin, Simone; Rossi, Carlo Riccardo

    2007-01-01

    The development of several gene expression profiling methods, such as comparative genomic hybridization (CGH), differential display, serial analysis of gene expression (SAGE), and gene microarray, together with the sequencing of the human genome, has provided an opportunity to monitor and investigate the complex cascade of molecular events leading to tumor development and progression. The availability of such large amounts of information has shifted the attention of scientists towards a nonreductionist approach to biological phenomena. High throughput technologies can be used to follow changing patterns of gene expression over time. Among them, gene microarray has become prominent because it is easier to use, does not require large-scale DNA sequencing, and allows for the parallel quantification of thousands of genes from multiple samples. Gene microarray technology is rapidly spreading worldwide and has the potential to drastically change the therapeutic approach to patients affected with tumor. Therefore, it is of paramount importance for both researchers and clinicians to know the principles underlying the analysis of the huge amount of data generated with microarray technology.

  10. Analysis of water hammer phenomena in RBMK-1500 reactor main circulation circuit

    International Nuclear Information System (INIS)

    Kaliatka, A.; Uspuras, E.; Vaisnoras, M.

    2006-01-01

    Water hammer can occur in any thermal-hydraulic systems. Water hammer can reach pressure levels far exceeding the pressure range of a pipe given by the manufacturer, and it can lead to the failure of the pipeline integrity. In the past three decades, since a large number of water hammer events occurred in the light-water- reactor power plants, a number of comprehensive studies on the phenomena associated with water hammer events have been performed. There are three basic types of severe water hammer occurring at power plants that can result in significant plant damage: rapid valve operation events; void-induced water hammer; condensation-induced water hammer. Correct prediction of water hammer transients, is therefore of paramount importance for the safe operation of the plant. Therefore verifying of computer codes capability to simulate water hammer type transients is very important issue at performing of safety analyses for nuclear power plants. Verification of RELAP5/MOD3.3 code capability to simulate water hammer type transients employing the experimental investigations is presented. Experience gained from benchmarking analyses has been used at development of the detail RELAP5 code RBMK-1500 model for simulation of water hammer effects in reactor main circulation circuit. Analysis of reactor cooling system shows, that water hammers can occur in main circulation circuit of RBMK-1500 reactor in cases of: (1) Guillotine break of the inlet piping upstream of the Group Distribution Header and (2) Guillotine break of the pressure piping upstream the Main Circulation Pump check valve. Analysis of above mentioned accident scenarios is presented in this paper. First scenario of the accident potentially is more dangerous, because the pressure pulses influence not only the reactor cooling circuit, but also the piping of safety related system (Emergency Core Cooling System pipeline) connected to affected Group Distribution Header. The performed analysis using RELAP5 code

  11. Modulation of learning and memory by the targeted deletion of the circadian clock gene Bmal1 in forebrain circuits.

    Science.gov (United States)

    Snider, Kaitlin H; Dziema, Heather; Aten, Sydney; Loeser, Jacob; Norona, Frances E; Hoyt, Kari; Obrietan, Karl

    2016-07-15

    A large body of literature has shown that the disruption of circadian clock timing has profound effects on mood, memory and complex thinking. Central to this time keeping process is the master circadian pacemaker located within the suprachiasmatic nucleus (SCN). Of note, within the central nervous system, clock timing is not exclusive to the SCN, but rather, ancillary oscillatory capacity has been detected in a wide range of cell types and brain regions, including forebrain circuits that underlie complex cognitive processes. These observations raise questions about the hierarchical and functional relationship between the SCN and forebrain oscillators, and, relatedly, about the underlying clock-gated synaptic circuitry that modulates cognition. Here, we utilized a clock knockout strategy in which the essential circadian timing gene Bmal1 was selectively deleted from excitatory forebrain neurons, whilst the SCN clock remained intact, to test the role of forebrain clock timing in learning, memory, anxiety, and behavioral despair. With this model system, we observed numerous effects on hippocampus-dependent measures of cognition. Mice lacking forebrain Bmal1 exhibited deficits in both acquisition and recall on the Barnes maze. Notably, loss of forebrain Bmal1 abrogated time-of-day dependent novel object location memory. However, the loss of Bmal1 did not alter performance on the elevated plus maze, open field assay, and tail suspension test, indicating that this phenotype specifically impairs cognition but not affect. Together, these data suggest that forebrain clock timing plays a critical role in shaping the efficiency of learning and memory retrieval over the circadian day. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Temporal Noise Analysis of Charge-Domain Sampling Readout Circuits for CMOS Image Sensors

    Directory of Open Access Journals (Sweden)

    Xiaoliang Ge

    2018-02-01

    Full Text Available This paper presents a temporal noise analysis of charge-domain sampling readout circuits for Complementary Metal-Oxide Semiconductor (CMOS image sensors. In order to address the trade-off between the low input-referred noise and high dynamic range, a Gm-cell-based pixel together with a charge-domain correlated-double sampling (CDS technique has been proposed to provide a way to efficiently embed a tunable conversion gain along the read-out path. Such readout topology, however, operates in a non-stationery large-signal behavior, and the statistical properties of its temporal noise are a function of time. Conventional noise analysis methods for CMOS image sensors are based on steady-state signal models, and therefore cannot be readily applied for Gm-cell-based pixels. In this paper, we develop analysis models for both thermal noise and flicker noise in Gm-cell-based pixels by employing the time-domain linear analysis approach and the non-stationary noise analysis theory, which help to quantitatively evaluate the temporal noise characteristic of Gm-cell-based pixels. Both models were numerically computed in MATLAB using design parameters of a prototype chip, and compared with both simulation and experimental results. The good agreement between the theoretical and measurement results verifies the effectiveness of the proposed noise analysis models.

  13. Circuit- and Diagnosis-Specific DNA Methylation Changes at γ-Aminobutyric Acid–Related Genes in Postmortem Human Hippocampus in Schizophrenia and Bipolar Disorder

    Science.gov (United States)

    Ruzicka, W. Brad; Subburaju, Sivan; Benes, Francine M.

    2017-01-01

    IMPORTANCE Dysfunction related to γ-aminobutyric acid (GABA)–ergic neurotransmission in the pathophysiology of major psychosis has been well established by the work of multiple groups across several decades, including the widely replicated downregulation of GAD1. Prior gene expression and network analyses within the human hippocampus implicate a broader network of genes, termed the GAD1 regulatory network, in regulation of GAD1 expression. Several genes within this GAD1 regulatory network show diagnosis- and sector-specific expression changes within the circuitry of the hippocampus, influencing abnormal GAD1 expression in schizophrenia and bipolar disorder. OBJECTIVE To investigate the hypothesis that aberrant DNA methylation contributes to circuit- and diagnosis-specific abnormal expression of GAD1 regulatory network genes in psychotic illness. DESIGN, SETTING, AND PARTICIPANTS This epigenetic association study targeting GAD1 regulatory network genes was conducted between July 1, 2012, and June 30, 2014. Postmortem human hippocampus tissue samples were obtained from 8patients with schizophrenia, 8 patients with bipolar disorder, and 8 healthy control participants matched for age, sex, postmortem interval, and other potential confounds from the Harvard Brain Tissue Resource Center, McLean Hospital, Belmont,Massachusetts. We extracted DNA from laser-microdissected stratum oriens tissue of cornu ammonis 2/3 (CA2/3) and CA1 postmortem human hippocampus, bisulfite modified it, and assessed it with the Infinium HumanMethylation450 BeadChip (Illumina, Inc). The subset of CpG loci associated with GAD1 regulatory network genes was analyzed in R version 3.1.0 software (R Foundation) using the minfi package. Findings were validated using bisulfite pyrosequencing. MAIN OUTCOMES AND MEASURES Methylation levels at 1308 GAD1 regulatory network–associated CpG loci were assessed both as individual sites to identify differentially methylated positions and by sharing

  14. Circuit- and Diagnosis-Specific DNA Methylation Changes at γ-Aminobutyric Acid-Related Genes in Postmortem Human Hippocampus in Schizophrenia and Bipolar Disorder.

    Science.gov (United States)

    Ruzicka, W Brad; Subburaju, Sivan; Benes, Francine M

    2015-06-01

    Dysfunction related to γ-aminobutyric acid (GABA)-ergic neurotransmission in the pathophysiology of major psychosis has been well established by the work of multiple groups across several decades, including the widely replicated downregulation of GAD1. Prior gene expression and network analyses within the human hippocampus implicate a broader network of genes, termed the GAD1 regulatory network, in regulation of GAD1 expression. Several genes within this GAD1 regulatory network show diagnosis- and sector-specific expression changes within the circuitry of the hippocampus, influencing abnormal GAD1 expression in schizophrenia and bipolar disorder. To investigate the hypothesis that aberrant DNA methylation contributes to circuit- and diagnosis-specific abnormal expression of GAD1 regulatory network genes in psychotic illness. This epigenetic association study targeting GAD1 regulatory network genes was conducted between July 1, 2012, and June 30, 2014. Postmortem human hippocampus tissue samples were obtained from 8 patients with schizophrenia, 8 patients with bipolar disorder, and 8 healthy control participants matched for age, sex, postmortem interval, and other potential confounds from the Harvard Brain Tissue Resource Center, McLean Hospital, Belmont, Massachusetts. We extracted DNA from laser-microdissected stratum oriens tissue of cornu ammonis 2/3 (CA2/3) and CA1 postmortem human hippocampus, bisulfite modified it, and assessed it with the Infinium HumanMethylation450 BeadChip (Illumina, Inc). The subset of CpG loci associated with GAD1 regulatory network genes was analyzed in R version 3.1.0 software (R Foundation) using the minfi package. Findings were validated using bisulfite pyrosequencing. Methylation levels at 1308 GAD1 regulatory network-associated CpG loci were assessed both as individual sites to identify differentially methylated positions and by sharing information among colocalized probes to identify differentially methylated regions. A total of

  15. Multi-Level Simulated Fault Injection for Data Dependent Reliability Analysis of RTL Circuit Descriptions

    Directory of Open Access Journals (Sweden)

    NIMARA, S.

    2016-02-01

    Full Text Available This paper proposes data-dependent reliability evaluation methodology for digital systems described at Register Transfer Level (RTL. It uses a hybrid hierarchical approach, combining the accuracy provided by Gate Level (GL Simulated Fault Injection (SFI and the low simulation overhead required by RTL fault injection. The methodology comprises the following steps: the correct simulation of the RTL system, according to a set of input vectors, hierarchical decomposition of the system into basic RTL blocks, logic synthesis of basic RTL blocks, data-dependent SFI for the GL netlists, and RTL SFI. The proposed methodology has been validated in terms of accuracy on a medium sized circuit – the parallel comparator used in Check Node Unit (CNU of the Low-Density Parity-Check (LDPC decoders. The methodology has been applied for the reliability analysis of a 128-bit Advanced Encryption Standard (AES crypto-core, for which the GL simulation was prohibitive in terms of required computational resources.

  16. The analysis of a novel 3-D autonomous system and circuit implementation

    International Nuclear Information System (INIS)

    Dong Gaogao; Zheng Song; Tian Lixin; Du Ruijin; Sun Mei; Shi Zhiyan

    2009-01-01

    This Letter presents a new three-dimensional autonomous system with four quadratic terms. The system with five equilibrium points has complex chaotic dynamics behaviors. It can generate many different single chaotic attractors and double coexisting chaotic attractors over a large range of parameters. We observe that these chaotic attractors were rarely reported in previous work. The complex dynamical behaviors of the system are further investigated by means of phase portraits, Lyapunov exponents spectrum, Lyapunov dimension, dissipativeness of system, bifurcation diagram and Poincare map. The physical circuit experimental results of the chaotic attractors show agreement with numerical simulations. More importantly, the analysis of frequency spectrum shows that the novel system has a broad frequency bandwidth, which is very desirable for engineering applications such as secure communications.

  17. Electric circuits and signals

    CERN Document Server

    Sabah, Nassir H

    2007-01-01

    Circuit Variables and Elements Overview Learning Objectives Electric Current Voltage Electric Power and Energy Assigned Positive Directions Active and Passive Circuit Elements Voltage and Current Sources The Resistor The Capacitor The Inductor Concluding Remarks Summary of Main Concepts and Results Learning Outcomes Supplementary Topics on CD Problems and Exercises Basic Circuit Connections and Laws Overview Learning Objectives Circuit Terminology Kirchhoff's Laws Voltage Division and Series Connection of Resistors Current Division and Parallel Connection of Resistors D-Y Transformation Source Equivalence and Transformation Reduced-Voltage Supply Summary of Main Concepts and Results Learning Outcomes Supplementary Topics and Examples on CD Problems and Exercises Basic Analysis of Resistive Circuits Overview Learning Objectives Number of Independent Circuit Equations Node-Voltage Analysis Special Considerations in Node-Voltage Analysis Mesh-Current Analysis Special Conside...

  18. Bioinformatic Analysis of Strawberry GSTF12 Gene

    Science.gov (United States)

    Wang, Xiran; Jiang, Leiyu; Tang, Haoru

    2018-01-01

    GSTF12 has always been known as a key factor of proanthocyanins accumulate in plant testa. Through bioinformatics analysis of the nucleotide and encoded protein sequence of GSTF12, it is more advantageous to the study of genes related to anthocyanin biosynthesis accumulation pathway. Therefore, we chosen GSTF12 gene of 11 kinds species, downloaded their nucleotide and protein sequence from NCBI as the research object, found strawberry GSTF12 gene via bioinformation analyse, constructed phylogenetic tree. At the same time, we analysed the strawberry GSTF12 gene of physical and chemical properties and its protein structure and so on. The phylogenetic tree showed that Strawberry and petunia were closest relative. By the protein prediction, we found that the protein owed one proper signal peptide without obvious transmembrane regions.

  19. Analysis of a distributed pulse power system using a circuit analysis code

    International Nuclear Information System (INIS)

    Hoeft, L.O.; BDM Corp., Albuquerque, NM)

    1979-01-01

    A sophisticated computer code (SCEPTRE), used to analyze electronic circuits, was used to evaluate the performance of a large flash x-ray machine. This device was considered to be a transmission line whose impedance varied with position. This distributed system was modeled by lumped parameter sections with time constants of 1 ns. The model was used to interpret voltage, current, and radiation measurements in terms of diode performance. The effects of tube impedance, diode model, switch behavior, and potential geometric modifications were determined. The principal conclusions were that, since radiation output depends strongly on voltage, diode impedance was much more important than the other parameters, and the charge voltage must be accurately known

  20. Analysis of electrical circuits with variable load regime parameters projective geometry method

    CERN Document Server

    Penin, A

    2015-01-01

    This book introduces electric circuits with variable loads and voltage regulators. It allows to define invariant relationships for various parameters of regime and circuit sections and to prove the concepts characterizing these circuits. Generalized equivalent circuits are introduced. Projective geometry is used for the interpretation of changes of operating regime parameters. Expressions of normalized regime parameters and their changes are presented. Convenient formulas for the calculation of currents are given. Parallel voltage sources and the cascade connection of multi-port networks are d

  1. Functional changes of neural circuits in stroke patients with dysphagia: A meta-analysis.

    Science.gov (United States)

    Liu, Lu; Xiao, Yuan; Zhang, Wenjing; Yao, Li; Gao, Xin; Chandan, Shah; Lui, Su

    2017-08-01

    Dysphagia is a common problem in stroke patients with unclear pathogenesis. Several recent functional magnetic resonance imaging (fMRI) studies had been carried out to explore the cerebral functional changes in dysphagic stroke patients. The aim of this study was to analysis these imaging findings using a meta-analysis. We used seed-based d mapping (SDM) to conduct a meta-analysis for dysphagic stroke patients prior to any kind of special treatment for dysphagia. A systematic search was conducted for the relevant studies. SDM meta-analysis method was used to examine regions of increased and decreased functional activation between dysphagic stroke patients and healthy controls. Finally, six studies including 81 stroke patients with dysphagia and 78 healthy controls met the inclusion standards. When compared with healthy controls, stroke patients with dysphagia showed hyperactivation in left cingulate gyrus, left precentral gyrus and right posterior cingulate gyrus, and hypoactivation in right cuneus and left middle frontal gyrus. The hyperactivity of precentral gyrus is crucial in stroke patients with dysphagia and may be associated with the severity of stroke. Besides the motor areas, the default-mode network regions (DMN) and affective network regions (AN) circuits are also involved in dysphagia after stroke. © 2017 Chinese Cochrane Center, West China Hospital of Sichuan University and John Wiley & Sons Australia, Ltd.

  2. A computer analysis code of radioactive corrosion product behaviour in primary circuits of LMFBRs (PSYCHE)

    International Nuclear Information System (INIS)

    Iizawa, Katsuyuki; Seki, Seiichi; Kawasaki, Yuji; Kano, Shigeki; Nihei, Isao

    1986-01-01

    Recently it has become an important subject to reduce exposure to radiation from radioactive corrosion products (CPs) during maintenance and repair works in reactor plants. Metallic sodium is used as cooling material in fast reactor plants, leading to different CP behaviours compared to light water reactors. In the present study, a computer code for analyzing behaviours of CPs in fast reactor plants is developed. The analysis code, called PSYCHE, makes it possible to perform consistent analysis of production, migration and deposition of CPs in primary circuits together with dose rate around piping of apparatus in cooling systems. An analysis model is developed based on test results on CP behaviour in out-pile sodium. The model, called the ''dissolution-deposition model'', can reproduce atom-selective behaviour, transient phenomenon and downstream effect of CPs, which represent mass transfer phenomena in sodium. Verification of this code is carried out on the basis of CP measurements made in ''Joyo''. The calculation vs. measurement ratio is found to be 0.5 - 2 for CP deposition density in piping for cooling systems and 0.7 - 1.3 for dose rate, demonstrating that this code can give reasonable results. Analysis is also made to predict future changes in total amount of deposited CP in ''Joyo''. (Nogami, K.)

  3. Circuit Analysis of a Drosophila Dopamine Type 2 Receptor That Supports Anesthesia-Resistant Memory.

    Science.gov (United States)

    Scholz-Kornehl, Sabrina; Schwärzel, Martin

    2016-07-27

    Dopamine is central to reinforcement processing and exerts this function in species ranging from humans to fruit flies. It can do so via two different types of receptors (i.e., D1 or D2) that mediate either augmentation or abatement of cellular cAMP levels. Whereas D1 receptors are known to contribute to Drosophila aversive odor learning per se, we here show that D2 receptors are specific for support of a consolidated form of odor memory known as anesthesia-resistant memory. By means of genetic mosaicism, we localize this function to Kenyon cells, the mushroom body intrinsic neurons, as well as GABAergic APL neurons and local interneurons of the antennal lobes, suggesting that consolidated anesthesia-resistant memory requires widespread dopaminergic modulation within the olfactory circuit. Additionally, dopaminergic neurons themselves require D2R, suggesting a critical role in dopamine release via its recognized autoreceptor function. Considering the dual role of dopamine in balancing memory acquisition (proactive function of dopamine) and its "forgetting" (retroactive function of dopamine), our analysis suggests D2R as central player of either process. Dopamine provides different information; while it mediates reinforcement during the learning act (proactive function), it balances memory performance between two antithetic processes thereafter (retroactive function) (i.e., forgetting and augmentation). Such bidirectional design can also be found at level of dopamine receptors, where augmenting D1 and abating D2 receptors are engaged to balance cellular cAMP levels. Here, we report that consolidated anesthesia-resistant memory (ARM), but not other concomitant memory phases, are sensitive to bidirectional dopaminergic signals. By means of genetic mosaicism, we identified widespread dopaminergic modulation within the olfactory circuit that suggests nonredundant and reiterating functions of D2R in support of ARM. Our results oppose ARM to its concomitant memory phases

  4. Gene set analysis for interpreting genetic studies

    DEFF Research Database (Denmark)

    Pers, Tune H

    2016-01-01

    Interpretation of genome-wide association study (GWAS) results is lacking behind the discovery of new genetic associations. Consequently, there is an urgent need for data-driven methods for interpreting genetic association studies. Gene set analysis (GSA) can identify aetiologic pathways...

  5. CFD Analysis on the Periodic Element of a Printed Circuit Heat Exchanger

    International Nuclear Information System (INIS)

    Tak, Nam-il; Kim, Min-Hwan; Lee, Won-Jae

    2007-01-01

    A typical printed circuit heat exchanger (PCHE) is composed of a large number of flow channels with lateral corrugations. In an effort to investigate fundamental thermo-fluid characteristics of a PCHE with corrugated channels, computational fluid dynamics (CFD) analyses were previously made in. One pair of flow channels (i.e., cold and hot channels) with the entire flow path was considered for the computational domain in the previous studies. Although only one pair of flow channels with coarse meshes was used, computational loads were found to be very high to simulate the entire flow path of the PCHE. Fortunately a recent study has shown that a simplified CFD methodology with a stream wise periodic assumption (called periodic CFD analysis) is feasible for a CFD evaluation of the thermo-fluid performance of compact heat exchangers. Since the periodic CFD analysis focuses on the periodic element of a flow channel, the required computing resources are dramatically reduced. In the present paper, the periodic CFD analysis has been applied to the periodic element of the PCHE. The results are compared with those of the full elements which have an entire flow path. Based on the periodic approach the effects of the corrugation parameters on the thermo-fluid performance of the PCHE are investigated

  6. Massively Parallel, Molecular Analysis Platform Developed Using a CMOS Integrated Circuit With Biological Nanopores

    Science.gov (United States)

    Roever, Stefan

    2012-01-01

    A massively parallel, low cost molecular analysis platform will dramatically change the nature of protein, molecular and genomics research, DNA sequencing, and ultimately, molecular diagnostics. An integrated circuit (IC) with 264 sensors was fabricated using standard CMOS semiconductor processing technology. Each of these sensors is individually controlled with precision analog circuitry and is capable of single molecule measurements. Under electronic and software control, the IC was used to demonstrate the feasibility of creating and detecting lipid bilayers and biological nanopores using wild type α-hemolysin. The ability to dynamically create bilayers over each of the sensors will greatly accelerate pore development and pore mutation analysis. In addition, the noise performance of the IC was measured to be 30fA(rms). With this noise performance, single base detection of DNA was demonstrated using α-hemolysin. The data shows that a single molecule, electrical detection platform using biological nanopores can be operationalized and can ultimately scale to millions of sensors. Such a massively parallel platform will revolutionize molecular analysis and will completely change the field of molecular diagnostics in the future.

  7. Experimental and theoretical analysis of vacuum circuit breaker prestrike effect on a transformer

    NARCIS (Netherlands)

    Popov, M.; Smeets, R.P.P.; Van der Sluis, L.; De Herdt, H.; Declerq, J.

    2009-01-01

    The work presented in this paper deals with the investigation of circuit breaker prestrike effect that occurs during energizing a distribution transformer. An experimental test setup that consists of a supply transformer, a vacuum circuit breaker (VCB), a cable and a test transformer is built, and

  8. MAGMA: generalized gene-set analysis of GWAS data.

    NARCIS (Netherlands)

    de Leeuw, C.A.; Mooij, J.M.; Heskes, T.; Posthuma, D.

    2015-01-01

    By aggregating data for complex traits in a biologically meaningful way, gene and gene-set analysis constitute a valuable addition to single-marker analysis. However, although various methods for gene and gene-set analysis currently exist, they generally suffer from a number of issues. Statistical

  9. MAGMA: Generalized Gene-Set Analysis of GWAS Data

    NARCIS (Netherlands)

    de Leeuw, C.A.; Mooij, J.M.; Heskes, T.; Posthuma, D.

    2015-01-01

    By aggregating data for complex traits in a biologically meaningful way, gene and gene-set analysis constitute a valuable addition to single-marker analysis. However, although various methods for gene and gene-set analysis currently exist, they generally suffer from a number of issues. Statistical

  10. [Lower urinary tract dysfunction and neuropathological findings of the neural circuits controlling micturition in familial amyotrophic lateral sclerosis with L106V mutation in the SOD1 gene].

    Science.gov (United States)

    Hineno, Akiyo; Oyanagi, Kiyomitsu; Nakamura, Akinori; Shimojima, Yoshio; Yoshida, Kunihiro; Ikeda, Shu-Ichi

    2016-01-01

    We report lower urinary tract dysfunction and neuropathological findings of the neural circuits controlling micturition in the patients with familial amyotrophic lateral sclerosis having L106V mutation in the SOD1 gene. Ten of 20 patients showed lower urinary tract dysfunction and 5 patients developed within 1 year after the onset of weakness. In 8 patients with an artificial respirator, 6 patients showed lower urinary tract dysfunction. Lower urinary tract dysfunction and respiratory failure requiring an artificial respirator occurred simultaneously in 3 patients. Neuronal loss and gliosis were observed in the neural circuits controlling micturition, such as frontal lobe, thalamus, hypothalamus, striatum, periaqueductal gray, ascending spinal tract, lateral corticospinal tract, intermediolateral nucleus and Onufrowicz' nucleus. Lower urinary tract dysfunction, especially storage symptoms, developed about 1 year after the onset of weakness, and the dysfunction occurred simultaneously with artificial respirator use in the patients.

  11. Full Wave Analysis of Passive Microwave Monolithic Integrated Circuit Devices Using a Generalized Finite Difference Time Domain (GFDTD) Algorithm

    Science.gov (United States)

    Lansing, Faiza S.; Rascoe, Daniel L.

    1993-01-01

    This paper presents a modified Finite-Difference Time-Domain (FDTD) technique using a generalized conformed orthogonal grid. The use of the Conformed Orthogonal Grid, Finite Difference Time Domain (GFDTD) enables the designer to match all the circuit dimensions, hence eliminating a major source o error in the analysis.

  12. General theory for integrated analysis of growth, gene, and protein expression in biofilms.

    Science.gov (United States)

    Zhang, Tianyu; Pabst, Breana; Klapper, Isaac; Stewart, Philip S

    2013-01-01

    A theory for analysis and prediction of spatial and temporal patterns of gene and protein expression within microbial biofilms is derived. The theory integrates phenomena of solute reaction and diffusion, microbial growth, mRNA or protein synthesis, biomass advection, and gene transcript or protein turnover. Case studies illustrate the capacity of the theory to simulate heterogeneous spatial patterns and predict microbial activities in biofilms that are qualitatively different from those of planktonic cells. Specific scenarios analyzed include an inducible GFP or fluorescent protein reporter, a denitrification gene repressed by oxygen, an acid stress response gene, and a quorum sensing circuit. It is shown that the patterns of activity revealed by inducible stable fluorescent proteins or reporter unstable proteins overestimate the region of activity. This is due to advective spreading and finite protein turnover rates. In the cases of a gene induced by either limitation for a metabolic substrate or accumulation of a metabolic product, maximal expression is predicted in an internal stratum of the biofilm. A quorum sensing system that includes an oxygen-responsive negative regulator exhibits behavior that is distinct from any stage of a batch planktonic culture. Though here the analyses have been limited to simultaneous interactions of up to two substrates and two genes, the framework applies to arbitrarily large networks of genes and metabolites. Extension of reaction-diffusion modeling in biofilms to the analysis of individual genes and gene networks is an important advance that dovetails with the growing toolkit of molecular and genetic experimental techniques.

  13. Evaluation of treatment effects for high-performance dye-sensitized solar cells using equivalent circuit analysis

    International Nuclear Information System (INIS)

    Murayama, Masaki; Mori, Tatsuo

    2006-01-01

    Equivalent circuit analysis using a one-diode model was carried out as a simpler, more convenient method to evaluate the electric mechanism and to employ effective treatment of a dye-sensitized solar cell (DSC). Cells treated using acetic acid or 4,t-butylpyridine were measured under irradiation (0.1 W/m 2 , AM 1.5) to obtain current-voltage (I-V) curves. Cell performance and equivalent circuit parameters were calculated from the I-V curves. Evaluation based on residual factors was useful for better fitting of the equivalent circuit to the I-V curve. The diode factor value was often over two for high-performance DSCs. Acetic acid treatment was effective to increase the short-circuit current by decreasing the series resistance of cells. In contrast, 4,t-butylpyridine was effective to increase open-circuit voltage by increasing the cell shunt resistance. Previous explanations considered that acetic acid worked to decrease the internal resistance of the TiO 2 layer and butylpyridine worked to lower the back-electron-transfer from the TiO 2 to the electrolyte

  14. Anti-electromagnetic interference analysis of equivalent circuit of ion channel based on the Hodgkin-Huxley model

    International Nuclear Information System (INIS)

    Chu, J; Chang, X L; Zhao, M; Man, M H; Wei, M; Yuan, L

    2013-01-01

    With the continuous improvement of circuit integration and working clock frequency in the electronic system, it is increasingly easy for the system to be affected by electromagnetic waves, and electromagnetic susceptibility and vulnerability become more severe. However, living beings in nature have shown extraordinary compatibility, immunity and adaptability to the electromagnetism at the same time. In addition, the ion channel on the neuron cytomembrane is a typical representation of b ioelectrical immunity . So the Hodgkin-Huxley circuit model with one capacitor in parallel with some power supplies and resistors was adopted to simulate the ion channel on the neuron cytomembrane. Through analysis, the circuit model can be used to simulate some electrical characteristics of biological neuron cells, and then acquire a certain level of anti-electromagnetic interference ability. This method will be useful for improving the reliability, compatibility and anti-interference capability of the electronic system in the complicated electromagnetic environment.

  15. Transient Analysis of Grid-Connected Wind Turbines with DFIG After an External Short-Circuit Fault

    DEFF Research Database (Denmark)

    Sun, Tao; Chen, Zhe; Blaabjerg, Frede

    2004-01-01

    The fast development of wind power generation brings new requirements for wind turbine integration to the network. After the clearance of an external short-circuit fault, the grid-connected wind turbine should restore its normal operation with minimized power losses. This paper concentrates...... on transient analysis of variable speed wind turbines with doubly fed induction generator (DFIG) after an external short-circuit fault. A simulation model of a MW-level variable speed wind turbine with DFIG developed in PSCAD/EMTDC is presented, and the control and protection schemes are described in detail....... After the clearance of an external short-circuit fault the control schemes manage to restore the wind turbine?s normal operation, and their performances are demonstrated by simulation results both during the fault and after the clearance of the fault....

  16. Computational Performance Optimisation for Statistical Analysis of the Effect of Nano-CMOS Variability on Integrated Circuits

    Directory of Open Access Journals (Sweden)

    Zheng Xie

    2013-01-01

    Full Text Available The intrinsic variability of nanoscale VLSI technology must be taken into account when analyzing circuit designs to predict likely yield. Monte-Carlo- (MC- and quasi-MC- (QMC- based statistical techniques do this by analysing many randomised or quasirandomised copies of circuits. The randomisation must model forms of variability that occur in nano-CMOS technology, including “atomistic” effects without intradie correlation and effects with intradie correlation between neighbouring devices. A major problem is the computational cost of carrying out sufficient analyses to produce statistically reliable results. The use of principal components analysis, behavioural modeling, and an implementation of “Statistical Blockade” (SB is shown to be capable of achieving significant reduction in the computational costs. A computation time reduction of 98.7% was achieved for a commonly used asynchronous circuit element. Replacing MC by QMC analysis can achieve further computation reduction, and this is illustrated for more complex circuits, with the results being compared with those of transistor-level simulations. The “yield prediction” analysis of SRAM arrays is taken as a case study, where the arrays contain up to 1536 transistors modelled using parameters appropriate to 35 nm technology. It is reported that savings of up to 99.85% in computation time were obtained.

  17. Situation analysis of physical independence of the equipment and safety circuits of Almaraz NPP regarding R.G. 1.75 rev.3 (2005)

    International Nuclear Information System (INIS)

    Seijas Portela, S.

    2010-01-01

    Situation analysis of physical independence of the electrical equipment and circuits CN safety Almaraz about R.G. 1.75 rev. 3. (2005) The aim of this paper is to present the work done in the analysis of the physical separation of redundant safety electrical equipment (emergency diesel generators, medium voltage, electrical cabinets, etc.) and physical separation of circuits and electrical conduits.

  18. Analysis of Electromagnetic Attractive Force : Examination by Magnetic Circuit, Finite Element Method and Experiment

    OpenAIRE

    薮野, 浩司; 大和田, 竜太郎; 青島, 伸治; Hiroshi, YABUNO; Ryotaro, OOWADA; Nobuharu, AOSHIMA; 筑波大学; 筑波大学院; 筑波大学

    1998-01-01

    This paper presents the limitation of the magnetic circuit method. The force between magnetic bodies can be approximated accurately by the magnetic circuit method. Therefore this method has been used widely for the estimation of magnetic force. However this method is limited by the magnetic leakage and can be not used in the case when the gap between the magnetic bodies is wide. It is very important to clarify the limitation of the magnetic circuit method. In this research, the force of an el...

  19. Feeding the developing brain: Juvenile rats fed diet rich in prebiotics and bioactive milk fractions exhibit reduced anxiety-related behavior and modified gene expression in emotion circuits.

    Science.gov (United States)

    Mika, Agnieszka; Gaffney, Michelle; Roller, Rachel; Hills, Abigail; Bouchet, Courtney A; Hulen, Kristina A; Thompson, Robert S; Chichlowski, Maciej; Berg, Brian M; Fleshner, Monika

    2018-01-30

    Early life nutrition is critical for brain development. Dietary prebiotics and bioactive milk fractions support brain development by increasing plasticity and altering activity in brain regions important for cognition and emotion regulation, perhaps through the gut-microbiome-brain axis. Here we examined the impact of a diet containing prebiotics, lactoferrin, and milk fat globule membrane (test diet) on beneficial gut bacteria, basal gene expression for activity and plasticity markers within brain circuits important for cognition and anxiety, and anxiety-related behavior in the open field. Juvenile male F344 rats were fed the test diet or a calorically matched control diet beginning postnatal day 24. After 4 weeks on diets, rats were sacrificed and brains were removed. Test diet significantly increased mRNA expression for cfos, brain derived neurotropic factor, and the GluN1 subunit of the NMDA receptor in the prefrontal cortex and reduced cfos mRNA within the amygdala. Diet-induced increases in fecal Lactobacillus spp., measured using selective bacterial culture, positively correlated with altered gene expression for cfos and serotonin receptors within multiple brain regions. In a separate cohort of juvenile rats, 4 weeks of the test diet increased time spent in the center of the open field, a behavior indicative of reduced anxiety. These data demonstrate that early life diets containing prebiotics and bioactive milk fractions can adaptively alter genes in neural circuits underlying emotion regulation and decrease anxiety-related behavior. Copyright © 2018. Published by Elsevier B.V.

  20. A cGMP-dependent protein kinase gene, foraging, modifies habituation-like response decrement of the giant fiber escape circuit in Drosophila.

    Science.gov (United States)

    Engel, J E; Xie, X J; Sokolowski, M B; Wu, C F

    2000-01-01

    The Drosophila giant fiber jump-and-flight escape response is a model for genetic analysis of both the physiology and the plasticity of a sensorimotor behavioral pathway. We previously established the electrically induced giant fiber response in intact tethered flies as a model for habituation, a form of nonassociative learning. Here, we show that the rate of stimulus-dependent response decrement of this neural pathway in a habituation protocol is correlated with PKG (cGMP-Dependent Protein Kinase) activity and foraging behavior. We assayed response decrement for natural and mutant rover and sitter alleles of the foraging (for) gene that encodes a Drosophila PKG. Rover larvae and adults, which have higher PKG activities, travel significantly farther while foraging than sitters with lower PKG activities. Response decrement was most rapid in genotypes previously shown to have low PKG activities and sitter-like foraging behavior. We also found differences in spontaneous recovery (the reversal of response decrement during a rest from stimulation) and a dishabituation-like phenomenon (the reversal of response decrement evoked by a novel stimulus). This electrophysiological study in an intact animal preparation provides one of the first direct demonstrations that PKG can affect plasticity in a simple learning paradigm. It increases our understanding of the complex interplay of factors that can modulate the sensitivity of the giant fiber escape response, and it defines a new adult-stage phenotype of the foraging locus. Finally, these results show that behaviorally relevant neural plasticity in an identified circuit can be influenced by a single-locus genetic polymorphism existing in a natural population of Drosophila.

  1. Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function.

    Science.gov (United States)

    Di, Chao; Xu, Wenying; Su, Zhen; Yuan, Joshua S

    2010-10-07

    PHB (Prohibitin) gene family is involved in a variety of functions important for different biological processes. PHB genes are ubiquitously present in divergent species from prokaryotes to eukaryotes. Human PHB genes have been found to be associated with various diseases. Recent studies by our group and others have shown diverse function of PHB genes in plants for development, senescence, defence, and others. Despite the importance of the PHB gene family, no comprehensive gene family analysis has been carried to evaluate the relatedness of PHB genes across different species. In order to better guide the gene function analysis and understand the evolution of the PHB gene family, we therefore carried out the comparative genome analysis of the PHB genes across different kingdoms. The relatedness, motif distribution, and intron/exon distribution all indicated that PHB genes is a relatively conserved gene family. The PHB genes can be classified into 5 classes and each class have a very deep evolutionary origin. The PHB genes within the class maintained the same motif patterns during the evolution. With Arabidopsis as the model species, we found that PHB gene intron/exon structure and domains are also conserved during the evolution. Despite being a conserved gene family, various gene duplication events led to the expansion of the PHB genes. Both segmental and tandem gene duplication were involved in Arabidopsis PHB gene family expansion. However, segmental duplication is predominant in Arabidopsis. Moreover, most of the duplicated genes experienced neofunctionalization. The results highlighted that PHB genes might be involved in important functions so that the duplicated genes are under the evolutionary pressure to derive new function. PHB gene family is a conserved gene family and accounts for diverse but important biological functions based on the similar molecular mechanisms. The highly diverse biological function indicated that more research needs to be carried out

  2. MAGMA: generalized gene-set analysis of GWAS data.

    Science.gov (United States)

    de Leeuw, Christiaan A; Mooij, Joris M; Heskes, Tom; Posthuma, Danielle

    2015-04-01

    By aggregating data for complex traits in a biologically meaningful way, gene and gene-set analysis constitute a valuable addition to single-marker analysis. However, although various methods for gene and gene-set analysis currently exist, they generally suffer from a number of issues. Statistical power for most methods is strongly affected by linkage disequilibrium between markers, multi-marker associations are often hard to detect, and the reliance on permutation to compute p-values tends to make the analysis computationally very expensive. To address these issues we have developed MAGMA, a novel tool for gene and gene-set analysis. The gene analysis is based on a multiple regression model, to provide better statistical performance. The gene-set analysis is built as a separate layer around the gene analysis for additional flexibility. This gene-set analysis also uses a regression structure to allow generalization to analysis of continuous properties of genes and simultaneous analysis of multiple gene sets and other gene properties. Simulations and an analysis of Crohn's Disease data are used to evaluate the performance of MAGMA and to compare it to a number of other gene and gene-set analysis tools. The results show that MAGMA has significantly more power than other tools for both the gene and the gene-set analysis, identifying more genes and gene sets associated with Crohn's Disease while maintaining a correct type 1 error rate. Moreover, the MAGMA analysis of the Crohn's Disease data was found to be considerably faster as well.

  3. Gene expression analysis of flax seed development

    Science.gov (United States)

    2011-01-01

    Background Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed. Results We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages) seed coats (globular and torpedo stages) and endosperm (pooled globular to torpedo stages) and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST) (GenBank accessions LIBEST_026995 to LIBEST_027011) were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152) had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development. Conclusions We have developed a foundational database of expressed sequences and collection of plasmid clones that comprise

  4. Gene expression analysis of flax seed development

    Directory of Open Access Journals (Sweden)

    Sharpe Andrew

    2011-04-01

    Full Text Available Abstract Background Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed. Results We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages seed coats (globular and torpedo stages and endosperm (pooled globular to torpedo stages and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST (GenBank accessions LIBEST_026995 to LIBEST_027011 were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152 had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development. Conclusions We have developed a foundational database of expressed sequences and collection of plasmid

  5. Analytical Analysis and Case Study of Transient Behavior of Inrush Current in Power Transformer for Designing of Efficient Circuit Breakers

    Science.gov (United States)

    Harmanpreet, Singh, Sukhwinder; Kumar, Ashok; Kaur, Parneet

    2010-11-01

    Stability & security are main aspects in electrical power systems. Transformer protection is major issue of concern to system operation. There are many mall-trip cases of transformer protection are caused by inrush current problems. The phenomenon of transformer inrush current has been discussed in many papers since 1958. In this paper analytical analysis of inrush current in a transformer switched on dc and ac supply has been done. This analysis will help in design aspects of circuit breakers for better performance.

  6. Maximum Acceleration Recording Circuit

    Science.gov (United States)

    Bozeman, Richard J., Jr.

    1995-01-01

    Coarsely digitized maximum levels recorded in blown fuses. Circuit feeds power to accelerometer and makes nonvolatile record of maximum level to which output of accelerometer rises during measurement interval. In comparison with inertia-type single-preset-trip-point mechanical maximum-acceleration-recording devices, circuit weighs less, occupies less space, and records accelerations within narrower bands of uncertainty. In comparison with prior electronic data-acquisition systems designed for same purpose, circuit simpler, less bulky, consumes less power, costs and analysis of data recorded in magnetic or electronic memory devices. Circuit used, for example, to record accelerations to which commodities subjected during transportation on trucks.

  7. Circuits and filters handbook

    CERN Document Server

    Chen, Wai-Kai

    2003-01-01

    A bestseller in its first edition, The Circuits and Filters Handbook has been thoroughly updated to provide the most current, most comprehensive information available in both the classical and emerging fields of circuits and filters, both analog and digital. This edition contains 29 new chapters, with significant additions in the areas of computer-aided design, circuit simulation, VLSI circuits, design automation, and active and digital filters. It will undoubtedly take its place as the engineer's first choice in looking for solutions to problems encountered in the design, analysis, and behavi

  8. Equivalent-circuit model for stacked slot-based 2D periodic arrays of arbitrary geometry for broadband analysis

    Science.gov (United States)

    Astorino, Maria Denise; Frezza, Fabrizio; Tedeschi, Nicola

    2018-03-01

    The analysis of the transmission and reflection spectra of stacked slot-based 2D periodic structures of arbitrary geometry and the ability to devise and control their electromagnetic responses have been a matter of extensive research for many decades. The purpose of this paper is to develop an equivalent Π circuit model based on the transmission-line theory and Floquet harmonic interactions, for broadband and short longitudinal period analysis. The proposed circuit model overcomes the limits of identical and symmetrical configurations imposed by the even/odd excitation approach, exploiting both the circuit topology of a single 2D periodic array of apertures and the ABCD matrix formalism. The transmission spectra obtained through the equivalent-circuit model have been validated by comparison with full-wave simulations carried out with a finite-element commercial electromagnetic solver. This allowed for a physical insight into the spectral and angular responses of multilayer devices with arbitrary aperture shapes, guaranteeing a noticeable saving of computational resources.

  9. Dynamic analysis and electronic circuit implementation of a novel 3D autonomous system without linear terms

    Science.gov (United States)

    Kengne, J.; Jafari, S.; Njitacke, Z. T.; Yousefi Azar Khanian, M.; Cheukem, A.

    2017-11-01

    Mathematical models (ODEs) describing the dynamics of almost all continuous time chaotic nonlinear systems (e.g. Lorenz, Rossler, Chua, or Chen system) involve at least a nonlinear term in addition to linear terms. In this contribution, a novel (and singular) 3D autonomous chaotic system without linear terms is introduced. This system has an especial feature of having two twin strange attractors: one ordinary and one symmetric strange attractor when the time is reversed. The complex behavior of the model is investigated in terms of equilibria and stability, bifurcation diagrams, Lyapunov exponent plots, time series and Poincaré sections. Some interesting phenomena are found including for instance, period-doubling bifurcation, antimonotonicity (i.e. the concurrent creation and annihilation of periodic orbits) and chaos while monitoring the system parameters. Compared to the (unique) case previously reported by Xu and Wang (2014) [31], the system considered in this work displays a more 'elegant' mathematical expression and experiences richer dynamical behaviors. A suitable electronic circuit (i.e. the analog simulator) is designed and used for the investigations. Pspice based simulation results show a very good agreement with the theoretical analysis.

  10. Inductive analysis of failure patterns and of their impact on thermohydraulic circuits of nuclear power plants

    International Nuclear Information System (INIS)

    Limnios, N.

    1983-01-01

    The APACHE code (Automatic Analysis of Failures of Hydraulic and Thermohydraulic Circuits more particularly of Water) situates in an important program of computer codes development in the field of studies on reliability and safety of systems in nuclear power plants. APACHE is an automatic generation code of failure pattern and of their effects. After a presentation of the theoretical basis, the methodological principles of the theory of networks are developed. Then, the model of the code is developed: model of individual behavior of each classical model component of normal behavior and model of failure pattern with specifications. The global model of hydraulic systems and the resolution systems are then developed. More particularly, some aspects of the theory of graphs, and the algorithms developed for the automatic construction of the equation systems and especially the algorithm of the research of meshes are presented. The computer aspect of the code and the programming of the code with its limits and some specifications are described. The practical aspect of utilization is finally presented [fr

  11. Micromachining of semiconductor by femtosecond laser for integrated circuit defect analysis

    International Nuclear Information System (INIS)

    Halbwax, M.; Sarnet, T.; Hermann, J.; Delaporte, Ph.; Sentis, M.; Fares, L.; Haller, G.

    2007-01-01

    The latest International Technology Roadmap for Semiconductors (ITRS) has highlighted the detection and analysis of defects in Integrated Circuits (IC) as a major challenge faced by the semiconductor industry. Advanced tools used today for defect cross sectioning include dual beams (focused ion- and electron-beam technologies) with resolution down to the sub-Angstrom level. However ion milling an IC with a FIB is time consuming because of the need to open wide cavities in front of the cross-sections that need to be analyzed. Therefore the use of a femtosecond laser as a tool for direct material removal is discussed in this paper. Experiments were performed on IC structures to reveal the different layers of fabrication: selective or total ablation can occur depending on the laser energy density, without delamination of the layers. Different laser irradiation conditions like pressure (air, vacuum), polarization, beam shaping, and scanning parameters have been used to produce different types of cavities. The femtosecond laser engraving of silicon-based structures could be useful for cross-sectioning devices but also for other applications like direct-write lithography, photomask repair, maskless implantation or reverse engineering/restructuring

  12. Micromachining of semiconductor by femtosecond laser for integrated circuit defect analysis

    Energy Technology Data Exchange (ETDEWEB)

    Halbwax, M. [Laboratoire LP3 CNRS UMR 6182, Parc Scientifique et Technologique de Luminy, Case 917, 163 Avenue de Luminy, 13009 Marseille (France); Sarnet, T. [Laboratoire LP3 CNRS UMR 6182, Parc Scientifique et Technologique de Luminy, Case 917, 163 Avenue de Luminy, 13009 Marseille (France)], E-mail: sarnet@lp3.univ-mrs.fr; Hermann, J.; Delaporte, Ph.; Sentis, M. [Laboratoire LP3 CNRS UMR 6182, Parc Scientifique et Technologique de Luminy, Case 917, 163 Avenue de Luminy, 13009 Marseille (France); Fares, L.; Haller, G. [STMicroelectronics, 190 Avenue Celestin Coq, ZI, 13106 Rousset Cedex (France)

    2007-12-15

    The latest International Technology Roadmap for Semiconductors (ITRS) has highlighted the detection and analysis of defects in Integrated Circuits (IC) as a major challenge faced by the semiconductor industry. Advanced tools used today for defect cross sectioning include dual beams (focused ion- and electron-beam technologies) with resolution down to the sub-Angstrom level. However ion milling an IC with a FIB is time consuming because of the need to open wide cavities in front of the cross-sections that need to be analyzed. Therefore the use of a femtosecond laser as a tool for direct material removal is discussed in this paper. Experiments were performed on IC structures to reveal the different layers of fabrication: selective or total ablation can occur depending on the laser energy density, without delamination of the layers. Different laser irradiation conditions like pressure (air, vacuum), polarization, beam shaping, and scanning parameters have been used to produce different types of cavities. The femtosecond laser engraving of silicon-based structures could be useful for cross-sectioning devices but also for other applications like direct-write lithography, photomask repair, maskless implantation or reverse engineering/restructuring.

  13. Magnetic Circuit Design and Multiphysics Analysis of a Novel MR Damper for Applications under High Velocity

    Directory of Open Access Journals (Sweden)

    Jiajia Zheng

    2014-02-01

    Full Text Available A novel magnetorheological (MR damper with a multistage piston and independent input currents is designed and analyzed. The equivalent magnetic circuit model is investigated along with the relation between magnetic induction density in the working gap and input currents of the electromagnetic coils. Finite element method (FEM is used to analyze the distribution of magnetic field through the MR fluid region. Considering the real situation, coupling equations are presented to analyze the electromagnetic-thermal-flow coupling problems. Software COMSOL is used to analyze the multiphysics, that is, electromagnetic, thermal dynamic, and fluid mechanic. A measurement index involving total damping force, dynamic range, and induction time needed for magnetic coil is put forward to evaluate the performance of the novel multistage MR damper. The simulation results show that it is promising for applications under high velocity and works better when more electromagnetic coils are applied with input currents separately. Besides, in order to reduce energy consumption, it is recommended to apply more electromagnetic coils with relative low currents based on the analysis of pressure drop along the annular gap.

  14. THE ANALYSIS OF STRUCTURAL RELIABILITY OF THE MAIN ELECTRIC CONNECTION CIRCUITS OF NUCLEAR POWER PLANTS

    Directory of Open Access Journals (Sweden)

    M. A. Korotkevich

    2017-01-01

    Full Text Available The reliability of the main circuit of electrical connections at a nuclear electric power plant that has two units with a capacity of 1,200 MW each has been determined. Reliability, economical, maneuverable properties of the atomic power plant under study are largely determined by its main circuit, so the choice of the circuit for the design and its status in the process of operation occur to be critical objectives. Main electrical connection circuits in nuclear electric power plants are selected on the basis of the schematic networks of the energy system and the land attached to the plant. The circuit of the connection of a nuclear power plant to the grid in the original normal operating modes at all stages of the construction of such a plant should provide the outcome of the full added capacity of a nuclear power plant and the preservation of its stability in the power system without the influence of the emergency system automatics when any outgoing transmission line is disabled. When selecting the main circuit the individual capacity of the installed units and their number are taken into account as well as the order of development of the plant and power supply system; the voltage on which the power of a plant is delivered; a shortcircuit current for switchgear high voltage and the need for their limitation by circuit means; the most power that can be lost when damage to any switch. A model of reliability of the main circuit of electrical connections is designed to detect all types of accidents that are possible at the coincidence of failures of elements with the repair and operational modes that differs in composition and damageability of the equipment, as well as under conditions of the development of accidents due to failure of operation of devices of relay protection and automation.

  15. Dynamic Analysis and Circuit Design of a Novel Hyperchaotic System with Fractional-Order Terms

    Directory of Open Access Journals (Sweden)

    Abir Lassoued

    2017-01-01

    Full Text Available A novel hyperchaotic system with fractional-order (FO terms is designed. Its highly complex dynamics are investigated in terms of equilibrium points, Lyapunov spectrum, and attractor forms. It will be shown that the proposed system exhibits larger Lyapunov exponents than related hyperchaotic systems. Finally, to enhance its potential application, a related circuit is designed by using the MultiSIM Software. Simulation results verify the effectiveness of the suggested circuit.

  16. Synthesis and Analysis of a Quaternary Static RAM Using Quantizing Circuits

    Science.gov (United States)

    Syuto, Makoto; Magata, Hiroshi; Tanno, Koichi; Ishizuka, Okihiko

    1999-09-01

    In this paper, a voltage mode multiple valued static random access memory (MVSRAM) with a multiple valued quantizer is described. The proposed circuit has the merits of simplicity and low cost on fabrication, since it is implemented by standard CMOs process, instead of the conventional multi-level ion implantation usually applied in the voltage-mode multi-valued logic (MVL) circuit. The performance of the proposed MVSRAM is estimated by HSPICE simulations with MOSIS 2.0 microns CMOs process parameter.

  17. Analysis of baseline gene expression levels from ...

    Science.gov (United States)

    The use of gene expression profiling to predict chemical mode of action would be enhanced by better characterization of variance due to individual, environmental, and technical factors. Meta-analysis of microarray data from untreated or vehicle-treated animals within the control arm of toxicogenomics studies has yielded useful information on baseline fluctuations in gene expression. A dataset of control animal microarray expression data was assembled by a working group of the Health and Environmental Sciences Institute's Technical Committee on the Application of Genomics in Mechanism Based Risk Assessment in order to provide a public resource for assessments of variability in baseline gene expression. Data from over 500 Affymetrix microarrays from control rat liver and kidney were collected from 16 different institutions. Thirty-five biological and technical factors were obtained for each animal, describing a wide range of study characteristics, and a subset were evaluated in detail for their contribution to total variability using multivariate statistical and graphical techniques. The study factors that emerged as key sources of variability included gender, organ section, strain, and fasting state. These and other study factors were identified as key descriptors that should be included in the minimal information about a toxicogenomics study needed for interpretation of results by an independent source. Genes that are the most and least variable, gender-selectiv

  18. Separate enrichment analysis of pathways for up- and downregulated genes.

    Science.gov (United States)

    Hong, Guini; Zhang, Wenjing; Li, Hongdong; Shen, Xiaopei; Guo, Zheng

    2014-03-06

    Two strategies are often adopted for enrichment analysis of pathways: the analysis of all differentially expressed (DE) genes together or the analysis of up- and downregulated genes separately. However, few studies have examined the rationales of these enrichment analysis strategies. Using both microarray and RNA-seq data, we show that gene pairs with functional links in pathways tended to have positively correlated expression levels, which could result in an imbalance between the up- and downregulated genes in particular pathways. We then show that the imbalance could greatly reduce the statistical power for finding disease-associated pathways through the analysis of all-DE genes. Further, using gene expression profiles from five types of tumours, we illustrate that the separate analysis of up- and downregulated genes could identify more pathways that are really pertinent to phenotypic difference. In conclusion, analysing up- and downregulated genes separately is more powerful than analysing all of the DE genes together.

  19. Failure Analysis of Short-Circuited Lithium-Ion Battery with Nickel-Manganese-Cobalt/Graphite Electrode.

    Science.gov (United States)

    Lee, Seung-Mi; Kim, Jea-Yeon; Byeon, Jai-Won

    2018-09-01

    Accidental failures and explosions of lithium-ion batteries have been reported in recent years. To determine the root causes and mechanisms of these failures from the perspective of material degradation, failure analysis was conducted for an intentionally shorted lithium-ion battery. The battery was subjected to electrical overcharging and mechanical pressing to simulate internal short-circuiting. After in situ measurement of the temperature increase during the short-circuiting of the electrodes, the disassembled battery components (i.e., the anode, cathode, and separator) were analyzed by scanning electron microscopy and energy-dispersive X-ray spectroscopy. Regardless of the simulated short-circuit method (mechanical or electrical), damage was observed in the shorted batteries. Numerous small cracks and chemical reaction products were observed on the electrode surface, along with pore shielding on the separator. The event of short-circuiting increased the surface temperature of the battery to approximately 90 °C, which prompted the deterioration and decomposition of the electrolyte, thus affecting the overall battery performance; this was attributed to the decomposition of the lithium salt at 60 °C. The gas generation due to the breakdown of the electrolyte causes pressure accumulation inside the cell; therefore, the electrolyte leaks.

  20. Displacement damage analysis and modified electrical equivalent circuit for electron and photon-irradiated silicon solar cells

    Science.gov (United States)

    Arjhangmehr, Afshin; Feghhi, Seyed Amir Hossein

    2014-10-01

    Solar modules and arrays are the conventional energy resources of space satellites. Outside the earth's atmosphere, solar panels experience abnormal radiation environments and because of incident particles, photovoltaic (PV) parameters degrade. This article tries to analyze the electrical performance of electron and photon-irradiated mono-crystalline silicon (mono-Si) solar cells. PV cells are irradiated by mono-energetic electrons and poly-energetic photons and immediately characterized after the irradiation. The mean degradation of the maximum power (Pmax) of silicon solar cells is presented and correlated using the displacement damage dose (Dd) methodology. This method simplifies evaluation of cell performance in space radiation environments and produces a single characteristic curve for Pmax degradation. Furthermore, complete analysis of the results revealed that the open-circuit voltage (Voc) and the filling factor of mono-Si cells did not significantly change during the irradiation and were independent of the radiation type and fluence. Moreover, a new technique is developed that adapts the irradiation-induced effects in a single-cell equivalent electrical circuit and adjusts its elements. The "modified circuit" is capable of modeling the "radiation damage" in the electrical behavior of mono-Si solar cells and simplifies the designing of the compensation circuits.

  1. Detection of inter-turn short-circuit at start-up of induction machine based on torque analysis

    Directory of Open Access Journals (Sweden)

    Pietrowski Wojciech

    2017-12-01

    Full Text Available Recently, interest in new diagnostics methods in a field of induction machines was observed. Research presented in the paper shows the diagnostics of induction machine based on torque pulsation, under inter-turn short-circuit, during start-up of a machine. In the paper three numerical techniques were used: finite element analysis, signal analysis and artificial neural networks (ANN. The elaborated numerical model of faulty machine consists of field, circuit and motion equations. Voltage excited supply allowed to determine the torque waveform during start-up. The inter-turn short-circuit was treated as a galvanic connection between two points of the stator winding. The waveforms were calculated for different amounts of shorted-turns from 0 to 55. Due to the non-stationary waveforms a wavelet packet decomposition was used to perform an analysis of the torque. The obtained results of analysis were used as input vector for ANN. The response of the neural network was the number of shorted-turns in the stator winding. Special attention was paid to compare response of general regression neural network (GRNN and multi-layer perceptron neural network (MLP. Based on the results of the research, the efficiency of the developed algorithm can be inferred.

  2. A circuit-level analysis of third order intermodulation mechanisms in CMOS mixers using time-invariant power and Volterra series

    NARCIS (Netherlands)

    Sakian, P.; Mahmoudi, R.; Roermund, van A.H.M.

    2011-01-01

    An in-depth analysis is performed on the third-order intermodulation distortions (IMD3) in the switching pair of active CMOS mixers. The nonlinear time-varying switching pair is described by a hypothetical circuit composed of a nonlinear time-invariant circuit cascaded with a linear time-varying

  3. 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.

  4. Digital-circuit analysis of short-gate tunnel FETs for low-voltage applications

    International Nuclear Information System (INIS)

    Zhuge, Jing; Huang, Ru; Wang, Yangyuan; Verhulst, Anne S; Vandenberghe, William G; Dehaene, Wim; Groeseneken, Guido

    2011-01-01

    This paper investigates the potential of tunnel field-effect transistors (TFETs), with emphasis on short-gate TFETs, by simulation for low-power digital applications having a supply voltage lower than 0.5 V. A transient study shows that the tunneling current has a negligible contribution in charging and discharging the gate capacitance of TFETs. In spite of a higher resistance region in the short-gate TFET, the gate (dis)charging speed still meets low-voltage application requirements. A circuit analysis is performed on short-gate TFETs with different materials, such as Si, Ge and heterostructures in terms of voltage overshoot, delay, static power, energy consumption and energy delay product (EDP). These results are compared to MOSFET and full-gate TFET performance. It is concluded that short-gate heterostructure TFETs (Ge–source for nTFET, In 0.6 Ga 0.4 As–source for pTFET) are promising candidates to extend the supply voltage to lower than 0.5 V because they combine the advantage of a low Miller capacitance, due to the short-gate structures, and strong drive current in TFETs, due to the narrow bandgap material in the source. At a supply voltage of 0.4 V and for an EOT and channel length of 0.6 nm and 40 nm, respectively, a three-stage inverter chain based on short-gate heterostructure TFETs saves 40% energy consumption per cycle at the same delay and shows 60%–75% improvement of EDP at the same static power, compared to its full-gate counterpart. When compared to the MOSFET, better EDP can be achieved in the heterostructure TFET especially at low static power consumption

  5. Theoretical analysis of a YBCO squirrel-cage type induction motor based on an equivalent circuit

    International Nuclear Information System (INIS)

    Morita, G; Nakamura, T; Muta, I

    2006-01-01

    A HTS induction motor, with a HTS squirrel-cage rotor, is analysed using an electrical equivalent circuit. The squirrel-cage winding in the rotor consists of rotor bars and end rings, and both are considered to be made of YBCO film conductors. A wide range of electric field versus current density in YBCO film is formulated based on the Weibull function, and analysed as a non-linear resistance in the equivalent circuit. It is shown that starting and accelerating torques of the HTS induction motor are improved drastically compared to those of a conventional induction motor. Furthermore, large synchronous torque can also be realized by trapping the magnetic flux in the rotor circuit because of the persistent current mode

  6. An analysis of latch-up characteristics and latch-up windows in CMOS integrated circuits

    International Nuclear Information System (INIS)

    Xu Xianguo; Yang Huaimin

    2004-01-01

    Because of topology's complexity, there may be several potential parasitic latch-up paths in a CMOS integrated circuit. All of the latch-up paths may have an effect on each other or one another due to different triggering dose rate, holding voltage and holding current and then one or more latch-up windows may appear. After we analyze the latch-up characteristic of CMOS integrated circuits in detail, a 'three-path' latch-up model is developed and used to explain the latch-up window phenomena reasonably. (authors)

  7. Gene coexpression network analysis as a source of functional annotation for rice genes.

    Directory of Open Access Journals (Sweden)

    Kevin L Childs

    Full Text Available With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional

  8. A Strategy for Identifying Quantitative Trait Genes Using Gene Expression Analysis and Causal Analysis

    Directory of Open Access Journals (Sweden)

    Akira Ishikawa

    2017-11-01

    Full Text Available Large numbers of quantitative trait loci (QTL affecting complex diseases and other quantitative traits have been reported in humans and model animals. However, the genetic architecture of these traits remains elusive due to the difficulty in identifying causal quantitative trait genes (QTGs for common QTL with relatively small phenotypic effects. A traditional strategy based on techniques such as positional cloning does not always enable identification of a single candidate gene for a QTL of interest because it is difficult to narrow down a target genomic interval of the QTL to a very small interval harboring only one gene. A combination of gene expression analysis and statistical causal analysis can greatly reduce the number of candidate genes. This integrated approach provides causal evidence that one of the candidate genes is a putative QTG for the QTL. Using this approach, I have recently succeeded in identifying a single putative QTG for resistance to obesity in mice. Here, I outline the integration approach and discuss its usefulness using my studies as an example.

  9. A Strategy for Identifying Quantitative Trait Genes Using Gene Expression Analysis and Causal Analysis.

    Science.gov (United States)

    Ishikawa, Akira

    2017-11-27

    Large numbers of quantitative trait loci (QTL) affecting complex diseases and other quantitative traits have been reported in humans and model animals. However, the genetic architecture of these traits remains elusive due to the difficulty in identifying causal quantitative trait genes (QTGs) for common QTL with relatively small phenotypic effects. A traditional strategy based on techniques such as positional cloning does not always enable identification of a single candidate gene for a QTL of interest because it is difficult to narrow down a target genomic interval of the QTL to a very small interval harboring only one gene. A combination of gene expression analysis and statistical causal analysis can greatly reduce the number of candidate genes. This integrated approach provides causal evidence that one of the candidate genes is a putative QTG for the QTL. Using this approach, I have recently succeeded in identifying a single putative QTG for resistance to obesity in mice. Here, I outline the integration approach and discuss its usefulness using my studies as an example.

  10. Load Flow and Short Circuit Analysis of the Class III Power System of HANARO

    Energy Technology Data Exchange (ETDEWEB)

    Kim, H. K.; Jung, H. S

    2005-12-15

    The planning, design, and operation of electric power system require engineering studies to assist in the evaluation of the system performance, reliability, safety and economics. The Class III power of HANARO supplies power for not only HANARO but also RIPF and IMEF. The starting current of most ac motors is five to ten times normal full load current. The loads of the Class III power are connected in consecutive orders at an interval for 10 seconds to avoid excessive voltage drop. This technical report deals with the load flow study and motor starting study for the Class III power of HANARO using ETAP(Electrical Transient Analyzer Program) to verify the capacity of the diesel generator. Short-circuit studies are done to determine the magnitude of the prospective currents flowing throughout the power system at various time intervals after a fault occurs. Short-circuit studies can be performed at the planning stage in order to help finalize the system layout, determine voltage levels, and size cables, transformers, and conductors. From this study, we verify the short circuit current capacity of air circuit breaker(ACB) and automatic transfer switch(ATS) of the Class III power.

  11. Design and Analysis of Compact DNA Strand Displacement Circuits for Analog Computation Using Autocatalytic Amplifiers.

    Science.gov (United States)

    Song, Tianqi; Garg, Sudhanshu; Mokhtar, Reem; Bui, Hieu; Reif, John

    2018-01-19

    A main goal in DNA computing is to build DNA circuits to compute designated functions using a minimal number of DNA strands. Here, we propose a novel architecture to build compact DNA strand displacement circuits to compute a broad scope of functions in an analog fashion. A circuit by this architecture is composed of three autocatalytic amplifiers, and the amplifiers interact to perform computation. We show DNA circuits to compute functions sqrt(x), ln(x) and exp(x) for x in tunable ranges with simulation results. A key innovation in our architecture, inspired by Napier's use of logarithm transforms to compute square roots on a slide rule, is to make use of autocatalytic amplifiers to do logarithmic and exponential transforms in concentration and time. In particular, we convert from the input that is encoded by the initial concentration of the input DNA strand, to time, and then back again to the output encoded by the concentration of the output DNA strand at equilibrium. This combined use of strand-concentration and time encoding of computational values may have impact on other forms of molecular computation.

  12. Dynamical Analysis, Synchronization, Circuit Design, and Secure Communication of a Novel Hyperchaotic System

    Directory of Open Access Journals (Sweden)

    Li Xiong

    2017-01-01

    Full Text Available This paper is devoted to introduce a novel fourth-order hyperchaotic system. The hyperchaotic system is constructed by adding a linear feedback control level based on a modified Lorenz-like chaotic circuit with reduced number of amplifiers. The local dynamical entities, such as the basic dynamical behavior, the divergence, the eigenvalue, and the Lyapunov exponents of the new hyperchaotic system, are all investigated analytically and numerically. Then, an active control method is derived to achieve global chaotic synchronization of the novel hyperchaotic system through making the synchronization error system asymptotically stable at the origin based on Lyapunov stability theory. Next, the proposed novel hyperchaotic system is applied to construct another new hyperchaotic system with circuit deformation and design a new hyperchaotic secure communication circuit. Furthermore, the implementation of two novel electronic circuits of the proposed hyperchaotic systems is presented, examined, and realized using physical components. A good qualitative agreement is shown between the simulations and the experimental results around 500 kHz and below 1 MHz.

  13. Battery open-circuit voltage estimation by a method of statistical analysis

    NARCIS (Netherlands)

    Snihir, Iryna; Rey, William; Verbitskiy, Evgeny; Belfadhel-Ayeb, Afifa; Notten, Peter H.L.

    2006-01-01

    The basic task of a battery management system (BMS) is the optimal utilization of the stored energy and minimization of degradation effects. It is critical for a BMS that the state-of-charge (SoC) be accurately determined. Open-circuit voltage (OCV) is directly related to the state-of-charge of the

  14. Analysis of the NPP-V1 primary circuit fast cooldown

    International Nuclear Information System (INIS)

    Filo, J.; Bazso, Z.; Vranka, L.

    1994-01-01

    Results of thermal-hydraulic calculations of the NPP-V1 primary circuit fast cooldown during small leakage through openings of diameter 20, 32 and 50 mm as well as analyses of cooldown following the steam pipeline break at nominal and null reactor power are given in this paper. 4 refs, 24 figs, 1 tab

  15. Analysis of the capability to effectively design complementary metal oxide semiconductor integrated circuits

    Science.gov (United States)

    McConkey, M. L.

    1984-12-01

    A complete CMOS/BULK design cycle has been implemented and fully tested to evaluate its effectiveness and a viable set of computer-aided design tools for the layout, verification, and simulation of CMOS/BULK integrated circuits. This design cycle is good for p-well, n-well, or twin-well structures, although current fabrication technique available limit this to p-well only. BANE, an integrated layout program from Stanford, is at the center of this design cycle and was shown to be simple to use in the layout of CMOS integrated circuits (it can be also used to layout NMOS integrated circuits). A flowchart was developed showing the design cycle from initial layout, through design verification, and to circuit simulation using NETLIST, PRESIM, and RNL from the University of Washington. A CMOS/BULK library was designed and includes logic gates that were designed and completely tested by following this flowchart. Also designed was an arithmetic logic unit as a more complex test of the CMOS/BULK design cycle.

  16. Analogue circuits simulation

    Energy Technology Data Exchange (ETDEWEB)

    Mendo, C

    1988-09-01

    Most analogue simulators have evolved from SPICE. The history and description of SPICE-like simulators are given. From a mathematical formulation of the electronic circuit the following analysis are possible: DC, AC, transient, noise, distortion, Worst Case and Statistical.

  17. Resonance circuits for adiabatic circuits

    Directory of Open Access Journals (Sweden)

    C. Schlachta

    2003-01-01

    Full Text Available One of the possible techniques to reduces the power consumption in digital CMOS circuits is to slow down the charge transport. This slowdown can be achieved by introducing an inductor in the charging path. Additionally, the inductor can act as an energy storage element, conserving the energy that is normally dissipated during discharging. Together with the parasitic capacitances from the circuit a LCresonant circuit is formed.

  18. CMOS analog circuit design

    CERN Document Server

    Allen, Phillip E

    1987-01-01

    This text presents the principles and techniques for designing analog circuits to be implemented in a CMOS technology. The level is appropriate for seniors and graduate students familiar with basic electronics, including biasing, modeling, circuit analysis, and some familiarity with frequency response. Students learn the methodology of analog integrated circuit design through a hierarchically-oriented approach to the subject that provides thorough background and practical guidance for designing CMOS analog circuits, including modeling, simulation, and testing. The authors' vast industrial experience and knowledge is reflected in the circuits, techniques, and principles presented. They even identify the many common pitfalls that lie in the path of the beginning designer--expert advice from veteran designers. The text mixes the academic and practical viewpoints in a treatment that is neither superficial nor overly detailed, providing the perfect balance.

  19. Effect of the absolute statistic on gene-sampling gene-set analysis methods.

    Science.gov (United States)

    Nam, Dougu

    2017-06-01

    Gene-set enrichment analysis and its modified versions have commonly been used for identifying altered functions or pathways in disease from microarray data. In particular, the simple gene-sampling gene-set analysis methods have been heavily used for datasets with only a few sample replicates. The biggest problem with this approach is the highly inflated false-positive rate. In this paper, the effect of absolute gene statistic on gene-sampling gene-set analysis methods is systematically investigated. Thus far, the absolute gene statistic has merely been regarded as a supplementary method for capturing the bidirectional changes in each gene set. Here, it is shown that incorporating the absolute gene statistic in gene-sampling gene-set analysis substantially reduces the false-positive rate and improves the overall discriminatory ability. Its effect was investigated by power, false-positive rate, and receiver operating curve for a number of simulated and real datasets. The performances of gene-set analysis methods in one-tailed (genome-wide association study) and two-tailed (gene expression data) tests were also compared and discussed.

  20. Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study

    KAUST Repository

    Fan, M.; Kuwahara, Hiroyuki; Wang, X.; Wang, S.; Gao, Xin

    2015-01-01

    Parameter estimation is a challenging computational problemin the reverse engineering of biological systems. Because advances in biotechnology have facilitated wide availability of time-series gene expression data, systematic parameter esti- mation

  1. Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data

    Directory of Open Access Journals (Sweden)

    Tintle Nathan L

    2012-08-01

    Full Text Available Abstract Background Statistical analyses of whole genome expression data require functional information about genes in order to yield meaningful biological conclusions. The Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG are common sources of functionally grouped gene sets. For bacteria, the SEED and MicrobesOnline provide alternative, complementary sources of gene sets. To date, no comprehensive evaluation of the data obtained from these resources has been performed. Results We define a series of gene set consistency metrics directly related to the most common classes of statistical analyses for gene expression data, and then perform a comprehensive analysis of 3581 Affymetrix® gene expression arrays across 17 diverse bacteria. We find that gene sets obtained from GO and KEGG demonstrate lower consistency than those obtained from the SEED and MicrobesOnline, regardless of gene set size. Conclusions Despite the widespread use of GO and KEGG gene sets in bacterial gene expression data analysis, the SEED and MicrobesOnline provide more consistent sets for a wide variety of statistical analyses. Increased use of the SEED and MicrobesOnline gene sets in the analysis of bacterial gene expression data may improve statistical power and utility of expression data.

  2. Thermo-hydraulic Analysis of a Water-cooled Printed Circuit Heat Exchanger in a Small-scale Nitrogen Loop

    International Nuclear Information System (INIS)

    Kim, Chan Soo; Hong, Sung Deok; Kim, Min Hwan; Shim, Jaesool; Lee, Gyung Dong

    2013-01-01

    The development of high-temperature heat exchangers is very important because of its higher operation temperature and pressure than those of common light water reactors and industrial process plants. In particular, the intermediate heat exchanger is a key-challenged high temperature component in a Very High Temperature gas-cooled Reactor (VHTR). A printed circuit heat exchanger is one of the candidates for an intermediate heat exchanger in a VHTR. The printed circuit heat exchanger (PCHE) was developed and commercialized by HEATRIC. The compactness is better than any other heat exchanger types, because its core matrices are fabricated by diffusion bonding with photo-chemically etched micro-channels. Various tests and analysis have been performed to verify the performance of PCHE. The thermal stress analysis of the high temperature PCHE is necessary to endure the extremely operation condition of IHX. In this study, the thermo-hydraulic analysis for the laboratory-scale PCHE is performed to provide the input data for the boundary conditions of a structural analysis. The results from the first-principal calculation are compared with those from computational fluid dynamics code analysis. COMSOL 4.3a analysis is successfully performed at the uniform pressure drop condition in a set of flow channel stacks. The heat-exchanged region concentrated to the nitrogen inlet cause the uniform mass velocity distribution in the channels, therefore there is little difference between two analytical results

  3. Electronic circuit encyclopedia 2

    International Nuclear Information System (INIS)

    Park, Sun Ho

    1992-10-01

    This book is composed of 15 chapters, which are amplification of weak signal and measurement circuit audio control and power amplification circuit, data transmission and wireless system, forwarding and isolation, signal converting circuit, counter and comparator, discriminator circuit, oscillation circuit and synthesizer, digital and circuit on computer image processing circuit, sensor drive circuit temperature sensor circuit, magnetic control and application circuit, motor driver circuit, measuring instrument and check tool and power control and stability circuit.

  4. Electronic circuit encyclopedia 2

    Energy Technology Data Exchange (ETDEWEB)

    Park, Sun Ho

    1992-10-15

    This book is composed of 15 chapters, which are amplification of weak signal and measurement circuit audio control and power amplification circuit, data transmission and wireless system, forwarding and isolation, signal converting circuit, counter and comparator, discriminator circuit, oscillation circuit and synthesizer, digital and circuit on computer image processing circuit, sensor drive circuit temperature sensor circuit, magnetic control and application circuit, motor driver circuit, measuring instrument and check tool and power control and stability circuit.

  5. Reporter gene bioassays in environmental analysis.

    Science.gov (United States)

    Köhler, S; Belkin, S; Schmid, R D

    2000-01-01

    In parallel to the continuous development of increasingly more sophisticated physical and chemical analytical technologies for the detection of environmental pollutants, there is a progressively more urgent need also for bioassays which report not only on the presence of a chemical but also on its bioavailability and its biological effects. As a partial fulfillment of that need, there has been a rapid development of biosensors based on genetically engineered bacteria. Such microorganisms typically combine a promoter-operator, which acts as the sensing element, with reporter gene(s) coding for easily detectable proteins. These sensors have the ability to detect global parameters such as stress conditions, toxicity or DNA-damaging agents as well as specific organic and inorganic compounds. The systems described in this review, designed to detect different groups of target chemicals, vary greatly in their detection limits, specificity, response times and more. These variations reflect on their potential applicability which, for most of the constructs described, is presently rather limited. Nevertheless, present trends promise that additional improvements will make microbial biosensors an important tool for future environmental analysis.

  6. Gene expression analysis identifies global gene dosage sensitivity in cancer

    DEFF Research Database (Denmark)

    Fehrmann, Rudolf S. N.; Karjalainen, Juha M.; Krajewska, Malgorzata

    2015-01-01

    Many cancer-associated somatic copy number alterations (SCNAs) are known. Currently, one of the challenges is to identify the molecular downstream effects of these variants. Although several SCNAs are known to change gene expression levels, it is not clear whether each individual SCNA affects gen...

  7. A nonlinear equivalent circuit method for analysis of passive intermodulation of mesh reflectors

    Directory of Open Access Journals (Sweden)

    Jiang Jie

    2014-08-01

    Full Text Available Passive intermodulation (PIM has gradually become a serious electromagnetic interference due to the development of high-power and high-sensitivity RF/microwave communication systems, especially large deployable mesh reflector antennas. This paper proposes a field-circuit coupling method to analyze the PIM level of mesh reflectors. With the existence of many metal–metal (MM contacts in mesh reflectors, the contact nonlinearity becomes the main reason for PIM generation. To analyze these potential PIM sources, an equivalent circuit model including nonlinear components is constructed to model a single MM contact so that the transient current through the MM contact point induced by incident electromagnetic waves can be calculated. Taking the electric current as a new electromagnetic wave source, the far-field scattering can be obtained by the use of electromagnetic numerical methods or the communication link method. Finally, a comparison between simulation and experimental results is illustrated to verify the validity of the proposed method.

  8. Analysis of surface insulation resistance related failures in electronics by circuit simulation

    DEFF Research Database (Denmark)

    Verdingovas, Vadimas; Joshy, Salil; Jellesen, Morten Stendahl

    2017-01-01

    conduction medium. Findings-This paper provides a summary of the effects of contamination with various weak organic acids representing the active components in no-clean solder flux residue, and demonstrates the effect of humidity and contamination on the possible malfunctions and errors in electronic...... of the circuits using a range of empirical leakage resistance values combined with the knowledge of the humidity and contamination profile of the electronics can be used for the robust design of a device, which is also important for electronic products relying on low current consumption for long battery lifetime....... Originality/value-Examples provide a basic link between the combined effect of humidity and contamination and the performance of electronic circuits. The methodology shown provides the possibility of addressing the climatic reliability of an electronic device at the early stage of device design by using...

  9. Nonlinear Analysis of Ring Oscillator and Cross-Coupled Oscillator Circuits

    KAUST Repository

    Ge, Xiaoqing

    2010-12-01

    Hassan Khalil’s research results and beautifully written textbook on nonlinear systems have influenced generations of researchers, including the authors of this paper. Using nonlinear systems techniques, this paper analyzes ring oscillator and cross-coupled oscillator circuits, which are essential building blocks in digital systems. The paper first investigates local and global stability properties of an n-stage ring oscillator by making use of its cyclic structure. It next studies global stability properties of a class of cross-coupled oscillators which admit the representation of a dynamic system in feedback with a static nonlinearity, and presents su cient conditions for almost global convergence of the solutions to a limit cycle when the feedback gain is in the vicinity of a bifurcation point. The result are also extended to the synchronization of interconnected identical oscillator circuits.

  10. Analysis of a PCB In-Circuit Test and Its Optimized Cycle

    International Nuclear Information System (INIS)

    Chi, Moon Goo; Lee, Eun Chan; Bae, Yeon Kyoung

    2011-01-01

    KHNP performs subcomponent performance tests of the PCBs (Printed Circuit Boards) installed in safety-related systems or plant trip-related systems with every outage. The characteristics of each subcomponent are measured by test equipment. The tests are known as an ICT (In-Circuit Test). If a degraded condition is detected by this test, the affected subcomponents are replaced. This test has been conducted for 17 years, since 1994, and its results have been compiled into a test system database. As part of the reliability improvement plan of critical PCBs, KHNP developed a program that analyzes the performance of various key PCBs based on this test data. Thus, it became possible to evaluate the performance trends related to PCBs by tracing the test history of the PCB subcomponents through the ICT over many years. The present study also estimates an optimized ICT cycle that can be implemented to prevent the degradation of PCBs before they fail due to aging

  11. Experimental and theoretical analysis of integrated circuit (IC) chips on flexible substrates subjected to bending

    Science.gov (United States)

    Chen, Ying; Yuan, Jianghong; Zhang, Yingchao; Huang, Yonggang; Feng, Xue

    2017-10-01

    The interfacial failure of integrated circuit (IC) chips integrated on flexible substrates under bending deformation has been studied theoretically and experimentally. A compressive buckling test is used to impose the bending deformation onto the interface between the IC chip and the flexible substrate quantitatively, after which the failed interface is investigated using scanning electron microscopy. A theoretical model is established based on the beam theory and a bi-layer interface model, from which an analytical expression of the critical curvature in relation to the interfacial failure is obtained. The relationships between the critical curvature, the material, and the geometric parameters of the device are discussed in detail, providing guidance for future optimization flexible circuits based on IC chips.

  12. analysis and implementation of reactor protection system circuits - case study Egypt's 2 nd research reactor-

    International Nuclear Information System (INIS)

    Elnokity, O.E.M.

    2006-01-01

    this work presents a way to design and implement the trip unit of a reactor protection system (RPS) using a field programmable gate arrays (FPGA). instead of the traditional embedded microprocessor based interface design method, a proposed tailor made FPGA based circuit is built to substitute the trip unit (TU), which is used in Egypt's 2 nd research reactor ETRR-2. the existing embedded system is built around the STD32 field computer bus which is used in industrial and process control applications. it is modular, rugged, reliable, and easy-to-use and is able to support a large mix of I/O cards and to easily change its configuration in the future. therefore, the same bus is still used in the proposed design. the state machine of this bus is designed based around its timing diagrams and implemented in VHDL to interface the designed TU circuit

  13. Nonlinear Analysis of Ring Oscillator and Cross-Coupled Oscillator Circuits

    KAUST Repository

    Ge, Xiaoqing; Arcak, Murat; Salama, Khaled N.

    2010-01-01

    Hassan Khalil’s research results and beautifully written textbook on nonlinear systems have influenced generations of researchers, including the authors of this paper. Using nonlinear systems techniques, this paper analyzes ring oscillator and cross-coupled oscillator circuits, which are essential building blocks in digital systems. The paper first investigates local and global stability properties of an n-stage ring oscillator by making use of its cyclic structure. It next studies global stability properties of a class of cross-coupled oscillators which admit the representation of a dynamic system in feedback with a static nonlinearity, and presents su cient conditions for almost global convergence of the solutions to a limit cycle when the feedback gain is in the vicinity of a bifurcation point. The result are also extended to the synchronization of interconnected identical oscillator circuits.

  14. Field analysis and enhancement of multi-pole magnetic components fabricated on printed circuit board

    International Nuclear Information System (INIS)

    Chiu, K.-C.; Chen, C.-S.

    2007-01-01

    A multi-pole magnetic component magnetized with a fine magnetic pole pitch of less than 1 mm is very difficult to achieve by using traditional methods. Moreover, it requires a precise mechanical process and a complicated magnetization system. Different fine magnetic pole pitches of 300, 350 and 400 μm have been accomplished on 9-pole magnetic components through the printed circuit board (PCB) manufacturing technology. Additionally, another fine magnetic pole pitch of 500 μm was also fabricated on a dual-layered (DL) wire circuit structure to investigate the field enhancement. After measurements, a gain factor of 1.37 was obtained in the field strength. The field variations among different magnetic pole pitches were analyzed in this paper

  15. Design analysis of a lead–lithium/supercritical CO2 Printed Circuit Heat Exchanger for primary power recovery

    International Nuclear Information System (INIS)

    Fernández, Iván; Sedano, Luis

    2013-01-01

    Highlights: • A design for a PbLi/CO 2 (SC) Printed Circuit Heat Exchanger which optimizes the pressure drop performance is proposed. • Numerical analyses have been performed to optimize the airfoil fins shape and arrangement. • SiC is proposed as structural material and tritium permeation barrier for the PCHE. • The integrated flux is larger than expected and allows reducing the CO 2 mass flow in this sector of the power cycle. • A transport model has been developed to evaluate the permeation of tritium from the liquid metal to the secondary CO 2 . -- Abstract: One of the key issues for fusion power plant technology is the efficient, reliable and safe recovery of the power extracted by the primary coolants. An interesting design option for power conversion cycles based on Dual Coolant Breeding Blankets (DCBB) is a Printed Circuit Heat Exchanger, which is supported by the advantages of its compactness, thermal effectiveness, high temperature and pressure capability and corrosion resistance. This work presents a design analysis of a silicon carbide Printed Circuit Heat Exchanger for lead–lithium/supercritical CO 2 at DEMO ranges (4× segmentation)

  16. Functional connectivity decreases in autism in emotion, self, and face circuits identified by Knowledge-based Enrichment Analysis.

    Science.gov (United States)

    Cheng, Wei; Rolls, Edmund T; Zhang, Jie; Sheng, Wenbo; Ma, Liang; Wan, Lin; Luo, Qiang; Feng, Jianfeng

    2017-03-01

    A powerful new method is described called Knowledge based functional connectivity Enrichment Analysis (KEA) for interpreting resting state functional connectivity, using circuits that are functionally identified using search terms with the Neurosynth database. The method derives its power by focusing on neural circuits, sets of brain regions that share a common biological function, instead of trying to interpret single functional connectivity links. This provides a novel way of investigating how task- or function-related networks have resting state functional connectivity differences in different psychiatric states, provides a new way to bridge the gap between task and resting-state functional networks, and potentially helps to identify brain networks that might be treated. The method was applied to interpreting functional connectivity differences in autism. Functional connectivity decreases at the network circuit level in 394 patients with autism compared with 473 controls were found in networks involving the orbitofrontal cortex, anterior cingulate cortex, middle temporal gyrus cortex, and the precuneus, in networks that are implicated in the sense of self, face processing, and theory of mind. The decreases were correlated with symptom severity. Copyright © 2017. Published by Elsevier Inc.

  17. Double-layer rotor magnetic shield performance analysis in high temperature superconducting synchronous generators under short circuit fault conditions

    Science.gov (United States)

    Hekmati, Arsalan; Aliahmadi, Mehdi

    2016-12-01

    High temperature superconducting, HTS, synchronous machines benefit from a rotor magnetic shield in order to protect superconducting coils against asynchronous magnetic fields. This magnetic shield, however, suffers from exerted Lorentz forces generated in light of induced eddy currents during transient conditions, e.g. stator windings short-circuit fault. In addition, to the exerted electromagnetic forces, eddy current losses and the associated effects on the cryogenic system are the other consequences of shielding HTS coils. This study aims at investigating the Rotor Magnetic Shield, RMS, performance in HTS synchronous generators under stator winding short-circuit fault conditions. The induced eddy currents in different circumferential positions of the rotor magnetic shield along with associated Joule heating losses would be studied using 2-D time-stepping Finite Element Analysis, FEA. The investigation of Lorentz forces exerted on the magnetic shield during transient conditions has also been performed in this paper. The obtained results show that double line-to-ground fault is of the most importance among different types of short-circuit faults. It was revealed that when it comes to the design of the rotor magnetic shields, in addition to the eddy current distribution and the associated ohmic losses, two phase-to-ground fault should be taken into account since the produced electromagnetic forces in the time of fault conditions are more severe during double line-to-ground fault.

  18. RNA amplification for successful gene profiling analysis

    Directory of Open Access Journals (Sweden)

    Wang Ena

    2005-07-01

    Full Text Available Abstract The study of clinical samples is often limited by the amount of material available to study. While proteins cannot be multiplied in their natural form, DNA and RNA can be amplified from small specimens and used for high-throughput analyses. Therefore, genetic studies offer the best opportunity to screen for novel insights of human pathology when little material is available. Precise estimates of DNA copy numbers in a given specimen are necessary. However, most studies investigate static variables such as the genetic background of patients or mutations within pathological specimens without a need to assess proportionality of expression among different genes throughout the genome. Comparative genomic hybridization of DNA samples represents a crude exception to this rule since genomic amplification or deletion is compared among different specimens directly. For gene expression analysis, however, it is critical to accurately estimate the proportional expression of distinct RNA transcripts since such proportions directly govern cell function by modulating protein expression. Furthermore, comparative estimates of relative RNA expression at different time points portray the response of cells to environmental stimuli, indirectly informing about broader biological events affecting a particular tissue in physiological or pathological conditions. This cognitive reaction of cells is similar to the detection of electroencephalographic patterns which inform about the status of the brain in response to external stimuli. As our need to understand human pathophysiology at the global level increases, the development and refinement of technologies for high fidelity messenger RNA amplification have become the focus of increasing interest during the past decade. The need to increase the abundance of RNA has been met not only for gene specific amplification, but, most importantly for global transcriptome wide, unbiased amplification. Now gene

  19. Analysis of the flow imbalance in the KSTAR PF cryo-circuit

    International Nuclear Information System (INIS)

    Lee, Hyun-Jung; Park, Dong-Seong; Kwag, Sang-Woo; Joo, Jae-Jun; Moon, Kyung-Mo; Kim, Nam-Won; Lee, Young-Joo; Park, Young-Min; Yang, Hyung-Lyeol

    2015-01-01

    Highlights: • Investigate of flow imbalance trend for the KSTAR PF superconducting magnet. • Flow imbalance is compared with individual magnet test and integration magnet test. • Intensifying of flow imbalance is proven from the flow monitoring in the KSTAR PF circuit. • Flow behavior is analyzed during magnet charging in the circulator circuit. • Variation of magnet outlet temperature is analyzed due to flow imbalance. - Abstract: The KSTAR PF cryo-circuit is a quasi-closed circulation system in which more than 370 g/s of supercritical helium (SHe) is circulated using a SHe circulator. The heated helium from superconducting magnet is cooled through sub cooler (4.3 K). The circulator is operated at 4.5 K and 6.5 bar, and the pressure drop of the circuit is kept at 2 bar in order to maintain the supercritical state and circulator stability. The circuit is connected with helium refrigerator system, distribution system, and supercritical magnet system. It has a hundred branches to supply supercritical helium to the poloidal field superconducting magnet. The branch was designed to optimize the operation conditions and they are grouped for one cryogenic valve has the same length within the cardinal principle of the optimization. Five cryogenic valves are installed to control the mass flow rate, and seven orifice mass flow meters, differential pressure gauges and temperature sensors were installed in front of the magnet in the distribution because upper magnet and lower magnet is symmetric theoretically. The cryogenic pipe line was manufactured with elevation about 10 m between upper magnet and lower magnet. The inlet and outlet helium feed-through were installed at the coil inside in case of KSTAR PF1–PF5 upper magnet and lower magnet. The flow imbalance is caused by void fraction and it could be changed due to manufacturing process even if it has the same length of cooling channel. This creates an imbalance among cooling channels and temperatures are

  20. Identification of Human HK Genes and Gene Expression Regulation Study in Cancer from Transcriptomics Data Analysis

    Science.gov (United States)

    Zhang, Zhang; Liu, Jingxing; Wu, Jiayan; Yu, Jun

    2013-01-01

    The regulation of gene expression is essential for eukaryotes, as it drives the processes of cellular differentiation and morphogenesis, leading to the creation of different cell types in multicellular organisms. RNA-Sequencing (RNA-Seq) provides researchers with a powerful toolbox for characterization and quantification of transcriptome. Many different human tissue/cell transcriptome datasets coming from RNA-Seq technology are available on public data resource. The fundamental issue here is how to develop an effective analysis method to estimate expression pattern similarities between different tumor tissues and their corresponding normal tissues. We define the gene expression pattern from three directions: 1) expression breadth, which reflects gene expression on/off status, and mainly concerns ubiquitously expressed genes; 2) low/high or constant/variable expression genes, based on gene expression level and variation; and 3) the regulation of gene expression at the gene structure level. The cluster analysis indicates that gene expression pattern is higher related to physiological condition rather than tissue spatial distance. Two sets of human housekeeping (HK) genes are defined according to cell/tissue types, respectively. To characterize the gene expression pattern in gene expression level and variation, we firstly apply improved K-means algorithm and a gene expression variance model. We find that cancer-associated HK genes (a HK gene is specific in cancer group, while not in normal group) are expressed higher and more variable in cancer condition than in normal condition. Cancer-associated HK genes prefer to AT-rich genes, and they are enriched in cell cycle regulation related functions and constitute some cancer signatures. The expression of large genes is also avoided in cancer group. These studies will help us understand which cell type-specific patterns of gene expression differ among different cell types, and particularly for cancer. PMID:23382867

  1. Mutation analysis of the preproghrelin gene

    DEFF Research Database (Denmark)

    Larsen, Lesli H; Gjesing, Anette P; Sørensen, Thorkild I A

    2005-01-01

    To investigate the preproghrelin gene for variants and their association with obesity and type 2 diabetes.......To investigate the preproghrelin gene for variants and their association with obesity and type 2 diabetes....

  2. Gene set analysis of purine and pyrimidine antimetabolites cancer therapies.

    Science.gov (United States)

    Fridley, Brooke L; Batzler, Anthony; Li, Liang; Li, Fang; Matimba, Alice; Jenkins, Gregory D; Ji, Yuan; Wang, Liewei; Weinshilboum, Richard M

    2011-11-01

    Responses to therapies, either with regard to toxicities or efficacy, are expected to involve complex relationships of gene products within the same molecular pathway or functional gene set. Therefore, pathways or gene sets, as opposed to single genes, may better reflect the true underlying biology and may be more appropriate units for analysis of pharmacogenomic studies. Application of such methods to pharmacogenomic studies may enable the detection of more subtle effects of multiple genes in the same pathway that may be missed by assessing each gene individually. A gene set analysis of 3821 gene sets is presented assessing the association between basal messenger RNA expression and drug cytotoxicity using ethnically defined human lymphoblastoid cell lines for two classes of drugs: pyrimidines [gemcitabine (dFdC) and arabinoside] and purines [6-thioguanine and 6-mercaptopurine]. The gene set nucleoside-diphosphatase activity was found to be significantly associated with both dFdC and arabinoside, whereas gene set γ-aminobutyric acid catabolic process was associated with dFdC and 6-thioguanine. These gene sets were significantly associated with the phenotype even after adjusting for multiple testing. In addition, five associated gene sets were found in common between the pyrimidines and two gene sets for the purines (3',5'-cyclic-AMP phosphodiesterase activity and γ-aminobutyric acid catabolic process) with a P value of less than 0.0001. Functional validation was attempted with four genes each in gene sets for thiopurine and pyrimidine antimetabolites. All four genes selected from the pyrimidine gene sets (PSME3, CANT1, ENTPD6, ADRM1) were validated, but only one (PDE4D) was validated for the thiopurine gene sets. In summary, results from the gene set analysis of pyrimidine and purine therapies, used often in the treatment of various cancers, provide novel insight into the relationship between genomic variation and drug response.

  3. Time-Course Gene Set Analysis for Longitudinal Gene Expression Data.

    Directory of Open Access Journals (Sweden)

    Boris P Hejblum

    2015-06-01

    Full Text Available Gene set analysis methods, which consider predefined groups of genes in the analysis of genomic data, have been successfully applied for analyzing gene expression data in cross-sectional studies. The time-course gene set analysis (TcGSA introduced here is an extension of gene set analysis to longitudinal data. The proposed method relies on random effects modeling with maximum likelihood estimates. It allows to use all available repeated measurements while dealing with unbalanced data due to missing at random (MAR measurements. TcGSA is a hypothesis driven method that identifies a priori defined gene sets with significant expression variations over time, taking into account the potential heterogeneity of expression within gene sets. When biological conditions are compared, the method indicates if the time patterns of gene sets significantly differ according to these conditions. The interest of the method is illustrated by its application to two real life datasets: an HIV therapeutic vaccine trial (DALIA-1 trial, and data from a recent study on influenza and pneumococcal vaccines. In the DALIA-1 trial TcGSA revealed a significant change in gene expression over time within 69 gene sets during vaccination, while a standard univariate individual gene analysis corrected for multiple testing as well as a standard a Gene Set Enrichment Analysis (GSEA for time series both failed to detect any significant pattern change over time. When applied to the second illustrative data set, TcGSA allowed the identification of 4 gene sets finally found to be linked with the influenza vaccine too although they were found to be associated to the pneumococcal vaccine only in previous analyses. In our simulation study TcGSA exhibits good statistical properties, and an increased power compared to other approaches for analyzing time-course expression patterns of gene sets. The method is made available for the community through an R package.

  4. Computational algorithms for analysis of data from thin-film thermoresistors on a radio-electronic printed circuit board

    International Nuclear Information System (INIS)

    Korneeva, Anna; Shaydurov, Vladimir

    2016-01-01

    In the paper, the data analysis is considered for thin-film thermoresistors coated on to a radio-electronic printed circuit board to determine possible zones of its overheating. A mathematical model consists in an underdetermined system of linear algebraic equations with an infinite set of solutions. For computing a more real solution, two additional conditions are used: the smoothness of a solution and the positiveness of an increase of temperature during overheating. Computational experiments demonstrate that an overheating zone is determined exactly with a tolerable accuracy of temperature in it.

  5. Simulation of TunneLadder traveling-wave tube cold-test characteristics: Implementation of the three-dimensional, electromagnetic circuit analysis code micro-SOS

    Science.gov (United States)

    Kory, Carol L.; Wilson, Jeffrey D.

    1993-01-01

    The three-dimensional, electromagnetic circuit analysis code, Micro-SOS, can be used to reduce expensive time-consuming experimental 'cold-testing' of traveling-wave tube (TWT) circuits. The frequency-phase dispersion characteristics and beam interaction impedance of a TunneLadder traveling-wave tube slow-wave structure were simulated using the code. When reasonable dimensional adjustments are made, computer results agree closely with experimental data. Modifications to the circuit geometry that would make the TunneLadder TWT easier to fabricate for higher frequency operation are explored.

  6. EDF operational experience of primary circuit filter usage. Analysis of results and strategy for optimizing filtration and reducing solid wastes

    International Nuclear Information System (INIS)

    Mascarenhas, Darren; Moleiro, Edgar; Bancelin, Estelle; Bretelle, Jean-Luc

    2014-01-01

    Pleated fibreglass media filter cartridges are used throughout the auxiliary systems at nuclear power plants across the 58 reactors of EDF fleet. The main role of these filters is to remove suspended solids from coolant to prevent them accumulating in circuits or in equipments. In the primary circuit, these filters therefore limit the deposition of solids that are active or could become active if allowed to recirculate throughout the primary circuit, avoiding potential consequences such as an increase in dose rates, axial offset anomalies, demineralisers fouling, higher pressure losses in primary loop, and clogging of the primary pumps. Since 2008, a steady increase in the consumption of filters has been noticed, and therefore an increase in the amount of solid waste to treat. Preliminary studies have identified the primary circuit high-flow filters of the 1300/1450 MWe reactors as the main source of this increase. Not only has this stretched of solid waste containers production to the limit, as well as strained site resources and increased risks of operational errors during periods of frequent filter changes; it has also suggested that there is an underlying problem that could pose a serious risk to the primary circuit if untreated. Further studies have been carried out to identify more precisely the impact of possible causes, including increased quality surveillance of the filters, correlation of consumption data with the concentrations of various conditioning products and typical pollutants, and an impact analysis of events such as steam generator replacements or new practices like zinc injection. Work has been done with the filter manufacturer to improve their service lifetime and a simulation tool has been developed in order to understand and optimise filtration. We are also working with sites on creating good practices and avoiding bad ones. These actions should reduce the consumption in the short term while still assuring a high quality of filtration and

  7. Coupled circuit numerical analysis of eddy currents in an open MRI system

    Science.gov (United States)

    Akram, Md. Shahadat Hossain; Terada, Yasuhiko; Keiichiro, Ishi; Kose, Katsumi

    2014-08-01

    We performed a new coupled circuit numerical simulation of eddy currents in an open compact magnetic resonance imaging (MRI) system. Following the coupled circuit approach, the conducting structures were divided into subdomains along the length (or width) and the thickness, and by implementing coupled circuit concepts we have simulated transient responses of eddy currents for subdomains in different locations. We implemented the Eigen matrix technique to solve the network of coupled differential equations to speed up our simulation program. On the other hand, to compute the coupling relations between the biplanar gradient coil and any other conducting structure, we implemented the solid angle form of Ampere’s law. We have also calculated the solid angle for three dimensions to compute inductive couplings in any subdomain of the conducting structures. Details of the temporal and spatial distribution of the eddy currents were then implemented in the secondary magnetic field calculation by the Biot-Savart law. In a desktop computer (Programming platform: Wolfram Mathematica 8.0®, Processor: Intel(R) Core(TM)2 Duo E7500 @ 2.93 GHz; OS: Windows 7 Professional; Memory (RAM): 4.00 GB), it took less than 3 min to simulate the entire calculation of eddy currents and fields, and approximately 6 min for X-gradient coil. The results are given in the time-space domain for both the direct and the cross-terms of the eddy current magnetic fields generated by the Z-gradient coil. We have also conducted free induction decay (FID) experiments of eddy fields using a nuclear magnetic resonance (NMR) probe to verify our simulation results. The simulation results were found to be in good agreement with the experimental results. In this study we have also conducted simulations for transient and spatial responses of secondary magnetic field induced by X-gradient coil. Our approach is fast and has much less computational complexity than the conventional electromagnetic numerical

  8. Stability analysis of a recycling circuit of a BWR type reactor. Theoretical study

    International Nuclear Information System (INIS)

    Salinas H, J.G.; Espinosa P, G.; Gonzalez M, V.M.

    2000-01-01

    The Technology, Regulation and Services Management of the National Commission of Nuclear Safety and Safeguards financed and in coordinate form with the I.P.H. Department of the Metropolitan Autonomous-Iztapalapa University developed the present project with the purpose of studying the effect of the recycling system on the linear stability of a BWR reactor whose reference central is the Laguna Verde power station. The present project forms part of a work series focused to the linear stability of the nuclear reactor of the Unit 1 at Laguna Verde power station. The components of the recycling system considered for the study of stability are the recycling external circuit (recycling pumps, valves) and the internal circuit (downcomer, jet pumps, lower full, driers, separators). The mathematical model is obtained applying mass balances and movement quantity in each one of the mentioned circuits. With respect to the nucleus model two regions are considered, the first one is made of a flow in one phase and the second one of a flow in two phases. For modelling the biphasic region it is considered homogenous flow. Generally it is studied the system behavior in the frequency domain starting from the transfer function applied to four operational states which correspond to the lower stability zone in the map power-flow of the Unit 1 of Laguna Verde power station. The Nyquist diagrams corresponding to each state as well as their characteristic frequency were determined. The results show that exists a very clear dependence of the power-flow relation on the stability of the system. It was found that the boiling length is an important parameter for the linear stability of the system. The obtained results show that the characteristic frequencies in unstability zones are similar to the reported data of the Unit 1 of the Laguna Verde power station in the event of power oscillations carried out in January 1995. (Author)

  9. Homogenization on Multi-Materials’ Elements: Application to Printed Circuit Boards and Warpage Analysis

    Directory of Open Access Journals (Sweden)

    Araújo Manuel

    2016-01-01

    Full Text Available Multi-material domains are often found in industrial applications. Modelling them can be computationally very expensive due to meshing requirements. The finite element properties comprising different materials are hardly accurate. In this work, a new homogenization method that simplifies the computation of the homogenized Young modulus, Poisson ratio and thermal expansion coefficient is proposed, and applied to composite-like material on a printed circuit board. The results show a good properties correspondence between the homogenized domain and the real geometry simulation.

  10. MeV He microbeam analysis of a semiconductor integrated circuit

    International Nuclear Information System (INIS)

    Zhu Peiran; Liu Jiarui; Zhang Jinping; Yin Shiduan

    1989-01-01

    An MeV He + microbeam has been used to analyse a microscale semiconductor structure. The 2 MeV He + ion beam is limited to 25 μm diameter by a set of diaphragms and is further focused by a quadrupole quadruplet to 3μm diameter. The incident beam current on the sample is about 0.3 nA. The Rutherford backscattering (RBS) technique is applied to the measurement of the composition and depth profile in the near-surface region of a semiconductor integrated circuit. (author)

  11. New domain for image analysis: VLSI circuits testing, with Romuald, specialized in parallel image processing

    Energy Technology Data Exchange (ETDEWEB)

    Rubat Du Merac, C; Jutier, P; Laurent, J; Courtois, B

    1983-07-01

    This paper describes some aspects of specifying, designing and evaluating a specialized machine, Romuald, for the capture, coding, and processing of video and scanning electron microscope (SEM) pictures. First the authors present the functional organization of the process unit of romuald and its hardware, giving details of its behaviour. Then they study the capture and display unit which, thanks to its flexibility, enables SEM images coding. Finally, they describe an application which is now being developed in their laboratory: testing VLSI circuits with new methods: sem+voltage contrast and image processing. 15 references.

  12. SEM analysis of ionizing radiation effects in linear integrated circuits. [Scanning Electron Microscope

    Science.gov (United States)

    Stanley, A. G.; Gauthier, M. K.

    1977-01-01

    A successful diagnostic technique was developed using a scanning electron microscope (SEM) as a precision tool to determine ionization effects in integrated circuits. Previous SEM methods radiated the entire semiconductor chip or major areas. The large area exposure methods do not reveal the exact components which are sensitive to radiation. To locate these sensitive components a new method was developed, which consisted in successively irradiating selected components on the device chip with equal doses of electrons /10 to the 6th rad (Si)/, while the whole device was subjected to representative bias conditions. A suitable device parameter was measured in situ after each successive irradiation with the beam off.

  13. CMOS circuits for piezoelectric energy harvesters efficient power extraction, interface modeling and loss analysis

    CERN Document Server

    Hehn, Thorsten

    2014-01-01

    This book deals with the challenge of exploiting ambient vibrational energy which can be used to power small and low-power electronic devices, e.g. wireless sensor nodes. Generally, particularly for low voltage amplitudes, low-loss rectification is required to achieve high conversion efficiency. In the special case of piezoelectric energy harvesting, pulsed charge extraction has the potential to extract more power compared to a single rectifier. For this purpose, a fully autonomous CMOS integrated interface circuit for piezoelectric generators which fulfills these requirements is presented.Due

  14. MeV He microbeam analysis of a semiconductor integrated circuit

    Energy Technology Data Exchange (ETDEWEB)

    Zhu Peiran; Liu Jiarui; Zhang Jinping; Yin Shiduan

    1989-01-01

    An MeV He/sup +/ microbeam has been used to analyse a microscale semiconductor structure. The 2 MeV He/sup +/ ion beam is limited to 25 /mu/m diameter by a set of diaphragms and is further focused by a quadrupole quadruplet to 3/mu/m diameter. The incident beam current on the sample is about 0.3 nA. The Rutherford backscattering (RBS) technique is applied to the measurement of the composition and depth profile in the near-surface region of a semiconductor integrated circuit.

  15. The Technical Analysis of the Impact of Circuit of Financial Capital on the Currency Stability in Ukraine

    Directory of Open Access Journals (Sweden)

    Iaroshevska Oksana V.

    2018-01-01

    Full Text Available The relevance of the article’s topic is determined by the aggravation of the monetary and financial crisis in Ukraine and the need to overcome imbalances arising from the complications of circuit of financial capital and its involvement by economic entities. The article is aimed at researching on the basis of technical analysis the influence of exchange rate factor on the formation of capital in the country. The general and distinctive features of technical and fundamental analysis of currency markets are defined. It is shown that despite the difference of views, technical analysis is an integral stage of forecasting the exchange rate. The main scientific result of the article is substantiating the temporary lags of fractals, which explain the change in the dynamics of the exchange rate and their impact on the circuit of financial capital. It has been proved that the systemic crisis in the currency market of Ukraine arose during 2012–2014, with its peak at the end of the specified period. To stop devaluation processes and to provide measures on regulation of the foreign exchange market it has been proposed to soften the conditions of doing business, to improve the methodology of quantitative and qualitative forecasting of the NBU exchange rates, to form system of foreign exchange risk insurance instruments, to increase international reserves to a secure level, etc. Prospect for further research is determining the impact of currency fluctuations on the financial performance of the use of capital of Ukrainian economic entities.

  16. Identifying key genes in rheumatoid arthritis by weighted gene co-expression network analysis.

    Science.gov (United States)

    Ma, Chunhui; Lv, Qi; Teng, Songsong; Yu, Yinxian; Niu, Kerun; Yi, Chengqin

    2017-08-01

    This study aimed to identify rheumatoid arthritis (RA) related genes based on microarray data using the WGCNA (weighted gene co-expression network analysis) method. Two gene expression profile datasets GSE55235 (10 RA samples and 10 healthy controls) and GSE77298 (16 RA samples and seven healthy controls) were downloaded from Gene Expression Omnibus database. Characteristic genes were identified using metaDE package. WGCNA was used to find disease-related networks based on gene expression correlation coefficients, and module significance was defined as the average gene significance of all genes used to assess the correlation between the module and RA status. Genes in the disease-related gene co-expression network were subject to functional annotation and pathway enrichment analysis using Database for Annotation Visualization and Integrated Discovery. Characteristic genes were also mapped to the Connectivity Map to screen small molecules. A total of 599 characteristic genes were identified. For each dataset, characteristic genes in the green, red and turquoise modules were most closely associated with RA, with gene numbers of 54, 43 and 79, respectively. These genes were enriched in totally enriched in 17 Gene Ontology terms, mainly related to immune response (CD97, FYB, CXCL1, IKBKE, CCR1, etc.), inflammatory response (CD97, CXCL1, C3AR1, CCR1, LYZ, etc.) and homeostasis (C3AR1, CCR1, PLN, CCL19, PPT1, etc.). Two small-molecule drugs sanguinarine and papaverine were predicted to have a therapeutic effect against RA. Genes related to immune response, inflammatory response and homeostasis presumably have critical roles in RA pathogenesis. Sanguinarine and papaverine have a potential therapeutic effect against RA. © 2017 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.

  17. A LabVIEW-based electrical bioimpedance spectroscopic data interpreter (LEBISDI) for biological tissue impedance analysis and equivalent circuit modelling

    KAUST Repository

    Bera, Tushar Kanti

    2016-12-05

    Under an alternating electrical signal, biological tissues produce a complex electrical bioimpedance that is a function of tissue composition and applied signal frequencies. By studying the bioimpedance spectra of biological tissues over a wide range of frequencies, we can noninvasively probe the physiological properties of these tissues to detect possible pathological conditions. Electrical impedance spectroscopy (EIS) can provide the spectra that are needed to calculate impedance parameters within a wide range of frequencies. Before impedance parameters can be calculated and tissue information extracted, impedance spectra should be processed and analyzed by a dedicated software program. National Instruments (NI) Inc. offers LabVIEW, a fast, portable, robust, user-friendly platform for designing dataanalyzing software. We developed a LabVIEW-based electrical bioimpedance spectroscopic data interpreter (LEBISDI) to analyze the electrical impedance spectra for tissue characterization in medical, biomedical and biological applications. Here, we test, calibrate and evaluate the performance of LEBISDI on the impedance data obtained from simulation studies as well as the practical EIS experimentations conducted on electronic circuit element combinations and the biological tissue samples. We analyze the Nyquist plots obtained from the EIS measurements and compare the equivalent circuit parameters calculated by LEBISDI with the corresponding original circuit parameters to assess the accuracy of the program developed. Calibration studies show that LEBISDI not only interpreted the simulated and circuitelement data accurately, but also successfully interpreted tissues impedance data and estimated the capacitive and resistive components produced by the compositions biological cells. Finally, LEBISDI efficiently calculated and analyzed variation in bioimpedance parameters of different tissue compositions, health and temperatures. LEBISDI can also be used for human tissue

  18. A LabVIEW-based electrical bioimpedance spectroscopic data interpreter (LEBISDI) for biological tissue impedance analysis and equivalent circuit modelling

    KAUST Repository

    Bera, Tushar Kanti; Jampana, Nagaraju; Lubineau, Gilles

    2016-01-01

    Under an alternating electrical signal, biological tissues produce a complex electrical bioimpedance that is a function of tissue composition and applied signal frequencies. By studying the bioimpedance spectra of biological tissues over a wide range of frequencies, we can noninvasively probe the physiological properties of these tissues to detect possible pathological conditions. Electrical impedance spectroscopy (EIS) can provide the spectra that are needed to calculate impedance parameters within a wide range of frequencies. Before impedance parameters can be calculated and tissue information extracted, impedance spectra should be processed and analyzed by a dedicated software program. National Instruments (NI) Inc. offers LabVIEW, a fast, portable, robust, user-friendly platform for designing dataanalyzing software. We developed a LabVIEW-based electrical bioimpedance spectroscopic data interpreter (LEBISDI) to analyze the electrical impedance spectra for tissue characterization in medical, biomedical and biological applications. Here, we test, calibrate and evaluate the performance of LEBISDI on the impedance data obtained from simulation studies as well as the practical EIS experimentations conducted on electronic circuit element combinations and the biological tissue samples. We analyze the Nyquist plots obtained from the EIS measurements and compare the equivalent circuit parameters calculated by LEBISDI with the corresponding original circuit parameters to assess the accuracy of the program developed. Calibration studies show that LEBISDI not only interpreted the simulated and circuitelement data accurately, but also successfully interpreted tissues impedance data and estimated the capacitive and resistive components produced by the compositions biological cells. Finally, LEBISDI efficiently calculated and analyzed variation in bioimpedance parameters of different tissue compositions, health and temperatures. LEBISDI can also be used for human tissue

  19. Analysis of each branch current of serial solar cells by using an equivalent circuit model

    International Nuclear Information System (INIS)

    Yi Shi-Guang; Zhang Wan-Hui; Ai Bin; Song Jing-Wei; Shen Hui

    2014-01-01

    In this paper, based on the equivalent single diode circuit model of the solar cell, an equivalent circuit diagram for two serial solar cells is drawn. Its equations of current and voltage are derived from Kirchhoff's current and voltage law. First, parameters are obtained from the I—V (current—voltage) curves for typical monocrystalline silicon solar cells (125 mm × 125 mm). Then, by regarding photo-generated current, shunt resistance, serial resistance of the first solar cell, and resistance load as the variables. The properties of shunt currents (I sh1 and I sh2 ), diode currents (I D1 and I D2 ), and load current (I L ) for the whole two serial solar cells are numerically analyzed in these four cases for the first time, and the corresponding physical explanations are made. We find that these parameters have different influences on the internal currents of solar cells. Our results will provide a reference for developing higher efficiency solar cell module and contribute to the better understanding of the reason of efficiency loss of solar cell module. (interdisciplinary physics and related areas of science and technology)

  20. Instantaneous charging & discharging cycle analysis of a novel supercapacitor based energy harvesting circuit

    Science.gov (United States)

    Khan, MD Shahrukh Adnan; Kuni, Sharsad Kara; Rajkumar, Rajprasad; Syed, Anas; Hawladar, Masum; Rahman, Md. Moshiur

    2017-12-01

    In this paper, an extensive effort has been made to design and develop a prototype in a laboratory setup environment in order to investigate experimentally the response of a novel Supercapacitor based energy harvesting circuit; particularly the phenomena of instantaneous charging and discharging cycle is analysed. To maximize battery lifespan and storage capacity, charging/discharging cycles need to be optimized in such a way, it ultimately enhances the system performances reliably. Keeping this into focus, an Arduino-MOSFET based control system is developed to charge the Supercapacitor from a low wind Vertical Axis Turbine (VAWT) and discharge it through a 6V battery. With a wind speed of 5m/s, the wind turbine requires approximately 8.1 hours to charge the 6V battery through Supercapacitor bank that constitutes 18 cycles in which each cycle consumes 27 minutes. The overall performance of the proposed system was quite convincing in a sense that the efficiency of the developed Energy Harvesting Circuit EHC raises to 19% in comparison to direct charging of the battery from the Vertical wind turbine. At low wind speed, such value of efficiency margin is quite encouraging which essentially validates the system design.

  1. A photonic circuit for complementary frequency shifting, in-phase quadrature/single sideband modulation and frequency multiplication: analysis and integration feasibility

    Science.gov (United States)

    Hasan, Mehedi; Hu, Jianqi; Nikkhah, Hamdam; Hall, Trevor

    2017-08-01

    A novel photonic integrated circuit architecture for implementing orthogonal frequency division multiplexing by means of photonic generation of phase-correlated sub-carriers is proposed. The circuit can also be used for implementing complex modulation, frequency up-conversion of the electrical signal to the optical domain and frequency multiplication. The principles of operation of the circuit are expounded using transmission matrices and the predictions of the analysis are verified by computer simulation using an industry-standard software tool. Non-ideal scenarios that may affect the correct function of the circuit are taken into consideration and quantified. The discussion of integration feasibility is illustrated by a photonic integrated circuit that has been fabricated using 'library' components and which features most of the elements of the proposed circuit architecture. The circuit is found to be practical and may be fabricated in any material platform that offers a linear electro-optic modulator such as organic or ferroelectric thin films hybridized with silicon photonics.

  2. Inferring gene expression dynamics via functional regression analysis

    Directory of Open Access Journals (Sweden)

    Leng Xiaoyan

    2008-01-01

    Full Text Available Abstract Background Temporal gene expression profiles characterize the time-dynamics of expression of specific genes and are increasingly collected in current gene expression experiments. In the analysis of experiments where gene expression is obtained over the life cycle, it is of interest to relate temporal patterns of gene expression associated with different developmental stages to each other to study patterns of long-term developmental gene regulation. We use tools from functional data analysis to study dynamic changes by relating temporal gene expression profiles of different developmental stages to each other. Results We demonstrate that functional regression methodology can pinpoint relationships that exist between temporary gene expression profiles for different life cycle phases and incorporates dimension reduction as needed for these high-dimensional data. By applying these tools, gene expression profiles for pupa and adult phases are found to be strongly related to the profiles of the same genes obtained during the embryo phase. Moreover, one can distinguish between gene groups that exhibit relationships with positive and others with negative associations between later life and embryonal expression profiles. Specifically, we find a positive relationship in expression for muscle development related genes, and a negative relationship for strictly maternal genes for Drosophila, using temporal gene expression profiles. Conclusion Our findings point to specific reactivation patterns of gene expression during the Drosophila life cycle which differ in characteristic ways between various gene groups. Functional regression emerges as a useful tool for relating gene expression patterns from different developmental stages, and avoids the problems with large numbers of parameters and multiple testing that affect alternative approaches.

  3. A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes

    OpenAIRE

    Mukherjee, Krishanu; Brocchieri, Luciano; B?rglin, Thomas R.

    2009-01-01

    The full complement of homeobox transcription factor sequences, including genes and pseudogenes, was determined from the analysis of 10 complete genomes from flowering plants, moss, Selaginella, unicellular green algae, and red algae. Our exhaustive genome-wide searches resulted in the discovery in each class of a greater number of homeobox genes than previously reported. All homeobox genes can be unambiguously classified by sequence evolutionary analysis into 14 distinct classes also charact...

  4. Analysis of multiplex gene expression maps obtained by voxelation.

    Science.gov (United States)

    An, Li; Xie, Hongbo; Chin, Mark H; Obradovic, Zoran; Smith, Desmond J; Megalooikonomou, Vasileios

    2009-04-29

    Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in cortex and corpus callosum. The experimental

  5. Analysis of multiplex gene expression maps obtained by voxelation

    Directory of Open Access Journals (Sweden)

    Smith Desmond J

    2009-04-01

    Full Text Available Abstract Background Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. Results To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in

  6. Analysis of Production and Delivery Center Hydrogen Applied to the Southern Patagonian Circuit

    Directory of Open Access Journals (Sweden)

    Maximiliano Fernando Medina

    2016-08-01

    Full Text Available The Desire department of the province of Santa Cruz, Argentina, presents the greatest potential electrolytic Hydrogen Production Country, From Three primary sources of sustainable energy: wind, solar, biomass. There, the Hydrogen Plant of Pico Truncado has capacity central production of hydrogen 100m3 of H2 / day, enough to supply 353 vehicles with hybrid fuel called HGNC, made by cutting 12% V / V of hydrogen in CNG (in situ at each station. Puerto Deseado, Fitz Roy, Caleta Olivia, Las Heras, Comodoro Rivadavia, Sarmiento and the Ancients: From the production cost, the cost of delivering hydrogen to the Southern Patagonian circuit comprised analyzed. Considering various local parameters are determined as a way of delivering more profitable virtual pipeline, with total cost of hydrogen estimated 6.5 USD / kg H2 and HGNC shipped in the station at 0.50 USD / Nm3.

  7. A Circuit Design and its Experimental Analysis for Electromagnetic Flowmeter in Measurement of Sewage

    Directory of Open Access Journals (Sweden)

    Huang Yu-Hang

    2014-02-01

    Full Text Available There are many problems in the traditional electromagnetic flowmeter. The problems involve three aspects. The first one is that the measurement precision is low. The second one is that the measurement range is narrow. The third one is that the test results are susceptible to interference. For the problems a new electromagnetic flowmeter controlled by single-chip microcomputer has been proposed. The medium/large-sized electromagnetic flowmeter is suitable for measurement of sewage. The software and hardware circuit of the electromagnetic flowmeter has been designed and tested. The tested data have been analyzed by the least square method and the error is 0.8 %. The result shown that the electromagnetic flowmeter controlled by single-chip microcomputer for measurement of sewage has reached the advanced level of similar products at home and abroad.

  8. A New Chaotic System with Multiple Attractors: Dynamic Analysis, Circuit Realization and S-Box Design

    Directory of Open Access Journals (Sweden)

    Qiang Lai

    2017-12-01

    Full Text Available This paper reports about a novel three-dimensional chaotic system with three nonlinearities. The system has one stable equilibrium, two stable equilibria and one saddle node, two saddle foci and one saddle node for different parameters. One salient feature of this novel system is its multiple attractors caused by different initial values. With the change of parameters, the system experiences mono-stability, bi-stability, mono-periodicity, bi-periodicity, one strange attractor, and two coexisting strange attractors. The complex dynamic behaviors of the system are revealed by analyzing the corresponding equilibria and using the numerical simulation method. In addition, an electronic circuit is given for implementing the chaotic attractors of the system. Using the new chaotic system, an S-Box is developed for cryptographic operations. Moreover, we test the performance of this produced S-Box and compare it to the existing S-Box studies.

  9. Growth Mechanism Studies of ZnO Nanowires: Experimental Observations and Short-Circuit Diffusion Analysis.

    Science.gov (United States)

    Shih, Po-Hsun; Wu, Sheng Yun

    2017-07-21

    Plenty of studies have been performed to probe the diverse properties of ZnO nanowires, but only a few have focused on the physical properties of a single nanowire since analyzing the growth mechanism along a single nanowire is difficult. In this study, a single ZnO nanowire was synthesized using a Ti-assisted chemical vapor deposition (CVD) method to avoid the appearance of catalytic contamination. Two-dimensional energy dispersive spectroscopy (EDS) mapping with a diffusion model was used to obtain the diffusion length and the activation energy ratio. The ratio value is close to 0.3, revealing that the growth of ZnO nanowires was attributed to the short-circuit diffusion.

  10. Numerical analysis of the influence of circuit arrangement on a fin-and-tube condenser performance

    Directory of Open Access Journals (Sweden)

    Cesare Maria Joppolo

    2015-09-01

    Full Text Available In the present paper a model for the steady-state simulation of fin-and-tube condenser is developed. The model is based on a finite volume approach that divides each tube into small elemental volumes where mass, momentum and energy conservation equations are solved using the effectiveness-NTU method and with appropriate correlations for void fraction, friction factor and heat transfer coefficient calculation. The model is validated against experimental data on two small condensers finding that the calculated heat transfer rate and refrigerant-side pressure drop agree within ±5% and ±21% respectively to the experimental values. The model is then used to numerically analyse the impact of different circuit arrangements on the condenser heat transfer rate, refrigerant-side pressure drop and refrigerant charge.

  11. Fluid elastic instability analysis of 1/6th experimental model of PFBR main vessel cooling circuit

    International Nuclear Information System (INIS)

    Jalaldeen, S.; Ravi, R.; Chellapandi, P.; Bhoje, S.B.

    1993-01-01

    In reactor assembly of Prototype Fast Breeder Reactor (PFBR), the main vessel (MV) temperature is kept below creep range i.e. less than 427 deg C by way of diverting a small fraction of core flow from the cold pool and sent through the passage between main vessel and an outer cylindrical baffle to cool the vessel. The sodium coning from this, is collected by another inner baffle and then returned to cold pool again. This system is termed as MV cooling circuit. The outer and inner baffles form feeding and restitution collectors respectively. The sodium from the feeding collector flows over the outer baffle and falls through a height of about 0.5 m before impacting on the free surface of sodium in the restitution collector. The fall of sodium may become a source of vibration of the baffles. Such vibrations have been already noted in case of SPX-I during its commissioning stage. For PFBR, the theoretical analysis was done to assess the fluid-elastic instability risks and stability charts were obtained. By this, it was concluded that the operating point (flow rate and fall height) lies within the stable zone. In order to confirm the above analysis results, a series of experiments were proposed. One preliminary experiment on 1/16 th model of MV cooling circuit has been completed. This model has also been analysed theoretically for the fluid- elastic instability, the theoretical analysis involves 2 stage computations. In the first stage, free vibration analysis with fluid structure interaction (FSI) effect for experimental model has been done using INCA (CASTEM 1985) code and all the mode shapes including sloshing are extracted. In the second stage the instability analysis is performed with the free vibration results from INCA. For the instability computations, a code WEIR has been written based on Aita's instability criteria [Aita.S. 1986

  12. Theoretical design and analysis of wideband active hard electromagnetic surfaces using non-Foster circuit loaded anisotropic metasurfaces

    Science.gov (United States)

    Li, Yunbo; Li, Aobo; Sievenpiper, Daniel

    2018-02-01

    The electromagnetic (EM) hard surface which can both support transverse electric and transverse magnetic surface wave modes has the important ability to reduce the EM blockage of metallic obstacles. We propose a method to design an electrically thin hard surface with wide bandwidth by loading with non-Foster elements. The wideband hard surface composed of an anisotropic impedance coating can be considered as a kind of active metasurface. We develop a method to determine the values of the loading non-Foster circuit which can minimize the dispersion of the unit cells. For this method, we derive accurate values for the loading non-Foster elements through theoretical analysis. We also determine the fundamental limitations on the bandwidth due to stability requirements. To verify our theoretical design, we simulate the transmission performance between the two ports on opposite sides of a metallic rhombus-shaped obstacle coated with the non-Foster based metasurface. The simulated results show that the blockage has been largely reduced over a broad bandwidth from 0.2 GHz to 1.5 GHz. Finally, we provide a discussion on how the resistive part of the non-Foster circuit can affect the performance of the wideband hard surface coating.

  13. Controllable circuit

    DEFF Research Database (Denmark)

    2010-01-01

    A switch-mode power circuit comprises a controllable element and a control unit. The controllable element is configured to control a current in response to a control signal supplied to the controllable element. The control unit is connected to the controllable element and provides the control...

  14. Circuit Training.

    Science.gov (United States)

    Nelson, Jane B.

    1998-01-01

    Describes a research-based activity for high school physics students in which they build an LC circuit and find its resonant frequency of oscillation using an oscilloscope. Includes a diagram of the apparatus and an explanation of the procedures. (DDR)

  15. A gene network bioinformatics analysis for pemphigoid autoimmune blistering diseases.

    Science.gov (United States)

    Barone, Antonio; Toti, Paolo; Giuca, Maria Rita; Derchi, Giacomo; Covani, Ugo

    2015-07-01

    In this theoretical study, a text mining search and clustering analysis of data related to genes potentially involved in human pemphigoid autoimmune blistering diseases (PAIBD) was performed using web tools to create a gene/protein interaction network. The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database was employed to identify a final set of PAIBD-involved genes and to calculate the overall significant interactions among genes: for each gene, the weighted number of links, or WNL, was registered and a clustering procedure was performed using the WNL analysis. Genes were ranked in class (leader, B, C, D and so on, up to orphans). An ontological analysis was performed for the set of 'leader' genes. Using the above-mentioned data network, 115 genes represented the final set; leader genes numbered 7 (intercellular adhesion molecule 1 (ICAM-1), interferon gamma (IFNG), interleukin (IL)-2, IL-4, IL-6, IL-8 and tumour necrosis factor (TNF)), class B genes were 13, whereas the orphans were 24. The ontological analysis attested that the molecular action was focused on extracellular space and cell surface, whereas the activation and regulation of the immunity system was widely involved. Despite the limited knowledge of the present pathologic phenomenon, attested by the presence of 24 genes revealing no protein-protein direct or indirect interactions, the network showed significant pathways gathered in several subgroups: cellular components, molecular functions, biological processes and the pathologic phenomenon obtained from the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database. The molecular basis for PAIBD was summarised and expanded, which will perhaps give researchers promising directions for the identification of new therapeutic targets.

  16. Rice Transcriptome Analysis to Identify Possible Herbicide Quinclorac Detoxification Genes

    Directory of Open Access Journals (Sweden)

    Wenying eXu

    2015-09-01

    Full Text Available Quinclorac is a highly selective auxin-type herbicide, and is widely used in the effective control of barnyard grass in paddy rice fields, improving the world’s rice yield. The herbicide mode of action of quinclorac has been proposed and hormone interactions affect quinclorac signaling. Because of widespread use, quinclorac may be transported outside rice fields with the drainage waters, leading to soil and water pollution and environmental health problems.In this study, we used 57K Affymetrix rice whole-genome array to identify quinclorac signaling response genes to study the molecular mechanisms of action and detoxification of quinclorac in rice plants. Overall, 637 probe sets were identified with differential expression levels under either 6 or 24 h of quinclorac treatment. Auxin-related genes such as GH3 and OsIAAs responded to quinclorac treatment. Gene Ontology analysis showed that genes of detoxification-related family genes were significantly enriched, including cytochrome P450, GST, UGT, and ABC and drug transporter genes. Moreover, real-time RT-PCR analysis showed that top candidate P450 families such as CYP81, CYP709C and CYP72A genes were universally induced by different herbicides. Some Arabidopsis genes for the same P450 family were up-regulated under quinclorac treatment.We conduct rice whole-genome GeneChip analysis and the first global identification of quinclorac response genes. This work may provide potential markers for detoxification of quinclorac and biomonitors of environmental chemical pollution.

  17. DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

    Directory of Open Access Journals (Sweden)

    Baseler Michael W

    2007-11-01

    Full Text Available Abstract Background Due to the complex and distributed nature of biological research, our current biological knowledge is spread over many redundant annotation databases maintained by many independent groups. Analysts usually need to visit many of these bioinformatics databases in order to integrate comprehensive annotation information for their genes, which becomes one of the bottlenecks, particularly for the analytic task associated with a large gene list. Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis. Description The DAVID Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene/protein identifiers from a variety of public genomic resources into DAVID gene clusters. The grouping of such identifiers improves the cross-reference capability, particularly across NCBI and UniProt systems, enabling more than 40 publicly available functional annotation sources to be comprehensively integrated and centralized by the DAVID gene clusters. The simple, pair-wise, text format files which make up the DAVID Knowledgebase are freely downloadable for various data analysis uses. In addition, a well organized web interface allows users to query different types of heterogeneous annotations in a high-throughput manner. Conclusion The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis. For a given gene list, it not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for an individual gene. Moreover, the entire DAVID Knowledgebase is freely downloadable or searchable at http://david.abcc.ncifcrf.gov/knowledgebase/.

  18. Hacking DNA copy number for circuit engineering.

    Science.gov (United States)

    Wu, Feilun; You, Lingchong

    2017-07-27

    DNA copy number represents an essential parameter in the dynamics of synthetic gene circuits but typically is not explicitly considered. A new study demonstrates how dynamic control of DNA copy number can serve as an effective strategy to program robust oscillations in gene expression circuits.

  19. Analysis of the Diurnal Variation of the Global Electric Circuit Obtained From Different Numerical Models

    Science.gov (United States)

    Jánský, Jaroslav; Lucas, Greg M.; Kalb, Christina; Bayona, Victor; Peterson, Michael J.; Deierling, Wiebke; Flyer, Natasha; Pasko, Victor P.

    2017-12-01

    This work analyzes different current source and conductivity parameterizations and their influence on the diurnal variation of the global electric circuit (GEC). The diurnal variations of the current source parameterizations obtained using electric field and conductivity measurements from plane overflights combined with global Tropical Rainfall Measuring Mission satellite data give generally good agreement with measured diurnal variation of the electric field at Vostok, Antarctica, where reference experimental measurements are performed. An approach employing 85 GHz passive microwave observations to infer currents within the GEC is compared and shows the best agreement in amplitude and phase with experimental measurements. To study the conductivity influence, GEC models solving the continuity equation in 3-D are used to calculate atmospheric resistance using yearly averaged conductivity obtained from the global circulation model Community Earth System Model (CESM). Then, using current source parameterization combining mean currents and global counts of electrified clouds, if the exponential conductivity is substituted by the conductivity from CESM, the peak to peak diurnal variation of the ionospheric potential of the GEC decreases from 24% to 20%. The main reason for the change is the presence of clouds while effects of 222Rn ionization, aerosols, and topography are less pronounced. The simulated peak to peak diurnal variation of the electric field at Vostok is increased from 15% to 18% from the diurnal variation of the global current in the GEC if conductivity from CESM is used.

  20. Advances on the analysis of fast reactor core and coolant circuit structures

    International Nuclear Information System (INIS)

    Livolant, M.; Imazu, A.; Chang, Y.W.; Eggen, D.T.

    1989-01-01

    For the 10th SMiRT Conference, it has been decided to make general reviews of the accomplishments throughout the conferences. The aim of this paper is to make such a review in the field of fast reactor core and coolant circuit structures, which is now fully treated in division E. That was not true in the past: at the earliest conferences up to the 5th, the division E dealt with accidental studies among which the hypothetical core disruptive accident was the most important. So, to cover the subject from the first SMiRT to now, it has been necessary to search into all the past division in order to recover the studies fitting into the scope of the present division E. This has allowed a table showing the number of presented papers on the various topics at the SMiRT conferences to be set up (table I). Then, some significant topics have been studied in detail, highlighting the main accomplishments, but trying also to point out the shortcomings and the work still to be done, in view of the present state of art

  1. Analysis of Power Transfer Efficiency of Standard Integrated Circuit Immunity Test Methods

    Directory of Open Access Journals (Sweden)

    Hai Au Huynh

    2015-01-01

    Full Text Available Direct power injection (DPI and bulk current injection (BCI methods are defined in IEC 62132-3 and IEC 62132-4 as the electromagnetic immunity test method of integrated circuits (IC. The forward power measured at the RF noise generator when the IC malfunctions is used as the measure of immunity level of the IC. However, the actual power that causes failure in ICs is different from forward power measured at the noise source. Power transfer efficiency is used as a measure of power loss of the noise injection path. In this paper, the power transfer efficiencies of DPI and BCI methods are derived and validated experimentally with immunity test setup of a clock divider IC. Power transfer efficiency varies significantly over the frequency range as a function of the test method used and the IC input impedance. For the frequency range of 15 kHz to 1 GHz, power transfer efficiency of the BCI test was constantly higher than that of the DPI test. In the DPI test, power transfer efficiency is particularly low in the lower test frequency range up to 10 MHz. When performing the IC immunity tests following the standards, these characteristics of the test methods need to be considered.

  2. A computational analysis of the carbon-nanotube-based resonant-circuit sensors

    International Nuclear Information System (INIS)

    Grujicic, M.; Cao, G.; Roy, W.N.

    2004-01-01

    Available values for the molecular polarizability and the dipole moment and the computed adsorption energies to single walled carbon nanotubes (SWCNTs) for a couple of polar (NH 3 and CO) and several non-polar (He, Ar, N 2 and O 2 ) gases are used to help establish a correlation between the adsorbed gas-induced changes in the dielectric constant of the SWCNTs (the sensing material) and the resulting reduction in the resonant frequency of the resonant circuit-based chemical gas sensors. It is found that simple weighting methods which neglect the effect of changes in the electronic structure of the carbon nanotubes during adsorption are generally incapable of predicting correctly the changes in the effective dielectric constant of the carbon nanotubes. Conversely, the use of adsorption-induced changes in the band gap of the carbon nanotubes and a relationship between the band gap and the dielectric constant is found to be a promising approach for assessing the adsorption-induced changes in the effective dielectric constant of the carbon nanotubes and for establishment of their effect on the resonant frequency of resonator-based chemical gas sensors

  3. A comparative analysis of soft computing techniques for gene prediction.

    Science.gov (United States)

    Goel, Neelam; Singh, Shailendra; Aseri, Trilok Chand

    2013-07-01

    The rapid growth of genomic sequence data for both human and nonhuman species has made analyzing these sequences, especially predicting genes in them, very important and is currently the focus of many research efforts. Beside its scientific interest in the molecular biology and genomics community, gene prediction is of considerable importance in human health and medicine. A variety of gene prediction techniques have been developed for eukaryotes over the past few years. This article reviews and analyzes the application of certain soft computing techniques in gene prediction. First, the problem of gene prediction and its challenges are described. These are followed by different soft computing techniques along with their application to gene prediction. In addition, a comparative analysis of different soft computing techniques for gene prediction is given. Finally some limitations of the current research activities and future research directions are provided. Copyright © 2013 Elsevier Inc. All rights reserved.

  4. Serial analysis of gene expression (SAGE) in rat liver regeneration

    International Nuclear Information System (INIS)

    Cimica, Velasco; Batusic, Danko; Haralanova-Ilieva, Borislava; Chen, Yonglong; Hollemann, Thomas; Pieler, Tomas; Ramadori, Giuliano

    2007-01-01

    We have applied serial analysis of gene expression for studying the molecular mechanism of the rat liver regeneration in the model of 70% partial hepatectomy. We generated three SAGE libraries from a normal control liver (NL library: 52,343 tags), from a sham control operated liver (Sham library: 51,028 tags), and from a regenerating liver (PH library: 53,061 tags). By SAGE bioinformatics analysis we identified 40 induced genes and 20 repressed genes during the liver regeneration. We verified temporal expression of such genes by real time PCR during the regeneration process and we characterized 13 induced genes and 3 repressed genes. We found connective tissue growth factor transcript and protein induced very early at 4 h after PH operation before hepatocytes proliferation is triggered. Our study suggests CTGF as a growth factor signaling mediator that could be involved directly in the mechanism of liver regeneration induction

  5. Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids.

    Science.gov (United States)

    Jiang, Jinjin; Wang, Yue; Zhu, Bao; Fang, Tingting; Fang, Yujie; Wang, Youping

    2015-01-27

    Brassica includes many successfully cultivated crop species of polyploid origin, either by ancestral genome triplication or by hybridization between two diploid progenitors, displaying complex repetitive sequences and transposons. The U's triangle, which consists of three diploids and three amphidiploids, is optimal for the analysis of complicated genomes after polyploidization. Next-generation sequencing enables the transcriptome profiling of polyploids on a global scale. We examined the gene expression patterns of three diploids (Brassica rapa, B. nigra, and B. oleracea) and three amphidiploids (B. napus, B. juncea, and B. carinata) via digital gene expression analysis. In total, the libraries generated between 5.7 and 6.1 million raw reads, and the clean tags of each library were mapped to 18547-21995 genes of B. rapa genome. The unambiguous tag-mapped genes in the libraries were compared. Moreover, the majority of differentially expressed genes (DEGs) were explored among diploids as well as between diploids and amphidiploids. Gene ontological analysis was performed to functionally categorize these DEGs into different classes. The Kyoto Encyclopedia of Genes and Genomes analysis was performed to assign these DEGs into approximately 120 pathways, among which the metabolic pathway, biosynthesis of secondary metabolites, and peroxisomal pathway were enriched. The non-additive genes in Brassica amphidiploids were analyzed, and the results indicated that orthologous genes in polyploids are frequently expressed in a non-additive pattern. Methyltransferase genes showed differential expression pattern in Brassica species. Our results provided an understanding of the transcriptome complexity of natural Brassica species. The gene expression changes in diploids and allopolyploids may help elucidate the morphological and physiological differences among Brassica species.

  6. Synchronisation, electronic circuit implementation, and fractional-order analysis of 5D ordinary differential equations with hidden hyperchaotic attractors

    Science.gov (United States)

    Wei, Zhouchao; Rajagopal, Karthikeyan; Zhang, Wei; Kingni, Sifeu Takougang; Akgül, Akif

    2018-04-01

    Hidden hyperchaotic attractors can be generated with three positive Lyapunov exponents in the proposed 5D hyperchaotic Burke-Shaw system with only one stable equilibrium. To the best of our knowledge, this feature has rarely been previously reported in any other higher-dimensional systems. Unidirectional linear error feedback coupling scheme is used to achieve hyperchaos synchronisation, which will be estimated by using two indicators: the normalised average root-mean squared synchronisation error and the maximum cross-correlation coefficient. The 5D hyperchaotic system has been simulated using a specially designed electronic circuit and viewed on an oscilloscope, thereby confirming the results of the numerical integration. In addition, fractional-order hidden hyperchaotic system will be considered from the following three aspects: stability, bifurcation analysis and FPGA implementation. Such implementations in real time represent hidden hyperchaotic attractors with important consequences for engineering applications.

  7. Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus

    Science.gov (United States)

    Repin, Rul Aisyah Mat; Mutalib, Sahilah Abdul; Shahimi, Safiyyah; Khalid, Rozida Mohd.; Ayob, Mohd. Khan; Bakar, Mohd. Faizal Abu; Isa, Mohd Noor Mat

    2016-11-01

    In this study, we performed bioinformatics analysis toward genome sequence of Lysinibacillussphaericus (L. sphaericus) to determine gene encoded for gelatinase. L. sphaericus was isolated from soil and gelatinase species-specific bacterium to porcine and bovine gelatin. This bacterium offers the possibility of enzymes production which is specific to both species of meat, respectively. The main focus of this research is to identify the gelatinase encoded gene within the bacteria of L. Sphaericus using bioinformatics analysis of partially sequence genome. From the research study, three candidate gene were identified which was, gelatinase candidate gene 1 (P1), NODE_71_length_93919_cov_158.931839_21 which containing 1563 base pair (bp) in size with 520 amino acids sequence; Secondly, gelatinase candidate gene 2 (P2), NODE_23_length_52851_cov_190.061386_17 which containing 1776 bp in size with 591 amino acids sequence; and Thirdly, gelatinase candidate gene 3 (P3), NODE_106_length_32943_cov_169.147919_8 containing 1701 bp in size with 566 amino acids sequence. Three pairs of oligonucleotide primers were designed and namely as, F1, R1, F2, R2, F3 and R3 were targeted short sequences of cDNA by PCR. The amplicons were reliably results in 1563 bp in size for candidate gene P1 and 1701 bp in size for candidate gene P3. Therefore, the results of bioinformatics analysis of L. Sphaericus resulting in gene encoded gelatinase were identified.

  8. Gastric Cancer Associated Genes Identified by an Integrative Analysis of Gene Expression Data

    Directory of Open Access Journals (Sweden)

    Bing Jiang

    2017-01-01

    Full Text Available Gastric cancer is one of the most severe complex diseases with high morbidity and mortality in the world. The molecular mechanisms and risk factors for this disease are still not clear since the cancer heterogeneity caused by different genetic and environmental factors. With more and more expression data accumulated nowadays, we can perform integrative analysis for these data to understand the complexity of gastric cancer and to identify consensus players for the heterogeneous cancer. In the present work, we screened the published gene expression data and analyzed them with integrative tool, combined with pathway and gene ontology enrichment investigation. We identified several consensus differentially expressed genes and these genes were further confirmed with literature mining; at last, two genes, that is, immunoglobulin J chain and C-X-C motif chemokine ligand 17, were screened as novel gastric cancer associated genes. Experimental validation is proposed to further confirm this finding.

  9. A comparative study of three different gene expression analysis methods.

    Science.gov (United States)

    Choe, Jae Young; Han, Hyung Soo; Lee, Seon Duk; Lee, Hanna; Lee, Dong Eun; Ahn, Jae Yun; Ryoo, Hyun Wook; Seo, Kang Suk; Kim, Jong Kun

    2017-12-04

    TNF-α regulates immune cells and acts as an endogenous pyrogen. Reverse transcription polymerase chain reaction (RT-PCR) is one of the most commonly used methods for gene expression analysis. Among the alternatives to PCR, loop-mediated isothermal amplification (LAMP) shows good potential in terms of specificity and sensitivity. However, few studies have compared RT-PCR and LAMP for human gene expression analysis. Therefore, in the present study, we compared one-step RT-PCR, two-step RT-LAMP and one-step RT-LAMP for human gene expression analysis. We compared three gene expression analysis methods using the human TNF-α gene as a biomarker from peripheral blood cells. Total RNA from the three selected febrile patients were subjected to the three different methods of gene expression analysis. In the comparison of three gene expression analysis methods, the detection limit of both one-step RT-PCR and one-step RT-LAMP were the same, while that of two-step RT-LAMP was inferior. One-step RT-LAMP takes less time, and the experimental result is easy to determine. One-step RT-LAMP is a potentially useful and complementary tool that is fast and reasonably sensitive. In addition, one-step RT-LAMP could be useful in environments lacking specialized equipment or expertise.

  10. An Integrated Circuit for Chip-Based Analysis of Enzyme Kinetics and Metabolite Quantification.

    Science.gov (United States)

    Cheah, Boon Chong; Macdonald, Alasdair Iain; Martin, Christopher; Streklas, Angelos J; Campbell, Gordon; Al-Rawhani, Mohammed A; Nemeth, Balazs; Grant, James P; Barrett, Michael P; Cumming, David R S

    2016-06-01

    We have created a novel chip-based diagnostic tools based upon quantification of metabolites using enzymes specific for their chemical conversion. Using this device we show for the first time that a solid-state circuit can be used to measure enzyme kinetics and calculate the Michaelis-Menten constant. Substrate concentration dependency of enzyme reaction rates is central to this aim. Ion-sensitive field effect transistors (ISFET) are excellent transducers for biosensing applications that are reliant upon enzyme assays, especially since they can be fabricated using mainstream microelectronics technology to ensure low unit cost, mass-manufacture, scaling to make many sensors and straightforward miniaturisation for use in point-of-care devices. Here, we describe an integrated ISFET array comprising 2(16) sensors. The device was fabricated with a complementary metal oxide semiconductor (CMOS) process. Unlike traditional CMOS ISFET sensors that use the Si3N4 passivation of the foundry for ion detection, the device reported here was processed with a layer of Ta2O5 that increased the detection sensitivity to 45 mV/pH unit at the sensor readout. The drift was reduced to 0.8 mV/hour with a linear pH response between pH 2-12. A high-speed instrumentation system capable of acquiring nearly 500 fps was developed to stream out the data. The device was then used to measure glucose concentration through the activity of hexokinase in the range of 0.05 mM-231 mM, encompassing glucose's physiological range in blood. Localised and temporal enzyme kinetics of hexokinase was studied in detail. These results present a roadmap towards a viable personal metabolome machine.

  11. Shrinkage Approach for Gene Expression Data Analysis

    Czech Academy of Sciences Publication Activity Database

    Haman, Jiří; Valenta, Zdeněk; Kalina, Jan

    2013-01-01

    Roč. 1, č. 1 (2013), s. 65-65 ISSN 1805-8698. [EFMI 2013 Special Topic Conference. 17.04.2013-19.04.2013, Prague] Institutional support: RVO:67985807 Keywords : shrinkage estimation * covariance matrix * high dimensional data * gene expression Subject RIV: IN - Informatics, Computer Science

  12. GenePublisher: automated analysis of DNA microarray data

    DEFF Research Database (Denmark)

    Knudsen, Steen; Workman, Christopher; Sicheritz-Ponten, T.

    2003-01-01

    GenePublisher, a system for automatic analysis of data from DNA microarray experiments, has been implemented with a web interface at http://www.cbs.dtu.dk/services/GenePublisher. Raw data are uploaded to the server together with aspecification of the data. The server performs normalization...

  13. Genomewide identification and expression analysis of the ARF gene ...

    Indian Academy of Sciences (India)

    Figure 1. Phylogenetic relation of apple ARF genes. The phylogenetic tree was constructed based on a complete protein sequence align- ment of MdARFs by the neighbour-joining method with bootstrapping analysis (1000 replicates). The scale bar represents 0.05 amino acid substitutions per site. Paralogous gene pairs ...

  14. Microarray analysis of the gene expression profile in triethylene ...

    African Journals Online (AJOL)

    Microarray analysis of the gene expression profile in triethylene glycol dimethacrylate-treated human dental pulp cells. ... Conclusions: Our results suggest that TEGDMA can change the many functions of hDPCs through large changes in gene expression levels and complex interactions with different signaling pathways.

  15. Validation of suitable reference genes for quantitative gene expression analysis in Panax ginseng

    Directory of Open Access Journals (Sweden)

    Meizhen eWang

    2016-01-01

    Full Text Available Reverse transcription-qPCR (RT-qPCR has become a popular method for gene expression studies. Its results require data normalization by housekeeping genes. No single gene is proved to be stably expressed under all experimental conditions. Therefore, systematic evaluation of reference genes is necessary. With the aim to identify optimum reference genes for RT-qPCR analysis of gene expression in different tissues of Panax ginseng and the seedlings grown under heat stress, we investigated the expression stability of eight candidate reference genes, including elongation factor 1-beta (EF1-β, elongation factor 1-gamma (EF1-γ, eukaryotic translation initiation factor 3G (IF3G, eukaryotic translation initiation factor 3B (IF3B, actin (ACT, actin11 (ACT11, glyceraldehyde-3-phosphate dehydrogenase (GAPDH and cyclophilin ABH-like protein (CYC, using four widely used computational programs: geNorm, Normfinder, BestKeeper, and the comparative ΔCt method. The results were then integrated using the web-based tool RefFinder. As a result, EF1-γ, IF3G and EF1-β were the three most stable genes in different tissues of P. ginseng, while IF3G, ACT11 and GAPDH were the top three-ranked genes in seedlings treated with heat. Using three better reference genes alone or in combination as internal control, we examined the expression profiles of MAR, a multiple function-associated mRNA-like non-coding RNA (mlncRNA in P. ginseng. Taken together, we recommended EF1-γ/IF3G and IF3G/ACT11 as the suitable pair of reference genes for RT-qPCR analysis of gene expression in different tissues of P. ginseng and the seedlings grown under heat stress, respectively. The results serve as a foundation for future studies on P. ginseng functional genomics.

  16. In silico analysis of miRNA-mediated gene regulation in OCA and OA genes.

    Science.gov (United States)

    Kamaraj, Balu; Gopalakrishnan, Chandrasekhar; Purohit, Rituraj

    2014-12-01

    Albinism is an autosomal recessive genetic disorder due to low secretion of melanin. The oculocutaneous albinism (OCA) and ocular albinism (OA) genes are responsible for melanin production and also act as a potential targets for miRNAs. The role of miRNA is to inhibit the protein synthesis partially or completely by binding with the 3'UTR of the mRNA thus regulating gene expression. In this analysis, we predicted the genetic variation that occurred in 3'UTR of the transcript which can be a reason for low melanin production thus causing albinism. The single nucleotide polymorphisms (SNPs) in 3'UTR cause more new binding sites for miRNA which binds with mRNA which leads to inhibit the translation process either partially or completely. The SNPs in the mRNA of OCA and OA genes can create new binding sites for miRNA which may control the gene expression and lead to hypopigmentation. We have developed a computational procedure to determine the SNPs in the 3'UTR region of mRNA of OCA (TYR, OCA2, TYRP1 and SLC45A2) and OA (GPR143) genes which will be a potential cause for albinism. We identified 37 SNPs in five genes that are predicted to create 87 new binding sites on mRNA, which may lead to abrogation of the translation process. Expression analysis confirms that these genes are highly expressed in skin and eye regions. It is well supported by enrichment analysis that these genes are mainly involved in eye pigmentation and melanin biosynthesis process. The network analysis also shows how the genes are interacting and expressing in a complex network. This insight provides clue to wet-lab researches to understand the expression pattern of OCA and OA genes and binding phenomenon of mRNA and miRNA upon mutation, which is responsible for inhibition of translation process at genomic levels.

  17. The primary circuit materials properties results analysis performed on archive material used in NPP V-1 and Kola NPP Units 1 and 2

    Energy Technology Data Exchange (ETDEWEB)

    Kupca, L.; Beno, P. [Nuclear Power Plants Research Institute Inc., Trnava (Slovakia)

    1997-04-01

    A very brief summary is provided of a primary circuit piping material properties analysis. The analysis was performed for the Bohunice V-1 reactor and the Kola-1 and -2 reactors. Assessment was performed on Bohunice V-1 archive materials and primary piping material cut from the Kola units after 100,000 hours of operation. Main research program tasks included analysis of mechanical properties, corrosion stability, and microstructural properties. Analysis results are not provided.

  18. Gene set analysis of the EADGENE chicken data-set

    DEFF Research Database (Denmark)

    Skarman, Axel; Jiang, Li; Hornshøj, Henrik

    2009-01-01

     Abstract Background: Gene set analysis is considered to be a way of improving our biological interpretation of the observed expression patterns. This paper describes different methods applied to analyse expression data from a chicken DNA microarray dataset. Results: Applying different gene set...... analyses to the chicken expression data led to different ranking of the Gene Ontology terms tested. A method for prediction of possible annotations was applied. Conclusion: Biological interpretation based on gene set analyses dependent on the statistical method used. Methods for predicting the possible...

  19. Dynamic association rules for gene expression data analysis.

    Science.gov (United States)

    Chen, Shu-Chuan; Tsai, Tsung-Hsien; Chung, Cheng-Han; Li, Wen-Hsiung

    2015-10-14

    The purpose of gene expression analysis is to look for the association between regulation of gene expression levels and phenotypic variations. This association based on gene expression profile has been used to determine whether the induction/repression of genes correspond to phenotypic variations including cell regulations, clinical diagnoses and drug development. Statistical analyses on microarray data have been developed to resolve gene selection issue. However, these methods do not inform us of causality between genes and phenotypes. In this paper, we propose the dynamic association rule algorithm (DAR algorithm) which helps ones to efficiently select a subset of significant genes for subsequent analysis. The DAR algorithm is based on association rules from market basket analysis in marketing. We first propose a statistical way, based on constructing a one-sided confidence interval and hypothesis testing, to determine if an association rule is meaningful. Based on the proposed statistical method, we then developed the DAR algorithm for gene expression data analysis. The method was applied to analyze four microarray datasets and one Next Generation Sequencing (NGS) dataset: the Mice Apo A1 dataset, the whole genome expression dataset of mouse embryonic stem cells, expression profiling of the bone marrow of Leukemia patients, Microarray Quality Control (MAQC) data set and the RNA-seq dataset of a mouse genomic imprinting study. A comparison of the proposed method with the t-test on the expression profiling of the bone marrow of Leukemia patients was conducted. We developed a statistical way, based on the concept of confidence interval, to determine the minimum support and minimum confidence for mining association relationships among items. With the minimum support and minimum confidence, one can find significant rules in one single step. The DAR algorithm was then developed for gene expression data analysis. Four gene expression datasets showed that the proposed

  20. Effectiveness of Circuit-Based Exercises on Gait Speed, Balance, and Functional Mobility in People Affected by Stroke: A Meta-Analysis.

    Science.gov (United States)

    Bonini-Rocha, Ana Clara; de Andrade, Anderson Lúcio Souza; Moraes, André Marques; Gomide Matheus, Liana Barbaresco; Diniz, Leonardo Rios; Martins, Wagner Rodrigues

    2018-04-01

    Several interventions have been proposed to rehabilitate patients with neurologic dysfunctions due to stroke. However, the effectiveness of circuit-based exercises according to its actual definition, ie, an overall program to improve strength, stamina, balance or functioning, was not provided. To examine the effectiveness of circuit-based exercise in the treatment of people affected by stroke. A search through PubMed, Embase, Cochrane Library, and Physiotherapy Evidence Database databases was performed to identify controlled clinical trials without language or date restriction. The overall mean difference with 95% confidence interval was calculated for all outcomes. Two independent reviewers assessed the risk of bias. Eleven studies met the inclusion criteria, and 8 presented suitable data to perform a meta-analysis. Quantitative analysis showed that circuit-based exercise was more effective than conventional intervention on gait speed (mean difference of 0.11 m/s) and circuit-based exercise was not significantly more effective than conventional intervention on balance and functional mobility. Our results demonstrated that circuit-based exercise presents better effects on gait when compared with conventional intervention and that its effects on balance and functional mobility were not better than conventional interventions. I. Copyright © 2018 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

  1. Model-based gene set analysis for Bioconductor.

    Science.gov (United States)

    Bauer, Sebastian; Robinson, Peter N; Gagneur, Julien

    2011-07-01

    Gene Ontology and other forms of gene-category analysis play a major role in the evaluation of high-throughput experiments in molecular biology. Single-category enrichment analysis procedures such as Fisher's exact test tend to flag large numbers of redundant categories as significant, which can complicate interpretation. We have recently developed an approach called model-based gene set analysis (MGSA), that substantially reduces the number of redundant categories returned by the gene-category analysis. In this work, we present the Bioconductor package mgsa, which makes the MGSA algorithm available to users of the R language. Our package provides a simple and flexible application programming interface for applying the approach. The mgsa package has been made available as part of Bioconductor 2.8. It is released under the conditions of the Artistic license 2.0. peter.robinson@charite.de; julien.gagneur@embl.de.

  2. Long SAGE analysis of genes differentially expressed in the midgut ...

    African Journals Online (AJOL)

    Long SAGE analysis of genes differentially expressed in the midgut and silk gland between the sexes of the silkwormBombyx mori. Liping Gan, Ying Wang, Jian Xi, Yanshan Niu, Hongyou Qin, Yanghu Sima, Shiqing Xu ...

  3. Genome-Wide Detection and Analysis of Multifunctional Genes

    Science.gov (United States)

    Pritykin, Yuri; Ghersi, Dario; Singh, Mona

    2015-01-01

    Many genes can play a role in multiple biological processes or molecular functions. Identifying multifunctional genes at the genome-wide level and studying their properties can shed light upon the complexity of molecular events that underpin cellular functioning, thereby leading to a better understanding of the functional landscape of the cell. However, to date, genome-wide analysis of multifunctional genes (and the proteins they encode) has been limited. Here we introduce a computational approach that uses known functional annotations to extract genes playing a role in at least two distinct biological processes. We leverage functional genomics data sets for three organisms—H. sapiens, D. melanogaster, and S. cerevisiae—and show that, as compared to other annotated genes, genes involved in multiple biological processes possess distinct physicochemical properties, are more broadly expressed, tend to be more central in protein interaction networks, tend to be more evolutionarily conserved, and are more likely to be essential. We also find that multifunctional genes are significantly more likely to be involved in human disorders. These same features also hold when multifunctionality is defined with respect to molecular functions instead of biological processes. Our analysis uncovers key features about multifunctional genes, and is a step towards a better genome-wide understanding of gene multifunctionality. PMID:26436655

  4. The voltage—current relationship and equivalent circuit implementation of parallel flux-controlled memristive circuits

    International Nuclear Information System (INIS)

    Bao Bo-Cheng; Feng Fei; Dong Wei; Pan Sai-Hu

    2013-01-01

    A flux-controlled memristor characterized by smooth cubic nonlinearity is taken as an example, upon which the voltage—current relationships (VCRs) between two parallel memristive circuits — a parallel memristor and capacitor circuit (the parallel MC circuit), and a parallel memristor and inductor circuit (the parallel ML circuit) — are investigated. The results indicate that the VCR between these two parallel memristive circuits is closely related to the circuit parameters, and the frequency and amplitude of the sinusoidal voltage stimulus. An equivalent circuit model of the memristor is built, upon which the circuit simulations and experimental measurements of both the parallel MC circuit and the parallel ML circuit are performed, and the results verify the theoretical analysis results

  5. A Magnetic Circuit Demonstration.

    Science.gov (United States)

    Vanderkooy, John; Lowe, June

    1995-01-01

    Presents a demonstration designed to illustrate Faraday's, Ampere's, and Lenz's laws and to reinforce the concepts through the analysis of a two-loop magnetic circuit. Can be made dramatic and challenging for sophisticated students but is suitable for an introductory course in electricity and magnetism. (JRH)

  6. Circuit design for reliability

    CERN Document Server

    Cao, Yu; Wirth, Gilson

    2015-01-01

    This book presents physical understanding, modeling and simulation, on-chip characterization, layout solutions, and design techniques that are effective to enhance the reliability of various circuit units.  The authors provide readers with techniques for state of the art and future technologies, ranging from technology modeling, fault detection and analysis, circuit hardening, and reliability management. Provides comprehensive review on various reliability mechanisms at sub-45nm nodes; Describes practical modeling and characterization techniques for reliability; Includes thorough presentation of robust design techniques for major VLSI design units; Promotes physical understanding with first-principle simulations.

  7. Global gene expression analysis for evaluation and design of biomaterials

    Directory of Open Access Journals (Sweden)

    Nobutaka Hanagata, Taro Takemura and Takashi Minowa

    2010-01-01

    Full Text Available Comprehensive gene expression analysis using DNA microarrays has become a widespread technique in molecular biological research. In the biomaterials field, it is used to evaluate the biocompatibility or cellular toxicity of metals, polymers and ceramics. Studies in this field have extracted differentially expressed genes in the context of differences in cellular responses among multiple materials. Based on these genes, the effects of materials on cells at the molecular level have been examined. Expression data ranging from several to tens of thousands of genes can be obtained from DNA microarrays. For this reason, several tens or hundreds of differentially expressed genes are often present in different materials. In this review, we outline the principles of DNA microarrays, and provide an introduction to methods of extracting information which is useful for evaluating and designing biomaterials from comprehensive gene expression data.

  8. Global gene expression analysis for evaluation and design of biomaterials

    International Nuclear Information System (INIS)

    Hanagata, Nobutaka; Takemura, Taro; Minowa, Takashi

    2010-01-01

    Comprehensive gene expression analysis using DNA microarrays has become a widespread technique in molecular biological research. In the biomaterials field, it is used to evaluate the biocompatibility or cellular toxicity of metals, polymers and ceramics. Studies in this field have extracted differentially expressed genes in the context of differences in cellular responses among multiple materials. Based on these genes, the effects of materials on cells at the molecular level have been examined. Expression data ranging from several to tens of thousands of genes can be obtained from DNA microarrays. For this reason, several tens or hundreds of differentially expressed genes are often present in different materials. In this review, we outline the principles of DNA microarrays, and provide an introduction to methods of extracting information which is useful for evaluating and designing biomaterials from comprehensive gene expression data. (topical review)

  9. Gene expression profiling of resting and activated vascular smooth muscle cells by serial analysis of gene expression and clustering analysis

    NARCIS (Netherlands)

    Beauchamp, Nicholas J.; van Achterberg, Tanja A. E.; Engelse, Marten A.; Pannekoek, Hans; de Vries, Carlie J. M.

    2003-01-01

    Migration and proliferation of vascular smooth muscle cells (SMCs) are key events in atherosclerosis. However, little is known about alterations in gene expression upon transition of the quiescent, contractile SMC to the proliferative SMC. We performed serial analysis of gene expression (SAGE) of

  10. Microarray gene expression profiling and analysis in renal cell carcinoma

    Directory of Open Access Journals (Sweden)

    Sadhukhan Provash

    2004-06-01

    Full Text Available Abstract Background Renal cell carcinoma (RCC is the most common cancer in adult kidney. The accuracy of current diagnosis and prognosis of the disease and the effectiveness of the treatment for the disease are limited by the poor understanding of the disease at the molecular level. To better understand the genetics and biology of RCC, we profiled the expression of 7,129 genes in both clear cell RCC tissue and cell lines using oligonucleotide arrays. Methods Total RNAs isolated from renal cell tumors, adjacent normal tissue and metastatic RCC cell lines were hybridized to affymatrix HuFL oligonucleotide arrays. Genes were categorized into different functional groups based on the description of the Gene Ontology Consortium and analyzed based on the gene expression levels. Gene expression profiles of the tissue and cell line samples were visualized and classified by singular value decomposition. Reverse transcription polymerase chain reaction was performed to confirm the expression alterations of selected genes in RCC. Results Selected genes were annotated based on biological processes and clustered into functional groups. The expression levels of genes in each group were also analyzed. Seventy-four commonly differentially expressed genes with more than five-fold changes in RCC tissues were identified. The expression alterations of selected genes from these seventy-four genes were further verified using reverse transcription polymerase chain reaction (RT-PCR. Detailed comparison of gene expression patterns in RCC tissue and RCC cell lines shows significant differences between the two types of samples, but many important expression patterns were preserved. Conclusions This is one of the initial studies that examine the functional ontology of a large number of genes in RCC. Extensive annotation, clustering and analysis of a large number of genes based on the gene functional ontology revealed many interesting gene expression patterns in RCC. Most

  11. GSMA: Gene Set Matrix Analysis, An Automated Method for Rapid Hypothesis Testing of Gene Expression Data

    Directory of Open Access Journals (Sweden)

    Chris Cheadle

    2007-01-01

    Full Text Available Background: Microarray technology has become highly valuable for identifying complex global changes in gene expression patterns. The assignment of functional information to these complex patterns remains a challenging task in effectively interpreting data and correlating results from across experiments, projects and laboratories. Methods which allow the rapid and robust evaluation of multiple functional hypotheses increase the power of individual researchers to data mine gene expression data more efficiently.Results: We have developed (gene set matrix analysis GSMA as a useful method for the rapid testing of group-wise up- or downregulation of gene expression simultaneously for multiple lists of genes (gene sets against entire distributions of gene expression changes (datasets for single or multiple experiments. The utility of GSMA lies in its flexibility to rapidly poll gene sets related by known biological function or as designated solely by the end-user against large numbers of datasets simultaneously.Conclusions: GSMA provides a simple and straightforward method for hypothesis testing in which genes are tested by groups across multiple datasets for patterns of expression enrichment.

  12. In Silico Analysis of FMR1 Gene Missense SNPs.

    Science.gov (United States)

    Tekcan, Akin

    2016-06-01

    The FMR1 gene, a member of the fragile X-related gene family, is responsible for fragile X syndrome (FXS). Missense single-nucleotide polymorphisms (SNPs) are responsible for many complex diseases. The effect of FMR1 gene missense SNPs is unknown. The aim of this study, using in silico techniques, was to analyze all known missense mutations that can affect the functionality of the FMR1 gene, leading to mental retardation (MR) and FXS. Data on the human FMR1 gene were collected from the Ensembl database (release 81), National Centre for Biological Information dbSNP Short Genetic Variations database, 1000 Genomes Browser, and NHLBI Exome Sequencing Project Exome Variant Server. In silico analysis was then performed. One hundred-twenty different missense SNPs of the FMR1 gene were determined. Of these, 11.66 % of the FMR1 gene missense SNPs were in highly conserved domains, and 83.33 % were in domains with high variety. The results of the in silico prediction analysis showed that 31.66 % of the FMR1 gene SNPs were disease related and that 50 % of SNPs had a pathogenic effect. The results of the structural and functional analysis revealed that although the R138Q mutation did not seem to have a damaging effect on the protein, the G266E and I304N SNPs appeared to disturb the interaction between the domains and affect the function of the protein. This is the first study to analyze all missense SNPs of the FMR1 gene. The results indicate the applicability of a bioinformatics approach to FXS and other FMR1-related diseases. I think that the analysis of FMR1 gene missense SNPs using bioinformatics methods would help diagnosis of FXS and other FMR1-related diseases.

  13. Robust dynamical pattern formation from a multifunctional minimal genetic circuit

    Directory of Open Access Journals (Sweden)

    Carrera Javier

    2010-04-01

    Full Text Available Abstract Background A practical problem during the analysis of natural networks is their complexity, thus the use of synthetic circuits would allow to unveil the natural mechanisms of operation. Autocatalytic gene regulatory networks play an important role in shaping the development of multicellular organisms, whereas oscillatory circuits are used to control gene expression under variable environments such as the light-dark cycle. Results We propose a new mechanism to generate developmental patterns and oscillations using a minimal number of genes. For this, we design a synthetic gene circuit with an antagonistic self-regulation to study the spatio-temporal control of protein expression. Here, we show that our minimal system can behave as a biological clock or memory, and it exhibites an inherent robustness due to a quorum sensing mechanism. We analyze this property by accounting for molecular noise in an heterogeneous population. We also show how the period of the oscillations is tunable by environmental signals, and we study the bifurcations of the system by constructing different phase diagrams. Conclusions As this minimal circuit is based on a single transcriptional unit, it provides a new mechanism based on post-translational interactions to generate targeted spatio-temporal behavior.

  14. Transient Thermal Analysis of 3-D Integrated Circuits Packages by the DGTD Method

    KAUST Repository

    Li, Ping; Dong, Yilin; Tang, Min; Mao, Junfa; Jiang, Li Jun; Bagci, Hakan

    2017-01-01

    Since accurate thermal analysis plays a critical role in the thermal design and management of the 3-D system-level integration, in this paper, a discontinuous Galerkin time-domain (DGTD) algorithm is proposed to achieve this purpose

  15. Computer circuit analysis of induced currents in the MFTF-B magnet system

    International Nuclear Information System (INIS)

    Magnuson, G.D.; Woods, E.L.

    1981-01-01

    An analysis was made of the induced current behavior of the MFTF-B magnet system. Although the magnet system consists of 22 coils, because of its symmetry we considered only 11 coils in the analysis. Various combinations of the coils were dumped either singly or in groups, with the current behavior in all magnets calculated as a function of time after initiation of the dump

  16. Statistical analysis of error rate of large-scale single flux quantum logic circuit by considering fluctuation of timing parameters

    International Nuclear Information System (INIS)

    Yamanashi, Yuki; Masubuchi, Kota; Yoshikawa, Nobuyuki

    2016-01-01

    The relationship between the timing margin and the error rate of the large-scale single flux quantum logic circuits is quantitatively investigated to establish a timing design guideline. We observed that the fluctuation in the set-up/hold time of single flux quantum logic gates caused by thermal noises is the most probable origin of the logical error of the large-scale single flux quantum circuit. The appropriate timing margin for stable operation of the large-scale logic circuit is discussed by taking the fluctuation of setup/hold time and the timing jitter in the single flux quantum circuits. As a case study, the dependence of the error rate of the 1-million-bit single flux quantum shift register on the timing margin is statistically analyzed. The result indicates that adjustment of timing margin and the bias voltage is important for stable operation of a large-scale SFQ logic circuit.

  17. Statistical analysis of error rate of large-scale single flux quantum logic circuit by considering fluctuation of timing parameters

    Energy Technology Data Exchange (ETDEWEB)

    Yamanashi, Yuki, E-mail: yamanasi@ynu.ac.jp [Department of Electrical and Computer Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama 240-8501 (Japan); Masubuchi, Kota; Yoshikawa, Nobuyuki [Department of Electrical and Computer Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama 240-8501 (Japan)

    2016-11-15

    The relationship between the timing margin and the error rate of the large-scale single flux quantum logic circuits is quantitatively investigated to establish a timing design guideline. We observed that the fluctuation in the set-up/hold time of single flux quantum logic gates caused by thermal noises is the most probable origin of the logical error of the large-scale single flux quantum circuit. The appropriate timing margin for stable operation of the large-scale logic circuit is discussed by taking the fluctuation of setup/hold time and the timing jitter in the single flux quantum circuits. As a case study, the dependence of the error rate of the 1-million-bit single flux quantum shift register on the timing margin is statistically analyzed. The result indicates that adjustment of timing margin and the bias voltage is important for stable operation of a large-scale SFQ logic circuit.

  18. Gene profile analysis of osteoblast genes differentially regulated by histone deacetylase inhibitors

    Directory of Open Access Journals (Sweden)

    Lamblin Anne-Francoise

    2007-10-01

    Full Text Available Abstract Background Osteoblast differentiation requires the coordinated stepwise expression of multiple genes. Histone deacetylase inhibitors (HDIs accelerate the osteoblast differentiation process by blocking the activity of histone deacetylases (HDACs, which alter gene expression by modifying chromatin structure. We previously demonstrated that HDIs and HDAC3 shRNAs accelerate matrix mineralization and the expression of osteoblast maturation genes (e.g. alkaline phosphatase, osteocalcin. Identifying other genes that are differentially regulated by HDIs might identify new pathways that contribute to osteoblast differentiation. Results To identify other osteoblast genes that are altered early by HDIs, we incubated MC3T3-E1 preosteoblasts with HDIs (trichostatin A, MS-275, or valproic acid for 18 hours in osteogenic conditions. The promotion of osteoblast differentiation by HDIs in this experiment was confirmed by osteogenic assays. Gene expression profiles relative to vehicle-treated cells were assessed by microarray analysis with Affymetrix GeneChip 430 2.0 arrays. The regulation of several genes by HDIs in MC3T3-E1 cells and primary osteoblasts was verified by quantitative real-time PCR. Nine genes were differentially regulated by at least two-fold after exposure to each of the three HDIs and six were verified by PCR in osteoblasts. Four of the verified genes (solute carrier family 9 isoform 3 regulator 1 (Slc9a3r1, sorbitol dehydrogenase 1, a kinase anchor protein, and glutathione S-transferase alpha 4 were induced. Two genes (proteasome subunit, beta type 10 and adaptor-related protein complex AP-4 sigma 1 were suppressed. We also identified eight growth factors and growth factor receptor genes that are significantly altered by each of the HDIs, including Frizzled related proteins 1 and 4, which modulate the Wnt signaling pathway. Conclusion This study identifies osteoblast genes that are regulated early by HDIs and indicates pathways that

  19. Structural analysis and incipient failure detection of primary circuit components based on correlation-analysis and finite-element models

    International Nuclear Information System (INIS)

    Olma, B.J.

    1977-01-01

    A method is presented to compute vibrational power spectral densities (VPSD's) of primary circuit components based on a finite-element representation of the primary circuit. First this method has been applied to the sodium cooled reactor KNK, Karlsruhe. Now a further application is being developed for a BWR-nuclear power plant. The experimentally determined VPSD's can be considered as the output of a multiple input-output system. They have to be explained as the frequency response of a multidimensional mechanical system, which is excited by stochastic and deterministic mechanical driving forces. The stochastic mechanical forces are generated by the dynamic pressure fluctuations of the fluid. The deterministic mechanical forces are caused by the pressure fluctuations, which are induced by the main coolant pumps or by standing waves. The excitation matrix can be obtained from measured pressure fluctuations. The vibration transfer function matrix can be computed from the mass matrix, damping matrix and stiffness matrix of a theoretical finite-element model or mass-spring model. Based on this theory the computer code 'STAMPO' has been established. This program has been applied to the KNK reactor. The excitation matrix was created from measured jet-noise pressure fluctuations. The mass-, stiffness- and damping matrix has been extracted from a SAP-IV-model of the primary system. Sequentially for each frequency point the complete VPSD matrix has been computed. The diagonal elements of this matrix represent the vibrational auto-power spectral densities, the off-diagonal elements represent the vibrational cross-power spectral densities. The calculations give good agreement with measured VPSD's. The comparison shows that the measured jet-noise pressure fluctuations act nearly uncorrelated on the structure, whereas the output VPSD's are well correlated

  20. Gene Ontology-Based Analysis of Zebrafish Omics Data Using the Web Tool Comparative Gene Ontology.

    Science.gov (United States)

    Ebrahimie, Esmaeil; Fruzangohar, Mario; Moussavi Nik, Seyyed Hani; Newman, Morgan

    2017-10-01

    Gene Ontology (GO) analysis is a powerful tool in systems biology, which uses a defined nomenclature to annotate genes/proteins within three categories: "Molecular Function," "Biological Process," and "Cellular Component." GO analysis can assist in revealing functional mechanisms underlying observed patterns in transcriptomic, genomic, and proteomic data. The already extensive and increasing use of zebrafish for modeling genetic and other diseases highlights the need to develop a GO analytical tool for this organism. The web tool Comparative GO was originally developed for GO analysis of bacterial data in 2013 ( www.comparativego.com ). We have now upgraded and elaborated this web tool for analysis of zebrafish genetic data using GOs and annotations from the Gene Ontology Consortium.

  1. System Biology Approach: Gene Network Analysis for Muscular Dystrophy.

    Science.gov (United States)

    Censi, Federica; Calcagnini, Giovanni; Mattei, Eugenio; Giuliani, Alessandro

    2018-01-01

    Phenotypic changes at different organization levels from cell to entire organism are associated to changes in the pattern of gene expression. These changes involve the entire genome expression pattern and heavily rely upon correlation patterns among genes. The classical approach used to analyze gene expression data builds upon the application of supervised statistical techniques to detect genes differentially expressed among two or more phenotypes (e.g., normal vs. disease). The use of an a posteriori, unsupervised approach based on principal component analysis (PCA) and the subsequent construction of gene correlation networks can shed a light on unexpected behaviour of gene regulation system while maintaining a more naturalistic view on the studied system.In this chapter we applied an unsupervised method to discriminate DMD patient and controls. The genes having the highest absolute scores in the discrimination between the groups were then analyzed in terms of gene expression networks, on the basis of their mutual correlation in the two groups. The correlation network structures suggest two different modes of gene regulation in the two groups, reminiscent of important aspects of DMD pathogenesis.

  2. Network graph analysis of gene-gene interactions in genome-wide association study data.

    Science.gov (United States)

    Lee, Sungyoung; Kwon, Min-Seok; Park, Taesung

    2012-12-01

    Most common complex traits, such as obesity, hypertension, diabetes, and cancers, are known to be associated with multiple genes, environmental factors, and their epistasis. Recently, the development of advanced genotyping technologies has allowed us to perform genome-wide association studies (GWASs). For detecting the effects of multiple genes on complex traits, many approaches have been proposed for GWASs. Multifactor dimensionality reduction (MDR) is one of the powerful and efficient methods for detecting high-order gene-gene (GxG) interactions. However, the biological interpretation of GxG interactions identified by MDR analysis is not easy. In order to aid the interpretation of MDR results, we propose a network graph analysis to elucidate the meaning of identified GxG interactions. The proposed network graph analysis consists of three steps. The first step is for performing GxG interaction analysis using MDR analysis. The second step is to draw the network graph using the MDR result. The third step is to provide biological evidence of the identified GxG interaction using external biological databases. The proposed method was applied to Korean Association Resource (KARE) data, containing 8838 individuals with 327,632 single-nucleotide polymorphisms, in order to perform GxG interaction analysis of body mass index (BMI). Our network graph analysis successfully showed that many identified GxG interactions have known biological evidence related to BMI. We expect that our network graph analysis will be helpful to interpret the biological meaning of GxG interactions.

  3. SIGNATURE: A workbench for gene expression signature analysis

    Directory of Open Access Journals (Sweden)

    Chang Jeffrey T

    2011-11-01

    Full Text Available Abstract Background The biological phenotype of a cell, such as a characteristic visual image or behavior, reflects activities derived from the expression of collections of genes. As such, an ability to measure the expression of these genes provides an opportunity to develop more precise and varied sets of phenotypes. However, to use this approach requires computational methods that are difficult to implement and apply, and thus there is a critical need for intelligent software tools that can reduce the technical burden of the analysis. Tools for gene expression analyses are unusually difficult to implement in a user-friendly way because their application requires a combination of biological data curation, statistical computational methods, and database expertise. Results We have developed SIGNATURE, a web-based resource that simplifies gene expression signature analysis by providing software, data, and protocols to perform the analysis successfully. This resource uses Bayesian methods for processing gene expression data coupled with a curated database of gene expression signatures, all carried out within a GenePattern web interface for easy use and access. Conclusions SIGNATURE is available for public use at http://genepattern.genome.duke.edu/signature/.

  4. LOGIC CIRCUIT

    Science.gov (United States)

    Strong, G.H.; Faught, M.L.

    1963-12-24

    A device for safety rod counting in a nuclear reactor is described. A Wheatstone bridge circuit is adapted to prevent de-energizing the hopper coils of a ball backup system if safety rods, sufficient in total control effect, properly enter the reactor core to effect shut down. A plurality of resistances form one arm of the bridge, each resistance being associated with a particular safety rod and weighted in value according to the control effect of the particular safety rod. Switching means are used to switch each of the resistances in and out of the bridge circuit responsive to the presence of a particular safety rod in its effective position in the reactor core and responsive to the attainment of a predetermined velocity by a particular safety rod enroute to its effective position. The bridge is unbalanced in one direction during normal reactor operation prior to the generation of a scram signal and the switching means and resistances are adapted to unbalance the bridge in the opposite direction if the safety rods produce a predetermined amount of control effect in response to the scram signal. The bridge unbalance reversal is then utilized to prevent the actuation of the ball backup system, or, conversely, a failure of the safety rods to produce the predetermined effect produces no unbalance reversal and the ball backup system is actuated. (AEC)

  5. Performance analysis of the closed digital control circuit of reactor A-1

    International Nuclear Information System (INIS)

    Karpeta, C.; Volf, K.; Stirsky, P.; Roubal, S.; Muellerova, H.

    A computer-aided analysis is presented of the optimum digital control of the A-1 nuclear power plant reactor. The effect of index weighting matrices on the quality of control processes was studied for a deterministic case using the Separation Theorem for a linear time-discrete regulator problem with a quadratic performance index. Some properties were also investigated of the Kalman filter serving the process state estimation. An analysis is reported for a stochastic case, this for both time-invariant and time-variant Kalman filter gain matrix. (author)

  6. Analysis of pan-genome to identify the core genes and essential genes of Brucella spp.

    Science.gov (United States)

    Yang, Xiaowen; Li, Yajie; Zang, Juan; Li, Yexia; Bie, Pengfei; Lu, Yanli; Wu, Qingmin

    2016-04-01

    Brucella spp. are facultative intracellular pathogens, that cause a contagious zoonotic disease, that can result in such outcomes as abortion or sterility in susceptible animal hosts and grave, debilitating illness in humans. For deciphering the survival mechanism of Brucella spp. in vivo, 42 Brucella complete genomes from NCBI were analyzed for the pan-genome and core genome by identification of their composition and function of Brucella genomes. The results showed that the total 132,143 protein-coding genes in these genomes were divided into 5369 clusters. Among these, 1710 clusters were associated with the core genome, 1182 clusters with strain-specific genes and 2477 clusters with dispensable genomes. COG analysis indicated that 44 % of the core genes were devoted to metabolism, which were mainly responsible for energy production and conversion (COG category C), and amino acid transport and metabolism (COG category E). Meanwhile, approximately 35 % of the core genes were in positive selection. In addition, 1252 potential essential genes were predicted in the core genome by comparison with a prokaryote database of essential genes. The results suggested that the core genes in Brucella genomes are relatively conservation, and the energy and amino acid metabolism play a more important role in the process of growth and reproduction in Brucella spp. This study might help us to better understand the mechanisms of Brucella persistent infection and provide some clues for further exploring the gene modules of the intracellular survival in Brucella spp.

  7. Analysis of gene and protein name synonyms in Entrez Gene and UniProtKB resources

    KAUST Repository

    Arkasosy, Basil

    2013-05-11

    Ambiguity in texts is a well-known problem: words can carry several meanings, and hence, can be read and interpreted differently. This is also true in the biological literature; names of biological concepts, such as genes and proteins, might be ambiguous, referring in some cases to more than one gene or one protein, or in others, to both genes and proteins at the same time. Public biological databases give a very useful insight about genes and proteins information, including their names. In this study, we made a thorough analysis of the nomenclatures of genes and proteins in two data sources and for six different species. We developed an automated process that parses, extracts, processes and stores information available in two major biological databases: Entrez Gene and UniProtKB. We analysed gene and protein synonyms, their types, frequencies, and the ambiguities within a species, in between data sources and cross-species. We found that at least 40% of the cross-species ambiguities are caused by names that are already ambiguous within the species. Our study shows that from the six species we analysed (Homo Sapiens, Mus Musculus, Arabidopsis Thaliana, Oryza Sativa, Bacillus Subtilis and Pseudomonas Fluorescens), rice (Oriza Sativa) has the best naming model in Entrez Gene database, with low ambiguities between data sources and cross-species.

  8. Advanced circuit simulation using Multisim workbench

    CERN Document Server

    Báez-López, David; Cervantes-Villagómez, Ofelia Delfina

    2012-01-01

    Multisim is now the de facto standard for circuit simulation. It is a SPICE-based circuit simulator which combines analog, discrete-time, and mixed-mode circuits. In addition, it is the only simulator which incorporates microcontroller simulation in the same environment. It also includes a tool for printed circuit board design.Advanced Circuit Simulation Using Multisim Workbench is a companion book to Circuit Analysis Using Multisim, published by Morgan & Claypool in 2011. This new book covers advanced analyses and the creation of models and subcircuits. It also includes coverage of transmissi

  9. Component-Level Electronic-Assembly Repair (CLEAR) Spacecraft Circuit Diagnostics by Analog and Complex Signature Analysis

    Science.gov (United States)

    Oeftering, Richard C.; Wade, Raymond P.; Izadnegahdar, Alain

    2011-01-01

    The Component-Level Electronic-Assembly Repair (CLEAR) project at the NASA Glenn Research Center is aimed at developing technologies that will enable space-flight crews to perform in situ component-level repair of electronics on Moon and Mars outposts, where there is no existing infrastructure for logistics spares. These technologies must provide effective repair capabilities yet meet the payload and operational constraints of space facilities. Effective repair depends on a diagnostic capability that is versatile but easy to use by crew members that have limited training in electronics. CLEAR studied two techniques that involve extensive precharacterization of "known good" circuits to produce graphical signatures that provide an easy-to-use comparison method to quickly identify faulty components. Analog Signature Analysis (ASA) allows relatively rapid diagnostics of complex electronics by technicians with limited experience. Because of frequency limits and the growing dependence on broadband technologies, ASA must be augmented with other capabilities. To meet this challenge while preserving ease of use, CLEAR proposed an alternative called Complex Signature Analysis (CSA). Tests of ASA and CSA were used to compare capabilities and to determine if the techniques provided an overlapping or complementary capability. The results showed that the methods are complementary.

  10. Experimental and CFD Analysis of Printed Circuit Heat Exchanger for Supercritical CO{sub 2} Power Cycle Application

    Energy Technology Data Exchange (ETDEWEB)

    Baik, Seungjoon; Kim, Hyeon Tae; Kim, Seong Gu; Lee, Jekyoung; Lee, Jeong Ik [KAIST, Daejeon (Korea, Republic of)

    2015-10-15

    The supercritical carbon dioxide (S-CO{sub 2}) power cycle has been suggested as an alternative for the SFR power generation system. First of all, relatively mild sodium-CO{sub 2} interaction can reduce the accident probability. Also the S-CO{sub 2} power conversion cycle can achieve high efficiency with SFR core thermal condition. Moreover, the S-CO{sub 2} power cycle can reduce cycle footprint due to high density of the working fluid. Recently, various compact heat exchangers have been studied for developing an optimal heat exchanger. In this paper, the printed circuit heat exchanger was selected for S-CO{sub 2} power cycle applications and was closely investigated experimentally and analytically. Recently, design and performance prediction of PCHE received attention due to its importance in high pressure power systems such as S-CO{sub 2} cycle. To evaluate a PCHE performance with CO{sub 2} to water, KAIST research team designed and tested a lab-scale PCHE. From the experimental data and CFD analysis, pressure drop and heat transfer correlations are obtained. For the CFD analysis, Ansys-CFX commercial code was utilized with RGP table implementation. In near future, the turbulence model sensitivity study will be followed.

  11. Short- circuit tests of circuit breakers

    OpenAIRE

    Chorovský, P.

    2015-01-01

    This paper deals with short-circuit tests of low voltage electrical devices. In the first part of this paper, there are described basic types of short- circuit tests and their principles. Direct and indirect (synthetic) tests with more details are described in the second part. Each test and principles are explained separately. Oscilogram is obtained from short-circuit tests of circuit breakers at laboratory. The aim of this research work is to propose a test circuit for performing indirect test.

  12. Genome-wide Analysis of Gene Regulation

    DEFF Research Database (Denmark)

    Chen, Yun

    to protein: through epigenetic modifications, transcription regulators or post-transcriptional controls. The following papers concern several layers of gene regulation with questions answered by different HTS approaches. Genome-wide screening of epigenetic changes by ChIP-seq allowed us to study both spatial...... and temporal alterations of histone modifications (Papers I and II). Coupling the data with machine learning approaches, we established a prediction framework to assess the most informative histone marks as well as their most influential nucleosome positions in predicting the promoter usages. (Papers I...... they regulated or if the sites had global elevated usage rates by multiple TFs. Using RNA-seq, 5’end-seq in combination with depletion of 5’exonuclease as well as nonsensemediated decay (NMD) factors, we systematically analyzed NMD substrates as well as their degradation intermediates in human cells (Paper V...

  13. Joint mapping of genes and conditions via multidimensional unfolding analysis

    Directory of Open Access Journals (Sweden)

    Engelen Kristof

    2007-06-01

    Full Text Available Abstract Background Microarray compendia profile the expression of genes in a number of experimental conditions. Such data compendia are useful not only to group genes and conditions based on their similarity in overall expression over profiles but also to gain information on more subtle relations between genes and conditions. Getting a clear visual overview of all these patterns in a single easy-to-grasp representation is a useful preliminary analysis step: We propose to use for this purpose an advanced exploratory method, called multidimensional unfolding. Results We present a novel algorithm for multidimensional unfolding that overcomes both general problems and problems that are specific for the analysis of gene expression data sets. Applying the algorithm to two publicly available microarray compendia illustrates its power as a tool for exploratory data analysis: The unfolding analysis of a first data set resulted in a two-dimensional representation which clearly reveals temporal regulation patterns for the genes and a meaningful structure for the time points, while the analysis of a second data set showed the algorithm's ability to go beyond a mere identification of those genes that discriminate between different patient or tissue types. Conclusion Multidimensional unfolding offers a useful tool for preliminary explorations of microarray data: By relying on an easy-to-grasp low-dimensional geometric framework, relations among genes, among conditions and between genes and conditions are simultaneously represented in an accessible way which may reveal interesting patterns in the data. An additional advantage of the method is that it can be applied to the raw data without necessitating the choice of suitable genewise transformations of the data.

  14. Collective of mechatronics circuit

    International Nuclear Information System (INIS)

    1987-02-01

    This book is composed of three parts, which deals with mechatronics system about sensor, circuit and motor. The contents of the first part are photo sensor of collector for output, locating detection circuit with photo interrupts, photo sensor circuit with CdS cell and lamp, interface circuit with logic and LED and temperature sensor circuit. The second part deals with oscillation circuit with crystal, C-R oscillation circuit, F-V converter, timer circuit, stability power circuit, DC amp and DC-DC converter. The last part is comprised of bridge server circuit, deformation bridge server, controlling circuit of DC motor, controlling circuit with IC for PLL and driver circuit of stepping motor and driver circuit of Brushless.

  15. Collective of mechatronics circuit

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1987-02-15

    This book is composed of three parts, which deals with mechatronics system about sensor, circuit and motor. The contents of the first part are photo sensor of collector for output, locating detection circuit with photo interrupts, photo sensor circuit with CdS cell and lamp, interface circuit with logic and LED and temperature sensor circuit. The second part deals with oscillation circuit with crystal, C-R oscillation circuit, F-V converter, timer circuit, stability power circuit, DC amp and DC-DC converter. The last part is comprised of bridge server circuit, deformation bridge server, controlling circuit of DC motor, controlling circuit with IC for PLL and driver circuit of stepping motor and driver circuit of Brushless.

  16. General Analysis of Vacuum Circuit Breaker Switching Overvoltages in Offshore Wind Farms

    DEFF Research Database (Denmark)

    Ghafourian, S. M.; Arana, I.; Holbøll, Joachim

    2016-01-01

    Understanding mechanisms of switching transient overvoltages in modern electrical power systems is a necessity to ensure a proper design of power plants and switchgear and the required level of reliable and secure system operation. High fidelity plant modelling and accurate transient analysis...... on the transformer terminal voltage during closing operation was studied. A wind farm power collection system was modelled in ATP-EMTP environment. To validate the results obtained through computer simulation, field measurements from an actual system were used....

  17. A Sparsity-based Framework for Resolution Enhancement in Optical Fault Analysis of Integrated Circuits

    Science.gov (United States)

    2015-01-01

    discussions and collaboration. I also want to thank other co-workers for discussions and their contributions, Dr. Helen Fawcett, Dr. Euan Ramsay , Dr...optical fault analysis techniques Gordon E. Moore predicted the rapid decrease in IC dimensions (Moore, 1998) and this decrease continues as predicted...Serrels, K. A., Ramsay , E., Warburton, R. J., and Reid, D. T. (2008). Nanoscale optical microscopy in the vectorial focusing regime. Nature Photonics, 2(5

  18. Prioritization of epilepsy associated candidate genes by convergent analysis.

    Science.gov (United States)

    Jia, Peilin; Ewers, Jeffrey M; Zhao, Zhongming

    2011-02-24

    Epilepsy is a severe neurological disorder affecting a large number of individuals, yet the underlying genetic risk factors for epilepsy remain unclear. Recent studies have revealed several recurrent copy number variations (CNVs) that are more likely to be associated with epilepsy. The responsible gene(s) within these regions have yet to be definitively linked to the disorder, and the implications of their interactions are not fully understood. Identification of these genes may contribute to a better pathological understanding of epilepsy, and serve to implicate novel therapeutic targets for further research. In this study, we examined genes within heterozygous deletion regions identified in a recent large-scale study, encompassing a diverse spectrum of epileptic syndromes. By integrating additional protein-protein interaction data, we constructed subnetworks for these CNV-region genes and also those previously studied for epilepsy. We observed 20 genes common to both networks, primarily concentrated within a small molecular network populated by GABA receptor, BDNF/MAPK signaling, and estrogen receptor genes. From among the hundreds of genes in the initial networks, these were designated by convergent evidence for their likely association with epilepsy. Importantly, the identified molecular network was found to contain complex interrelationships, providing further insight into epilepsy's underlying pathology. We further performed pathway enrichment and crosstalk analysis and revealed a functional map which indicates the significant enrichment of closely related neurological, immune, and kinase regulatory pathways. The convergent framework we proposed here provides a unique and powerful approach to screening and identifying promising disease genes out of typically hundreds to thousands of genes in disease-related CNV-regions. Our network and pathway analysis provides important implications for the underlying molecular mechanisms for epilepsy. The strategy can be

  19. Prioritization of epilepsy associated candidate genes by convergent analysis.

    Directory of Open Access Journals (Sweden)

    Peilin Jia

    2011-02-01

    Full Text Available Epilepsy is a severe neurological disorder affecting a large number of individuals, yet the underlying genetic risk factors for epilepsy remain unclear. Recent studies have revealed several recurrent copy number variations (CNVs that are more likely to be associated with epilepsy. The responsible gene(s within these regions have yet to be definitively linked to the disorder, and the implications of their interactions are not fully understood. Identification of these genes may contribute to a better pathological understanding of epilepsy, and serve to implicate novel therapeutic targets for further research.In this study, we examined genes within heterozygous deletion regions identified in a recent large-scale study, encompassing a diverse spectrum of epileptic syndromes. By integrating additional protein-protein interaction data, we constructed subnetworks for these CNV-region genes and also those previously studied for epilepsy. We observed 20 genes common to both networks, primarily concentrated within a small molecular network populated by GABA receptor, BDNF/MAPK signaling, and estrogen receptor genes. From among the hundreds of genes in the initial networks, these were designated by convergent evidence for their likely association with epilepsy. Importantly, the identified molecular network was found to contain complex interrelationships, providing further insight into epilepsy's underlying pathology. We further performed pathway enrichment and crosstalk analysis and revealed a functional map which indicates the significant enrichment of closely related neurological, immune, and kinase regulatory pathways.The convergent framework we proposed here provides a unique and powerful approach to screening and identifying promising disease genes out of typically hundreds to thousands of genes in disease-related CNV-regions. Our network and pathway analysis provides important implications for the underlying molecular mechanisms for epilepsy. The

  20. Microphone triggering circuit for elimination of mechanically induced frequency-jitter in diode laser spectrometers: implications for quantitative analysis.

    Science.gov (United States)

    Sams, R L; Fried, A

    1987-09-01

    An electronic timing circuit using a microphone triggering device has been developed for elimination of mechanically induced frequency-jitter in diode laser spectrometers employing closed-cycle refrigerators. Mechanical compressor piston shocks are detected by the microphone and actuate an electronic circuit which ultimately interrupts data acquisition until the mechanical vibrations are completely quenched. In this way, laser sweeps contaminated by compressor frequency-jitter are not co-averaged. Employing this circuit, measured linewidths were in better agreement with that calculated. The importance of eliminating this mechanically induced frequency-jitter when carrying out quantitative diode laser measurements is further discussed.

  1. General oscillation damping analysis of the L-C filter circuit in the high-power rectifying power supply

    International Nuclear Information System (INIS)

    Xu Weihua; Chen Yonghao; Wu Junshuan; Kuang Guangli

    1998-06-01

    Rectifier circuit is the most popular converter. For the ripple demand of high-power load, the L-C filter with invert 'L' type has been used universally. Due to the influence of the second-order link, damped oscillation will occur with proper condition while the circuit state is changed. The ideal cascade damping condition and the parallel one can be obtained easily. Generally, the damping condition of the step response of the L-C filter circuit is induced, and the discussion is given

  2. Sequence comparison and phylogenetic analysis of core gene of ...

    African Journals Online (AJOL)

    Phylogenetic analysis suggests that our sequences are clustered with sequences reported from Japan. This is the first phylogenetic analysis of HCV core gene from Pakistani population. Our sequences and sequences from Japan are grouped into same cluster in the phylogenetic tree. Sequence comparison and ...

  3. Molecular responses and expression analysis of genes in a ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-17

    Jun 17, 2009 ... Molecular responses and expression analysis of genes in a xerophytic desert shrub Haloxylon ammodendron .... physiological determination and cDNA-AFLP analysis, three groups of seeds were sowed in pots with sand and .... HaDR27. U. 234. PDR-like ABC transporter. AT1G59870. HaDR28. U. 135.

  4. GWATCH: a web platform for automated gene association discovery analysis

    Science.gov (United States)

    2014-01-01

    Background As genome-wide sequence analyses for complex human disease determinants are expanding, it is increasingly necessary to develop strategies to promote discovery and validation of potential disease-gene associations. Findings Here we present a dynamic web-based platform – GWATCH – that automates and facilitates four steps in genetic epidemiological discovery: 1) Rapid gene association search and discovery analysis of large genome-wide datasets; 2) Expanded visual display of gene associations for genome-wide variants (SNPs, indels, CNVs), including Manhattan plots, 2D and 3D snapshots of any gene region, and a dynamic genome browser illustrating gene association chromosomal regions; 3) Real-time validation/replication of candidate or putative genes suggested from other sources, limiting Bonferroni genome-wide association study (GWAS) penalties; 4) Open data release and sharing by eliminating privacy constraints (The National Human Genome Research Institute (NHGRI) Institutional Review Board (IRB), informed consent, The Health Insurance Portability and Accountability Act (HIPAA) of 1996 etc.) on unabridged results, which allows for open access comparative and meta-analysis. Conclusions GWATCH is suitable for both GWAS and whole genome sequence association datasets. We illustrate the utility of GWATCH with three large genome-wide association studies for HIV-AIDS resistance genes screened in large multicenter cohorts; however, association datasets from any study can be uploaded and analyzed by GWATCH. PMID:25374661

  5. Detection of non-stationary leak signals at NPP primary circuit by cross-correlation analysis

    International Nuclear Information System (INIS)

    Shimanskij, S.B.

    2007-01-01

    A leak-detection system employing high-temperature microphones has been developed for the RBMK and ATR (Japan) reactors. Further improvement of the system focused on using cross-correlation analysis of the spectral components of the signal to detect a small leak at an early stage of development. Since envelope processes are less affected by distortions than are wave processes, they give a higher-degree of correlation and can be used to detect leaks with lower signal-noise ratios. Many simulation tests performed at nuclear power plants have shown that the proposed methods can be used to detect and find the location of a small leak [ru

  6. Gene Expression Signature in Endemic Osteoarthritis by Microarray Analysis

    Directory of Open Access Journals (Sweden)

    Xi Wang

    2015-05-01

    Full Text Available Kashin-Beck Disease (KBD is an endemic osteochondropathy with an unknown pathogenesis. Diagnosis of KBD is effective only in advanced cases, which eliminates the possibility of early treatment and leads to an inevitable exacerbation of symptoms. Therefore, we aim to identify an accurate blood-based gene signature for the detection of KBD. Previously published gene expression profile data on cartilage and peripheral blood mononuclear cells (PBMCs from adults with KBD were compared to select potential target genes. Microarray analysis was conducted to evaluate the expression of the target genes in a cohort of 100 KBD patients and 100 healthy controls. A gene expression signature was identified using a training set, which was subsequently validated using an independent test set with a minimum redundancy maximum relevance (mRMR algorithm and support vector machine (SVM algorithm. Fifty unique genes were differentially expressed between KBD patients and healthy controls. A 20-gene signature was identified that distinguished between KBD patients and controls with 90% accuracy, 85% sensitivity, and 95% specificity. This study identified a 20-gene signature that accurately distinguishes between patients with KBD and controls using peripheral blood samples. These results promote the further development of blood-based genetic biomarkers for detection of KBD.

  7. QTL global meta-analysis: are trait determining genes clustered?

    Directory of Open Access Journals (Sweden)

    Adelson David L

    2009-04-01

    Full Text Available Abstract Background A key open question in biology is if genes are physically clustered with respect to their known functions or phenotypic effects. This is of particular interest for Quantitative Trait Loci (QTL where a QTL region could contain a number of genes that contribute to the trait being measured. Results We observed a significant increase in gene density within QTL regions compared to non-QTL regions and/or the entire bovine genome. By grouping QTL from the Bovine QTL Viewer database into 8 categories of non-redundant regions, we have been able to analyze gene density and gene function distribution, based on Gene Ontology (GO with relation to their location within QTL regions, outside of QTL regions and across the entire bovine genome. We identified a number of GO terms that were significantly over represented within particular QTL categories. Furthermore, select GO terms expected to be associated with the QTL category based on common biological knowledge have also proved to be significantly over represented in QTL regions. Conclusion Our analysis provides evidence of over represented GO terms in QTL regions. This increased GO term density indicates possible clustering of gene functions within QTL regions of the bovine genome. Genes with similar functions may be grouped in specific locales and could be contributing to QTL traits. Moreover, we have identified over-represented GO terminology that from a biological standpoint, makes sense with respect to QTL category type.

  8. Semi-supervised consensus clustering for gene expression data analysis

    OpenAIRE

    Wang, Yunli; Pan, Youlian

    2014-01-01

    Background Simple clustering methods such as hierarchical clustering and k-means are widely used for gene expression data analysis; but they are unable to deal with noise and high dimensionality associated with the microarray gene expression data. Consensus clustering appears to improve the robustness and quality of clustering results. Incorporating prior knowledge in clustering process (semi-supervised clustering) has been shown to improve the consistency between the data partitioning and do...

  9. Circuit parties.

    Science.gov (United States)

    Guzman, R

    2000-03-01

    Circuit parties are extended celebrations, lasting from a day to a week, primarily attended by gay and bisexual men in their thirties and forties. These large-scale dance parties move from city to city and draw thousands of participants. The risks for contracting HIV during these parties include recreational drug use and unsafe sex. Limited data exists on the level of risk at these parties, and participants are skeptical of outside help because of past criticism of these events. Health care and HIV advocates can promote risk-reduction strategies with the cooperation of party planners and can counsel individuals to personally reduce their own risk. To convey the message, HIV prevention workers should emphasize positive and community-centered aspects of the parties, such as taking care of friends and avoiding overdose.

  10. Genome-wide analysis of E. coli cell-gene interactions.

    Science.gov (United States)

    Cardinale, S; Cambray, G

    2017-11-23

    The pursuit of standardization and reliability in synthetic biology has achieved, in recent years, a number of advances in the design of more predictable genetic parts for biological circuits. However, even with the development of high-throughput screening methods and whole-cell models, it is still not possible to predict reliably how a synthetic genetic construct interacts with all cellular endogenous systems. This study presents a genome-wide analysis of how the expression of synthetic genes is affected by systematic perturbations of cellular functions. We found that most perturbations modulate expression indirectly through an effect on cell size, putting forward the existence of a generic Size-Expression interaction in the model prokaryote Escherichia coli. The Size-Expression interaction was quantified by inserting a dual fluorescent reporter gene construct into each of the 3822 single-gene deletion strains comprised in the KEIO collection. Cellular size was measured for single cells via flow cytometry. Regression analyses were used to discriminate between expression-specific and gene-specific effects. Functions of the deleted genes broadly mapped onto three systems with distinct primary influence on the Size-Expression map. Perturbations in the Division and Biosynthesis (DB) system led to a large-cell and high-expression phenotype. In contrast, disruptions of the Membrane and Motility (MM) system caused small-cell and low-expression phenotypes. The Energy, Protein synthesis and Ribosome (EPR) system was predominantly associated with smaller cells and positive feedback on ribosome function. Feedback between cell growth and gene expression is widespread across cell systems. Even though most gene disruptions proximally affect one component of the Size-Expression interaction, the effect therefore ultimately propagates to both. More specifically, we describe the dual impact of growth on cell size and gene expression through cell division and ribosomal content

  11. Gene expression patterns combined with network analysis identify hub genes associated with bladder cancer.

    Science.gov (United States)

    Bi, Dongbin; Ning, Hao; Liu, Shuai; Que, Xinxiang; Ding, Kejia

    2015-06-01

    To explore molecular mechanisms of bladder cancer (BC), network strategy was used to find biomarkers for early detection and diagnosis. The differentially expressed genes (DEGs) between bladder carcinoma patients and normal subjects were screened using empirical Bayes method of the linear models for microarray data package. Co-expression networks were constructed by differentially co-expressed genes and links. Regulatory impact factors (RIF) metric was used to identify critical transcription factors (TFs). The protein-protein interaction (PPI) networks were constructed by the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and clusters were obtained through molecular complex detection (MCODE) algorithm. Centralities analyses for complex networks were performed based on degree, stress and betweenness. Enrichment analyses were performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Co-expression networks and TFs (based on expression data of global DEGs and DEGs in different stages and grades) were identified. Hub genes of complex networks, such as UBE2C, ACTA2, FABP4, CKS2, FN1 and TOP2A, were also obtained according to analysis of degree. In gene enrichment analyses of global DEGs, cell adhesion, proteinaceous extracellular matrix and extracellular matrix structural constituent were top three GO terms. ECM-receptor interaction, focal adhesion, and cell cycle were significant pathways. Our results provide some potential underlying biomarkers of BC. However, further validation is required and deep studies are needed to elucidate the pathogenesis of BC. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. The Software Reliability of Large Scale Integration Circuit and Very Large Scale Integration Circuit

    OpenAIRE

    Artem Ganiyev; Jan Vitasek

    2010-01-01

    This article describes evaluation method of faultless function of large scale integration circuits (LSI) and very large scale integration circuits (VLSI). In the article there is a comparative analysis of factors which determine faultless of integrated circuits, analysis of already existing methods and model of faultless function evaluation of LSI and VLSI. The main part describes a proposed algorithm and program for analysis of fault rate in LSI and VLSI circuits.

  13. Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean) Cattle.

    Science.gov (United States)

    Lim, Dajeong; Lee, Seung-Hwan; Kim, Nam-Kuk; Cho, Yong-Min; Chai, Han-Ha; Seong, Hwan-Hoo; Kim, Heebal

    2013-01-01

    Marbling (intramuscular fat) is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the 'marbling score' trait and systemically analyzed the network topology in Hanwoo (Korean cattle). As a result, we determined 3 modules (gene groups) that showed statistically significant results for marbling score. In particular, one module (denoted as red) has a statistically significant result for marbling score (p = 0.008) and intramuscular fat (p = 0.02) and water capacity (p = 0.006). From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA) have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.

  14. Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean Cattle

    Directory of Open Access Journals (Sweden)

    Dajeong Lim

    2013-01-01

    Full Text Available Marbling (intramuscular fat is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the ‘marbling score’ trait and systemically analyzed the network topology in Hanwoo (Korean cattle. As a result, we determined 3 modules (gene groups that showed statistically significant results for marbling score. In particular, one module (denoted as red has a statistically significant result for marbling score (p = 0.008 and intramuscular fat (p = 0.02 and water capacity (p = 0.006. From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.

  15. A multicolor panel of novel lentiviral "gene ontology" (LeGO) vectors for functional gene analysis.

    Science.gov (United States)

    Weber, Kristoffer; Bartsch, Udo; Stocking, Carol; Fehse, Boris

    2008-04-01

    Functional gene analysis requires the possibility of overexpression, as well as downregulation of one, or ideally several, potentially interacting genes. Lentiviral vectors are well suited for this purpose as they ensure stable expression of complementary DNAs (cDNAs), as well as short-hairpin RNAs (shRNAs), and can efficiently transduce a wide spectrum of cell targets when packaged within the coat proteins of other viruses. Here we introduce a multicolor panel of novel lentiviral "gene ontology" (LeGO) vectors designed according to the "building blocks" principle. Using a wide spectrum of different fluorescent markers, including drug-selectable enhanced green fluorescent protein (eGFP)- and dTomato-blasticidin-S resistance fusion proteins, LeGO vectors allow simultaneous analysis of multiple genes and shRNAs of interest within single, easily identifiable cells. Furthermore, each functional module is flanked by unique cloning sites, ensuring flexibility and individual optimization. The efficacy of these vectors for analyzing multiple genes in a single cell was demonstrated in several different cell types, including hematopoietic, endothelial, and neural stem and progenitor cells, as well as hepatocytes. LeGO vectors thus represent a valuable tool for investigating gene networks using conditional ectopic expression and knock-down approaches simultaneously.

  16. Implementation, Test Pattern Generation, and Comparative Analysis of Different Adder Circuits

    Directory of Open Access Journals (Sweden)

    Vikas K. Saini

    2016-01-01

    Full Text Available Addition usually affects the overall performance of digital systems and an arithmetic function. Adders are most widely used in applications like multipliers, DSP (i.e., FFT, FIR, and IIR. In digital adders, the speed of addition is constrained by the time required to propagate a carry through the adder. Various techniques have been proposed to design fast adders. We have derived architectures for carry-select adder (CSA, Common Boolean Logic (CBL based adders, ripple carry adder (RCA, and Carry Look-Ahead Adder (CLA for 8-, 16-, 32-, and 64-bit length. In this work we have done comparative analysis of different types of adders in Synopsis Design Compiler using different standard cell libraries at 32/28 nm. Also, the designs are analyzed for the stuck at faults (s-a-0, s-a-1 using Synopsis TetraMAX.

  17. Theoretical and experimental analysis of a linear accelerator endowed with single feed coupler with movable short-circuit

    International Nuclear Information System (INIS)

    Forno, Massimo Dal; Craievich, Paolo; Penco, Giuseppe; Vescovo, Roberto

    2013-01-01

    The front-end injection systems of the FERMI@Elettra linac produce high brightness electron beams that define the performance of the Free Electron Laser. The photoinjector mainly consists of the radiofrequency (rf) gun and of two S-band rf structures which accelerate the beam. Accelerating structures endowed with a single feed coupler cause deflection and degradation of the electron beam properties, due to the asymmetry of the electromagnetic field. In this paper, a new type of single feed structure with movable short-circuit is proposed. It has the advantage of having only one waveguide input, but we propose a novel design where the dipolar component is reduced. Moreover, the racetrack geometry allows to reduce the quadrupolar component. This paper presents the microwave design and the analysis of the particle motion inside the linac. A prototype has been machined at the Elettra facility to verify the new coupler design and the rf field has been measured by adopting the bead-pull method. The results are here presented, showing good agreement with the expectations

  18. Theoretical and experimental analysis of a linear accelerator endowed with single feed coupler with movable short-circuit.

    Science.gov (United States)

    Dal Forno, Massimo; Craievich, Paolo; Penco, Giuseppe; Vescovo, Roberto

    2013-11-01

    The front-end injection systems of the FERMI@Elettra linac produce high brightness electron beams that define the performance of the Free Electron Laser. The photoinjector mainly consists of the radiofrequency (rf) gun and of two S-band rf structures which accelerate the beam. Accelerating structures endowed with a single feed coupler cause deflection and degradation of the electron beam properties, due to the asymmetry of the electromagnetic field. In this paper, a new type of single feed structure with movable short-circuit is proposed. It has the advantage of having only one waveguide input, but we propose a novel design where the dipolar component is reduced. Moreover, the racetrack geometry allows to reduce the quadrupolar component. This paper presents the microwave design and the analysis of the particle motion inside the linac. A prototype has been machined at the Elettra facility to verify the new coupler design and the rf field has been measured by adopting the bead-pull method. The results are here presented, showing good agreement with the expectations.

  19. Analysis of the Nonlinear Characteristics of Microwave Power Heterojunction Bipolar Transistors and Optoelectronic Integrated Circuits.

    Science.gov (United States)

    Samelis, Apostolos

    A physical basis for large-signal HBT modeling was established in terms of transit times using a Monte Carlo analysis of AlGaAs/GaAs and GaInP/GaAs designs. Static carriers located in the collector-subcollector interface were found to prohibit accurate evaluation of transit times from electron velocity profiles. These carriers also influence the bias dependence of device capacitances. Analytical parameter extraction techniques for DC, thermal and high frequency HBT parameters were developed and applied to HBT large-signal modeling. The "impedance block" conditioned optimization technique was introduced to facilitate parameter extraction. Physical analysis of HBTs by means of Volterra Series techniques showed that C_{bc } dominates nonlinear distortion in high gain amplifiers. Designs with that C_{bc }-V_{cb} characteristics i.e. p -n collector HBTs lead to more than 10 dB IP3 improvement over n-collector HBTs. Nonlinear current cancellation was found to improve intermodulation distortion. A Gummel -Poon-based HBT large-signal model incorporating self-heating effects was developed and applied to AlGaAs/GaAs HBTs. Maximum power drive was shown to occur using constant V _{be} father than I_ {b} bias. The device temperature of constant I_{b} biased HBTs decreases at increased rf-drive levels ensuring in this case safer device operation. A large-signal model incorporating "soft" -breakdown effects typical of InP/InGaAs HBTs was developed and found to model succesfully the power characteristics of OEICs built with them. The effective large-signal transimpedance of a cascode transimpedance preamplifier was evaluated using this model and found to degrade by 3dBOmega for a variation of P_{in} from -65 to -5 dBm. Self-bias of individual transistors was studied and found to be related to variations of the amplifier characteristics at higher rf-drive levels. The power characteristics of CE and CB AlGaAs/GaAs HBTs were investigated using an on -wafer source/load pull setup

  20. Commutation circuit for an HVDC circuit breaker

    Science.gov (United States)

    Premerlani, William J.

    1981-01-01

    A commutation circuit for a high voltage DC circuit breaker incorporates a resistor capacitor combination and a charging circuit connected to the main breaker, such that a commutating capacitor is discharged in opposition to the load current to force the current in an arc after breaker opening to zero to facilitate arc interruption. In a particular embodiment, a normally open commutating circuit is connected across the contacts of a main DC circuit breaker to absorb the inductive system energy trapped by breaker opening and to limit recovery voltages to a level tolerable by the commutating circuit components.

  1. Thermal analysis of wirelessly powered thermo-pneumatic micropump based on planar LC circuit

    International Nuclear Information System (INIS)

    Chee, Pei Song; Nafea, Marwan; Leow, Pei Ling; Ali, Mohamed Sultan Mohamed

    2016-01-01

    This paper studies the thermal behavior of a wireless powered micropump operated using thermo-pneumatic actuation. Numerical analysis was performed to investigate the temporal conduction of the planar inductor-capacitor (LC) wireless heater and the heating chamber. The result shows that the temperature at the heating chamber reaches steady state temperature of 46.7.deg.C within 40 seconds. The finding was further verified with experimental works through the fabrication of the planar LC heater (RF sensitive actuator) and micropump device using MEMS fabrication technique. The fabricated device delivers a minimum volume of 0.096 μL at the temperature of 29.deg.C after being thermally activated for 10 s. The volume dispensed from the micropump device can precisely controlled by an increase of the electrical heating power within the cut-off input power of 0.22 W. Beyond the power, the heat transfer to the heating chamber exhibits non-linear behavior. In addition, wireless operation of the fabricated device shows successful release of color dye when the micropump is immersed in DI-water containing dish and excited by tuning the RF power.

  2. Thermal analysis of wirelessly powered thermo-pneumatic micropump based on planar LC circuit

    Energy Technology Data Exchange (ETDEWEB)

    Chee, Pei Song; Nafea, Marwan; Leow, Pei Ling; Ali, Mohamed Sultan Mohamed [Universiti Teknologi Malaysia, Skudai (Malaysia)

    2016-06-15

    This paper studies the thermal behavior of a wireless powered micropump operated using thermo-pneumatic actuation. Numerical analysis was performed to investigate the temporal conduction of the planar inductor-capacitor (LC) wireless heater and the heating chamber. The result shows that the temperature at the heating chamber reaches steady state temperature of 46.7.deg.C within 40 seconds. The finding was further verified with experimental works through the fabrication of the planar LC heater (RF sensitive actuator) and micropump device using MEMS fabrication technique. The fabricated device delivers a minimum volume of 0.096 μL at the temperature of 29.deg.C after being thermally activated for 10 s. The volume dispensed from the micropump device can precisely controlled by an increase of the electrical heating power within the cut-off input power of 0.22 W. Beyond the power, the heat transfer to the heating chamber exhibits non-linear behavior. In addition, wireless operation of the fabricated device shows successful release of color dye when the micropump is immersed in DI-water containing dish and excited by tuning the RF power.

  3. Transient Thermal Analysis of 3-D Integrated Circuits Packages by the DGTD Method

    KAUST Repository

    Li, Ping

    2017-03-11

    Since accurate thermal analysis plays a critical role in the thermal design and management of the 3-D system-level integration, in this paper, a discontinuous Galerkin time-domain (DGTD) algorithm is proposed to achieve this purpose. Such as the parabolic partial differential equation (PDE), the transient thermal equation cannot be directly solved by the DGTD method. To address this issue, the heat flux, as an auxiliary variable, is introduced to reduce the Laplace operator to a divergence operator. The resulting PDE is hyperbolic, which can be further written into a conservative form. By properly choosing the definition of the numerical flux used for the information exchange between neighboring elements, the hyperbolic thermal PDE can be solved by the DGTD together with the auxiliary differential equation. The proposed algorithm is a kind of element-level domain decomposition method, which is suitable to deal with multiscale geometries in 3-D integrated systems. To verify the accuracy and robustness of the developed DGTD algorithm, several representative examples are benchmarked.

  4. Transcriptome profiling and digital gene expression analysis of genes associated with salinity resistance in peanut

    Directory of Open Access Journals (Sweden)

    Jiongming Sui

    2018-03-01

    Full Text Available Background: Soil salinity can significantly reduce crop production, but the molecular mechanism of salinity tolerance in peanut is poorly understood. A mutant (S1 with higher salinity resistance than its mutagenic parent HY22 (S3 was obtained. Transcriptome sequencing and digital gene expression (DGE analysis were performed with leaves of S1 and S3 before and after plants were irrigated with 250 mM NaCl. Results: A total of 107,725 comprehensive transcripts were assembled into 67,738 unigenes using TIGR Gene Indices clustering tools (TGICL. All unigenes were searched against the euKaryotic Ortholog Groups (KOG, gene ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG databases, and these unigenes were assigned to 26 functional KOG categories, 56 GO terms, 32 KEGG groups, respectively. In total 112 differentially expressed genes (DEGs between S1 and S3 after salinity stress were screened, among them, 86 were responsive to salinity stress in S1 and/or S3. These 86 DEGs included genes that encoded the following kinds of proteins that are known to be involved in resistance to salinity stress: late embryogenesis abundant proteins (LEAs, major intrinsic proteins (MIPs or aquaporins, metallothioneins (MTs, lipid transfer protein (LTP, calcineurin B-like protein-interacting protein kinases (CIPKs, 9-cis-epoxycarotenoid dioxygenase (NCED and oleosins, etc. Of these 86 DEGs, 18 could not be matched with known proteins. Conclusion: The results from this study will be useful for further research on the mechanism of salinity resistance and will provide a useful gene resource for the variety breeding of salinity resistance in peanut. Keywords: Digital gene expression, Gene, Mutant, NaCl, Peanut (Arachis hypogaea L., RNA-seq, Salinity stress, Salinity tolerance, Soil salinity, Transcripts, Unigenes

  5. Quantitative DNA methylation analysis of candidate genes in cervical cancer.

    Directory of Open Access Journals (Sweden)

    Erin M Siegel

    Full Text Available Aberrant DNA methylation has been observed in cervical cancer; however, most studies have used non-quantitative approaches to measure DNA methylation. The objective of this study was to quantify methylation within a select panel of genes previously identified as targets for epigenetic silencing in cervical cancer and to identify genes with elevated methylation that can distinguish cancer from normal cervical tissues. We identified 49 women with invasive squamous cell cancer of the cervix and 22 women with normal cytology specimens. Bisulfite-modified genomic DNA was amplified and quantitative pyrosequencing completed for 10 genes (APC, CCNA, CDH1, CDH13, WIF1, TIMP3, DAPK1, RARB, FHIT, and SLIT2. A Methylation Index was calculated as the mean percent methylation across all CpG sites analyzed per gene (~4-9 CpG site per sequence. A binary cut-point was defined at >15% methylation. Sensitivity, specificity and area under ROC curve (AUC of methylation in individual genes or a panel was examined. The median methylation index was significantly higher in cases compared to controls in 8 genes, whereas there was no difference in median methylation for 2 genes. Compared to HPV and age, the combination of DNA methylation level of DAPK1, SLIT2, WIF1 and RARB with HPV and age significantly improved the AUC from 0.79 to 0.99 (95% CI: 0.97-1.00, p-value = 0.003. Pyrosequencing analysis confirmed that several genes are common targets for aberrant methylation in cervical cancer and DNA methylation level of four genes appears to increase specificity to identify cancer compared to HPV detection alone. Alterations in DNA methylation of specific genes in cervical cancers, such as DAPK1, RARB, WIF1, and SLIT2, may also occur early in cervical carcinogenesis and should be evaluated.

  6. IGSA: Individual Gene Sets Analysis, including Enrichment and Clustering.

    Science.gov (United States)

    Wu, Lingxiang; Chen, Xiujie; Zhang, Denan; Zhang, Wubing; Liu, Lei; Ma, Hongzhe; Yang, Jingbo; Xie, Hongbo; Liu, Bo; Jin, Qing

    2016-01-01

    Analysis of gene sets has been widely applied in various high-throughput biological studies. One weakness in the traditional methods is that they neglect the heterogeneity of genes expressions in samples which may lead to the omission of some specific and important gene sets. It is also difficult for them to reflect the severities of disease and provide expression profiles of gene sets for individuals. We developed an application software called IGSA that leverages a powerful analytical capacity in gene sets enrichment and samples clustering. IGSA calculates gene sets expression scores for each sample and takes an accumulating clustering strategy to let the samples gather into the set according to the progress of disease from mild to severe. We focus on gastric, pancreatic and ovarian cancer data sets for the performance of IGSA. We also compared the results of IGSA in KEGG pathways enrichment with David, GSEA, SPIA, ssGSEA and analyzed the results of IGSA clustering and different similarity measurement methods. Notably, IGSA is proved to be more sensitive and specific in finding significant pathways, and can indicate related changes in pathways with the severity of disease. In addition, IGSA provides with significant gene sets profile for each sample.

  7. CANDIDATE GENE ANALYSIS IN ISRAELI SOLDIERS WITH STRESS FRACTURES

    Directory of Open Access Journals (Sweden)

    Ran Yanovich

    2012-03-01

    Full Text Available To investigate the association of polymorphisms within candidate genes which we hypothesized may contribute to stress fracture predisposition, a case-control, cross- sectional study design was employed. Genotyping 268 Single Nucleotide Polymorphisms- SNPs within 17 genes in 385 Israeli young male and female recruits (182 with and 203 without stress fractures. Twenty-five polymorphisms within 9 genes (NR3C1, ANKH, VDR, ROR2, CALCR, IL6, COL1A2, CBG, and LRP4 showed statistically significant differences (p < 0.05 in the distribution between stress fracture cases and non stress fracture controls. Seventeen genetic variants were associated with an increased stress fracture risk, and eight variants with a decreased stress fracture risk. None of the SNP associations remained significant after correcting for multiple comparisons (false discovery rate- FDR. Our findings suggest that genes may be involved in stress fracture pathogenesis. Specifically, the CALCR and the VDR genes are intriguing candidates. The putative involvement of these genes in stress fracture predisposition requires analysis of more cases and controls and sequencing the relevant genomic regions, in order to define the specific gene mutations

  8. Singular Perturbation Analysis and Gene Regulatory Networks with Delay

    Science.gov (United States)

    Shlykova, Irina; Ponosov, Arcady

    2009-09-01

    There are different ways of how to model gene regulatory networks. Differential equations allow for a detailed description of the network's dynamics and provide an explicit model of the gene concentration changes over time. Production and relative degradation rate functions used in such models depend on the vector of steeply sloped threshold functions which characterize the activity of genes. The most popular example of the threshold functions comes from the Boolean network approach, where the threshold functions are given by step functions. The system of differential equations becomes then piecewise linear. The dynamics of this system can be described very easily between the thresholds, but not in the switching domains. For instance this approach fails to analyze stationary points of the system and to define continuous solutions in the switching domains. These problems were studied in [2], [3], but the proposed model did not take into account a time delay in cellular systems. However, analysis of real gene expression data shows a considerable number of time-delayed interactions suggesting that time delay is essential in gene regulation. Therefore, delays may have a great effect on the dynamics of the system presenting one of the critical factors that should be considered in reconstruction of gene regulatory networks. The goal of this work is to apply the singular perturbation analysis to certain systems with delay and to obtain an analog of Tikhonov's theorem, which provides sufficient conditions for constracting the limit system in the delay case.

  9. Ranking metrics in gene set enrichment analysis: do they matter?

    Science.gov (United States)

    Zyla, Joanna; Marczyk, Michal; Weiner, January; Polanska, Joanna

    2017-05-12

    There exist many methods for describing the complex relation between changes of gene expression in molecular pathways or gene ontologies under different experimental conditions. Among them, Gene Set Enrichment Analysis seems to be one of the most commonly used (over 10,000 citations). An important parameter, which could affect the final result, is the choice of a metric for the ranking of genes. Applying a default ranking metric may lead to poor results. In this work 28 benchmark data sets were used to evaluate the sensitivity and false positive rate of gene set analysis for 16 different ranking metrics including new proposals. Furthermore, the robustness of the chosen methods to sample size was tested. Using k-means clustering algorithm a group of four metrics with the highest performance in terms of overall sensitivity, overall false positive rate and computational load was established i.e. absolute value of Moderated Welch Test statistic, Minimum Significant Difference, absolute value of Signal-To-Noise ratio and Baumgartner-Weiss-Schindler test statistic. In case of false positive rate estimation, all selected ranking metrics were robust with respect to sample size. In case of sensitivity, the absolute value of Moderated Welch Test statistic and absolute value of Signal-To-Noise ratio gave stable results, while Baumgartner-Weiss-Schindler and Minimum Significant Difference showed better results for larger sample size. Finally, the Gene Set Enrichment Analysis method with all tested ranking metrics was parallelised and implemented in MATLAB, and is available at https://github.com/ZAEDPolSl/MrGSEA . Choosing a ranking metric in Gene Set Enrichment Analysis has critical impact on results of pathway enrichment analysis. The absolute value of Moderated Welch Test has the best overall sensitivity and Minimum Significant Difference has the best overall specificity of gene set analysis. When the number of non-normally distributed genes is high, using Baumgartner

  10. Stochastic biological response to radiation. Comprehensive analysis of gene expression

    International Nuclear Information System (INIS)

    Inoue, Tohru; Hirabayashi, Yoko

    2012-01-01

    Authors explain that the radiation effect on biological system is stochastic along the law of physics, differing from chemical effect, using instances of Cs-137 gamma-ray (GR) and benzene (BZ) exposures to mice and of resultant comprehensive analyses of gene expression. Single GR irradiation is done with Gamma Cell 40 (CSR) to C57BL/6 or C3H/He mouse at 0, 0.6 and 3 Gy. BE is given orally at 150 mg/kg/day for 5 days x 2 weeks. Bone marrow cells are sampled 1 month after the exposure. Comprehensive gene expression is analyzed by Gene Chip Mouse Genome 430 2.0 Array (Affymetrix) and data are processed by programs like case normalization, statistics, network generation, functional analysis etc. GR irradiation brings about changes of gene expression, which are classifiable in common genes variable commonly on the dose change and stochastic genes variable stochastically within each dose: e.g., with Welch-t-test, significant differences are between 0/3 Gy (dose-specific difference, 455 pbs (probe set), in stochastic 2113 pbs), 0/0.6 Gy (267 in 1284 pbs) and 0.6/3 Gy (532 pbs); and with one-way analysis of variation (ANOVA) and hierarchial/dendrographic analyses, 520 pbs are shown to involve the dose-dependent 226 and dose-specific 294 pbs. It is also shown that at 3 Gy, expression of common genes are rather suppressed, including those related to the proliferation/apoptosis of B/T cells, and of stochastic genes, related to cell division/signaling. Ven diagram of the common genes of above 520 pbs, stochastic 2113 pbs at 3 Gy and 1284 pbs at 0.6 Gy shows the overlapping genes 29, 2 and 4, respectively, indicating only 35 pbs are overlapping in total. Network analysis of changes by GR shows the rather high expression of genes around hub of cAMP response element binding protein (CREB) at 0.6 Gy, and rather variable expression around CREB hub/suppressed expression of kinesin hub at 3 Gy; in the network by BZ exposure, unchanged or low expression around p53 hub and suppression

  11. Detection and sequence analysis of accessory gene regulator genes of Staphylococcus pseudintermedius isolates

    Directory of Open Access Journals (Sweden)

    M. Ananda Chitra

    2015-07-01

    Full Text Available Background: Staphylococcus pseudintermedius (SP is the major pathogenic species of dogs involved in a wide variety of skin and soft tissue infections. The accessory gene regulator (agr locus of Staphylococcus aureus has been extensively studied, and it influences the expression of many virulence genes. It encodes a two-component signal transduction system that leads to down-regulation of surface proteins and up-regulation of secreted proteins during in vitro growth of S. aureus. The objective of this study was to detect and sequence analyzing the AgrA, B, and D of SP isolated from canine skin infections. Materials and Methods: In this study, we have isolated and identified SP from canine pyoderma and otitis cases by polymerase chain reaction (PCR and confirmed by PCR-restriction fragment length polymorphism. Primers for SP agrA and agrBD genes were designed using online primer designing software and BLAST searched for its specificity. Amplification of the agr genes was carried out for 53 isolates of SP by PCR and sequencing of agrA, B, and D were carried out for five isolates and analyzed using DNAstar and Mega5.2 software. Results: A total of 53 (59% SP isolates were obtained from 90 samples. 15 isolates (28% were confirmed to be methicillinresistant SP (MRSP with the detection of the mecA gene. Accessory gene regulator A, B, and D genes were detected in all the SP isolates. Complete nucleotide sequences of the above three genes for five isolates were submitted to GenBank, and their accession numbers are from KJ133557 to KJ133571. AgrA amino acid sequence analysis showed that it is mainly made of alpha-helices and is hydrophilic in nature. AgrB is a transmembrane protein, and AgrD encodes the precursor of the autoinducing peptide (AIP. Sequencing of the agrD gene revealed that the 5 canine SP strains tested could be divided into three Agr specificity groups (RIPTSTGFF, KIPTSTGFF, and RIPISTGFF based on the putative AIP produced by each strain

  12. Evolutionary Analysis of Minor Histocompatibility Genes In Hydra

    KAUST Repository

    Aalismail, Nojood

    2016-01-01

    In the present study we took initiative to study the self/nonself recognition in hydra and its relation to the immune response. Moreover, performing phylogenetic analysis to look for annotated immune genes in hydra gave us a potential to analyze the expression of minor histocompatibility genes that have been shown to play a major role in grafting and transplantation in mammals. Here we obtained the cDNA library that shows expression of minor histocompatibility genes and confirmed that the annotated sequences in databases are actually present. In addition, grafting experiments suggested, although still preliminary, that homograft showed less rejection response than in heterograft. Involvement of possible minor histocompatibility gene orthologous in immune response was examined by qPCR.

  13. Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser

    LENUS (Irish Health Repository)

    Fitzpatrick, David A

    2010-05-10

    Abstract Background Candida species are the most common cause of opportunistic fungal infection worldwide. Recent sequencing efforts have provided a wealth of Candida genomic data. We have developed the Candida Gene Order Browser (CGOB), an online tool that aids comparative syntenic analyses of Candida species. CGOB incorporates all available Candida clade genome sequences including two Candida albicans isolates (SC5314 and WO-1) and 8 closely related species (Candida dubliniensis, Candida tropicalis, Candida parapsilosis, Lodderomyces elongisporus, Debaryomyces hansenii, Pichia stipitis, Candida guilliermondii and Candida lusitaniae). Saccharomyces cerevisiae is also included as a reference genome. Results CGOB assignments of homology were manually curated based on sequence similarity and synteny. In total CGOB includes 65617 genes arranged into 13625 homology columns. We have also generated improved Candida gene sets by merging\\/removing partial genes in each genome. Interrogation of CGOB revealed that the majority of tandemly duplicated genes are under strong purifying selection in all Candida species. We identified clusters of adjacent genes involved in the same metabolic pathways (such as catabolism of biotin, galactose and N-acetyl glucosamine) and we showed that some clusters are species or lineage-specific. We also identified one example of intron gain in C. albicans. Conclusions Our analysis provides an important resource that is now available for the Candida community. CGOB is available at http:\\/\\/cgob.ucd.ie.

  14. Evaluation of reference genes for gene expression analysis using quantitative RT-PCR in Azospirillum brasilense.

    Science.gov (United States)

    McMillan, Mary; Pereg, Lily

    2014-01-01

    Azospirillum brasilense is a nitrogen fixing bacterium that has been shown to have various beneficial effects on plant growth and yield. Under normal conditions A. brasilense exists in a motile flagellated form, which, under starvation or stress conditions, can undergo differentiation into an encapsulated, cyst-like form. Quantitative RT-PCR can be used to analyse changes in gene expression during this differentiation process. The accuracy of quantification of mRNA levels by qRT-PCR relies on the normalisation of data against stably expressed reference genes. No suitable set of reference genes has yet been described for A. brasilense. Here we evaluated the expression of ten candidate reference genes (16S rRNA, gapB, glyA, gyrA, proC, pykA, recA, recF, rpoD, and tpiA) in wild-type and mutant A. brasilense strains under different culture conditions, including conditions that induce differentiation. Analysis with the software programs BestKeeper, NormFinder and GeNorm indicated that gyrA, glyA and recA are the most stably expressed reference genes in A. brasilense. The results also suggested that the use of two reference genes (gyrA and glyA) is sufficient for effective normalisation of qRT-PCR data.

  15. Evaluation of reference genes for gene expression analysis using quantitative RT-PCR in Azospirillum brasilense.

    Directory of Open Access Journals (Sweden)

    Mary McMillan

    Full Text Available Azospirillum brasilense is a nitrogen fixing bacterium that has been shown to have various beneficial effects on plant growth and yield. Under normal conditions A. brasilense exists in a motile flagellated form, which, under starvation or stress conditions, can undergo differentiation into an encapsulated, cyst-like form. Quantitative RT-PCR can be used to analyse changes in gene expression during this differentiation process. The accuracy of quantification of mRNA levels by qRT-PCR relies on the normalisation of data against stably expressed reference genes. No suitable set of reference genes has yet been described for A. brasilense. Here we evaluated the expression of ten candidate reference genes (16S rRNA, gapB, glyA, gyrA, proC, pykA, recA, recF, rpoD, and tpiA in wild-type and mutant A. brasilense strains under different culture conditions, including conditions that induce differentiation. Analysis with the software programs BestKeeper, NormFinder and GeNorm indicated that gyrA, glyA and recA are the most stably expressed reference genes in A. brasilense. The results also suggested that the use of two reference genes (gyrA and glyA is sufficient for effective normalisation of qRT-PCR data.

  16. Analog circuit design designing dynamic circuit response

    CERN Document Server

    Feucht, Dennis

    2010-01-01

    This second volume, Designing Dynamic Circuit Response builds upon the first volume Designing Amplifier Circuits by extending coverage to include reactances and their time- and frequency-related behavioral consequences.

  17. Trigger circuit

    International Nuclear Information System (INIS)

    Verity, P.R.; Chaplain, M.D.; Turner, G.D.J.

    1984-01-01

    A monostable trigger circuit comprises transistors TR2 and TR3 arranged with their collectors and bases interconnected. The collector of the transistor TR2 is connected to the base of transistor TR3 via a capacitor C2 the main current path of a grounded base transistor TR1 and resistive means R2,R3. The collector of transistor TR3 is connected to the base of transistor TR2 via resistive means R6, R7. In the stable state all the transistors are OFF, the capacitor C2 is charged, and the output is LOW. A positive pulse input to the base of TR2 switches it ON, which in turn lowers the voltage at points A and B and so switches TR1 ON so that C2 can discharge via R2, R3, which in turn switches TR3 ON making the output high. Thus all three transistors are latched ON. When C2 has discharged sufficiently TR1 switches OFF, followed by TR3 (making the output low again) and TR2. The components C1, C3 and R4 serve to reduce noise, and the diode D1 is optional. (author)

  18. Network Graph Analysis of Gene-Gene Interactions in Genome-Wide Association Study Data

    Directory of Open Access Journals (Sweden)

    Sungyoung Lee

    2012-12-01

    Full Text Available Most common complex traits, such as obesity, hypertension, diabetes, and cancers, are known to be associated with multiple genes, environmental factors, and their epistasis. Recently, the development of advanced genotyping technologies has allowed us to perform genome-wide association studies (GWASs. For detecting the effects of multiple genes on complex traits, many approaches have been proposed for GWASs. Multifactor dimensionality reduction (MDR is one of the powerful and efficient methods for detecting high-order gene-gene (GxG interactions. However, the biological interpretation of GxG interactions identified by MDR analysis is not easy. In order to aid the interpretation of MDR results, we propose a network graph analysis to elucidate the meaning of identified GxG interactions. The proposed network graph analysis consists of three steps. The first step is for performing GxG interaction analysis using MDR analysis. The second step is to draw the network graph using the MDR result. The third step is to provide biological evidence of the identified GxG interaction using external biological databases. The proposed method was applied to Korean Association Resource (KARE data, containing 8838 individuals with 327,632 single-nucleotide polymorphisms, in order to perform GxG interaction analysis of body mass index (BMI. Our network graph analysis successfully showed that many identified GxG interactions have known biological evidence related to BMI. We expect that our network graph analysis will be helpful to interpret the biological meaning of GxG interactions.

  19. The identification of functional motifs in temporal gene expression analysis

    Directory of Open Access Journals (Sweden)

    Michael G. Surette

    2005-01-01

    Full Text Available The identification of transcription factor binding sites is essential to the understanding of the regulation of gene expression and the reconstruction of genetic regulatory networks. The in silico identification of cis-regulatory motifs is challenging due to sequence variability and lack of sufficient data to generate consensus motifs that are of quantitative or even qualitative predictive value. To determine functional motifs in gene expression, we propose a strategy to adopt false discovery rate (FDR and estimate motif effects to evaluate combinatorial analysis of motif candidates and temporal gene expression data. The method decreases the number of predicted motifs, which can then be confirmed by genetic analysis. To assess the method we used simulated motif/expression data to evaluate parameters. We applied this approach to experimental data for a group of iron responsive genes in Salmonella typhimurium 14028S. The method identified known and potentially new ferric-uptake regulator (Fur binding sites. In addition, we identified uncharacterized functional motif candidates that correlated with specific patterns of expression. A SAS code for the simulation and analysis gene expression data is available from the first author upon request.

  20. Analysis of the clonal repertoire of gene-corrected cells in gene therapy.

    Science.gov (United States)

    Paruzynski, Anna; Glimm, Hanno; Schmidt, Manfred; Kalle, Christof von

    2012-01-01

    Gene therapy-based clinical phase I/II studies using integrating retroviral vectors could successfully treat different monogenetic inherited diseases. However, with increased efficiency of this therapy, severe side effects occurred in various gene therapy trials. In all cases, integration of the vector close to or within a proto-oncogene contributed substantially to the development of the malignancies. Thus, the in-depth analysis of integration site patterns is of high importance to uncover potential clonal outgrowth and to assess the safety of gene transfer vectors and gene therapy protocols. The standard and nonrestrictive linear amplification-mediated PCR (nrLAM-PCR) in combination with high-throughput sequencing exhibits technologies that allow to comprehensively analyze the clonal repertoire of gene-corrected cells and to assess the safety of the used vector system at an early stage on the molecular level. It enables clarifying the biological consequences of the vector system on the fate of the transduced cell. Furthermore, the downstream performance of real-time PCR allows a quantitative estimation of the clonality of individual cells and their clonal progeny. Here, we present a guideline that should allow researchers to perform comprehensive integration site analysis in preclinical and clinical studies. Copyright © 2012 Elsevier Inc. All rights reserved.

  1. Integrative analysis of RUNX1 downstream pathways and target genes

    Directory of Open Access Journals (Sweden)

    Liu Marjorie

    2008-07-01

    Full Text Available Abstract Background The RUNX1 transcription factor gene is frequently mutated in sporadic myeloid and lymphoid leukemia through translocation, point mutation or amplification. It is also responsible for a familial platelet disorder with predisposition to acute myeloid leukemia (FPD-AML. The disruption of the largely unknown biological pathways controlled by RUNX1 is likely to be responsible for the development of leukemia. We have used multiple microarray platforms and bioinformatic techniques to help identify these biological pathways to aid in the understanding of why RUNX1 mutations lead to leukemia. Results Here we report genes regulated either directly or indirectly by RUNX1 based on the study of gene expression profiles generated from 3 different human and mouse platforms. The platforms used were global gene expression profiling of: 1 cell lines with RUNX1 mutations from FPD-AML patients, 2 over-expression of RUNX1 and CBFβ, and 3 Runx1 knockout mouse embryos using either cDNA or Affymetrix microarrays. We observe that our datasets (lists of differentially expressed genes significantly correlate with published microarray data from sporadic AML patients with mutations in either RUNX1 or its cofactor, CBFβ. A number of biological processes were identified among the differentially expressed genes and functional assays suggest that heterozygous RUNX1 point mutations in patients with FPD-AML impair cell proliferation, microtubule dynamics and possibly genetic stability. In addition, analysis of the regulatory regions of the differentially expressed genes has for the first time systematically identified numerous potential novel RUNX1 target genes. Conclusion This work is the first large-scale study attempting to identify the genetic networks regulated by RUNX1, a master regulator in the development of the hematopoietic system and leukemia. The biological pathways and target genes controlled by RUNX1 will have considerable importance in disease

  2. Biclustering methods: biological relevance and application in gene expression analysis.

    Directory of Open Access Journals (Sweden)

    Ali Oghabian

    Full Text Available DNA microarray technologies are used extensively to profile the expression levels of thousands of genes under various conditions, yielding extremely large data-matrices. Thus, analyzing this information and extracting biologically relevant knowledge becomes a considerable challenge. A classical approach for tackling this challenge is to use clustering (also known as one-way clustering methods where genes (or respectively samples are grouped together based on the similarity of their expression profiles across the set of all samples (or respectively genes. An alternative approach is to develop biclustering methods to identify local patterns in the data. These methods extract subgroups of genes that are co-expressed across only a subset of samples and may feature important biological or medical implications. In this study we evaluate 13 biclustering and 2 clustering (k-means and hierarchical methods. We use several approaches to compare their performance on two real gene expression data sets. For this purpose we apply four evaluation measures in our analysis: (1 we examine how well the considered (biclustering methods differentiate various sample types; (2 we evaluate how well the groups of genes discovered by the (biclustering methods are annotated with similar Gene Ontology categories; (3 we evaluate the capability of the methods to differentiate genes that are known to be specific to the particular sample types we study and (4 we compare the running time of the algorithms. In the end, we conclude that as long as the samples are well defined and annotated, the contamination of the samples is limited, and the samples are well replicated, biclustering methods such as Plaid and SAMBA are useful for discovering relevant subsets of genes and samples.

  3. Spectral map-analysis: a method to analyze gene expression data

    OpenAIRE

    Bijnens, Luc J.M.; Lewi, Paul J.; Göhlmann, Hinrich W.; Molenberghs, Geert; Wouters, Luc

    2004-01-01

    bioinformatics; biplot; correspondence factor analysis; data mining; data visualization; gene expression data; microarray data; multivariate exploratory data analysis; principal component analysis; Spectral map analysis

  4. Comprehensive analysis of gene expression patterns of hedgehog-related genes

    Directory of Open Access Journals (Sweden)

    Baillie David

    2006-10-01

    Full Text Available Abstract Background The Caenorhabditis elegans genome encodes ten proteins that share sequence similarity with the Hedgehog signaling molecule through their C-terminal autoprocessing Hint/Hog domain. These proteins contain novel N-terminal domains, and C. elegans encodes dozens of additional proteins containing only these N-terminal domains. These gene families are called warthog, groundhog, ground-like and quahog, collectively called hedgehog (hh-related genes. Previously, the expression pattern of seventeen genes was examined, which showed that they are primarily expressed in the ectoderm. Results With the completion of the C. elegans genome sequence in November 2002, we reexamined and identified 61 hh-related ORFs. Further, we identified 49 hh-related ORFs in C. briggsae. ORF analysis revealed that 30% of the genes still had errors in their predictions and we improved these predictions here. We performed a comprehensive expression analysis using GFP fusions of the putative intergenic regulatory sequence with one or two transgenic lines for most genes. The hh-related genes are expressed in one or a few of the following tissues: hypodermis, seam cells, excretory duct and pore cells, vulval epithelial cells, rectal epithelial cells, pharyngeal muscle or marginal cells, arcade cells, support cells of sensory organs, and neuronal cells. Using time-lapse recordings, we discovered that some hh-related genes are expressed in a cyclical fashion in phase with molting during larval development. We also generated several translational GFP fusions, but they did not show any subcellular localization. In addition, we also studied the expression patterns of two genes with similarity to Drosophila frizzled, T23D8.1 and F27E11.3A, and the ortholog of the Drosophila gene dally-like, gpn-1, which is a heparan sulfate proteoglycan. The two frizzled homologs are expressed in a few neurons in the head, and gpn-1 is expressed in the pharynx. Finally, we compare the

  5. Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis

    Directory of Open Access Journals (Sweden)

    Ueki Masao

    2012-05-01

    Full Text Available Abstract Background Genome-wide gene-gene interaction analysis using single nucleotide polymorphisms (SNPs is an attractive way for identification of genetic components that confers susceptibility of human complex diseases. Individual hypothesis testing for SNP-SNP pairs as in common genome-wide association study (GWAS however involves difficulty in setting overall p-value due to complicated correlation structure, namely, the multiple testing problem that causes unacceptable false negative results. A large number of SNP-SNP pairs than sample size, so-called the large p small n problem, precludes simultaneous analysis using multiple regression. The method that overcomes above issues is thus needed. Results We adopt an up-to-date method for ultrahigh-dimensional variable selection termed the sure independence screening (SIS for appropriate handling of numerous number of SNP-SNP interactions by including them as predictor variables in logistic regression. We propose ranking strategy using promising dummy coding methods and following variable selection procedure in the SIS method suitably modified for gene-gene interaction analysis. We also implemented the procedures in a software program, EPISIS, using the cost-effective GPGPU (General-purpose computing on graphics processing units technology. EPISIS can complete exhaustive search for SNP-SNP interactions in standard GWAS dataset within several hours. The proposed method works successfully in simulation experiments and in application to real WTCCC (Wellcome Trust Case–control Consortium data. Conclusions Based on the machine-learning principle, the proposed method gives powerful and flexible genome-wide search for various patterns of gene-gene interaction.

  6. Realization of a counter/timer circuit used in digital pulse height analysis in a single chip

    International Nuclear Information System (INIS)

    Mahmoud, I.I.

    2000-01-01

    This paper presents a single chip realization of a counter circuit, which is used in random signal processing and nuclear gamma ray spectrometers. The circuit contains a counter to count the repetition rate of a selected pulse train coming from a single channel analyzer circuit. Also, it contains a timer to measure the accumulation period. The timer possesses a predetermined time facility so that processing lasts for a certain adjustable predetermined period. The counter and the timer are synchronized to start and stop simultaneously at the beginning and end of the counting interval. A multiplexed BCD to 7-segment decoder/driver is also included in the circuit. The multiplexing allows the decrease of pin count of the chip.Two stages are designed, simulated for a single channel, however more stages and channels can be added by copying the designed circuits. Schematic flow of Xilinx v.1.2I is used as the design strategy with top-level schematic design containing VHDL and schematic macros

  7. Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm

    Science.gov (United States)

    Rosli, Rozana; Amiruddin, Nadzirah; Ab Halim, Mohd Amin; Chan, Pek-Lan; Chan, Kuang-Lim; Azizi, Norazah; Morris, Priscilla E.; Leslie Low, Eng-Ti; Ong-Abdullah, Meilina; Sambanthamurthi, Ravigadevi; Singh, Rajinder

    2018-01-01

    Comparative genomics and transcriptomic analyses were performed on two agronomically important groups of genes from oil palm versus other major crop species and the model organism, Arabidopsis thaliana. The first analysis was of two gene families with key roles in regulation of oil quality and in particular the accumulation of oleic acid, namely stearoyl ACP desaturases (SAD) and acyl-acyl carrier protein (ACP) thioesterases (FAT). In both cases, these were found to be large gene families with complex expression profiles across a wide range of tissue types and developmental stages. The detailed classification of the oil palm SAD and FAT genes has enabled the updating of the latest version of the oil palm gene model. The second analysis focused on disease resistance (R) genes in order to elucidate possible candidates for breeding of pathogen tolerance/resistance. Ortholog analysis showed that 141 out of the 210 putative oil palm R genes had homologs in banana and rice. These genes formed 37 clusters with 634 orthologous genes. Classification of the 141 oil palm R genes showed that the genes belong to the Kinase (7), CNL (95), MLO-like (8), RLK (3) and Others (28) categories. The CNL R genes formed eight clusters. Expression data for selected R genes also identified potential candidates for breeding of disease resistance traits. Furthermore, these findings can provide information about the species evolution as well as the identification of agronomically important genes in oil palm and other major crops. PMID:29672525

  8. Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm.

    Science.gov (United States)

    Rosli, Rozana; Amiruddin, Nadzirah; Ab Halim, Mohd Amin; Chan, Pek-Lan; Chan, Kuang-Lim; Azizi, Norazah; Morris, Priscilla E; Leslie Low, Eng-Ti; Ong-Abdullah, Meilina; Sambanthamurthi, Ravigadevi; Singh, Rajinder; Murphy, Denis J

    2018-01-01

    Comparative genomics and transcriptomic analyses were performed on two agronomically important groups of genes from oil palm versus other major crop species and the model organism, Arabidopsis thaliana. The first analysis was of two gene families with key roles in regulation of oil quality and in particular the accumulation of oleic acid, namely stearoyl ACP desaturases (SAD) and acyl-acyl carrier protein (ACP) thioesterases (FAT). In both cases, these were found to be large gene families with complex expression profiles across a wide range of tissue types and developmental stages. The detailed classification of the oil palm SAD and FAT genes has enabled the updating of the latest version of the oil palm gene model. The second analysis focused on disease resistance (R) genes in order to elucidate possible candidates for breeding of pathogen tolerance/resistance. Ortholog analysis showed that 141 out of the 210 putative oil palm R genes had homologs in banana and rice. These genes formed 37 clusters with 634 orthologous genes. Classification of the 141 oil palm R genes showed that the genes belong to the Kinase (7), CNL (95), MLO-like (8), RLK (3) and Others (28) categories. The CNL R genes formed eight clusters. Expression data for selected R genes also identified potential candidates for breeding of disease resistance traits. Furthermore, these findings can provide information about the species evolution as well as the identification of agronomically important genes in oil palm and other major crops.

  9. Genomewide analysis of TCP transcription factor gene family in ...

    Indian Academy of Sciences (India)

    2014-12-09

    Dec 9, 2014 ... study of a genomewide analysis of apple TCP gene family. These results provide .... synthesize the first-strand cDNA using the PrimeScript First. Strand cDNA ..... only detected in the stem, leaf and fruit (figure 8). When.

  10. Genomewide analysis of TCP transcription factor gene family in ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 93; Issue 3. Genomewide ... Teosinte branched1/cycloidea/proliferating cell factor1 (TCP) proteins are a large family of transcriptional regulators in angiosperms. They are ... To the best of our knowledge, this is the first study of a genomewide analysis of apple TCP gene family.

  11. Expression and functional analysis of apoptosis-related gene ...

    African Journals Online (AJOL)

    Administrator

    2011-10-19

    Oct 19, 2011 ... conducted a molecular cloning and functional analysis to study a specific silkworm gene BmICAD related to apoptosis. .... blocking with 5% non-fat milk for 1 h at room temperature, the .... requirements for all next experiments.

  12. Characterization and phylogenetic analysis of α-gliadin gene ...

    Indian Academy of Sciences (India)

    Supplementary data: Characterization and phylogenetic analysis of α-gliadin gene sequences reveals significant genomic divergence in Triticeae species. Guang-Rong Li, Tao Lang, En-Nian Yang, Cheng Liu ... The MITE insertion at the 3 UTR is boxed. Figure 2. The secondary structure of MITE insertion in HM452949.

  13. Comparative modular analysis of gene expression in vertebrate organs

    Directory of Open Access Journals (Sweden)

    Piasecka Barbara

    2012-03-01

    Full Text Available Abstract Background The degree of conservation of gene expression between homologous organs largely remains an open question. Several recent studies reported some evidence in favor of such conservation. Most studies compute organs' similarity across all orthologous genes, whereas the expression level of many genes are not informative about organ specificity. Results Here, we use a modularization algorithm to overcome this limitation through the identification of inter-species co-modules of organs and genes. We identify such co-modules using mouse and human microarray expression data. They are functionally coherent both in terms of genes and of organs from both organisms. We show that a large proportion of genes belonging to the same co-module are orthologous between mouse and human. Moreover, their zebrafish orthologs also tend to be expressed in the corresponding homologous organs. Notable exceptions to the general pattern of conservation are the testis and the olfactory bulb. Interestingly, some co-modules consist of single organs, while others combine several functionally related organs. For instance, amygdala, cerebral cortex, hypothalamus and spinal cord form a clearly discernible unit of expression, both in mouse and human. Conclusions Our study provides a new framework for comparative analysis which will be applicable also to other sets of large-scale phenotypic data collected across different species.

  14. Comparative modular analysis of gene expression in vertebrate organs.

    Science.gov (United States)

    Piasecka, Barbara; Kutalik, Zoltán; Roux, Julien; Bergmann, Sven; Robinson-Rechavi, Marc

    2012-03-29

    The degree of conservation of gene expression between homologous organs largely remains an open question. Several recent studies reported some evidence in favor of such conservation. Most studies compute organs' similarity across all orthologous genes, whereas the expression level of many genes are not informative about organ specificity. Here, we use a modularization algorithm to overcome this limitation through the identification of inter-species co-modules of organs and genes. We identify such co-modules using mouse and human microarray expression data. They are functionally coherent both in terms of genes and of organs from both organisms. We show that a large proportion of genes belonging to the same co-module are orthologous between mouse and human. Moreover, their zebrafish orthologs also tend to be expressed in the corresponding homologous organs. Notable exceptions to the general pattern of conservation are the testis and the olfactory bulb. Interestingly, some co-modules consist of single organs, while others combine several functionally related organs. For instance, amygdala, cerebral cortex, hypothalamus and spinal cord form a clearly discernible unit of expression, both in mouse and human. Our study provides a new framework for comparative analysis which will be applicable also to other sets of large-scale phenotypic data collected across different species.

  15. Xylella fastidiosa gene expression analysis by DNA microarrays

    Directory of Open Access Journals (Sweden)

    Regiane F. Travensolo

    2009-01-01

    Full Text Available Xylella fastidiosa genome sequencing has generated valuable data by identifying genes acting either on metabolic pathways or in associated pathogenicity and virulence. Based on available information on these genes, new strategies for studying their expression patterns, such as microarray technology, were employed. A total of 2,600 primer pairs were synthesized and then used to generate fragments using the PCR technique. The arrays were hybridized against cDNAs labeled during reverse transcription reactions and which were obtained from bacteria grown under two different conditions (liquid XDM2 and liquid BCYE. All data were statistically analyzed to verify which genes were differentially expressed. In addition to exploring conditions for X. fastidiosa genome-wide transcriptome analysis, the present work observed the differential expression of several classes of genes (energy, protein, amino acid and nucleotide metabolism, transport, degradation of substances, toxins and hypothetical proteins, among others. The understanding of expressed genes in these two different media will be useful in comprehending the metabolic characteristics of X. fastidiosa, and in evaluating how important certain genes are for the functioning and survival of these bacteria in plants.

  16. Expression analysis of dihydroflavonol 4-reductase genes in Petunia hybrida.

    Science.gov (United States)

    Chu, Y X; Chen, H R; Wu, A Z; Cai, R; Pan, J S

    2015-05-12

    Dihydroflavonol 4-reductase (DFR) genes from Rosa chinensis (Asn type) and Calibrachoa hybrida (Asp type), driven by a CaMV 35S promoter, were integrated into the petunia (Petunia hybrida) cultivar 9702. Exogenous DFR gene expression characteristics were similar to flower-color changes, and effects on anthocyanin concentration were observed in both types of DFR gene transformants. Expression analysis showed that exogenous DFR genes were expressed in all of the tissues, but the expression levels were significantly different. However, both of them exhibited a high expression level in petals that were starting to open. The introgression of DFR genes may significantly change DFR enzyme activity. Anthocyanin ultra-performance liquid chromatography results showed that anthocyanin concentrations changed according to DFR enzyme activity. Therefore, the change in flower color was probably the result of a DFR enzyme change. Pelargonidin 3-O-glucoside was found in two different transgenic petunias, indicating that both CaDFR and RoDFR could catalyze dihydrokaempferol. Our results also suggest that transgenic petunias with DFR gene of Asp type could biosynthesize pelargonidin 3-O-glucoside.

  17. Transient analysis of the output short-circuit fault of high power and high voltage DC power supply

    International Nuclear Information System (INIS)

    Yang Zhigang; Zhang Jian; Huang Yiyun; Hao Xu; Sun Haozhang; Guo Fei

    2014-01-01

    The transient conditions of output short-circuit fault of high voltage DC power supply was introduced, and the energy of power supply injecting into klystron during the protection process of three-electrode gas switch were analyzed and calculated in detail when klystron load happening electrode arc faults. The results of calculation and simulation are consistent with the results of the experiment. When the output short-circuit fault of high voltage power supply occurs, switch can be shut off in the microsecond, and the short circuit current can be controlled in 200 A. It has verified the rapidity and reliability of the three-electrode gas switch protection, and it has engineering application value. (authors)

  18. A comparative mathematical analysis of RL and RC electrical circuits via Atangana-Baleanu and Caputo-Fabrizio fractional derivatives

    Science.gov (United States)

    Abro, Kashif Ali; Memon, Anwar Ahmed; Uqaili, Muhammad Aslam

    2018-03-01

    This research article is analyzed for the comparative study of RL and RC electrical circuits by employing newly presented Atangana-Baleanu and Caputo-Fabrizio fractional derivatives. The governing ordinary differential equations of RL and RC electrical circuits have been fractionalized in terms of fractional operators in the range of 0 ≤ ξ ≤ 1 and 0 ≤ η ≤ 1. The analytic solutions of fractional differential equations for RL and RC electrical circuits have been solved by using the Laplace transform with its inversions. General solutions have been investigated for periodic and exponential sources by implementing the Atangana-Baleanu and Caputo-Fabrizio fractional operators separately. The investigated solutions have been expressed in terms of simple elementary functions with convolution product. On the basis of newly fractional derivatives with and without singular kernel, the voltage and current have interesting behavior with several similarities and differences for the periodic and exponential sources.

  19. Analysis of multiple spurions and associated circuits in Cofrentes; Analisis de espurios multiples y circuitos asociados en C.N. Cofrentes

    Energy Technology Data Exchange (ETDEWEB)

    Molina, J. J.; Celaya, M. A.

    2015-07-01

    The article describes the process followed by the Cofrentes Nuclear Power Plant (CNC) to conduct the analysis of multiple spurious in compliance with regulatory standards IS-30 rev 1 and CSN Safety Guide 1.19 based on the recommendations of the NEI-00-01 Guidance for Post-fire Safe Shutdown Circuit and NUREG/CR-6850. Fire PRA Methodology for Nuclear Power Facilities. (Author)

  20. Analysis of the impact of connecting a larger number of small hydroelectric power plants to the short-circuit currents values and relay protection system of distribution network

    Directory of Open Access Journals (Sweden)

    Sučević Nikola

    2017-01-01

    Full Text Available In this paper the influence of a large number of small hydro power plants on the short-circuit currents is analysed, as well as the operation of the relay protection system within the real distribution network in Serbia. The necessary modification of the existing protection functions, as well as the implementation of the new proposed protection functions, are presented and discussed. Network modeling and analysis are performed using the program tool DIgSILENT PowerFactory.

  1. Evolutionary Analysis of Minor Histocompatibility Genes In Hydra

    KAUST Repository

    Aalismail, Nojood

    2016-05-01

    Hydra is a simple freshwater solitary polyp used as a model system to study evolutionary aspects. The immune response of this organism has not been studied extensively and the immune response genes have not been identified and characterized. On the other hand, immune response has been investigated and genetic analysis has been initiated in other lower invertebrates. In the present study we took initiative to study the self/nonself recognition in hydra and its relation to the immune response. Moreover, performing phylogenetic analysis to look for annotated immune genes in hydra gave us a potential to analyze the expression of minor histocompatibility genes that have been shown to play a major role in grafting and transplantation in mammals. Here we obtained the cDNA library that shows expression of minor histocompatibility genes and confirmed that the annotated sequences in databases are actually present. In addition, grafting experiments suggested, although still preliminary, that homograft showed less rejection response than in heterograft. Involvement of possible minor histocompatibility gene orthologous in immune response was examined by qPCR.

  2. Network Analysis of Human Genes Influencing Susceptibility to Mycobacterial Infections

    Science.gov (United States)

    Lipner, Ettie M.; Garcia, Benjamin J.; Strong, Michael

    2016-01-01

    Tuberculosis and nontuberculous mycobacterial infections constitute a high burden of pulmonary disease in humans, resulting in over 1.5 million deaths per year. Building on the premise that genetic factors influence the instance, progression, and defense of infectious disease, we undertook a systems biology approach to investigate relationships among genetic factors that may play a role in increased susceptibility or control of mycobacterial infections. We combined literature and database mining with network analysis and pathway enrichment analysis to examine genes, pathways, and networks, involved in the human response to Mycobacterium tuberculosis and nontuberculous mycobacterial infections. This approach allowed us to examine functional relationships among reported genes, and to identify novel genes and enriched pathways that may play a role in mycobacterial susceptibility or control. Our findings suggest that the primary pathways and genes influencing mycobacterial infection control involve an interplay between innate and adaptive immune proteins and pathways. Signaling pathways involved in autoimmune disease were significantly enriched as revealed in our networks. Mycobacterial disease susceptibility networks were also examined within the context of gene-chemical relationships, in order to identify putative drugs and nutrients with potential beneficial immunomodulatory or anti-mycobacterial effects. PMID:26751573

  3. Serial analysis of gene expression in the silkworm, Bombyx mori.

    Science.gov (United States)

    Huang, Jianhua; Miao, Xuexia; Jin, Weirong; Couble, Pierre; Mita, Kasuei; Zhang, Yong; Liu, Wenbin; Zhuang, Leijun; Shen, Yan; Keime, Celine; Gandrillon, Olivier; Brouilly, Patrick; Briolay, Jerome; Zhao, Guoping; Huang, Yongping

    2005-08-01

    The silkworm Bombyx mori is one of the most economically important insects and serves as a model for Lepidoptera insects. We used serial analysis of gene expression (SAGE) to derive profiles of expressed genes during the developmental life cycle of the silkworm and to create a reference for understanding silkworm metamorphosis. We generated four SAGE libraries, one from each of the four developmental stages of the silkworm. In total we obtained 257,964 SAGE tags, of which 39,485 were unique tags. Sorted by copy number, 14.1% of the unique tags were detected at a median to high level (five or more copies), 24.2% at lower levels (two to four copies), and 61.7% as single copies. Using a basic local alignment search tool on the EST database, 35% of the tags matched known silkworm expressed sequence tags. SAGE demonstrated that a number of the genes were up- or down-regulated during the four developmental phases of the egg, larva, pupa, and adult. Furthermore, we found that the generation of longer cDNA fragments from SAGE tags constituted the most efficient method of gene identification, which facilitated the analysis of a large number of unknown genes.

  4. Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool.

    Science.gov (United States)

    Clark, Neil R; Szymkiewicz, Maciej; Wang, Zichen; Monteiro, Caroline D; Jones, Matthew R; Ma'ayan, Avi

    2015-11-01

    Gene set analysis of differential expression, which identifies collectively differentially expressed gene sets, has become an important tool for biology. The power of this approach lies in its reduction of the dimensionality of the statistical problem and its incorporation of biological interpretation by construction. Many approaches to gene set analysis have been proposed, but benchmarking their performance in the setting of real biological data is difficult due to the lack of a gold standard. In a previously published work we proposed a geometrical approach to differential expression which performed highly in benchmarking tests and compared well to the most popular methods of differential gene expression. As reported, this approach has a natural extension to gene set analysis which we call Principal Angle Enrichment Analysis (PAEA). PAEA employs dimensionality reduction and a multivariate approach for gene set enrichment analysis. However, the performance of this method has not been assessed nor its implementation as a web-based tool. Here we describe new benchmarking protocols for gene set analysis methods and find that PAEA performs highly. The PAEA method is implemented as a user-friendly web-based tool, which contains 70 gene set libraries and is freely available to the community.

  5. Sensitivity analysis of an LCL-filter-based three-phase active rectifier via a virtual circuit approach

    DEFF Research Database (Denmark)

    Blaabjerg, Frede; Chiarantoni, Ernesto; Aquila, Antonio Dell’

    2004-01-01

    Three-phase active rectifiers based on the voltage source converter topology can successfully replace traditional thyristor based rectifiers or diode bridge plus chopper in interfacing dc-systems to the grid. However, if the application in which they are employed has a high safety issue......, to the grid side stiffness and to the parameters of the controller has never been detailed considered. In this paper the experimental results of an LCL-filter-based three-phase active rectifier are analysed with the circuit theory approach. A ?virtual circuit? is synthesized in role of the digital controller...

  6. Whole Gene Capture Analysis of 15 CRC Susceptibility Genes in Suspected Lynch Syndrome Patients.

    Science.gov (United States)

    Jansen, Anne M L; Geilenkirchen, Marije A; van Wezel, Tom; Jagmohan-Changur, Shantie C; Ruano, Dina; van der Klift, Heleen M; van den Akker, Brendy E W M; Laros, Jeroen F J; van Galen, Michiel; Wagner, Anja; Letteboer, Tom G W; Gómez-García, Encarna B; Tops, Carli M J; Vasen, Hans F; Devilee, Peter; Hes, Frederik J; Morreau, Hans; Wijnen, Juul T

    2016-01-01

    Lynch Syndrome (LS) is caused by pathogenic germline variants in one of the mismatch repair (MMR) genes. However, up to 60% of MMR-deficient colorectal cancer cases are categorized as suspected Lynch Syndrome (sLS) because no pathogenic MMR germline variant can be identified, which leads to difficulties in clinical management. We therefore analyzed the genomic regions of 15 CRC susceptibility genes in leukocyte DNA of 34 unrelated sLS patients and 11 patients with MLH1 hypermethylated tumors with a clear family history. Using targeted next-generation sequencing, we analyzed the entire non-repetitive genomic sequence, including intronic and regulatory sequences, of 15 CRC susceptibility genes. In addition, tumor DNA from 28 sLS patients was analyzed for somatic MMR variants. Of 1979 germline variants found in the leukocyte DNA of 34 sLS patients, one was a pathogenic variant (MLH1 c.1667+1delG). Leukocyte DNA of 11 patients with MLH1 hypermethylated tumors was negative for pathogenic germline variants in the tested CRC susceptibility genes and for germline MLH1 hypermethylation. Somatic DNA analysis of 28 sLS tumors identified eight (29%) cases with two pathogenic somatic variants, one with a VUS predicted to pathogenic and LOH, and nine cases (32%) with one pathogenic somatic variant (n = 8) or one VUS predicted to be pathogenic (n = 1). This is the first study in sLS patients to include the entire genomic sequence of CRC susceptibility genes. An underlying somatic or germline MMR gene defect was identified in ten of 34 sLS patients (29%). In the remaining sLS patients, the underlying genetic defect explaining the MMRdeficiency in their tumors might be found outside the genomic regions harboring the MMR and other known CRC susceptibility genes.

  7. Multiscale Embedded Gene Co-expression Network Analysis.

    Directory of Open Access Journals (Sweden)

    Won-Min Song

    2015-11-01

    Full Text Available Gene co-expression network analysis has been shown effective in identifying functional co-expressed gene modules associated with complex human diseases. However, existing techniques to construct co-expression networks require some critical prior information such as predefined number of clusters, numerical thresholds for defining co-expression/interaction, or do not naturally reproduce the hallmarks of complex systems such as the scale-free degree distribution of small-worldness. Previously, a graph filtering technique called Planar Maximally Filtered Graph (PMFG has been applied to many real-world data sets such as financial stock prices and gene expression to extract meaningful and relevant interactions. However, PMFG is not suitable for large-scale genomic data due to several drawbacks, such as the high computation complexity O(|V|3, the presence of false-positives due to the maximal planarity constraint, and the inadequacy of the clustering framework. Here, we developed a new co-expression network analysis framework called Multiscale Embedded Gene Co-expression Network Analysis (MEGENA by: i introducing quality control of co-expression similarities, ii parallelizing embedded network construction, and iii developing a novel clustering technique to identify multi-scale clustering structures in Planar Filtered Networks (PFNs. We applied MEGENA to a series of simulated data and the gene expression data in breast carcinoma and lung adenocarcinoma from The Cancer Genome Atlas (TCGA. MEGENA showed improved performance over well-established clustering methods and co-expression network construction approaches. MEGENA revealed not only meaningful multi-scale organizations of co-expressed gene clusters but also novel targets in breast carcinoma and lung adenocarcinoma.

  8. Multiscale Embedded Gene Co-expression Network Analysis.

    Science.gov (United States)

    Song, Won-Min; Zhang, Bin

    2015-11-01

    Gene co-expression network analysis has been shown effective in identifying functional co-expressed gene modules associated with complex human diseases. However, existing techniques to construct co-expression networks require some critical prior information such as predefined number of clusters, numerical thresholds for defining co-expression/interaction, or do not naturally reproduce the hallmarks of complex systems such as the scale-free degree distribution of small-worldness. Previously, a graph filtering technique called Planar Maximally Filtered Graph (PMFG) has been applied to many real-world data sets such as financial stock prices and gene expression to extract meaningful and relevant interactions. However, PMFG is not suitable for large-scale genomic data due to several drawbacks, such as the high computation complexity O(|V|3), the presence of false-positives due to the maximal planarity constraint, and the inadequacy of the clustering framework. Here, we developed a new co-expression network analysis framework called Multiscale Embedded Gene Co-expression Network Analysis (MEGENA) by: i) introducing quality control of co-expression similarities, ii) parallelizing embedded network construction, and iii) developing a novel clustering technique to identify multi-scale clustering structures in Planar Filtered Networks (PFNs). We applied MEGENA to a series of simulated data and the gene expression data in breast carcinoma and lung adenocarcinoma from The Cancer Genome Atlas (TCGA). MEGENA showed improved performance over well-established clustering methods and co-expression network construction approaches. MEGENA revealed not only meaningful multi-scale organizations of co-expressed gene clusters but also novel targets in breast carcinoma and lung adenocarcinoma.

  9. Capturing heterogeneity in gene expression studies by surrogate variable analysis.

    Directory of Open Access Journals (Sweden)

    Jeffrey T Leek

    2007-09-01

    Full Text Available It has unambiguously been shown that genetic, environmental, demographic, and technical factors may have substantial effects on gene expression levels. In addition to the measured variable(s of interest, there will tend to be sources of signal due to factors that are unknown, unmeasured, or too complicated to capture through simple models. We show that failing to incorporate these sources of heterogeneity into an analysis can have widespread and detrimental effects on the study. Not only can this reduce power or induce unwanted dependence across genes, but it can also introduce sources of spurious signal to many genes. This phenomenon is true even for well-designed, randomized studies. We introduce "surrogate variable analysis" (SVA to overcome the problems caused by heterogeneity in expression studies. SVA can be applied in conjunction with standard analysis techniques to accurately capture the relationship between expression and any modeled variables of interest. We apply SVA to disease class, time course, and genetics of gene expression studies. We show that SVA increases the biological accuracy and reproducibility of analyses in genome-wide expression studies.

  10. Genomic analysis of primordial dwarfism reveals novel disease genes.

    Science.gov (United States)

    Shaheen, Ranad; Faqeih, Eissa; Ansari, Shinu; Abdel-Salam, Ghada; Al-Hassnan, Zuhair N; Al-Shidi, Tarfa; Alomar, Rana; Sogaty, Sameera; Alkuraya, Fowzan S

    2014-02-01

    Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in defining clinical subgroups. In this study, we present the results of clinical and genomic characterization of 16 new patients in whom a broad definition of PD was used (e.g., 3M syndrome was included). We report a novel PD syndrome with distinct facies in two unrelated patients, each with a different homozygous truncating mutation in CRIPT. Our analysis also reveals, in addition to mutations in known PD disease genes, the first instance of biallelic truncating BRCA2 mutation causing PD with normal bone marrow analysis. In addition, we have identified a novel locus for Seckel syndrome based on a consanguineous multiplex family and identified a homozygous truncating mutation in DNA2 as the likely cause. An additional novel PD disease candidate gene XRCC4 was identified by autozygome/exome analysis, and the knockout mouse phenotype is highly compatible with PD. Thus, we add a number of novel genes to the growing list of PD-linked genes, including one which we show to be linked to a novel PD syndrome with a distinct facial appearance. PD is extremely heterogeneous genetically and clinically, and genomic tools are often required to reach a molecular diagnosis.

  11. Tracking difference in gene expression in a time-course experiment using gene set enrichment analysis.

    Directory of Open Access Journals (Sweden)

    Pui Shan Wong

    Full Text Available Fistulifera sp. strain JPCC DA0580 is a newly sequenced pennate diatom that is capable of simultaneously growing and accumulating lipids. This is a unique trait, not found in other related microalgae so far. It is able to accumulate between 40 to 60% of its cell weight in lipids, making it a strong candidate for the production of biofuel. To investigate this characteristic, we used RNA-Seq data gathered at four different times while Fistulifera sp. strain JPCC DA0580 was grown in oil accumulating and non-oil accumulating conditions. We then adapted gene set enrichment analysis (GSEA to investigate the relationship between the difference in gene expression of 7,822 genes and metabolic functions in our data. We utilized information in the KEGG pathway database to create the gene sets and changed GSEA to use re-sampling so that data from the different time points could be included in the analysis. Our GSEA method identified photosynthesis, lipid synthesis and amino acid synthesis related pathways as processes that play a significant role in oil production and growth in Fistulifera sp. strain JPCC DA0580. In addition to GSEA, we visualized the results by creating a network of compounds and reactions, and plotted the expression data on top of the network. This made existing graph algorithms available to us which we then used to calculate a path that metabolizes glucose into triacylglycerol (TAG in the smallest number of steps. By visualizing the data this way, we observed a separate up-regulation of genes at different times instead of a concerted response. We also identified two metabolic paths that used less reactions than the one shown in KEGG and showed that the reactions were up-regulated during the experiment. The combination of analysis and visualization methods successfully analyzed time-course data, identified important metabolic pathways and provided new hypotheses for further research.

  12. Circuit card failures and industry mitigation strategy

    Energy Technology Data Exchange (ETDEWEB)

    Mondal, U. [Candu Owners Group, Toronto, Ontario (Canada)

    2012-07-01

    In recent years the nuclear industry has experienced an increase in circuit card failures due to ageing of components, inadequate Preventive Maintenance (PM), lack of effective circuit card health monitoring, etc. Circuit card failures have caused loss of critical equipment, e.g., electro hydraulic governors, Safety Systems, resulting in loss of function and in some cases loss of generation. INPO completed a root cause analysis of 40 Reactor Trips/Scrams in US reactors and has recommended several actions to mitigate Circuit Card failures. Obsolescence of discrete components has posed many challenges in conducting effective preventative maintenance on circuit cards. In many cases, repairs have resulted in installation of components that compromise performance of the circuit cards. Improper termination and worn edge connectors have caused intermittent contacts contributing to circuit card failures. Traditionally, little attention is paid to relay functions and preventative maintenance of relay. Relays contribute significantly to circuit card failures and have dominated loss of generation across the power industry. The INPO study recommended a number of actions to mitigate circuit card failures, such as; identification of critical components and single point vulnerabilities; strategic preventative maintenance; protection of circuit boards against electrostatic discharge; limiting power cycles; performing an effective burn-in prior to commissioning of the circuit cards; monitoring performance of DC power supplies; limiting cabinet temperatures; managing of component aging/degradation mechanism, etc. A subcommittee has been set up under INPO sponsorship to understand the causes of circuit card failure and to develop an effective mitigation strategy. (author)

  13. Analysis of specification of an electrode type sensor equivalent circuit on the base of impedance spectroscopy simulation

    International Nuclear Information System (INIS)

    Ogurtsov, V I; Mathewson, A; Sheehan, M M

    2005-01-01

    Simulation of electrochemical impedance spectroscopy (EIS) based on a LabVIEW model of a complex impedance measuring system in the frequency domain has been investigated to specify parameters of Randle's equivalent circuit, which is ordinarily used for electrode sensors. The model was based on a standard system for EIS instrumentation and consisted of a sensor modelled by Randle's equivalent circuit, a source of harmonic frequency sweep voltage applied to the sensor and a transimpedance amplifier, which transformed the sensor current to voltage. It provided impedance spectroscopy data for different levels of noise, modelled by current and voltage equivalent noise sources applied to the amplifier input. The noise influence on Randle's equivalent circuit specification was analysed by considering the behaviour of the approximation error. Different metrics including absolute, relative, semilogarithmic and logarithmic based distance between complex numbers on a complex plane were considered and compared to one another for evaluating this error. It was shown that the relative and logarithmic based metrics provide more reliable results for the determination of circuit parameters

  14. Analysis of specification of an electrode type sensor equivalent circuit on the base of impedance spectroscopy simulation

    Energy Technology Data Exchange (ETDEWEB)

    Ogurtsov, V I; Mathewson, A; Sheehan, M M [Tyndall National Institute, Lee Maltings, Prospect Row, Cork (Ireland)

    2005-01-01

    Simulation of electrochemical impedance spectroscopy (EIS) based on a LabVIEW model of a complex impedance measuring system in the frequency domain has been investigated to specify parameters of Randle's equivalent circuit, which is ordinarily used for electrode sensors. The model was based on a standard system for EIS instrumentation and consisted of a sensor modelled by Randle's equivalent circuit, a source of harmonic frequency sweep voltage applied to the sensor and a transimpedance amplifier, which transformed the sensor current to voltage. It provided impedance spectroscopy data for different levels of noise, modelled by current and voltage equivalent noise sources applied to the amplifier input. The noise influence on Randle's equivalent circuit specification was analysed by considering the behaviour of the approximation error. Different metrics including absolute, relative, semilogarithmic and logarithmic based distance between complex numbers on a complex plane were considered and compared to one another for evaluating this error. It was shown that the relative and logarithmic based metrics provide more reliable results for the determination of circuit parameters.

  15. An analysis of the operation of a single-pole relay integrated circuit device with a controlled reset ratio

    Energy Technology Data Exchange (ETDEWEB)

    Reshetov, N.E.

    1980-01-01

    Relay equipment using semiconductor components (such as those containing gates using planar transformers, and a relay in networks which control the operational time of a relay) are widely used in the automation equipment of electric power systems. A scheme where a gate in the form of an integrated circuit is used is given.

  16. Modelling the transient analysis of flat miniature heat pipes in printed circuit boards using a control volume approacht

    NARCIS (Netherlands)

    Wits, W.W.; Kok, J.B.W.; van Steenhoven, A.A.; van der Meer, T.H.; Stoffels, G.G.M.

    2008-01-01

    The heat pipe is a two-phase cooling solution, offering very high thermal coefficients, for heat transport. Therefore, it is increasingly used in the design of electronic products. Flat miniature heat pipes are able to effectively remove heat from several hot spots on a Printed Circuit Board (PCB).

  17. GECKO: a complete large-scale gene expression analysis platform

    Directory of Open Access Journals (Sweden)

    Heuer Michael

    2004-12-01

    Full Text Available Abstract Background Gecko (Gene Expression: Computation and Knowledge Organization is a complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community. Results Based on a client-server architecture, with a centralized repository of typically many tens of thousands of Affymetrix scans, Gecko includes automatic processing pipelines for uploading data from remote sites, a data base, a computational engine implementing ~ 50 different analysis tools, and a client application. Among available analysis tools are clustering methods, principal component analysis, supervised classification including feature selection and cross-validation, multi-factorial ANOVA, statistical contrast calculations, and various post-processing tools for extracting data at given error rates or significance levels. On account of its open architecture, Gecko also allows for the integration of new algorithms. The Gecko framework is very general: non-Affymetrix and non-gene expression data can be analyzed as well. A unique feature of the Gecko architecture is the concept of the Analysis Tree (actually, a directed acyclic graph, in which all successive results in ongoing analyses are saved. This approach has proven invaluable in allowing a large (~ 100 users and distributed community to share results, and to repeatedly return over a span of years to older and potentially very complex analyses of gene expression data. Conclusions The Gecko system is being made publicly available as free software http://sourceforge.net/projects/geckoe. In totality or in parts, the Gecko framework should prove useful to users and system developers with a broad range of analysis needs.

  18. [FANCA gene mutation analysis in Fanconi anemia patients].

    Science.gov (United States)

    Chen, Fei; Peng, Guang-Jie; Zhang, Kejian; Hu, Qun; Zhang, Liu-Qing; Liu, Ai-Guo

    2005-10-01

    To screen the FANCA gene mutation and explore the FANCA protein function in Fanconi anemia (FA) patients. FANCA protein expression and its interaction with FANCF were analyzed using Western blot and immunoprecipitation in 3 cases of FA-A. Genomic DNA was used for MLPA analysis followed by sequencing. FANCA protein was undetectable and FANCA and FANCF protein interaction was impaired in these 3 cases of FA-A. Each case of FA-A contained biallelic pathogenic mutations in FANCA gene. No functional FANCA protein was found in these 3 cases of FA-A, and intragenic deletion, frame shift and splice site mutation were the major pathogenic mutations found in FANCA gene.

  19. Pattern Recognition of Gene Expression with Singular Spectrum Analysis

    Directory of Open Access Journals (Sweden)

    Hossein Hassani

    2014-07-01

    Full Text Available Drosophila segmentation as a model organism is one of the most highly studied. Among many maternal segmentation coordinate genes, bicoid protein pattern plays a significant role during Drosophila embryogenesis, since this gradient determines most aspects of head and thorax development. Despite the fact that several models have been proposed to describe the bicoid gradient, due to its association with considerable error, each can only partially explain bicoid characteristics. In this paper, a modified version of singular spectrum analysis is examined for filtering and extracting the bicoid gene expression signal. The results with strong evidence indicate that the proposed technique is able to remove noise more effectively and can be considered as a promising method for filtering gene expression measurements for other applications.

  20. Integrative sparse principal component analysis of gene expression data.

    Science.gov (United States)

    Liu, Mengque; Fan, Xinyan; Fang, Kuangnan; Zhang, Qingzhao; Ma, Shuangge

    2017-12-01

    In the analysis of gene expression data, dimension reduction techniques have been extensively adopted. The most popular one is perhaps the PCA (principal component analysis). To generate more reliable and more interpretable results, the SPCA (sparse PCA) technique has been developed. With the "small sample size, high dimensionality" characteristic of gene expression data, the analysis results generated from a single dataset are often unsatisfactory. Under contexts other than dimension reduction, integrative analysis techniques, which jointly analyze the raw data of multiple independent datasets, have been developed and shown to outperform "classic" meta-analysis and other multidatasets techniques and single-dataset analysis. In this study, we conduct integrative analysis by developing the iSPCA (integrative SPCA) method. iSPCA achieves the selection and estimation of sparse loadings using a group penalty. To take advantage of the similarity across datasets and generate more accurate results, we further impose contrasted penalties. Different penalties are proposed to accommodate different data conditions. Extensive simulations show that iSPCA outperforms the alternatives under a wide spectrum of settings. The analysis of breast cancer and pancreatic cancer data further shows iSPCA's satisfactory performance. © 2017 WILEY PERIODICALS, INC.

  1. Transcriptomic analysis of salt stress responsive genes in Rhazya stricta.

    Directory of Open Access Journals (Sweden)

    Nahid H Hajrah

    Full Text Available Rhazya stricta is an evergreen shrub that is widely distributed across Western and South Asia, and like many other members of the Apocynaceae produces monoterpene indole alkaloids that have anti-cancer properties. This species is adapted to very harsh desert conditions making it an excellent system for studying tolerance to high temperatures and salinity. RNA-Seq analysis was performed on R. stricta exposed to severe salt stress (500 mM NaCl across four time intervals (0, 2, 12 and 24 h to examine mechanisms of salt tolerance. A large number of transcripts including genes encoding tetrapyrroles and pentatricopeptide repeat (PPR proteins were regulated only after 12 h of stress of seedlings grown in controlled greenhouse conditions. Mechanisms of salt tolerance in R. stricta may involve the upregulation of genes encoding chaperone protein Dnaj6, UDP-glucosyl transferase 85a2, protein transparent testa 12 and respiratory burst oxidase homolog protein b. Many of the highly-expressed genes act on protecting protein folding during salt stress and the production of flavonoids, key secondary metabolites in stress tolerance. Other regulated genes encode enzymes in the porphyrin and chlorophyll metabolic pathway with important roles during plant growth, photosynthesis, hormone signaling and abiotic responses. Heme biosynthesis in R. stricta leaves might add to the level of salt stress tolerance by maintaining appropriate levels of photosynthesis and normal plant growth as well as by the participation in reactive oxygen species (ROS production under stress. We speculate that the high expression levels of PPR genes may be dependent on expression levels of their targeted editing genes. Although the results of PPR gene family indicated regulation of a large number of transcripts under salt stress, PPR actions were independent of the salt stress because their RNA editing patterns were unchanged.

  2. Microarray analysis of gene expression profiles in ripening pineapple fruits.

    Science.gov (United States)

    Koia, Jonni H; Moyle, Richard L; Botella, Jose R

    2012-12-18

    Pineapple (Ananas comosus) is a tropical fruit crop of significant commercial importance. Although the physiological changes that occur during pineapple fruit development have been well characterized, little is known about the molecular events that occur during the fruit ripening process. Understanding the molecular basis of pineapple fruit ripening will aid the development of new varieties via molecular breeding or genetic modification. In this study we developed a 9277 element pineapple microarray and used it to profile gene expression changes that occur during pineapple fruit ripening. Microarray analyses identified 271 unique cDNAs differentially expressed at least 1.5-fold between the mature green and mature yellow stages of pineapple fruit ripening. Among these 271 sequences, 184 share significant homology with genes encoding proteins of known function, 53 share homology with genes encoding proteins of unknown function and 34 share no significant homology with any database accession. Of the 237 pineapple sequences with homologs, 160 were up-regulated and 77 were down-regulated during pineapple fruit ripening. DAVID Functional Annotation Cluster (FAC) analysis of all 237 sequences with homologs revealed confident enrichment scores for redox activity, organic acid metabolism, metalloenzyme activity, glycolysis, vitamin C biosynthesis, antioxidant activity and cysteine peptidase activity, indicating the functional significance and importance of these processes and pathways during pineapple fruit development. Quantitative real-time PCR analysis validated the microarray expression results for nine out of ten genes tested. This is the first report of a microarray based gene expression study undertaken in pineapple. Our bioinformatic analyses of the transcript profiles have identified a number of genes, processes and pathways with putative involvement in the pineapple fruit ripening process. This study extends our knowledge of the molecular basis of pineapple fruit

  3. A new approach to magnetic circuit analysis and its application to the optimal design of a bi-directional magnetorheological brake

    International Nuclear Information System (INIS)

    Nguyen, Phuong-Bac; Choi, Seung-Bok

    2011-01-01

    This paper proposes a new approach to modeling the magnetic circuit of an MR brake and applies it to explore an engineering optimization problem. The MR brake used in this work is a bi-directional type whose range of braking torque varies from negative to positive values. The model of the bi-directional MR brake can be split into two components: the mechanical part and the magnetic circuit. While the mechanical part is modeled using Bingham's equation, an approach to modeling the magnetic circuit is proposed in this work. For verification of the effectiveness of this method, an optimal design aiming to minimize the mass subjected to the geometric and desired torque constraints is undertaken. In order to solve such an optimization problem, which consists of numerous constraints and potential local optima, a particle swarm optimization (PSO) algorithm in combination with a gradient-based repair method is proposed. The optimal solution of the problem obtained from the proposed method is then investigated and compared with that obtained from finite element analysis (FEA). In addition, an experiment on a manufactured bi-directional MR brake with the optimal parameters is undertaken to validate the accuracy of the proposed analysis methodology

  4. Signal Network Analysis of Plant Genes Responding to Ionizing Radiation

    International Nuclear Information System (INIS)

    Kim, Dong Sub; Kim, Jinbaek; Kim, Sang Hoon

    2012-12-01

    In this project, we irradiated Arabidopsis plants with various doses of gamma-rays at the vegetative and reproductive stages to assess their radiation sensitivity. After the gene expression profiles and an analysis of the antioxidant response, we selected several Arabidopsis genes for uses of 'Radio marker genes (RMG)' and conducted over-expression and knock-down experiments to confirm the radio sensitivity. Based on these results, we applied two patents for the detection of two RMG (At3g28210 and At4g37990) and development of transgenic plants. Also, we developed a Genechip for use of high-throughput screening of Arabidopsis genes responding only to ionizing radiation and identified RMG to detect radiation leaks. Based on these results, we applied two patents associated with the use of Genechip for different types of radiation and different growth stages. Also, we conducted co-expression network study of specific expressed probes against gamma-ray stress and identified expressed patterns of duplicated genes formed by whole/500kb segmental genome duplication

  5. Mining the archives: a cross-platform analysis of gene ...

    Science.gov (United States)

    Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a potentially invaluable resource for genomic research into the molecular basis of disease. However, use of FFPE samples in gene expression studies has been limited by technical challenges resulting from degradation of nucleic acids. Here we evaluated gene expression profiles derived from fresh-frozen (FRO) and FFPE mouse liver tissues using two DNA microarray protocols and two whole transcriptome sequencing (RNA-seq) library preparation methodologies. The ribo-depletion protocol outperformed the other three methods by having the highest correlations of differentially expressed genes (DEGs) and best overlap of pathways between FRO and FFPE groups. We next tested the effect of sample time in formalin (18 hours or 3 weeks) on gene expression profiles. Hierarchical clustering of the datasets indicated that test article treatment, and not preservation method, was the main driver of gene expression profiles. Meta- and pathway analyses indicated that biological responses were generally consistent for 18-hour and 3-week FFPE samples compared to FRO samples. However, clear erosion of signal intensity with time in formalin was evident, and DEG numbers differed by platform and preservation method. Lastly, we investigated the effect of age in FFPE block on genomic profiles. RNA-seq analysis of 8-, 19-, and 26-year-old control blocks using the ribo-depletion protocol resulted in comparable quality metrics, inc

  6. Molecular genetic analysis of phosphomannomutase genes in Triticum monococcum

    Institute of Scientific and Technical Information of China (English)

    Chunmei; Yu; Xinyan; Liu; Qian; Zhang; Xinyu; He; Wan; Huai; Baohua; Wang; Yunying; Cao; Rong; Zhou

    2015-01-01

    In higher plants, phosphomannomutase(PMM) is essential for synthesizing the antioxidant ascorbic acid through the Smirnoff–Wheeler pathway. Previously, we characterized six PMM genes(Ta PMM-A1, A2, B1, B2, D1 and D2) in common wheat(Triticum aestivum, AABBDD).Here, we report a molecular genetic analysis of PMM genes in Triticum monococcum(AmAm), a diploid wheat species whose Amgenome is closely related to the A genome of common wheat. Two distinct PMM genes, Tm PMM-1 and Tm PMM-2, were found in T. monococcum. The coding region of Tm PMM-1 was intact and highly conserved. In contrast, two main Tm PMM-2 alleles were identified, with Tm PMM-2a possessing an intact coding sequence and Tm PMM-2b being a pseudogene. The transcript level of Tm PMM-2a was much higher than that of Tm PMM-2b, and a bacterially expressed Tm PMM-2a recombinant protein displayed relatively high PMM activity. In general, the total transcript level of PMM was substantially higher in accessions carrying Tm PMM-1 and Tm PMM-2a than those harboring Tm PMM-1 and Tm PMM-2b. However, total PMM protein and activity levels did not differ drastically between the two genotypes. This work provides new information on PMM genes in T. monococcum and expands our understanding on Triticeae PMM genes, which may aid further functional and applied studies of PMM in crop plants.

  7. Serial Analysis of Gene Expression: Applications in Human Studies

    Directory of Open Access Journals (Sweden)

    Tuteja Renu

    2004-01-01

    Full Text Available Serial analysis of gene expression (SAGE is a powerful tool, which provides quantitative and comprehensive expression profile of genes in a given cell population. It works by isolating short fragments of genetic information from the expressed genes that are present in the cell being studied. These short sequences, called SAGE tags, are linked together for efficient sequencing. The frequency of each SAGE tag in the cloned multimers directly reflects the transcript abundance. Therefore, SAGE results in an accurate picture of gene expression at both the qualitative and the quantitative levels. It does not require a hybridization probe for each transcript and allows new genes to be discovered. This technique has been applied widely in human studies and various SAGE tags/SAGE libraries have been generated from different cells/tissues such as dendritic cells, lung fibroblast cells, oocytes, thyroid tissue, B-cell lymphoma, cultured keratinocytes, muscles, brain tissues, sciatic nerve, cultured Schwann cells, cord blood-derived mast cells, retina, macula, retinal pigment epithelial cells, skin cells, and so forth. In this review we present the updated information on the applications of SAGE technology mainly to human studies.

  8. GxGrare: gene-gene interaction analysis method for rare variants from high-throughput sequencing data.

    Science.gov (United States)

    Kwon, Minseok; Leem, Sangseob; Yoon, Joon; Park, Taesung

    2018-03-19

    With the rapid advancement of array-based genotyping techniques, genome-wide association studies (GWAS) have successfully identified common genetic variants associated with common complex diseases. However, it has been shown that only a small proportion of the genetic etiology of complex diseases could be explained by the genetic factors identified from GWAS. This missing heritability could possibly be explained by gene-gene interaction (epistasis) and rare variants. There has been an exponential growth of gene-gene interaction analysis for common variants in terms of methodological developments and practical applications. Also, the recent advancement of high-throughput sequencing technologies makes it possible to conduct rare variant analysis. However, little progress has been made in gene-gene interaction analysis for rare variants. Here, we propose GxGrare which is a new gene-gene interaction method for the rare variants in the framework of the multifactor dimensionality reduction (MDR) analysis. The proposed method consists of three steps; 1) collapsing the rare variants, 2) MDR analysis for the collapsed rare variants, and 3) detect top candidate interaction pairs. GxGrare can be used for the detection of not only gene-gene interactions, but also interactions within a single gene. The proposed method is illustrated with 1080 whole exome sequencing data of the Korean population in order to identify causal gene-gene interaction for rare variants for type 2 diabetes. The proposed GxGrare performs well for gene-gene interaction detection with collapsing of rare variants. GxGrare is available at http://bibs.snu.ac.kr/software/gxgrare which contains simulation data and documentation. Supported operating systems include Linux and OS X.

  9. A novel joint analysis framework improves identification of differentially expressed genes in cross disease transcriptomic analysis

    Directory of Open Access Journals (Sweden)

    Wenyi Qin

    2018-02-01

    Full Text Available Abstract Motivation Detecting differentially expressed (DE genes between disease and normal control group is one of the most common analyses in genome-wide transcriptomic data. Since most studies don’t have a lot of samples, researchers have used meta-analysis to group different datasets for the same disease. Even then, in many cases the statistical power is still not enough. Taking into account the fact that many diseases share the same disease genes, it is desirable to design a statistical framework that can identify diseases’ common and specific DE genes simultaneously to improve the identification power. Results We developed a novel empirical Bayes based mixture model to identify DE genes in specific study by leveraging the shared information across multiple different disease expression data sets. The effectiveness of joint analysis was demonstrated through comprehensive simulation studies and two real data applications. The simulation results showed that our method consistently outperformed single data set analysis and two other meta-analysis methods in identification power. In real data analysis, overall our method demonstrated better identification power in detecting DE genes and prioritized more disease related genes and disease related pathways than single data set analysis. Over 150% more disease related genes are identified by our method in application to Huntington’s disease. We expect that our method would provide researchers a new way of utilizing available data sets from different diseases when sample size of the focused disease is limited.

  10. Solid-state circuits

    CERN Document Server

    Pridham, G J

    2013-01-01

    Solid-State Circuits provides an introduction to the theory and practice underlying solid-state circuits, laying particular emphasis on field effect transistors and integrated circuits. Topics range from construction and characteristics of semiconductor devices to rectification and power supplies, low-frequency amplifiers, sine- and square-wave oscillators, and high-frequency effects and circuits. Black-box equivalent circuits of bipolar transistors, physical equivalent circuits of bipolar transistors, and equivalent circuits of field effect transistors are also covered. This volume is divided

  11. Current limiter circuit system

    Science.gov (United States)

    Witcher, Joseph Brandon; Bredemann, Michael V.

    2017-09-05

    An apparatus comprising a steady state sensing circuit, a switching circuit, and a detection circuit. The steady state sensing circuit is connected to a first, a second and a third node. The first node is connected to a first device, the second node is connected to a second device, and the steady state sensing circuit causes a scaled current to flow at the third node. The scaled current is proportional to a voltage difference between the first and second node. The switching circuit limits an amount of current that flows between the first and second device. The detection circuit is connected to the third node and the switching circuit. The detection circuit monitors the scaled current at the third node and controls the switching circuit to limit the amount of the current that flows between the first and second device when the scaled current is greater than a desired level.

  12. A Serial Analysis of Gene Expression (SAGE) database analysis of chemosensitivity

    DEFF Research Database (Denmark)

    Stein, Wilfred D; Litman, Thomas; Fojo, Tito

    2004-01-01

    are their corresponding solid tumors. We used the Serial Analysis of Gene Expression (SAGE) database to identify differences between solid tumors and cell lines, hoping to detect genes that could potentially explain differences in drug sensitivity. SAGE libraries were available for both solid tumors and cell lines from...

  13. LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights.

    Science.gov (United States)

    Dong, Xinran; Hao, Yun; Wang, Xiao; Tian, Weidong

    2016-01-11

    Pathway or gene set over-representation analysis (ORA) has become a routine task in functional genomics studies. However, currently widely used ORA tools employ statistical methods such as Fisher's exact test that reduce a pathway into a list of genes, ignoring the constitutive functional non-equivalent roles of genes and the complex gene-gene interactions. Here, we develop a novel method named LEGO (functional Link Enrichment of Gene Ontology or gene sets) that takes into consideration these two types of information by incorporating network-based gene weights in ORA analysis. In three benchmarks, LEGO achieves better performance than Fisher and three other network-based methods. To further evaluate LEGO's usefulness, we compare LEGO with five gene expression-based and three pathway topology-based methods using a benchmark of 34 disease gene expression datasets compiled by a recent publication, and show that LEGO is among the top-ranked methods in terms of both sensitivity and prioritization for detecting target KEGG pathways. In addition, we develop a cluster-and-filter approach to reduce the redundancy among the enriched gene sets, making the results more interpretable to biologists. Finally, we apply LEGO to two lists of autism genes, and identify relevant gene sets to autism that could not be found by Fisher.

  14. The Reconstruction and Analysis of Gene Regulatory Networks.

    Science.gov (United States)

    Zheng, Guangyong; Huang, Tao

    2018-01-01

    In post-genomic era, an important task is to explore the function of individual biological molecules (i.e., gene, noncoding RNA, protein, metabolite) and their organization in living cells. For this end, gene regulatory networks (GRNs) are constructed to show relationship between biological molecules, in which the vertices of network denote biological molecules and the edges of network present connection between nodes (Strogatz, Nature 410:268-276, 2001; Bray, Science 301:1864-1865, 2003). Biologists can understand not only the function of biological molecules but also the organization of components of living cells through interpreting the GRNs, since a gene regulatory network is a comprehensively physiological map of living cells and reflects influence of genetic and epigenetic factors (Strogatz, Nature 410:268-276, 2001; Bray, Science 301:1864-1865, 2003). In this paper, we will review the inference methods of GRN reconstruction and analysis approaches of network structure. As a powerful tool for studying complex diseases and biological processes, the applications of the network method in pathway analysis and disease gene identification will be introduced.

  15. Bioinformatics Analysis of MAPKKK Family Genes in Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Wei Li

    2016-04-01

    Full Text Available Mitogen‐activated protein kinase kinase kinase (MAPKKK is a component of the MAPK cascade pathway that plays an important role in plant growth, development, and response to abiotic stress, the functions of which have been well characterized in several plant species, such as Arabidopsis, rice, and maize. In this study, we performed genome‐wide and systemic bioinformatics analysis of MAPKKK family genes in Medicago truncatula. In total, there were 73 MAPKKK family members identified by search of homologs, and they were classified into three subfamilies, MEKK, ZIK, and RAF. Based on the genomic duplication function, 72 MtMAPKKK genes were located throughout all chromosomes, but they cluster in different chromosomes. Using microarray data and high‐throughput sequencing‐data, we assessed their expression profiles in growth and development processes; these results provided evidence for exploring their important functions in developmental regulation, especially in the nodulation process. Furthermore, we investigated their expression in abiotic stresses by RNA‐seq, which confirmed their critical roles in signal transduction and regulation processes under stress. In summary, our genome‐wide, systemic characterization and expressional analysis of MtMAPKKK genes will provide insights that will be useful for characterizing the molecular functions of these genes in M. truncatula.

  16. Gene expression analysis of FABP4 in gastric cancer

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    Abdulkarim Yasin Karim

    2016-06-01

    Full Text Available Purpose: Gastric cancer has high incidence and mortality rate in several countries and is still one of the most frequent and lethal disease. In this study, we aimed to determine diagnostic markers in gastric cancer by molecular techniques; include mRNA expression analysis of FABP4 gene. Fatty acid binding protein 4 (FABP4 gene encodes the fatty acid binding protein found in adipocytes. The protein encoded by FABP4 are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands. It is thought that FABPs roles include fatty acid uptake, transport, and metabolism. Material and Methods: Total RNA were extracted from paired tumor and normal tissues of 47 gastric cancer. The mRNA expression level of FABP4 was measured employing semi- quantitative reverse transcription- polymerase chain reaction (RT- PCR. Results: The mRNA expression level of FABP4 was significantly decreased (down- regulated. Conclusion: Down-regulation of FABP4 gene seems to occur at the initial steps of gastric cancer development. In order to confirm the relationship between the gastric tumor and FABP4 gene, further analysis like immunohistochemistry and epigenetc techniques are necessary. [Cukurova Med J 2016; 41(2.000: 248-252

  17. Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton

    Directory of Open Access Journals (Sweden)

    Xueqiang Su

    2017-10-01

    Full Text Available Plant type III polyketide synthase (PKS can catalyse the formation of a series of secondary metabolites with different structures and different biological functions; the enzyme plays an important role in plant growth, development and resistance to stress. At present, the PKS gene has been identified and studied in a variety of plants. Here, we identified 11 PKS genes from upland cotton (Gossypium hirsutum and compared them with 41 PKS genes in Populus tremula, Vitis vinifera, Malus domestica and Arabidopsis thaliana. According to the phylogenetic tree, a total of 52 PKS genes can be divided into four subfamilies (I–IV. The analysis of gene structures and conserved motifs revealed that most of the PKS genes were composed of two exons and one intron and there are two characteristic conserved domains (Chal_sti_synt_N and Chal_sti_synt_C of the PKS gene family. In our study of the five species, gene duplication was found in addition to Arabidopsis thaliana and we determined that purifying selection has been of great significance in maintaining the function of PKS gene family. From qRT-PCR analysis and a combination of the role of the accumulation of proanthocyanidins (PAs in brown cotton fibers, we concluded that five PKS genes are candidate genes involved in brown cotton fiber pigment synthesis. These results are important for the further study of brown cotton PKS genes. It not only reveals the relationship between PKS gene family and pigment in brown cotton, but also creates conditions for improving the quality of brown cotton fiber.

  18. Global Analysis of miRNA Gene Clusters and Gene Families Reveals Dynamic and Coordinated Expression

    Directory of Open Access Journals (Sweden)

    Li Guo

    2014-01-01

    Full Text Available To further understand the potential expression relationships of miRNAs in miRNA gene clusters and gene families, a global analysis was performed in 4 paired tumor (breast cancer and adjacent normal tissue samples using deep sequencing datasets. The compositions of miRNA gene clusters and families are not random, and clustered and homologous miRNAs may have close relationships with overlapped miRNA species. Members in the miRNA group always had various expression levels, and even some showed larger expression divergence. Despite the dynamic expression as well as individual difference, these miRNAs always indicated consistent or similar deregulation patterns. The consistent deregulation expression may contribute to dynamic and coordinated interaction between different miRNAs in regulatory network. Further, we found that those clustered or homologous miRNAs that were also identified as sense and antisense miRNAs showed larger expression divergence. miRNA gene clusters and families indicated important biological roles, and the specific distribution and expression further enrich and ensure the flexible and robust regulatory network.

  19. Phylogenetic analysis of ferlin genes reveals ancient eukaryotic origins

    Directory of Open Access Journals (Sweden)

    Lek Monkol

    2010-07-01

    Full Text Available Abstract Background The ferlin gene family possesses a rare and identifying feature consisting of multiple tandem C2 domains and a C-terminal transmembrane domain. Much currently remains unknown about the fundamental function of this gene family, however, mutations in its two most well-characterised members, dysferlin and otoferlin, have been implicated in human disease. The availability of genome sequences from a wide range of species makes it possible to explore the evolution of the ferlin family, providing contextual insight into characteristic features that define the ferlin gene family in its present form in humans. Results Ferlin genes were detected from all species of representative phyla, with two ferlin subgroups partitioned within the ferlin phylogenetic tree based on the presence or absence of a DysF domain. Invertebrates generally possessed two ferlin genes (one with DysF and one without, with six ferlin genes in most vertebrates (three DysF, three non-DysF. Expansion of the ferlin gene family is evident between the divergence of lamprey (jawless vertebrates and shark (cartilaginous fish. Common to almost all ferlins is an N-terminal C2-FerI-C2 sandwich, a FerB motif, and two C-terminal C2 domains (C2E and C2F adjacent to the transmembrane domain. Preservation of these structural elements throughout eukaryotic evolution suggests a fundamental role of these motifs for ferlin function. In contrast, DysF, C2DE, and FerA are optional, giving rise to subtle differences in domain topologies of ferlin genes. Despite conservation of multiple C2 domains in all ferlins, the C-terminal C2 domains (C2E and C2F displayed higher sequence conservation and greater conservation of putative calcium binding residues across paralogs and orthologs. Interestingly, the two most studied non-mammalian ferlins (Fer-1 and Misfire in model organisms C. elegans and D. melanogaster, present as outgroups in the phylogenetic analysis, with results suggesting

  20. Meta Analysis of Gene Expression Data within and Across Species.

    Science.gov (United States)

    Fierro, Ana C; Vandenbussche, Filip; Engelen, Kristof; Van de Peer, Yves; Marchal, Kathleen

    2008-12-01

    Since the second half of the 1990s, a large number of genome-wide analyses have been described that study gene expression at the transcript level. To this end, two major strategies have been adopted, a first one relying on hybridization techniques such as microarrays, and a second one based on sequencing techniques such as serial analysis of gene expression (SAGE), cDNA-AFLP, and analysis based on expressed sequence tags (ESTs). Despite both types of profiling experiments becoming routine techniques in many research groups, their application remains costly and laborious. As a result, the number of conditions profiled in individual studies is still relatively small and usually varies from only two to few hundreds of samples for the largest experiments. More and more, scientific journals require the deposit of these high throughput experiments in public databases upon publication. Mining the information present in these databases offers molecular biologists the possibility to view their own small-scale analysis in the light of what is already available. However, so far, the richness of the public information remains largely unexploited. Several obstacles such as the correct association between ESTs and microarray probes with the corresponding gene transcript, the incompleteness and inconsistency in the annotation of experimental conditions, and the lack of standardized experimental protocols to generate gene expression data, all impede the successful mining of these data. Here, we review the potential and difficulties of combining publicly available expression data from respectively EST analyses and microarray experiments. With examples from literature, we show how meta-analysis of expression profiling experiments can be used to study expression behavior in a single organism or between organisms, across a wide range of experimental conditions. We also provide an overview of the methods and tools that can aid molecular biologists in exploiting these public data.

  1. Screening strategies for a highly polymorphic gene: DHPLC analysis of the Fanconi anemia group A gene.

    Science.gov (United States)

    Rischewski, J; Schneppenheim, R

    2001-01-30

    Patients with Fanconi anemia (Fanc) are at risk of developing leukemia. Mutations of the group A gene (FancA) are most common. A multitude of polymorphisms and mutations within the 43 exons of the gene are described. To examine the role of heterozygosity as a risk factor for malignancies, a partially automatized screening method to identify aberrations was needed. We report on our experience with DHPLC (WAVE (Transgenomic)). PCR amplification of all 43 exons from one individual was performed on one microtiter plate on a gradient thermocycler. DHPLC analysis conditions were established via melting curves, prediction software, and test runs with aberrant samples. PCR products were analyzed twice: native, and after adding a WT-PCR product. Retention patterns were compared with previously identified polymorphic PCR products or mutants. We have defined the mutation screening conditions for all 43 exons of FancA using DHPLC. So far, 40 different sequence variations have been detected in more than 100 individuals. The native analysis identifies heterozygous individuals, and the second run detects homozygous aberrations. Retention patterns are specific for the underlying sequence aberration, thus reducing sequencing demand and costs. DHPLC is a valuable tool for reproducible recognition of known sequence aberrations and screening for unknown mutations in the highly polymorphic FancA gene.

  2. Theoretical analysis and modeling of a photonic integrated circuit for frequency 8-tupled and 24-tupled millimeter wave signal generation.

    Science.gov (United States)

    Hasan, Mehedi; Guemri, Rabiaa; Maldonado-Basilio, Ramón; Lucarz, Frédéric; de Bougrenet de la Tocnaye, Jean-Louis; Hall, Trevor

    2014-12-15

    A photonic circuit design for implementing frequency 8-tupling and 24-tupling is proposed. The front- and back-end of the circuit comprises 4×4 MMI couplers enclosing an array of four pairs of phase modulators and 2×2 MMI couplers. The proposed design for frequency multiplication requires no optical or electrical filters, the operation is not limited to carefully adjusted modulation indexes, and the drift originated from static DC bias is mitigated by making use of the intrinsic phase relations of multi-mode interference couplers. A transfer matrix approach is used to represent the main building blocks of the design and hence to describe the operation of the frequency 8-tupling and 24-tupling. The concept is theoretically developed and demonstrated by simulations. Ideal and imperfect power imbalances in the multi-mode interference couplers, as well as ideal and imperfect phases of the electric drives to the phase modulators, are analyzed.

  3. Analysis of SEL on Commercial SRAM Memories and Mixed-Field Characterization of a Latchup Detection Circuit for LEO Space Applications

    Science.gov (United States)

    Secondo, R.; Alía, R. Garcia; Peronnard, P.; Brugger, M.; Masi, A.; Danzeca, S.; Merlenghi, A.; Vaillé, J.-R.; Dusseau, L.

    2017-08-01

    A single event latchup (SEL) experiment based on commercial static random access memory (SRAM) memories has recently been proposed in the framework of the European Organization for Nuclear Research (CERN) Latchup Experiment and Student Satellite nanosatellite low Earth orbit (LEO) space mission. SEL characterization of three commercial SRAM memories has been carried out at the Paul Scherrer Institut (PSI) facility, using monoenergetic focused proton beams and different acquisition setups. The best target candidate was selected and a circuit for SEL detection has been proposed and tested at CERN, in the CERN High Energy AcceleRator Mixed-field facility (CHARM). Experimental results were carried out at test locations representative of the LEO environment, thus providing a full characterization of the SRAM cross sections, together with the analysis of the single-event effect and total ionizing dose of the latchup detection circuit in relation to the particle spectra expected during mission. The setups used for SEL monitoring are described, and details of the proposed circuit components and topology are presented. Experimental results obtained both at PSI and at CHARM facilities are discussed.

  4. Laminar and dorsoventral molecular organization of the medial entorhinal cortex revealed by large-scale anatomical analysis of gene expression.

    Directory of Open Access Journals (Sweden)

    Helen L Ramsden

    2015-01-01

    Full Text Available Neural circuits in the medial entorhinal cortex (MEC encode an animal's position and orientation in space. Within the MEC spatial representations, including grid and directional firing fields, have a laminar and dorsoventral organization that corresponds to a similar topography of neuronal connectivity and cellular properties. Yet, in part due to the challenges of integrating anatomical data at the resolution of cortical layers and borders, we know little about the molecular components underlying this organization. To address this we develop a new computational pipeline for high-throughput analysis and comparison of in situ hybridization (ISH images at laminar resolution. We apply this pipeline to ISH data for over 16,000 genes in the Allen Brain Atlas and validate our analysis with RNA sequencing of MEC tissue from adult mice. We find that differential gene expression delineates the borders of the MEC with neighboring brain structures and reveals its laminar and dorsoventral organization. We propose a new molecular basis for distinguishing the deep layers of the MEC and show that their similarity to corresponding layers of neocortex is greater than that of superficial layers. Our analysis identifies ion channel-, cell adhesion- and synapse-related genes as candidates for functional differentiation of MEC layers and for encoding of spatial information at different scales along the dorsoventral axis of the MEC. We also reveal laminar organization of genes related to disease pathology and suggest that a high metabolic demand predisposes layer II to neurodegenerative pathology. In principle, our computational pipeline can be applied to high-throughput analysis of many forms of neuroanatomical data. Our results support the hypothesis that differences in gene expression contribute to functional specialization of superficial layers of the MEC and dorsoventral organization of the scale of spatial representations.

  5. Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer.

    Directory of Open Access Journals (Sweden)

    Verena Jabs

    Full Text Available Non-small cell lung cancer (NSCLC represents a genomically unstable cancer type with extensive copy number aberrations. The relationship of gene copy number alterations and subsequent mRNA levels has only fragmentarily been described. The aim of this study was to conduct a genome-wide analysis of gene copy number gains and corresponding gene expression levels in a clinically well annotated NSCLC patient cohort (n = 190 and their association with survival. While more than half of all analyzed gene copy number-gene expression pairs showed statistically significant correlations (10,296 of 18,756 genes, high correlations, with a correlation coefficient >0.7, were obtained only in a subset of 301 genes (1.6%, including KRAS, EGFR and MDM2. Higher correlation coefficients were associated with higher copy number and expression levels. Strong correlations were frequently based on few tumors with high copy number gains and correspondingly increased mRNA expression. Among the highly correlating genes, GO groups associated with posttranslational protein modifications were particularly frequent, including ubiquitination and neddylation. In a meta-analysis including 1,779 patients we found that survival associated genes were overrepresented among highly correlating genes (61 of the 301 highly correlating genes, FDR adjusted p<0.05. Among them are the chaperone CCT2, the core complex protein NUP107 and the ubiquitination and neddylation associated protein CAND1. In conclusion, in a comprehensive analysis we described a distinct set of highly correlating genes. These genes were found to be overrepresented among survival-associated genes based on gene expression in a large collection of publicly available datasets.

  6. Identification of pathogenic genes related to rheumatoid arthritis through integrated analysis of DNA methylation and gene expression profiling.

    Science.gov (United States)

    Zhang, Lei; Ma, Shiyun; Wang, Huailiang; Su, Hang; Su, Ke; Li, Longjie

    2017-11-15

    The purpose of our study was to identify new pathogenic genes used for exploring the pathogenesis of rheumatoid arthritis (RA). To screen pathogenic genes of RA, an integrated analysis was performed by using the microarray datasets in RA derived from the Gene Expression Omnibus (GEO) database. The functional annotation and potential pathways of differentially expressed genes (DEGs) were further discovered by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Afterwards, the integrated analysis of DNA methylation and gene expression profiling was used to screen crucial genes. In addition, we used RT-PCR and MSP to verify the expression levels and methylation status of these crucial genes in 20 synovial biopsy samples obtained from 10 RA model mice and 10 normal mice. BCL11B, CCDC88C, FCRLA and APOL6 were both up-regulated and hypomethylated in RA according to integrated analysis, RT-PCR and MSP verification. Four crucial genes (BCL11B, CCDC88C, FCRLA and APOL6) identified and analyzed in this study might be closely connected with the pathogenesis of RA. Copyright © 2017. Published by Elsevier B.V.

  7. Planarian homeobox genes: cloning, sequence analysis, and expression.

    Science.gov (United States)

    Garcia-Fernàndez, J; Baguñà, J; Saló, E

    1991-01-01

    Freshwater planarians (Platyhelminthes, Turbellaria, and Tricladida) are acoelomate, triploblastic, unsegmented, and bilaterally symmetrical organisms that are mainly known for their ample power to regenerate a complete organism from a small piece of their body. To identify potential pattern-control genes in planarian regeneration, we have isolated two homeobox-containing genes, Dth-1 and Dth-2 [Dugesia (Girardia) tigrina homeobox], by using degenerate oligonucleotides corresponding to the most conserved amino acid sequence from helix-3 of the homeodomain. Dth-1 and Dth-2 homeodomains are closely related (68% at the nucleotide level and 78% at the protein level) and show the conserved residues characteristic of the homeodomains identified to data. Similarity with most homeobox sequences is low (30-50%), except with Drosophila NK homeodomains (80-82% with NK-2) and the rodent TTF-1 homeodomain (77-87%). Some unusual amino acid residues specific to NK-2, TTF-1, Dth-1, and Dth-2 can be observed in the recognition helix (helix-3) and may define a family of homeodomains. The deduced amino acid sequences from the cDNAs contain, in addition to the homeodomain, other domains also present in various homeobox-containing genes. The expression of both genes, detected by Northern blot analysis, appear slightly higher in cephalic regions than in the rest of the intact organism, while a slight increase is detected in the central period (5 days) or regeneration. Images PMID:1714599

  8. Association and linkage analysis of aluminum tolerance genes in maize.

    Directory of Open Access Journals (Sweden)

    Allison M Krill

    Full Text Available BACKGROUND: Aluminum (Al toxicity is a major worldwide constraint to crop productivity on acidic soils. Al becomes soluble at low pH, inhibiting root growth and severely reducing yields. Maize is an important staple food and commodity crop in acidic soil regions, especially in South America and Africa where these soils are very common. Al exclusion and intracellular tolerance have been suggested as two important mechanisms for Al tolerance in maize, but little is known about the underlying genetics. METHODOLOGY: An association panel of 282 diverse maize inbred lines and three F2 linkage populations with approximately 200 individuals each were used to study genetic variation in this complex trait. Al tolerance was measured as net root growth in nutrient solution under Al stress, which exhibited a wide range of variation between lines. Comparative and physiological genomics-based approaches were used to select 21 candidate genes for evaluation by association analysis. CONCLUSIONS: Six candidate genes had significant results from association analysis, but only four were confirmed by linkage analysis as putatively contributing to Al tolerance: Zea mays AltSB like (ZmASL, Zea mays aluminum-activated malate transporter2 (ALMT2, S-adenosyl-L-homocysteinase (SAHH, and Malic Enzyme (ME. These four candidate genes are high priority subjects for follow-up biochemical and physiological studies on the mechanisms of Al tolerance in maize. Immediately, elite haplotype-specific molecular markers can be developed for these four genes and used for efficient marker-assisted selection of superior alleles in Al tolerance maize breeding programs.

  9. Synthetic Biology: A Unifying View and Review Using Analog Circuits.

    Science.gov (United States)

    Teo, Jonathan J Y; Woo, Sung Sik; Sarpeshkar, Rahul

    2015-08-01

    We review the field of synthetic biology from an analog circuits and analog computation perspective, focusing on circuits that have been built in living cells. This perspective is well suited to pictorially, symbolically, and quantitatively representing the nonlinear, dynamic, and stochastic (noisy) ordinary and partial differential equations that rigorously describe the molecular circuits of synthetic biology. This perspective enables us to construct a canonical analog circuit schematic that helps unify and review the operation of many fundamental circuits that have been built in synthetic biology at the DNA, RNA, protein, and small-molecule levels over nearly two decades. We review 17 circuits in the literature as particular examples of feedforward and feedback analog circuits that arise from special topological cases of the canonical analog circuit schematic. Digital circuit operation of these circuits represents a special case of saturated analog circuit behavior and is automatically incorporated as well. Many issues that have prevented synthetic biology from scaling are naturally represented in analog circuit schematics. Furthermore, the deep similarity between the Boltzmann thermodynamic equations that describe noisy electronic current flow in subthreshold transistors and noisy molecular flux in biochemical reactions has helped map analog circuit motifs in electronics to analog circuit motifs in cells and vice versa via a `cytomorphic' approach. Thus, a body of knowledge in analog electronic circuit design, analysis, simulation, and implementation may also be useful in the robust and efficient design of molecular circuits in synthetic biology, helping it to scale to more complex circuits in the future.

  10. Large scale gene expression meta-analysis reveals tissue-specific, sex-biased gene expression in humans

    Directory of Open Access Journals (Sweden)

    Benjamin Mayne

    2016-10-01

    Full Text Available The severity and prevalence of many diseases are known to differ between the sexes. Organ specific sex-biased gene expression may underpin these and other sexually dimorphic traits. To further our understanding of sex differences in transcriptional regulation, we performed meta-analyses of sex biased gene expression in multiple human tissues. We analysed 22 publicly available human gene expression microarray data sets including over 2500 samples from 15 different tissues and 9 different organs. Briefly, by using an inverse-variance method we determined the effect size difference of gene expression between males and females. We found the greatest sex differences in gene expression in the brain, specifically in the anterior cingulate cortex, (1818 genes, followed by the heart (375 genes, kidney (224 genes, colon (218 genes and thyroid (163 genes. More interestingly, we found different parts of the brain with varying numbers and identity of sex-biased genes, indicating that specific cortical regions may influence sexually dimorphic traits. The majority of sex-biased genes in other tissues such as the bladder, liver, lungs and pancreas were on the sex chromosomes or involved in sex hormone production. On average in each tissue, 32% of autosomal genes that were expressed in a sex-biased fashion contained androgen or estrogen hormone response elements. Interestingly, across all tissues, we found approximately two-thirds of autosomal genes that were sex-biased were not under direct influence of sex hormones. To our knowledge this is the largest analysis of sex-biased gene expression in human tissues to date. We identified many sex-biased genes that were not under the direct influence of sex chromosome genes or sex hormones. These may provide targets for future development of sex-specific treatments for diseases.

  11. Intuitive analog circuit design

    CERN Document Server

    Thompson, Marc

    2013-01-01

    Intuitive Analog Circuit Design outlines ways of thinking about analog circuits and systems that let you develop a feel for what a good, working analog circuit design should be. This book reflects author Marc Thompson's 30 years of experience designing analog and power electronics circuits and teaching graduate-level analog circuit design, and is the ideal reference for anyone who needs a straightforward introduction to the subject. In this book, Dr. Thompson describes intuitive and ""back-of-the-envelope"" techniques for designing and analyzing analog circuits, including transistor amplifi

  12. The circuit designer's companion

    CERN Document Server

    Williams, Tim

    1991-01-01

    The Circuit Designer's Companion covers the theoretical aspects and practices in analogue and digital circuit design. Electronic circuit design involves designing a circuit that will fulfill its specified function and designing the same circuit so that every production model of it will fulfill its specified function, and no other undesired and unspecified function.This book is composed of nine chapters and starts with a review of the concept of grounding, wiring, and printed circuits. The subsequent chapters deal with the passive and active components of circuitry design. These topics are foll

  13. Information dimension analysis of bacterial essential and nonessential genes based on chaos game representation

    International Nuclear Information System (INIS)

    Zhou, Qian; Yu, Yong-ming

    2014-01-01

    Essential genes are indispensable for the survival of an organism. Investigating features associated with gene essentiality is fundamental to the prediction and identification of the essential genes. Selecting features associated with gene essentiality is fundamental to predict essential genes with computational techniques. We use fractal theory to make comparative analysis of essential and nonessential genes in bacteria. The information dimensions of essential genes and nonessential genes available in the DEG database for 27 bacteria are calculated based on their gene chaos game representations (CGRs). It is found that weak positive linear correlation exists between information dimension and gene length. Moreover, for genes of similar length, the average information dimension of essential genes is larger than that of nonessential genes. This indicates that essential genes show less regularity and higher complexity than nonessential genes. Our results show that for bacterium with a similar number of essential genes and nonessential genes, the CGR information dimension is helpful for the classification of essential genes and nonessential genes. Therefore, the gene CGR information dimension is very probably a useful gene feature for a genetic algorithm predicting essential genes. (paper)

  14. Multilocus analysis reveals three candidate genes for Chinese migraine susceptibility.

    Science.gov (United States)

    An, X-K; Fang, J; Yu, Z-Z; Lin, Q; Lu, C-X; Qu, H-L; Ma, Q-L

    2017-08-01

    Several genome-wide association studies (GWASs) in Caucasian populations have identified 12 loci that are significantly associated with migraine. More evidence suggests that serotonin receptors are also involved in migraine pathophysiology. In the present study, a case-control study was conducted in a cohort of 581 migraine cases and 533 ethnically matched controls among a Chinese population. Eighteen polymorphisms from serotonin receptors and GWASs were selected, and genotyping was performed using a Sequenom MALDI-TOF mass spectrometry iPLEX platform. The genotypic and allelic distributions of MEF2D rs2274316 and ASTN2 rs6478241 were significantly different between migraine patients and controls. Univariate and multivariate analysis revealed significant associations of polymorphisms in the MEF2D and ASTN2 genes with migraine susceptibility. MEF2D, PRDM16 and ASTN2 were also found to be associated with migraine without aura (MO) and migraine with family history. And, MEF2D and ASTN2 also served as genetic risk factors for the migraine without family history. The generalized multifactor dimensionality reduction analysis identified that MEF2D and HTR2E constituted the two-factor interaction model. Our study suggests that the MEF2D, PRDM16 and ASTN2 genes from GWAS are associated with migraine susceptibility, especially MO, among Chinese patients. It appears that there is no association with serotonin receptor related genes. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  15. Transcriptome sequencing and positive selected genes analysis of Bombyx mandarina.

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    Tingcai Cheng

    Full Text Available The wild silkworm Bombyx mandarina is widely believed to be an ancestor of the domesticated silkworm, Bombyx mori. Silkworms are often used as a model for studying the mechanism of species domestication. Here, we performed transcriptome sequencing of the wild silkworm using an Illumina HiSeq2000 platform. We produced 100,004,078 high-quality reads and assembled them into 50,773 contigs with an N50 length of 1764 bp and a mean length of 941.62 bp. A total of 33,759 unigenes were identified, with 12,805 annotated in the Nr database, 8273 in the Pfam database, and 9093 in the Swiss-Prot database. Expression profile analysis found significant differential expression of 1308 unigenes between the middle silk gland (MSG and posterior silk gland (PSG. Three sericin genes (sericin 1, sericin 2, and sericin 3 were expressed specifically in the MSG and three fibroin genes (fibroin-H, fibroin-L, and fibroin/P25 were expressed specifically in the PSG. In addition, 32,297 Single-nucleotide polymorphisms (SNPs and 361 insertion-deletions (INDELs were detected. Comparison with the domesticated silkworm p50/Dazao identified 5,295 orthologous genes, among which 400 might have experienced or to be experiencing positive selection by Ka/Ks analysis. These data and analyses presented here provide insights into silkworm domestication and an invaluable resource for wild silkworm genomics research.

  16. Molecular Characterization and Expression Analysis of Equine ( Gene in Horse (

    Directory of Open Access Journals (Sweden)

    Ki-Duk Song

    2014-05-01

    Full Text Available The objective of this study was to determine the molecular characteristics of the horse vascular endothelial growth factor alpha gene (VEGFα by constructing a phylogenetic tree, and to investigate gene expression profiles in tissues and blood leukocytes after exercise for development of suitable biomarkers. Using published amino acid sequences of other vertebrate species (human, chimpanzee, mouse, rat, cow, pig, chicken and dog, we constructed a phylogenetic tree which showed that equine VEGFα belonged to the same clade of the pig VEGFα. Analysis for synonymous (Ks and non-synonymous substitution ratios (Ka revealed that the horse VEGFα underwent positive selection. RNA was extracted from blood samples before and after exercise and different tissue samples of three horses. Expression analyses using reverse transcription-polymerase chain reaction (RT-PCR and quantitative-polymerase chain reaction (qPCR showed ubiquitous expression of VEGFα mRNA in skeletal muscle, kidney, thyroid, lung, appendix, colon, spinal cord, and heart tissues. Analysis of differential expression of VEGFα gene in blood leukocytes after exercise indicated a unimodal pattern. These results will be useful in developing biomarkers that can predict the recovery capacity of racing horses.

  17. Reference genes for gene expression analysis by real-time reverse transcription polymerase chain reaction of renal cell carcinoma.

    Science.gov (United States)

    Bjerregaard, Henriette; Pedersen, Shona; Kristensen, Søren Risom; Marcussen, Niels

    2011-12-01

    Differentiation between malignant renal cell carcinoma and benign oncocytoma is of great importance to choose the optimal treatment. Accurate preoperative diagnosis of renal tumor is therefore crucial; however, existing imaging techniques and histologic examinations are incapable of providing an optimal differentiation profile. Analysis of gene expression of molecular markers is a new possibility but relies on appropriate standardization to compare different samples. The aim of this study was to identify stably expressed reference genes suitable for the normalization of results extracted from gene expression analysis of renal tumors. Expression levels of 8 potential reference genes (ATP5J, HMBS, HPRT1, PPIA, TBP, 18S, GAPDH, and POLR2A) were examined by real-time reverse transcription polymerase chain reaction in tumor and normal tissue from removed kidneys from 13 patients with renal cell carcinoma and 5 patients with oncocytoma. The expression levels of genes were compared by gene stability value M, average gene stability M, pairwise variation V, and coefficient of variation CV. More candidates were not suitable for the purpose, but a combination of HMBS, PPIA, ATP5J, and TBP was found to be the best combination with an average gene stability value M of 0.9 and a CV of 0.4 in the 18 tumors and normal tissues. A combination of 4 genes, HMBS, PPIA, ATP5J, and TBP, is a possible reference in renal tumor gene expression analysis by reverse transcription polymerase chain reaction. A combination of four genes, HMBS, PPIA, ATP5J and TBP, being stably expressed in tissues from RCC is possible reference genes for gene expression analysis.

  18. Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray.

    Directory of Open Access Journals (Sweden)

    Kouji Satoh

    Full Text Available Rice (Oryza sativa L. is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly. Based on the annotation status and the presence of corresponding cDNA clones, genes were classified into 23K annotated expressed (AE genes, 33K annotated non-expressed (ANE genes, and 5.5K non-annotated expressed (NAE genes. We developed a 60mer oligo-array for analysis of gene expression from each locus. Analysis of gene structures and expression levels revealed that the general features of gene structure and expression of NAE and ANE genes were considerably different from those of AE genes. The results also suggested that the cloning efficiency of rice FL-cDNA is associated with the transcription activity of the corresponding genetic locus, although other factors may also have an effect. Comparison of the coverage of FL-cDNA among gene families suggested that FL-cDNA from genes encoding rice- or eukaryote-specific domains, and those involved in regulatory functions were difficult to produce in bacterial cells. Collectively, these results indicate that rice genes can be divided into distinct groups based on transcription activity and gene structure, and that the coverage bias of FL-cDNA clones exists due to the incompatibility of certain eukaryotic genes in bacteria.

  19. A comparative analysis of biclustering algorithms for gene expression data

    Science.gov (United States)

    Eren, Kemal; Deveci, Mehmet; Küçüktunç, Onur; Çatalyürek, Ümit V.

    2013-01-01

    The need to analyze high-dimension biological data is driving the development of new data mining methods. Biclustering algorithms have been successfully applied to gene expression data to discover local patterns, in which a subset of genes exhibit similar expression levels over a subset of conditions. However, it is not clear which algorithms are best suited for this task. Many algorithms have been published in the past decade, most of which have been compared only to a small number of algorithms. Surveys and comparisons exist in the literature, but because of the large number and variety of biclustering algorithms, they are quickly outdated. In this article we partially address this problem of evaluating the strengths and weaknesses of existing biclustering methods. We used the BiBench package to compare 12 algorithms, many of which were recently published or have not been extensively studied. The algorithms were tested on a suite of synthetic data sets to measure their performance on data with varying conditions, such as different bicluster models, varying noise, varying numbers of biclusters and overlapping biclusters. The algorithms were also tested on eight large gene expression data sets obtained from the Gene Expression Omnibus. Gene Ontology enrichment analysis was performed on the resulting biclusters, and the best enrichment terms are reported. Our analyses show that the biclustering method and its parameters should be selected based on the desired model, whether that model allows overlapping biclusters, and its robustness to noise. In addition, we observe that the biclustering algorithms capable of finding more than one model are more successful at capturing biologically relevant clusters. PMID:22772837

  20. Mutational analysis of the HGO gene in Finnish alkaptonuria patients

    Science.gov (United States)

    de Bernabe, D. B.-V.; Peterson, P.; Luopajarvi, K.; Matintalo, P.; Alho, A.; Konttinen, Y.; Krohn, K.; de Cordoba, S. R.; Ranki, A.

    1999-01-01

    Alkaptonuria (AKU), the prototypic inborn error of metabolism, has recently been shown to be caused by loss of function mutations in the homogentisate-1,2-dioxygenase gene (HGO). So far 17 mutations have been characterised in AKU patients of different ethnic origin. We describe three novel mutations (R58fs, R330S, and H371R) and one common AKU mutation (M368V), detected by mutational and polymorphism analysis of the HGO gene in five Finnish AKU pedigrees. The three novel AKU mutations are most likely specific for the Finnish population and have originated recently.


Keywords: alkaptonuria; homogentisate-1,2-dioxygenase; Finland PMID:10594001

  1. [Weighted gene co-expression network analysis in biomedicine research].

    Science.gov (United States)

    Liu, Wei; Li, Li; Ye, Hua; Tu, Wei

    2017-11-25

    High-throughput biological technologies are now widely applied in biology and medicine, allowing scientists to monitor thousands of parameters simultaneously in a specific sample. However, it is still an enormous challenge to mine useful information from high-throughput data. The emergence of network biology provides deeper insights into complex bio-system and reveals the modularity in tissue/cellular networks. Correlation networks are increasingly used in bioinformatics applications. Weighted gene co-expression network analysis (WGCNA) tool can detect clusters of highly correlated genes. Therefore, we systematically reviewed the application of WGCNA in the study of disease diagnosis, pathogenesis and other related fields. First, we introduced principle, workflow, advantages and disadvantages of WGCNA. Second, we presented the application of WGCNA in disease, physiology, drug, evolution and genome annotation. Then, we indicated the application of WGCNA in newly developed high-throughput methods. We hope this review will help to promote the application of WGCNA in biomedicine research.

  2. Gene Regulation, Modulation, and Their Applications in Gene Expression Data Analysis

    Directory of Open Access Journals (Sweden)

    Mario Flores

    2013-01-01

    Full Text Available Common microarray and next-generation sequencing data analysis concentrate on tumor subtype classification, marker detection, and transcriptional regulation discovery during biological processes by exploring the correlated gene expression patterns and their shared functions. Genetic regulatory network (GRN based approaches have been employed in many large studies in order to scrutinize for dysregulation and potential treatment controls. In addition to gene regulation and network construction, the concept of the network modulator that has significant systemic impact has been proposed, and detection algorithms have been developed in past years. Here we provide a unified mathematic description of these methods, followed with a brief survey of these modulator identification algorithms. As an early attempt to extend the concept to new RNA regulation mechanism, competitive endogenous RNA (ceRNA, into a modulator framework, we provide two applications to illustrate the network construction, modulation effect, and the preliminary finding from these networks. Those methods we surveyed and developed are used to dissect the regulated network under different modulators. Not limit to these, the concept of “modulation” can adapt to various biological mechanisms to discover the novel gene regulation mechanisms.

  3. Development of gene diagnosis for diabetes and cholecystitis based on gene analysis of CCK-A receptor

    International Nuclear Information System (INIS)

    Kono, Akira

    1999-01-01

    Base sequence analysis of CCKAR gene (a gene of A-type receptor for cholecystokinin) from OLETF rat, a model rat for insulin-independent diabetes was made based on the base sequence of wild CCKAR gene, which had been clarified in the previous year. From the pancreas of OLETF rat, DNA was extracted and transduced into λphage after fragmentation to construct the gene library of OLETF. Then, λphage DNA clone bound with labelled cDNA of CCKAR gene was analyzed and the gene structure was compared with that of the wild gene. It was demonstrated that CCKAR gene of OLETF had a deletion (6800 b.p.) ranging from the promoter region to the Exon 2, suggesting that CCKAR gene is not functional in OLETF rat. The whole sequence of this mutant gene was registered into Japan DNA Bank (D 50610). Then, F 2 offspring rats were obtained through crossing OLETF (female) and F344 (male) and the time course-changes in the blood glucose level after glucose loading were compared among them. The blood glucose level after glucose loading was significantly higher in the homo-mutant F 2 (CCKAR,-/-) as well as the parent OLETF rat than hetero-mutant F 2 (CCKARm-/+) or the wild rat (CCKAR,+/+). This suggests that CCKAR gene might be involved in the control of blood glucose level and an alteration of the expression level or the functions of CCKAR gene might affect the blood glucose level. (M.N.)

  4. An analog integrated circuit design laboratory

    OpenAIRE

    Mondragon-Torres, A.F.; Mayhugh, Jr.; Pineda de Gyvez, J.; Silva-Martinez, J.; Sanchez-Sinencio, E.

    2003-01-01

    We present the structure of an analog integrated circuit design laboratory to instruct at both, senior undergraduate and entry graduate levels. The teaching material includes: a laboratory manual with analog circuit design theory, pre-laboratory exercises and circuit design specifications; a reference web page with step by step instructions and examples; the use of mathematical tools for automation and analysis; and state of the art CAD design tools in use by industry. Upon completion of the ...

  5. Project and analysis of the toroidal magnetic field production circuits and the plasma formation of the ETE (Spherical Tokamak Experiment) tokamak

    International Nuclear Information System (INIS)

    Barbosa, Luis Filipe F.P.W.; Bosco, Edson del.

    1994-01-01

    This report presents the project and analysis of the circuit for production of the toroidal magnetic field in the Tokamak ETE (Spherical Tokamak Experiment). The ETE is a Tokamak with a small-aspect-ratio parameter to be used for studying the plasma physics for the research on thermonuclear fusion. This machine is being constructed at the Laboratorio Associado de Plasma (LAP) of the Instituto Nacional de Pesquisas Espaciais (INPE) in Sao Jose dos Campos, SP, Brazil. (author). 20 refs., 39 figs., 4 tabs

  6. Theory, analysis and applications of the operation of the superconducting transformer supplying a direct current to a non-dissipative superconducting charge circuit

    International Nuclear Information System (INIS)

    Sole, J.

    1967-01-01

    The author derives the very simple equations governing the operation of a transformer with superconducting windings supplying direct current to a non-dissipative superconducting charge circuit. An analysis of the various possible modes of operation with direct or slowly varying current raises the problem of the magnetic core. The study. leads to a conclusion which a priori might be surprising: the elimination of the magnetic core and the use of a primary super-conductor. An example of a possible realization of such a transformer is given as an indication, and the present prospects for different applications are considered. (author) [fr

  7. Feasibility analysis of a novel hybrid-type superconducting circuit breaker in multi-terminal HVDC networks

    International Nuclear Information System (INIS)

    Khan, Umer Amir; Lee, Jong-Geon; Seo, In-Jin; Amir, Faisal; Lee, Bang-Wook

    2015-01-01

    Highlights: • A novel hybrid-type superconducting circuit breaker (SDCCB) is proposed. • SDCCB has SFCL located in the main current path to limit the fault current until the final trip signal. • SFCL in SDCCB suppressed the fast rising DC fault current for a predefined time. • SFCL significantly reduced the DC current breaking stress on SDCCB components. • SDCCB isolated the HVDC faulty line in three, four, and five converter stations MTDC. - Abstract: Voltage source converter-based HVDC systems (VSC-HVDC) are a better alternative than conventional thyristor-based HVDC systems, especially for developing multi-terminal HVDC systems (MTDC). However, one of the key obstacles in developing MTDC is the absence of an adequate protection system that can quickly detect faults, locate the faulty line and trip the HVDC circuit breakers (DCCBs) to interrupt the DC fault current. In this paper, a novel hybrid-type superconducting circuit breaker (SDCCB) is proposed and feasibility analyses of its application in MTDC are presented. The SDCCB has a superconducting fault current limiter (SFCL) located in the main current path to limit fault currents until the final trip signal is received. After the trip signal the IGBT located in the main line commutates the current into a parallel line where DC current is forced to zero by the combination of IGBTs and surge arresters. Fault simulations for three-, four- and five-terminal MTDC were performed and SDCCB performance was evaluated in these MTDC. Passive current limitation by SFCL caused a significant reduction of fault current interruption stress in the SDCCB. It was observed that the DC current could change direction in MTDC after a fault and the SDCCB was modified to break the DC current in both the forward and reverse directions. The simulation results suggest that the proposed SDCCB could successfully suppress the DC fault current, cause a timely interruption, and isolate the faulty HVDC line in MTDC.

  8. Feasibility analysis of a novel hybrid-type superconducting circuit breaker in multi-terminal HVDC networks

    Energy Technology Data Exchange (ETDEWEB)

    Khan, Umer Amir [Hanyang University, Sa-3dong, Sangrok-gu, Ansan 426-791 (Korea, Republic of); National University of Sciences and Technology, PNEC Campus, Habib Rehmatullah Road, Karachi (Pakistan); Lee, Jong-Geon; Seo, In-Jin [Hanyang University, Sa-3dong, Sangrok-gu, Ansan 426-791 (Korea, Republic of); Amir, Faisal [National University of Sciences and Technology, PNEC Campus, Habib Rehmatullah Road, Karachi (Pakistan); Lee, Bang-Wook, E-mail: bangwook@hanyang.ac.kr [Hanyang University, Sa-3dong, Sangrok-gu, Ansan 426-791 (Korea, Republic of)

    2015-11-15

    Highlights: • A novel hybrid-type superconducting circuit breaker (SDCCB) is proposed. • SDCCB has SFCL located in the main current path to limit the fault current until the final trip signal. • SFCL in SDCCB suppressed the fast rising DC fault current for a predefined time. • SFCL significantly reduced the DC current breaking stress on SDCCB components. • SDCCB isolated the HVDC faulty line in three, four, and five converter stations MTDC. - Abstract: Voltage source converter-based HVDC systems (VSC-HVDC) are a better alternative than conventional thyristor-based HVDC systems, especially for developing multi-terminal HVDC systems (MTDC). However, one of the key obstacles in developing MTDC is the absence of an adequate protection system that can quickly detect faults, locate the faulty line and trip the HVDC circuit breakers (DCCBs) to interrupt the DC fault current. In this paper, a novel hybrid-type superconducting circuit breaker (SDCCB) is proposed and feasibility analyses of its application in MTDC are presented. The SDCCB has a superconducting fault current limiter (SFCL) located in the main current path to limit fault currents until the final trip signal is received. After the trip signal the IGBT located in the main line commutates the current into a parallel line where DC current is forced to zero by the combination of IGBTs and surge arresters. Fault simulations for three-, four- and five-terminal MTDC were performed and SDCCB performance was evaluated in these MTDC. Passive current limitation by SFCL caused a significant reduction of fault current interruption stress in the SDCCB. It was observed that the DC current could change direction in MTDC after a fault and the SDCCB was modified to break the DC current in both the forward and reverse directions. The simulation results suggest that the proposed SDCCB could successfully suppress the DC fault current, cause a timely interruption, and isolate the faulty HVDC line in MTDC.

  9. Reliability and Availability Analysis of Some Systems with Common-Cause Failures Using SPICE Circuit Simulation Program

    Directory of Open Access Journals (Sweden)

    Muhammad Taher Abuelma'atti

    1999-01-01

    Full Text Available The effectiveness of SPICE circuit simulation program in calculating probabilities, reliability, steady-state availability and mean-time to failure of repairable systems described by Markov models is demonstrated. Two examples are presented. The first example is a warm standby system with common-cause failures and human errors. The second example is a non-identical unit parallel system with common-cause failures. In both cases recourse to numerical solution is inevitable to obtain the Laplace transforms of the probabilities. Results obtained using SPICE are compared with previously published results obtained using the Laplace transform method. Full SPICE listings are included.

  10. Nonlinear analysis of a family of LC tuned inverters. [dc to square wave circuits for power conditioning

    Science.gov (United States)

    Lee, F. C. Y.; Wilson, T. G.

    1974-01-01

    A family of four dc-to-square-wave LC tuned inverters are analyzed using singular point. Limit cycles and waveshape characteristics are given for three modes of oscillation: quasi-harmonic, relaxation, and discontinuous. An inverter in which the avalanche breakdown of the transistor emitter-to-base junction occurs is discussed and the starting characteristics of this family of inverters are presented. The LC tuned inverters are shown to belong to a family of inverters with a common equivalent circuit consisting of only three 'series' elements: a five-segment piecewise-linear current-controlled resistor, linear inductor, and linear capacitor.

  11. Electrical Circuits and Water Analogies

    Science.gov (United States)

    Smith, Frederick A.; Wilson, Jerry D.

    1974-01-01

    Briefly describes water analogies for electrical circuits and presents plans for the construction of apparatus to demonstrate these analogies. Demonstrations include series circuits, parallel circuits, and capacitors. (GS)

  12. Analysis of deterministic cyclic gene regulatory network models with delays

    CERN Document Server

    Ahsen, Mehmet Eren; Niculescu, Silviu-Iulian

    2015-01-01

    This brief examines a deterministic, ODE-based model for gene regulatory networks (GRN) that incorporates nonlinearities and time-delayed feedback. An introductory chapter provides some insights into molecular biology and GRNs. The mathematical tools necessary for studying the GRN model are then reviewed, in particular Hill functions and Schwarzian derivatives. One chapter is devoted to the analysis of GRNs under negative feedback with time delays and a special case of a homogenous GRN is considered. Asymptotic stability analysis of GRNs under positive feedback is then considered in a separate chapter, in which conditions leading to bi-stability are derived. Graduate and advanced undergraduate students and researchers in control engineering, applied mathematics, systems biology and synthetic biology will find this brief to be a clear and concise introduction to the modeling and analysis of GRNs.

  13. GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data.

    Science.gov (United States)

    Ben-Ari Fuchs, Shani; Lieder, Iris; Stelzer, Gil; Mazor, Yaron; Buzhor, Ella; Kaplan, Sergey; Bogoch, Yoel; Plaschkes, Inbar; Shitrit, Alina; Rappaport, Noa; Kohn, Asher; Edgar, Ron; Shenhav, Liraz; Safran, Marilyn; Lancet, Doron; Guan-Golan, Yaron; Warshawsky, David; Shtrichman, Ronit

    2016-03-01

    Postgenomics data are produced in large volumes by life sciences and clinical applications of novel omics diagnostics and therapeutics for precision medicine. To move from "data-to-knowledge-to-innovation," a crucial missing step in the current era is, however, our limited understanding of biological and clinical contexts associated with data. Prominent among the emerging remedies to this challenge are the gene set enrichment tools. This study reports on GeneAnalytics™ ( geneanalytics.genecards.org ), a comprehensive and easy-to-apply gene set analysis tool for rapid contextualization of expression patterns and functional signatures embedded in the postgenomics Big Data domains, such as Next Generation Sequencing (NGS), RNAseq, and microarray experiments. GeneAnalytics' differentiating features include in-depth evidence-based scoring algorithms, an intuitive user interface and proprietary unified data. GeneAnalytics employs the LifeMap Science's GeneCards suite, including the GeneCards®--the human gene database; the MalaCards-the human diseases database; and the PathCards--the biological pathways database. Expression-based analysis in GeneAnalytics relies on the LifeMap Discovery®--the embryonic development and stem cells database, which includes manually curated expression data for normal and diseased tissues, enabling advanced matching algorithm for gene-tissue association. This assists in evaluating differentiation protocols and discovering biomarkers for tissues and cells. Results are directly linked to gene, disease, or cell "cards" in the GeneCards suite. Future developments aim to enhance the GeneAnalytics algorithm as well as visualizations, employing varied graphical display items. Such attributes make GeneAnalytics a broadly applicable postgenomics data analyses and interpretation tool for translation of data to knowledge-based innovation in various Big Data fields such as precision medicine, ecogenomics, nutrigenomics, pharmacogenomics, vaccinomics

  14. Serial Expression Analysis: a web tool for the analysis of serial gene expression data

    Science.gov (United States)

    Nueda, Maria José; Carbonell, José; Medina, Ignacio; Dopazo, Joaquín; Conesa, Ana

    2010-01-01

    Serial transcriptomics experiments investigate the dynamics of gene expression changes associated with a quantitative variable such as time or dosage. The statistical analysis of these data implies the study of global and gene-specific expression trends, the identification of significant serial changes, the comparison of expression profiles and the assessment of transcriptional changes in terms of cellular processes. We have created the SEA (Serial Expression Analysis) suite to provide a complete web-based resource for the analysis of serial transcriptomics data. SEA offers five different algorithms based on univariate, multivariate and functional profiling strategies framed within a user-friendly interface and a project-oriented architecture to facilitate the analysis of serial gene expression data sets from different perspectives. SEA is available at sea.bioinfo.cipf.es. PMID:20525784

  15. Fine Mapping and Candidate Gene Analysis of the Leaf-Color Gene ygl-1 in Maize.

    Directory of Open Access Journals (Sweden)

    Haiying Guan

    Full Text Available A novel yellow-green leaf mutant yellow-green leaf-1 (ygl-1 was isolated in self-pollinated progenies from the cross of maize inbred lines Ye478 and Yuanwu02. The mutant spontaneously showed yellow-green character throughout the lifespan. Meanwhile, the mutant reduced contents of chlorophyll and Car, arrested chloroplast development and lowered the capacity of photosynthesis compared with the wild-type Lx7226. Genetic analysis revealed that the mutant phenotype was controlled by a recessive nuclear gene. The ygl-1 locus was initially mapped to an interval of about 0.86 Mb in bin 1.01 on the short arm of chromosome 1 using 231 yellow-green leaf individuals of an F2 segregating population from ygl-1/Lx7226. Utilizing four new polymorphic SSR markers, the ygl-1 locus was narrowed down to a region of about 48 kb using 2930 and 2247 individuals of F2 and F3 mapping populations, respectively. Among the three predicted genes annotated within this 48 kb region, GRMZM2G007441, which was predicted to encode a cpSRP43 protein, had a 1-bp nucleotide deletion in the coding region of ygl-1 resulting in a frame shift mutation. Semi-quantitative RT-PCR analysis revealed that YGL-1 was constitutively expressed in all tested tissues and its expression level was not significantly affected in the ygl-1 mutant from early to mature stages, while light intensity regulated its expression both in the ygl-1 mutant and wild type seedlings. Furthermore, the mRNA levels of some genes involved in chloroplast development were affected in the six-week old ygl-1 plants. These findings suggested that YGL-1 plays an important role in chloroplast development of maize.

  16. Suitable Reference Genes for Accurate Gene Expression Analysis in Parsley (Petroselinum crispum) for Abiotic Stresses and Hormone Stimuli.

    Science.gov (United States)

    Li, Meng-Yao; Song, Xiong; Wang, Feng; Xiong, Ai-Sheng

    2016-01-01

    Parsley, one of the most important vegetables in the Apiaceae family, is widely used in the food, medicinal, and cosmetic industries. Recent studies on parsley mainly focus on its chemical composition, and further research involving the analysis of the plant's gene functions and expressions is required. qPCR is a powerful method for detecting very low quantities of target transcript levels and is widely used to study gene expression. To ensure the accuracy of results, a suitable reference gene is necessary for expression normalization. In this study, four software, namely geNorm, NormFinder, BestKeeper, and RefFinder were used to evaluate the expression stabilities of eight candidate reference genes of parsley ( GAPDH, ACTIN, eIF-4 α, SAND, UBC, TIP41, EF-1 α, and TUB ) under various conditions, including abiotic stresses (heat, cold, salt, and drought) and hormone stimuli treatments (GA, SA, MeJA, and ABA). Results showed that EF-1 α and TUB were the most stable genes for abiotic stresses, whereas EF-1 α, GAPDH , and TUB were the top three choices for hormone stimuli treatments. Moreover, EF-1 α and TUB were the most stable reference genes among all tested samples, and UBC was the least stable one. Expression analysis of PcDREB1 and PcDREB2 further verified that the selected stable reference genes were suitable for gene expression normalization. This study can guide the selection of suitable reference genes in gene expression in parsley.

  17. Suitable reference genes for accurate gene expression analysis in parsley (Petroselinum crispum for abiotic stresses and hormone stimuli

    Directory of Open Access Journals (Sweden)

    Meng-Yao Li

    2016-09-01

    Full Text Available Parsley is one of the most important vegetable in Apiaceae family and widely used in food industry, medicinal and cosmetic. The recent studies in parsley are mainly focus on chemical composition, further research involving the analysis of the gene functions and expressions will be required. qPCR is a powerful method for detecting very low quantities of target transcript levels and widely used for gene expression studies. To ensure the accuracy of results, a suitable reference gene is necessary for expression normalization. In this study, three software geNorm, NormFinder, and BestKeeper were used to evaluate the expression stabilities of eight candidate reference genes (GAPDH, ACTIN, eIF-4α, SAND, UBC, TIP41, EF-1α, and TUB under various conditions including abiotic stresses (heat, cold, salt, and drought and hormone stimuli treatments (GA, SA, MeJA, and ABA. The results showed that EF-1α and TUB were identified as the most stable genes for abiotic stresses, while EF-1α, GAPDH, and TUB were the top three choices for hormone stimuli treatments. Moreover, EF-1α and TUB were the most stable reference genes across all the tested samples, while UBC was the least stable one. The expression analysis of PcDREB1 and PcDREB2 further verified that the selected stable reference genes were suitable for gene expression normalization. This study provides a guideline for selection the suitable reference genes in gene expression in parsley.

  18. Piezoelectric drive circuit

    Science.gov (United States)

    Treu, C.A. Jr.

    1999-08-31

    A piezoelectric motor drive circuit is provided which utilizes the piezoelectric elements as oscillators and a Meacham half-bridge approach to develop feedback from the motor ground circuit to produce a signal to drive amplifiers to power the motor. The circuit automatically compensates for shifts in harmonic frequency of the piezoelectric elements due to pressure and temperature changes. 7 figs.

  19. Load testing circuit

    DEFF Research Database (Denmark)

    2009-01-01

    A load testing circuit a circuit tests the load impedance of a load connected to an amplifier. The load impedance includes a first terminal and a second terminal, the load testing circuit comprising a signal generator providing a test signal of a defined bandwidth to the first terminal of the load...

  20. Short-circuit logic

    NARCIS (Netherlands)

    Bergstra, J.A.; Ponse, A.

    2010-01-01

    Short-circuit evaluation denotes the semantics of propositional connectives in which the second argument is only evaluated if the first argument does not suffice to determine the value of the expression. In programming, short-circuit evaluation is widely used. A short-circuit logic is a variant of