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Sample records for metabolic scaling theory

  1. Plant interactions alter the predictions of metabolic scaling theory

    Lin, Yue; Berger, Uta; Grimm, Volker

    2013-01-01

    Metabolic scaling theory (MST) is an attempt to link physiological processes of individual organisms with macroecology. It predicts a power law relationship with an exponent of 24/3 between mean individual biomass and density during densitydependent mortality (self-thinning). Empirical tests have...... processes can scale up to the population level. MST, like thermodynamics or biomechanics, sets limits within which organisms can live and function, but there may be stronger limits determined by ecological interactions. In such cases MST will not be predictive....... of plant stand development that includes three elements: a model of individual plant growth based on MST, different modes of local competition (size-symmetric vs. -asymmetric), and different resource levels. Our model is consistent with the observed variation in the slopes of self-thinning trajectories...

  2. Plant interactions alter the predictions of metabolic scaling theory.

    Yue Lin

    Full Text Available Metabolic scaling theory (MST is an attempt to link physiological processes of individual organisms with macroecology. It predicts a power law relationship with an exponent of -4/3 between mean individual biomass and density during density-dependent mortality (self-thinning. Empirical tests have produced variable results, and the validity of MST is intensely debated. MST focuses on organisms' internal physiological mechanisms but we hypothesize that ecological interactions can be more important in determining plant mass-density relationships induced by density. We employ an individual-based model of plant stand development that includes three elements: a model of individual plant growth based on MST, different modes of local competition (size-symmetric vs. -asymmetric, and different resource levels. Our model is consistent with the observed variation in the slopes of self-thinning trajectories. Slopes were significantly shallower than -4/3 if competition was size-symmetric. We conclude that when the size of survivors is influenced by strong ecological interactions, these can override predictions of MST, whereas when surviving plants are less affected by interactions, individual-level metabolic processes can scale up to the population level. MST, like thermodynamics or biomechanics, sets limits within which organisms can live and function, but there may be stronger limits determined by ecological interactions. In such cases MST will not be predictive.

  3. Body shape shifting during growth permits tests that distinguish between competing geometric theories of metabolic scaling

    Hirst, Andrew G.; Glazier, Douglas S.; Atkinson, David

    2014-01-01

    Metabolism fuels all of life’s activities, from biochemical reactions to ecological interactions. According to two intensely debated theories, body size affects metabolism via geometrical influences on the transport of resources and wastes. However, these theories differ crucially in whether...... the size dependence of metabolism is derived from material transport across external surfaces, or through internal resource-transport networks. We show that when body shape changes during growth, these models make opposing predictions. These models are tested using pelagic invertebrates, because...... these animals exhibit highly variable intraspecific scaling relationships for metabolic rate and body shape. Metabolic scaling slopes of diverse integument-breathing species were significantly positively correlated with degree of body flattening or elongation during ontogeny, as expected from surface area...

  4. Scaling of Metabolic Scaling within Physical Limits

    Douglas S. Glazier

    2014-10-01

    Full Text Available Both the slope and elevation of scaling relationships between log metabolic rate and log body size vary taxonomically and in relation to physiological or developmental state, ecological lifestyle and environmental conditions. Here I discuss how the recently proposed metabolic-level boundaries hypothesis (MLBH provides a useful conceptual framework for explaining and predicting much, but not all of this variation. This hypothesis is based on three major assumptions: (1 various processes related to body volume and surface area exert state-dependent effects on the scaling slope for metabolic rate in relation to body mass; (2 the elevation and slope of metabolic scaling relationships are linked; and (3 both intrinsic (anatomical, biochemical and physiological and extrinsic (ecological factors can affect metabolic scaling. According to the MLBH, the diversity of metabolic scaling relationships occurs within physical boundary limits related to body volume and surface area. Within these limits, specific metabolic scaling slopes can be predicted from the metabolic level (or scaling elevation of a species or group of species. In essence, metabolic scaling itself scales with metabolic level, which is in turn contingent on various intrinsic and extrinsic conditions operating in physiological or evolutionary time. The MLBH represents a “meta-mechanism” or collection of multiple, specific mechanisms that have contingent, state-dependent effects. As such, the MLBH is Darwinian in approach (the theory of natural selection is also meta-mechanistic, in contrast to currently influential metabolic scaling theory that is Newtonian in approach (i.e., based on unitary deterministic laws. Furthermore, the MLBH can be viewed as part of a more general theory that includes other mechanisms that may also affect metabolic scaling.

  5. Tree Morphologic Plasticity Explains Deviation from Metabolic Scaling Theory in Semi-Arid Conifer Forests, Southwestern USA.

    Tyson L Swetnam

    Full Text Available A significant concern about Metabolic Scaling Theory (MST in real forests relates to consistent differences between the values of power law scaling exponents of tree primary size measures used to estimate mass and those predicted by MST. Here we consider why observed scaling exponents for diameter and height relationships deviate from MST predictions across three semi-arid conifer forests in relation to: (1 tree condition and physical form, (2 the level of inter-tree competition (e.g. open vs closed stand structure, (3 increasing tree age, and (4 differences in site productivity. Scaling exponent values derived from non-linear least-squares regression for trees in excellent condition (n = 381 were above the MST prediction at the 95% confidence level, while the exponent for trees in good condition were no different than MST (n = 926. Trees that were in fair or poor condition, characterized as diseased, leaning, or sparsely crowned had exponent values below MST predictions (n = 2,058, as did recently dead standing trees (n = 375. Exponent value of the mean-tree model that disregarded tree condition (n = 3,740 was consistent with other studies that reject MST scaling. Ostensibly, as stand density and competition increase trees exhibited greater morphological plasticity whereby the majority had characteristically fair or poor growth forms. Fitting by least-squares regression biases the mean-tree model scaling exponent toward values that are below MST idealized predictions. For 368 trees from Arizona with known establishment dates, increasing age had no significant impact on expected scaling. We further suggest height to diameter ratios below MST relate to vertical truncation caused by limitation in plant water availability. Even with environmentally imposed height limitation, proportionality between height and diameter scaling exponents were consistent with the predictions of MST.

  6. Tree Morphologic Plasticity Explains Deviation from Metabolic Scaling Theory in Semi-Arid Conifer Forests, Southwestern USA.

    Swetnam, Tyson L; O'Connor, Christopher D; Lynch, Ann M

    2016-01-01

    A significant concern about Metabolic Scaling Theory (MST) in real forests relates to consistent differences between the values of power law scaling exponents of tree primary size measures used to estimate mass and those predicted by MST. Here we consider why observed scaling exponents for diameter and height relationships deviate from MST predictions across three semi-arid conifer forests in relation to: (1) tree condition and physical form, (2) the level of inter-tree competition (e.g. open vs closed stand structure), (3) increasing tree age, and (4) differences in site productivity. Scaling exponent values derived from non-linear least-squares regression for trees in excellent condition (n = 381) were above the MST prediction at the 95% confidence level, while the exponent for trees in good condition were no different than MST (n = 926). Trees that were in fair or poor condition, characterized as diseased, leaning, or sparsely crowned had exponent values below MST predictions (n = 2,058), as did recently dead standing trees (n = 375). Exponent value of the mean-tree model that disregarded tree condition (n = 3,740) was consistent with other studies that reject MST scaling. Ostensibly, as stand density and competition increase trees exhibited greater morphological plasticity whereby the majority had characteristically fair or poor growth forms. Fitting by least-squares regression biases the mean-tree model scaling exponent toward values that are below MST idealized predictions. For 368 trees from Arizona with known establishment dates, increasing age had no significant impact on expected scaling. We further suggest height to diameter ratios below MST relate to vertical truncation caused by limitation in plant water availability. Even with environmentally imposed height limitation, proportionality between height and diameter scaling exponents were consistent with the predictions of MST.

  7. A theoretical framework for whole-plant carbon assimilation efficiency based on metabolic scaling theory: a test case using Picea seedlings.

    Wang, Zhiqiang; Ji, Mingfei; Deng, Jianming; Milne, Richard I; Ran, Jinzhi; Zhang, Qiang; Fan, Zhexuan; Zhang, Xiaowei; Li, Jiangtao; Huang, Heng; Cheng, Dongliang; Niklas, Karl J

    2015-06-01

    Simultaneous and accurate measurements of whole-plant instantaneous carbon-use efficiency (ICUE) and annual total carbon-use efficiency (TCUE) are difficult to make, especially for trees. One usually estimates ICUE based on the net photosynthetic rate or the assumed proportional relationship between growth efficiency and ICUE. However, thus far, protocols for easily estimating annual TCUE remain problematic. Here, we present a theoretical framework (based on the metabolic scaling theory) to predict whole-plant annual TCUE by directly measuring instantaneous net photosynthetic and respiratory rates. This framework makes four predictions, which were evaluated empirically using seedlings of nine Picea taxa: (i) the flux rates of CO(2) and energy will scale isometrically as a function of plant size, (ii) whole-plant net and gross photosynthetic rates and the net primary productivity will scale isometrically with respect to total leaf mass, (iii) these scaling relationships will be independent of ambient temperature and humidity fluctuations (as measured within an experimental chamber) regardless of the instantaneous net photosynthetic rate or dark respiratory rate, or overall growth rate and (iv) TCUE will scale isometrically with respect to instantaneous efficiency of carbon use (i.e., the latter can be used to predict the former) across diverse species. These predictions were experimentally verified. We also found that the ranking of the nine taxa based on net photosynthetic rates differed from ranking based on either ICUE or TCUE. In addition, the absolute values of ICUE and TCUE significantly differed among the nine taxa, with both ICUE and temperature-corrected ICUE being highest for Picea abies and lowest for Picea schrenkiana. Nevertheless, the data are consistent with the predictions of our general theoretical framework, which can be used to access annual carbon-use efficiency of different species at the level of an individual plant based on simple, direct

  8. Genome scale metabolic modeling of cancer

    Nilsson, Avlant; Nielsen, Jens

    2017-01-01

    of metabolism which allows simulation and hypotheses testing of metabolic strategies. It has successfully been applied to many microorganisms and is now used to study cancer metabolism. Generic models of human metabolism have been reconstructed based on the existence of metabolic genes in the human genome......Cancer cells reprogram metabolism to support rapid proliferation and survival. Energy metabolism is particularly important for growth and genes encoding enzymes involved in energy metabolism are frequently altered in cancer cells. A genome scale metabolic model (GEM) is a mathematical formalization...

  9. Finite size scaling theory

    Rittenberg, V.

    1983-01-01

    Fischer's finite-size scaling describes the cross over from the singular behaviour of thermodynamic quantities at the critical point to the analytic behaviour of the finite system. Recent extensions of the method--transfer matrix technique, and the Hamiltonian formalism--are discussed in this paper. The method is presented, with equations deriving scaling function, critical temperature, and exponent v. As an application of the method, a 3-states Hamiltonian with Z 3 global symmetry is studied. Diagonalization of the Hamiltonian for finite chains allows one to estimate the critical exponents, and also to discover new phase transitions at lower temperatures. The critical points lambda, and indices v estimated for finite-scaling are given

  10. Unified theory of interspecific allometric scaling

    Silva, Jafferson K L da; Barbosa, Lauro A; Silva, Paulo Roberto

    2007-01-01

    A general simple theory for the interspecific allometric scaling is developed in the d + 1-dimensional space (d biological lengths and a physiological time) of metabolic states of organisms. It is assumed that natural selection shaped the metabolic states in such a way that the mass and energy d + 1-densities are size-invariant quantities (independent of body mass). The different metabolic states (basal and maximum) are described by considering that the biological lengths and the physiological time are related by different transport processes of energy and mass. In the basal metabolism, transportation occurs by ballistic and diffusion processes. In d = 3, the 3/4 law occurs if the ballistic movement is the dominant process, while the 2/3 law appears when both transport processes are equivalent. Accelerated movement during the biological time is related to the maximum aerobic sustained metabolism, which is characterized by the scaling exponent 2d/(2d + 1) (6/7 in d = 3). The results are in good agreement with empirical data and a verifiable empirical prediction about the aorta blood velocity in maximum metabolic rate conditions is made. (fast track communication)

  11. Size structure, not metabolic scaling rules, determines fisheries reference points

    Andersen, Ken Haste; Beyer, Jan

    2015-01-01

    Impact assessments of fishing on a stock require parameterization of vital rates: growth, mortality and recruitment. For 'data-poor' stocks, vital rates may be estimated from empirical size-based relationships or from life-history invariants. However, a theoretical framework to synthesize...... these empirical relations is lacking. Here, we combine life-history invariants, metabolic scaling and size-spectrum theory to develop a general size- and trait-based theory for demography and recruitment of exploited fish stocks. Important concepts are physiological or metabolic scaled mortalities and flux...... is that larger species have a higher egg production per recruit than small species. This means that density dependence is stronger for large than for small species and has the consequence that fisheries reference points that incorporate recruitment do not obey metabolic scaling rules. This result implies...

  12. Genome scale engineering techniques for metabolic engineering.

    Liu, Rongming; Bassalo, Marcelo C; Zeitoun, Ramsey I; Gill, Ryan T

    2015-11-01

    Metabolic engineering has expanded from a focus on designs requiring a small number of genetic modifications to increasingly complex designs driven by advances in genome-scale engineering technologies. Metabolic engineering has been generally defined by the use of iterative cycles of rational genome modifications, strain analysis and characterization, and a synthesis step that fuels additional hypothesis generation. This cycle mirrors the Design-Build-Test-Learn cycle followed throughout various engineering fields that has recently become a defining aspect of synthetic biology. This review will attempt to summarize recent genome-scale design, build, test, and learn technologies and relate their use to a range of metabolic engineering applications. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  13. Scaling Theory of Polyelectrolyte Nanogels

    Qu, Li-Jian

    2017-08-01

    The present paper develops the scaling theory of polyelectrolyte nanogels in dilute and semidilute solutions. The dependencies of the nanogel dimension on branching topology, charge fraction, subchain length, segment number, solution concentration are obtained. For a single polyelectrolyte nanogel in salt free solution, the nanogel may be swelled by the Coulombic repulsion (the so-called polyelectrolyte regime) or the osmotic counterion pressure (the so-called osmotic regime). Characteristics and boundaries between different regimes of a single polyelectrolyte nanogel are summarized. In dilute solution, the nanogels in polyelectrolyte regime will distribute orderly with the increase of concentration. While the nanogels in osmotic regime will always distribute randomly. Different concentration dependencies of the size of a nanogel in polyelectrolyte regime and in osmotic regime are also explored. Supported by China Earthquake Administration under Grant No. 20150112 and National Natural Science Foundation of China under Grant No. 21504014

  14. Scaling Theory of Polyelectrolyte Nanogels

    Qu Li-Jian

    2017-01-01

    The present paper develops the scaling theory of polyelectrolyte nanogels in dilute and semidilute solutions. The dependencies of the nanogel dimension on branching topology, charge fraction, subchain length, segment number, solution concentration are obtained. For a single polyelectrolyte nanogel in salt free solution, the nanogel may be swelled by the Coulombic repulsion (the so-called polyelectrolyte regime) or the osmotic counterion pressure (the so-called osmotic regime). Characteristics and boundaries between different regimes of a single polyelectrolyte nanogel are summarized. In dilute solution, the nanogels in polyelectrolyte regime will distribute orderly with the increase of concentration. While the nanogels in osmotic regime will always distribute randomly. Different concentration dependencies of the size of a nanogel in polyelectrolyte regime and in osmotic regime are also explored. (paper)

  15. The scaling of maximum and basal metabolic rates of mammals and birds

    Barbosa, Lauro A.; Garcia, Guilherme J. M.; da Silva, Jafferson K. L.

    2006-01-01

    Allometric scaling is one of the most pervasive laws in biology. Its origin, however, is still a matter of dispute. Recent studies have established that maximum metabolic rate scales with an exponent larger than that found for basal metabolism. This unpredicted result sets a challenge that can decide which of the concurrent hypotheses is the correct theory. Here, we show that both scaling laws can be deduced from a single network model. Besides the 3/4-law for basal metabolism, the model predicts that maximum metabolic rate scales as M, maximum heart rate as M, and muscular capillary density as M, in agreement with data.

  16. Scaling of Theory-of-Mind Tasks

    Wellman, Henry M.; Liu, David

    2004-01-01

    Two studies address the sequence of understandings evident in preschoolers' developing theory of mind. The first, preliminary study provides a meta-analysis of research comparing different types of mental state understandings (e.g., desires vs. beliefs, ignorance vs. false belief). The second, primary study tests a theory-of-mind scale for…

  17. Critical PO2 is size-independent in insects: implications for the metabolic theory of ecology.

    Harrison, Jon F; Klok, C J; Waters, James S

    2014-10-01

    Insects, and all animals, exhibit hypometric scaling of metabolic rate, with larger species having lower mass-specific metabolic rates. The metabolic theory of ecology (MTE) is based on models ascribing hypometric scaling of metabolic rate to constrained O 2 supply systems in larger animals. We compiled critical PO 2 of metabolic and growth rates for more than 40 insect species with a size range spanning four orders of magnitude. Critical PO 2 values vary from far below 21kPa for resting animals to near 21kPa for growing or flying animals and are size-independent, demonstrating that supply capacity matches oxygen demand. These data suggest that hypometric scaling of resting metabolic rate in insects is not driven by constraints on oxygen availability. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. Shape shifting predicts ontogenetic changes in metabolic scaling in diverse aquatic invertebrates.

    Glazier, Douglas S; Hirst, Andrew G; Atkinson, David

    2015-03-07

    Metabolism fuels all biological activities, and thus understanding its variation is fundamentally important. Much of this variation is related to body size, which is commonly believed to follow a 3/4-power scaling law. However, during ontogeny, many kinds of animals and plants show marked shifts in metabolic scaling that deviate from 3/4-power scaling predicted by general models. Here, we show that in diverse aquatic invertebrates, ontogenetic shifts in the scaling of routine metabolic rate from near isometry (bR = scaling exponent approx. 1) to negative allometry (bR < 1), or the reverse, are associated with significant changes in body shape (indexed by bL = the scaling exponent of the relationship between body mass and body length). The observed inverse correlations between bR and bL are predicted by metabolic scaling theory that emphasizes resource/waste fluxes across external body surfaces, but contradict theory that emphasizes resource transport through internal networks. Geometric estimates of the scaling of surface area (SA) with body mass (bA) further show that ontogenetic shifts in bR and bA are positively correlated. These results support new metabolic scaling theory based on SA influences that may be applied to ontogenetic shifts in bR shown by many kinds of animals and plants. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  19. Finite size scaling and lattice gauge theory

    Berg, B.A.

    1986-01-01

    Finite size (Fisher) scaling is investigated for four dimensional SU(2) and SU(3) lattice gauge theories without quarks. It allows to disentangle violations of (asymptotic) scaling and finite volume corrections. Mass spectrum, string tension, deconfinement temperature and lattice β-function are considered. For appropriate volumes, Monte Carlo investigations seem to be able to control the finite volume continuum limit. Contact is made with Luescher's small volume expansion and possibly also with the asymptotic large volume behavior. 41 refs., 19 figs

  20. A scale distortion theory of anchoring.

    Frederick, Shane W; Mochon, Daniel

    2012-02-01

    We propose that anchoring is often best interpreted as a scaling effect--that the anchor changes how the response scale is used, not how the focal stimulus is perceived. Of importance, we maintain that this holds true even for so-called objective scales (e.g., pounds, calories, meters, etc.). In support of this theory of scale distortion, we show that prior exposure to a numeric standard changes respondents' use of that specific response scale but does not generalize to conceptually affiliated judgments rendered on similar scales. Our findings highlight the necessity of distinguishing response language effects from representational effects in places where the need for that distinction has often been assumed away.

  1. Scaling in the sine-Gordon theory

    Ben-Abraham, S.I.

    1976-01-01

    It is shown that both the classical and the quantum sine-Gordon theory depend on a single scaling parameter and therefore the coupling constant cannot be freely chosen. To introduce a meaningful coupling constant it is proposed to include higher Fourier terms in the sine-Gordon potential. The two term case is exactly solvable. (Auth.)

  2. Genome-scale modeling for metabolic engineering.

    Simeonidis, Evangelos; Price, Nathan D

    2015-03-01

    We focus on the application of constraint-based methodologies and, more specifically, flux balance analysis in the field of metabolic engineering, and enumerate recent developments and successes of the field. We also review computational frameworks that have been developed with the express purpose of automatically selecting optimal gene deletions for achieving improved production of a chemical of interest. The application of flux balance analysis methods in rational metabolic engineering requires a metabolic network reconstruction and a corresponding in silico metabolic model for the microorganism in question. For this reason, we additionally present a brief overview of automated reconstruction techniques. Finally, we emphasize the importance of integrating metabolic networks with regulatory information-an area which we expect will become increasingly important for metabolic engineering-and present recent developments in the field of metabolic and regulatory integration.

  3. Effects of Contingency versus Constraints on the Body-Mass Scaling of Metabolic Rate

    Douglas S. Glazier

    2018-01-01

    Full Text Available I illustrate the effects of both contingency and constraints on the body-mass scaling of metabolic rate by analyzing the significantly different influences of ambient temperature (Ta on metabolic scaling in ectothermic versus endothermic animals. Interspecific comparisons show that increasing Ta results in decreasing metabolic scaling slopes in ectotherms, but increasing slopes in endotherms, a pattern uniquely predicted by the metabolic-level boundaries hypothesis, as amended to include effects of the scaling of thermal conductance in endotherms outside their thermoneutral zone. No other published theoretical model explicitly predicts this striking variation in metabolic scaling, which I explain in terms of contingent effects of Ta and thermoregulatory strategy in the context of physical and geometric constraints related to the scaling of surface area, volume, and heat flow across surfaces. My analysis shows that theoretical models focused on an ideal 3/4-power law, as explained by a single universally applicable mechanism, are clearly inadequate for explaining the diversity and environmental sensitivity of metabolic scaling. An important challenge is to develop a theory of metabolic scaling that recognizes the contingent effects of multiple mechanisms that are modulated by several extrinsic and intrinsic factors within specified constraints.

  4. Genome-Scale Reconstruction of the Human Astrocyte Metabolic Network

    Mart?n-Jim?nez, Cynthia A.; Salazar-Barreto, Diego; Barreto, George E.; Gonz?lez, Janneth

    2017-01-01

    Astrocytes are the most abundant cells of the central nervous system; they have a predominant role in maintaining brain metabolism. In this sense, abnormal metabolic states have been found in different neuropathological diseases. Determination of metabolic states of astrocytes is difficult to model using current experimental approaches given the high number of reactions and metabolites present. Thus, genome-scale metabolic networks derived from transcriptomic data can be used as a framework t...

  5. Electrodynamics in scale-covariant gravity theory

    Mansfield, V.N.; Malin, S.

    1980-01-01

    Utilizing the inherent scale-invariance of Maxwell's Equations, classical electrodynamics is incorporated into the theory of scale-invariant gravity. In this incorporation the gravitational constant G is shown to transform like β -2 (β is the gauge function), the generalized Lorentz Force Law is derived, the electric charge is shown to be invariant under gauge transformation, and matter creation is shown to be a necessity. In all nontrivial gauges a modified version of QED is obtained. The deviation from standard QED, however, is shown to be beyond the range of experimental detection when G α β -2 . (orig.)

  6. Gaussian-3 theory using scaled energies

    Curtiss, Larry A.; Raghavachari, Krishnan; Redfern, Paul C.; Pople, John A.

    2000-01-01

    A modification of Guassian-3 (G3) theory using multiplicative scale factors, instead of the additive higher level correction, is presented. In this method, referred to as G3S, the correlation energy is scaled by five parameters and the Hartree-Fock energy by one parameter. The six parameters are fitted to the G2/97 test set of 299 energies and the resulting mean absolute deviation from experiment is 0.99 kcal/mol compared to 1.01 kcal/mol for G3 theory. The G3S method has the advantage compared to G3 theory in that it can be used for studying potential energy surfaces where the products and reactants have a different number of paired electrons. In addition, versions of the computationally less intensive G3(MP3) and G3(MP2) methods that use scaled energies are also presented. These methods, referred to as G3S(MP3) and G3S(MP2), have mean absolute deviations of 1.16 and 1.35 kcal/mol, respectively. (c) 2000 American Institute of Physics

  7. Bridging food webs, ecosystem metabolism, and biogeochemistry using ecological stoichiometry theory

    Welti, Nina; Striebel, Maren; Ulseth, Amber J.

    2017-01-01

    process rates). ES theory holds the promise to be a unifying concept to link across hierarchical scales of patterns and processes in ecology, but this has not been fully achieved. Therefore, we propose connecting the expertise of aquatic ecologists and biogeochemists with ES theory as a common currency......, we propose that using ES to link nutrient cycling, trophic dynamics, and ecosystem metabolism would allow for a more holistic understanding of ecosystem functions in a changing environment....

  8. Next-generation genome-scale models for metabolic engineering

    King, Zachary A.; Lloyd, Colton J.; Feist, Adam M.

    2015-01-01

    Constraint-based reconstruction and analysis (COBRA) methods have become widely used tools for metabolic engineering in both academic and industrial laboratories. By employing a genome-scale in silico representation of the metabolic network of a host organism, COBRA methods can be used to predict...... examples of applying COBRA methods to strain optimization are presented and discussed. Then, an outlook is provided on the next generation of COBRA models and the new types of predictions they will enable for systems metabolic engineering....

  9. SCALE Sensitivity Calculations Using Contributon Theory

    Rearden, Bradley T.; Perfetti, Chris; Williams, Mark L.; Petrie, Lester M. Jr.

    2010-01-01

    The SCALE TSUNAMI-3D sensitivity and uncertainty analysis sequence computes the sensitivity of k-eff to each constituent multigroup cross section using adjoint techniques with the KENO Monte Carlo codes. A new technique to simultaneously obtain the product of the forward and adjoint angular flux moments within a single Monte Carlo calculation has been developed and implemented in the SCALE TSUNAMI-3D analysis sequence. A new concept in Monte Carlo theory has been developed for this work, an eigenvalue contributon estimator, which is an extension of previously developed fixed-source contributon estimators. A contributon is a particle for which the forward solution is accumulated, and its importance to the response, which is equivalent to the adjoint solution, is simultaneously accumulated. Thus, the contributon is a particle coupled with its contribution to the response, in this case k-eff. As implemented in SCALE, the contributon provides the importance of a particle exiting at any energy or direction for each location, energy and direction at which the forward flux solution is sampled. Although currently implemented for eigenvalue calculations in multigroup mode in KENO, this technique is directly applicable to continuous-energy calculations for many other responses such as fixed-source sensitivity analysis and quantification of reactor kinetics parameters. This paper provides the physical bases of eigenvalue contributon theory, provides details of implementation into TSUNAMI-3D, and provides results of sample calculations.

  10. On the character of scale symmetry breaking in gauge theories

    Gusijnin, V.P.; Kushnir, V.A.; Miransky, V.A.

    1988-01-01

    The problem of scale symmetry breaking in gauge theories is discussed. It is shown that the phenomenon of spontaneous breaking of scale symmetry in gauge theories is incompatible with the PCAAC dynamics. 12 refs

  11. Experimental signature of scaling violation implied by field theories

    Tung, W.

    1975-01-01

    Renormalizable field theories are found to predict a surprisingly specific pattern of scaling violation in deep inelastic scattering. Comparison with experiments is discussed. The feasibility of distinguishing asymptotically free field theories from conventional field theories is evaluated

  12. Analysis of Aspergillus nidulans metabolism at the genome-scale

    David, Helga; Ozcelik, İlknur Ş; Hofmann, Gerald

    2008-01-01

    of relevant secondary metabolites, was reconstructed based on detailed metabolic reconstructions available for A. niger and Saccharomyces cerevisiae, and information on the genetics, biochemistry and physiology of A. nidulans. Thereby, it was possible to identify metabolic functions without a gene associated...... a function. Results: In this work, we have manually assigned functions to 472 orphan genes in the metabolism of A. nidulans, by using a pathway-driven approach and by employing comparative genomics tools based on sequence similarity. The central metabolism of A. nidulans, as well as biosynthetic pathways......, in an objective and systematic manner. The functional assignments served as a basis to develop a mathematical model, linking 666 genes (both previously and newly annotated) to metabolic roles. The model was used to simulate metabolic behavior and additionally to integrate, analyze and interpret large-scale gene...

  13. Integration of Genome Scale Metabolic Networks and Gene Regulation of Metabolic Enzymes With Physiologically Based Pharmacokinetics.

    Maldonado, Elaina M; Leoncikas, Vytautas; Fisher, Ciarán P; Moore, J Bernadette; Plant, Nick J; Kierzek, Andrzej M

    2017-11-01

    The scope of physiologically based pharmacokinetic (PBPK) modeling can be expanded by assimilation of the mechanistic models of intracellular processes from systems biology field. The genome scale metabolic networks (GSMNs) represent a whole set of metabolic enzymes expressed in human tissues. Dynamic models of the gene regulation of key drug metabolism enzymes are available. Here, we introduce GSMNs and review ongoing work on integration of PBPK, GSMNs, and metabolic gene regulation. We demonstrate example models. © 2017 The Authors CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

  14. Inflationary perturbations in no-scale theories

    Salvio, Alberto [CERN, Theoretical Physics Department, Geneva (Switzerland)

    2017-04-15

    We study the inflationary perturbations in general (classically) scale-invariant theories. Such scenario is motivated by the hierarchy problem and provides natural inflationary potentials and dark matter candidates. We analyse in detail all sectors (the scalar, vector and tensor perturbations) giving general formulae for the potentially observable power spectra, as well as for the curvature spectral index n{sub s} and the tensor-to-scalar ratio r. We show that the conserved Hamiltonian for all perturbations does not feature negative energies even in the presence of the Weyl-squared term if the appropriate quantisation is performed and argue that this term does not lead to phenomenological problems at least in some relevant setups. The general formulae are then applied to a concrete no-scale model, which includes the Higgs and a scalar, ''the planckion'', whose vacuum expectation value generates the Planck mass. Inflation can be triggered by a combination of the planckion and the Starobinsky scalar and we show that no tension with observations is present even in the case of pure planckion inflation, if the coefficient of the Weyl-squared term is large enough. In general, even quadratic inflation is allowed in this case. Moreover, the Weyl-squared term leads to an isocurvature mode, which currently satisfies the observational bounds, but it may be detectable with future experiments. (orig.)

  15. Exercise-induced maximum metabolic rate scaled to body mass by ...

    Exercise-induced maximum metabolic rate scaled to body mass by the fractal ... rate scaling is that exercise-induced maximum aerobic metabolic rate (MMR) is ... muscle stress limitation, and maximized oxygen delivery and metabolic rates.

  16. A quantitative theory of solid tumor growth, metabolic rate and vascularization.

    Alexander B Herman

    Full Text Available The relationships between cellular, structural and dynamical properties of tumors have traditionally been studied separately. Here, we construct a quantitative, predictive theory of solid tumor growth, metabolic rate, vascularization and necrosis that integrates the relationships between these properties. To accomplish this, we develop a comprehensive theory that describes the interface and integration of the tumor vascular network and resource supply with the cardiovascular system of the host. Our theory enables a quantitative understanding of how cells, tissues, and vascular networks act together across multiple scales by building on recent theoretical advances in modeling both healthy vasculature and the detailed processes of angiogenesis and tumor growth. The theory explicitly relates tumor vascularization and growth to metabolic rate, and yields extensive predictions for tumor properties, including growth rates, metabolic rates, degree of necrosis, blood flow rates and vessel sizes. Besides these quantitative predictions, we explain how growth rates depend on capillary density and metabolic rate, and why similar tumors grow slower and occur less frequently in larger animals, shedding light on Peto's paradox. Various implications for potential therapeutic strategies and further research are discussed.

  17. Use of genome-scale microbial models for metabolic engineering

    Patil, Kiran Raosaheb; Åkesson, M.; Nielsen, Jens

    2004-01-01

    Metabolic engineering serves as an integrated approach to design new cell factories by providing rational design procedures and valuable mathematical and experimental tools. Mathematical models have an important role for phenotypic analysis, but can also be used for the design of optimal metaboli...... network structures. The major challenge for metabolic engineering in the post-genomic era is to broaden its design methodologies to incorporate genome-scale biological data. Genome-scale stoichiometric models of microorganisms represent a first step in this direction....

  18. Environmental versatility promotes modularity in genome-scale metabolic networks.

    Samal, Areejit; Wagner, Andreas; Martin, Olivier C

    2011-08-24

    The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new arrangements that may benefit their carrier. Conversely, modularity may emerge as a by-product of some trait. We here ask whether this last scenario may play a role in genome-scale metabolic networks that need to sustain life in one or more chemical environments. For such networks, we define a network module as a maximal set of reactions that are fully coupled, i.e., whose fluxes can only vary in fixed proportions. This definition overcomes limitations of purely graph based analyses of metabolism by exploiting the functional links between reactions. We call a metabolic network viable in a given chemical environment if it can synthesize all of an organism's biomass compounds from nutrients in this environment. An organism's metabolism is highly versatile if it can sustain life in many different chemical environments. We here ask whether versatility affects the modularity of metabolic networks. Using recently developed techniques to randomly sample large numbers of viable metabolic networks from a vast space of metabolic networks, we use flux balance analysis to study in silico metabolic networks that differ in their versatility. We find that highly versatile networks are also highly modular. They contain more modules and more reactions that are organized into modules. Most or all reactions in a module are associated with the same biochemical pathways. Modules that arise in highly versatile networks generally involve reactions that process nutrients or closely related chemicals. We also observe that the metabolism of E. coli is significantly more modular than even our most versatile networks. Our work shows that modularity in metabolic networks can be a by-product of functional constraints, e.g., the need to sustain life in multiple

  19. Environmental versatility promotes modularity in genome-scale metabolic networks

    Wagner Andreas

    2011-08-01

    Full Text Available Abstract Background The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new arrangements that may benefit their carrier. Conversely, modularity may emerge as a by-product of some trait. We here ask whether this last scenario may play a role in genome-scale metabolic networks that need to sustain life in one or more chemical environments. For such networks, we define a network module as a maximal set of reactions that are fully coupled, i.e., whose fluxes can only vary in fixed proportions. This definition overcomes limitations of purely graph based analyses of metabolism by exploiting the functional links between reactions. We call a metabolic network viable in a given chemical environment if it can synthesize all of an organism's biomass compounds from nutrients in this environment. An organism's metabolism is highly versatile if it can sustain life in many different chemical environments. We here ask whether versatility affects the modularity of metabolic networks. Results Using recently developed techniques to randomly sample large numbers of viable metabolic networks from a vast space of metabolic networks, we use flux balance analysis to study in silico metabolic networks that differ in their versatility. We find that highly versatile networks are also highly modular. They contain more modules and more reactions that are organized into modules. Most or all reactions in a module are associated with the same biochemical pathways. Modules that arise in highly versatile networks generally involve reactions that process nutrients or closely related chemicals. We also observe that the metabolism of E. coli is significantly more modular than even our most versatile networks. Conclusions Our work shows that modularity in metabolic networks can be a by-product of functional

  20. Dynamic optimal metabolic control theory: a cybernetic approach for modelling of the central nitrogen metabolism of S. cerevisiae

    Riel, van N.A.W.; Giuseppin, M.L.F.; Verrips, C.T.

    2000-01-01

    The theory of dynamic optimal metabolic control (DOMC), as developed by Giuseppin and Van Riel (Metab. Eng., 2000), is applied to model the central nitrogen metabolism (CNM) in Saccharomyces cerevisiae. The CNM represents a typical system encountered in advanced metabolic engineering. The CNM is the

  1. Use of density functional theory in drug metabolism studies

    Rydberg, Patrik; Jørgensen, Flemming Steen; Olsen, Lars

    2014-01-01

    INTRODUCTION: The cytochrome P450 enzymes (CYPs) metabolize many drug compounds. They catalyze a wide variety of reactions, and potentially, a large number of different metabolites can be generated. Density functional theory (DFT) has, over the past decade, been shown to be a powerful tool...... isoforms. This is probably due to the fact that the binding of the substrates is not the major determinant. When binding of the substrate plays a significant role, the well-known issue of determining the free energy of binding is the challenge. How approaches taking the protein environment into account...

  2. On the scaling limits in the Euclidean (quantum) field theory

    Gielerak, R.

    1983-01-01

    The author studies the concept of scaling limits in the context of the constructive field theory. He finds that the domain of attraction of a free massless Euclidean scalar field in the two-dimensional space time contains almost all Euclidean self-interacting models of quantum fields so far constructed. The renormalized scaling limit of the Wick polynomials of several self-interacting Euclidean field theory models are shown to be the same as in the free field theory. (Auth.)

  3. Mokken scale analysis : Between the Guttman scale and parametric item response theory

    van Schuur, Wijbrandt H.

    2003-01-01

    This article introduces a model of ordinal unidimensional measurement known as Mokken scale analysis. Mokken scaling is based on principles of Item Response Theory (IRT) that originated in the Guttman scale. I compare the Mokken model with both Classical Test Theory (reliability or factor analysis)

  4. Environmental versatility promotes modularity in large scale metabolic networks

    Samal A.; Wagner Andreas; Martin O.C.

    2011-01-01

    Abstract Background The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new arrangements that may benefit their carrier. Conversely, modularity may emerge as a by-product of some trait. We here ask whether this last scenario may play a role in genome-scale metabolic networks that need to sustain life in one or more chem...

  5. Two-Scale 13C Metabolic Flux Analysis for Metabolic Engineering.

    Ando, David; Garcia Martin, Hector

    2018-01-01

    Accelerating the Design-Build-Test-Learn (DBTL) cycle in synthetic biology is critical to achieving rapid and facile bioengineering of organisms for the production of, e.g., biofuels and other chemicals. The Learn phase involves using data obtained from the Test phase to inform the next Design phase. As part of the Learn phase, mathematical models of metabolic fluxes give a mechanistic level of comprehension to cellular metabolism, isolating the principle drivers of metabolic behavior from the peripheral ones, and directing future experimental designs and engineering methodologies. Furthermore, the measurement of intracellular metabolic fluxes is specifically noteworthy as providing a rapid and easy-to-understand picture of how carbon and energy flow throughout the cell. Here, we present a detailed guide to performing metabolic flux analysis in the Learn phase of the DBTL cycle, where we show how one can take the isotope labeling data from a 13 C labeling experiment and immediately turn it into a determination of cellular fluxes that points in the direction of genetic engineering strategies that will advance the metabolic engineering process.For our modeling purposes we use the Joint BioEnergy Institute (JBEI) Quantitative Metabolic Modeling (jQMM) library, which provides an open-source, python-based framework for modeling internal metabolic fluxes and making actionable predictions on how to modify cellular metabolism for specific bioengineering goals. It presents a complete toolbox for performing different types of flux analysis such as Flux Balance Analysis, 13 C Metabolic Flux Analysis, and it introduces the capability to use 13 C labeling experimental data to constrain comprehensive genome-scale models through a technique called two-scale 13 C Metabolic Flux Analysis (2S- 13 C MFA) [1]. In addition to several other capabilities, the jQMM is also able to predict the effects of knockouts using the MoMA and ROOM methodologies. The use of the jQMM library is

  6. Non-Abelian gauge field theory in scale relativity

    Nottale, Laurent; Celerier, Marie-Noeelle; Lehner, Thierry

    2006-01-01

    Gauge field theory is developed in the framework of scale relativity. In this theory, space-time is described as a nondifferentiable continuum, which implies it is fractal, i.e., explicitly dependent on internal scale variables. Owing to the principle of relativity that has been extended to scales, these scale variables can themselves become functions of the space-time coordinates. Therefore, a coupling is expected between displacements in the fractal space-time and the transformations of these scale variables. In previous works, an Abelian gauge theory (electromagnetism) has been derived as a consequence of this coupling for global dilations and/or contractions. We consider here more general transformations of the scale variables by taking into account separate dilations for each of them, which yield non-Abelian gauge theories. We identify these transformations with the usual gauge transformations. The gauge fields naturally appear as a new geometric contribution to the total variation of the action involving these scale variables, while the gauge charges emerge as the generators of the scale transformation group. A generalized action is identified with the scale-relativistic invariant. The gauge charges are the conservative quantities, conjugates of the scale variables through the action, which find their origin in the symmetries of the ''scale-space.'' We thus found in a geometric way and recover the expression for the covariant derivative of gauge theory. Adding the requirement that under the scale transformations the fermion multiplets and the boson fields transform such that the derived Lagrangian remains invariant, we obtain gauge theories as a consequence of scale symmetries issued from a geometric space-time description

  7. The physics of musical scales: Theory and experiment

    Durfee, Dallin S.; Colton, John S.

    2015-10-01

    The theory of musical scales involves mathematical ratios, harmonic resonators, beats, and human perception and provides an interesting application of the physics of waves and sound. We first review the history and physics of musical scales, with an emphasis on four historically important scales: twelve-tone equal temperament, Pythagorean, quarter-comma meantone, and Ptolemaic just intonation. We then present an easy way for students and teachers to directly experience the qualities of different scales using MIDI synthesis.

  8. Theory and Validity of Life Satisfaction Scales

    Diener, Ed; Inglehart, Ronald; Tay, Louis

    2013-01-01

    National accounts of subjective well-being are being considered and adopted by nations. In order to be useful for policy deliberations, the measures of life satisfaction must be psychometrically sound. The reliability, validity, and sensitivity to change of life satisfaction measures are reviewed. The scales are stable under unchanging conditions,…

  9. A quantization scheme for scale-invariant pure gauge theories

    Hortacsu, M.

    1988-01-01

    A scheme is suggested for the quantization of the recently proposed scale-invariant gauge theories in higher dimensions. The model is minimally coupled to a spinor field. Regularization algorithms are proposed. (orig.)

  10. Astrophysical tests of scale-covariant gravity theories

    Mansfield, V.N.; Malin, S.

    1980-01-01

    Starting from the most general form of the conservation laws in scale-covariant gravitation theory, a conservation of energy equation appropriate for stars is derived. Applications to white dwarfs and neutron stars reveal serious difficulties for some choices of gauge that have been frequently employed in the literature on scale-covariant gravity. We also show how to restrict some of the possible gauges that result from theories which are independent of the Large Numbers Hypothesis

  11. Graph-based linear scaling electronic structure theory

    Niklasson, Anders M. N., E-mail: amn@lanl.gov; Negre, Christian F. A.; Cawkwell, Marc J.; Swart, Pieter J.; Germann, Timothy C.; Bock, Nicolas [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Mniszewski, Susan M.; Mohd-Yusof, Jamal; Wall, Michael E.; Djidjev, Hristo [Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Rubensson, Emanuel H. [Division of Scientific Computing, Department of Information Technology, Uppsala University, Box 337, SE-751 05 Uppsala (Sweden)

    2016-06-21

    We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

  12. Another scheme for quantization of scale invariant gauge theories

    Hortacsu, M.

    1987-10-01

    A new scheme is proposed for the quantization of scale invariant gauge theories for all even dimensions when they are minimally coupled to a spinor field. A cut-off procedure suggests an algorithm which may regularize the theory. (author). 10 refs

  13. Genome scale metabolic network reconstruction of Spirochaeta cellobiosiphila

    Bharat Manna

    2017-10-01

    Full Text Available Substantial rise in the global energy demand is one of the biggest challenges in this century. Environmental pollution due to rapid depletion of the fossil fuel resources and its alarming impact on the climate change and Global Warming have motivated researchers to look for non-petroleum-based sustainable, eco-friendly, renewable, low-cost energy alternatives, such as biofuel. Lignocellulosic biomass is one of the most promising bio-resources with huge potential to contribute to this worldwide energy demand. However, the complex organization of the Cellulose, Hemicellulose and Lignin in the Lignocellulosic biomass requires extensive pre-treatment and enzymatic hydrolysis followed by fermentation, raising overall production cost of biofuel. This encourages researchers to design cost-effective approaches for the production of second generation biofuels. The products from enzymatic hydrolysis of cellulose are mostly glucose monomer or cellobiose unit that are subjected to fermentation. Spirochaeta genus is a well-known group of obligate or facultative anaerobes, living primarily on carbohydrate metabolism. Spirochaeta cellobiosiphila sp. is a facultative anaerobe under this genus, which uses a variety of monosaccharides and disaccharides as energy sources. However, most rapid growth occurs on cellobiose and fermentation yields significant amount of ethanol, acetate, CO2, H2 and small amounts of formate. It is predicted to be promising microbial machinery for industrial fermentation processes for biofuel production. The metabolic pathways that govern cellobiose metabolism in Spirochaeta cellobiosiphila are yet to be explored. The function annotation of the genome sequence of Spirochaeta cellobiosiphila is in progress. In this work we aim to map all the metabolic activities for reconstruction of genome-scale metabolic model of Spirochaeta cellobiosiphila.

  14. Challenges for Large Scale Structure Theory

    CERN. Geneva

    2018-01-01

    I will describe some of the outstanding questions in Cosmology where answers could be provided by observations of the Large Scale Structure of the Universe at late times.I will discuss some of the theoretical challenges which will have to be overcome to extract this information from the observations. I will describe some of the theoretical tools that might be useful to achieve this goal. 

  15. Scaling anomalies in Kaluza-Klein theory

    Delbourgo, R.; Thompson, G.; Weber, R.O.

    1987-01-01

    The effect of Pauli interactions on the scaling anomaly is to add F/sup 4/, (∂F)/sup 2/ and m/sup 2/F/sup 2/ terms to the trace of the stress-tensor at one loop level, such terms being connected with renormalization. However, when the sum over all modes is taken, these extra contributions vanish upon zeta-function regularisation

  16. Scaling theory of drying in porous media

    Tsimpanogiannis, I.N.; Yortsos, Y.C.; Poulou, S.; Kanellopoulos, N.; Stubos, A.K.

    1999-01-01

    Concepts of immiscible displacements in porous media driven by mass transfer are utilized to model drying of porous media. Visualization experiments of drying in two-dimensional glass micromodels are conducted to identify pore-scale mechanisms. Then, a pore network approach is used to analyze the advancing drying front. It is shown that in a porous medium, capillarity induces a flow that effectively limits the extent of the front, which would otherwise be of the percolation type, to a finite width. In conjuction with the predictions of a macroscale stable front, obtained from a linear stability analysis, the process is shown to be equivalent to invasion percolation in a stabilizing gradient. A power-law scaling relation of the front width with a diffusion-based capillary number is also obtained. This capillary number reflects the fact that drying is controlled by diffusion in contrast to external drainage. The scaling exponent predicted is compatible with the experimental results of Shaw [Phys Rev. Lett. 59, 1671 (1987)]. A framework for a continuum description of the upstream drying regimes is also developed. copyright 1999 The American Physical Society

  17. Genome-scale metabolic representation of Amycolatopsis balhimycina

    Vongsangnak, Wanwipa; Figueiredo, L. F.; Förster, Jochen

    2012-01-01

    Infection caused by methicillin‐resistant Staphylococcus aureus (MRSA) is an increasing societal problem. Typically, glycopeptide antibiotics are used in the treatment of these infections. The most comprehensively studied glycopeptide antibiotic biosynthetic pathway is that of balhimycin...... to reconstruct a genome‐scale metabolic model for the organism. Here we generated an almost complete A. balhimycina genome sequence comprising 10,562,587 base pairs assembled into 2,153 contigs. The high GC‐genome (∼69%) includes 8,585 open reading frames (ORFs). We used our integrative toolbox called SEQTOR...

  18. Nonperturbative scale anomaly and composite operators in gauge field theories

    Gusynin, V.P.; Miranskij, V.A.

    1987-01-01

    In non-asymptotically free gauge theories with a non-trivial ultraviolet fixed point scale symmetry breaking (the scale anomaly) caused by the nonperturbative PCAC dynamics is studied. In the two-loop approximation the analytical expression for the gluon condensate is obtained. It is shown that the form of the anomaly depends on the type of the phase of a theory to which it relates. The hypothesis about the soft behaviour at small distances of composite operators in such theories is confirmed. 14 refs.; 1 fig

  19. Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

    Saha, Rajib; Suthers, Patrick F.; Maranas, Costas D.

    2011-01-01

    The scope and breadth of genome-scale metabolic reconstructions have continued to expand over the last decade. Herein, we introduce a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize). Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. The developed model is designed to meet rigorous standards on gene-protein-reaction (GPR) associations, elementally and charged balanced reactions and a biomass reaction abstracting the relative contribution of all biomass constituents. The metabolic network contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct literature evidence for the participation of the reaction in maize was found. As many as 445 reactions and 369 metabolites are unique to the maize model compared to the AraGEM model for A. thaliana. 674 metabolites and 893 reactions are present in Zea mays iRS1563 that are not accounted for in maize C4GEM. All reactions are elementally and charged balanced and localized into six different compartments (i.e., cytoplasm, mitochondrion, plastid, peroxisome, vacuole and extracellular). GPR associations are also established based on the functional annotation information and homology prediction accounting for monofunctional, multifunctional and multimeric proteins, isozymes and protein complexes. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration) of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3). The developed model corresponds to the largest and more complete to-date effort at cataloguing metabolism for a plant species. PMID:21755001

  20. Metabolic engineering of strains: from industrial-scale to lab-scale chemical production.

    Sun, Jie; Alper, Hal S

    2015-03-01

    A plethora of successful metabolic engineering case studies have been published over the past several decades. Here, we highlight a collection of microbially produced chemicals using a historical framework, starting with titers ranging from industrial scale (more than 50 g/L), to medium-scale (5-50 g/L), and lab-scale (0-5 g/L). Although engineered Escherichia coli and Saccharomyces cerevisiae emerge as prominent hosts in the literature as a result of well-developed genetic engineering tools, several novel native-producing strains are gaining attention. This review catalogs the current progress of metabolic engineering towards production of compounds such as acids, alcohols, amino acids, natural organic compounds, and others.

  1. Renormalization and scaling behaviour of eikonal perturbation theories. [Eikonal approximation

    Din, A M [Chalmers Tekniska Hoegskola, Goeteborg (Sweden). Institutionen foer Teoretisk Fysik; Nielsen, N K [Aarhus Univ. (Denmark)

    1975-01-04

    Some observations on the renormalization and scaling behaviour of the charged-particle propagator in scalar quantum electrodynamics, in the ordinary eikonal approximation as well as in the eikonal perturbation theory, are reported. The conclusions indicate that scaling behaviour is not realized in the simple sense.

  2. Neoclassical theory of electromagnetic interactions a single theory for macroscopic and microscopic scales

    Babin, Anatoli

    2016-01-01

    In this monograph, the authors present their recently developed theory of electromagnetic interactions. This neoclassical approach extends the classical electromagnetic theory down to atomic scales and allows the explanation of various non-classical phenomena in the same framework. While the classical Maxwell–Lorentz electromagnetism theory succeeds in describing the physical reality at macroscopic scales, it struggles at atomic scales. Here, quantum mechanics traditionally takes over to describe non-classical phenomena such as the hydrogen spectrum and de Broglie waves. By means of modifying the classical theory, the approach presented here is able to consistently explain quantum-mechanical effects, and while similar to quantum mechanics in some respects, this neoclassical theory also differs markedly from it. In particular, the newly developed framework omits probabilistic interpretations of the wave function and features a new fundamental spatial scale which, at the size of the free electron, is much lar...

  3. Renormalization Group Theory of Bolgiano Scaling in Boussinesq Turbulence

    Rubinstein, Robert

    1994-01-01

    Bolgiano scaling in Boussinesq turbulence is analyzed using the Yakhot-Orszag renormalization group. For this purpose, an isotropic model is introduced. Scaling exponents are calculated by forcing the temperature equation so that the temperature variance flux is constant in the inertial range. Universal amplitudes associated with the scaling laws are computed by expanding about a logarithmic theory. Connections between this formalism and the direct interaction approximation are discussed. It is suggested that the Yakhot-Orszag theory yields a lowest order approximate solution of a regularized direct interaction approximation which can be corrected by a simple iterative procedure.

  4. Scaling theory of quantum resistance distributions in disordered systems

    Jayannavar, A.M.

    1991-01-01

    The large scale distribution of quantum Ohmic resistance of a disorderd one-dimensional conductor is derived explicitly. It is shown that in the thermodynamic limit this distribution is characterized by two independent parameters for strong disorder, leading to a two-parameter scaling theory of localization. Only in the limit of weak disorder single parameter scaling consistent with existing theoretical treatments is recovered. (author). 33 refs., 4 figs

  5. Scaling theory of quantum resistance distributions in disordered systems

    Jayannavar, A.M.

    1990-05-01

    We have derived explicitly, the large scale distribution of quantum Ohmic resistance of a disordered one-dimensional conductor. We show that in the thermodynamic limit this distribution is characterized by two independent parameters for strong disorder, leading to a two-parameter scaling theory of localization. Only in the limit of weak disorder we recover single parameter scaling, consistent with existing theoretical treatments. (author). 32 refs, 4 figs

  6. Scaling algebras and renormalization group in algebraic quantum field theory

    Buchholz, D.; Verch, R.

    1995-01-01

    For any given algebra of local observables in Minkowski space an associated scaling algebra is constructed on which renormalization group (scaling) transformations act in a canonical manner. The method can be carried over to arbitrary spacetime manifolds and provides a framework for the systematic analysis of the short distance properties of local quantum field theories. It is shown that every theory has a (possibly non-unique) scaling limit which can be classified according to its classical or quantum nature. Dilation invariant theories are stable under the action of the renormalization group. Within this framework the problem of wedge (Bisognano-Wichmann) duality in the scaling limit is discussed and some of its physical implications are outlined. (orig.)

  7. Little string theory from double-scaling limits of field theories

    Ling, Henry; Shieh, H.-H.; Anders, Greg van

    2007-01-01

    We show that little string theory on S 5 can be obtained as double-scaling limits of the maximally supersymmetric Yang-Mills theories on R x S 2 and R x S 3 /Z k . By matching the gauge theory parameters with those in the dual supergravity solutions found by Lin and Maldacena, we determine the limits in the gauge theories that correspond to decoupling of NS5-brane degrees of freedom. We find that for the theory on R x S 2 , the 't Hooft coupling must be scaled like ln 3 N, and on R x S 3 /Z k , like ln 2 N. Accordingly, taking these limits in these field theories gives Lagrangian definitions of little string theory on S 5

  8. Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities.

    Zomorrodi, Ali R; Segrè, Daniel

    2017-11-16

    Metabolite exchanges in microbial communities give rise to ecological interactions that govern ecosystem diversity and stability. It is unclear, however, how the rise of these interactions varies across metabolites and organisms. Here we address this question by integrating genome-scale models of metabolism with evolutionary game theory. Specifically, we use microbial fitness values estimated by metabolic models to infer evolutionarily stable interactions in multi-species microbial "games". We first validate our approach using a well-characterized yeast cheater-cooperator system. We next perform over 80,000 in silico experiments to infer how metabolic interdependencies mediated by amino acid leakage in Escherichia coli vary across 189 amino acid pairs. While most pairs display shared patterns of inter-species interactions, multiple deviations are caused by pleiotropy and epistasis in metabolism. Furthermore, simulated invasion experiments reveal possible paths to obligate cross-feeding. Our study provides genomically driven insight into the rise of ecological interactions, with implications for microbiome research and synthetic ecology.

  9. Shape shifting predicts ontogenetic changes in metabolic scaling in diverse aquatic invertebrates

    Glazier, Douglas S.; Hirst, Andrew G.; Atkinson, D.

    2016-01-01

    in metabolic scaling that deviate from 3/4-power scaling predicted by general models. Here, we show that in diverse aquatic invertebrates, ontogenetic shifts in the scaling of routine metabolic rate from near isometry (bR = scaling exponent approx. 1) to negative allometry (bR

  10. Why allometric variation in mammalian metabolism is curvilinear on the logarithmic scale.

    Packard, Gary C

    2017-11-01

    Studies performed over the last 20 years have repeatedly documented a slight convex curvature (relative to the x-axis) in double-logarithmic plots of basal metabolic rate (BMR) versus body mass in mammals. This curvilinear pattern has usually been interpreted in the context of a simple, two-parameter power function on the arithmetic scale, y  =  a  ×  x b , with the exponent in the equation supposedly increasing systematically with body size. An equation of this form has caused concern among ecologists because a variable exponent is inconsistent with an assumption underlying the metabolic theory of ecology (MTE). However, the appearance of an exponent that varies with body size is an artifact resulting from the widespread use of logarithmic transformations in allometric analyses. Curvature in the distribution on the logarithmic scale actually is caused by a requirement for an explicit, non-zero intercept-and not a variable exponent-in the model describing the distribution on the arithmetic scale. Thus, the MTE need not be revised to accommodate an exponent that varies with body size in the scaling of mammalian BMR, but the theory may need to be tweaked to accommodate an intercept in the allometric equation. In general, any bivariate dataset that is well described by a three-parameter power equation on the arithmetic scale will follow a curvilinear path when displayed on the logarithmic scale. Consequently, reports of curvilinearity in log domain (i.e., "complex allometry") need to be revisited because conclusions from those investigations are likely to be flawed. © 2018 Wiley Periodicals, Inc.

  11. Metabolite coupling in genome-scale metabolic networks

    Palsson Bernhard Ø

    2006-03-01

    Full Text Available Abstract Background Biochemically detailed stoichiometric matrices have now been reconstructed for various bacteria, yeast, and for the human cardiac mitochondrion based on genomic and proteomic data. These networks have been manually curated based on legacy data and elementally and charge balanced. Comparative analysis of these well curated networks is now possible. Pairs of metabolites often appear together in several network reactions, linking them topologically. This co-occurrence of pairs of metabolites in metabolic reactions is termed herein "metabolite coupling." These metabolite pairs can be directly computed from the stoichiometric matrix, S. Metabolite coupling is derived from the matrix ŜŜT, whose off-diagonal elements indicate the number of reactions in which any two metabolites participate together, where Ŝ is the binary form of S. Results Metabolite coupling in the studied networks was found to be dominated by a relatively small group of highly interacting pairs of metabolites. As would be expected, metabolites with high individual metabolite connectivity also tended to be those with the highest metabolite coupling, as the most connected metabolites couple more often. For metabolite pairs that are not highly coupled, we show that the number of reactions a pair of metabolites shares across a metabolic network closely approximates a line on a log-log scale. We also show that the preferential coupling of two metabolites with each other is spread across the spectrum of metabolites and is not unique to the most connected metabolites. We provide a measure for determining which metabolite pairs couple more often than would be expected based on their individual connectivity in the network and show that these metabolites often derive their principal biological functions from existing in pairs. Thus, analysis of metabolite coupling provides information beyond that which is found from studying the individual connectivity of individual

  12. The fractal geometry of nutrient exchange surfaces does not provide an explanation for 3/4-power metabolic scaling

    Painter Page R

    2005-08-01

    Full Text Available Abstract Background A prominent theoretical explanation for 3/4-power allometric scaling of metabolism proposes that the nutrient exchange surface of capillaries has properties of a space-filling fractal. The theory assumes that nutrient exchange surface area has a fractal dimension equal to or greater than 2 and less than or equal to 3 and that the volume filled by the exchange surface area has a fractal dimension equal to or greater than 3 and less than or equal to 4. Results It is shown that contradicting predictions can be derived from the assumptions of the model. When errors in the model are corrected, it is shown to predict that metabolic rate is proportional to body mass (proportional scaling. Conclusion The presence of space-filling fractal nutrient exchange surfaces does not provide a satisfactory explanation for 3/4-power metabolic rate scaling.

  13. Constraining genome-scale models to represent the bow tie structure of metabolism for 13C metabolic flux analysis

    Backman, Tyler W.H.; Ando, David; Singh, Jahnavi

    2018-01-01

    for a minimum of fluxes into core metabolism to satisfy these experimental constraints. Together, these methods accelerate and automate the identification of a biologically reasonable set of core reactions for use with 13C MFA or 2S- 13C MFA, as well as provide for a substantially lower set of flux bounds......Determination of internal metabolic fluxes is crucial for fundamental and applied biology because they map how carbon and electrons flow through metabolism to enable cell function. 13C Metabolic Flux Analysis (13C MFA) and Two-Scale 13C Metabolic Flux Analysis (2S-13C MFA) are two techniques used...

  14. Perturbation theory instead of large scale shell model calculations

    Feldmeier, H.; Mankos, P.

    1977-01-01

    Results of large scale shell model calculations for (sd)-shell nuclei are compared with a perturbation theory provides an excellent approximation when the SU(3)-basis is used as a starting point. The results indicate that perturbation theory treatment in an SU(3)-basis including 2hω excitations should be preferable to a full diagonalization within the (sd)-shell. (orig.) [de

  15. Scaling theory of depinning in the Sneppen model

    Maslov, S.; Paczuski, M.

    1994-01-01

    We develop a scaling theory for the critical depinning behavior of the Sneppen interface model [Phys. Rev. Lett. 69, 3539 (1992)]. This theory is based on a ''gap'' equation that describes the self-organization process to a critical state of the depinning transition. All of the critical exponents can be expressed in terms of two independent exponents, ν parallel (d) and ν perpendicular (d), characterizing the divergence of the parallel and perpendicular correlation lengths as the interface approaches its dynamical attractor

  16. Large-scale structure in the universe: Theory vs observations

    Kashlinsky, A.; Jones, B.J.T.

    1990-01-01

    A variety of observations constrain models of the origin of large scale cosmic structures. We review here the elements of current theories and comment in detail on which of the current observational data provide the principal constraints. We point out that enough observational data have accumulated to constrain (and perhaps determine) the power spectrum of primordial density fluctuations over a very large range of scales. We discuss the theories in the light of observational data and focus on the potential of future observations in providing even (and ever) tighter constraints. (orig.)

  17. Genome-scale reconstruction of the Streptococcus pyogenes M49 metabolic network reveals growth requirements and indicates potential drug targets

    Levering, J.; Fiedler, T.; Sieg, A.; van Grinsven, K.W.A.; Hering, S.; Veith, N.; Olivier, B.G.; Klett, L.; Hugenholtz, J.; Teusink, B.; Kreikemeyer, B.; Kummer, U.

    2016-01-01

    Genome-scale metabolic models comprise stoichiometric relations between metabolites, as well as associations between genes and metabolic reactions and facilitate the analysis of metabolism. We computationally reconstructed the metabolic network of the lactic acid bacterium Streptococcus pyogenes

  18. The evolving Planck mass in classically scale-invariant theories

    Kannike, K.; Raidal, M.; Spethmann, C.; Veermäe, H. [National Institute of Chemical Physics and Biophysics,Rävala 10, 10143 Tallinn (Estonia)

    2017-04-05

    We consider classically scale-invariant theories with non-minimally coupled scalar fields, where the Planck mass and the hierarchy of physical scales are dynamically generated. The classical theories possess a fixed point, where scale invariance is spontaneously broken. In these theories, however, the Planck mass becomes unstable in the presence of explicit sources of scale invariance breaking, such as non-relativistic matter and cosmological constant terms. We quantify the constraints on such classical models from Big Bang Nucleosynthesis that lead to an upper bound on the non-minimal coupling and require trans-Planckian field values. We show that quantum corrections to the scalar potential can stabilise the fixed point close to the minimum of the Coleman-Weinberg potential. The time-averaged motion of the evolving fixed point is strongly suppressed, thus the limits on the evolving gravitational constant from Big Bang Nucleosynthesis and other measurements do not presently constrain this class of theories. Field oscillations around the fixed point, if not damped, contribute to the dark matter density of the Universe.

  19. Characterizing Sources of Uncertainty in Item Response Theory Scale Scores

    Yang, Ji Seung; Hansen, Mark; Cai, Li

    2012-01-01

    Traditional estimators of item response theory scale scores ignore uncertainty carried over from the item calibration process, which can lead to incorrect estimates of the standard errors of measurement (SEMs). Here, the authors review a variety of approaches that have been applied to this problem and compare them on the basis of their statistical…

  20. The evolving Planck mass in classically scale-invariant theories

    Kannike, K.; Raidal, M.; Spethmann, C.; Veermäe, H.

    2017-04-01

    We consider classically scale-invariant theories with non-minimally coupled scalar fields, where the Planck mass and the hierarchy of physical scales are dynamically generated. The classical theories possess a fixed point, where scale invariance is spontaneously broken. In these theories, however, the Planck mass becomes unstable in the presence of explicit sources of scale invariance breaking, such as non-relativistic matter and cosmological constant terms. We quantify the constraints on such classical models from Big Bang Nucleosynthesis that lead to an upper bound on the non-minimal coupling and require trans-Planckian field values. We show that quantum corrections to the scalar potential can stabilise the fixed point close to the minimum of the Coleman-Weinberg potential. The time-averaged motion of the evolving fixed point is strongly suppressed, thus the limits on the evolving gravitational constant from Big Bang Nucleosynthesis and other measurements do not presently constrain this class of theories. Field oscillations around the fixed point, if not damped, contribute to the dark matter density of the Universe.

  1. Scale transformation and massless limit in neutral-vector field theory. [Gauge transformation unified theory

    Kubo, R; Takahashi, Y; Yokoyama, K

    1975-01-01

    In a wide class of neutral vector field theories, in which massive and massless fields are described in a unified way and a unique massless limit exists to quantum electrodynamics in covariant gauges, the commutability of the scale transformation and the massless limit is examined. It is shown that there occurs no anomaly with respect to the assignment for scale dimensions of relevant fields. Connection of scale transformation and gauge transformation is also discussed.

  2. Divergence of perturbation theory in large scale structures

    Pajer, Enrico; van der Woude, Drian

    2018-05-01

    We make progress towards an analytical understanding of the regime of validity of perturbation theory for large scale structures and the nature of some non-perturbative corrections. We restrict ourselves to 1D gravitational collapse, for which exact solutions before shell crossing are known. We review the convergence of perturbation theory for the power spectrum, recently proven by McQuinn and White [1], and extend it to non-Gaussian initial conditions and the bispectrum. In contrast, we prove that perturbation theory diverges for the real space two-point correlation function and for the probability density function (PDF) of the density averaged in cells and all the cumulants derived from it. We attribute these divergences to the statistical averaging intrinsic to cosmological observables, which, even on very large and "perturbative" scales, gives non-vanishing weight to all extreme fluctuations. Finally, we discuss some general properties of non-perturbative effects in real space and Fourier space.

  3. Scaling theory and the classification of phase transitions

    Hilfer, R.

    1992-01-01

    In this paper, the recent classification theory for phase transitions and its relation with the foundations of statistical physics is reviewed. First it is outlined how Ehrenfests classification scheme can be generalized into a general thermodynamic classification theory for phase transitions. The classification theory implies scaling and multiscaling thereby eliminating the need to postulate the scaling hypothesis as a fourth law of thermodynamics. The new classification has also led to the discovery and distinction of nonequilibrium transitions within equilibrium statistical physics. Nonequilibrium phase transitions are distinguished from equilibrium transitions by orders less than unity and by the fact the equilibrium thermodynamics and statistical mechanics become inapplicable at the critical point. The latter fact requires a change in the Gibbs assumption underlying the canonical and grandcanonical ensembles in order to recover the thermodynamic description in the critical limit

  4. Incorporating Protein Biosynthesis into the Saccharomyces cerevisiae Genome-scale Metabolic Model

    Olivares Hernandez, Roberto

    Based on stoichiometric biochemical equations that occur into the cell, the genome-scale metabolic models can quantify the metabolic fluxes, which are regarded as the final representation of the physiological state of the cell. For Saccharomyces Cerevisiae the genome scale model has been construc......Based on stoichiometric biochemical equations that occur into the cell, the genome-scale metabolic models can quantify the metabolic fluxes, which are regarded as the final representation of the physiological state of the cell. For Saccharomyces Cerevisiae the genome scale model has been...

  5. The effective field theory of cosmological large scale structures

    Carrasco, John Joseph M. [Stanford Univ., Stanford, CA (United States); Hertzberg, Mark P. [Stanford Univ., Stanford, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States); Senatore, Leonardo [Stanford Univ., Stanford, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States)

    2012-09-20

    Large scale structure surveys will likely become the next leading cosmological probe. In our universe, matter perturbations are large on short distances and small at long scales, i.e. strongly coupled in the UV and weakly coupled in the IR. To make precise analytical predictions on large scales, we develop an effective field theory formulated in terms of an IR effective fluid characterized by several parameters, such as speed of sound and viscosity. These parameters, determined by the UV physics described by the Boltzmann equation, are measured from N-body simulations. We find that the speed of sound of the effective fluid is c2s ≈ 10–6c2 and that the viscosity contributions are of the same order. The fluid describes all the relevant physics at long scales k and permits a manifestly convergent perturbative expansion in the size of the matter perturbations δ(k) for all the observables. As an example, we calculate the correction to the power spectrum at order δ(k)4. As a result, the predictions of the effective field theory are found to be in much better agreement with observation than standard cosmological perturbation theory, already reaching percent precision at this order up to a relatively short scale k ≃ 0.24h Mpc–1.

  6. Scaling of theory-of-mind understandings in Chinese children.

    Wellman, Henry M; Fang, Fuxi; Liu, David; Zhu, Liqi; Liu, Guoxiong

    2006-12-01

    Prior research demonstrates that understanding of theory of mind develops at different paces in children raised in different cultures. Are these differences simply differences in timing, or do they represent different patterns of cultural learning? That is, to what extent are sequences of theory-of-mind understanding universal, and to what extent are they culture-specific? We addressed these questions by using a theory-of-mind scale to examine performance of 140 Chinese children living in Beijing and to compare their performance with that of 135 English-speaking children living in the United States and Australia. Results reveal a common sequence of understanding, as well as sociocultural differences in children's developing theories of mind.

  7. Sequential Progressions in a Theory of Mind Scale: Longitudinal Perspectives

    Wellman, Henry M.; Fuxi, Fang; Peterson, Candida C.

    2011-01-01

    Consecutive re-testings of 92 U.S. preschoolers (n = 30), Chinese preschoolers (n = 31), and deaf children (n = 31) examined whether the sequences of development apparent in cross-sectional results with a theory-of-mind scale also appeared in longitudinal assessment. Longitudinal data confirmed that theory-of-mind progressions apparent in cross-sectional scaling data also characterized longitudinal sequences of understanding for individual children. The match between cross-sectional and longitudinal sequences appeared for children who exhibit different progressions across cultures (U.S. vs. China) and for children with substantial delays (deaf children of hearing parents). Moreover, greater scale distances reflected larger longitudinal age differences. PMID:21428982

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

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

    2003-01-01

    The metabolic network in the yeast Saccharomyces cerevisiae was reconstructed using currently available genomic, biochemical, and physiological information. The metabolic reactions were compartmentalized between the cytosol and the mitochondria, and transport steps between the compartments...

  9. Quantum no-scale regimes in string theory

    Coudarchet, Thibaut; Fleming, Claude; Partouche, Hervé

    2018-05-01

    We show that in generic no-scale models in string theory, the flat, expanding cosmological evolutions found at the quantum level can be attracted to a "quantum no-scale regime", where the no-scale structure is restored asymptotically. In this regime, the quantum effective potential is dominated by the classical kinetic energies of the no-scale modulus and dilaton. We find that this natural preservation of the classical no-scale structure at the quantum level occurs when the initial conditions of the evolutions sit in a subcritical region of their space. On the contrary, supercritical initial conditions yield solutions that have no analogue at the classical level. The associated intrinsically quantum universes are sentenced to collapse and their histories last finite cosmic times. Our analysis is done at 1-loop, in perturbative heterotic string compactified on tori, with spontaneous supersymmetry breaking implemented by a stringy version of the Scherk-Schwarz mechanism.

  10. Constraining Genome-Scale Models to Represent the Bow Tie Structure of Metabolism for 13C Metabolic Flux Analysis

    Tyler W. H. Backman

    2018-01-01

    Full Text Available Determination of internal metabolic fluxes is crucial for fundamental and applied biology because they map how carbon and electrons flow through metabolism to enable cell function. 13 C Metabolic Flux Analysis ( 13 C MFA and Two-Scale 13 C Metabolic Flux Analysis (2S- 13 C MFA are two techniques used to determine such fluxes. Both operate on the simplifying approximation that metabolic flux from peripheral metabolism into central “core” carbon metabolism is minimal, and can be omitted when modeling isotopic labeling in core metabolism. The validity of this “two-scale” or “bow tie” approximation is supported both by the ability to accurately model experimental isotopic labeling data, and by experimentally verified metabolic engineering predictions using these methods. However, the boundaries of core metabolism that satisfy this approximation can vary across species, and across cell culture conditions. Here, we present a set of algorithms that (1 systematically calculate flux bounds for any specified “core” of a genome-scale model so as to satisfy the bow tie approximation and (2 automatically identify an updated set of core reactions that can satisfy this approximation more efficiently. First, we leverage linear programming to simultaneously identify the lowest fluxes from peripheral metabolism into core metabolism compatible with the observed growth rate and extracellular metabolite exchange fluxes. Second, we use Simulated Annealing to identify an updated set of core reactions that allow for a minimum of fluxes into core metabolism to satisfy these experimental constraints. Together, these methods accelerate and automate the identification of a biologically reasonable set of core reactions for use with 13 C MFA or 2S- 13 C MFA, as well as provide for a substantially lower set of flux bounds for fluxes into the core as compared with previous methods. We provide an open source Python implementation of these algorithms at https://github.com/JBEI/limitfluxtocore.

  11. Testing the Grandchildren's Received Affection Scale using Affection Exchange Theory.

    Mansson, Daniel H

    2013-04-01

    The purpose of this study was to test the Grandchildren's Received Affection Scale (GRAS) using Affection Exchange Theory (Floyd, 2006). In accordance with Affection Exchange Theory, it was hypothesized that grandchildren's scores on the Trait Affection Received Scale (i.e., the extent to which individuals by nature receive affection) would be related significantly and positively to their reports of received affection from their grandparents (i.e., their scores on the GRAS). Additionally, a research question was asked to explore if grandchildren's received affection from their grandparents is dependent on their grandparent's biological sex or lineage (i.e., maternal vs paternal). Thus, young adult grandchildren (N = 422) completed the GRAS and the Trait Affection Received Scale. The results of zero-order Pearson correlational analyses provided support for the hypothesis, whereas the results of MANOVAs tests only partially support extant grandparent-grandchild theory and research. These findings broaden the scope of Affection Exchange Theory and also bolster the GRAS's utility in future grandparent-grandchild affectionate communication research.

  12. Chemical theory and modelling through density across length scales

    Ghosh, Swapan K.

    2016-01-01

    One of the concepts that has played a major role in the conceptual as well as computational developments covering all the length scales of interest in a number of areas of chemistry, physics, chemical engineering and materials science is the concept of single-particle density. Density functional theory has been a versatile tool for the description of many-particle systems across length scales. Thus, in the microscopic length scale, an electron density based description has played a major role in providing a deeper understanding of chemical binding in atoms, molecules and solids. Density concept has been used in the form of single particle number density in the intermediate mesoscopic length scale to obtain an appropriate picture of the equilibrium and dynamical processes, dealing with a wide class of problems involving interfacial science and soft condensed matter. In the macroscopic length scale, however, matter is usually treated as a continuous medium and a description using local mass density, energy density and other related property density functions has been found to be quite appropriate. The basic ideas underlying the versatile uses of the concept of density in the theory and modelling of materials and phenomena, as visualized across length scales, along with selected illustrative applications to some recent areas of research on hydrogen energy, soft matter, nucleation phenomena, isotope separation, and separation of mixture in condensed phase, will form the subject matter of the talk. (author)

  13. The algebraic construction of the scale-invariant asymtotic theory

    Gatto, R.; Sartori, G.

    1975-01-01

    The procedure proposed in the preceding paper to construct the asymptotic scale-invariant theory is applied to massive free fields. The contracted fields (of the asymptotic theory) are calculated in terms of the original fields by two different procedures. The contracted charges are calculated and their general relation to the original charges is verified. The problem of defining a vacuum state for the contracted fields and charges is solved. The relation to the problem of non-equivalent representations of the commutator relations is pointed out

  14. Validation of Theory of Consumption Values Scales for Deal Sites

    Sudzina, Frantisek

    2016-01-01

    Deal sites became a widely used artefact. But there is still only a limited number of papers investigating their adoption and use. Most of the research published on the topic is qualitative. It is typical for an early stage of investigation of any new artefact. The Theory of Consumption Values ex...... explains purchase behavior. The aim of this paper is to validate scales for the Theory of Consumption Values for deal sites. This should pave a way for quantitative investigation of motives for purchasing using deal sites....

  15. Departures from scaling in SU(2) lattice gauge theory

    Gutbrod, F.

    1987-01-01

    High statistics Monte Carlo Data in SU(2) lattice gauge theory are presented. At β = 2.6 and β = 2.7 large deviations form scaling are observed for Creutz ratios, when 12 4 and 24 4 lattice data are compared. There is a trend towards a restauration of asymptotic scaling with increasing β, which vanishes if at the higher value of β larger loops are considered than at lower β. The static qanti q-potential and an upper limit for the string tension are given. (orig.)

  16. Detailed treatment of scaling violations in asymptotically free gauge theories

    Hinchliffe, I.; Llewellyn Smith, C.H.

    1977-01-01

    Scaling violations in lepto-production are discussed on the basis of asymptotically free gauge theories. Detailed attention is given to the problems of operator mixing and data parametrisation. All the electro-/muo-production data for F 2 can be accommodated. The calculated values for Fsub(L) are also compatible with the data in the region where the theory may be trusted. It is shown that the FNAL data for sigmasup(anti γ)/sigmasup(γ) and sup(anti γ) can be explained if the freedom to input rather large amounts of antiquarks is exploited. It is therefore premature to conclude that new flavours are required. Predictions are given for very high energies which are relevant for possible new experimental facilities. The consequences of a conjecture about the possible pattern of scaling violations in the production of W's, Z's and μ-pairs are explored. Some theoretical problems and uncertainties in testing asymptotic freedom are discussed. (Auth.)

  17. Construction of a Genome-Scale Metabolic Model of Arthrospira platensis NIES-39 and Metabolic Design for Cyanobacterial Bioproduction.

    Katsunori Yoshikawa

    Full Text Available Arthrospira (Spirulina platensis is a promising feedstock and host strain for bioproduction because of its high accumulation of glycogen and superior characteristics for industrial production. Metabolic simulation using a genome-scale metabolic model and flux balance analysis is a powerful method that can be used to design metabolic engineering strategies for the improvement of target molecule production. In this study, we constructed a genome-scale metabolic model of A. platensis NIES-39 including 746 metabolic reactions and 673 metabolites, and developed novel strategies to improve the production of valuable metabolites, such as glycogen and ethanol. The simulation results obtained using the metabolic model showed high consistency with experimental results for growth rates under several trophic conditions and growth capabilities on various organic substrates. The metabolic model was further applied to design a metabolic network to improve the autotrophic production of glycogen and ethanol. Decreased flux of reactions related to the TCA cycle and phosphoenolpyruvate reaction were found to improve glycogen production. Furthermore, in silico knockout simulation indicated that deletion of genes related to the respiratory chain, such as NAD(PH dehydrogenase and cytochrome-c oxidase, could enhance ethanol production by using ammonium as a nitrogen source.

  18. A global evaluation of metabolic theory as an explanation for terrestrial species richness gradients

    Hawkins, Bradford A.; Albuquerque, Fabio S.; Araújo, Miguel B.

    2007-01-01

    We compiled 46 broadscale data sets of species richness for a wide range of terrestrial plant, invertebrate, and ectothermic vertebrate groups in all parts of the world to test the ability of metabolic theory to account for observed diversity gradients. The theory makes two related predictions: (...

  19. Bridging Food Webs, Ecosystem Metabolism, and Biogeochemistry Using Ecological Stoichiometry Theory

    Nina Welti

    2017-07-01

    Full Text Available Although aquatic ecologists and biogeochemists are well aware of the crucial importance of ecosystem functions, i.e., how biota drive biogeochemical processes and vice-versa, linking these fields in conceptual models is still uncommon. Attempts to explain the variability in elemental cycling consequently miss an important biological component and thereby impede a comprehensive understanding of the underlying processes governing energy and matter flow and transformation. The fate of multiple chemical elements in ecosystems is strongly linked by biotic demand and uptake; thus, considering elemental stoichiometry is important for both biogeochemical and ecological research. Nonetheless, assessments of ecological stoichiometry (ES often focus on the elemental content of biota rather than taking a more holistic view by examining both elemental pools and fluxes (e.g., organismal stoichiometry and ecosystem process rates. ES theory holds the promise to be a unifying concept to link across hierarchical scales of patterns and processes in ecology, but this has not been fully achieved. Therefore, we propose connecting the expertise of aquatic ecologists and biogeochemists with ES theory as a common currency to connect food webs, ecosystem metabolism, and biogeochemistry, as they are inherently concatenated by the transfer of carbon, nitrogen, and phosphorous through biotic and abiotic nutrient transformation and fluxes. Several new studies exist that demonstrate the connections between food web ecology, biogeochemistry, and ecosystem metabolism. In addition to a general introduction into the topic, this paper presents examples of how these fields can be combined with a focus on ES. In this review, a series of concepts have guided the discussion: (1 changing biogeochemistry affects trophic interactions and ecosystem processes by altering the elemental ratios of key species and assemblages; (2 changing trophic dynamics influences the transformation and

  20. Translation Fidelity of Psychological Scales: An Item Response Theory Analysis of an Individualism-Collectivism Scale.

    Bontempo, Robert

    1993-01-01

    Describes a method for assessing the quality of translations based on item response theory (IRT). Results from the IRT technique with French and Chinese versions of a scale measuring individualism-collectivism for samples of 250 U.S., 357 French, and 290 Chinese undergraduates show how several biased items are detected. (SLD)

  1. The natural selection of metabolism explains curvature in allometric scaling

    Witting, Lars

    2016-01-01

    I simulate the evolution of metabolism and mass to explain the curvature in the metabolic allometry for placental and marsupial mammals. I assume that the release of inter-specific competition by the extinction of dinosaurs 65 million years ago made it possible for each clade to diversity into a multitude of species across a wide range of niches. The natural selection of metabolism and mass was then fitted to explain the maximum observed body masses over time, as well as the current inter-spe...

  2. Comprehensive Mapping of Pluripotent Stem Cell Metabolism Using Dynamic Genome-Scale Network Modeling

    Sriram Chandrasekaran

    2017-12-01

    Full Text Available Summary: Metabolism is an emerging stem cell hallmark tied to cell fate, pluripotency, and self-renewal, yet systems-level understanding of stem cell metabolism has been limited by the lack of genome-scale network models. Here, we develop a systems approach to integrate time-course metabolomics data with a computational model of metabolism to analyze the metabolic state of naive and primed murine pluripotent stem cells. Using this approach, we find that one-carbon metabolism involving phosphoglycerate dehydrogenase, folate synthesis, and nucleotide synthesis is a key pathway that differs between the two states, resulting in differential sensitivity to anti-folates. The model also predicts that the pluripotency factor Lin28 regulates this one-carbon metabolic pathway, which we validate using metabolomics data from Lin28-deficient cells. Moreover, we identify and validate metabolic reactions related to S-adenosyl-methionine production that can differentially impact histone methylation in naive and primed cells. Our network-based approach provides a framework for characterizing metabolic changes influencing pluripotency and cell fate. : Chandrasekaran et al. use computational modeling, metabolomics, and metabolic inhibitors to discover metabolic differences between various pluripotent stem cell states and infer their impact on stem cell fate decisions. Keywords: systems biology, stem cell biology, metabolism, genome-scale modeling, pluripotency, histone methylation, naive (ground state, primed state, cell fate, metabolic network

  3. Boomerang RG flows in M-theory with intermediate scaling

    Donos, Aristomenis; Gauntlett, Jerome P.; Rosen, Christopher; Sosa-Rodriguez, Omar

    2017-07-01

    We construct novel RG flows of D=11 supergravity that asymptotically approach AdS 4 × S 7 in the UV with deformations that break spatial translations in the dual field theory. In the IR the solutions return to exactly the same AdS 4 × S 7 vacuum, with a renormalisation of relative length scales, and hence we refer to the flows as `boomerang RG flows'. For sufficiently large deformations, on the way to the IR the solutions also approach two distinct intermediate scaling regimes, each with hyperscaling violation. The first regime is Lorentz invariant with dynamical exponent z = 1 while the second has z = 5/2. Neither ofthe two intermediatescaling regimesare associatedwith exact hyperscaling violation solutions of D = 11 supergravity. The RG flow solutions are constructed using the four dimensional N = 2 STU gauged supergravity theory with vanishing gauge fields, but non-vanishing scalar and pseudoscalar fields. In the ABJM dual field theory the flows are driven by spatially modulated deformation parameters for scalar and fermion bilinear operators.

  4. TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

    Jensen Paul A

    2011-09-01

    Full Text Available Abstract Background Several methods have been developed for analyzing genome-scale models of metabolism and transcriptional regulation. Many of these methods, such as Flux Balance Analysis, use constrained optimization to predict relationships between metabolic flux and the genes that encode and regulate enzyme activity. Recently, mixed integer programming has been used to encode these gene-protein-reaction (GPR relationships into a single optimization problem, but these techniques are often of limited generality and lack a tool for automating the conversion of rules to a coupled regulatory/metabolic model. Results We present TIGER, a Toolbox for Integrating Genome-scale Metabolism, Expression, and Regulation. TIGER converts a series of generalized, Boolean or multilevel rules into a set of mixed integer inequalities. The package also includes implementations of existing algorithms to integrate high-throughput expression data with genome-scale models of metabolism and transcriptional regulation. We demonstrate how TIGER automates the coupling of a genome-scale metabolic model with GPR logic and models of transcriptional regulation, thereby serving as a platform for algorithm development and large-scale metabolic analysis. Additionally, we demonstrate how TIGER's algorithms can be used to identify inconsistencies and improve existing models of transcriptional regulation with examples from the reconstructed transcriptional regulatory network of Saccharomyces cerevisiae. Conclusion The TIGER package provides a consistent platform for algorithm development and extending existing genome-scale metabolic models with regulatory networks and high-throughput data.

  5. Reconstruction of genome-scale human metabolic models using omics data

    Ryu, Jae Yong; Kim, Hyun Uk; Lee, Sang Yup

    2015-01-01

    used to describe metabolic phenotypes of healthy and diseased human tissues and cells, and to predict therapeutic targets. Here we review recent trends in genome-scale human metabolic modeling, including various generic and tissue/cell type-specific human metabolic models developed to date, and methods......, databases and platforms used to construct them. For generic human metabolic models, we pay attention to Recon 2 and HMR 2.0 with emphasis on data sources used to construct them. Draft and high-quality tissue/cell type-specific human metabolic models have been generated using these generic human metabolic...... refined through gap filling, reaction directionality assignment and the subcellular localization of metabolic reactions. We review relevant tools for this model refinement procedure as well. Finally, we suggest the direction of further studies on reconstructing an improved human metabolic model....

  6. Systematic renormalization of the effective theory of Large Scale Structure

    Abolhasani, Ali Akbar; Mirbabayi, Mehrdad; Pajer, Enrico

    2016-01-01

    A perturbative description of Large Scale Structure is a cornerstone of our understanding of the observed distribution of matter in the universe. Renormalization is an essential and defining step to make this description physical and predictive. Here we introduce a systematic renormalization procedure, which neatly associates counterterms to the UV-sensitive diagrams order by order, as it is commonly done in quantum field theory. As a concrete example, we renormalize the one-loop power spectrum and bispectrum of both density and velocity. In addition, we present a series of results that are valid to all orders in perturbation theory. First, we show that while systematic renormalization requires temporally non-local counterterms, in practice one can use an equivalent basis made of local operators. We give an explicit prescription to generate all counterterms allowed by the symmetries. Second, we present a formal proof of the well-known general argument that the contribution of short distance perturbations to large scale density contrast δ and momentum density π(k) scale as k 2 and k, respectively. Third, we demonstrate that the common practice of introducing counterterms only in the Euler equation when one is interested in correlators of δ is indeed valid to all orders.

  7. Scale-covariant theory of gravitation and astrophysical applications

    Canuto, V.; Adams, P.J.; Hsieh, S.; Tsiang, E.

    1977-01-01

    By associating the mathematical operation of scale transformation with the physics of using different dynamical systems to measure space-time distances, we formulate a scale-covariant theory of gravitation. Corresponding to each dynamical system of units is a gauge condition which determines the otherwise arbitrary gauge function. For gravitational units, the gauge condition is chosen so that the standard Einstein equations are recovered. Assuming the atomic units, derivable from atomic dynamics, to be distinct from the gravitational units, a different gauge condition must be imposed. It is suggested that Dirac's large-number hypothesis be used for the determination of this condition so that gravitational phenomena can be described in atomic units. The result allows a natural interpretation of the possible variation of the gravitational constant without compromising the validity of general relativity. A geometrical interpretation of the scale-covariant theory is possible if the covariant tensors in Riemannian space are replaced by cocovariant cotensors in an integrable Weyl space. A scale-invariant action principle is constructed from the metrical potentials of the integrable Weyl space. Application of the dynamical equations in atomic units to cosmology yields a family of homogeneous solutions characterized by R approx. t for large cosmological times. Equations of motion in atomic units are solved for spherically symmetric gravitational fields. Expressions for perihelion shift and light deflection are derived. They do not differ from the predictions of general relativity except for secular variations, having the age of the universe as a time scale. Similar variations of periods and radii for planetary orbits are also derived

  8. Adiposopathy, metabolic syndrome, quantum physics, general relativity, chaos and the Theory of Everything.

    Bays, Harold

    2005-05-01

    Excessive fat (adiposity) and dysfunctional fat (adiposopathy) constitute the most common worldwide epidemics of our time -- and perhaps of all time. Ongoing efforts to explain how the micro (adipocyte) and macro (body organ) biologic systems interact through function and dysfunction in promoting Type 2 diabetes mellitus, hypertension and dyslipidemia are not unlike the mechanistic and philosophical thinking processes involved in reconciling the micro (quantum physics) and macro (general relativity) theories in physics. Currently, the term metabolic syndrome refers to a constellation of consequences often associated with excess body fat and is an attempt to unify the associations known to exist between the four fundamental metabolic diseases of obesity, hyperglycemia (including Type 2 diabetes mellitus), hypertension and dyslipidemia. However, the association of adiposity with these metabolic disorders is not absolute and the metabolic syndrome does not describe underlying causality, nor does the metabolic syndrome necessarily reflect any reasonably related pathophysiologic process. Just as with quantum physics, general relativity and the four fundamental forces of the universe, the lack of an adequate unifying theory of micro causality and macro consequence is unsatisfying, and in medicine, impairs the development of agents that may globally improve both obesity and obesity-related metabolic disease. Emerging scientific and clinical evidence strongly supports the novel concept that it is not adiposity alone, but rather it is adiposopathy that is the underlying cause of most cases of Type 2 diabetes mellitus, hypertension and dyslipidemia. Adiposopathy is a plausible Theory of Everything for mankind's greatest metabolic epidemics.

  9. F-theory, GUTs, and the weak scale

    Heckman, Jonathan J.; Vafa, Cumrun

    2009-01-01

    In this paper we study a deformation of gauge mediated supersymmetry breaking in a class of local F-theory GUT models where the scale of supersymmetry breaking determines the value of the μ term. Geometrically correlating these two scales constrains the soft SUSY breaking parameters of the MSSM. In this scenario, the hidden SUSY breaking sector involves an anomalous U(1) Peccei-Quinn symmetry which forbids bare μ and Bμ terms. This sector typically breaks supersymmetry at the desired range of energy scales through a simple stringy hybrid of a Fayet and Polonyi model. A variant of the Giudice-Masiero mechanism generates the value μ ∼ 10 2 -10 3 GeV when the hidden sector scale of supersymmetry breaking is F 1/2 ∼ 10 8.5 GeV. Further, the Bμ problem is solved due to the mild hierarchy between the GUT scale and Planck scale. These models relate SUSY breaking with the QCD axion, and solve the strong CP problem through an axion with decay constant f a ∼ M GUT cμ/Λ, where Λ ∼ 10 5 GeV is the characteristic scale of gaugino mass unification in gauge mediated models, and the ratio μ/Λ ∼ M GUT /M pl ∼ 10 -3 . We find f a ∼ 10 12 GeV, which is near the high end of the phenomenologically viable window. Here, the axino is the goldstino mode which is eaten by the gravitino. The gravitino is the LSP with a mass of about 10 1 -10 2 MeV, and a bino-like neutralino is (typically) the NLSP with mass of about 10 2 -10 3 GeV. Compatibility with electroweak symmetry breaking also determines the value of tanβ ∼ 30±7.

  10. The role of instantons in scale-invariant gauge theories

    Affleck, I.

    1980-01-01

    Instanton calculations in scale-invariant gauge theories, such as QCD, have long been plagued by divergences at large distances where strong coupling effects are important. Furthermore, Witten has argued that quantum effects may cause the instanton gas to disappear and has displayed this phenomenon in the CPsup(N-1) model at large N. It is argued here that instantons can play a role in calculations involving an inherent infrared cut-off, and this is demonstrated in the CPsup(N-1) model for large N at a finite temperature. Some results on finite-temperature QED are also obtained in passing. (orig.)

  11. On the GUT scale of F-theory SU(5)

    Leontaris, G.K.; Vlachos, N.D.

    2011-01-01

    In F-theory GUTs, threshold corrections from Kaluza-Klein (KK) massive modes arising from gauge and matter multiplets play an important role in the determination of the weak mixing angle and the strong gauge coupling of the effective low energy model. In this Letter we further explore the induced modifications on the gauge couplings running and the GUT scale. In particular, we focus on the KK-contributions from matter curves and analyze the conditions on the chiral and Higgs matter spectrum which imply a GUT scale consistent with the minimal unification scenario. As an application, we present an explicit computation of these thresholds for matter fields residing on specific non-trivial Riemann surfaces.

  12. Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico.

    McAnulty, Michael J; Yen, Jiun Y; Freedman, Benjamin G; Senger, Ryan S

    2012-05-14

    Genome-scale metabolic networks and flux models are an effective platform for linking an organism genotype to its phenotype. However, few modeling approaches offer predictive capabilities to evaluate potential metabolic engineering strategies in silico. A new method called "flux balance analysis with flux ratios (FBrAtio)" was developed in this research and applied to a new genome-scale model of Clostridium acetobutylicum ATCC 824 (iCAC490) that contains 707 metabolites and 794 reactions. FBrAtio was used to model wild-type metabolism and metabolically engineered strains of C. acetobutylicum where only flux ratio constraints and thermodynamic reversibility of reactions were required. The FBrAtio approach allowed solutions to be found through standard linear programming. Five flux ratio constraints were required to achieve a qualitative picture of wild-type metabolism for C. acetobutylicum for the production of: (i) acetate, (ii) lactate, (iii) butyrate, (iv) acetone, (v) butanol, (vi) ethanol, (vii) CO2 and (viii) H2. Results of this simulation study coincide with published experimental results and show the knockdown of the acetoacetyl-CoA transferase increases butanol to acetone selectivity, while the simultaneous over-expression of the aldehyde/alcohol dehydrogenase greatly increases ethanol production. FBrAtio is a promising new method for constraining genome-scale models using internal flux ratios. The method was effective for modeling wild-type and engineered strains of C. acetobutylicum.

  13. Finite-size scaling theory and quantum hamiltonian Field theory: the transverse Ising model

    Hamer, C.J.; Barber, M.N.

    1979-01-01

    Exact results for the mass gap, specific heat and susceptibility of the one-dimensional transverse Ising model on a finite lattice are generated by constructing a finite matrix representation of the Hamiltonian using strong-coupling eigenstates. The critical behaviour of the limiting infinite chain is analysed using finite-size scaling theory. In this way, excellent estimates (to within 1/2% accuracy) are found for the critical coupling and the exponents α, ν and γ

  14. In silico analysis of human metabolism: Reconstruction, contextualization and application of genome-scale models

    Geng, Jun; Nielsen, Jens

    2017-01-01

    The arising prevalence of metabolic diseases calls for a holistic approach for analysis of the underlying nature of abnormalities in cellular functions. Through mathematic representation and topological analysis of cellular metabolism, GEnome scale metabolic Models (GEMs) provide a promising fram...... that correctly describe interactions between cells or tissues, and we therefore discuss how GEMs can be integrated with blood circulation models. Finally, we end the review with proposing some possible future research directions....

  15. Scaling theory for the quasideterministic limit of continuous bifurcations.

    Kessler, David A; Shnerb, Nadav M

    2012-05-01

    Deterministic rate equations are widely used in the study of stochastic, interacting particles systems. This approach assumes that the inherent noise, associated with the discreteness of the elementary constituents, may be neglected when the number of particles N is large. Accordingly, it fails close to the extinction transition, when the amplitude of stochastic fluctuations is comparable with the size of the population. Here we present a general scaling theory of the transition regime for spatially extended systems. We demonstrate this through a detailed study of two fundamental models for out-of-equilibrium phase transitions: the Susceptible-Infected-Susceptible (SIS) that belongs to the directed percolation equivalence class and the Susceptible-Infected-Recovered (SIR) model belonging to the dynamic percolation class. Implementing the Ginzburg criteria we show that the width of the fluctuation-dominated region scales like N^{-κ}, where N is the number of individuals per site and κ=2/(d_{u}-d), d_{u} is the upper critical dimension. Other exponents that control the approach to the deterministic limit are shown to be calculable once κ is known. The theory is extended to include the corrections to the front velocity above the transition. It is supported by the results of extensive numerical simulations for systems of various dimensionalities.

  16. A critical review on the scaling theory of dispersion

    Zech, Alraune; Mai, Juliane; Attinger, Sabine; Dietrich, Peter; Teutsch, Georg; Fiori, Aldo; Rubin, Yoram

    2014-05-01

    The phenomenon of dispersive mixing of solutes in aquifers is subject of research since decades. The characterization of dispersivity at a particular field site is a prerequisite to predict the movement and spreading of a contaminant plume. Experimental investigations have shown, that field-scale dispersivities vary over orders of magnitude, which apparently depends on the scale of measurement. Gelhar et al. [1992] and Schulze-Makuch [2005] have reviewed a large number of transport experiments reported in the literature. Based on that data Schulze-Makuch [2005] performed a trend analysis of longitudinal dispersivity, fostering the empirical relationship of a power law between dispersivities and the scale of measurement without an upper bound. The goal of our study is to critically revisit not only the data used for the trend analysis but the power-law scale dependence of longitudinal dispersivity (e.g. Neuman [1990], Xu and Eckstein [1995]). Our particular focus is on the reported dispersivities of large amount (larger than 100m) and large measurement scales (in the order of kilometers). We aim to evaluate current theories of transport against a critical "mass" of field experiments and to bracket the conditions of their applicability. We further aim to evaluate the adequacy of the field sampling techniques that were employed from the perspective of more than 30 years development in modeling and field characterization. Given the tremendous progress in field data acquisition techniques and new insights gained, it is reasonable to expect that interpretations of past experiments may be flawed due to the limitations or inadequacy of field sampling techniques. Gelhar, L.W., C. Welty, and K.R. Rehfeldt, 1992, A critical review of data on field-scale dispersion in aquifers, Water Resources Research 28, No. 7: 1955-1974. Schulze-Makuch, D., 2005, Longitudinal dispersivity data and implications for scaling behavior, Ground Water, Vol. 43, No. 3, 443-456. Neuman, S.P., 1990

  17. Conductance of finite systems and scaling in localization theory

    Suslov, I. M.

    2012-11-01

    The conductance of finite systems plays a central role in the scaling theory of localization (Abrahams et al., Phys. Rev. Lett. 42, 673 (1979)). Usually it is defined by the Landauer-type formulas, which remain open the following questions: (a) exclusion of the contact resistance in the many-channel case; (b) correspondence of the Landauer conductance with internal properties of the system; (c) relation with the diffusion coefficient D(ω, q) of an infinite system. The answers to these questions are obtained below in the framework of two approaches: (1) self-consistent theory of localization by Vollhardt and Wölfle, and (2) quantum mechanical analysis based on the shell model. Both approaches lead to the same definition for the conductance of a finite system, closely related to the Thouless definition. In the framework of the self-consistent theory, the relations of finite-size scaling are derived and the Gell-Mann-Low functions β( g) for space dimensions d = 1, 2, 3 are calculated. In contrast to the previous attempt by Vollhardt and Wölfle (1982), the metallic and localized phase are considered from the same standpoint, and the conductance of a finite system has no singularity at the critical point. In the 2D case, the expansion of β( g) in 1/ g coincides with results of the σ-model approach on the two-loop level and depends on the renormalization scheme in higher loops; the use of dimensional regularization for transition to dimension d = 2 + ɛ looks incompatible with the physical essence of the problem. The results are compared with numerical and physical experiments. A situation in higher dimensions and the conditions for observation of the localization law σ(ω) ∝ - iω for conductivity are discussed.

  18. Cosmological tests of a scale covariant theory of gravitation

    Owen, J.R.

    1979-01-01

    The Friedmann models with #betta# = 0 are subjected to several optical and radio tests within the standard and scale covariant theories of gravitation. Within standard cosmology, both interferometric and scintillation data are interpreted in terms of selection effects and evolution. Within the context of scale covariant cosmology are derived: (1) the full solution to Einstein's gravitational equations in atomic units for a matter dominated universe, (2) the study of the magnitude vs. redshift relation for elliptical galaxies, (3) the derivation of the evolutionary parameter used in (2), (4) the isophotal angular diameter vs. redshift relation, (5) the metric angular diameter vs. redshift relation, (6) the N(m) vs. magnitude relation for QSO's and their m vs z relation, and finally (7) the integrated and differential expressions for the number count vs. radio flux test. The results, both in graphical and tabular form, are presented for four gauges (i.e. parametrized relations between atomic and gravitational units). No contradiction between the new theory and the data is found with any of the tests studied. For some gauges, which are suggested by a recent analysis of the time variation of the Moon's period which is discussed in the text in terms of the new theory, the effect of the deceleration parameter on cosmological predictions is enhanced over standard cosmology and it is possible to say that the data are more easily reconciled with an open universe. Within the same gauge, the main features of both the N(m) vs. m and m-z test are accounted for by the same simple evolutionary parametrization whereas different evolutionary rates were indicated by interpretation within standard cosmology. The same consistency, lacking in standard cosmology on this level of analysis, is achieved for the integrated and differential number count - radio flux tests within the same gauge

  19. Conductance of finite systems and scaling in localization theory

    Suslov, I. M.

    2012-01-01

    The conductance of finite systems plays a central role in the scaling theory of localization (Abrahams et al., Phys. Rev. Lett. 42, 673 (1979)). Usually it is defined by the Landauer-type formulas, which remain open the following questions: (a) exclusion of the contact resistance in the many-channel case; (b) correspondence of the Landauer conductance with internal properties of the system; (c) relation with the diffusion coefficient D(ω, q) of an infinite system. The answers to these questions are obtained below in the framework of two approaches: (1) self-consistent theory of localization by Vollhardt and Wölfle, and (2) quantum mechanical analysis based on the shell model. Both approaches lead to the same definition for the conductance of a finite system, closely related to the Thouless definition. In the framework of the self-consistent theory, the relations of finite-size scaling are derived and the Gell-Mann-Low functions β(g) for space dimensions d = 1, 2, 3 are calculated. In contrast to the previous attempt by Vollhardt and Wölfle (1982), the metallic and localized phase are considered from the same standpoint, and the conductance of a finite system has no singularity at the critical point. In the 2D case, the expansion of β(g) in 1/g coincides with results of the σ-model approach on the two-loop level and depends on the renormalization scheme in higher loops; the use of dimensional regularization for transition to dimension d = 2 + ε looks incompatible with the physical essence of the problem. The results are compared with numerical and physical experiments. A situation in higher dimensions and the conditions for observation of the localization law σ(ω) ∝ −iω for conductivity are discussed.

  20. Determining the Control Circuitry of Redox Metabolism at the Genome-Scale

    Federowicz, Stephen; Kim, Donghyuk; Ebrahim, Ali

    2014-01-01

    -scale metabolic model to show that ArcA and Fnr regulate >80% of total metabolic flux and 96% of differential gene expression across fermentative and nitrate respiratory conditions. Based on the data, we propose a feedforward with feedback trim regulatory scheme, given the extensive repression of catabolic genes...

  1. In Silico Genome-Scale Reconstruction and Validation of the Staphylococcus aureus Metabolic Network

    Heinemann, Matthias; Kümmel, Anne; Ruinatscha, Reto; Panke, Sven

    2005-01-01

    A genome-scale metabolic model of the Gram-positive, facultative anaerobic opportunistic pathogen Staphylococcus aureus N315 was constructed based on current genomic data, literature, and physiological information. The model comprises 774 metabolic processes representing approximately 23% of all

  2. Exercise-induced maximum metabolic rate scaled to body mass by ...

    user

    2016-10-27

    Oct 27, 2016 ... maximum aerobic metabolic rate (MMR) is proportional to the fractal extent ... metabolic rate with body mass can be obtained by taking body .... blood takes place. ..... MMR and BMR is that MMR is owing mainly to respiration in skeletal .... the spectra of surface area scaling strategies of cells and organisms:.

  3. Neutral Theory and Scale-Free Neural Dynamics

    Martinello, Matteo; Hidalgo, Jorge; Maritan, Amos; di Santo, Serena; Plenz, Dietmar; Muñoz, Miguel A.

    2017-10-01

    Neural tissues have been consistently observed to be spontaneously active and to generate highly variable (scale-free distributed) outbursts of activity in vivo and in vitro. Understanding whether these heterogeneous patterns of activity stem from the underlying neural dynamics operating at the edge of a phase transition is a fascinating possibility, as criticality has been argued to entail many possible important functional advantages in biological computing systems. Here, we employ a well-accepted model for neural dynamics to elucidate an alternative scenario in which diverse neuronal avalanches, obeying scaling, can coexist simultaneously, even if the network operates in a regime far from the edge of any phase transition. We show that perturbations to the system state unfold dynamically according to a "neutral drift" (i.e., guided only by stochasticity) with respect to the background of endogenous spontaneous activity, and that such a neutral dynamics—akin to neutral theories of population genetics and of biogeography—implies marginal propagation of perturbations and scale-free distributed causal avalanches. We argue that causal information, not easily accessible to experiments, is essential to elucidate the nature and statistics of neural avalanches, and that neutral dynamics is likely to play an important role in the cortex functioning. We discuss the implications of these findings to design new empirical approaches to shed further light on how the brain processes and stores information.

  4. Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis

    Broddrick, Jared T.; Rubin, Benjamin E.; Welkie, David G.; Du, Niu; Mih, Nathan; Diamond, Spencer; Lee, Jenny J.; Golden, Susan S.; Palsson, Bernhard O.

    2016-01-01

    The model cyanobacterium, Synechococcus elongatus PCC 7942, is a genetically tractable obligate phototroph that is being developed for the bioproduction of high-value chemicals. Genome-scale models (GEMs) have been successfully used to assess and engineer cellular metabolism; however, GEMs of phototrophic metabolism have been limited by the lack of experimental datasets for model validation and the challenges of incorporating photon uptake. Here, we develop a GEM of metabolism in S. elongatus using random barcode transposon site sequencing (RB-TnSeq) essential gene and physiological data specific to photoautotrophic metabolism. The model explicitly describes photon absorption and accounts for shading, resulting in the characteristic linear growth curve of photoautotrophs. GEM predictions of gene essentiality were compared with data obtained from recent dense-transposon mutagenesis experiments. This dataset allowed major improvements to the accuracy of the model. Furthermore, discrepancies between GEM predictions and the in vivo dataset revealed biological characteristics, such as the importance of a truncated, linear TCA pathway, low flux toward amino acid synthesis from photorespiration, and knowledge gaps within nucleotide metabolism. Coupling of strong experimental support and photoautotrophic modeling methods thus resulted in a highly accurate model of S. elongatus metabolism that highlights previously unknown areas of S. elongatus biology. PMID:27911809

  5. Large-scale transcriptome analysis reveals arabidopsis metabolic pathways are frequently influenced by different pathogens.

    Jiang, Zhenhong; He, Fei; Zhang, Ziding

    2017-07-01

    Through large-scale transcriptional data analyses, we highlighted the importance of plant metabolism in plant immunity and identified 26 metabolic pathways that were frequently influenced by the infection of 14 different pathogens. Reprogramming of plant metabolism is a common phenomenon in plant defense responses. Currently, a large number of transcriptional profiles of infected tissues in Arabidopsis (Arabidopsis thaliana) have been deposited in public databases, which provides a great opportunity to understand the expression patterns of metabolic pathways during plant defense responses at the systems level. Here, we performed a large-scale transcriptome analysis based on 135 previously published expression samples, including 14 different pathogens, to explore the expression pattern of Arabidopsis metabolic pathways. Overall, metabolic genes are significantly changed in expression during plant defense responses. Upregulated metabolic genes are enriched on defense responses, and downregulated genes are enriched on photosynthesis, fatty acid and lipid metabolic processes. Gene set enrichment analysis (GSEA) identifies 26 frequently differentially expressed metabolic pathways (FreDE_Paths) that are differentially expressed in more than 60% of infected samples. These pathways are involved in the generation of energy, fatty acid and lipid metabolism as well as secondary metabolite biosynthesis. Clustering analysis based on the expression levels of these 26 metabolic pathways clearly distinguishes infected and control samples, further suggesting the importance of these metabolic pathways in plant defense responses. By comparing with FreDE_Paths from abiotic stresses, we find that the expression patterns of 26 FreDE_Paths from biotic stresses are more consistent across different infected samples. By investigating the expression correlation between transcriptional factors (TFs) and FreDE_Paths, we identify several notable relationships. Collectively, the current study

  6. Recent development of linear scaling quantum theories in GAMESS

    Choi, Cheol Ho [Kyungpook National Univ., Daegu (Korea, Republic of)

    2003-06-01

    Linear scaling quantum theories are reviewed especially focusing on the method adopted in GAMESS. The three key translation equations of the fast multipole method (FMM) are deduced from the general polypolar expansions given earlier by Steinborn and Rudenberg. Simplifications are introduced for the rotation-based FMM that lead to a very compact FMM formalism. The OPS (optimum parameter searching) procedure, a stable and efficient way of obtaining the optimum set of FMM parameters, is established with complete control over the tolerable error {epsilon}. In addition, a new parallel FMM algorithm requiring virtually no inter-node communication, is suggested which is suitable for the parallel construction of Fock matrices in electronic structure calculations.

  7. Stability theory for dynamic equations on time scales

    Martynyuk, Anatoly A

    2016-01-01

    This monograph is a first in the world to present three approaches for stability analysis of solutions of dynamic equations. The first approach is based on the application of dynamic integral inequalities and the fundamental matrix of solutions of linear approximation of dynamic equations. The second is based on the generalization of the direct Lyapunovs method for equations on time scales, using scalar, vector and matrix-valued auxiliary functions. The third approach is the application of auxiliary functions (scalar, vector, or matrix-valued ones) in combination with differential dynamic inequalities. This is an alternative comparison method, developed for time continuous and time discrete systems. In recent decades, automatic control theory in the study of air- and spacecraft dynamics and in other areas of modern applied mathematics has encountered problems in the analysis of the behavior of solutions of time continuous-discrete linear and/or nonlinear equations of perturbed motion. In the book “Men of Ma...

  8. Gravitational theory in atomic scale units in Dirac cosmology

    Davidson, W.

    1984-01-01

    The implication of Dirac's large numbers hypothesis (LNH) that there are two cosmological space-time metrics, gravitational (E) and atomic (A), is used to formulate the gravitational laws for a general mass system in atomic scale units within such a cosmology. The gravitational laws are illustrated in application to the case of a single spherical mass immersed in the smoothed out expanding universe. The condition is determined for such a metric to apply approximately just outside a typical member of a cosmic distribution of such masses. Conversely, the condition is given when the influence of the universe as a whole can be neglected outside such a mass. In the latter situation, which applies in particular to stars, a Schwarzschild-type metric is derived which incorporates variable G in accordance with the LNH. The dynamics of freely moving particles and photons in such a metric are examined according to the theory and observational tests are formulated. (author)

  9. Density Functional Theory and Materials Modeling at Atomistic Length Scales

    Swapan K. Ghosh

    2002-04-01

    Full Text Available Abstract: We discuss the basic concepts of density functional theory (DFT as applied to materials modeling in the microscopic, mesoscopic and macroscopic length scales. The picture that emerges is that of a single unified framework for the study of both quantum and classical systems. While for quantum DFT, the central equation is a one-particle Schrodinger-like Kohn-Sham equation, the classical DFT consists of Boltzmann type distributions, both corresponding to a system of noninteracting particles in the field of a density-dependent effective potential, the exact functional form of which is unknown. One therefore approximates the exchange-correlation potential for quantum systems and the excess free energy density functional or the direct correlation functions for classical systems. Illustrative applications of quantum DFT to microscopic modeling of molecular interaction and that of classical DFT to a mesoscopic modeling of soft condensed matter systems are highlighted.

  10. On the consistency of scale among experiments, theory, and simulation

    McClure, James E.; Dye, Amanda L.; Miller, Cass T.; Gray, William G.

    2017-02-01

    As a tool for addressing problems of scale, we consider an evolving approach known as the thermodynamically constrained averaging theory (TCAT), which has broad applicability to hydrology. We consider the case of modeling of two-fluid-phase flow in porous media, and we focus on issues of scale as they relate to various measures of pressure, capillary pressure, and state equations needed to produce solvable models. We apply TCAT to perform physics-based data assimilation to understand how the internal behavior influences the macroscale state of two-fluid porous medium systems. A microfluidic experimental method and a lattice Boltzmann simulation method are used to examine a key deficiency associated with standard approaches. In a hydrologic process such as evaporation, the water content will ultimately be reduced below the irreducible wetting-phase saturation determined from experiments. This is problematic since the derived closure relationships cannot predict the associated capillary pressures for these states. We demonstrate that the irreducible wetting-phase saturation is an artifact of the experimental design, caused by the fact that the boundary pressure difference does not approximate the true capillary pressure. Using averaging methods, we compute the true capillary pressure for fluid configurations at and below the irreducible wetting-phase saturation. Results of our analysis include a state function for the capillary pressure expressed as a function of fluid saturation and interfacial area.

  11. Universality and scaling in SU(2) lattice gauge theory

    Michael, C.; Teper, M.; Oxford Univ.

    1988-01-01

    We calculate the lowest glueball masses and the string tension for both Manton's action and for Symanzik's tree-level improved action. We do so on large lattices and for small lattice spacings using techniques recently employed in an extensive investigation of the Wilson plaquette action. Comparing all these results we find that the ratios of the lightest masses are universal to a high degree of accuracy. In particular, we confirm that on large volumes the tensor glueball is heavier than the scalar glueball: m[2 + ] ≅ 1.5 m[0 + ]. We repeat these calculations for larger lattice spacings and find that the string tension follows 2-loop perturbation theory more closely in the case of these alternative actions than in the case of the standard plaquette action. Our attempt to repeat the analysis with Wilson's block-spin improved action foundered on the strong breakdown of positivity apparent in the calculated correlation functions. In all the cases which we were able to study the observed violations of scaling are in the same direction. This suggests that the causes of the scaling violations observed with Wilson's plaquette action are 'semi-universal'. It also weakens the implication of the observed universality for the question of how close we are to the continuum limit. (orig.)

  12. A model for allometric scaling of mammalian metabolism with ambient heat loss

    Kwak, Ho Sang; Im, Hong G.; Shim, Eun Bo

    2016-01-01

    The finding that additional radiative heat loss and the consideration of an outer insulation fur layer attenuate these deviation effects and render the scaling law closer to 2/3 provides in silico evidence for a functional impact of heat transfer mode on the allometric scaling law in mammalian metabolism.

  13. A flux-scaling scenario for high-scale moduli stabilization in string theory

    Ralph Blumenhagen

    2015-08-01

    Full Text Available Tree-level moduli stabilization via geometric and non-geometric fluxes in type IIB orientifolds on Calabi–Yau manifolds is investigated. The focus is on stable non-supersymmetric minima, where all moduli are fixed except for some massless axions. The scenario includes the purely axionic orientifold-odd moduli. A set of vacua allowing for parametric control over the moduli vacuum expectation values and their masses is presented, featuring a specific scaling with the fluxes. Uplift mechanisms and supersymmetry breaking soft masses on MSSM-like D7-branes are discussed as well. This scenario provides a complete effective framework for realizing the idea of F-term axion monodromy inflation in string theory. It is argued that, with all masses close to the Planck and GUT scales, one is confronted with working at the threshold of controlling all mass hierarchies.

  14. A flux-scaling scenario for high-scale moduli stabilization in string theory

    Blumenhagen, Ralph [Max-Planck-Institut für Physik (Werner-Heisenberg-Institut), Föhringer Ring 6, 80805 München (Germany); Font, Anamaría [Max-Planck-Institut für Physik (Werner-Heisenberg-Institut), Föhringer Ring 6, 80805 München (Germany); Arnold Sommerfeld Center for Theoretical Physics, LMU, Theresienstr. 37, 80333 München (Germany); Fuchs, Michael [Max-Planck-Institut für Physik (Werner-Heisenberg-Institut), Föhringer Ring 6, 80805 München (Germany); Herschmann, Daniela, E-mail: herschma@mpp.mpg.de [Max-Planck-Institut für Physik (Werner-Heisenberg-Institut), Föhringer Ring 6, 80805 München (Germany); Plauschinn, Erik [Dipartimento di Fisica e Astronomia “Galileo Galilei”, Università di Padova, Via Marzolo 8, 35131 Padova (Italy); INFN, Sezione di Padova, Via Marzolo 8, 35131 Padova (Italy); Sekiguchi, Yuta; Wolf, Florian [Max-Planck-Institut für Physik (Werner-Heisenberg-Institut), Föhringer Ring 6, 80805 München (Germany); Arnold Sommerfeld Center for Theoretical Physics, LMU, Theresienstr. 37, 80333 München (Germany)

    2015-08-15

    Tree-level moduli stabilization via geometric and non-geometric fluxes in type IIB orientifolds on Calabi–Yau manifolds is investigated. The focus is on stable non-supersymmetric minima, where all moduli are fixed except for some massless axions. The scenario includes the purely axionic orientifold-odd moduli. A set of vacua allowing for parametric control over the moduli vacuum expectation values and their masses is presented, featuring a specific scaling with the fluxes. Uplift mechanisms and supersymmetry breaking soft masses on MSSM-like D7-branes are discussed as well. This scenario provides a complete effective framework for realizing the idea of F-term axion monodromy inflation in string theory. It is argued that, with all masses close to the Planck and GUT scales, one is confronted with working at the threshold of controlling all mass hierarchies.

  15. Probing the genome-scale metabolic landscape of Bordetella pertussis, the causative agent of whooping cough.

    Branco Dos Santos, Filipe; Olivier, Brett G; Boele, Joost; Smessaert, Vincent; De Rop, Philippe; Krumpochova, Petra; Klau, Gunnar W; Giera, Martin; Dehottay, Philippe; Teusink, Bas; Goffin, Philippe

    2017-08-25

    Whooping cough is a highly-contagious respiratory disease caused by Bordetella pertussi s. Despite vaccination, its incidence has been rising alarmingly, and yet, the physiology of B. pertussis remains poorly understood. We combined genome-scale metabolic reconstruction, a novel optimization algorithm and experimental data to probe the full metabolic potential of this pathogen, using strain Tohama I as a reference. Experimental validation showed that B. pertussis secretes a significant proportion of nitrogen as arginine and purine nucleosides, which may contribute to modulation of the host response. We also found that B. pertussis can be unexpectedly versatile, being able to metabolize many compounds while displaying minimal nutrient requirements. It can grow without cysteine - using inorganic sulfur sources such as thiosulfate - and it can grow on organic acids such as citrate or lactate as sole carbon sources, providing in vivo demonstration that its TCA cycle is functional. Although the metabolic reconstruction of eight additional strains indicates that the structural genes underlying this metabolic flexibility are widespread, experimental validation suggests a role of strain-specific regulatory mechanisms in shaping metabolic capabilities. Among five alternative strains tested, three were shown to grow on substrate combinations requiring a functional TCA cycle, but only one could use thiosulfate. Finally, the metabolic model was used to rationally design growth media with over two-fold improvements in pertussis toxin production. This study thus provides novel insights into B. pertussis physiology, and highlights the potential, but also limitations of models solely based on metabolic gene content. IMPORTANCE The metabolic capabilities of Bordetella pertussis - the causative agent of whooping cough - were investigated from a systems-level perspective. We constructed a comprehensive genome-scale metabolic model for B. pertussis , and challenged its predictions

  16. A protocol for generating a high-quality genome-scale metabolic reconstruction.

    Thiele, Ines; Palsson, Bernhard Ø

    2010-01-01

    Network reconstructions are a common denominator in systems biology. Bottom-up metabolic network reconstructions have been developed over the last 10 years. These reconstructions represent structured knowledge bases that abstract pertinent information on the biochemical transformations taking place within specific target organisms. The conversion of a reconstruction into a mathematical format facilitates a myriad of computational biological studies, including evaluation of network content, hypothesis testing and generation, analysis of phenotypic characteristics and metabolic engineering. To date, genome-scale metabolic reconstructions for more than 30 organisms have been published and this number is expected to increase rapidly. However, these reconstructions differ in quality and coverage that may minimize their predictive potential and use as knowledge bases. Here we present a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction, as well as the common trials and tribulations. Therefore, this protocol provides a helpful manual for all stages of the reconstruction process.

  17. A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks.

    Hojung Nam

    2014-09-01

    Full Text Available Altered metabolism in cancer cells has been viewed as a passive response required for a malignant transformation. However, this view has changed through the recently described metabolic oncogenic factors: mutated isocitrate dehydrogenases (IDH, succinate dehydrogenase (SDH, and fumarate hydratase (FH that produce oncometabolites that competitively inhibit epigenetic regulation. In this study, we demonstrate in silico predictions of oncometabolites that have the potential to dysregulate epigenetic controls in nine types of cancer by incorporating massive scale genetic mutation information (collected from more than 1,700 cancer genomes, expression profiling data, and deploying Recon 2 to reconstruct context-specific genome-scale metabolic models. Our analysis predicted 15 compounds and 24 substructures of potential oncometabolites that could result from the loss-of-function and gain-of-function mutations of metabolic enzymes, respectively. These results suggest a substantial potential for discovering unidentified oncometabolites in various forms of cancers.

  18. Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling

    Ghaffari, Pouyan; Mardinoglu, Adil; Asplund, Anna

    2015-01-01

    Human cancer cell lines are used as important model systems to study molecular mechanisms associated with tumor growth, hereunder how genomic and biological heterogeneity found in primary tumors affect cellular phenotypes. We reconstructed Genome scale metabolic models (GEMs) for eleven cell lines...... based on RNA-Seq data and validated the functionality of these models with data from metabolite profiling. We used cell line-specific GEMs to analyze the differences in the metabolism of cancer cell lines, and to explore the heterogeneous expression of the metabolic subsystems. Furthermore, we predicted...... for inhibition of cell growth may provide leads for the development of efficient cancer treatment strategies....

  19. Identifying all moiety conservation laws in genome-scale metabolic networks.

    De Martino, Andrea; De Martino, Daniele; Mulet, Roberto; Pagnani, Andrea

    2014-01-01

    The stoichiometry of a metabolic network gives rise to a set of conservation laws for the aggregate level of specific pools of metabolites, which, on one hand, pose dynamical constraints that cross-link the variations of metabolite concentrations and, on the other, provide key insight into a cell's metabolic production capabilities. When the conserved quantity identifies with a chemical moiety, extracting all such conservation laws from the stoichiometry amounts to finding all non-negative integer solutions of a linear system, a programming problem known to be NP-hard. We present an efficient strategy to compute the complete set of integer conservation laws of a genome-scale stoichiometric matrix, also providing a certificate for correctness and maximality of the solution. Our method is deployed for the analysis of moiety conservation relationships in two large-scale reconstructions of the metabolism of the bacterium E. coli, in six tissue-specific human metabolic networks, and, finally, in the human reactome as a whole, revealing that bacterial metabolism could be evolutionarily designed to cover broader production spectra than human metabolism. Convergence to the full set of moiety conservation laws in each case is achieved in extremely reduced computing times. In addition, we uncover a scaling relation that links the size of the independent pool basis to the number of metabolites, for which we present an analytical explanation.

  20. Identifying all moiety conservation laws in genome-scale metabolic networks.

    Andrea De Martino

    Full Text Available The stoichiometry of a metabolic network gives rise to a set of conservation laws for the aggregate level of specific pools of metabolites, which, on one hand, pose dynamical constraints that cross-link the variations of metabolite concentrations and, on the other, provide key insight into a cell's metabolic production capabilities. When the conserved quantity identifies with a chemical moiety, extracting all such conservation laws from the stoichiometry amounts to finding all non-negative integer solutions of a linear system, a programming problem known to be NP-hard. We present an efficient strategy to compute the complete set of integer conservation laws of a genome-scale stoichiometric matrix, also providing a certificate for correctness and maximality of the solution. Our method is deployed for the analysis of moiety conservation relationships in two large-scale reconstructions of the metabolism of the bacterium E. coli, in six tissue-specific human metabolic networks, and, finally, in the human reactome as a whole, revealing that bacterial metabolism could be evolutionarily designed to cover broader production spectra than human metabolism. Convergence to the full set of moiety conservation laws in each case is achieved in extremely reduced computing times. In addition, we uncover a scaling relation that links the size of the independent pool basis to the number of metabolites, for which we present an analytical explanation.

  1. Genome-scale metabolic models as platforms for strain design and biological discovery.

    Mienda, Bashir Sajo

    2017-07-01

    Genome-scale metabolic models (GEMs) have been developed and used in guiding systems' metabolic engineering strategies for strain design and development. This strategy has been used in fermentative production of bio-based industrial chemicals and fuels from alternative carbon sources. However, computer-aided hypotheses building using established algorithms and software platforms for biological discovery can be integrated into the pipeline for strain design strategy to create superior strains of microorganisms for targeted biosynthetic goals. Here, I described an integrated workflow strategy using GEMs for strain design and biological discovery. Specific case studies of strain design and biological discovery using Escherichia coli genome-scale model are presented and discussed. The integrated workflow presented herein, when applied carefully would help guide future design strategies for high-performance microbial strains that have existing and forthcoming genome-scale metabolic models.

  2. Story of the string theory. From hadrons to Planck scale

    Petropoulos, P.M.

    2010-01-01

    Originally the string theory was devised to describe the scattering between hadron particles but was quickly put aside by the success of the quantum chromodynamics. Now string theory appears in the quantum gravity theory and has been involved in almost all attempts to define a physics beyond the standard model and to unify basic interactions. (A.C.)

  3. Construction and analysis of a genome-scale metabolic network for Bacillus licheniformis WX-02.

    Guo, Jing; Zhang, Hong; Wang, Cheng; Chang, Ji-Wei; Chen, Ling-Ling

    2016-05-01

    We constructed the genome-scale metabolic network of Bacillus licheniformis (B. licheniformis) WX-02 by combining genomic annotation, high-throughput phenotype microarray (PM) experiments and literature-based metabolic information. The accuracy of the metabolic network was assessed by an OmniLog PM experiment. The final metabolic model iWX1009 contains 1009 genes, 1141 metabolites and 1762 reactions, and the predicted metabolic phenotypes showed an agreement rate of 76.8% with experimental PM data. In addition, key metabolic features such as growth yield, utilization of different substrates and essential genes were identified by flux balance analysis. A total of 195 essential genes were predicted from LB medium, among which 149 were verified with the experimental essential gene set of B. subtilis 168. With the removal of 5 reactions from the network, pathways for poly-γ-glutamic acid (γ-PGA) synthesis were optimized and the γ-PGA yield reached 83.8 mmol/h. Furthermore, the important metabolites and pathways related to γ-PGA synthesis and bacterium growth were comprehensively analyzed. The present study provides valuable clues for exploring the metabolisms and metabolic regulation of γ-PGA synthesis in B. licheniformis WX-02. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  4. Allometric Scaling and Cell Ratios in Multi-Organ in vitro Models of Human Metabolism

    Ucciferri, Nadia; Sbrana, Tommaso; Ahluwalia, Arti

    2014-01-01

    Intelligent in vitro models able to recapitulate the physiological interactions between tissues in the body have enormous potential as they enable detailed studies on specific two-way or higher order tissue communication. These models are the first step toward building an integrated picture of systemic metabolism and signaling in physiological or pathological conditions. However, the rational design of in vitro models of cell–cell or cell–tissue interaction is difficult as quite often cell culture experiments are driven by the device used, rather than by design considerations. Indeed, very little research has been carried out on in vitro models of metabolism connecting different cell or tissue types in a physiologically and metabolically relevant manner. Here, we analyze the physiological relationship between cells, cell metabolism, and exchange in the human body using allometric rules, downscaling them to an organ-on-a-plate device. In particular, in order to establish appropriate cell ratios in the system in a rational manner, two different allometric scaling models (cell number scaling model and metabolic and surface scaling model) are proposed and applied to a two compartment model of hepatic-vascular metabolic cross-talk. The theoretical scaling studies illustrate that the design and hence relevance of multi-organ models is principally determined by experimental constraints. Two experimentally feasible model configurations are then implemented in a multi-compartment organ-on-a-plate device. An analysis of the metabolic response of the two configurations demonstrates that their glucose and lipid balance is quite different, with only one of the two models recapitulating physiological-like homeostasis. In conclusion, not only do cross-talk and physical stimuli play an important role in in vitro models, but the numeric relationship between cells is also crucial to recreate in vitro interactions, which can be extrapolated to the in vivo reality.

  5. Allometric scaling and cell ratios in multi-organ in vitro models of human metabolism

    Nadia eUcciferri

    2014-12-01

    Full Text Available Intelligent in vitro models able to recapitulate the physiological interactions between tissues in the body have enormous potential as they enable detailed studies on specific two-way or higher order tissue communication. These models are the first step towards building an integrated picture of systemic metabolism and signalling in physiological or pathological conditions. However the rational design of in vitro models of cell-cell or cell-tissue interaction is difficult as quite often cell culture experiments are driven by the device used, rather than by design considerations. Indeed very little research has been carried out on in vitro models of metabolism connecting different cell or tissue types in a physiologically and metabolically relevant manner. Here we analyse the physiologic relationship between cells, cell metabolism and exchange in the human body using allometric rules, downscaling them to an organ-on-a plate device. In particular, in order to establish appropriate cell ratios in the system in a rational manner, two different allometric scaling models (Cell Number Scaling Model, CNSM, and Metabolic and Surface Scaling model, MSSM are proposed and applied to a two compartment model of hepatic-vascular metabolic cross-talk. The theoretical scaling studies illustrate that the design and hence relevance of multi-organ models is principally determined by experimental constraints. Two experimentally feasible model configurations are then implemented in a multi-compartment organ-on-a plate device. An analysis of the metabolic response of the two configurations demonstrates that their glucose and lipid balance is quite different, with only one of the two models recapitulating physiological-like homeostasis. In conclusion, not only do cross-talk and physical stimuli play an important role in in vitro models, but the numeric relationship between cells is also crucial to recreate in vitro interactions which can be extrapolated to the in vivo

  6. Allometric Scaling and Cell Ratios in Multi-Organ in vitro Models of Human Metabolism.

    Ucciferri, Nadia; Sbrana, Tommaso; Ahluwalia, Arti

    2014-01-01

    Intelligent in vitro models able to recapitulate the physiological interactions between tissues in the body have enormous potential as they enable detailed studies on specific two-way or higher order tissue communication. These models are the first step toward building an integrated picture of systemic metabolism and signaling in physiological or pathological conditions. However, the rational design of in vitro models of cell-cell or cell-tissue interaction is difficult as quite often cell culture experiments are driven by the device used, rather than by design considerations. Indeed, very little research has been carried out on in vitro models of metabolism connecting different cell or tissue types in a physiologically and metabolically relevant manner. Here, we analyze the physiological relationship between cells, cell metabolism, and exchange in the human body using allometric rules, downscaling them to an organ-on-a-plate device. In particular, in order to establish appropriate cell ratios in the system in a rational manner, two different allometric scaling models (cell number scaling model and metabolic and surface scaling model) are proposed and applied to a two compartment model of hepatic-vascular metabolic cross-talk. The theoretical scaling studies illustrate that the design and hence relevance of multi-organ models is principally determined by experimental constraints. Two experimentally feasible model configurations are then implemented in a multi-compartment organ-on-a-plate device. An analysis of the metabolic response of the two configurations demonstrates that their glucose and lipid balance is quite different, with only one of the two models recapitulating physiological-like homeostasis. In conclusion, not only do cross-talk and physical stimuli play an important role in in vitro models, but the numeric relationship between cells is also crucial to recreate in vitro interactions, which can be extrapolated to the in vivo reality.

  7. Allometric Scaling and Cell Ratios in Multi-Organ in vitro Models of Human Metabolism

    Ucciferri, Nadia [CNR Institute of Clinical Physiology, Pisa (Italy); Interdepartmental Research Center “E. Piaggio”, University of Pisa, Pisa (Italy); Sbrana, Tommaso [Interdepartmental Research Center “E. Piaggio”, University of Pisa, Pisa (Italy); Ahluwalia, Arti, E-mail: arti.ahluwalia@unipi.it [CNR Institute of Clinical Physiology, Pisa (Italy); Interdepartmental Research Center “E. Piaggio”, University of Pisa, Pisa (Italy)

    2014-12-17

    Intelligent in vitro models able to recapitulate the physiological interactions between tissues in the body have enormous potential as they enable detailed studies on specific two-way or higher order tissue communication. These models are the first step toward building an integrated picture of systemic metabolism and signaling in physiological or pathological conditions. However, the rational design of in vitro models of cell–cell or cell–tissue interaction is difficult as quite often cell culture experiments are driven by the device used, rather than by design considerations. Indeed, very little research has been carried out on in vitro models of metabolism connecting different cell or tissue types in a physiologically and metabolically relevant manner. Here, we analyze the physiological relationship between cells, cell metabolism, and exchange in the human body using allometric rules, downscaling them to an organ-on-a-plate device. In particular, in order to establish appropriate cell ratios in the system in a rational manner, two different allometric scaling models (cell number scaling model and metabolic and surface scaling model) are proposed and applied to a two compartment model of hepatic-vascular metabolic cross-talk. The theoretical scaling studies illustrate that the design and hence relevance of multi-organ models is principally determined by experimental constraints. Two experimentally feasible model configurations are then implemented in a multi-compartment organ-on-a-plate device. An analysis of the metabolic response of the two configurations demonstrates that their glucose and lipid balance is quite different, with only one of the two models recapitulating physiological-like homeostasis. In conclusion, not only do cross-talk and physical stimuli play an important role in in vitro models, but the numeric relationship between cells is also crucial to recreate in vitro interactions, which can be extrapolated to the in vivo reality.

  8. Metabolic activation and carcinogenicity of polycyclic hydrocarbons: A new quantum mechanical theory

    Mohammad, S.N.

    1986-01-01

    This investigation aims to describe a quantum mechanical theory of cancer, which, on the basis of certain electronic indices calculated for the parent compound, would give prediction of its P-450 mediated metabolic activation and would provide better representation of its relative carcinogenic potency when activated to its PUM. The author's theory is based on the assumption that electronic charge distribution of activated species resembles at least qualitatively the charge distribution of the parent compound, and a careful analysis of electronic characteristics of the parent compound would suffice to give reasonable estimation of the carcinogenic activities of the metabolic products. The details of the theoretical method is given and the results for some alternant and non-alternant PAHs are presented

  9. A model for allometric scaling of mammalian metabolism with ambient heat loss

    Kwak, Ho Sang

    2016-02-02

    Background Allometric scaling, which represents the dependence of biological trait or process relates on body size, is a long-standing subject in biological science. However, there has been no study to consider heat loss to the ambient and an insulation layer representing mammalian skin and fur for the derivation of the scaling law of metabolism. Methods A simple heat transfer model is proposed to analyze the allometry of mammalian metabolism. The present model extends existing studies by incorporating various external heat transfer parameters and additional insulation layers. The model equations were solved numerically and by an analytic heat balance approach. Results A general observation is that the present heat transfer model predicted the 2/3 surface scaling law, which is primarily attributed to the dependence of the surface area on the body mass. External heat transfer effects introduced deviations in the scaling law, mainly due to natural convection heat transfer which becomes more prominent at smaller mass. These deviations resulted in a slight modification of the scaling exponent to a value smaller than 2/3. Conclusion The finding that additional radiative heat loss and the consideration of an outer insulation fur layer attenuate these deviation effects and render the scaling law closer to 2/3 provides in silico evidence for a functional impact of heat transfer mode on the allometric scaling law in mammalian metabolism.

  10. On the Renormalization of the Effective Field Theory of Large Scale Structures

    Pajer, Enrico; Zaldarriaga, Matias

    2013-01-01

    Standard perturbation theory (SPT) for large-scale matter inhomogeneities is unsatisfactory for at least three reasons: there is no clear expansion parameter since the density contrast is not small on all scales; it does not fully account for deviations at large scales from a perfect pressureless fluid induced by short-scale non-linearities; for generic initial conditions, loop corrections are UV-divergent, making predictions cutoff dependent and hence unphysical. The Effective Field Theory o...

  11. Predicting growth of the healthy infant using a genome scale metabolic model.

    Nilsson, Avlant; Mardinoglu, Adil; Nielsen, Jens

    2017-01-01

    An estimated 165 million children globally have stunted growth, and extensive growth data are available. Genome scale metabolic models allow the simulation of molecular flux over each metabolic enzyme, and are well adapted to analyze biological systems. We used a human genome scale metabolic model to simulate the mechanisms of growth and integrate data about breast-milk intake and composition with the infant's biomass and energy expenditure of major organs. The model predicted daily metabolic fluxes from birth to age 6 months, and accurately reproduced standard growth curves and changes in body composition. The model corroborates the finding that essential amino and fatty acids do not limit growth, but that energy is the main growth limiting factor. Disruptions to the supply and demand of energy markedly affected the predicted growth, indicating that elevated energy expenditure may be detrimental. The model was used to simulate the metabolic effect of mineral deficiencies, and showed the greatest growth reduction for deficiencies in copper, iron, and magnesium ions which affect energy production through oxidative phosphorylation. The model and simulation method were integrated to a platform and shared with the research community. The growth model constitutes another step towards the complete representation of human metabolism, and may further help improve the understanding of the mechanisms underlying stunting.

  12. Optimal knockout strategies in genome-scale metabolic networks using particle swarm optimization.

    Nair, Govind; Jungreuthmayer, Christian; Zanghellini, Jürgen

    2017-02-01

    Knockout strategies, particularly the concept of constrained minimal cut sets (cMCSs), are an important part of the arsenal of tools used in manipulating metabolic networks. Given a specific design, cMCSs can be calculated even in genome-scale networks. We would however like to find not only the optimal intervention strategy for a given design but the best possible design too. Our solution (PSOMCS) is to use particle swarm optimization (PSO) along with the direct calculation of cMCSs from the stoichiometric matrix to obtain optimal designs satisfying multiple objectives. To illustrate the working of PSOMCS, we apply it to a toy network. Next we show its superiority by comparing its performance against other comparable methods on a medium sized E. coli core metabolic network. PSOMCS not only finds solutions comparable to previously published results but also it is orders of magnitude faster. Finally, we use PSOMCS to predict knockouts satisfying multiple objectives in a genome-scale metabolic model of E. coli and compare it with OptKnock and RobustKnock. PSOMCS finds competitive knockout strategies and designs compared to other current methods and is in some cases significantly faster. It can be used in identifying knockouts which will force optimal desired behaviors in large and genome scale metabolic networks. It will be even more useful as larger metabolic models of industrially relevant organisms become available.

  13. The corrections to scaling within Mazenko's theory in the limit of low ...

    functions'. In fact both the scaling functions and scaling exponents describe only the leading behaviour in the theory of scaling phenomena. There may be, and usually are, subdominant corrections, known as corrections to scaling. These corrections cannot be neglected in practice if more accurate values for exponents and ...

  14. Do Performance-Safety Tradeoffs Cause Hypometric Metabolic Scaling in Animals?

    Harrison, Jon F

    2017-09-01

    Hypometric scaling of aerobic metabolism in animals has been widely attributed to constraints on oxygen (O 2 ) supply in larger animals, but recent findings demonstrate that O 2 supply balances with need regardless of size. Larger animals also do not exhibit evidence of compensation for O 2 supply limitation. Because declining metabolic rates (MRs) are tightly linked to fitness, this provides significant evidence against the hypothesis that constraints on supply drive hypometric scaling. As an alternative, ATP demand might decline in larger animals because of performance-safety tradeoffs. Larger animals, which typically reproduce later, exhibit risk-reducing strategies that lower MR. Conversely, smaller animals are more strongly selected for growth and costly neurolocomotory performance, elevating metabolism. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Metingear: a development environment for annotating genome-scale metabolic models.

    May, John W; James, A Gordon; Steinbeck, Christoph

    2013-09-01

    Genome-scale metabolic models often lack annotations that would allow them to be used for further analysis. Previous efforts have focused on associating metabolites in the model with a cross reference, but this can be problematic if the reference is not freely available, multiple resources are used or the metabolite is added from a literature review. Associating each metabolite with chemical structure provides unambiguous identification of the components and a more detailed view of the metabolism. We have developed an open-source desktop application that simplifies the process of adding database cross references and chemical structures to genome-scale metabolic models. Annotated models can be exported to the Systems Biology Markup Language open interchange format. Source code, binaries, documentation and tutorials are freely available at http://johnmay.github.com/metingear. The application is implemented in Java with bundles available for MS Windows and Macintosh OS X.

  16. Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm

    Seaver, Samuel M. D.; Bradbury, Louis M. T.; Frelin, Océane; Zarecki, Raphy; Ruppin, Eytan; Hanson, Andrew D.; Henry, Christopher S.

    2015-03-10

    There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and possible generation of unreliable metabolic phenotype predictions. Here we introduce a new evidence-based genome-scale metabolic reconstruction of maize, with significant improvements in the quality of the gene-reaction associations included within our model. We also present a new approach for applying our model to predict active metabolic genes based on transcriptome data. This method includes a minimal set of reactions associated with low expression genes to enable activity of a maximum number of reactions associated with high expression genes. We apply this method to construct an organ-specific model for the maize leaf, and tissue specific models for maize embryo and endosperm cells. We validate our models using fluxomics data for the endosperm and embryo, demonstrating an improved capacity of our models to fit the available fluxomics data. All models are publicly available via the DOE Systems Biology Knowledgebase and PlantSEED, and our new method is generally applicable for analysis transcript profiles from any plant, paving the way for further in silico studies with a wide variety of plant genomes.

  17. Advanced computational workflow for the multi-scale modeling of the bone metabolic processes.

    Dao, Tien Tuan

    2017-06-01

    Multi-scale modeling of the musculoskeletal system plays an essential role in the deep understanding of complex mechanisms underlying the biological phenomena and processes such as bone metabolic processes. Current multi-scale models suffer from the isolation of sub-models at each anatomical scale. The objective of this present work was to develop a new fully integrated computational workflow for simulating bone metabolic processes at multi-scale levels. Organ-level model employs multi-body dynamics to estimate body boundary and loading conditions from body kinematics. Tissue-level model uses finite element method to estimate the tissue deformation and mechanical loading under body loading conditions. Finally, cell-level model includes bone remodeling mechanism through an agent-based simulation under tissue loading. A case study on the bone remodeling process located on the human jaw was performed and presented. The developed multi-scale model of the human jaw was validated using the literature-based data at each anatomical level. Simulation outcomes fall within the literature-based ranges of values for estimated muscle force, tissue loading and cell dynamics during bone remodeling process. This study opens perspectives for accurately simulating bone metabolic processes using a fully integrated computational workflow leading to a better understanding of the musculoskeletal system function from multiple length scales as well as to provide new informative data for clinical decision support and industrial applications.

  18. Basal metabolic rate scaled to body mass within species by the ...

    Basal metabolic rate scaled to body mass within species by the fractal dimension of the vascular system and body composition. ... The postulate bd = c is shown to hold for both these species within the limits of experimental error, with the crucian carp evidence being especially convincing, since b, c and d are estimated from ...

  19. Ontogenetic scaling of fish metabolism in the mouse-to-elephant mass magnitude range

    Moran, Damian; Wells, R.M.G.

    2007-01-01

    , and are therefore not statistically comparable. In this study the metabolic rate of yellowtail kingfish was measured from 0.6 mg-2.2 kg, a mass range comparable to that between a mouse and an elephant. Linear regression of the log transformed data resulted in a scaling exponent of 0.90 and high correlation...

  20. Basal metabolic rate scaled to body mass between species by the ...

    The principal reason that basal metabolic rate (BMR) and MMR scale with different power exponents to whole body mass is that MMR is due mainly to respiration in skeletal muscle during exercise and BMR to respiration in the viscera during rest. It follows, therefore, from the self-similarity of the vascular system that BMR is ...

  1. A New Likert Scale Based on Fuzzy Sets Theory

    Li, Cheryl Qing

    2010-01-01

    In social science research, the Likert method is commonly used as a psychometric scale to measure responses. This measurement scale has a procedure that facilitates survey construction and administration, and data coding and analysis. However, there are some problems with Likert scaling. This dissertation addresses the information distortion and…

  2. Reconstruction and analysis of a genome-scale metabolic model for Scheffersomyces stipitis

    Balagurunathan Balaji

    2012-02-01

    Full Text Available Abstract Background Fermentation of xylose, the major component in hemicellulose, is essential for economic conversion of lignocellulosic biomass to fuels and chemicals. The yeast Scheffersomyces stipitis (formerly known as Pichia stipitis has the highest known native capacity for xylose fermentation and possesses several genes for lignocellulose bioconversion in its genome. Understanding the metabolism of this yeast at a global scale, by reconstructing the genome scale metabolic model, is essential for manipulating its metabolic capabilities and for successful transfer of its capabilities to other industrial microbes. Results We present a genome-scale metabolic model for Scheffersomyces stipitis, a native xylose utilizing yeast. The model was reconstructed based on genome sequence annotation, detailed experimental investigation and known yeast physiology. Macromolecular composition of Scheffersomyces stipitis biomass was estimated experimentally and its ability to grow on different carbon, nitrogen, sulphur and phosphorus sources was determined by phenotype microarrays. The compartmentalized model, developed based on an iterative procedure, accounted for 814 genes, 1371 reactions, and 971 metabolites. In silico computed growth rates were compared with high-throughput phenotyping data and the model could predict the qualitative outcomes in 74% of substrates investigated. Model simulations were used to identify the biosynthetic requirements for anaerobic growth of Scheffersomyces stipitis on glucose and the results were validated with published literature. The bottlenecks in Scheffersomyces stipitis metabolic network for xylose uptake and nucleotide cofactor recycling were identified by in silico flux variability analysis. The scope of the model in enhancing the mechanistic understanding of microbial metabolism is demonstrated by identifying a mechanism for mitochondrial respiration and oxidative phosphorylation. Conclusion The genome-scale

  3. MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory.

    Marchetti, Luca; Manca, Vincenzo

    2015-04-15

    MpTheory Java library is an open-source project collecting a set of objects and algorithms for modeling observed dynamics by means of the Metabolic P (MP) theory, that is, a mathematical theory introduced in 2004 for modeling biological dynamics. By means of the library, it is possible to model biological systems both at continuous and at discrete time. Moreover, the library comprises a set of regression algorithms for inferring MP models starting from time series of observations. To enhance the modeling experience, beside a pure Java usage, the library can be directly used within the most popular computing environments, such as MATLAB, GNU Octave, Mathematica and R. The library is open-source and licensed under the GNU Lesser General Public License (LGPL) Version 3.0. Source code, binaries and complete documentation are available at http://mptheory.scienze.univr.it. luca.marchetti@univr.it, marchetti@cosbi.eu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  4. Deconfinement phase transition and finite-size scaling in SU(2) lattice gauge theory

    Mogilevskij, O.A.

    1988-01-01

    Calculation technique for deconfinement phase transition parameters based on application of finite-size scaling theory is suggested. The essence of the technique lies in plotting of universal scaling function on the basis of numerical data obtained at different-size final lattices and discrimination of phase transition parameters for infinite lattice system. Finite-size scaling technique was developed as applied to spin system theory. β critical index for Polyakov loop and SU(2) deconfinement temperature of lattice gauge theory are calculated on the basis of finite-size scaling technique. The obtained value agrees with critical index of magnetization in Ising three-dimensional model

  5. Genome-scale reconstruction of metabolic networks of Lactobacillus casei ATCC 334 and 12A.

    Elena Vinay-Lara

    Full Text Available Lactobacillus casei strains are widely used in industry and the utility of this organism in these industrial applications is strain dependent. Hence, tools capable of predicting strain specific phenotypes would have utility in the selection of strains for specific industrial processes. Genome-scale metabolic models can be utilized to better understand genotype-phenotype relationships and to compare different organisms. To assist in the selection and development of strains with enhanced industrial utility, genome-scale models for L. casei ATCC 334, a well characterized strain, and strain 12A, a corn silage isolate, were constructed. Draft models were generated from RAST genome annotations using the Model SEED database and refined by evaluating ATP generating cycles, mass-and-charge-balances of reactions, and growth phenotypes. After the validation process was finished, we compared the metabolic networks of these two strains to identify metabolic, genetic and ortholog differences that may lead to different phenotypic behaviors. We conclude that the metabolic capabilities of the two networks are highly similar. The L. casei ATCC 334 model accounts for 1,040 reactions, 959 metabolites and 548 genes, while the L. casei 12A model accounts for 1,076 reactions, 979 metabolites and 640 genes. The developed L. casei ATCC 334 and 12A metabolic models will enable better understanding of the physiology of these organisms and be valuable tools in the development and selection of strains with enhanced utility in a variety of industrial applications.

  6. Genome-scale metabolic modeling of Mucor circinelloides and comparative analysis with other oleaginous species.

    Vongsangnak, Wanwipa; Klanchui, Amornpan; Tawornsamretkit, Iyarest; Tatiyaborwornchai, Witthawin; Laoteng, Kobkul; Meechai, Asawin

    2016-06-01

    We present a novel genome-scale metabolic model iWV1213 of Mucor circinelloides, which is an oleaginous fungus for industrial applications. The model contains 1213 genes, 1413 metabolites and 1326 metabolic reactions across different compartments. We demonstrate that iWV1213 is able to accurately predict the growth rates of M. circinelloides on various nutrient sources and culture conditions using Flux Balance Analysis and Phenotypic Phase Plane analysis. Comparative analysis of three oleaginous genome-scale models, including M. circinelloides (iWV1213), Mortierella alpina (iCY1106) and Yarrowia lipolytica (iYL619_PCP) revealed that iWV1213 possesses a higher number of genes involved in carbohydrate, amino acid, and lipid metabolisms that might contribute to its versatility in nutrient utilization. Moreover, the identification of unique and common active reactions among the Zygomycetes oleaginous models using Flux Variability Analysis unveiled a set of gene/enzyme candidates as metabolic engineering targets for cellular improvement. Thus, iWV1213 offers a powerful metabolic engineering tool for multi-level omics analysis, enabling strain optimization as a cell factory platform of lipid-based production. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Low-energy limit of two-scale field theories

    Leon, J.; Perez-Mercader, J.; Sanchez, M.F.

    1991-01-01

    We present a full and self-contained discussion of the decoupling theorem applied to several general models in four-dimensional field theory. We compute in each case the low-energy effective action and show the explicit one-loop expressions for each of the effective parameters. We find that for suitable conditions one can always build an effective low-energy theory where the conditions of the decoupling theorem are satisfied

  8. Integration of expression data in genome-scale metabolic network reconstructions

    Anna S. Blazier

    2012-08-01

    Full Text Available With the advent of high-throughput technologies, the field of systems biology has amassed an abundance of omics data, quantifying thousands of cellular components across a variety of scales, ranging from mRNA transcript levels to metabolite quantities. Methods are needed to not only integrate this omics data but to also use this data to heighten the predictive capabilities of computational models. Several recent studies have successfully demonstrated how flux balance analysis (FBA, a constraint-based modeling approach, can be used to integrate transcriptomic data into genome-scale metabolic network reconstructions to generate predictive computational models. In this review, we summarize such FBA-based methods for integrating expression data into genome-scale metabolic network reconstructions, highlighting their advantages as well as their limitations.

  9. Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing

    María P. Cortés

    2017-12-01

    Full Text Available Piscirickettsia salmonis is an intracellular bacterial fish pathogen that causes piscirickettsiosis, a disease with highly adverse impact in the Chilean salmon farming industry. The development of effective treatment and control methods for piscireckttsiosis is still a challenge. To meet it the number of studies on P. salmonis has grown in the last couple of years but many aspects of the pathogen’s biology are still poorly understood. Studies on its metabolism are scarce and only recently a metabolic model for reference strain LF-89 was developed. We present a new genome-scale model for P. salmonis LF-89 with more than twice as many genes as in the previous model and incorporating specific elements of the fish pathogen metabolism. Comparative analysis with models of different bacterial pathogens revealed a lower flexibility in P. salmonis metabolic network. Through constraint-based analysis, we determined essential metabolites required for its growth and showed that it can benefit from different carbon sources tested experimentally in new defined media. We also built an additional model for strain A1-15972, and together with an analysis of P. salmonis pangenome, we identified metabolic features that differentiate two main species clades. Both models constitute a knowledge-base for P. salmonis metabolism and can be used to guide the efficient culture of the pathogen and the identification of specific drug targets.

  10. Computational solution to automatically map metabolite libraries in the context of genome scale metabolic networks

    Benjamin eMerlet

    2016-02-01

    Full Text Available This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc and flat file formats (SBML and Matlab files. We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics and Glasgow Polyomics on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks.In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks.In order to achieve this goal we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities.

  11. Novel insights into obesity and diabetes through genome-scale metabolic modeling

    Leif eVäremo

    2013-04-01

    Full Text Available The growing prevalence of metabolic diseases, such as obesity and diabetes, are putting a high strain on global healthcare systems as well as increasing the demand for efficient treatment strategies. More than 360 million people worldwide are suffering from type 2 diabetes and, with the current trends, the projection is that 10% of the global adult population will be affected by 2030. In light of the systemic properties of metabolic diseases as well as the interconnected nature of metabolism, it is necessary to begin taking a holistic approach to study these diseases. Human genome-scale metabolic models (GEMs are topological and mathematical representations of cell metabolism and have proven to be valuable tools in the area of systems biology. Successful applications of GEMs include the process of gaining further biological and mechanistic understanding of diseases, finding potential biomarkers and identifying new drug targets. This review will focus on the modeling of human metabolism in the field of obesity and diabetes, showing its vast range of applications of clinical importance as well as point out future challenges.

  12. Deriving metabolic engineering strategies from genome-scale modeling with flux ratio constraints.

    Yen, Jiun Y; Nazem-Bokaee, Hadi; Freedman, Benjamin G; Athamneh, Ahmad I M; Senger, Ryan S

    2013-05-01

    Optimized production of bio-based fuels and chemicals from microbial cell factories is a central goal of systems metabolic engineering. To achieve this goal, a new computational method of using flux balance analysis with flux ratios (FBrAtio) was further developed in this research and applied to five case studies to evaluate and design metabolic engineering strategies. The approach was implemented using publicly available genome-scale metabolic flux models. Synthetic pathways were added to these models along with flux ratio constraints by FBrAtio to achieve increased (i) cellulose production from Arabidopsis thaliana; (ii) isobutanol production from Saccharomyces cerevisiae; (iii) acetone production from Synechocystis sp. PCC6803; (iv) H2 production from Escherichia coli MG1655; and (v) isopropanol, butanol, and ethanol (IBE) production from engineered Clostridium acetobutylicum. The FBrAtio approach was applied to each case to simulate a metabolic engineering strategy already implemented experimentally, and flux ratios were continually adjusted to find (i) the end-limit of increased production using the existing strategy, (ii) new potential strategies to increase production, and (iii) the impact of these metabolic engineering strategies on product yield and culture growth. The FBrAtio approach has the potential to design "fine-tuned" metabolic engineering strategies in silico that can be implemented directly with available genomic tools. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks.

    Merlet, Benjamin; Paulhe, Nils; Vinson, Florence; Frainay, Clément; Chazalviel, Maxime; Poupin, Nathalie; Gloaguen, Yoann; Giacomoni, Franck; Jourdan, Fabien

    2016-01-01

    This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc) and flat file formats (SBML and Matlab files). We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics) and Glasgow Polyomics (GP) on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks. In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks. In order to achieve this goal, we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities.

  14. ReacKnock: identifying reaction deletion strategies for microbial strain optimization based on genome-scale metabolic network.

    Zixiang Xu

    Full Text Available Gene knockout has been used as a common strategy to improve microbial strains for producing chemicals. Several algorithms are available to predict the target reactions to be deleted. Most of them apply mixed integer bi-level linear programming (MIBLP based on metabolic networks, and use duality theory to transform bi-level optimization problem of large-scale MIBLP to single-level programming. However, the validity of the transformation was not proved. Solution of MIBLP depends on the structure of inner problem. If the inner problem is continuous, Karush-Kuhn-Tucker (KKT method can be used to reformulate the MIBLP to a single-level one. We adopt KKT technique in our algorithm ReacKnock to attack the intractable problem of the solution of MIBLP, demonstrated with the genome-scale metabolic network model of E. coli for producing various chemicals such as succinate, ethanol, threonine and etc. Compared to the previous methods, our algorithm is fast, stable and reliable to find the optimal solutions for all the chemical products tested, and able to provide all the alternative deletion strategies which lead to the same industrial objective.

  15. The necessity of a theory of biology for tissue engineering: metabolism-repair systems.

    Ganguli, Suman; Hunt, C Anthony

    2004-01-01

    Since there is no widely accepted global theory of biology, tissue engineering and bioengineering lack a theoretical understanding of the systems being engineered. By default, tissue engineering operates with a "reductionist" theoretical approach, inherited from traditional engineering of non-living materials. Long term, that approach is inadequate, since it ignores essential aspects of biology. Metabolism-repair systems are a theoretical framework which explicitly represents two "functional" aspects of living organisms: self-repair and self-replication. Since repair and replication are central to tissue engineering, we advance metabolism-repair systems as a potential theoretical framework for tissue engineering. We present an overview of the framework, and indicate directions to pursue for extending it to the context of tissue engineering. We focus on biological networks, both metabolic and cellular, as one such direction. The construction of these networks, in turn, depends on biological protocols. Together these concepts may help point the way to a global theory of biology appropriate for tissue engineering.

  16. A general model for metabolic scaling in self-similar asymmetric networks.

    Alexander Byers Brummer

    2017-03-01

    Full Text Available How a particular attribute of an organism changes or scales with its body size is known as an allometry. Biological allometries, such as metabolic scaling, have been hypothesized to result from selection to maximize how vascular networks fill space yet minimize internal transport distances and resistances. The West, Brown, Enquist (WBE model argues that these two principles (space-filling and energy minimization are (i general principles underlying the evolution of the diversity of biological networks across plants and animals and (ii can be used to predict how the resulting geometry of biological networks then governs their allometric scaling. Perhaps the most central biological allometry is how metabolic rate scales with body size. A core assumption of the WBE model is that networks are symmetric with respect to their geometric properties. That is, any two given branches within the same generation in the network are assumed to have identical lengths and radii. However, biological networks are rarely if ever symmetric. An open question is: Does incorporating asymmetric branching change or influence the predictions of the WBE model? We derive a general network model that relaxes the symmetric assumption and define two classes of asymmetrically bifurcating networks. We show that asymmetric branching can be incorporated into the WBE model. This asymmetric version of the WBE model results in several theoretical predictions for the structure, physiology, and metabolism of organisms, specifically in the case for the cardiovascular system. We show how network asymmetry can now be incorporated in the many allometric scaling relationships via total network volume. Most importantly, we show that the 3/4 metabolic scaling exponent from Kleiber's Law can still be attained within many asymmetric networks.

  17. Toward the automated generation of genome-scale metabolic networks in the SEED.

    DeJongh, Matthew; Formsma, Kevin; Boillot, Paul; Gould, John; Rycenga, Matthew; Best, Aaron

    2007-04-26

    Current methods for the automated generation of genome-scale metabolic networks focus on genome annotation and preliminary biochemical reaction network assembly, but do not adequately address the process of identifying and filling gaps in the reaction network, and verifying that the network is suitable for systems level analysis. Thus, current methods are only sufficient for generating draft-quality networks, and refinement of the reaction network is still largely a manual, labor-intensive process. We have developed a method for generating genome-scale metabolic networks that produces substantially complete reaction networks, suitable for systems level analysis. Our method partitions the reaction space of central and intermediary metabolism into discrete, interconnected components that can be assembled and verified in isolation from each other, and then integrated and verified at the level of their interconnectivity. We have developed a database of components that are common across organisms, and have created tools for automatically assembling appropriate components for a particular organism based on the metabolic pathways encoded in the organism's genome. This focuses manual efforts on that portion of an organism's metabolism that is not yet represented in the database. We have demonstrated the efficacy of our method by reverse-engineering and automatically regenerating the reaction network from a published genome-scale metabolic model for Staphylococcus aureus. Additionally, we have verified that our method capitalizes on the database of common reaction network components created for S. aureus, by using these components to generate substantially complete reconstructions of the reaction networks from three other published metabolic models (Escherichia coli, Helicobacter pylori, and Lactococcus lactis). We have implemented our tools and database within the SEED, an open-source software environment for comparative genome annotation and analysis. Our method sets the

  18. Toward the automated generation of genome-scale metabolic networks in the SEED

    Gould John

    2007-04-01

    Full Text Available Abstract Background Current methods for the automated generation of genome-scale metabolic networks focus on genome annotation and preliminary biochemical reaction network assembly, but do not adequately address the process of identifying and filling gaps in the reaction network, and verifying that the network is suitable for systems level analysis. Thus, current methods are only sufficient for generating draft-quality networks, and refinement of the reaction network is still largely a manual, labor-intensive process. Results We have developed a method for generating genome-scale metabolic networks that produces substantially complete reaction networks, suitable for systems level analysis. Our method partitions the reaction space of central and intermediary metabolism into discrete, interconnected components that can be assembled and verified in isolation from each other, and then integrated and verified at the level of their interconnectivity. We have developed a database of components that are common across organisms, and have created tools for automatically assembling appropriate components for a particular organism based on the metabolic pathways encoded in the organism's genome. This focuses manual efforts on that portion of an organism's metabolism that is not yet represented in the database. We have demonstrated the efficacy of our method by reverse-engineering and automatically regenerating the reaction network from a published genome-scale metabolic model for Staphylococcus aureus. Additionally, we have verified that our method capitalizes on the database of common reaction network components created for S. aureus, by using these components to generate substantially complete reconstructions of the reaction networks from three other published metabolic models (Escherichia coli, Helicobacter pylori, and Lactococcus lactis. We have implemented our tools and database within the SEED, an open-source software environment for comparative

  19. [Modeling continuous scaling of NDVI based on fractal theory].

    Luan, Hai-Jun; Tian, Qing-Jiu; Yu, Tao; Hu, Xin-Li; Huang, Yan; Du, Ling-Tong; Zhao, Li-Min; Wei, Xi; Han, Jie; Zhang, Zhou-Wei; Li, Shao-Peng

    2013-07-01

    Scale effect was one of the very important scientific problems of remote sensing. The scale effect of quantitative remote sensing can be used to study retrievals' relationship between different-resolution images, and its research became an effective way to confront the challenges, such as validation of quantitative remote sensing products et al. Traditional up-scaling methods cannot describe scale changing features of retrievals on entire series of scales; meanwhile, they are faced with serious parameters correction issues because of imaging parameters' variation of different sensors, such as geometrical correction, spectral correction, etc. Utilizing single sensor image, fractal methodology was utilized to solve these problems. Taking NDVI (computed by land surface radiance) as example and based on Enhanced Thematic Mapper Plus (ETM+) image, a scheme was proposed to model continuous scaling of retrievals. Then the experimental results indicated that: (a) For NDVI, scale effect existed, and it could be described by fractal model of continuous scaling; (2) The fractal method was suitable for validation of NDVI. All of these proved that fractal was an effective methodology of studying scaling of quantitative remote sensing.

  20. Factors associated with metabolic syndrome and related medical costs by the scale of enterprise in Korea.

    Kong, Hyung-Sik; Lee, Kang-Sook; Yim, Eun-Shil; Lee, Seon-Young; Cho, Hyun-Young; Lee, Bin Na; Park, Jee Young

    2013-10-21

    The purpose of this study was to identify the risk factors of metabolic syndrome (MS) and to analyze the relationship between the risk factors of MS and medical cost of major diseases related to MS in Korean workers, according to the scale of the enterprise. Data was obtained from annual physical examinations, health insurance qualification and premiums, and health insurance benefits of 4,094,217 male and female workers who underwent medical examinations provided by the National Health Insurance Corporation in 2009. Logistic regression analyses were used to the identify risk factors of MS and multiple regression was used to find factors associated with medical expenditures due to major diseases related to MS. The study found that low-income workers were more likely to work in small-scale enterprises. The prevalence rate of MS in males and females, respectively, was 17.2% and 9.4% in small-scale enterprises, 15.9% and 8.9% in medium-scale enterprises, and 15.9% and 5.5% in large-scale enterprises. The risks of MS increased with age, lower income status, and smoking in small-scale enterprise workers. The medical costs increased in workers with old age and past smoking history. There was also a gender difference in the pattern of medical expenditures related to MS. Health promotion programs to manage metabolic syndrome should be developed to focus on workers who smoke, drink, and do little exercise in small scale enterprises.

  1. Association of metabolic syndrome and change in Unified Parkinson's Disease Rating Scale scores.

    Leehey, Maureen; Luo, Sheng; Sharma, Saloni; Wills, Anne-Marie A; Bainbridge, Jacquelyn L; Wong, Pei Shieen; Simon, David K; Schneider, Jay; Zhang, Yunxi; Pérez, Adriana; Dhall, Rohit; Christine, Chadwick W; Singer, Carlos; Cambi, Franca; Boyd, James T

    2017-10-24

    To explore the association between metabolic syndrome and the Unified Parkinson's Disease Rating Scale (UPDRS) scores and, secondarily, the Symbol Digit Modalities Test (SDMT). This is a secondary analysis of data from 1,022 of 1,741 participants of the National Institute of Neurological Disorders and Stroke Exploratory Clinical Trials in Parkinson Disease Long-Term Study 1, a randomized, placebo-controlled trial of creatine. Participants were categorized as having or not having metabolic syndrome on the basis of modified criteria from the National Cholesterol Education Program Adult Treatment Panel III. Those who had the same metabolic syndrome status at consecutive annual visits were included. The change in UPDRS and SDMT scores from randomization to 3 years was compared in participants with and without metabolic syndrome. Participants with metabolic syndrome (n = 396) compared to those without (n = 626) were older (mean [SD] 63.9 [8.1] vs 59.9 [9.4] years; p metabolic syndrome experienced an additional 0.6- (0.2) unit annual increase in total UPDRS ( p = 0.02) and 0.5- (0.2) unit increase in motor UPDRS ( p = 0.01) scores compared with participants without metabolic syndrome. There was no difference in the change in SDMT scores. Persons with Parkinson disease meeting modified criteria for metabolic syndrome experienced a greater increase in total UPDRS scores over time, mainly as a result of increases in motor scores, compared to those who did not. Further studies are needed to confirm this finding. NCT00449865. © 2017 American Academy of Neurology.

  2. Scaling of Advanced Theory-of-Mind Tasks

    Osterhaus, Christopher; Koerber, Susanne; Sodian, Beate

    2016-01-01

    Advanced theory-of-mind (AToM) development was investigated in three separate studies involving 82, 466, and 402 elementary school children (8-, 9-, and 10-year-olds). Rasch and factor analyses assessed whether common conceptual development underlies higher-order false-belief understanding, social understanding, emotion recognition, and…

  3. Symmetry-guided large-scale shell-model theory

    Launey, K. D.; Dytrych, Tomáš; Draayer, J. P.

    2016-01-01

    Roč. 89, JUL (2016), s. 101-136 ISSN 0146-6410 R&D Projects: GA ČR GA16-16772S Institutional support: RVO:61389005 Keywords : Ab intio shell -model theory * Symplectic symmetry * Collectivity * Clusters * Hoyle state * Orderly patterns in nuclei from first principles Subject RIV: BE - Theoretical Physics Impact factor: 11.229, year: 2016

  4. Characterizing steady states of genome-scale metabolic networks in continuous cell cultures.

    Jorge Fernandez-de-Cossio-Diaz

    2017-11-01

    Full Text Available In the continuous mode of cell culture, a constant flow carrying fresh media replaces culture fluid, cells, nutrients and secreted metabolites. Here we present a model for continuous cell culture coupling intra-cellular metabolism to extracellular variables describing the state of the bioreactor, taking into account the growth capacity of the cell and the impact of toxic byproduct accumulation. We provide a method to determine the steady states of this system that is tractable for metabolic networks of arbitrary complexity. We demonstrate our approach in a toy model first, and then in a genome-scale metabolic network of the Chinese hamster ovary cell line, obtaining results that are in qualitative agreement with experimental observations. We derive a number of consequences from the model that are independent of parameter values. The ratio between cell density and dilution rate is an ideal control parameter to fix a steady state with desired metabolic properties. This conclusion is robust even in the presence of multi-stability, which is explained in our model by a negative feedback loop due to toxic byproduct accumulation. A complex landscape of steady states emerges from our simulations, including multiple metabolic switches, which also explain why cell-line and media benchmarks carried out in batch culture cannot be extrapolated to perfusion. On the other hand, we predict invariance laws between continuous cell cultures with different parameters. A practical consequence is that the chemostat is an ideal experimental model for large-scale high-density perfusion cultures, where the complex landscape of metabolic transitions is faithfully reproduced.

  5. An item response theory analysis of the Olweus Bullying scale.

    Breivik, Kyrre; Olweus, Dan

    2014-12-02

    In the present article, we used IRT (graded response) modeling as a useful technology for a detailed and refined study of the psychometric properties of the various items of the Olweus Bullying scale and the scale itself. The sample consisted of a very large number of Norwegian 4th-10th grade students (n = 48 926). The IRT analyses revealed that the scale was essentially unidimensional and had excellent reliability in the upper ranges of the latent bullying tendency trait, as intended and desired. Gender DIF effects were identified with regard to girls' use of indirect bullying by social exclusion and boys' use of physical bullying by hitting and kicking but these effects were small and worked in opposite directions, having negligible effects at the scale level. Also scale scores adjusted for DIF effects differed very little from non-adjusted scores. In conclusion, the empirical data were well characterized by the chosen IRT model and the Olweus Bullying scale was considered well suited for the conduct of fair and reliable comparisons involving different gender-age groups. Information Aggr. Behav. 9999:XX-XX, 2014. © 2014 Wiley Periodicals, Inc. © 2014 Wiley Periodicals, Inc.

  6. Network Thermodynamic Curation of Human and Yeast Genome-Scale Metabolic Models

    Martínez, Verónica S.; Quek, Lake-Ee; Nielsen, Lars K.

    2014-01-01

    Genome-scale models are used for an ever-widening range of applications. Although there has been much focus on specifying the stoichiometric matrix, the predictive power of genome-scale models equally depends on reaction directions. Two-thirds of reactions in the two eukaryotic reconstructions Homo sapiens Recon 1 and Yeast 5 are specified as irreversible. However, these specifications are mainly based on biochemical textbooks or on their similarity to other organisms and are rarely underpinned by detailed thermodynamic analysis. In this study, a to our knowledge new workflow combining network-embedded thermodynamic and flux variability analysis was used to evaluate existing irreversibility constraints in Recon 1 and Yeast 5 and to identify new ones. A total of 27 and 16 new irreversible reactions were identified in Recon 1 and Yeast 5, respectively, whereas only four reactions were found with directions incorrectly specified against thermodynamics (three in Yeast 5 and one in Recon 1). The workflow further identified for both models several isolated internal loops that require further curation. The framework also highlighted the need for substrate channeling (in human) and ATP hydrolysis (in yeast) for the essential reaction catalyzed by phosphoribosylaminoimidazole carboxylase in purine metabolism. Finally, the framework highlighted differences in proline metabolism between yeast (cytosolic anabolism and mitochondrial catabolism) and humans (exclusively mitochondrial metabolism). We conclude that network-embedded thermodynamics facilitates the specification and validation of irreversibility constraints in compartmentalized metabolic models, at the same time providing further insight into network properties. PMID:25028891

  7. Investigating host-pathogen behavior and their interaction using genome-scale metabolic network models.

    Sadhukhan, Priyanka P; Raghunathan, Anu

    2014-01-01

    Genome Scale Metabolic Modeling methods represent one way to compute whole cell function starting from the genome sequence of an organism and contribute towards understanding and predicting the genotype-phenotype relationship. About 80 models spanning all the kingdoms of life from archaea to eukaryotes have been built till date and used to interrogate cell phenotype under varying conditions. These models have been used to not only understand the flux distribution in evolutionary conserved pathways like glycolysis and the Krebs cycle but also in applications ranging from value added product formation in Escherichia coli to predicting inborn errors of Homo sapiens metabolism. This chapter describes a protocol that delineates the process of genome scale metabolic modeling for analysing host-pathogen behavior and interaction using flux balance analysis (FBA). The steps discussed in the process include (1) reconstruction of a metabolic network from the genome sequence, (2) its representation in a precise mathematical framework, (3) its translation to a model, and (4) the analysis using linear algebra and optimization. The methods for biological interpretations of computed cell phenotypes in the context of individual host and pathogen models and their integration are also discussed.

  8. Net Community Metabolism and Seawater Carbonate Chemistry Scale Non-intuitively with Coral Cover

    Heather N. Page

    2017-05-01

    Full Text Available Coral cover and reef health have been declining globally as reefs face local and global stressors including higher temperature and ocean acidification (OA. Ocean warming and acidification will alter rates of benthic reef metabolism (i.e., primary production, respiration, calcification, and CaCO3 dissolution, but our understanding of community and ecosystem level responses is limited in terms of functional, spatial, and temporal scales. Furthermore, dramatic changes in coral cover and benthic metabolism could alter seawater carbonate chemistry on coral reefs, locally alleviating or exacerbating OA. This study examines how benthic metabolic rates scale with changing coral cover (0–100%, and the subsequent influence of these coral communities on seawater carbonate chemistry based on mesocosm experiments in Bermuda and Hawaii. In Bermuda, no significant differences in benthic metabolism or seawater carbonate chemistry were observed for low (40% and high (80% coral cover due to large variability within treatments. In contrast, significant differences were detected between treatments in Hawaii with benthic metabolic rates increasing with increasing coral cover. Observed increases in daily net community calcification and nighttime net respiration scaled proportionally with coral cover. This was not true for daytime net community organic carbon production rates, which increased the most between 0 and 20% coral cover and then less so between 20 and 100%. Consequently, diel variability in seawater carbonate chemistry increased with increasing coral cover, but absolute values of pH, Ωa, and pCO2 were not significantly different during daytime. To place the results of the mesocosm experiments into a broader context, in situ seawater carbon dioxide (CO2 at three reef sites in Bermuda and Hawaii were also evaluated; reefs with higher coral cover experienced a greater range of diel CO2 levels, complementing the mesocosm results. The results from this study

  9. Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism

    2016-03-15

    RESEARCH ARTICLE Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism Francisco G...jaques.reifman.civ@mail.mil Abstract A hallmark of Pseudomonas aeruginosa is its ability to establish biofilm -based infections that are difficult to...eradicate. Biofilms are less susceptible to host inflammatory and immune responses and have higher antibiotic tolerance than free-living planktonic

  10. Scale-invariant entropy-based theory for dynamic ordering

    Mahulikar, Shripad P.; Kumari, Priti

    2014-01-01

    Dynamically Ordered self-organized dissipative structure exists in various forms and at different scales. This investigation first introduces the concept of an isolated embedding system, which embeds an open system, e.g., dissipative structure and its mass and/or energy exchange with its surroundings. Thereafter, scale-invariant theoretical analysis is presented using thermodynamic principles for Order creation, existence, and destruction. The sustainability criterion for Order existence based on its structured mass and/or energy interactions with the surroundings is mathematically defined. This criterion forms the basis for the interrelationship of physical parameters during sustained existence of dynamic Order. It is shown that the sufficient condition for dynamic Order existence is approached if its sustainability criterion is met, i.e., its destruction path is blocked. This scale-invariant approach has the potential to unify the physical understanding of universal dynamic ordering based on entropy considerations

  11. Self-similarity and scaling theory of complex networks

    Song, Chaoming

    Scale-free networks have been studied extensively due to their relevance to many real systems as diverse as the World Wide Web (WWW), the Internet, biological and social networks. We present a novel approach to the analysis of scale-free networks, revealing that their structure is self-similar. This result is achieved by the application of a renormalization procedure which coarse-grains the system into boxes containing nodes within a given "size". Concurrently, we identify a power-law relation between the number of boxes needed to cover the network and the size of the box defining a self-similar exponent, which classifies fractal and non-fractal networks. By using the concept of renormalization as a mechanism for the growth of fractal and non-fractal modular networks, we show that the key principle that gives rise to the fractal architecture of networks is a strong effective "repulsion" between the most connected nodes (hubs) on all length scales, rendering them very dispersed. We show that a robust network comprised of functional modules, such as a cellular network, necessitates a fractal topology, suggestive of a evolutionary drive for their existence. These fundamental properties help to understand the emergence of the scale-free property in complex networks.

  12. Scale-covariant theory of gravitation and astrophysical applications

    Canuto, V.; Hsieh, S.H.; Adams, P.J.

    1977-01-01

    We present generalized Einstein equations, invariant under scale transformations, and study several astrophysical tests. It is assumed that the dynamics of atoms or clocks used as measuring apparatus is given a priori. Connection with gauge fields and broken symmetries is made through the cosmological constant

  13. Metabolism

    ... Are More Common in People With Type 1 Diabetes Metabolic Syndrome Your Child's Weight Healthy Eating Endocrine System Blood Test: Basic Metabolic Panel (BMP) Activity: Endocrine System Growth Disorders Diabetes Center Thyroid Disorders Your Endocrine System Movie: Endocrine ...

  14. Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production

    Brooks J Paul

    2010-03-01

    Full Text Available Abstract Background Microorganisms possess diverse metabolic capabilities that can potentially be leveraged for efficient production of biofuels. Clostridium thermocellum (ATCC 27405 is a thermophilic anaerobe that is both cellulolytic and ethanologenic, meaning that it can directly use the plant sugar, cellulose, and biochemically convert it to ethanol. A major challenge in using microorganisms for chemical production is the need to modify the organism to increase production efficiency. The process of properly engineering an organism is typically arduous. Results Here we present a genome-scale model of C. thermocellum metabolism, iSR432, for the purpose of establishing a computational tool to study the metabolic network of C. thermocellum and facilitate efforts to engineer C. thermocellum for biofuel production. The model consists of 577 reactions involving 525 intracellular metabolites, 432 genes, and a proteomic-based representation of a cellulosome. The process of constructing this metabolic model led to suggested annotation refinements for 27 genes and identification of areas of metabolism requiring further study. The accuracy of the iSR432 model was tested using experimental growth and by-product secretion data for growth on cellobiose and fructose. Analysis using this model captures the relationship between the reduction-oxidation state of the cell and ethanol secretion and allowed for prediction of gene deletions and environmental conditions that would increase ethanol production. Conclusions By incorporating genomic sequence data, network topology, and experimental measurements of enzyme activities and metabolite fluxes, we have generated a model that is reasonably accurate at predicting the cellular phenotype of C. thermocellum and establish a strong foundation for rational strain design. In addition, we are able to draw some important conclusions regarding the underlying metabolic mechanisms for observed behaviors of C. thermocellum

  15. Scaling theory put into practice: First-principles modeling of transport in doped silicon nanowires

    Markussen, Troels; Rurali, R.; Jauho, Antti-Pekka

    2007-01-01

    We combine the ideas of scaling theory and universal conductance fluctuations with density-functional theory to analyze the conductance properties of doped silicon nanowires. Specifically, we study the crossover from ballistic to diffusive transport in boron or phosphorus doped Si nanowires...

  16. Sequential Progressions in a Theory-of-Mind Scale: Longitudinal Perspectives

    Wellman, Henry M.; Fang, Fuxi; Peterson, Candida C.

    2011-01-01

    Consecutive retestings of 92 U.S. preschoolers (n = 30), Chinese preschoolers (n = 31), and deaf children (n = 31) examined whether the sequences of development apparent in cross-sectional results with a theory-of-mind scale also appeared in longitudinal assessment. Longitudinal data confirmed that theory-of-mind progressions apparent in…

  17. Necessity of intermediate mass scales in grand unified theories with spontaneously broken CP invariance

    Senjanovic, G.

    1982-07-01

    It is demonstrated that the spontaneous breakdown of CP invariance in grand unified theories requires the presence of intermediate mass scales. The simplest realization is provided by weakly broken left-right symmetry in the context of SU(2)sub(L) x SU(2)sub(R) x U(1)sub(B-L) model embedded in grand unified theories. (author)

  18. Quasi-potential and Two-Scale Large Deviation Theory for Gillespie Dynamics

    Li, Tiejun; Li, Fangting; Li, Xianggang; Lu, Cheng

    2016-01-01

    theory for Gillespie-type jump dynamics. In the application to a typical genetic switching model, the two-scale large deviation theory is developed to take into account the fast switching of DNA states. The comparison with other proposals are also

  19. On the non-linear scale of cosmological perturbation theory

    Blas, Diego; Konstandin, Thomas

    2013-01-01

    We discuss the convergence of cosmological perturbation theory. We prove that the polynomial enhancement of the non-linear corrections expected from the effects of soft modes is absent in equal-time correlators like the power or bispectrum. We first show this at leading order by resumming the most important corrections of soft modes to an arbitrary skeleton of hard fluctuations. We derive the same result in the eikonal approximation, which also allows us to show the absence of enhancement at any order. We complement the proof by an explicit calculation of the power spectrum at two-loop order, and by further numerical checks at higher orders. Using these insights, we argue that the modification of the power spectrum from soft modes corresponds at most to logarithmic corrections. Finally, we discuss the asymptotic behavior in the large and small momentum regimes and identify the expansion parameter pertinent to non-linear corrections.

  20. On the non-linear scale of cosmological perturbation theory

    Blas, Diego; Garny, Mathias; Konstandin, Thomas

    2013-04-01

    We discuss the convergence of cosmological perturbation theory. We prove that the polynomial enhancement of the non-linear corrections expected from the effects of soft modes is absent in equal-time correlators like the power or bispectrum. We first show this at leading order by resumming the most important corrections of soft modes to an arbitrary skeleton of hard fluctuations. We derive the same result in the eikonal approximation, which also allows us to show the absence of enhancement at any order. We complement the proof by an explicit calculation of the power spectrum at two-loop order, and by further numerical checks at higher orders. Using these insights, we argue that the modification of the power spectrum from soft modes corresponds at most to logarithmic corrections. Finally, we discuss the asymptotic behavior in the large and small momentum regimes and identify the expansion parameter pertinent to non-linear corrections.

  1. On the non-linear scale of cosmological perturbation theory

    Blas, Diego [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Garny, Mathias; Konstandin, Thomas [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2013-04-15

    We discuss the convergence of cosmological perturbation theory. We prove that the polynomial enhancement of the non-linear corrections expected from the effects of soft modes is absent in equal-time correlators like the power or bispectrum. We first show this at leading order by resumming the most important corrections of soft modes to an arbitrary skeleton of hard fluctuations. We derive the same result in the eikonal approximation, which also allows us to show the absence of enhancement at any order. We complement the proof by an explicit calculation of the power spectrum at two-loop order, and by further numerical checks at higher orders. Using these insights, we argue that the modification of the power spectrum from soft modes corresponds at most to logarithmic corrections. Finally, we discuss the asymptotic behavior in the large and small momentum regimes and identify the expansion parameter pertinent to non-linear corrections.

  2. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism

    Hefzi, Hooman

    2016-11-23

    Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess optimization, we reconstructed the metabolic pathways in CHO and associated them with >1,700 genes in the Cricetulus griseus genome. The genome-scale metabolic model based on this reconstruction, iCHO1766, and cell-line-specific models for CHO-K1, CHO-S, and CHO-DG44 cells provide the biochemical basis of growth and recombinant protein production. The models accurately predict growth phenotypes and known auxotrophies in CHO cells. With the models, we quantify the protein synthesis capacity of CHO cells and demonstrate that common bioprocess treatments, such as histone deacetylase inhibitors, inefficiently increase product yield. However, our simulations show that the metabolic resources in CHO are more than three times more efficiently utilized for growth or recombinant protein synthesis following targeted efforts to engineer the CHO secretory pathway. This model will further accelerate CHO cell engineering and help optimize bioprocesses.

  3. Genome-scale metabolic models applied to human health and disease.

    Cook, Daniel J; Nielsen, Jens

    2017-11-01

    Advances in genome sequencing, high throughput measurement of gene and protein expression levels, data accessibility, and computational power have allowed genome-scale metabolic models (GEMs) to become a useful tool for understanding metabolic alterations associated with many different diseases. Despite the proven utility of GEMs, researchers confront multiple challenges in the use of GEMs, their application to human health and disease, and their construction and simulation in an organ-specific and disease-specific manner. Several approaches that researchers are taking to address these challenges include using proteomic and transcriptomic-informed methods to build GEMs for individual organs, diseases, and patients and using constraints on model behavior during simulation to match observed metabolic fluxes. We review the challenges facing researchers in the use of GEMs, review the approaches used to address these challenges, and describe advances that are on the horizon and could lead to a better understanding of human metabolism. WIREs Syst Biol Med 2017, 9:e1393. doi: 10.1002/wsbm.1393 For further resources related to this article, please visit the WIREs website. © 2017 Wiley Periodicals, Inc.

  4. Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins.

    Irani, Zahra Azimzadeh; Kerkhoven, Eduard J; Shojaosadati, Seyed Abbas; Nielsen, Jens

    2016-05-01

    Pichia pastoris is used for commercial production of human therapeutic proteins, and genome-scale models of P. pastoris metabolism have been generated in the past to study the metabolism and associated protein production by this yeast. A major challenge with clinical usage of recombinant proteins produced by P. pastoris is the difference in N-glycosylation of proteins produced by humans and this yeast. However, through metabolic engineering, a P. pastoris strain capable of producing humanized N-glycosylated proteins was constructed. The current genome-scale models of P. pastoris do not address native nor humanized N-glycosylation, and we therefore developed ihGlycopastoris, an extension to the iLC915 model with both native and humanized N-glycosylation for recombinant protein production, but also an estimation of N-glycosylation of P. pastoris native proteins. This new model gives a better prediction of protein yield, demonstrates the effect of the different types of N-glycosylation of protein yield, and can be used to predict potential targets for strain improvement. The model represents a step towards a more complete description of protein production in P. pastoris, which is required for using these models to understand and optimize protein production processes. © 2015 Wiley Periodicals, Inc.

  5. A mixed-integer linear programming approach to the reduction of genome-scale metabolic networks.

    Röhl, Annika; Bockmayr, Alexander

    2017-01-03

    Constraint-based analysis has become a widely used method to study metabolic networks. While some of the associated algorithms can be applied to genome-scale network reconstructions with several thousands of reactions, others are limited to small or medium-sized models. In 2015, Erdrich et al. introduced a method called NetworkReducer, which reduces large metabolic networks to smaller subnetworks, while preserving a set of biological requirements that can be specified by the user. Already in 2001, Burgard et al. developed a mixed-integer linear programming (MILP) approach for computing minimal reaction sets under a given growth requirement. Here we present an MILP approach for computing minimum subnetworks with the given properties. The minimality (with respect to the number of active reactions) is not guaranteed by NetworkReducer, while the method by Burgard et al. does not allow specifying the different biological requirements. Our procedure is about 5-10 times faster than NetworkReducer and can enumerate all minimum subnetworks in case there exist several ones. This allows identifying common reactions that are present in all subnetworks, and reactions appearing in alternative pathways. Applying complex analysis methods to genome-scale metabolic networks is often not possible in practice. Thus it may become necessary to reduce the size of the network while keeping important functionalities. We propose a MILP solution to this problem. Compared to previous work, our approach is more efficient and allows computing not only one, but even all minimum subnetworks satisfying the required properties.

  6. Enumeration of smallest intervention strategies in genome-scale metabolic networks.

    Axel von Kamp

    2014-01-01

    Full Text Available One ultimate goal of metabolic network modeling is the rational redesign of biochemical networks to optimize the production of certain compounds by cellular systems. Although several constraint-based optimization techniques have been developed for this purpose, methods for systematic enumeration of intervention strategies in genome-scale metabolic networks are still lacking. In principle, Minimal Cut Sets (MCSs; inclusion-minimal combinations of reaction or gene deletions that lead to the fulfilment of a given intervention goal provide an exhaustive enumeration approach. However, their disadvantage is the combinatorial explosion in larger networks and the requirement to compute first the elementary modes (EMs which itself is impractical in genome-scale networks. We present MCSEnumerator, a new method for effective enumeration of the smallest MCSs (with fewest interventions in genome-scale metabolic network models. For this we combine two approaches, namely (i the mapping of MCSs to EMs in a dual network, and (ii a modified algorithm by which shortest EMs can be effectively determined in large networks. In this way, we can identify the smallest MCSs by calculating the shortest EMs in the dual network. Realistic application examples demonstrate that our algorithm is able to list thousands of the most efficient intervention strategies in genome-scale networks for various intervention problems. For instance, for the first time we could enumerate all synthetic lethals in E.coli with combinations of up to 5 reactions. We also applied the new algorithm exemplarily to compute strain designs for growth-coupled synthesis of different products (ethanol, fumarate, serine by E.coli. We found numerous new engineering strategies partially requiring less knockouts and guaranteeing higher product yields (even without the assumption of optimal growth than reported previously. The strength of the presented approach is that smallest intervention strategies can be

  7. The string tension and the scaling behavior of SU(2) gauge theory on a random lattice

    Qui Zhaoming; Ren Haichang; Academia Sinica, Beijing; Wang Xiaoqun; Yang Zhixing; Zhao Enping

    1987-01-01

    The SU(2) gauge theory on an 8 4 random lattice has been studied by the Monte Carlo method. The string tensions have been evaluated. They display the expected scaling behavior for β = 1.2-1.3. The scale parameter Λ RAN has been determined approximately. (orig.)

  8. Item Response Theory Models for Wording Effects in Mixed-Format Scales

    Wang, Wen-Chung; Chen, Hui-Fang; Jin, Kuan-Yu

    2015-01-01

    Many scales contain both positively and negatively worded items. Reverse recoding of negatively worded items might not be enough for them to function as positively worded items do. In this study, we commented on the drawbacks of existing approaches to wording effect in mixed-format scales and used bi-factor item response theory (IRT) models to…

  9. An Item Response Theory Analysis of the Community of Inquiry Scale

    Horzum, Mehmet Baris; Uyanik, Gülden Kaya

    2015-01-01

    The aim of this study is to examine validity and reliability of Community of Inquiry Scale commonly used in online learning by the means of Item Response Theory. For this purpose, Community of Inquiry Scale version 14 is applied on 1,499 students of a distance education center's online learning programs at a Turkish state university via internet.…

  10. Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

    Vongsangnak, Wanwipa; Olsen, Peter; Hansen, Kim

    2008-01-01

    Background: Since ancient times the filamentous fungus Aspergillus oryzae has been used in the fermentation industry for the production of fermented sauces and the production of industrial enzymes. Recently, the genome sequence of A. oryzae with 12,074 annotated genes was released but the number...... to a genome scale metabolic model of A. oryzae. Results: Our assembled EST sequences we identified 1,046 newly predicted genes in the A. oryzae genome. Furthermore, it was possible to assign putative protein functions to 398 of the newly predicted genes. Noteworthy, our annotation strategy resulted...... model was validated and shown to correctly describe the phenotypic behavior of A. oryzae grown on different carbon sources. Conclusion: A much enhanced annotation of the A. oryzae genome was performed and a genomescale metabolic model of A. oryzae was reconstructed. The model accurately predicted...

  11. Systematic construction of kinetic models from genome-scale metabolic networks.

    Natalie J Stanford

    Full Text Available The quantitative effects of environmental and genetic perturbations on metabolism can be studied in silico using kinetic models. We present a strategy for large-scale model construction based on a logical layering of data such as reaction fluxes, metabolite concentrations, and kinetic constants. The resulting models contain realistic standard rate laws and plausible parameters, adhere to the laws of thermodynamics, and reproduce a predefined steady state. These features have not been simultaneously achieved by previous workflows. We demonstrate the advantages and limitations of the workflow by translating the yeast consensus metabolic network into a kinetic model. Despite crudely selected data, the model shows realistic control behaviour, a stable dynamic, and realistic response to perturbations in extracellular glucose concentrations. The paper concludes by outlining how new data can continuously be fed into the workflow and how iterative model building can assist in directing experiments.

  12. Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks

    Smallbone, Kieran; Klipp, Edda; Mendes, Pedro; Liebermeister, Wolfram

    2013-01-01

    The quantitative effects of environmental and genetic perturbations on metabolism can be studied in silico using kinetic models. We present a strategy for large-scale model construction based on a logical layering of data such as reaction fluxes, metabolite concentrations, and kinetic constants. The resulting models contain realistic standard rate laws and plausible parameters, adhere to the laws of thermodynamics, and reproduce a predefined steady state. These features have not been simultaneously achieved by previous workflows. We demonstrate the advantages and limitations of the workflow by translating the yeast consensus metabolic network into a kinetic model. Despite crudely selected data, the model shows realistic control behaviour, a stable dynamic, and realistic response to perturbations in extracellular glucose concentrations. The paper concludes by outlining how new data can continuously be fed into the workflow and how iterative model building can assist in directing experiments. PMID:24324546

  13. Scaled unscented transform Gaussian sum filter: Theory and application

    Luo, Xiaodong

    2010-05-01

    In this work we consider the state estimation problem in nonlinear/non-Gaussian systems. We introduce a framework, called the scaled unscented transform Gaussian sum filter (SUT-GSF), which combines two ideas: the scaled unscented Kalman filter (SUKF) based on the concept of scaled unscented transform (SUT) (Julier and Uhlmann (2004) [16]), and the Gaussian mixture model (GMM). The SUT is used to approximate the mean and covariance of a Gaussian random variable which is transformed by a nonlinear function, while the GMM is adopted to approximate the probability density function (pdf) of a random variable through a set of Gaussian distributions. With these two tools, a framework can be set up to assimilate nonlinear systems in a recursive way. Within this framework, one can treat a nonlinear stochastic system as a mixture model of a set of sub-systems, each of which takes the form of a nonlinear system driven by a known Gaussian random process. Then, for each sub-system, one applies the SUKF to estimate the mean and covariance of the underlying Gaussian random variable transformed by the nonlinear governing equations of the sub-system. Incorporating the estimations of the sub-systems into the GMM gives an explicit (approximate) form of the pdf, which can be regarded as a "complete" solution to the state estimation problem, as all of the statistical information of interest can be obtained from the explicit form of the pdf (Arulampalam et al. (2002) [7]). In applications, a potential problem of a Gaussian sum filter is that the number of Gaussian distributions may increase very rapidly. To this end, we also propose an auxiliary algorithm to conduct pdf re-approximation so that the number of Gaussian distributions can be reduced. With the auxiliary algorithm, in principle the SUT-GSF can achieve almost the same computational speed as the SUKF if the SUT-GSF is implemented in parallel. As an example, we will use the SUT-GSF to assimilate a 40-dimensional system due to

  14. Building an Evaluation Scale using Item Response Theory.

    Lalor, John P; Wu, Hao; Yu, Hong

    2016-11-01

    Evaluation of NLP methods requires testing against a previously vetted gold-standard test set and reporting standard metrics (accuracy/precision/recall/F1). The current assumption is that all items in a given test set are equal with regards to difficulty and discriminating power. We propose Item Response Theory (IRT) from psychometrics as an alternative means for gold-standard test-set generation and NLP system evaluation. IRT is able to describe characteristics of individual items - their difficulty and discriminating power - and can account for these characteristics in its estimation of human intelligence or ability for an NLP task. In this paper, we demonstrate IRT by generating a gold-standard test set for Recognizing Textual Entailment. By collecting a large number of human responses and fitting our IRT model, we show that our IRT model compares NLP systems with the performance in a human population and is able to provide more insight into system performance than standard evaluation metrics. We show that a high accuracy score does not always imply a high IRT score, which depends on the item characteristics and the response pattern.

  15. Explaining the electroweak scale and stabilizing moduli in M theory

    Acharya, Bobby S.; Bobkov, Konstantin; Kane, Gordon L.; Kumar, Piyush; Shao Jing

    2007-01-01

    In a recent paper [B. Acharya, K. Bobkov, G. Kane, P. Kumar, and D. Vaman, Phys. Rev. Lett. 97, 191601 (2006).] it was shown that in fluxless M theory vacua with at least two hidden sectors undergoing strong gauge dynamics and a particular form of the Kaehler potential, all moduli are stabilized by the effective potential and a stable hierarchy is generated, consistent with standard gauge unification. This paper explains the results of [B. Acharya, K. Bobkov, G. Kane, P. Kumar, and D. Vaman, Phys. Rev. Lett. 97, 191601 (2006).] in more detail and generalizes them, finding an essentially unique de Sitter vacuum under reasonable conditions. One of the main phenomenological consequences is a prediction which emerges from this entire class of vacua: namely, gaugino masses are significantly suppressed relative to the gravitino mass. We also present evidence that, for those vacua in which the vacuum energy is small, the gravitino mass, which sets all the superpartner masses, is automatically in the TeV-100 TeV range

  16. Explaining the electroweak scale and stabilizing moduli in M theory

    Acharya, Bobby S.; Bobkov, Konstantin; Kane, Gordon L.; Kumar, Piyush; Shao, Jing

    2007-12-01

    In a recent paper [B. Acharya, K. Bobkov, G. Kane, P. Kumar, and D. Vaman, Phys. Rev. Lett. 97, 191601 (2006).PRLTAO0031-900710.1103/PhysRevLett.97.191601] it was shown that in fluxless M theory vacua with at least two hidden sectors undergoing strong gauge dynamics and a particular form of the Kähler potential, all moduli are stabilized by the effective potential and a stable hierarchy is generated, consistent with standard gauge unification. This paper explains the results of [B. Acharya, K. Bobkov, G. Kane, P. Kumar, and D. Vaman, Phys. Rev. Lett. 97, 191601 (2006).PRLTAO0031-900710.1103/PhysRevLett.97.191601] in more detail and generalizes them, finding an essentially unique de Sitter vacuum under reasonable conditions. One of the main phenomenological consequences is a prediction which emerges from this entire class of vacua: namely, gaugino masses are significantly suppressed relative to the gravitino mass. We also present evidence that, for those vacua in which the vacuum energy is small, the gravitino mass, which sets all the superpartner masses, is automatically in the TeV 100 TeV range.

  17. Low mass-scale parity restoration in expanded gauge theories

    Rajpoot, S.

    1982-07-01

    It is shown that schemes of grand unification with SU(2n) 4 gauge symmetry permit the embedding of the left-right symmetric SU(2)sub(L)xSU(2)sub(R)xU(1)xSU(3) intermediate symmetry at relatively low energies (between 250 GeV and 1 TeV) as well as allowing light unification mass-scales ( 5 TeV) if n>=3 for values of the weak angle Sin 2 thetasub(W) and the strong coupling αsub(s) in the ranges 0.20 2 thetasub(W)<=0.25, 0.10<=αsub(s)<=0.15. (author)

  18. Theory-based transport simulation of tokamaks: density scaling

    Ghanem, E.S.; Kinsey, J.; Singer, C.; Bateman, G.

    1992-01-01

    There has been a sizeable amount of work in the past few years using theoretically based flux-surface-average transport models to simulate various types of experimental tokamak data. Here we report two such studies, concentrating on the response of the plasma to variation of the line averaged electron density. The first study reported here uses a transport model described by Ghanem et al. to examine the response of global energy confinement time in ohmically heated discharges. The second study reported here uses a closely related and more recent transport model described by Bateman to examine the response of temperature profiles to changes in line-average density in neutral-beam-heated discharges. Work on developing a common theoretical model for these and other scaling experiments is in progress. (author) 5 refs., 2 figs

  19. Network thermodynamic curation of human and yeast genome-scale metabolic models.

    Martínez, Verónica S; Quek, Lake-Ee; Nielsen, Lars K

    2014-07-15

    Genome-scale models are used for an ever-widening range of applications. Although there has been much focus on specifying the stoichiometric matrix, the predictive power of genome-scale models equally depends on reaction directions. Two-thirds of reactions in the two eukaryotic reconstructions Homo sapiens Recon 1 and Yeast 5 are specified as irreversible. However, these specifications are mainly based on biochemical textbooks or on their similarity to other organisms and are rarely underpinned by detailed thermodynamic analysis. In this study, a to our knowledge new workflow combining network-embedded thermodynamic and flux variability analysis was used to evaluate existing irreversibility constraints in Recon 1 and Yeast 5 and to identify new ones. A total of 27 and 16 new irreversible reactions were identified in Recon 1 and Yeast 5, respectively, whereas only four reactions were found with directions incorrectly specified against thermodynamics (three in Yeast 5 and one in Recon 1). The workflow further identified for both models several isolated internal loops that require further curation. The framework also highlighted the need for substrate channeling (in human) and ATP hydrolysis (in yeast) for the essential reaction catalyzed by phosphoribosylaminoimidazole carboxylase in purine metabolism. Finally, the framework highlighted differences in proline metabolism between yeast (cytosolic anabolism and mitochondrial catabolism) and humans (exclusively mitochondrial metabolism). We conclude that network-embedded thermodynamics facilitates the specification and validation of irreversibility constraints in compartmentalized metabolic models, at the same time providing further insight into network properties. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  20. Development and psychometric validation of social cognitive theory scales in an oral health context.

    Jones, Kelly; Parker, Eleanor J; Steffens, Margaret A; Logan, Richard M; Brennan, David; Jamieson, Lisa M

    2016-04-01

    This study aimed to develop and evaluate scales reflecting potentially modifiable social cognitive theory-based risk indicators associated with homeless populations' oral health. The scales are referred to as the social cognitive theory risk scales in an oral health context (SCTOH) and are referred to as SCTOH(SE), SCTOH(K) and SCTOH(F), respectively. The three SCTOH scales assess the key constructs of social cognitive theory: self-efficacy, knowledge and fatalism. The reliability and validity of the three scales were evaluated in a convenience sample of 248 homeless participants (age range 17-78 years, 79% male) located in a metropolitan setting in Australia. The scales were supported by exploratory factor analysis and established three distinct and internally consistent domains of social cognition: oral health-related self-efficacy, oral health-related knowledge and oral health-related fatalism, with Cronbach's alphas of 0.95, 0.85 and Spearman's-Brown ρ of 0.69. Concurrent ability was confirmed by each SCTOH scale's association with oral health status in the expected directions. The three SCTOH scales appear to be internally valid and reliable. If confirmed by further research, these scales could potentially be used for tailored educational and cognitive-behavioural interventions to reduce oral health inequalities among homeless and other vulnerable populations. © 2015 Public Health Association of Australia.

  1. Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test

    Pinu, Farhana R.; Granucci, Ninna; Daniell, James

    2018-01-01

    Introduction Microbial cells secrete many metabolites during growth, including important intermediates of the central carbon metabolism. This has not been taken into account by researchers when modeling microbial metabolism for metabolic engineering and systems biology studies. Materials and Meth...

  2. BPS ZN string tensions, sine law and Casimir scaling, and integrable field theories

    Kneipp, Marco A. C.

    2007-01-01

    We consider a Yang-Mills-Higgs theory with spontaneous symmetry breaking of the gauge group G→U(1) r →C G , with C G being the center of G. We study two vacua solutions of the theory which produce this symmetry breaking. We show that for one of these vacua, the theory in the Coulomb phase has the mass spectrum of particles and monopoles which is exactly the same as the mass spectrum of particles and solitons of two-dimensional affine Toda field theory, for suitable coupling constants. That result holds also for N=4 super Yang-Mills theories. On the other hand, in the Higgs phase, we show that for each of the two vacua the ratio of the tensions of the BPS Z N strings satisfy either the Casimir scaling or the sine law scaling for G=SU(N). These results are extended to other gauge groups: for the Casimir scaling, the ratios of the tensions are equal to the ratios of the quadratic Casimir constant of specific representations; for the sine law scaling, the tensions are proportional to the components of the left Perron-Frobenius eigenvector of Cartan matrix K ij and the ratios of tensions are equal to the ratios of the soliton masses of affine Toda field theories

  3. Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model

    Dash, Satyakam; Mueller, Thomas J.; Venkataramanan, Keerthi P.; Papoutsakis, Eleftherios T.; Maranas, Costas D.

    2014-01-01

    Clostridia are anaerobic Gram-positive Firmicutes containing broad and flexible systems for substrate utilization, which have been used successfully to produce a range of industrial compounds. Clostridium acetobutylicum has been used to produce butanol on an industrial scale through acetone-butanol-ethanol (ABE) fermentation. A genome-scale metabolic (GSM) model is a powerful tool for understanding the metabolic capacities of an organism and developing metabolic engineering strategies for strain development. The integration of stress related specific transcriptomics information with the GSM model provides opportunities for elucidating the focal points of regulation

  4. Metabolism

    ... lin), which signals cells to increase their anabolic activities. Metabolism is a complicated chemical process, so it's not ... how those enzymes or hormones work. When the metabolism of body chemicals is ... Hyperthyroidism (pronounced: hi-per-THIGH-roy-dih-zum). Hyperthyroidism ...

  5. Genome-scale modelling of microbial metabolism with temporal and spatial resolution.

    Henson, Michael A

    2015-12-01

    Most natural microbial systems have evolved to function in environments with temporal and spatial variations. A major limitation to understanding such complex systems is the lack of mathematical modelling frameworks that connect the genomes of individual species and temporal and spatial variations in the environment to system behaviour. The goal of this review is to introduce the emerging field of spatiotemporal metabolic modelling based on genome-scale reconstructions of microbial metabolism. The extension of flux balance analysis (FBA) to account for both temporal and spatial variations in the environment is termed spatiotemporal FBA (SFBA). Following a brief overview of FBA and its established dynamic extension, the SFBA problem is introduced and recent progress is described. Three case studies are reviewed to illustrate the current state-of-the-art and possible future research directions are outlined. The author posits that SFBA is the next frontier for microbial metabolic modelling and a rapid increase in methods development and system applications is anticipated. © 2015 Authors; published by Portland Press Limited.

  6. Reframed Genome-Scale Metabolic Model to Facilitate Genetic Design and Integration with Expression Data.

    Gu, Deqing; Jian, Xingxing; Zhang, Cheng; Hua, Qiang

    2017-01-01

    Genome-scale metabolic network models (GEMs) have played important roles in the design of genetically engineered strains and helped biologists to decipher metabolism. However, due to the complex gene-reaction relationships that exist in model systems, most algorithms have limited capabilities with respect to directly predicting accurate genetic design for metabolic engineering. In particular, methods that predict reaction knockout strategies leading to overproduction are often impractical in terms of gene manipulations. Recently, we proposed a method named logical transformation of model (LTM) to simplify the gene-reaction associations by introducing intermediate pseudo reactions, which makes it possible to generate genetic design. Here, we propose an alternative method to relieve researchers from deciphering complex gene-reactions by adding pseudo gene controlling reactions. In comparison to LTM, this new method introduces fewer pseudo reactions and generates a much smaller model system named as gModel. We showed that gModel allows two seldom reported applications: identification of minimal genomes and design of minimal cell factories within a modified OptKnock framework. In addition, gModel could be used to integrate expression data directly and improve the performance of the E-Fmin method for predicting fluxes. In conclusion, the model transformation procedure will facilitate genetic research based on GEMs, extending their applications.

  7. On the renormalization of the effective field theory of large scale structures

    Pajer, Enrico; Zaldarriaga, Matias

    2013-01-01

    Standard perturbation theory (SPT) for large-scale matter inhomogeneities is unsatisfactory for at least three reasons: there is no clear expansion parameter since the density contrast is not small on all scales; it does not fully account for deviations at large scales from a perfect pressureless fluid induced by short-scale non-linearities; for generic initial conditions, loop corrections are UV-divergent, making predictions cutoff dependent and hence unphysical. The Effective Field Theory of Large Scale Structures successfully addresses all three issues. Here we focus on the third one and show explicitly that the terms induced by integrating out short scales, neglected in SPT, have exactly the right scale dependence to cancel all UV-divergences at one loop, and this should hold at all loops. A particularly clear example is an Einstein deSitter universe with no-scale initial conditions P in ∼ k n . After renormalizing the theory, we use self-similarity to derive a very simple result for the final power spectrum for any n, excluding two-loop corrections and higher. We show how the relative importance of different corrections depends on n. For n ∼ −1.5, relevant for our universe, pressure and dissipative corrections are more important than the two-loop corrections

  8. On the renormalization of the effective field theory of large scale structures

    Pajer, Enrico [Department of Physics, Princeton University, Princeton, NJ 08544 (United States); Zaldarriaga, Matias, E-mail: enrico.pajer@gmail.com, E-mail: matiasz@ias.edu [Institute for Advanced Study, Princeton, NJ 08544 (United States)

    2013-08-01

    Standard perturbation theory (SPT) for large-scale matter inhomogeneities is unsatisfactory for at least three reasons: there is no clear expansion parameter since the density contrast is not small on all scales; it does not fully account for deviations at large scales from a perfect pressureless fluid induced by short-scale non-linearities; for generic initial conditions, loop corrections are UV-divergent, making predictions cutoff dependent and hence unphysical. The Effective Field Theory of Large Scale Structures successfully addresses all three issues. Here we focus on the third one and show explicitly that the terms induced by integrating out short scales, neglected in SPT, have exactly the right scale dependence to cancel all UV-divergences at one loop, and this should hold at all loops. A particularly clear example is an Einstein deSitter universe with no-scale initial conditions P{sub in} ∼ k{sup n}. After renormalizing the theory, we use self-similarity to derive a very simple result for the final power spectrum for any n, excluding two-loop corrections and higher. We show how the relative importance of different corrections depends on n. For n ∼ −1.5, relevant for our universe, pressure and dissipative corrections are more important than the two-loop corrections.

  9. Determining the control circuitry of redox metabolism at the genome-scale.

    Stephen Federowicz

    2014-04-01

    Full Text Available Determining how facultative anaerobic organisms sense and direct cellular responses to electron acceptor availability has been a subject of intense study. However, even in the model organism Escherichia coli, established mechanisms only explain a small fraction of the hundreds of genes that are regulated during electron acceptor shifts. Here we propose a qualitative model that accounts for the full breadth of regulated genes by detailing how two global transcription factors (TFs, ArcA and Fnr of E. coli, sense key metabolic redox ratios and act on a genome-wide basis to regulate anabolic, catabolic, and energy generation pathways. We first fill gaps in our knowledge of this transcriptional regulatory network by carrying out ChIP-chip and gene expression experiments to identify 463 regulatory events. We then interfaced this reconstructed regulatory network with a highly curated genome-scale metabolic model to show that ArcA and Fnr regulate >80% of total metabolic flux and 96% of differential gene expression across fermentative and nitrate respiratory conditions. Based on the data, we propose a feedforward with feedback trim regulatory scheme, given the extensive repression of catabolic genes by ArcA and extensive activation of chemiosmotic genes by Fnr. We further corroborated this regulatory scheme by showing a 0.71 r(2 (p<1e-6 correlation between changes in metabolic flux and changes in regulatory activity across fermentative and nitrate respiratory conditions. Finally, we are able to relate the proposed model to a wealth of previously generated data by contextualizing the existing transcriptional regulatory network.

  10. Between theory and quantification: An integrated analysis of metabolic patterns of informal urban settlements

    Kovacic, Zora; Giampietro, Mario

    2017-01-01

    As informal urban settlements grow in size and population across the developing world, the issue of how to design and implement effective policies to provide for the needs and the aspirations of dwellers becomes ever more pressing. This paper addresses the challenge of how to characterise in quantitative terms the complex and fast-changing phenomenon of informal urban settlements without falling into oversimplification and a narrow focus on the material deficits of informal settlements. Energy policies are taken as an example to illustrate the shortcomings of oversimplification in producing policy relevant information. We adopt a semantically open representation of informal settlements that can capture the diversity of adaptive strategies used by different settlement typologies, based on the societal metabolism approach. Results show that as settlements grow in size and complexity, they remain economically and politically marginalised and fail to integrate into the city. We argue that in the case of energy policy, the analysis must go beyond the definition of problems such as access to energy at the level of the individual, and focus on a multi-scale assessment including the household and community levels studying the capacity of the household to increase it energy throughput through exosomatic devices and infrastructure. - Highlights: • The policy challenges of fast changing informal urban settlements are assessed. • Metabolic patterns are used to assess and compare different typologies of slums. • Semantically open representations are used to capture the complexity of slums.

  11. Scaling Law for Photon Transmission through Optically Turbid Slabs Based on Random Walk Theory

    Xuesong Li

    2012-03-01

    Full Text Available Past work has demonstrated the value of a random walk theory (RWT to solve multiple-scattering problems arising in numerous contexts. This paper’s goal is to investigate the application range of the RWT using Monte Carlo simulations and extending it to anisotropic media using scaling laws. Meanwhile, this paper also reiterates rules for converting RWT formulas to real physical dimensions, and corrects some errors which appear in an earlier publication. The RWT theory, validated by the Monte Carlo simulations and combined with the scaling law, is expected to be useful to study multiple scattering and to greatly reduce the computation cost.

  12. Experimental verification of the statistical theories of scaling factor effect in fatigue fracture of steel

    Svistun, R.P.; Babej, Yu.I.; Tkachenko, N.N.

    1976-01-01

    Statistical theories of the scale effect in the fatigue failure of 40KH18N9T, 10 and 20 steels have been verified. The theories are shown to be not invariably suitable for a satisfactory exlanation of the fatigue strength of the samples with respect to their dimensions. One of the main reasons for displaying the scale effect in the process of steel fatigue is the sample self-heating, i.e. a temperature factor which in many cases overlaps a statistical one

  13. Experimental verification of the statistical theories of scaling factor effect in fatigue fracture of steel

    Svistun, R P; Babei, Yu I; Tkachenko, N N [AN Ukrainskoj SSR, Lvov. Fiziko-Mekhanicheskij Inst.; L' vovskij Lesotekhnicheskij Inst. (Ukrainian SSR))

    1976-01-01

    Statistical theories of the scale effect in the fatigue failure of 40KH18N9T, 10 and 20 steels have been verified. The theories are shown to be not invariably suitable for a satisfactory exlanation of the fatigue strength of the samples with respect to their dimensions. One of the main reasons for displaying the scale effect in the process of steel fatigue is the sample self-heating, i.e. a temperature factor which in many cases overlaps a statistical one.

  14. Theory-based scaling of the SOL width in circular limited tokamak plasmas

    Halpern, F.D.; Ricci, P.; Labit, B.; Furno, I.; Jolliet, S.; Loizu, J.; Mosetto, A.; Arnoux, G.; Silva, C.; Gunn, J.P.; Horacek, J.; Kočan, M.; LaBombard, B.

    2013-01-01

    A theory-based scaling for the characteristic length of a circular, limited tokamak scrape-off layer (SOL) is obtained by considering the balance between parallel losses and non-linearly saturated resistive ballooning mode turbulence driving anomalous perpendicular transport. The SOL size increases with plasma size, resistivity, and safety factor q. The scaling is verified against flux-driven non-linear turbulence simulations, which reveal good agreement within a wide range of dimensionless parameters, including parameters closely matching the TCV tokamak. An initial comparison of the theory against experimental data from several tokamaks also yields good agreement. (letter)

  15. Comparison of relativity theories with observer-independent scales of both velocity and length/mass

    Amelino-Camelia, Giovanni; Benedetti, Dario; D'Andrea, Francesco; Procaccini, Andrea

    2003-01-01

    We consider the two most studied proposals of relativity theories with observer-independent scales of both velocity and length/mass: the one discussed by Amelino-Camelia as an illustrative example for the original proposal (Preprint gr-qc/0012051) of theories with two relativistic invariants, and an alternative more recently proposed by Magueijo and Smolin (Preprint hep-th/0112090). We show that these two relativistic theories are much more closely connected than it would appear on the basis of a naive analysis of their original formulations. In particular, in spite of adopting a rather different formal description of the deformed boost generators, they end up assigning the same dependence of momentum on rapidity, which can be described as the core feature of these relativistic theories. We show that this observation can be used to clarify the concepts of particle mass, particle velocity and energy-momentum conservation rules in these theories with two relativistic invariants

  16. Theory of critical phenomena in finite-size systems scaling and quantum effects

    Brankov, Jordan G; Tonchev, Nicholai S

    2000-01-01

    The aim of this book is to familiarise the reader with the rich collection of ideas, methods and results available in the theory of critical phenomena in systems with confined geometry. The existence of universal features of the finite-size effects arising due to highly correlated classical or quantum fluctuations is explained by the finite-size scaling theory. This theory (1) offers an interpretation of experimental results on finite-size effects in real systems; (2) gives the most reliable tool for extrapolation to the thermodynamic limit of data obtained by computer simulations; (3) reveals

  17. Non-equilibrium mean-field theories on scale-free networks

    Caccioli, Fabio; Dall'Asta, Luca

    2009-01-01

    Many non-equilibrium processes on scale-free networks present anomalous critical behavior that is not explained by standard mean-field theories. We propose a systematic method to derive stochastic equations for mean-field order parameters that implicitly account for the degree heterogeneity. The method is used to correctly predict the dynamical critical behavior of some binary spin models and reaction–diffusion processes. The validity of our non-equilibrium theory is further supported by showing its relation with the generalized Landau theory of equilibrium critical phenomena on networks

  18. Watching More Closely: Shot Scale Affects Film Viewers’ Theory of Mind Tendency But Not Ability

    Rooney, Brendan; Bálint, Katalin E.

    2018-01-01

    Recent research debates the effects of exposure to narrative fiction on recognition of mental states in others and self, referred to as Theory of Mind. The current study explores the mechanisms by which such effects could occur in fictional film. Using manipulated film scenes, we conducted a between subject experiment (N = 136) exploring how film shot-scale affects viewers’ Theory of Mind. Specifically, in our methods we distinguish between the trait Theory of Mind abilities (ToM ability), and the state-like tendency to recognize mental states in others and self (ToM tendency). Results showed that close-up shots (compared to long shots) of a character was associated with higher levels of Theory of Mind tendency, when the facial expression was sad but not when it was neutral. And this effect did not transfer to other characters in the film. There was also no observable effect of character depiction on viewers’ general Theory of Mind ability. Together the findings suggest that formal and content features of shot scale can elicit Theory of Mind responses by directing attention toward character mental states rather than improving viewers’ general Theory of Mind ability. PMID:29387032

  19. Watching More Closely: Shot Scale Affects Film Viewers’ Theory of Mind Tendency But Not Ability

    Brendan Rooney

    2018-01-01

    Full Text Available Recent research debates the effects of exposure to narrative fiction on recognition of mental states in others and self, referred to as Theory of Mind. The current study explores the mechanisms by which such effects could occur in fictional film. Using manipulated film scenes, we conducted a between subject experiment (N = 136 exploring how film shot-scale affects viewers’ Theory of Mind. Specifically, in our methods we distinguish between the trait Theory of Mind abilities (ToM ability, and the state-like tendency to recognize mental states in others and self (ToM tendency. Results showed that close-up shots (compared to long shots of a character was associated with higher levels of Theory of Mind tendency, when the facial expression was sad but not when it was neutral. And this effect did not transfer to other characters in the film. There was also no observable effect of character depiction on viewers’ general Theory of Mind ability. Together the findings suggest that formal and content features of shot scale can elicit Theory of Mind responses by directing attention toward character mental states rather than improving viewers’ general Theory of Mind ability.

  20. Metabolic Profile and Inflammatory Responses in Dairy Cows with Left Displaced Abomasum Kept under Small-Scaled Farm Conditions

    Fenja Klevenhusen

    2015-10-01

    Full Text Available Left displaced abomasum (LDA is a severe metabolic disease of cattle with a strong negative impact on production efficiency of dairy farms. Metabolic and inflammatory alterations associated with this disease have been reported in earlier studies, conducted mostly in large dairy farms. This research aimed to: (1 evaluate metabolic and inflammatory responses in dairy cows affected by LDA in small-scaled dairy farms; and (2 establish an Animals 2015, 5 1022 association between lactation number and milk production with the outcome of metabolic variables. The cows with LDA had lower serum calcium (Ca, but greater concentrations of non-esterified fatty acids (NEFA and beta-hydroxy-butyrate (BHBA, in particular when lactation number was >2. Cows with LDA showed elevated levels of aspartate aminotransferase, glutamate dehydrogenase, and serum amyloid A (SAA, regardless of lactation number. In addition, this study revealed strong associations between milk yield and the alteration of metabolic profile but not with inflammation in the sick cows. Results indicate metabolic alterations, liver damage, and inflammation in LDA cows kept under small-scale farm conditions. Furthermore, the data suggest exacerbation of metabolic profile and Ca metabolism but not of inflammation and liver health with increasing lactation number and milk yield in cows affected by LDA.

  1. Metabolic Profile and Inflammatory Responses in Dairy Cows with Left Displaced Abomasum Kept under Small-Scaled Farm Conditions.

    Klevenhusen, Fenja; Humer, Elke; Metzler-Zebeli, Barbara; Podstatzky-Lichtenstein, Leopold; Wittek, Thomas; Zebeli, Qendrim

    2015-10-13

    Left displaced abomasum (LDA) is a severe metabolic disease of cattle with a strong negative impact on production efficiency of dairy farms. Metabolic and inflammatory alterations associated with this disease have been reported in earlier studies, conducted mostly in large dairy farms. This research aimed to: (1) evaluate metabolic and inflammatory responses in dairy cows affected by LDA in small-scaled dairy farms; and (2) establish an Animals 2015, 5 1022 association between lactation number and milk production with the outcome of metabolic variables. The cows with LDA had lower serum calcium (Ca), but greater concentrations of non-esterified fatty acids (NEFA) and beta-hydroxy-butyrate (BHBA), in particular when lactation number was >2. Cows with LDA showed elevated levels of aspartate aminotransferase, glutamate dehydrogenase, and serum amyloid A (SAA), regardless of lactation number. In addition, this study revealed strong associations between milk yield and the alteration of metabolic profile but not with inflammation in the sick cows. Results indicate metabolic alterations, liver damage, and inflammation in LDA cows kept under small-scale farm conditions. Furthermore, the data suggest exacerbation of metabolic profile and Ca metabolism but not of inflammation and liver health with increasing lactation number and milk yield in cows affected by LDA.

  2. Theory of finite-entanglement scaling at one-dimensional quantum critical points.

    Pollmann, Frank; Mukerjee, Subroto; Turner, Ari M; Moore, Joel E

    2009-06-26

    Studies of entanglement in many-particle systems suggest that most quantum critical ground states have infinitely more entanglement than noncritical states. Standard algorithms for one-dimensional systems construct model states with limited entanglement, which are a worse approximation to quantum critical states than to others. We give a quantitative theory of previously observed scaling behavior resulting from finite entanglement at quantum criticality. Finite-entanglement scaling in one-dimensional systems is governed not by the scaling dimension of an operator but by the "central charge" of the critical point. An important ingredient is the universal distribution of density-matrix eigenvalues at a critical point [P. Calabrese and A. Lefevre, Phys. Rev. A 78, 032329 (2008)10.1103/PhysRevA.78.032329]. The parameter-free theory is checked against numerical scaling at several quantum critical points.

  3. Nonlocal strain gradient theory calibration using molecular dynamics simulation based on small scale vibration of nanotubes

    Mehralian, Fahimeh [Mechanical Engineering Department, Shahrekord University, Shahrekord (Iran, Islamic Republic of); Tadi Beni, Yaghoub, E-mail: tadi@eng.sku.ac.ir [Faculty of Engineering, Shahrekord University, Shahrekord (Iran, Islamic Republic of); Karimi Zeverdejani, Mehran [Mechanical Engineering Department, Shahrekord University, Shahrekord (Iran, Islamic Republic of)

    2017-06-01

    Featured by two small length scale parameters, nonlocal strain gradient theory is utilized to investigate the free vibration of nanotubes. A new size-dependent shell model formulation is developed by using the first order shear deformation theory. The governing equations and boundary conditions are obtained using Hamilton's principle and solved for simply supported boundary condition. As main purpose of this study, since the values of two small length scale parameters are still unknown, they are calibrated by the means of molecular dynamics simulations (MDs). Then, the influences of different parameters such as nonlocal parameter, scale factor, length and thickness on vibration characteristics of nanotubes are studied. It is also shown that increase in thickness and decrease in length parameters intensify the effect of nonlocal parameter and scale factor.

  4. Thermodynamic scaling of dynamics in polymer melts: predictions from the generalized entropy theory.

    Xu, Wen-Sheng; Freed, Karl F

    2013-06-21

    Many glass-forming fluids exhibit a remarkable thermodynamic scaling in which dynamic properties, such as the viscosity, the relaxation time, and the diffusion constant, can be described under different thermodynamic conditions in terms of a unique scaling function of the ratio ρ(γ)∕T, where ρ is the density, T is the temperature, and γ is a material dependent constant. Interest in the scaling is also heightened because the exponent γ enters prominently into considerations of the relative contributions to the dynamics from pressure effects (e.g., activation barriers) vs. volume effects (e.g., free volume). Although this scaling is clearly of great practical use, a molecular understanding of the scaling remains elusive. Providing this molecular understanding would greatly enhance the utility of the empirically observed scaling in assisting the rational design of materials by describing how controllable molecular factors, such as monomer structures, interactions, flexibility, etc., influence the scaling exponent γ and, hence, the dynamics. Given the successes of the generalized entropy theory in elucidating the influence of molecular details on the universal properties of glass-forming polymers, this theory is extended here to investigate the thermodynamic scaling in polymer melts. The predictions of theory are in accord with the appearance of thermodynamic scaling for pressures not in excess of ~50 MPa. (The failure at higher pressures arises due to inherent limitations of a lattice model.) In line with arguments relating the magnitude of γ to the steepness of the repulsive part of the intermolecular potential, the abrupt, square-well nature of the lattice model interactions lead, as expected, to much larger values of the scaling exponent. Nevertheless, the theory is employed to study how individual molecular parameters affect the scaling exponent in order to extract a molecular understanding of the information content contained in the exponent. The chain

  5. Constraints on Interacting Scalars in 2T Field Theory and No Scale Models in 1T Field Theory

    Bars, Itzhak

    2010-01-01

    In this paper I determine the general form of the physical and mathematical restrictions that arise on the interactions of gravity and scalar fields in the 2T field theory setting, in d+2 dimensions, as well as in the emerging shadows in d dimensions. These constraints on scalar fields follow from an underlying Sp(2,R) gauge symmetry in phase space. Determining these general constraints provides a basis for the construction of 2T supergravity, as well as physical applications in 1T-field theory, that are discussed briefly here, and more detail elsewhere. In particular, no scale models that lead to a vanishing cosmological constant at the classical level emerge naturally in this setting.

  6. Genome-scale reconstruction of the metabolic network in Yersinia pestis, strain 91001

    Navid, A; Almaas, E

    2009-01-13

    The gram-negative bacterium Yersinia pestis, the aetiological agent of bubonic plague, is one the deadliest pathogens known to man. Despite its historical reputation, plague is a modern disease which annually afflicts thousands of people. Public safety considerations greatly limit clinical experimentation on this organism and thus development of theoretical tools to analyze the capabilities of this pathogen is of utmost importance. Here, we report the first genome-scale metabolic model of Yersinia pestis biovar Mediaevalis based both on its recently annotated genome, and physiological and biochemical data from literature. Our model demonstrates excellent agreement with Y. pestis known metabolic needs and capabilities. Since Y. pestis is a meiotrophic organism, we have developed CryptFind, a systematic approach to identify all candidate cryptic genes responsible for known and theoretical meiotrophic phenomena. In addition to uncovering every known cryptic gene for Y. pestis, our analysis of the rhamnose fermentation pathway suggests that betB is the responsible cryptic gene. Despite all of our medical advances, we still do not have a vaccine for bubonic plague. Recent discoveries of antibiotic resistant strains of Yersinia pestis coupled with the threat of plague being used as a bioterrorism weapon compel us to develop new tools for studying the physiology of this deadly pathogen. Using our theoretical model, we can study the cell's phenotypic behavior under different circumstances and identify metabolic weaknesses which may be harnessed for the development of therapeutics. Additionally, the automatic identification of cryptic genes expands the usage of genomic data for pharmaceutical purposes.

  7. Friedmann cosmology with a cosmological 'constant' in the scale covariant theory

    Beesham, A.

    1986-01-01

    Homogeneous isotropic cosmologies in the presence of a cosmological 'constant' are studied in the scale covariant theory. A class of solutions is obtained for kappa = 0 for models filled with dust, radiation or stiff matter. For kappa not= 0, solutions are presented for the radiation models. (author)

  8. A Polytomous Item Response Theory Analysis of Social Physique Anxiety Scale

    Fletcher, Richard B.; Crocker, Peter

    2014-01-01

    The present study investigated the social physique anxiety scale's factor structure and item properties using confirmatory factor analysis and item response theory. An additional aim was to identify differences in response patterns between groups (gender). A large sample of high school students aged 11-15 years (N = 1,529) consisting of n =…

  9. Catalonia's energy metabolism: Using the MuSIASEM approach at different scales

    Ramos-Martin, Jesus; Canellas-Bolta, Silvia; Giampietro, Mario; Gamboa, Gonzalo

    2009-01-01

    This paper applies the so-called Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism (MuSIASEM), based on Georgescu-Roegen's fund-flow model, to the Spanish region of Catalonia. It arrives to the conclusion that within the context of the end of cheap oil, the current development model of the Catalan economy, based on the growth of low-productivity sectors such as services and construction, must be changed. The change is needed not only because of the increasing scarcity of affordable energy and the increasing environmental impact of present development, but also because of the aging population. Moreover, the situation experienced by Catalonia is similar to that of other European countries and many other developed countries. This implies that we can expect a wave of major structural changes in the economy of developed countries worldwide. To make things more challenging, according to current trends, the energy intensity and exosomatic energy metabolism of Catalonia will keep increasing in the near future. To avoid a reduction in the standard of living of Catalans due to a reduction in the available energy it is important that the Government of Catalonia implement major adjustments and conservation efforts in both the household and paid-work sectors.

  10. Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica

    Chatterjee, Ankita; Kundu, Sudip

    2015-01-01

    Chlorophyll is one of the most important pigments present in green plants and rice is one of the major food crops consumed worldwide. We curated the existing genome scale metabolic model (GSM) of rice leaf by incorporating new compartment, reactions and transporters. We used this modified GSM to elucidate how the chlorophyll is synthesized in a leaf through a series of bio-chemical reactions spanned over different organelles using inorganic macronutrients and light energy. We predicted the essential reactions and the associated genes of chlorophyll synthesis and validated against the existing experimental evidences. Further, ammonia is known to be the preferred source of nitrogen in rice paddy fields. The ammonia entering into the plant is assimilated in the root and leaf. The focus of the present work is centered on rice leaf metabolism. We studied the relative importance of ammonia transporters through the chloroplast and the cytosol and their interlink with other intracellular transporters. Ammonia assimilation in the leaves takes place by the enzyme glutamine synthetase (GS) which is present in the cytosol (GS1) and chloroplast (GS2). Our results provided possible explanation why GS2 mutants show normal growth under minimum photorespiration and appear chlorotic when exposed to air. PMID:26443104

  11. Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production.

    Agren, Rasmus; Otero, José Manuel; Nielsen, Jens

    2013-07-01

    In this work, we describe the application of a genome-scale metabolic model and flux balance analysis for the prediction of succinic acid overproduction strategies in Saccharomyces cerevisiae. The top three single gene deletion strategies, Δmdh1, Δoac1, and Δdic1, were tested using knock-out strains cultivated anaerobically on glucose, coupled with physiological and DNA microarray characterization. While Δmdh1 and Δoac1 strains failed to produce succinate, Δdic1 produced 0.02 C-mol/C-mol glucose, in close agreement with model predictions (0.03 C-mol/C-mol glucose). Transcriptional profiling suggests that succinate formation is coupled to mitochondrial redox balancing, and more specifically, reductive TCA cycle activity. While far from industrial titers, this proof-of-concept suggests that in silico predictions coupled with experimental validation can be used to identify novel and non-intuitive metabolic engineering strategies.

  12. Chiral symmetry breaking and nonperturbative scale anomaly in gauge field theories

    Miranskij, V.A.; Gusynin, V.P.

    1987-01-01

    The nonperturbative dynamics of chiral and scale symmetry breaking in asymtotically free and non-asymptotically free (with an ultraviolet stable fixed point) vector-like gauge theories is investigated. In the two-loop approximation analytical expressions for the chiral and gluon condensates are obtained. The hypothesis about a soft behaviour at small distances of composite operators in non-asymptotically free gauge theories with a fixed point is put forward and substantiated. It is shown that in these theories the form of the scale anomaly depends on the type of the phase in coupling constant to which it relates. A new dilaton effective lagrangian for glueball and chiral fields is suggested. The mass relation for the single scalar fermion-antifermion bound state is obtained. The important ingredient of this approach is a large (d≅ 2) dynamical dimension of composite chiral fields. The application of this approach to QCD and technicolour models is discussed

  13. Bending of marble with intrinsic length scales: a gradient theory with surface energy and size effects

    Vardoulakis, I.; Kourkoulis, S.K.; Exadaktylos, G.

    1998-01-01

    A gradient bending theory is developed based on a strain energy function that includes the classical Bernoulli-Euler term, the shape correction term (microstructural length scale) introduced by Timoshenko, and a term associated with surface energy (micromaterial length scale) accounting for the bending moment gradient effect. It is shown that the last term is capable to interpret the size effect in three-point bending (3PB), namely the decrease of the failure load with decreasing beam length for the same aspect ratio. This theory is used to describe the mechanical behaviour of Dionysos-Pentelikon marble in 3PB. Series of tests with prismatic marble beams of the same aperture but with different lengths were conducted and it was concluded that the present theory predicts well the size effect. (orig.)

  14. In Silico Genome-Scale Reconstruction and Validation of the Corynebacterium glutamicum Metabolic Network

    Kjeldsen, Kjeld Raunkjær; Nielsen, J.

    2009-01-01

    A genome-scale metabolic model of the Gram-positive bacteria Corynebacterium glutamicum ATCC 13032 was constructed comprising 446 reactions and 411 metabolite, based on the annotated genome and available biochemical information. The network was analyzed using constraint based methods. The model...... was extensively validated against published flux data, and flux distribution values were found to correlate well between simulations and experiments. The split pathway of the lysine synthesis pathway of C. glutamicum was investigated, and it was found that the direct dehydrogenase variant gave a higher lysine...... yield than the alternative succinyl pathway at high lysine production rates. The NADPH demand of the network was not found to be critical for lysine production until lysine yields exceeded 55% (mmol lysine (mmol glucose)(-1)). The model was validated during growth on the organic acids acetate...

  15. Energy analysis for a sustainable future multi-scale integrated analysis of societal and ecosystem metabolism

    Giampietro, Mario; Sorman, Alevgül H

    2013-01-01

    The vast majority of the countries of the world are now facing an imminent energy crisis, particularly the USA, China, India, Japan and EU countries, but also developing countries having to boost their economic growth precisely when more powerful economies will prevent them from using the limited supply of fossil energy. Despite this crisis, current protocols of energy accounting have been developed for dealing with fossil energy exclusively and are therefore not useful for the analysis of alternative energy sources. The first part of the book illustrates the weakness of existing analyses of energy problems: the science of energy was born and developed neglecting the issue of scale. The authors argue that it is necessary to adopt more complex protocols of accounting and analysis in order to generate robust energy scenarios and effective assessments of the quality of alternative energy sources. The second part of the book introduces the concept of energetic metabolism of modern societies and uses empirical res...

  16. Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

    Ma, Ding; Yang, Laurence; Fleming, Ronan M. T.

    2017-01-01

    orders of magnitude. Data values also have greatly varying magnitudes. Standard double-precision solvers may return inaccurate solutions or report that no solution exists. Exact simplex solvers based on rational arithmetic require a near-optimal warm start to be practical on large problems (current ME......Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many...... models have 70,000 constraints and variables and will grow larger). We have developed a quadrupleprecision version of our linear and nonlinear optimizer MINOS, and a solution procedure (DQQ) involving Double and Quad MINOS that achieves reliability and efficiency for ME models and other challenging...

  17. Direct gauging of the Poincare group V. Group scaling, classical gauge theory, and gravitational corrections

    Edelen, D.G.B.

    1986-01-01

    Homogeneous scaling of the group space of the Poincare group, P 10 , is shown to induce scalings of all geometric quantities associated with the local action of P 10 . The field equations for both the translation and the Lorentz rotation compensating fields reduce to O(1) equations if the scaling parameter is set equal to the general relativistic gravitational coupling constant 8πGc -4 . Standard expansions of all field variables in power series in the scaling parameter give the following results. The zeroth-order field equations are exactly the classical field equations for matter fields on Minkowski space subject to local action of an internal symmetry group (classical gauge theory). The expansion process is shown to break P 10 -gauge covariance of the theory, and hence solving the zeroth-order field equations imposes an implicit system of P 10 -gauge conditions. Explicit systems of field equations are obtained for the first- and higher-order approximations. The first-order translation field equations are driven by the momentum-energy tensor of the matter and internal compensating fields in the zeroth order (classical gauge theory), while the first-order Lorentz rotation field equations are driven by the spin currents of the same classical gauge theory. Field equations for the first-order gravitational corrections to the matter fields and the gauge fields for the internal symmetry group are obtained. Direct Poincare gauge theory is thus shown to satisfy the first two of the three-part acid test of any unified field theory. Satisfaction of the third part of the test, at least for finite neighborhoods, seems probable

  18. Multi-scale connectivity and graph theory highlight critical areas for conservation under climate change

    Dilts, Thomas E.; Weisberg, Peter J.; Leitner, Phillip; Matocq, Marjorie D.; Inman, Richard D.; Nussear, Ken E.; Esque, Todd C.

    2016-01-01

    Conservation planning and biodiversity management require information on landscape connectivity across a range of spatial scales from individual home ranges to large regions. Reduction in landscape connectivity due changes in land-use or development is expected to act synergistically with alterations to habitat mosaic configuration arising from climate change. We illustrate a multi-scale connectivity framework to aid habitat conservation prioritization in the context of changing land use and climate. Our approach, which builds upon the strengths of multiple landscape connectivity methods including graph theory, circuit theory and least-cost path analysis, is here applied to the conservation planning requirements of the Mohave ground squirrel. The distribution of this California threatened species, as for numerous other desert species, overlaps with the proposed placement of several utility-scale renewable energy developments in the American Southwest. Our approach uses information derived at three spatial scales to forecast potential changes in habitat connectivity under various scenarios of energy development and climate change. By disentangling the potential effects of habitat loss and fragmentation across multiple scales, we identify priority conservation areas for both core habitat and critical corridor or stepping stone habitats. This approach is a first step toward applying graph theory to analyze habitat connectivity for species with continuously-distributed habitat, and should be applicable across a broad range of taxa.

  19. The maximum sizes of large scale structures in alternative theories of gravity

    Bhattacharya, Sourav [IUCAA, Pune University Campus, Post Bag 4, Ganeshkhind, Pune, 411 007 India (India); Dialektopoulos, Konstantinos F. [Dipartimento di Fisica, Università di Napoli ' Federico II' , Complesso Universitario di Monte S. Angelo, Edificio G, Via Cinthia, Napoli, I-80126 Italy (Italy); Romano, Antonio Enea [Instituto de Física, Universidad de Antioquia, Calle 70 No. 52–21, Medellín (Colombia); Skordis, Constantinos [Department of Physics, University of Cyprus, 1 Panepistimiou Street, Nicosia, 2109 Cyprus (Cyprus); Tomaras, Theodore N., E-mail: sbhatta@iitrpr.ac.in, E-mail: kdialekt@gmail.com, E-mail: aer@phys.ntu.edu.tw, E-mail: skordis@ucy.ac.cy, E-mail: tomaras@physics.uoc.gr [Institute of Theoretical and Computational Physics and Department of Physics, University of Crete, 70013 Heraklion (Greece)

    2017-07-01

    The maximum size of a cosmic structure is given by the maximum turnaround radius—the scale where the attraction due to its mass is balanced by the repulsion due to dark energy. We derive generic formulae for the estimation of the maximum turnaround radius in any theory of gravity obeying the Einstein equivalence principle, in two situations: on a spherically symmetric spacetime and on a perturbed Friedman-Robertson-Walker spacetime. We show that the two formulae agree. As an application of our formula, we calculate the maximum turnaround radius in the case of the Brans-Dicke theory of gravity. We find that for this theory, such maximum sizes always lie above the ΛCDM value, by a factor 1 + 1/3ω, where ω>> 1 is the Brans-Dicke parameter, implying consistency of the theory with current data.

  20. Eliminating infinities in the λφ4 theory by simple scaling

    Aragao, Cristiane M.L. de; Carneiro, C.E.I.

    2006-01-01

    We present an alternative method to remove infinities in the perturbative φ 4 theory. In our method, the renormalization is performed in two stages. Firstly, the infinities are eliminated by rescaling the Lagrangian. The Green functions obtained from this rescaled Lagrangian are finite to all orders in perturbation. Secondly, we fix the values of parameters of the resulting finite theory at a certain mass scale by using the standard renormalization conditions. This second stage allows us to derive renormalization equations which yields the critical behavior of the theory. We show that our method does not change the critical behavior of the λφ 4 theory in 4-ε dimensions. In particular, we recover the usual critical exponents

  1. Creation and validation of the barriers to alcohol reduction (BAR) scale using classical test theory and item response theory.

    Kunicki, Zachary J; Schick, Melissa R; Spillane, Nichea S; Harlow, Lisa L

    2018-06-01

    Those who binge drink are at increased risk for alcohol-related consequences when compared to non-binge drinkers. Research shows individuals may face barriers to reducing their drinking behavior, but few measures exist to assess these barriers. This study created and validated the Barriers to Alcohol Reduction (BAR) scale. Participants were college students ( n  = 230) who endorsed at least one instance of past-month binge drinking (4+ drinks for women or 5+ drinks for men). Using classical test theory, exploratory structural equation modeling found a two-factor structure of personal/psychosocial barriers and perceived program barriers. The sub-factors, and full scale had reasonable internal consistency (i.e., coefficient omega = 0.78 (personal/psychosocial), 0.82 (program barriers), and 0.83 (full measure)). The BAR also showed evidence for convergent validity with the Brief Young Adult Alcohol Consequences Questionnaire ( r  = 0.39, p  Theory (IRT) analysis showed the two factors separately met the unidimensionality assumption, and provided further evidence for severity of the items on the two factors. Results suggest that the BAR measure appears reliable and valid for use in an undergraduate student population of binge drinkers. Future studies may want to re-examine this measure in a more diverse sample.

  2. Integration of genome-scale metabolic networks into whole-body PBPK models shows phenotype-specific cases of drug-induced metabolic perturbation.

    Cordes, Henrik; Thiel, Christoph; Baier, Vanessa; Blank, Lars M; Kuepfer, Lars

    2018-01-01

    Drug-induced perturbations of the endogenous metabolic network are a potential root cause of cellular toxicity. A mechanistic understanding of such unwanted side effects during drug therapy is therefore vital for patient safety. The comprehensive assessment of such drug-induced injuries requires the simultaneous consideration of both drug exposure at the whole-body and resulting biochemical responses at the cellular level. We here present a computational multi-scale workflow that combines whole-body physiologically based pharmacokinetic (PBPK) models and organ-specific genome-scale metabolic network (GSMN) models through shared reactions of the xenobiotic metabolism. The applicability of the proposed workflow is illustrated for isoniazid, a first-line antibacterial agent against Mycobacterium tuberculosis , which is known to cause idiosyncratic drug-induced liver injuries (DILI). We combined GSMN models of a human liver with N-acetyl transferase 2 (NAT2)-phenotype-specific PBPK models of isoniazid. The combined PBPK-GSMN models quantitatively describe isoniazid pharmacokinetics, as well as intracellular responses, and changes in the exometabolome in a human liver following isoniazid administration. Notably, intracellular and extracellular responses identified with the PBPK-GSMN models are in line with experimental and clinical findings. Moreover, the drug-induced metabolic perturbations are distributed and attenuated in the metabolic network in a phenotype-dependent manner. Our simulation results show that a simultaneous consideration of both drug pharmacokinetics at the whole-body and metabolism at the cellular level is mandatory to explain drug-induced injuries at the patient level. The proposed workflow extends our mechanistic understanding of the biochemistry underlying adverse events and may be used to prevent drug-induced injuries in the future.

  3. Quantitative Assessment of Thermodynamic Constraints on the Solution Space of Genome-Scale Metabolic Models

    Hamilton, Joshua J.; Dwivedi, Vivek; Reed, Jennifer L.

    2013-01-01

    Constraint-based methods provide powerful computational techniques to allow understanding and prediction of cellular behavior. These methods rely on physiochemical constraints to eliminate infeasible behaviors from the space of available behaviors. One such constraint is thermodynamic feasibility, the requirement that intracellular flux distributions obey the laws of thermodynamics. The past decade has seen several constraint-based methods that interpret this constraint in different ways, including those that are limited to small networks, rely on predefined reaction directions, and/or neglect the relationship between reaction free energies and metabolite concentrations. In this work, we utilize one such approach, thermodynamics-based metabolic flux analysis (TMFA), to make genome-scale, quantitative predictions about metabolite concentrations and reaction free energies in the absence of prior knowledge of reaction directions, while accounting for uncertainties in thermodynamic estimates. We applied TMFA to a genome-scale network reconstruction of Escherichia coli and examined the effect of thermodynamic constraints on the flux space. We also assessed the predictive performance of TMFA against gene essentiality and quantitative metabolomics data, under both aerobic and anaerobic, and optimal and suboptimal growth conditions. Based on these results, we propose that TMFA is a useful tool for validating phenotypes and generating hypotheses, and that additional types of data and constraints can improve predictions of metabolite concentrations. PMID:23870272

  4. Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models.

    Hamilton, Joshua J; Dwivedi, Vivek; Reed, Jennifer L

    2013-07-16

    Constraint-based methods provide powerful computational techniques to allow understanding and prediction of cellular behavior. These methods rely on physiochemical constraints to eliminate infeasible behaviors from the space of available behaviors. One such constraint is thermodynamic feasibility, the requirement that intracellular flux distributions obey the laws of thermodynamics. The past decade has seen several constraint-based methods that interpret this constraint in different ways, including those that are limited to small networks, rely on predefined reaction directions, and/or neglect the relationship between reaction free energies and metabolite concentrations. In this work, we utilize one such approach, thermodynamics-based metabolic flux analysis (TMFA), to make genome-scale, quantitative predictions about metabolite concentrations and reaction free energies in the absence of prior knowledge of reaction directions, while accounting for uncertainties in thermodynamic estimates. We applied TMFA to a genome-scale network reconstruction of Escherichia coli and examined the effect of thermodynamic constraints on the flux space. We also assessed the predictive performance of TMFA against gene essentiality and quantitative metabolomics data, under both aerobic and anaerobic, and optimal and suboptimal growth conditions. Based on these results, we propose that TMFA is a useful tool for validating phenotypes and generating hypotheses, and that additional types of data and constraints can improve predictions of metabolite concentrations. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  5. A genome-scale metabolic network reconstruction of tomato (Solanum lycopersicum L.) and its application to photorespiratory metabolism

    Yuan, H.; Cheung, C.Y. Maurice; Poolman, M.G.; Hilbers, P.A.J.; van Riel, N.A.W.

    2016-01-01

    Tomato (Solanum lycopersicum L.) has been studied extensively due to its high economic value in the market, and high content in health-promoting antioxidant compounds. Tomato is also considered as an excellent model organism for studying the development and metabolism of fleshy fruits. However, the

  6. Renormalization group scale-setting from the action—a road to modified gravity theories

    Domazet, Silvije; Štefančić, Hrvoje

    2012-01-01

    The renormalization group (RG) corrected gravitational action in Einstein–Hilbert and other truncations is considered. The running scale of the RG is treated as a scalar field at the level of the action and determined in a scale-setting procedure recently introduced by Koch and Ramirez for the Einstein–Hilbert truncation. The scale-setting procedure is elaborated for other truncations of the gravitational action and applied to several phenomenologically interesting cases. It is shown how the logarithmic dependence of the Newton's coupling on the RG scale leads to exponentially suppressed effective cosmological constant and how the scale-setting in particular RG-corrected gravitational theories yields the effective f(R) modified gravity theories with negative powers of the Ricci scalar R. The scale-setting at the level of the action at the non-Gaussian fixed point in Einstein–Hilbert and more general truncations is shown to lead to universal effective action quadratic in the Ricci tensor. (paper)

  7. Renormalization group scale-setting from the action—a road to modified gravity theories

    Domazet, Silvije; Štefančić, Hrvoje

    2012-12-01

    The renormalization group (RG) corrected gravitational action in Einstein-Hilbert and other truncations is considered. The running scale of the RG is treated as a scalar field at the level of the action and determined in a scale-setting procedure recently introduced by Koch and Ramirez for the Einstein-Hilbert truncation. The scale-setting procedure is elaborated for other truncations of the gravitational action and applied to several phenomenologically interesting cases. It is shown how the logarithmic dependence of the Newton's coupling on the RG scale leads to exponentially suppressed effective cosmological constant and how the scale-setting in particular RG-corrected gravitational theories yields the effective f(R) modified gravity theories with negative powers of the Ricci scalar R. The scale-setting at the level of the action at the non-Gaussian fixed point in Einstein-Hilbert and more general truncations is shown to lead to universal effective action quadratic in the Ricci tensor.

  8. Metabolic Trade-offs between Biomass Synthesis and Photosynthate Export at Different Light Intensities in a Genome–Scale Metabolic Model of Rice

    Mark Graham Poolman

    2014-11-01

    Full Text Available Previously we have used a genome scale model of rice metabolism to describe how metabolism reconfigures at different light intensities in an expanding leaf of rice. Although this established that the metabolism of the leaf was adequatelyrepresented, in the model, the scenario was not that of the typical function of the leaf --- to provide material for the rest of the plant. Here we extend our analysis to explore the transition to a source leaf as export of photosynthate increases at the expense of making leaf biomass precursors, again as a function of light intensity. In particular we investigate whether, when the leaf is making a smaller range of compounds for export to the phloem, the same changes occur in the interactions between mitochondrial and chloroplast metabolism as seen in biomass synthesis for growth when light intensity increases. Our results show that the same changes occur qualitatively, though there are slight quantitative differences reflecting differences in the energy and redox requirements for the different metabolic outputs.

  9. Planar plane-wave matrix theory at the four loop order: integrability without BMN scaling

    Fischbacher, Thomas; Klose, Thomas; Plefka, Jan

    2005-01-01

    We study SU(N) plane-wave matrix theory up to fourth perturbative order in its large N planar limit. The effective hamiltonian in the closed su(2) subsector of the model is explicitly computed through a specially tailored computer program to perform large scale distributed symbolic algebra and generation of planar graphs. The number of graphs here was in the deep billions. The outcome of our computation establishes the four-loop integrability of the planar plane-wave matrix model. To elucidate the integrable structure we apply the recent technology of the perturbative asymptotic Bethe ansatz to our model. The resulting S-matrix turns out to be structurally similar but nevertheless distinct to the so far considered long-range spin-chain S-matrices of Inozemtsev, Beisert-Dippel-Staudacher and Arutyunov-Frolov-Staudacher in the AdS/CFT context. In particular our result displays a breakdown of BMN scaling at the four-loop order. That is, while there exists an appropriate identification of the matrix theory mass parameter with the coupling constant of the N=4 superconformal Yang-Mills theory which yields an eighth order lattice derivative for well separated impurities (naively implying BMN scaling) the detailed impurity contact interactions ruin this scaling property at the four-loop order. Moreover we study the issue of 'wrapping' interactions, which show up for the first time at this loop-order through a Konishi descendant length four operator. (author)

  10. Time-sliced perturbation theory for large scale structure I: general formalism

    Blas, Diego; Garny, Mathias; Sibiryakov, Sergey [Theory Division, CERN, CH-1211 Genève 23 (Switzerland); Ivanov, Mikhail M., E-mail: diego.blas@cern.ch, E-mail: mathias.garny@cern.ch, E-mail: mikhail.ivanov@cern.ch, E-mail: sergey.sibiryakov@cern.ch [FSB/ITP/LPPC, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne (Switzerland)

    2016-07-01

    We present a new analytic approach to describe large scale structure formation in the mildly non-linear regime. The central object of the method is the time-dependent probability distribution function generating correlators of the cosmological observables at a given moment of time. Expanding the distribution function around the Gaussian weight we formulate a perturbative technique to calculate non-linear corrections to cosmological correlators, similar to the diagrammatic expansion in a three-dimensional Euclidean quantum field theory, with time playing the role of an external parameter. For the physically relevant case of cold dark matter in an Einstein-de Sitter universe, the time evolution of the distribution function can be found exactly and is encapsulated by a time-dependent coupling constant controlling the perturbative expansion. We show that all building blocks of the expansion are free from spurious infrared enhanced contributions that plague the standard cosmological perturbation theory. This paves the way towards the systematic resummation of infrared effects in large scale structure formation. We also argue that the approach proposed here provides a natural framework to account for the influence of short-scale dynamics on larger scales along the lines of effective field theory.

  11. Quasi-potential and Two-Scale Large Deviation Theory for Gillespie Dynamics

    Li, Tiejun

    2016-01-07

    The construction of energy landscape for bio-dynamics is attracting more and more attention recent years. In this talk, I will introduce the strategy to construct the landscape from the connection to rare events, which relies on the large deviation theory for Gillespie-type jump dynamics. In the application to a typical genetic switching model, the two-scale large deviation theory is developed to take into account the fast switching of DNA states. The comparison with other proposals are also discussed. We demonstrate different diffusive limits arise when considering different regimes for genetic translation and switching processes.

  12. Higgs mass scales and matter-antimatter oscillations in grand unified theories

    Senjanovic, G.

    1982-01-01

    A general discussion of mass scales in grand unified theories is presented, with special emphasis on Higgs scalars which mediate neutron-antineutron (n-anti n) and hydrogen-antihydrogen (H-anti H) oscillations. It is shown that the analogue of survival hypothesis for fermions naturally makes such particles superheavy, thus leading to unobservable lifetimes. If this hypothesis is relaxed, an interesting possibility of potentially observable n-anti n and H-anti H transitions, mutually related arises in the context of SU(5) theory with spontaneously broken B-L symmetry

  13. Conservation laws and radiation in the scale covariant theory of gravitation

    Beesham, A.

    1988-01-01

    The conservation laws for mass, energy, and momentum are derived in the scale covariant theory of gravitation. The entropy problem which exists in the standard Friedmann-Lemaitre-Robertson-Walker models can be solved in the present context. Since the weak and strong energy conditions may be violated, a big bang singularity may be avoided, in contrast to general relativity. Since beta is shown to be constant during the radiation-dominated era, the difficulties in the theory associated with nucleosynthesis are avoided. 10 references

  14. Autotrophs' challenge to Dynamic Energy Budget theory: Comment on ;Physics of metabolic organization; by Marko Jusup et al.

    Geček, Sunčana

    2017-03-01

    Jusup and colleagues in the recent review on physics of metabolic organization [1] discuss in detail motivational considerations and common assumptions of Dynamic Energy Budget (DEB) theory, supply readers with a practical guide to DEB-based modeling, demonstrate the construction and dynamics of the standard DEB model, and illustrate several applications. The authors make a step forward from the existing literature by seamlessly bridging over the dichotomy between (i) thermodynamic foundations of the theory (which are often more accessible and understandable to physicists and mathematicians), and (ii) the resulting bioenergetic models (mostly used by biologists in real-world applications).

  15. Molecular evolutionary rates are not correlated with temperature and latitude in Squamata: an exception to the metabolic theory of ecology?

    Rolland, Jonathan; Loiseau, Oriane; Romiguier, Jonathan; Salamin, Nicolas

    2016-05-20

    The metabolic theory of ecology stipulates that molecular evolutionary rates should correlate with temperature and latitude in ectothermic organisms. Previous studies have shown that most groups of vertebrates, such as amphibians, turtles and even endothermic mammals, have higher molecular evolutionary rates in regions where temperature is high. However, the association between molecular evolutionary rates and temperature or latitude has never been tested in Squamata. We used a large dataset including the spatial distributions and environmental variables for 1,651 species of Squamata and compared the contrast of the rates of molecular evolution with the contrast of temperature and latitude between sister species. Using major axis regressions and a new algorithm to choose independent sister species pairs, we found that temperature and absolute latitude were not associated with molecular evolutionary rates. This absence of association in such a diverse ectothermic group questions the mechanisms explaining current pattern of species diversity in Squamata and challenges the presupposed universality of the metabolic theory of ecology.

  16. Characterizing the multi–scale spatial structure of remotely sensed evapotranspiration with information theory

    N. A. Brunsell

    2011-08-01

    Full Text Available A more thorough understanding of the multi-scale spatial structure of land surface heterogeneity will enhance understanding of the relationships and feedbacks between land surface conditions, mass and energy exchanges between the surface and the atmosphere, and regional meteorological and climatological conditions. The objectives of this study were to (1 quantify which spatial scales are dominant in determining the evapotranspiration flux between the surface and the atmosphere and (2 to quantify how different spatial scales of atmospheric and surface processes interact for different stages of the phenological cycle. We used the ALEXI/DisALEXI model for three days (DOY 181, 229 and 245 in 2002 over the Ft. Peck Ameriflux site to estimate the latent heat flux from Landsat, MODIS and GOES satellites. We then applied a multiresolution information theory methodology to quantify these interactions across different spatial scales and compared the dynamics across the different sensors and different periods. We note several important results: (1 spatial scaling characteristics vary with day, but are usually consistent for a given sensor, but (2 different sensors give different scalings, and (3 the different sensors exhibit different scaling relationships with driving variables such as fractional vegetation and near surface soil moisture. In addition, we note that while the dominant length scale of the vegetation index remains relatively constant across the dates, the contribution of the vegetation index to the derived latent heat flux varies with time. We also note that length scales determined from MODIS are consistently larger than those determined from Landsat, even at scales that should be detectable by MODIS. This may imply an inability of the MODIS sensor to accurately determine the fine scale spatial structure of the land surface. These results aid in identifying the dominant cross-scale nature of local to regional biosphere

  17. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism

    Hefzi, Hooman; Ang, Kok Siong; Hanscho, Michael

    2016-01-01

    Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess optimization, we reconstructed the metabolic pathways...

  18. Nutrient Uptake and Metabolism Along a Large Scale Tropical Physical-Chemical Gradient

    Tromboni, F.; Neres-Lima, V.; Saltarelli, W. A.; Miwa, A. C. P.; Cunha, D. G. F.

    2016-12-01

    Nutrient spiraling is a whole-system approach for estimating nutrient uptake that can be used to assess aquatic ecosystems' responses to environmental change and anthropogenic impacts. Historically research on nutrient dynamic uptake in streams has focused on single nutrient dynamics and only rarely the stoichiometric uptake has been considered and linked to carbon metabolism driven by autotrophic and heterotrophic production. We investigated the relationship between uptake of phosphate (PO43-), nitrate (NO3-) ammonium (NH4+) and total dissolve nitrogen (DIN)/ PO43-; and gross primary production (GPP), respiration (R), and net ecosystem productivity (NEP) in six relatively pristine streams with differences regarding canopy cover and physical characteristics, located in a large scale gradient from tropical Atlantic Forest to an Atlantic forest/Cerrado (Brazilian Savanna) transition. We carried out whole stream instantaneous additions of PO43-, NO3- and NH4+ added to each stream in combination, using the TASCC (Tracer Additions for Spiraling Curve Characterization) method. Metabolism measurements were performed in the same streams right after uptake was measured, using one-station open channel method and re-aeration estimations for those sites. We found different background concentrations in the streams located in the Atlantic forest compared with the transition area with Cerrado. In general PO43- and NO3- uptake increased with the decreasing of canopy cover, while a positive relation with background concentration better explained NH4+uptake. DIN/PO43- uptake increased with increasing R and NEP. Little work on functional characteristics of pristine streams has been conducted in this region and this work provides an initial characterization on nitrogen and phosphorus dynamics as well as their stoichiometric uptake in streams.

  19. Physics on all scales. Scalar-tensor theories of quantum gravity in particle physics and cosmology

    Henz, Tobias

    2016-05-10

    In this thesis, we investigate dilaton quantum gravity using a functional renormalization group approach. We derive and discuss flow equations both in the background field approximation and using a vertex expansion as well as solve the fixed point equations globally to show how realistic gravity, connecting ultraviolet and infrared physics, can be realized on a pure fixed point trajectory by virtue of spontaneous breaking of scale invariance. The emerging physical system features a dynamically generated moving Planck scale resembling the Newton coupling as well as slow roll inflation with an exponentially decreasing effective cosmological constant that vanishes completely in the infrared. The moving Planck scale might make quantum gravity experimentally accessible at a different energy scale than previously believed. We therefore not only provide further evidence for the existence of a consistent quantum theory of gravity based on general relativity, but also offer potential solutions towards the hierarchy and cosmological constant problems, thereby opening up exciting opportunities for further research.

  20. A computational comparison of theory and practice of scale intonation in Byzantine chant

    Panteli, Maria; Purwins, Hendrik

    2013-01-01

    Byzantine Chant performance practice is quantitatively compared to the Chrysanthine theory. The intonation of scale degrees is quantified, based on pitch class profiles. An analysis procedure is introduced that consists of the following steps: 1) Pitch class histograms are calculated via non-parametric...... kernel smoothing. 2) Histogram peaks are detected. 3) Phrase ending analysis aids the finding of the tonic to align histogram peaks. 4) The theoretical scale degrees are mapped to the practical ones. 5) A schema of statistical tests detects significant deviations of theoretical scale tuning from...... the estimated ones in performance practice. The analysis of 94 echoi shows a tendency of the singer to level theoretic particularities of the echos that stand out of the general norm in the octoechos: theoretically extremely large scale steps are diminished in performance....

  1. Psychometric Properties of the Theory of Mind Assessment Scale in a Sample of Adolescents and Adults.

    Bosco, Francesca M; Gabbatore, Ilaria; Tirassa, Maurizio; Testa, Silvia

    2016-01-01

    This research aimed at the evaluation of the psychometric properties of the Theory of Mind Assessment Scale (Th.o.m.a.s.). Th.o.m.a.s. is a semi-structured interview meant to evaluate a person's Theory of Mind (ToM). It is composed of several questions organized in four scales, each focusing on one of the areas of knowledge in which such faculty may manifest itself: Scale A (I-Me) investigates first-order first-person ToM; Scale B (Other-Self) investigates third-person ToM from an allocentric perspective; Scale C (I-Other) again investigates third-person ToM, but from an egocentric perspective; and Scale D (Other-Me) investigates second-order ToM. The psychometric proprieties of Th.o.m.a.s. were evaluated in a sample of 156 healthy persons: 80 preadolescent and adolescent (aged 11-17 years, 42 females) and 76 adults (aged from 20 to 67 years, 35 females). Th.o.m.a.s. scores show good inter-rater agreement and internal consistency; the scores increase with age. Evidence of criterion validity was found as Scale B scores were correlated with those of an independent instrument for the evaluation of ToM, the Strange Stories task. Confirmatory factor analysis (CFA) showed good fit of the four-factors theoretical model to the data, although the four factors were highly correlated. For each of the four scales, Rasch analyses showed that, with few exceptions, items fitted the Partial credit model and their functioning was invariant for gender and age. The results of this study, along with those of previous researches with clinical samples, show that Th.o.m.a.s. is a promising instrument to assess ToM in different populations.

  2. A simplified density matrix minimization for linear scaling self-consistent field theory

    Challacombe, M.

    1999-01-01

    A simplified version of the Li, Nunes and Vanderbilt [Phys. Rev. B 47, 10891 (1993)] and Daw [Phys. Rev. B 47, 10895 (1993)] density matrix minimization is introduced that requires four fewer matrix multiplies per minimization step relative to previous formulations. The simplified method also exhibits superior convergence properties, such that the bulk of the work may be shifted to the quadratically convergent McWeeny purification, which brings the density matrix to idempotency. Both orthogonal and nonorthogonal versions are derived. The AINV algorithm of Benzi, Meyer, and Tuma [SIAM J. Sci. Comp. 17, 1135 (1996)] is introduced to linear scaling electronic structure theory, and found to be essential in transformations between orthogonal and nonorthogonal representations. These methods have been developed with an atom-blocked sparse matrix algebra that achieves sustained megafloating point operations per second rates as high as 50% of theoretical, and implemented in the MondoSCF suite of linear scaling SCF programs. For the first time, linear scaling Hartree - Fock theory is demonstrated with three-dimensional systems, including water clusters and estane polymers. The nonorthogonal minimization is shown to be uncompetitive with minimization in an orthonormal representation. An early onset of linear scaling is found for both minimal and double zeta basis sets, and crossovers with a highly optimized eigensolver are achieved. Calculations with up to 6000 basis functions are reported. The scaling of errors with system size is investigated for various levels of approximation. copyright 1999 American Institute of Physics

  3. Scale dependence of the average potential around the maximum in Φ4 theories

    Tetradis, N.; Wetterich, C.

    1992-04-01

    The average potential describes the physics at a length scale k - 1 by averaging out the degrees of freedom with characteristic moments larger than k. The dependence on k can be described by differential evolution equations. We solve these equations for the nonconvex part of the potential around the origin in φ 4 theories, in the phase with spontaneous symmetry breaking. The average potential is real and approaches the convex effective potential in the limit k → 0. Our calculation is relevant for processes for which the shape of the potential at a given scale is important, such as tunneling phenomena or inflation. (orig.)

  4. On Δβ and the search for asymptotic scaling in lattice gauge theory

    Petcher, D.

    1986-01-01

    An ansatz for the β-function of SU(3) lattice gauge theory in four dimensions whose parameters are determined by Monte Carlo data is used both to compare different sets of data for Δβ and to study systematic errors. The data for Δβ obtained from different values of the block spin renormalization group scaling factor are shown to be compatible within statistical errors. However the data is easily consistent with sizeable deviations (ca. 30% or more) from the two loop approximation to the renormalization group scaling formula for physical quantities in the region of coupling for which Δβ essentially takes on its asymptotic value. (orig.)

  5. ONETEP: linear-scaling density-functional theory with plane-waves

    Haynes, P D; Mostof, A A; Skylaris, C-K; Payne, M C

    2006-01-01

    This paper provides a general overview of the methodology implemented in onetep (Order-N Electronic Total Energy Package), a parallel density-functional theory code for largescale first-principles quantum-mechanical calculations. The distinctive features of onetep are linear-scaling in both computational effort and resources, obtained by making well-controlled approximations which enable simulations to be performed with plane-wave accuracy. Titanium dioxide clusters of increasing size designed to mimic surfaces are studied to demonstrate the accuracy and scaling of onetep

  6. Scaling of the quark-antiquark potential and improved actions in SU(2) lattice gauge theory

    Montvay, I.; Gutbrod, F.

    1983-11-01

    The scaling behaviour of the quark-antiquark potential is investigated by a high statistics Monte Carlo calculation in SU(2) lattice gauge theory. Besides the standard one-plaquette action we also use Symanzik's tree-level improved action and Wilson's block-spin improved action. No significant differences between Symanzik's action and the standard action have been observed. For small β Wilson's action scales differently. The string tension value chi extracted from the data corresponds to Λsub(latt) = (0.018 +- 0.001) √chi for the one-plaquette action. (orig.)

  7. Features and New Physical Scales in Primordial Observables: Theory and Observation

    Chluba, Jens; Patil, Subodh P.

    2015-01-01

    All cosmological observations to date are consistent with adiabatic, Gaussian and nearly scale invariant initial conditions. These findings provide strong evidence for a particular symmetry breaking pattern in the very early universe (with a close to vanishing order parameter, $\\epsilon$), widely accepted as conforming to the predictions of the simplest realizations of the inflationary paradigm. However, given that our observations are only privy to perturbations, in inferring something about the background that gave rise to them, it should be clear that many different underlying constructions project onto the same set of cosmological observables. Features in the primordial correlation functions, if present, would offer a unique and discriminating window onto the parent theory in which the mechanism that generated the initial conditions is embedded. In certain contexts, simple linear response theory allows us to infer new characteristic scales from the presence of features that can break the aforementioned de...

  8. [Scale Relativity Theory in living beings morphogenesis: fratal, determinism and chance].

    Chaline, J

    2012-10-01

    The Scale Relativity Theory has many biological applications from linear to non-linear and, from classical mechanics to quantum mechanics. Self-similar laws have been used as model for the description of a huge number of biological systems. Theses laws may explain the origin of basal life structures. Log-periodic behaviors of acceleration or deceleration can be applied to branching macroevolution, to the time sequences of major evolutionary leaps. The existence of such a law does not mean that the role of chance in evolution is reduced, but instead that randomness and contingency may occur within a framework which may itself be structured in a partly statistical way. The scale relativity theory can open new perspectives in evolution. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  9. Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model

    Teusink, B.; Wiersma, A.; Molenaar, D.; Francke, C.; Vos, de W.M.; Siezen, R.J.; Smid, E.J.

    2006-01-01

    A genome-scale metabolic model of the lactic acid bacterium Lactobacillus plantarum WCFS1 was constructed based on genomic content and experimental data. The complete model includes 721 genes, 643 reactions, and 531 metabolites. Different stoichiometric modeling techniques were used for

  10. Analysis of critical neutron- scattering data from iron and dynamical scaling theory

    Als-Nielsen, Jens Aage

    1970-01-01

    Experimental three- axis spectrometer data of critical neutron- scattering data from Fe are reanalyzed and compared with the recent theoretical prediction by P. Resibois and C. Piette. The reason why the spin- diffusion parameter did not obey the prediction of dynamical scaling theory is indicated....... Double- axis spectrometer data have previously been interpreted in terms of a non- Lorentzian susceptibility. It is shown that with proper corrections for the inelasticity of the scattering the data are consistent with a Lorentzian form of susceptibility....

  11. Scale relativity theory and integrative systems biology: 2. Macroscopic quantum-type mechanics.

    Nottale, Laurent; Auffray, Charles

    2008-05-01

    In these two companion papers, we provide an overview and a brief history of the multiple roots, current developments and recent advances of integrative systems biology and identify multiscale integration as its grand challenge. Then we introduce the fundamental principles and the successive steps that have been followed in the construction of the scale relativity theory, which aims at describing the effects of a non-differentiable and fractal (i.e., explicitly scale dependent) geometry of space-time. The first paper of this series was devoted, in this new framework, to the construction from first principles of scale laws of increasing complexity, and to the discussion of some tentative applications of these laws to biological systems. In this second review and perspective paper, we describe the effects induced by the internal fractal structures of trajectories on motion in standard space. Their main consequence is the transformation of classical dynamics into a generalized, quantum-like self-organized dynamics. A Schrödinger-type equation is derived as an integral of the geodesic equation in a fractal space. We then indicate how gauge fields can be constructed from a geometric re-interpretation of gauge transformations as scale transformations in fractal space-time. Finally, we introduce a new tentative development of the theory, in which quantum laws would hold also in scale space, introducing complexergy as a measure of organizational complexity. Initial possible applications of this extended framework to the processes of morphogenesis and the emergence of prokaryotic and eukaryotic cellular structures are discussed. Having founded elements of the evolutionary, developmental, biochemical and cellular theories on the first principles of scale relativity theory, we introduce proposals for the construction of an integrative theory of life and for the design and implementation of novel macroscopic quantum-type experiments and devices, and discuss their potential

  12. Dark energy and modified gravity in the Effective Field Theory of Large-Scale Structure

    Cusin, Giulia; Lewandowski, Matthew; Vernizzi, Filippo

    2018-04-01

    We develop an approach to compute observables beyond the linear regime of dark matter perturbations for general dark energy and modified gravity models. We do so by combining the Effective Field Theory of Dark Energy and Effective Field Theory of Large-Scale Structure approaches. In particular, we parametrize the linear and nonlinear effects of dark energy on dark matter clustering in terms of the Lagrangian terms introduced in a companion paper [1], focusing on Horndeski theories and assuming the quasi-static approximation. The Euler equation for dark matter is sourced, via the Newtonian potential, by new nonlinear vertices due to modified gravity and, as in the pure dark matter case, by the effects of short-scale physics in the form of the divergence of an effective stress tensor. The effective fluid introduces a counterterm in the solution to the matter continuity and Euler equations, which allows a controlled expansion of clustering statistics on mildly nonlinear scales. We use this setup to compute the one-loop dark-matter power spectrum.

  13. Genome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis.

    Hong Yang

    2014-09-01

    Full Text Available Transposon mutagenesis, in combination with parallel sequencing, is becoming a powerful tool for en-masse mutant analysis. A probability generating function was used to explain observed miniHimar transposon insertion patterns, and gene essentiality calls were made by transposon insertion frequency analysis (TIFA. TIFA incorporated the observed genome and sequence motif bias of the miniHimar transposon. The gene essentiality calls were compared to: 1 previous genome-wide direct gene-essentiality assignments; and, 2 flux balance analysis (FBA predictions from an existing genome-scale metabolic model of Shewanella oneidensis MR-1. A three-way comparison between FBA, TIFA, and the direct essentiality calls was made to validate the TIFA approach. The refinement in the interpretation of observed transposon insertions demonstrated that genes without insertions are not necessarily essential, and that genes that contain insertions are not always nonessential. The TIFA calls were in reasonable agreement with direct essentiality calls for S. oneidensis, but agreed more closely with E. coli essentiality calls for orthologs. The TIFA gene essentiality calls were in good agreement with the MR-1 FBA essentiality predictions, and the agreement between TIFA and FBA predictions was substantially better than between the FBA and the direct gene essentiality predictions.

  14. The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

    Agren, Rasmus; Liu, Liming; Shoaie, Saeed; Vongsangnak, Wanwipa; Nookaew, Intawat; Nielsen, Jens

    2013-01-01

    We present the RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox: a software suite that allows for semi-automated reconstruction of genome-scale models. It makes use of published models and/or the KEGG database, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology. The RAVEN Toolbox workflow was applied in order to reconstruct a genome-scale metabolic model for the important microbial cell factory Penicillium chrysogenum Wisconsin54-1255. The model was validated in a bibliomic study of in total 440 references, and it comprises 1471 unique biochemical reactions and 1006 ORFs. It was then used to study the roles of ATP and NADPH in the biosynthesis of penicillin, and to identify potential metabolic engineering targets for maximization of penicillin production. PMID:23555215

  15. Genome-scale reconstruction of the Streptococcus pyogenes M49 metabolic network reveals growth requirements and indicates potential drug targets.

    Levering, Jennifer; Fiedler, Tomas; Sieg, Antje; van Grinsven, Koen W A; Hering, Silvio; Veith, Nadine; Olivier, Brett G; Klett, Lara; Hugenholtz, Jeroen; Teusink, Bas; Kreikemeyer, Bernd; Kummer, Ursula

    2016-08-20

    Genome-scale metabolic models comprise stoichiometric relations between metabolites, as well as associations between genes and metabolic reactions and facilitate the analysis of metabolism. We computationally reconstructed the metabolic network of the lactic acid bacterium Streptococcus pyogenes M49. Initially, we based the reconstruction on genome annotations and already existing and curated metabolic networks of Bacillus subtilis, Escherichia coli, Lactobacillus plantarum and Lactococcus lactis. This initial draft was manually curated with the final reconstruction accounting for 480 genes associated with 576 reactions and 558 metabolites. In order to constrain the model further, we performed growth experiments of wild type and arcA deletion strains of S. pyogenes M49 in a chemically defined medium and calculated nutrient uptake and production fluxes. We additionally performed amino acid auxotrophy experiments to test the consistency of the model. The established genome-scale model can be used to understand the growth requirements of the human pathogen S. pyogenes and define optimal and suboptimal conditions, but also to describe differences and similarities between S. pyogenes and related lactic acid bacteria such as L. lactis in order to find strategies to reduce the growth of the pathogen and propose drug targets. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. An Analysis of the Connectedness to Nature Scale Based on Item Response Theory.

    Pasca, Laura; Aragonés, Juan I; Coello, María T

    2017-01-01

    The Connectedness to Nature Scale (CNS) is used as a measure of the subjective cognitive connection between individuals and nature. However, to date, it has not been analyzed at the item level to confirm its quality. In the present study, we conduct such an analysis based on Item Response Theory. We employed data from previous studies using the Spanish-language version of the CNS, analyzing a sample of 1008 participants. The results show that seven items presented appropriate indices of discrimination and difficulty, in addition to a good fit. The remaining six have inadequate discrimination indices and do not present a good fit. A second study with 321 participants shows that the seven-item scale has adequate levels of reliability and validity. Therefore, it would be appropriate to use a reduced version of the scale after eliminating the items that display inappropriate behavior, since they may interfere with research results on connectedness to nature.

  17. A New Functional Health Literacy Scale for Japanese Young Adults Based on Item Response Theory.

    Tsubakita, Takashi; Kawazoe, Nobuo; Kasano, Eri

    2017-03-01

    Health literacy predicts health outcomes. Despite concerns surrounding the health of Japanese young adults, to date there has been no objective assessment of health literacy in this population. This study aimed to develop a Functional Health Literacy Scale for Young Adults (funHLS-YA) based on item response theory. Each item in the scale requires participants to choose the most relevant term from 3 choices in relation to a target item, thus assessing objective rather than perceived health literacy. The 20-item scale was administered to 1816 university students and 1751 responded. Cronbach's α coefficient was .73. Difficulty and discrimination parameters of each item were estimated, resulting in the exclusion of 1 item. Some items showed different difficulty parameters for male and female participants, reflecting that some aspects of health literacy may differ by gender. The current 19-item version of funHLS-YA can reliably assess the objective health literacy of Japanese young adults.

  18. Wave-particle duality through an extended model of the scale relativity theory

    Ioannou, P D; Nica, P; Agop, M; Paun, V; Vizureanu, P

    2008-01-01

    Considering that the chaotic effect of associated wave packet on the particle itself results in movements on the fractal (continuous and non-differentiable) curves of fractal dimension D F , wave-particle duality through an extension of the scale relativity theory is given. It results through an equation of motion for the complex speed field, that in a fractal fluid, the convection, dissipation and dispersion are reciprocally compensating at any scale (differentiable or non-differentiable). From here, for an irrotational movement, a generalized Schroedinger equation is obtained. The absence of dispersion implies a generalized Navier-Stokes type equation, whereas, for the irrotational movement and the fractal dimension, D F = 2, the usual Schroedinger equation results. The absence of dissipation implies a generalized Korteweg-de Vries type equation. In such conjecture, at the differentiable scale, the duality is achieved through the flowing regimes of the fractal fluid, i.e. the wave character by means of the non-quasi-autonomous flowing regime and the particle character by means of the quasi-autonomous flowing regime. These flowing regimes are separated by '0.7 structure'. At the non-differentiable scale, a fractal potential acts as an energy accumulator and controls through the coherence the duality. The correspondence between the differentiable and non-differentiable scales implies a Cantor space-time. Moreover, the wave-particle duality implies at any scale a fractal.

  19. Genome-scale reconstruction of the metabolic network in Yersinia pestis CO92

    Navid, Ali; Almaas, Eivind

    2007-03-01

    The gram-negative bacterium Yersinia pestis is the causative agent of bubonic plague. Using publicly available genomic, biochemical and physiological data, we have developed a constraint-based flux balance model of metabolism in the CO92 strain (biovar Orientalis) of this organism. The metabolic reactions were appropriately compartmentalized, and the model accounts for the exchange of metabolites, as well as the import of nutrients and export of waste products. We have characterized the metabolic capabilities and phenotypes of this organism, after comparing the model predictions with available experimental observations to evaluate accuracy and completeness. We have also begun preliminary studies into how cellular metabolism affects virulence.

  20. Theory and evidence for using the economy-of-scale law in power plant economics

    Phung, D.L.

    1987-05-01

    This report compiles theory and evidence for the use of the economy-of-scale law in energy economics, particularly in the estimation of capital costs for coal-fired and nuclear power plants. The economy-of-scale law is widely used in its simplest form: cost is directly proportional to capacity raised to an exponent. An additive constant is an important component that is not generally taken into account. Also, the economy of scale is perforce valid only over a limited size range. The majority of engineering studies have estimated an economy of scale exponent of 0.7 to 0.9 for coal-fired plants and an exponent of 0.4 to 0.6 for nuclear plants in the capacity ranges of 400 to 1000 MWe. However, the majority of econometric analyses found little or no economy of scale for coal-fired plants and only a slight economy of scale for nuclear plants. This disparity is explained by the fact that economists have included regulatory and time-related costs in addition to the direct and indirect costs used by the engineers. Regulatory and time-related costs have become an increasingly larger portion of total costs during the last decade. In addition, these costs appeared to have either a very small economy of scale or to be increasing as the size of the power plant increased. We conclude that gains in economy of scale can only be made by reducing regulatory and time-related costs through design standardization and regulatory stability, in combination with more favorable economic conditions. 59 refs

  1. [Theory humoral pathology K Rokitansky, cellular phathology R Virchov and new phylogenetic theory disease development. Ethyology and pathogenesis of metabolic pandemias].

    Titov, V N

    2013-01-01

    Virchow's cellular pathology indirectly points at structural units between cells and organs in vivo and at universal mechanisms underlying the condition of health or disease. In order to substantiate similarity of pathogeneses of atherosclerosis, diabetes mellitus, metabolic syndrome and obesity we suggest a phylogenetic theory which includes: 1) consideration of physiological and pathological processes in vivo from the viewpoint of biological functions and biological reactions. 2) Phylogenesis of metabolic regulation at the levels of: a) cells (autocrine), b) paracrine cell communities, i.e., structural and functional units of each organ (paracrine), and c) the entire organism. Biological functions are: trophology, homeostasis, endoecology ( of the intercellular medium), adaptation, locomotion, reproduction, and cognition. 3) A three-step successive phylogenesis of biological functions and pathological responses. Methodological approaches in phylogenesis are: a) succession of biological functions and reactions and b) biological subordination where phylogenetically late humoral mediators cannot abolish the effects of phylogenetically early mediators. Incompliance of humoral regulation at different steps of phylogenesis, autocrine, paracrine and the organism levels is the basis for similarity between pathogeneses of all metabolic pandemias, including essential hypertension and insulin resistance syndrome.

  2. Solution to the hierarchy problem from an almost decoupled hidden sector within a classically scale invariant theory

    Foot, Robert; Kobakhidze, Archil; Volkas, Raymond R.; McDonald, Kristian L.

    2008-01-01

    If scale invariance is a classical symmetry then both the Planck scale and the weak scale should emerge as quantum effects. We show that this can be realized in simple scale invariant theories with a hidden sector. The weak/Planck scale hierarchy emerges in the (technically natural) limit in which the hidden sector decouples from the ordinary sector. In this limit, finite corrections to the weak scale are consequently small, while quadratic divergences are absent by virtue of classical scale invariance, so there is no hierarchy problem

  3. Challenges for dynamic energy budget theory. Comment on ;Physics of metabolic organization; by Marko Jusup et al.

    Nisbet, Roger M.

    2017-03-01

    Jusup et al. [1] provide a comprehensive review of Dynamic Energy Budget (DEB) theory - a theory of metabolic organization that has its roots in a model by S.A.L.M Kooijman [2] and has evolved over three decades into a remarkable general theory whose use appears to be growing exponentially. The definitive text on DEB theory [3] is a challenging (though exceptionally rewarding) read, and previous reviews (e.g. [4,5]) have provided focused summaries of some of its main themes, targeted at specific groups of readers. The strong case for a further review is well captured in the abstract: ;Hitherto, the foundations were more accessible to physicists or mathematicians, and the applications to biologists, causing a dichotomy in what always should have been a single body of work.; In response to this need, Jusup et al. provide a review that combines a lucid, rigorous exposition of the core components of DEB theory with a diverse collection of DEB applications. They also highlight some recent advances, notably the rapidly growing on-line database of DEB model parameters (451 species on 15 August 2016 according to [1], now, just a few months later, over 500 species).

  4. The validity and scalability of the Theory of Mind Scale with toddlers and preschoolers.

    Hiller, Rachel M; Weber, Nathan; Young, Robyn L

    2014-12-01

    Despite the importance of theory of mind (ToM) for typical development, there remain 2 key issues affecting our ability to draw robust conclusions. One is the continued focus on false belief as the sole measure of ToM. The second is the lack of empirically validated measures of ToM as a broad construct. Our key aim was to examine the validity and reliability of the 5-item ToM scale (Peterson, Wellman, & Liu, 2005). In particular, we extended on previous research of this scale by assessing its scalability and validity for use with children from 2 years of age. Sixty-eight typically developing children (aged 24 to 61 months) were assessed on the scale's 5 tasks, along with a sixth Sally-Anne false-belief task. Our data replicated the scalability of the 5 tasks for a Rasch-but not Guttman-scale. Guttman analysis showed that a 4-item scale may be more suitable for this age range. Further, the tasks showed good internal consistency and validity for use with children as young as 2 years of age. Overall, the measure provides a valid and reliable tool for the assessment of ToM, and in particular, the longitudinal assessment of this ability as a construct. (c) 2014 APA, all rights reserved.

  5. Time-Sliced Perturbation Theory for Large Scale Structure I: General Formalism

    Blas, Diego; Ivanov, Mikhail M.; Sibiryakov, Sergey

    2016-01-01

    We present a new analytic approach to describe large scale structure formation in the mildly non-linear regime. The central object of the method is the time-dependent probability distribution function generating correlators of the cosmological observables at a given moment of time. Expanding the distribution function around the Gaussian weight we formulate a perturbative technique to calculate non-linear corrections to cosmological correlators, similar to the diagrammatic expansion in a three-dimensional Euclidean quantum field theory, with time playing the role of an external parameter. For the physically relevant case of cold dark matter in an Einstein--de Sitter universe, the time evolution of the distribution function can be found exactly and is encapsulated by a time-dependent coupling constant controlling the perturbative expansion. We show that all building blocks of the expansion are free from spurious infrared enhanced contributions that plague the standard cosmological perturbation theory. This pave...

  6. De Sitter and scaling solutions in a higher-order modified teleparallel theory

    Paliathanasis, Andronikos, E-mail: anpaliat@phys.uoa.gr [Instituto de Ciencias Físicas y Matemáticas, Universidad Austral de Chile, Valdivia (Chile)

    2017-08-01

    The existence and the stability conditions for some exact relativistic solutions of special interest are studied in a higher-order modified teleparallel gravitational theory. The theory with the use of a Lagrange multiplier is equivalent with that of General Relativity with a minimally coupled noncanonical field. The conditions for the existence of de Sitter solutions and ideal gas solutions in the case of vacuum are studied as also the stability criteria. Furthermore, in the presence of matter the behaviour of scaling solutions is given. Finally, we discuss the degrees of freedom of the field equations and we reduce the field equations in an algebraic equation, where in order to demonstrate our result we show how this noncanonical scalar field can reproduce the Hubble function of Λ-cosmology.

  7. Developing Scale for Assimilate the Integration between Learning Theories and E-learning.

    George Maher Iskander

    2014-03-01

    Full Text Available As e-learning tend to get more and more significant for all kind of universities, researchers and consultants are becoming aware of the fact that a high technology approach and Blackboard do not guarantee successful teaching and learning. Thus, a move to pedagogy-based theories can be observed within the field of e-learning. This study describes the procedure of the development of an empirically-based psychometrically-sound instrument to measure instructional model for e-learning system at Middle East universities. In order to accelerate the acceptance of e-learning and implementation of institution-wide adoption of e-learning, it is important to understand students' perceptions with instructional model for e- learning. The 19-item scale developed shows a high probability of differentiating between positive and negative perceptions and the methods which can be used for embedding the traditional learning theories into e-learning.

  8. Atomic-scale simulation of dust grain collisions: Surface chemistry and dissipation beyond existing theory

    Quadery, Abrar H.; Doan, Baochi D.; Tucker, William C.; Dove, Adrienne R.; Schelling, Patrick K.

    2017-10-01

    The early stages of planet formation involve steps where submicron-sized dust particles collide to form aggregates. However, the mechanism through which millimeter-sized particles aggregate to kilometer-sized planetesimals is still not understood. Dust grain collision experiments carried out in the environment of the Earth lead to the prediction of a 'bouncing barrier' at millimeter-sizes. Theoretical models, e.g., Johnson-Kendall-Roberts and Derjaguin-Muller-Toporov theories, lack two key features, namely the chemistry of dust grain surfaces, and a mechanism for atomic-scale dissipation of energy. Moreover, interaction strengths in these models are parameterized based on experiments done in the Earth's environment. To address these issues, we performed atomic-scale simulations of collisions between nonhydroxylated and hydroxylated amorphous silica nanoparticles. We used the ReaxFF approach which enables modeling chemical reactions using an empirical potential. We found that nonhydroxylated nanograins tend to adhere with much higher probability than suggested by existing theories. By contrast, hydroxylated nanograins exhibit a strong tendency to bounce. Also, the interaction between dust grains has the characteristics of a strong chemical force instead of weak van der Waals forces. This suggests that the formation of strong chemical bonds and dissipation via internal atomic vibration may result in aggregation beyond what is expected based on our current understanding. Our results also indicate that experiments should more carefully consider surface conditions to mimic the space environment. We also report results of simulations with molten silica nanoparticles. It is found that molten particles are more likely to adhere due to viscous dissipation, which supports theories that suggest aggregation to kilometer scales might require grains to be in a molten state.

  9. Front-end vision and multi-scale image analysis multi-scale computer vision theory and applications, written in Mathematica

    Romeny, Bart M Haar

    2008-01-01

    Front-End Vision and Multi-Scale Image Analysis is a tutorial in multi-scale methods for computer vision and image processing. It builds on the cross fertilization between human visual perception and multi-scale computer vision (`scale-space') theory and applications. The multi-scale strategies recognized in the first stages of the human visual system are carefully examined, and taken as inspiration for the many geometric methods discussed. All chapters are written in Mathematica, a spectacular high-level language for symbolic and numerical manipulations. The book presents a new and effective

  10. Absolute calibration of the mass scale in the inverse problem of the physical theory of fireballs

    Kalenichenko, V. V.

    1992-08-01

    A method of the absolute calibration of the mass scale is proposed for solving the inverse problem of the physical theory of fireballs. The method is based on data on the masses of fallen meteorites whose fireballs have been photographed in flight. The method can be applied to fireballs whose bodies have not experienced significant fragmentation during their flight in the atmosphere and have kept their shape relatively well. Data on the Lost City and Innisfree meteorites are used to calculate the calibration coefficients.

  11. Absolute mass scale calibration in the inverse problem of the physical theory of fireballs.

    Kalenichenko, V. V.

    A method of the absolute mass scale calibration is suggested for solving the inverse problem of the physical theory of fireballs. The method is based on the data on the masses of the fallen meteorites whose fireballs have been photographed in their flight. The method may be applied to those fireballs whose bodies have not experienced considerable fragmentation during their destruction in the atmosphere and have kept their form well enough. Statistical analysis of the inverse problem solution for a sufficiently representative sample makes it possible to separate a subsample of such fireballs. The data on the Lost City and Innisfree meteorites are used to obtain calibration coefficients.

  12. Cosmological models with a hybrid scale factor in an extended gravity theory

    Mishra, B.; Tripathy, S. K.; Tarai, Sankarsan

    2018-03-01

    A general formalism to investigate Bianchi type V Ih universes is developed in an extended theory of gravity. A minimally coupled geometry and matter field is considered with a rescaled function of f(R,T) substituted in place of the Ricci scalar R in the geometrical action. Dynamical aspects of the models are discussed by using a hybrid scale factor (HSF) that behaves as power law in an initial epoch and as an exponential form at late epoch. The power law behavior and the exponential behavior appear as two extreme cases of the present model.

  13. The O(epsilon2) scaling law for dsigma/dt in the Reggeon field theory

    Dash, J.W.; Grandou, Thierry.

    1979-04-01

    The two loop contributions were calculated within the epsilon-expansion to the Reggeon Field Theory scaling law for dsigma/dt, derived using the renormalization group and a general renormalization point for the Pomeron propagator. This generalizes the O(epsilon) work of Abarbanel, Bartels, Bronzan, and Sidhu. The invariance of the results under certain coupling constant rescalings is demonstrated. Some qualitative comments were made regarding phenomenological applications. Our amplitude in a certain limit approximates the form of the low energy diffractive amplitude advocated by Kane

  14. Bridging scales from molecular simulations to classical thermodynamics: density functional theory of capillary condensation in nanopores

    Neimark, Alexander V; Ravikovitch, Peter I; Vishnyakov, Aleksey

    2003-01-01

    With the example of the capillary condensation of Lennard-Jones fluid in nanopores ranging from 1 to 10 nm, we show that the non-local density functional theory (NLDFT) with properly chosen parameters of intermolecular interactions bridges the scale gap from molecular simulations to macroscopic thermodynamics. On the one hand, NLDFT correctly approximates the results of Monte Carlo simulations (shift of vapour-liquid equilibrium, spinodals, density profiles, adsorption isotherms) for pores wider than about 2 nm. On the other hand, NLDFT smoothly merges (above 7-10 nm) with the Derjaguin-Broekhoff-de Boer equations which represent augmented Laplace-Kelvin equations of capillary condensation and desorption

  15. Effective field theory analysis on μ problem in low-scale gauge mediation

    Zheng Sibo

    2012-01-01

    Supersymmetric models based on the scenario of gauge mediation often suffer from the well-known μ problem. In this paper, we reconsider this problem in low-scale gauge mediation in terms of effective field theory analysis. In this paradigm, all high energy input soft mass can be expressed via loop expansions. If the corrections coming from messenger thresholds are small, as we assume in this letter, then all RG evaluations can be taken as linearly approximation for low-scale supersymmetric breaking. Due to these observations, the parameter space can be systematically classified and studied after constraints coming from electro-weak symmetry breaking are imposed. We find that some old proposals in the literature are reproduced, and two new classes are uncovered. We refer to a microscopic model, where the specific relations among coefficients in one of the new classes are well motivated. Also, we discuss some primary phenomenologies.

  16. On Δβ and the search for asymptotic scaling in lattice gauge theory

    Petcher, D.

    1986-01-01

    An ansatz for the β-function of SU(3) lattice gauge theory in four dimensions whose parameters are determined by Monte Carlo data is used both to compare different sets of data for Δβ and to study systematic errors. The data for Δβ obtained from different values of the block-spin renormalization group scaling factor are shown to be compatible within statistical errors. However the data is easily consistent with sizeable deviations (ca. 30% or more) from the two-loop approximation to the renormalization group scaling formula for physical quantities in the region of coupling for which Δβ essentially takes on its asymptotic value. (orig.)

  17. Cosmological large-scale structures beyond linear theory in modified gravity

    Bernardeau, Francis; Brax, Philippe, E-mail: francis.bernardeau@cea.fr, E-mail: philippe.brax@cea.fr [CEA, Institut de Physique Théorique, 91191 Gif-sur-Yvette Cédex (France)

    2011-06-01

    We consider the effect of modified gravity on the growth of large-scale structures at second order in perturbation theory. We show that modified gravity models changing the linear growth rate of fluctuations are also bound to change, although mildly, the mode coupling amplitude in the density and reduced velocity fields. We present explicit formulae which describe this effect. We then focus on models of modified gravity involving a scalar field coupled to matter, in particular chameleons and dilatons, where it is shown that there exists a transition scale around which the existence of an extra scalar degree of freedom induces significant changes in the coupling properties of the cosmic fields. We obtain the amplitude of this effect for realistic dilaton models at the tree-order level for the bispectrum, finding them to be comparable in amplitude to those obtained in the DGP and f(R) models.

  18. Item response theory analysis of the Lichtenberg Financial Decision Screening Scale.

    Teresi, Jeanne A; Ocepek-Welikson, Katja; Lichtenberg, Peter A

    2017-01-01

    The focus of these analyses was to examine the psychometric properties of the Lichtenberg Financial Decision Screening Scale (LFDSS). The purpose of the screen was to evaluate the decisional abilities and vulnerability to exploitation of older adults. Adults aged 60 and over were interviewed by social, legal, financial, or health services professionals who underwent in-person training on the administration and scoring of the scale. Professionals provided a rating of the decision-making abilities of the older adult. The analytic sample included 213 individuals with an average age of 76.9 (SD = 10.1). The majority (57%) were female. Data were analyzed using item response theory (IRT) methodology. The results supported the unidimensionality of the item set. Several IRT models were tested. Ten ordinal and binary items evidenced a slightly higher reliability estimate (0.85) than other versions and better coverage in terms of the range of reliable measurement across the continuum of financial incapacity.

  19. Techniques for Large-Scale Bacterial Genome Manipulation and Characterization of the Mutants with Respect to In Silico Metabolic Reconstructions.

    diCenzo, George C; Finan, Turlough M

    2018-01-01

    The rate at which all genes within a bacterial genome can be identified far exceeds the ability to characterize these genes. To assist in associating genes with cellular functions, a large-scale bacterial genome deletion approach can be employed to rapidly screen tens to thousands of genes for desired phenotypes. Here, we provide a detailed protocol for the generation of deletions of large segments of bacterial genomes that relies on the activity of a site-specific recombinase. In this procedure, two recombinase recognition target sequences are introduced into known positions of a bacterial genome through single cross-over plasmid integration. Subsequent expression of the site-specific recombinase mediates recombination between the two target sequences, resulting in the excision of the intervening region and its loss from the genome. We further illustrate how this deletion system can be readily adapted to function as a large-scale in vivo cloning procedure, in which the region excised from the genome is captured as a replicative plasmid. We next provide a procedure for the metabolic analysis of bacterial large-scale genome deletion mutants using the Biolog Phenotype MicroArray™ system. Finally, a pipeline is described, and a sample Matlab script is provided, for the integration of the obtained data with a draft metabolic reconstruction for the refinement of the reactions and gene-protein-reaction relationships in a metabolic reconstruction.

  20. Forests as Patrimonies? From Theory to Tangible Processes at Various Scales

    Genevieve Michon

    2012-09-01

    Full Text Available Among theoretical fields addressing the conceptualization of interrelationships between nature and society, patrimonial approaches remain relatively unexplored. Stressing the multiplication of local dynamics where elements of nature are redefined as "patrimonies" (ranging from local patrimonies to world heritage by various social groups, this conceptual field tries to qualify these dynamics and their determiners to understand how they allow us to better address contemporary environmental challenges. Through a multidisciplinary approach in social sciences, centered on rural forests, we analyze the multiplication of patrimonial processes in forest development at various scales. First, we elaborate on the concept of patrimony and on patrimonial processes and present the current construction and dynamics of forest patrimonies. A crucial question concerns the links that form between the many spatial-temporal levels where these processes develop. Moreover, these patrimonial processes can be quite divergent, not only across scales from local to global, but also between "endogenous" (or bottom-up and "exogenous" (or top-down processes. We present two detailed examples in Morocco and Sumatra, where patrimonial constructions are developing simultaneously at various scales and through various actors who treat the forest in very different ways. Drawing from these examples, we discuss how and why the simultaneous development of different, often overlapping, patrimonial constructions along these scales allows collaboration or, conversely, can lead their holders into conflict. Lastly, we discuss the contribution of patrimonial concepts to resilience thinking and social-ecological systems theory.

  1. Scaling dynamic response and destructive metabolism in an immunosurveillant anti-tumor system modulated by different external periodic interventions.

    Yuanzhi Shao

    Full Text Available On the basis of two universal power-law scaling laws, i.e. the scaling dynamic hysteresis in physics and the allometric scaling metabolism in biosystem, we studied the dynamic response and the evolution of an immunosurveillant anti-tumor system subjected to a periodic external intervention, which is equivalent to the scheme of a radiotherapy or chemotherapy, within the framework of the growth dynamics of tumor. Under the modulation of either an abrupt or a gradual change external intervention, the population density of tumors exhibits a dynamic hysteresis to the intervention. The area of dynamic hysteresis loop characterizes a sort of dissipative-therapeutic relationship of the dynamic responding of treated tumors with the dose consumption of accumulated external intervention per cycle of therapy. Scaling the area of dynamic hysteresis loops against the intensity of an external intervention, we deduced a characteristic quantity which was defined as the theoretical therapeutic effectiveness of treated tumor and related with the destructive metabolism of tumor under treatment. The calculated dose-effectiveness profiles, namely the dose cumulant per cycle of intervention versus the therapeutic effectiveness, could be well scaled into a universal quadratic formula regardless of either an abrupt or a gradual change intervention involved. We present a new concept, i.e., the therapy-effect matrix and the dose cumulant matrix, to expound the new finding observed in the growth and regression dynamics of a modulated anti-tumor system.

  2. Examining the validity of the Academic Motivation Scale by comparing scale construction to self-determination theory.

    Cokley, K O

    2000-04-01

    This study examined the construct validity of the Academic Motivation Scale. Specifically, subscale correlations were examined to assess whether support for a continuum of self-determination would be provided. The three types of Intrinsic Motivation were significantly and positively correlated with each other .67, .62, and .58, while the three types of Extrinsic Motivation were significantly and positively intercorrelated .50, .49, and .45. The former subscales, however, correlated higher with Introjected Regulation than Identified Regulation, suggesting that Introjected Regulation may be indicative of more self-determined behavior than has previously been believed. Also, the Intrinsic Motivation To Accomplish subscale had a stronger relationship with two of the Extrinsic Motivation subscales, Identified Regulation and Introjected Regulation, than did the Extrinsic Motivation subscales with each other. This suggests that the differences between Extrinsic and Intrinsic Motivation are not as obvious as has been believed. Also, contrary to self-determination theory, Amotivation had a stronger negative correlation with Identified Regulation (r = -.31) than with any of the Intrinsic Motivation subscales (rs = -.27, -.19, and -.11).

  3. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism

    Hefzi, Hooman; Ang, Kok  Siong; Hanscho, Michael; Bordbar, Aarash; Ruckerbauer, David; Lakshmanan, Meiyappan; Orellana, Camila  A.; Baycin-Hizal, Deniz; Huang, Yingxiang; Ley, Daniel; Martinez, Veronica  S.; Kyriakopoulos, Sarantos; Jimé nez, Natalia  E.; Zielinski, Daniel  C.; Quek, Lake-Ee; Wulff, Tune; Arnsdorf, Johnny; Li, Shangzhong; Lee, Jae  Seong; Paglia, Giuseppe; Loira, Nicolas; Spahn, Philipp  N.; Pedersen, Lasse  E.; Gutierrez, Jahir  M.; King, Zachary  A.; Lund, Anne  Mathilde; Nagarajan, Harish; Thomas, Alex; Abdel-Haleem, Alyaa M.; Zanghellini, Juergen; Kildegaard, Helene  F.; Voldborg, Bjø rn  G.; Gerdtzen, Ziomara  P.; Betenbaugh, Michael  J.; Palsson, Bernhard  O.; Andersen, Mikael  R.; Nielsen, Lars  K.; Borth, Nicole; Lee, Dong-Yup; Lewis, Nathan  E.

    2016-01-01

    Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess

  4. In silico method for modelling metabolism and gene product expression at genome scale

    Lerman, Joshua A.; Hyduke, Daniel R.; Latif, Haythem; Portnoy, Vasiliy A.; Lewis, Nathan E.; Orth, Jeffrey D.; Rutledge, Alexandra C.; Smith, Richard D.; Adkins, Joshua N.; Zengler, Karsten; Palsson, Bernard O.

    2012-07-03

    Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism.

  5. Nonsingular cosmology with a scale-invariant spectrum of cosmological perturbations from Lee-Wick theory

    Cai Yifu; Qiu Taotao; Brandenberger, Robert; Zhang Xinmin

    2009-01-01

    We study the cosmology of a Lee-Wick type scalar field theory. First, we consider homogeneous and isotropic background solutions and find that they are nonsingular, leading to cosmological bounces. Next, we analyze the spectrum of cosmological perturbations which result from this model. Unless either the potential of the Lee-Wick theory or the initial conditions are finely tuned, it is impossible to obtain background solutions which have a sufficiently long period of inflation after the bounce. More interestingly, however, we find that in the generic noninflationary bouncing cosmology, perturbations created from quantum vacuum fluctuations in the contracting phase have the correct form to lead to a scale-invariant spectrum of metric inhomogeneities in the expanding phase. Since the background is nonsingular, the evolution of the fluctuations is defined unambiguously through the bounce. We also analyze the evolution of fluctuations which emerge from thermal initial conditions in the contracting phase. The spectrum of gravitational waves stemming from quantum vacuum fluctuations in the contracting phase is also scale-invariant, and the tensor to scalar ratio is not suppressed.

  6. Simulation of electron energy loss spectra of nanomaterials with linear-scaling density functional theory

    Tait, E W; Payne, M C; Ratcliff, L E; Haynes, P D; Hine, N D M

    2016-01-01

    Experimental techniques for electron energy loss spectroscopy (EELS) combine high energy resolution with high spatial resolution. They are therefore powerful tools for investigating the local electronic structure of complex systems such as nanostructures, interfaces and even individual defects. Interpretation of experimental electron energy loss spectra is often challenging and can require theoretical modelling of candidate structures, which themselves may be large and complex, beyond the capabilities of traditional cubic-scaling density functional theory. In this work, we present functionality to compute electron energy loss spectra within the onetep linear-scaling density functional theory code. We first demonstrate that simulated spectra agree with those computed using conventional plane wave pseudopotential methods to a high degree of precision. The ability of onetep to tackle large problems is then exploited to investigate convergence of spectra with respect to supercell size. Finally, we apply the novel functionality to a study of the electron energy loss spectra of defects on the (1 0 1) surface of an anatase slab and determine concentrations of defects which might be experimentally detectable. (paper)

  7. Multiple spatial scaling and the weak-coupling approximation. I. General formulation and equilibrium theory

    Kleinsmith, P E [Carnegie-Mellon Univ., Pittsburgh, Pa. (USA)

    1976-04-01

    Multiple spatial scaling is incorporated in a modified form of the Bogoliubov plasma cluster expansion; then this proposed reformulation of the plasma weak-coupling approximation is used to derive, from the BBGKY Hierarchy, a decoupled set of equations for the one-and two-particle distribution functions in the limit as the plasma parameter goes to zero. Because the reformulated cluster expansion permits retention of essential two-particle collisional information in the limiting equations, while simultaneously retaining the well-established Debye-scale relative ordering of the correlation functions, decoupling of the Hierarchy is accomplished without introduction of the divergence problems encountered in the Bogoliubov theory, as is indicated by an exact solution of the limiting equations for the equilibrium case. To establish additional links with existing plasma equilibrium theories, the two-particle equilibrium correlation function is used to calculate the interaction energy and the equation of state. The limiting equation for the equilibrium three-particle correlation function is then developed, and a formal solution is obtained.

  8. Large-scale transportation network congestion evolution prediction using deep learning theory.

    Ma, Xiaolei; Yu, Haiyang; Wang, Yunpeng; Wang, Yinhai

    2015-01-01

    Understanding how congestion at one location can cause ripples throughout large-scale transportation network is vital for transportation researchers and practitioners to pinpoint traffic bottlenecks for congestion mitigation. Traditional studies rely on either mathematical equations or simulation techniques to model traffic congestion dynamics. However, most of the approaches have limitations, largely due to unrealistic assumptions and cumbersome parameter calibration process. With the development of Intelligent Transportation Systems (ITS) and Internet of Things (IoT), transportation data become more and more ubiquitous. This triggers a series of data-driven research to investigate transportation phenomena. Among them, deep learning theory is considered one of the most promising techniques to tackle tremendous high-dimensional data. This study attempts to extend deep learning theory into large-scale transportation network analysis. A deep Restricted Boltzmann Machine and Recurrent Neural Network architecture is utilized to model and predict traffic congestion evolution based on Global Positioning System (GPS) data from taxi. A numerical study in Ningbo, China is conducted to validate the effectiveness and efficiency of the proposed method. Results show that the prediction accuracy can achieve as high as 88% within less than 6 minutes when the model is implemented in a Graphic Processing Unit (GPU)-based parallel computing environment. The predicted congestion evolution patterns can be visualized temporally and spatially through a map-based platform to identify the vulnerable links for proactive congestion mitigation.

  9. Large-scale transportation network congestion evolution prediction using deep learning theory.

    Xiaolei Ma

    Full Text Available Understanding how congestion at one location can cause ripples throughout large-scale transportation network is vital for transportation researchers and practitioners to pinpoint traffic bottlenecks for congestion mitigation. Traditional studies rely on either mathematical equations or simulation techniques to model traffic congestion dynamics. However, most of the approaches have limitations, largely due to unrealistic assumptions and cumbersome parameter calibration process. With the development of Intelligent Transportation Systems (ITS and Internet of Things (IoT, transportation data become more and more ubiquitous. This triggers a series of data-driven research to investigate transportation phenomena. Among them, deep learning theory is considered one of the most promising techniques to tackle tremendous high-dimensional data. This study attempts to extend deep learning theory into large-scale transportation network analysis. A deep Restricted Boltzmann Machine and Recurrent Neural Network architecture is utilized to model and predict traffic congestion evolution based on Global Positioning System (GPS data from taxi. A numerical study in Ningbo, China is conducted to validate the effectiveness and efficiency of the proposed method. Results show that the prediction accuracy can achieve as high as 88% within less than 6 minutes when the model is implemented in a Graphic Processing Unit (GPU-based parallel computing environment. The predicted congestion evolution patterns can be visualized temporally and spatially through a map-based platform to identify the vulnerable links for proactive congestion mitigation.

  10. Planck-scale induced left–right gauge theory at LHC and experimental tests

    M.K. Parida

    2016-05-01

    Full Text Available Recent measurements at LHC have inspired searches for TeV scale left–right gauge theory originating from grand unified theories. We show that inclusion of Planck-scale induced effects due to dim.5 operator not only does away with all the additional intermediate symmetries, but also it predicts the minimal set of light Higgs scalars tailored after neutrino masses and dilepton, or trilepton signals. The heavy-light neutrino mixings are predicted from charged fermion mass fits in SO(10 and LFV constraints which lead to new predictions for dilepton or trilepton production signals. Including fine-structure constant matching and two-loop, and threshold effects predict MWR=g2R104.3±1.5±0.2 GeV and proton lifetime τp=1036.15±5.8±0.2 yrs with WR gauge boson coupling g2R=0.56–0.57. Predictions on lepton flavour and lepton number violations are accessible to ongoing experiments. Current CMS data on di-electron excess at s=8 TeV are found to be consistent with WR gauge boson mass MWR≥1.9–2.2 TeV which also agrees with the values obtained from dijet resonance production data. We also discuss plausible explanations for diboson production excesses observed at LHC and make predictions expected at s=14 TeV.

  11. A preliminary and qualitative study of resource ratio theory to nitrifying lab-scale bioreactors.

    Bellucci, Micol; Ofiţeru, Irina D; Beneduce, Luciano; Graham, David W; Head, Ian M; Curtis, Thomas P

    2015-05-01

    The incorporation of microbial diversity in design would ideally require predictive theory that would relate operational parameters to the numbers and distribution of taxa. Resource ratio-theory (RRT) might be one such theory. Based on Monod kinetics, it explains diversity in function of resource-ratio and richness. However, to be usable in biological engineered system, the growth parameters of all the bacteria under consideration and the resource supply and diffusion parameters for all the relevant nutrients should be determined. This is challenging, but plausible, at least for low diversity groups with simple resource requirements like the ammonia oxidizing bacteria (AOB). One of the major successes of RRT was its ability to explain the 'paradox of enrichment' which states that diversity first increases and then decreases with resource richness. Here, we demonstrate that this pattern can be seen in lab-scale-activated sludge reactors and parallel simulations that incorporate the principles of RRT in a floc-based system. High and low ammonia and oxygen were supplied to continuous flow bioreactors with resource conditions correlating with the composition and diversity of resident AOB communities based on AOB 16S rDNA clone libraries. Neither the experimental work nor the simulations are definitive proof for the application of RRT in this context. However, it is sufficient evidence that such approach might work and justify a more rigorous investigation. © 2015 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  12. Large wood influence on stream metabolism at a reach-scale in the Assabet River, Massachusetts

    David, G. C. L.; Snyder, N. P.; Rosario, G. M.

    2016-12-01

    Total stream metabolism (TSM) represents the transfer of carbon through a channel by both primary production and respiration, and thus represents the movement of energy through a watershed. Large wood (LW) creates geomorphically complex channels by diverting flows, altering shear stresses on the channel bed and banks, and pool development. The increase in habitat complexity around LW is expected to increase TSM, but this change has not been directly measured. In this study, we measured changes in TSM around a LW jam in a Massachusetts river. Dissolved oxygen (DO) time series data are used to quantify gross primary production (GPP), ecosystem respiration (ER), which equal TSM when summed. Two primary objectives of this study are to (1) assess changes in TSM around LW and (2) compare empirical methods of deriving TSM to Grace et al.'s (2015) BASE model. We hypothesized that LW would increase TSM by providing larger pools, increasing coverage for fish and macroinvertebrates, increasing organic matter accumulation, and providing a place for primary producers to anchor and grow. The Assabet River is a 78 km2 drainage basin in central Massachusetts that provides public water supply to 7 towns. A change in TSM over a reach-scale was assessed using two YSI 6-Series Multiparameter Water Quality sondes over a 140 m long pool-riffle open meadow section. The reach included 6 pools and one LW jam. Every two weeks from July to November 2015, the sondes were moved to different pools. The sondes collected DO, temperature, depth, pH, salinity, light intensity, and turbidity at 15-minute intervals. Velocity (V) and discharge (Q) were measured weekly around the sondes and at established cross sections. Instantaneous V and Q were calculated for each sonde by modeling flows in HEC-RAS. Overall, TSM was heavily influenced by the pool size and indirectly to the LW jam which was associated with the largest pool. The largest error in TSM calculations is related to the empirically

  13. Chaos, scaling and existence of a continuum limit in classical non-Abelian lattice gauge theory

    Nielsen, H.B.; Rugh, H.H.; Rugh, S.E.

    1996-01-01

    We discuss space-time chaos and scaling properties for classical non-Abelian gauge fields discretized on a spatial lattice. We emphasize that there is a open-quote no goclose quotes for simulating the original continuum classical gauge fields over a long time span since there is a never ending dynamical cascading towards the ultraviolet. We note that the temporal chaotic properties of the original continuum gauge fields and the lattice gauge system have entirely different scaling properties thereby emphasizing that they are entirely different dynamical systems which have only very little in common. Considered as a statistical system in its own right the lattice gauge system in a situation where it has reached equilibrium comes closest to what could be termed a open-quotes continuum limitclose quotes in the limit of very small energies (weak non-linearities). We discuss the lattice system both in the limit for small energies and in the limit of high energies where we show that there is a saturation of the temporal chaos as a pure lattice artifact. Our discussion focuses not only on the temporal correlations but to a large extent also on the spatial correlations in the lattice system. We argue that various conclusions of physics have been based on monitoring the non-Abelian lattice system in regimes where the fields are correlated over few lattice units only. This is further evidenced by comparison with results for Abelian lattice gauge theory. How the real time simulations of the classical lattice gauge theory may reach contact with the real time evolution of (semi-classical aspects of) the quantum gauge theory (e.g. Q.C.D.) is left an important question to be further examined

  14. Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1).

    de la Torre, Andrea; Metivier, Aisha; Chu, Frances; Laurens, Lieve M L; Beck, David A C; Pienkos, Philip T; Lidstrom, Mary E; Kalyuzhnaya, Marina G

    2015-11-25

    Methane-utilizing bacteria (methanotrophs) are capable of growth on methane and are attractive systems for bio-catalysis. However, the application of natural methanotrophic strains to large-scale production of value-added chemicals/biofuels requires a number of physiological and genetic alterations. An accurate metabolic model coupled with flux balance analysis can provide a solid interpretative framework for experimental data analyses and integration. A stoichiometric flux balance model of Methylomicrobium buryatense strain 5G(B1) was constructed and used for evaluating metabolic engineering strategies for biofuels and chemical production with a methanotrophic bacterium as the catalytic platform. The initial metabolic reconstruction was based on whole-genome predictions. Each metabolic step was manually verified, gapfilled, and modified in accordance with genome-wide expression data. The final model incorporates a total of 841 reactions (in 167 metabolic pathways). Of these, up to 400 reactions were recruited to produce 118 intracellular metabolites. The flux balance simulations suggest that only the transfer of electrons from methanol oxidation to methane oxidation steps can support measured growth and methane/oxygen consumption parameters, while the scenario employing NADH as a possible source of electrons for particulate methane monooxygenase cannot. Direct coupling between methane oxidation and methanol oxidation accounts for most of the membrane-associated methane monooxygenase activity. However the best fit to experimental results is achieved only after assuming that the efficiency of direct coupling depends on growth conditions and additional NADH input (about 0.1-0.2 mol of incremental NADH per one mol of methane oxidized). The additional input is proposed to cover loss of electrons through inefficiency and to sustain methane oxidation at perturbations or support uphill electron transfer. Finally, the model was used for testing the carbon conversion

  15. Using a genome-scale metabolic network model to elucidate the mechanism of chloroquine action in Plasmodium falciparum

    Shivendra G. Tewari

    2017-08-01

    Full Text Available Chloroquine, long the default first-line treatment against malaria, is now abandoned in large parts of the world because of widespread drug-resistance in Plasmodium falciparum. In spite of its importance as a cost-effective and efficient drug, a coherent understanding of the cellular mechanisms affected by chloroquine and how they influence the fitness and survival of the parasite remains elusive. Here, we used a systems biology approach to integrate genome-scale transcriptomics to map out the effects of chloroquine, identify targeted metabolic pathways, and translate these findings into mechanistic insights. Specifically, we first developed a method that integrates transcriptomic and metabolomic data, which we independently validated against a recently published set of such data for Krebs-cycle mutants of P. falciparum. We then used the method to calculate the effect of chloroquine treatment on the metabolic flux profiles of P. falciparum during the intraerythrocytic developmental cycle. The model predicted dose-dependent inhibition of DNA replication, in agreement with earlier experimental results for both drug-sensitive and drug-resistant P. falciparum strains. Our simulations also corroborated experimental findings that suggest differences in chloroquine sensitivity between ring- and schizont-stage P. falciparum. Our analysis also suggests that metabolic fluxes that govern reduced thioredoxin and phosphoenolpyruvate synthesis are significantly decreased and are pivotal to chloroquine-based inhibition of P. falciparum DNA replication. The consequences of impaired phosphoenolpyruvate synthesis and redox metabolism are reduced carbon fixation and increased oxidative stress, respectively, both of which eventually facilitate killing of the parasite. Our analysis suggests that a combination of chloroquine (or an analogue and another drug, which inhibits carbon fixation and/or increases oxidative stress, should increase the clearance of P

  16. Measurement with multiple indicators and psychophysical scaling in the context of Fishbein and Ajzen's theory of reasoned action

    van den Putte, B.; Saris, W.E.; Hoogstraten, J.

    1995-01-01

    Two experiments were carried out to test the theory of reasoned action of Fishbein and Ajzen. The measurements were done using two category scales and two psychophysical scales. No consistent difference in results was found between the four modalities. However, if the latter were used as multiple

  17. Item Response Theory Analyses of the Parent and Teacher Ratings of the DSM-IV ADHD Rating Scale

    Gomez, Rapson

    2008-01-01

    The graded response model (GRM), which is based on item response theory (IRT), was used to evaluate the psychometric properties of the inattention and hyperactivity/impulsivity symptoms in an ADHD rating scale. To accomplish this, parents and teachers completed the DSM-IV ADHD Rating Scale (DARS; Gomez et al., "Journal of Child Psychology and…

  18. Toward city-scale water quality control: building a theory for smart stormwater systems

    Kerkez, B.; Mullapudi, A. M.; Wong, B. P.

    2016-12-01

    Urban stormwater systems are rarely designed as actual systems. Rather, it is often assumed that individual Best Management Practices (BMPs) will add up to achieve desired watershed outcomes. Given the rise of BMPs and green infrastructure, we ask: does doing "best" at the local scale guarantee the "best" at the global scale? Existing studies suggest that the system-level performance of distributed stormwater practices may actually adversely impact watersheds by increasing downstream erosion and reducing water quality. Optimizing spatial placement may not be sufficient, however, since precipitation variability and other sources of uncertainty can drive the overall system into undesirable states. To that end, it is also important to control the temporal behavior of the system, which can be achieved by equipping stormwater elements (ponds, wetlands, basins, bioswales, etc.) with "smart" sensors and valves. Rather than building new infrastructure, this permits for existing assets to be repurposed and controlled to adapt to individual storm events. While we have learned how to build and deploy the necessary sensing and control technologies, we do not have a framework or theory that combines our knowledge of hydrology, hydraulics, water quality and control. We discuss the development of such a framework and investigate how existing water domain knowledge can be transferred into a system-theoretic context to enable real-time, city-scale stormwater control. We apply this framework to water quality control in an urban watershed in southeast Michigan, which has been heavily instrumented and retrofitted for control over the past year.

  19. Theory and evidence of economies of scale in the development of waste management systems

    Chang, Shoou-Yuh; Rivera, A.L.

    1989-01-01

    Waste is a cost of doing business. This cost can be considered in terms of the potential adverse health and environmental impacts, or the waste management costs associated with avoiding, minimizing, and controlling those impacts. There is an anticipated increase in the cost of waste management as a result of the increasing requirements for regulatory compliance. To meet the total waste management capacity needs of the organization and the compliance requirements, low-level radioactive, hazardous, and mixed waste management will need demonstrated technologies strategically managed as a technology portfolio. The role of the decision maker is to select the optimum mix of technologies and facilities to provide the waste management capacity needed for the next twenty years. The waste management system resulting from this mix includes multiple small-scale fixed facilities, large-scale centralized facilities, and waste management subcontracts. This study was conducted to examine the theory and evidence of economies of scale in the development of waste management systems as as exploratory research on the economic considerations in the process of technology selection and implementation. 25 refs., 24 figs., 11 tabs

  20. The Australian Racism, Acceptance, and Cultural-Ethnocentrism Scale (RACES): item response theory findings.

    Grigg, Kaine; Manderson, Lenore

    2016-03-17

    Racism and associated discrimination are pervasive and persistent challenges with multiple cumulative deleterious effects contributing to inequities in various health outcomes. Globally, research over the past decade has shown consistent associations between racism and negative health concerns. Such research confirms that race endures as one of the strongest predictors of poor health. Due to the lack of validated Australian measures of racist attitudes, RACES (Racism, Acceptance, and Cultural-Ethnocentrism Scale) was developed. Here, we examine RACES' psychometric properties, including the latent structure, utilising Item Response Theory (IRT). Unidimensional and Multidimensional Rating Scale Model (RSM) Rasch analyses were utilised with 296 Victorian primary school students and 182 adolescents and 220 adults from the Australian community. RACES was demonstrated to be a robust 24-item three-dimensional scale of Accepting Attitudes (12 items), Racist Attitudes (8 items), and Ethnocentric Attitudes (4 items). RSM Rasch analyses provide strong support for the instrument as a robust measure of racist attitudes in the Australian context, and for the overall factorial and construct validity of RACES across primary school children, adolescents, and adults. RACES provides a reliable and valid measure that can be utilised across the lifespan to evaluate attitudes towards all racial, ethnic, cultural, and religious groups. A core function of RACES is to assess the effectiveness of interventions to reduce community levels of racism and in turn inequities in health outcomes within Australia.

  1. MOST-visualization: software for producing automated textbook-style maps of genome-scale metabolic networks.

    Kelley, James J; Maor, Shay; Kim, Min Kyung; Lane, Anatoliy; Lun, Desmond S

    2017-08-15

    Visualization of metabolites, reactions and pathways in genome-scale metabolic networks (GEMs) can assist in understanding cellular metabolism. Three attributes are desirable in software used for visualizing GEMs: (i) automation, since GEMs can be quite large; (ii) production of understandable maps that provide ease in identification of pathways, reactions and metabolites; and (iii) visualization of the entire network to show how pathways are interconnected. No software currently exists for visualizing GEMs that satisfies all three characteristics, but MOST-Visualization, an extension of the software package MOST (Metabolic Optimization and Simulation Tool), satisfies (i), and by using a pre-drawn overview map of metabolism based on the Roche map satisfies (ii) and comes close to satisfying (iii). MOST is distributed for free on the GNU General Public License. The software and full documentation are available at http://most.ccib.rutgers.edu/. dslun@rutgers.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  2. Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints

    Sanchez, Benjamin J.; Zhang, Xi-Cheng; Nilsson, Avlant

    2017-01-01

    , which act as limitations on metabolic fluxes, are not taken into account. Here, we present GECKO, a method that enhances a GEM to account for enzymes as part of reactions, thereby ensuring that each metabolic flux does not exceed its maximum capacity, equal to the product of the enzyme's abundance...... and turnover number. We applied GECKO to a Saccharomyces cerevisiae GEM and demonstrated that the new model could correctly describe phenotypes that the previous model could not, particularly under high enzymatic pressure conditions, such as yeast growing on different carbon sources in excess, coping...... with stress, or overexpressing a specific pathway. GECKO also allows to directly integrate quantitative proteomics data; by doing so, we significantly reduced flux variability of the model, in over 60% of metabolic reactions. Additionally, the model gives insight into the distribution of enzyme usage between...

  3. Lawton IADL scale in dementia: can item response theory make it more informative?

    McGrory, Sarah; Shenkin, Susan D; Austin, Elizabeth J; Starr, John M

    2014-07-01

    impairment of functional abilities represents a crucial component of dementia diagnosis. Current functional measures rely on the traditional aggregate method of summing raw scores. While this summary score provides a quick representation of a person's ability, it disregards useful information on the item level. to use item response theory (IRT) methods to increase the interpretive power of the Lawton Instrumental Activities of Daily Living (IADL) scale by establishing a hierarchy of item 'difficulty' and 'discrimination'. this cross-sectional study applied IRT methods to the analysis of IADL outcomes. Participants were 202 members of the Scottish Dementia Research Interest Register (mean age = 76.39, range = 56-93, SD = 7.89 years) with complete itemised data available. a Mokken scale with good reliability (Molenaar Sijtsama statistic 0.79) was obtained, satisfying the IRT assumption that the items comprise a single unidimensional scale. The eight items in the scale could be placed on a hierarchy of 'difficulty' (H coefficient = 0.55), with 'Shopping' being the most 'difficult' item and 'Telephone use' being the least 'difficult' item. 'Shopping' was the most discriminatory item differentiating well between patients of different levels of ability. IRT methods are capable of providing more information about functional impairment than a summed score. 'Shopping' and 'Telephone use' were identified as items that reveal key information about a patient's level of ability, and could be useful screening questions for clinicians. © The Author 2013. Published by Oxford University Press on behalf of the British Geriatrics Society. All rights reserved. For Permissions, please email: journals.permissions@ oup.com.

  4. IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models.

    Ye, Chao; Xu, Nan; Dong, Chuan; Ye, Yuannong; Zou, Xuan; Chen, Xiulai; Guo, Fengbiao; Liu, Liming

    2017-04-07

    Genome-scale metabolic models (GSMMs) constitute a platform that combines genome sequences and detailed biochemical information to quantify microbial physiology at the system level. To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD database was built in the LAMP (Linux + Apache + MySQL + PHP) system by integrating and standardizing 328 GSMMs constructed for 139 microorganisms. The IMGMD database can help microbial researchers download manually curated GSMMs, rapidly reconstruct standard GSMMs, design pathways, and identify metabolic targets for strategies on strain improvement. Moreover, the IMGMD database facilitates the integration of wet-lab and in silico data to gain an additional insight into microbial physiology. The IMGMD database is freely available, without any registration requirements, at http://imgmd.jiangnan.edu.cn/database.

  5. Leo Szilard Lectureship Award Talk - Universal Scaling Laws from Cells to Cities; A Physicist's Search for Quantitative, Unified Theories of Biological and Social Structure and Dynamics

    West, Geoffrey

    2013-04-01

    Many of the most challenging, exciting and profound questions facing science and society, from the origins of life to global sustainability, fall under the banner of ``complex adaptive systems.'' This talk explores how scaling can be used to begin to develop physics-inspired quantitative, predictive, coarse-grained theories for understanding their structure, dynamics and organization based on underlying mathematisable principles. Remarkably, most physiological, organisational and life history phenomena in biology and socio-economic systems scale in a simple and ``universal'' fashion: metabolic rate scales approximately as the 3/4-power of mass over 27 orders of magnitude from complex molecules to the largest organisms. Time-scales (such as lifespans and growth-rates) and sizes (such as genome lengths and RNA densities) scale with exponents which are typically simple multiples of 1/4, suggesting that fundamental constraints underlie much of the generic structure and dynamics of living systems. These scaling laws follow from dynamical and geometrical properties of space-filling, fractal-like, hierarchical branching networks, presumed optimised by natural selection. This leads to a general framework that potentially captures essential features of diverse systems including vasculature, ontogenetic growth, cancer, aging and mortality, sleep, cell size, and DNA nucleotide substitution rates. Cities and companies also scale: wages, profits, patents, crime, disease, pollution, road lengths scale similarly across the globe, reflecting underlying universal social network dynamics which point to general principles of organization transcending their individuality. These have dramatic implications for global sustainability: innovation and wealth creation that fuel social systems, left unchecked, potentially sow the seeds for their inevitable collapse.

  6. Presentation : Development of an age-specific genome-scale model of skeletal muscle metabolism

    Cabbia, A.; van Riel, N.A.W.

    2017-01-01

    Skeletal myocytes are among the most metabolically active cell types, implicated in nutrient balance, contributing to the insulin-stimulated clearance of glucose from the blood, and secreting myokines that contribute in regulating inflammation and the ageing process. The loss of muscle mass and

  7. Predicting growth of the healthy infant using a genome scale metabolic model

    Nilsson, Avlant; Mardinoglu, Adil; Nielsen, Jens

    2017-01-01

    to simulate the mechanisms of growth and integrate data about breast-milk intake and composition with the infant's biomass and energy expenditure of major organs. The model predicted daily metabolic fluxes from birth to age 6 months, and accurately reproduced standard growth curves and changes in body...

  8. Flux balance analysis of genome-scale metabolic model of rice ...

    2015-09-28

    Sep 28, 2015 ... biologists are also trying to understand the plant's systems level biochemistry ... metabolism to observe the effect of intracellular transporters' transport ..... [The information about this pathway and associated genes in .... 2013 A method for accounting for mainte- ... Biological control of rice diseases pp 1–11.

  9. Random sampling of elementary flux modes in large-scale metabolic networks.

    Machado, Daniel; Soons, Zita; Patil, Kiran Raosaheb; Ferreira, Eugénio C; Rocha, Isabel

    2012-09-15

    The description of a metabolic network in terms of elementary (flux) modes (EMs) provides an important framework for metabolic pathway analysis. However, their application to large networks has been hampered by the combinatorial explosion in the number of modes. In this work, we develop a method for generating random samples of EMs without computing the whole set. Our algorithm is an adaptation of the canonical basis approach, where we add an additional filtering step which, at each iteration, selects a random subset of the new combinations of modes. In order to obtain an unbiased sample, all candidates are assigned the same probability of getting selected. This approach avoids the exponential growth of the number of modes during computation, thus generating a random sample of the complete set of EMs within reasonable time. We generated samples of different sizes for a metabolic network of Escherichia coli, and observed that they preserve several properties of the full EM set. It is also shown that EM sampling can be used for rational strain design. A well distributed sample, that is representative of the complete set of EMs, should be suitable to most EM-based methods for analysis and optimization of metabolic networks. Source code for a cross-platform implementation in Python is freely available at http://code.google.com/p/emsampler. dmachado@deb.uminho.pt Supplementary data are available at Bioinformatics online.

  10. Microfluidics Enables Small-Scale Tissue-Based Drug Metabolism Studies With Scarce Human Tissue

    van Midwoud, Paul M.; Verpoorte, Elisabeth; Groothuis, Geny M. M.; Merema, M.T.

    2011-01-01

    Early information on the metabolism and toxicity properties of new drug candidates is crucial for selecting the right candidates for further development. Preclinical trials rely on cell-based in vitro tests and animal studies to characterize the in vivo behavior of drug candidates, although neither

  11. Genome-scale model of Streptococcus thermophilus LMG18311 for metabolic comparison.

    Pastink, M.I.; Teusink, B.; Hols, P.; Visser, S.; Vos, W.M.; Hugenholtz, J.

    2009-01-01

    In this report, we describe the amino acid metabolism and amino acid dependency of the dairy bacterium Streptococcus thermophilus LMG18311 and compare them with those of two other characterized lactic acid bacteria, Lactococcus lactis and Lactobacillus plantarum. Through the construction of a

  12. Mean field theory of EM algorithm for Bayesian grey scale image restoration

    Inoue, Jun-ichi; Tanaka, Kazuyuki

    2003-01-01

    The EM algorithm for the Bayesian grey scale image restoration is investigated in the framework of the mean field theory. Our model system is identical to the infinite range random field Q-Ising model. The maximum marginal likelihood method is applied to the determination of hyper-parameters. We calculate both the data-averaged mean square error between the original image and its maximizer of posterior marginal estimate, and the data-averaged marginal likelihood function exactly. After evaluating the hyper-parameter dependence of the data-averaged marginal likelihood function, we derive the EM algorithm which updates the hyper-parameters to obtain the maximum likelihood estimate analytically. The time evolutions of the hyper-parameters and so-called Q function are obtained. The relation between the speed of convergence of the hyper-parameters and the shape of the Q function is explained from the viewpoint of dynamics

  13. Simulations of nanocrystals under pressure: Combining electronic enthalpy and linear-scaling density-functional theory

    Corsini, Niccolò R. C., E-mail: niccolo.corsini@imperial.ac.uk; Greco, Andrea; Haynes, Peter D. [Department of Physics and Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ (United Kingdom); Hine, Nicholas D. M. [Department of Physics and Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ (United Kingdom); Cavendish Laboratory, J. J. Thompson Avenue, Cambridge CB3 0HE (United Kingdom); Molteni, Carla [Department of Physics, King' s College London, Strand, London WC2R 2LS (United Kingdom)

    2013-08-28

    We present an implementation in a linear-scaling density-functional theory code of an electronic enthalpy method, which has been found to be natural and efficient for the ab initio calculation of finite systems under hydrostatic pressure. Based on a definition of the system volume as that enclosed within an electronic density isosurface [M. Cococcioni, F. Mauri, G. Ceder, and N. Marzari, Phys. Rev. Lett.94, 145501 (2005)], it supports both geometry optimizations and molecular dynamics simulations. We introduce an approach for calibrating the parameters defining the volume in the context of geometry optimizations and discuss their significance. Results in good agreement with simulations using explicit solvents are obtained, validating our approach. Size-dependent pressure-induced structural transformations and variations in the energy gap of hydrogenated silicon nanocrystals are investigated, including one comparable in size to recent experiments. A detailed analysis of the polyamorphic transformations reveals three types of amorphous structures and their persistence on depressurization is assessed.

  14. Universality in quantum chaos and the one-parameter scaling theory.

    García-García, Antonio M; Wang, Jiao

    2008-02-22

    The one-parameter scaling theory is adapted to the context of quantum chaos. We define a generalized dimensionless conductance, g, semiclassically and then study Anderson localization corrections by renormalization group techniques. This analysis permits a characterization of the universality classes associated to a metal (g-->infinity), an insulator (g-->0), and the metal-insulator transition (g-->g(c)) in quantum chaos provided that the classical phase space is not mixed. According to our results the universality class related to the metallic limit includes all the systems in which the Bohigas-Giannoni-Schmit conjecture holds but automatically excludes those in which dynamical localization effects are important. The universality class related to the metal-insulator transition is characterized by classical superdiffusion or a fractal spectrum in low dimensions (d < or = 2). Several examples are discussed in detail.

  15. Recommendations to improve the positive and negative syndrome scale (PANSS) based on item response theory.

    Levine, Stephen Z; Rabinowitz, Jonathan; Rizopoulos, Dimitris

    2011-08-15

    The adequacy of the Positive and Negative Syndrome Scale (PANSS) items in measuring symptom severity in schizophrenia was examined using Item Response Theory (IRT). Baseline PANSS assessments were analyzed from two multi-center clinical trials of antipsychotic medication in chronic schizophrenia (n=1872). Generally, the results showed that the PANSS (a) item ratings discriminated symptom severity best for the negative symptoms; (b) has an excess of "Severe" and "Extremely severe" rating options; and (c) assessments are more reliable at medium than very low or high levels of symptom severity. Analysis also showed that the detection of statistically and non-statistically significant differences in treatment were highly similar for the original and IRT-modified PANSS. In clinical trials of chronic schizophrenia, the PANSS appears to require the following modifications: fewer rating options, adjustment of 'Lack of judgment and insight', and improved severe symptom assessment. 2011 Elsevier Ltd. All rights reserved.

  16. DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems.

    Smith, Robert W; van Rosmalen, Rik P; Martins Dos Santos, Vitor A P; Fleck, Christian

    2018-06-19

    Models of metabolism are often used in biotechnology and pharmaceutical research to identify drug targets or increase the direct production of valuable compounds. Due to the complexity of large metabolic systems, a number of conclusions have been drawn using mathematical methods with simplifying assumptions. For example, constraint-based models describe changes of internal concentrations that occur much quicker than alterations in cell physiology. Thus, metabolite concentrations and reaction fluxes are fixed to constant values. This greatly reduces the mathematical complexity, while providing a reasonably good description of the system in steady state. However, without a large number of constraints, many different flux sets can describe the optimal model and we obtain no information on how metabolite levels dynamically change. Thus, to accurately determine what is taking place within the cell, finer quality data and more detailed models need to be constructed. In this paper we present a computational framework, DMPy, that uses a network scheme as input to automatically search for kinetic rates and produce a mathematical model that describes temporal changes of metabolite fluxes. The parameter search utilises several online databases to find measured reaction parameters. From this, we take advantage of previous modelling efforts, such as Parameter Balancing, to produce an initial mathematical model of a metabolic pathway. We analyse the effect of parameter uncertainty on model dynamics and test how recent flux-based model reduction techniques alter system properties. To our knowledge this is the first time such analysis has been performed on large models of metabolism. Our results highlight that good estimates of at least 80% of the reaction rates are required to accurately model metabolic systems. Furthermore, reducing the size of the model by grouping reactions together based on fluxes alters the resulting system dynamics. The presented pipeline automates the

  17. Formation factor in Bentheimer and Fontainebleau sandstones: Theory compared with pore-scale numerical simulations

    Ghanbarian, Behzad; Berg, Carl F.

    2017-09-01

    Accurate quantification of formation resistivity factor F (also called formation factor) provides useful insight into connectivity and pore space topology in fully saturated porous media. In particular the formation factor has been extensively used to estimate permeability in reservoir rocks. One of the widely applied models to estimate F is Archie's law (F = ϕ- m in which ϕ is total porosity and m is cementation exponent) that is known to be valid in rocks with negligible clay content, such as clean sandstones. In this study we compare formation factors determined by percolation and effective-medium theories as well as Archie's law with numerical simulations of electrical resistivity on digital rock models. These digital models represent Bentheimer and Fontainebleau sandstones and are derived either by reconstruction or directly from micro-tomographic images. Results show that the universal quadratic power law from percolation theory accurately estimates the calculated formation factor values in network models over the entire range of porosity. However, it crosses over to the linear scaling from the effective-medium approximation at the porosity of 0.75 in grid models. We also show that the effect of critical porosity, disregarded in Archie's law, is nontrivial, and the Archie model inaccurately estimates the formation factor in low-porosity homogeneous sandstones.

  18. Generation of large-scale vorticity in rotating stratified turbulence with inhomogeneous helicity: mean-field theory

    Kleeorin, N.

    2018-06-01

    We discuss a mean-field theory of the generation of large-scale vorticity in a rotating density stratified developed turbulence with inhomogeneous kinetic helicity. We show that the large-scale non-uniform flow is produced due to either a combined action of a density stratified rotating turbulence and uniform kinetic helicity or a combined effect of a rotating incompressible turbulence and inhomogeneous kinetic helicity. These effects result in the formation of a large-scale shear, and in turn its interaction with the small-scale turbulence causes an excitation of the large-scale instability (known as a vorticity dynamo) due to a combined effect of the large-scale shear and Reynolds stress-induced generation of the mean vorticity. The latter is due to the effect of large-scale shear on the Reynolds stress. A fast rotation suppresses this large-scale instability.

  19. Snake scales, partial exposure, and the Snake Detection Theory: A human event-related potentials study

    Van Strien, Jan W.; Isbell, Lynne A.

    2017-01-01

    Studies of event-related potentials in humans have established larger early posterior negativity (EPN) in response to pictures depicting snakes than to pictures depicting other creatures. Ethological research has recently shown that macaques and wild vervet monkeys respond strongly to partially exposed snake models and scale patterns on the snake skin. Here, we examined whether snake skin patterns and partially exposed snakes elicit a larger EPN in humans. In Task 1, we employed pictures with close-ups of snake skins, lizard skins, and bird plumage. In task 2, we employed pictures of partially exposed snakes, lizards, and birds. Participants watched a random rapid serial visual presentation of these pictures. The EPN was scored as the mean activity (225–300 ms after picture onset) at occipital and parieto-occipital electrodes. Consistent with previous studies, and with the Snake Detection Theory, the EPN was significantly larger for snake skin pictures than for lizard skin and bird plumage pictures, and for lizard skin pictures than for bird plumage pictures. Likewise, the EPN was larger for partially exposed snakes than for partially exposed lizards and birds. The results suggest that the EPN snake effect is partly driven by snake skin scale patterns which are otherwise rare in nature. PMID:28387376

  20. DGDFT: A massively parallel method for large scale density functional theory calculations.

    Hu, Wei; Lin, Lin; Yang, Chao

    2015-09-28

    We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10(-4) Hartree/atom in terms of the error of energy and 6.2 × 10(-4) Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail.

  1. Evaporation of Liquid Droplet in Nano and Micro Scales from Statistical Rate Theory.

    Duan, Fei; He, Bin; Wei, Tao

    2015-04-01

    The statistical rate theory (SRT) is applied to predict the average evaporation flux of liquid droplet after the approach is validated in the sessile droplet experiments of the water and heavy water. The steady-state experiments show a temperature discontinuity at the evaporating interface. The average evaporation flux is evaluated by individually changing the measurement at a liquid-vapor interface, including the interfacial liquid temperature, the interfacial vapor temperature, the vapor-phase pressure, and the droplet size. The parameter study shows that a higher temperature jump would reduce the average evaporation flux. The average evaporation flux can significantly be influenced by the interfacial liquid temperature and the vapor-phase pressure. The variation can switch the evaporation into condensation. The evaporation flux is found to remain relative constant if the droplet is larger than a micro scale, while the smaller diameters in nano scale can produce a much higher evaporation flux. In addition, a smaller diameter of droplets with the same liquid volume has a larger surface area. It is suggested that the evaporation rate increases dramatically as the droplet shrinks into nano size.

  2. DGDFT: A massively parallel method for large scale density functional theory calculations

    Hu, Wei, E-mail: whu@lbl.gov; Yang, Chao, E-mail: cyang@lbl.gov [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Lin, Lin, E-mail: linlin@math.berkeley.edu [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Department of Mathematics, University of California, Berkeley, California 94720 (United States)

    2015-09-28

    We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10{sup −4} Hartree/atom in terms of the error of energy and 6.2 × 10{sup −4} Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail.

  3. DGDFT: A massively parallel method for large scale density functional theory calculations

    Hu, Wei; Yang, Chao; Lin, Lin

    2015-01-01

    We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10 −4 Hartree/atom in terms of the error of energy and 6.2 × 10 −4 Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail

  4. Gas production in the Barnett Shale obeys a simple scaling theory.

    Patzek, Tad W; Male, Frank; Marder, Michael

    2013-12-03

    Natural gas from tight shale formations will provide the United States with a major source of energy over the next several decades. Estimates of gas production from these formations have mainly relied on formulas designed for wells with a different geometry. We consider the simplest model of gas production consistent with the basic physics and geometry of the extraction process. In principle, solutions of the model depend upon many parameters, but in practice and within a given gas field, all but two can be fixed at typical values, leading to a nonlinear diffusion problem we solve exactly with a scaling curve. The scaling curve production rate declines as 1 over the square root of time early on, and it later declines exponentially. This simple model provides a surprisingly accurate description of gas extraction from 8,294 wells in the United States' oldest shale play, the Barnett Shale. There is good agreement with the scaling theory for 2,057 horizontal wells in which production started to decline exponentially in less than 10 y. The remaining 6,237 horizontal wells in our analysis are too young for us to predict when exponential decline will set in, but the model can nevertheless be used to establish lower and upper bounds on well lifetime. Finally, we obtain upper and lower bounds on the gas that will be produced by the wells in our sample, individually and in total. The estimated ultimate recovery from our sample of 8,294 wells is between 10 and 20 trillion standard cubic feet.

  5. A compact to revitalise large-scale irrigation systems: A ‘theory of change’ approach

    Bruce A. Lankford

    2016-02-01

    Full Text Available In countries with transitional economies such as those found in South Asia, large-scale irrigation systems (LSIS with a history of public ownership account for about 115 million ha (Mha or approximately 45% of their total area under irrigation. In terms of the global area of irrigation (320 Mha for all countries, LSIS are estimated at 130 Mha or 40% of irrigated land. These systems can potentially deliver significant local, regional and global benefits in terms of food, water and energy security, employment, economic growth and ecosystem services. For example, primary crop production is conservatively valued at about US$355 billion. However, efforts to enhance these benefits and reform the sector have been costly and outcomes have been underwhelming and short-lived. We propose the application of a 'theory of change' (ToC as a foundation for promoting transformational change in large-scale irrigation centred upon a 'global irrigation compact' that promotes new forms of leadership, partnership and ownership (LPO. The compact argues that LSIS can change by switching away from the current channelling of aid finances controlled by government irrigation agencies. Instead it is for irrigators, closely partnered by private, public and NGO advisory and regulatory services, to develop strong leadership models and to find new compensatory partnerships with cities and other river basin neighbours. The paper summarises key assumptions for change in the LSIS sector including the need to initially test this change via a handful of volunteer systems. Our other key purpose is to demonstrate a ToC template by which large-scale irrigation policy can be better elaborated and discussed.

  6. Improving Measurement Efficiency of the Inner EAR Scale with Item Response Theory.

    Jessen, Annika; Ho, Andrew D; Corrales, C Eduardo; Yueh, Bevan; Shin, Jennifer J

    2018-02-01

    Objectives (1) To assess the 11-item Inner Effectiveness of Auditory Rehabilitation (Inner EAR) instrument with item response theory (IRT). (2) To determine whether the underlying latent ability could also be accurately represented by a subset of the items for use in high-volume clinical scenarios. (3) To determine whether the Inner EAR instrument correlates with pure tone thresholds and word recognition scores. Design IRT evaluation of prospective cohort data. Setting Tertiary care academic ambulatory otolaryngology clinic. Subjects and Methods Modern psychometric methods, including factor analysis and IRT, were used to assess unidimensionality and item properties. Regression methods were used to assess prediction of word recognition and pure tone audiometry scores. Results The Inner EAR scale is unidimensional, and items varied in their location and information. Information parameter estimates ranged from 1.63 to 4.52, with higher values indicating more useful items. The IRT model provided a basis for identifying 2 sets of items with relatively lower information parameters. Item information functions demonstrated which items added insubstantial value over and above other items and were removed in stages, creating a 8- and 3-item Inner EAR scale for more efficient assessment. The 8-item version accurately reflected the underlying construct. All versions correlated moderately with word recognition scores and pure tone averages. Conclusion The 11-, 8-, and 3-item versions of the Inner EAR scale have strong psychometric properties, and there is correlational validity evidence for the observed scores. Modern psychometric methods can help streamline care delivery by maximizing relevant information per item administered.

  7. Item response theory analysis applied to the Spanish version of the Personal Outcomes Scale.

    Guàrdia-Olmos, J; Carbó-Carreté, M; Peró-Cebollero, M; Giné, C

    2017-11-01

    The study of measurements of quality of life (QoL) is one of the great challenges of modern psychology and psychometric approaches. This issue has greater importance when examining QoL in populations that were historically treated on the basis of their deficiency, and recently, the focus has shifted to what each person values and desires in their life, as in cases of people with intellectual disability (ID). Many studies of QoL scales applied in this area have attempted to improve the validity and reliability of their components by incorporating various sources of information to achieve consistency in the data obtained. The adaptation of the Personal Outcomes Scale (POS) in Spanish has shown excellent psychometric attributes, and its administration has three sources of information: self-assessment, practitioner and family. The study of possible congruence or incongruence of observed distributions of each item between sources is therefore essential to ensure a correct interpretation of the measure. The aim of this paper was to analyse the observed distribution of items and dimensions from the three Spanish POS information sources cited earlier, using the item response theory. We studied a sample of 529 people with ID and their respective practitioners and family member, and in each case, we analysed items and factors using Samejima's model of polytomic ordinal scales. The results indicated an important number of items with differential effects regarding sources, and in some cases, they indicated significant differences in the distribution of items, factors and sources of information. As a result of this analysis, we must affirm that the administration of the POS, considering three sources of information, was adequate overall, but a correct interpretation of the results requires that it obtain much more information to consider, as well as some specific items in specific dimensions. The overall ratings, if these comments are considered, could result in bias. © 2017

  8. Development and validation of an item response theory-based Social Responsiveness Scale short form.

    Sturm, Alexandra; Kuhfeld, Megan; Kasari, Connie; McCracken, James T

    2017-09-01

    Research and practice in autism spectrum disorder (ASD) rely on quantitative measures, such as the Social Responsiveness Scale (SRS), for characterization and diagnosis. Like many ASD diagnostic measures, SRS scores are influenced by factors unrelated to ASD core features. This study further interrogates the psychometric properties of the SRS using item response theory (IRT), and demonstrates a strategy to create a psychometrically sound short form by applying IRT results. Social Responsiveness Scale analyses were conducted on a large sample (N = 21,426) of youth from four ASD databases. Items were subjected to item factor analyses and evaluation of item bias by gender, age, expressive language level, behavior problems, and nonverbal IQ. Item selection based on item psychometric properties, DIF analyses, and substantive validity produced a reduced item SRS short form that was unidimensional in structure, highly reliable (α = .96), and free of gender, age, expressive language, behavior problems, and nonverbal IQ influence. The short form also showed strong relationships with established measures of autism symptom severity (ADOS, ADI-R, Vineland). Degree of association between all measures varied as a function of expressive language. Results identified specific SRS items that are more vulnerable to non-ASD-related traits. The resultant 16-item SRS short form may possess superior psychometric properties compared to the original scale and emerge as a more precise measure of ASD core symptom severity, facilitating research and practice. Future research using IRT is needed to further refine existing measures of autism symptomatology. © 2017 Association for Child and Adolescent Mental Health.

  9. Data-driven integration of genome-scale regulatory and metabolic network models

    Imam, Saheed; Schäuble, Sascha; Brooks, Aaron N.; Baliga, Nitin S.; Price, Nathan D.

    2015-01-01

    Microbes are diverse and extremely versatile organisms that play vital roles in all ecological niches. Understanding and harnessing microbial systems will be key to the sustainability of our planet. One approach to improving our knowledge of microbial processes is through data-driven and mechanism-informed computational modeling. Individual models of biological networks (such as metabolism, transcription, and signaling) have played pivotal roles in driving microbial research through the years. These networks, however, are highly interconnected and function in concert—a fact that has led to the development of a variety of approaches aimed at simulating the integrated functions of two or more network types. Though the task of integrating these different models is fraught with new challenges, the large amounts of high-throughput data sets being generated, and algorithms being developed, means that the time is at hand for concerted efforts to build integrated regulatory-metabolic networks in a data-driven fashion. In this perspective, we review current approaches for constructing integrated regulatory-metabolic models and outline new strategies for future development of these network models for any microbial system. PMID:25999934

  10. Data-driven integration of genome-scale regulatory and metabolic network models

    Saheed eImam

    2015-05-01

    Full Text Available Microbes are diverse and extremely versatile organisms that play vital roles in all ecological niches. Understanding and harnessing microbial systems will be key to the sustainability of our planet. One approach to improving our knowledge of microbial processes is through data-driven and mechanism-informed computational modeling. Individual models of biological networks (such as metabolism, transcription and signaling have played pivotal roles in driving microbial research through the years. These networks, however, are highly interconnected and function in concert – a fact that has led to the development of a variety of approaches aimed at simulating the integrated functions of two or more network types. Though the task of integrating these different models is fraught with new challenges, the large amounts of high-throughput data sets being generated, and algorithms being developed, means that the time is at hand for concerted efforts to build integrated regulatory-metabolic networks in a data-driven fashion. In this perspective, we review current approaches for constructing integrated regulatory-metabolic models and outline new strategies for future development of these network models for any microbial system.

  11. Effect of vibration on osteoblastic and osteoclastic activities: Analysis of bone metabolism using goldfish scale as a model for bone

    Suzuki, N.; Kitamura, K.; Nemoto, T.; Shimizu, N.; Wada, S.; Kondo, T.; Tabata, M. J.; Sodeyama, F.; Ijiri, K.; Hattori, A.

    In osteoclastic activity during space flight as well as hind limb unloading by tail suspension, inconsistent results have been reported in an in vivo study. The bone matrix plays an important role in the response to physical stress. However, there is no suitable in vitro co-culture system of osteoblasts and osteoclasts including bone matrix. On the other hand, fish scale is a calcified tissue that contains osteoblasts, osteoclasts, and bone matrix, all of which are similar to those found in human bones. Recently, we developed a new in vitro model system using goldfish scale. This system can detect the activities of osteoclasts and osteoblasts with tartrate-resistant acid phosphatase and alkaline phosphatase as the respective markers and precisely analyze the co-relationship between osteoblasts and osteoclasts. Using this system, we analyzed the bone metabolism under various degrees of acceleration (0.5-, 1-, 2-, 4-, and 6-G) by vibration with a G-load apparatus. After loading for 5 and 10 min, the scales were incubated for 6 and 24 h. The osteoblastic and osteoclastic activities were then measured. The osteoblastic activities gradually increased corresponding to 1-G to 6-G acceleration. In addition, ER mRNA expression was the highest under 6-G acceleration. On the other hand, the osteoclastic activity decreased at 24 h of incubation under low acceleration (0.5- and 1-G). This change coincided with TRAP mRNA expression. Under 2-G acceleration, the strength of suppression in osteoclastic activity was the highest. The strength of the inhibitory action under 4- and 6-G acceleration was lower than that under 2-G acceleration. In our co-culture system, osteoblasts and osteoclasts in the scale sensitively responded to several degrees of acceleration. Therefore, we strongly believe that our in vitro co-culture system is useful for the analysis of bone metabolism under loading or unloading.

  12. Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling

    Dorines Rosario

    2018-06-01

    Full Text Available Dysbiosis in the gut microbiome composition may be promoted by therapeutic drugs such as metformin, the world’s most prescribed antidiabetic drug. Under metformin treatment, disturbances of the intestinal microbes lead to increased abundance of Escherichia spp., Akkermansia muciniphila, Subdoligranulum variabile and decreased abundance of Intestinibacter bartlettii. This alteration may potentially lead to adverse effects on the host metabolism, with the depletion of butyrate producer genus. However, an increased production of butyrate and propionate was verified in metformin-treated Type 2 diabetes (T2D patients. The mechanisms underlying these nutritional alterations and their relation with gut microbiota dysbiosis remain unclear. Here, we used Genome-scale Metabolic Models of the representative gut bacteria Escherichia spp., I. bartlettii, A. muciniphila, and S. variabile to elucidate their bacterial metabolism and its effect on intestinal nutrient pool, including macronutrients (e.g., amino acids and short chain fatty acids, minerals and chemical elements (e.g., iron and oxygen. We applied flux balance analysis (FBA coupled with synthetic lethality analysis interactions to identify combinations of reactions and extracellular nutrients whose absence prevents growth. Our analyses suggest that Escherichia sp. is the bacteria least vulnerable to nutrient availability. We have also examined bacterial contribution to extracellular nutrients including short chain fatty acids, amino acids, and gasses. For instance, Escherichia sp. and S. variabile may contribute to the production of important short chain fatty acids (e.g., acetate and butyrate, respectively involved in the host physiology under aerobic and anaerobic conditions. We have also identified pathway susceptibility to nutrient availability and reaction changes among the four bacteria using both FBA and flux variability analysis. For instance, lipopolysaccharide synthesis, nucleotide sugar

  13. Comprehensive reconstruction and in silico analysis of Aspergillus niger genome-scale metabolic network model that accounts for 1210 ORFs.

    Lu, Hongzhong; Cao, Weiqiang; Ouyang, Liming; Xia, Jianye; Huang, Mingzhi; Chu, Ju; Zhuang, Yingping; Zhang, Siliang; Noorman, Henk

    2017-03-01

    Aspergillus niger is one of the most important cell factories for industrial enzymes and organic acids production. A comprehensive genome-scale metabolic network model (GSMM) with high quality is crucial for efficient strain improvement and process optimization. The lack of accurate reaction equations and gene-protein-reaction associations (GPRs) in the current best model of A. niger named GSMM iMA871, however, limits its application scope. To overcome these limitations, we updated the A. niger GSMM by combining the latest genome annotation and literature mining technology. Compared with iMA871, the number of reactions in iHL1210 was increased from 1,380 to 1,764, and the number of unique ORFs from 871 to 1,210. With the aid of our transcriptomics analysis, the existence of 63% ORFs and 68% reactions in iHL1210 can be verified when glucose was used as the only carbon source. Physiological data from chemostat cultivations, 13 C-labeled and molecular experiments from the published literature were further used to check the performance of iHL1210. The average correlation coefficients between the predicted fluxes and estimated fluxes from 13 C-labeling data were sufficiently high (above 0.89) and the prediction of cell growth on most of the reported carbon and nitrogen sources was consistent. Using the updated genome-scale model, we evaluated gene essentiality on synthetic and yeast extract medium, as well as the effects of NADPH supply on glucoamylase production in A. niger. In summary, the new A. niger GSMM iHL1210 contains significant improvements with respect to the metabolic coverage and prediction performance, which paves the way for systematic metabolic engineering of A. niger. Biotechnol. Bioeng. 2017;114: 685-695. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  14. Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III-reducer Rhodoferax ferrireducens

    Daugherty Sean

    2009-09-01

    Full Text Available Abstract Background Rhodoferax ferrireducens is a metabolically versatile, Fe(III-reducing, subsurface microorganism that is likely to play an important role in the carbon and metal cycles in the subsurface. It also has the unique ability to convert sugars to electricity, oxidizing the sugars to carbon dioxide with quantitative electron transfer to graphite electrodes in microbial fuel cells. In order to expand our limited knowledge about R. ferrireducens, the complete genome sequence of this organism was further annotated and then the physiology of R. ferrireducens was investigated with a constraint-based, genome-scale in silico metabolic model and laboratory studies. Results The iterative modeling and experimental approach unveiled exciting, previously unknown physiological features, including an expanded range of substrates that support growth, such as cellobiose and citrate, and provided additional insights into important features such as the stoichiometry of the electron transport chain and the ability to grow via fumarate dismutation. Further analysis explained why R. ferrireducens is unable to grow via photosynthesis or fermentation of sugars like other members of this genus and uncovered novel genes for benzoate metabolism. The genome also revealed that R. ferrireducens is well-adapted for growth in the subsurface because it appears to be capable of dealing with a number of environmental insults, including heavy metals, aromatic compounds, nutrient limitation and oxidative stress. Conclusion This study demonstrates that combining genome-scale modeling with the annotation of a new genome sequence can guide experimental studies and accelerate the understanding of the physiology of under-studied yet environmentally relevant microorganisms.

  15. Using G-Theory to Enhance Evidence of Reliability and Validity for Common Uses of the Paulhus Deception Scales.

    Vispoel, Walter P; Morris, Carrie A; Kilinc, Murat

    2018-01-01

    We applied a new approach to Generalizability theory (G-theory) involving parallel splits and repeated measures to evaluate common uses of the Paulhus Deception Scales based on polytomous and four types of dichotomous scoring. G-theory indices of reliability and validity accounting for specific-factor, transient, and random-response measurement error supported use of polytomous over dichotomous scores as contamination checks; as control, explanatory, and outcome variables; as aspects of construct validation; and as indexes of environmental effects on socially desirable responding. Polytomous scoring also provided results for flagging faking as dependable as those when using dichotomous scoring methods. These findings argue strongly against the nearly exclusive use of dichotomous scoring for the Paulhus Deception Scales in practice and underscore the value of G-theory in demonstrating this. We provide guidelines for applying our G-theory techniques to other objectively scored clinical assessments, for using G-theory to estimate how changes to a measure might improve reliability, and for obtaining software to conduct G-theory analyses free of charge.

  16. The Protective Behavioral Strategies for Marijuana Scale: Further examination using item response theory.

    Pedersen, Eric R; Huang, Wenjing; Dvorak, Robert D; Prince, Mark A; Hummer, Justin F

    2017-08-01

    Given recent state legislation legalizing marijuana for recreational purposes and majority popular opinion favoring these laws, we developed the Protective Behavioral Strategies for Marijuana scale (PBSM) to identify strategies that may mitigate the harms related to marijuana use among those young people who choose to use the drug. In the current study, we expand on the initial exploratory study of the PBSM to further validate the measure with a large and geographically diverse sample (N = 2,117; 60% women, 30% non-White) of college students from 11 different universities across the United States. We sought to develop a psychometrically sound item bank for the PBSM and to create a short assessment form that minimizes respondent burden and time. Quantitative item analyses, including exploratory and confirmatory factor analyses with item response theory (IRT) and evaluation of differential item functioning (DIF), revealed an item bank of 36 items that was examined for unidimensionality and good content coverage, as well as a short form of 17 items that is free of bias in terms of gender (men vs. women), race (White vs. non-White), ethnicity (Hispanic vs. non-Hispanic), and recreational marijuana use legal status (state recreational marijuana was legal for 25.5% of participants). We also provide a scoring table for easy transformation from sum scores to IRT scale scores. The PBSM item bank and short form associated strongly and negatively with past month marijuana use and consequences. The measure may be useful to researchers and clinicians conducting intervention and prevention programs with young adults. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  17. iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE.

    Norsigian, Charles J; Kavvas, Erol; Seif, Yara; Palsson, Bernhard O; Monk, Jonathan M

    2018-01-01

    Acinetobacter baumannii has become an urgent clinical threat due to the recent emergence of multi-drug resistant strains. There is thus a significant need to discover new therapeutic targets in this organism. One means for doing so is through the use of high-quality genome-scale reconstructions. Well-curated and accurate genome-scale models (GEMs) of A. baumannii would be useful for improving treatment options. We present an updated and improved genome-scale reconstruction of A. baumannii AYE, named iCN718, that improves and standardizes previous A. baumannii AYE reconstructions. iCN718 has 80% accuracy for predicting gene essentiality data and additionally can predict large-scale phenotypic data with as much as 89% accuracy, a new capability for an A. baumannii reconstruction. We further demonstrate that iCN718 can be used to analyze conserved metabolic functions in the A. baumannii core genome and to build strain-specific GEMs of 74 other A. baumannii strains from genome sequence alone. iCN718 will serve as a resource to integrate and synthesize new experimental data being generated for this urgent threat pathogen.

  18. Testing the Metabolic Theory of Ecology with marine bacteria: Different temperature sensitivity of major phylogenetic groups during the spring phytoplankton bloom

    Arandia-Gorostidi, Nestor; Huete-Stauffer, Tamara Megan; Alonso-Sá ez, Laura; Moran, Xose Anxelu G.

    2017-01-01

    in general lower than 0.65 eV, the value predicted by the Metabolic Theory of Ecology (MTE). Contrary to MTE predictions, carrying capacity tended to increase with warming for all bacterial groups. Our analysis confirms that resource availability is key when

  19. Energy harvesting with stacked dielectric elastomer transducers: Nonlinear theory, optimization, and linearized scaling law

    Tutcuoglu, A.; Majidi, C.

    2014-12-01

    Using principles of damped harmonic oscillation with continuous media, we examine electrostatic energy harvesting with a "soft-matter" array of dielectric elastomer (DE) transducers. The array is composed of infinitely thin and deformable electrodes separated by layers of insulating elastomer. During vibration, it deforms longitudinally, resulting in a change in the capacitance and electrical enthalpy of the charged electrodes. Depending on the phase of electrostatic loading, the DE array can function as either an actuator that amplifies small vibrations or a generator that converts these external excitations into electrical power. Both cases are addressed with a comprehensive theory that accounts for the influence of viscoelasticity, dielectric breakdown, and electromechanical coupling induced by Maxwell stress. In the case of a linearized Kelvin-Voigt model of the dielectric, we obtain a closed-form estimate for the electrical power output and a scaling law for DE generator design. For the complete nonlinear model, we obtain the optimal electrostatic voltage input for maximum electrical power output.

  20. Single-polymer dynamics under constraints: scaling theory and computer experiment

    Milchev, Andrey

    2011-01-01

    The relaxation, diffusion and translocation dynamics of single linear polymer chains in confinement is briefly reviewed with emphasis on the comparison between theoretical scaling predictions and observations from experiment or, most frequently, from computer simulations. Besides cylindrical, spherical and slit-like constraints, related problems such as the chain dynamics in a random medium and the translocation dynamics through a nanopore are also considered. Another particular kind of confinement is imposed by polymer adsorption on attractive surfaces or selective interfaces-a short overview of single-chain dynamics is also contained in this survey. While both theory and numerical experiments consider predominantly coarse-grained models of self-avoiding linear chain molecules with typically Rouse dynamics, we also note some recent studies which examine the impact of hydrodynamic interactions on polymer dynamics in confinement. In all of the aforementioned cases we focus mainly on the consequences of imposed geometric restrictions on single-chain dynamics and try to check our degree of understanding by assessing the agreement between theoretical predictions and observations. (topical review)

  1. Subgrid-scale scalar flux modelling based on optimal estimation theory and machine-learning procedures

    Vollant, A.; Balarac, G.; Corre, C.

    2017-09-01

    New procedures are explored for the development of models in the context of large eddy simulation (LES) of a passive scalar. They rely on the combination of the optimal estimator theory with machine-learning algorithms. The concept of optimal estimator allows to identify the most accurate set of parameters to be used when deriving a model. The model itself can then be defined by training an artificial neural network (ANN) on a database derived from the filtering of direct numerical simulation (DNS) results. This procedure leads to a subgrid scale model displaying good structural performance, which allows to perform LESs very close to the filtered DNS results. However, this first procedure does not control the functional performance so that the model can fail when the flow configuration differs from the training database. Another procedure is then proposed, where the model functional form is imposed and the ANN used only to define the model coefficients. The training step is a bi-objective optimisation in order to control both structural and functional performances. The model derived from this second procedure proves to be more robust. It also provides stable LESs for a turbulent plane jet flow configuration very far from the training database but over-estimates the mixing process in that case.

  2. Salting out of methane by sodium chloride: A scaled particle theory study.

    Graziano, Giuseppe

    2008-08-28

    The salting out of methane by adding NaCl to water at 25 degrees C and 1 atm is investigated by calculating the work of cavity creation by means of scaled particle theory and the methane-solvent energy of attraction. The latter quantity changes to little extent on passing from pure water to an aqueous 4M NaCl solution, whereas the magnitude of the work of cavity creation increases significantly, accounting for the salting out effect. There is quantitative agreement between the experimental values of the hydration Gibbs energy and the calculated ones. The behavior of the work of cavity creation is due to the increase in the volume packing density of NaCl solutions, since the average effective molecular diameter does not change, being always 2.80 A. The same approach allows the rationalization of the difference in methane salting out along the alkali chloride series. These results indicate that, fixed the aqueous solution density, the solubility of nonpolar species is mainly determined by the effective diameter of solvent molecules and the corresponding volume packing density. There is no need to take into account the H-bond rearrangement because it is characterized by an almost complete enthalpy-entropy compensation.

  3. Principal shapes and squeezed limits in the effective field theory of large scale structure

    Bertolini, Daniele; Solon, Mikhail P., E-mail: dbertolini@lbl.gov, E-mail: mpsolon@lbl.gov [Berkeley Center for Theoretical Physics, University of California, South Hall Road, Berkeley, CA, 94720 (United States)

    2016-11-01

    We apply an orthogonalization procedure on the effective field theory of large scale structure (EFT of LSS) shapes, relevant for the angle-averaged bispectrum and non-Gaussian covariance of the matter power spectrum at one loop. Assuming natural-sized EFT parameters, this identifies a linear combination of EFT shapes—referred to as the principal shape—that gives the dominant contribution for the whole kinematic plane, with subdominant combinations suppressed by a few orders of magnitude. For the covariance, our orthogonal transformation is in excellent agreement with a principal component analysis applied to available data. Additionally we find that, for both observables, the coefficients of the principal shapes are well approximated by the EFT coefficients appearing in the squeezed limit, and are thus measurable from power spectrum response functions. Employing data from N-body simulations for the growth-only response, we measure the single EFT coefficient describing the angle-averaged bispectrum with Ο (10%) precision. These methods of shape orthogonalization and measurement of coefficients from response functions are valuable tools for developing the EFT of LSS framework, and can be applied to more general observables.

  4. An item-response theory approach to safety climate measurement: The Liberty Mutual Safety Climate Short Scales.

    Huang, Yueng-Hsiang; Lee, Jin; Chen, Zhuo; Perry, MacKenna; Cheung, Janelle H; Wang, Mo

    2017-06-01

    Zohar and Luria's (2005) safety climate (SC) scale, measuring organization- and group- level SC each with 16 items, is widely used in research and practice. To improve the utility of the SC scale, we shortened the original full-length SC scales. Item response theory (IRT) analysis was conducted using a sample of 29,179 frontline workers from various industries. Based on graded response models, we shortened the original scales in two ways: (1) selecting items with above-average discriminating ability (i.e. offering more than 6.25% of the original total scale information), resulting in 8-item organization-level and 11-item group-level SC scales; and (2) selecting the most informative items that together retain at least 30% of original scale information, resulting in 4-item organization-level and 4-item group-level SC scales. All four shortened scales had acceptable reliability (≥0.89) and high correlations (≥0.95) with the original scale scores. The shortened scales will be valuable for academic research and practical survey implementation in improving occupational safety. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  5. Decision support for large-scale remediation strategies by fused urban metabolism and life cycle assessment

    Ohms, Pernille; Andersen, Camilla; Landgren, Mathilde

    2018-01-01

    Purpose: This paper seeks to identify the most environmental friendly way of conducting a refurbishment of Broendby Strand, with focus on PCB remediation. The actual identification is conducted by comparing four remediation techniques using urban metabolism fused with life cycle assessment (UM......-LCA) in combination with information relating to cost and efficiency of the compared techniques. The methodological goal of our paper is to test UM-LCA as a decision support tool and discuss application of the method in relation to large refurbishment projects. Methods: To assess the environmental performance of PCB......-remediation techniques, the UM-LCA method was applied. By combining UM and LCA methodologies, the total environmental impact potentials of the remediation techniques were calculated. To build an inventory for each technique, we contacted and interviewed experts and studied existing literature, cases, and projects...

  6. El Naschie's ε (∞) space-time and scale relativity theory in the topological dimension D = 4

    Agop, M.; Murgulet, C.

    2007-01-01

    In the topological dimension D = 4 of the scale relativity theory, the self-structuring of a coherent quantum fluid implies the Golden mean renormalization group. Then, the transfinite set of El Naschie's ε (∞) space-time becomes the background of a new physics (the transfinite physics)

  7. The Development of the Functional Literacy Experience Scale Based upon Ecological Theory (FLESBUET) and Validity-Reliability Study

    Özenç, Emine Gül; Dogan, M. Cihangir

    2014-01-01

    This study aims to perform a validity-reliability test by developing the Functional Literacy Experience Scale based upon Ecological Theory (FLESBUET) for primary education students. The study group includes 209 fifth grade students at Sabri Taskin Primary School in the Kartal District of Istanbul, Turkey during the 2010-2011 academic year.…

  8. A Cultural Insight into the Development of Teacher Autonomy Support Scale: A Self-Determination Theory Perspective

    Awang-Hashim, Rosna; Thaliah, Rajaletchumi; Kaur, Amrita

    2017-01-01

    Purpose: The cross-cultural significance of autonomy within self-determination theory is divisive on universal significance. This paper aims to report a sequential exploratory mixed methods study conducted to construct and validate a scale to investigate how, in Malaysian context, the construct of autonomy is conceptualized in comparison with the…

  9. An Analysis of Cross Racial Identity Scale Scores Using Classical Test Theory and Rasch Item Response Models

    Sussman, Joshua; Beaujean, A. Alexander; Worrell, Frank C.; Watson, Stevie

    2013-01-01

    Item response models (IRMs) were used to analyze Cross Racial Identity Scale (CRIS) scores. Rasch analysis scores were compared with classical test theory (CTT) scores. The partial credit model demonstrated a high goodness of fit and correlations between Rasch and CTT scores ranged from 0.91 to 0.99. CRIS scores are supported by both methods.…

  10. Development and Standardization of the Diagnostic Adaptive Behavior Scale: Application of Item Response Theory to the Assessment of Adaptive Behavior

    Tassé, Marc J.; Schalock, Robert L.; Thissen, David; Balboni, Giulia; Bersani, Henry, Jr.; Borthwick-Duffy, Sharon A.; Spreat, Scott; Widaman, Keith F.; Zhang, Dalun; Navas, Patricia

    2016-01-01

    The Diagnostic Adaptive Behavior Scale (DABS) was developed using item response theory (IRT) methods and was constructed to provide the most precise and valid adaptive behavior information at or near the cutoff point of making a decision regarding a diagnosis of intellectual disability. The DABS initial item pool consisted of 260 items. Using IRT…

  11. LIDAR-based urban metabolism approach to neighbourhood scale energy and carbon emissions modelling

    Christen, A. [British Columbia Univ., Vancouver, BC (Canada). Dept. of Geography; Coops, N. [British Columbia Univ., Vancouver, BC (Canada). Dept. of Forest Sciences; Canada Research Chairs, Ottawa, ON (Canada); Kellet, R. [British Columbia Univ., Vancouver, BC (Canada). School of Architecture and Landscape Architecture

    2010-07-01

    A remote sensing technology was used to model neighbourhood scale energy and carbon emissions in a case study set in Vancouver, British Columbia (BC). The study was used to compile and aggregate atmospheric carbon flux, urban form, and energy and emissions data in a replicable neighbourhood-scale approach. The study illustrated methods of integrating diverse emission and uptake processes on a range of scales and resolutions, and benchmarked comparisons of modelled estimates with measured energy consumption data obtained over a 2-year period from a research tower located in the study area. The study evaluated carbon imports, carbon exports and sequestration, and relevant emissions processes. Fossil fuel emissions produced in the neighbourhood were also estimated. The study demonstrated that remote sensing technologies such as LIDAR and multispectral satellite imagery can be an effective means of generating and extracting urban form and land cover data at fine scales. Data from the study were used to develop several emissions reduction and energy conservation scenarios. 6 refs.

  12. Consensus for linear multi-agent system with intermittent information transmissions using the time-scale theory

    Taousser, Fatima; Defoort, Michael; Djemai, Mohamed

    2016-01-01

    This paper investigates the consensus problem for linear multi-agent system with fixed communication topology in the presence of intermittent communication using the time-scale theory. Since each agent can only obtain relative local information intermittently, the proposed consensus algorithm is based on a discontinuous local interaction rule. The interaction among agents happens at a disjoint set of continuous-time intervals. The closed-loop multi-agent system can be represented using mixed linear continuous-time and linear discrete-time models due to intermittent information transmissions. The time-scale theory provides a powerful tool to combine continuous-time and discrete-time cases and study the consensus protocol under a unified framework. Using this theory, some conditions are derived to achieve exponential consensus under intermittent information transmissions. Simulations are performed to validate the theoretical results.

  13. Games microbes play: The game theory behind cooperative sucrose metabolism in yeast

    Gore, Jeff

    2010-03-01

    The origin of cooperation is a central challenge to our understanding of evolution. Microbial interactions can be manipulated in ways that animal interactions cannot, thus leading to growing interest in microbial models of cooperation and competition. In order for the budding yeast S. cerevisiae to grow on sucrose, the disaccharide must first be hydrolyzed by the enzyme invertase. This hydrolysis reaction is performed outside of the cytoplasm in the periplasmic space between the plasma membrane and the cell wall. Here we demonstrate that the vast majority (˜99%) of the monosaccharides created by sucrose hydrolysis diffuse away before they can be imported into the cell, thus making invertase production and secretion a cooperative behavior [1]. A mutant cheater strain that does not produce invertase is able to take advantage of and invade a population of wildtype cooperator cells. However, over a wide range of conditions, the wildtype cooperator can also invade a population of cheater cells. Therefore, we observe coexistence between the two strains in well-mixed culture at steady state resulting from the fact that rare strategies outperform common strategies---the defining features of what game theorists call the snowdrift game. A simple model of the cooperative interaction incorporating nonlinear benefits explains the origin of this coexistence. Glucose repression of invertase expression in wildtype cells produces a strategy which is optimal for the snowdrift game---wildtype cells cooperate only when competing against cheater cells. In disagreement with recent theory [2], we find that spatial structure always aids the evolution of cooperation in our experimental snowdrift game. [4pt] [1] Gore, J., Youk, H. & van Oudenaarden, A., Nature 459, 253 -- 256 (2009) [0pt] [2] Hauert, C. & Doebeli, M., Nature 428, 643 -- 646 (2004)

  14. Inferring physiological energetics of loggerhead turtle (Caretta caretta) from existing data using a general metabolic theory.

    Marn, Nina; Kooijman, S A L M; Jusup, Marko; Legović, Tarzan; Klanjšček, Tin

    2017-05-01

    Loggerhead turtle is an endangered sea turtle species with a migratory lifestyle and worldwide distribution, experiencing markedly different habitats throughout its lifetime. Environmental conditions, especially food availability and temperature, constrain the acquisition and the use of available energy, thus affecting physiological processes such as growth, maturation, and reproduction. These physiological processes at the population level determine survival, fecundity, and ultimately the population growth rate-a key indicator of the success of conservation efforts. As a first step towards the comprehensive understanding of how environment shapes the physiology and the life cycle of a loggerhead turtle, we constructed a full life cycle model based on the principles of energy acquisition and utilization embedded in the Dynamic Energy Budget (DEB) theory. We adapted the standard DEB model using data from published and unpublished sources to obtain parameter estimates and model predictions that could be compared with data. The outcome was a successful mathematical description of ontogeny and life history traits of the loggerhead turtle. Some deviations between the model and the data existed (such as an earlier age at sexual maturity and faster growth of the post-hatchlings), yet probable causes for these deviations were found informative and discussed in great detail. Physiological traits such as the capacity to withstand starvation, trade-offs between reproduction and growth, and changes in the energy budget throughout the ontogeny were inferred from the model. The results offer new insights into physiology and ecology of loggerhead turtle with the potential to lead to novel approaches in conservation of this endangered species. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. High Agreement was Obtained Across Scores from Multiple Equated Scales for Social Anxiety Disorder using Item Response Theory.

    Sunderland, Matthew; Batterham, Philip; Calear, Alison; Carragher, Natacha; Baillie, Andrew; Slade, Tim

    2018-04-10

    There is no standardized approach to the measurement of social anxiety. Researchers and clinicians are faced with numerous self-report scales with varying strengths, weaknesses, and psychometric properties. The lack of standardization makes it difficult to compare scores across populations that utilise different scales. Item response theory offers one solution to this problem via equating different scales using an anchor scale to set a standardized metric. This study is the first to equate several scales for social anxiety disorder. Data from two samples (n=3,175 and n=1,052), recruited from the Australian community using online advertisements, were utilised to equate a network of 11 self-report social anxiety scales via a fixed parameter item calibration method. Comparisons between actual and equated scores for most of the scales indicted a high level of agreement with mean differences <0.10 (equivalent to a mean difference of less than one point on the standardized metric). This study demonstrates that scores from multiple scales that measure social anxiety can be converted to a common scale. Re-scoring observed scores to a common scale provides opportunities to combine research from multiple studies and ultimately better assess social anxiety in treatment and research settings. Copyright © 2018. Published by Elsevier Inc.

  16. Analysis of genetic variation and potential applications in genome-scale metabolic modeling

    Cardoso, Joao; Andersen, Mikael Rørdam; Herrgard, Markus

    2015-01-01

    scale and resolution by re-sequencing thousands of strains systematically. In this article, we review challenges in the integration and analysis of large-scale re-sequencing data, present an extensive overview of bioinformatics methods for predicting the effects of genetic variants on protein function......Genetic variation is the motor of evolution and allows organisms to overcome the environmental challenges they encounter. It can be both beneficial and harmful in the process of engineering cell factories for the production of proteins and chemicals. Throughout the history of biotechnology......, there have been efforts to exploit genetic variation in our favor to create strains with favorable phenotypes. Genetic variation can either be present in natural populations or it can be artificially created by mutagenesis and selection or adaptive laboratory evolution. On the other hand, unintended genetic...

  17. Scaling measurements of metabolism in stream ecosystems: challenges and approaches to estimating reaeration

    Bowden, W. B.; Parker, S.; Song, C.

    2016-12-01

    Stream ecologists have used various formulations of an oxygen budget approach as a surrogate to measure "whole-stream metabolism" (WSM) of carbon in rivers and streams. Improvements in sensor technologies that provide reliable, high-frequency measurements of dissolved oxygen concentrations in adverse field conditions has made it much easier to acquire the basic data needed to estimate WSM in remote locations over long periods (weeks to months). However, accurate estimates of WSM require reliable measurements or estimates of the reaeration coefficient (k). Small errors in estimates of k can lead to large errors in estimates of gross ecosystem production and ecosystem respiration and so the magnitude of the biological flux of CO2 to or from streams. This is an especially challenging problem in unproductive, oligotrophic streams. Unfortunately, current methods to measure reaeration directly (gas evasion) are expensive, labor-intensive, and time-consuming. As a consequence, there is a substantial mismatch between the time steps at which we can measure reaeration versus most of the other variables required to calculate WSM. As a part of the NSF Arctic Long-Term Ecological Research Project we have refined methods to measure WSM in Arctic streams and found a good relationship between measured k values and those calculated by the Energy Dissipation Model (EDM). Other researchers have also noted that this equation works well for both low- and high-order streams. The EDM is dependent on stream slope (relatively constant) and velocity (which is related to discharge or stage). These variables are easy to measure and can be used to estimate k a high frequency (minutes) over large areas (river networks). As a key part of the NSF MacroSystems Biology SCALER project we calculated WSM for multiple reaches in nested stream networks in six biomes across the United States and Australia. We calculated k by EDM and fitted k via a Bayesian model for WSM. The relationships between

  18. Scaling of brain metabolism with a fixed energy budget per neuron: implications for neuronal activity, plasticity and evolution.

    Herculano-Houzel, Suzana

    2011-03-01

    It is usually considered that larger brains have larger neurons, which consume more energy individually, and are therefore accompanied by a larger number of glial cells per neuron. These notions, however, have never been tested. Based on glucose and oxygen metabolic rates in awake animals and their recently determined numbers of neurons, here I show that, contrary to the expected, the estimated glucose use per neuron is remarkably constant, varying only by 40% across the six species of rodents and primates (including humans). The estimated average glucose use per neuron does not correlate with neuronal density in any structure. This suggests that the energy budget of the whole brain per neuron is fixed across species and brain sizes, such that total glucose use by the brain as a whole, by the cerebral cortex and also by the cerebellum alone are linear functions of the number of neurons in the structures across the species (although the average glucose consumption per neuron is at least 10× higher in the cerebral cortex than in the cerebellum). These results indicate that the apparently remarkable use in humans of 20% of the whole body energy budget by a brain that represents only 2% of body mass is explained simply by its large number of neurons. Because synaptic activity is considered the major determinant of metabolic cost, a conserved energy budget per neuron has several profound implications for synaptic homeostasis and the regulation of firing rates, synaptic plasticity, brain imaging, pathologies, and for brain scaling in evolution.

  19. Scaling of brain metabolism with a fixed energy budget per neuron: implications for neuronal activity, plasticity and evolution.

    Suzana Herculano-Houzel

    Full Text Available It is usually considered that larger brains have larger neurons, which consume more energy individually, and are therefore accompanied by a larger number of glial cells per neuron. These notions, however, have never been tested. Based on glucose and oxygen metabolic rates in awake animals and their recently determined numbers of neurons, here I show that, contrary to the expected, the estimated glucose use per neuron is remarkably constant, varying only by 40% across the six species of rodents and primates (including humans. The estimated average glucose use per neuron does not correlate with neuronal density in any structure. This suggests that the energy budget of the whole brain per neuron is fixed across species and brain sizes, such that total glucose use by the brain as a whole, by the cerebral cortex and also by the cerebellum alone are linear functions of the number of neurons in the structures across the species (although the average glucose consumption per neuron is at least 10× higher in the cerebral cortex than in the cerebellum. These results indicate that the apparently remarkable use in humans of 20% of the whole body energy budget by a brain that represents only 2% of body mass is explained simply by its large number of neurons. Because synaptic activity is considered the major determinant of metabolic cost, a conserved energy budget per neuron has several profound implications for synaptic homeostasis and the regulation of firing rates, synaptic plasticity, brain imaging, pathologies, and for brain scaling in evolution.

  20. Scaling of Brain Metabolism with a Fixed Energy Budget per Neuron: Implications for Neuronal Activity, Plasticity and Evolution

    Herculano-Houzel, Suzana

    2011-01-01

    It is usually considered that larger brains have larger neurons, which consume more energy individually, and are therefore accompanied by a larger number of glial cells per neuron. These notions, however, have never been tested. Based on glucose and oxygen metabolic rates in awake animals and their recently determined numbers of neurons, here I show that, contrary to the expected, the estimated glucose use per neuron is remarkably constant, varying only by 40% across the six species of rodents and primates (including humans). The estimated average glucose use per neuron does not correlate with neuronal density in any structure. This suggests that the energy budget of the whole brain per neuron is fixed across species and brain sizes, such that total glucose use by the brain as a whole, by the cerebral cortex and also by the cerebellum alone are linear functions of the number of neurons in the structures across the species (although the average glucose consumption per neuron is at least 10× higher in the cerebral cortex than in the cerebellum). These results indicate that the apparently remarkable use in humans of 20% of the whole body energy budget by a brain that represents only 2% of body mass is explained simply by its large number of neurons. Because synaptic activity is considered the major determinant of metabolic cost, a conserved energy budget per neuron has several profound implications for synaptic homeostasis and the regulation of firing rates, synaptic plasticity, brain imaging, pathologies, and for brain scaling in evolution. PMID:21390261

  1. Mechanics of Platelet-Matrix Composites across Scales: Theory, Multiscale Modeling, and 3D Fabrication

    Sakhavand, Navid

    Many natural and biomimetic composites - such as nacre, silk and clay-polymer - exhibit a remarkable balance of strength, toughness, and/or stiffness, which call for a universal measure to quantify this outstanding feature given the platelet-matrix structure and material characteristics of the constituents. Analogously, there is an urgent need to quantify the mechanics of emerging electronic and photonic systems such as stacked heterostructures, which are composed of strong in-plane bonding networks but weak interplanar bonding matrices. In this regard, development of a universal composition-structure-property map for natural platelet-matrix composites, and stacked heterostructures opens up new doors for designing materials with superior mechanical performance. In this dissertation, a multiscale bottom-up approach is adopted to analyze and predict the mechanical properties of platelet-matrix composites. Design guidelines are provided by developing universally valid (across different length scales) diagrams for science-based engineering of numerous natural and synthetic platelet-matrix composites and stacked heterostructures while significantly broadening the spectrum of strategies for fabricating new composites with specific and optimized mechanical properties. First, molecular dynamics simulations are utilized to unravel the fundamental underlying physics and chemistry of the binding nature at the atomic-level interface of organic-inorganic composites. Polymer-cementitious composites are considered as case studies to understand bonding mechanism at the nanoscale and open up new venues for potential mechanical enhancement at the macro-scale. Next, sophisticated mathematical derivations based on elasticity and plasticity theories are presented to describe pre-crack (intrinsic) mechanical performance of platelet-matrix composites at the microscale. These derivations lead to developing a unified framework to construct series of universal composition

  2. Statistical theory and transition in multiple-scale-lengths turbulence in plasmas

    Itoh, Sanae-I. [Research Institute for Applied Mechanics, Kyushu Univ., Kasuga, Fukuoka (Japan); Itoh, Kimitaka [National Inst. for Fusion Science, Toki, Gifu (Japan)

    2001-06-01

    The statistical theory of strong turbulence in inhomogeneous plasmas is developed for the cases where fluctuations with different scale-lengths coexist. Nonlinear interactions in the same kind of fluctuations as well as nonlinear interplay between different classes of fluctuations are kept in the analysis. Nonlinear interactions are modelled as turbulent drag, nonlinear noise and nonlinear drive, and a set of Langevin equations is formulated. With the help of an Ansatz of a large number of degrees of freedom with positive Lyapunov number, Langevin equations are solved and the fluctuation dissipation theorem in the presence of strong plasma turbulence has been derived. A case where two driving mechanisms (one for micro mode and the other for semi-micro mode) coexist is investigated. It is found that there are several states of fluctuations: in one state, the micro mode is excited and the semi-micro mode is quenched; in the other state, the semi-micro mode is excited, and the micro mode remains at finite but suppressed level. New type of turbulence transition is obtained, and a cusp type catastrophe is revealed. A phase diagram is drawn for turbulence which is composed of multiple classes of fluctuations. Influence of the inhomogeneous global radial electric field is discussed. A new insight is given for the physics of internal transport barrier. Finally, the nonlocal heat transport due to the long-wave-length fluctuations, which are noise-pumped by shorter-wave-length ones, is analyzed and the impact on transient transport problems is discussed. (author)

  3. The e-MSWS-12: improving the multiple sclerosis walking scale using item response theory.

    Engelhard, Matthew M; Schmidt, Karen M; Engel, Casey E; Brenton, J Nicholas; Patek, Stephen D; Goldman, Myla D

    2016-12-01

    The Multiple Sclerosis Walking Scale (MSWS-12) is the predominant patient-reported measure of multiple sclerosis (MS) -elated walking ability, yet it had not been analyzed using item response theory (IRT), the emerging standard for patient-reported outcome (PRO) validation. This study aims to reduce MSWS-12 measurement error and facilitate computerized adaptive testing by creating an IRT model of the MSWS-12 and distributing it online. MSWS-12 responses from 284 subjects with MS were collected by mail and used to fit and compare several IRT models. Following model selection and assessment, subpopulations based on age and sex were tested for differential item functioning (DIF). Model comparison favored a one-dimensional graded response model (GRM). This model met fit criteria and explained 87 % of response variance. The performance of each MSWS-12 item was characterized using category response curves (CRCs) and item information. IRT-based MSWS-12 scores correlated with traditional MSWS-12 scores (r = 0.99) and timed 25-foot walk (T25FW) speed (r =  -0.70). Item 2 showed DIF based on age (χ 2  = 19.02, df = 5, p Item 11 showed DIF based on sex (χ 2  = 13.76, df = 5, p = 0.02). MSWS-12 measurement error depends on walking ability, but could be lowered by improving or replacing items with low information or DIF. The e-MSWS-12 includes IRT-based scoring, error checking, and an estimated T25FW derived from MSWS-12 responses. It is available at https://ms-irt.shinyapps.io/e-MSWS-12 .

  4. Psychometric properties of the Epworth Sleepiness Scale: A factor analysis and item-response theory approach.

    Pilcher, June J; Switzer, Fred S; Munc, Alec; Donnelly, Janet; Jellen, Julia C; Lamm, Claus

    2018-04-01

    The purpose of this study is to examine the psychometric properties of the Epworth Sleepiness Scale (ESS) in two languages, German and English. Students from a university in Austria (N = 292; 55 males; mean age = 18.71 ± 1.71 years; 237 females; mean age = 18.24 ± 0.88 years) and a university in the US (N = 329; 128 males; mean age = 18.71 ± 0.88 years; 201 females; mean age = 21.59 ± 2.27 years) completed the ESS. An exploratory-factor analysis was completed to examine dimensionality of the ESS. Item response theory (IRT) analyses were used to provide information about the response rates on the items on the ESS and provide differential item functioning (DIF) analyses to examine whether the items were interpreted differently between the two languages. The factor analyses suggest that the ESS measures two distinct sleepiness constructs. These constructs indicate that the ESS is probing sleepiness in settings requiring active versus passive responding. The IRT analyses found that overall, the items on the ESS perform well as a measure of sleepiness. However, Item 8 and to a lesser extent Item 6 were being interpreted differently by respondents in comparison to the other items. In addition, the DIF analyses showed that the responses between German and English were very similar indicating that there are only minor measurement differences between the two language versions of the ESS. These findings suggest that the ESS provides a reliable measure of propensity to sleepiness; however, it does convey a two-factor approach to sleepiness. Researchers and clinicians can use the German and English versions of the ESS but may wish to exclude Item 8 when calculating a total sleepiness score.

  5. Workshop report on large-scale matrix diagonalization methods in chemistry theory institute

    Bischof, C.H.; Shepard, R.L.; Huss-Lederman, S. [eds.

    1996-10-01

    The Large-Scale Matrix Diagonalization Methods in Chemistry theory institute brought together 41 computational chemists and numerical analysts. The goal was to understand the needs of the computational chemistry community in problems that utilize matrix diagonalization techniques. This was accomplished by reviewing the current state of the art and looking toward future directions in matrix diagonalization techniques. This institute occurred about 20 years after a related meeting of similar size. During those 20 years the Davidson method continued to dominate the problem of finding a few extremal eigenvalues for many computational chemistry problems. Work on non-diagonally dominant and non-Hermitian problems as well as parallel computing has also brought new methods to bear. The changes and similarities in problems and methods over the past two decades offered an interesting viewpoint for the success in this area. One important area covered by the talks was overviews of the source and nature of the chemistry problems. The numerical analysts were uniformly grateful for the efforts to convey a better understanding of the problems and issues faced in computational chemistry. An important outcome was an understanding of the wide range of eigenproblems encountered in computational chemistry. The workshop covered problems involving self- consistent-field (SCF), configuration interaction (CI), intramolecular vibrational relaxation (IVR), and scattering problems. In atomic structure calculations using the Hartree-Fock method (SCF), the symmetric matrices can range from order hundreds to thousands. These matrices often include large clusters of eigenvalues which can be as much as 25% of the spectrum. However, if Cl methods are also used, the matrix size can be between 10{sup 4} and 10{sup 9} where only one or a few extremal eigenvalues and eigenvectors are needed. Working with very large matrices has lead to the development of

  6. A Scale Elasticity Measure for Directional Distance Function and its Dual: Theory and DEA Estimation

    Valentin Zelenyuk

    2012-01-01

    In this paper we focus on scale elasticity measure based on directional distance function for multi-output-multi-input technologies, explore its fundamental properties and show its equivalence with the input oriented and output oriented scale elasticity measures. We also establish duality relationship between the scale elasticity measure based on the directional distance function with scale elasticity measure based on the profit function. Finally, we discuss the estimation issues of the scale...

  7. Reach‐scale river metabolism across contrasting sub‐catchment geologies: Effect of light and hydrology

    Rovelli, Lorenzo; Attard, Karl; Binley, Andrew

    2017-01-01

    and reaches followed a general linear relationship with increasing stream light availability. Sub‐catchment specific NEM proved to be linearly related to the local hydrological connectivity, quantified as the ratio between base flow and stream discharge, and expressed on a timescale of 9 d on average....... This timescale apparently represents the average period of hydrological imprint for carbon turnover within the reaches. Combining a general light response and sub‐catchment specific base flow ratio provided a robust functional relationship for predicting NEM at the reach scale. The novel approach proposed...

  8. Thresholds, switches and hysteresis in hydrology from the pedon to the catchment scale: a non-linear systems theory

    2007-01-01

    Full Text Available Hysteresis is a rate-independent non-linearity that is expressed through thresholds, switches, and branches. Exceedance of a threshold, or the occurrence of a turning point in the input, switches the output onto a particular output branch. Rate-independent branching on a very large set of switches with non-local memory is the central concept in the new definition of hysteresis. Hysteretic loops are a special case. A self-consistent mathematical description of hydrological systems with hysteresis demands a new non-linear systems theory of adequate generality. The goal of this paper is to establish this and to show how this may be done. Two results are presented: a conceptual model for the hysteretic soil-moisture characteristic at the pedon scale and a hysteretic linear reservoir at the catchment scale. Both are based on the Preisach model. A result of particular significance is the demonstration that the independent domain model of the soil moisture characteristic due to Childs, Poulavassilis, Mualem and others, is equivalent to the Preisach hysteresis model of non-linear systems theory, a result reminiscent of the reduction of the theory of the unit hydrograph to linear systems theory in the 1950s. A significant reduction in the number of model parameters is also achieved. The new theory implies a change in modelling paradigm.

  9. Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

    Kim Pan-Jun

    2011-08-01

    Full Text Available Abstract Background Solventogenic clostridia offer a sustainable alternative to petroleum-based production of butanol--an important chemical feedstock and potential fuel additive or replacement. C. beijerinckii is an attractive microorganism for strain design to improve butanol production because it (i naturally produces the highest recorded butanol concentrations as a byproduct of fermentation; and (ii can co-ferment pentose and hexose sugars (the primary products from lignocellulosic hydrolysis. Interrogating C. beijerinckii metabolism from a systems viewpoint using constraint-based modeling allows for simulation of the global effect of genetic modifications. Results We present the first genome-scale metabolic model (iCM925 for C. beijerinckii, containing 925 genes, 938 reactions, and 881 metabolites. To build the model we employed a semi-automated procedure that integrated genome annotation information from KEGG, BioCyc, and The SEED, and utilized computational algorithms with manual curation to improve model completeness. Interestingly, we found only a 34% overlap in reactions collected from the three databases--highlighting the importance of evaluating the predictive accuracy of the resulting genome-scale model. To validate iCM925, we conducted fermentation experiments using the NCIMB 8052 strain, and evaluated the ability of the model to simulate measured substrate uptake and product production rates. Experimentally observed fermentation profiles were found to lie within the solution space of the model; however, under an optimal growth objective, additional constraints were needed to reproduce the observed profiles--suggesting the existence of selective pressures other than optimal growth. Notably, a significantly enriched fraction of actively utilized reactions in simulations--constrained to reflect experimental rates--originated from the set of reactions that overlapped between all three databases (P = 3.52 × 10-9, Fisher's exact test

  10. An evaluation of string theory for the prediction of dynamic tire properties using scale model aircraft tires

    Clark, S. K.; Dodge, R. N.; Nybakken, G. H.

    1972-01-01

    The string theory was evaluated for predicting lateral tire dynamic properties as obtained from scaled model tests. The experimental data and string theory predictions are in generally good agreement using lateral stiffness and relaxation length values obtained from the static or slowly rolling tire. The results indicate that lateral forces and self-aligning torques are linearly proportional to tire lateral stiffness and to the amplitude of either steer or lateral displacement. In addition, the results show that the ratio of input excitation frequency to road speed is the proper independent variable by which frequency should be measured.

  11. An Institutional Theory Analysis of Charter Schools: Addressing Institutional Challenges to Scale

    Huerta, Luis A.; Zuckerman, Andrew

    2009-01-01

    This article presents a conceptual framework derived from institutional theory in sociology that offers two competing policy contexts in which charter schools operate--a bureaucratic frame versus a decentralized frame. An analysis of evolving charter school types based on three underlying theories of action is considered. As charter school leaders…

  12. Scaling laws and triviality bounds in the lattice Φ4 theory. Pt. 1

    Luescher, M.; Weisz, P.

    1987-01-01

    The lattice Φ 4 theory in four space-time dimensions is most likely 'trivial', i.e. its continuum limit is a free field theory. However, for small but positive lattice spacing a and at energies well below the cutoff mass Λ=1/a, the theory effectively behaves like a continuum theory with particle interactions, which may be appreciable. By a combination of known analytical methods, we here determine the maximal value of the renormalized coupling at zero momentum as a function of Λ/m, where m denotes the mass of the scalar particle in the theory. Moreover, a complete solution of the model is obtained in the sense that all low energy amplitudes can be computed with reasonable estimated accuracy for arbitrarily chosen bare coupling and mass in the symmetric phase region. (orig.)

  13. Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth

    2012-01-01

    Background Over the last decade, the genome-scale metabolic models have been playing increasingly important roles in elucidating metabolic characteristics of biological systems for a wide range of applications including, but not limited to, system-wide identification of drug targets and production of high value biochemical compounds. However, these genome-scale metabolic models must be able to first predict known in vivo phenotypes before it is applied towards these applications with high confidence. One benchmark for measuring the in silico capability in predicting in vivo phenotypes is the use of single-gene mutant libraries to measure the accuracy of knockout simulations in predicting mutant growth phenotypes. Results Here we employed a systematic and iterative process, designated as Reconciling In silico/in vivo mutaNt Growth (RING), to settle discrepancies between in silico prediction and in vivo observations to a newly reconstructed genome-scale metabolic model of the fission yeast, Schizosaccharomyces pombe, SpoMBEL1693. The predictive capabilities of the genome-scale metabolic model in predicting single-gene mutant growth phenotypes were measured against the single-gene mutant library of S. pombe. The use of RING resulted in improving the overall predictive capability of SpoMBEL1693 by 21.5%, from 61.2% to 82.7% (92.5% of the negative predictions matched the observed growth phenotype and 79.7% the positive predictions matched the observed growth phenotype). Conclusion This study presents validation and refinement of a newly reconstructed metabolic model of the yeast S. pombe, through improving the metabolic model’s predictive capabilities by reconciling the in silico predicted growth phenotypes of single-gene knockout mutants, with experimental in vivo growth data. PMID:22631437

  14. Evaluation of a Genome-Scale In Silico Metabolic Model for Geobacter metallireducens by Using Proteomic Data from a Field Biostimulation Experiment

    Fang, Yilin; Yabusaki, Steven B.; Lipton, Mary S.; Long, Philip E.

    2012-01-01

    Accurately predicting the interactions between microbial metabolism and the physical subsurface environment is necessary to enhance subsurface energy development, soil and groundwater cleanup, and carbon management. This study was an initial attempt to confirm the metabolic functional roles within an in silico model using environmental proteomic data collected during field experiments. Shotgun global proteomics data collected during a subsurface biostimulation experiment were used to validate a genome-scale metabolic model of Geobacter metallireducens—specifically, the ability of the metabolic model to predict metal reduction, biomass yield, and growth rate under dynamic field conditions. The constraint-based in silico model of G. metallireducens relates an annotated genome sequence to the physiological functions with 697 reactions controlled by 747 enzyme-coding genes. Proteomic analysis showed that 180 of the 637 G. metallireducens proteins detected during the 2008 experiment were associated with specific metabolic reactions in the in silico model. When the field-calibrated Fe(III) terminal electron acceptor process reaction in a reactive transport model for the field experiments was replaced with the genome-scale model, the model predicted that the largest metabolic fluxes through the in silico model reactions generally correspond to the highest abundances of proteins that catalyze those reactions. Central metabolism predicted by the model agrees well with protein abundance profiles inferred from proteomic analysis. Model discrepancies with the proteomic data, such as the relatively low abundances of proteins associated with amino acid transport and metabolism, revealed pathways or flux constraints in the in silico model that could be updated to more accurately predict metabolic processes that occur in the subsurface environment. PMID:23042184

  15. Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming

    Song, Hyun-Seob; Goldberg, Noam; Mahajan, Ashutosh; Ramkrishna, Doraiswami

    2017-03-27

    Elementary (flux) modes (EMs) have served as a valuable tool for investigating structural and functional properties of metabolic networks. Identification of the full set of EMs in genome-scale networks remains challenging due to combinatorial explosion of EMs in complex networks. It is often, however, that only a small subset of relevant EMs needs to be known, for which optimization-based sequential computation is a useful alternative. Most of the currently available methods along this line are based on the iterative use of mixed integer linear programming (MILP), the effectiveness of which significantly deteriorates as the number of iterations builds up. To alleviate the computational burden associated with the MILP implementation, we here present a novel optimization algorithm termed alternate integer linear programming (AILP). Results: Our algorithm was designed to iteratively solve a pair of integer programming (IP) and linear programming (LP) to compute EMs in a sequential manner. In each step, the IP identifies a minimal subset of reactions, the deletion of which disables all previously identified EMs. Thus, a subsequent LP solution subject to this reaction deletion constraint becomes a distinct EM. In cases where no feasible LP solution is available, IP-derived reaction deletion sets represent minimal cut sets (MCSs). Despite the additional computation of MCSs, AILP achieved significant time reduction in computing EMs by orders of magnitude. The proposed AILP algorithm not only offers a computational advantage in the EM analysis of genome-scale networks, but also improves the understanding of the linkage between EMs and MCSs.

  16. Development of a Scale to Assess Knowledge about Suicide Postvention Using Item Response Theory

    Nader, Ingo W.; Niederkrotenthaler, Thomas; Schild, Anne H. E.; Koller, Ingrid; Tran, Ulrich S.; Kapusta, Nestor D.; Sonneck, Gernot; Voracek, Martin

    2013-01-01

    Knowledge about suicide postvention (KSPV) is an important distal outcome in the evaluation of suicide prevention programs that focus on the bereaved. However, most scales are specifically tailored to the evaluation study in question and psychometric properties are often unsatisfactory. Therefore, we developed the KSPV scale. Scale properties were…

  17. Localized multi-scale energy and vorticity analysis. II. Finite-amplitude instability theory and validation

    San Liang, X.; Robinson, Allan R.

    2007-12-01

    A novel localized finite-amplitude hydrodynamic stability analysis is established in a unified treatment for the study of real oceanic and atmospheric processes, which are in general highly nonlinear, and intermittent in space and time. We first re-state the classical definition using the multi-scale energy and vorticity analysis (MS-EVA) developed in Liang and Robinson [Liang, X.S., Robinson, A.R., 2005. Localized multiscale energy and vorticity analysis. I. Fundamentals. Dyn. Atmos. Oceans 38, 195-230], and then manipulate certain global operators to achieve the temporal and spatial localization. The key of the spatial localization is transfer-transport separation, which is made precise with the concept of perfect transfer, while relaxation of marginalization leads to the localization of time. In doing so the information of transfer lost in the averages is retrieved and an easy-to-use instability metric is obtained. The resulting metric is field-like (Eulerian), conceptually generalizing the classical formalism, a bulk notion over the whole system. In this framework, an instability has a structure, which is of particular use for open flow processes. We check the structure of baroclinic instability with the benchmark Eady model solution, and the Iceland-Faeroe Frontal (IFF) intrusion, a highly localized and nonlinear process occurring frequently in the region between Iceland and Faeroe Islands. A clear isolated baroclinic instability is identified around the intrusion, which is further found to be characterized by the transition from a spatially growing mode to a temporally growing mode. We also check the consistency of the MS-EVA dynamics with the barotropic Kuo model. An observation is that a local perturbation burst does not necessarily imply an instability: the perturbation energy could be transported from other processes occurring elsewhere. We find that our analysis yields a Kuo theorem-consistent mean-eddy interaction, which is not seen in a conventional

  18. Canonical-ensemble extended Lagrangian Born-Oppenheimer molecular dynamics for the linear scaling density functional theory.

    Hirakawa, Teruo; Suzuki, Teppei; Bowler, David R; Miyazaki, Tsuyoshi

    2017-10-11

    We discuss the development and implementation of a constant temperature (NVT) molecular dynamics scheme that combines the Nosé-Hoover chain thermostat with the extended Lagrangian Born-Oppenheimer molecular dynamics (BOMD) scheme, using a linear scaling density functional theory (DFT) approach. An integration scheme for this canonical-ensemble extended Lagrangian BOMD is developed and discussed in the context of the Liouville operator formulation. Linear scaling DFT canonical-ensemble extended Lagrangian BOMD simulations are tested on bulk silicon and silicon carbide systems to evaluate our integration scheme. The results show that the conserved quantity remains stable with no systematic drift even in the presence of the thermostat.

  19. Henry's Constants of Persistent Organic Pollutants by a Group-Contribution Method Based on Scaled-Particle Theory.

    Razdan, Neil K; Koshy, David M; Prausnitz, John M

    2017-11-07

    A group-contribution method based on scaled-particle theory was developed to predict Henry's constants for six families of persistent organic pollutants: polychlorinated benzenes, polychlorinated biphenyls, polychlorinated dibenzodioxins, polychlorinated dibenzofurans, polychlorinated naphthalenes, and polybrominated diphenyl ethers. The group-contribution model uses limited experimental data to obtain group-interaction parameters for an easy-to-use method to predict Henry's constants for systems where reliable experimental data are scarce. By using group-interaction parameters obtained from data reduction, scaled-particle theory gives the partial molar Gibbs energy of dissolution, Δg̅ 2 , allowing calculation of Henry's constant, H 2 , for more than 700 organic pollutants. The average deviation between predicted values of log H 2 and experiment is 4%. Application of an approximate van't Hoff equation gives the temperature dependence of Henry's constants for polychlorinated biphenyls, polychlorinated naphthalenes, and polybrominated diphenyl ethers in the environmentally relevant range 0-40 °C.

  20. Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions.

    Zuñiga, Cristal; Li, Chien-Ting; Huelsman, Tyler; Levering, Jennifer; Zielinski, Daniel C; McConnell, Brian O; Long, Christopher P; Knoshaug, Eric P; Guarnieri, Michael T; Antoniewicz, Maciek R; Betenbaugh, Michael J; Zengler, Karsten

    2016-09-01

    The green microalga Chlorella vulgaris has been widely recognized as a promising candidate for biofuel production due to its ability to store high lipid content and its natural metabolic versatility. Compartmentalized genome-scale metabolic models constructed from genome sequences enable quantitative insight into the transport and metabolism of compounds within a target organism. These metabolic models have long been utilized to generate optimized design strategies for an improved production process. Here, we describe the reconstruction, validation, and application of a genome-scale metabolic model for C. vulgaris UTEX 395, iCZ843. The reconstruction represents the most comprehensive model for any eukaryotic photosynthetic organism to date, based on the genome size and number of genes in the reconstruction. The highly curated model accurately predicts phenotypes under photoautotrophic, heterotrophic, and mixotrophic conditions. The model was validated against experimental data and lays the foundation for model-driven strain design and medium alteration to improve yield. Calculated flux distributions under different trophic conditions show that a number of key pathways are affected by nitrogen starvation conditions, including central carbon metabolism and amino acid, nucleotide, and pigment biosynthetic pathways. Furthermore, model prediction of growth rates under various medium compositions and subsequent experimental validation showed an increased growth rate with the addition of tryptophan and methionine. © 2016 American Society of Plant Biologists. All rights reserved.

  1. Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions1

    Zuñiga, Cristal; Li, Chien-Ting; Zielinski, Daniel C.; Guarnieri, Michael T.; Antoniewicz, Maciek R.; Zengler, Karsten

    2016-01-01

    The green microalga Chlorella vulgaris has been widely recognized as a promising candidate for biofuel production due to its ability to store high lipid content and its natural metabolic versatility. Compartmentalized genome-scale metabolic models constructed from genome sequences enable quantitative insight into the transport and metabolism of compounds within a target organism. These metabolic models have long been utilized to generate optimized design strategies for an improved production process. Here, we describe the reconstruction, validation, and application of a genome-scale metabolic model for C. vulgaris UTEX 395, iCZ843. The reconstruction represents the most comprehensive model for any eukaryotic photosynthetic organism to date, based on the genome size and number of genes in the reconstruction. The highly curated model accurately predicts phenotypes under photoautotrophic, heterotrophic, and mixotrophic conditions. The model was validated against experimental data and lays the foundation for model-driven strain design and medium alteration to improve yield. Calculated flux distributions under different trophic conditions show that a number of key pathways are affected by nitrogen starvation conditions, including central carbon metabolism and amino acid, nucleotide, and pigment biosynthetic pathways. Furthermore, model prediction of growth rates under various medium compositions and subsequent experimental validation showed an increased growth rate with the addition of tryptophan and methionine. PMID:27372244

  2. Find_tfSBP: find thermodynamics-feasible and smallest balanced pathways with high yield from large-scale metabolic networks.

    Xu, Zixiang; Sun, Jibin; Wu, Qiaqing; Zhu, Dunming

    2017-12-11

    Biologically meaningful metabolic pathways are important references in the design of industrial bacterium. At present, constraint-based method is the only way to model and simulate a genome-scale metabolic network under steady-state criteria. Due to the inadequate assumption of the relationship in gene-enzyme-reaction as one-to-one unique association, computational difficulty or ignoring the yield from substrate to product, previous pathway finding approaches can't be effectively applied to find out the high yield pathways that are mass balanced in stoichiometry. In addition, the shortest pathways may not be the pathways with high yield. At the same time, a pathway, which exists in stoichiometry, may not be feasible in thermodynamics. By using mixed integer programming strategy, we put forward an algorithm to identify all the smallest balanced pathways which convert the source compound to the target compound in large-scale metabolic networks. The resulting pathways by our method can finely satisfy the stoichiometric constraints and non-decomposability condition. Especially, the functions of high yield and thermodynamics feasibility have been considered in our approach. This tool is tailored to direct the metabolic engineering practice to enlarge the metabolic potentials of industrial strains by integrating the extensive metabolic network information built from systems biology dataset.

  3. River Metabolism and Nutrient Cycling at the Point Scale: Insights from In Situ Sensors in Benthic Chambers

    Cohen, M. J.; Reijo, C. J.; Hensley, R. T.

    2017-12-01

    Riverine processing of nutrients and carbon is a local process, subject to heterogeneity in sediment, biotic, insolation, and flow velocity drivers. Measurements at the reach scale aggregate across riverscapes, limiting their utility for enumerating these drivers, and thus for scaling to river networks. Using a combination of in situ sensors that sample water chemistry at high temporal resolution and open benthic chambers that isolate the biogeochemical impacts of a small footprint of benthic surface area, we explored controls on metabolism and nutrient cycling. We specifically sought to answer two questions. First, what are the controls on primary production, with a particular emphasis on the relative roles of light vs. nutrient limitation? Second, what are the pathways of nutrient retention, and do the reaction kinetics of these different pathways differ? We demonstrate the considerable utility of these benthic chambers, reasoning that they provide experimental units for river processes that are not attainable at the reach or network scale. Specifically, in addition to their ability to sample the heterogeneity of the river bed as well as observe nutrient depletion to create concentrations well below ambient levels, they enable manipulative experiments (e.g., nutrient enrichment, light reduction, grazer adjustments) while retaining key elements of the natural system. Across several of Florida's spring-fed river sites, our results strongly support the primacy of light limitation of primary production, with very little evidence of any incremental effects of nutrient enrichment. Nutrient depletion assays further support the dominance of two N retention mechanisms (denitrification and assimilation), the kinetics of which differ markedly, with denitrification exhibiting nearly first-order reactions, and assimilation following zero-order or Michaelis-Menten kinetics over the range of observed concentrations. This latter result helps explain the absence of strong

  4. Generic mechanism of optimal energy transfer efficiency: a scaling theory of the mean first-passage time in exciton systems.

    Wu, Jianlan; Silbey, Robert J; Cao, Jianshu

    2013-05-17

    An asymptotic scaling theory is presented using the conceptual basis of trapping-free subspace (i.e., orthogonal subspace) to establish the generic mechanism of optimal efficiency of excitation energy transfer in light-harvesting systems. A quantum state orthogonal to the trap will exhibit noise-assisted transfer, clarifying the significance of initial preparation. For such an initial state, the efficiency is enhanced in the weak damping limit (⟨t⟩ ∼ 1/Γ), and suppressed in the strong damping limit (⟨t⟩ ∼ Γ), analogous to Kramers turnover in classical rate theory. An interpolating expression ⟨t⟩ = A/Γ + B + CΓ quantitatively describes the trapping time over the entire range of the dissipation strength, and predicts the optimal efficiency at Γ(opt) ∼ J for homogenous systems. In the presence of static disorder, the scaling law of transfer time with respect to dephasing rate changes from linear to square root, suggesting a weaker dependence on the environment. The prediction of the scaling theory is verified in a symmetric dendrimer system by numerically exact quantum calculations. Though formulated in the context of excitation energy transfer, the analysis and conclusions apply in general to open quantum processes, including electron transfer, fluorescence emission, and heat conduction.

  5. On the cooperativity of association and reference energy scales in thermodynamic perturbation theory

    Marshall, Bennett D.

    2016-11-01

    Equations of state for hydrogen bonding fluids are typically described by two energy scales. A short range highly directional hydrogen bonding energy scale as well as a reference energy scale which accounts for dispersion and orientationally averaged multi-pole attractions. These energy scales are always treated independently. In recent years, extensive first principles quantum mechanics calculations on small water clusters have shown that both hydrogen bond and reference energy scales depend on the number of incident hydrogen bonds of the water molecule. In this work, we propose a new methodology to couple the reference energy scale to the degree of hydrogen bonding in the fluid. We demonstrate the utility of the new approach by showing that it gives improved predictions of water-hydrocarbon mutual solubilities.

  6. Scaling Factor Estimation Using an Optimized Mass Change Strategy, Part 1: Theory

    Aenlle, Manuel López; Fernández, Pelayo Fernández; Brincker, Rune

    2007-01-01

    In natural input modal analysis, only un-scaled mode shapes can be obtained. The mass change method is, in many cases, the simplest way to estimate the scaling factors, which involves repeated modal testing after changing the mass in different points of the structure where the mode shapes are known....... The scaling factors are determined using the natural frequencies and mode shapes of both the modified and the unmodified structure. However, the uncertainty on the scaling factor estimation depends on the modal analysis and the mass change strategy (number, magnitude and location of the masses) used to modify...

  7. Scaling Theory for Pulsed Jet Mixed Vessels, Sparging, and Cyclic Feed Transport Systems for Slurries

    Kuhn, William L.; Rector, David R.; Rassat, Scot D.; Enderlin, Carl W.; Minette, Michael J.; Bamberger, Judith A.; Josephson, Gary B.; Wells, Beric E.; Berglin, Eric J.

    2013-09-27

    This document is a previously unpublished work based on a draft report prepared by Pacific Northwest National Laboratory (PNNL) for the Hanford Waste Treatment and Immobilization Plant (WTP) in 2012. Work on the report stopped when WTP’s approach to testing changed. PNNL is issuing a modified version of the document a year later to preserve and disseminate the valuable technical work that was completed. This document establishes technical bases for evaluating the mixing performance of Waste Treatment Plant (WTP) pretreatment process tanks based on data from less-than-full-scale testing, relative to specified mixing requirements. The technical bases include the fluid mechanics affecting mixing for specified vessel configurations, operating parameters, and simulant properties. They address scaling vessel physical performance, simulant physical performance, and “scaling down” the operating conditions at full scale to define test conditions at reduced scale and “scaling up” the test results at reduced scale to predict the performance at full scale. Essentially, this document addresses the following questions: • Why and how can the mixing behaviors in a smaller vessel represent those in a larger vessel? • What information is needed to address the first question? • How should the information be used to predict mixing performance in WTP? The design of Large Scale Integrated Testing (LSIT) is being addressed in other, complementary documents.

  8. A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism.

    Mih, Nathan; Brunk, Elizabeth; Bordbar, Aarash; Palsson, Bernhard O

    2016-07-01

    Progress in systems medicine brings promise to addressing patient heterogeneity and individualized therapies. Recently, genome-scale models of metabolism have been shown to provide insight into the mechanistic link between drug therapies and systems-level off-target effects while being expanded to explicitly include the three-dimensional structure of proteins. The integration of these molecular-level details, such as the physical, structural, and dynamical properties of proteins, notably expands the computational description of biochemical network-level properties and the possibility of understanding and predicting whole cell phenotypes. In this study, we present a multi-scale modeling framework that describes biological processes which range in scale from atomistic details to an entire metabolic network. Using this approach, we can understand how genetic variation, which impacts the structure and reactivity of a protein, influences both native and drug-induced metabolic states. As a proof-of-concept, we study three enzymes (catechol-O-methyltransferase, glucose-6-phosphate dehydrogenase, and glyceraldehyde-3-phosphate dehydrogenase) and their respective genetic variants which have clinically relevant associations. Using all-atom molecular dynamic simulations enables the sampling of long timescale conformational dynamics of the proteins (and their mutant variants) in complex with their respective native metabolites or drug molecules. We find that changes in a protein's structure due to a mutation influences protein binding affinity to metabolites and/or drug molecules, and inflicts large-scale changes in metabolism.

  9. A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism.

    Nathan Mih

    2016-07-01

    Full Text Available Progress in systems medicine brings promise to addressing patient heterogeneity and individualized therapies. Recently, genome-scale models of metabolism have been shown to provide insight into the mechanistic link between drug therapies and systems-level off-target effects while being expanded to explicitly include the three-dimensional structure of proteins. The integration of these molecular-level details, such as the physical, structural, and dynamical properties of proteins, notably expands the computational description of biochemical network-level properties and the possibility of understanding and predicting whole cell phenotypes. In this study, we present a multi-scale modeling framework that describes biological processes which range in scale from atomistic details to an entire metabolic network. Using this approach, we can understand how genetic variation, which impacts the structure and reactivity of a protein, influences both native and drug-induced metabolic states. As a proof-of-concept, we study three enzymes (catechol-O-methyltransferase, glucose-6-phosphate dehydrogenase, and glyceraldehyde-3-phosphate dehydrogenase and their respective genetic variants which have clinically relevant associations. Using all-atom molecular dynamic simulations enables the sampling of long timescale conformational dynamics of the proteins (and their mutant variants in complex with their respective native metabolites or drug molecules. We find that changes in a protein's structure due to a mutation influences protein binding affinity to metabolites and/or drug molecules, and inflicts large-scale changes in metabolism.

  10. Spatial connections in regional climate model rainfall outputs at different temporal scales: Application of network theory

    Naufan, Ihsan; Sivakumar, Bellie; Woldemeskel, Fitsum M.; Raghavan, Srivatsan V.; Vu, Minh Tue; Liong, Shie-Yui

    2018-01-01

    Understanding the spatial and temporal variability of rainfall has always been a great challenge, and the impacts of climate change further complicate this issue. The present study employs the concepts of complex networks to study the spatial connections in rainfall, with emphasis on climate change and rainfall scaling. Rainfall outputs (during 1961-1990) from a regional climate model (i.e. Weather Research and Forecasting (WRF) model that downscaled the European Centre for Medium-range Weather Forecasts, ECMWF ERA-40 reanalyses) over Southeast Asia are studied, and data corresponding to eight different temporal scales (6-hr, 12-hr, daily, 2-day, 4-day, weekly, biweekly, and monthly) are analyzed. Two network-based methods are applied to examine the connections in rainfall: clustering coefficient (a measure of the network's local density) and degree distribution (a measure of the network's spread). The influence of rainfall correlation threshold (T) on spatial connections is also investigated by considering seven different threshold levels (ranging from 0.5 to 0.8). The results indicate that: (1) rainfall networks corresponding to much coarser temporal scales exhibit properties similar to that of small-world networks, regardless of the threshold; (2) rainfall networks corresponding to much finer temporal scales may be classified as either small-world networks or scale-free networks, depending upon the threshold; and (3) rainfall spatial connections exhibit a transition phase at intermediate temporal scales, especially at high thresholds. These results suggest that the most appropriate model for studying spatial connections may often be different at different temporal scales, and that a combination of small-world and scale-free network models might be more appropriate for rainfall upscaling/downscaling across all scales, in the strict sense of scale-invariance. The results also suggest that spatial connections in the studied rainfall networks in Southeast Asia are

  11. Reliability and Structure of the TALIS Social Desirability Scale: An Assessment Based on Item Response Theory

    Kapuza, A. V.; Tyumeneva, Yu. A.

    2017-01-01

    One of the ways of controlling for the influence of social expectations on the answers given by survey respondents is to use a social desirability scale together with the main questions. The social desirability scale, which was included in the Teaching and Learning International Survey (TALIS) international comparative study for this purpose, was…

  12. Large-scale atomistic simulations of nanostructured materials based on divide-and-conquer density functional theory

    Vashishta P.

    2011-05-01

    Full Text Available A linear-scaling algorithm based on a divide-and-conquer (DC scheme is designed to perform large-scale molecular-dynamics simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT. This scheme is applied to the thermite reaction at an Al/Fe2O3 interface. It is found that mass diffusion and reaction rate at the interface are enhanced by a concerted metal-oxygen flip mechanism. Preliminary simulations are carried out for an aluminum particle in water based on the conventional DFT, as a target system for large-scale DC-DFT simulations. A pair of Lewis acid and base sites on the aluminum surface preferentially catalyzes hydrogen production in a low activation-barrier mechanism found in the simulations

  13. Scales

    Scales are a visible peeling or flaking of outer skin layers. These layers are called the stratum ... Scales may be caused by dry skin, certain inflammatory skin conditions, or infections. Examples of disorders that ...

  14. Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming.

    Song, Hyun-Seob; Goldberg, Noam; Mahajan, Ashutosh; Ramkrishna, Doraiswami

    2017-08-01

    Elementary (flux) modes (EMs) have served as a valuable tool for investigating structural and functional properties of metabolic networks. Identification of the full set of EMs in genome-scale networks remains challenging due to combinatorial explosion of EMs in complex networks. It is often, however, that only a small subset of relevant EMs needs to be known, for which optimization-based sequential computation is a useful alternative. Most of the currently available methods along this line are based on the iterative use of mixed integer linear programming (MILP), the effectiveness of which significantly deteriorates as the number of iterations builds up. To alleviate the computational burden associated with the MILP implementation, we here present a novel optimization algorithm termed alternate integer linear programming (AILP). Our algorithm was designed to iteratively solve a pair of integer programming (IP) and linear programming (LP) to compute EMs in a sequential manner. In each step, the IP identifies a minimal subset of reactions, the deletion of which disables all previously identified EMs. Thus, a subsequent LP solution subject to this reaction deletion constraint becomes a distinct EM. In cases where no feasible LP solution is available, IP-derived reaction deletion sets represent minimal cut sets (MCSs). Despite the additional computation of MCSs, AILP achieved significant time reduction in computing EMs by orders of magnitude. The proposed AILP algorithm not only offers a computational advantage in the EM analysis of genome-scale networks, but also improves the understanding of the linkage between EMs and MCSs. The software is implemented in Matlab, and is provided as supplementary information . hyunseob.song@pnnl.gov. Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2017. This work is written by US Government employees and are in the public domain in the US.

  15. Understanding urban water performance at the city-region scale using an urban water metabolism evaluation framework.

    Renouf, Marguerite A; Kenway, Steven J; Lam, Ka Leung; Weber, Tony; Roux, Estelle; Serrao-Neumann, Silvia; Choy, Darryl Low; Morgan, Edward A

    2018-06-15

    Water sensitive interventions are being promoted to reduce the adverse impacts of urban development on natural water cycles. However it is currently difficult to know the best strategy for their implementation because current and desired urban water performance is not well quantified. This is particularly at the city-region scale, which is important for strategic urban planning. This work aimed to fill this gap by quantifying the water performance of urban systems within city-regions using 'urban water metabolism' evaluation, to inform decisions about water sensitive interventions. To do this we adapted an existing evaluation framework with new methods. In particular, we used land use data for defining system boundaries, and for estimating natural hydrological flows. The criteria for gauging the water performance were water efficiency (in terms of water extracted externally) and hydrological performance (how much natural hydrological flows have changed relative to a nominated pre-urbanised state). We compared these performance criteria for urban systems within three Australian city-regions (South East Queensland, Melbourne and Perth metropolitan areas), under current conditions, and after implementation of example water sensitive interventions (demand management, rainwater/stormwater harvesting, wastewater recycling and increasing perviousness). The respective water efficiencies were found to be 79, 90 and 133 kL/capita/yr. In relation to hydrological performance, stormwater runoff relative to pre-urbanised flows was of most note, estimated to be 2-, 6- and 3- fold, respectively. The estimated performance benefits from water sensitive interventions suggested different priorities for each region, and that combined implementation of a range of interventions may be necessary to make substantive gains in performance. We concluded that the framework is suited to initial screening of the type and scale of water sensitive interventions needed to achieve desired water

  16. Cerebral metabolic alterations and cognitive dysfunction in children with chronic kidney disease using Magnetic Resonance Spectroscopy and Wechsler intelligence scale.

    Youssef, Doaa Mohammed; Mohamed, Ahmed Hosny; Kamel Attia, Wafaa Mahmoud; Mohammad, Faten Fawzy; El Fatah, Nelly Rafaat Abd; Elshal, Amal Saeed

    2017-06-16

    Many studies described Impaired intelligence, attention, memory and executive function in patients with chronic kidney disease (CKD) dialyzed and non-dialyzed, but there is still lacking the early and sensitive method of detection of these deficits. The purpose of this study is to investigate relation between the brain metabolic alteration [measured by magnetic resonance spectroscopy (MRS)] and cognitive dysfunction in CKD children (detected by psychometric analysis). One hundred and forty patients with CKD were included [ 40 patients with stage 5 CKD on dialysis, 30 patients with stage 4 to 5 CKD without dialysis, and 70 patients with stage 1 to 3 CKD]. All patients with previous neurological disorders were excluded. Conventional MRI, MRS and psychometric assessment by using Wechsler intelligence scale for children third edition was done in all subjects. We found a significant negative correlation between MRS abnormalities and Wechsler IQ Test scores. But there was a significantly positive correlation between the CKD stages and MRS abnormalities in patients with CKD and negative significant correlation between CKD stages and Wechsler IQ test scores in patients with CKD. There were correlations between "the electrolyte disturbance, blood hemoglobin and hypertension" and "the CKD staging, cognitive functions IQ scores and MRS parameter changes". We concluded that both MRS and psychometric tests are sensitive methods for detection of cognitive function affection in CKD children, particularly in dialyzed group and these findings appears before the clinical diagnosis. This article is protected by copyright. All rights reserved.

  17. From Fancy to Reason: Scaling Deaf and Hearing Children's Understanding of Theory of Mind and Pretence

    Peterson, Candida C.; Wellman, Henry M.

    2009-01-01

    We examined deaf and hearing children's progression of steps in theory of mind (ToM) development including their understanding of social pretending. Ninety-three children (33 deaf; 60 hearing) aged 3-13 years were tested on a set of six closely matched ToM tasks. Results showed that deaf children were delayed substantially behind hearing children…

  18. Application of Item Response Theory to Modeling of Expanded Disability Status Scale in Multiple Sclerosis.

    Novakovic, A.M.; Krekels, E.H.; Munafo, A.; Ueckert, S.; Karlsson, M.O.

    2016-01-01

    In this study, we report the development of the first item response theory (IRT) model within a pharmacometrics framework to characterize the disease progression in multiple sclerosis (MS), as measured by Expanded Disability Status Score (EDSS). Data were collected quarterly from a 96-week phase III

  19. Teaching a lay theory before college narrows achievement gaps at scale.

    Yeager, David S; Walton, Gregory M; Brady, Shannon T; Akcinar, Ezgi N; Paunesku, David; Keane, Laura; Kamentz, Donald; Ritter, Gretchen; Duckworth, Angela Lee; Urstein, Robert; Gomez, Eric M; Markus, Hazel Rose; Cohen, Geoffrey L; Dweck, Carol S

    2016-06-14

    Previous experiments have shown that college students benefit when they understand that challenges in the transition to college are common and improvable and, thus, that early struggles need not portend a permanent lack of belonging or potential. Could such an approach-called a lay theory intervention-be effective before college matriculation? Could this strategy reduce a portion of racial, ethnic, and socioeconomic achievement gaps for entire institutions? Three double-blind experiments tested this possibility. Ninety percent of first-year college students from three institutions were randomly assigned to complete single-session, online lay theory or control materials before matriculation (n > 9,500). The lay theory interventions raised first-year full-time college enrollment among students from socially and economically disadvantaged backgrounds exiting a high-performing charter high school network or entering a public flagship university (experiments 1 and 2) and, at a selective private university, raised disadvantaged students' cumulative first-year grade point average (experiment 3). These gains correspond to 31-40% reductions of the raw (unadjusted) institutional achievement gaps between students from disadvantaged and nondisadvantaged backgrounds at those institutions. Further, follow-up surveys suggest that the interventions improved disadvantaged students' overall college experiences, promoting use of student support services and the development of friendship networks and mentor relationships. This research therefore provides a basis for further tests of the generalizability of preparatory lay theories interventions and of their potential to reduce social inequality and improve other major life transitions.

  20. Enforced Scale Selection in Field Theories of Mechanical and Biological Systems

    Tarp, Jens Magelund

    The collective motion of driven or self-propelled interacting units is in many natural systems known to produce complex patterns. This thesis considers two continuum field theories commonly used in describing pattern formation and dynamics: The first one, the phase field crystal model, which...

  1. Nonparametric Item Response Theory for Investigating Dimensionality of Marketing Scales: A SERVQUAL application

    Paas, L.J.; Sijtsma, K.

    2008-01-01

    Assessing scale dimensionality is an important issue in the marketing literature. In an exploratory context, principal axis factoring and principal components analysis receive emphasis, while other fields apply suitable alternatives. This article introduces a promising procedure known as Mokken

  2. Single Mode Theory for Impedance Eduction in Large-Scale Ducts with Grazing Flow

    Watson, Willie R.; Gerhold, Carl H.; Jones, Michael G.; June, Jason C.

    2014-01-01

    An impedance eduction theory for a rigid wall duct containing an acoustic liner with an unknown impedance and uniform grazing flow is presented. The unique features of the theory are: 1) non-planar waves propagate in the hard wall sections of the duct, 2) input data consist solely of complex acoustic pressures acquired on a wall adjacent to the liner, and 3) multiple higher-order modes may exist in the direction perpendicular to the liner and the opposite rigid wall. The approach is to first measure the axial propagation constant of a dominant higher-order mode in the liner sample section. This axial propagation constant is then used in conjunction with a closed-form solution to a reduced form of the convected Helmholtz equation and the wall impedance boundary condition to educe the liner impedance. The theory is validated on a conventional liner whose impedance spectrum is educed in two flow ducts with different cross sections. For the frequencies and Mach numbers of interest, no higher-order modes propagate in the hard wall sections of the smaller duct. A benchmark method is used to educe the impedance spectrum in this duct. A dominant higher-order vertical mode propagates in the larger duct for similar test conditions, and the current theory is applied to educe the impedance spectrum. Results show that when the theory is applied to data acquired in the larger duct with a dominant higher-order vertical mode, the same impedance spectra is educed as that obtained in the small duct where only the plane wave mode is present and the benchmark method is used. This result holds for each higher-order vertical mode that is considered.

  3. Reconstruction of Oryza sativa indica Genome Scale Metabolic Model and Its Responses to Varying RuBisCO Activity, Light Intensity, and Enzymatic Cost Conditions

    Ankita Chatterjee

    2017-11-01

    Full Text Available To combat decrease in rice productivity under different stresses, an understanding of rice metabolism is needed. Though there are different genome scale metabolic models (GSMs of Oryza sativa japonica, no GSM with gene-protein-reaction association exist for Oryza sativa indica. Here, we report a GSM, OSI1136 of O.s. indica, which includes 3602 genes and 1136 metabolic reactions and transporters distributed across the cytosol, mitochondrion, peroxisome, and chloroplast compartments. Flux balance analysis of the model showed that for varying RuBisCO activity (Vc/Vo (i the activity of the chloroplastic malate valve increases to transport reducing equivalents out of the chloroplast under increased photorespiratory conditions and (ii glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase can act as source of cytosolic ATP under decreased photorespiration. Under increasing light conditions we observed metabolic flexibility, involving photorespiration, chloroplastic triose phosphate and the dicarboxylate transporters of the chloroplast and mitochondrion for redox and ATP exchanges across the intracellular compartments. Simulations under different enzymatic cost conditions revealed (i participation of peroxisomal glutathione-ascorbate cycle in photorespiratory H2O2 metabolism (ii different modes of the chloroplastic triose phosphate transporters and malate valve, and (iii two possible modes of chloroplastic Glu–Gln transporter which were related with the activity of chloroplastic and cytosolic isoforms of glutamine synthetase. Altogether, our results provide new insights into plant metabolism.

  4. Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory

    Riplinger, Christoph; Pinski, Peter; Becker, Ute; Neese, Frank; Valeev, Edward F.

    2016-01-01

    Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate

  5. Polymer density functional theory approach based on scaling second-order direct correlation function.

    Zhou, Shiqi

    2006-06-01

    A second-order direct correlation function (DCF) from solving the polymer-RISM integral equation is scaled up or down by an equation of state for bulk polymer, the resultant scaling second-order DCF is in better agreement with corresponding simulation results than the un-scaling second-order DCF. When the scaling second-order DCF is imported into a recently proposed LTDFA-based polymer DFT approach, an originally associated adjustable but mathematically meaningless parameter now becomes mathematically meaningful, i.e., the numerical value lies now between 0 and 1. When the adjustable parameter-free version of the LTDFA is used instead of the LTDFA, i.e., the adjustable parameter is fixed at 0.5, the resultant parameter-free version of the scaling LTDFA-based polymer DFT is also in good agreement with the corresponding simulation data for density profiles. The parameter-free version of the scaling LTDFA-based polymer DFT is employed to investigate the density profiles of a freely jointed tangent hard sphere chain near a variable sized central hard sphere, again the predictions reproduce accurately the simulational results. Importance of the present adjustable parameter-free version lies in its combination with a recently proposed universal theoretical way, in the resultant formalism, the contact theorem is still met by the adjustable parameter associated with the theoretical way.

  6. Aerodynamic loads calculation and analysis for large scale wind turbine based on combining BEM modified theory with dynamic stall model

    Dai, J.C. [College of Mechanical and Electrical Engineering, Central South University, Changsha (China); School of Electromechanical Engineering, Hunan University of Science and Technology, Xiangtan (China); Hu, Y.P.; Liu, D.S. [School of Electromechanical Engineering, Hunan University of Science and Technology, Xiangtan (China); Long, X. [Hara XEMC Windpower Co., Ltd., Xiangtan (China)

    2011-03-15

    The aerodynamic loads for MW scale horizontal-axis wind turbines are calculated and analyzed in the established coordinate systems which are used to describe the wind turbine. In this paper, the blade element momentum (BEM) theory is employed and some corrections, such as Prandtl and Buhl models, are carried out. Based on the B-L semi-empirical dynamic stall (DS) model, a new modified DS model for NACA63-4xx airfoil is adopted. Then, by combing BEM modified theory with DS model, a set of calculation method of aerodynamic loads for large scale wind turbines is proposed, in which some influence factors such as wind shear, tower, tower and blade vibration are considered. The research results show that the presented dynamic stall model is good enough for engineering purpose; the aerodynamic loads are influenced by many factors such as tower shadow, wind shear, dynamic stall, tower and blade vibration, etc, with different degree; the single blade endures periodical changing loads but the variations of the rotor shaft power caused by the total aerodynamic torque in edgewise direction are very small. The presented study approach of aerodynamic loads calculation and analysis is of the university, and helpful for thorough research of loads reduction on large scale wind turbines. (author)

  7. Psychometric analysis of the Generalized Anxiety Disorder scale (GAD-7) in primary care using modern item response theory.

    Jordan, Pascal; Shedden-Mora, Meike C; Löwe, Bernd

    2017-01-01

    The Generalized Anxiety Disorder scale (GAD-7) is one of the most frequently used diagnostic self-report scales for screening, diagnosis and severity assessment of anxiety disorder. Its psychometric properties from the view of the Item Response Theory paradigm have rarely been investigated. We aimed to close this gap by analyzing the GAD-7 within a large sample of primary care patients with respect to its psychometric properties and its implications for scoring using Item Response Theory. Robust, nonparametric statistics were used to check unidimensionality of the GAD-7. A graded response model was fitted using a Bayesian approach. The model fit was evaluated using posterior predictive p-values, item information functions were derived and optimal predictions of anxiety were calculated. The sample included N = 3404 primary care patients (60% female; mean age, 52,2; standard deviation 19.2) The analysis indicated no deviations of the GAD-7 scale from unidimensionality and a decent fit of a graded response model. The commonly suggested ultra-brief measure consisting of the first two items, the GAD-2, was supported by item information analysis. The first four items discriminated better than the last three items with respect to latent anxiety. The information provided by the first four items should be weighted more heavily. Moreover, estimates corresponding to low to moderate levels of anxiety show greater variability. The psychometric validity of the GAD-2 was supported by our analysis.

  8. The plasma transport equations derived by multiple time-scale expansions and turbulent transport. I. General theory

    Edenstrasser, J.W.

    1995-01-01

    A multiple time-scale derivative expansion scheme is applied to the dimensionless Fokker--Planck equation and to Maxwell's equations, where the parameter range of a typical fusion plasma was assumed. Within kinetic theory, the four time scales considered are those of Larmor gyration, particle transit, collisions, and classical transport. The corresponding magnetohydrodynamic (MHD) time scales are those of ion Larmor gyration, Alfven, MHD collision, and resistive diffusion. The solution of the zeroth-order equations results in the force-free equilibria and ideal Ohm's law. The solution of the first-order equations leads under the assumption of a weak collisional plasma to the ideal MHD equations. On the MHD-collision time scale, not only the full set of the MHD transport equations is obtained, but also turbulent terms, where the related transport quantities are one order in the expansion parameter larger than those of classical transport. Finally, at the resistive diffusion time scale the known transport equations are arrived at including, however, also turbulent contributions. copyright 1995 American Institute of Physics

  9. Measuring health workers' motivation composition: validation of a scale based on Self-Determination Theory in Burkina Faso.

    Lohmann, Julia; Souares, Aurélia; Tiendrebéogo, Justin; Houlfort, Nathalie; Robyn, Paul Jacob; Somda, Serge M A; De Allegri, Manuela

    2017-05-22

    Although motivation of health workers in low- and middle-income countries (LMICs) has become a topic of increasing interest by policy makers and researchers in recent years, many aspects are not well understood to date. This is partly due to a lack of appropriate measurement instruments. This article presents evidence on the construct validity of a psychometric scale developed to measure motivation composition, i.e., the extent to which motivation of different origin within and outside of a person contributes to their overall work motivation. It is theoretically grounded in Self-Determination Theory (SDT). We conducted a cross-sectional survey of 1142 nurses in 522 government health facilities in 24 districts of Burkina Faso. We assessed the scale's validity in a confirmatory factor analysis framework, investigating whether the scale measures what it was intended to measure (content, structural, and convergent/discriminant validity) and whether it does so equally well across health worker subgroups (measurement invariance). Our results show that the scale measures a slightly modified version of the SDT continuum of motivation well. Measurements were overall comparable between subgroups, but results indicate that caution is warranted if a comparison of motivation scores between groups is the focus of analysis. The scale is a valuable addition to the repository of measurement tools for health worker motivation in LMICs. We expect it to prove useful in the quest for a more comprehensive understanding of motivation as well as of the effects and potential side effects of interventions intended to enhance motivation.

  10. Detectable states, cycle fluxes, and motility scaling of molecular motor kinesin: An integrative kinetic graph theory analysis

    Ren, Jie

    2017-12-01

    The process by which a kinesin motor couples its ATPase activity with concerted mechanical hand-over-hand steps is a foremost topic of molecular motor physics. Two major routes toward elucidating kinesin mechanisms are the motility performance characterization of velocity and run length, and single-molecular state detection experiments. However, these two sets of experimental approaches are largely uncoupled to date. Here, we introduce an integrative motility state analysis based on a theorized kinetic graph theory for kinesin, which, on one hand, is validated by a wealth of accumulated motility data, and, on the other hand, allows for rigorous quantification of state occurrences and chemomechanical cycling probabilities. An interesting linear scaling for kinesin motility performance across species is discussed as well. An integrative kinetic graph theory analysis provides a powerful tool to bridge motility and state characterization experiments, so as to forge a unified effort for the elucidation of the working mechanisms of molecular motors.

  11. Scaling of the low-energy structure in above-threshold ionization in the tunneling regime: theory and experiment.

    Guo, L; Han, S S; Liu, X; Cheng, Y; Xu, Z Z; Fan, J; Chen, J; Chen, S G; Becker, W; Blaga, C I; DiChiara, A D; Sistrunk, E; Agostini, P; DiMauro, L F

    2013-01-04

    A calculation of the second-order (rescattering) term in the S-matrix expansion of above-threshold ionization is presented for the case when the binding potential is the unscreened Coulomb potential. Technical problems related to the divergence of the Coulomb scattering amplitude are avoided in the theory by considering the depletion of the atomic ground state due to the applied laser field, which is well defined and does not require the introduction of a screening constant. We focus on the low-energy structure, which was observed in recent experiments with a midinfrared wavelength laser field. Both the spectra and, in particular, the observed scaling versus the Keldysh parameter and the ponderomotive energy are reproduced. The theory provides evidence that the origin of the structure lies in the long-range Coulomb interaction.

  12. A dual theory of price and value in a meso-scale economic model with stochastic profit rate

    Greenblatt, R. E.

    2014-12-01

    The problem of commodity price determination in a market-based, capitalist economy has a long and contentious history. Neoclassical microeconomic theories are based typically on marginal utility assumptions, while classical macroeconomic theories tend to be value-based. In the current work, I study a simplified meso-scale model of a commodity capitalist economy. The production/exchange model is represented by a network whose nodes are firms, workers, capitalists, and markets, and whose directed edges represent physical or monetary flows. A pair of multivariate linear equations with stochastic input parameters represent physical (supply/demand) and monetary (income/expense) balance. The input parameters yield a non-degenerate profit rate distribution across firms. Labor time and price are found to be eigenvector solutions to the respective balance equations. A simple relation is derived relating the expected value of commodity price to commodity labor content. Results of Monte Carlo simulations are consistent with the stochastic price/labor content relation.

  13. Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface

    Bushell Michael E

    2011-05-01

    Full Text Available Abstract Background Constraint-based approaches facilitate the prediction of cellular metabolic capabilities, based, in turn on predictions of the repertoire of enzymes encoded in the genome. Recently, genome annotations have been used to reconstruct genome scale metabolic reaction networks for numerous species, including Homo sapiens, which allow simulations that provide valuable insights into topics, including predictions of gene essentiality of pathogens, interpretation of genetic polymorphism in metabolic disease syndromes and suggestions for novel approaches to microbial metabolic engineering. These constraint-based simulations are being integrated with the functional genomics portals, an activity that requires efficient implementation of the constraint-based simulations in the web-based environment. Results Here, we present Acorn, an open source (GNU GPL grid computing system for constraint-based simulations of genome scale metabolic reaction networks within an interactive web environment. The grid-based architecture allows efficient execution of computationally intensive, iterative protocols such as Flux Variability Analysis, which can be readily scaled up as the numbers of models (and users increase. The web interface uses AJAX, which facilitates efficient model browsing and other search functions, and intuitive implementation of appropriate simulation conditions. Research groups can install Acorn locally and create user accounts. Users can also import models in the familiar SBML format and link reaction formulas to major functional genomics portals of choice. Selected models and simulation results can be shared between different users and made publically available. Users can construct pathway map layouts and import them into the server using a desktop editor integrated within the system. Pathway maps are then used to visualise numerical results within the web environment. To illustrate these features we have deployed Acorn and created a

  14. Brans-Dicke Theory with Λ>0: Black Holes and Large Scale Structures.

    Bhattacharya, Sourav; Dialektopoulos, Konstantinos F; Romano, Antonio Enea; Tomaras, Theodore N

    2015-10-30

    A step-by-step approach is followed to study cosmic structures in the context of Brans-Dicke theory with positive cosmological constant Λ and parameter ω. First, it is shown that regular stationary black-hole solutions not only have constant Brans-Dicke field ϕ, but can exist only for ω=∞, which forces the theory to coincide with the general relativity. Generalizations of the theory in order to evade this black-hole no-hair theorem are presented. It is also shown that in the absence of a stationary cosmological event horizon in the asymptotic region, a stationary black-hole horizon can support a nontrivial Brans-Dicke hair. Even more importantly, it is shown next that the presence of a stationary cosmological event horizon rules out any regular stationary solution, appropriate for the description of a star. Thus, to describe a star one has to assume that there is no such stationary horizon in the faraway asymptotic region. Under this implicit assumption generic spherical cosmic structures are studied perturbatively and it is shown that only for ω>0 or ω≲-5 their predicted maximum sizes are consistent with observations. We also point out how, many of the conclusions of this work differ qualitatively from the Λ=0 spacetimes.

  15. Psychological Trait Resilience Within Ecological Systems Theory: The Resilient Systems Scales.

    Maltby, John; Day, Liz; Flowe, Heather D; Vostanis, Panos; Chivers, Sally

    2017-07-14

    This project describes the development of the Resilient Systems Scales, created to address conceptual and methodological ambiguities in assessing the ecological systems model of resilience. Across a number of samples (total N = 986), our findings suggest that the Resilient Systems Scales show equivalence to a previously reported assessment (Maltby, Day, & Hall, 2015 ) in demonstrating the same factor structure, adequate intercorrelation between the 2 measures of resilience, and equivalent associations with personality and well-being. The findings also suggest that the Resilient Systems Scales demonstrate adequate test-retest reliability, compare well with other extant measures of resilience in predicting well-being, and map, to varying degrees, onto positive expression of several cognitive, social, and emotional traits. The findings suggest that the new measure can be used alongside existing measures of resilience, or singly, to assess positive life outcomes within psychology research.

  16. A note on finite-scale Navier–Stokes theory: The case of constant viscosity, strictly adiabatic flow

    Jordan, P.M.; Keiffer, R.S.

    2015-01-01

    We investigate the “piston problem” for the case of a viscous, but non-thermally conducting, gas with constant transport coefficients under the recently introduced generalization of the Navier–Stokes (NS) equations known as the finite-scale Navier–Stokes (FSNS) equations. Along with determining and analyzing the integral curves of the resulting kink-type traveling wave solutions (TWS)s, the present study also reveals the importance of the bulk viscosity vis-a-vis this special case of FSNS theory and highlights the impact that averaging has on the structure of the shock profile

  17. Analysis of effectiveness of possible queuing models at gas stations using the large-scale queuing theory

    Slaviša M. Ilić

    2011-10-01

    Full Text Available This paper analyzes the effectiveness of possible models for queuing at gas stations, using a mathematical model of the large-scale queuing theory. Based on actual data collected and the statistical analysis of the expected intensity of vehicle arrivals and queuing at gas stations, the mathematical modeling of the real process of queuing was carried out and certain parameters quantified, in terms of perception of the weaknesses of the existing models and the possible benefits of an automated queuing model.

  18. Isotropic-nematic transition in a mixture of hard spheres and hard spherocylinders: scaled particle theory description

    M.F. Holovko

    2017-12-01

    Full Text Available The scaled particle theory is developed for the description of thermodynamical properties of a mixture of hard spheres and hard spherocylinders. Analytical expressions for free energy, pressure and chemical potentials are derived. From the minimization of free energy, a nonlinear integral equation for the orientational singlet distribution function is formulated. An isotropic-nematic phase transition in this mixture is investigated from the bifurcation analysis of this equation. It is shown that with an increase of concentration of hard spheres, the total packing fraction of a mixture on phase boundaries slightly increases. The obtained results are compared with computer simulations data.

  19. Exact form factors for the scaling ZN-Ising and the affine AN-1-Toda quantum field theories

    Babujian, H.; Karowski, M.

    2003-01-01

    Previous results on form factors for the scaling Ising and the sinh-Gordon models are extended to general Z N -Ising and affine A N-1 -Toda quantum field theories. In particular result for order, disorder parameters and para-Fermi fields σ Q (x), μ Q-tilde (x) and ψ Q (x) are presented for the Z N -model. For the A N-1 -Toda model form factors for exponentials of the Toda fields are proposed. The quantum field equation of motion is proved and the mass and wave function renormalization are calculated exactly

  20. From Fancy to Reason: Scaling Deaf and Hearing Children’s Understanding of Theory of Mind and Pretence

    Peterson, Candida C.; Wellman, Henry M.

    2009-01-01

    We examined deaf and hearing children’s progression of steps in theory-of-mind (ToM) development including their understanding of social pretending. Ninety-three children (33 deaf; 60 hearing) aged 3 to 13 years were tested on a set of six closely-matched ToM tasks. Results showed that deaf children were delayed substantially behind hearing children in understanding pretending, false belief and other ToM concepts, in line with their delayed uptake of social pretend play. By using a scaling me...

  1. Basin-scale variability in plankton biomass and community metabolism in the sub-tropical North Atlantic Ocean

    Harrison, W. G.; Arístegui, J.; Head, E. J. H.; Li, W. K. W.; Longhurst, A. R.; Sameoto, D. D.

    Three trans-Atlantic oceanographic surveys (Nova Scotia to Canary Islands) were carried out during fall 1992 and spring 1993 to describe the large-scale variability in hydrographic, chemical and biological properties of the upper water column of the subtropical gyre and adjacent waters. Significant spatial and temporal variability characterized a number of the biological pools and rate processes whereas others were relatively invariant. Systematic patterns were observed in the zonal distribution of some properties. Most notable were increases (eastward) in mixed-layer temperature and salinity, depths of the nitracline and chlorophyll- a maximum, regenerated production (NH 4 uptake) and bacterial production. Dissolved inorganic carbon (DIC) concentrations, phytoplankton biomass, mesozooplankton biomass and new production (NO 3 uptake) decreased (eastward). Bacterial biomass, primary production, and community respiration exhibited no discernible zonal distribution patterns. Seasonal variability was most evident in hydrography (cooler/fresher mixed-layer in spring), and chemistry (mixed-layer DIC concentration higher and nitracline shallower in spring) although primary production and bacterial production were significantly higher in spring than in fall. In general, seasonal variability was greater in the west than in the east; seasonality in most properties was absent west of Canary Islands (˜20°W). The distribution of autotrophs could be reasonably well explained by hydrography and nutrient structure, independent of location or season. Processes underlying the distribution of the microheterophs, however, were less clear. Heterotrophic biomass and metabolism was less variable than autotrophs and appeared to dominate the upper ocean carbon balance of the subtropical North Atlantic in both fall and spring. Geographical patterns in distribution are considered in the light of recent efforts to partition the ocean into distinct "biogeochemical provinces".

  2. Using Item Response Theory Methods with the Brazilian Temperament Scale for Students

    Primi, Ricardo; Wechsler, Solange Muglia; de Cassia Nakano, Tatiana; Oakland, Thomas; Guzzo, Raquel Souza Lobo

    2014-01-01

    The development and validation of the Brazilian Temperament Scale for Students (BTSS) are examined through the use of data from 1,258 children and adolescents, ages 10 through 21 (M = 15.0, SD = 2.1, 56% females). Three psychometric properties of BTSS are reported: its internal structure (e.g., validity), its reliability, and cut points to best…

  3. Application of Hierarchy Theory to Cross-Scale Hydrologic Modeling of Nutrient Loads

    We describe a model called Regional Hydrologic Modeling for Environmental Evaluation 16 (RHyME2) for quantifying annual nutrient loads in stream networks and watersheds. RHyME2 is 17 a cross-scale statistical and process-based water-quality model. The model ...

  4. Work Adjustment Theory: An Empirical Test Using a Fuzzy Rating Scale.

    Hesketh, Beryl; And Others

    1992-01-01

    A fuzzy graphic rating scale elicited work preferences and job perceptions of 166 (of 170) Australian bank employees. Correspondence between preferences and perceptions correlated significantly with job satisfaction. Satisfaction and performance related to tenure intentions; this relation was higher for poorer performers. (SK)

  5. Bifactor and Item Response Theory Analyses of Interviewer Report Scales of Cognitive Impairment in Schizophrenia

    Reise, Steven P.; Ventura, Joseph; Keefe, Richard S. E.; Baade, Lyle E.; Gold, James M.; Green, Michael F.; Kern, Robert S.; Mesholam-Gately, Raquelle; Nuechterlein, Keith H.; Seidman, Larry J.; Bilder, Robert

    2011-01-01

    A psychometric analysis of 2 interview-based measures of cognitive deficits was conducted: the 21-item Clinical Global Impression of Cognition in Schizophrenia (CGI-CogS; Ventura et al., 2008), and the 20-item Schizophrenia Cognition Rating Scale (SCoRS; Keefe et al., 2006), which were administered on 2 occasions to a sample of people with…

  6. [New theory of holistic integrative physiology and medicine. III: New insight of neurohumoral mechanism and pattern of control and regulation for core axe of respiration, circulation and metabolism].

    Sun, Xing-guo

    2015-07-01

    Systemic mechanism of neurohumoral control and regulation for human is limited. We used the new theory of holistic integrative physiology and medicine to approach the mechanism and pattern of neurohumoral control and regulation for life. As the core of human life, there are two core axes of functions. The first one is the common goal of respiration and circulation to transport oxygen and carbon dioxide for cells, and the second one is the goal of gastrointestinal tract and circulation to transport energy material and metabolic product for cells. These two core axes maintain the metabolism. The neurohumoral regulation is holistically integrated and unified for all functions in human body. We simplified explain the mechanism of neurohumoral control and regulation life (respiration and circulation) as the example pattern of sound system. Based upon integrated regulation of life, we described the neurohumoral pattern to control respiration and circulation.

  7. Topological charge and cooling scales in pure SU(2) lattice gauge theory

    Berg, Bernd A.; Clarke, David A.

    2018-01-01

    Using Monte Carlo simulations with overrelaxation, we have equilibrated lattices up to β=2.928, size 604, for pure SU(2) lattice gauge theory with the Wilson action. We calculate topological charges with the standard cooling method and find that they become more reliable with increasing β values and lattice sizes. Continuum limit estimates of the topological susceptibility χ are obtained of which we favor χ1/4/Tc=0.643(12), where Tc is the SU(2) deconfinement temperature. Differences between ...

  8. Validation of Sustainable Development Practices Scale Using the Bayesian Approach to Item Response Theory

    Martin Hernani Merino

    2014-12-01

    Full Text Available There has been growing recognition of the importance of creating performance measurement tools for the economic, social and environmental management of micro and small enterprise (MSE. In this context, this study aims to validate an instrument to assess perceptions of sustainable development practices by MSEs by means of a Graded Response Model (GRM with a Bayesian approach to Item Response Theory (IRT. The results based on a sample of 506 university students in Peru, suggest that a valid measurement instrument was achieved. At the end of the paper, methodological and managerial contributions are presented.

  9. Large-scale perturbations of magnetohydrodynamic regimes linear and weakly nonlinear stability theory

    Zheligovsky, Vladislav

    2011-01-01

    New developments for hydrodynamical dynamo theory have been spurred by recent evidence of self-sustained dynamo activity in laboratory experiments with liquid metals. The emphasis in the present volume is on the introduction of powerful mathematical techniques required to tackle modern multiscale analysis of continous systems and there application to a number of realistic model geometries of increasing complexity. This introductory and self-contained research monograph summarizes the theoretical state-of-the-art to which the author has made pioneering contributions.

  10. Development and psychometric properties of an informant assessment scale of theory of mind for adults with traumatic brain injury.

    Zhang, Dengke; Pang, Yanxia; Cai, Weixiong; Fazio, Rachel L; Ge, Jianrong; Su, Qiaorong; Xu, Shuiqin; Pan, Yinan; Chen, Sanmei; Zhang, Hongwei

    2016-08-01

    Impairment of theory of mind (ToM) is a common phenomenon following traumatic brain injury (TBI) that has clear effects on patients' social functioning. A growing body of research has focused on this area, and several methods have been developed to assess ToM deficiency. Although an informant assessment scale would be useful for examining individuals with TBI, very few studies have adopted this approach. The purpose of the present study was to develop an informant assessment scale of ToM for adults with traumatic brain injury (IASToM-aTBI) and to test its reliability and validity with 196 adults with TBI and 80 normal adults. A 44-item scale was developed following a literature review, interviews with patient informants, consultations with experts, item analysis, and exploratory factor analysis (EFA). The following three common factors were extracted: social interaction, understanding of beliefs, and understanding of emotions. The psychometric analyses indicate that the scale has good internal consistency reliability, split-half reliability, test-retest reliability, inter-rater reliability, structural validity, discriminate validity and criterion validity. These results provide preliminary evidence that supports the reliability and validity of the IASToM-aTBI as a ToM assessment tool for adults with TBI.

  11. Using Procedure Based on Item Response Theory to Evaluate Classification Consistency Indices in the Practice of Large-Scale Assessment

    Shanshan Zhang

    2017-09-01

    Full Text Available In spite of the growing interest in the methods of evaluating the classification consistency (CC indices, only few researches are available in the field of applying these methods in the practice of large-scale educational assessment. In addition, only few studies considered the influence of practical factors, for example, the examinee ability distribution, the cut score location and the score scale, on the performance of CC indices. Using the newly developed Lee's procedure based on the item response theory (IRT, the main purpose of this study is to investigate the performance of CC indices when practical factors are taken into consideration. A simulation study and an empirical study were conducted under comprehensive conditions. Results suggested that with negatively skewed distribution, the CC indices were larger than with other distributions. Interactions occurred among ability distribution, cut score location, and score scale. Consequently, Lee's IRT procedure is reliable to be used in the field of large-scale educational assessment, and when reporting the indices, it should be treated with caution as testing conditions may vary a lot.

  12. Past and future corollaries of theories on causes of metabolic syndrome and obesity related co-morbidities part 2: a composite unifying theory review of human-specific co-adaptations to brain energy consumption.

    McGill, Anne-Thea

    2014-01-01

    Metabolic syndrome (MetS) predicts type II diabetes mellitus (TIIDM), cardiovascular disease (CVD) and cancer, and their rates have escalated over the last few decades. Obesity related co-morbidities also overlap the concept of the metabolic syndrome (MetS). However, understanding of the syndrome's underlying causes may have been misapprehended. The current paper follows on from a theory review by McGill, A-T in Archives of Public Health, 72: 30. This accompanying paper utilises research on human evolution and new biochemistry to theorise on why MetS and obesity arise and how they affect the population. The basis of this composite unifying theory is that the proportionately large, energy-demanding human brain may have driven co-adaptive mechanisms to provide, or conserve, energy for the brain. A 'dual system' is proposed. 1) The enlarged, complex cortico-limbic-striatal system increases dietary energy by developing strong neural self-reward/motivation pathways for the acquisition of energy dense food, and (2) the nuclear factor-erythroid 2-related factor 2 (NRF2) cellular protection system amplifies antioxidant, antitoxicant and repair activity by employing plant chemicals. In humans who consume a nutritious diet, the NRF2 system has become highly energy efficient. Other relevant human-specific co-adaptations are explored. In order to 'test' this composite unifying theory it is important to show that the hypothesis and sub-theories pertain throughout the whole of human evolution and history up till the current era. Corollaries of the composite unifying theory of MetS are examined with respect to past under-nutrition and malnutrition since agriculture began 10,000 years ago. The effects of man-made pollutants on degenerative change are examined. Projections are then made from current to future patterns on the state of 'insufficient micronutrient and/or unbalanced high energy malnutrition with central obesity and metabolic dysregulation' or 'malnubesity'. Forecasts

  13. Plasmon mass scale in two-dimensional classical nonequilibrium gauge theory

    Lappi, T.; Peuron, J.

    2018-02-01

    We study the plasmon mass scale in classical gluodynamics in a two-dimensional configuration that mimics the boost-invariant initial color fields in a heavy-ion collision. We numerically measure the plasmon mass scale using three different methods: a hard thermal loop (HTL) expression involving the quasiparticle spectrum constructed from Coulomb gauge field correlators, an effective dispersion relation, and the measurement of oscillations between electric and magnetic energies after introducing a spatially uniform perturbation to the electric field. We find that the HTL expression and the uniform electric field measurement are in rough agreement. The effective dispersion relation agrees with other methods within a factor of 2. We also study the dependence on time and occupation number, observing similar trends as in three spatial dimensions, where a power-law dependence sets in after an occupation-number-dependent transient time. We observe a decrease of the plasmon mass squared as t-1 / 3 at late times.

  14. Self-consistent field theory based molecular dynamics with linear system-size scaling

    Richters, Dorothee [Institute of Mathematics and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 9, D-55128 Mainz (Germany); Kühne, Thomas D., E-mail: kuehne@uni-mainz.de [Institute of Physical Chemistry and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 7, D-55128 Mainz (Germany); Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn (Germany)

    2014-04-07

    We present an improved field-theoretic approach to the grand-canonical potential suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is circumvented by means of a properly modified Langevin equation. The predictive power of the present approach is illustrated using the example of liquid methane under extreme conditions.

  15. Gas production in the Barnett Shale obeys a simple scaling theory

    Patzek, Tad W.; Male, Frank; Marder, Michael

    2013-01-01

    Ten years ago, US natural gas cost 50% more than that from Russia. Now, it is threefold less. US gas prices plummeted because of the shale gas revolution. However, a key question remains: At what rate will the new hydrofractured horizontal wells in shales continue to produce gas? We analyze the simplest model of gas production consistent with basic physics of the extraction process. Its exact solution produces a nearly universal scaling law for gas wells in each shale play, where production f...

  16. On the 'hysteresis' effect in the biological nitrogen removal :theory and full scale experimental evaluation

    Tatano, F.

    1996-01-01

    The wastewater treatments plants localized in the Ruhr River (Germany), generally present a typical wastewater temperature variation curve during the winter period. These temperature changes produce specific effects on the nitrogen removal efficiencies in the activated sludge systems. The so called 'hysteresis' phenomenon is responsible for these effects. The paper deals with some simplified theoretical considerations and with a full scale experimental evaluations of the effects caused by the hysteresis phenomenon in the biological nitrogen removal

  17. Renormalization group and relations between scattering amplitudes in a theory with different mass scales

    Gulov, A.V.; Skalozub, V.V.

    2000-01-01

    In the Yukawa model with two different mass scales the renormalization group equation is used to obtain relations between scattering amplitudes at low energies. Considering fermion-fermion scattering as an example, a basic one-loop renormalization group relation is derived which gives possibility to reduce the problem to the scattering of light particles on the external field substituting a heavy virtual state. Applications of the results to problem of searching new physics beyond the Standard Model are discussed [ru

  18. Nonlinear power spectrum from resummed perturbation theory: a leap beyond the BAO scale

    Anselmi, Stefano; Pietroni, Massimo

    2012-01-01

    A new computational scheme for the nonlinear cosmological matter power spectrum (PS) is presented. Our method is based on evolution equations in time, which can be cast in a form extremely convenient for fast numerical evaluations. A nonlinear PS is obtained in a time comparable to that needed for a simple 1-loop computation, and the numerical implementation is very simple. Our results agree with N-body simulations at the percent level in the BAO range of scales, and at the few-percent level up to k ≅ 1 h/Mpc at z∼>0.5, thereby opening the possibility of applying this tool to scales interesting for weak lensing. We clarify the approximations inherent to this approach as well as its relations to previous ones, such as the Time Renormalization Group, and the multi-point propagator expansion. We discuss possible lines of improvements of the method and its intrinsic limitations by multi streaming at small scales and low redshifts

  19. GPU-Accelerated Large-Scale Electronic Structure Theory on Titan with a First-Principles All-Electron Code

    Huhn, William Paul; Lange, Björn; Yu, Victor; Blum, Volker; Lee, Seyong; Yoon, Mina

    Density-functional theory has been well established as the dominant quantum-mechanical computational method in the materials community. Large accurate simulations become very challenging on small to mid-scale computers and require high-performance compute platforms to succeed. GPU acceleration is one promising approach. In this talk, we present a first implementation of all-electron density-functional theory in the FHI-aims code for massively parallel GPU-based platforms. Special attention is paid to the update of the density and to the integration of the Hamiltonian and overlap matrices, realized in a domain decomposition scheme on non-uniform grids. The initial implementation scales well across nodes on ORNL's Titan Cray XK7 supercomputer (8 to 64 nodes, 16 MPI ranks/node) and shows an overall speed up in runtime due to utilization of the K20X Tesla GPUs on each Titan node of 1.4x, with the charge density update showing a speed up of 2x. Further acceleration opportunities will be discussed. Work supported by the LDRD Program of ORNL managed by UT-Battle, LLC, for the U.S. DOE and by the Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC05-00OR22725.

  20. Extensions of Island Biogeography Theory predict the scaling of functional trait composition with habitat area and isolation.

    Jacquet, Claire; Mouillot, David; Kulbicki, Michel; Gravel, Dominique

    2017-02-01

    The Theory of Island Biogeography (TIB) predicts how area and isolation influence species richness equilibrium on insular habitats. However, the TIB remains silent about functional trait composition and provides no information on the scaling of functional diversity with area, an observation that is now documented in many systems. To fill this gap, we develop a probabilistic approach to predict the distribution of a trait as a function of habitat area and isolation, extending the TIB beyond the traditional species-area relationship. We compare model predictions to the body-size distribution of piscivorous and herbivorous fishes found on tropical reefs worldwide. We find that small and isolated reefs have a higher proportion of large-sized species than large and connected reefs. We also find that knowledge of species body-size and trophic position improves the predictions of fish occupancy on tropical reefs, supporting both the allometric and trophic theory of island biogeography. The integration of functional ecology to island biogeography is broadly applicable to any functional traits and provides a general probabilistic approach to study the scaling of trait distribution with habitat area and isolation. © 2016 John Wiley & Sons Ltd/CNRS.

  1. THE HALO MASS FUNCTION FROM EXCURSION SET THEORY. I. GAUSSIAN FLUCTUATIONS WITH NON-MARKOVIAN DEPENDENCE ON THE SMOOTHING SCALE

    Maggiore, Michele; Riotto, Antonio

    2010-01-01

    A classic method for computing the mass function of dark matter halos is provided by excursion set theory, where density perturbations evolve stochastically with the smoothing scale, and the problem of computing the probability of halo formation is mapped into the so-called first-passage time problem in the presence of a barrier. While the full dynamical complexity of halo formation can only be revealed through N-body simulations, excursion set theory provides a simple analytic framework for understanding various aspects of this complex process. In this series of papers we propose improvements of both technical and conceptual aspects of excursion set theory, and we explore up to which point the method can reproduce quantitatively the data from N-body simulations. In Paper I of the series, we show how to derive excursion set theory from a path integral formulation. This allows us both to derive rigorously the absorbing barrier boundary condition, that in the usual formulation is just postulated, and to deal analytically with the non-Markovian nature of the random walk. Such a non-Markovian dynamics inevitably enters when either the density is smoothed with filters such as the top-hat filter in coordinate space (which is the only filter associated with a well-defined halo mass) or when one considers non-Gaussian fluctuations. In these cases, beside 'Markovian' terms, we find 'memory' terms that reflect the non-Markovianity of the evolution with the smoothing scale. We develop a general formalism for evaluating perturbatively these non-Markovian corrections, and in this paper we perform explicitly the computation of the halo mass function for Gaussian fluctuations, to first order in the non-Markovian corrections due to the use of a top-hat filter in coordinate space. In Paper II of this series we propose to extend excursion set theory by treating the critical threshold for collapse as a stochastic variable, which better captures some of the dynamical complexity of the

  2. Light Condensation and Localization in Disordered Photonic Media: Theory and Large Scale ab initio Simulations

    Toth, Laszlo Daniel

    2013-05-07

    Disordered photonics is the study of light in random media. In a disordered photonic medium, multiple scattering of light and coherence, together with the fundamental principle of reciprocity, produce a wide range of interesting phenomena, such as enhanced backscattering and Anderson localization of light. They are also responsible for the existence of modes in these random systems. It is known that analogous processes to Bose-Einstein condensation can occur in classical wave systems, too. Classical condensation has been studied in several contexts in photonics: pulse formation in lasers, mode-locking theory and coherent emission of disordered lasers. All these systems have the common theme of possessing a large ensemble of waves or modes, together with nonlinearity, dispersion or gain. In this work, we study light condensation and its connection with light localization in a disordered, passive dielectric medium. We develop a theory for the modes inside the disordered resonator, which combines the Feshbach projection technique with spin-glass theory and statistical physics. In particular, starting from the Maxwell’s equations, we map the system to a spherical p-spin model with p = 2. The spins are replaced by modes and the temperature is related to the fluctuations in the environment. We study the equilibrium thermodynamics of the system in a general framework and show that two distinct phases exist: a paramagnetic phase, where all the modes are randomly oscillating and a condensed phase, where the energy condensates on a single mode. The thermodynamic quantities can be explicitly interpreted and can also be computed from the disorder-averaged time domain correlation function. We launch an ab initio simulation campaign using our own code and the Shaheen supercomputer to test the theoretical predictions. We construct photonic samples of varying disorder and find computationally relevant ways to obtain the thermodynamic quantities. We observe the phase transition

  3. Critical dynamics a field theory approach to equilibrium and non-equilibrium scaling behavior

    Täuber, Uwe C

    2014-01-01

    Introducing a unified framework for describing and understanding complex interacting systems common in physics, chemistry, biology, ecology, and the social sciences, this comprehensive overview of dynamic critical phenomena covers the description of systems at thermal equilibrium, quantum systems, and non-equilibrium systems. Powerful mathematical techniques for dealing with complex dynamic systems are carefully introduced, including field-theoretic tools and the perturbative dynamical renormalization group approach, rapidly building up a mathematical toolbox of relevant skills. Heuristic and qualitative arguments outlining the essential theory behind each type of system are introduced at the start of each chapter, alongside real-world numerical and experimental data, firmly linking new mathematical techniques to their practical applications. Each chapter is supported by carefully tailored problems for solution, and comprehensive suggestions for further reading, making this an excellent introduction to critic...

  4. Validity and reliability analysis of the planned behavior theory scale related to the testicular self-examination in a Turkish context.

    Iyigun, Emine; Tastan, Sevinc; Ayhan, Hatice; Kose, Gulsah; Acikel, Cengizhan

    2016-06-01

    This study aimed to determine the validity and reliability levels of the Planned Behavior Theory Scale as related to a testicular self-examination. The study was carried out in a health-profession higher-education school in Ankara, Turkey, from April to June 2012. The study participants comprised 215 male students. Study data were collected by using a questionnaire, a planned behavior theory scale related to testicular self-examination, and Champion's Health Belief Model Scale (CHBMS). The sub-dimensions of the planned behavior theory scale, namely those of intention, attitude, subjective norms and self-efficacy, were found to have Cronbach's alpha values of between 0.81 and 0.89. Exploratory factor analysis showed that items of the scale had five factors that accounted for 75% of the variance. Of these, the sub-dimension of intention was found to have the highest level of contribution. A significant correlation was found between the sub-dimensions of the testicular self-examination planned behavior theory scale and those of CHBMS (p Planned Behavior Theory Scale is a valid and reliable measurement for Turkish society.

  5. Linear perturbation theory for tidal streams and the small-scale CDM power spectrum

    Bovy, Jo; Erkal, Denis; Sanders, Jason L.

    2017-04-01

    Tidal streams in the Milky Way are sensitive probes of the population of low-mass dark matter subhaloes predicted in cold dark matter (CDM) simulations. We present a new calculus for computing the effect of subhalo fly-bys on cold streams based on the action-angle representation of streams. The heart of this calculus is a line-of-parallel-angle approach that calculates the perturbed distribution function of a stream segment by undoing the effect of all relevant impacts. This approach allows one to compute the perturbed stream density and track in any coordinate system in minutes for realizations of the subhalo distribution down to 105 M⊙, accounting for the stream's internal dispersion and overlapping impacts. We study the statistical properties of density and track fluctuations with large suites of simulations of the effect of subhalo fly-bys. The one-dimensional density and track power spectra along the stream trace the subhalo mass function, with higher mass subhaloes producing power only on large scales, while lower mass subhaloes cause structure on smaller scales. We also find significant density and track bispectra that are observationally accessible. We further demonstrate that different projections of the track all reflect the same pattern of perturbations, facilitating their observational measurement. We apply this formalism to data for the Pal 5 stream and make a first rigorous determination of 10^{+11}_{-6} dark matter subhaloes with masses between 106.5 and 109 M⊙ within 20 kpc from the Galactic centre [corresponding to 1.4^{+1.6}_{-0.9} times the number predicted by CDM-only simulations or to fsub(r matter is clumpy on the smallest scales relevant for galaxy formation.

  6. The method of arbitrarily large moments to calculate single scale processes in quantum field theory

    Bluemlein, Johannes [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Schneider, Carsten [Johannes Kepler Univ., Linz (Austria). Research Inst. for Symbolic Computation (RISC)

    2017-01-15

    We device a new method to calculate a large number of Mellin moments of single scale quantities using the systems of differential and/or difference equations obtained by integration-by-parts identities between the corresponding Feynman integrals of loop corrections to physical quantities. These scalar quantities have a much simpler mathematical structure than the complete quantity. A sufficiently large set of moments may even allow the analytic reconstruction of the whole quantity considered, holding in case of first order factorizing systems. In any case, one may derive highly precise numerical representations in general using this method, which is otherwise completely analytic.

  7. The method of arbitrarily large moments to calculate single scale processes in quantum field theory

    Johannes Blümlein

    2017-08-01

    Full Text Available We devise a new method to calculate a large number of Mellin moments of single scale quantities using the systems of differential and/or difference equations obtained by integration-by-parts identities between the corresponding Feynman integrals of loop corrections to physical quantities. These scalar quantities have a much simpler mathematical structure than the complete quantity. A sufficiently large set of moments may even allow the analytic reconstruction of the whole quantity considered, holding in case of first order factorizing systems. In any case, one may derive highly precise numerical representations in general using this method, which is otherwise completely analytic.

  8. Managing common resources in local and global systems. Applying theory across scales

    Karlsson, Sylvia [ed.

    1997-12-31

    The main point brought forward in this publication is the productiveness of applying theoretical elements, developed within common property resource (CPR) literature, to a broader field of cases on different scales. The common framework for the contributions is a series of seminars held at the Department of Water and Environmental Studies in the spring of 1996, covering expanding work during the last decade on common property resource (CPR) management. It is obvious that there were a broad range of definitions of the concept CPR in the literature. The common pool/property resource concepts are both used, often depending on the resource studied, and authors in this volume have used both terms accordingly. Certain points are raised from empirical cases presented in this volume that are partly missing or not thoroughly stressed in other work in the area of CPR management and which crystallized much clearer when contrasting the situation for cases from different scales. Separate abstracts have been performed for five of the seven contributions

  9. Scaling theory of tunneling diffusion of a heavy particle interacting with phonons

    Itai, K.

    1988-05-01

    The author discusses motion of a heavy particle in a d-dimensional lattice interacting with phonons by different couplings. The models discussed are characterized by the dimension (d) and the set of two indices (λ,ν) which specify the momentum dependence of the dispersion of phonon energy (ω~kν) and of the particle-phonon coupling (~kλ). Scaling equations are derived by eliminating the short-time behavior in a renormalization-group scheme using Feynman's path-integral method, and the technique developed by Anderson, Yuval, and Hamann for the Kondo problem. The scaling equations show that the particle is localized in the strict sense when (2λ+d+2)/ν2. In the marginal case, i.e., (2λ+d+2)/ν=2, localization occurs for couplings larger than a critical value. This marginal case shows Ohmic dissipation and is a close analogy to the Caldeira-Leggett model for macroscopic quantum tunneling and the hopping models of Schmid's type. For large-enough (2λ+d+2)/ν, the particle is considered practically localized, but the origin of the localization is quite different from that for (2λ+d+2)/ν<=2. .AE

  10. Managing common resources in local and global systems. Applying theory across scales

    Karlsson, Sylvia [ed.

    1998-12-31

    The main point brought forward in this publication is the productiveness of applying theoretical elements, developed within common property resource (CPR) literature, to a broader field of cases on different scales. The common framework for the contributions is a series of seminars held at the Department of Water and Environmental Studies in the spring of 1996, covering expanding work during the last decade on common property resource (CPR) management. It is obvious that there were a broad range of definitions of the concept CPR in the literature. The common pool/property resource concepts are both used, often depending on the resource studied, and authors in this volume have used both terms accordingly. Certain points are raised from empirical cases presented in this volume that are partly missing or not thoroughly stressed in other work in the area of CPR management and which crystallized much clearer when contrasting the situation for cases from different scales. Separate abstracts have been performed for five of the seven contributions

  11. Cut-off scaling and multiplicative reformalization in the theory of critical phenomena

    Forgacs, G.; Solyom, J.; Zawadowski, A.

    1976-03-01

    In the paper a new method to study the critical fluctuations in systems of 4-epsilon dimensions around the phase transition point is developed. This method unifies the Kadanoff scaling hypothesis as formulated by Wilson by help of his renormalization group technique and the simple mathematical structure of the Lie equations of the Gell-Mann-Low multiplicative renormalization. The basic idea of the new method is that a change in the physical cut-off can be compensated by an effective coupling in such a way that the Green's function and vertex in the original and transformed system differ only by a multiplicative factor. The critical indices, the anomalous dimensions and the critical exponent describing the correction to scaling are determined to second order in epsilon. The specific heat exponent is also calculated, in four dimensions the effect of fluctuations appears in the form of logarithmic corrections. In the last sections the new method is compared to other ones and the differences are discussed. (Sz.N.Z.)

  12. Improved production of cytotoxic thailanstatins A and D through metabolic engineering of Burkholderia thailandensis MSMB43 and pilot scale fermentation

    Xiangyang Liu

    2016-03-01

    Full Text Available Thailanstatin A (TST-A is a potent antiproliferative natural product discovered by our group from Burkholderia thailandensis MSMB43 through a genome-guided approach. The limited supply of TST-A, due to its low titer in bacterial fermentation, modest stability and very low recovery rate during purification, has hindered the investigations of TST-A as an anticancer drug candidate. Here we report the significant yield improvement of TST-A and its direct precursor, thailanstatin D (TST-D, through metabolic engineering of the thailanstatin biosynthetic pathway in MSMB43. Deletion of tstP, which encodes a dioxygenase involved in converting TST-A to downstream products including FR901464 (FR, resulted in 58% increase of the TST-A titer to 144.7 ± 2.3 mg/L and 132% increase of the TST-D titer to 14.6 ± 0.5 mg/L in the fermentation broth, respectively. Deletion of tstR, which encodes a cytochrome P450 involved in converting TST-D to TST-A, resulted in more than 7-fold increase of the TST-D titer to 53.2 ± 12.1 mg/L in the fermentation broth. An execution of 90 L pilot-scale fed-batch fermentation of the tstP deletion mutant in a 120-L fermentor led to the preparation of 714 mg of TST-A with greater than 98.5% purity. The half-life of TST-D in a phosphate buffer was found to be at least 202 h, significantly longer than that of TST-A or FR, suggesting superior stability. However, the IC50 values of TST-D against representative human cancer cell lines were determined to be greater than those of TST-A, indicating weaker antiproliferative activity. This work enabled us to prepare sufficient quantities of TST-A and TST-D for our ongoing translational research.

  13. Why Japanese workers show low work engagement: An item response theory analysis of the Utrecht Work Engagement scale.

    Shimazu, Akihito; Schaufeli, Wilmar B; Miyanaka, Daisuke; Iwata, Noboru

    2010-11-05

    With the globalization of occupational health psychology, more and more researchers are interested in applying employee well-being like work engagement (i.e., a positive, fulfilling, work-related state of mind that is characterized by vigor, dedication, and absorption) to diverse populations. Accurate measurement contributes to our further understanding and to the generalizability of the concept of work engagement across different cultures. The present study investigated the measurement accuracy of the Japanese and the original Dutch versions of the Utrecht Work Engagement Scale (9-item version, UWES-9) and the comparability of this scale between both countries. Item Response Theory (IRT) was applied to the data from Japan (N = 2,339) and the Netherlands (N = 13,406). Reliability of the scale was evaluated at various levels of the latent trait (i.e., work engagement) based the test information function (TIF) and the standard error of measurement (SEM). The Japanese version had difficulty in differentiating respondents with extremely low work engagement, whereas the original Dutch version had difficulty in differentiating respondents with high work engagement. The measurement accuracy of both versions was not similar. Suppression of positive affect among Japanese people and self-enhancement (the general sensitivity to positive self-relevant information) among Dutch people may have caused decreased measurement accuracy. Hence, we should be cautious when interpreting low engagement scores among Japanese as well as high engagement scores among western employees.

  14. Why Japanese workers show low work engagement: An item response theory analysis of the Utrecht Work Engagement scale

    Iwata Noboru

    2010-11-01

    Full Text Available Abstract With the globalization of occupational health psychology, more and more researchers are interested in applying employee well-being like work engagement (i.e., a positive, fulfilling, work-related state of mind that is characterized by vigor, dedication, and absorption to diverse populations. Accurate measurement contributes to our further understanding and to the generalizability of the concept of work engagement across different cultures. The present study investigated the measurement accuracy of the Japanese and the original Dutch versions of the Utrecht Work Engagement Scale (9-item version, UWES-9 and the comparability of this scale between both countries. Item Response Theory (IRT was applied to the data from Japan (N = 2,339 and the Netherlands (N = 13,406. Reliability of the scale was evaluated at various levels of the latent trait (i.e., work engagement based the test information function (TIF and the standard error of measurement (SEM. The Japanese version had difficulty in differentiating respondents with extremely low work engagement, whereas the original Dutch version had difficulty in differentiating respondents with high work engagement. The measurement accuracy of both versions was not similar. Suppression of positive affect among Japanese people and self-enhancement (the general sensitivity to positive self-relevant information among Dutch people may have caused decreased measurement accuracy. Hence, we should be cautious when interpreting low engagement scores among Japanese as well as high engagement scores among western employees.

  15. Density functional theory studies on the nano-scaled composites consisted of graphene and acyl hydrazone molecules

    Ren, J. L.; Zhou, L.; Lv, Z. C.; Ding, C. H.; Wu, Y. H.; Bai, H. C.

    2016-07-01

    Graphene, which is the first obtained single atomic layer 2D materials, has drawn a great of concern in nano biotechnology due to the unique property. On one hand, acyl hydrazone compounds belonging to the Schif bases have aroused considerable attention in medicine, pharmacy, and analytical reagent. However, few understanding about the interaction between graphene and acyl hydrazone molecules is now available. And such investigations are much crucial for the applications of these new nano-scaled composites. The current work revealed theoretical investigations on the nano-scaled composites built by acyl hydrazone molecules loaded on the surface of graphene. The relative energy, electronic property and the interaction between the counterparts of graphene/acyl hydrazone composites are investigated based on the density functional theory calculations. According to the obtained adsorption energy, the formation of the nano-scaled composite from the isolated graphene and acyl hydrazone molecule is exothermic, and thus it is energetically favorable to form these nano composites in viewpoint of total energy change. The frontier molecular orbital for the nano composite is mainly distributed at the graphene part, leading to that the energy levels of the frontier molecular orbital of the nano composites are very close to that of isolated graphene. Moreover, the counterpart interaction for the graphene/acyl hydrazone composites is also explored based on the discussions of orbital hybridization, charge redistribution and Van der Waals interaction.

  16. The multi-dimensional model of Māori identity and cultural engagement: item response theory analysis of scale properties.

    Sibley, Chris G; Houkamau, Carla A

    2013-01-01

    We argue that there is a need for culture-specific measures of identity that delineate the factors that most make sense for specific cultural groups. One such measure, recently developed specifically for Māori peoples, is the Multi-Dimensional Model of Māori Identity and Cultural Engagement (MMM-ICE). Māori are the indigenous peoples of New Zealand. The MMM-ICE is a 6-factor measure that assesses the following aspects of identity and cultural engagement as Māori: (a) group membership evaluation, (b) socio-political consciousness, (c) cultural efficacy and active identity engagement, (d) spirituality, (e) interdependent self-concept, and (f) authenticity beliefs. This article examines the scale properties of the MMM-ICE using item response theory (IRT) analysis in a sample of 492 Māori. The MMM-ICE subscales showed reasonably even levels of measurement precision across the latent trait range. Analysis of age (cohort) effects further indicated that most aspects of Māori identification tended to be higher among older Māori, and these cohort effects were similar for both men and women. This study provides novel support for the reliability and measurement precision of the MMM-ICE. The study also provides a first step in exploring change and stability in Māori identity across the life span. A copy of the scale, along with recommendations for scale scoring, is included.

  17. Evaluation of the Multiple Sclerosis Walking Scale-12 (MSWS-12) in a Dutch sample: Application of item response theory.

    Mokkink, Lidwine Brigitta; Galindo-Garre, Francisca; Uitdehaag, Bernard Mj

    2016-12-01

    The Multiple Sclerosis Walking Scale-12 (MSWS-12) measures walking ability from the patients' perspective. We examined the quality of the MSWS-12 using an item response theory model, the graded response model (GRM). A total of 625 unique Dutch multiple sclerosis (MS) patients were included. After testing for unidimensionality, monotonicity, and absence of local dependence, a GRM was fit and item characteristics were assessed. Differential item functioning (DIF) for the variables gender, age, duration of MS, type of MS and severity of MS, reliability, total test information, and standard error of the trait level (θ) were investigated. Confirmatory factor analysis showed a unidimensional structure of the 12 items of the scale, explaining 88% of the variance. Item 2 did not fit into the GRM model. Reliability was 0.93. Items 8 and 9 (of the 11 and 12 item version respectively) showed DIF on the variable severity, based on the Expanded Disability Status Scale (EDSS). However, the EDSS is strongly related to the content of both items. Our results confirm the good quality of the MSWS-12. The trait level (θ) scores and item parameters of both the 12- and 11-item versions were highly comparable, although we do not suggest to change the content of the MSWS-12. © The Author(s), 2016.

  18. Unified nano-mechanics based probabilistic theory of quasibrittle and brittle structures: I. Strength, static crack growth, lifetime and scaling

    Le, Jia-Liang; Bažant, Zdeněk P.; Bazant, Martin Z.

    2011-07-01

    Engineering structures must be designed for an extremely low failure probability such as 10 -6, which is beyond the means of direct verification by histogram testing. This is not a problem for brittle or ductile materials because the type of probability distribution of structural strength is fixed and known, making it possible to predict the tail probabilities from the mean and variance. It is a problem, though, for quasibrittle materials for which the type of strength distribution transitions from Gaussian to Weibullian as the structure size increases. These are heterogeneous materials with brittle constituents, characterized by material inhomogeneities that are not negligible compared to the structure size. Examples include concrete, fiber composites, coarse-grained or toughened ceramics, rocks, sea ice, rigid foams and bone, as well as many materials used in nano- and microscale devices. This study presents a unified theory of strength and lifetime for such materials, based on activation energy controlled random jumps of the nano-crack front, and on the nano-macro multiscale transition of tail probabilities. Part I of this study deals with the case of monotonic and sustained (or creep) loading, and Part II with fatigue (or cyclic) loading. On the scale of the representative volume element of material, the probability distribution of strength has a Gaussian core onto which a remote Weibull tail is grafted at failure probability of the order of 10 -3. With increasing structure size, the Weibull tail penetrates into the Gaussian core. The probability distribution of static (creep) lifetime is related to the strength distribution by the power law for the static crack growth rate, for which a physical justification is given. The present theory yields a simple relation between the exponent of this law and the Weibull moduli for strength and lifetime. The benefit is that the lifetime distribution can be predicted from short-time tests of the mean size effect on

  19. Universal scaling of the logarithmic negativity in massive quantum field theory

    Blondeau-Fournier, Olivier; Castro-Alvaredo, Olalla A.; Doyon, Benjamin

    2016-03-01

    We consider the logarithmic negativity, a measure of bipartite entanglement, in a general unitary 1 + 1-dimensional massive quantum field theory, not necessarily integrable. We compute the negativity between a finite region of length r and an adjacent semi-infinite region, and that between two semi-infinite regions separated by a distance r. We show that the former saturates to a finite value, and that the latter tends to zero, as r\\to ∞ . We show that in both cases, the leading corrections are exponential decays in r (described by modified Bessel functions) that are solely controlled by the mass spectrum of the model, independently of its scattering matrix. This implies that, like the entanglement entropy (EE), the logarithmic negativity displays a very high level of universality, allowing one to extract information about the mass spectrum. Further, a study of sub-leading terms shows that, unlike the EE, a large-r analysis of the negativity allows for the detection of bound states.

  20. Thermalization time scales for WIMP capture by the Sun in effective theories

    Widmark, A., E-mail: axel.widmark@fysik.su.se [The Oskar Klein Centre for Cosmoparticle Physics, AlbaNova, SE-106 91 Stockholm (Sweden)

    2017-05-01

    I study the process of dark matter capture by the Sun, under the assumption of a Weakly Interacting Massive Particle (WIMP), in the framework of non-relativistic effective field theory. Hypothetically, WIMPs from the galactic halo can scatter against atomic nuclei in the solar interior, settle to thermal equilibrium with the solar core and annihilate to produce an observable flux of neutrinos. In particular, I examine the thermalization process using Monte-Carlo integration of WIMP trajectories. I consider WIMPs in a mass range of 10–1000 GeV and WIMP-nucleon interaction operators with different dependence on spin and transferred momentum. I find that the density profiles of captured WIMPs are in accordance with a thermal profile described by the Sun's gravitational potential and core temperature. Depending on the operator that governs the interaction, the majority of the thermalization time is spent in either the solar interior or exterior. If normalizing the WIMP-nuclei interaction strength to a specific capture rate, I find that the thermalization time differs at most by 3 orders of magnitude between operators. In most cases of interest, the thermalization time is many orders of magnitude shorter than the age of the solar system.