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Sample records for generalized beta model

  1. Bayesian Analysis for Binomial Models with Generalized Beta Prior Distributions.

    ERIC Educational Resources Information Center

    Chen, James J.; Novick, Melvin, R.

    1984-01-01

    The Libby-Novick class of three-parameter generalized beta distributions is shown to provide a rich class of prior distributions for the binomial model that removes some restrictions of the standard beta class. A numerical example indicates the desirability of using these wider classes of densities for binomial models. (Author/BW)

  2. A Generalized QMRA Beta-Poisson Dose-Response Model.

    PubMed

    Xie, Gang; Roiko, Anne; Stratton, Helen; Lemckert, Charles; Dunn, Peter K; Mengersen, Kerrie

    2016-10-01

    Quantitative microbial risk assessment (QMRA) is widely accepted for characterizing the microbial risks associated with food, water, and wastewater. Single-hit dose-response models are the most commonly used dose-response models in QMRA. Denoting PI(d) as the probability of infection at a given mean dose d, a three-parameter generalized QMRA beta-Poisson dose-response model, PI(d|α,β,r*), is proposed in which the minimum number of organisms required for causing infection, Kmin , is not fixed, but a random variable following a geometric distribution with parameter 0beta-Poisson model, PI(d|α,β), is a special case of the generalized model with Kmin = 1 (which implies r*=1). The generalized beta-Poisson model is based on a conceptual model with greater detail in the dose-response mechanism. Since a maximum likelihood solution is not easily available, a likelihood-free approximate Bayesian computation (ABC) algorithm is employed for parameter estimation. By fitting the generalized model to four experimental data sets from the literature, this study reveals that the posterior median r* estimates produced fall short of meeting the required condition of r* = 1 for single-hit assumption. However, three out of four data sets fitted by the generalized models could not achieve an improvement in goodness of fit. These combined results imply that, at least in some cases, a single-hit assumption for characterizing the dose-response process may not be appropriate, but that the more complex models may be difficult to support especially if the sample size is small. The three-parameter generalized model provides a possibility to investigate the mechanism of a dose-response process in greater detail than is possible under a single-hit model.

  3. Spatial Double Generalized Beta Regression Models: Extensions and Application to Study Quality of Education in Colombia

    ERIC Educational Resources Information Center

    Cepeda-Cuervo, Edilberto; Núñez-Antón, Vicente

    2013-01-01

    In this article, a proposed Bayesian extension of the generalized beta spatial regression models is applied to the analysis of the quality of education in Colombia. We briefly revise the beta distribution and describe the joint modeling approach for the mean and dispersion parameters in the spatial regression models' setting. Finally, we motivate…

  4. Distributional Assumptions in Educational Assessments Analysis: Normal Distributions versus Generalized Beta Distribution in Modeling the Phenomenon of Learning

    ERIC Educational Resources Information Center

    Campos, Jose Alejandro Gonzalez; Moraga, Paulina Saavedra; Del Pozo, Manuel Freire

    2013-01-01

    This paper introduces the generalized beta (GB) model as a new modeling tool in the educational assessment area and evaluation analysis, specifically. Unlike normal model, GB model allows us to capture some real characteristics of data and it is an important tool for understanding the phenomenon of learning. This paper develops a contrast with the…

  5. Modeling of Beta Diversity in Tunisian Waters: Predictions Using Generalized Dissimilarity Modeling and Bioregionalisation Using Fuzzy Clustering

    PubMed Central

    Lasram, Frida Ben Rais; Hattab, Tarek; Halouani, Ghassen; Romdhane, Mohamed Salah; Le Loc'h, François

    2015-01-01

    Spatial patterns of beta diversity are a major focus of ecology. They can be especially valuable in conservation planning. In this study, we used a generalized dissimilarity modeling approach to analyze and predict the spatial patterns of beta diversity for commercially exploited, demersal marine species assemblages along the Tunisian coasts. For this study, we used a presence/absence dataset which included information on 174 species (invertebrates and fishes) and 9 environmental variables. We first performed the modeling analyses and assessed beta diversity using the turnover component of the Jaccard’s dissimilarity index. We then performed nonmetric multidimensional scaling to map predicted beta diversity. To delineate the biogeographical regions, we used fuzzy cluster analysis. Finally, we also identified a set of indicator species which characterized the species assemblages in each identified biogeographical region. The predicted beta diversity map revealed two patterns: an inshore-offshore gradient and a south-north latitudinal gradient. Three biogeographical regions were identified and 14 indicator species. These results constitute a first contribution of the bioregionalisation of the Tunisian waters and highlight the issues associated with current fisheries management zones and conservation strategies. Results could be useful to follow an Ecosystem Based Management approach by proposing an objective spatial partitioning of the Tunisian waters. This partitioning could be used to prioritize the adjustment of the actual fisheries management entities, identify current data gaps, inform future scientific surveys and improve current MPA network. PMID:26147371

  6. Generalized Beta Mixtures of Gaussians.

    PubMed

    Armagan, Artin; Dunson, David B; Clyde, Merlise

    2011-01-01

    In recent years, a rich variety of shrinkage priors have been proposed that have great promise in addressing massive regression problems. In general, these new priors can be expressed as scale mixtures of normals, but have more complex forms and better properties than traditional Cauchy and double exponential priors. We first propose a new class of normal scale mixtures through a novel generalized beta distribution that encompasses many interesting priors as special cases. This encompassing framework should prove useful in comparing competing priors, considering properties and revealing close connections. We then develop a class of variational Bayes approximations through the new hierarchy presented that will scale more efficiently to the types of truly massive data sets that are now encountered routinely.

  7. Multivariate Generalized Beta Distributions with Applications to Utility Assessment.

    ERIC Educational Resources Information Center

    Libby, David L.; Novick, Melvin R.

    1982-01-01

    Two multivariate probability distributions, a generalized beta distribution and a generalized F distribution, are derived. Formulas for the moments of these distributions are given and an example of the bivariate generalized beta is presented. (Author/JKS)

  8. Beta Regression Finite Mixture Models of Polarization and Priming

    ERIC Educational Resources Information Center

    Smithson, Michael; Merkle, Edgar C.; Verkuilen, Jay

    2011-01-01

    This paper describes the application of finite-mixture general linear models based on the beta distribution to modeling response styles, polarization, anchoring, and priming effects in probability judgments. These models, in turn, enhance our capacity for explicitly testing models and theories regarding the aforementioned phenomena. The mixture…

  9. Fundamental processes in the interacting boson model: 0{nu}{beta}{beta} decay

    SciTech Connect

    Iachello, F.; Barea, J.

    2011-05-06

    A program to calculate nuclear matrix elements for fundamental processes in the interacting boson model has been initiated. Results for the nuclear matrix elements in neutrinoless double beta decay 0{nu}{beta}{beta} are presented.

  10. Modeling the beta diversity of coral reefs.

    PubMed

    Harborne, Alastair R; Mumby, Peter J; Zychaluk, Kamila; Hedley, John D; Blackwell, Paul G

    2006-11-01

    Quantifying the beta diversity (species replacement along spatiotemporal gradients) of ecosystems is important for understanding and conserving patterns of biodiversity. However, virtually all studies of beta diversity focus on one-dimensional transects orientated along a specific environmental gradient that is defined a priori. By ignoring a second spatial dimension and the associated changes in species composition and environmental gradients, this approach may provide limited insight into the full pattern of beta diversity. Here, we use remotely sensed imagery to quantify beta diversity continuously, in two dimensions, and at multiple scales across an entire tropical marine seascape. We then show that beta diversity can be modeled (0.852 > or = r2 > or = 0.590) at spatial scales between 0.5 and 5.0 km2, using the environmental variables of mean and variance of depth and wave exposure. Beta diversity, quantified within a "window" of a given size, is positively correlated to the range of environmental conditions within that window. For example, beta diversity increases with increasing variance of depth. By analyzing such relationships across seascapes, this study provides a framework for a range of disparate coral reef literature including studies of zonation, diversity, and disturbance. Using supporting evidence from soft-bottom communities, we hypothesize that depth will be an important variable for modeling beta diversity in a range of marine systems. We discuss the implications of our results for the design of marine reserves.

  11. Generalized Latent Trait Models.

    ERIC Educational Resources Information Center

    Moustaki, Irini; Knott, Martin

    2000-01-01

    Discusses a general model framework within which manifest variables with different distributions in the exponential family can be analyzed with a latent trait model. Presents a unified maximum likelihood method for estimating the parameters of the generalized latent trait model and discusses the scoring of individuals on the latent dimensions.…

  12. Decoding {beta}-decay systematics: A global statistical model for {beta}{sup -} half-lives

    SciTech Connect

    Costiris, N. J.; Mavrommatis, E.; Gernoth, K. A.; Clark, J. W.

    2009-10-15

    Statistical modeling of nuclear data provides a novel approach to nuclear systematics complementary to established theoretical and phenomenological approaches based on quantum theory. Continuing previous studies in which global statistical modeling is pursued within the general framework of machine learning theory, we implement advances in training algorithms designed to improve generalization, in application to the problem of reproducing and predicting the half-lives of nuclear ground states that decay 100% by the {beta}{sup -} mode. More specifically, fully connected, multilayer feed-forward artificial neural network models are developed using the Levenberg-Marquardt optimization algorithm together with Bayesian regularization and cross-validation. The predictive performance of models emerging from extensive computer experiments is compared with that of traditional microscopic and phenomenological models as well as with the performance of other learning systems, including earlier neural network models as well as the support vector machines recently applied to the same problem. In discussing the results, emphasis is placed on predictions for nuclei that are far from the stability line, and especially those involved in r-process nucleosynthesis. It is found that the new statistical models can match or even surpass the predictive performance of conventional models for {beta}-decay systematics and accordingly should provide a valuable additional tool for exploring the expanding nuclear landscape.

  13. The General Teaching Model.

    ERIC Educational Resources Information Center

    Miles, David T.; Robinson, Roger E.

    The General Teaching Model is a procedural guide for the design, implementation, evaluation, and improvement of instruction. The Model is considered applicable to all levels of education, all subject matters, and any length of instructional unit. It consists of four components: 1) instructional objectives, 2) pre-assessment, 3) instructional…

  14. Functional Generalized Additive Models.

    PubMed

    McLean, Mathew W; Hooker, Giles; Staicu, Ana-Maria; Scheipl, Fabian; Ruppert, David

    2014-01-01

    We introduce the functional generalized additive model (FGAM), a novel regression model for association studies between a scalar response and a functional predictor. We model the link-transformed mean response as the integral with respect to t of F{X(t), t} where F(·,·) is an unknown regression function and X(t) is a functional covariate. Rather than having an additive model in a finite number of principal components as in Müller and Yao (2008), our model incorporates the functional predictor directly and thus our model can be viewed as the natural functional extension of generalized additive models. We estimate F(·,·) using tensor-product B-splines with roughness penalties. A pointwise quantile transformation of the functional predictor is also considered to ensure each tensor-product B-spline has observed data on its support. The methods are evaluated using simulated data and their predictive performance is compared with other competing scalar-on-function regression alternatives. We illustrate the usefulness of our approach through an application to brain tractography, where X(t) is a signal from diffusion tensor imaging at position, t, along a tract in the brain. In one example, the response is disease-status (case or control) and in a second example, it is the score on a cognitive test. R code for performing the simulations and fitting the FGAM can be found in supplemental materials available online.

  15. General composite Higgs models

    NASA Astrophysics Data System (ADS)

    Marzocca, David; Serone, Marco; Shu, Jing

    2012-08-01

    We construct a general class of pseudo-Goldstone composite Higgs models, within the minimal SO(5)/SO(4) coset structure, that are not necessarily of moose-type. We characterize the main properties these models should have in order to give rise to a Higgs mass around 125 GeV. We assume the existence of relatively light and weakly coupled spin 1 and 1/2 resonances. In absence of a symmetry principle, we introduce the Minimal Higgs Potential (MHP) hypothesis: the Higgs potential is assumed to be one-loop dominated by the SM fields and the above resonances, with a contribution that is made calculable by imposing suitable generalizations of the first and second Weinberg sum rules. We show that a 125 GeV Higgs requires light, often sub-TeV, fermion resonances. Their presence can also be important for the models to successfully pass the electroweak precision tests. Interestingly enough, the latter can also be passed by models with a heavy Higgs around 320 GeV. The composite Higgs models of the moose-type considered in the literature can be seen as particular limits of our class of models.

  16. Meta-analysis of studies with bivariate binary outcomes: a marginal beta-binomial model approach.

    PubMed

    Chen, Yong; Hong, Chuan; Ning, Yang; Su, Xiao

    2016-01-15

    When conducting a meta-analysis of studies with bivariate binary outcomes, challenges arise when the within-study correlation and between-study heterogeneity should be taken into account. In this paper, we propose a marginal beta-binomial model for the meta-analysis of studies with binary outcomes. This model is based on the composite likelihood approach and has several attractive features compared with the existing models such as bivariate generalized linear mixed model (Chu and Cole, 2006) and Sarmanov beta-binomial model (Chen et al., 2012). The advantages of the proposed marginal model include modeling the probabilities in the original scale, not requiring any transformation of probabilities or any link function, having closed-form expression of likelihood function, and no constraints on the correlation parameter. More importantly, because the marginal beta-binomial model is only based on the marginal distributions, it does not suffer from potential misspecification of the joint distribution of bivariate study-specific probabilities. Such misspecification is difficult to detect and can lead to biased inference using currents methods. We compare the performance of the marginal beta-binomial model with the bivariate generalized linear mixed model and the Sarmanov beta-binomial model by simulation studies. Interestingly, the results show that the marginal beta-binomial model performs better than the Sarmanov beta-binomial model, whether or not the true model is Sarmanov beta-binomial, and the marginal beta-binomial model is more robust than the bivariate generalized linear mixed model under model misspecifications. Two meta-analyses of diagnostic accuracy studies and a meta-analysis of case-control studies are conducted for illustration.

  17. New model for nucleon generalized parton distributions

    SciTech Connect

    Radyushkin, Anatoly V.

    2014-01-01

    We describe a new type of models for nucleon generalized parton distributions (GPDs) H and E. They are heavily based on the fact nucleon GPDs require to use two forms of double distribution (DD) representations. The outcome of the new treatment is that the usual DD+D-term construction should be amended by an extra term, {xi} E{sub +}{sup 1} (x,{xi}) which has the DD structure {alpha}/{beta} e({beta},{alpha}, with e({beta},{alpha}) being the DD that generates GPD E(x,{xi}). We found that this function, unlike the D-term, has support in the whole -1 <= x <= 1 region. Furthermore, it does not vanish at the border points |x|={xi}.

  18. Generalized Nonlinear Yule Models

    NASA Astrophysics Data System (ADS)

    Lansky, Petr; Polito, Federico; Sacerdote, Laura

    2016-11-01

    With the aim of considering models related to random graphs growth exhibiting persistent memory, we propose a fractional nonlinear modification of the classical Yule model often studied in the context of macroevolution. Here the model is analyzed and interpreted in the framework of the development of networks such as the World Wide Web. Nonlinearity is introduced by replacing the linear birth process governing the growth of the in-links of each specific webpage with a fractional nonlinear birth process with completely general birth rates. Among the main results we derive the explicit distribution of the number of in-links of a webpage chosen uniformly at random recognizing the contribution to the asymptotics and the finite time correction. The mean value of the latter distribution is also calculated explicitly in the most general case. Furthermore, in order to show the usefulness of our results, we particularize them in the case of specific birth rates giving rise to a saturating behaviour, a property that is often observed in nature. The further specialization to the non-fractional case allows us to extend the Yule model accounting for a nonlinear growth.

  19. Ocean General Circulation Models

    SciTech Connect

    Yoon, Jin-Ho; Ma, Po-Lun

    2012-09-30

    1. Definition of Subject The purpose of this text is to provide an introduction to aspects of oceanic general circulation models (OGCMs), an important component of Climate System or Earth System Model (ESM). The role of the ocean in ESMs is described in Chapter XX (EDITOR: PLEASE FIND THE COUPLED CLIMATE or EARTH SYSTEM MODELING CHAPTERS). The emerging need for understanding the Earth’s climate system and especially projecting its future evolution has encouraged scientists to explore the dynamical, physical, and biogeochemical processes in the ocean. Understanding the role of these processes in the climate system is an interesting and challenging scientific subject. For example, a research question how much extra heat or CO2 generated by anthropogenic activities can be stored in the deep ocean is not only scientifically interesting but also important in projecting future climate of the earth. Thus, OGCMs have been developed and applied to investigate the various oceanic processes and their role in the climate system.

  20. Generalized Multilevel Structural Equation Modeling

    ERIC Educational Resources Information Center

    Rabe-Hesketh, Sophia; Skrondal, Anders; Pickles, Andrew

    2004-01-01

    A unifying framework for generalized multilevel structural equation modeling is introduced. The models in the framework, called generalized linear latent and mixed models (GLLAMM), combine features of generalized linear mixed models (GLMM) and structural equation models (SEM) and consist of a response model and a structural model for the latent…

  1. The Generalized DINA Model Framework

    ERIC Educational Resources Information Center

    de la Torre, Jimmy

    2011-01-01

    The G-DINA ("generalized deterministic inputs, noisy and gate") model is a generalization of the DINA model with more relaxed assumptions. In its saturated form, the G-DINA model is equivalent to other general models for cognitive diagnosis based on alternative link functions. When appropriate constraints are applied, several commonly used…

  2. A Beta-splitting model for evolutionary trees

    PubMed Central

    Sainudiin, Raazesh

    2016-01-01

    In this article, we construct a generalization of the Blum–François Beta-splitting model for evolutionary trees, which was itself inspired by Aldous' Beta-splitting model on cladograms. The novelty of our approach allows for asymmetric shares of diversification rates (or diversification ‘potential’) between two sister species in an evolutionarily interpretable manner, as well as the addition of extinction to the model in a natural way. We describe the incremental evolutionary construction of a tree with n leaves by splitting or freezing extant lineages through the generating, organizing and deleting processes. We then give the probability of any (binary rooted) tree under this model with no extinction, at several resolutions: ranked planar trees giving asymmetric roles to the first and second offspring species of a given species and keeping track of the order of the speciation events occurring during the creation of the tree, unranked planar trees, ranked non-planar trees and finally (unranked non-planar) trees. We also describe a continuous-time equivalent of the generating, organizing and deleting processes where tree topology and branch lengths are jointly modelled and provide code in SageMath/Python for these algorithms. PMID:27293780

  3. General Graded Response Model.

    ERIC Educational Resources Information Center

    Samejima, Fumiko

    This paper describes the graded response model. The graded response model represents a family of mathematical models that deal with ordered polytomous categories, such as: (1) letter grading; (2) an attitude survey with "strongly disagree, disagree, agree, and strongly agree" choices; (3) partial credit given in accord with an…

  4. Order-disorder transition in conflicting dynamics leading to rank-frequency generalized beta distributions

    NASA Astrophysics Data System (ADS)

    Alvarez-Martinez, R.; Martinez-Mekler, G.; Cocho, G.

    2011-01-01

    The behavior of rank-ordered distributions of phenomena present in a variety of fields such as biology, sociology, linguistics, finance and geophysics has been a matter of intense research. Often power laws have been encountered; however, their validity tends to hold mainly for an intermediate range of rank values. In a recent publication (Martínez-Mekler et al., 2009 [7]), a generalization of the functional form of the beta distribution has been shown to give excellent fits for many systems of very diverse nature, valid for the whole range of rank values, regardless of whether or not a power law behavior has been previously suggested. Here we give some insight on the significance of the two free parameters which appear as exponents in the functional form, by looking into discrete probabilistic branching processes with conflicting dynamics. We analyze a variety of realizations of these so-called expansion-modification models first introduced by Wentian Li (1989) [10]. We focus our attention on an order-disorder transition we encounter as we vary the modification probability p. We characterize this transition by means of the fitting parameters. Our numerical studies show that one of the fitting exponents is related to the presence of long-range correlations exhibited by power spectrum scale invariance, while the other registers the effect of disordering elements leading to a breakdown of these properties. In the absence of long-range correlations, this parameter is sensitive to the occurrence of unlikely events. We also introduce an approximate calculation scheme that relates this dynamics to multinomial multiplicative processes. A better understanding through these models of the meaning of the generalized beta-fitting exponents may contribute to their potential for identifying and characterizing universality classes.

  5. The beta distribution: A statistical model for world cloud cover

    NASA Technical Reports Server (NTRS)

    Falls, L. W.

    1973-01-01

    Much work has been performed in developing empirical global cloud cover models. This investigation was made to determine an underlying theoretical statistical distribution to represent worldwide cloud cover. The beta distribution with probability density function is given to represent the variability of this random variable. It is shown that the beta distribution possesses the versatile statistical characteristics necessary to assume the wide variety of shapes exhibited by cloud cover. A total of 160 representative empirical cloud cover distributions were investigated and the conclusion was reached that this study provides sufficient statical evidence to accept the beta probability distribution as the underlying model for world cloud cover.

  6. A Quantitative Model for the Exchange Current of Porous Molybdenum Electrodes on Sodium Beta-Alumina in Sodium Vapor

    NASA Technical Reports Server (NTRS)

    Williams, R. M.; Ryan, M. A.; LeDuc, H.; Cortez, R. H.; Saipetch, C.; Shields, V.; Manatt, K.; Homer, M. L.

    1998-01-01

    This paper presents a model of the exchange current developed for porous molybdenum electrodes on sodium beta-alumina ceramics in low pressure sodium vapor, but which has general applicability to gas/porous metal electrodes on solid electrolytes.

  7. Numerical models for high beta magnetohydrodynamic flow

    SciTech Connect

    Brackbill, J.U.

    1987-01-01

    The fundamentals of numerical magnetohydrodynamics for highly conducting, high-beta plasmas are outlined. The discussions emphasize the physical properties of the flow, and how elementary concepts in numerical analysis can be applied to the construction of finite difference approximations that capture these features. The linear and nonlinear stability of explicit and implicit differencing in time is examined, the origin and effect of numerical diffusion in the calculation of convective transport is described, and a technique for maintaining solenoidality in the magnetic field is developed. Many of the points are illustrated by numerical examples. The techniques described are applicable to the time-dependent, high-beta flows normally encountered in magnetically confined plasmas, plasma switches, and space and astrophysical plasmas. 40 refs.

  8. Model of Break-Bone Fever via Beta-Derivatives

    PubMed Central

    Atangana, Abdon; Oukouomi Noutchie, Suares Clovis

    2014-01-01

    Using the new derivative called beta-derivative, we modelled the well-known infectious disease called break-bone fever or the dengue fever. We presented the endemic equilibrium points under certain conditions of the physical parameters included in the model. We made use of an iteration method to solve the extended model. To show the efficiency of the method used, we have presented in detail the stability and the convergence of the method for solving the system (2). We presented the uniqueness of the special solution of system (2) and finally the numerical simulations were presented for various values of beta. PMID:25295263

  9. In vivo modeling of beta-glucan degradation in contrasting barley (Hordeum vulgare L.) genotypes.

    PubMed

    Gianinetti, Alberto; Ferrari, Barbara; Frigeri, Paolo; Stanca, Antonio Michele

    2007-04-18

    An important determinative of malt quality is the malt beta-glucan content, which in turn depends on the initial barley beta-glucan content as well as the beta-glucan depolymerization by beta-glucanase (EC 3.2.1.73) during malting. Another enzyme, named beta-glucan solubilase, has been suggested to act prior to beta-glucanase; its existence, however, has not been unequivocally proven. We monitored changes in beta-glucan levels and in the development of beta-glucan-degrading enzymes during malting of five lots of contrasting barley genotypes. Two models of in vivo kinetics for beta-glucan degradation were then compared as follows: (i) a biphasic model based on the sequential action of beta-glucan solubilase and beta-glucanase and (ii) a monophasic model assuming that all beta-glucans are depolymerized by beta-glucanase without the previous intervention of another enzyme. Confirmatory regression analysis was used to test the fit of the models to the observed data. Our results show that beta-glucan degradation is mostly monophasic, although some enzyme other than beta-glucanase seems to be required for the early solubilization of a small fraction of insoluble beta-glucans (on average, 7% of total beta-glucans). Furthermore, the genotype-dependent kinetic rate constant (indicating beta-glucan degradability), in addition to beta-glucanase activity, is suggested to play a major role in malting quality.

  10. Comparison of the [ital pn] quasiparticle RPA and shell model for Gamow-Teller beta and double-beta decays

    SciTech Connect

    Zhao, L.; Brown, B.A. )

    1993-06-01

    We examine the validity of the [ital pn] quasiparticle RPA ([ital pn]QRPA) as a model for calculating [beta][sup +] and 2[nu][beta][beta] Gamow-Teller decays by making a comparison of the [ital pn]QRPA with a large-basis shell-model calculation within the 0[ital f]1[ital p] shell. We employ [ital A]=46 nuclei (those with six valence nucleons) for this comparison. Our comparison includes the decay matrix elements summed over final states, the strength distributions, and, for the first time, the coherent transition matrix elements (CTME). The [ital pn]QRPA overestimates the total [beta][sup +] and 2[nu][beta][beta] matrix elements. There are large differences in the shape of the spectra as well as in the CTME between the [ital pn]QRPA and shell-model results. Empirical improvements for the [ital pn]QRPA are discussed.

  11. Generalized Ordinary Differential Equation Models.

    PubMed

    Miao, Hongyu; Wu, Hulin; Xue, Hongqi

    2014-10-01

    Existing estimation methods for ordinary differential equation (ODE) models are not applicable to discrete data. The generalized ODE (GODE) model is therefore proposed and investigated for the first time. We develop the likelihood-based parameter estimation and inference methods for GODE models. We propose robust computing algorithms and rigorously investigate the asymptotic properties of the proposed estimator by considering both measurement errors and numerical errors in solving ODEs. The simulation study and application of our methods to an influenza viral dynamics study suggest that the proposed methods have a superior performance in terms of accuracy over the existing ODE model estimation approach and the extended smoothing-based (ESB) method.

  12. One loop beta functions and fixed points in higher derivative sigma models

    SciTech Connect

    Percacci, Roberto; Zanusso, Omar

    2010-03-15

    We calculate the one loop beta functions of nonlinear sigma models in four dimensions containing general two- and four-derivative terms. In the O(N) model there are four such terms and nontrivial fixed points exist for all N{>=}4. In the chiral SU(N) models there are in general six couplings, but only five for N=3 and four for N=2; we find fixed points only for N=2, 3. In the approximation considered, the four-derivative couplings are asymptotically free but the coupling in the two-derivative term has a nonzero limit. These results support the hypothesis that certain sigma models may be asymptotically safe.

  13. Quantitative analysis of cyclic beta-turn models.

    PubMed Central

    Perczel, A.; Fasman, G. D.

    1992-01-01

    The beta-turn is a frequently found structural unit in the conformation of globular proteins. Although the circular dichroism (CD) spectra of the alpha-helix and beta-pleated sheet are well defined, there remains some ambiguity concerning the pure component CD spectra of the different types of beta-turns. Recently, it has been reported (Hollósi, M., Kövér, K.E., Holly, S., Radics, L., & Fasman, G.D., 1987, Biopolymers 26, 1527-1572; Perczel, A., Hollósi, M., Foxman, B.M., & Fasman, G.D., 1991a, J. Am. Chem. Soc. 113, 9772-9784) that some pseudohexapeptides (e.g., the cyclo[(delta)Ava-Gly-Pro-Aaa-Gly] where Aaa = Ser, Ser(OtBu), or Gly) in many solvents adopt a conformational mixture of type I and the type II beta-turns, although the X-ray-determined conformation was an ideal type I beta-turn. In addition to these pseudohexapeptides, conformational analysis was also carried out on three pseudotetrapeptides and three pseudooctapeptides. The target of the conformation analysis reported herein was to determine whether the ring stress of the above beta-turn models has an influence on their conformational properties. Quantitative nuclear Overhauser effect (NOE) measurements yielded interproton distances. The conformational average distances so obtained were interpreted utilizing molecular dynamics (MD) simulations to yield the conformational percentages. These conformational ratios were correlated with the conformational weights obtained by quantitative CD analysis of the same compounds. The pure component CD curves of type I and type II beta-turns were also obtained, using a recently developed algorithm (Perczel, A., Tusnády, G., Hollósi, M., & Fasman, G.D., 1991b, Protein Eng. 4(6), 669-679). For the first time the results of a CD deconvolution, based on the CD spectra of 14 beta-turn models, were assigned by quantitative NOE results. The NOE experiments confirmed the ratios of the component curves found for the two major beta-turns by CD analysis. These results

  14. Fermions as generalized Ising models

    NASA Astrophysics Data System (ADS)

    Wetterich, C.

    2017-04-01

    We establish a general map between Grassmann functionals for fermions and probability or weight distributions for Ising spins. The equivalence between the two formulations is based on identical transfer matrices and expectation values of products of observables. The map preserves locality properties and can be realized for arbitrary dimensions. We present a simple example where a quantum field theory for free massless Dirac fermions in two-dimensional Minkowski space is represented by an asymmetric Ising model on a euclidean square lattice.

  15. Fluxon modeling of low-beta plasmas

    NASA Astrophysics Data System (ADS)

    Deforest, C. E.; Kankelborg, C. C.

    2007-02-01

    We have developed a new, quasi-Lagrangian approach for numerical modeling of magnetohydrodynamics in low to moderate β plasmas such as the solar corona. We introduce the concept of a “fluxon”, a discretized field line. Fluxon models represent the magnetic field as a skeleton of such discrete field lines, and interpolate field values from the geometry of the skeleton where needed, reversing the usual direction of the field line transform. The fluxon skeleton forms the grid for a collection of 1-D Eulerian models of plasma along individual flux tubes. Fluxon models have no numerical resistivity, because they preserve topology explicitly. Our prototype code, FLUX, is currently able to find 3-D nonlinear force-free field solutions with a specified field topology, and work is ongoing to validate and extend the code to full magnetohydrodynamics. FLUX has significant scaling advantages over conventional models: for “magnetic carpet” models, with photospheric line-tied boundary conditions, FLUX simulations scale in complexity like a conventional 2-D grid although the full 3-D field is represented. The code is free software and is available online. In this current paper we introduce fluxons and our prototype code, and describe the course of future work with the code.

  16. Generalized waste package containment model

    SciTech Connect

    Liebetrau, A.M.; Apted, M.J.

    1985-02-01

    The US Department of Energy (DOE) is developing a performance assessment strategy to demonstrate compliance with standards and technical requirements of the Environmental Protection Agency (EPA) and the Nuclear Regulatory Commission (NRC) for the permanent disposal of high-level nuclear wastes in geologic repositories. One aspect of this strategy is the development of a unified performance model of the entire geologic repository system. Details of a generalized waste package containment (WPC) model and its relationship with other components of an overall repository model are presented in this paper. The WPC model provides stochastically determined estimates of the distributions of times-to-failure of the barriers of a waste package by various corrosion mechanisms and degradation processes. The model consists of a series of modules which employ various combinations of stochastic (probabilistic) and mechanistic process models, and which are individually designed to reflect the current state of knowledge. The WPC model is designed not only to take account of various site-specific conditions and processes, but also to deal with a wide range of site, repository, and waste package configurations. 11 refs., 3 figs., 2 tabs.

  17. General O-glycosylation of 2-furfuryl alcohol using beta-glucuronidase.

    PubMed

    Martin, Brett D; Welsh, Eric R; Mastrangelo, Jonathan C; Aggarwal, Renu

    2002-10-20

    beta-Glucuronidase from bovine liver is able to catalyze transfer of several carbohydrates to furfuryl alcohol, an acid-sensitive diene, with transfer yields as high as 84%. Carbohydrates that were transferred in yields of 30% or higher include gluco-, galacto-, xylo-, and fucopyranose. Small variations in the configuration of the substrate hydroxyls lead to large variations in the catalytic behavior of the enzyme in terms of both the initial reaction velocities and the final ratios of transfer-to-hydrolysis. The high transfer yields and surprising nonspecificity towards carbohydrate suggest that the enzyme may be a versatile tool for the general O-glycosylation of dienic alcohols.

  18. Smart Grid Interoperability Maturity Model Beta Version

    SciTech Connect

    Widergren, Steven E.; Drummond, R.; Giroti, Tony; Houseman, Doug; Knight, Mark; Levinson, Alex; longcore, Wayne; Lowe, Randy; Mater, J.; Oliver, Terry V.; Slack, Phil; Tolk, Andreas; Montgomery, Austin

    2011-12-02

    The GridWise Architecture Council was formed by the U.S. Department of Energy to promote and enable interoperability among the many entities that interact with the electric power system. This balanced team of industry representatives proposes principles for the development of interoperability concepts and standards. The Council provides industry guidance and tools that make it an available resource for smart grid implementations. In the spirit of advancing interoperability of an ecosystem of smart grid devices and systems, this document presents a model for evaluating the maturity of the artifacts and processes that specify the agreement of parties to collaborate across an information exchange interface. You are expected to have a solid understanding of large, complex system integration concepts and experience in dealing with software component interoperation. Those without this technical background should read the Executive Summary for a description of the purpose and contents of the document. Other documents, such as checklists, guides, and whitepapers, exist for targeted purposes and audiences. Please see the www.gridwiseac.org website for more products of the Council that may be of interest to you.

  19. Beta

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter covers the use of wild beets in sugar beet improvement, including the basic botany of the species, its distribution; geographical locations of genetic diversity; morphology; cytology and karyotype; genome size; taxonomic position; agricultural status (model plant/weeds/invasive species/...

  20. Guidelines for Use of the Approximate Beta-Poisson Dose-Response Model.

    PubMed

    Xie, Gang; Roiko, Anne; Stratton, Helen; Lemckert, Charles; Dunn, Peter K; Mengersen, Kerrie

    2016-10-05

    For dose-response analysis in quantitative microbial risk assessment (QMRA), the exact beta-Poisson model is a two-parameter mechanistic dose-response model with parameters α>0 and β>0, which involves the Kummer confluent hypergeometric function. Evaluation of a hypergeometric function is a computational challenge. Denoting PI(d) as the probability of infection at a given mean dose d, the widely used dose-response model PI(d)=1-(1+dβ)-α is an approximate formula for the exact beta-Poisson model. Notwithstanding the required conditions α<β and β>1, issues related to the validity and approximation accuracy of this approximate formula have remained largely ignored in practice, partly because these conditions are too general to provide clear guidance. Consequently, this study proposes a probability measure Pr(0 < r < 1 | α̂, β̂) as a validity measure (r is a random variable that follows a gamma distribution; α̂ and β̂ are the maximum likelihood estimates of α and β in the approximate model); and the constraint conditions β̂>(22α̂)0.50 for 0.02<α̂<2 as a rule of thumb to ensure an accurate approximation (e.g., Pr(0 < r < 1 | α̂, β̂) >0.99) . This validity measure and rule of thumb were validated by application to all the completed beta-Poisson models (related to 85 data sets) from the QMRA community portal (QMRA Wiki). The results showed that the higher the probability Pr(0 < r < 1 | α̂, β̂), the better the approximation. The results further showed that, among the total 85 models examined, 68 models were identified as valid approximate model applications, which all had a near perfect match to the corresponding exact beta-Poisson model dose-response curve.

  1. Neural mechanisms of transient neocortical beta rhythms: Converging evidence from humans, computational modeling, monkeys, and mice

    PubMed Central

    Sherman, Maxwell A.; Lee, Shane; Law, Robert; Haegens, Saskia; Thorn, Catherine A.; Hämäläinen, Matti S.; Moore, Christopher I.; Jones, Stephanie R.

    2016-01-01

    Human neocortical 15–29-Hz beta oscillations are strong predictors of perceptual and motor performance. However, the mechanistic origin of beta in vivo is unknown, hindering understanding of its functional role. Combining human magnetoencephalography (MEG), computational modeling, and laminar recordings in animals, we present a new theory that accounts for the origin of spontaneous neocortical beta. In our MEG data, spontaneous beta activity from somatosensory and frontal cortex emerged as noncontinuous beta events typically lasting <150 ms with a stereotypical waveform. Computational modeling uniquely designed to infer the electrical currents underlying these signals showed that beta events could emerge from the integration of nearly synchronous bursts of excitatory synaptic drive targeting proximal and distal dendrites of pyramidal neurons, where the defining feature of a beta event was a strong distal drive that lasted one beta period (∼50 ms). This beta mechanism rigorously accounted for the beta event profiles; several other mechanisms did not. The spatial location of synaptic drive in the model to supragranular and infragranular layers was critical to the emergence of beta events and led to the prediction that beta events should be associated with a specific laminar current profile. Laminar recordings in somatosensory neocortex from anesthetized mice and awake monkeys supported these predictions, suggesting this beta mechanism is conserved across species and recording modalities. These findings make several predictions about optimal states for perceptual and motor performance and guide causal interventions to modulate beta for optimal function. PMID:27469163

  2. Earthquake Early Warning Beta Users: Java, Modeling, and Mobile Apps

    NASA Astrophysics Data System (ADS)

    Strauss, J. A.; Vinci, M.; Steele, W. P.; Allen, R. M.; Hellweg, M.

    2014-12-01

    Earthquake Early Warning (EEW) is a system that can provide a few to tens of seconds warning prior to ground shaking at a user's location. The goal and purpose of such a system is to reduce, or minimize, the damage, costs, and casualties resulting from an earthquake. A demonstration earthquake early warning system (ShakeAlert) is undergoing testing in the United States by the UC Berkeley Seismological Laboratory, Caltech, ETH Zurich, University of Washington, the USGS, and beta users in California and the Pacific Northwest. The beta users receive earthquake information very rapidly in real-time and are providing feedback on their experiences of performance and potential uses within their organization. Beta user interactions allow the ShakeAlert team to discern: which alert delivery options are most effective, what changes would make the UserDisplay more useful in a pre-disaster situation, and most importantly, what actions users plan to take for various scenarios. Actions could include: personal safety approaches, such as drop cover, and hold on; automated processes and procedures, such as opening elevator or fire stations doors; or situational awareness. Users are beginning to determine which policy and technological changes may need to be enacted, and funding requirements to implement their automated controls. The use of models and mobile apps are beginning to augment the basic Java desktop applet. Modeling allows beta users to test their early warning responses against various scenarios without having to wait for a real event. Mobile apps are also changing the possible response landscape, providing other avenues for people to receive information. All of these combine to improve business continuity and resiliency.

  3. Generalized model of island biodiversity

    NASA Astrophysics Data System (ADS)

    Kessler, David A.; Shnerb, Nadav M.

    2015-04-01

    The dynamics of a local community of competing species with weak immigration from a static regional pool is studied. Implementing the generalized competitive Lotka-Volterra model with demographic noise, a rich dynamics with four qualitatively distinct phases is unfolded. When the overall interspecies competition is weak, the island species recapitulate the mainland species. For higher values of the competition parameter, the system still admits an equilibrium community, but now some of the mainland species are absent on the island. Further increase in competition leads to an intermittent "disordered" phase, where the dynamics is controlled by invadable combinations of species and the turnover rate is governed by the migration. Finally, the strong competition phase is glasslike, dominated by uninvadable states and noise-induced transitions. Our model contains, as a special case, the celebrated neutral island theories of Wilson-MacArthur and Hubbell. Moreover, we show that slight deviations from perfect neutrality may lead to each of the phases, as the Hubbell point appears to be quadracritical.

  4. Modeling the transmission of beta rays through thin foils in planar geometry.

    PubMed

    Stanga, D; De Felice, P; Keightley, J; Capogni, M; Ionescu, E

    2016-01-01

    This paper is concerned with the modeling of the transmission of beta rays through thin foils in planar geometry based on the plane source concept, using Monte Carlo simulation of electron transport and least squares fitting. Applications of modeling results for calculating the efficiency of large-area beta sources, transmission coefficient of beta rays through thin foils and the beta detection efficiency of large-area detectors used in surface contamination measurements are also presented.

  5. The nature and structure of correlations among Big Five ratings: the halo-alpha-beta model.

    PubMed

    Anusic, Ivana; Schimmack, Ulrich; Pinkus, Rebecca T; Lockwood, Penelope

    2009-12-01

    In light of consistently observed correlations among Big Five ratings, the authors developed and tested a model that combined E. L. Thorndike's (1920) general evaluative bias (halo) model and J. M. Digman's (1997) higher order personality factors (alpha and beta) model. With 4 multitrait-multimethod analyses, Study 1 revealed moderate convergent validity for alpha and beta across raters, whereas halo was mainly a unique factor for each rater. In Study 2, the authors showed that the halo factor was highly correlated with a validated measure of evaluative biases in self-ratings. Study 3 showed that halo is more strongly correlated with self-ratings of self-esteem than self-ratings of the Big Five, which suggests that halo is not a mere rating bias but actually reflects overly positive self-evaluations. Finally, Study 4 demonstrated that the halo bias in Big Five ratings is stable over short retest intervals. Taken together, the results suggest that the halo-alpha-beta model integrates the main findings in structural analyses of Big Five correlations. Accordingly, halo bias in self-ratings is a reliable and stable bias in individuals' perceptions of their own attributes. Implications of the present findings for the assessment of Big Five personality traits in monomethod studies are discussed.

  6. Generalized complex geometry, generalized branes and the Hitchin sigma model

    NASA Astrophysics Data System (ADS)

    Zucchini, Roberto

    2005-03-01

    Hitchin's generalized complex geometry has been shown to be relevant in compactifications of superstring theory with fluxes and is expected to lead to a deeper understanding of mirror symmetry. Gualtieri's notion of generalized complex submanifold seems to be a natural candidate for the description of branes in this context. Recently, we introduced a Batalin-Vilkovisky field theoretic realization of generalized complex geometry, the Hitchin sigma model, extending the well known Poisson sigma model. In this paper, exploiting Gualtieri's formalism, we incorporate branes into the model. A detailed study of the boundary conditions obeyed by the world sheet fields is provided. Finally, it is found that, when branes are present, the classical Batalin-Vilkovisky cohomology contains an extra sector that is related non trivially to a novel cohomology associated with the branes as generalized complex submanifolds.

  7. Protoplanetary Nebula Evolution using the Beta Viscosity Model

    NASA Technical Reports Server (NTRS)

    Davis, Sanford S.

    2003-01-01

    The evolutionary dynamics of a protoplanetary disk is an important component of the planet formation process. In particular, the dynamic and thermodynamic field plays a critical role in chemical evolution, the migration of dust particles in the nebula, and the radial transport of meteoritic components. The dynamic evolution is investigated using analytical solutions of the surface density transport equations using a turbulence model based on hydrodynamic generation of turbulence. It captures the major properties of the disk including region of separation between radial inflow and-outflow and the evolution of the central plane temperature. The analytical formulas are compared with available numerical solutions based on the alpha viscosity model. The beta viscosity model, heretofore used for steady-state disks, is shown to be a useful approximation for unsteady problems.

  8. A 3D structure model of integrin alpha 4 beta 1 complex: I. Construction of a homology model of beta 1 and ligand binding analysis.

    PubMed Central

    You, Tony J; Maxwell, David S; Kogan, Timothy P; Chen, Qi; Li, Jian; Kassir, Jamal; Holland, George W; Dixon, Richard A F

    2002-01-01

    It is well established that integrin alpha 4 beta 1 binds to the vascular cell adhesion molecule (VCAM) and fibronectin and plays an important role in signal transduction. Blocking the binding of VCAM to alpha 4 beta 1 is thought to be a way of controlling a number of disease processes. To better understand how various inhibitors might block the interaction of VCAM and fibronectin with alpha 4 beta 1, we began constructing a structure model for the integrin alpha 4 beta 1 complex. As the first step, we have built a homology model of the beta 1 subunit based on the I domain of the integrin CD11B subunit. The model, including a bound Mg(2+) ion, was optimized through a specially designed relaxation scheme involving restrained minimization and dynamics steps. The native ligand VCAM and two highly active small molecules (TBC772 and TBC3486) shown to inhibit binding of CS-1 and VCAM to alpha 4 beta 1 were docked into the active site of the refined model. Results from the binding analysis fit well with a pharmacophore model that was independently derived from active analog studies. A critical examination of residues in the binding site and analysis of docked ligands that are both potent and selective led to the proposal of a mechanism for beta 1/beta 7 ligand binding selectivity. PMID:11751331

  9. Neuroprotective effects of thymosin beta4 in experimental models of excitotoxicity.

    PubMed

    Popoli, Patrizia; Pepponi, Rita; Martire, Alberto; Armida, Monica; Pèzzola, Antonella; Galluzzo, Mariangela; Domenici, M Rosaria; Potenza, Rosa Luisa; Tebano, M Teresa; Mollinari, Cristiana; Merlo, Daniela; Garaci, Enrico

    2007-09-01

    The aim of this study was to evaluate the possible neuroprotective effects of thymosin beta(4) in different models of excitotoxicity. The application of thymosin beta(4) significantly attenuated glutamate-induced toxicity both in primary cultures of cortical neurons and in rat hippocampal slices. In in vivo experiments, the intracerebroventricular administration of thymosin beta(4) significantly reduced hippocampal neuronal loss induced by kainic acid. These results show that thymosin beta(4) induced a protective effect in models of excitotoxicity. The mechanisms underlying such an effect, as well as the real neuroprotective potential of thymosin beta(4), are worthy of further investigations.

  10. Generalized Environment for Modeling Systems

    SciTech Connect

    2012-02-07

    GEMS is an integrated environment that allows technical analysts, modelers, researchers, etc. to integrate and deploy models and/or decision tools with associated data to the internet for direct use by customers. GEMS does not require that the model developer know how to code or script and therefore delivers this capability to a large group of technical specialists. Customers gain the benefit of being able to execute their own scenarios directly without need for technical support. GEMS is a process that leverages commercial software products with specialized codes that add connectivity and unique functions to support the overall capability. Users integrate pre-existing models with a commercial product and store parameters and input trajectories in a companion commercial database. The model is then exposed into a commercial web environment and a graphical user interface (GUI) is applied by the model developer. Users execute the model through the web based GUI and GEMS manages supply of proper inputs, execution of models, routing of data to models and display of results back to users. GEMS works in layers, the following description is from the bottom up. Modelers create models in the modeling tool of their choice such as Excel, Matlab, or Fortran. They can also use models from a library of previously wrapped legacy codes (models). Modelers integrate the models (or a single model) by wrapping and connecting the models using the Phoenix Integration tool entitled ModelCenter. Using a ModelCenter/SAS plugin (DOE copyright CW-10-08) the modeler gets data from either an SAS or SQL database and sends results back to SAS or SQL. Once the model is working properly, the ModelCenter file is saved and stored in a folder location to which a SharePoint server tool created at INL is pointed. This enables the ModelCenter model to be run from SharePoint. The modeler then goes into Microsoft SharePoint and creates a graphical user interface (GUI) using the ModelCenter WebPart (CW-12

  11. Generalized exponential function and discrete growth models

    NASA Astrophysics Data System (ADS)

    Souto Martinez, Alexandre; Silva González, Rodrigo; Lauri Espíndola, Aquino

    2009-07-01

    Here we show that a particular one-parameter generalization of the exponential function is suitable to unify most of the popular one-species discrete population dynamic models into a simple formula. A physical interpretation is given to this new introduced parameter in the context of the continuous Richards model, which remains valid for the discrete case. From the discretization of the continuous Richards’ model (generalization of the Gompertz and Verhulst models), one obtains a generalized logistic map and we briefly study its properties. Notice, however that the physical interpretation for the introduced parameter persists valid for the discrete case. Next, we generalize the (scramble competition) θ-Ricker discrete model and analytically calculate the fixed points as well as their stabilities. In contrast to previous generalizations, from the generalized θ-Ricker model one is able to retrieve either scramble or contest models.

  12. General, stereoselective synthesis of (Z)-beta,gamma-unsaturated nitriles promoted by samarium diiodide.

    PubMed

    Concellón, José M; Rodríguez-Solla, Humberto; Simal, Carmen; Santos, David; Paz, Nieves R

    2008-10-16

    A method to obtain (Z)-beta,gamma-unsaturated nitriles in high or good yields and with moderate or high stereoselectivity is described. The products were achieved through the photoinduced metalation of 3-acetoxy-4-chloronitriles with SmI2. The starting compounds were readily prepared, and a mechanism is proposed to explain this stereoselective beta-elimination reaction.

  13. Inhomogeneous generalization of some Bianchi models

    NASA Astrophysics Data System (ADS)

    Carmeli, M.; Charach, Ch.

    1980-02-01

    Vacuum Bianchi models which can be transformed to the Einstein-Rosen metric are considered. The models are used in order to construct new inhomogeneous universes, which are generalizations of Bianchi cosmologies of types III, V and VIh. Recent generalizations of these Bianchi models, considered by Wainwright et al., are also discussed.

  14. LLNL Ocean General Circulation Model

    SciTech Connect

    Wickett, M. E.; Caldeira, K.; Duffy, P.

    2005-12-29

    The LLNL OGCM is a numerical ocean modeling tool for use in studying ocean circulation over a wide range of space and time scales, with primary applications to climate change and carbon cycle science.

  15. Theoretical Models of Generalized Quasispecies.

    PubMed

    Wagner, Nathaniel; Atsmon-Raz, Yoav; Ashkenasy, Gonen

    2016-01-01

    Theoretical modeling of quasispecies has progressed in several directions. In this chapter, we review the works of Emmanuel Tannenbaum, who, together with Eugene Shakhnovich at Harvard University and later with colleagues and students at Ben-Gurion University in Beersheva, implemented one of the more useful approaches, by progressively setting up various formulations for the quasispecies model and solving them analytically. Our review will focus on these papers that have explored new models, assumed the relevant mathematical approximations, and proceeded to analytically solve for the steady-state solutions and run stochastic simulations . When applicable, these models were related to real-life problems and situations, including changing environments, presence of chemical mutagens, evolution of cancer and tumor cells , mutations in Escherichia coli, stem cells , chromosomal instability (CIN), propagation of antibiotic drug resistance , dynamics of bacteria with plasmids , DNA proofreading mechanisms, and more.

  16. Trending in Probability of Collision Measurements via a Bayesian Zero-Inflated Beta Mixed Model

    NASA Technical Reports Server (NTRS)

    Vallejo, Jonathon; Hejduk, Matt; Stamey, James

    2015-01-01

    We investigate the performance of a generalized linear mixed model in predicting the Probabilities of Collision (Pc) for conjunction events. Specifically, we apply this model to the log(sub 10) transformation of these probabilities and argue that this transformation yields values that can be considered bounded in practice. Additionally, this bounded random variable, after scaling, is zero-inflated. Consequently, we model these values using the zero-inflated Beta distribution, and utilize the Bayesian paradigm and the mixed model framework to borrow information from past and current events. This provides a natural way to model the data and provides a basis for answering questions of interest, such as what is the likelihood of observing a probability of collision equal to the effective value of zero on a subsequent observation.

  17. General Pressurization Model in Simscape

    NASA Technical Reports Server (NTRS)

    Servin, Mario; Garcia, Vicky

    2010-01-01

    System integration is an essential part of the engineering design process. The Ares I Upper Stage (US) is a complex system which is made up of thousands of components assembled into subsystems including a J2-X engine, liquid hydrogen (LH2) and liquid oxygen (LO2) tanks, avionics, thrust vector control, motors, etc. System integration is the task of connecting together all of the subsystems into one large system. To ensure that all the components will "fit together" as well as safety and, quality, integration analysis is required. Integration analysis verifies that, as an integrated system, the system will behave as designed. Models that represent the actual subsystems are built for more comprehensive analysis. Matlab has been an instrument widely use by engineers to construct mathematical models of systems. Simulink, one of the tools offered by Matlab, provides multi-domain graphical environment to simulate and design time-varying systems. Simulink is a powerful tool to analyze the dynamic behavior of systems over time. Furthermore, Simscape, a tool provided by Simulink, allows users to model physical (such as mechanical, thermal and hydraulic) systems using physical networks. Using Simscape, a model representing an inflow of gas to a pressurized tank was created where the temperature and pressure of the tank are measured over time to show the behavior of the gas. By further incorporation of Simscape into model building, the full potential of this software can be discovered and it hopefully can become a more utilized tool.

  18. NASA Orbital Debris Engineering Model ORDEM2008 (Beta Version)

    NASA Technical Reports Server (NTRS)

    Stansbery, Eugene G.; Krisko, Paula H.

    2009-01-01

    This is an interim document intended to accompany the beta-release of the ORDEM2008 model. As such it provides the user with a guide for its use, a list of its capabilities, a brief summary of model development, and appendices included to educate the user as to typical runtimes for different orbit configurations. More detailed documentation will be delivered with the final product. ORDEM2008 supersedes NASA's previous model - ORDEM2000. The availability of new sensor and in situ data, the re-analysis of older data, and the development of new analytical techniques, has enabled the construction of this more comprehensive and sophisticated model. Integrated with the software is an upgraded graphical user interface (GUI), which uses project-oriented organization and provides the user with graphical representations of numerous output data products. These range from the conventional average debris size vs. flux magnitude for chosen analysis orbits, to the more complex color-contoured two-dimensional (2-D) directional flux diagrams in terms of local spacecraft pitch and yaw.

  19. Extended Generalized Linear Latent and Mixed Model

    ERIC Educational Resources Information Center

    Segawa, Eisuke; Emery, Sherry; Curry, Susan J.

    2008-01-01

    The generalized linear latent and mixed modeling (GLLAMM framework) includes many models such as hierarchical and structural equation models. However, GLLAMM cannot currently accommodate some models because it does not allow some parameters to be random. GLLAMM is extended to overcome the limitation by adding a submodel that specifies a…

  20. Classical integrability for beta-ensembles and general Fokker-Planck equations

    SciTech Connect

    Rumanov, Igor

    2015-01-15

    Beta-ensembles of random matrices are naturally considered as quantum integrable systems, in particular, due to their relation with conformal field theory, and more recently appeared connection with quantized Painlevé Hamiltonians. Here, we demonstrate that, at least for even integer beta, these systems are classically integrable, e.g., there are Lax pairs associated with them, which we explicitly construct. To come to the result, we show that a solution of every Fokker-Planck equation in one space (and one time) dimensions can be considered as a component of an eigenvector of a Lax pair. The explicit finding of the Lax pair depends on finding a solution of a governing system–a closed system of two nonlinear partial differential equations (PDEs) of hydrodynamic type. This result suggests that there must be a solution for all values of beta. We find the solution of this system for even integer beta in the particular case of quantum Painlevé II related to the soft edge of the spectrum for beta-ensembles. The solution is given in terms of Calogero system of β/2 particles in an additional time-dependent potential. Thus, we find another situation where quantum integrability is reduced to classical integrability.

  1. Three-dimensional MR mapping of angiogenesis with alpha5beta1(alpha nu beta3)-targeted theranostic nanoparticles in the MDA-MB-435 xenograft mouse model.

    PubMed

    Schmieder, Anne H; Caruthers, Shelton D; Zhang, Huiying; Williams, Todd A; Robertson, J David; Wickline, Samuel A; Lanza, Gregory M

    2008-12-01

    Our objectives were 1) to characterize angiogenesis in the MDA-MB-435 xenograft mouse model with three-dimensional (3D) MR molecular imaging using alpha(5)beta(1)(RGD)- or irrelevant RGS-targeted paramagnetic nanoparticles and 2) to use MR molecular imaging to assess the antiangiogenic effectiveness of alpha(5)beta(1)(alpha(nu)beta(3))- vs. alpha(nu)beta(3)-targeted fumagillin (50 mug/kg) nanoparticles. Tumor-bearing mice were imaged with MR before and after administration of either alpha(5)beta(1)(RGD) or irrelevant RGS-paramagnetic nanoparticles. In experiment 2, mice received saline or alpha(5)beta(1)(alpha(nu)beta(3))- or alpha(nu)beta(3)-targeted fumagillin nanoparticles on days 7, 11, 15, and 19 posttumor implant. On day 22, MRI was performed using alpha(5)beta(1)(alpha(nu)beta(3))-targeted paramagnetic nanoparticles to monitor the antiangiogenic response. 3D reconstructions of alpha(5)beta(1)(RGD)-signal enhancement revealed a sparse, asymmetrical pattern of angiogenesis along the tumor periphery, which occupied <2.0% tumor surface area. alpha(5)beta(1)-targeted rhodamine nanoparticles colocalized with FITC-lectin corroborated the peripheral neovascular signal. alpha(5)beta(1)(alpha(nu)beta(3))-fumagillin nanoparticles decreased neovasculature to negligible levels relative to control; alpha(nu)beta(3)-targeted fumagillin nanoparticles were less effective (P>0.05). Reduction of angiogenesis in MDA-MB-435 tumors from low to negligible levels did not decrease tumor volume. MR molecular imaging may be useful for characterizing tumors with sparse neovasculature that are unlikely to have a reduced growth response to targeted antiangiogenic therapy.

  2. A general consumer-resource population model

    USGS Publications Warehouse

    Lafferty, Kevin D.; DeLeo, Giulio; Briggs, Cheryl J.; Dobson, Andrew P.; Gross, Thilo; Kuris, Armand M.

    2015-01-01

    Food-web dynamics arise from predator-prey, parasite-host, and herbivore-plant interactions. Models for such interactions include up to three consumer activity states (questing, attacking, consuming) and up to four resource response states (susceptible, exposed, ingested, resistant). Articulating these states into a general model allows for dissecting, comparing, and deriving consumer-resource models. We specify this general model for 11 generic consumer strategies that group mathematically into predators, parasites, and micropredators and then derive conditions for consumer success, including a universal saturating functional response. We further show how to use this framework to create simple models with a common mathematical lineage and transparent assumptions. Underlying assumptions, missing elements, and composite parameters are revealed when classic consumer-resource models are derived from the general model.

  3. Conformity and Dissonance in Generalized Voter Models

    NASA Astrophysics Data System (ADS)

    Page, Scott E.; Sander, Leonard M.; Schneider-Mizell, Casey M.

    2007-09-01

    We generalize the voter model to include social forces that produce conformity among voters and avoidance of cognitive dissonance of opinions within a voter. The time for both conformity and consistency (which we call the exit time) is, in general, much longer than for either process alone. We show that our generalized model can be applied quite widely: it is a form of Wright's island model of population genetics, and is related to problems in the physical sciences. We give scaling arguments, numerical simulations, and analytic estimates for the exit time for a range of relative strengths in the tendency to conform and to avoid dissonance.

  4. A Bayesian beta distribution model for estimating rainfall IDF curves in a changing climate

    NASA Astrophysics Data System (ADS)

    Lima, Carlos H. R.; Kwon, Hyun-Han; Kim, Jin-Young

    2016-09-01

    The estimation of intensity-duration-frequency (IDF) curves for rainfall data comprises a classical task in hydrology studies to support a variety of water resources projects, including urban drainage and the design of flood control structures. In a changing climate, however, traditional approaches based on historical records of rainfall and on the stationary assumption can be inadequate and lead to poor estimates of rainfall intensity quantiles. Climate change scenarios built on General Circulation Models offer a way to access and estimate future changes in spatial and temporal rainfall patterns at the daily scale at the utmost, which is not as fine temporal resolution as required (e.g. hours) to directly estimate IDF curves. In this paper we propose a novel methodology based on a four-parameter beta distribution to estimate IDF curves conditioned on the observed (or simulated) daily rainfall, which becomes the time-varying upper bound of the updated nonstationary beta distribution. The inference is conducted in a Bayesian framework that provides a better way to take into account the uncertainty in the model parameters when building the IDF curves. The proposed model is tested using rainfall data from four stations located in South Korea and projected climate change Representative Concentration Pathways (RCPs) scenarios 6 and 8.5 from the Met Office Hadley Centre HadGEM3-RA model. The results show that the developed model fits the historical data as good as the traditional Generalized Extreme Value (GEV) distribution but is able to produce future IDF curves that significantly differ from the historically based IDF curves. The proposed model predicts for the stations and RCPs scenarios analysed in this work an increase in the intensity of extreme rainfalls of short duration with long return periods.

  5. Modeling the Production of Beta-Delayed Gamma Rays for the Detection of Special Nuclear Materials

    SciTech Connect

    Hall, J M; Pruet, J A; Brown, D A; Descalle, M; Hedstrom, G W; Prussin, S G

    2005-02-14

    The objective of this LDRD project was to develop one or more models for the production of {beta}-delayed {gamma} rays following neutron-induced fission of a special nuclear material (SNM) and to define a standardized formatting scheme which will allow them to be incorporated into some of the modern, general-purpose Monte Carlo transport codes currently being used to simulate inspection techniques proposed for detecting fissionable material hidden in sea-going cargo containers. In this report, we will describe a Monte Carlo model for {beta}-delayed {gamma}-ray emission following the fission of SNM that can accommodate arbitrary time-dependent fission rates and photon collection histories. The model involves direct sampling of the independent fission yield distributions of the system, the branching ratios for decay of individual fission products and spectral distributions representing photon emission from each fission product and for each decay mode. While computationally intensive, it will be shown that this model can provide reasonably detailed estimates of the spectra that would be recorded by an arbitrary spectrometer and may prove quite useful in assessing the quality of evaluated data libraries and identifying gaps in the libraries. The accuracy of the model will be illustrated by comparing calculated and experimental spectra from the decay of short-lived fission products following the reactions {sup 235}U(n{sub th}, f) and {sup 239}Pu(n{sub th}, f). For general-purpose transport calculations, where a detailed consideration of the large number of individual {gamma}-ray transitions in a spectrum may not be necessary, it will be shown that a simple parameterization of the {gamma}-ray source function can be defined which provides high-quality average spectral distributions that should suffice for calculations describing photons being transported through thick attenuating media. Finally, a proposal for ENDF-compatible formats that describe each of the models and

  6. Anisotropic Generalized Ghost Pilgrim Dark Energy Model in General Relativity

    NASA Astrophysics Data System (ADS)

    Santhi, M. Vijaya; Rao, V. U. M.; Aditya, Y.

    2017-02-01

    A spatially homogeneous and anisotropic locally rotationally symmetric (LRS) Bianchi type- I Universe filled with matter and generalized ghost pilgrim dark energy (GGPDE) has been studied in general theory of relativity. To obtain determinate solution of the field equations we have used scalar expansion proportional to the shear scalar which leads to a relation between the metric potentials. Some well-known cosmological parameters (equation of state (EoS) parameter ( ω Λ), deceleration parameter ( q) and squared speed of sound {vs2}) and planes (ω _{Λ }-dot {ω }_{Λ } and statefinder) are constructed for obtained model. The discussion and significance of these parameters is totally done through pilgrim dark energy parameter ( β) and cosmic time ( t).

  7. Building a generalized distributed system model

    NASA Technical Reports Server (NTRS)

    Mukkamala, Ravi

    1991-01-01

    A number of topics related to building a generalized distributed system model are discussed. The effects of distributed database modeling on evaluation of transaction rollbacks, the measurement of effects of distributed database models on transaction availability measures, and a performance analysis of static locking in replicated distributed database systems are covered.

  8. A General Model for Free Response Data

    ERIC Educational Resources Information Center

    Samejima, Fumiko

    1972-01-01

    This paper proposes a general model for free-response data collected for measuring a specified unidimensional psychological process; systematizes situations which vary with respect to the scoring level of items; and finds out general conditions for the operating characteristic of an item response category to provide a unique maximum likelihood…

  9. GENERALIZED VISCOPLASTIC MODELING OF DEBRIS FLOW.

    USGS Publications Warehouse

    Chen, Cheng-lung

    1988-01-01

    The earliest model developed by R. A. Bagnold was based on the concept of the 'dispersive' pressure generated by grain collisions. Some efforts have recently been made by theoreticians in non-Newtonian fluid mechanics to modify or improve Bagnold's concept or model. A viable rheological model should consist both of a rate-independent part and a rate-dependent part. A generalized viscoplastic fluid (GVF) model that has both parts as well as two major rheological properties (i. e. , the normal stress effect and soil yield criterion) is shown to be sufficiently accurate, yet practical for general use in debris-flow modeling. In fact, Bagnold's model is found to be only a particular case of the GVF model. analytical solutions for (steady) uniform debris flows in wide channels are obtained from the GVF model based on Bagnold's simplified assumption of constant grain concentration.

  10. Simple implementation of general dark energy models

    SciTech Connect

    Bloomfield, Jolyon K.; Pearson, Jonathan A. E-mail: jonathan.pearson@durham.ac.uk

    2014-03-01

    We present a formalism for the numerical implementation of general theories of dark energy, combining the computational simplicity of the equation of state for perturbations approach with the generality of the effective field theory approach. An effective fluid description is employed, based on a general action describing single-scalar field models. The formalism is developed from first principles, and constructed keeping the goal of a simple implementation into CAMB in mind. Benefits of this approach include its straightforward implementation, the generality of the underlying theory, the fact that the evolved variables are physical quantities, and that model-independent phenomenological descriptions may be straightforwardly investigated. We hope this formulation will provide a powerful tool for the comparison of theoretical models of dark energy with observational data.

  11. A probabilistic respiratory tract dosimetry model with application to beta-particle and photon emitters

    NASA Astrophysics Data System (ADS)

    Farfan, Eduardo Balderrama

    2002-01-01

    Predicting equivalent dose in the human respiratory tract is significant in the assessment of health risks associated with the inhalation of radioactive aerosols. A complete respiratory tract methodology based on the International Commission on Radiological Protection Publication 66 model was used in this research project for beta-particle and photon emitters. The conventional methodology has been to use standard values (from Reference Man) for parameters to obtain a single dose value. However, the methods used in the current study allow lung dose values to be determined as probability distributions to reflect the spread or variability in doses. To implement the methodology, a computer code, LUDUC, has been modified to include inhalation scenarios of beta-particle and photon emitters. For beta particles, a new methodology was implemented into Monte Carlo simulations to determine absorbed fractions in target tissues within the thoracic region of the respiratory tract. For photons, a new mathematical phantom of extrathoracic and thoracic regions was created based on previous studies to determine specific absorbed fractions in several tissues and organs of the human body due to inhalation of radioactive materials. The application of the methodology and developed data will be helpful in dose reconstruction and prediction efforts concerning the inhalation of short-lived radionuclides or radionuclides of Inhalation Class S. The resulting dose distributions follow a lognormal distribution shape for all scenarios examined. Applying the probabilistic computer code LUDUC to inhalation of strontium and yttrium aerosols has shown several trends, which could also be valid for many S radionuclide compounds that are beta-particle emitters. The equivalent doses are, in general, found to follow lognormal distributions. Therefore, these distributions can be described by geometric means and geometric standard deviations. Furthermore, a mathematical phantom of the extrathoracic and

  12. Bayesian inferences for beta semiparametric-mixed models to analyze longitudinal neuroimaging data.

    PubMed

    Wang, Xiao-Feng; Li, Yingxing

    2014-07-01

    Diffusion tensor imaging (DTI) is a quantitative magnetic resonance imaging technique that measures the three-dimensional diffusion of water molecules within tissue through the application of multiple diffusion gradients. This technique is rapidly increasing in popularity for studying white matter properties and structural connectivity in the living human brain. One of the major outcomes derived from the DTI process is known as fractional anisotropy, a continuous measure restricted on the interval (0,1). Motivated from a longitudinal DTI study of multiple sclerosis, we use a beta semiparametric-mixed regression model for the neuroimaging data. This work extends the generalized additive model methodology with beta distribution family and random effects. We describe two estimation methods with penalized splines, which are formalized under a Bayesian inferential perspective. The first one is carried out by Markov chain Monte Carlo (MCMC) simulations while the second one uses a relatively new technique called integrated nested Laplace approximation (INLA). Simulations and the neuroimaging data analysis show that the estimates obtained from both approaches are stable and similar, while the INLA method provides an efficient alternative to the computationally expensive MCMC method.

  13. Targeting of Beta Adrenergic Receptors Results in Therapeutic Efficacy against Models of Hemangioendothelioma and Angiosarcoma

    PubMed Central

    Stiles, Jessica M.; Amaya, Clarissa; Rains, Steven; Diaz, Dolores; Pham, Robert; Battiste, James; Modiano, Jaime F.; Kokta, Victor; Boucheron, Laura E.; Mitchell, Dianne C.; Bryan, Brad A.

    2013-01-01

    Therapeutic targeting of the beta-adrenergic receptors has recently shown remarkable efficacy in the treatment of benign vascular tumors such as infantile hemangiomas. As infantile hemangiomas are reported to express high levels of beta adrenergic receptors, we examined the expression of these receptors on more aggressive vascular tumors such as hemangioendotheliomas and angiosarcomas, revealing beta 1, 2, and 3 receptors were indeed present and therefore aggressive vascular tumors may similarly show increased susceptibility to the inhibitory effects of beta blockade. Using a panel of hemangioendothelioma and angiosarcoma cell lines, we demonstrate that beta adrenergic inhibition blocks cell proliferation and induces apoptosis in a dose dependent manner. Beta blockade is selective for vascular tumor cells over normal endothelial cells and synergistically effective when combined with standard chemotherapeutic or cytotoxic agents. We demonstrate that inhibition of beta adrenergic signaling induces large scale changes in the global gene expression patterns of vascular tumors, including alterations in the expression of established cell cycle and apoptotic regulators. Using in vivo tumor models we demonstrate that beta blockade shows remarkable efficacy as a single agent in reducing the growth of angiosarcoma tumors. In summary, these experiments demonstrate the selective cytotoxicity and tumor suppressive ability of beta adrenergic inhibition on malignant vascular tumors and have laid the groundwork for a promising treatment of angiosarcomas in humans. PMID:23555867

  14. A generalized model for coincidence counting

    SciTech Connect

    Lu, Ming-Shih; Teichmann, T.

    1993-12-31

    A generalized model for coincidence counting has been developed based on the dual probability generating function introduced. The model accounts explicitly and simultaneously the effects of multiplication, absorption by poison and instrument detection and is applicable for a wide class of NDA including Pu in waste.

  15. Modeling GABA Alterations in Schizophrenia: A Link Between Impaired Inhibition and Altered Gamma and Beta Range Auditory Entrainment

    PubMed Central

    Vierling-Claassen, Dorea; Siekmeier, Peter; Stufflebeam, Steven; Kopell, Nancy

    2009-01-01

    The disorganized symptoms of schizophrenia, including severely disordered thought patterns, may be indicative of a problem with the construction and maintenance of cell assemblies during sensory processing and attention. The gamma and beta frequency bands (15–70 Hz) are believed relevant to such processing. This paper addresses the results of an experimental examination of the cortical response of 12 schizophrenia patients and 12 control subjects when presented with auditory click-train stimuli in the gamma/beta frequency band during measurement using magnetoencephalography (MEG), as well as earlier work by Kwon et al. These data indicate that control subjects show an increased 40-Hz response to both 20- and 40-Hz stimulation as compared with patients, whereas schizophrenic subjects show a preference for 20-Hz response to the same driving frequencies. In this work, two computational models of the auditory cortex are constructed based on postmortem studies that indicate cortical interneurons in schizophrenic subjects have decreased GAT-1 (a GABA transporter) and GAD67 (1 of 2 enzymes responsible for GABA synthesis). The models transition from control to schizophrenic frequency response when an extended inhibitory decay time is introduced; this change captures a possible effect of these GABA alterations. Modeling gamma/beta range auditory entrainment in schizophrenia provides insight into how biophysical mechanisms can impact cognitive function. In addition, the study of dynamics that underlie auditory entrainment in schizophrenia may contribute to the understanding of how gamma and beta rhythms impact cognition in general. PMID:18287555

  16. Modeling GABA alterations in schizophrenia: a link between impaired inhibition and altered gamma and beta range auditory entrainment.

    PubMed

    Vierling-Claassen, Dorea; Siekmeier, Peter; Stufflebeam, Steven; Kopell, Nancy

    2008-05-01

    The disorganized symptoms of schizophrenia, including severely disordered thought patterns, may be indicative of a problem with the construction and maintenance of cell assemblies during sensory processing and attention. The gamma and beta frequency bands (15-70 Hz) are believed relevant to such processing. This paper addresses the results of an experimental examination of the cortical response of 12 schizophrenia patients and 12 control subjects when presented with auditory click-train stimuli in the gamma/beta frequency band during measurement using magnetoencephalography (MEG), as well as earlier work by Kwon et al. These data indicate that control subjects show an increased 40-Hz response to both 20- and 40-Hz stimulation as compared with patients, whereas schizophrenic subjects show a preference for 20-Hz response to the same driving frequencies. In this work, two computational models of the auditory cortex are constructed based on postmortem studies that indicate cortical interneurons in schizophrenic subjects have decreased GAT-1 (a GABA transporter) and GAD(67) (1 of 2 enzymes responsible for GABA synthesis). The models transition from control to schizophrenic frequency response when an extended inhibitory decay time is introduced; this change captures a possible effect of these GABA alterations. Modeling gamma/beta range auditory entrainment in schizophrenia provides insight into how biophysical mechanisms can impact cognitive function. In addition, the study of dynamics that underlie auditory entrainment in schizophrenia may contribute to the understanding of how gamma and beta rhythms impact cognition in general.

  17. Generalized force model of traffic dynamics

    NASA Astrophysics Data System (ADS)

    Helbing, Dirk; Tilch, Benno

    1998-07-01

    Floating car data of car-following behavior in cities were compared to existing microsimulation models, after their parameters had been calibrated to the experimental data. With these parameter values, additional simulations have been carried out, e.g., of a moving car which approaches a stopped car. It turned out that, in order to manage such kinds of situations without producing accidents, improved traffic models are needed. Good results were obtained with the proposed generalized force model.

  18. Semi-Parametric Generalized Linear Models.

    DTIC Science & Technology

    1985-08-01

    is nonsingular, upper triangular, and of full rank r. It is known (Dongarra et al., 1979) that G-1 FT is the Moore - Penrose inverse of L . Therefore... GENERALIZED LINEAR pq Mathematics Research Center University of Wisconsin-Madison 610 Walnut Street Madison, Wisconsin 53705 TI C August 1985 E T NOV 7 8...North Carolina 27709 -. -.. . - -.-. g / 6 O5’o UNIVERSITY OF WISCONSIN-MADISON MATHD4ATICS RESEARCH CENTER SD4I-PARAMETRIC GENERALIZED LINEAR MODELS

  19. A Tailored Testing Model Employing the Beta Distribution and Conditional Difficulties

    ERIC Educational Resources Information Center

    Kalisch, Stanley J.

    1974-01-01

    A tailored testing model employing the beta distribution, whose mean equals the difficulty of an item and whose variance is approximately equal to the sampling variance of the item difficulty, and employing conditional item difficulties, is proposed. (Author)

  20. Nonlinear enhancement of oxygen evolution in thylakoid membranes: modeling the effect of light intensity and beta-cyclodextrin concentration.

    PubMed

    Fragata, Mário; Dudekula, Subhan

    2005-08-04

    Electron transport through photosystem II, measured as oxygen evolution (OE), was investigated in isolated thylakoid membranes treated with beta-cyclodextrin (beta-CD, a cyclic oligosaccharide constituted of seven alpha-d-glucose residues linked by alpha-1,4 glycosidic bonds) and irradiated with white light of variable intensity. First, we found that the light-response curves of oxygen evolution are well fitted with a hyperbolic function, the shape of which is not affected by the beta-CD concentration. Second, we showed that under conditions of irradiation with white light of saturating intensity ( approximately 5000 mumol of photons/m(2).s) beta-CD enhances the oxygen evolution in the thylakoid membranes according to a sigmoid function displaying a sharp inflection point, or transition. Unexpectedely, this beta-CD effect is not observed at irradiances of less than approximately 300 mumol of photons/m(2).s. We attempted a theoretical analysis of the combined effect of irradiance and beta-CD concentration on oxygen evolution (OE(th)). For this purpose, the effect of irradiance (I) was modeled with a hyperbola (i) and the beta-CD concentration (C) contribution with a Hill equation, that is, a sigmoid function (ii). The mathematical simulations generated the following general expressions: (i) OE(th) = [OE(max)(0) G(1)(C)]I/[L(1/2)(0) G(2)(C) + I] and (ii) G(i)()(C) = 1 + p[C(n)()/(K(1/2)(n)() + C(n)())], where OE(max)(0) is the OE maximum (OE(max)) in the absence of beta-CD, L(1/2)(0) is the photon flux density giving OE(max)/2 in the absence of beta-CD, G(1)(C) or G(2)(C) is obtained from G(i)()(C) where i is 1 or 2, n is the Hill coefficient, p is a parameter to account for the beta-CD-mediated maximum OE increase, and K(1/2) is the beta-CD concentration giving half-maximal OE activity. The results of the calculations yielded the expression (iii) OE(th) = 151[1 + 3.3C(4.8)/(13.1(4.8) + C(4.8))]I/{97.5[1 + 5.2C(7.8)/(14.8(7.8) + C(7.8))] + I} which agrees well with

  1. General Equilibrium Models: Improving the Microeconomics Classroom

    ERIC Educational Resources Information Center

    Nicholson, Walter; Westhoff, Frank

    2009-01-01

    General equilibrium models now play important roles in many fields of economics including tax policy, environmental regulation, international trade, and economic development. The intermediate microeconomics classroom has not kept pace with these trends, however. Microeconomics textbooks primarily focus on the insights that can be drawn from the…

  2. Space Station Freedom Beta Gimbal Control via Sensitivity Models

    NASA Technical Reports Server (NTRS)

    Schoenwald, David A.; Ozguner, Umit; Graham, Ronald E.

    1993-01-01

    Tracking control of the Space Station Freedom solar array beta gimbals is investigated. Of particular interest is the issue of control in the presence of uncertainty in gimbal friction parameters. Sensitivity functions are incorporated into the feedback loop to desensitize the gimbal control law to parameter variations. Simulation results indicated that one such sensitivity function improves the closed-loop performance of the gimbals in the presence of unexpected friction parameter dispersions.

  3. The effects of interferon-alpha/beta in a model of rat heart transplantation

    NASA Technical Reports Server (NTRS)

    Slater, A. D.; Klein, J. B.; Sonnenfeld, G.; Ogden, L. L. 2nd; Gray, L. A. Jr

    1992-01-01

    Interferons have multiple immunologic effects. One such effect is the activation of expression of cell surface antigens. Interferon alpha/beta enhance expression of class I but not class II histocompatibility antigens. Contradictory information has been published regarding the effect of interferon-alpha/beta administration in patients with kidney transplantation. In a model of rat heart transplantation we demonstrated that administration of interferon-alpha/beta accelerated rejection in a dose-dependent fashion in the absence of maintenance cyclosporine. Animals treated with maintenance cyclosporine had evidence of increased rejection at 20 days that was resolved completely at 45 days with cyclosporine alone.

  4. A realistic model of neutrino masses with a large neutrinoless double beta decay rate

    NASA Astrophysics Data System (ADS)

    del Aguila, Francisco; Aparici, Alberto; Bhattacharya, Subhaditya; Santamaria, Arcadi; Wudka, Jose

    2012-05-01

    The minimal Standard Model extension with the Weinberg operator does accommodate the observed neutrino masses and mixing, but predicts a neutrinoless double beta (0 νββ) decay rate proportional to the effective electron neutrino mass, which can be then arbitrarily small within present experimental limits. However, in general 0 νββ decay can have an independent origin and be near its present experimental bound; whereas neutrino masses are generated radiatively, contributing negligibly to 0 νββ decay. We provide a realization of this scenario in a simple, well defined and testable model, with potential LHC effects and calculable neutrino masses, whose two-loop expression we derive exactly. We also discuss the connection of this model to others that have appeared in the literature, and remark on the significant differences that result from various choices of quantum number assignments and symmetry assumptions. In this type of models lepton flavor violating rates are also preferred to be relatively large, at the reach of foreseen experiments. Interestingly enough, in our model this stands for a large third mixing angle, {{si}}{{{n}}^{{2}}}{θ_{{{13}}}}{˜}}}{ > }}0.00{8} , when μ→ eee is required to lie below its present experimental limit.

  5. BetaMol: A Molecular Modeling, Analysis and Visualization Software Based on the Beta-Complex and the Quasi-Triangulation

    NASA Astrophysics Data System (ADS)

    Cho, Youngsong; Kim, Jae-Kwan; Ryu, Joonghyun; Won, Chung-In; Kim, Chong-Min; Kim, Donguk; Kim, Deok-Soo

    Molecular shape is one of the most critical factors that determines molecular function. Therefore, it is frequently desirable to understand geometric characteristics of a molecule more precisely and efficiently. In this paper, we introduce the BetaMol, a molecular modeling, analysis, and visualization software based on the recent theory of the beta-complex and the quasi-triangulation that are derived from the Voronoi diagram of three-dimensional spherical atoms. The powerful features of the BetaMol are solely based on a unified, single framework of the mathematically rigorous and computationally efficient beta-complex theory. The BetaMol is implemented in the standard C++ language with OpenGL graphics library and freely available at Voronoi Diagram Research Center web site (http://voronoi.hanyang.ac.kr).

  6. Neutrinoless double beta decay in the left-right symmetric models for linear seesaw

    NASA Astrophysics Data System (ADS)

    Gu, Pei-Hong

    2016-09-01

    In a class of left-right symmetric models for linear seesaw, a neutrinoless double beta decay induced by the left- and right-handed charged currents together will only depend on the breaking details of left-right and electroweak symmetries. This neutrinoless double beta decay can reach the experimental sensitivities if the right-handed charged gauge boson is below the 100TeV scale.

  7. The ToI-beta transgenic mouse: a model to study the specific role of NF-kappaB in beta-cells.

    PubMed

    Eldor, Roy; Baum, Ketty; Abel, Roy; Sever, Dror; Melloul, Danielle

    2009-12-01

    Type 1 diabetes is characterized by the infiltration of inflammatory cells into pancreatic islets of Langerhans, followed by the selective and progressive destruction of insulin-secreting beta-cells. Islet infiltrating leukocytes secrete cytokines including IL-1beta and IFN-gamma, which contribute to beta-cell death. In vitro evidence suggests that cytokine-induced activation of the transcription factor NF-kappaB is an important component of the signal triggering beta-cell apoptosis. To study the role of NF-kappaB in vivo we generated a transgenic mouse line expressing a degradation-resistant NF-kappaB protein inhibitor (DeltaNIkappaBalpha) and the luciferase gene, acting specifically in beta-cells, in an inducible and reversible manner, by using the tet-on regulation system. Using this new mouse model, termed the ToI-beta mouse (for Tet-Ondelta I kappaB in beta-cells) we have previously shown in vitro, that islets expressing the DeltaNIkappaBalpha protein were resistant to the deleterious effects of IL-1beta and IFN-gamma, as assessed by reduced NO production and beta-cell apoptosis. In vivo, a nearly complete protection against multiple low dose streptozocin-induced diabetes was observed, with reduced intra-islet lymphocytic infiltration. In the present study we demonstrate the tight regulated and reversible expression of the DeltaNIkappaBalpha transgene in the ToI-beta mouse model as well as the effect of its overexpression on glucose metabolism and insulin secretion. The results show a lack of effect of transgene induction on both in vivo glucose tolerance tests and in vitro islet insulin secretion and content. Furthermore, to prove the tight control of induction in the model, luciferase mediated light emission was only detected at constant levels in Dox-treated double transgenic mice or islets as well as in a model of islet transplantation. Upon removal of the inducing stimulus, complete reversal of both NF-kappaB inhibition and luciferase activity were

  8. Higher dimensional generalizations of the SYK model

    NASA Astrophysics Data System (ADS)

    Berkooz, Micha; Narayan, Prithvi; Rozali, Moshe; Simón, Joan

    2017-01-01

    We discuss a 1+1 dimensional generalization of the Sachdev-Ye-Kitaev model. The model contains N Majorana fermions at each lattice site with a nearest-neighbour hopping term. The SYK random interaction is restricted to low momentum fermions of definite chirality within each lattice site. This gives rise to an ordinary 1+1 field theory above some energy scale and a low energy SYK-like behavior. We exhibit a class of low-pass filters which give rise to a rich variety of hyperscaling behaviour in the IR. We also discuss another set of generalizations which describes probing an SYK system with an external fermion, together with the new scaling behavior they exhibit in the IR.

  9. Beta-cryptoxanthin from citrus juices: assessment of bioaccessibility using an in vitro digestion/Caco-2 cell culture model.

    PubMed

    Dhuique-Mayer, Claudie; Borel, Patrick; Reboul, Emmanuelle; Caporiccio, Bertrand; Besancon, Pierre; Amiot, Marie-Josèphe

    2007-05-01

    Beta-Cryptoxanthin (beta-CX), a provitaminic carotenoid of potential interest for health, is found principally in Citrus fruit in both free and esterified forms. Little is known about the intestinal absorption of beta-CX especially with regard to the esterified forms. The aim of this study was to evaluate the absorption of free and esterified beta-CX using simulated digestion coupled with the Caco-2 model. Bioaccessibility was investigated by measuring the transfer of carotenoids from different citrus juices into micelles using an in vitro digestion system. Then, carotenoid uptake was evaluated by adding carotenoid-rich micelles (from the in vitro digestion) or synthetic micelles (made from synthetic lipids and carotenoids purified from citrus juice) to human intestinal cells (Caco-2 TC7 clone). Our results showed that beta-cryptoxanthin esters (beta-CXE) were partially hydrolysed during the in vitro digestion. The bioaccessibility of free beta-CX measured was significantly higher (40 (SD 1.05) %) than that of beta-carotene (30 (SD 1.9) %) and beta-CXE (16 (SD 1.5) %). In the same way, the incorporation of free beta-CX (27 (SD 1.01) %) into synthetic micelles exceeded (P<0.05) that of beta-carotene (10 (SD 0.7) %) and beta-CXE (8.8 (SD 0.4) %). In the case of micelles from in vitro digestion, the uptake of beta-carotene, free beta-CX and beta-CXE forms by Caco-2 cells was 14.3 (SD 1.8), 3.9 (SD 1.3), and 0.7 (SD 0.08) % respectively. These results showed a preferential uptake by Caco-2 cells of beta-carotene and free beta-CX compared with the two esters of beta-CX.

  10. Two Simple Classes of Mastery Scores Based On the Beta-Binomial Model

    ERIC Educational Resources Information Center

    Huynh, Huynh

    1977-01-01

    A model for the setting of mastery cut scores is presented. The model, based on the beta-binomial test distribution, allows for hand calculation of cut scores. The model provides a simple way to explore the consequences of selecting a particular cut score. (Author/JKS)

  11. A General Business Model for Marine Reserves

    PubMed Central

    Sala, Enric; Costello, Christopher; Dougherty, Dawn; Heal, Geoffrey; Kelleher, Kieran; Murray, Jason H.; Rosenberg, Andrew A.; Sumaila, Rashid

    2013-01-01

    Marine reserves are an effective tool for protecting biodiversity locally, with potential economic benefits including enhancement of local fisheries, increased tourism, and maintenance of ecosystem services. However, fishing communities often fear short-term income losses associated with closures, and thus may oppose marine reserves. Here we review empirical data and develop bioeconomic models to show that the value of marine reserves (enhanced adjacent fishing + tourism) may often exceed the pre-reserve value, and that economic benefits can offset the costs in as little as five years. These results suggest the need for a new business model for creating and managing reserves, which could pay for themselves and turn a profit for stakeholder groups. Our model could be expanded to include ecosystem services and other benefits, and it provides a general framework to estimate costs and benefits of reserves and to develop such business models. PMID:23573192

  12. A general business model for marine reserves.

    PubMed

    Sala, Enric; Costello, Christopher; Dougherty, Dawn; Heal, Geoffrey; Kelleher, Kieran; Murray, Jason H; Rosenberg, Andrew A; Sumaila, Rashid

    2013-01-01

    Marine reserves are an effective tool for protecting biodiversity locally, with potential economic benefits including enhancement of local fisheries, increased tourism, and maintenance of ecosystem services. However, fishing communities often fear short-term income losses associated with closures, and thus may oppose marine reserves. Here we review empirical data and develop bioeconomic models to show that the value of marine reserves (enhanced adjacent fishing + tourism) may often exceed the pre-reserve value, and that economic benefits can offset the costs in as little as five years. These results suggest the need for a new business model for creating and managing reserves, which could pay for themselves and turn a profit for stakeholder groups. Our model could be expanded to include ecosystem services and other benefits, and it provides a general framework to estimate costs and benefits of reserves and to develop such business models.

  13. Effects of concomitant use of fibroblast growth factor (FGF)-2 with beta-tricalcium phosphate ({beta}-TCP) on the beagle dog 1-wall periodontal defect model

    SciTech Connect

    Anzai, Jun; Kitamura, Masahiro; Nozaki, Takenori; Nagayasu, Toshie; Terashima, Akio; Asano, Taiji; Murakami, Shinya

    2010-12-17

    Research highlights: {yields} Concomitant use of FGF-2 and {beta}-TCP (an osteo-conductive scaffold) significantly promotes periodontal regeneration in the severe periodontitis model (1-wall defect model) of beagle dog. {yields} FGF-2 enhanced new bone formation via {beta}-TCP at the defects. {yields} In particular, FGF-2 dramatically regenerated new periodontal ligament and cementum formations at the defects, that is one of the most important healing outcomes during the process of periodontal regeneration. {yields} Epithelial downgrowth (undesirable wound healing) was decreased by administration of FGF-2. {yields} This manuscript indicates for the first time that concomitant use of FGF-2 and {beta}-TCP is efficacious in regenerating periodontal tissue following severe destruction of the tissue by progression of periodontitis. -- Abstract: The effects of concomitant use of fibroblast growth factor-2 (FGF-2) and beta-tricalcium phosphate ({beta}-TCP) on periodontal regeneration were investigated in the beagle dog 1-wall periodontal defect model. One-wall periodontal defects were created in the mesial portion of both sides of the mandibular first molars, and 0.3% FGF-2 plus {beta}-TCP or {beta}-TCP alone was administered. Radiographic evaluation was performed at 0, 3, and 6 weeks. At 6 weeks, the periodontium with the defect site was removed and histologically analyzed. Radiographic findings showed that co-administration of FGF-2 significantly increased bone mineral contents of the defect sites compared with {beta}-TCP alone. Histologic analysis revealed that the length of the regenerated periodontal ligament, the cementum, distance to the junctional epithelium, new bone height, and area of newly formed bone were significantly increased in the FGF-2 group. No abnormal inflammatory response or ankylosis was observed in either group. These findings indicate the efficacy of concomitant use of FGF-2 and {beta}-TCP as an osteoconductive material for periodontal

  14. Computational Models Describing Possible Mechanisms for Generation of Excessive Beta Oscillations in Parkinson’s Disease

    PubMed Central

    Pavlides, Alex; Hogan, S. John; Bogacz, Rafal

    2015-01-01

    In Parkinson’s disease, an increase in beta oscillations within the basal ganglia nuclei has been shown to be associated with difficulty in movement initiation. An important role in the generation of these oscillations is thought to be played by the motor cortex and by a network composed of the subthalamic nucleus (STN) and the external segment of globus pallidus (GPe). Several alternative models have been proposed to describe the mechanisms for generation of the Parkinsonian beta oscillations. However, a recent experimental study of Tachibana and colleagues yielded results which are challenging for all published computational models of beta generation. That study investigated how the presence of beta oscillations in a primate model of Parkinson’s disease is affected by blocking different connections of the STN-GPe circuit. Due to a large number of experimental conditions, the study provides strong constraints that any mechanistic model of beta generation should satisfy. In this paper we present two models consistent with the data of Tachibana et al. The first model assumes that Parkinsonian beta oscillation are generated in the cortex and the STN-GPe circuits resonates at this frequency. The second model additionally assumes that the feedback from STN-GPe circuit to cortex is important for maintaining the oscillations in the network. Predictions are made about experimental evidence that is required to differentiate between the two models, both of which are able to reproduce firing rates, oscillation frequency and effects of lesions carried out by Tachibana and colleagues. Furthermore, an analysis of the models reveals how the amplitude and frequency of the generated oscillations depend on parameters. PMID:26683341

  15. Matrix elements for the ground-state to ground-state 2{nu}{beta}{sup -}{beta}{sup -} decay of Te isotopes in a hybrid model

    SciTech Connect

    Bes, D. R.; Civitarese, O.

    2010-01-15

    Theoretical matrix elements, for the ground-state to ground-state two-neutrino double-{beta}-decay mode (2{nu}{beta}{sup -}{beta}{sup -}gs->gs) of {sup 128,130}Te isotopes, are calculated within a formalism that describes interactions between neutrons in a superfluid phase and protons in a normal phase. The elementary degrees of freedom of the model are proton-pair modes and pairs of protons and quasineutrons. The calculation is basically a parameter-free one, because all relevant parameters are fixed from the phenomenology. A comparison with the available experimental data is presented.

  16. Formulation and Application of the Generalized Multilevel Facets Model

    ERIC Educational Resources Information Center

    Wang, Wen-Chung; Liu, Chih-Yu

    2007-01-01

    In this study, the authors develop a generalized multilevel facets model, which is not only a multilevel and two-parameter generalization of the facets model, but also a multilevel and facet generalization of the generalized partial credit model. Because the new model is formulated within a framework of nonlinear mixed models, no efforts are…

  17. 75 FR 41104 - Airworthiness Directives; Robinson Helicopter Company (Robinson) Model R22, R22 Alpha, R22 Beta...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-15

    ... Company (Robinson) Model R22, R22 Alpha, R22 Beta, and R22 Mariner Helicopters, and Model R44, and R44 II...). SUMMARY: This document proposes adopting a new airworthiness directive (AD) for Robinson Model R22, R22 Alpha, R22 Beta, and R22 Mariner helicopters, and Model R44 and R44 II helicopters. The AD would...

  18. Neutrinoless Double Beta Nuclear Matrix Elements Around Mass 80 in the Nuclear Shell Model

    NASA Astrophysics Data System (ADS)

    Yoshinaga, Naotaka; Higashiyama, Koji; Taguchi, Daisuke; Teruya, Eri

    The observation of the neutrinoless double-beta decay can determine whether the neutrino is a Majorana particle or not. In its theoretical nuclear side it is particularly important to estimate three types of nuclear matrix elements, namely, Fermi (F), Gamow-Teller (GT), and tensor (T) types matrix elements. The shell model calculations and also the pair-truncated shell model calculations are carried out to check the model dependence on nuclear matrix elements. In this work the neutrinoless double-beta decay for mass A = 82 nuclei is studied. It is found that the matrix elements are quite sensitive to the ground state wavefunctions.

  19. Generalized model of brushless dc generator

    NASA Astrophysics Data System (ADS)

    Vadher, V. V.; Kettleborough, J. Gordon; Smith, I. R.; Gerges, Wahid R.

    1989-07-01

    A generalized model is described for a brushless dc machine consisting of a multiphase synchronous machine with a full-wave bridge rectifier connected to its output terminals. The state-variable equations for the machine are suitable for numerical integration on a digital computer, and are assembled in a form which permits investigations to be made on the effects of different numbers of armature phase windings and different winding connections. The model has been used in both steady-state and transient studies on a number of generating units, with the detailed information which is provided being beneficial to design engineers. Comparisons presented between predicted and measured results illustrate the validity of the model and the mathematical techniques adopted, and confirm that accurate information on the performance of a brushless generator may be obtained prior to manufacture.

  20. Core histone hyperacetylation co-maps with generalized DNase I sensitivity in the chicken beta-globin chromosomal domain.

    PubMed Central

    Hebbes, T R; Clayton, A L; Thorne, A W; Crane-Robinson, C

    1994-01-01

    The distribution of core histone acetylation across the chicken beta-globin locus has been mapped in 15 day chicken embryo erythrocytes by immunoprecipitation of mononucleosomes with an antibody recognizing acetylated histones, followed by hybridization probing at several points in the locus. A continuum of acetylation was observed, covering both genes and intergenic regions. Using the same probes, the generalized sensitivity to DNase I was mapped by monitoring the disappearance of intact genomic restriction fragments from Southern transfers. Close correspondence between the 33 kb of sensitive chromatin and the extent of acetylation indicates that one role of the modification could be the generation and/or maintenance of the open conformation. The precision of acetylation mapping makes it a possible approach to the definition of chromosomal domain boundaries. Images PMID:8168481

  1. On improvements of Double Beta Decay using FQTDA Model

    NASA Astrophysics Data System (ADS)

    de Oliveira, L.; Samana, A. R.; Krmpotic, F.; Mariano, A. E.; Barbero, C. A.

    2015-07-01

    The Quasiparticle Tamm-Dancoff Approximation (QTDA) is applied to describe the nuclear double beta decay with two neutrinos. Several serious inconveniences found in the Quasiparticle Random Phase Approximation (QRPA) are not present in the QTDA, as such as the ambiguity in treating the intermediary states, and further approximations necessary for evaluation of the nuclear matrix elements (NMEs) or, the extreme sensitivity of NME with the ratio between the pn and pp + nn pairings. Some years ago, the decay 48Ca → 48Ti was discussed within the particle-hole limit of QTDA. We found some mismatch in the numerical calculations when the full QTDA was being implemented, and a new performance in the particle-hole limit of QTDA is required to guarantee the fidelity of the approximation.

  2. Generalized model of the microwave auditory effect

    NASA Astrophysics Data System (ADS)

    Yitzhak, N. M.; Ruppin, R.; Hareuveny, R.

    2009-07-01

    A generalized theoretical model for evaluating the amplitudes of the sound waves generated in a spherical head model, which is irradiated by microwave pulses, is developed. The thermoelastic equation of motion is solved for a spherically symmetric heating pattern of arbitrary form. For previously treated heating patterns that are peaked at the sphere centre, the results reduce to those presented before. The generalized model is applied to the case in which the microwave absorption is concentrated near the sphere surface. It is found that, for equal average specific absorption rates, the sound intensity generated by a surface localized heating pattern is comparable to that generated by a heating pattern that is peaked at the centre. The dependence of the induced sound pressure on the shape of the microwave pulse is explored. Another theoretical extension, to the case of repeated pulses, is developed and applied to the interpretation of existing experimental data on the dependence of the human hearing effect threshold on the pulse repetition frequency.

  3. Generalized model of the microwave auditory effect.

    PubMed

    Yitzhak, N M; Ruppin, R; Hareuveny, R

    2009-07-07

    A generalized theoretical model for evaluating the amplitudes of the sound waves generated in a spherical head model, which is irradiated by microwave pulses, is developed. The thermoelastic equation of motion is solved for a spherically symmetric heating pattern of arbitrary form. For previously treated heating patterns that are peaked at the sphere centre, the results reduce to those presented before. The generalized model is applied to the case in which the microwave absorption is concentrated near the sphere surface. It is found that, for equal average specific absorption rates, the sound intensity generated by a surface localized heating pattern is comparable to that generated by a heating pattern that is peaked at the centre. The dependence of the induced sound pressure on the shape of the microwave pulse is explored. Another theoretical extension, to the case of repeated pulses, is developed and applied to the interpretation of existing experimental data on the dependence of the human hearing effect threshold on the pulse repetition frequency.

  4. The Application of Global Kinetic Models to HMX Beta-Delta Transition and Cookoff Processes

    SciTech Connect

    Wemhoff, A P; Burnham, A K; Nichols III, A L

    2006-12-07

    The reduction of the number of reactions in kinetic models for both the HMX beta-delta phase transition and thermal cookoff provides an attractive alternative to traditional multi-stage kinetic models due to reduced calibration effort requirements. In this study, we use the LLNL code ALE3D to provide calibrated kinetic parameters for a two-reaction bidirectional beta-delta HMX phase transition model based on Sandia Instrumented Thermal Ignition (SITI) and Scaled Thermal Explosion (STEX) temperature history curves, and a Prout-Tompkins cookoff model based on One-Dimensional Time to Explosion (ODTX) data. Results show that the two-reaction bidirectional beta-delta transition model presented here agrees as well with STEX and SITI temperature history curves as a reversible four-reaction Arrhenius model, yet requires an order of magnitude less computational effort. In addition, a single-reaction Prout-Tompkins model calibrated to ODTX data provides better agreement with ODTX data than a traditional multi-step Arrhenius model, and can contain up to 90% less chemistry-limited time steps for low-temperature ODTX simulations. Manual calibration methods for the Prout-Tompkins kinetics provide much better agreement with ODTX experimental data than parameters derived from Differential Scanning Calorimetry (DSC) measurements at atmospheric pressure. The predicted surface temperature at explosion for STEX cookoff simulations is a weak function of the cookoff model used, and a reduction of up to 15% of chemistry-limited time steps can be achieved by neglecting the beta-delta transition for this type of simulation. Finally, the inclusion of the beta-delta transition model in the overall kinetics model can affect the predicted time to explosion by 1% for the traditional multi-step Arrhenius approach, while up to 11% using a Prout-Tompkins cookoff model.

  5. Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps.

    PubMed

    Si, Dong; He, Jing

    2017-01-01

    Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Although α-helices can be detected from density maps at 5-8 Å resolutions, β-strands are challenging to detect at such density maps due to close-spacing of β-strands. The variety of shapes of β-sheets adds the complexity of β-strands detection from density maps. We propose a new approach to model traces of β-strands for β-barrel density regions that are extracted from cryo-EM density maps. In the test containing eight β-barrels extracted from experimental cryo-EM density maps at 5.5 Å-8.25 Å resolution, StrandRoller detected about 74.26% of the amino acids in the β-strands with an overall 2.05 Å 2-way distance between the detected β-traces and the observed ones, if the best of the fifteen detection cases is considered.

  6. Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps

    PubMed Central

    Si, Dong

    2017-01-01

    Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Although α-helices can be detected from density maps at 5–8 Å resolutions, β-strands are challenging to detect at such density maps due to close-spacing of β-strands. The variety of shapes of β-sheets adds the complexity of β-strands detection from density maps. We propose a new approach to model traces of β-strands for β-barrel density regions that are extracted from cryo-EM density maps. In the test containing eight β-barrels extracted from experimental cryo-EM density maps at 5.5 Å–8.25 Å resolution, StrandRoller detected about 74.26% of the amino acids in the β-strands with an overall 2.05 Å 2-way distance between the detected β-traces and the observed ones, if the best of the fifteen detection cases is considered. PMID:28164115

  7. A Tailored Testing Model Employing the Beta Distribution and Conditional Difficulties.

    ERIC Educational Resources Information Center

    Kalisch, Stanley J.

    A tailored testing model employing the beta distribution, whose mean equals the difficulty of an item and whose variance is approximately equal to the sampling variance of the item difficulty, and employing conditional item difficulties, is proposed. The model provides a procedure by which a minimum number of items of a test, consisting of a set…

  8. General Model for Multicomponent Ablation Thermochemistry

    NASA Technical Reports Server (NTRS)

    Milos, Frank S.; Marschall, Jochen; Rasky, Daniel J. (Technical Monitor)

    1994-01-01

    A previous paper (AIAA 94-2042) presented equations and numerical procedures for modeling the thermochemical ablation and pyrolysis of thermal protection materials which contain multiple surface species. This work describes modifications and enhancements to the Multicomponent Ablation Thermochemistry (MAT) theory and code for application to the general case which includes surface area constraints, rate limited surface reactions, and non-thermochemical mass loss (failure). Detailed results and comparisons with data are presented for the Shuttle Orbiter reinforced carbon-carbon oxidation protection system which contains a mixture of sodium silicate (Na2SiO3), silica (SiO2), silicon carbide (SiC), and carbon (C).

  9. Generalized Drift-Diffusion Model In Semiconductors

    SciTech Connect

    Mesbah, S.; Bendib-Kalache, K.; Bendib, A.

    2008-09-23

    A new drift-diffusion model is proposed based on the computation of the stationary nonlocal current density. The semi classical Boltzmann equation is solved keeping all the anisotropies of the distribution function with the use of the continued fractions. The conductivity is calculated in the linear approximation and for arbitrary collision frequency with respect to Kv{sub t} where K{sup -1} is the characteristic length scale of the system and V{sub t} is the thermal velocity. The nonlocal conductivity can be used to close the generalized drift-diffusion equations valid for arbitrary collisionality.

  10. Snow hydrology in a general circulation model

    NASA Technical Reports Server (NTRS)

    Marshall, Susan; Roads, John O.; Glatzmaier, Gary

    1994-01-01

    A snow hydrology has been implemented in an atmospheric general circulation model (GCM). The snow hydrology consists of parameterizations of snowfall and snow cover fraction, a prognostic calculation of snow temperature, and a model of the snow mass and hydrologic budgets. Previously, only snow albedo had been included by a specified snow line. A 3-year GCM simulation with this now more complete surface hydrology is compared to a previous GCM control run with the specified snow line, as well as with observations. In particular, the authors discuss comparisons of the atmospheric and surface hydrologic budgets and the surface energy budget for U.S. and Canadian areas. The new snow hydrology changes the annual cycle of the surface moisture and energy budgets in the model. There is a noticeable shift in the runoff maximum from winter in the control run to spring in the snow hydrology run. A substantial amount of GCM winter precipitation is now stored in the seasonal snowpack. Snow cover also acts as an important insulating layer between the atmosphere and the ground. Wintertime soil temperatures are much higher in the snow hydrology experiment than in the control experiment. Seasonal snow cover is important for dampening large fluctuations in GCM continental skin temperature during the Northern Hemisphere winter. Snow depths and snow extent show good agreement with observations over North America. The geographic distribution of maximum depths is not as well simulated by the model due, in part, to the coarse resolution of the model. The patterns of runoff are qualitatively and quantitatively similar to observed patterns of streamflow averaged over the continental United States. The seasonal cycles of precipitation and evaporation are also reasonably well simulated by the model, although their magnitudes are larger than is observed. This is due, in part, to a cold bias in this model, which results in a dry model atmosphere and enhances the hydrologic cycle everywhere.

  11. Snow hydrology in a general circulation model

    SciTech Connect

    Marshall, S. ); Roads, J.O. ); Glatzmaier, G. )

    1994-08-01

    A snow hydrology has been implemented in an atmospheric general circulation model (GCM). The snow hydrology consists of parameterizations of snowfall and snow cover fraction, a prognostic calculation of snow temperature, and a model of the snow mass and hydrologic budgets. Previously, only snow albedo had been included. A 3-year GCM simulation with this more complete surface hydrology is compared to a previous GCM control run with the specified snow line, as well as with observations. In particular, the authors discuss comparisons of the atmospheric and surface hydrologic budgets and the surface energy budget for U.S. and Canadian areas. The new snow hydrology changes the annual cycle of the surface moisture and energy budgets in the model. There is a noticeable shift in the runoff maximum from winter in the control run to spring in the snow hydrology run. A substantial amount of GCM winter precipitation is now stored in the seasonal snowpack. Snow cover also acts as an important insulating layer between the atmosphere and the ground. Wintertime soil temperatures are much higher in the snow, hydrology experiment than in the control experiment. Seasonal snow cover is important for dampening large fluctuations in GCM continental skin temperature during the Northern Hemisphere winter. Snow depths and snow extent show good agreement with observations over North America. The geographic distribution of maximum depths is not as well simulated by the model due, in part, to the coarse resolution of the model. The patterns of runoff are qualitatively and quantitatively similar to observed patterns of streamflow averaged over the continental United States. The seasonal cycles of precipitation and evaporation are also reasonably well simulated by the model, although their magnitudes are larger than is observed. This is due, in part, to a cold bias in this model, which results in a dry model atmosphere and enhances the hydrologic cycle everywhere. 52 refs., 13 figs., 5 tabs.

  12. The Generalized Quantum Episodic Memory Model.

    PubMed

    Trueblood, Jennifer S; Hemmer, Pernille

    2016-12-21

    Recent evidence suggests that experienced events are often mapped to too many episodic states, including those that are logically or experimentally incompatible with one another. For example, episodic over-distribution patterns show that the probability of accepting an item under different mutually exclusive conditions violates the disjunction rule. A related example, called subadditivity, occurs when the probability of accepting an item under mutually exclusive and exhaustive instruction conditions sums to a number >1. Both the over-distribution effect and subadditivity have been widely observed in item and source-memory paradigms. These phenomena are difficult to explain using standard memory frameworks, such as signal-detection theory. A dual-trace model called the over-distribution (OD) model (Brainerd & Reyna, 2008) can explain the episodic over-distribution effect, but not subadditivity. Our goal is to develop a model that can explain both effects. In this paper, we propose the Generalized Quantum Episodic Memory (GQEM) model, which extends the Quantum Episodic Memory (QEM) model developed by Brainerd, Wang, and Reyna (2013). We test GQEM by comparing it to the OD model using data from a novel item-memory experiment and a previously published source-memory experiment (Kellen, Singmann, & Klauer, 2014) examining the over-distribution effect. Using the best-fit parameters from the over-distribution experiments, we conclude by showing that the GQEM model can also account for subadditivity. Overall these results add to a growing body of evidence suggesting that quantum probability theory is a valuable tool in modeling recognition memory.

  13. A More General, Quasineutral Plasma Model

    NASA Astrophysics Data System (ADS)

    Fernsler, Richard

    2003-10-01

    More than seventy-five years ago, Irving Langmuir proposed a quasineutral plasma model still widely used today. The electrostatic field is derived from the electron density using the Boltzmann approximation, while the electron density is obtained from the ion densities using quasineutrality. However, the Boltzmann approximation is not always valid and has no relationship to quasineutrality. Moreover, the solutions thus obtained are usually singular near the ion sound speed, thus necessitating an additional boundary condition known as the Bohm condition. This condition is difficult to use when multiple ion species are present, is ill posed in kinetic treatments, and does not always apply. In this talk, a more general quasineutral model is presented to circumvent these limitations.

  14. Generalized mathematical models in design optimization

    NASA Technical Reports Server (NTRS)

    Papalambros, Panos Y.; Rao, J. R. Jagannatha

    1989-01-01

    The theory of optimality conditions of extremal problems can be extended to problems continuously deformed by an input vector. The connection between the sensitivity, well-posedness, stability and approximation of optimization problems is steadily emerging. The authors believe that the important realization here is that the underlying basis of all such work is still the study of point-to-set maps and of small perturbations, yet what has been identified previously as being just related to solution procedures is now being extended to study modeling itself in its own right. Many important studies related to the theoretical issues of parametric programming and large deformation in nonlinear programming have been reported in the last few years, and the challenge now seems to be in devising effective computational tools for solving these generalized design optimization models.

  15. Conserved Current for General Teleparallel Models

    NASA Astrophysics Data System (ADS)

    Itin, Y.

    The obstruction for the existence of an energy-momentum tensor for the gravitational field in GR is connected with vanishing of first order invariants in (pseudo) Riemannian geometry. This specific geometric property is not valid in alternative geometrical structures1,2. A parallelizable differentiable 4D-manifold endowed with a class of smooth coframe fields ϑa is considered. A general 3-parameter class of global Lorentz invariant teleparallel models is considered. It includes a 1-parameter subclass of models with the Schwarzschild coframe solution (generalized teleparallel equivalent of gravity) 3. By introducing the notion of a 3-parameter conjugate field strength F linear in the strength Ca = dϑa the coframe Lagrangian is rewritten in the Maxwell-Yang-Mills form L = 1/2Fa ∧ Ca. The field equation turns out to have a form d * Fa = Ta completely similar to the Maxwell field equation. By applying the Noether procedure, the source 3-form Ta is shown to be connected with the diffeomorphism invariance of the Lagrangian. Thus the source Ta of the coframe field is interpreted as the total conserved energy-momentum current of the coframe field and matter4. The energy-momentum tensor is defined as a map of the module of current 3-forms into the module of vector fields 5. Thus an energy-momentum tensor for the coframe is defined in a diffeomorphism invariant and a translational covariant way. The total energy-momentum current of a system is conserved. Thus a redistribution of the energy-momentum current between material and coframe (gravity) field is possible in principle, unlike as in the standard GR. The result is: The standard GR has a neighborhood of viable models with the same Schwarzschild solutions. These models however have a better Lagrangian behavior and produce an invariant energy-momentum tensor.

  16. Numerical modeling of large-area beta sources constructed from anodized-aluminum foils.

    PubMed

    Stanga, D

    2012-09-01

    The numerical modeling of large-area beta sources constructed from anodized-aluminum foils is described in this paper. Based on a realistic model for the activity depth distribution, theoretical lower and upper bounds for the efficiency and the transmission coefficient were calculated and used to analyze the comparison method recommended by ISO 8769 for measuring the surface emission rate. The analysis shows that this method can provide measurement results with relative standard uncertainties smaller than 3% for high energy beta emitters such as (90)Sr-(90)Y, (36)Cl and (204)Tl.

  17. A Synthetic Model of Human Beta-Thalassemia Erythropoiesis Using CD34+ Cells from Healthy Adult Donors

    PubMed Central

    Byrnes, Colleen; de Vasconcellos, Jaira F.; Noh, Seung-Jae; Rabel, Antoinette; Meier, Emily R.; Miller, Jeffery L.

    2013-01-01

    Based upon the lack of clinical samples available for research in many laboratories worldwide, a significant gap exists between basic and clinical studies of beta-thalassemia major. To bridge this gap, we developed an artificially engineered model for human beta thalassemia by knocking down beta-globin gene and protein expression in cultured CD34+ cells obtained from healthy adults. Lentiviral-mediated transduction of beta-globin shRNA (beta-KD) caused imbalanced globin chain production. Beta-globin mRNA was reduced by 90% compared to controls, while alpha-globin mRNA levels were maintained. HPLC analyses revealed a 96% reduction in HbA with only a minor increase in HbF. During the terminal phases of differentiation (culture days 14–21), beta-KD cells demonstrated increased levels of insoluble alpha-globin, as well as activated caspase-3. The majority of the beta-KD cells underwent apoptosis around the polychromatophilic stage of maturation. GDF15, a marker of ineffective erythropoiesis in humans with thalassemia, was significantly increased in the culture supernatants from the beta-KD cells. Knockdown of beta-globin expression in cultured primary human erythroblasts provides a robust ex vivo model for beta-thalassemia. PMID:23861885

  18. A neural mass model of basal ganglia nuclei simulates pathological beta rhythm in Parkinson's disease

    NASA Astrophysics Data System (ADS)

    Liu, Fei; Wang, Jiang; Liu, Chen; Li, Huiyan; Deng, Bin; Fietkiewicz, Chris; Loparo, Kenneth A.

    2016-12-01

    An increase in beta oscillations within the basal ganglia nuclei has been shown to be associated with movement disorder, such as Parkinson's disease. The motor cortex and an excitatory-inhibitory neuronal network composed of the subthalamic nucleus (STN) and the external globus pallidus (GPe) are thought to play an important role in the generation of these oscillations. In this paper, we propose a neuron mass model of the basal ganglia on the population level that reproduces the Parkinsonian oscillations in a reciprocal excitatory-inhibitory network. Moreover, it is shown that the generation and frequency of these pathological beta oscillations are varied by the coupling strength and the intrinsic characteristics of the basal ganglia. Simulation results reveal that increase of the coupling strength induces the generation of the beta oscillation, as well as enhances the oscillation frequency. However, for the intrinsic properties of each nucleus in the excitatory-inhibitory network, the STN primarily influences the generation of the beta oscillation while the GPe mainly determines its frequency. Interestingly, describing function analysis applied on this model theoretically explains the mechanism of pathological beta oscillations.

  19. Effects of beta-adrenoceptor drug stimulation on various models of gastric ulcer in rats.

    PubMed Central

    Esplugues, J.; Lloris, J. M.; Martí-Bonmatí, E.; Morcillo, E. J.

    1982-01-01

    1. Experiments were designed to evaluate the effect of the pharmacological activation of beta-adrenoceptors on various models of gastric ulcer in the rat. 2. Pretreatment with the beta-adrenoceptor stimulant drugs, isoprenaline or salbutamol, significantly inhibited stress-induced gastric ulcers. This anti-ulcer effect was abolished by propranolol but not by atenolol, suggesting that beta 2-adrenoceptors mediate this response. 3. In the pylorus-ligation model, salbutamol inhibited lesion formation and reduced the intragastric content of hydrogen ions, histamine and pepsin although the latter was only affected with the higher dose of salbutamol. 4. Salbutamol also prevented the ulcerogenic action on the gastric mucosa of an exogenously perfused artificial gastric juice, showing that the anti-ulcer effect is not necessarily dependent on acid inhibition. 5. Salbutamol also reduced the formation of acute ulcers induced by various iatrogenic means (histamine, polymyxin B, reserpine and indomethacin). 6. Long-term treatment with salbutamol accelerated the healing of experimental chronic gastric ulcer. 7. In anaesthetized rats, salbutamol produced a dose-related increase in mucosal blood flow which may contribute to its mode of action. 8. It is concluded that beta-adrenoceptor agonists exert preventive and curative effects on gastric damage induced in the rat. This effect seems specific and mediated through beta-adrenoceptor activation. PMID:6125225

  20. Pharmacodynamic models of various beta blockers: an explanation for the long duration of action of bopindolol.

    PubMed

    Grevel, J

    1986-01-01

    Models describing the time course of effects (pharmacodynamic models) of various beta blockers in man are used to explain the long duration of action of bopindolol. No matter what effect is used [reduction in exercise heart rate (RER) or isoproterenol dose ratio (DR)] human data show clearly that bopindolol is very potent compared to other beta blockers such as atenolol, metoprolol, pindolol, practolol, and propranolol. In pharmacokinetic terms, however, these drugs show no pronounced difference in their elimination half-life (ranging between 4 and 8 h). Also the site of action of the therapeutic effects (beta 1 receptors) is obviously identical for all beta blockers. Furthermore, there is no evidence to suggest that bopindolol (the prodrug) or hydrolyzed bopindolol (the active substance) is further metabolized to a slowly eliminated active metabolite. Thus, drug disposition provides no argument to explain the long-lasting effects of bopindolol as compared other beta blockers. The long duration of action of bopindolol seems to reflect an usually flat plasma concentration-response curve.

  1. Evaluating the double Poisson generalized linear model.

    PubMed

    Zou, Yaotian; Geedipally, Srinivas Reddy; Lord, Dominique

    2013-10-01

    The objectives of this study are to: (1) examine the applicability of the double Poisson (DP) generalized linear model (GLM) for analyzing motor vehicle crash data characterized by over- and under-dispersion and (2) compare the performance of the DP GLM with the Conway-Maxwell-Poisson (COM-Poisson) GLM in terms of goodness-of-fit and theoretical soundness. The DP distribution has seldom been investigated and applied since its first introduction two decades ago. The hurdle for applying the DP is related to its normalizing constant (or multiplicative constant) which is not available in closed form. This study proposed a new method to approximate the normalizing constant of the DP with high accuracy and reliability. The DP GLM and COM-Poisson GLM were developed using two observed over-dispersed datasets and one observed under-dispersed dataset. The modeling results indicate that the DP GLM with its normalizing constant approximated by the new method can handle crash data characterized by over- and under-dispersion. Its performance is comparable to the COM-Poisson GLM in terms of goodness-of-fit (GOF), although COM-Poisson GLM provides a slightly better fit. For the over-dispersed data, the DP GLM performs similar to the NB GLM. Considering the fact that the DP GLM can be easily estimated with inexpensive computation and that it is simpler to interpret coefficients, it offers a flexible and efficient alternative for researchers to model count data.

  2. GPU Developments for General Circulation Models

    NASA Astrophysics Data System (ADS)

    Appleyard, Jeremy; Posey, Stan; Ponder, Carl; Eaton, Joe

    2014-05-01

    Current trends in high performance computing (HPC) are moving towards the use of graphics processing units (GPUs) to achieve speedups through the extraction of fine-grain parallelism of application software. GPUs have been developed exclusively for computational tasks as massively-parallel co-processors to the CPU, and during 2013 an extensive set of new HPC architectural features were developed in a 4th generation of NVIDIA GPUs that provide further opportunities for GPU acceleration of general circulation models used in climate science and numerical weather prediction. Today computational efficiency and simulation turnaround time continue to be important factors behind scientific decisions to develop models at higher resolutions and deploy increased use of ensembles. This presentation will examine the current state of GPU parallel developments for stencil based numerical operations typical of dynamical cores, and introduce new GPU-based implicit iterative schemes with GPU parallel preconditioning and linear solvers based on ILU, Krylov methods, and multigrid. Several GCMs show substantial gain in parallel efficiency from second-level fine-grain parallelism under first-level distributed memory parallel through a hybrid parallel implementation. Examples are provided relevant to science-scale HPC practice of CPU-GPU system configurations based on model resolution requirements of a particular simulation. Performance results compare use of the latest conventional CPUs with and without GPU acceleration. Finally a forward looking discussion is provided on the roadmap of GPU hardware, software, tools, and programmability for GCM development.

  3. A Simple General Model of Evolutionary Dynamics

    NASA Astrophysics Data System (ADS)

    Thurner, Stefan

    Evolution is a process in which some variations that emerge within a population (of, e.g., biological species or industrial goods) get selected, survive, and proliferate, whereas others vanish. Survival probability, proliferation, or production rates are associated with the "fitness" of a particular variation. We argue that the notion of fitness is an a posteriori concept in the sense that one can assign higher fitness to species or goods that survive but one can generally not derive or predict fitness per se. Whereas proliferation rates can be measured, fitness landscapes, that is, the inter-dependence of proliferation rates, cannot. For this reason we think that in a physical theory of evolution such notions should be avoided. Here we review a recent quantitative formulation of evolutionary dynamics that provides a framework for the co-evolution of species and their fitness landscapes (Thurner et al., 2010, Physica A 389, 747; Thurner et al., 2010, New J. Phys. 12, 075029; Klimek et al., 2009, Phys. Rev. E 82, 011901 (2010). The corresponding model leads to a generic evolutionary dynamics characterized by phases of relative stability in terms of diversity, followed by phases of massive restructuring. These dynamical modes can be interpreted as punctuated equilibria in biology, or Schumpeterian business cycles (Schumpeter, 1939, Business Cycles, McGraw-Hill, London) in economics. We show that phase transitions that separate phases of high and low diversity can be approximated surprisingly well by mean-field methods. We demonstrate that the mathematical framework is suited to understand systemic properties of evolutionary systems, such as their proneness to collapse, or their potential for diversification. The framework suggests that evolutionary processes are naturally linked to self-organized criticality and to properties of production matrices, such as their eigenvalue spectra. Even though the model is phrased in general terms it is also practical in the sense

  4. Neutrinoless double beta nuclear matrix elements around mass 80 in the nuclear shell-model

    NASA Astrophysics Data System (ADS)

    Yoshinaga, N.; Higashiyama, K.; Taguchi, D.; Teruya, E.

    2015-05-01

    The observation of the neutrinoless double-beta decay can determine whether the neutrino is a Majorana particle or not. For theoretical nuclear physics it is particularly important to estimate three types of matrix elements, namely Fermi (F), Gamow-Teller (GT), and tensor (T) matrix elements. In this paper, we carry out shell-model calculations and also pair-truncated shell-model calculations to check the model dependence in the case of mass A=82 nuclei.

  5. Study on the C-terminal beta-hairpin of protein G in AB heteropolymer model

    NASA Astrophysics Data System (ADS)

    Kim, Seung-Yeon

    2016-08-01

    The off-lattice AB heteropolymer model, consisting of the hydrophobic (A) and hydrophilic (B) polymers, is one of popular protein models. Its energy function includes the bending energy and the van der Waals interaction energy. The properties and the energy landscape of the C-terminal beta-hairpin of protein G are studied in the off-lattice AB heteropolymer model with conformational space annealing, a powerful global optimization method.

  6. Boosted Beta Regression

    PubMed Central

    Schmid, Matthias; Wickler, Florian; Maloney, Kelly O.; Mitchell, Richard; Fenske, Nora; Mayr, Andreas

    2013-01-01

    Regression analysis with a bounded outcome is a common problem in applied statistics. Typical examples include regression models for percentage outcomes and the analysis of ratings that are measured on a bounded scale. In this paper, we consider beta regression, which is a generalization of logit models to situations where the response is continuous on the interval (0,1). Consequently, beta regression is a convenient tool for analyzing percentage responses. The classical approach to fit a beta regression model is to use maximum likelihood estimation with subsequent AIC-based variable selection. As an alternative to this established - yet unstable - approach, we propose a new estimation technique called boosted beta regression. With boosted beta regression estimation and variable selection can be carried out simultaneously in a highly efficient way. Additionally, both the mean and the variance of a percentage response can be modeled using flexible nonlinear covariate effects. As a consequence, the new method accounts for common problems such as overdispersion and non-binomial variance structures. PMID:23626706

  7. Modeling of turbulent supersonic H2-air combustion with a multivariate beta PDF

    NASA Technical Reports Server (NTRS)

    Baurle, R. A.; Hassan, H. A.

    1993-01-01

    Recent calculations of turbulent supersonic reacting shear flows using an assumed multivariate beta PDF (probability density function) resulted in reduced production rates and a delay in the onset of combustion. This result is not consistent with available measurements. The present research explores two possible reasons for this behavior: use of PDF's that do not yield Favre averaged quantities, and the gradient diffusion assumption. A new multivariate beta PDF involving species densities is introduced which makes it possible to compute Favre averaged mass fractions. However, using this PDF did not improve comparisons with experiment. A countergradient diffusion model is then introduced. Preliminary calculations suggest this to be the cause of the discrepancy.

  8. Entropy maximization under the constraints on the generalized Gini index and its application in modeling income distributions

    NASA Astrophysics Data System (ADS)

    Khosravi Tanak, A.; Mohtashami Borzadaran, G. R.; Ahmadi, J.

    2015-11-01

    In economics and social sciences, the inequality measures such as Gini index, Pietra index etc., are commonly used to measure the statistical dispersion. There is a generalization of Gini index which includes it as special case. In this paper, we use principle of maximum entropy to approximate the model of income distribution with a given mean and generalized Gini index. Many distributions have been used as descriptive models for the distribution of income. The most widely known of these models are the generalized beta of second kind and its subclass distributions. The obtained maximum entropy distributions are fitted to the US family total money income in 2009, 2011 and 2013 and their relative performances with respect to generalized beta of second kind family are compared.

  9. General approach for the stereocontrolled construction of the beta-lactam ring in amino acid-derived 4-alkyl-4-carboxy-2-azetidinones.

    PubMed

    Gerona-Navarro, Guillermo; García-López, M Teresa; González-Muñiz, Rosario

    2002-05-31

    The first general approach toward the asymmetric synthesis of 4-alkyl-4-carboxy-2-azetidinones derived from amino acids is described. The stereoselective construction of the beta-lactam ring was achieved through base-mediated intramolecular cyclization of the corresponding N(alpha)-chloroacetyl derivatives bearing (+)- or (-)-10-(N,N-dicyclohexylsulfamoyl)isoborneol as chiral auxiliary (ee up to 82%).

  10. General single phase wellbore flow model

    SciTech Connect

    Ouyang, Liang-Biao; Arbabi, S.; Aziz, K.

    1997-02-05

    A general wellbore flow model, which incorporates not only frictional, accelerational and gravitational pressure drops, but also the pressure drop caused by inflow, is presented in this report. The new wellbore model is readily applicable to any wellbore perforation patterns and well completions, and can be easily incorporated in reservoir simulators or analytical reservoir inflow models. Three dimensionless numbers, the accelerational to frictional pressure gradient ratio R{sub af}, the gravitational to frictional pressure gradient ratio R{sub gf}, and the inflow-directional to accelerational pressure gradient ratio R{sub da}, have been introduced to quantitatively describe the relative importance of different pressure gradient components. For fluid flow in a production well, it is expected that there may exist up to three different regions of the wellbore: the laminar flow region, the partially-developed turbulent flow region, and the fully-developed turbulent flow region. The laminar flow region is located near the well toe, the partially-turbulent flow region lies in the middle of the wellbore, while the fully-developed turbulent flow region is at the downstream end or the heel of the wellbore. Length of each region depends on fluid properties, wellbore geometry and flow rate. As the distance from the well toe increases, flow rate in the wellbore increases and the ratios R{sub af} and R{sub da} decrease. Consequently accelerational and inflow-directional pressure drops have the greatest impact in the toe region of the wellbore. Near the well heel the local wellbore flow rate becomes large and close to the total well production rate, here R{sub af} and R{sub da} are small, therefore, both the accelerational and inflow-directional pressure drops can be neglected.

  11. Generalized Reduced Order Modeling of Aeroservoelastic Systems

    NASA Astrophysics Data System (ADS)

    Gariffo, James Michael

    Transonic aeroelastic and aeroservoelastic (ASE) modeling presents a significant technical and computational challenge. Flow fields with a mixture of subsonic and supersonic flow, as well as moving shock waves, can only be captured through high-fidelity CFD analysis. With modern computing power, it is realtively straightforward to determine the flutter boundary for a single structural configuration at a single flight condition, but problems of larger scope remain quite costly. Some such problems include characterizing a vehicle's flutter boundary over its full flight envelope, optimizing its structural weight subject to aeroelastic constraints, and designing control laws for flutter suppression. For all of these applications, reduced-order models (ROMs) offer substantial computational savings. ROM techniques in general have existed for decades, and the methodology presented in this dissertation builds on successful previous techniques to create a powerful new scheme for modeling aeroelastic systems, and predicting and interpolating their transonic flutter boundaries. In this method, linear ASE state-space models are constructed from modal structural and actuator models coupled to state-space models of the linearized aerodynamic forces through feedback loops. Flutter predictions can be made from these models through simple eigenvalue analysis of their state-transition matrices for an appropriate set of dynamic pressures. Moreover, this analysis returns the frequency and damping trend of every aeroelastic branch. In contrast, determining the critical dynamic pressure by direct time-marching CFD requires a separate run for every dynamic pressure being analyzed simply to obtain the trend for the critical branch. The present ROM methodology also includes a new model interpolation technique that greatly enhances the benefits of these ROMs. This enables predictions of the dynamic behavior of the system for flight conditions where CFD analysis has not been explicitly

  12. Transferability of regional permafrost disturbance susceptibility modelling using generalized linear and generalized additive models

    NASA Astrophysics Data System (ADS)

    Rudy, Ashley C. A.; Lamoureux, Scott F.; Treitz, Paul; van Ewijk, Karin Y.

    2016-07-01

    To effectively assess and mitigate risk of permafrost disturbance, disturbance-prone areas can be predicted through the application of susceptibility models. In this study we developed regional susceptibility models for permafrost disturbances using a field disturbance inventory to test the transferability of the model to a broader region in the Canadian High Arctic. Resulting maps of susceptibility were then used to explore the effect of terrain variables on the occurrence of disturbances within this region. To account for a large range of landscape characteristics, the model was calibrated using two locations: Sabine Peninsula, Melville Island, NU, and Fosheim Peninsula, Ellesmere Island, NU. Spatial patterns of disturbance were predicted with a generalized linear model (GLM) and generalized additive model (GAM), each calibrated using disturbed and randomized undisturbed locations from both locations and GIS-derived terrain predictor variables including slope, potential incoming solar radiation, wetness index, topographic position index, elevation, and distance to water. Each model was validated for the Sabine and Fosheim Peninsulas using independent data sets while the transferability of the model to an independent site was assessed at Cape Bounty, Melville Island, NU. The regional GLM and GAM validated well for both calibration sites (Sabine and Fosheim) with the area under the receiver operating curves (AUROC) > 0.79. Both models were applied directly to Cape Bounty without calibration and validated equally with AUROC's of 0.76; however, each model predicted disturbed and undisturbed samples differently. Additionally, the sensitivity of the transferred model was assessed using data sets with different sample sizes. Results indicated that models based on larger sample sizes transferred more consistently and captured the variability within the terrain attributes in the respective study areas. Terrain attributes associated with the initiation of disturbances were

  13. Permutation inference for the general linear model

    PubMed Central

    Winkler, Anderson M.; Ridgway, Gerard R.; Webster, Matthew A.; Smith, Stephen M.; Nichols, Thomas E.

    2014-01-01

    Permutation methods can provide exact control of false positives and allow the use of non-standard statistics, making only weak assumptions about the data. With the availability of fast and inexpensive computing, their main limitation would be some lack of flexibility to work with arbitrary experimental designs. In this paper we report on results on approximate permutation methods that are more flexible with respect to the experimental design and nuisance variables, and conduct detailed simulations to identify the best method for settings that are typical for imaging research scenarios. We present a generic framework for permutation inference for complex general linear models (glms) when the errors are exchangeable and/or have a symmetric distribution, and show that, even in the presence of nuisance effects, these permutation inferences are powerful while providing excellent control of false positives in a wide range of common and relevant imaging research scenarios. We also demonstrate how the inference on glm parameters, originally intended for independent data, can be used in certain special but useful cases in which independence is violated. Detailed examples of common neuroimaging applications are provided, as well as a complete algorithm – the “randomise” algorithm – for permutation inference with the glm. PMID:24530839

  14. Appropriate model selection methods for nonstationary generalized extreme value models

    NASA Astrophysics Data System (ADS)

    Kim, Hanbeen; Kim, Sooyoung; Shin, Hongjoon; Heo, Jun-Haeng

    2017-04-01

    Several evidences of hydrologic data series being nonstationary in nature have been found to date. This has resulted in the conduct of many studies in the area of nonstationary frequency analysis. Nonstationary probability distribution models involve parameters that vary over time. Therefore, it is not a straightforward process to apply conventional goodness-of-fit tests to the selection of an appropriate nonstationary probability distribution model. Tests that are generally recommended for such a selection include the Akaike's information criterion (AIC), corrected Akaike's information criterion (AICc), Bayesian information criterion (BIC), and likelihood ratio test (LRT). In this study, the Monte Carlo simulation was performed to compare the performances of these four tests, with regard to nonstationary as well as stationary generalized extreme value (GEV) distributions. Proper model selection ratios and sample sizes were taken into account to evaluate the performances of all the four tests. The BIC demonstrated the best performance with regard to stationary GEV models. In case of nonstationary GEV models, the AIC proved to be better than the other three methods, when relatively small sample sizes were considered. With larger sample sizes, the AIC, BIC, and LRT presented the best performances for GEV models which have nonstationary location and/or scale parameters, respectively. Simulation results were then evaluated by applying all four tests to annual maximum rainfall data of selected sites, as observed by the Korea Meteorological Administration.

  15. A general approach to mixed effects modeling of residual variances in generalized linear mixed models

    PubMed Central

    Kizilkaya, Kadir; Tempelman, Robert J

    2005-01-01

    We propose a general Bayesian approach to heteroskedastic error modeling for generalized linear mixed models (GLMM) in which linked functions of conditional means and residual variances are specified as separate linear combinations of fixed and random effects. We focus on the linear mixed model (LMM) analysis of birth weight (BW) and the cumulative probit mixed model (CPMM) analysis of calving ease (CE). The deviance information criterion (DIC) was demonstrated to be useful in correctly choosing between homoskedastic and heteroskedastic error GLMM for both traits when data was generated according to a mixed model specification for both location parameters and residual variances. Heteroskedastic error LMM and CPMM were fitted, respectively, to BW and CE data on 8847 Italian Piemontese first parity dams in which residual variances were modeled as functions of fixed calf sex and random herd effects. The posterior mean residual variance for male calves was over 40% greater than that for female calves for both traits. Also, the posterior means of the standard deviation of the herd-specific variance ratios (relative to a unitary baseline) were estimated to be 0.60 ± 0.09 for BW and 0.74 ± 0.14 for CE. For both traits, the heteroskedastic error LMM and CPMM were chosen over their homoskedastic error counterparts based on DIC values. PMID:15588567

  16. Application of Improved Radiation Modeling to General Circulation Models

    SciTech Connect

    Michael J Iacono

    2011-04-07

    This research has accomplished its primary objectives of developing accurate and efficient radiation codes, validating them with measurements and higher resolution models, and providing these advancements to the global modeling community to enhance the treatment of cloud and radiative processes in weather and climate prediction models. A critical component of this research has been the development of the longwave and shortwave broadband radiative transfer code for general circulation model (GCM) applications, RRTMG, which is based on the single-column reference code, RRTM, also developed at AER. RRTMG is a rigorously tested radiation model that retains a considerable level of accuracy relative to higher resolution models and measurements despite the performance enhancements that have made it possible to apply this radiation code successfully to global dynamical models. This model includes the radiative effects of all significant atmospheric gases, and it treats the absorption and scattering from liquid and ice clouds and aerosols. RRTMG also includes a statistical technique for representing small-scale cloud variability, such as cloud fraction and the vertical overlap of clouds, which has been shown to improve cloud radiative forcing in global models. This development approach has provided a direct link from observations to the enhanced radiative transfer provided by RRTMG for application to GCMs. Recent comparison of existing climate model radiation codes with high resolution models has documented the improved radiative forcing capability provided by RRTMG, especially at the surface, relative to other GCM radiation models. Due to its high accuracy, its connection to observations, and its computational efficiency, RRTMG has been implemented operationally in many national and international dynamical models to provide validated radiative transfer for improving weather forecasts and enhancing the prediction of global climate change.

  17. A new theoretical framework for modeling respiratory protection based on the beta distribution.

    PubMed

    Klausner, Ziv; Fattal, Eyal

    2014-08-01

    The problem of modeling respiratory protection is well known and has been dealt with extensively in the literature. Often the efficiency of respiratory protection is quantified in terms of penetration, defined as the proportion of an ambient contaminant concentration that penetrates the respiratory protection equipment. Typically, the penetration modeling framework in the literature is based on the assumption that penetration measurements follow the lognormal distribution. However, the analysis in this study leads to the conclusion that the lognormal assumption is not always valid, making it less adequate for analyzing respiratory protection measurements. This work presents a formulation of the problem from first principles, leading to a stochastic differential equation whose solution is the probability density function of the beta distribution. The data of respiratory protection experiments were reexamined, and indeed the beta distribution was found to provide the data a better fit than the lognormal. We conclude with a suggestion for a new theoretical framework for modeling respiratory protection.

  18. Generalized resistance to thyroid hormone associated with a mutation in the ligand-binding domain of the human thyroid hormone receptor. beta

    SciTech Connect

    Sakurai, A.; Takeda, K.; Ain, K.; Ceccarelli, P.; Nakai, A.; Seino, S.; Bell, G.I.; Refetoff, S.; DeGroot, L.J. )

    1989-11-01

    The syndrome of generalized resistance to thyroid hormone is characterized by elevated circulating levels of thyroid hormone in the presence of an overall eumetabolic state and failure to respond normally to triiodothyronine. The authors have evaluated a family with inherited generalized resistance to thyroid hormone for abnormalities in the thyroid hormone nuclear receptors. A single guanine {yields} cytosine replacement in the codon for amino acid 340 resulted in a glycine {yields} arginine substitution in the hormone-binding domain of one of two alleles of the patient's thyroid hormone nuclear receptor {beta} gene. In vitro translation products of this mutant human thyroid hormone nuclear receptor {beta} gene did not bind triiodothyronine. Thus, generalized resistance to thyroid hormone can result from expression of an abnormal thyroid hormone nuclear receptor molecule.

  19. Remote Sensing of Alpha and Beta Sources - Modeling Summary

    SciTech Connect

    Dignon, J; Frank, M; Cherepy, N

    2005-10-20

    Evaluating the potential for optical detection of the products of interactions of energetic electrons or other particles with the background atmosphere depends on predictions of change in atmospheric concentrations of species which would generate detectable spectral signals within the range of observation. The solar blind region of the spectrum, in the ultra violet, would be the logical band for outdoor detection (see Figure 1). The chemistry relevant to these processes is composed of ion-molecule reactions involving the initially created N{sub 2}{sup +} and O{sub 2}{sup +} ions, and their subsequent interactions with ambient trace atmospheric constituents. Effective modeling of the atmospheric chemical system acted upon by energetic particles requires knowledge of the dominant mechanism that exchange charge and associate it with atmospheric constituents, kinetic parameters of the individual processes (see e.g. Brasseur and Solomon, 1995), and a solver for the coupled differential equations that is accurate for the very stiff set of time constants involved. The LLNL box model, VOLVO, simulates the diel cycle of trace constituent photochemistry for any point on the globe over the wide range of time scales present using a stiff Gear-type ODE solver, i.e. LSODE. It has been applied to problems such as tropospheric and stratospheric nitrogen oxides, stratospheric ozone production and loss, and tropospheric hydrocarbon oxidation. For this study we have included the appropriate ion flux.

  20. Beta-binomial model for meta-analysis of odds ratios.

    PubMed

    Bakbergenuly, Ilyas; Kulinskaya, Elena

    2017-01-25

    In meta-analysis of odds ratios (ORs), heterogeneity between the studies is usually modelled via the additive random effects model (REM). An alternative, multiplicative REM for ORs uses overdispersion. The multiplicative factor in this overdispersion model (ODM) can be interpreted as an intra-class correlation (ICC) parameter. This model naturally arises when the probabilities of an event in one or both arms of a comparative study are themselves beta-distributed, resulting in beta-binomial distributions. We propose two new estimators of the ICC for meta-analysis in this setting. One is based on the inverted Breslow-Day test, and the other on the improved gamma approximation by Kulinskaya and Dollinger (2015, p. 26) to the distribution of Cochran's Q. The performance of these and several other estimators of ICC on bias and coverage is studied by simulation. Additionally, the Mantel-Haenszel approach to estimation of ORs is extended to the beta-binomial model, and we study performance of various ICC estimators when used in the Mantel-Haenszel or the inverse-variance method to combine ORs in meta-analysis. The results of the simulations show that the improved gamma-based estimator of ICC is superior for small sample sizes, and the Breslow-Day-based estimator is the best for n⩾100. The Mantel-Haenszel-based estimator of OR is very biased and is not recommended. The inverse-variance approach is also somewhat biased for ORs≠1, but this bias is not very large in practical settings. Developed methods and R programs, provided in the Web Appendix, make the beta-binomial model a feasible alternative to the standard REM for meta-analysis of ORs. © 2017 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.

  1. Top-Down Beta Rhythms Support Selective Attention via Interlaminar Interaction: A Model

    PubMed Central

    Lee, Jung H.; Whittington, Miles A.; Kopell, Nancy J.

    2013-01-01

    Cortical rhythms have been thought to play crucial roles in our cognitive abilities. Rhythmic activity in the beta frequency band, around 20 Hz, has been reported in recent studies that focused on neural correlates of attention, indicating that top-down beta rhythms, generated in higher cognitive areas and delivered to earlier sensory areas, can support attentional gain modulation. To elucidate functional roles of beta rhythms and underlying mechanisms, we built a computational model of sensory cortical areas. Our simulation results show that top-down beta rhythms can activate ascending synaptic projections from L5 to L4 and L2/3, responsible for biased competition in superficial layers. In the simulation, slow-inhibitory interneurons are shown to resonate to the 20 Hz input and modulate the activity in superficial layers in an attention-related manner. The predicted critical roles of these cells in attentional gain provide a potential mechanism by which cholinergic drive can support selective attention. PMID:23950699

  2. Modeling beta-adrenergic control of cardiac myocyte contractility in silico

    NASA Technical Reports Server (NTRS)

    Saucerman, Jeffrey J.; Brunton, Laurence L.; Michailova, Anushka P.; McCulloch, Andrew D.; McCullough, A. D. (Principal Investigator)

    2003-01-01

    The beta-adrenergic signaling pathway regulates cardiac myocyte contractility through a combination of feedforward and feedback mechanisms. We used systems analysis to investigate how the components and topology of this signaling network permit neurohormonal control of excitation-contraction coupling in the rat ventricular myocyte. A kinetic model integrating beta-adrenergic signaling with excitation-contraction coupling was formulated, and each subsystem was validated with independent biochemical and physiological measurements. Model analysis was used to investigate quantitatively the effects of specific molecular perturbations. 3-Fold overexpression of adenylyl cyclase in the model allowed an 85% higher rate of cyclic AMP synthesis than an equivalent overexpression of beta 1-adrenergic receptor, and manipulating the affinity of Gs alpha for adenylyl cyclase was a more potent regulator of cyclic AMP production. The model predicted that less than 40% of adenylyl cyclase molecules may be stimulated under maximal receptor activation, and an experimental protocol is suggested for validating this prediction. The model also predicted that the endogenous heat-stable protein kinase inhibitor may enhance basal cyclic AMP buffering by 68% and increasing the apparent Hill coefficient of protein kinase A activation from 1.0 to 2.0. Finally, phosphorylation of the L-type calcium channel and phospholamban were found sufficient to predict the dominant changes in myocyte contractility, including a 2.6x increase in systolic calcium (inotropy) and a 28% decrease in calcium half-relaxation time (lusitropy). By performing systems analysis, the consequences of molecular perturbations in the beta-adrenergic signaling network may be understood within the context of integrative cellular physiology.

  3. Comprehensive investigation of hydroxypropyl methylcellulose, propylene glycol, polysorbate 80, and hydroxypropyl-beta-cyclodextrin for use in general toxicology studies.

    PubMed

    Thackaberry, Evan A; Kopytek, Stephen; Sherratt, Phillip; Trouba, Kevin; McIntyre, Barry

    2010-10-01

    This study was conducted to assess the safety and tolerability of the alternative formulation vehicles polysorbate 80 (PS80), propylene glycol (PG), and hydroxypropyl-beta-cyclodextrin (HPβCD) in general toxicology studies in the mouse, rat, dog, and monkey. Twenty (20) mg/kg of hydroxypropyl methylcellulose (MC, control), 10 mg/kg PS80, 1000 mg/kg PG, 500 mg/kg HPβCD, or 1000 mg/kg HPβCD were administered by oral gavage to mice, rats, dogs, and cynomolgus monkeys for approximately 90 days. The effects of these formulations on clinical observations, body weight and food consumption parameters, clinical pathology, and histopathology were evaluated across all species. The suitability of formulations containing up to 20 mg/kg MC, 10 mg/kg PS80, and 1000 mg/kg PG for use in preclinical safety studies was confirmed by a lack of effects on all parameters examined. However, formulations containing HPβCD produced elevated transaminase (aspartate and alanine aminotransferase) levels in rats and mice and fecal changes (loose and soft stool) in large animals. Although the etiology and toxicological significance of the transaminase elevations in rats and mice is uncertain, this finding could represent a significant liability for a preclinical formulation because of the critical importance of these biomarkers in the risk assessment of novel therapeutic agents. Based on these data, PS80 and PG are considered to be practical alternatives to MC in preclinical toxicology studies. However, formulations containing HPβCD should be used with caution because of the elevations in rodent transaminase levels.

  4. A generalized multivariate regression model for modelling ocean wave heights

    NASA Astrophysics Data System (ADS)

    Wang, X. L.; Feng, Y.; Swail, V. R.

    2012-04-01

    In this study, a generalized multivariate linear regression model is developed to represent the relationship between 6-hourly ocean significant wave heights (Hs) and the corresponding 6-hourly mean sea level pressure (MSLP) fields. The model is calibrated using the ERA-Interim reanalysis of Hs and MSLP fields for 1981-2000, and is validated using the ERA-Interim reanalysis for 2001-2010 and ERA40 reanalysis of Hs and MSLP for 1958-2001. The performance of the fitted model is evaluated in terms of Pierce skill score, frequency bias index, and correlation skill score. Being not normally distributed, wave heights are subjected to a data adaptive Box-Cox transformation before being used in the model fitting. Also, since 6-hourly data are being modelled, lag-1 autocorrelation must be and is accounted for. The models with and without Box-Cox transformation, and with and without accounting for autocorrelation, are inter-compared in terms of their prediction skills. The fitted MSLP-Hs relationship is then used to reconstruct historical wave height climate from the 6-hourly MSLP fields taken from the Twentieth Century Reanalysis (20CR, Compo et al. 2011), and to project possible future wave height climates using CMIP5 model simulations of MSLP fields. The reconstructed and projected wave heights, both seasonal means and maxima, are subject to a trend analysis that allows for non-linear (polynomial) trends.

  5. Modeling the inhibition of the bacteral reduction of U(VI) by beta-MnO2(s).

    PubMed

    Liu, Chongxuan; Zachara, John M; Fredrickson, James K; Kennedy, David W; Dohnalkova, Alice

    2002-04-01

    Pyrolusite (beta-MnO2(s)) was used to assess the influence of a competitive electron acceptor on the kinetics of reduction of aqueous uranyl carbonate by a dissimilatory metal-reducing bacterium (DMRB), Shewanella putrefaciens strain CN32. The enzymatic reduction of U(VI) and beta-MnO2(s) and the abiotic redox reaction between beta-MnO2(s) and biogenic uraninite (UO2(s)) were independently investigated to allow for interpretation of studies of U(VI) bioreduction in the presence of beta-MnO2(s). Uranyl bioreduction to UO2(s) by CN32 with H2 as the electron donor followed Monod kinetics, with a maximum specific reduction rate of 110 M/h/10(8) cells/mL and a half-saturation constant of 370 microM. The bioreduction rate of beta-MnO2(s) by CN32 was described by a pseudo-first-order model with respect to beta-MnO2(s) surface sites, with a rate constant of 7.92 x 10(-2) h(-1)/10(8) cells/mL. Uraninite that precipitated as a result of microbial U(VI) reduction was abiotically reoxidized to U(VI) by beta-MnO2(s), with concomitant reduction to Mn(II). The oxidation of biogenic UO2(s) coupled with beta-MnO2(s) reduction was well-described by an electrochemical model. However, a simple model that coupled the bacterial reduction of U(VI) and beta-MnO2(s) with an abiotic redox reaction between UO2(s) and beta-MnO2(s) failed to describe the mass loss of U(VI) in the presence of beta-MnO2(s). Transmission electron microscopy (TEM) and energy dispersive spectroscopy (EDS) revealed that the particle size and spatial distribution of the biogenic UO2(s) changed dynamically in systems with, as compared to without, beta-MnO2(s)). These observations suggested that the surface properties and localization of UO2(s) in relation to the cell and beta-MnO2(s) surfaces was an important factor controlling the abiotic oxidation of UO2(s) and, thus, the overall rate and extent of U(VI) bioreduction. The coupled model that was modified to account for the "effective" contact surface area between UO2

  6. Comparison of the Beta and the Hidden Markov Models of Trust in Dynamic Environments

    NASA Astrophysics Data System (ADS)

    Moe, Marie E. G.; Helvik, Bjarne E.; Knapskog, Svein J.

    Computational trust and reputation models are used to aid the decision-making process in complex dynamic environments, where we are unable to obtain perfect information about the interaction partners. In this paper we present a comparison of our proposed hidden Markov trust model to the Beta reputation system. The hidden Markov trust model takes the time between observations into account, it also distinguishes between system states and uses methods previously applied to intrusion detection for the prediction of which state an agent is in. We show that the hidden Markov trust model performs better when it comes to the detection of changes in behavior of agents, due to its larger richness in model features. This means that our trust model may be more realistic in dynamic environments. However, the increased model complexity also leads to bigger challenges in estimating parameter values for the model. We also show that the hidden Markov trust model can be parameterized so that it responds similarly to the Beta reputation system.

  7. A Continuous Correlated Beta Process Model for Genetic Ancestry in Admixed Populations

    PubMed Central

    Gompert, Zachariah

    2016-01-01

    Admixture and recombination create populations and genomes with genetic ancestry from multiple source populations. Analyses of genetic ancestry in admixed populations are relevant for trait and disease mapping, studies of speciation, and conservation efforts. Consequently, many methods have been developed to infer genome-average ancestry and to deconvolute ancestry into continuous local ancestry blocks or tracts within individuals. Current methods for local ancestry inference perform well when admixture occurred recently or hybridization is ongoing, or when admixture occurred in the distant past such that local ancestry blocks have fixed in the admixed population. However, methods to infer local ancestry frequencies in isolated admixed populations still segregating for ancestry do not exist. In the current paper, I develop and test a continuous correlated beta process model to fill this analytical gap. The method explicitly models autocorrelations in ancestry frequencies at the population-level and uses discriminant analysis of SNP windows to take advantage of ancestry blocks within individuals. Analyses of simulated data sets show that the method is generally accurate such that ancestry frequency estimates exhibited low root-mean-square error and were highly correlated with the true values, particularly when large (±10 or ±20) SNP windows were used. Along these lines, the proposed method outperformed post hoc inference of ancestry frequencies from a traditional hidden Markov model (i.e., the linkage model in structure), particularly when admixture occurred more distantly in the past with little on-going gene flow or was followed by natural selection. The reliability and utility of the method was further assessed by analyzing genetic ancestry in an admixed human population (Uyghur) and three populations from a hybrid zone between Mus domesticus and M. musculus. Considerable variation in ancestry frequencies was detected within and among chromosomes in the Uyghur

  8. A Continuous Correlated Beta Process Model for Genetic Ancestry in Admixed Populations.

    PubMed

    Gompert, Zachariah

    2016-01-01

    Admixture and recombination create populations and genomes with genetic ancestry from multiple source populations. Analyses of genetic ancestry in admixed populations are relevant for trait and disease mapping, studies of speciation, and conservation efforts. Consequently, many methods have been developed to infer genome-average ancestry and to deconvolute ancestry into continuous local ancestry blocks or tracts within individuals. Current methods for local ancestry inference perform well when admixture occurred recently or hybridization is ongoing, or when admixture occurred in the distant past such that local ancestry blocks have fixed in the admixed population. However, methods to infer local ancestry frequencies in isolated admixed populations still segregating for ancestry do not exist. In the current paper, I develop and test a continuous correlated beta process model to fill this analytical gap. The method explicitly models autocorrelations in ancestry frequencies at the population-level and uses discriminant analysis of SNP windows to take advantage of ancestry blocks within individuals. Analyses of simulated data sets show that the method is generally accurate such that ancestry frequency estimates exhibited low root-mean-square error and were highly correlated with the true values, particularly when large (±10 or ±20) SNP windows were used. Along these lines, the proposed method outperformed post hoc inference of ancestry frequencies from a traditional hidden Markov model (i.e., the linkage model in structure), particularly when admixture occurred more distantly in the past with little on-going gene flow or was followed by natural selection. The reliability and utility of the method was further assessed by analyzing genetic ancestry in an admixed human population (Uyghur) and three populations from a hybrid zone between Mus domesticus and M. musculus. Considerable variation in ancestry frequencies was detected within and among chromosomes in the Uyghur

  9. Towards a General Model of Temporal Discounting

    ERIC Educational Resources Information Center

    van den Bos, Wouter; McClure, Samuel M.

    2013-01-01

    Psychological models of temporal discounting have now successfully displaced classical economic theory due to the simple fact that many common behavior patterns, such as impulsivity, were unexplainable with classic models. However, the now dominant hyperbolic model of discounting is itself becoming increasingly strained. Numerous factors have…

  10. Connecting the X(5)-{beta}{sup 2}, X(5)-{beta}{sup 4}, and X(3) models to the shape/phase transition region of the interacting boson model

    SciTech Connect

    McCutchan, E. A. Bonatsos, D. Zamfir, N. V.

    2007-08-15

    The parameter-independent (up to overall scale factors) predictions of the X(5)-{beta}{sup 2},X(5)-{beta}{sup 4}, and X(3) models, which are variants of the X(5) critical point symmetry developed within the framework of the geometric collective model, are compared to two-parameter calculations in the framework of the interacting boson approximation (IBA) model. The results show that these geometric models coincide with IBA parameters consistent with the phase/shape transition region of the IBA for boson numbers of physical interest (close to 10). {sup 186}Pt and {sup 172}Os are identified as good examples of X(3), while {sup 146}Ce, {sup 174}Os, and {sup 158}Er, {sup 176}Os are identified as good examples of X(5)-{beta}{sub 2} and X(5)-{beta}{sup 4} behavior, respectively.

  11. A case of acute generalized exanthematous pustulosis due to amoxicillin-clavulanate with multiple positivity to beta-lactam patch testing.

    PubMed

    Bomarrito, L; Zisa, G; Delrosso, G; Farinelli, P; Galimberti, M

    2013-09-01

    We present a case of acute generalized exanthematous pustolosis (AGEP) induced by amoxicillin-clavulanate. Clinical diagnosis was confirmed by symptoms presentation and  histological features (Euroscar score point compatible with definite diagnosis). Patch testing performer six months later confirmed sensitization to the culprit drug and showed positivity also to other beta-lactam antibiotics (penicillin G and cephalexin). We believe that a T cell delayed response to betalactams common ring could be involved.

  12. Study of the determination of the coefficients beta and gamma of the generalized metric of Robertson and of the dynamical oblateness of the sun

    NASA Technical Reports Server (NTRS)

    Marchal, C.

    1971-01-01

    Motion of a space probe about a spherical center of attraction is considered, applying the general theory of relativity. Motion of a probe under the influence of the sun's oblateness is also discussed. Estimates of beta, gamma, and J20 using solar probe motion are presented. It is concluded that such measurements are possible if the unknown long-period perturbing acceleration is of the order of 10 to the -11th or -12th power m/sec. sq.

  13. Sharpening Low-Energy, Standard-Model Tests via Correlation Coefficients in Neutron {beta} Decay

    SciTech Connect

    Gardner, S.; Zhang, C.

    2001-06-18

    The correlation coefficients a , A , and B in neutron {beta} decay are proportional to the ratio of the axial-vector-to-vector weak coupling constants, g{sub A}/g{sub V} , to leading recoil order. With the advent of the next generation of neutron-decay experiments, the recoil-order corrections to these expressions become experimentally accessible, admitting a plurality of standard model (SM) tests. The measurement of both a and A , e.g., allows one to test the conserved-vector-current (CVC) hypothesis and to search for second-class currents (SCC) independently. The anticipated precision of these measurements suggests that the bounds on CVC violation and SCC from studies of nuclear {beta} decay can be qualitatively bettered.

  14. Optimal determination of steric mass action model parameters for beta-lactoglobulin using static batch experiments.

    PubMed

    Barz, Tilman; Löffler, Verena; Arellano-Garcia, Harvey; Wozny, Günter

    2010-06-25

    In this work, parameters of the steric mass-formalism SMA are optimally ascertained for a reliable determination of the adsorption isotherms of beta-lactoglobulin A and B under non-isocratic conditions. For this purpose, static batch experiments are used in contrast to the protocols based on different experimental steps, which use a chromatographic column. It is shown that parameters can already be determined for a small number of experiments by using a systematic procedure based on optimal model-based experimental design and an efficient NLP-solver. The in different works observed anti-Langmuir shape of the isotherm for small concentrations of beta-lactoglobulin A was corroborated. Moreover, we also found indications for a porosity variation with changing protein concentrations.

  15. Modeling of Antarctic sea ice in a general circulation model

    SciTech Connect

    Wu, Xingren; Budd, W.F.; Simmonds, I.

    1997-04-01

    A dynamic-thermodynamic sea ice model is developed and coupled with the Melbourne University general circulation model to simulate the seasonal cycle of the Antarctic sea ice distributions The model is efficient, rapid to compute, and useful for a range of climate studies. The thermodynamic part of the sea ice model is similar to that developed by Parkinson and Washington, the dynamics contain a simplified ice rheology that resists compression. The thermodynamics is based on energy conservation at the top surface of the ice/snow, the ice/water interface, and the open water area to determine the ice formation, accretion, and ablation. A lead parameterization is introduced with an effective partitioning scheme for freezing between and under the ice floes. The dynamic calculation determines the motion of ice, which is forced with the atmospheric wind, taking account of ice resistance and rafting. The simulated sea ice distribution compares reasonably well with observations. The seasonal cycle of ice extent is well simulated in phase as well as in magnitude. Simulated sea ice thickness and concentration are also in good agreement with observations over most regions and serve to indicate the importance of advection and ocean drift in the determination of the sea ice distribution. 64 refs., 15 figs., 2 tabs.

  16. Stratospheric General Circulation with Chemistry Model (SGCCM)

    NASA Technical Reports Server (NTRS)

    Rood, Richard B.; Douglass, Anne R.; Geller, Marvin A.; Kaye, Jack A.; Nielsen, J. Eric; Rosenfield, Joan E.; Stolarski, Richard S.

    1990-01-01

    In the past two years constituent transport and chemistry experiments have been performed using both simple single constituent models and more complex reservoir species models. Winds for these experiments have been taken from the data assimilation effort, Stratospheric Data Analysis System (STRATAN).

  17. Specification of the Model 3 General Lexicon.

    ERIC Educational Resources Information Center

    Rhode, Mary

    The Model 3 communication skills lexicon consists of three lists of words developed by the Southwest Regional Laboratory (SWRL) for use in communication skills instruction in K-6. This report documents the procedures followed in the specification and generation of the second component of the Model 3 communication skills lexicon, the general…

  18. Evidence for a General Factor Model of ADHD in Adults

    ERIC Educational Resources Information Center

    Gibbins, Christopher; Toplak, Maggie E.; Flora, David B.; Weiss, Margaret D.; Tannock, Rosemary

    2012-01-01

    Objective: To examine factor structures of "Diagnostic and Statistical Manual of Mental Disorders" (4th ed.) symptoms of ADHD in adults. Method: Two sets of models were tested: (a) models with inattention and hyperactivity/impulsivity as separate but correlated latent constructs and (b) hierarchical general factor models with a general factor for…

  19. Universality in generalized models of inflation

    NASA Astrophysics Data System (ADS)

    Binétruy, P.; Mabillard, J.; Pieroni, M.

    2017-03-01

    We discuss the cosmological evolution of a scalar field with non standard kinetic term in terms of a Renormalization Group Equation (RGE). In this framework inflation corresponds to the slow evolution in a neighborhood of a fixed point and universality classes for inflationary models naturally arise. Using some examples we show the application of the formalism. The predicted values for the speed of sound cs2 and for the amount of non-Gaussianities produced in these models are discussed. In particular, we show that it is possible to introduce models with cs2 ≠ 1 that can be in agreement with present cosmological observations.

  20. beta2-adrenergic receptor signaling and desensitization elucidated by quantitative modeling of real time cAMP dynamics.

    PubMed

    Violin, Jonathan D; DiPilato, Lisa M; Yildirim, Necmettin; Elston, Timothy C; Zhang, Jin; Lefkowitz, Robert J

    2008-02-01

    G protein-coupled receptor signaling is dynamically regulated by multiple feedback mechanisms, which rapidly attenuate signals elicited by ligand stimulation, causing desensitization. The individual contributions of these mechanisms, however, are poorly understood. Here, we use an improved fluorescent biosensor for cAMP to measure second messenger dynamics stimulated by endogenous beta(2)-adrenergic receptor (beta(2)AR) in living cells. beta(2)AR stimulation with isoproterenol results in a transient pulse of cAMP, reaching a maximal concentration of approximately 10 microm and persisting for less than 5 min. We investigated the contributions of cAMP-dependent kinase, G protein-coupled receptor kinases, and beta-arrestin to the regulation of beta(2)AR signal kinetics by using small molecule inhibitors, small interfering RNAs, and mouse embryonic fibroblasts. We found that the cAMP response is restricted in duration by two distinct mechanisms in HEK-293 cells: G protein-coupled receptor kinase (GRK6)-mediated receptor phosphorylation leading to beta-arrestin mediated receptor inactivation and cAMP-dependent kinase-mediated induction of cAMP metabolism by phosphodiesterases. A mathematical model of beta(2)AR signal kinetics, fit to these data, revealed that direct receptor inactivation by cAMP-dependent kinase is insignificant but that GRK6/beta-arrestin-mediated inactivation is rapid and profound, occurring with a half-time of 70 s. This quantitative system analysis represents an important advance toward quantifying mechanisms contributing to the physiological regulation of receptor signaling.

  1. Flavor constraints on two-Higgs-doublet models with general diagonal Yukawa couplings

    SciTech Connect

    Mahmoudi, F.

    2010-02-01

    We consider constraints from flavor physics on two-Higgs-doublet models (2HDM) with general, flavor-diagonal, Yukawa couplings. Analyzing the charged Higgs contribution to different observables, we find that b{yields}s{gamma} transitions and {Delta}M{sub B{sub d}} restrict the coupling {lambda}{sub tt} of the top quark (corresponding to cot{beta} in models with a Z{sub 2} symmetry) to |{lambda}{sub tt}|<1 for m{sub H}{sup +} < or approx. 500 GeV. Stringent constraints from B meson decays are obtained also on the other third generation couplings {lambda}{sub bb} and {lambda}{sub {tau}{tau},} but with stronger dependence on m{sub H}{sup +}. For the second generation, we obtain constraints on combinations of {lambda}{sub ss}, {lambda}{sub cc}, and {lambda}{sub {mu}{mu}}from leptonic K and D{sub s} decays. The limits on the general couplings are translated to the common 2HDM types I-IV with a Z{sub 2} symmetry, and presented on the (m{sub H}{sup +},tan{beta}) plane. The flavor constraints are most excluding in the type II model which lacks a decoupling limit in tan{beta}. We obtain a lower limit m{sub H}{sup +} > or approx. 300 GeV in models of type II and III, while no lower bound on m{sub H}{sup +} is found for types I and IV.

  2. Response-surface models for deterministic effects of localized irradiation of the skin by discrete {beta}/{gamma} -emitting sources

    SciTech Connect

    Scott, B.R.

    1995-12-01

    Individuals who work at nuclear reactor facilities can be at risk for deterministic effects in the skin from exposure to discrete {Beta}- and {gamma}-emitting ({Beta}{gamma}E) sources (e.g., {Beta}{gamma}E hot particles) on the skin or clothing. Deterministic effects are non-cancer effects that have a threshold and increase in severity as dose increases (e.g., ulcer in skin). Hot {Beta}{gamma}E particles are {sup 60}Co- or nuclear fuel-derived particles with diameters > 10 {mu}m and < 3 mm and contain at least 3.7 kBq (0.1 {mu}Ci) of radioactivity. For such {Beta}{gamma}E sources on the skin, it is the beta component of the dose that is most important. To develop exposure limitation systems that adequately control exposure of workers to discrete {Beta}{gamma}E sources, models are needed for systems that adequately control exposure of workers to discrete {Beta}{gamma}E sources, models are needed for evaluating the risk of deterministic effects of localized {Beta} irradiation of the skin. The purpose of this study was to develop dose-rate and irradiated-area dependent, response-surface models for evaluating risks of significant deterministic effects of localized irradiation of the skin by discrete {Beta}{gamma}E sources and to use modeling results to recommend approaches to limiting occupational exposure to such sources. The significance of the research results as follows: (1) response-surface models are now available for evaluating the risk of specific deterministic effects of localized irradiation of the skin; (2) modeling results have been used to recommend approaches to limiting occupational exposure of workers to {Beta} radiation from {Beta}{gamma}E sources on the skin or on clothing; and (3) the generic irradiated-volume, weighting-factor approach to limiting exposure can be applied to other organs including the eye, the ear, and organs of the respiratory or gastrointestinal tract and can be used for both deterministic and stochastic effects.

  3. Generalized Model of a Skeletal Muscle

    NASA Astrophysics Data System (ADS)

    Shil'ko, S. V.; Chernous, D. A.; Bondarenko, K. K.

    2016-01-01

    A new phenomenological model of a skeletal muscle consisting of a contractile and two nonlinear viscoelastic elements is proposed. The corresponding system of differential equations of the model is obtained, which allows one to derive time-dependent relations between the axial stress and the longitudinal strain in passive and activated states of the muscle. Methods for determining the viscoelastic and functional characteristics of the muscle as input parameters of the equations mentioned above are developed. These methods are based on the joint application of known experimental relations for a single muscle fiber and the results of muscle indentation in vivo on a "Miometer UT 98-01" device.

  4. Generalized Hertz model for bimodal nanomechanical mapping

    PubMed Central

    Kocuń, Marta; Meinhold, Waiman; Walters, Deron; Proksch, Roger

    2016-01-01

    Summary Bimodal atomic force microscopy uses a cantilever that is simultaneously driven at two of its eigenmodes (resonant modes). Parameters associated with both resonances can be measured and used to extract quantitative nanomechanical information about the sample surface. Driving the first eigenmode at a large amplitude and a higher eigenmode at a small amplitude simultaneously provides four independent observables that are sensitive to the tip–sample nanomechanical interaction parameters. To demonstrate this, a generalized theoretical framework for extracting nanomechanical sample properties from bimodal experiments is presented based on Hertzian contact mechanics. Three modes of operation for measuring cantilever parameters are considered: amplitude, phase, and frequency modulation. The experimental equivalence of all three modes is demonstrated on measurements of the second eigenmode parameters. The contact mechanics theory is then extended to power-law tip shape geometries, which is applied to analyze the experimental data and extract a shape and size of the tip interacting with a polystyrene surface. PMID:27547614

  5. Invariance Properties for General Diagnostic Classification Models

    ERIC Educational Resources Information Center

    Bradshaw, Laine P.; Madison, Matthew J.

    2016-01-01

    In item response theory (IRT), the invariance property states that item parameter estimates are independent of the examinee sample, and examinee ability estimates are independent of the test items. While this property has long been established and understood by the measurement community for IRT models, the same cannot be said for diagnostic…

  6. Generalized IRT Models for Extreme Response Style

    ERIC Educational Resources Information Center

    Jin, Kuan-Yu; Wang, Wen-Chung

    2014-01-01

    Extreme response style (ERS) is a systematic tendency for a person to endorse extreme options (e.g., strongly disagree, strongly agree) on Likert-type or rating-scale items. In this study, we develop a new class of item response theory (IRT) models to account for ERS so that the target latent trait is free from the response style and the tendency…

  7. A General Model for Shallow Magmatic Intrusions

    NASA Astrophysics Data System (ADS)

    Thorey, C.; Michaut, C.

    2015-12-01

    Shallow magmatic intrusions make room for themselves by upward bending of the elastic overburden. Previous studies have shown that the bending of the overlying layer first controls the dynamics. Then, when the radius reaches a few times the flexural wavelength of the overburden, it transitions to a gravity current regime. This model predicts the appropriate geometry for both terrestrial laccoliths and large mafic sills. However, it underestimates the absolute dimensions of these magmatic intrusions; in particular, it requires abnormally high viscosity to reconcile both observations and predictions. To get some insights into the effective flow viscosity, we develop a model that account for the cooling of such elastic-plated gravity currents. We show that the coupling between the temperature field and the flow itself leads to the formation of a highly viscous region at the tip that slows down the spreading in both regimes. The intrusions are predicted to be thicker and their dimensions, especially in the bending regime, are now consistent with observations. By introducing the potentially complex structure of the overburden, we also show that the topography largely contributes to constrain the final intrusion morphology. For instance, in the case of an intrusion centered below a circular depression, the model predicts that the lithostatic increase at the crater rim prevents the magma from spreading laterally and enhances the thickening of the intrusion. This model has already proven successful in reproducing the deformations observed on potential intrusion centered below lunar impact craters. Caldera complexes often exhibit ground deformations that might be associated to the formation of shallow magmatic intrusions. InSAR imaging and GPS measurements now provide efficient tools to monitor these deformations. We conclude this study by examining the ability of the model to reproduce the deformation observed in several caldera complexes.

  8. Mixed-effects beta regression for modeling continuous bounded outcome scores using NONMEM when data are not on the boundaries.

    PubMed

    Xu, Xu Steven; Samtani, Mahesh N; Dunne, Adrian; Nandy, Partha; Vermeulen, An; De Ridder, Filip

    2013-08-01

    Beta regression models have been recommended for continuous bounded outcome scores that are often collected in clinical studies. Implementing beta regression in NONMEM presents difficulties since it does not provide gamma functions required by the beta distribution density function. The objective of the study was to implement mixed-effects beta regression models in NONMEM using Nemes' approximation to the gamma function and to evaluate the performance of the NONMEM implementation of mixed-effects beta regression in comparison to the commonly used SAS approach. Monte Carlo simulations were conducted to simulate continuous outcomes within an interval of (0, 70) based on a beta regression model in the context of Alzheimer's disease. Six samples per subject over a 3 years period were simulated at 0, 0.5, 1, 1.5, 2, and 3 years. One thousand trials were simulated and each trial had 250 subjects. The simulation-reestimation exercise indicated that the NONMEM implementation using Laplace and Nemes' approximations provided only slightly higher bias and relative RMSE (RRMSE) compared to the commonly used SAS approach with adaptive Gaussian quadrature and built-in gamma functions, i.e., the difference in bias and RRMSE for fixed-effect parameters, random effects on intercept, and the precision parameter were <1-3 %, while the difference in the random effects on the slope was <3-7 % under the studied simulation conditions. The mixed-effect beta regression model described the disease progression for the cognitive component of the Alzheimer's disease assessment scale from the Alzheimer's Disease Neuroimaging Initiative study. In conclusion, with Nemes' approximation of the gamma function, NONMEM provided comparable estimates to those from SAS for both fixed and random-effect parameters. In addition, the NONMEM run time for the mixed beta regression models appeared to be much shorter compared to SAS, i.e., 1-2 versus 20-40 s for the model and data used in the manuscript.

  9. A Mechanistic Beta-Binomial Probability Model for mRNA Sequencing Data.

    PubMed

    Smith, Gregory R; Birtwistle, Marc R

    2016-01-01

    A main application for mRNA sequencing (mRNAseq) is determining lists of differentially-expressed genes (DEGs) between two or more conditions. Several software packages exist to produce DEGs from mRNAseq data, but they typically yield different DEGs, sometimes markedly so. The underlying probability model used to describe mRNAseq data is central to deriving DEGs, and not surprisingly most softwares use different models and assumptions to analyze mRNAseq data. Here, we propose a mechanistic justification to model mRNAseq as a binomial process, with data from technical replicates given by a binomial distribution, and data from biological replicates well-described by a beta-binomial distribution. We demonstrate good agreement of this model with two large datasets. We show that an emergent feature of the beta-binomial distribution, given parameter regimes typical for mRNAseq experiments, is the well-known quadratic polynomial scaling of variance with the mean. The so-called dispersion parameter controls this scaling, and our analysis suggests that the dispersion parameter is a continually decreasing function of the mean, as opposed to current approaches that impose an asymptotic value to the dispersion parameter at moderate mean read counts. We show how this leads to current approaches overestimating variance for moderately to highly expressed genes, which inflates false negative rates. Describing mRNAseq data with a beta-binomial distribution thus may be preferred since its parameters are relatable to the mechanistic underpinnings of the technique and may improve the consistency of DEG analysis across softwares, particularly for moderately to highly expressed genes.

  10. Limitations of animal models in predicting beta-lactam efficacy for endocarditis and meningitis.

    PubMed

    Gerberding, J L; Sande, M A

    1986-01-01

    Animal models are important in predicting the efficacy in humans of antimicrobial agents for various disease conditions, including endocarditis and meningitis. Screening models are useful in assessing antibiotic effectiveness and toxicity; their advantages include simplicity, a reproducible course of infection, a well-defined therapeutic end point, and low cost. However, the inoculum size, the virulence of the organism, and the production of beta-lactamases can have important effects on outcome and must be considered in the interpretation of data obtained from such models. Discriminative models are those designed to mimic human disease as closely as possible with respect to infectious inoculum, host response, and course of disease. Each drug's pharmacokinetics must be carefully documented before being extrapolated to humans. Rigid criteria must be established to minimize misinterpretation of results from animal studies before conclusions from in vivo animal models are applied to human disease.

  11. Reduced Order Modeling in General Relativity

    NASA Astrophysics Data System (ADS)

    Tiglio, Manuel

    2014-03-01

    Reduced Order Modeling is an emerging yet fast developing filed in gravitational wave physics. The main goals are to enable fast modeling and parameter estimation of any detected signal, along with rapid matched filtering detecting. I will focus on the first two. Some accomplishments include being able to replace, with essentially no lost of physical accuracy, the original models with surrogate ones (which are not effective ones, that is, they do not simplify the physics but go on a very different track, exploiting the particulars of the waveform family under consideration and state of the art dimensional reduction techniques) which are very fast to evaluate. For example, for EOB models they are at least around 3 orders of magnitude faster than solving the original equations, with physically equivalent results. For numerical simulations the speedup is at least 11 orders of magnitude. For parameter estimation our current numbers are about bringing ~100 days for a single SPA inspiral binary neutron star Bayesian parameter estimation analysis to under a day. More recently, it has been shown that the full precessing problem for, say, 200 cycles, can be represented, through some new ideas, by a remarkably compact set of carefully chosen reduced basis waveforms (~10-100, depending on the accuracy requirements). I will highlight what I personally believe are the challenges to face next in this subarea of GW physics and where efforts should be directed. This talk will summarize work in collaboration with: Harbir Antil (GMU), Jonathan Blackman (Caltech), Priscila Canizares (IoA, Cambridge, UK), Sarah Caudill (UWM), Jonathan Gair (IoA. Cambridge. UK), Scott Field (UMD), Chad R. Galley (Caltech), Frank Herrmann (Germany), Han Hestahven (EPFL, Switzerland), Jason Kaye (Brown, Stanford & Courant). Evan Ochsner (UWM), Ricardo Nochetto (UMD), Vivien Raymond (LIGO, Caltech), Rory Smith (LIGO, Caltech) Bela Ssilagyi (Caltech) and MT (UMD & Caltech).

  12. Ego Development and a General Model for Counseling and Psychotherapy.

    ERIC Educational Resources Information Center

    Swensen, Clifford H.

    1980-01-01

    Describes a general model within which various techniques of counseling and psychotherapy may be integrated. This model is based on Lewin's formula, that is, behavior is a function of the person and the environment. (Author)

  13. Surrogate oracles, generalized dependency and simpler models

    NASA Technical Reports Server (NTRS)

    Wilson, Larry

    1990-01-01

    Software reliability models require the sequence of interfailure times from the debugging process as input. It was previously illustrated that using data from replicated debugging could greatly improve reliability predictions. However, inexpensive replication of the debugging process requires the existence of a cheap, fast error detector. Laboratory experiments can be designed around a gold version which is used as an oracle or around an n-version error detector. Unfortunately, software developers can not be expected to have an oracle or to bear the expense of n-versions. A generic technique is being investigated for approximating replicated data by using the partially debugged software as a difference detector. It is believed that the failure rate of each fault has significant dependence on the presence or absence of other faults. Thus, in order to discuss a failure rate for a known fault, the presence or absence of each of the other known faults needs to be specified. Also, in simpler models which use shorter input sequences without sacrificing accuracy are of interest. In fact, a possible gain in performance is conjectured. To investigate these propositions, NASA computers running LIC (RTI) versions are used to generate data. This data will be used to label the debugging graph associated with each version. These labeled graphs will be used to test the utility of a surrogate oracle, to analyze the dependent nature of fault failure rates and to explore the feasibility of reliability models which use the data of only the most recent failures.

  14. Shell-model calculations of beta-decay rates for s- and r-process nucleosyntheses

    NASA Astrophysics Data System (ADS)

    Takahashi, K.; Mathews, G. J.; Bloom, S. D.

    1985-10-01

    Examples of large-basis shell-model calculations of Gamow-Teller (BETA)-decay properties of specific interest in the astrophysical s- and r- processes are presented. Numerical results are given for: (1) the GT-matrix elements for the excited state decays of the unstable s-process nucleus Tc-99; and (2) the GT-strength function for the neutron-rich nucleus Cd-130, which lies on the r-process path. The results are discussed in conjunction with the astrophysics problems.

  15. Generalizing in Interaction: Middle School Mathematics Students Making Mathematical Generalizations in a Population-Modeling Project

    ERIC Educational Resources Information Center

    Jurow, A. Susan

    2004-01-01

    Generalizing or making claims that extend beyond particular situations is a central mathematical practice and a focus of classroom mathematics instruction. This study examines how aspects of generality are produced through the situated activities of a group of middle school mathematics students working on an 8-week population-modeling project. The…

  16. A General Model for Measurement Improvement

    NASA Astrophysics Data System (ADS)

    Dumke, Reiner; Yazbek, Hashem; Asfoura, Evan; Georgieva, Konstantina

    The following paper describes our approach for characterizing software measurement in a holistic manner. Therefore software measurement was defined as a system including all aspects of software measurement, evaluation, estimation and exploration. First of all, we define these components of software measurement considering the different levels of each component in order to classify the different levels of the software measurement itself. First examples have shown the appropriateness of this approach for paradigm related measurement comparisons and improvements. In this paper, we extend our modelling approach and demonstrate the meaningfulness of comparing software measurement practices for different standards and process improvement approaches. These examples help for identifying essential key areas for measurement improvement as basics of quality assurance.

  17. Building a generalized distributed system model

    NASA Technical Reports Server (NTRS)

    Mukkamala, R.

    1992-01-01

    The key elements in the second year (1991-92) of our project are: (1) implementation of the distributed system prototype; (2) successful passing of the candidacy examination and a PhD proposal acceptance by the funded student; (3) design of storage efficient schemes for replicated distributed systems; and (4) modeling of gracefully degrading reliable computing systems. In the third year of the project (1992-93), we propose to: (1) complete the testing of the prototype; (2) enhance the functionality of the modules by enabling the experimentation with more complex protocols; (3) use the prototype to verify the theoretically predicted performance of locking protocols, etc.; and (4) work on issues related to real-time distributed systems. This should result in efficient protocols for these systems.

  18. Large deviation approach to the generalized random energy model

    NASA Astrophysics Data System (ADS)

    Dorlas, T. C.; Dukes, W. M. B.

    2002-05-01

    The generalized random energy model is a generalization of the random energy model introduced by Derrida to mimic the ultrametric structure of the Parisi solution of the Sherrington-Kirkpatrick model of a spin glass. It was solved exactly in two special cases by Derrida and Gardner. A complete solution for the thermodynamics in the general case was given by Capocaccia et al. Here we use large deviation theory to analyse the model in a very straightforward way. We also show that the variational expression for the free energy can be evaluated easily using the Cauchy-Schwarz inequality.

  19. A Generalized Kinetic Model for Heterogeneous Gas-Solid Reactions

    SciTech Connect

    Xu, Zhijie; Sun, Xin; Khaleel, Mohammad A.

    2012-08-15

    We present a generalized kinetic model for gas-solid heterogeneous reactions taking place at the interface between two phases. The model studies the reaction kinetics by taking into account the reactions at the interface, as well as the transport process within the product layer. The standard unreacted shrinking core model relies on the assumption of quasi-static diffusion that results in a steady-state concentration profile of gas reactant in the product layer. By relaxing this assumption and resolving the entire problem, general solutions can be obtained for reaction kinetics, including the reaction front velocity and the conversion (volume fraction of reacted solid). The unreacted shrinking core model is shown to be accurate and in agreement with the generalized model for slow reaction (or fast diffusion), low concentration of gas reactant, and small solid size. Otherwise, a generalized kinetic model should be used.

  20. Layered Kondo lattice model for quantum critical beta-YbAlB4.

    PubMed

    Nevidomskyy, Andriy H; Coleman, P

    2009-02-20

    We analyze the magnetic and electronic properties of the quantum critical heavy fermion superconductor beta-YbAlB4, calculating the Fermi surface and the angular dependence of the extremal orbits relevant to the de Haas-van Alphen measurements. Using a combination of the realistic materials modeling and single-ion crystal field analysis, we are led to propose a layered Kondo lattice model for this system, in which two-dimensional boron layers are Kondo coupled via interlayer Yb moments in a Jz=+/-5/2 state. This model fits the measured single-ion magnetic susceptibility and predicts a substantial change in the electronic anisotropy as the system is pressure tuned through the quantum critical point.

  1. Shell-Model Calculations of Two-Nucleon Tansfer Related to Double Beta Decay

    NASA Astrophysics Data System (ADS)

    Brown, Alex

    2013-10-01

    I will discuss theoretical results for two-nucleon transfer cross sections for nuclei in the regions of 48Ca, 76Ge and 136Xe of interest for testing the wavefuntions used for the nuclear matrix elements in double-beta decay. Various reaction models are used. A simple cluster transfer model gives relative cross sections. Thompson's code Fresco with direct and sequential transfer is used for absolute cross sections. Wavefunctions are obtained in large-basis proton-neutron coupled model spaces with the code NuShellX with realistic effecive Hamiltonians such as those used for the recent results for 136Xe [M. Horoi and B. A. Brown, Phys. Rev. Lett. 110, 222502 (2013)]. I acknowledge support from NSF grant PHY-1068217.

  2. An Ultrahigh Resolution Structure of TEM-1 beta-Lactamase Suggests a Role for Glu166 as the General Base in Acylation

    SciTech Connect

    Minasov, George; Wang, Xiaojun; Shoichet, Brian K.

    2010-03-08

    Although TEM-1 {beta}-lactamase is among the best studied enzymes, its acylation mechanism remains controversial. To investigate this problem, the structure of TEM-1 in complex with an acylation transition-state analogue was determined at ultrahigh resolution (0.85 {angstrom}) by X-ray crystallography. The quality of the data was such as to allow for refinement to an R-factor of 9.1% and an R{sub free} of 11.2%. In the resulting structure, the electron density features were clear enough to differentiate between single and double bonds in carboxylate groups, to identify multiple conformations that are occupied by residues and loops, and to assign 70% of the protons in the protein. Unexpectedly, even at pH 8.0 where the protein was crystallized, the active site residue Glu166 is clearly protonated. This supports the hypothesis that Glu166 is the general base in the acylation half of the reaction cycle. This structure suggests that Glu166 acts through the catalytic water to activate Ser70 for nucleophilic attack on the {beta}-lactam ring of the substrate. The hydrolytic mechanism of class A {beta}-lactamases, such as TEM-1, appears to be symmetrical, as are the serine proteases. Apart from its mechanistic implications, this atomic resolution structure affords an unusually detailed view of the structure, dynamics, and hydrogen-bonding networks of TEM-1, which may be useful for the design of inhibitors against this key antibiotic resistance target.

  3. Immunolocalization of alpha-keratins and feather beta-proteins in feather cells and comparison with the general process of cornification in the skin of mammals.

    PubMed

    Alibardi, L

    2013-03-01

    The maturation of the corneous material of feathers is a special case of cornification in vertebrate epidermis and is believed to occur mainly by the accumulation of small proteins of about 100 amino acids and a central beta-pleated sheet region known as feather keratins. The present immunocytochemical study carried out using double-labeling immunogold shows that a small amount of alpha-keratins of intermediate filament type form the early keratin clumps in barb and barbule cells. These initial nuclei of formation of corneous material are rapidly coated by the deposition of large amounts of small feather keratin-associated beta-proteins (feather keratins). The latter proteins turn the keratin bundles of barb and barbule cells into a compact and apparently amorphous mass of corneous material where no sign of intermediate filaments are seen. Feather beta-proteins however form an irregular filamentous network of 2-3nm thick electron-pale filaments and produce the characteristic feather X-ray pattern due to their prevalent amount over any other protein present in feather cells. The modality of cornification in feathers is discussed in relation to the process of formation of corneous material in the skin of vertebrates in general that occurs by the association of intermediate filament proteins and keratin-associated proteins.

  4. Quasideterminant solutions of the generalized Heisenberg magnet model

    NASA Astrophysics Data System (ADS)

    Saleem, U.; Hassan, M.

    2010-01-01

    In this paper we present the Darboux transformation for the generalized Heisenberg magnet (GHM) model based on the general linear Lie group GL(n) and construct multi-soliton solutions in terms of quasideterminants. Further we relate the quasideterminant multi-soliton solutions obtained by means of Darboux transformation with those obtained by the dressing method. We also discuss the model based on the Lie group SU(n) and obtain explicit soliton solutions of the model based on SU(2).

  5. Tokamak disruption alarm based on a neural network model of the high- beta limit

    NASA Astrophysics Data System (ADS)

    Wroblewski, D.; Jahns, G. L.; Leuer, J. A.

    1997-06-01

    An artificial neural network, combining signals from a large number of plasma diagnostics, was used to estimate the high- beta disruption boundary in the DIII-D tokamak. It is shown that inclusion of many diagnostic measurements results in a much more accurate prediction of the disruption boundary than that provided by the traditional Troyon limit. A trained neural network constitutes a non-linear, non-parametric model of the disruption boundary. Through the analysis of the input-output sensitivities, the relative statistical significance of various diagnostic measurements (plasma parameters) for the determination of the disruption boundary is directly assessed and the number of diagnostics used by the neural network model is reduced to the necessary minimum. The neural network is trained to map the disruption boundary throughout most of the discharge. As a result, it can predict the high- beta disruption boundary on a time-scale of the order of 100 ms (much longer than the precursor growth time), which makes this approach ideally suitable for real time application in a disruption avoidance scheme. Owing to the relative simplicity of the required computations, the neural network is easily implemented in a real time system. A prototype of the neural network disruption alarm was installed within the DIII-D digital plasma control system, and its real time operation, with a typical time resolution of 10 ms, was demonstrated

  6. Analysis of a compartmental model of amyloid beta production, irreversible loss and exchange in humans.

    PubMed

    Elbert, Donald L; Patterson, Bruce W; Bateman, Randall J

    2015-03-01

    Amyloid beta (Aβ) peptides, and in particular Aβ42, are found in senile plaques associated with Alzheimer's disease. A compartmental model of Aβ production, exchange and irreversible loss was recently developed to explain the kinetics of isotope-labeling of Aβ peptides collected in cerebrospinal fluid (CSF) following infusion of stable isotope-labeled leucine in humans. The compartmental model allowed calculation of the rates of production, irreversible loss (or turnover) and short-term exchange of Aβ peptides. Exchange of Aβ42 was particularly pronounced in amyloid plaque-bearing participants. In the current work, we describe in much greater detail the characteristics of the compartmental model to two distinct audiences: physician-scientists and biokineticists. For physician-scientists, we describe through examples the types of questions the model can and cannot answer, as well as correct some misunderstandings of previous kinetic analyses applied to this type of isotope labeling data. For biokineticists, we perform a system identifiability analysis and a sensitivity analysis of the kinetic model to explore the global and local properties of the model. Combined, these analyses motivate simplifications from a more comprehensive physiological model to the final model that was previously presented. The analyses clearly demonstrate that the current dataset and compartmental model allow determination with confidence a single 'turnover' parameter, a single 'exchange' parameter and a single 'delay' parameter. When combined with CSF concentration data for the Aβ peptides, production rates may also be obtained.

  7. Association between genetic variants of IL-1beta, IL-6 and TNF-alpha cytokines and cognitive performance in the elderly general population of the MEMO-study.

    PubMed

    Baune, Bernhard T; Ponath, Gerald; Rothermundt, Matthias; Riess, Olaf; Funke, Harald; Berger, Klaus

    2008-01-01

    This study is to investigate the associations between specific polymorphisms in three cytokine genes and domains of cognitive functioning in a population based study in the elderly. In a cross-sectional study of 369 community dwelling elderly subjects we examined the relationships between the polymorphisms IL-1beta-1418C-->T, IL-6-572G-->C and TNF-alpha-308G-->A and the cognitive function domains memory, processing speed and motor function using an extensive neuropsychological test battery. Linear regression models were used in the analysis and results adjusted for multiple comparisons. A significant association between the IL-1beta-1418C-->T polymorphism and memory performance was found with carriers of the T allele (dominant model) having worse memory performance than those with the C allele. In addition, a significant association between the TNF-alpha-308G-->A polymorphism and processing speed was observed, indicating better performance for heterozygous or homozygous carriers of the A allele. These results remained significant after adjustment for known confounders of cognitive function and additional Bonferroni correction for multiple comparisons. Our study provides first results on detrimental effects of the IL-1beta-1418C-->T polymorphism on memory performance and neuroprotective effects of the TNF-alpha-308G-->A polymorphism on processing speed in elderly individuals. Further research is needed to prospectively examine changes in cognitive performance in relation to cytokine genotypes.

  8. Cloud Feedback in Atmospheric General Circulation Models: An Update

    NASA Technical Reports Server (NTRS)

    Cess, R. D.; Zhang, M. H.; Ingram, W. J.; Potter, G. L.; Alekseev, V.; Barker, H. W.; Cohen-Solal, E.; Colman, R. A.; Dazlich, D. A.; DelGenio, A. D.; Dix, M. R.; Dymnikov, V.; Esch, M.; Fowler, L. D.; Fraser, J. R.; Galin, V.; Gates, W. L.; Hack, J. J.; Kiehl, J. T.; LeTreut, H.

    1996-01-01

    Six years ago, we compared the climate sensitivity of 19 atmospheric general circulation models and found a roughly threefold variation among the models; most of this variation was attributed to differences in the models' depictions of cloud feedback. In an update of this comparison, current models showed considerably smaller differences in net cloud feedback, with most producing modest values. There are, however, substantial differences in the feedback components, indicating that the models still have physical disagreements.

  9. Conserved Quantities in the Generalized Heisenberg Magnet (ghm) Model

    NASA Astrophysics Data System (ADS)

    Mushahid, N.; Hassan, M.; Saleem, U.

    2013-03-01

    We study the conserved quantities of the generalized Heisenberg magnet (GHM) model. We derive the nonlocal conserved quantities of the model using the iterative procedure of Brezin et al. [Phys. Lett. B82, 442 (1979).] We show that the nonlocal conserved quantities Poisson commute with local conserved quantities of the model.

  10. Calibrating the ECCO ocean general circulation model using Green's functions

    NASA Technical Reports Server (NTRS)

    Menemenlis, D.; Fu, L. L.; Lee, T.; Fukumori, I.

    2002-01-01

    Green's functions provide a simple, yet effective, method to test and calibrate General-Circulation-Model(GCM) parameterizations, to study and quantify model and data errors, to correct model biases and trends, and to blend estimates from different solutions and data products.

  11. Equating Parameter Estimates from the Generalized Graded Unfolding Model.

    ERIC Educational Resources Information Center

    Roberts, James S.

    Three common methods for equating parameter estimates from binary item response theory models are extended to the generalized grading unfolding model (GGUM). The GGUM is an item response model in which single-peaked, nonmonotonic expected value functions are implemented for polytomous responses. GGUM parameter estimates are equated using extended…

  12. Critical Comments on the General Model of Instructional Communication

    ERIC Educational Resources Information Center

    Walton, Justin D.

    2014-01-01

    This essay presents a critical commentary on McCroskey et al.'s (2004) general model of instructional communication. In particular, five points are examined which make explicit and problematize the meta-theoretical assumptions of the model. Comments call attention to the limitations of the model and argue for a broader approach to…

  13. Ising model on the generalized Bruhat-Tits tree

    NASA Astrophysics Data System (ADS)

    Zinoviev, Yu. M.

    1990-06-01

    The partition function and the correlation functions of the Ising model on the generalized Bruhat-Tits tree are calculated. We computed also the averages of these correlation functions when the corresponding vertices are attached to the boundary of the generalized Bruhat-Tits tree.

  14. Ising model on the generalized Bruhat-Tits tree

    NASA Astrophysics Data System (ADS)

    Zinoviev, Yu. M.

    1991-08-01

    The partition function and the correlation functions of the Ising model on the generalized Bruhat-Tits tree are calculated. We computed also the averages of these correlation functions when the corresponding vertices are attached to the boundary of the generalized Bruhat-Tits tree.

  15. Symmetric Fold/Super-Hopf Bursting, Chaos and Mixed-Mode Oscillations in Pernarowski Model of Pancreatic Beta-Cells

    NASA Astrophysics Data System (ADS)

    Fallah, Haniyeh

    Pancreatic beta-cells produce insulin to regularize the blood glucose level. Bursting is important in beta cells due to its relation to the release of insulin. Pernarowski model is a simple polynomial model of beta-cell activities indicating bursting oscillations in these cells. This paper presents bursting behaviors of symmetric type in this model. In addition, it is shown that the current system exhibits the phenomenon of period doubling cascades of canards which is a route to chaos. Canards are also observed symmetrically near folds of slow manifold which results in a chaotic transition between n and n + 1 spikes symmetric bursting. Furthermore, mixed-mode oscillations (MMOs) and combination of symmetric bursting together with MMOs are illustrated during the transition between symmetric bursting and continuous spiking.

  16. Low-dose paclitaxel ameliorates renal fibrosis in rat UUO model by inhibition of TGF-beta/Smad activity.

    PubMed

    Zhang, Dongshan; Sun, Lin; Xian, Wang; Liu, Fuyou; Ling, Guanghui; Xiao, Li; Liu, Yanhong; Peng, Youmin; Haruna, Yoshisuke; Kanwar, Yashpal S

    2010-03-01

    Transforming growth factor-beta (TGF-beta) has a pivotal function in the progression of renal fibrosis in a wide variety of renal diseases. Smad proteins have been identified to have an important function in regulating the expression of extracellular matrix (ECM) proteins through TGF-beta signaling pathway. Aberrant TGF-beta/Smad signaling can be modulated by stabilization of microtubules with paclitaxel. In this study, we investigated if paclitaxel can attenuate tubulointerstitial fibrosis in a rat model of unilateral ureteral obstruction (UUO). Rats in groups of six were subjected to UUO and received low-dose intraperitoneal injection of paclitaxel (0.3 mg/kg) twice a week. They were killed at day 7 and 14 after UUO or Sham operation. TGF-beta signaling cascade and status of various ECM proteins were evaluated by RT-PCR, western blotting and immunohistochemical or immunofluorescence staining. The paclitaxel treatment markedly suppressed Smad2 and Smad3 phosphorylation. This was associated with attenuated expression of integrin-linked kinase, collagens I and III, fibronectin (FN) and alpha-smooth muscle actin, and a substantial decrease in renal fibrosis in animals that underwent UUO and received paclitaxel. These data indicate that the low-dose paclitaxel ameliorates renal tubulointerstitial fibrosis by modulating TGF-beta signaling, and thus, the paclitaxel may have some therapeutic value in humans.

  17. Haloacetic acid and trihalomethane formation from the chlorination and bromination of aliphatic beta-dicarbonyl acid model compounds.

    PubMed

    Dickenson, Eric R V; Summers, R Scott; Croué, Jean-Philippe; Gallard, Hervé

    2008-05-01

    While it is known that resorcinol- and phenol-type aromatic structures within natural organic matter (NOM) react during drinking water chlorination to form trihalomethanes (THMs), limited studies have examined aliphatic-type structures as THM and haloacetic acid (HAA) precursors. A suite of aliphatic acid model compounds were chlorinated and brominated separately in controlled laboratory-scale batch experiments. Four and two beta-dicarbonyl acid compounds were found to be important precursors for the formation of THMs (chloroform and bromoform (71-91% mol/mol)), and dihaloacetic acids (DXAAs) (dichloroacetic acid and dibromoacetic acid (5-68% mol/mol)), respectively, after 24 h at pH 8. Based upon adsorbable organic halide formation, THMs and DXAAs, and to a lesser extent mono and trihaloacetic acids, were the majority (> 80%) of the byproducts produced for most of the aliphatic beta-dicarbonyl acid compounds. Aliphatic beta-diketone-acid-type and beta-keto-acid-type structures could be possible fast- and slow-reacting THM precursors, respectively, and aliphatic beta-keto-acid-type structures are possible slow-reacting DXAA precursors. Aliphatic beta-dicarbonyl acid moieties in natural organic matter, particularly in the hydrophilic fraction, could contribute to the significant formation of THMs and DXAAs observed after chlorination of natural waters.

  18. The DINA model as a constrained general diagnostic model: Two variants of a model equivalency.

    PubMed

    von Davier, Matthias

    2014-02-01

    The 'deterministic-input noisy-AND' (DINA) model is one of the more frequently applied diagnostic classification models for binary observed responses and binary latent variables. The purpose of this paper is to show that the model is equivalent to a special case of a more general compensatory family of diagnostic models. Two equivalencies are presented. Both project the original DINA skill space and design Q-matrix using mappings into a transformed skill space as well as a transformed Q-matrix space. Both variants of the equivalency produce a compensatory model that is mathematically equivalent to the (conjunctive) DINA model. This equivalency holds for all DINA models with any type of Q-matrix, not only for trivial (simple-structure) cases. The two versions of the equivalency presented in this paper are not implied by the recently suggested log-linear cognitive diagnosis model or the generalized DINA approach. The equivalencies presented here exist independent of these recently derived models since they solely require a linear - compensatory - general diagnostic model without any skill interaction terms. Whenever it can be shown that one model can be viewed as a special case of another more general one, conclusions derived from any particular model-based estimates are drawn into question. It is widely known that multidimensional models can often be specified in multiple ways while the model-based probabilities of observed variables stay the same. This paper goes beyond this type of equivalency by showing that a conjunctive diagnostic classification model can be expressed as a constrained special case of a general compensatory diagnostic modelling framework.

  19. Adaptation of a general circulation model to ocean dynamics

    NASA Technical Reports Server (NTRS)

    Turner, R. E.; Rees, T. H.; Woodbury, G. E.

    1976-01-01

    A primitive-variable general circulation model of the ocean was formulated in which fast external gravity waves are suppressed with rigid-lid surface constraint pressires which also provide a means for simulating the effects of large-scale free-surface topography. The surface pressure method is simpler to apply than the conventional stream function models, and the resulting model can be applied to both global ocean and limited region situations. Strengths and weaknesses of the model are also presented.

  20. Two field BPS solutions for generalized Lorentz breaking models

    SciTech Connect

    Souza Dutra, A. de; Hott, M.; Barone, F. A.

    2006-10-15

    In this work we present nonlinear models in two-dimensional space-time of two interacting scalar fields in the Lorentz and CPT violating scenarios. We discuss the soliton solutions for these models as well as the question of stability for them. This is done by generalizing a model recently published by Barreto and collaborators and also by getting new solutions for the model introduced by them.

  1. A spin foam model for general Lorentzian 4-geometries

    NASA Astrophysics Data System (ADS)

    Conrady, Florian; Hnybida, Jeff

    2010-09-01

    We derive simplicity constraints for the quantization of general Lorentzian 4-geometries. Our method is based on the correspondence between coherent states and classical bivectors and the minimization of associated uncertainties. For triangulations with spacelike triangles, this scheme agrees with the master constraint method of the model by Engle, Pereira, Rovelli and Livine (EPRL). When it is applied to general triangulations of Lorentzian geometries, we obtain new constraints that include the EPRL constraints as a special case. They imply a discrete area spectrum for both spacelike and timelike surfaces. We use these constraints to define a spin foam model for general Lorentzian 4-geometries.

  2. General autocatalytic theory and simple model of financial markets

    NASA Astrophysics Data System (ADS)

    Thuy Anh, Chu; Lan, Nguyen Tri; Viet, Nguyen Ai

    2015-06-01

    The concept of autocatalytic theory has become a powerful tool in understanding evolutionary processes in complex systems. A generalization of autocatalytic theory was assumed by considering that the initial element now is being some distribution instead of a constant value as in traditional theory. This initial condition leads to that the final element might have some distribution too. A simple physics model for financial markets is proposed, using this general autocatalytic theory. Some general behaviours of evolution process and risk moment of a financial market also are investigated in framework of this simple model.

  3. Generalized Kähler Geometry from Supersymmetric Sigma Models

    NASA Astrophysics Data System (ADS)

    Bredthauer, Andreas; Lindström, Ulf; Persson, Jonas; Zabzine, Maxim

    2006-09-01

    We give a physical derivation of generalized Kähler geometry. Starting from a supersymmetric nonlinear sigma model, we rederive and explain the results of Gualtieri (Generalized complex geometry, DPhil thesis, Oxford University, 2004) regarding the equivalence between generalized Kähler geometry and the bi-hermitean geometry of Gates et al. (Nucl Phys B248:157, 1984). When cast in the language of supersymmetric sigma models, this relation maps precisely to that between the Lagrangian and the Hamiltonian formalisms. We also discuss topological twist in this context.

  4. A potential field model using generalized sigmoid functions.

    PubMed

    Ren, Jing; McIsaac, Kenneth A; Patel, Rajni V; Peters, Terry M

    2007-04-01

    The lack of a potential field model capable of providing accurate representations of objects of arbitrary shapes is considered one major limitation in applying the artificial potential field method in many practical applications. In this correspondence, we propose a potential function based on generalized sigmoid functions. The generalized sigmoid model can be constructed from combinations of implicit primitives or from sampled surface data. The constructed potential field model can achieve an accurate analytic description of objects in two or three dimensions and requires very modest computation at run time. In this correspondence, applications of the generalized sigmoid model in path-planning tasks for mobile robots and in haptic feedback tasks are presented. The validation results in this correspondence show that the model can effectively allow the user or mobile robot to avoid penetrations of obstacles while successfully accomplishing the task.

  5. A generalized statistical model for the size distribution of wealth

    NASA Astrophysics Data System (ADS)

    Clementi, F.; Gallegati, M.; Kaniadakis, G.

    2012-12-01

    In a recent paper in this journal (Clementi et al 2009 J. Stat. Mech. P02037), we proposed a new, physically motivated, distribution function for modeling individual incomes, having its roots in the framework of the κ-generalized statistical mechanics. The performance of the κ-generalized distribution was checked against real data on personal income for the United States in 2003. In this paper we extend our previous model so as to be able to account for the distribution of wealth. Probabilistic functions and inequality measures of this generalized model for wealth distribution are obtained in closed form. In order to check the validity of the proposed model, we analyze the US household wealth distributions from 1984 to 2009 and conclude an excellent agreement with the data that is superior to any other model already known in the literature.

  6. Generalized linear and generalized additive models in studies of species distributions: Setting the scene

    USGS Publications Warehouse

    Guisan, A.; Edwards, T.C.; Hastie, T.

    2002-01-01

    An important statistical development of the last 30 years has been the advance in regression analysis provided by generalized linear models (GLMs) and generalized additive models (GAMs). Here we introduce a series of papers prepared within the framework of an international workshop entitled: Advances in GLMs/GAMs modeling: from species distribution to environmental management, held in Riederalp, Switzerland, 6-11 August 2001. We first discuss some general uses of statistical models in ecology, as well as provide a short review of several key examples of the use of GLMs and GAMs in ecological modeling efforts. We next present an overview of GLMs and GAMs, and discuss some of their related statistics used for predictor selection, model diagnostics, and evaluation. Included is a discussion of several new approaches applicable to GLMs and GAMs, such as ridge regression, an alternative to stepwise selection of predictors, and methods for the identification of interactions by a combined use of regression trees and several other approaches. We close with an overview of the papers and how we feel they advance our understanding of their application to ecological modeling. ?? 2002 Elsevier Science B.V. All rights reserved.

  7. A generalized model via random walks for information filtering

    NASA Astrophysics Data System (ADS)

    Ren, Zhuo-Ming; Kong, Yixiu; Shang, Ming-Sheng; Zhang, Yi-Cheng

    2016-08-01

    There could exist a simple general mechanism lurking beneath collaborative filtering and interdisciplinary physics approaches which have been successfully applied to online E-commerce platforms. Motivated by this idea, we propose a generalized model employing the dynamics of the random walk in the bipartite networks. Taking into account the degree information, the proposed generalized model could deduce the collaborative filtering, interdisciplinary physics approaches and even the enormous expansion of them. Furthermore, we analyze the generalized model with single and hybrid of degree information on the process of random walk in bipartite networks, and propose a possible strategy by using the hybrid degree information for different popular objects to toward promising precision of the recommendation.

  8. Standard-Model Tests with Superallowed {beta} Decay: Nuclear Data Applied to Fundamental Physics

    SciTech Connect

    Hardy, J.C.

    2005-05-24

    The study of superallowed nuclear {beta} decay currently provides the most precise and convincing confirmation of the conservation of the vector current (CVC) and is a key component of the most demanding available test of the unitarity of the Cabibbo-Kobayashi-Maskawa (CKM) matrix, a basic pillar of the Electroweak Standard Model. Experimentally, the Q-value, half-life, and branching ratio for superallowed transitions must be determined with a precision better than 0.1%. This demands metrological techniques be applied to short-lived ({approx}1 s) activities and that strict standards be employed in surveying the body of world data. The status of these fundamental studies is summarized and recent work described.

  9. Deformed shell model results for neutrinoless double beta decay of nuclei in A = 60 - 90 region

    NASA Astrophysics Data System (ADS)

    Sahu, R.; Kota, V. K. B.

    2015-03-01

    Nuclear transition matrix elements (NTME) for the neutrinoless double beta decay (Oνββ or OνDBD) of 70Zn, 80Se and 82Se nuclei are calculated within the framework of the deformed shell model (DSM) based on Hartree-Fock (HF) states. For 70Zn, jj44b interaction in 2p3/2, 1f5/2, 2p1/2 and 1g9/2 space with 56Ni as the core is employed. However, for 80Se and 82Se nuclei, a modified Kuo interaction with the above core and model space are employed. Most of our calculations in this region were performed with this effective interaction. However, jj44b interaction has been found to be better for 70Zn. The above model space was used in many recent shell model (SM) and interacting boson model (IBM) calculations for nuclei in this region. After ensuring that DSM gives good description of the spectroscopic properties of low-lying levels in these three nuclei considered, the NTME are calculated. The deduced half-lives with these NTME, assuming neutrino mass is 1 eV, are 1.1 × 1026, 2.3 × 1027 and 2.2 × 1024 yr for 70Zn, 80Se and 82Se, respectively.

  10. Inefficiency in GM2 ganglioside elimination by human lysosomal beta-hexosaminidase beta-subunit gene transfer to fibroblastic cell line derived from Sandhoff disease model mice.

    PubMed

    Itakura, Tomohiro; Kuroki, Aya; Ishibashi, Yasuhiro; Tsuji, Daisuke; Kawashita, Eri; Higashine, Yukari; Sakuraba, Hitoshi; Yamanaka, Shoji; Itoh, Kohji

    2006-08-01

    Sandhoff disease (SD) is an autosomal recessive GM2 gangliosidosis caused by the defect of lysosomal beta-hexosaminidase (Hex) beta-subunit gene associated with neurosomatic manifestations. Therapeutic effects of Hex subunit gene transduction have been examined on Sandhoff disease model mice (SD mice) produced by the allelic disruption of Hexb gene encoding the murine beta-subunit. We demonstrate here that elimination of GM2 ganglioside (GM2) accumulated in the fibroblastic cell line derived from SD mice (FSD) did not occur when the HEXB gene only was transfected. In contrast, a significant increase in the HexB (betabeta homodimer) activity toward neutral substrates, including GA2 (asialo-GM2) and oligosaccharides carrying the terminal N-acetylglucosamine residues at their non-reducing ends (GlcNAc-oligosaccharides) was observed. Immunoblotting with anti-human HexA (alphabeta heterodimer) serum after native polyacrylamide gel electrophoresis (Native-PAGE) revealed that the human HEXB gene product could hardly form the chimeric HexA through associating with the murine alpha-subunit. However, co-introduction of the HEXA encoding the human alpha-subunit and HEXB genes caused significant corrective effect on the GM2 degradation by producing the human HexA. These results indicate that the recombinant human HexA could interspeciesly associate with the murine GM2 activator protein to degrade GM2 accumulated in the FSD cells. Thus, therapeutic effects of the recombinant human HexA isozyme but not human HEXB gene product could be evaluated by using the SD mice.

  11. A generalized item response tree model for psychological assessments.

    PubMed

    Jeon, Minjeong; De Boeck, Paul

    2016-09-01

    A new item response theory (IRT) model with a tree structure has been introduced for modeling item response processes with a tree structure. In this paper, we present a generalized item response tree model with a flexible parametric form, dimensionality, and choice of covariates. The utilities of the model are demonstrated with two applications in psychological assessments for investigating Likert scale item responses and for modeling omitted item responses. The proposed model is estimated with the freely available R package flirt (Jeon et al., 2014b).

  12. Modeling of conformational transitions of fibrillogenic peptide, homologous to beta-domain of human alpha-lactalbumin

    NASA Astrophysics Data System (ADS)

    Kadochnikov, V. V.; Egorov, V. V.; Shvetsov, A. V.; Kuklin, A. I.; Isaev-Ivanov, V. V.; Lebedev, D. V.

    2016-01-01

    The behavior of the peptide corresponding to beta domain of human alpha-lactalbumin (GYDTQAIVENNESTEYG, WT) has been simulated by the molecular dynamics method. It is shown that, within the model considered, the monomer of this peptide does not tend to form a stable secondary structure; however, simulation of the behavior of several peptide molecules revealed the occurrence of beta structures due to the formation of intermolecular hydrogen bonds. Since the aforementioned interactions involve the terminal portions of peptides, the influence of the tetrapeptide corresponding to the N-terminal portion of WT, TDYG (R), on the secondary structure has been analyzed. The model calculations show that the interaction of this peptide with WT monomer facilitates formation of beta-structures. It is suggested that peptide R may affect the quaternary structure of WT.

  13. A Generalized Evaluation Model for Primary Prevention Programs.

    ERIC Educational Resources Information Center

    Barling, Phillip W.; Cramer, Kathryn D.

    A generalized evaluation model (GEM) has been developed to evaluate primary prevention program impact. The GEM model views primary prevention dynamically; delineating four structural components (program, organization, target population, system) and four developmental stages (initiation, establishment, integration, continuation). The interaction of…

  14. A General Method for Modeling Macromolecular Shape in Solution

    PubMed Central

    Harding, Stephen E.

    1987-01-01

    A general method for modeling macromolecular shape in solution is described involving measurements of viscosity, radius of gyration, and the second thermodynamic virial coefficient. The method, which should be relatively straightforward to apply, does not suffer from uniqueness problems, involves shape functions that are independent of hydration, and models the gross conformation of the macromolecule in solution as a general triaxial ellipsoid. The method is illustrated by application to myosin, and the relevance and applicability of ellipsoid modeling to biological structures is discussed. PMID:19431695

  15. A generalized cholera model and epidemic-endemic analysis.

    PubMed

    Wang, Jin; Liao, Shu

    2012-01-01

    The transmission of cholera involves both human-to-human and environment-to-human pathways that complicate its dynamics. In this paper, we present a new and unified deterministic model that incorporates a general incidence rate and a general formulation of the pathogen concentration to analyse the dynamics of cholera. Particularly, this work unifies many existing cholera models proposed by different authors. We conduct equilibrium analysis to carefully study the complex epidemic and endemic behaviour of the disease. Our results show that despite the incorporation of the environmental component, there exists a forward transcritical bifurcation at R (0)=1 for the combined human-environment epidemiological model under biologically reasonable conditions.

  16. Residuals analysis of the generalized linear models for longitudinal data.

    PubMed

    Chang, Y C

    2000-05-30

    The generalized estimation equation (GEE) method, one of the generalized linear models for longitudinal data, has been used widely in medical research. However, the related sensitivity analysis problem has not been explored intensively. One of the possible reasons for this was due to the correlated structure within the same subject. We showed that the conventional residuals plots for model diagnosis in longitudinal data could mislead a researcher into trusting the fitted model. A non-parametric method, named the Wald-Wolfowitz run test, was proposed to check the residuals plots both quantitatively and graphically. The rationale proposedin this paper is well illustrated with two real clinical studies in Taiwan.

  17. Flexible Approaches to Computing Mediated Effects in Generalized Linear Models: Generalized Estimating Equations and Bootstrapping

    ERIC Educational Resources Information Center

    Schluchter, Mark D.

    2008-01-01

    In behavioral research, interest is often in examining the degree to which the effect of an independent variable X on an outcome Y is mediated by an intermediary or mediator variable M. This article illustrates how generalized estimating equations (GEE) modeling can be used to estimate the indirect or mediated effect, defined as the amount by…

  18. Chop deletion reduces oxidative stress, improves beta cell function, and promotes cell survival in multiple mouse models of diabetes.

    PubMed

    Song, Benbo; Scheuner, Donalyn; Ron, David; Pennathur, Subramaniam; Kaufman, Randal J

    2008-10-01

    The progression from insulin resistance to type 2 diabetes is caused by the failure of pancreatic beta cells to produce sufficient levels of insulin to meet the metabolic demand. Recent studies indicate that nutrient fluctuations and insulin resistance increase proinsulin synthesis in beta cells beyond the capacity for folding of nascent polypeptides within the endoplasmic reticulum (ER) lumen, thereby disrupting ER homeostasis and triggering the unfolded protein response (UPR). Chronic ER stress promotes apoptosis, at least in part through the UPR-induced transcription factor C/EBP homologous protein (CHOP). We assessed the effect of Chop deletion in multiple mouse models of type 2 diabetes and found that Chop-/- mice had improved glycemic control and expanded beta cell mass in all conditions analyzed. In both genetic and diet-induced models of insulin resistance, CHOP deficiency improved beta cell ultrastructure and promoted cell survival. In addition, we found that isolated islets from Chop-/- mice displayed increased expression of UPR and oxidative stress response genes and reduced levels of oxidative damage. These findings suggest that CHOP is a fundamental factor that links protein misfolding in the ER to oxidative stress and apoptosis in beta cells under conditions of increased insulin demand.

  19. A Generalized Information Theoretical Model for Quantum Secret Sharing

    NASA Astrophysics Data System (ADS)

    Bai, Chen-Ming; Li, Zhi-Hui; Xu, Ting-Ting; Li, Yong-Ming

    2016-11-01

    An information theoretical model for quantum secret sharing was introduced by H. Imai et al. (Quantum Inf. Comput. 5(1), 69-80 2005), which was analyzed by quantum information theory. In this paper, we analyze this information theoretical model using the properties of the quantum access structure. By the analysis we propose a generalized model definition for the quantum secret sharing schemes. In our model, there are more quantum access structures which can be realized by our generalized quantum secret sharing schemes than those of the previous one. In addition, we also analyse two kinds of important quantum access structures to illustrate the existence and rationality for the generalized quantum secret sharing schemes and consider the security of the scheme by simple examples.

  20. Partially Observed Mixtures of IRT Models: An Extension of the Generalized Partial-Credit Model

    ERIC Educational Resources Information Center

    Von Davier, Matthias; Yamamoto, Kentaro

    2004-01-01

    The generalized partial-credit model (GPCM) is used frequently in educational testing and in large-scale assessments for analyzing polytomous data. Special cases of the generalized partial-credit model are the partial-credit model--or Rasch model for ordinal data--and the two parameter logistic (2PL) model. This article extends the GPCM to the…

  1. Muon capture in a general class of weak models

    NASA Astrophysics Data System (ADS)

    Botella, F. J.

    1985-10-01

    We study muon capture by 12C in a general class of weak models. There is always a parameter characteristic of the weak model that can be extracted in a nuclear-model-independent way from the average polarization Pav, the longitudinal polarization PNL and the asymmetry α in the angular distribution of recoils. For a less general class of models the asymmetry α is unnecessary. Using the experimental values of PNL and Pav we get a lower bound for the mass of the right-handed gauge boson of the left-right-symmetric model, MWR>=2.5MWL, in a nuclear-model-independent way. The dependence of this bound on the experimental values is also discussed.

  2. A general non-linear multilevel structural equation mixture model

    PubMed Central

    Kelava, Augustin; Brandt, Holger

    2014-01-01

    In the past 2 decades latent variable modeling has become a standard tool in the social sciences. In the same time period, traditional linear structural equation models have been extended to include non-linear interaction and quadratic effects (e.g., Klein and Moosbrugger, 2000), and multilevel modeling (Rabe-Hesketh et al., 2004). We present a general non-linear multilevel structural equation mixture model (GNM-SEMM) that combines recent semiparametric non-linear structural equation models (Kelava and Nagengast, 2012; Kelava et al., 2014) with multilevel structural equation mixture models (Muthén and Asparouhov, 2009) for clustered and non-normally distributed data. The proposed approach allows for semiparametric relationships at the within and at the between levels. We present examples from the educational science to illustrate different submodels from the general framework. PMID:25101022

  3. General Hubbard Model for Fermions in an Optical Lattice

    NASA Astrophysics Data System (ADS)

    Kestner, Jason; Duan, Luming

    2009-03-01

    For two-component fermions in an optical lattice, an effective general Hubbard model (GHM) with tunable on-site attraction/repulsion and occupation-dependent hopping rates emerges from very general arguments [1]. This model is quite interesting, containing as special cases both the t-J and the XXZ models. However, the experimental range of applicability and the connection between the model parameters and the actual experimental parameters must be determined explicitly. To this end, we have used a stochastic variational approach with a correlated gaussian wavefunction to numerically find the eigenstates of two atoms interacting in a 3D few-well trap. By matching the few-site spectrum of the GHM to the variational spectrum obtained, the validity of the model and the relationship between experimental and model parameters are determined. [1] L.-M. Duan, Euro. Phys. Lett. 81, 20001 (2008).

  4. Lifetime Measurements of ^170Hf and a test of the Confined Beta Soft Rotor Model

    NASA Astrophysics Data System (ADS)

    Smith, M. K.; Werner, V.; Heinz, A.; Terry, J. R.; Qian, J.; Winkler, R.; Casperson, R.; Williams, E.; Berant, Z.; L"Uttke, R.; Shoraka, B.; Henning, G.

    2009-10-01

    Significant deviations from rigid rotor model energy level predictions have been known to occur in rare earth nuclei. Recently, it was shown these deviations may be caused by centrifugal stretching effects within the nucleus [1]. New geometrical models have been proposed that account for centrifugal stretching, such as the confined beta soft model (CBS). We present the results from a high precision lifetime experiment performed with the New Yale Plunger Device at WNSL, Yale University. The ground state band of ^170Hf was measured through the J=12^+ level using the Recoil Distance Doppler Shift method. Excited states were populated in the ^124Sn(^50Ti,γ)^170Hf fusion evaporation reaction. Using the lifetimes, the B(E2) values and the quadrupole deformation parameter are determined. Centrifugal stretching is observed as an increased deviation in energy at higher spins in 170Hf. These results are compared to theoretical predictions from the CBS rotor model. Supported by grant DE-FG02-91ER40609.[4pt] [1] Costin et al, Phys.Rev. C 79, 024307 (2009)

  5. Geometric critical exponent inequalities for general random cluster models

    NASA Astrophysics Data System (ADS)

    Tasaki, Hal

    1987-11-01

    A set of new critical exponent inequalities, d(1 -1 / δ)≥2 - η, dv(1 - 1/ δ)≥ γ, and dμ> 1, is proved for a general class of random cluster models, which includes (independent or dependent) percolations, lattice animals (with any interactions), and various stochastic cluster growth models. The inequalities imply that the critical phenomena in the models are inevitably not mean-field-like in the dimensions one, two, and three.

  6. Asian Summer Monsoon Intraseasonal Variability in General Circulation Models

    SciTech Connect

    Sperber, K R; Annamalai, H

    2004-02-24

    The goals of this report are: (1) Analyze boreal summer Asian monsoon intraseasonal variability general circulation models--How well do the models represent the eastward and northward propagating components of the convection and how well do the models represent the interactive control that the western tropical Pacific rainfall exerts on the rainfall over India and vice-versa? (2) Role of air-sea interactions--prescribed vs. interactive ocean; and (3) Mean monsoon vs. variability.

  7. Generalization of Richardson-Gaudin models to rank-2 algebras

    SciTech Connect

    Errea, B; Lerma, S; Dukelsky, J; Dimitrova, S S; Pittel, S; Van Isacker, P; Gueorguiev, V G

    2006-07-20

    A generalization of Richardson-Gaudin models to the rank-2 SO(5) and SO(3,2) algebras is used to describe systems of two kinds of fermions or bosons interacting through a pairing force. They are applied to the proton-neutron neutron isovector pairing model and to the Interacting Boson Model 2, in the transition from vibration to gamma-soft nuclei, respectively. In both cases, the integrals of motion and their eigenvalues are obtained.

  8. Australian and overseas models of general practice training.

    PubMed

    Hays, Richard B; Morgan, Simon

    2011-06-06

    General practice training in Australia continues to evolve. It is now the responsibility of an independent organisation, is delivered by regional training providers, and comprises a structured training program. Overseas, general practice varies in its importance to health care systems, and training models differ considerably. In some cases training is mandatory, in others voluntary, but the aim is always similar--to improve the quality of care delivered to the large majority of populations that access health care through primary care. We review the current status of vocational general practice training in Australia, compare it with selected training programs in international contexts, and describe how the local model is well placed to address future challenges. Challenges include changes in population demographics, increasing comorbidity, increasing costs of technology-based health care, increasing globalisation of health, and workforce shortages. Although general practice training in Australia is strong, it can improve further by learning from other training programs to meet these challengers.

  9. Comparison of the pn quasiparticle RPA and shell model for Gamow-Teller beta and double-beta decays

    NASA Astrophysics Data System (ADS)

    Zhao, Liang; Brown, B. Alex

    1993-06-01

    We examine the validity of the pn quasiparticle RPA (pnQRPA) as a model for calculating β+ and 2νββ Gamow-Teller decays by making a comparison of the pnQRPA with a large-basis shell-model calculation within the 0f1p shell. We employ A=46 nuclei (those with six valence nucleons) for this comparison. Our comparison includes the decay matrix elements summed over final states, the strength distributions, and, for the first time, the coherent transition matrix elements (CTME). The pnQRPA overestimates the total β+ and 2νββ matrix elements. There are large differences in the shape of the spectra as well as in the CTME between the pnQRPA and shell-model results. Empirical improvements for the pnQRPA are discussed.

  10. The involvement of Opaque 2 on beta-prolamin gene regulation in maize and Coix suggests a more general role for this transcriptional activator.

    PubMed

    Cord Neto, G; Yunes, J A; da Silva, M J; Vettore, A L; Arruda, P; Leite, A

    1995-03-01

    The maize opaque 2 (o2) mutation is known to have numerous pleiotropic effects. Some polypeptides have their expression depressed while others are enhanced. The best characterized effects of the o2 mutation are those exerted on endosperm genes encoding the storage protein class of the 22 kDa alpha-zeins and the ribosome inactivating protein b-32. The Opaque 2 (O2) locus encodes a basic domain-leucine zipper DNA-binding factor, O2, which transcriptionally regulates these genes. In the maize-related grass Coix lacryma-jobi, an O2-homologous protein regulates the 25 kDa alpha-coixin family. We show in this paper that O2 transcriptionally regulates the structurally and developmentally different class of the beta-prolamins. A new O2-binding box was identified in beta-prolamin genes from maize and Coix that, together with the boxes previously identified in other endosperm expressed genes, forms a curious collection of O2 cis elements. This may have regulatory implications on the role of O2 in the mechanism that controls coordinated gene expression in the developing endosperm. Considering that the O2 locus controls at least three distinct classes of genes in maize endosperm, we propose that the O2 protein may play a more general role in maize endosperm development than previously conceived.

  11. Coding and noncoding variation of the human calcium-channel beta4-subunit gene CACNB4 in patients with idiopathic generalized epilepsy and episodic ataxia.

    PubMed Central

    Escayg, A; De Waard, M; Lee, D D; Bichet, D; Wolf, P; Mayer, T; Johnston, J; Baloh, R; Sander, T; Meisler, M H

    2000-01-01

    Inactivation of the beta4 subunit of the calcium channel in the mouse neurological mutant lethargic results in a complex neurological disorder that includes absence epilepsy and ataxia. To determine the role of the calcium-channel beta4-subunit gene CACNB4 on chromosome 2q22-23 in related human disorders, we screened for mutations in small pedigrees with familial epilepsy and ataxia. The premature-termination mutation R482X was identified in a patient with juvenile myoclonic epilepsy. The R482X protein lacks the 38 C-terminal amino acids containing part of an interaction domain for the alpha1 subunit. The missense mutation C104F was identified both in a German family with generalized epilepsy and praxis-induced seizures and in a French Canadian family with episodic ataxia. These coding mutations were not detected in 255 unaffected control individuals (510 chromosomes), and they may be considered candidate disease mutations. The results of functional tests of the truncated protein R482X in Xenopus laevis oocytes demonstrated a small decrease in the fast time constant for inactivation of the cotransfected alpha1 subunit. Further studies will be required to evaluate the in vivo consequences of these mutations. We also describe eight noncoding single-nucleotide substitutions, two of which are present at polymorphic frequency, and a previously unrecognized first intron of CACNB4 that interrupts exon 1 at codon 21. PMID:10762541

  12. Modeling the brain morphology distribution in the general aging population

    NASA Astrophysics Data System (ADS)

    Huizinga, W.; Poot, D. H. J.; Roshchupkin, G.; Bron, E. E.; Ikram, M. A.; Vernooij, M. W.; Rueckert, D.; Niessen, W. J.; Klein, S.

    2016-03-01

    Both normal aging and neurodegenerative diseases such as Alzheimer's disease cause morphological changes of the brain. To better distinguish between normal and abnormal cases, it is necessary to model changes in brain morphology owing to normal aging. To this end, we developed a method for analyzing and visualizing these changes for the entire brain morphology distribution in the general aging population. The method is applied to 1000 subjects from a large population imaging study in the elderly, from which 900 were used to train the model and 100 were used for testing. The results of the 100 test subjects show that the model generalizes to subjects outside the model population. Smooth percentile curves showing the brain morphology changes as a function of age and spatiotemporal atlases derived from the model population are publicly available via an interactive web application at agingbrain.bigr.nl.

  13. Phase-field modeling of the beta to omega phase transformation in Zr–Nb alloys

    SciTech Connect

    Yeddu, Hemantha Kumar; Lookman, Turab

    2015-05-01

    A three-dimensional elastoplastic phase-field model is developed, using the Finite Element Method (FEM), for modeling the athermal beta to omega phase transformation in Zr–Nb alloys by including plastic deformation and strain hardening of the material. The microstructure evolution during athermal transformation as well as under different stress states, e.g. uni-axial tensile and compressive, bi-axial tensile and compressive, shear and tri-axial loadings, is studied. The effects of plasticity, stress states and the stress loading direction on the microstructure evolution as well as on the mechanical properties are studied. The input data corresponding to a Zr – 8 at.% Nb alloy are acquired from experimental studies as well as by using the CALPHAD method. Our simulations show that the four different omega variants grow as ellipsoidal shaped particles. Our results show that due to stress relaxation, the athermal phase transformation occurs slightly more readily in the presence of plasticity compared to that in its absence. The evolution of omega phase is different under different stress states, which leads to the differences in the mechanical properties of the material. The variant selection mechanism, i.e. formation of different variants under different stress loading directions, is also nicely captured by our model.

  14. Phase-field modeling of the beta to omega phase transformation in Zr–Nb alloys

    DOE PAGES

    Yeddu, Hemantha Kumar; Lookman, Turab

    2015-05-01

    A three-dimensional elastoplastic phase-field model is developed, using the Finite Element Method (FEM), for modeling the athermal beta to omega phase transformation in Zr–Nb alloys by including plastic deformation and strain hardening of the material. The microstructure evolution during athermal transformation as well as under different stress states, e.g. uni-axial tensile and compressive, bi-axial tensile and compressive, shear and tri-axial loadings, is studied. The effects of plasticity, stress states and the stress loading direction on the microstructure evolution as well as on the mechanical properties are studied. The input data corresponding to a Zr – 8 at.% Nb alloy aremore » acquired from experimental studies as well as by using the CALPHAD method. Our simulations show that the four different omega variants grow as ellipsoidal shaped particles. Our results show that due to stress relaxation, the athermal phase transformation occurs slightly more readily in the presence of plasticity compared to that in its absence. The evolution of omega phase is different under different stress states, which leads to the differences in the mechanical properties of the material. The variant selection mechanism, i.e. formation of different variants under different stress loading directions, is also nicely captured by our model.« less

  15. Analyzing and modeling the kinetics of amyloid beta pores associated with Alzheimer’s disease pathology

    DOE PAGES

    Ullah, Ghanim; Demuro, Angelo; Parker, Ian; ...

    2015-09-08

    Amyloid beta (Aβ) oligomers associated with Alzheimer’s disease (AD) form Ca2+-permeable plasma membrane pores, leading to a disruption of the otherwise well-controlled intracellular calcium (Ca2+) homeostasis. The resultant up-regulation of intracellular Ca2+ concentration has detrimental implications for memory formation and cell survival. The gating kinetics and Ca2+ permeability of Aβ pores are not well understood. We have used computational modeling in conjunction with the ability of optical patch-clamping for massively parallel imaging of Ca2+ flux through thousands of pores in the cell membrane of Xenopus oocytes to elucidate the kinetic properties of Aβ pores. The fluorescence time-series data from individualmore » pores were idealized and used to develop data-driven Markov chain models for the kinetics of the Aβ pore at different stages of its evolution. Our study provides the first demonstration of developing Markov chain models for ion channel gating that are driven by optical-patch clamp data with the advantage of experiments being performed under close to physiological conditions. As a result, we demonstrate the up-regulation of gating of various Ca2+ release channels due to Aβ pores and show that the extent and spatial range of such up-regulation increases as Aβ pores with low open probability and Ca2+ permeability transition into those with high open probability and Ca2+ permeability.« less

  16. A mathematical model of the kinetics of beta-amyloid fibril growth from the denatured state.

    PubMed Central

    Pallitto, M M; Murphy, R M

    2001-01-01

    Spontaneous conversion of beta-amyloid peptide (Abeta) from soluble monomer to insoluble fibril may underlie the neurodegeneration associated with Alzheimer's disease. A complete description of Abeta self-association kinetics requires identification of the oligomeric species present and the pathway of association, as well as quantitation of rate constants and reaction order. Abeta was rendered monomeric and denatured by dissolution in 8 M urea, pH 10. "Refolding" and fibrillization were initiated by rapid dilution into phosphate-buffered saline, pH 7.4. The kinetics of growth were followed at three different concentrations, using size exclusion chromatography, dynamic light scattering, and static light scattering. A multi-step pathway for fibril formation and growth was postulated. This pathway included 1) rapid commitment to either stable monomer/dimer or unstable intermediate, 2) cooperative association of intermediate into a multimeric "nucleus," 3) elongation of the "nucleus" into filaments via addition of intermediate, 4) lateral aggregation of filaments into fibrils, and 5) fibril elongation via end-to-end association. Differential and algebraic equations describing this kinetic pathway were derived, and model parameters were determined by fitting the data. The utility of the model for identifying toxic Abeta oligomeric specie(s) is demonstrated. The model should prove useful for designing compounds that inhibit Abeta aggregation and/or toxicity. PMID:11509390

  17. Coexistence of interacting opinions in a generalized Sznajd model

    NASA Astrophysics Data System (ADS)

    Timpanaro, André M.; Prado, Carmen P. C.

    2011-08-01

    The Sznajd model is a sociophysics model that mimics the propagation of opinions in a closed society, where the interactions favor groups of agreeing people. It is based in the Ising and Potts ferromagnetic models and, although the original model used only linear chains, it has since been adapted to general networks. This model has a very rich transient, which has been used to model several aspects of elections, but its stationary states are always consensus states. In order to model more complex behaviors, we have, in a recent work, introduced the idea of biases and prejudices to the Sznajd model by generalizing the bounded confidence rule, which is common to many continuous opinion models, to what we called confidence rules. In that work we have found that the mean field version of this model (corresponding to a complete network) allows for stationary states where noninteracting opinions survive, but never for the coexistence of interacting opinions. In the present work, we provide networks that allow for the coexistence of interacting opinions for certain confidence rules. Moreover, we show that the model does not become inactive; that is, the opinions keep changing, even in the stationary regime. This is an important result in the context of understanding how a rule that breeds local conformity is still able to sustain global diversity while avoiding a frozen stationary state. We also provide results that give some insights on how this behavior approaches the mean field behavior as the networks are changed.

  18. A general diagnostic model applied to language testing data.

    PubMed

    von Davier, Matthias

    2008-11-01

    Probabilistic models with one or more latent variables are designed to report on a corresponding number of skills or cognitive attributes. Multidimensional skill profiles offer additional information beyond what a single test score can provide, if the reported skills can be identified and distinguished reliably. Many recent approaches to skill profile models are limited to dichotomous data and have made use of computationally intensive estimation methods such as Markov chain Monte Carlo, since standard maximum likelihood (ML) estimation techniques were deemed infeasible. This paper presents a general diagnostic model (GDM) that can be estimated with standard ML techniques and applies to polytomous response variables as well as to skills with two or more proficiency levels. The paper uses one member of a larger class of diagnostic models, a compensatory diagnostic model for dichotomous and partial credit data. Many well-known models, such as univariate and multivariate versions of the Rasch model and the two-parameter logistic item response theory model, the generalized partial credit model, as well as a variety of skill profile models, are special cases of this GDM. In addition to an introduction to this model, the paper presents a parameter recovery study using simulated data and an application to real data from the field test for TOEFL Internet-based testing.

  19. Generalized model for incoherent detection in confocal optical microscopy.

    PubMed

    Hammoum, Rachid; Hamady, Sidi Ould Saad; Fontana, Marc D

    2010-06-01

    We develop a generalized model in order to calculate the point spread functions in both the focal and the detection planes for the electric field strengths. In these calculations, based on the generalized Jones matrices, we introduce all of the interdependent parameters that could influence the spatial resolution of a confocal optical microscope. Our proposed model is more nearly complete, since we make no approximations of the scattered electric fields. These results can be successfully applied to standard confocal optical techniques to get a better understanding for more quantitative interpretations of the probe.

  20. Glycogen synthase kinase-3beta heterozygote knockout mice as a model of findings in postmortem schizophrenia brain or as a model of behaviors mimicking lithium action: negative results.

    PubMed

    Bersudsky, Yuly; Shaldubina, Alona; Kozlovsky, Nitzan; Woodgett, James R; Agam, Galila; Belmaker, R H

    2008-05-01

    In mice glycogen synthase kinase (GSK)-3beta heterozygote knockout status was reported to cause reduced immobility in the Porsolt forced swim test and reduced amphetamine-induced hyperactivity, behaviors that mimic the effects of lithium. GSK-3beta protein and mRNA level and activity have been reported to be reduced in the postmortem brain of schizophrenia patients and this could suggest the involvement of GSK-3beta in the etiology of schizophrenia. However, apomorphine-induced stereotyping was reported to be unchanged in GSK-3beta heterozygote (HZ) knockout (KO) mice. As such behaviors are not always robust, study in another laboratory seemed indicated. Motor activity and coordination were assessed in the rotarod test. Behavior was studied in the following tests: pilocarpine-induced seizures model for lithium action, Porsolt forced swim test, tail suspension test, elevated plus-maze, large open field, startle response and prepulse inhibition of acoustic startle response, amphetamine-induced hyperactivity, and apomorphine-induced stereotypic climbing. We could not confirm the report that GSK-3beta HZ KO mice exhibit reduced immobility in the Porsolt forced swim or reduced amphetamine-induced hyperactivity in a manner mimicking the behavioral effects of lithium. We did not find increased apomorphine-induced stereotypic climbing or disruption of prepulse inhibition, suggesting that human postmortem findings regarding GSK-3beta in schizophrenia are not mediated by changes in dopamine receptors and are not the cause of prepulse inhibition deficits in schizophrenia. These data do not support the role of GSK-3beta in schizophrenia or in the mechanism of therapeutic action of lithium. Although differences in the genetic background of the GSK-3beta HZ KOs used in the present study compared with that of the previous study could be responsible, such results could suggest that the previously reported effects of GSK-3beta knockout on behavior are not robust.

  1. Generalized gas-solid adsorption modeling: Single-component equilibria

    SciTech Connect

    Ladshaw, Austin; Yiacoumi, Sotira; Tsouris, Costas; DePaoli, David W.

    2015-01-07

    Over the last several decades, modeling of gas–solid adsorption at equilibrium has generally been accomplished through the use of isotherms such as the Freundlich, Langmuir, Tóth, and other similar models. While these models are relatively easy to adapt for describing experimental data, their simplicity limits their generality to be used with many different sets of data. This limitation forces engineers and scientists to test each different model in order to evaluate which one can best describe their data. Additionally, the parameters of these models all have a different physical interpretation, which may have an effect on how they can be further extended into kinetic, thermodynamic, and/or mass transfer models for engineering applications. Therefore, it is paramount to adopt not only a more general isotherm model, but also a concise methodology to reliably optimize for and obtain the parameters of that model. A model of particular interest is the Generalized Statistical Thermodynamic Adsorption (GSTA) isotherm. The GSTA isotherm has enormous flexibility, which could potentially be used to describe a variety of different adsorption systems, but utilizing this model can be fairly difficult due to that flexibility. To circumvent this complication, a comprehensive methodology and computer code has been developed that can perform a full equilibrium analysis of adsorption data for any gas-solid system using the GSTA model. The code has been developed in C/C++ and utilizes a Levenberg–Marquardt’s algorithm to handle the non-linear optimization of the model parameters. Since the GSTA model has an adjustable number of parameters, the code iteratively goes through all number of plausible parameters for each data set and then returns the best solution based on a set of scrutiny criteria. Data sets at different temperatures are analyzed serially and then linear correlations with temperature are made for the parameters of the model. The end result is a full set of

  2. Generalized gas-solid adsorption modeling: Single-component equilibria

    DOE PAGES

    Ladshaw, Austin; Yiacoumi, Sotira; Tsouris, Costas; ...

    2015-01-07

    Over the last several decades, modeling of gas–solid adsorption at equilibrium has generally been accomplished through the use of isotherms such as the Freundlich, Langmuir, Tóth, and other similar models. While these models are relatively easy to adapt for describing experimental data, their simplicity limits their generality to be used with many different sets of data. This limitation forces engineers and scientists to test each different model in order to evaluate which one can best describe their data. Additionally, the parameters of these models all have a different physical interpretation, which may have an effect on how they can bemore » further extended into kinetic, thermodynamic, and/or mass transfer models for engineering applications. Therefore, it is paramount to adopt not only a more general isotherm model, but also a concise methodology to reliably optimize for and obtain the parameters of that model. A model of particular interest is the Generalized Statistical Thermodynamic Adsorption (GSTA) isotherm. The GSTA isotherm has enormous flexibility, which could potentially be used to describe a variety of different adsorption systems, but utilizing this model can be fairly difficult due to that flexibility. To circumvent this complication, a comprehensive methodology and computer code has been developed that can perform a full equilibrium analysis of adsorption data for any gas-solid system using the GSTA model. The code has been developed in C/C++ and utilizes a Levenberg–Marquardt’s algorithm to handle the non-linear optimization of the model parameters. Since the GSTA model has an adjustable number of parameters, the code iteratively goes through all number of plausible parameters for each data set and then returns the best solution based on a set of scrutiny criteria. Data sets at different temperatures are analyzed serially and then linear correlations with temperature are made for the parameters of the model. The end result is a full set

  3. Generalized memory associativity in a network model for the neuroses

    NASA Astrophysics Data System (ADS)

    Wedemann, Roseli S.; Donangelo, Raul; de Carvalho, Luís A. V.

    2009-03-01

    We review concepts introduced in earlier work, where a neural network mechanism describes some mental processes in neurotic pathology and psychoanalytic working-through, as associative memory functioning, according to the findings of Freud. We developed a complex network model, where modules corresponding to sensorial and symbolic memories interact, representing unconscious and conscious mental processes. The model illustrates Freud's idea that consciousness is related to symbolic and linguistic memory activity in the brain. We have introduced a generalization of the Boltzmann machine to model memory associativity. Model behavior is illustrated with simulations and some of its properties are analyzed with methods from statistical mechanics.

  4. Generalized memory associativity in a network model for the neuroses.

    PubMed

    Wedemann, Roseli S; Donangelo, Raul; de Carvalho, Luís A V

    2009-03-01

    We review concepts introduced in earlier work, where a neural network mechanism describes some mental processes in neurotic pathology and psychoanalytic working-through, as associative memory functioning, according to the findings of Freud. We developed a complex network model, where modules corresponding to sensorial and symbolic memories interact, representing unconscious and conscious mental processes. The model illustrates Freud's idea that consciousness is related to symbolic and linguistic memory activity in the brain. We have introduced a generalization of the Boltzmann machine to model memory associativity. Model behavior is illustrated with simulations and some of its properties are analyzed with methods from statistical mechanics.

  5. Generalized F test and generalized deviance test in two-way ANOVA models for randomized trials.

    PubMed

    Shen, Juan; He, Xuming

    2014-01-01

    We consider the problem of detecting treatment effects in a randomized trial in the presence of an additional covariate. By reexpressing a two-way analysis of variance (ANOVA) model in a logistic regression framework, we derive generalized F tests and generalized deviance tests, which provide better power in detecting common location-scale changes of treatment outcomes than the classical F test. The null distributions of the test statistics are independent of the nuisance parameters in the models, so the critical values can be easily determined by Monte Carlo methods. We use simulation studies to demonstrate how the proposed tests perform compared with the classical F test. We also use data from a clinical study to illustrate possible savings in sample sizes.

  6. Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations.

    PubMed

    Luo, Zhonglin; Ding, Jiandong; Zhou, Yaoqi

    2008-06-14

    This paper examines the folding mechanism of an individual beta-hairpin in the presence of other hairpins by using an off-lattice model of a small triple-stranded antiparallel beta-sheet protein, Pin1 WW domain. The turn zipper model and the hydrophobic collapse model originally developed for a single beta-hairpin in literature is confirmed to be useful in describing beta-hairpins in model Pin1 WW domain. We find that the mechanism for folding a specific hairpin is independent of whether it folds first or second, but the formation process are significantly dependent on temperature. More specifically, beta1-beta2 hairpin folds via the turn zipper model at a low temperature and the hydrophobic collapse model at a high temperature, while the folding of beta2-beta3 hairpin follows the turn zipper model at both temperatures. The change in folding mechanisms is interpreted by the interplay between contact stability (enthalpy) and loop lengths (entropy), the effect of which is temperature dependent.

  7. A general graphical user interface for automatic reliability modeling

    NASA Technical Reports Server (NTRS)

    Liceaga, Carlos A.; Siewiorek, Daniel P.

    1991-01-01

    Reported here is a general Graphical User Interface (GUI) for automatic reliability modeling of Processor Memory Switch (PMS) structures using a Markov model. This GUI is based on a hierarchy of windows. One window has graphical editing capabilities for specifying the system's communication structure, hierarchy, reconfiguration capabilities, and requirements. Other windows have field texts, popup menus, and buttons for specifying parameters and selecting actions. An example application of the GUI is given.

  8. p75 reduces beta-amyloid-induced sympathetic innervation deficits in an Alzheimer's disease mouse model.

    PubMed

    Bengoechea, Tasha G; Chen, Zhijiang; O'Leary, Debra A; O'Leary, Deborah; Masliah, Eliezer; Lee, Kuo-Fen

    2009-05-12

    Beta-amyloid (Abeta) has adverse effects on brain cells, but little is known about its effects on the peripheral nervous system in Alzheimer's disease (AD). Several lines of in vitro evidence suggest that the neurotrophin receptor p75 mediates or exacerbates Abeta-induced neurotoxicity. Here, we show that p75-deficient sympathetic neurons are more sensitive to Abeta-induced neurite growth inhibition. To investigate the role of p75 in the sympathetic nervous system of AD, p75 mutant mice were crossed with a mouse line of AD model. The majority of p75-deficient AD mice died by 3 weeks of age. The lethality is associated with severe defects in sympathetic innervation to multiple organs. When 1 copy of the BACE1 gene encoding a protein essential in Abeta production was deleted in p75-deficient AD mice, sympathetic innervation was significantly restored. These results suggest that p75 is neuroprotective for the sympathetic nervous system in a mouse model of AD.

  9. Benchmarking the thermodynamic analysis of water molecules around a model beta sheet.

    PubMed

    Huggins, David J

    2012-06-05

    Water molecules play a vital role in biological and engineered systems by controlling intermolecular interactions in the aqueous phase. Inhomogeneous fluid solvation theory provides a method to quantify solvent thermodynamics from molecular dynamics or Monte Carlo simulations and provides an insight into intermolecular interactions. In this study, simulations of TIP4P-2005 and TIP5P-Ewald water molecules around a model beta sheet are used to investigate the orientational correlations and predicted thermodynamic properties of water molecules at a protein surface. This allows the method to be benchmarked and provides information about the effect of a protein on the thermodynamics of nearby water molecules. The results show that the enthalpy converges with relatively little sampling, but the entropy and thus the free energy require considerably more sampling to converge. The two water models yield a very similar pattern of hydration sites, and these hydration sites have very similar thermodynamic properties, despite notable differences in their orientational preferences. The results also predict that a protein surface affects the free energy of water molecules to a distance of approximately 4.0 Å, which is in line with previous work. In addition, all hydration sites have a favorable free energy with respect to bulk water, but only when the water-water entropy term is included. A new technique for calculating this term is presented and its use is expected to be very important in accurately calculating solvent thermodynamics for quantitative application.

  10. Modeling Pseudomonas syringae ice-nucleation protein as a beta-helical protein.

    PubMed Central

    Graether, S P; Jia, Z

    2001-01-01

    Antifreeze proteins (AFPs) inhibit the growth of ice, whereas ice-nucleation proteins (INPs) promote its formation. Although the structures of several AFPs are known, the structure of INP has been modeled thus far because of the difficulty in determining membrane protein structures. Here, we present a novel model of an INP structure from Pseudomonas syringae based on comparison with two newly determined insect AFP structures. The results suggest that both this class of AFPs and INPs may have a similar beta-helical fold and that they could interact with water through the repetitive TXT motif. By theoretical arguments, we show that the distinguishing feature between an ice inhibitor and an ice nucleator lies in the size of the ice-interacting surface. For INPs, the larger surface area acts as a template that is larger than the critical ice embryo surface area required for growth. In contrast, AFPs are small enough so that they bind to ice and inhibit further growth without acting as a nucleator. PMID:11222281

  11. Cellulose hydrolysis in evolving substrate morphologies I: A general modeling formalism.

    PubMed

    Zhou, Wen; Schüttler, Heinz-Bernd; Hao, Zhiqian; Xu, Ying

    2009-10-01

    We develop a general framework for a realistic rate equation modeling of cellulose hydrolysis using non-complexed cellulase. Our proposed formalism, for the first time, takes into account explicitly the time evolution of the random substrate morphology resulting from the hydrolytic cellulose chain fragmentation and solubilization. This is achieved by integrating novel geometrical concepts to quantitatively capture the time-dependent random morphology, together with the enzymatic chain fragmentation, into a coupled morphology-plus-kinetics rate equation approach. In addition, an innovative site number representation, based on tracking available numbers of beta(1,4) glucosidic bonds, of different "site" types, exposed to attacks by different enzyme types, is presented. This site number representation results in an ordinary differential equation (ODE) system, with a substantially reduced ODE system size, compared to earlier chain fragmentation kinetics approaches. This formalism enables us to quantitatively simulate both the hydrolytically evolving random substrate morphology and the profound, and heretofore neglected, morphology effects on the hydrolysis kinetics. By incorporating the evolving morphology on an equal footing with the hydrolytic chain fragmentation, our formalism provides a framework for the realistic modeling of the entire solubilization process, beyond the short-time limit and through near-complete hydrolytic conversion. As part I of two companion papers, the present paper focuses on the development of the general modelling formalism. Results and testable experimental predictions from detailed numerical simulations are presented in part II.

  12. Photometric Stereo for General BRDFs via Reflection Sparsity Modeling.

    PubMed

    Han, Tian-Qi; Shen, Hui-Liang

    2015-12-01

    This paper proposes a pixelwise photometric stereo method for object surfaces with general bidirectional reflectance distribution functions (BRDFs) via appropriate reflection modeling. The modeling is based on three general characteristics of reflection components, i.e., the smooth variation of diffuse reflection, the concentration of specular reflection, and the low-intensity nature of shadow. A graph, whose nodes are light directions, is introduced to model these characteristics. In the graph, the neighborhood of nodes is determined by finding the light sources with close directions. The smoothness of the diffuse component is termed as the summation of local variations under all light sources. The specular reflection is modeled by group sparsity, and the shadow is determined via weighted l1 -norm modeling. The optimization problem, which incorporates these three modeling terms, is cast as a second-order cone programming problem. The proposed method is evaluated on both synthetic and real-world scenes with both isotropic and anisotropic materials. The experimental results show that the method is effective for object surfaces with general BRDFs and outperforms the state-of-the-arts.

  13. Computerized Classification Testing under the Generalized Graded Unfolding Model

    ERIC Educational Resources Information Center

    Wang, Wen-Chung; Liu, Chen-Wei

    2011-01-01

    The generalized graded unfolding model (GGUM) has been recently developed to describe item responses to Likert items (agree-disagree) in attitude measurement. In this study, the authors (a) developed two item selection methods in computerized classification testing under the GGUM, the current estimate/ability confidence interval method and the cut…

  14. Suggesting a General ESP Model for Adult Learners

    ERIC Educational Resources Information Center

    Al-Jumaily, Samir

    2011-01-01

    The study suggests a general model that could guarantee the cooperation between teachers and their students to overcome the difficulties encountered in ESP learning. It tries to join together different perspectives in the research of adult education, specifically in the teaching of English for Specific Purposes. It also provides some sort of trust…

  15. A general circulation model (GCM) parameterization of Pinatubo aerosols

    SciTech Connect

    Lacis, A.A.; Carlson, B.E.; Mishchenko, M.I.

    1996-04-01

    The June 1991 volcanic eruption of Mt. Pinatubo is the largest and best documented global climate forcing experiment in recorded history. The time development and geographical dispersion of the aerosol has been closely monitored and sampled. Based on preliminary estimates of the Pinatubo aerosol loading, general circulation model predictions of the impact on global climate have been made.

  16. Confidence Intervals for Assessing Heterogeneity in Generalized Linear Mixed Models

    ERIC Educational Resources Information Center

    Wagler, Amy E.

    2014-01-01

    Generalized linear mixed models are frequently applied to data with clustered categorical outcomes. The effect of clustering on the response is often difficult to practically assess partly because it is reported on a scale on which comparisons with regression parameters are difficult to make. This article proposes confidence intervals for…

  17. A Novel Multipurpose Model Set for Teaching General Chemistry.

    ERIC Educational Resources Information Center

    Gupta, H. O.; Parkash, Brahm

    1999-01-01

    Reports on a low-cost and unique molecular model set capable of generating a large number of structures for teaching and learning general chemistry. An important component of the kit is an 11-hole ball that gives tetrahedral, octahedral, trigonal, trigonal bipyramidal, and square planar symmetries. (WRM)

  18. Generalized universality in the massive sine-Gordon model

    SciTech Connect

    Nagy, S.; Sailer, K.; Nandori, I.; Polonyi, J.

    2008-01-15

    A nontrivial interplay of the UV and IR scaling laws, a generalization of the universality is demonstrated in the framework of the massive sine-Gordon model, as a result of a detailed study of the global behavior of the renormalization group flow and the phase structure.

  19. Institutional Quality and Generalized Trust: A Nonrecursive Causal Model

    ERIC Educational Resources Information Center

    Robbins, Blaine G.

    2012-01-01

    This paper investigates the association between institutional quality and generalized trust. Despite the importance of the topic, little quantitative empirical evidence exists to support either unidirectional or bidirectional causality for the reason that cross-sectional studies rarely model the reciprocal relationship between institutional…

  20. Beta measurements

    NASA Technical Reports Server (NTRS)

    Schotland, R. M.; Warren, A. J.; Funariu, O. M.

    1991-01-01

    The second year's results of the BETA project research are presented. The program is divided into two areas, aerosol modification and climatology in the trade wind region and the climatology of BETA (CO2) on remote mountain top locations. Limited data is available on the aerosol climatology of the marine free troposphere (MFT) in the trade wind region. In order to study the effects of cumulus convection on the MFT values of BETA, a cloud model was developed to simulate the evolution of a typical Pacific trade wind cumulus cloud. The stages involved in this development are outlined. The assembly of the major optical components of the lidar was made. Tests were run of the spectral bandwidth of the Synrad laser when a portion of the beam is mixed with a component which has traveled 450 meters corresponding to a delay of 1.5 microsecs. The bandwidth of the beat signal was measured to be 3 KHz. The data processing system based on a parallel processing filter bank analyzer using true time squaring detectors at each filter was completed.

  1. Self-assembly of the beta2-microglobulin NHVTLSQ peptide using a coarse-grained protein model reveals a beta-barrel species.

    PubMed

    Song, Wei; Wei, Guanghong; Mousseau, Normand; Derreumaux, Philippe

    2008-04-10

    Although a wide variety of proteins can assemble into amyloid fibrils, the structure of the early oligomeric species on the aggregation pathways remains unknown at an atomic level of detail. In this paper we report, using molecular dynamics simulations with the OPEP coarse-grained force field, the free energy landscape of a tetramer and a heptamer of the beta2-microglobulin NHVTLSQ peptide. On the basis of a total of more than 17 ns trajectories started from various states, we find that both species are in equilibrium between amorphous and well-ordered aggregates with cross-beta-structure, a perpendicular bilayer beta-sheet, and, for the heptamer, six- or seven-stranded closed and open beta-barrels. Moreover, analysis of the heptamer trajectories shows that the perpendicular bilayer beta-sheet is one possible precursor of the beta-barrel, but that this barrel can also be formed from a twisted monolayer beta-sheet with successive addition of chains. Comparison with previous aggregation simulations and the fact that nature constructs transmembrane beta-sheet proteins with pores open the possibility that beta-barrels with small inner diameters may represent a common intermediate during the early steps of aggregation.

  2. Molecular basis of feline beta-glucuronidase deficiency: an animal model of mucopolysaccharidosis VII.

    PubMed

    Fyfe, J C; Kurzhals, R L; Lassaline, M E; Henthorn, P S; Alur, P R; Wang, P; Wolfe, J H; Giger, U; Haskins, M E; Patterson, D F; Sun, H; Jain, S; Yuhki, N

    1999-06-01

    A family of domestic cats was found that exhibited clinical and biochemical abnormalities consistent with mucopolysaccharidosis VII, an autosomal recessive lysosomal storage disorder caused by beta-glucuronidase deficiency. beta-Glucuronidase activity was undetectable in affected cat fibroblasts and restored by retroviral gene transfer of rat beta-glucuronidase cDNA. beta-Glucuronidase mRNA was normal in affected cat testis by Northern blot analysis. Normal feline beta-glucuronidase cDNA was cloned and characterized, and amplified from affected cat fibroblasts by reverse transcription coupled polymerase chain reaction. There was a G-to-A transition in the affected cat cDNA that predicted an E351K substitution, destroyed a BssSI site, and eliminated GUSB enzymatic activity in expression studies. Multiple species comparison and the crystal structure of human beta-glucuronidase indicated that E351 is a highly conserved residue most likely essential in maintenance of the enzyme's conformation. BssSI digestion of polymerase chain reaction products amplified from genomic DNA indicated that affected cats were homozygous and cats with half-normal beta-glucuronidase activity were heterozygous for the missense mutation. Carriers identified in this manner produced affected kittens in prospective breedings, and a feline MPS VII breeding colony has been established.

  3. 75 FR 71532 - Airworthiness Directives; Robinson Helicopter Company (Robinson) Model R22, R22 Alpha, R22 Beta...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-24

    ...This amendment adopts a new airworthiness directive (AD) for Robinson Model R22, R22 Alpha, R22 Beta, and R22 Mariner helicopters, and Model R44 and R44 II helicopters. This AD requires visually inspecting each tail rotor (T/R) control pedal bearing block support (support) for a crack, measuring the thickness of each support, installing support safety tabs on certain supports, and replacing......

  4. Micro RNA-214 contributes to proteasome independent downregulation of beta catenin in Huntington's disease knock-in striatal cell model STHdhQ111/Q111.

    PubMed

    Ghatak, Supratim; Raha, Sanghamitra

    2015-04-10

    Role of beta catenin in Huntington's disease (HD) is not clear. Previous studies on HD reported varied levels of beta catenin. In the present study we showed that beta catenin is post transcriptionally down-regulated in mutant huntingtin knock-in cell model STHdhQ111/Q111. This in turn leads to decreased level of wnt/beta catenin responsive genes. We observed that Gsk3beta or Gsk3beta (phospho Ser 9) is unaltered in HD and this down-regulation of beta catenin is independent of proteasomal degradation. Finally, we showed that the overexpression of miR-214 leads to the down-regulation of beta catenin at protein level only and reduces its transcriptional activity. We concluded that, miR-214 contributes to the processes that result in proteasome independent post transcriptional down-regulation of beta catenin in STHdhQ111/Q111, probably through inhibition of protein synthesis from beta catenin mRNA.

  5. Commensurate Priors for Incorporating Historical Information in Clinical Trials Using General and Generalized Linear Models.

    PubMed

    Hobbs, Brian P; Sargent, Daniel J; Carlin, Bradley P

    2012-08-28

    Assessing between-study variability in the context of conventional random-effects meta-analysis is notoriously difficult when incorporating data from only a small number of historical studies. In order to borrow strength, historical and current data are often assumed to be fully homogeneous, but this can have drastic consequences for power and Type I error if the historical information is biased. In this paper, we propose empirical and fully Bayesian modifications of the commensurate prior model (Hobbs et al., 2011) extending Pocock (1976), and evaluate their frequentist and Bayesian properties for incorporating patient-level historical data using general and generalized linear mixed regression models. Our proposed commensurate prior models lead to preposterior admissible estimators that facilitate alternative bias-variance trade-offs than those offered by pre-existing methodologies for incorporating historical data from a small number of historical studies. We also provide a sample analysis of a colon cancer trial comparing time-to-disease progression using a Weibull regression model.

  6. Interaction of osteopontin with neutrophil {alpha}{sub 4}{beta}{sub 1} and {alpha}{sub 9}{beta}{sub 1} integrins in a rodent model of alcoholic liver disease

    SciTech Connect

    Banerjee, Atrayee; Lee, Jin-Hyung; Ramaiah, Shashi K

    2008-12-01

    Previous studies from our laboratory have reported that osteopontin (OPN) mediated higher hepatic neutrophil infiltration makes female rats more susceptible to alcoholic steatohepatitis (ASH) than their male counterparts. The objective of the current work was to investigate the patho-mechanism by which OPN attracts the hepatic neutrophils in ASH. We hypothesized that OPN-mediated hepatic neutrophil infiltration is a result of signaling by N-terminal integrin binding motif (SLAYGLR) of OPN through its receptor {alpha}{sub 9}{beta}{sub 1} (VLA9) and {alpha}{sub 4}{beta}{sub 1} (VLA4) integrins on neutrophils. Compared to the males, females in the ASH group exhibited higher expression of {alpha}{sub 4}{beta}{sub 1} and {alpha}{sub 9}{beta}{sub 1} protein and mRNA and a significant decrease in the expression of these integrins was observed in rats treated with neutralizing OPN antibody. Immunoprecipitation experiments suggested the binding of OPN to {alpha}{sub 4}{beta}{sub 1} and {alpha}{sub 9}{beta}{sub 1} integrins. OPN-mediated neutrophil infiltration was also confirmed using Boyden chamber assays, and antibodies directed against {alpha}{sub 4} and {beta}{sub 1} integrins was found to significantly inhibit neutrophilic migration in vitro. In conclusion, these data suggest that SLAYGLR-mediated {alpha}{sub 4}{beta}{sub 1} and {alpha}{sub 9}{beta}{sub 1} integrin signaling may be responsible for higher hepatic neutrophil infiltration and higher liver injury in the rat ASH model.

  7. Generalized Levy-walk model for DNA nucleotide sequences

    NASA Technical Reports Server (NTRS)

    Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Simons, M.; Stanley, H. E.

    1993-01-01

    We propose a generalized Levy walk to model fractal landscapes observed in noncoding DNA sequences. We find that this model provides a very close approximation to the empirical data and explains a number of statistical properties of genomic DNA sequences such as the distribution of strand-biased regions (those with an excess of one type of nucleotide) as well as local changes in the slope of the correlation exponent alpha. The generalized Levy-walk model simultaneously accounts for the long-range correlations in noncoding DNA sequences and for the apparently paradoxical finding of long subregions of biased random walks (length lj) within these correlated sequences. In the generalized Levy-walk model, the lj are chosen from a power-law distribution P(lj) varies as lj(-mu). The correlation exponent alpha is related to mu through alpha = 2-mu/2 if 2 < mu < 3. The model is consistent with the finding of "repetitive elements" of variable length interspersed within noncoding DNA.

  8. Concurrent approaches to Generalized Parton Distribution modeling: the pion's case

    NASA Astrophysics Data System (ADS)

    Chouika, N.; Mezrag, C.; Moutarde, H.; Rodríguez-Quintero, J.

    2017-03-01

    The concept of Generalized Parton Distributions promises an understanding of the generation of the charge, spin, and energy-momentum structure of hadrons by quarks and gluons. Forthcoming measurements with unprecedented accuracy at Jefferson Lab and at CERN will challenge our quantitative description of the three-dimensional structure of hadrons. To fully exploit these future measurements, new tools and models are currently being developed. We explain the difficulties of Generalized Parton Distribution modeling, and present some recent progresses. In particular we describe the symmetry-preserving Dyson-Schwinger and Bethe-Salpeter framework. We also discuss various equivalent parameterizations and sketch how to combine them to obtain models satisfying a priori all required theoretical constraints. At last we explain why these developments naturally fit in a versatile software framework, named PARTONS, dedicated to the theory and phenomenology of GPDs.

  9. Generalized Jaynes-Cummings model as a quantum search algorithm

    SciTech Connect

    Romanelli, A.

    2009-07-15

    We propose a continuous time quantum search algorithm using a generalization of the Jaynes-Cummings model. In this model the states of the atom are the elements among which the algorithm realizes the search, exciting resonances between the initial and the searched states. This algorithm behaves like Grover's algorithm; the optimal search time is proportional to the square root of the size of the search set and the probability to find the searched state oscillates periodically in time. In this frame, it is possible to reinterpret the usual Jaynes-Cummings model as a trivial case of the quantum search algorithm.

  10. A general kinetic model for the hydrothermal liquefaction of microalgae.

    PubMed

    Valdez, Peter J; Tocco, Vincent J; Savage, Phillip E

    2014-07-01

    We developed a general kinetic model for hydrothermal liquefaction (HTL) of microalgae. The model, which allows the protein, lipid, and carbohydrate fractions of the cell to react at different rates, successfully correlated experimental data for the hydrothermal liquefaction of Chlorella protothecoides, Scenedesmus sp., and Nannochloropsis sp. The model can faithfully account for the influence of time and temperature on the gravimetric yields of gas, solid, biocrude, and aqueous-phase products from isothermal HTL of a 15 wt% slurry. Examination of the rate constants shows that lipids and proteins are the major contributors to the biocrude, while other algal cell constituents contribute very little to the biocrude.

  11. A parallel coupled oceanic-atmospheric general circulation model

    SciTech Connect

    Wehner, M.F.; Bourgeois, A.J.; Eltgroth, P.G.; Duffy, P.B.; Dannevik, W.P.

    1994-12-01

    The Climate Systems Modeling group at LLNL has developed a portable coupled oceanic-atmospheric general circulation model suitable for use on a variety of massively parallel (MPP) computers of the multiple instruction, multiple data (MIMD) class. The model is composed of parallel versions of the UCLA atmospheric general circulation model, the GFDL modular ocean model (MOM) and a dynamic sea ice model based on the Hiber formulation extracted from the OPYC ocean model. The strategy to achieve parallelism is twofold. One level of parallelism is accomplished by applying two dimensional domain decomposition techniques to each of the three constituent submodels. A second level of parallelism is attained by a concurrent execution of AGCM and OGCM/sea ice components on separate sets of processors. For this functional decomposition scheme, a flux coupling module has been written to calculate the heat, moisture and momentum fluxes independent of either the AGCM or the OGCM modules. The flux coupler`s other roles are to facilitate the transfer of data between subsystem components and processors via message passing techniques and to interpolate and aggregate between the possibly incommensurate meshes.

  12. Short duration of breast-feeding as a risk-factor for beta-cell autoantibodies in 5-year-old children from the general population.

    PubMed

    Holmberg, Hanna; Wahlberg, Jeanette; Vaarala, Outi; Ludvigsson, Johnny

    2007-01-01

    Breast-feeding has been suggested to have a protective effect against the development of type 1 diabetes. In the present study, we investigated the relation between duration of breast-feeding and beta-cell autoantibodies in 5-year-old non-diabetic children who participated in a prospective population-based follow-up study (the All Babies in Southeast Sweden study). Autoantibodies to insulin (IAA), glutamic acid decarboxylase (GADA) and the protein tryosine phosphatase-like IA-2 (IA-2A) were measured by radiobinding assays. A short duration of total breast-feeding was associated with an increased risk of GADA and/or IAA above the ninety-fifth percentile at 5 years of age (OR 2.09, 95% CI 1.45, 3.02; P<0.000) as well as with an increased risk of IAA above the ninety-fifth percentile at this age (OR 2.89, 95% CI 1.81, 4.62, P<0.000). A short duration of exclusive breast-feeding was associated with an increased risk of GADA, IAA and/or IA-2A above the ninety-ninth percentile (OR 2.01, 95% CI 1.08, 3.73; P=0.028) as well as with an increased risk of IA-2A above the ninety-ninth percentile (OR 3.50, 95% CI 1.38, 8.92, P=0.009) at 5 years of age. An early introduction of formula was associated with an increased risk of GADA, IAA and/or IA-2A above the ninety-ninth percentile (OR 1.84, 95% CI 1.01, 3.37; P=0.047) at 5 years of age. The positive association between a short duration of both total and exclusive breast-feeding, as well as an early introduction of formula, and positivity for beta-cell autoantibodies in children from the general population suggest that breast-feeding modifies the risk of beta-cell autoimmunity, even years after finishing breast-feeding.

  13. AIP-1 ameliorates beta-amyloid peptide toxicity in a Caenorhabditis elegans Alzheimer's disease model.

    PubMed

    Hassan, Wail M; Merin, David A; Fonte, Virginia; Link, Christopher D

    2009-08-01

    Multiple neurodegenerative diseases are causally linked to aggregation-prone proteins. Cellular mechanisms involving protein turnover may be key defense mechanisms against aggregating protein disorders. We have used a transgenic Caenorhabditis elegans Alzheimer's disease model to identify cellular responses to proteotoxicity resulting from expression of the human beta amyloid peptide (Abeta). We show up-regulation of aip-1 in Abeta-expressing animals. Mammalian homologues of AIP-1 have been shown to associate with, and regulate the function of, the 26S proteasome, leading us to hypothesize that induction of AIP-1 may be a protective cellular response directed toward modulating proteasomal function in response to toxic protein aggregation. Using our transgenic model, we show that overexpression of AIP-1 protected against, while RNAi knockdown of AIP-1 exacerbated, Abeta toxicity. AIP-1 overexpression also reduced accumulation of Abeta in this model, which is consistent with AIP-1 enhancing protein degradation. Transgenic expression of one of the two human aip-1 homologues (AIRAPL), but not the other (AIRAP), suppressed Abeta toxicity in C. elegans, which advocates the biological relevance of the data to human biology. Interestingly, AIRAPL and AIP-1 contain a predicted farnesylation site, which is absent from AIRAP. This farnesylation site was shown by others to be essential for an AIP-1 prolongevity function. Consistent with this, we show that an AIP-1 mutant lacking the predicted farnesylation site failed to protect against Abeta toxicity. Our results implicate AIP-1 in the regulation of protein turnover and protection against Abeta toxicity and point at AIRAPL as the functional mammalian homologue of AIP-1.

  14. Analyzing and modeling the kinetics of amyloid beta pores associated with Alzheimer’s disease pathology

    SciTech Connect

    Ullah, Ghanim; Demuro, Angelo; Parker, Ian; Pearson, John E.; Xu, Shang -Zhong

    2015-09-08

    Amyloid beta (Aβ) oligomers associated with Alzheimer’s disease (AD) form Ca2+-permeable plasma membrane pores, leading to a disruption of the otherwise well-controlled intracellular calcium (Ca2+) homeostasis. The resultant up-regulation of intracellular Ca2+ concentration has detrimental implications for memory formation and cell survival. The gating kinetics and Ca2+ permeability of Aβ pores are not well understood. We have used computational modeling in conjunction with the ability of optical patch-clamping for massively parallel imaging of Ca2+ flux through thousands of pores in the cell membrane of Xenopus oocytes to elucidate the kinetic properties of Aβ pores. The fluorescence time-series data from individual pores were idealized and used to develop data-driven Markov chain models for the kinetics of the Aβ pore at different stages of its evolution. Our study provides the first demonstration of developing Markov chain models for ion channel gating that are driven by optical-patch clamp data with the advantage of experiments being performed under close to physiological conditions. As a result, we demonstrate the up-regulation of gating of various Ca2+ release channels due to Aβ pores and show that the extent and spatial range of such up-regulation increases as Aβ pores with low open probability and Ca2+ permeability transition into those with high open probability and Ca2+ permeability.

  15. Gene therapy by allele selection in a mouse model of beta-thalassemia.

    PubMed

    Eckardt, Sigrid; Leu, N Adrian; Yanchik, Ashley; Hatada, Seigo; Kyba, Michael; McLaughlin, K John

    2011-02-01

    To be of therapeutic use, autologous stem cells derived from patients with inherited genetic disorders require genetic modification via gene repair or insertion. Here, we present proof of principle that, for diseases associated with dominant alleles (gain-of-function or haploinsufficient loss-of-function), disease allele–free ES cells can be derived from afflicted individuals without genome manipulation. This approach capitalizes on the derivation of uniparental cells, such as parthenogenetic (PG) ES cell lines from disease allele–free gametes. Diploid mammalian uniparental embryos with only maternally (oocyte-) or paternally (sperm-)derived genomes fail early in development due to the nonequivalence of parental genomes caused by genomic imprinting. However, these uniparental embryos develop to the blastocyst stage, allowing the derivation of ES cell lines. Using a mouse model for dominant beta-thalassemia, we developed disease allele–free PG ES cell lines from the oocytes of affected animals. Phenotype correction was obtained in donor-genotype recipients after transplantation of in vitro hematopoietic ES cell derivatives. This genetic correction strategy without gene targeting is potentially applicable to any dominant disease. It could also be the sole approach for larger or more complex mutations that cannot be corrected by homologous recombination.

  16. Energetics of beta-oxidation. Reduction potentials of general fatty acyl-CoA dehydrogenase, electron transfer flavoprotein, and fatty acyl-CoA substrates.

    PubMed

    Gustafson, W G; Feinberg, B A; McFarland, J T

    1986-06-15

    We have determined reduction potentials for porcine mitochondrial general fatty acyl-CoA dehydrogenase (GAD) and electron transfer flavoprotein (ETF) using an anaerobic spectroelectrochemical titration method. Computer simulation techniques were used to analyze the absorbance data. Nernst plots of the simulated data gave E'0, 7.1, quinone/semiquinone = -0.014 V and E'0, 7.1, semiquinone/hydroquinone = -0.036 V for ETF and E'0, 7.1, quinone/semiquinone = -0.155 V and E'0, 7.1, semiquinone/hydroquinone = -0.122 V for GAD. Using these techniques we have also determined a conditional reduction potential of -0.156 V for the chromophore producing fatty acyl-CoA substrate beta-2-furylpropionyl-CoA. From this value and our previous determination of the equilibrium constant for the transhydrogenation reaction between beta-2-furylpropionyl-CoA and the oxidized substrate crotonyl-CoA (Keq = 10.4), we have determined a reduction potential of -0.126 V for the butyryl-CoA/crotonyl-CoA couple. In light of the structural similarity between butyryl-CoA and octanoyl-CoA, the optimal substrate for GAD, the reduction potential for octanoyl-CoA should be similar to that for butyryl-CoA; i.e. fatty acyl-CoA substrates and GAD are essentially isopotential. The ability of octanoyl-CoA to reduce GAD quantitatively (Keq = 9.0) poses a dilemma in light of the nearly equal reduction potentials. We postulate that the stable charge-transfer complex formed between enzyme and optimal product is significantly lower in energy than enzyme and product and thus is responsible for pulling the reaction toward completion.

  17. UWB microwave breast cancer detection: generalized models and performance prediction.

    PubMed

    Chen, Yifan; Gunawan, Erry; Kim, Yongmin; Low, Kay Soon; Soh, Cheong Boon; Thi, Lin Lin

    2006-01-01

    This paper presents a generic framework for the modeling of ultra-wideband (UWB) signal propagation in human breast, which facilitates system-level simulations and provides performance prediction. The clutter associated with the breast tissue heterogeneity is modeled through several key parameters depending on the tissue compositions. Subsequently, important channel properties such as the backscatter energy and the probability density function of time-of-arrival are derived. The modified Hermite polynomials, which fit well into the real pulse shapes, are then used to model the UWB signals. Armed with the channel/signal model preliminaries, three metrics are proposed, namely, the mean clutter response, the clean tumor response, and the worst-case clutter response. The generalized model provides a parsimonious way to study the effects of tissue structures, pulse templates, and array setup on the performance of a specified UWB imaging system. Numerical examples are used to demonstrate the usefulness of the proposed approach.

  18. Generalized slave-particle method for extended Hubbard models

    NASA Astrophysics Data System (ADS)

    Georgescu, Alexandru B.; Ismail-Beigi, Sohrab

    2015-12-01

    We introduce a set of generalized slave-particle models for extended Hubbard models that treat localized electronic correlations using slave-boson decompositions. Our models automatically include two slave-particle methods of recent interest, the slave-rotor and slave-spin methods, as well as a ladder of new intermediate models where one can choose which of the electronic degrees of freedom (e.g., spin or orbital labels) are treated as correlated degrees of freedom by the slave bosons. In addition, our method removes the aberrant behavior of the slave-rotor model, where it systematically overestimates the importance of electronic correlation effects for weak interaction strength, by removing the contribution of unphysical states from the bosonic Hilbert space. The flexibility of our formalism permits one to separate and isolate the effect of correlations on the key degrees of freedom.

  19. A comparison of observation-level random effect and Beta-Binomial models for modelling overdispersion in Binomial data in ecology & evolution.

    PubMed

    Harrison, Xavier A

    2015-01-01

    Overdispersion is a common feature of models of biological data, but researchers often fail to model the excess variation driving the overdispersion, resulting in biased parameter estimates and standard errors. Quantifying and modeling overdispersion when it is present is therefore critical for robust biological inference. One means to account for overdispersion is to add an observation-level random effect (OLRE) to a model, where each data point receives a unique level of a random effect that can absorb the extra-parametric variation in the data. Although some studies have investigated the utility of OLRE to model overdispersion in Poisson count data, studies doing so for Binomial proportion data are scarce. Here I use a simulation approach to investigate the ability of both OLRE models and Beta-Binomial models to recover unbiased parameter estimates in mixed effects models of Binomial data under various degrees of overdispersion. In addition, as ecologists often fit random intercept terms to models when the random effect sample size is low (<5 levels), I investigate the performance of both model types under a range of random effect sample sizes when overdispersion is present. Simulation results revealed that the efficacy of OLRE depends on the process that generated the overdispersion; OLRE failed to cope with overdispersion generated from a Beta-Binomial mixture model, leading to biased slope and intercept estimates, but performed well for overdispersion generated by adding random noise to the linear predictor. Comparison of parameter estimates from an OLRE model with those from its corresponding Beta-Binomial model readily identified when OLRE were performing poorly due to disagreement between effect sizes, and this strategy should be employed whenever OLRE are used for Binomial data to assess their reliability. Beta-Binomial models performed well across all contexts, but showed a tendency to underestimate effect sizes when modelling non-Beta-Binomial data

  20. A generalized conditional heteroscedastic model for temperature downscaling

    NASA Astrophysics Data System (ADS)

    Modarres, R.; Ouarda, T. B. M. J.

    2014-11-01

    This study describes a method for deriving the time varying second order moment, or heteroscedasticity, of local daily temperature and its association to large Coupled Canadian General Circulation Models predictors. This is carried out by applying a multivariate generalized autoregressive conditional heteroscedasticity (MGARCH) approach to construct the conditional variance-covariance structure between General Circulation Models (GCMs) predictors and maximum and minimum temperature time series during 1980-2000. Two MGARCH specifications namely diagonal VECH and dynamic conditional correlation (DCC) are applied and 25 GCM predictors were selected for a bivariate temperature heteroscedastic modeling. It is observed that the conditional covariance between predictors and temperature is not very strong and mostly depends on the interaction between the random process governing temporal variation of predictors and predictants. The DCC model reveals a time varying conditional correlation between GCM predictors and temperature time series. No remarkable increasing or decreasing change is observed for correlation coefficients between GCM predictors and observed temperature during 1980-2000 while weak winter-summer seasonality is clear for both conditional covariance and correlation. Furthermore, the stationarity and nonlinearity Kwiatkowski-Phillips-Schmidt-Shin (KPSS) and Brock-Dechert-Scheinkman (BDS) tests showed that GCM predictors, temperature and their conditional correlation time series are nonlinear but stationary during 1980-2000 according to BDS and KPSS test results. However, the degree of nonlinearity of temperature time series is higher than most of the GCM predictors.

  1. Generalized Modeling of the Human Lower Limb Assembly

    NASA Astrophysics Data System (ADS)

    Cofaru, Ioana; Huzu, Iulia

    2014-11-01

    The main reason for creating a generalized assembly of the main bones of the lower human member is to create the premises of realizing a biomechanic assisted study which could be used for the study of the high range of varieties of pathologies that exist at this level. Starting from 3D CAD models of the main bones of the lower human member, which were realized in previous researches, in this study a generalized assembly system was developed, system in which are highlighted both the situation of an healthy subject and the situation of the situation of a subject affected by axial deviations. In order to achieve these purpose reference systems were created, systems that are in accordance with the mechanical axes and the anatomic axes of the lower member, which were later generally assembled in a manner that provides an easy customization option

  2. Harnessing the theoretical foundations of the exponential and beta-Poisson dose-response models to quantify parameter uncertainty using Markov Chain Monte Carlo.

    PubMed

    Schmidt, Philip J; Pintar, Katarina D M; Fazil, Aamir M; Topp, Edward

    2013-09-01

    Dose-response models are the essential link between exposure assessment and computed risk values in quantitative microbial risk assessment, yet the uncertainty that is inherent to computed risks because the dose-response model parameters are estimated using limited epidemiological data is rarely quantified. Second-order risk characterization approaches incorporating uncertainty in dose-response model parameters can provide more complete information to decisionmakers by separating variability and uncertainty to quantify the uncertainty in computed risks. Therefore, the objective of this work is to develop procedures to sample from posterior distributions describing uncertainty in the parameters of exponential and beta-Poisson dose-response models using Bayes's theorem and Markov Chain Monte Carlo (in OpenBUGS). The theoretical origins of the beta-Poisson dose-response model are used to identify a decomposed version of the model that enables Bayesian analysis without the need to evaluate Kummer confluent hypergeometric functions. Herein, it is also established that the beta distribution in the beta-Poisson dose-response model cannot address variation among individual pathogens, criteria to validate use of the conventional approximation to the beta-Poisson model are proposed, and simple algorithms to evaluate actual beta-Poisson probabilities of infection are investigated. The developed MCMC procedures are applied to analysis of a case study data set, and it is demonstrated that an important region of the posterior distribution of the beta-Poisson dose-response model parameters is attributable to the absence of low-dose data. This region includes beta-Poisson models for which the conventional approximation is especially invalid and in which many beta distributions have an extreme shape with questionable plausibility.

  3. Attractive Hubbard model with disorder and the generalized Anderson theorem

    SciTech Connect

    Kuchinskii, E. Z. Kuleeva, N. A. Sadovskii, M. V.

    2015-06-15

    Using the generalized DMFT+Σ approach, we study the influence of disorder on single-particle properties of the normal phase and the superconducting transition temperature in the attractive Hubbard model. A wide range of attractive potentials U is studied, from the weak coupling region, where both the instability of the normal phase and superconductivity are well described by the BCS model, to the strong-coupling region, where the superconducting transition is due to Bose-Einstein condensation (BEC) of compact Cooper pairs, formed at temperatures much higher than the superconducting transition temperature. We study two typical models of the conduction band with semi-elliptic and flat densities of states, respectively appropriate for three-dimensional and two-dimensional systems. For the semi-elliptic density of states, the disorder influence on all single-particle properties (e.g., density of states) is universal for an arbitrary strength of electronic correlations and disorder and is due to only the general disorder widening of the conduction band. In the case of a flat density of states, universality is absent in the general case, but still the disorder influence is mainly due to band widening, and the universal behavior is restored for large enough disorder. Using the combination of DMFT+Σ and Nozieres-Schmitt-Rink approximations, we study the disorder influence on the superconducting transition temperature T{sub c} for a range of characteristic values of U and disorder, including the BCS-BEC crossover region and the limit of strong-coupling. Disorder can either suppress T{sub c} (in the weak-coupling region) or significantly increase T{sub c} (in the strong-coupling region). However, in all cases, the generalized Anderson theorem is valid and all changes of the superconducting critical temperature are essentially due to only the general disorder widening of the conduction band.

  4. Beta-triketone inhibitors of plant p-hydroxyphenylpyruvate dioxygenase: modeling and comparative molecular field analysis of their interactions.

    PubMed

    Dayan, Franck E; Singh, Nidhi; McCurdy, Christopher R; Godfrey, Colette A; Larsen, Lesley; Weavers, Rex T; Van Klink, John W; Perry, Nigel B

    2009-06-24

    p-Hydroxyphenylpyruvate dioxygenase (HPPD) is the target site of beta-triketone herbicides in current use. Nineteen beta-triketones and analogues, including the naturally occurring leptospermone and grandiflorone, were synthesized and tested as inhibitors of purified Arabidopsis thaliana HPPD. The most active compound was a beta-triketone with a C(9) alkyl side chain, not reported as natural, which inhibited HPPD with an I(50) of 19 +/- 1 nM. This is significantly more active than sulcotrione, which had an I(50) of 250 +/- 21 nM in this assay system. The most active naturally occurring beta-triketone was grandiflorone, which had an I(50) of 750 +/- 70 nM. This compound is of potential interest as a natural herbicide because it can be extracted with good yield and purity from some Leptospermum shrubs. Analogues without the 1,3-diketone group needed to interact with Fe(2+) at the HPPD active site were inactive (I(50)s > 50 microM), as were analogues with prenyl or ethyl groups on the triketone ring. Modeling of the binding of the triketones to HPPD, three-dimensional QSAR analysis using CoMFA (comparative molecular field analysis), and evaluation of the hydrophobic contribution with HINT (hydropathic interactions) provided a structural basis to describe the ligand/receptor interactions.

  5. Microstrain temperature evolution in beta-eurcryptite ceramics: Measurement and model

    SciTech Connect

    Bruno, Giovanni; Garlea, Vasile O; Muth, Joseph T.; Efremov, Alexander; Watkins, Thomas R; Shyam, Amit

    2012-01-01

    Mechanisms of microcracking and stress release in {beta}-eucryptite ceramics were investigated by applying a combination of neutron diffraction (ND), dilatometry and the Integrity Factor Model (IFM). It was observed that the macroscopic thermal expansion of solid samples closely follows the lattice thermal expansion as a function of temperature, and both are dominated by microcracks closing (during heating) and opening (during cooling). Analogous experiments on powders showed that the stresses that manifest peak shift are indeed relieved by comminution, and that the resulting lattice thermal expansion can be considered as unconstrained. By means of Rietveld refinement of the ND data, the evolution with temperature of peak width parameters linked to strain distributions along the basal, pyramidal and axial planes could also be extracted. The peak width parameters S{sub HKL} correlated well with the strains calculated by peak shift and with the model results. Furthermore, while the peak shifts showed that the powders are basically stress free, the S{sub HKL} showed a strong evolution of the peak width. Powders carry, therefore, a measurable strain distribution inside the particles, owing to the thermal expansion anisotropy of the crystallites. The IFM allowed this behavior to be rationalized, and the effect of microcracking on thermal expansion to be quantified. Experimental data allowed accurate numerical prediction of microcracking on cooling and of the evolution of microstresses. They also allowed the derivation of the material elastic modulus from bulk thermal expansion curves through the IFM concept. Ultrasound resonance measurements of the elastic modulus strongly support these theoretical predictions.

  6. Net diffusivity in ocean general circulation models with nonuniform grids

    NASA Technical Reports Server (NTRS)

    Yin, F. L.; Fung, I. Y.

    1991-01-01

    The numerical vertical diffusivity K(num), embedded in a numerical ocean general circulation model with nonuniform vertical grid, is estimated. It is shown that in a downwelling region, K(num) is negative for a grid with grid size increasing with depth. When the grid size increment, or the downward vertical velocity, is large, K(num) may exceed the vertical diffusivity specified and may result in a negative effective vertical diffusivity. Therefore care needs to be taken to specify the vertical diffusivity in a numerical model with nonuniform grid, and a lower bound is generally imposed in order to avoid an unphysical negative value. Some possible effects of the negative effective diffusivity are discussed.

  7. Yang-Mills generalization of the geometrical collective model

    NASA Astrophysics Data System (ADS)

    Rosensteel, George; Sparks, Nick

    2015-04-01

    The geometrical or Bohr-Mottelson model is generalized and recast as a Yang-Mills theory. The gauge symmetry determines conservation of Kelvin circulation. The circulation commutes with the Hamiltonian when it is the sum of the kinetic energy and a potential that depends only on deformation. The conventional Bohr-Mottelson model is the special case of circulation zero, and wave functions are complex-valued. In the generalization, any quantized value of the circulation is allowed, and the wave functions are vector-valued. The Yang-Mills formulation introduces a new coupling between the geometrical and intrinsic degrees of freedom. The coupling appears in the covariant derivative term of the collective kinetic energy. This kind of coupling is sometimes called ``magnetic'' because of the analogy with electrodynamics.

  8. A Coupled General Circulation Model of the Archean Earth

    NASA Astrophysics Data System (ADS)

    Wolf, E. T.; Toon, O. B.

    2011-12-01

    We present results from a new coupled general circulation model suitable for deep paleoclimate studies. Particular interest is given to the faint young Sun paradox. The model is based on the Community Earth System Model maintained by the National Center for Atmospheric Research [1]. Prognostic atmosphere, ocean, land, ice, and hydrological cycle models are coupled. A new correlated-k radiative transfer model has been implemented allowing accurate flux calculations for anoxic atmospheres containing high concentrations of CO2 and CH4 [2, 3]. This model represents a significant improvement upon one-dimensional radiative-convective climate models used previously to study ancient climate [4]. Cloud and ice albedo feedbacks will be accurately quantified and new constraints on Archean surface temperatures will be revealed. References [1] Collins W.D. et al. "Description of the NCAR Community Atmosphere Model (CAM 3.0)." NCAR Technical Note, 2004. [2] Toon O.B., McKay, C.P., Ackerman, T.P. "Rapid Calculation of Radiative Heating Rates and Photodissociation Rates in Inhomogeneous Multiple Scattering Atmospheres." J. Geo. Res., 94(D13), 16287 - 16301, 1989. [3] Mlawer, E.J., et al. "Radiative transfer for inhomogeneous atmospheres: RRTM, a validated correlated-k model for the longwave." J. Geo. Res., 102(D14), 16663 - 16682, 1997. [4] Kasting J.F., Pollack, J.B., Crisp, D. "Effects of High CO2 Levels on Surface Temperature and Atmospheric Oxidation State of the Early Earth." J. Atm. Chem., 1, 403-428, 1984.

  9. EPA`s emissions models for general nonroad sources

    SciTech Connect

    Fieber, J.; Rosenbaum, A.; Vranka, R.; Kleinhesselink, D.

    1996-12-31

    Under the sponsorship of the US EPA`s Office of Mobile Sources, SAI has developed a computer model for nonroad mobile sources. Although data and methodologies continue to be revisited, the alpha version of the model has been completed and is currently under review at EPA. The model contains modules for estimating equipment populations, activity, emission factors, and total emissions. It adjusts these estimates to predict total emissions for the calendar year and at a level of detail specified by the user (e.g., average annual estimates at a national level, hourly estimates for a specific county). The EPA`s nonroad model provides estimates for the following general classes of nonroad equipment: General Nonroad Sources: (1) Lawn and garden equipment; (2) Airport service equipment; (3) Recreational; (4) Light Commercial; (5) Industrial; (6) Construction; (7) Agricultural; and (8) Logging. Special Nonroad Sources: (1) Locomotives; (2) Aircraft; and (3) Marine Vessels. With the exception of locomotives, aircraft, and marine vessels, the methodologies used within the model are quite similar for all these source groupings. Information for specific equipment types (e.g., 15-25 horsepower, gasoline 2-stroke engine commercial turf equipment) will also be provided if the user requests this level of detail. Written in FORTRAN and designed for personal computers (though it can be ported to workstations), this new emissions tool includes an interface to improve its ease of use and flexibility. We present here some of the features of the model and provide an overview of the internal methods used for the equipment groups listed under general nonroad sources.

  10. Generalized cable equation model for myelinated nerve fiber.

    PubMed

    Einziger, Pinchas D; Livshitz, Leonid M; Mizrahi, Joseph

    2005-10-01

    Herein, the well-known cable equation for nonmyelinated axon model is extended analytically for myelinated axon formulation. The myelinated membrane conductivity is represented via the Fourier series expansion. The classical cable equation is thereby modified into a linear second order ordinary differential equation with periodic coefficients, known as Hill's equation. The general internal source response, expressed via repeated convolutions, uniformly converges provided that the entire periodic membrane is passive. The solution can be interpreted as an extended source response in an equivalent nonmyelinated axon (i.e., the response is governed by the classical cable equation). The extended source consists of the original source and a novel activation function, replacing the periodic membrane in the myelinated axon model. Hill's equation is explicitly integrated for the specific choice of piecewise constant membrane conductivity profile, thereby resulting in an explicit closed form expression for the transmembrane potential in terms of trigonometric functions. The Floquet's modes are recognized as the nerve fiber activation modes, which are conventionally associated with the nonlinear Hodgkin-Huxley formulation. They can also be incorporated in our linear model, provided that the periodic membrane point-wise passivity constraint is properly modified. Indeed, the modified condition, enforcing the periodic membrane passivity constraint on the average conductivity only leads, for the first time, to the inclusion of the nerve fiber activation modes in our novel model. The validity of the generalized transmission-line and cable equation models for a myelinated nerve fiber, is verified herein through a rigorous Green's function formulation and numerical simulations for transmembrane potential induced in three-dimensional myelinated cylindrical cell. It is shown that the dominant pole contribution of the exact modal expansion is the transmembrane potential solution of our

  11. Generalized Bogoliubov Polariton Model: An Application to Stock Exchange Market

    NASA Astrophysics Data System (ADS)

    Thuy Anh, Chu; Anh, Truong Thi Ngoc; Lan, Nguyen Tri; Viet, Nguyen Ai

    2016-06-01

    A generalized Bogoliubov method for investigation non-simple and complex systems was developed. We take two branch polariton Hamiltonian model in second quantization representation and replace the energies of quasi-particles by two distribution functions of research objects. Application to stock exchange market was taken as an example, where the changing the form of return distribution functions from Boltzmann-like to Gaussian-like was studied.

  12. Treatment of cloud radiative effects in general circulation models

    SciTech Connect

    Wang, W.C.; Dudek, M.P.; Liang, X.Z.; Ding, M.

    1996-04-01

    We participate in the Atmospheric Radiation Measurement (ARM) program with two objectives: (1) to improve the general circulation model (GCM) cloud/radiation treatment with a focus on cloud verticle overlapping and layer cloud optical properties, and (2) to study the effects of cloud/radiation-climate interaction on GCM climate simulations. This report summarizes the project progress since the Fourth ARM Science Team meeting February 28-March 4, 1994, in Charleston, South Carolina.

  13. Credibility analysis of risk classes by generalized linear model

    NASA Astrophysics Data System (ADS)

    Erdemir, Ovgucan Karadag; Sucu, Meral

    2016-06-01

    In this paper generalized linear model (GLM) and credibility theory which are frequently used in nonlife insurance pricing are combined for reliability analysis. Using full credibility standard, GLM is associated with limited fluctuation credibility approach. Comparison criteria such as asymptotic variance and credibility probability are used to analyze the credibility of risk classes. An application is performed by using one-year claim frequency data of a Turkish insurance company and results of credible risk classes are interpreted.

  14. Baroclinic Rossby Wave Signature in a General Circulation Ocean Model.

    DTIC Science & Technology

    1983-06-01

    northwest with a wavelength cf 300 km. For other laritudes of the North acific Ocean , Price and Maqaard (1980) determined that first mode baroclinic Rossby...role in the latitude belt 40-50N in the North acific 10 -. - !o Ocean . Magaard (1983) ir. a paper discussing bariclin _c Rossty wave energetics...HD-AI132 219 BAROCLINIC ROSSBY WAVE SIGNATURE IN A GENERAL CIRCULATION OCEAN MODEL(U) NAVAL POSTGRADUATE SCHOOLU MONTEREY CA A H RUTSCH JUN 83

  15. Interactive data exploration and particle tracking for general circulation models

    NASA Technical Reports Server (NTRS)

    Rosenbaum, R. I.; Peskin, R. L.; Walther, S. S.; Zinn, H. P.

    1995-01-01

    The SCENE environment for interactive visualization of complex data sets is discussed. This environment is used to create tools for graphical exploration of atmospheric flow models. These tools may be extended by the user in a seamless manner, so that no programming is required. A module for accurately tracing field lines and particle trajectories in SCENE is presented. This is used to examine the flowfield qualitatively with streamlines and pathlines and to identify critical points in the velocity field. The paper also describes a visualization tool for general circulation models on which the primary features of the environment are demonstrated.

  16. Tropical disturbances in relation to general circulation modeling

    NASA Technical Reports Server (NTRS)

    Estoque, M. A.

    1982-01-01

    The initial results of an evaluation of the performance of the Goddard Laboratory of Atmospheric Simulation general circulation model depicting the tropical atmosphere during the summer are presented. Because the results show the existence of tropical wave disturbances throughout the tropics, the characteristics of synoptic disturbances over Africa were studied and a synoptic case study of a selected disturbance in this area was conducted. It is shown that the model is able to reproduce wave type synoptic disturbances in the tropics. The findings show that, in one of the summers simulated, the disturbances are predominantly closed vortices; in another summer, the predominant disturbances are open waves.

  17. A Moist Idealized Test Case for Atmospheric General Circulation Models

    NASA Astrophysics Data System (ADS)

    Thatcher, D.; Jablonowski, C.; Zarzycki, C.

    2013-12-01

    The vast array of dynamical and physical processes within atmospheric general circulation models (GCMs) makes it difficult to correctly distinguish the sources of error within a model. Therefore, simplified test cases are important in testing the accuracy of individual model components, such as the fluid flow component in the dynamical core. Typically, dynamical cores are coupled to complex subgrid-scale physical parameterization packages, and the nonlinear interactions mask the causes and effects of atmospheric phenomena. Idealized tests are a computationally efficient method for analyzing the underlying numerical techniques of dynamical cores. The newly proposed test case is based on the widely-used Held and Suarez (1994) (HS) test for dry dynamical cores. The latter replaces the full physical parameterization package with a Newtonian temperature relaxation and Rayleigh damping of low-level winds on a flat planet. However, the impact of moisture, a crucial physics-dynamics coupling process, is missing from the HS test. Here we present a moist variant of the HS test case to create a test case of intermediate complexity with idealized moisture feedbacks. It uses simplified physical processes to model large-scale condensation, boundary layer turbulence, and surface fluxes of horizontal momentum, latent heat, and sensible heat between the atmosphere and an ocean-covered planet (Reed and Jablonowski, 2012). We apply this test to four dynamical cores within NCAR's Community Atmosphere Model version 5.3, including the Finite Volume, Eulerian spectral transform, semi-Lagrangian spectral transform, and Spectral Element dynamical cores. We analyze the kinetic energy spectra, general circulation, and precipitation of this new moist idealized test case across all four dynamical cores. Simulations of the moist idealized test case are compared to aqua-planet experiments with complex physical parameterizations. The moist idealized test case successfully reproduces many features

  18. Anisotropic Mesoscale Eddy Transport in Ocean General Circulation Models

    NASA Astrophysics Data System (ADS)

    Reckinger, S. J.; Fox-Kemper, B.; Bachman, S.; Bryan, F.; Dennis, J.; Danabasoglu, G.

    2014-12-01

    Modern climate models are limited to coarse-resolution representations of large-scale ocean circulation that rely on parameterizations for mesoscale eddies. The effects of eddies are typically introduced by relating subgrid eddy fluxes to the resolved gradients of buoyancy or other tracers, where the proportionality is, in general, governed by an eddy transport tensor. The symmetric part of the tensor, which represents the diffusive effects of mesoscale eddies, is universally treated isotropically in general circulation models. Thus, only a single parameter, namely the eddy diffusivity, is used at each spatial and temporal location to impart the influence of mesoscale eddies on the resolved flow. However, the diffusive processes that the parameterization approximates, such as shear dispersion, potential vorticity barriers, oceanic turbulence, and instabilities, typically have strongly anisotropic characteristics. Generalizing the eddy diffusivity tensor for anisotropy extends the number of parameters to three: a major diffusivity, a minor diffusivity, and the principal axis of alignment. The Community Earth System Model (CESM) with the anisotropic eddy parameterization is used to test various choices for the newly introduced parameters, which are motivated by observations and the eddy transport tensor diagnosed from high resolution simulations. Simply setting the ratio of major to minor diffusivities to a value of five globally, while aligning the major axis along the flow direction, improves biogeochemical tracer ventilation and reduces global temperature and salinity biases. These effects can be improved even further by parameterizing the anisotropic transport mechanisms in the ocean.

  19. Integrated and spectral energetics of the GLAS general circulation model

    NASA Technical Reports Server (NTRS)

    Tenenbaum, J.

    1982-01-01

    Integrated and spectral error energetics of the GLAS General circulation model are compared with observations for periods in January 1975, 1976, and 1977. For two cases the model shows significant skill in predicting integrated energetics quantities out to two weeks, and for all three cases, the integrated monthly mean energetics show qualitative improvements over previous versions of the model in eddy kinetic energy and barotropic conversions. Fundamental difficulties remain with leakage of energy to the stratospheric level, particularly above strong initial jet streams associated in part with regions of steep terrain. The spectral error growth study represents the first comparison of general circulation model spectral energetics predictions with the corresponding observational spectra on a day by day basis. The major conclusion is that eddy kinetics energy can be correct while significant errors occur in the kinetic energy of wavenumber 3. Both the model and observations show evidence of single wavenumber dominance in eddy kinetic energy and the correlation of spectral kinetics and potential energy.

  20. Pharmaceutical Industry and Trade Liberalization Using Computable General Equilibrium Model

    PubMed Central

    Barouni, M; Ghaderi, H; Banouei, AA

    2012-01-01

    Background Computable general equilibrium models are known as a powerful instrument in economic analyses and widely have been used in order to evaluate trade liberalization effects. The purpose of this study was to provide the impacts of trade openness on pharmaceutical industry using CGE model. Methods: Using a computable general equilibrium model in this study, the effects of decrease in tariffs as a symbol of trade liberalization on key variables of Iranian pharmaceutical products were studied. Simulation was performed via two scenarios in this study. The first scenario was the effect of decrease in tariffs of pharmaceutical products as 10, 30, 50, and 100 on key drug variables, and the second was the effect of decrease in other sectors except pharmaceutical products on vital and economic variables of pharmaceutical products. The required data were obtained and the model parameters were calibrated according to the social accounting matrix of Iran in 2006. Results: The results associated with simulation demonstrated that the first scenario has increased import, export, drug supply to markets and household consumption, while import, export, supply of product to market, and household consumption of pharmaceutical products would averagely decrease in the second scenario. Ultimately, society welfare would improve in all scenarios. Conclusion: We presents and synthesizes the CGE model which could be used to analyze trade liberalization policy issue in developing countries (like Iran), and thus provides information that policymakers can use to improve the pharmacy economics. PMID:23641393

  1. Unitarity-violation in generalized Higgs inflation models

    SciTech Connect

    Lerner, Rose N.; McDonald, John E-mail: j.mcdonald@lancaster.ac.uk

    2012-11-01

    Unitarity-violation presents a challenge for non-minimally coupled models of inflation based on weak-scale particle physics. We examine the energy scale of tree-level unitarity-violation in scattering processes for generalized models with multiple scalar fields where the inflaton is either a singlet scalar or the Higgs. In the limit that the non-minimal couplings are all equal (e.g. in the case of Higgs or other complex inflaton), the scale of tree-level unitarity-violation matches the existing result. However if the inflaton is a singlet, and if it has a larger non-minimal coupling than other scalars in the model, then this hierarchy increases the scale of tree-level unitarity-violation. A sufficiently strong hierarchy pushes the scale of tree-level unitarity-violation above the Planck scale. We also discuss models which attempt to resolve the issue of unitarity-violation in Higgs Inflation.

  2. Generalized Dynamic Factor Models for Mixed-Measurement Time Series

    PubMed Central

    Cui, Kai; Dunson, David B.

    2013-01-01

    In this article, we propose generalized Bayesian dynamic factor models for jointly modeling mixed-measurement time series. The framework allows mixed-scale measurements associated with each time series, with different measurements having different distributions in the exponential family conditionally on time-varying latent factor(s). Efficient Bayesian computational algorithms are developed for posterior inference on both the latent factors and model parameters, based on a Metropolis Hastings algorithm with adaptive proposals. The algorithm relies on a Greedy Density Kernel Approximation (GDKA) and parameter expansion with latent factor normalization. We tested the framework and algorithms in simulated studies and applied them to the analysis of intertwined credit and recovery risk for Moody’s rated firms from 1982–2008, illustrating the importance of jointly modeling mixed-measurement time series. The article has supplemental materials available online. PMID:24791133

  3. Generalized Dynamic Factor Models for Mixed-Measurement Time Series.

    PubMed

    Cui, Kai; Dunson, David B

    2014-02-12

    In this article, we propose generalized Bayesian dynamic factor models for jointly modeling mixed-measurement time series. The framework allows mixed-scale measurements associated with each time series, with different measurements having different distributions in the exponential family conditionally on time-varying latent factor(s). Efficient Bayesian computational algorithms are developed for posterior inference on both the latent factors and model parameters, based on a Metropolis Hastings algorithm with adaptive proposals. The algorithm relies on a Greedy Density Kernel Approximation (GDKA) and parameter expansion with latent factor normalization. We tested the framework and algorithms in simulated studies and applied them to the analysis of intertwined credit and recovery risk for Moody's rated firms from 1982-2008, illustrating the importance of jointly modeling mixed-measurement time series. The article has supplemental materials available online.

  4. Generalized Optoelectronic Model of Series-Connected Multijunction Solar Cells

    SciTech Connect

    Geisz, John F.; Steiner, Myles A.; Garcia, Ivan; France, Ryan M.; McMahon, William E.; Osterwald, Carl R.; Friedman, Daniel J.

    2015-10-02

    The emission of light from each junction in a series-connected multijunction solar cell, we found, both complicates and elucidates the understanding of its performance under arbitrary conditions. Bringing together many recent advances in this understanding, we present a general 1-D model to describe luminescent coupling that arises from both voltage-driven electroluminescence and voltage-independent photoluminescence in nonideal junctions that include effects such as Sah-Noyce-Shockley (SNS) recombination with n ≠ 2, Auger recombination, shunt resistance, reverse-bias breakdown, series resistance, and significant dark area losses. The individual junction voltages and currents are experimentally determined from measured optical and electrical inputs and outputs of the device within the context of the model to fit parameters that describe the devices performance under arbitrary input conditions. Furthermore, our techniques to experimentally fit the model are demonstrated for a four-junction inverted metamorphic solar cell, and the predictions of the model are compared with concentrator flash measurements.

  5. An evaluation of the assumed beta probability density function subgrid-scale model for large eddy simulation of nonpremixed, turbulent combustion with heat release

    SciTech Connect

    Wall, Clifton; Boersma, Bendiks Jan; Moin, Parviz

    2000-10-01

    The assumed beta distribution model for the subgrid-scale probability density function (PDF) of the mixture fraction in large eddy simulation of nonpremixed, turbulent combustion is tested, a priori, for a reacting jet having significant heat release (density ratio of 5). The assumed beta distribution is tested as a model for both the subgrid-scale PDF and the subgrid-scale Favre PDF of the mixture fraction. The beta model is successful in approximating both types of PDF but is slightly more accurate in approximating the normal (non-Favre) PDF. To estimate the subgrid-scale variance of mixture fraction, which is required by the beta model, both a scale similarity model and a dynamic model are used. Predictions using the dynamic model are found to be more accurate. The beta model is used to predict the filtered value of a function chosen to resemble the reaction rate. When no model is used, errors in the predicted value are of the same order as the actual value. The beta model is found to reduce this error by about a factor of two, providing a significant improvement. (c) 2000 American Institute of Physics.

  6. Planetary-Scale Flow on a Two-Layer Beta-Plane Channel Model with Topography

    NASA Astrophysics Data System (ADS)

    Shin, Won-Tae Kwon

    A two-layer low-order spectral model on a beta-plane channel with topographic, thermal and frictional forcing is designed as a compromise to resolve the relative importance and interaction of several relevant processes. The model is truncated at three zonal modes and three meridional modes. Topography forces the largest scale; the intermediate scale may be destabilized by zonal thermal forcing; the smallest scale permits barotropic scale-interaction and a rudimentary energy cascade. Multiple steady states of the simple one zonal mode and one wave mode (the 1 x 1 model) have been found. There are seven possible steady states: a zonally symmetric state, a topographically resonant state, and five baroclinic and equivalent barotropic wave states. New results emphasize relevance of the barotropic and baroclinic zonal flows; most significantly, multiple steady states exist only for a restricted range of zonal wind and vertical shear in the vicinity of the topographically resonant values. The time-dependent behavior for the 3 x 3 model is classified into six different types: zonally symmetric, steady wave state, steady propagating (Rossby wave), periodic, quasi-periodic and chaotic solutions. The regimes of the solutions for three parameters (thermal forcing, topography and friction) are investigated. The amplitude of zonal flow in wave solutions is weaker with moderate topography and is stronger with larger friction, smaller thermal forcing and higher topography or no topography. The characteristics of solutions are related to the strength of the resultant zonal flow with small or moderate topography. When the intermediate scale wave with largest meridional scale (MODE 12) is baroclinically unstable, this wave maintains the topographic wave ridge upstream of the mountain through the wave-wave interaction and also maintains other waves through form-drag; then, other modes are maintained by various mechanisms. When the topographic wave (MODE 11) becomes unstable with

  7. Beta Blockers

    MedlinePlus

    Diseases and Conditions High blood pressure (hypertension) Beta blockers, also called beta-adrenergic blocking agents, treat a variety of conditions, such as high blood pressure and migraines. Find out more about this ...

  8. Reshocks, rarefactions, and the generalized Layzer model for hydrodynamic instabilities

    SciTech Connect

    Mikaelian, K O

    2008-06-10

    We report numerical simulations and analytic modeling of shock tube experiments on Rayleigh-Taylor and Richtmyer-Meshkov instabilities. We examine single interfaces of the type A/B where the incident shock is initiated in A and the transmitted shock proceeds into B. Examples are He/air and air/He. In addition, we study finite-thickness or double-interface A/B/A configurations like air/SF{sub 6}/air gas-curtain experiments. We first consider conventional shock tubes that have a 'fixed' boundary: A solid endwall which reflects the transmitted shock and reshocks the interface(s). Then we focus on new experiments with a 'free' boundary--a membrane disrupted mechanically or by the transmitted shock, sending back a rarefaction towards the interface(s). Complex acceleration histories are achieved, relevant for Inertial Confinement Fusion implosions. We compare our simulation results with a generalized Layzer model for two fluids with time-dependent densities, and derive a new freeze-out condition whereby accelerating and compressive forces cancel each other out. Except for the recently reported failures of the Layzer model, the generalized Layzer model and hydrocode simulations for reshocks and rarefactions agree well with each other, and remain to be verified experimentally.

  9. Bayesian generalized linear mixed modeling of Tuberculosis using informative priors

    PubMed Central

    Woldegerima, Woldegebriel Assefa

    2017-01-01

    TB is rated as one of the world’s deadliest diseases and South Africa ranks 9th out of the 22 countries with hardest hit of TB. Although many pieces of research have been carried out on this subject, this paper steps further by inculcating past knowledge into the model, using Bayesian approach with informative prior. Bayesian statistics approach is getting popular in data analyses. But, most applications of Bayesian inference technique are limited to situations of non-informative prior, where there is no solid external information about the distribution of the parameter of interest. The main aim of this study is to profile people living with TB in South Africa. In this paper, identical regression models are fitted for classical and Bayesian approach both with non-informative and informative prior, using South Africa General Household Survey (GHS) data for the year 2014. For the Bayesian model with informative prior, South Africa General Household Survey dataset for the year 2011 to 2013 are used to set up priors for the model 2014. PMID:28257437

  10. Bayesian generalized linear mixed modeling of Tuberculosis using informative priors.

    PubMed

    Ojo, Oluwatobi Blessing; Lougue, Siaka; Woldegerima, Woldegebriel Assefa

    2017-01-01

    TB is rated as one of the world's deadliest diseases and South Africa ranks 9th out of the 22 countries with hardest hit of TB. Although many pieces of research have been carried out on this subject, this paper steps further by inculcating past knowledge into the model, using Bayesian approach with informative prior. Bayesian statistics approach is getting popular in data analyses. But, most applications of Bayesian inference technique are limited to situations of non-informative prior, where there is no solid external information about the distribution of the parameter of interest. The main aim of this study is to profile people living with TB in South Africa. In this paper, identical regression models are fitted for classical and Bayesian approach both with non-informative and informative prior, using South Africa General Household Survey (GHS) data for the year 2014. For the Bayesian model with informative prior, South Africa General Household Survey dataset for the year 2011 to 2013 are used to set up priors for the model 2014.

  11. Fermion masses and mixing in general warped extra dimensional models

    NASA Astrophysics Data System (ADS)

    Frank, Mariana; Hamzaoui, Cherif; Pourtolami, Nima; Toharia, Manuel

    2015-06-01

    We analyze fermion masses and mixing in a general warped extra dimensional model, where all the Standard Model (SM) fields, including the Higgs, are allowed to propagate in the bulk. In this context, a slightly broken flavor symmetry imposed universally on all fermion fields, without distinction, can generate the full flavor structure of the SM, including quarks, charged leptons and neutrinos. For quarks and charged leptons, the exponential sensitivity of their wave functions to small flavor breaking effects yield hierarchical masses and mixing as it is usual in warped models with fermions in the bulk. In the neutrino sector, the exponential wave-function factors can be flavor blind and thus insensitive to the small flavor symmetry breaking effects, directly linking their masses and mixing angles to the flavor symmetric structure of the five-dimensional neutrino Yukawa couplings. The Higgs must be localized in the bulk and the model is more successful in generalized warped scenarios where the metric background solution is different than five-dimensional anti-de Sitter (AdS5 ). We study these features in two simple frameworks, flavor complimentarity and flavor democracy, which provide specific predictions and correlations between quarks and leptons, testable as more precise data in the neutrino sector becomes available.

  12. Generalized linear mixed model for segregation distortion analysis

    PubMed Central

    2011-01-01

    Background Segregation distortion is a phenomenon that the observed genotypic frequencies of a locus fall outside the expected Mendelian segregation ratio. The main cause of segregation distortion is viability selection on linked marker loci. These viability selection loci can be mapped using genome-wide marker information. Results We developed a generalized linear mixed model (GLMM) under the liability model to jointly map all viability selection loci of the genome. Using a hierarchical generalized linear mixed model, we can handle the number of loci several times larger than the sample size. We used a dataset from an F2 mouse family derived from the cross of two inbred lines to test the model and detected a major segregation distortion locus contributing 75% of the variance of the underlying liability. Replicated simulation experiments confirm that the power of viability locus detection is high and the false positive rate is low. Conclusions Not only can the method be used to detect segregation distortion loci, but also used for mapping quantitative trait loci of disease traits using case only data in humans and selected populations in plants and animals. PMID:22078575

  13. Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

    PubMed Central

    Hayes, Ryan L.; Noel, Jeffrey K.; Mandic, Ana; Whitford, Paul C.; Sanbonmatsu, Karissa Y.; Mohanty, Udayan; Onuchic, José N.

    2016-01-01

    RNA is highly sensitive to the ionic environment, and typically requires Mg2+ to form compact structures. There is a need for models capable of describing the ion atmosphere surrounding RNA with quantitative accuracy. We present a model of RNA electrostatics and apply it within coarse-grained molecular dynamics simulation. The model treats Mg2+ ions explicitly to account for ion-ion correlations neglected by mean field theories. Since mean-field theories capture KCl well, it is treated implicitly by a generalized Manning counterion condensation model. The model extends Manning condensation to deal with arbitrary RNA conformations, non-limiting KCl concentrations, and the ion inaccessible volume of RNA. The model is tested against experimental measurements of the excess Mg2+ associated with the RNA, Γ2+, because Γ2+ is directly related to the Mg2+-RNA interaction free energy. The excellent agreement with experiment demonstrates the model captures the ionic dependence of the RNA free energy landscape. PMID:26197147

  14. Symmetry in the Generalized Rotor Model for Extremely Floppy Molecules

    NASA Astrophysics Data System (ADS)

    Schmiedt, Hanno; Jensen, Per; Schlemmer, Stephan

    2016-06-01

    Protonated methane CH_5^+ is unique: It is an extremely fluxional molecule. All attempts to assign quantum numbers to the high-resolution transitions obtained over the last 20 years have failed because molecular rotation and vibration cannot be separated in the conventional way. The first step towards a theoretical description is to include internal rotational degrees of freedom into the overall ones, which can be used to formulate a fundamentally new zero order approximation for the (now) generalized rotational states and energies. Predictions from this simple five-dimensional rotor model compare very favorably with the combination differences of protonated methane found in recent low temperature experiments. This talk will focus on symmetry aspects and implications of permutation symmetry for the generalized rotational states. Furthermore, refinements of the theory will be discussed, ranging from the generalization to even higher-dimensional rotors to explicit symmetry breaking and corresponding energy splittings. The latter includes the link to well-known theories of internal rotation dynamics and will show the general validity of the presented theory. Schmiedt, H., et al.; J. Chem. Phys. 143 (15), 154302 (2015) Wodraszka, R. et al.; J. Phys. Chem. Lett. 6, 4229-4232 (2015) Asvany, O. et al.; Science, 347, (6228), 1346-1349 (2015)

  15. A generalized analytical compliance model for cartwheel flexure hinges

    NASA Astrophysics Data System (ADS)

    Wu, Jianwei; Cai, Shuai; Cui, Jiwen; Tan, Jiubin

    2015-10-01

    Normal cartwheel flexure hinge (NCFH) typically consists of two flexible springs crossing at their mid points. These have been used in compliant mechanism applications owing to the large motion range of such hinges. In this paper, a novel generalized cartwheel flexure hinge (GCFH) is proposed by modifying spring number and varying the angle between two springs on the basis of the NCFH. A 6 degrees of freedom (6-DOF) compliance model of the GCFH was derived. Validity of this model was demonstrated using finite element analysis simulation and experimental results on a GCFH with 3 pairs of springs and 70° angle. According to the model, influence of distribution and shape parameters of GCFH on performance was analyzed. Characteristics such as compliance, off-axis/axis compliance ratio, motion precision, and capacity of rotation were determined. Results show that the GCFH can achieve improved performance compared to NCFH with optimized GCFH parameters.

  16. Generalized linear mixed models for meta-analysis.

    PubMed

    Platt, R W; Leroux, B G; Breslow, N

    1999-03-30

    We examine two strategies for meta-analysis of a series of 2 x 2 tables with the odds ratio modelled as a linear combination of study level covariates and random effects representing between-study variation. Penalized quasi-likelihood (PQL), an approximate inference technique for generalized linear mixed models, and a linear model fitted by weighted least squares to the observed log-odds ratios are used to estimate regression coefficients and dispersion parameters. Simulation results demonstrate that both methods perform adequate approximate inference under many conditions, but that neither method works well in the presence of highly sparse data. Under certain conditions with small cell frequencies the PQL method provides better inference.

  17. Cache Allocation in CDN: An Evolutionary Game Generalized Particle Model

    NASA Astrophysics Data System (ADS)

    Feng, Xiang; Lau, Francis C. M.; Gao, Daqi

    Content distribution networks (CDNs) increasingly have been used to reduce the response times experienced by Internet users through placing surrogates close to the clients. This paper presents an object replacement approach based on an evolutionary game generalized particle model (G-GPM). We first propose a problem model for CDNs. The CDN model is then fit into a gravitational field. The origin servers and surrogates are regarded as two kinds of particles which are located in two force-fields. The cache allocation problem is thus transformed into the kinematics and dynamics of the particles in the annular and the round force-fields. The G-GPM approach is unique in four aspects: 1) direct viewing of individual and overall optimization; 2) parallel computing (lower time complexity); 3) multi-objective solution; and 4) being able to deal with some social interactions behaviors.

  18. Dimensional Reduction for the General Markov Model on Phylogenetic Trees.

    PubMed

    Sumner, Jeremy G

    2017-03-01

    We present a method of dimensional reduction for the general Markov model of sequence evolution on a phylogenetic tree. We show that taking certain linear combinations of the associated random variables (site pattern counts) reduces the dimensionality of the model from exponential in the number of extant taxa, to quadratic in the number of taxa, while retaining the ability to statistically identify phylogenetic divergence events. A key feature is the identification of an invariant subspace which depends only bilinearly on the model parameters, in contrast to the usual multi-linear dependence in the full space. We discuss potential applications including the computation of split (edge) weights on phylogenetic trees from observed sequence data.

  19. Trichotomous noise controlled signal amplification in a generalized Verhulst model

    NASA Astrophysics Data System (ADS)

    Mankin, Romi; Soika, Erkki; Lumi, Neeme

    2014-10-01

    The long-time limit of the probability distribution and statistical moments for a population size are studied by means of a stochastic growth model with generalized Verhulst self-regulation. The effect of variable environment on the carrying capacity of a population is modeled by a multiplicative three-level Markovian noise and by a time periodic deterministic component. Exact expressions for the moments of the population size have been calculated. It is shown that an interplay of a small periodic forcing and colored noise can cause large oscillations of the mean population size. The conditions for the appearance of such a phenomenon are found and illustrated by graphs. Implications of the results on models of symbiotic metapopulations are also discussed. Particularly, it is demonstrated that the effect of noise-generated amplification of an input signal gets more pronounced as the intensity of symbiotic interaction increases.

  20. Eigen model with general fitness functions and degradation rates

    NASA Astrophysics Data System (ADS)

    Hu, Chin-Kun; Saakian, David B.

    2006-03-01

    We present an exact solution of Eigen's quasispecies model with a general degradation rate and fitness functions, including a square root decrease of fitness with increasing Hamming distance from the wild type. The found behavior of the model with a degradation rate is analogous to a viral quasi-species under attack by the immune system of the host. Our exact solutions also revise the known results of neutral networks in quasispecies theory. To explain the existence of mutants with large Hamming distances from the wild type, we propose three different modifications of the Eigen model: mutation landscape, multiple adjacent mutations, and frequency-dependent fitness in which the steady state solution shows a multi-center behavior.

  1. Extensive investigation of the generalized dark matter model

    NASA Astrophysics Data System (ADS)

    Kopp, Michael; Skordis, Constantinos; Thomas, Dan B.

    2016-08-01

    The cold dark matter (CDM) model, wherein the dark matter is treated as a pressureless perfect fluid, provides a good fit to galactic and cosmological data. With the advent of precision cosmology, it should be asked whether this simplest model needs to be extended, and whether doing so could improve our understanding of the properties of dark matter. One established parametrization for generalizing the CDM fluid is the generalized dark matter (GDM) model, in which dark matter is an imperfect fluid with pressure and shear viscosity that fulfill certain postulated closure equations. We investigate these closure equations and the three new parametric functions they contain: the background equation of state w , the speed of sound cs2 and the viscosity cvis2. Taking these functions to be constant parameters, we analyze an exact solution of the perturbed Einstein equations in a flat GDM-dominated universe and discuss the main effects of the three parameters on the cosmic microwave background (CMB). Our analysis suggests that the CMB alone is not able to distinguish between the GDM sound speed and viscosity parameters, but that other observables, such as the matter power spectrum, are required to break this degeneracy. In order to elucidate further the meaning of the GDM closure equations, we also consider other descriptions of imperfect fluids that have a nonperturbative definition and relate these to the GDM model. In particular, we consider scalar fields, an effective field theory (EFT) of fluids, an EFT of large-scale structure, nonequilibrium thermodynamics and tightly coupled fluids. These descriptions could be used to extend the GDM model into the nonlinear regime of structure formation, which is necessary if the wealth of data available on those scales is to be employed in constraining the model. We also derive the initial conditions for adiabatic and isocurvature perturbations in the presence of GDM and standard cosmological fluids and provide the result in a

  2. A general two-cycle network model of molecular motors

    NASA Astrophysics Data System (ADS)

    Zhang, Yunxin

    2009-09-01

    Molecular motors are single macromolecules that generate forces at the piconewton range and nanometer scale. They convert chemical energy into mechanical work by moving along filamentous structures. In this paper, we study the velocity of two-head molecular motors in the framework of a mechanochemical network theory. The network model, a generalization of the recently work of Liepelt and Lipowsky [Steffen Liepelt, Reinhard Lipowsky, Kinesins network of chemomechanical motor cycles, Physical Review Letters 98 (25) (2007) 258102], is based on the discrete mechanochemical states of a molecular motor with multiple cycles. By generalizing the mathematical method developed by Fisher and Kolomeisky for a single cycle motor [Michael E. Fisher, Anatoly B. Kolomeisky, Simple mechanochemistry describes the dynamics of kinesin molecules, Proceedings of the National Academy of Sciences 98 (14) (2001) 7748-7753], we are able to obtain an explicit formula for the velocity of a molecular motor.

  3. Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides.

    PubMed

    Villegas, Myriam E; Vila, Jorge A; Scheraga, Harold A

    2007-02-01

    The dependence of the (13)C chemical shift on side-chain orientation was investigated at the density functional level for a two-strand antiparallel beta-sheet model peptide represented by the amino acid sequence Ac-(Ala)(3)-X-(Ala)(12)-NH(2) where X represents any of the 17 naturally occurring amino acids, i.e., not including alanine, glycine and proline. The dihedral angles adopted for the backbone were taken from, and fixed at, observed experimental values of an antiparallel beta-sheet. We carried out a cluster analysis of the ensembles of conformations generated by considering the side-chain dihedral angles for each residue X as variables, and use them to compute the (13)C chemical shifts at the density functional theory level. It is shown that the adoption of the locally-dense basis set approach for the quantum chemical calculations enabled us to reduce the length of the chemical-shift calculations while maintaining good accuracy of the results. For the 17 naturally occurring amino acids in an antiparallel beta-sheet, there is (i) good agreement between computed and observed (13)C(alpha) and (13)C(beta) chemical shifts, with correlation coefficients of 0.95 and 0.99, respectively; (ii) significant variability of the computed (13)C(alpha) and (13)C(beta) chemical shifts as a function of chi(1) for all amino acid residues except Ser; and (iii) a smaller, although significant, dependence of the computed (13)C(alpha) chemical shifts on chi(xi) (with xi > or = 2) compared to chi(1) for eleven out of seventeen residues. Our results suggest that predicted (13)C(alpha) and (13)C(beta) chemical shifts, based only on backbone (phi,psi) dihedral angles from high-resolution X-ray structure data or from NMR-derived models, may differ significantly from those observed in solution if the dihedral-angle preferences for the side chains are not taken into account.

  4. a Measurement of the Beta Decay Asymmetry of Neon -19 as a Test of the Standard Model

    NASA Astrophysics Data System (ADS)

    Jones, Gordon Lyman

    We have performed an accurate measurement of the parity-violating beta asymmetry of ^{19 }Ne decay. This asymmetry can be calculated in the standard electro-weak model using the measured ft value for ^{19}Ne and a value of G_{V}V_{ud }, where G_{V} is the Fermi coupling constant and V_{ud } is the u-d element of the Cabibbo-Kobayashi -Maskawa mass mixing matrix. The asymmetry is particularly sensitive to the existence of right-handed weak currents. In addition, if we assume that right-handed currents do not exist, the ^{19}Ne asymmetry and ft value provide an independent measurement of G _{V}V_{ud}.. The zero energy intercept of the asymmetry was measured to be A_0=-{0.0360} _sp{-0.0006}{+0.0008}+/-0.0003. The errors are systematic and statistical, respectively. The measured value is in good agreement with the value predicted by the standard model together with the ft values for ^{19}Ne decay and the 0^+ to 0^+ decays (A_0=-{0.0361}+/-0.0007). However, the value of V_{ud } derived from the measured asymmetry, the ^{19}Ne ft value, and mu decay violates unitarity by 1.5 sigma.. The slope of the asymmetry as a function of beta energy was measured to be {dAover dE }=(-{4.2}+/-0.7+/-0.8) times 10^{-3}/MeV. The standard model prediction for the slope is -3.5(1) times 10^{-3}/MeV. The slope is sensitive to second class currents which are not present in the standard model. The implied value of the second class form factor, d^ {II} is -60 +/- 54 +/- 60 which is consistent with the standard model value of 0. The beta asymmetry was measured from the difference in the beta emission rate parallel to and anti-parallel to the polarization of the decaying ^{19 }Ne. Polarized ^{19} Ne atoms were trapped in a thin walled cell at the center of a solenoidal magnetic field. Positrons from ^{19}Ne beta decay spiraled along the magnetic field lines and were detected in Si(Li) detectors at either end of the solenoid. The asymmetry was determined from the ratio of the rates in these two

  5. Modeling SAR images with a generalization of the Rayleigh distribution.

    PubMed

    Kuruoğlu, Ercan E; Zerubia, Josiane

    2004-04-01

    Synthetic aperture radar (SAR) imagery has found important applications due to its clear advantages over optical satellite imagery one of them being able to operate in various weather conditions. However, due to the physics of the radar imaging process, SAR images contain unwanted artifacts in the form of a granular look which is called speckle. The assumptions of the classical SAR image generation model lead to a Rayleigh distribution model for the histogram of the SAR image. However, some experimental data such as images of urban areas show impulsive characteristics that correspond to underlying heavy-tailed distributions, which are clearly non-Rayleigh. Some alternative distributions have been suggested such as the Weibull, log-normal, and the k-distribution which had success in varying degrees depending on the application. Recently, an alternative model namely the alpha-stable distribution has been suggested for modeling radar clutter. In this paper, we show that the amplitude distribution of the complex wave, the real and the imaginery components of which are assumed to be distributed by the alpha-stable distribution, is a generalization of the Rayleigh distribution. We demonstrate that the amplitude distribution is a mixture of Rayleighs as is the k-distribution in accordance with earlier work on modeling SAR images which showed that almost all successful SAR image models could be expressed as mixtures of Rayleighs. We also present parameter estimation techniques based on negative order moments for the new model. Finally, we test the performance of the model on urban images and compare with other models such as Rayleigh, Weibull, and the k-distribution.

  6. Generalized semiparametric varying-coefficient models for longitudinal data

    NASA Astrophysics Data System (ADS)

    Qi, Li

    In this dissertation, we investigate the generalized semiparametric varying-coefficient models for longitudinal data that can flexibly model three types of covariate effects: time-constant effects, time-varying effects, and covariate-varying effects, i.e., the covariate effects that depend on other possibly time-dependent exposure variables. First, we consider the model that assumes the time-varying effects are unspecified functions of time while the covariate-varying effects are parametric functions of an exposure variable specified up to a finite number of unknown parameters. The estimation procedures are developed using multivariate local linear smoothing and generalized weighted least squares estimation techniques. The asymptotic properties of the proposed estimators are established. The simulation studies show that the proposed methods have satisfactory finite sample performance. ACTG 244 clinical trial of HIV infected patients are applied to examine the effects of antiretroviral treatment switching before and after HIV developing the 215-mutation. Our analysis shows benefit of treatment switching before developing the 215-mutation. The proposed methods are also applied to the STEP study with MITT cases showing that they have broad applications in medical research.

  7. Generalized Magnetic Field Effects in Burgers' Nanofluid Model

    PubMed Central

    Rashidi, M. M.; Yang, Z.; Awais, Muhammad; Nawaz, Maria; Hayat, Tasawar

    2017-01-01

    Analysis has been conducted to present the generalized magnetic field effects on the flow of a Burgers' nanofluid over an inclined wall. Mathematical modelling for hydro-magnetics reveals that the term “σB02u/ρ” is for the Newtonian model whereas the generalized magnetic field term (as mentioned in Eq 4) is for the Burgers’ model which is incorporated in the current analysis to get the real insight of the problem for hydro-magnetics. Brownian motion and thermophoresis phenomenon are presented to analyze the nanofluidics for the non-Newtonian fluid. Mathematical analysis is completed in the presence of non-uniform heat generation/absorption. The constructed set of partial differential system is converted into coupled nonlinear ordinary differential system by employing the suitable transformations. Homotopy approach is employed to construct the analytical solutions which are shown graphically for sundr5y parameters including Deborah numbers, magnetic field, thermophoresis, Brownian motion and non-uniform heat generation/absorption. A comparative study is also presented showing the comparison of present results with an already published data. PMID:28045965

  8. The selection of the starting field: General versus tailored model

    NASA Astrophysics Data System (ADS)

    Lerch, F. S.; Wagner, C. A.; Colombo, O. L.; Klosko, S. M.; Williamson, R. G.

    1985-04-01

    The E-mats (normal equations) were solved for both the methods of the tailor-made a priori model and the general a priori model. Errors in the solutions of the 21 geopotential coefficients were plotted for comparison of the two methods. An ideal Topex accuracy goal of 1/4 the errors in the GEM-9 model (1/4 GEM-9 sigma's) was also plotted as a significance level to compare the differences in the solution of the two methods. Both cases of simulation with noise on the data and without noise were plotted. The following additional information were plotted in Figure 1: (1) the general a priori starting values (GEM9 + or - 3 sigma), (2) the standard deviations (error estimate) of the recovered coefficients for the case where noise was applied to the data, and (3) the Topex accuracy goal of 1/4 GEM-9 error sigma's for comparison. A log scale was used since over 6 orders of magnitude are seen in the plots.

  9. A fast method for a generalized nonlocal elastic model

    NASA Astrophysics Data System (ADS)

    Du, Ning; Wang, Hong; Wang, Che

    2015-09-01

    We develop a numerical method for a generalized nonlocal elastic model, which is expressed as a composition of a Riesz potential operator with a fractional differential operator, by composing a collocation method with a finite difference discretization. By carefully exploring the structure of the coefficient matrix of the numerical method, we develop a preconditioned fast Krylov subspace method, which reduces the computations to (Nlog ⁡ N) per iteration and the memory to O (N). The use of the preconditioner significantly reduces the number of iterations, and the preconditioner can be inverted in O (Nlog ⁡ N) computations. Numerical results show the utility of the method.

  10. Consolidation of data base for Army generalized missile model

    NASA Technical Reports Server (NTRS)

    Klenke, D. J.; Hemsch, M. J.

    1980-01-01

    Data from plume interaction tests, nose mounted canard configuration tests, and high angle of attack tests on the Army Generalized Missile model are consolidated in a computer program which makes them readily accessible for plotting, listing, and evaluation. The program is written in FORTRAN and will run on an ordinary minicomputer. It has the capability of retrieving any coefficient from the existing DATAMAN tapes and displaying it in tabular or plotted form. Comparisons of data taken in several wind tunnels and of data with the predictions of Program MISSILE2 are also presented.

  11. Generalized double-gradient model of flapping oscillations: Oblique waves

    NASA Astrophysics Data System (ADS)

    Korovinskiy, D. B.; Kiehas, S. A.

    2016-09-01

    The double-gradient model of flapping oscillations is generalized for oblique plane waves, propagating in the equatorial plane. It is found that longitudinal propagation (ky = 0) is prohibited, while transversal (kx = 0) or nearly transversal waves should possess a maximum frequency, diminishing with the reduction of | k y / k x | ratio. It turns out that the sausage mode may propagate in a narrow range of directions only, | k y / k x | ≫ 1 . A simple analytical expression for the dispersion relation of the kink mode, valid in most part of wave numbers range, | k y / k x | < 9 , is derived.

  12. Superconductivity in the two-dimensional generalized Hubbard model

    NASA Astrophysics Data System (ADS)

    Lima, L. S.

    2016-08-01

    We have used the Green's functions method at finite temperature and the Kubo's formalism, to calculate the electron conductivity σ(ω) in the generalized two-dimensional Hubbard model. We have obtained a behavior superconductor for the system to T > T0. The AC conductivity falls to zero in ω =ω0 , where ω0 depends on Δ, which is the gap of the system. The behavior gotten is according of with the behavior of the superconductors of high Tc where there is a changes abruptly from a Mott's insulator state to superconductor.

  13. A generalized methodology to characterize composite materials for pyrolysis models

    NASA Astrophysics Data System (ADS)

    McKinnon, Mark B.

    The predictive capabilities of computational fire models have improved in recent years such that models have become an integral part of many research efforts. Models improve the understanding of the fire risk of materials and may decrease the number of expensive experiments required to assess the fire hazard of a specific material or designed space. A critical component of a predictive fire model is the pyrolysis sub-model that provides a mathematical representation of the rate of gaseous fuel production from condensed phase fuels given a heat flux incident to the material surface. The modern, comprehensive pyrolysis sub-models that are common today require the definition of many model parameters to accurately represent the physical description of materials that are ubiquitous in the built environment. Coupled with the increase in the number of parameters required to accurately represent the pyrolysis of materials is the increasing prevalence in the built environment of engineered composite materials that have never been measured or modeled. The motivation behind this project is to develop a systematic, generalized methodology to determine the requisite parameters to generate pyrolysis models with predictive capabilities for layered composite materials that are common in industrial and commercial applications. This methodology has been applied to four common composites in this work that exhibit a range of material structures and component materials. The methodology utilizes a multi-scale experimental approach in which each test is designed to isolate and determine a specific subset of the parameters required to define a material in the model. Data collected in simultaneous thermogravimetry and differential scanning calorimetry experiments were analyzed to determine the reaction kinetics, thermodynamic properties, and energetics of decomposition for each component of the composite. Data collected in microscale combustion calorimetry experiments were analyzed to

  14. The Digital Astronaut Project Computational Bone Remodeling Model (Beta Version) Bone Summit Summary Report

    NASA Technical Reports Server (NTRS)

    Pennline, James; Mulugeta, Lealem

    2013-01-01

    Under the conditions of microgravity, astronauts lose bone mass at a rate of 1% to 2% a month, particularly in the lower extremities such as the proximal femur [1-3]. The most commonly used countermeasure against bone loss in microgravity has been prescribed exercise [4]. However, data has shown that existing exercise countermeasures are not as effective as desired for preventing bone loss in long duration, 4 to 6 months, spaceflight [1,3,5,6]. This spaceflight related bone loss may cause early onset of osteoporosis to place the astronauts at greater risk of fracture later in their lives. Consequently, NASA seeks to have improved understanding of the mechanisms of bone demineralization in microgravity in order to appropriately quantify this risk, and to establish appropriate countermeasures [7]. In this light, NASA's Digital Astronaut Project (DAP) is working with the NASA Bone Discipline Lead to implement well-validated computational models to help predict and assess bone loss during spaceflight, and enhance exercise countermeasure development. More specifically, computational modeling is proposed as a way to augment bone research and exercise countermeasure development to target weight-bearing skeletal sites that are most susceptible to bone loss in microgravity, and thus at higher risk for fracture. Given that hip fractures can be debilitating, the initial model development focused on the femoral neck. Future efforts will focus on including other key load bearing bone sites such as the greater trochanter, lower lumbar, proximal femur and calcaneus. The DAP has currently established an initial model (Beta Version) of bone loss due to skeletal unloading in femoral neck region. The model calculates changes in mineralized volume fraction of bone in this segment and relates it to changes in bone mineral density (vBMD) measured by Quantitative Computed Tomography (QCT). The model is governed by equations describing changes in bone volume fraction (BVF), and rates of

  15. Urinary Benzene Biomarkers and DNA Methylation in Bulgarian Petrochemical Workers: Study Findings and Comparison of Linear and Beta Regression Models

    PubMed Central

    Seow, Wei Jie; Pesatori, Angela Cecilia; Dimont, Emmanuel; Farmer, Peter B.; Albetti, Benedetta; Ettinger, Adrienne S.; Bollati, Valentina; Bolognesi, Claudia; Roggieri, Paola; Panev, Teodor I.; Georgieva, Tzveta; Merlo, Domenico Franco; Bertazzi, Pier Alberto; Baccarelli, Andrea A.

    2012-01-01

    Chronic occupational exposure to benzene is associated with an increased risk of hematological malignancies such as acute myeloid leukemia (AML), but the underlying mechanisms are still unclear. The main objective of this study was to investigate the association between benzene exposure and DNA methylation, both in repeated elements and candidate genes, in a population of 158 Bulgarian petrochemical workers and 50 unexposed office workers. Exposure assessment included personal monitoring of airborne benzene at work and urinary biomarkers of benzene metabolism (S-phenylmercapturic acid [SPMA] and trans,trans-muconic acid [t,t-MA]) at the end of the work-shift. The median levels of airborne benzene, SPMA and t,t-MA in workers were 0.46 ppm, 15.5 µg/L and 711 µg/L respectively, and exposure levels were significantly lower in the controls. Repeated-element DNA methylation was measured in Alu and LINE-1, and gene-specific methylation in MAGE and p15. DNA methylation levels were not significantly different between exposed workers and controls (P>0.05). Both ordinary least squares (OLS) and beta-regression models were used to estimate benzene-methylation associations. Beta-regression showed better model specification, as reflected in improved coefficient of determination (pseudo R2) and Akaike’s information criterion (AIC). In beta-regression, we found statistically significant reductions in LINE-1 (−0.15%, P<0.01) and p15 (−0.096%, P<0.01) mean methylation levels with each interquartile range (IQR) increase in SPMA. This study showed statistically significant but weak associations of LINE-1 and p15 hypomethylation with SPMA in Bulgarian petrochemical workers. We showed that beta-regression is more appropriate than OLS regression for fitting methylation data. PMID:23227177

  16. Statistical Inference for Two Reliability Indices in Mastery Testing Based on the Beta-Binomial Model.

    ERIC Educational Resources Information Center

    Huynh, Huynh

    1979-01-01

    In mastery testing, the raw agreement index and the kappa index may be estimated via one test administration when the test scores follow beta-binomial distributions. This paper reports formulae, tables, and a computer program which facilitate the computation of the standard errors of the estimates. (Author/CTM)

  17. Generalization Technique for 2D+SCALE Dhe Data Model

    NASA Astrophysics Data System (ADS)

    Karim, Hairi; Rahman, Alias Abdul; Boguslawski, Pawel

    2016-10-01

    Different users or applications need different scale model especially in computer application such as game visualization and GIS modelling. Some issues has been raised on fulfilling GIS requirement of retaining the details while minimizing the redundancy of the scale datasets. Previous researchers suggested and attempted to add another dimension such as scale or/and time into a 3D model, but the implementation of scale dimension faces some problems due to the limitations and availability of data structures and data models. Nowadays, various data structures and data models have been proposed to support variety of applications and dimensionality but lack research works has been conducted in terms of supporting scale dimension. Generally, the Dual Half Edge (DHE) data structure was designed to work with any perfect 3D spatial object such as buildings. In this paper, we attempt to expand the capability of the DHE data structure toward integration with scale dimension. The description of the concept and implementation of generating 3D-scale (2D spatial + scale dimension) for the DHE data structure forms the major discussion of this paper. We strongly believed some advantages such as local modification and topological element (navigation, query and semantic information) in scale dimension could be used for the future 3D-scale applications.

  18. Computable general equilibrium model fiscal year 2013 capability development report

    SciTech Connect

    Edwards, Brian Keith; Rivera, Michael Kelly; Boero, Riccardo

    2016-05-17

    This report documents progress made on continued developments of the National Infrastructure Simulation and Analysis Center (NISAC) Computable General Equilibrium Model (NCGEM), developed in fiscal year 2012. In fiscal year 2013, NISAC the treatment of the labor market and tests performed with the model to examine the properties of the solutions computed by the model. To examine these, developers conducted a series of 20 simulations for 20 U.S. States. Each of these simulations compared an economic baseline simulation with an alternative simulation that assumed a 20-percent reduction in overall factor productivity in the manufacturing industries of each State. Differences in the simulation results between the baseline and alternative simulations capture the economic impact of the reduction in factor productivity. While not every State is affected in precisely the same way, the reduction in manufacturing industry productivity negatively affects the manufacturing industries in each State to an extent proportional to the reduction in overall factor productivity. Moreover, overall economic activity decreases when manufacturing sector productivity is reduced. Developers ran two additional simulations: (1) a version of the model for the State of Michigan, with manufacturing divided into two sub-industries (automobile and other vehicle manufacturing as one sub-industry and the rest of manufacturing as the other subindustry); and (2) a version of the model for the United States, divided into 30 industries. NISAC conducted these simulations to illustrate the flexibility of industry definitions in NCGEM and to examine the simulation properties of in more detail.

  19. A revised model for AMP-activated protein kinase structure: The alpha-subunit binds to both the beta- and gamma-subunits although there is no direct binding between the beta- and gamma-subunits.

    PubMed

    Wong, Kelly A; Lodish, Harvey F

    2006-11-24

    The 5'-AMP-activated protein kinase (AMPK) is a master sensor for cellular metabolic energy state. It is activated by a high AMP/ATP ratio and leads to metabolic changes that conserve energy and utilize alternative cellular fuel sources. The kinase is composed of a heterotrimeric protein complex containing a catalytic alpha-subunit, an AMP-binding gamma-subunit, and a scaffolding beta-subunit thought to bind directly both the alpha- and gamma-subunits. Here, we use coimmunoprecipitation of proteins in transiently transfected cells to show that the alpha2-subunit binds directly not only to the beta-subunit, confirming previous work, but also to the gamma1-subunit. Deletion analysis of the alpha2-subunit reveals that the C-terminal 386-552 residues are sufficient to bind to the beta-subunit. The gamma1-subunit binds directly to the alpha2-subunit at two interaction sites, one within the catalytic domain consisting of alpha2 amino acids 1-312 and a second within residues 386-552. Binding of the alpha2 and the gamma1-subunits was not affected by 400 mum AMP or ATP. Furthermore, we show that the beta-subunit C terminus is essential for binding to the alpha2-subunit but, in contrast to previous work, the beta-subunit does not bind directly to the gamma1-subunit. Taken together, this study presents a new model for AMPK heterotrimer structure where through its C terminus the beta-subunit binds to the alpha-subunit that, in turn, binds to the gamma-subunit. There is no direct interaction between the beta- and gamma-subunits.

  20. Relaxation of polymers modeled by generalized Husimi cacti

    NASA Astrophysics Data System (ADS)

    Galiceanu, M.

    2010-07-01

    We focus on the generalized Husimi cacti, which are dual structures to the dendrimers but, distinct from the latter, contain loops. We determine their complete spectra by making use of the normal mode analysis. These spectra have been used in computing some physical quantities, such as the averaged monomer displacement and the mechanical relaxation moduli with its two components: the storage and the loss modulus. We also study the dynamics of Husimi cacti in solutions, introducing the hydrodynamic interactions in a preaveraged Oseen fashion, the so-called Zimm model. We observe that the relaxation quantities mentioned above do not scale, in the presence or in the absence of the hydrodynamic interactions. Our results show that all the relaxation forms depend on the number of monomers in the networks in the absence of the hydrodynamic interactions (Rouse model), while by taking into account the hydrodynamic interactions the results do not vary too much.

  1. Metastability of solitons in a generalized Skyrme model

    NASA Astrophysics Data System (ADS)

    Pottinger, D. E. L.; Rathske, E.

    1986-04-01

    We consider soliton solutions in the generalized chirally symmetric Skyrme model which includes, in addition to the usual commutator term, a symmetric term of fourth order in the field derivatives. The classical energy of static hedgehog field configurations is determined numerically as a function of the angle characterizing the relative contribution of these two terms. Next to the Skyrme combination, we find a region where numerical solutions either are metastable (due to the energy being unbounded from below) or do not exist at all. We also study the exact quantization of the isorotational collective coordinates. Our conclusion is that, demanding consistency with meson phenomenology for the signs of the parameters, the model discussed in this paper can lead to reliable physical results only for small deviations from Skyrme's original stabilizing term.

  2. Generalized Skyrme model with the loosely bound potential

    NASA Astrophysics Data System (ADS)

    Gudnason, Sven Bjarke; Zhang, Baiyang; Ma, Nana

    2016-12-01

    We study a generalization of the loosely bound Skyrme model which consists of the Skyrme model with a sixth-order derivative term—motivated by its fluidlike properties—and the second-order loosely bound potential—motivated by lowering the classical binding energies of higher-charged Skyrmions. We use the rational map approximation for the Skyrmion of topological charge B =4 , calculate the binding energy of the latter, and estimate the systematic error in using this approximation. In the parameter space that we can explore within the rational map approximation, we find classical binding energies as low as 1.8%, and once taking into account the contribution from spin-isospin quantization, we obtain binding energies as low as 5.3%. We also calculate the contribution from the sixth-order derivative term to the electric charge density and axial coupling.

  3. A Chemical Containment Model for the General Purpose Work Station

    NASA Technical Reports Server (NTRS)

    Flippen, Alexis A.; Schmidt, Gregory K.

    1994-01-01

    Contamination control is a critical safety requirement imposed on experiments flying on board the Spacelab. The General Purpose Work Station, a Spacelab support facility used for life sciences space flight experiments, is designed to remove volatile compounds from its internal airpath and thereby minimize contamination of the Spacelab. This is accomplished through the use of a large, multi-stage filter known as the Trace Contaminant Control System. Many experiments planned for the Spacelab require the use of toxic, volatile fixatives in order to preserve specimens prior to postflight analysis. The NASA-Ames Research Center SLS-2 payload, in particular, necessitated the use of several toxic, volatile compounds in order to accomplish the many inflight experiment objectives of this mission. A model was developed based on earlier theories and calculations which provides conservative predictions of the resultant concentrations of these compounds given various spill scenarios. This paper describes the development and application of this model.

  4. Dynamic regulation of erythropoiesis: A computer model of general applicability

    NASA Technical Reports Server (NTRS)

    Leonard, J. I.

    1979-01-01

    A mathematical model for the control of erythropoiesis was developed based on the balance between oxygen supply and demand at a renal oxygen detector which controls erythropoietin release and red cell production. Feedback regulation of tissue oxygen tension is accomplished by adjustments of hemoglobin levels resulting from the output of a renal-bone marrow controller. Special consideration was given to the determinants of tissue oxygenation including evaluation of the influence of blood flow, capillary diffusivity, oxygen uptake and oxygen-hemoglobin affinity. A theoretical analysis of the overall control system is presented. Computer simulations of altitude hypoxia, red cell infusion hyperoxia, and homolytic anemia demonstrate validity of the model for general human application in health and disease.

  5. Applying generalized Padé approximants in analytic QCD models

    NASA Astrophysics Data System (ADS)

    Cvetič, Gorazd; Kögerler, Reinhart

    2011-09-01

    A method of resummation of truncated perturbation series, related to diagonal Padé approximants but giving results independent of the renormalization scale, was developed more than ten years ago by us with a view of applying it in perturbative QCD. We now apply this method in analytic QCD models, i.e., models where the running coupling has no unphysical singularities, and we show that the method has attractive features, such as a rapid convergence. The method can be regarded as a generalization of the scale-setting methods of Stevenson, Grunberg, and Brodsky-Lepage-Mackenzie. The method involves the fixing of various scales and weight coefficients via an auxiliary construction of diagonal Padé approximant. In low-energy QCD observables, some of these scales become sometimes low at high order, which prevents the method from being effective in perturbative QCD, where the coupling has unphysical singularities at low spacelike momenta. There are no such problems in analytic QCD.

  6. The generalized hedgehog and the projected chiral soliton model

    NASA Astrophysics Data System (ADS)

    Fiolhais, M.; Goeke, K.; Grümmer, F.; Urbano, J. N.

    1988-05-01

    The linear chiral soliton model with quark fields and elementary pion and sigma fields is solved in order to describe static properties of the nucleon and the delta resonance. To this end a Fock state of the system is constructed which consists of three valence quarks in a 1s orbit with a generalized hedgehog spin-flavour configuration cos η¦u↓> - sin η¦d↑> . Coherent states are used to provide a quantum description for the mesonic parts of the total wave function. The corresponding classical pion field also exhibits a generalized hedgehog structure. In a pure mean field approximation the variation of the total energy results in the ordinary hedgehog form ( η = 45°). In a quantized approach, however, the generalized hedgehog baryon is projected onto states with good spin and isospin and then noticeable deviations from the simple hedgehog form occur (η ≅ 20°), if the relevant degrees of freedom of the wave functions are varied after the projection. Various nucleon properties are calculated. These include proton and neutron charge radii, and the magnetic moment of the proton for which good agreement with experiment is obtained. The absolute value of the neutron magnetic moment comes out too large, similarly as the axial vector coupling constant and the pion-nucleon-nucleon coupling constant. However, due to the generalization of the hedgehog, the Goldberger-Treiman relation and a corresponding virial theorem are fulfilled. Variation of the quark-meson coupling parameter g and the sigma mass mσ shows that the gA is always about 40% too large compared to experiment. The concepts and results of the projections are compared with the semiclassical collective quantization method. It is demonstrated that noticeable deviations occur for the delta-nucleon splitting, the isovector squared charge radius and the axial vector coupling constant.

  7. Anisotropic mesoscale eddy transport in ocean general circulation models

    NASA Astrophysics Data System (ADS)

    Reckinger, Scott; Fox-Kemper, Baylor; Bachman, Scott; Bryan, Frank; Dennis, John; Danabasoglu, Gokhan

    2014-11-01

    In modern climate models, the effects of oceanic mesoscale eddies are introduced by relating subgrid eddy fluxes to the resolved gradients of buoyancy or other tracers, where the proportionality is, in general, governed by an eddy transport tensor. The symmetric part of the tensor, which represents the diffusive effects of mesoscale eddies, is universally treated isotropically. However, the diffusive processes that the parameterization approximates, such as shear dispersion and potential vorticity barriers, typically have strongly anisotropic characteristics. Generalizing the eddy diffusivity tensor for anisotropy extends the number of parameters from one to three: major diffusivity, minor diffusivity, and alignment. The Community Earth System Model (CESM) with the anisotropic eddy parameterization is used to test various choices for the parameters, which are motivated by observations and the eddy transport tensor diagnosed from high resolution simulations. Simply setting the ratio of major to minor diffusivities to a value of five globally, while aligning the major axis along the flow direction, improves biogeochemical tracer ventilation and reduces temperature and salinity biases. These effects can be improved by parameterizing the oceanic anisotropic transport mechanisms.

  8. On the General Class of Models of Adiabatic Evolution

    NASA Astrophysics Data System (ADS)

    Sun, Jie; Lu, Songfeng; Liu, Fang

    2016-10-01

    The general class of models of adiabatic evolution was proposed to speed up the usual adiabatic computation in the case of quantum search problem. It was shown [8] that, by temporarily increasing the ground state energy of a time-dependent Hamiltonian to a suitable quantity, the quantum computation can perform the calculation in time complexity O(1). But it is also known that if the overlap between the initial and final states of the system is zero, then the computation based on the generalized models of adiabatic evolution can break down completely. In this paper, we find another severe limitation for this class of adiabatic evolution-based algorithms, which should be taken into account in applications. That is, it is still possible that this kind of evolution designed to deal with the quantum search problem fails completely if the interpolating paths in the system Hamiltonian are chosen inappropriately, while the usual adiabatic evolutions can do the same job relatively effectively. This implies that it is not always recommendable to use nonlinear paths in adiabatic computation. On the contrary, the usual simple adiabatic evolution may be sufficient for effective use.

  9. Risk prediction for myocardial infarction via generalized functional regression models.

    PubMed

    Ieva, Francesca; Paganoni, Anna M

    2016-08-01

    In this paper, we propose a generalized functional linear regression model for a binary outcome indicating the presence/absence of a cardiac disease with multivariate functional data among the relevant predictors. In particular, the motivating aim is the analysis of electrocardiographic traces of patients whose pre-hospital electrocardiogram (ECG) has been sent to 118 Dispatch Center of Milan (the Italian free-toll number for emergencies) by life support personnel of the basic rescue units. The statistical analysis starts with a preprocessing of ECGs treated as multivariate functional data. The signals are reconstructed from noisy observations. The biological variability is then removed by a nonlinear registration procedure based on landmarks. Thus, in order to perform a data-driven dimensional reduction, a multivariate functional principal component analysis is carried out on the variance-covariance matrix of the reconstructed and registered ECGs and their first derivatives. We use the scores of the Principal Components decomposition as covariates in a generalized linear model to predict the presence of the disease in a new patient. Hence, a new semi-automatic diagnostic procedure is proposed to estimate the risk of infarction (in the case of interest, the probability of being affected by Left Bundle Brunch Block). The performance of this classification method is evaluated and compared with other methods proposed in literature. Finally, the robustness of the procedure is checked via leave-j-out techniques.

  10. Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures.

    PubMed

    Chatzieleftheriou, Stavros; Adendorff, Matthew R; Lagaros, Nikos D

    2016-10-24

    The potential energy of molecules and nanostructures is commonly calculated in the molecular mechanics formalism by superimposing bonded and nonbonded atomic energy terms, i.e. bonds between two atoms, bond angles involving three atoms, dihedral angles involving four atoms, nonbonded terms expressing the Coulomb and Lennard-Jones interactions, etc. In this work a new, generalized numerical simulation is presented for studying the mechanical behavior of three-dimensional nanostructures at the atomic scale. The energy gradient and Hessian matrix of such assemblies are usually computed numerically; a potential energy finite element model is proposed herein where these two components are expressed analytically. In particular, generalized finite elements are developed that express the interactions among atoms in a manner equivalent to that invoked in simulations performed based on the molecular dynamics method. Thus, the global tangent stiffness matrix for any nanostructure is formed as an assembly of the generalized finite elements and is directly equivalent to the Hessian matrix of the potential energy. The advantages of the proposed model are identified in terms of both accuracy and computational efficiency. In the case of popular force fields (e.g., CHARMM), the computation of the Hessian matrix by implementing the proposed method is of the same order as that of the gradient. This analysis can be used to minimize the potential energy of molecular systems under nodal loads in order to derive constitutive laws for molecular systems where the entropy and solvent effects are neglected and can be approximated as solids, such as double stranded DNA nanostructures. In this context, the sequence dependent stretch modulus for some typical base pairs step is calculated.

  11. General Methods for Evolutionary Quantitative Genetic Inference from Generalized Mixed Models

    PubMed Central

    de Villemereuil, Pierre; Schielzeth, Holger; Nakagawa, Shinichi; Morrissey, Michael

    2016-01-01

    Methods for inference and interpretation of evolutionary quantitative genetic parameters, and for prediction of the response to selection, are best developed for traits with normal distributions. Many traits of evolutionary interest, including many life history and behavioral traits, have inherently nonnormal distributions. The generalized linear mixed model (GLMM) framework has become a widely used tool for estimating quantitative genetic parameters for nonnormal traits. However, whereas GLMMs provide inference on a statistically convenient latent scale, it is often desirable to express quantitative genetic parameters on the scale upon which traits are measured. The parameters of fitted GLMMs, despite being on a latent scale, fully determine all quantities of potential interest on the scale on which traits are expressed. We provide expressions for deriving each of such quantities, including population means, phenotypic (co)variances, variance components including additive genetic (co)variances, and parameters such as heritability. We demonstrate that fixed effects have a strong impact on those parameters and show how to deal with this by averaging or integrating over fixed effects. The expressions require integration of quantities determined by the link function, over distributions of latent values. In general cases, the required integrals must be solved numerically, but efficient methods are available and we provide an implementation in an R package, QGglmm. We show that known formulas for quantities such as heritability of traits with binomial and Poisson distributions are special cases of our expressions. Additionally, we show how fitted GLMM can be incorporated into existing methods for predicting evolutionary trajectories. We demonstrate the accuracy of the resulting method for evolutionary prediction by simulation and apply our approach to data from a wild pedigreed vertebrate population. PMID:27591750

  12. General Methods for Evolutionary Quantitative Genetic Inference from Generalized Mixed Models.

    PubMed

    de Villemereuil, Pierre; Schielzeth, Holger; Nakagawa, Shinichi; Morrissey, Michael

    2016-11-01

    Methods for inference and interpretation of evolutionary quantitative genetic parameters, and for prediction of the response to selection, are best developed for traits with normal distributions. Many traits of evolutionary interest, including many life history and behavioral traits, have inherently nonnormal distributions. The generalized linear mixed model (GLMM) framework has become a widely used tool for estimating quantitative genetic parameters for nonnormal traits. However, whereas GLMMs provide inference on a statistically convenient latent scale, it is often desirable to express quantitative genetic parameters on the scale upon which traits are measured. The parameters of fitted GLMMs, despite being on a latent scale, fully determine all quantities of potential interest on the scale on which traits are expressed. We provide expressions for deriving each of such quantities, including population means, phenotypic (co)variances, variance components including additive genetic (co)variances, and parameters such as heritability. We demonstrate that fixed effects have a strong impact on those parameters and show how to deal with this by averaging or integrating over fixed effects. The expressions require integration of quantities determined by the link function, over distributions of latent values. In general cases, the required integrals must be solved numerically, but efficient methods are available and we provide an implementation in an R package, QGglmm. We show that known formulas for quantities such as heritability of traits with binomial and Poisson distributions are special cases of our expressions. Additionally, we show how fitted GLMM can be incorporated into existing methods for predicting evolutionary trajectories. We demonstrate the accuracy of the resulting method for evolutionary prediction by simulation and apply our approach to data from a wild pedigreed vertebrate population.

  13. Generalized Optoelectronic Model of Series-Connected Multijunction Solar Cells

    DOE PAGES

    Geisz, John F.; Steiner, Myles A.; Garcia, Ivan; ...

    2015-10-02

    The emission of light from each junction in a series-connected multijunction solar cell, we found, both complicates and elucidates the understanding of its performance under arbitrary conditions. Bringing together many recent advances in this understanding, we present a general 1-D model to describe luminescent coupling that arises from both voltage-driven electroluminescence and voltage-independent photoluminescence in nonideal junctions that include effects such as Sah-Noyce-Shockley (SNS) recombination with n ≠ 2, Auger recombination, shunt resistance, reverse-bias breakdown, series resistance, and significant dark area losses. The individual junction voltages and currents are experimentally determined from measured optical and electrical inputs and outputs ofmore » the device within the context of the model to fit parameters that describe the devices performance under arbitrary input conditions. Furthermore, our techniques to experimentally fit the model are demonstrated for a four-junction inverted metamorphic solar cell, and the predictions of the model are compared with concentrator flash measurements.« less

  14. A generalized Potts model for confocal microscopy images

    NASA Astrophysics Data System (ADS)

    Máté, Gabriell; Heermann, Dieter W.

    2015-01-01

    Much as being among the least invasive mainstream imaging technologies in life sciences, the resolution of confocal microscopy is limited. Imaged structures, e.g., chromatin-fiber loops, have diameters around or beyond the diffraction limit, and microscopy images show seemingly random spatial density distributions only. While such images are important because the organization of the chromosomes influences different cell mechanisms, many interesting questions can also be related to the observed patterns. These concern their spatial aspects, the role of randomness, the possibility of modeling these images with a random generative process, the interaction between the densities of adjacent loci, the length-scales of these influences, etc. We answer these questions by implementing a generalization of the Potts model. We show how to estimate the model parameters, test the performance of the estimation process and numerically prove that the obtained values converge to the ground truth. Finally, we generate images with a trained model and show that they compare well to real cell images.

  15. Solitons and kinks in a general car-following model

    NASA Astrophysics Data System (ADS)

    Kurtze, Douglas A.

    2013-09-01

    We study a general car-following model of traffic flow on an infinitely long single-lane road, which assumes that a car's acceleration depends on time-delayed values of its own speed, the headway between it and the car ahead, and the rate of change of headway, but makes minimal assumptions about the functional form of that dependence. We present a detailed characterization of the onset of linear instability; in particular we find a specific limit on the delay time below which the marginal wave number at the onset of instability is zero, and another specific limit on the delay time above which steady flow is always unstable. Crucially, the threshold of absolute stability generally does not coincide with an inflection point of the steady-state velocity function. When the marginal perturbation at onset has wave number 0, we show that Burgers and Korteweg-de Vries (KdV) equations can be derived under the usual assumptions, and that corrections to the KdV equation “select” a single member of the one-parameter set of its one-soliton solutions by driving a slow evolution of the soliton parameter. While in previous models this selected soliton has always marked the threshold of a finite-amplitude instability of linearly stable steady flow, we find that it can alternatively be a stable, small-amplitude jam that occurs when steady flow is linearly unstable. The model reduces to the usual modified Korteweg-de Vries (mKdV) equation only in the special situation that the threshold of absolute stability coincides with an inflection point of the steady-state velocity function; in general, near the threshold of absolute stability the model reduces instead to a KdV equation in the regime of small solitons, while near an inflection point it reduces to a Hayakawa-Nakanishi equation. Like the mKdV equation, the Hayakawa-Nakanishi equation admits a continuous family of kink solutions, and the selection criterion arising from the corrections to this equation can be written down

  16. Complex Environmental Data Modelling Using Adaptive General Regression Neural Networks

    NASA Astrophysics Data System (ADS)

    Kanevski, Mikhail

    2015-04-01

    The research deals with an adaptation and application of Adaptive General Regression Neural Networks (GRNN) to high dimensional environmental data. GRNN [1,2,3] are efficient modelling tools both for spatial and temporal data and are based on nonparametric kernel methods closely related to classical Nadaraya-Watson estimator. Adaptive GRNN, using anisotropic kernels, can be also applied for features selection tasks when working with high dimensional data [1,3]. In the present research Adaptive GRNN are used to study geospatial data predictability and relevant feature selection using both simulated and real data case studies. The original raw data were either three dimensional monthly precipitation data or monthly wind speeds embedded into 13 dimensional space constructed by geographical coordinates and geo-features calculated from digital elevation model. GRNN were applied in two different ways: 1) adaptive GRNN with the resulting list of features ordered according to their relevancy; and 2) adaptive GRNN applied to evaluate all possible models N [in case of wind fields N=(2^13 -1)=8191] and rank them according to the cross-validation error. In both cases training were carried out applying leave-one-out procedure. An important result of the study is that the set of the most relevant features depends on the month (strong seasonal effect) and year. The predictabilities of precipitation and wind field patterns, estimated using the cross-validation and testing errors of raw and shuffled data, were studied in detail. The results of both approaches were qualitatively and quantitatively compared. In conclusion, Adaptive GRNN with their ability to select features and efficient modelling of complex high dimensional data can be widely used in automatic/on-line mapping and as an integrated part of environmental decision support systems. 1. Kanevski M., Pozdnoukhov A., Timonin V. Machine Learning for Spatial Environmental Data. Theory, applications and software. EPFL Press

  17. The effect of topical dexamethasone and preoperative beta irradiation on a model of glaucoma fistulizing surgery in the rabbit

    SciTech Connect

    Miller, M.H.; Grierson, I.; Unger, W.G.; Hitchings, R.A. )

    1990-01-01

    We studied the effect of topical dexamethasone (1%) and preoperative beta irradiation on a model of glaucoma fistulizing surgery in the rabbit. Intraocular pressure and gross facility of aqueous outflow following surgery were not influenced by either treatment, although blebs persisted longer in the irradiated eyes. Steroids reduced clinically observable inflammation as well as the number of inflammatory cells identifiable by microscopy. Fibroblast production temporarily slowed, and ultrastructural examination demonstrated lipid-filled vacuoles and dilated mitochondria in these eyes. Also, the scar was thinner at 24 days. Beta irradiation delayed wound healing and the scar was thinner in the early postoperative stages, but the light microscopic appearance of the scar was unaltered at 59 days. Inflammation was more pronounced initially, with abundant fibrin in the wound. Recovery of the conjunctival epithelium was delayed. The delay in fibroblast recruitment and wound contraction, the thinner scar tissue, and the increased survival of the bleb are all factors that suggest that beta irradiation may be a useful adjunct to glaucoma surgery.

  18. Erythropoietin and interleukin-1beta modulate nitrite production in a Swiss 3T3 cell model of rheumatoid synovial fibroblasts.

    PubMed

    Baig, S; Patel, Y; Coussons, P; Grant, R

    2002-11-01

    Erythropoietin (EPO), a haemopoietic growth factor and a primary regulator of erythropoiesis, is widely used to treat anaemia in various chronic complications of rheumatoid arthritis (RA). Fibroblast-like cells, found in the pannus tissue of joints, are thought to contribute to the inflammatory pathology of RA. Thus for the current study we investigated the effects of recombinant human EPO (rHuEPO) on NO metabolism, using an interleukin-1beta (IL-1beta)-stimulated Swiss 3T3 fibroblast monolayer as a model for fibroblast activity in RA. The results show that, over 3 days, both alone and in combination with the pro-inflammatory cytokine IL-1beta (10 ng/ml), rHuEPO (25 micro-units/ml) induced significant production of nitrite in cell culture supernatants. This is an indicator of NO production by nitric oxide synthase (NOS), which is a well-documented mediator of metalloproteinase-mediated tissue remodelling in RA. It therefore appears that, through modulation of NOS-dependent NO production, rHuEPO may influence remodelling of connective tissue in RA, independently of its established erythropoietic role.

  19. Adaptive Error Estimation in Linearized Ocean General Circulation Models

    NASA Technical Reports Server (NTRS)

    Chechelnitsky, Michael Y.

    1999-01-01

    Data assimilation methods are routinely used in oceanography. The statistics of the model and measurement errors need to be specified a priori. This study addresses the problem of estimating model and measurement error statistics from observations. We start by testing innovation based methods of adaptive error estimation with low-dimensional models in the North Pacific (5-60 deg N, 132-252 deg E) to TOPEX/POSEIDON (TIP) sea level anomaly data, acoustic tomography data from the ATOC project, and the MIT General Circulation Model (GCM). A reduced state linear model that describes large scale internal (baroclinic) error dynamics is used. The methods are shown to be sensitive to the initial guess for the error statistics and the type of observations. A new off-line approach is developed, the covariance matching approach (CMA), where covariance matrices of model-data residuals are "matched" to their theoretical expectations using familiar least squares methods. This method uses observations directly instead of the innovations sequence and is shown to be related to the MT method and the method of Fu et al. (1993). Twin experiments using the same linearized MIT GCM suggest that altimetric data are ill-suited to the estimation of internal GCM errors, but that such estimates can in theory be obtained using acoustic data. The CMA is then applied to T/P sea level anomaly data and a linearization of a global GFDL GCM which uses two vertical modes. We show that the CMA method can be used with a global model and a global data set, and that the estimates of the error statistics are robust. We show that the fraction of the GCM-T/P residual variance explained by the model error is larger than that derived in Fukumori et al.(1999) with the method of Fu et al.(1993). Most of the model error is explained by the barotropic mode. However, we find that impact of the change in the error statistics on the data assimilation estimates is very small. This is explained by the large

  20. The Generalized FLaIR Model (GFM) for landslide forecasting

    NASA Astrophysics Data System (ADS)

    De Luca, Davide Luciano; Versace, Pasquale

    2015-04-01

    A new version of the hydrological model named FLaIR (Forecasting of Landslides Induced by Rainfall, Capparelli and Versace 2011) is proposed, named as GFM (Generalized FLaIR Model). Non stationary rainfall thresholds, depending on antecedent precipitation, are introduced in this new release, which allow for a better prediction of landslide occurrences. It is possible to demonstrate that GFM reproduces all the Antecedent Precipitation models (AP) proposed in technical literature as particular cases, besides Intensity-Duration schemes (ID) and more conceptual approaches, whose reconstruction with the first release of FlaIR model, which adopts only stationary thresholds, was already discussed in Capparelli and Versace (2011). GFM is extremely flexible, and the main advantage of the model is represented by the possibility of using well-established procedures for the choice of the most appropriate configuration for the selected case study, and of facilitating the comparison between several options, through the use of a mobility function. Gimigliano municipality, located in Calabria region (southern Italy) was chosen as case study, where a consistent number of landslides occurred in the past years; in particular, during the period 2008-2010 this area (like the whole Calabria region) was affected by persistent rainfall events, which induced several damages related to infrastructures and buildings. For the selected case study GFM allows to obtain significant improvements in landslide prediction; in details a substantial reduction of False Alarms is obtained with respect to application of classical ID and AP schemes. REFERENCES Capparelli G, Versace P (2011). FLaIR and SUSHI: Two mathematical models for Early Warning Systems for rainfall induced landslides. Landslides 8:67-79. doi: 10.1007/s10346-010-0228-6

  1. A generalized model for estimating the energy density of invertebrates

    USGS Publications Warehouse

    James, Daniel A.; Csargo, Isak J.; Von Eschen, Aaron; Thul, Megan D.; Baker, James M.; Hayer, Cari-Ann; Howell, Jessica; Krause, Jacob; Letvin, Alex; Chipps, Steven R.

    2012-01-01

    Invertebrate energy density (ED) values are traditionally measured using bomb calorimetry. However, many researchers rely on a few published literature sources to obtain ED values because of time and sampling constraints on measuring ED with bomb calorimetry. Literature values often do not account for spatial or temporal variability associated with invertebrate ED. Thus, these values can be unreliable for use in models and other ecological applications. We evaluated the generality of the relationship between invertebrate ED and proportion of dry-to-wet mass (pDM). We then developed and tested a regression model to predict ED from pDM based on a taxonomically, spatially, and temporally diverse sample of invertebrates representing 28 orders in aquatic (freshwater, estuarine, and marine) and terrestrial (temperate and arid) habitats from 4 continents and 2 oceans. Samples included invertebrates collected in all seasons over the last 19 y. Evaluation of these data revealed a significant relationship between ED and pDM (r2  =  0.96, p < 0.0001), where ED (as J/g wet mass) was estimated from pDM as ED  =  22,960pDM − 174.2. Model evaluation showed that nearly all (98.8%) of the variability between observed and predicted values for invertebrate ED could be attributed to residual error in the model. Regression of observed on predicted values revealed that the 97.5% joint confidence region included the intercept of 0 (−103.0 ± 707.9) and slope of 1 (1.01 ± 0.12). Use of this model requires that only dry and wet mass measurements be obtained, resulting in significant time, sample size, and cost savings compared to traditional bomb calorimetry approaches. This model should prove useful for a wide range of ecological studies because it is unaffected by taxonomic, seasonal, or spatial variability.

  2. General Description of Fission Observables: GEF Model Code

    NASA Astrophysics Data System (ADS)

    Schmidt, K.-H.; Jurado, B.; Amouroux, C.; Schmitt, C.

    2016-01-01

    The GEF ("GEneral description of Fission observables") model code is documented. It describes the observables for spontaneous fission, neutron-induced fission and, more generally, for fission of a compound nucleus from any other entrance channel, with given excitation energy and angular momentum. The GEF model is applicable for a wide range of isotopes from Z = 80 to Z = 112 and beyond, up to excitation energies of about 100 MeV. The results of the GEF model are compared with fission barriers, fission probabilities, fission-fragment mass- and nuclide distributions, isomeric ratios, total kinetic energies, and prompt-neutron and prompt-gamma yields and energy spectra from neutron-induced and spontaneous fission. Derived properties of delayed neutrons and decay heat are also considered. The GEF model is based on a general approach to nuclear fission that explains a great part of the complex appearance of fission observables on the basis of fundamental laws of physics and general properties of microscopic systems and mathematical objects. The topographic theorem is used to estimate the fission-barrier heights from theoretical macroscopic saddle-point and ground-state masses and experimental ground-state masses. Motivated by the theoretically predicted early localisation of nucleonic wave functions in a necked-in shape, the properties of the relevant fragment shells are extracted. These are used to determine the depths and the widths of the fission valleys corresponding to the different fission channels and to describe the fission-fragment distributions and deformations at scission by a statistical approach. A modified composite nuclear-level-density formula is proposed. It respects some features in the superfluid regime that are in accordance with new experimental findings and with theoretical expectations. These are a constant-temperature behaviour that is consistent with a considerably increased heat capacity and an increased pairing condensation energy that is

  3. 2-Hydroxy-4-glutathion-S-yl-17beta-estradiol and 2-hydroxy-1-glutathion-S-yl-17beta-estradiol produce oxidative stress and renal toxicity in an animal model of 17beta-estradiol-mediated nephrocarcinogenicity.

    PubMed

    Butterworth, M; Lau, S S; Monks, T J

    1998-01-01

    Chronic exposure of male Syrian hamsters to a variety of estrogens has been linked with a high incidence of renal carcinoma. The basis of this species and tissue specificity remains to be resolved. We have recently shown that (i) 17beta-estradiol is nephrotoxic in the hamster in a manner dependent upon the activity of gamma-glutamyl transpeptidase and (ii) 17beta-estradiol is metabolized to a variety of catechol estrogen glutathione conjugates (Butterworth et al., Carcinogenesis, 18, 561-567, 1997). We report that the catechol estrogen glutathione conjugates exhibit redox properties similar to those of the catechol estrogens, and maintain the ability to generate superoxide radicals. Administration of 2-hydroxy-4-glutathion-S-yl-17beta-estradiol or 2-hydroxy-1-glutathion-S-yl-17beta-estradiol (0.27-5.0 micromol/kg) to Syrian hamsters, produces mild nephrotoxicity. Repeated daily administration of 2-hydroxy-4-glutathion-S-yl-17beta-estradiol causes a sustained elevation in urinary markers of renal damage and in the concentration of renal protein carbonyls and lipid hydroperoxides. Catechol estrogen oxidation and conjugation of glutathione in the liver, followed by the selective uptake of the redox active conjugates in tissues rich in gamma-glutamyl transpeptidase may contribute to 17beta-estradiol-induced renal tumors in the hamster.

  4. Modeling of space environment impact on nanostructured materials. General principles

    NASA Astrophysics Data System (ADS)

    Voronina, Ekaterina; Novikov, Lev

    2016-07-01

    In accordance with the resolution of ISO TC20/SC14 WG4/WG6 joint meeting, Technical Specification (TS) 'Modeling of space environment impact on nanostructured materials. General principles' which describes computer simulation methods of space environment impact on nanostructured materials is being prepared. Nanomaterials surpass traditional materials for space applications in many aspects due to their unique properties associated with nanoscale size of their constituents. This superiority in mechanical, thermal, electrical and optical properties will evidently inspire a wide range of applications in the next generation spacecraft intended for the long-term (~15-20 years) operation in near-Earth orbits and the automatic and manned interplanetary missions. Currently, ISO activity on developing standards concerning different issues of nanomaterials manufacturing and applications is high enough. Most such standards are related to production and characterization of nanostructures, however there is no ISO documents concerning nanomaterials behavior in different environmental conditions, including the space environment. The given TS deals with the peculiarities of the space environment impact on nanostructured materials (i.e. materials with structured objects which size in at least one dimension lies within 1-100 nm). The basic purpose of the document is the general description of the methodology of applying computer simulation methods which relate to different space and time scale to modeling processes occurring in nanostructured materials under the space environment impact. This document will emphasize the necessity of applying multiscale simulation approach and present the recommendations for the choice of the most appropriate methods (or a group of methods) for computer modeling of various processes that can occur in nanostructured materials under the influence of different space environment components. In addition, TS includes the description of possible

  5. The DSM-5 dimensional trait model and five-factor models of general personality.

    PubMed

    Gore, Whitney L; Widiger, Thomas A

    2013-08-01

    The current study tests empirically the relationship of the dimensional trait model proposed for the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) with five-factor models of general personality. The DSM-5 maladaptive trait dimensional model proposal included 25 traits organized within five broad domains (i.e., negative affectivity, detachment, antagonism, disinhibition, and psychoticism). Consistent with the authors of the proposal, it was predicted that negative affectivity would align with five-factor model (FFM) neuroticism, detachment with FFM introversion, antagonism with FFM antagonism, disinhibition with low FFM conscientiousness and, contrary to the proposal; psychoticism would align with FFM openness. Three measures of alternative five-factor models of general personality were administered to 445 undergraduates along with the Personality Inventory for DSM-5. The results provided support for the hypothesis that all five domains of the DSM-5 dimensional trait model are maladaptive variants of general personality structure, including the domain of psychoticism.

  6. Development of hormone-dependent prostate cancer models for the evaluation of inhibitors of 17beta-hydroxysteroid dehydrogenase type 3.

    PubMed

    Day, Joanna M; Tutill, Helena J; Foster, Paul A; Bailey, Helen V; Heaton, Wesley B; Sharland, Christopher M; Vicker, Nigel; Potter, Barry V L; Purohit, Atul; Reed, Michael J

    2009-03-25

    17beta-Hydroxysteroid dehydrogenases (17beta-HSDs) are responsible for the pre-receptor reduction/oxidation of steroids at the 17-position into active/inactive hormones, and the 15 known enzymes vary in their substrate specificity, localisation, and directional activity. 17beta-HSD Type 3 (17beta-HSD3) has been seen to be over-expressed in prostate cancer, and catalyses the reduction of androstenedione (Adione) to testosterone (T), which stimulates prostate tumour growth. Specific inhibitors of 17beta-HSD3 may have a role in the treatment of hormone-dependent prostate cancer and benign prostate hyperplasia, and also have potential as male anti-fertility agents. A 293-EBNA-based cell line with stable expression of transfected human 17beta-HSD3 was created and used to develop a whole cell radiometric TLC-based assay to assess the 17beta-HSD3 inhibitory potency of a series of compounds. STX2171 and STX2624 (IC(50) values in the 200-450nM range) were two of several active inhibitors identified. In similar TLC-based assays these compounds were found to be inactive against 17beta-HSD1 and 17beta-HSD2, indicating selectivity. A novel proof of concept model was developed to study the efficacy of the compounds in vitro using the androgen receptor positive hormone-dependent prostate cancer cell line, LNCaPwt, and its derivative, LNCaP[17beta-HSD3], transfected and selected for stable expression of 17beta-HSD3. The proliferation of the parental cell line was most efficiently stimulated by 5alpha-dihydrotestosterone (DHT), but the LNCaP[17beta-HSD3] cells were equally stimulated by Adione, indicating that 17beta-HSD3 efficiently converts Adione to T in this model. Adione-stimulated proliferation of LNCaP[17beta-HSD3] cells was inhibited in the presence of either STX2171 or STX2624. The compounds alone neither stimulated proliferation of the cells nor caused significant cell death, indicating that they are non-androgenic with low cytotoxicity. STX2171 inhibited Adione

  7. Polyelectrolyte stabilized drug nanoparticles via flash nanoprecipitation: a model study with beta-carotene.

    PubMed

    Zhu, Zhengxi; Margulis-Goshen, Katrin; Magdassi, Shlomo; Talmon, Yeshayahu; Macosko, Christopher W

    2010-10-01

    Polyelectrolyte protected beta-carotene nanoparticles (nanosuspensions) with average diameter of <100 nm were achieved by turbulent mixing and flash nanoprecipitation (FNP). Three types of multi-amine functional polyelectrolytes, epsilon-polylysine (epsilon-PL), poly(ethylene imine) (PEI), and chitosan, were investigated to electrosterically protect the nanoparticles. Particle size and distribution were measured by dynamic light scattering (DLS); particles were imaged via scanning electron microscopy (SEM) and cryogenic transmission electron microscopy (cryo-TEM). Low pH and high polyelectrolyte molecular weight gave the smallest and most stable particles. High drug loading capacity, >80 wt%, was achieved by using either PEI or chitosan. X-ray diffraction (XRD) patterns showed that beta-carotene nanoparticles were amorphous. These findings open the way for utilization of FNP for preparation of nanoparticles with enhanced bioavailability for highly water insoluble drugs.

  8. A general formulation for a mathematical PEM fuel cell model

    NASA Astrophysics Data System (ADS)

    Baschuk, J. J.; Li, Xianguo

    A general formulation for a comprehensive fuel cell model, based on the conservation principle is presented. The model formulation includes the electro-chemical reactions, proton migration, and the mass transport of the gaseous reactants and liquid water. Additionally, the model formulation can be applied to all regions of the PEM fuel cell: the bipolar plates, gas flow channels, electrode backing, catalyst, and polymer electrolyte layers. The model considers the PEM fuel cell to be composed of three phases: reactant gas, liquid water, and solid. These three phases can co-exist within the gas flow channels, electrode backing, catalyst, and polymer electrolyte layers. The conservation of mass, momentum, species, and energy are applied to each phase, with the technique of volume averaging being used to incorporate the interactions between the phases as interfacial source terms. In order to avoid problems arising from phase discontinuities, the gas and liquid phases are considered as a mixture. The momentum interactions between the fluid and solid phases are modeled by the Darcy-Forchheimer term. The electro-oxidation of H and CO, the reduction of O, and the heterogeneous oxidation of H and CO are considered in the catalyst layers. Due to the small pore size of the polymer electrolyte layer, the generalized Stefan-Maxwell equations, with the polymer considered as a diffusing species, are used to describe species transport. One consequence of considering the gas and liquid phases as a mixture is that expressions for the velocity of the individual phases relative to the mixture must be developed. In the gas flow channels, the flow is assumed homogeneous, while the Darcy and Schlögl equations are used to describe liquid water transport in the electrode backing and polymer electrolyte layers. Thus, two sets of equations, one for the mixture and another for the solid phase, can be developed to describe the processes occurring within a PEM fuel cell. These equations are in

  9. Biosynthesis of ketomycin. (II) biomimetic model for beta-lactamase catalysis: host-guest interactions in cyclodextrin-penicillin inclusion complex

    SciTech Connect

    Mak, H.W.

    1986-01-01

    The antibiotic ketomycin is formed from shikimic acid via chorismic acid and prephenic acid. Phenylalanine and 2',5'-dihydrophenylalanine derived from shikimic acid are not intermediates in the biosynthesis. Degradation of ketomycin derived from (1,6-/sup 14/C)shikimic acid showed that prephenic acid is converted into ketomycin with stereospecific discrimination between the two enantiotopic edges of the ring, the pro-S-R edge giving rise to the C-2', C-3' side of the cyclohexane ring of ketomycin. The resistance of pathogenic bacteria to the action of ..beta..-lactam antibiotics is mainly ascribed to their ability to produce ..beta..-lactamase to cleave the ..beta..-lactam ring. It is essential to understand the molecular nature of ..beta..-lactamase-penicillin recognition for designing and formulating more effective ..beta..-lactam antibiotics. A biomimetic study of ..beta..-lactamase is therefore initiated. To meet the requirements of hydrophobic and serine protease characteristics of ..beta..-lactamase, ..cap alpha..-cyclodextrin is chosen as a biomimetic model for ..beta..-lactamase. The structural specificity and the chemical dynamics of ..cap alpha..-cyclodextrin-phenoxymethyl penicillin inclusion complex in solid state and in solution have been determined by IR and NMR spectroscopy. The spectral results strongly indicate that the phenyl portion of the phenoxymethyl penicillin forms a stable inclusion complex with the hydrophobic cavity of ..cap alpha..-cyclodextrin in solution as well as in the solid state. Kinetic studies followed by /sup 1/HNMR and HPLC analyses under alkaline condition have shown that the ..cap alpha..-cyclodextrin mimics the catalytic function of serine of ..beta..-lactamase in the stereospecific hydrolysis of the ..beta..-lactam ring of phenoxymethyl penicillin.

  10. Generalized multiplicative error models: Asymptotic inference and empirical analysis

    NASA Astrophysics Data System (ADS)

    Li, Qian

    This dissertation consists of two parts. The first part focuses on extended Multiplicative Error Models (MEM) that include two extreme cases for nonnegative series. These extreme cases are common phenomena in high-frequency financial time series. The Location MEM(p,q) model incorporates a location parameter so that the series are required to have positive lower bounds. The estimator for the location parameter turns out to be the minimum of all the observations and is shown to be consistent. The second case captures the nontrivial fraction of zero outcomes feature in a series and combines a so-called Zero-Augmented general F distribution with linear MEM(p,q). Under certain strict stationary and moment conditions, we establish a consistency and asymptotic normality of the semiparametric estimation for these two new models. The second part of this dissertation examines the differences and similarities between trades in the home market and trades in the foreign market of cross-listed stocks. We exploit the multiplicative framework to model trading duration, volume per trade and price volatility for Canadian shares that are cross-listed in the New York Stock Exchange (NYSE) and the Toronto Stock Exchange (TSX). We explore the clustering effect, interaction between trading variables, and the time needed for price equilibrium after a perturbation for each market. The clustering effect is studied through the use of univariate MEM(1,1) on each variable, while the interactions among duration, volume and price volatility are captured by a multivariate system of MEM(p,q). After estimating these models by a standard QMLE procedure, we exploit the Impulse Response function to compute the calendar time for a perturbation in these variables to be absorbed into price variance, and use common statistical tests to identify the difference between the two markets in each aspect. These differences are of considerable interest to traders, stock exchanges and policy makers.

  11. Relativistic model of anisotropic charged fluid sphere in general relativity

    NASA Astrophysics Data System (ADS)

    Pant, Neeraj; Pradhan, N.; Bansal, Rajeev K.

    2016-01-01

    In this present paper, we present a class of static, spherically symmetric charged anisotropic fluid models of super dense stars in isotropic coordinates by considering a particular type of metric potential, a specific choice of electric field intensity E and pressure anisotropy factor Δ which involve parameters K (charge) and α (anisotropy) respectively. The solutions so obtained are utilized to construct the models for super-dense stars like neutron stars and strange quark stars. Our solutions are well behaved within the following ranges of different constant parameters. In the absence of pressure anisotropy and charge present model reduces to the isotropic model Pant et al. (Astrophys. Space Sci. 330:353-359, 2010). Our solution is well behaved in all respects for all values of X lying in the range 0< X ≤ 0.18, α lying in the range 0 ≤ α ≤6.6, K lying in the range 0< K ≤ 6.6 and Schwarzschild compactness parameter "u" lying in the range 0< u ≤ 0.38. Since our solution is well behaved for a wide ranges of the parameters, we can model many different types of ultra-cold compact stars like quark stars and neutron stars. We have shown that corresponding to X=0.088, α=0.6 and K=4.3 for which u=0.2054 and by assuming surface density ρb = 4.6888 × 10^{14} g/cm3 the mass and radius are found to be 1.51 M_{\\varTheta} and 10.90 km respectively. Assuming surface density ρb = 2 × 10^{14} g/cm3 the mass and radius for a neutron star candidate are found to be 2.313 M_{\\varTheta} and 16.690 km respectively. Hence we obtain masses and radii that fall in the range of what is generally expected for quark stars and neutron stars.

  12. Beta experiment

    NASA Technical Reports Server (NTRS)

    1982-01-01

    A focused laser doppler velocimeter (LDV) system was developed for the measurement of atmospheric backscatter (beta) from aerosols at infrared wavelengths. A Doppler signal generator was used in mapping the coherent sensitive focal volume of a focused LDV system. System calibration data was analyzed during the flight test activity scheduled for the Beta system. These analyses were performed to determine the acceptability of the Beta measurement system's performance.

  13. Correcting precipitation feature location in general circulation models

    NASA Astrophysics Data System (ADS)

    Levy, Adam A. L.; Jenkinson, Mark; Ingram, William; Allen, Myles

    2014-12-01

    There is much evidence that precipitation responses to global warming involve wet regions becoming wetter and dry regions drier. This presents challenges for the interpretation of projections from general circulation models (GCMs) which have substantial biases in the location of precipitation features. While improving GCM simulated precipitation is the most desirable solution, adaptation and mitigation decisions must be made with the models already available. Many techniques have been developed to correct biases in grid point precipitation intensities, but few have been introduced to correct for location biases. Here, we describe a new technique for correcting the spatial and seasonal location of climatological precipitation features. We design this technique to respect the geometry of the problem (spherical spatial dimensions, with cyclic seasons), while conserving either precipitation intensities, or integrated precipitation amount. We discuss the mathematical basis of the technique and investigate its behaviour in different regimes. We find that the resulting warps depend smoothly on the most influential parameter, which determines the balance between smoothness and closeness of fit. We show that the technique is capable of removing more than half the RMS error in a model's climatology, obtaining consistently better results when conserving integrated precipitation. To demonstrate the ability of the new technique to improve simulated precipitation changes, we apply our transformations to historical anomalies and show that RMS error is reduced relative to GPCP's anomalies by approximately 10% for both types of warp. This verifies that errors in precipitation changes can be reduced by correcting underlying location errors in a GCM's climatology.

  14. A Pacific Ocean general circulation model for satellite data assimilation

    NASA Technical Reports Server (NTRS)

    Chao, Y.; Halpern, D.; Mechoso, C. R.

    1991-01-01

    A tropical Pacific Ocean General Circulation Model (OGCM) to be used in satellite data assimilation studies is described. The transfer of the OGCM from a CYBER-205 at NOAA's Geophysical Fluid Dynamics Laboratory to a CRAY-2 at NASA's Ames Research Center is documented. Two 3-year model integrations from identical initial conditions but performed on those two computers are compared. The model simulations are very similar to each other, as expected, but the simulations performed with the higher-precision CRAY-2 is smoother than that with the lower-precision CYBER-205. The CYBER-205 and CRAY-2 use 32 and 64-bit mantissa arithmetic, respectively. The major features of the oceanic circulation in the tropical Pacific, namely the North Equatorial Current, the North Equatorial Countercurrent, the South Equatorial Current, and the Equatorial Undercurrent, are realistically produced and their seasonal cycles are described. The OGCM provides a powerful tool for study of tropical oceans and for the assimilation of satellite altimetry data.

  15. A bulk cloud parameterization in a Venus General Circulation Model

    NASA Astrophysics Data System (ADS)

    Lee, Christopher; Lewis, Stephen R.; Read, Peter L.

    2010-04-01

    A condensing cloud parameterization is included in a super-rotating Venus General Circulation Model. A parameterization including condensation, evaporation and sedimentation of mono-modal sulfuric acid cloud particles is described. Saturation vapor pressure of sulfuric acid vapor is used to determine cloud formation through instantaneous condensation and destruction through evaporation, while pressure dependent viscosity of a carbon dioxide atmosphere is used to determine sedimentation rates assuming particles fall at their terminal Stokes velocity. Modifications are described to account for the large range of the Reynolds number seen in the Venus atmosphere. Two GCM experiments initialized with 10 ppm-equivalent of sulfuric acid are integrated for 30 Earth years and the results are discussed with reference to "Y" shaped cloud structures observed on Venus. The GCM is able to produce an analog of the "Y" shaped cloud structure through dynamical processes alone, with contributions from the mean westward wind, the equatorial Kelvin wave, and the mid-latitude/polar Mixed Rossby/Gravity waves. The cloud top height in the GCM decreases from equator to pole and latitudinal gradients of cloud top height are comparable to those observed by Pioneer Venus and Venus Express, and those produced in more complex microphysical models of the sulfur cycle on Venus. Differences between the modeled cloud structures and observations are described and dynamical explanations are suggested for the most prominent differences.

  16. Generalized Symbolic Execution for Model Checking and Testing

    NASA Technical Reports Server (NTRS)

    Khurshid, Sarfraz; Pasareanu, Corina; Visser, Willem; Kofmeyer, David (Technical Monitor)

    2003-01-01

    Modern software systems, which often are concurrent and manipulate complex data structures must be extremely reliable. We present a novel framework based on symbolic execution, for automated checking of such systems. We provide a two-fold generalization of traditional symbolic execution based approaches: one, we define a program instrumentation, which enables standard model checkers to perform symbolic execution; two, we give a novel symbolic execution algorithm that handles dynamically allocated structures (e.g., lists and trees), method preconditions (e.g., acyclicity of lists), data (e.g., integers and strings) and concurrency. The program instrumentation enables a model checker to automatically explore program heap configurations (using a systematic treatment of aliasing) and manipulate logical formulae on program data values (using a decision procedure). We illustrate two applications of our framework: checking correctness of multi-threaded programs that take inputs from unbounded domains with complex structure and generation of non-isomorphic test inputs that satisfy a testing criterion. Our implementation for Java uses the Java PathFinder model checker.

  17. Toward a general psychological model of tension and suspense

    PubMed Central

    Lehne, Moritz; Koelsch, Stefan

    2015-01-01

    Tension and suspense are powerful emotional experiences that occur in a wide variety of contexts (e.g., in music, film, literature, and everyday life). The omnipresence of tension and suspense suggests that they build on very basic cognitive and affective mechanisms. However, the psychological underpinnings of tension experiences remain largely unexplained, and tension and suspense are rarely discussed from a general, domain-independent perspective. In this paper, we argue that tension experiences in different contexts (e.g., musical tension or suspense in a movie) build on the same underlying psychological processes. We discuss key components of tension experiences and propose a domain-independent model of tension and suspense. According to this model, tension experiences originate from states of conflict, instability, dissonance, or uncertainty that trigger predictive processes directed at future events of emotional significance. We also discuss possible neural mechanisms underlying tension and suspense. The model provides a theoretical framework that can inform future empirical research on tension phenomena. PMID:25717309

  18. A model for straight and helical solar jets. II. Parametric study of the plasma beta

    NASA Astrophysics Data System (ADS)

    Pariat, E.; Dalmasse, K.; DeVore, C. R.; Antiochos, S. K.; Karpen, J. T.

    2016-11-01

    Context. Jets are dynamic, impulsive, well-collimated plasma events that develop at many different scales and in different layers of the solar atmosphere. Aims: Jets are believed to be induced by magnetic reconnection, a process central to many astrophysical phenomena. Within the solar atmosphere, jet-like events develop in many different environments, e.g., in the vicinity of active regions, as well as in coronal holes, and at various scales, from small photospheric spicules to large coronal jets. In all these events, signatures of helical structure and/or twisting/rotating motions are regularly observed. We aim to establish that a single model can generally reproduce the observed properties of these jet-like events. Methods: Using our state-of-the-art numerical solver ARMS, we present a parametric study of a numerical tridimensional magnetohydrodynamic (MHD) model of solar jet-like events. Within the MHD paradigm, we study the impact of varying the atmospheric plasma β on the generation and properties of solar-like jets. Results: The parametric study validates our model of jets for plasma β ranging from 10-3 to 1, typical of the different layers and magnetic environments of the solar atmosphere. Our model of jets can robustly explain the generation of helical solar jet-like events at various β ≤ 1. We introduces the new result that the plasma β modifies the morphology of the helical jet, explaining the different observed shapes of jets at different scales and in different layers of the solar atmosphere. Conclusions: Our results enable us to understand the energisation, triggering, and driving processes of jet-like events. Our model enables us to make predictions of the impulsiveness and energetics of jets as determined by the surrounding environment, as well as the morphological properties of the resulting jets.

  19. Convex foundations for generalized MaxEnt models

    NASA Astrophysics Data System (ADS)

    Frongillo, Rafael; Reid, Mark D.

    2014-12-01

    We present an approach to maximum entropy models that highlights the convex geometry and duality of generalized exponential families (GEFs) and their connection to Bregman divergences. Using our framework, we are able to resolve a puzzling aspect of the bijection of Banerjee and coauthors between classical exponential families and what they call regular Bregman divergences. Their regularity condition rules out all but Bregman divergences generated from log-convex generators. We recover their bijection and show that a much broader class of divergences correspond to GEFs via two key observations: 1) Like classical exponential families, GEFs have a "cumulant" C whose subdifferential contains the mean: Eo˜pθ[φ(o)]∈∂C(θ) ; 2) Generalized relative entropy is a C-Bregman divergence between parameters: DF(pθ,pθ')= D C(θ,θ') , where DF becomes the KL divergence for F = -H. We also show that every incomplete market with cost function C can be expressed as a complete market, where the prices are constrained to be a GEF with cumulant C. This provides an entirely new interpretation of prediction markets, relating their design back to the principle of maximum entropy.

  20. Developing general acoustic model for noise sources and parameters estimation

    NASA Astrophysics Data System (ADS)

    Madoliat, Reza; Nouri, Nowrouz Mohammad; Rahrovi, Ali

    2017-02-01

    Noise measured at various points around the environment can be evaluated by a series of acoustic sources. Acoustic sources with wide surface can be broken down in fluid environment using some smaller acoustic sources. The aim of this study is to make a model to indicate the type, number, direction, position and strength of these sources in a way that the main sound and the sound of equivalent sources match together in an acceptable way. When position and direction of the source is given, the strength of the source can be found using inverse method. On the other hand, considering the non-uniqueness of solution in inverse method, a different acoustic strength is obtained for the sources if different positions are selected. Selecting an arrangement of general source and using the optimization algorithm, the least possible mismatch between the main sound and the sound of equivalent sources can be achieved.

  1. Mathematical Modeling of Yarn Dynamics in a Generalized Twisting System

    PubMed Central

    Yin, R.; Tao, X. M.; Xu, B. G.

    2016-01-01

    Twisting is an important process to form a continuous yarn from short fibres and to determine the structure and properties of the resultant yarn. This paper proposes a new theoretical model of yarn dynamics in a generalized twisting system, which deals with two important phenomena simultaneously, that is, twist generation and twist propagation. Equations of yarn motion are established and the boundary value problems are numerically solved by Newton-Raphson method. The simulation results are validated by experiments and a good agreement has been demonstrated for the system with a moving rigid cylinder as the twisting element. For the first time, influences of several parameters on the twisting process have been revealed in terms of twist efficiency of the moving rigid cylinder, propagation coefficients of twist trapping and congestion. It was found that the wrap angle and yarn tension have large influence on the twisting process, and the yarn torsional rigidity varies with the twisting parameters. PMID:27079187

  2. Optimization in generalized linear models: A case study

    NASA Astrophysics Data System (ADS)

    Silva, Eliana Costa e.; Correia, Aldina; Lopes, Isabel Cristina

    2016-06-01

    The maximum likelihood method is usually chosen to estimate the regression parameters of Generalized Linear Models (GLM) and also for hypothesis testing and goodness of fit tests. The classical method for estimating GLM parameters is the Fisher scores. In this work we propose to compute the estimates of the parameters with two alternative methods: a derivative-based optimization method, namely the BFGS method which is one of the most popular of the quasi-Newton algorithms, and the PSwarm derivative-free optimization method that combines features of a pattern search optimization method with a global Particle Swarm scheme. As a case study we use a dataset of biological parameters (phytoplankton) and chemical and environmental parameters of the water column of a Portuguese reservoir. The results show that, for this dataset, BFGS and PSwarm methods provided a better fit, than Fisher scores method, and can be good alternatives for finding the estimates for the parameters of a GLM.

  3. Development of a hybrid cloud parameterization for general circulation models

    SciTech Connect

    Kao, C.Y.J.; Kristjansson, J.E.; Langley, D.L.

    1995-04-01

    We have developed a cloud package with state-of-the-art physical schemes that can parameterize low-level stratus or stratocumulus, penetrative cumulus, and high-level cirrus. Such parameterizations will improve cloud simulations in general circulation models (GCMs). The principal tool in this development comprises the physically based Arakawa-Schubert scheme for convective clouds and the Sundqvist scheme for layered, nonconvective clouds. The term {open_quotes}hybrid{close_quotes} addresses the fact that the generation of high-attitude layered clouds can be associated with preexisting convective clouds. Overall, the cloud parameterization package developed should better determine cloud heating and drying effects in the thermodynamic budget, realistic precipitation patterns, cloud coverage and liquid/ice water content for radiation purposes, and the cloud-induced transport and turbulent diffusion for atmospheric trace gases.

  4. Estimation of propensity scores using generalized additive models.

    PubMed

    Woo, Mi-Ja; Reiter, Jerome P; Karr, Alan F

    2008-08-30

    Propensity score matching is often used in observational studies to create treatment and control groups with similar distributions of observed covariates. Typically, propensity scores are estimated using logistic regressions that assume linearity between the logistic link and the predictors. We evaluate the use of generalized additive models (GAMs) for estimating propensity scores. We compare logistic regressions and GAMs in terms of balancing covariates using simulation studies with artificial and genuine data. We find that, when the distributions of covariates in the treatment and control groups overlap sufficiently, using GAMs can improve overall covariate balance, especially for higher-order moments of distributions. When the distributions in the two groups overlap insufficiently, GAM more clearly reveals this fact than logistic regression does. We also demonstrate via simulation that matching with GAMs can result in larger reductions in bias when estimating treatment effects than matching with logistic regression.

  5. The Internal/External Frame of Reference Model Revisited: Incorporating General Cognitive Ability and General Academic Self-Concept.

    PubMed

    Brunner, Martin; Lüdtke, Oliver; Trautwein, Ulrich

    2008-01-01

    The internal/external frame of reference model (I/E model; Marsh, 1986 ) is a highly influential model of self-concept formation, which predicts that domain-specific abilities have positive effects on academic self-concepts in the corresponding domain and negative effects across domains. Investigations of the I/E model do not typically incorporate general cognitive ability or general academic self-concept. This article investigates alternative measurement models for domain-specific and domain-general cognitive abilities and academic self-concepts within an extended I/E model framework using representative data from 25,301 9th-grade students. Empirical support was found for the external validity of a new measurement model for academic self-concepts with respect to key student characteristics (gender, school satisfaction, educational aspirations, domain-specific interests, grades). Moreover, the basic predictions of the I/E model were confirmed, and the new extension of the traditional I/E model permitted meaningful relations to be drawn between domain-general cognitive ability and domain-general academic self-concept as well as between the domain-specific elements of the model.

  6. Sensitivity simulations of superparameterised convection in a general circulation model

    NASA Astrophysics Data System (ADS)

    Rybka, Harald; Tost, Holger

    2015-04-01

    Cloud Resolving Models (CRMs) covering a horizontal grid spacing from a few hundred meters up to a few kilometers have been used to explicitly resolve small-scale and mesoscale processes. Special attention has been paid to realistically represent cloud dynamics and cloud microphysics involving cloud droplets, ice crystals, graupel and aerosols. The entire variety of physical processes on the small-scale interacts with the larger-scale circulation and has to be parameterised on the coarse grid of a general circulation model (GCM). Since more than a decade an approach to connect these two types of models which act on different scales has been developed to resolve cloud processes and their interactions with the large-scale flow. The concept is to use an ensemble of CRM grid cells in a 2D or 3D configuration in each grid cell of the GCM to explicitly represent small-scale processes avoiding the use of convection and large-scale cloud parameterisations which are a major source for uncertainties regarding clouds. The idea is commonly known as superparameterisation or cloud-resolving convection parameterisation. This study presents different simulations of an adapted Earth System Model (ESM) connected to a CRM which acts as a superparameterisation. Simulations have been performed with the ECHAM/MESSy atmospheric chemistry (EMAC) model comparing conventional GCM runs (including convection and large-scale cloud parameterisations) with the improved superparameterised EMAC (SP-EMAC) modeling one year with prescribed sea surface temperatures and sea ice content. The sensitivity of atmospheric temperature, precipiation patterns, cloud amount and types is observed changing the embedded CRM represenation (orientation, width, no. of CRM cells, 2D vs. 3D). Additionally, we also evaluate the radiation balance with the new model configuration, and systematically analyse the impact of tunable parameters on the radiation budget and hydrological cycle. Furthermore, the subgrid

  7. Analysis of the noise-induced bursting-spiking transition in a pancreatic beta-cell model.

    PubMed

    Aguirre, Jacobo; Mosekilde, Erik; Sanjuán, Miguel A F

    2004-04-01

    A stochastic model of the electrophysiological behavior of the pancreatic beta cell is studied, as a paradigmatic example of a bursting biological cell embedded in a noisy environment. The analysis is focused on the distortion that a growing noise causes to the basic properties of the membrane potential signals, such as their periodic or chaotic nature, and their bursting or spiking behavior. We present effective computational tools to obtain as much information as possible from these signals, and we suggest that the methods could be applied to real time series. Finally, a universal dependence of the main characteristics of the membrane potential on the size of the considered cell cluster is presented.

  8. Application of nuclear magnetic resonance spectroscopy, Fourier transform infrared spectroscopy, UV-Visible spectroscopy and kinetic modeling for elucidation of adsorption chemistry in uptake of tetracycline by zeolite beta.

    PubMed

    Kang, Jin; Liu, Huijuan; Zheng, Yu-Ming; Qu, Jiuhui; Chen, J Paul

    2011-02-01

    Extensive usage of tetracycline has resulted in its contamination in surface water and groundwater. The adsorption of tetracycline on zeolite beta was systematically investigated for the decontamination of the antibiotic polluted water in this study. Ninety percent of uptake by the zeolite beta occured in 0.25h, and the adsorption equilibrium was obtained within 3h, which was well described by an intraparticle diffusion model. The adsorption generally increased when pH was increased from 4.0 to 5.0, and then decreased significantly as the pH was further increased, which was caused by the pH-dependent speciation of tetracycline and surface charge of zeolite beta. Both Freundlich and Langmuir equations well described the adsorption isotherm. A thermodynamic analysis showed that the sorption process was spontaneous and endothermic. Aluminum atoms in the zeolite played a crucial role in the uptake; the adsorption increased with the increasing aluminum content in zeolite. The UV-Visible spectroscopy study showed that the spectra of tetracycline changed upon the interaction with zeolite beta, which could be ascribed to the formation of complexes of tetracycline and aluminum atoms in the zeolite surface. Nuclear magnetic resonance spectroscopy study further confirmed the participation of Al in the tetracycline adsorption. Fourier transform infrared spectroscopy studies showed that the amino functional groups in tetracycline were involved in the complexation with the zeolite surface.

  9. Hospitable archean climates simulated by a general circulation model.

    PubMed

    Wolf, E T; Toon, O B

    2013-07-01

    Evidence from ancient sediments indicates that liquid water and primitive life were present during the Archean despite the faint young Sun. To date, studies of Archean climate typically utilize simplified one-dimensional models that ignore clouds and ice. Here, we use an atmospheric general circulation model coupled to a mixed-layer ocean model to simulate the climate circa 2.8 billion years ago when the Sun was 20% dimmer than it is today. Surface properties are assumed to be equal to those of the present day, while ocean heat transport varies as a function of sea ice extent. Present climate is duplicated with 0.06 bar of CO2 or alternatively with 0.02 bar of CO2 and 0.001 bar of CH4. Hot Archean climates, as implied by some isotopic reconstructions of ancient marine cherts, are unattainable even in our warmest simulation having 0.2 bar of CO2 and 0.001 bar of CH4. However, cooler climates with significant polar ice, but still dominated by open ocean, can be maintained with modest greenhouse gas amounts, posing no contradiction with CO2 constraints deduced from paleosols or with practical limitations on CH4 due to the formation of optically thick organic hazes. Our results indicate that a weak version of the faint young Sun paradox, requiring only that some portion of the planet's surface maintain liquid water, may be resolved with moderate greenhouse gas inventories. Thus, hospitable late Archean climates are easily obtained in our climate model.

  10. Beneficial effect of 17{beta}-estradiol on hyperglycemia and islet {beta}-cell functions in a streptozotocin-induced diabetic rat model

    SciTech Connect

    Yamabe, Noriko; Kang, Ki Sung; Zhu Baoting

    2010-11-15

    The modulating effect of estrogen on glucose homeostasis remains a controversial issue at present. In this study, we sought to determine the beneficial effect of 17{beta}-estradiol (E{sub 2}) on hyperglycemia and islet {beta}-cell functions in streptozotocin (STZ)-induced diabetic rats. Male Sprague-Dawley rats were injected i.p. with STZ to induce a relatively mild diabetic condition. The rats were then treated with E{sub 2} orally at 500 {mu}g/kg body weight/day for 15 days to evaluate the modulating effect on hyperglycemia, insulin secretion, and islet {beta}-cell proliferation. E{sub 2} administration for 10 days significantly lowered plasma glucose levels, increased plasma insulin levels, and improved glucose tolerance by attenuating insulin response to oral glucose loading. These beneficial effects of E{sub 2} were accompanied by increases in islet number and volume, rate of islet cell proliferation, and the amount of insulin secreted. The growth-stimulatory effect of E{sub 2} on islet cells was linked to the functions of the estrogen receptor {alpha}. Notably, these protective effects of E{sub 2} on diabetic conditions were basically not observed when the STZ-treated rats had a more severe degree of islet damage and hyperglycemia. Taken together, we conclude that E{sub 2} can promote the regeneration of damaged pancreatic islets by stimulating {beta}-cell proliferation in diabetic rats, and this effect is accompanied by improvements in glucose tolerance and a decrease in plasma glucose levels. These findings suggest that oral administration of E{sub 2} may be beneficial in diabetic patients with an accelerated loss of islet {beta}-cells.

  11. Screening of nineteen unrelated families with generalized resistance to thyroid hormone for known point mutations in the thyroid hormone receptor beta gene and the detection of a new mutation.

    PubMed Central

    Takeda, K; Balzano, S; Sakurai, A; DeGroot, L J; Refetoff, S

    1991-01-01

    Generalized resistance to thyroid hormone (GRTH) is a syndrome characterized by impaired tissue responsiveness to thyroid hormone. Two distinct point mutations in the hormone binding domain of the thyroid hormone receptor (TR) beta have recently been identified in two unrelated families with GRTH. One, Mf, involves a replacement of the normal glycine-345 for arginine in exon 7 and another, Mh, replaces the normal proline-453 for histidine in exon 8. To probe for the presence of the Mf and Mh defect in 19 unrelated families with GRTH, we applied separate polymerase chain reactions using allele-specific oligonucleotide primers containing the normal and each of the two mutant nucleotides at the 3'-position. A total of 24 affected subjects and 13 normal family members were studied. The mode of inheritance was dominant in 13 families, was unknown in 5 families, and was clearly recessive in 1 family in which only the consanguineous subjects were affected. Primers containing the substitutions specific for Mf and Mh amplified exons 7 and 8, respectively, only in affected members of each of the two index families. Primers containing the normal sequences amplified exons 7 and 8 of the TR beta gene in all subjects except affected members of one family. In this family with recessively inherited GRTH, neither exon could be amplified using any combinations of primers and DNA blot revealed absence of all coding exons. These results indicate a major deletion of the TR beta gene, including both DNA and hormone binding domains. Since heterozygous members of this family are not affected, the presence of a single normal allele is sufficient for normal function of the TR beta. These data also support the hypothesis that in the dominant mode of GRTH inheritance the presence of an abnormal TR beta interferes with the function of the normal TR beta. Distinct mutations are probably responsible for GRTH in unrelated families. Images PMID:1991834

  12. Digital terrain model generalization incorporating scale, semantic and cognitive constraints

    NASA Astrophysics Data System (ADS)

    Partsinevelos, Panagiotis; Papadogiorgaki, Maria

    2014-05-01

    Cartographic generalization is a well-known process accommodating spatial data compression, visualization and comprehension under various scales. In the last few years, there are several international attempts to construct tangible GIS systems, forming real 3D surfaces using a vast number of mechanical parts along a matrix formation (i.e., bars, pistons, vacuums). Usually, moving bars upon a structured grid push a stretching membrane resulting in a smooth visualization for a given surface. Most of these attempts suffer either in their cost, accuracy, resolution and/or speed. Under this perspective, the present study proposes a surface generalization process that incorporates intrinsic constrains of tangible GIS systems including robotic-motor movement and surface stretching limitations. The main objective is to provide optimized visualizations of 3D digital terrain models with minimum loss of information. That is, to minimize the number of pixels in a raster dataset used to define a DTM, while reserving the surface information. This neighborhood type of pixel relations adheres to the basics of Self Organizing Map (SOM) artificial neural networks, which are often used for information abstraction since they are indicative of intrinsic statistical features contained in the input patterns and provide concise and characteristic representations. Nevertheless, SOM remains more like a black box procedure not capable to cope with possible particularities and semantics of the application at hand. E.g. for coastal monitoring applications, the near - coast areas, surrounding mountains and lakes are more important than other features and generalization should be "biased"-stratified to fulfill this requirement. Moreover, according to the application objectives, we extend the SOM algorithm to incorporate special types of information generalization by differentiating the underlying strategy based on topologic information of the objects included in the application. The final

  13. Extrapolation of the DIII-D high poloidal beta scenario to ITER steady-state using transport modeling

    NASA Astrophysics Data System (ADS)

    McClenaghan, J.; Garofalo, A. M.; Meneghini, O.; Smith, S. P.

    2016-10-01

    Transport modeling of a proposed ITER steady-state scenario based on DIII-D high βP discharges finds that the core confinement may be improved with either sufficient rotation or a negative central shear q-profile. The high poloidal beta scenario is characterized by a large bootstrap current fraction( 80%) which reduces the demands on the external current drive, and a large radius internal transport barrier which is associated with improved normalized confinement. Typical temperature and density profiles from the non-inductive high poloidal beta scenario on DIII-D are scaled according to 0D modeling predictions of the requirements for achieving Q=5 steady state performance in ITER with ``day one'' H&CD capabilities. Then, TGLF turbulence modeling is carried out under systematic variations of the toroidal rotation and the core q-profile. Either strong negative central magnetic shear or rotation are found to successfully provide the turbulence suppression required to maintain the temperature and density profiles. This work supported by the US Department of Energy under DE-FC02-04ER54698.

  14. Centering, Scale Indeterminacy, and Differential Item Functioning Detection in Hierarchical Generalized Linear and Generalized Linear Mixed Models

    ERIC Educational Resources Information Center

    Cheong, Yuk Fai; Kamata, Akihito

    2013-01-01

    In this article, we discuss and illustrate two centering and anchoring options available in differential item functioning (DIF) detection studies based on the hierarchical generalized linear and generalized linear mixed modeling frameworks. We compared and contrasted the assumptions of the two options, and examined the properties of their DIF…

  15. A general method for modeling population dynamics and its applications.

    PubMed

    Shestopaloff, Yuri K

    2013-12-01

    Studying populations, be it a microbe colony or mankind, is important for understanding how complex systems evolve and exist. Such knowledge also often provides insights into evolution, history and different aspects of human life. By and large, populations' prosperity and decline is about transformation of certain resources into quantity and other characteristics of populations through growth, replication, expansion and acquisition of resources. We introduce a general model of population change, applicable to different types of populations, which interconnects numerous factors influencing population dynamics, such as nutrient influx and nutrient consumption, reproduction period, reproduction rate, etc. It is also possible to take into account specific growth features of individual organisms. We considered two recently discovered distinct growth scenarios: first, when organisms do not change their grown mass regardless of nutrients availability, and the second when organisms can reduce their grown mass by several times in a nutritionally poor environment. We found that nutrient supply and reproduction period are two major factors influencing the shape of population growth curves. There is also a difference in population dynamics between these two groups. Organisms belonging to the second group are significantly more adaptive to reduction of nutrients and far more resistant to extinction. Also, such organisms have substantially more frequent and lesser in amplitude fluctuations of population quantity for the same periodic nutrient supply (compared to the first group). Proposed model allows adequately describing virtually any possible growth scenario, including complex ones with periodic and irregular nutrient supply and other changing parameters, which present approaches cannot do.

  16. A general geomorphological recession flow model for river basins

    NASA Astrophysics Data System (ADS)

    Biswal, Basudev; Nagesh Kumar, D.

    2013-08-01

    Recession flows in a basin are controlled by the temporal evolution of its active drainage network (ADN). The geomorphological recession flow model (GRFM) assumes that both the rate of flow generation per unit ADN length (q) and the speed at which ADN heads move downstream (c) remain constant during a recession event. Thereby, it connects the power law exponent of -dQ/dt versus Q (discharge at the outlet at time t) curve, α, with the structure of the drainage network, a fixed entity. In this study, we first reformulate the GRFM for Horton-Strahler networks and show that the geomorphic α (αg) is equal to D/>(D-1>), where D is the fractal dimension of the drainage network. We then propose a more general recession flow model by expressing both q and c as functions of Horton-Strahler stream order. We show that it is possible to have α =α g for a recession event even when q and c do not remain constant. The modified GRFM suggests that α is controlled by the spatial distribution of subsurface storage within the basin. By analyzing streamflow data from 39 U.S. Geological Survey basins, we show that α is having a power law relationship with recession curve peak, which indicates that the spatial distribution of subsurface storage varies across recession events.

  17. Hydraulic Conductivity Estimation using Bayesian Model Averaging and Generalized Parameterization

    NASA Astrophysics Data System (ADS)

    Tsai, F. T.; Li, X.

    2006-12-01

    Non-uniqueness in parameterization scheme is an inherent problem in groundwater inverse modeling due to limited data. To cope with the non-uniqueness problem of parameterization, we introduce a Bayesian Model Averaging (BMA) method to integrate a set of selected parameterization methods. The estimation uncertainty in BMA includes the uncertainty in individual parameterization methods as the within-parameterization variance and the uncertainty from using different parameterization methods as the between-parameterization variance. Moreover, the generalized parameterization (GP) method is considered in the geostatistical framework in this study. The GP method aims at increasing the flexibility of parameterization through the combination of a zonation structure and an interpolation method. The use of BMP with GP avoids over-confidence in a single parameterization method. A normalized least-squares estimation (NLSE) is adopted to calculate the posterior probability for each GP. We employee the adjoint state method for the sensitivity analysis on the weighting coefficients in the GP method. The adjoint state method is also applied to the NLSE problem. The proposed methodology is implemented to the Alamitos Barrier Project (ABP) in California, where the spatially distributed hydraulic conductivity is estimated. The optimal weighting coefficients embedded in GP are identified through the maximum likelihood estimation (MLE) where the misfits between the observed and calculated groundwater heads are minimized. The conditional mean and conditional variance of the estimated hydraulic conductivity distribution using BMA are obtained to assess the estimation uncertainty.

  18. General Model for Light Curves of Chromospherically Active Binary Stars

    NASA Astrophysics Data System (ADS)

    Jetsu, L.; Henry, G. W.; Lehtinen, J.

    2017-04-01

    The starspots on the surface of many chromospherically active binary stars concentrate on long-lived active longitudes separated by 180°. Shifts in activity between these two longitudes, the “flip-flop” events, have been observed in single stars like FK Comae and binary stars like σ Geminorum. Recently, interferometry has revealed that ellipticity may at least partly explain the flip-flop events in σ Geminorum. This idea was supported by the double-peaked shape of the long-term mean light curve of this star. Here we show that the long-term mean light curves of 14 chromospherically active binaries follow a general model that explains the connection between orbital motion, changes in starspot distribution, ellipticity, and flip-flop events. Surface differential rotation is probably weak in these stars, because the interference of two constant period waves may explain the observed light curve changes. These two constant periods are the active longitude period ({P}{act}) and the orbital period ({P}{orb}). We also show how to apply the same model to single stars, where only the value of P act is known. Finally, we present a tentative interference hypothesis about the origin of magnetic fields in all spectral types of stars. The CPS results are available electronically at the Vizier database.

  19. Classification images in a very general decision model.

    PubMed

    Murray, Richard F

    2016-06-01

    Most of the theory supporting our understanding of classification images relies on standard signal detection models and the use of normally distributed stimulus noise. Here I show that the most common methods of calculating classification images by averaging stimulus noise samples within stimulus-response classes of trials are much more general than has previously been demonstrated, and that they give unbiased estimates of an observer's template for a wide range of decision rules and non-Gaussian stimulus noise distributions. These results are similar to findings on reverse correlation and related methods in the neurophysiology literature, but here I formulate them in terms that are tailored to signal detection analyses of visual tasks, in order to make them more accessible and useful to visual psychophysicists. I examine 2AFC and yes-no designs. These findings make it possible to use and interpret classification images in tasks where observers' decision strategies may not conform to classic signal detection models such as the difference rule, and in tasks where the stimulus noise is non-Gaussian.

  20. Host-parasitoid dynamics of a generalized Thompson model.

    PubMed

    Schreiber, Sebastian J

    2006-06-01

    A discrete-time host-parasitoid model including host-density dependence and a generalized Thompson escape function is analyzed. This model assumes that parasitoids are egg-limited but not search-limited, and is proven to exhibit five types of dynamics: host failure in which the host goes extinct in the parasitoid's presence or absence, unconditional parasitoid failure in which the parasitoid always goes extinct while the host persists, conditional parasitoid failure in the host and the parasitoid go extinct or coexist depending on the initial host-parasitoid ratio, parasitoid driven extinction in which the parasitoid invariably drives the host to extinction, and coexistence in which the host and parasitoid coexist about a global attractor. The latter two dynamics only occur when the parasitoid's maximal rate of growth exceeds the host's maximal rate of growth. Moreover, coexistence requires parasitism events to be sufficiently aggregated. Small additive noise is proven to alter the dynamical outcomes in two ways. The addition of noise to parasitoid driven extinction results in random outbreaks of the host and parasitoid with varying intensity. Additive noise converts conditional parasitoid failure to unconditional parasitoid failure. Implications for classical biological control are discussed.

  1. A generalized model of atomic processes in dense plasmas

    NASA Astrophysics Data System (ADS)

    Chung, Hyun-Kyung; Chen, M.; Ciricosta, O.; Vinko, S.; Wark, J.; Lee, R. W.

    2015-11-01

    A generalized model of atomic processes in plasmas, FLYCHK, has been developed over a decade to provide experimentalists fast and simple but reasonable predictions of atomic properties of plasmas. For a given plasma condition, it provides charge state distributions and spectroscopic properties, which have been extensively used for experimental design and data analysis and currently available through NIST web site. In recent years, highly transient and non-equilibrium plasmas have been created with X-ray free electron lasers (XFEL). As high intensity x-rays interact with matter, the inner-shell electrons are ionized and Auger electrons and photo electrons are generated. With time, electrons participate in the ionization processes and collisional ionization by these electrons dominates photoionization as electron density increases. To study highly complex XFEL produced plasmas, SCFLY, an extended version of FLYCHK code has been used. The code accepts the time-dependent history of x-ray energy and intensity to compute population distribution and ionization distribution self-consistently with electron temperature and density assuming an instantaneous equilibration. The model and its applications to XFEL experiments will be presented as well as its limitations.

  2. Generalized Pure Density Matrices and the Standard Model

    NASA Astrophysics Data System (ADS)

    Brannen, Carl

    2015-04-01

    We consider generalizations of pure density matrices that have ρρ = ρ , but give up the trace=1 requirement. Given a representation of a quantum algebra in N × N complex matrices, the elements that satisfy ρρ = ρ can be taken to be pure density matrix states. In the Standard Model, particles from different ``superselection sectors'' cannot form linear superpositions. For example, it is impossible to form a linear superposition between an electron and a neutrino. We report that some quantum algebras give symmetry, particle and generation content, gauge freedom, and superselection sectors that are similar to those of the Standard Model. Our lecture will consider as an example the 4 × 4 complex matrices. There are 16 that are diagonal with ρρ = ρ . The 4 with trace=1 give the usual pure density matrices. We will show that the 6 with trace=2 form an SU(3) triplet of three superselection sectors, with each sector consisting of an SU(2) doublet. Considering one of these sectors, the mapping to SU(2) is not unique; there is an SU(2) gauge freedom. This gauge freedom is an analogy to the U(1) gauge freedom that arises when converting a pure density matrix to a state vector.

  3. Critical rotation of general-relativistic polytropic models revisited

    NASA Astrophysics Data System (ADS)

    Geroyannis, V.; Karageorgopoulos, V.

    2013-09-01

    We develop a perturbation method for computing the critical rotational parameter as a function of the equatorial radius of a rigidly rotating polytropic model in the "post-Newtonia approximation" (PNA). We treat our models as "initial value problems" (IVP) of ordinary differential equations in the complex plane. The computations are carried out by the code dcrkf54.f95 (Geroyannis and Valvi 2012 [P1]; modified Runge-Kutta-Fehlberg code of fourth and fifth order for solving initial value problems in the complex plane). Such a complex-plane treatment removes the syndromes appearing in this particular family of IVPs (see e.g. P1, Sec. 3) and allows continuation of the numerical integrations beyond the surface of the star. Thus all the required values of the Lane-Emden function(s) in the post-Newtonian approximation are calculated by interpolation (so avoiding any extrapolation). An interesting point is that, in our computations, we take into account the complete correction due to the gravitational term, and this issue is a remarkable difference compared to the classical PNA. We solve the generalized density as a function of the equatorial radius and find the critical rotational parameter. Our computations are extended to certain other physical characteristics (like mass, angular momentum, rotational kinetic energy, etc). We find that our method yields results comparable with those of other reliable methods. REFERENCE: V.S. Geroyannis and F.N. Valvi 2012, International Journal of Modern Physics C, 23, No 5, 1250038:1-15.

  4. Modeling Differential Item Functioning Using a Generalization of the Multiple-Group Bifactor Model

    ERIC Educational Resources Information Center

    Jeon, Minjeong; Rijmen, Frank; Rabe-Hesketh, Sophia

    2013-01-01

    The authors present a generalization of the multiple-group bifactor model that extends the classical bifactor model for categorical outcomes by relaxing the typical assumption of independence of the specific dimensions. In addition to the means and variances of all dimensions, the correlations among the specific dimensions are allowed to differ…

  5. Modelling of filariasis in East Java with Poisson regression and generalized Poisson regression models

    NASA Astrophysics Data System (ADS)

    Darnah

    2016-04-01

    Poisson regression has been used if the response variable is count data that based on the Poisson distribution. The Poisson distribution assumed equal dispersion. In fact, a situation where count data are over dispersion or under dispersion so that Poisson regression inappropriate because it may underestimate the standard errors and overstate the significance of the regression parameters, and consequently, giving misleading inference about the regression parameters. This paper suggests the generalized Poisson regression model to handling over dispersion and under dispersion on the Poisson regression model. The Poisson regression model and generalized Poisson regression model will be applied the number of filariasis cases in East Java. Based regression Poisson model the factors influence of filariasis are the percentage of families who don't behave clean and healthy living and the percentage of families who don't have a healthy house. The Poisson regression model occurs over dispersion so that we using generalized Poisson regression. The best generalized Poisson regression model showing the factor influence of filariasis is percentage of families who don't have healthy house. Interpretation of result the model is each additional 1 percentage of families who don't have healthy house will add 1 people filariasis patient.

  6. Efficient decoding algorithms for generalized hidden Markov model gene finders

    PubMed Central

    Majoros, William H; Pertea, Mihaela; Delcher, Arthur L; Salzberg, Steven L

    2005-01-01

    Background The Generalized Hidden Markov Model (GHMM) has proven a useful framework for the task of computational gene prediction in eukaryotic genomes, due to its flexibility and probabilistic underpinnings. As the focus of the gene finding community shifts toward the use of homology information to improve prediction accuracy, extensions to the basic GHMM model are being explored as possible ways to integrate this homology information into the prediction process. Particularly prominent among these extensions are those techniques which call for the simultaneous prediction of genes in two or more genomes at once, thereby increasing significantly the computational cost of prediction and highlighting the importance of speed and memory efficiency in the implementation of the underlying GHMM algorithms. Unfortunately, the task of implementing an efficient GHMM-based gene finder is already a nontrivial one, and it can be expected that this task will only grow more onerous as our models increase in complexity. Results As a first step toward addressing the implementation challenges of these next-generation systems, we describe in detail two software architectures for GHMM-based gene finders, one comprising the common array-based approach, and the other a highly optimized algorithm which requires significantly less memory while achieving virtually identical speed. We then show how both of these architectures can be accelerated by a factor of two by optimizing their content sensors. We finish with a brief illustration of the impact these optimizations have had on the feasibility of our new homology-based gene finder, TWAIN. Conclusions In describing a number of optimizations for GHMM-based gene finders and making available two complete open-source software systems embodying these methods, it is our hope that others will be more enabled to explore promising extensions to the GHMM framework, thereby improving the state-of-the-art in gene prediction techniques. PMID:15667658

  7. Design and implementation of a generalized laboratory data model

    PubMed Central

    Wendl, Michael C; Smith, Scott; Pohl, Craig S; Dooling, David J; Chinwalla, Asif T; Crouse, Kevin; Hepler, Todd; Leong, Shin; Carmichael, Lynn; Nhan, Mike; Oberkfell, Benjamin J; Mardis, Elaine R; Hillier, LaDeana W; Wilson, Richard K

    2007-01-01

    Background Investigators in the biological sciences continue to exploit laboratory automation methods and have dramatically increased the rates at which they can generate data. In many environments, the methods themselves also evolve in a rapid and fluid manner. These observations point to the importance of robust information management systems in the modern laboratory. Designing and implementing such systems is non-trivial and it appears that in many cases a database project ultimately proves unserviceable. Results We describe a general modeling framework for laboratory data and its implementation as an information management system. The model utilizes several abstraction techniques, focusing especially on the concepts of inheritance and meta-data. Traditional approaches commingle event-oriented data with regular entity data in ad hoc ways. Instead, we define distinct regular entity and event schemas, but fully integrate these via a standardized interface. The design allows straightforward definition of a "processing pipeline" as a sequence of events, obviating the need for separate workflow management systems. A layer above the event-oriented schema integrates events into a workflow by defining "processing directives", which act as automated project managers of items in the system. Directives can be added or modified in an almost trivial fashion, i.e., without the need for schema modification or re-certification of applications. Association between regular entities and events is managed via simple "many-to-many" relationships. We describe the programming interface, as well as techniques for handling input/output, process control, and state transitions. Conclusion The implementation described here has served as the Washington University Genome Sequencing Center's primary information system for several years. It handles all transactions underlying a throughput rate of about 9 million sequencing reactions of various kinds per month and has handily weathered a number

  8. A General Model for the Homogeneous Case of the Continuous Response.

    ERIC Educational Resources Information Center

    Samejima, Fumiko

    A general model for the homogeneous case of the continuous response is proposed. The model is an expansion and generalization of the one proposed by the author in 1974, in which the open response situation is dealt with. In this generalized model, the closed response situation is dealt with, and it includes the model for the open response…

  9. Beta-glucosidase I variants with improved properties

    SciTech Connect

    Bott, Richard R.; Kaper, Thijs; Kelemen, Bradley; Goedegebuur, Frits; Hommes, Ronaldus Wilhelmus; Kralj, Slavko; Kruithof, Paulien; Nikolaev, Igor; Van Der Kley, Wilhelmus Antonious Hendricus; Van Lieshout, Johannes Franciscus Thomas; Van Stigt Thans, Sander

    2016-09-20

    The present disclosure is generally directed to enzymes and in particular beta-glucosidase variants. Also described are nucleic acids encoding beta-glucosidase variants, compositions comprising beta-glucosidase variants, methods of using beta-glucosidase variants, and methods of identifying additional useful beta-glucosidase variants.

  10. Recovery of the endogenous beta cell function in the NOD model of autoimmune diabetes.

    PubMed

    Zorina, Tatiana D; Subbotin, Vladimir M; Bertera, Suzanne; Alexander, Angela M; Haluszczak, Catherine; Gambrell, Beverley; Bottino, Rita; Styche, Alexis J; Trucco, Massimo

    2003-01-01

    In light of accumulating evidence that the endocrine pancreas has regenerative properties and that hematopoietic chimerism can abrogate destruction of beta cells in autoimmune diabetes, we addressed the question of whether recovery of physiologically adequate endogenous insulin regulation could be achieved in the nonobese diabetic (NOD) mice rendered allogeneic chimerae. Allogeneic bone marrow (BM) was transplanted into NOD mice at the preclinical and overtly clinical stages of the disease using lethal and nonlethal doses of radiation for recipient conditioning. Islets of Langerhans, syngeneic to the BM donors, were transplanted under kidney capsules of the overtly diabetic animals to sustain euglycemia for the time span required for recovery of the endogenous pancreas. Nephrectomies of the graft-bearing organs were performed 14 weeks later to confirm the restoration of endogenous insulin regulation. Reparative processes in the pancreata were assessed histologically and immunohistochemically. The level of chimerism in NOD recipients was evaluated by flow cytometric analysis. We have shown that as low as 1% of initial allogeneic chimerism can reverse the diabetogenic processes in islets of Langerhans in prediabetic NOD mice, and that restoration of endogenous beta cell function to physiologically sufficient levels is achievable even if the allogeneic BM transplantation is performed after the clinical onset of diabetes. If the same pattern of islet regeneration were shown in humans, induction of an autoimmunity-free status by establishment of a low level of chimerism, or other alternative means, might become a new therapy for type 1 diabetes.

  11. Preparation, characterization and molecular modeling studies of the inclusion complex of Caffeine with Beta-cyclodextrin

    NASA Astrophysics Data System (ADS)

    Prabu, Samikannu; Swaminathan, Meenakshisundaram; Sivakumar, Krishnamoorthy; Rajamohan, Rajaram

    2015-11-01

    The formation through supramolecular interaction of a host-guest inclusion complex of caffeine (CA) with nano-hydrophobic cavity beta-cyclodextrin (β-CD) is achieved by a physical mixture, a kneading method and a co-precipitation method. The formation of the inclusion complex of CA with β-CD in solution state is confirmed by UV-visible spectrophotometer, fluorescence spectrophotometer and time-resolved fluorescence spectrophotometer. The stoichiometry of the inclusion complex is 1:1; the imidazole ring and pyrimidine ring of caffeine is deeply entrapped in the beta-cyclodextrin as confirmed by spectral shifts. The Benesi-Hildebrand plot is used to calculate the binding constant of the inclusion complex of CA with β-CD at room temperature. The Gibbs free energy change of the inclusion complex process is calculated and the process is found to be spontaneous. The thermal stability of the inclusion complex of CA with β-CD is analyzed using differential scanning calorimetry. The crystal structure modification of a solid inclusion complex is confirmed by scanning electron microscopy image analysis. The formation of the inclusion complex of CA with β-CD in the solid phase is also confirmed by FT-IR and XRD. The formation of the inclusion complex between CA and β-CD, as confirmed by molecular docking studies, is in good relationship with the results obtained through different experimental methods.

  12. A model system to study the effects of beta-carotene on radon-stimulated oncogenesis

    SciTech Connect

    Seifter, E.; Mendecki, J.; Dawson, H.; Goodwin, P.; Friedenthal, E.

    1992-12-31

    Work from our laboratory has established that, in mice, the radioprotective action of supplemental beta-carotene provides protection against several insults: low-dose, gamma-irradiation-enhanced mammary tumor appearance and death in C3H mice carrying the mammary tumor virus but not in mouse strains not carrying the virus; low-dose, whole-body, gamma-irradiation-stimulated lung metastasis of Swiss and C57 mice bearing transplants of 10{sup 4} Lewis lung tumor cells injected into the hind limb, but not causing lung tumors in mice inoculated only with a buffer carrier or the same carrier containing 10{sup 2} tumor cells. Similarly, gamma-irradiation or the radiomimetic chemical cyclophosphamide decreased the amount of viral inoculum (Moloney sarcoma virus) required to cause sarcomas at the injection site, i.e., it decreased the TD{sub 50}. We now propose long-term (20- to 30-mo) studies on the effects of exposure to radon in these systems. The second aim of this study (and major thrust of this paper) is to determine how supplemental beta-carotene might modify the effect of exposure to radon in mice subjected to the insults described.

  13. Towards a General Model for Volcanic Caldera Dynamics

    NASA Astrophysics Data System (ADS)

    Macedonio, G.; Giudicepietro, F.; D'auria, L.; Martini, M.

    2014-12-01

    Volcanic calderas often show a behavior different from that of other volcanoes. In caldera complexes, it is not unusual to record long-term unrests, with remarkable ground deformation, seismicity, and geochemical changes, that do not culminate in an eruption. On the contrary, in certain cases, an unrest accompanied by minor geophysical changes can be followed in few months by an eruption, as in the case of Rabaul Caldera in 1994. Those behaviors are not simple to interpret. The dramatic advances in volcano monitoring over the last years has allowed us to record the dynamic phenomena of several calderas with great detail. This, highlighted characteristics that are typical of a single caldera, but also some features common to several calderas. The main common features are remarkable ground deformation with intense uplift episodes, that are often followed by subsidence. The ground deformations are generally characterized by strong horizontal components. The seismicity is almost always in swarms and has a spatial distribution that often shows seismic gaps. Moreover, calderas are the largest geothermal systems in the world. We think that a process of sill intrusion can explain the common features highlighted by many observations carried out on different calderas. We developed a dynamic model of sill intrusion in a shallow volcanic environment. In our model, the sill, fed by a deeper magma reservoir, intrudes below a horizontal elastic plate, representing the overlying rocks, and expands with axisymmetric geometry. The model is based on the numerical solution of the equation for the elastic plate, coupled with a Navier-Stokes equation for simulating the dynamics of the sill intrusion. We performed a number of simulations, with the objective of showing the main features of the model. In the experiments, when the feeding process stops, the vertical movement reverses its trend and the area of maximum uplift undergoes subsidence. Under certain conditions the subsidence can

  14. Early effects of aluminum chloride on beta-secretase mRNA expression in a neuronal model of beta-amyloid toxicity.

    PubMed

    Castorina, Alessandro; Tiralongo, Adriana; Giunta, Salvatore; Carnazza, Maria Luisa; Scapagnini, Giovanni; D'Agata, Velia

    2010-08-01

    Amyloid beta peptide (Abeta), generated by proteolytic cleavage of the amyloid precursor protein (APP), plays a pivotal role in the pathogenesis of Alzheimer's disease (AD). The key step in the generation of Abeta is cleavage of APP by beta-secretases (beta-site APP-cleaving enzyme 1 (BACE1) and BACE2). There has been suggestion of interaction between aluminum and several AD-associated pathways. However, the underlying mechanisms still remain unclear. Here, we report the effects of aluminum chloride (AlCl(3)) in Abeta-induced toxicity using differentiated neuronal SH-SY5Y cells. The metal significantly enhances Abeta-induced cell death at concentrations ranging from 50 to 300 microM after 24 and 48 h. After 72 and 96 h treatment, cell death is increased already at 10 microM. Early coexposure of cells to 10 microM AlCl(3) and 2 microM Abeta differentially affected beta-secretase mRNA levels as compared to single Abeta treatment after 1 and 3 h. BACE1 levels were slightly reduced after 1 h and significantly increased after 3 h exposure, whereas BACE2 levels were increased at both times considered. Both genes' mRNA levels were downregulated at longer times (6, 12, and 24 h). Although these results indicate that aluminum toxicity is correlated to changes in both BACE1 and BACE2 expression levels, the subsequent common downregulation observed suggests that aluminum involvement in the Abeta cascade is subtle, and other underlying mechanisms might be involved.

  15. Venusian Polar Vortex reproduced by a general circulation model

    NASA Astrophysics Data System (ADS)

    Ando, Hiroki; Sugimoto, Norihiko; Takagi, Masahiro

    2016-10-01

    Unlike the polar vortices observed in the Earth, Mars and Titan atmospheres, the observed Venus polar vortex is warmer than the mid-latitudes at cloud-top levels (~65 km). This warm polar vortex is zonally surrounded by a cold latitude band located at ~60 degree latitude, which is a unique feature called 'cold collar' in the Venus atmosphere [e.g. Taylor et al. 1980; Piccioni et al. 2007]. Although these structures have been observed in numerous previous observations, the formation mechanism is still unknown. In addition, an axi-asymmetric feature is always seen in the warm polar vortex. It changes temporally and sometimes shows a hot polar dipole or S-shaped structure as shown by a lot of infrared measurements [e.g. Garate-Lopez et al. 2013; 2015]. However, its vertical structure has not been investigated. To solve these problems, we performed a numerical simulation of the Venus atmospheric circulation using a general circulation model named AFES for Venus [Sugimoto et al. 2014] and reproduced these puzzling features.And then, the reproduced structures of the atmosphere and the axi-asymmetirc feature are compared with some previous observational results.In addition, the quasi-periodical zonal-mean zonal wind fluctuation is also seen in the Venus polar vortex reproduced in our model. This might be able to explain some observational results [e.g. Luz et al. 2007] and implies that the polar vacillation might also occur in the Venus atmosphere, which is silimar to the Earth's polar atmosphere. We will also show some initial results about this point in this presentation.

  16. A General Framework for Multiphysics Modeling Based on Numerical Averaging

    NASA Astrophysics Data System (ADS)

    Lunati, I.; Tomin, P.

    2014-12-01

    In the last years, multiphysics (hybrid) modeling has attracted increasing attention as a tool to bridge the gap between pore-scale processes and a continuum description at the meter-scale (laboratory scale). This approach is particularly appealing for complex nonlinear processes, such as multiphase flow, reactive transport, density-driven instabilities, and geomechanical coupling. We present a general framework that can be applied to all these classes of problems. The method is based on ideas from the Multiscale Finite-Volume method (MsFV), which has been originally developed for Darcy-scale application. Recently, we have reformulated MsFV starting with a local-global splitting, which allows us to retain the original degree of coupling for the local problems and to use spatiotemporal adaptive strategies. The new framework is based on the simple idea that different characteristic temporal scales are inherited from different spatial scales, and the global and the local problems are solved with different temporal resolutions. The global (coarse-scale) problem is constructed based on a numerical volume-averaging paradigm and a continuum (Darcy-scale) description is obtained by introducing additional simplifications (e.g., by assuming that pressure is the only independent variable at the coarse scale, we recover an extended Darcy's law). We demonstrate that it is possible to adaptively and dynamically couple the Darcy-scale and the pore-scale descriptions of multiphase flow in a single conceptual and computational framework. Pore-scale problems are solved only in the active front region where fluid distribution changes with time. In the rest of the domain, only a coarse description is employed. This framework can be applied to other important problems such as reactive transport and crack propagation. As it is based on a numerical upscaling paradigm, our method can be used to explore the limits of validity of macroscopic models and to illuminate the meaning of

  17. Generalized internal model robust control for active front steering intervention

    NASA Astrophysics Data System (ADS)

    Wu, Jian; Zhao, Youqun; Ji, Xuewu; Liu, Yahui; Zhang, Lipeng

    2015-03-01

    Because of the tire nonlinearity and vehicle's parameters' uncertainties, robust control methods based on the worst cases, such as H ∞, µ synthesis, have been widely used in active front steering control, however, in order to guarantee the stability of active front steering system (AFS) controller, the robust control is at the cost of performance so that the robust controller is a little conservative and has low performance for AFS control. In this paper, a generalized internal model robust control (GIMC) that can overcome the contradiction between performance and stability is used in the AFS control. In GIMC, the Youla parameterization is used in an improved way. And GIMC controller includes two sections: a high performance controller designed for the nominal vehicle model and a robust controller compensating the vehicle parameters' uncertainties and some external disturbances. Simulations of double lane change (DLC) maneuver and that of braking on split- µ road are conducted to compare the performance and stability of the GIMC control, the nominal performance PID controller and the H ∞ controller. Simulation results show that the high nominal performance PID controller will be unstable under some extreme situations because of large vehicle's parameters variations, H ∞ controller is conservative so that the performance is a little low, and only the GIMC controller overcomes the contradiction between performance and robustness, which can both ensure the stability of the AFS controller and guarantee the high performance of the AFS controller. Therefore, the GIMC method proposed for AFS can overcome some disadvantages of control methods used by current AFS system, that is, can solve the instability of PID or LQP control methods and the low performance of the standard H ∞ controller.

  18. A generalized Brownian motion model for turbulent relative particle dispersion

    NASA Astrophysics Data System (ADS)

    Shivamoggi, B. K.

    2016-08-01

    There is speculation that the difficulty in obtaining an extended range with Richardson-Obukhov scaling in both laboratory experiments and numerical simulations is due to the finiteness of the flow Reynolds number Re in these situations. In this paper, a generalized Brownian motion model has been applied to describe the relative particle dispersion problem in more realistic turbulent flows and to shed some light on this issue. The fluctuating pressure forces acting on a fluid particle are taken to be a colored noise and follow a stationary process and are described by the Uhlenbeck-Ornstein model while it appears plausible to take their correlation time to have a power-law dependence on Re, thus introducing a bridge between the Lagrangian quantities and the Eulerian parameters for this problem. This ansatz is in qualitative agreement with the possibility of a connection speculated earlier by Corrsin [26] between the white-noise representation for the fluctuating pressure forces and the large-Re assumption in the Kolmogorov [4] theory for the 3D fully developed turbulence (FDT) as well as a similar argument of Monin and Yaglom [23] and a similar result of Sawford [13] and Borgas and Sawford [24]. It also provides an insight into the result that the Richardson-Obukhov scaling holds only in the infinite-Re limit and disappears otherwise. This ansatz further provides a determination of the Richardson-Obukhov constant g as a function of Re, with an asymptotic constant value in the infinite-Re limit. It is shown to lead to full agreement, in the small-Re limit as well, with the Batchelor-Townsend [27] scaling for the rate of change of the mean square interparticle separation in 3D FDT, hence validating its soundness further.

  19. Generalized least-squares fit of multiequation models

    NASA Astrophysics Data System (ADS)

    Marshall, Simon L.; Blencoe, James G.

    2005-01-01

    A method for fitting multiequation models to data sets of finite precision is proposed. This is based on the Gauss-Newton algorithm devised by Britt and Luecke (1973); the inclusion of several equations of condition to be satisfied at each data point results in a block diagonal form for the effective weighting matrix. This method allows generalized nonlinear least-squares fitting of functions that are more easily represented in the parametric form (x(t),y(t)) than as an explicit functional relationship of the form y=f(x). The Aitken (1935) formulas appropriate to multiequation weighted nonlinear least squares are recovered in the limiting case where the variances and covariances of the independent variables are zero. Practical considerations relevant to the performance of such calculations, such as the evaluation of the required partial derivatives and matrix products, are discussed in detail, and the operation of the algorithm is illustrated by applying it to the fit of complex permittivity data to the Debye equation.

  20. Epidemic extinction in a generalized susceptible-infected-susceptible model

    NASA Astrophysics Data System (ADS)

    Chen, Hanshuang; Huang, Feng; Zhang, Haifeng; Li, Guofeng

    2017-01-01

    We study the extinction of epidemics in a generalized susceptible-infected-susceptible model, where a susceptible individual becomes infected at the rate λ when contacting m infective individual(s) simultaneously, and an infected individual spontaneously recovers at the rate μ. By employing the Wentzel-Kramers-Brillouin approximation for the master equation, the problem is reduced to finding the zero-energy trajectories in an effective Hamiltonian system, and the mean extinction time < T> depends exponentially on the associated action S and the size of the population N, < T> ˜ \\exp ≤ft(NS\\right) . Because of qualitatively different bifurcation features for m  =  1 and m≥slant 2 , we derive independently the expressions of S as a function of the rescaled infection rate λ /μ . For the weak infection, S scales to the distance to the bifurcation with an exponent 2 for m  =  1 and 3/2 for m≥slant 2 . Finally, a rare-event simulation method is used to validate the theory.

  1. Process Setting through General Linear Model and Response Surface Method

    NASA Astrophysics Data System (ADS)

    Senjuntichai, Angsumalin

    2010-10-01

    The objective of this study is to improve the efficiency of the flow-wrap packaging process in soap industry through the reduction of defectives. At the 95% confidence level, with the regression analysis, the sealing temperature, temperatures of upper and lower crimper are found to be the significant factors for the flow-wrap process with respect to the number/percentage of defectives. Twenty seven experiments have been designed and performed according to three levels of each controllable factor. With the general linear model (GLM), the suggested values for the sealing temperature, temperatures of upper and lower crimpers are 185, 85 and 85° C, respectively while the response surface method (RSM) provides the optimal process conditions at 186, 89 and 88° C. Due to different assumptions between percentage of defective and all three temperature parameters, the suggested conditions from the two methods are then slightly different. Fortunately, the estimated percentage of defectives at 5.51% under GLM process condition and the predicted percentage of defectives at 4.62% under RSM process condition are not significant different. But at 95% confidence level, the percentage of defectives under RSM condition can be much lower approximately 2.16% than those under GLM condition in accordance with wider variation. Lastly, the percentages of defectives under the conditions suggested by GLM and RSM are reduced by 55.81% and 62.95%, respectively.

  2. Late Early Silurian (Wenlockian) paleoclimate using a general circulation model

    SciTech Connect

    Moore, G.T.; Hayashida, D.N.; Jacobson, S.R. ) Ross, C.A. )

    1992-01-01

    The Silurian Period (439--409 Ma) is synonymous with organic-rich, graptolitic, black shales. The physical conditions that prevailed during the Mid-Silurian drove the paleoclimate and controlled the deposition of this globally ubiquitous, lithotope. The paleoclimate in turn concomitantly created a paleoceanic environment favorable for the generation, deposition, and preservation of phytoplankton. A study of the relationship of the paleogeographic framework on the paleoclimate conditions that forced the deposition of this unique rock type is a problem suitable for study with a general circulation model. For this study the authors chose the Wenlockian Stage (430--424 Ma), the late Early Silurian. The Wenlockian physical world was composed of an oceanic northern hemisphere and a southern hemisphere dominated by the giant continent of Gondwana. The high latitude position of Gondwana placed much of its extensive margin in the mid-latitudes. Laurentia and Baltica occupied a tropical position while Siberia and Kazakh laid to the north. The Silurian fits a paleoatmosphere with an elevated greenhouse effect. Estimated Silurian values of atmospheric CO[sub 2] vary. They chose 1,120 ppm CO[sub 2], a value of 4[times] that of the pre-industrial level. The overall paleoclimate is forced by the diverse paleogeography of the two hemispheres. The northern hemisphere is dominated by strong zonality in all seasons. In contrast, the continental southern hemisphere reactors to the summer heating and winter cooling of Gondwana.

  3. Meta-analysis for diagnostic accuracy studies: a new statistical model using beta-binomial distributions and bivariate copulas.

    PubMed

    Kuss, Oliver; Hoyer, Annika; Solms, Alexander

    2014-01-15

    There are still challenges when meta-analyzing data from studies on diagnostic accuracy. This is mainly due to the bivariate nature of the response where information on sensitivity and specificity must be summarized while accounting for their correlation within a single trial. In this paper, we propose a new statistical model for the meta-analysis for diagnostic accuracy studies. This model uses beta-binomial distributions for the marginal numbers of true positives and true negatives and links these margins by a bivariate copula distribution. The new model comes with all the features of the current standard model, a bivariate logistic regression model with random effects, but has the additional advantages of a closed likelihood function and a larger flexibility for the correlation structure of sensitivity and specificity. In a simulation study, which compares three copula models and two implementations of the standard model, the Plackett and the Gauss copula do rarely perform worse but frequently better than the standard model. We use an example from a meta-analysis to judge the diagnostic accuracy of telomerase (a urinary tumor marker) for the diagnosis of primary bladder cancer for illustration.

  4. Failure of Clindamycin To Eradicate Infection with Beta-Hemolytic Streptococci Inducibly Resistant to Clindamycin in an Animal Model and in Human Infections

    PubMed Central

    Lewis, James S.; Lepak, Alex J.; Thompson, George R.; Craig, William A.; Andes, David R.; Sabol-Dzintars, Kathryn E.

    2014-01-01

    Inducible clindamycin resistance in beta-hemolytic streptococci remains an underrecognized phenomenon of unknown clinical significance. We performed an evaluation of inducible clindamycin resistance using an animal model as well as retrospectively reviewing the charts of patients treated with clindamycin monotherapy who were infected with beta-hemolytic streptococci inducibly resistant to clindamycin. The neutropenic mouse thigh model of infection was used to evaluate the in vivo activity of clindamycin against beta-hemolytic streptococci, including isolates susceptible, inducibly resistant, or constitutively resistant to clindamycin. The clinical microbiology laboratory information system and pharmacy databases were cross-referenced to identify patients with infections due to inducibly clindamycin-resistant beta-hemolytic streptococci who were treated with clindamycin monotherapy. Medical records of these patients were reviewed to evaluate microbiologic and clinical outcomes. Inducible clindamycin resistance resulted in impaired killing of beta-hemolytic streptococci in the animal model. Though suppressed initially, compared to those with constitutive resistance (P = 0.0429), by 48 h, colony counts of inducibly clindamycin-resistant organisms were similar to those of constitutively resistant isolates (P = 0.1142). In addition, we identified 8 patients infected with inducibly clindamycin-resistant beta-hemolytic streptococci who experienced clinical and microbiologic failure when treated with clindamycin monotherapy. These patients either improved initially and subsequently failed or never responded to clindamycin therapy. We have demonstrated in a murine model of infection and from human cases that inducible clindamycin resistance in beta-hemolytic streptococci is clinically significant. Routine testing and reporting by clinical laboratories should be encouraged and alternative antimicrobial agents considered when these organisms are encountered in clinical care

  5. Extending two Higgs doublet models for two-loop neutrino mass generation and one-loop neutrinoless double beta decay

    NASA Astrophysics Data System (ADS)

    Liu, Zhen; Gu, Pei-Hong

    2017-02-01

    We extend some two Higgs doublet models, where the Yukawa couplings for the charged fermion mass generation only involve one Higgs doublet, by two singlet scalars respectively carrying a singly electric charge and a doubly electric charge. The doublet and singlet scalars together can mediate a two-loop diagram to generate a tiny Majorana mass matrix of the standard model neutrinos. Remarkably, the structure of the neutrino mass matrix is fully determined by the symmetric Yukawa couplings of the doubly charged scalar to the right-handed leptons. Meanwhile, a one-loop induced neutrinoless double beta decay can arrive at a testable level even if the electron neutrino has an extremely small Majorana mass. We also study other experimental constraints and implications including some rare processes and Higgs phenomenology.

  6. Triton College and General Motors: The Partnership Model.

    ERIC Educational Resources Information Center

    Fonte, Richard; Magnesen, Vernon

    1983-01-01

    The cooperative training program between Illinois's Triton College and General Motors is described. Illustrates the mutual benefits of this problem and recommends that other colleges follow suit. (NJ)

  7. Fitting host-parasitoid models with CV2 > 1 using hierarchical generalized linear models.

    PubMed Central

    Perry, J N; Noh, M S; Lee, Y; Alston, R D; Norowi, H M; Powell, W; Rennolls, K

    2000-01-01

    The powerful general Pacala-Hassell host-parasitoid model for a patchy environment, which allows host density-dependent heterogeneity (HDD) to be distinguished from between-patch, host density-independent heterogeneity (HDI), is reformulated within the class of the generalized linear model (GLM) family. This improves accessibility through the provision of general software within well-known statistical systems, and allows a rich variety of models to be formulated. Covariates such as age class, host density and abiotic factors may be included easily. For the case where there is no HDI, the formulation is a simple GLM. When there is HDI in addition to HDD, the formulation is a hierarchical generalized linear model. Two forms of HDI model are considered, both with between-patch variability: one has binomial variation within patches and one has extra-binomial, overdispersed variation within patches. Examples are given demonstrating parameter estimation with standard errors, and hypothesis testing. For one example given, the extra-binomial component of the HDI heterogeneity in parasitism is itself shown to be strongly density dependent. PMID:11416907

  8. Geodesic acoustic modes in a fluid model of tokamak plasma: the effects of finite beta and collisionality

    NASA Astrophysics Data System (ADS)

    Singh, Rameswar; Storelli, A.; Gürcan, Ö. D.; Hennequin, P.; Vermare, L.; Morel, P.; Singh, R.

    2015-12-01

    Starting from the Braginskii equations, relevant for the tokamak edge region, a complete set of nonlinear equations for the geodesic acoustic modes (GAM) has been derived which includes collisionality, plasma beta and external sources of particle, momentum and heat. Local linear analysis shows that the GAM frequency increases with collisionality at low radial wave number {{k}\\text{r}} and decreases at high {{k}\\text{r}} . GAM frequency also decreases with plasma beta. Radial profiles of GAM frequency for two Tore Supra shots, which were part of a collisionality scan, are compared with these calculations. A discrepancy between experiment and theory is observed, which seems to be explained by a finite {{k}\\text{r}} for the GAM when flux surface averaged density < n> and temperature < T> are assumed to vanish. It is shown that this agreement is incidental and self-consistent inclusion of < n> and < T> responses enhances the disagreement more with {{k}\\text{r}} at high {{k}\\text{r}} . So the discrepancy between the linear GAM calculation and experiment, (which also persist for more ‘complete’ linear models such as gyrokinetics) can probably not be resolved by simply adding a finite {{k}\\text{r}} .

  9. Hierarchical General Diagnostic Models. Research Report. ETS RR-07-19

    ERIC Educational Resources Information Center

    von Davier, Matthias

    2007-01-01

    This paper introduces multilevel extensions for the general diagnostic model (GDM) following recent developments on extensions of latent class analysis (LCA) to hierarchical models. The GDM is based on LCA as well as discrete latent trait models and may be viewed as a general modeling framework for conrmatory multidimensional item response models.…

  10. Evaluation of the Majorana phases of a general Majorana neutrino mass matrix: Testability of hierarchical flavour models

    NASA Astrophysics Data System (ADS)

    Samanta, Rome; Chakraborty, Mainak; Ghosal, Ambar

    2016-03-01

    We evaluate the Majorana phases for a general 3 × 3 complex symmetric neutrino mass matrix on the basis of Mohapatra-Rodejohann's phase convention using the three rephasing invariant quantities I12, I13 and I23 proposed by Sarkar and Singh. We find them interesting as they allow us to evaluate each Majorana phase in a model independent way even if one eigenvalue is zero. Utilizing the solution of a general complex symmetric mass matrix for eigenvalues and mixing angles we determine the Majorana phases for both the hierarchies, normal and inverted, taking into account the constraints from neutrino oscillation global fit data as well as bound on the sum of the three light neutrino masses (Σimi) and the neutrinoless double beta decay (ββ0ν) parameter |m11 |. This methodology of finding the Majorana phases is applied thereafter in some predictive models for both the hierarchical cases (normal and inverted) to evaluate the corresponding Majorana phases and it is shown that all the sub cases presented in inverted hierarchy section can be realized in a model with texture zeros and scaling ansatz within the framework of inverse seesaw although one of the sub cases following the normal hierarchy is yet to be established. Except the case of quasi degenerate neutrinos, the methodology obtained in this work is able to evaluate the corresponding Majorana phases, given any model of neutrino masses.

  11. A general moment expansion method for stochastic kinetic models

    NASA Astrophysics Data System (ADS)

    Ale, Angelique; Kirk, Paul; Stumpf, Michael P. H.

    2013-05-01

    Moment approximation methods are gaining increasing attention for their use in the approximation of the stochastic kinetics of chemical reaction systems. In this paper we derive a general moment expansion method for any type of propensities and which allows expansion up to any number of moments. For some chemical reaction systems, more than two moments are necessary to describe the dynamic properties of the system, which the linear noise approximation is unable to provide. Moreover, also for systems for which the mean does not have a strong dependence on higher order moments, moment approximation methods give information about higher order moments of the underlying probability distribution. We demonstrate the method using a dimerisation reaction, Michaelis-Menten kinetics and a model of an oscillating p53 system. We show that for the dimerisation reaction and Michaelis-Menten enzyme kinetics system higher order moments have limited influence on the estimation of the mean, while for the p53 system, the solution for the mean can require several moments to converge to the average obtained from many stochastic simulations. We also find that agreement between lower order moments does not guarantee that higher moments will agree. Compared to stochastic simulations, our approach is numerically highly efficient at capturing the behaviour of stochastic systems in terms of the average and higher moments, and we provide expressions for the computational cost for different system sizes and orders of approximation. We show how the moment expansion method can be employed to efficiently quantify parameter sensitivity. Finally we investigate the effects of using too few moments on parameter estimation, and provide guidance on how to estimate if the distribution can be accurately approximated using only a few moments.

  12. Venusian Polar Vortex reproduced in an Atmospheric General Circulation Model

    NASA Astrophysics Data System (ADS)

    Ando, Hiroki; Imamura, Takeshi; Takagi, Masahiro; Sugimoto, Norihiko; Kashimura, Hiroki

    The Venus atmosphere has a polar vortex rotating in the retrograde direction with a period of about three days. The vortex has a warm feature surrounded by a cold collar (e.g., Taylor et al. 1980; Piccioni et al. 2006). Although the Venusian polar vortex has been reported by many observations, its mechanism is still unknown. Elson (1982, 1989) examined the structure of the polar vortex by linear calculations. However, the background zonal wind assumed in the calculations was much stronger or weaker than those retrieved in the previous measurements (e.g., Peralta et al. 2008; Kouyama et al. 2012). Lee et al. (2010) and Yamamoto and Takahashi (2012) performed numerical simulations with general circulation models (GCMs) of the Venus atmosphere and obtained vertical structure in the polar region. However, the models included artificial forcing of Kelvin and/or Rossby waves. We have developed a new Venusian GCM by modifying the Atmospheric GCM For the Earth Simulator (Sugimoto et al. 2012; 2013). The basic equations of the GCM are primitive ones in the sigma coordinate on a sphere without topography. The model resolution is T42 (i.e., about 2.8 deg x 2.8 deg grids) and L60 (Deltaz is about 2 km). Rayleigh friction (sponge layer) in the upper layer (>80 km) is applied to prevent the reflection of waves, whose effect increases gradually with height. In the model, the atmosphere is dry and forced by the solar heating and Newtonian cooling. The vertical profile of the solar heating is based on Crisp (1986), and zonally averaged distribution is used. In addition diurnal component of the solar heating, which excites the diurnal and semi-diurnal tides, is also included. Newtonian cooling relaxes the temperature to the zonally uniform basic temperature which has a virtual static stability of Venus with almost neutral layers, and its coefficient is based on Crisp (1986). To prevent numerical instability, the biharmonic hyper-diffusion is included with 0.8 days of e-folding time

  13. Allosteric equilibrium model explains steady-state coupling of beta-adrenergic receptors to adenylate cyclase in turkey erythrocyte membranes.

    PubMed

    Ugur, O; Onaran, H O

    1997-05-01

    We used a simple experimental approach to clarify some contradictory predictions of the collision coupling and equilibrium models (e.g. ternary complex, two-state ternary complex or quinternary complex), which describe G-protein-mediated beta-adrenergic receptor signalling in essentially different manners. Analysis of the steady-state coupling of beta-adrenoceptors to adenylate cyclase in turkey erythrocyte membranes showed that: (1) in the absence of an agonist, Gpp(NH)p (a hydrolysis-resistant analogue of GTP) can activate adenylate cyclase very slowly; (2) this activity reaches a steady state in approx. 5 h, the extent of activity depending on the concentration of the nucleotide; (3) isoprenaline-activated steady-state adenylate cyclase can be inactivated by propranolol (a competitive antagonist that relaxes the receptor activation), in the presence of Gpp(NH)p (which provides a virtual absence of GTPase) and millimolar concentrations of Mg2+ (the rate of this inactivation is relatively fast); (4) increasing the concentration of Gpp(NH)p can saturate the steady-state activity of adenylate cyclase. The saturated enzyme activity was lower than that induced by isoprenaline under the same conditions. This additional agonist-induced activation was reversible. In the light of these results, we conclude that agonist can also activate the guanine nucleotide-saturated system in the absence of GTPase by a mechanism other than guanine nucleotide exchange. We explain these phenomena in the framework of a quinternary complex model as an agonist-induced and receptor-mediated dissociation of guanine nucleotide-saturated residual heterotrimer, the equilibrium concentration of which is not necessarily zero. These results, which suggest a continuous interaction between receptor and G-protein, can hardly be accommodated by the collision coupling model that was originally suggested for the present experimental system and then applied to many other G-protein systems. Therefore we

  14. Modeling Classroom Discourse: Do Models That Predict Dialogic Instruction Properties Generalize across Populations?

    ERIC Educational Resources Information Center

    Samei, Borhan; Olney, Andrew M.; Kelly, Sean; Nystrand, Martin; D'Mello, Sidney; Blanchard, Nathan; Graesser, Art

    2015-01-01

    It has previously been shown that the effective use of dialogic instruction has a positive impact on student achievement. In this study, we investigate whether linguistic features used to classify properties of classroom discourse generalize across different subpopulations. Results showed that the machine learned models perform equally well when…

  15. Documentation of the GLAS fourth order general circulation model. Volume 1: Model documentation

    NASA Technical Reports Server (NTRS)

    Kalnay, E.; Balgovind, R.; Chao, W.; Edelmann, J.; Pfaendtner, J.; Takacs, L.; Takano, K.

    1983-01-01

    The volume 1, of a 3 volume technical memoranda which contains a documentation of the GLAS Fourth Order General Circulation Model is presented. Volume 1 contains the documentation, description of the stratospheric/tropospheric extension, user's guide, climatological boundary data, and some climate simulation studies.

  16. A general model for estimating lower extremity inertial properties of individuals with transtibial amputation.

    PubMed

    Ferris, Abbie E; Smith, Jeremy D; Heise, Gary D; Hinrichs, Richard N; Martin, Philip E

    2017-03-21

    Lower extremity joint moment magnitudes during swing are dependent on the inertial properties of the prosthesis and residual limb of individuals with transtibial amputation (TTA). Often, intact limb inertial properties (INTACT) are used for prosthetic limb values in an inverse dynamics model even though these values overestimate the amputated limb's inertial properties. The purpose of this study was to use subject-specific (SPECIFIC) measures of prosthesis inertial properties to generate a general model (GENERAL) for estimating TTA prosthesis inertial properties. Subject-specific mass, center of mass, and moment of inertia were determined for the shank and foot segments of the prosthesis (n=11) using an oscillation technique and reaction board. The GENERAL model was derived from the means of the SPECIFIC model. Mass and segment lengths are required GENERAL model inputs. Comparisons of segment inertial properties and joint moments during walking were made using three inertial models (unique sample; n=9): (1) SPECIFIC, (2) GENERAL, and (3) INTACT. Prosthetic shank inertial properties were significantly smaller with the SPECIFIC and GENERAL model than the INTACT model, but the SPECIFIC and GENERAL model did not statistically differ. Peak knee and hip joint moments during swing were significantly smaller for the SPECIFIC and GENERAL model compared with the INTACT model and were not significantly different between SPECIFIC and GENERAL models. When subject-specific measures are unavailable, using the GENERAL model produces a better estimate of prosthetic side inertial properties resulting in more accurate joint moment measurements for individuals with TTA than the INTACT model.

  17. Logarithmic correction in the deformed AdS{sub 5} model to produce the heavy quark potential and QCD beta function

    SciTech Connect

    He Song; Huang Mei; Yan Qishu

    2011-02-15

    We study the holographic QCD model, which contains a quadratic term -{sigma}z{sup 2} and a logarithmic term -c{sub 0}log[(z{sub IR}-z)/z{sub IR}] with an explicit infrared cutoff z{sub IR} in the deformed AdS{sub 5} warp factor. We investigate the heavy-quark potential for three cases, i.e., with only a quadratic correction, with both quadratic and logarithmic corrections, and with only a logarithmic correction. We solve the dilaton field and dilation potential from the Einstein equation and investigate the corresponding beta function in the Guersoy-Kiritsis-Nitti framework. Our studies show that in the case with only a quadratic correction, a negative {sigma} or the Andreev-Zakharov model is favored to fit the heavy-quark potential and to produce the QCD beta function at 2-loop level; however, the dilaton potential is unbounded in the infrared regime. One interesting observation for the case of positive {sigma} is that the corresponding beta function exists in an infrared fixed point. In the case with only a logarithmic correction, the heavy-quark Cornell potential can be fitted very well, the corresponding beta function agrees with the QCD beta function at 2-loop level reasonably well, and the dilaton potential is bounded from below in the infrared. At the end, we propose a more compact model which has only a logarithmic correction in the deformed warp factor and has less free parameters.

  18. Spectral Representation of the Vertical Coordinate in Three-Dimensional Atmospheric Models on Tropical Beta - and F-Planes

    NASA Astrophysics Data System (ADS)

    Mizzi, Arthur Paul

    This research examines the application of the spectral method to the vertical coordinate of atmospheric models. Specifically, we use the vertical normal modes as basis functions in spectral expansion of the vertical structure of dependent variables in an equatorial beta-plane and a tropical f-plane model of the atmosphere. Previous attempts by Francis (1972) and Machenhauer and Daley (1972) found that use of vertical spectral methods was associated with an unrealistic acceleration of velocities near the top of the model. Machenhauer and Daley (1972) showed that this acceleration was associated with temperature not zero at the upper boundary where pressure is zero. They concluded that artificial constraints on temperature were necessary to control the upper-level accelerations. We show that artificial constraints are not required when the model uses prognostic equations for velocity and geopotential instead of velocity and temperature. We use the vertical normal modes of Staniforth et al. (1985), and our analysis shows that these vertical structure functions are bounded while all derivatives are unbounded at the upper boundary. Further analysis shows that the boundary conditions from the vertical structure problem ensure that temperature vanishes at the upper boundary. This analysis suggests that any basis set, for which the inverse of the first derivative approaches zero more slowly than pressure at the upper boundary, is suitable for the vertical spectral expansion. Using these ideas we coded tropical beta - and f-plane models using the basic state temperature and vertical normal modes of Staniforth et al. (1985). During model development we encountered the following problems. (1) The meridional grid is dependent upon the vertical mode. (2) The vertical quadrature is problematic due to presence of integrand derivative singularities. (3) The convergence of the vertical spectral expansion is slow due to the singularity at the upper boundary. (4) The projection of

  19. Charged lepton flavour violcxmation and neutrinoless double beta decay in left-right symmetric models with type I+II seesaw

    NASA Astrophysics Data System (ADS)

    Borah, Debasish; Dasgupta, Arnab

    2016-07-01

    We study the new physics contributions to neutrinoless double beta decay (0 νββ) half-life and lepton flavour violation (LFV) amplitude within the framework of the minimal left-right symmetric model (MLRSM). Considering all possible new physics contributions to 0 νββ and charged lepton flavour violation μ → eγ , μ → 3 e in MLRSM, we constrain the parameter space of the model from the requirement of satisfying existing experimental bounds. Assuming the breaking scale of the left-right symmetry to be O (1) TeV accessible at ongoing and near future collider experiments, we consider the most general type I+II seesaw mechanism for the origin of tiny neutrino masses. Choosing the relative contribution of the type II seesaw term allows us to calculate the right handed neutrino mass matrix as well as Dirac neutrino mass matrix as a function of the model parameters, required for the calculation of 0νββ and LFV amplitudes. We show that such a general type I+II seesaw structure results in more allowed parameter space compared to individual type I or type II seesaw cases considered in earlier works. In particular, we show that the doubly charged scalar masses M Δ are allowed to be smaller than the heaviest right handed neutrino mass M N from the present experimental bounds in these scenarios which is in contrast to earlier results with individual type I or type II seesaw showing M Δ > M N .

  20. Optimal Scaling of Interaction Effects in Generalized Linear Models

    ERIC Educational Resources Information Center

    van Rosmalen, Joost; Koning, Alex J.; Groenen, Patrick J. F.

    2009-01-01

    Multiplicative interaction models, such as Goodman's (1981) RC(M) association models, can be a useful tool for analyzing the content of interaction effects. However, most models for interaction effects are suitable only for data sets with two or three predictor variables. Here, we discuss an optimal scaling model for analyzing the content of…

  1. Hydraulic fracturing model based on the discrete fracture model and the generalized J integral

    NASA Astrophysics Data System (ADS)

    Liu, Z. Q.; Liu, Z. F.; Wang, X. H.; Zeng, B.

    2016-08-01

    The hydraulic fracturing technique is an effective stimulation for low permeability reservoirs. In fracturing models, one key point is to accurately calculate the flux across the fracture surface and the stress intensity factor. To achieve high precision, the discrete fracture model is recommended to calculate the flux. Using the generalized J integral, the present work obtains an accurate simulation of the stress intensity factor. Based on the above factors, an alternative hydraulic fracturing model is presented. Examples are included to demonstrate the reliability of the proposed model and its ability to model the fracture propagation. Subsequently, the model is used to describe the relationship between the geometry of the fracture and the fracturing equipment parameters. The numerical results indicate that the working pressure and the pump power will significantly influence the fracturing process.

  2. Hyperbolic value addition and general models of animal choice.

    PubMed

    Mazur, J E

    2001-01-01

    Three mathematical models of choice--the contextual-choice model (R. Grace, 1994), delay-reduction theory (N. Squires & E. Fantino, 1971), and a new model called the hyperbolic value-added model--were compared in their ability to predict the results from a wide variety of experiments with animal subjects. When supplied with 2 or 3 free parameters, all 3 models made fairly accurate predictions for a large set of experiments that used concurrent-chain procedures. One advantage of the hyperbolic value-added model is that it is derived from a simpler model that makes accurate predictions for many experiments using discrete-trial adjusting-delay procedures. Some results favor the hyperbolic value-added model and delay-reduction theory over the contextual-choice model, but more data are needed from choice situations for which the models make distinctly different predictions.

  3. Development of an atmospheric model based on a generalized vertical coordinate. Final report, September 12, 1991--August 31, 1997

    SciTech Connect

    Arakawa, Akio; Konor, C.S.

    1997-12-31

    There are great conceptual advantages in the use of an isentropic vertical coordinate in atmospheric models. Design of such a model, however, requires to overcome computational problems due to intersection of coordinate surfaces with the earth`s surface. Under this project, the authors have completed the development of a model based on a generalized vertical coordinate, {zeta} = F({Theta}, p, p{sub s}), in which an isentropic coordinate can be combined with a terrain-following {sigma}-coordinate a smooth transition between the two. One of the key issues in developing such a model is to satisfy the consistency between the predictions of pressure and potential temperature. In the model, the consistency is satisfied by the use of an equation that determines the vertical mass flux. A procedure to properly choose {zeta} = F({Theta}, p, p{sub s}) is also developed, which guarantees that {zeta} is a monotonic function of height even when unstable stratification occurs. There are two versions of the model constructed in parallel: one is the middle-latitude {beta}-plane version and the other is the global version. Both of these versions include moisture prediction, relaxed large-scale condensation and relaxed moist-convective adjustment schemes. A well-mixed planetary boundary layer (PBL) is also added.

  4. Activity of imipenem against VIM-1 metallo-beta-lactamase-producing Klebsiella pneumoniae in the murine thigh infection model.

    PubMed

    Daikos, G L; Panagiotakopoulou, A; Tzelepi, E; Loli, A; Tzouvelekis, L S; Miriagou, V

    2007-02-01

    The in-vivo activity of imipenem against VIM-1-producing Klebsiella pneumoniae (VPKP) was assessed in a thigh infection model in neutropenic mice. Animals were infected with three VPKP isolates (imipenem MICs 2, 4 and 32 mg/L, respectively) and a susceptible clinical isolate (MIC 0.125 mg/L) that did not produce any beta-lactamase with broad-spectrum activity. Bacterial density at the site of infection was determined after imipenem treatment (30 and 60 mg/kg every 2 h for 24 h). The log(10) reduction in CFU/thigh was greatest for the wild-type isolate, intermediate for the two imipenem-susceptible VPKP isolates, and lowest for the imipenem-resistant VPKP isolate. Whilst in-vivo imipenem activity appeared reduced against in-vitro susceptible VIM-1 producers compared with a VIM-1-negative control, an increased drug dosage could moderate this reduction.

  5. MAGNETO-STATIC MODELING OF THE MIXED PLASMA BETA SOLAR ATMOSPHERE BASED ON SUNRISE/IMaX DATA

    SciTech Connect

    Wiegelmann, T.; Solanki, S. K.; Neukirch, T.; Nickeler, D. H.; Pillet, V. Martínez; Borrero, J. M.

    2015-12-10

    Our aim is to model the three-dimensional magnetic field structure of the upper solar atmosphere, including regions of non-negligible plasma beta. We use high-resolution photospheric magnetic field measurements from SUNRISE/IMaX as the boundary condition for a magneto-static magnetic field model. The high resolution of IMaX allows us to resolve the interface region between the photosphere and corona, but modeling this region is challenging for the following reasons. While the coronal magnetic field is thought to be force-free (the Lorentz force vanishes), this is not the case in the mixed plasma β environment in the photosphere and lower chromosphere. In our model, pressure gradients and gravity forces are self-consistently taken into account and compensate for the non-vanishing Lorentz force. Above a certain height (about 2 Mm) the non-magnetic forces become very weak and consequently the magnetic field becomes almost force-free. Here, we apply a linear approach where the electric current density consists of a superposition of a field-line parallel current and a current perpendicular to the Sun's gravity field. We illustrate the prospects and limitations of this approach and give an outlook for an extension toward a nonlinear model.

  6. Reduction of beta-glucuronidase and nitroreductase activity by yoghurt in a murine colon cancer model.

    PubMed

    de Moreno de LeBlanc, A; Perdigón, G

    2005-04-01

    Yoghurt feeding inhibits induced colon cancer in mice. Several studies showed the immunomodulatory effect of yoghurt which can explain this inhibition. It is possible that yoghurt bacteria can also affect gut flora enzymes related to colon carcinogenesis as reported for other probiotics in different animal tumours. The aim of this work was to evaluate the role of yoghurt starter bacteria and their cell-free fermentation products on the reduction of procarcinogen enzyme activities (beta-glucuronidase and nitroreductase). Mice injected with 1,2-dimethylhydrazine (DMH) and fed with yoghurt were used for this study. Mice given milk or yoghurt supernatant (cell free extract) were used to evaluate if the yoghurt antitumour effect is due to the starter bacteria or other components released during fermentation, that could inhibit these enzymes. We determined that yoghurt by itself maintained enzymes activities similar or lower than non-treatment control group, and the enzyme activity was also lower than milk or yoghurt supernatant groups. DMH increased the activity of the enzymes. Mice injected with DMH and fed cyclically with yoghurt presented lower enzymes activities than the tumour control group. Feeding yoghurt decreased procarcinogenic enzyme levels in the large intestine contents of mice bearing colon tumour. The results of this study provide another mechanism by which yoghurt starter bacteria interact with the large intestine of the mice and prevent colon cancer.

  7. Double-beta decay in pn-QRPA model with isospin and SU(4) symmetry constraints

    NASA Astrophysics Data System (ADS)

    Krmpotić, F.; Sharma, S. Shelly

    1994-05-01

    The transition matrix elements for the 0 + → 0 + double-beta decays are calculated for 48Ca, 76Ge, 82Se, 100Mo, 128Te and 130Te nuclei, using a δ-interaction. As a guide, to fix the particle-particle interaction strengths, we exploit the fact that the missing symmetries of the mean-field approximation are restored in the random phase approximation by the residual interaction. Thus, the T = 1, S = 0 and T = 0, S = 1 coupling strengths have been estimated by invoking the partial restoration of the isospin and Wigner SU(4) symmetries, respectively. When this recipe is strictly applied, the calculation is consistent with the experimental limit for the 2ν lifetime of 48Ca and it also correctly reproduces the 2ν lifetime of 82Se. In this way, however, the two-neutrino matrix elements for the remaining nuclei are either underestimated (for 76Ge and 100Mo) or overestimated (for 128Te and 130Te) approximately by a factor of 3. With a comparatively small variation (< 10%) of the spin-triplet parameter, near the value suggested by the SU(4) symmetry, it is possible to reproduce the measured T 2ν{1}/{2} all the cases. The upper limit for the effective neutrino mass, as obtained from the theoretical estimates of 0ν matrix elements, is < m> ˜- 1 eV. The dependence of the nuclear matrix elements on the size of the configuration space has been also analyzed.

  8. Retrofitting Non-Cognitive-Diagnostic Reading Assessment under the Generalized DINA Model Framework

    ERIC Educational Resources Information Center

    Chen, Huilin; Chen, Jinsong

    2016-01-01

    Cognitive diagnosis models (CDMs) are psychometric models developed mainly to assess examinees' specific strengths and weaknesses in a set of skills or attributes within a domain. By adopting the Generalized-DINA model framework, the recently developed general modeling framework, we attempted to retrofit the PISA reading assessments, a…

  9. Selective destruction of mouse islet beta cells by human T lymphocytes in a newly-established humanized type 1 diabetic model

    SciTech Connect

    Zhao, Yong; Guo, Chengshan; Hwang, David; Lin, Brian; Dingeldein, Michael; Mihailescu, Dan; Sam, Susan; Sidhwani, Seema; Zhang, Yongkang; Jain, Sumit; Skidgel, Randal A.; Prabhakar, Bellur S.; Mazzone, Theodore; Holterman, Mark J.

    2010-09-03

    Research highlights: {yields} Establish a human immune-mediated type 1 diabetic model in NOD-scid IL2r{gamma}{sup null} mice. {yields} Using the irradiated diabetic NOD mouse spleen mononuclear cells as trigger. {yields} The islet {beta} cells were selectively destroyed by infiltrated human T cells. {yields} The model can facilitate translational research to find a cure for type 1 diabetes. -- Abstract: Type 1 diabetes (T1D) is caused by a T cell-mediated autoimmune response that leads to the loss of insulin-producing {beta} cells. The optimal preclinical testing of promising therapies would be aided by a humanized immune-mediated T1D model. We develop this model in NOD-scid IL2r{gamma}{sup null} mice. The selective destruction of pancreatic islet {beta} cells was mediated by human T lymphocytes after an initial trigger was supplied by the injection of irradiated spleen mononuclear cells (SMC) from diabetic nonobese diabetic (NOD) mice. This resulted in severe insulitis, a marked loss of total {beta}-cell mass, and other related phenotypes of T1D. The migration of human T cells to pancreatic islets was controlled by the {beta} cell-produced highly conserved chemokine stromal cell-derived factor 1 (SDF-1) and its receptor C-X-C chemokine receptor (CXCR) 4, as demonstrated by in vivo blocking experiments using antibody to CXCR4. The specificity of humanized T cell-mediated immune responses against islet {beta} cells was generated by the local inflammatory microenvironment in pancreatic islets including human CD4{sup +} T cell infiltration and clonal expansion, and the mouse islet {beta}-cell-derived CD1d-mediated human iNKT activation. The selective destruction of mouse islet {beta} cells by a human T cell-mediated immune response in this humanized T1D model can mimic those observed in T1D patients. This model can provide a valuable tool for translational research into T1D.

  10. Optimization of a Parallel Ocean General Circulation Model

    NASA Technical Reports Server (NTRS)

    Chao, Yi

    1997-01-01

    Global climate modeling is one of the grand chalenges of computational science, and ocean modeling plays an important role in both understanding the current climatic conditions and predicting the future climate change.

  11. Statistical multifragmentation model with discretized energy and the generalized Fermi breakup: Formulation of the model

    NASA Astrophysics Data System (ADS)

    Souza, S. R.; Carlson, B. V.; Donangelo, R.; Lynch, W. G.; Tsang, M. B.

    2013-07-01

    The generalized Fermi breakup model, recently demonstrated to be formally equivalent to the statistical multifragmentation model, if the contribution of excited states is included in the state densities of the former, is implemented. Because this treatment requires application of the statistical multifragmentation model repeatedly on hot fragments until they have decayed to their ground states, it becomes extremely computationally demanding, making its application to the systems of interest extremely difficult. Based on exact recursion formulas previously developed by Chase and Mekjian to calculate statistical weights very efficiently, we present an implementation which is efficient enough to allow it to be applied to large systems at high excitation energies. Comparison with the gemini++ sequential decay code and the Weisskopf-Ewing evaporation model shows that the predictions obtained with our treatment are fairly similar to those obtained with these more traditional models.

  12. The History and Generality of AQUATOX, a Robust Mechanistic Model

    EPA Science Inventory

    In 1987, the U.S. Environmental Protection Agency sponsored a workshop in Baltimore on modeling the fate and effects of toxic organics. The specifications for the AQUATOX model came out of this workshop, and the first paper on the modeling concept was published soon after. Since ...

  13. On the Bayesian Nonparametric Generalization of IRT-Type Models

    ERIC Educational Resources Information Center

    San Martin, Ernesto; Jara, Alejandro; Rolin, Jean-Marie; Mouchart, Michel

    2011-01-01

    We study the identification and consistency of Bayesian semiparametric IRT-type models, where the uncertainty on the abilities' distribution is modeled using a prior distribution on the space of probability measures. We show that for the semiparametric Rasch Poisson counts model, simple restrictions ensure the identification of a general…

  14. A General Bayesian Model for Testlets: Theory and Applications.

    ERIC Educational Resources Information Center

    Wang, Xiaohui; Bradlow, Eric T.; Wainer, Howard

    2002-01-01

    Proposes a modified version of commonly employed item response models in a fully Bayesian framework and obtains inferences under the model using Markov chain Monte Carlo techniques. Demonstrates use of the model in a series of simulations and with operational data from the North Carolina Test of Computer Skills and the Test of Spoken English…

  15. The Generalized Multilevel Facets Model for Longitudinal Data

    ERIC Educational Resources Information Center

    Hung, Lai-Fa; Wang, Wen-Chung

    2012-01-01

    In the human sciences, ability tests or psychological inventories are often repeatedly conducted to measure growth. Standard item response models do not take into account possible autocorrelation in longitudinal data. In this study, the authors propose an item response model to account for autocorrelation. The proposed three-level model consists…

  16. Modelo de Alfabetizacion: A Poblacion Urbana y Rural. Documento General (Literacy Model: Urban and Rural Populations. General Document).

    ERIC Educational Resources Information Center

    Instituto Nacional para la Educacion de los Adultos, Mexico City (Mexico).

    This document describes literacy models for urban and rural populations in Mexico. It contains four sections. The first two sections (generalizations about the population and considerations about the teaching of adults) discuss the environment that creates illiterate adults and also describe some of the conditions under which learning takes place…

  17. Testing the Generalized Partial Credit Model. Research Report 96-03.

    ERIC Educational Resources Information Center

    Glas, Cees A. W.

    The partial credit model (PCM) (G. N. Masters, 1982) can be viewed as a generalization of the Rasch model for dichotomous items to the case of polytomous items. In many cases, the PCM is too restrictive to fit the data. Several generalizations of the PCM have been proposed. In this paper, a generalization of the PCM (GPCM), a further…

  18. Looking beyond general metrics for model evaluation - lessons from an international model intercomparison study

    NASA Astrophysics Data System (ADS)

    Bouaziz, Laurène; de Boer-Euser, Tanja; Brauer, Claudia; Drogue, Gilles; Fenicia, Fabrizio; Grelier, Benjamin; de Niel, Jan; Nossent, Jiri; Pereira, Fernando; Savenije, Hubert; Thirel, Guillaume; Willems, Patrick

    2016-04-01

    International collaboration between institutes and universities is a promising way to reach consensus on hydrological model development. Education, experience and expert knowledge of the hydrological community have resulted in the development of a great variety of model concepts, calibration methods and analysis techniques. Although comparison studies are very valuable for international cooperation, they do often not lead to very clear new insights regarding the relevance of the modelled processes. We hypothesise that this is partly caused by model complexity and the used comparison methods, which focus on a good overall performance instead of focusing on specific events. We propose an approach that focuses on the evaluation of specific events. Eight international research groups calibrated their model for the Ourthe catchment in Belgium (1607 km2) and carried out a validation in time for the Ourthe (i.e. on two different periods, one of them on a blind mode for the modellers) and a validation in space for nested and neighbouring catchments of the Meuse in a completely blind mode. For each model, the same protocol was followed and an ensemble of best performing parameter sets was selected. Signatures were first used to assess model performances in the different catchments during validation. Comparison of the models was then followed by evaluation of selected events, which include: low flows, high flows and the transition from low to high flows. While the models show rather similar performances based on general metrics (i.e. Nash-Sutcliffe Efficiency), clear differences can be observed for specific events. While most models are able to simulate high flows well, large differences are observed during low flows and in the ability to capture the first peaks after drier months. The transferability of model parameters to neighbouring and nested catchments is assessed as an additional measure in the model evaluation. This suggested approach helps to select, among competing

  19. Determining tan {beta} at the NLC with SUSY Higgs bosons

    SciTech Connect

    Feng, J.L.; Moroi, Takeo |

    1997-07-01

    The authors examine the prospects for determining tan {beta} from heavy Higgs scalar production in the minimal supersymmetric standard model at a future e{sup +}e{sup {minus}} collider. Their analysis is independent of assumptions of parameter unification, and they consider general radiative corrections in the Higgs sector. Bounds are presented for {radical}s = 500 GeV and 1 TeV, several Higgs masses, and a variety of integrated luminosities. For all cases considered, it is possible to distinguish low, moderate, and high tan {beta}. In addition, the authors find stringent constraints for 3 {approx_lt} tan{beta} {approx_lt} 10, and, for some scenarios, also interesting bounds on high tan {beta} through tbH{sup {+-}} production. Such measurements may provide strong tests of the Yukawa unifications in grand unified theories and make possible highly precise determinations of soft SUSY breaking mass parameters.

  20. A simple hydrologically based model of land surface water and energy fluxes for general circulation models

    NASA Technical Reports Server (NTRS)

    Liang, XU; Lettenmaier, Dennis P.; Wood, Eric F.; Burges, Stephen J.

    1994-01-01

    A generalization of the single soil layer variable infiltration capacity (VIC) land surface hydrological model previously implemented in the Geophysical Fluid Dynamics Laboratory (GFDL) general circulation model (GCM) is described. The new model is comprised of a two-layer characterization of the soil column, and uses an aerodynamic representation of the latent and sensible heat fluxes at the land surface. The infiltration algorithm for the upper layer is essentially the same as for the single layer VIC model, while the lower layer drainage formulation is of the form previously implemented in the Max-Planck-Institut GCM. The model partitions the area of interest (e.g., grid cell) into multiple land surface cover types; for each land cover type the fraction of roots in the upper and lower zone is specified. Evapotranspiration consists of three components: canopy evaporation, evaporation from bare soils, and transpiration, which is represented using a canopy and architectural resistance formulation. Once the latent heat flux has been computed, the surface energy balance is iterated to solve for the land surface temperature at each time step. The model was tested using long-term hydrologic and climatological data for Kings Creek, Kansas to estimate and validate the hydrological parameters, and surface flux data from three First International Satellite Land Surface Climatology Project Field Experiment (FIFE) intensive field campaigns in the summer-fall of 1987 to validate the surface energy fluxes.

  1. Hierarchical framework for coupling a biogeochemical trace gas model to a general circulation model

    SciTech Connect

    Miller, N.L.; Foster, I.T.

    1994-04-01

    A scheme is described for the computation of terrestrial biogeochemical trace gas fluxes in the context of a general circulation model. This hierarchical system flux scheme (HSFS) incorporates five major components: (1) a general circulation model (GCM), which provides a medium-resolution (i.e., 1{degrees} by 1{degrees}) simulation of the atmospheric circulation; (2) a procedure for identifying regions of defined homogeneity of surface type within GCM grid cells; (3) a set of surface process models, to be run within each homogeneous region, which include a biophysical model, the Biosphere Atmospheric Transfer Scheme (BATS), and a biogeochemical model (BGCM); (4) an interpolation/integration system that transfers information between the GCM and surface process models with finer resolution; and (5) an interactive data array based on a geographic information system (GIS), which provides land characteristic information via the interpolator. The goals of this detailed investigation are to compute the local and global sensitivities of trace gas fluxes to GCM and BATS variables, the effects of trace gas fluxes on global climate, and the effects of global climate on specific biomes.

  2. Shoreline Change Modeling Using One- Line Models: General Model Comparison and Literature Review

    DTIC Science & Technology

    2013-12-01

    long term shoreline evolution primarily using (1) measurement and analysis of historical shoreline position, (2) models based on the conservation of...sand volume equation (one-line models), (3) coastal morphodynamics models, and (4) physical models (Dean and Dalrymple 2002). Statistical analysis of...not well suited to the large spatial and temporal scales over which beaches evolve. Physical models (method 4) are well suited to local analysis but

  3. AGATE concept model for a future general aviation airplane

    NASA Technical Reports Server (NTRS)

    1996-01-01

    Photo illustrates an advanced general aviation concept airplane. The pusher propeller - driven configuration seats 4 to 6 people (including pilot) in mid-wing, three-surface twin tail-boom configuration. The design concept incorporates natural laminar flow, ice protection, winglets and stall-departure-resistant flight dynamics.

  4. Modular and Stochastic Approaches to Molecular Pathway Models of ATM, TGF beta, and WNT Signaling

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; O'Neill, Peter; Ponomarev, Artem; Carra, Claudio; Whalen, Mary; Pluth, Janice M.

    2009-01-01

    Deterministic pathway models that describe the biochemical interactions of a group of related proteins, their complexes, activation through kinase, etc. are often the basis for many systems biology models. Low dose radiation effects present a unique set of challenges to these models including the importance of stochastic effects due to the nature of radiation tracks and small number of molecules activated, and the search for infrequent events that contribute to cancer risks. We have been studying models of the ATM, TGF -Smad and WNT signaling pathways with the goal of applying pathway models to the investigation of low dose radiation cancer risks. Modeling challenges include introduction of stochastic models of radiation tracks, their relationships to more than one substrate species that perturb pathways, and the identification of a representative set of enzymes that act on the dominant substrates. Because several pathways are activated concurrently by radiation the development of modular pathway approach is of interest.

  5. Stereopentads derived from a sequence of Mukaiyama aldolization and free radical reduction on alpha-methyl-beta-alkoxy aldehydes: a general strategy for efficient polypropionate synthesis.

    PubMed

    Brazeau, Jean-François; Mochirian, Philippe; Prévost, Michel; Guindon, Yvan

    2009-01-02

    In a stereodivergent manner, all 16 diastereomeric stereopentads 7-22 were synthesized starting with alpha-methyl-beta-alkoxy aldehydes 25 and 27. We designed an approach based on a sequence of a Mukaiyama aldolization with enoxysilane 24 followed by a hydrogen transfer reaction. Recent advancements concerning these reactions are described, and novel key intermediates are characterized in the aldol step. The synthesis of C(1)-C(11) fragment 60 of zincophorin, which contains a synthetically challenging stereopentad unit, is described attesting the usefulness of our strategy.

  6. Comparative Neuroregenerative Effects of C-Phycocyanin and IFN-Beta in a Model of Multiple Sclerosis in Mice.

    PubMed

    Pentón-Rol, Giselle; Lagumersindez-Denis, Nielsen; Muzio, Luca; Bergami, Alessandra; Furlan, Roberto; Fernández-Massó, Julio R; Nazabal-Galvez, Marcelo; Llópiz-Arzuaga, Alexey; Herrera-Rolo, Tania; Veliz-Rodriguez, Tania; Polentarutti, Nadia; Marín-Prida, Javier; Raíces-Cruz, Ivette; Valenzuela-Silva, Carmen; Teixeira, Mauro Martins; Pentón-Arias, Eduardo

    2016-03-01

    Multiple Sclerosis (MS) therapies approved so far are unable to effectively reverse the chronic phase of the disease or improve the remyelination process. Here our aim is to evaluate the effects of C-Phycocyanin (C-Pc), a biliprotein from Spirulina platensis with anti-oxidant, anti-inflammatory and cytoprotective properties, in a chronic model of experimental autoimmune encephalomyelitis (EAE) in mice. C-Pc (2, 4 or 8 mg/kg i.p.) or IFN-beta (2000 IU, s.c.) was administered daily once a day or every other day, respectively, starting at disease onset, which differ among EAE mice between 11 and 15 days postinduction. Histological and immunohistochemistry (anti-Mac-3, anti-CD3 and anti-APP) assessments were performed in spinal cord in the postinduction time. Global gene expression in the brain was analyzed with the Illumina Mouse WG-6_V2 BeadChip microarray and the expression of particular genes, assessed by qPCR using the Fast SYBR Green RT-PCR Master Mix. Oxidative stress parameters (malondialdehyde, peroxidation potential, CAT/SOD ratio and GSH) were determined spectrophoto-metrically. Results showed that C-Pc ameliorates the clinical deterioration of animals, an effect that expresses the reduction of the inflammatory infiltrates invading the spinal cord tissue, the axonal preservation and the down-regulation of IL-17 expression in brain tissue and serum. C-Pc and IFN-beta improved the redox status in mice subjected to EAE, while microarray analysis showed that both treatments shared a common subset of differentially expressed genes, although they also differentially modulated another subset of genes. Specifically, C-Pc mainly modulated the expression of genes related to remyelination, gliogenesis and axon-glia processes. Taken together, our results indicate that C-Pc has significant therapeutic effects against EAE, mediated by the dynamic regulation of multiple biological processes.

  7. Toward a General Nonlinear Model of Reduced Scale UAVs

    NASA Astrophysics Data System (ADS)

    Chriette, A.; Cheviron, T.; Plestan, F.

    2009-03-01

    This paper proposes, through a survey of models of several UAV-Structures, a generic nonlinear model for reduced scale aerial robotic vehicles (6 DOF)*. Dynamics of an aircraft and some VTOL UAV (quadricopter, ducted fan and classical helicopter) are illustrated. This generic model focuses only on the key physical efforts acting on the dynamics in order to be sufficiently simple to design a controller. The Small Body Forces expression which can introduce a zero dynamics is then discussed.

  8. General model and control of an n rotor helicopter

    NASA Astrophysics Data System (ADS)

    Sidea, A. G.; Yding Brogaard, R.; Andersen, N. A.; Ravn, O.

    2014-12-01

    The purpose of this study was to create a dynamic, nonlinear mathematical model of a multirotor that would be valid for different numbers of rotors. Furthermore, a set of Single Input Single Output (SISO) controllers were implemented for attitude control. Both model and controllers were tested experimentally on a quadcopter. Using the combined model and controllers, simple system simulation and control is possible, by replacing the physical values for the individual systems.

  9. GENERAL: Self-organized Criticality Model for Ocean Internal Waves

    NASA Astrophysics Data System (ADS)

    Wang, Gang; Lin, Min; Qiao, Fang-Li; Hou, Yi-Jun

    2009-03-01

    In this paper, we present a simple spring-block model for ocean internal waves based on the self-organized criticality (SOC). The oscillations of the water blocks in the model display power-law behavior with an exponent of -2 in the frequency domain, which is similar to the current and sea water temperature spectra in the actual ocean and the universal Garrett and Munk deep ocean internal wave model [Geophysical Fluid Dynamics 2 (1972) 225; J. Geophys. Res. 80 (1975) 291]. The influence of the ratio of the driving force to the spring coefficient to SOC behaviors in the model is also discussed.

  10. A general dynamic model of flexible robot arms for control

    NASA Technical Reports Server (NTRS)

    Ding, X.; Tarn, T. J.; Bejczy, A. K.

    1989-01-01

    Hamilton's principle is used to derive the dynamic model for a large class of flexible robot arms. The resultant dynamic model consists of a system of partial differential-integral equations and the dynamic boundary conditions associated with it. Some properties of the model are observed, and its application to control is discussed. This model represents an infinite-dimensional nonlinear dynamic system and yet can be turned into a finite-dimensional system that could be obtained by modal expansion, if it is desired. This provides more flexibility for control purposes as well as for the analysis of the system.

  11. GENERAL: A modified weighted probabilistic cellular automaton traffic flow model

    NASA Astrophysics Data System (ADS)

    Zhuang, Qian; Jia, Bin; Li, Xin-Gang

    2009-08-01

    This paper modifies the weighted probabilistic cellular automaton model (Li X L, Kuang H, Song T, et al 2008 Chin. Phys. B 17 2366) which considered a diversity of traffic behaviors under real traffic situations induced by various driving characters and habits. In the new model, the effects of the velocity at the last time step and drivers' desire for acceleration are taken into account. The fundamental diagram, spatial-temporal diagram, and the time series of one-minute data are analyzed. The results show that this model reproduces synchronized flow. Finally, it simulates the on-ramp system with the proposed model. Some characteristics including the phase diagram are studied.

  12. Neutron beta decay studies with Nab

    NASA Astrophysics Data System (ADS)

    Baeßler, S.; Alarcon, R.; Alonzi, L. P.; Balascuta, S.; Barrón-Palos, L.; Bowman, J. D.; Bychkov, M. A.; Byrne, J.; Calarco, J. R.; Chupp, T.; Cianciolo, T. V.; Crawford, C.; Frlež, E.; Gericke, M. T.; Glück, F.; Greene, G. L.; Grzywacz, R. K.; Gudkov, V.; Harrison, D.; Hersman, F. W.; Ito, T.; Makela, M.; Martin, J.; McGaughey, P. L.; McGovern, S.; Page, S.; Penttilä, S. I.; Počanić, D.; Rykaczewski, K. P.; Salas-Bacci, A.; Tompkins, Z.; Wagner, D.; Wilburn, W. S.; Young, A. R.

    2013-10-01

    Precision measurements in neutron beta decay serve to determine the coupling constants of beta decay and allow for several stringent tests of the standard model. This paper discusses the design and the expected performance of the Nab spectrometer.

  13. The NASA/Ames Mars General Circulation Model: Model Improvements and Comparison with Observations

    NASA Technical Reports Server (NTRS)

    Haberle, R. M.; Hollingsworth, J. L.; Colaprete, A.; Bridger, A. F. C.; McKay, C. P.; Murphy, J. R.; Schaeffer, J.; Freedman, R.; Fonda, Mark (Technical Monitor)

    2003-01-01

    For many years, the NASA/Ames Mars General Circulation Model (GCM) has been built around the UCLA B-grid dynamical core. An attached tracer transport scheme based on the aerosol microphysical model of Toon et al. (1988) provided a tool for studying dust storm transport and feedbacks (Murphy et al., 1995). While we still use a B-grid version of the model, the Ames group is now transitioning to the ARIES/GEOS Goddard C-grid dynamical core (Suarez and Takacs, 1995). The C-grid produces smoother fields when the model top is raised above 50 km, and has a built in transport scheme for an arbitrary number of tracers. All of our transport simulations are now carried out with the C-grid. We have also been updating our physics package. Several years ago we replaced our bulk boundary layer scheme with a level 2 type diffusive scheme, and added a multi-level soil model (Haberle et al., 2000). More recently we replaced our radiation code with a more generalized two-stream code that accounts for aerosol multiple scattering and gaseous absorption. This code gives us much more flexibility in choosing aerosol optical properties and radiatively active gases.

  14. A simple biosphere model (SiB) for use within general circulation models

    NASA Technical Reports Server (NTRS)

    Sellers, P. J.; Mintz, Y.; Sud, Y. C.; Dalcher, A.

    1986-01-01

    A simple realistic biosphere model for calculating the transfer of energy, mass and momentum between the atmosphere and the vegetated surface of the earth has been developed for use in atmospheric general circulation models. The vegetation in each terrestrial model grid is represented by an upper level, representing the perennial canopy of trees and shrubs, and a lower level, representing the annual cover of grasses and other heraceous species. The vegetation morphology and the physical and physiological properties of the vegetation layers determine such properties as: the reflection, transmission, absorption and emission of direct and diffuse radiation; the infiltration, drainage, and storage of the residual rainfall in the soil; and the control over the stomatal functioning. The model, with prescribed vegetation parameters and soil interactive soil moisture, can be used for prediction of the atmospheric circulation and precipitaion fields for short periods of up to a few weeks.

  15. Evolutionary optimization of life-history traits in the sea beet Beta vulgaris subsp. maritima: Comparing model to data

    NASA Astrophysics Data System (ADS)

    Hautekèete, N.-C.; Van Dijk, H.; Piquot, Y.; Teriokhin, A.

    2009-01-01

    At evolutionary equilibrium, ecological factors will determine the optimal combination of life-history trait values of an organism. This optimum can be assessed by assuming that the species maximizes some criterion of fitness such as the Malthusian coefficient or lifetime reproductive success depending on the degree of density-dependence. We investigated the impact of the amount of resources and habitat stability on a plant's age at maturity and life span by using an evolutionary optimization model in combination with empirical data. We conducted this study on sea beet, Beta vulgaris subsp. maritima, because of its large variation in life span and age at first reproduction along a latitudinal gradient including considerable ecological variation. We also compared the consequence in our evolutionary model of maximizing either the Malthusian coefficient or the lifetime reproductive success. Both the data analysis and the results of evolutionary modeling pointed to habitat disturbance and resources like length of the growing season as factors negatively related to life span and age at maturity in sea beet. Resource availability had a negative theoretical influence with the Malthusian coefficient as the chosen optimality criterion, while there was no influence in the case of lifetime reproductive success. As suggested by previous theoretical work the final conclusion on what criterion is more adequate depends on the assumptions of how in reality density-dependence restrains population growth. In our case of sea beet data R0 seems to be less appropriate than λ.

  16. Modelling Nonlinearities and Reference Dependence in General Practitioners' Income Preferences.

    PubMed

    Holte, Jon Helgheim; Sivey, Peter; Abelsen, Birgit; Olsen, Jan Abel

    2016-08-01

    This paper tests for the existence of nonlinearity and reference dependence in income preferences for general practitioners. Confirming the theory of reference dependent utility within the context of a discrete choice experiment, we find that losses loom larger than gains in income for Norwegian general practitioners, i.e. they value losses from their current income level around three times higher than the equivalent gains. Our results are validated by comparison with equivalent contingent valuation values for marginal willingness to pay and marginal willingness to accept compensation for changes in job characteristics. Physicians' income preferences determine the effectiveness of 'pay for performance' and other incentive schemes. Our results may explain the relative ineffectiveness of financial incentive schemes that rely on increasing physicians' incomes. Copyright © 2015 John Wiley & Sons, Ltd.

  17. Cystathionine beta synthase gene dose dependent vascular remodeling in murine model of hyperhomocysteinemia.

    PubMed

    Tyagi, Neetu; Qipshidze, Natia; Sen, Utpal; Rodriguez, Walter; Ovechkin, Alexander; Tyagi, Suresh C

    2011-09-30

    Although children born with severe homocystinurea (i.e. cystathionine beta synthase homozygote knockout, CBS-/-) develop deleterious vascular complications with structural malformation and do not live past teenage, the heterozygote (CBS-/+) lives with apparently normal phenotype. Interestingly, this differential role of CBS expression in vascular remodeling is unclear. Peroxisome proliferator activated receptor gamma (PPARγ) is nuclear transcription factor that mitigates vascular complications. The hypothesis was that homocysteine (Hcy) decreased thioredoxin (Trx), peroxiredoxin (Prx), increased NADPH oxidase (NOX1), mitochondrial nitric oxide synthase (mtNOS) activity and reactive oxygen species (ROS) in mitochondria in a CBS gene dose-dependent manner. ROS transduced matrix metalloproteinase (MMP) activation causing thickening (fibrosis) of the basement membrane, rendering ineffective endothelial nitric oxide synthase (eNOS) and promoted endothelial-smooth muscle disconnection/uncoupling by antagonizing PPARγ. Wild type (WT-CBS+/+), CBS-/+ and CBS -/- mice were treated with or without ciglitazone (CZ, a PPARγ agonist) in food at birth. Aortic nuclear PPARγ expression was measured by EMSA. Aortic mtNOS activity and ROS production was measured using NO- and H(2)O(2)-electrodes, respectively. Aorta was analyzed for Trx, Prx, by Western blot, and PCR. MMP activity was by in situ zymography. Aortic function was measured in tissue myobath. The results suggested 90% morbidity in CBS-/- allele at 12 wks. However, treatment with the PPARγ agonist, CZ significantly reduced the morbidity to 20%. In addition, CZ restored the PPARγ activity in CBS-/+ and -/- mice to normal levels. The oxidative stress was alleviated by CZ treatment. In situ labeling with mito-tracker suggests co-localization of ROS with mitochondrial mitophagy. The mtNOS activity was increased in HHcy compared to WT. The data support the notion that Hcy decreases redoxins, increases mtNOS activity and

  18. Iterative Approximate Byzantine Consensus under a Generalized Fault Model

    DTIC Science & Technology

    2012-05-21

    on Principles of distributed computing , PODC ’05, pages 138–147, New York, NY, USA, 2005. ACM. [3] S. Dasgupta, C. Papadimitriou , and U. Vazirani...Iterative Approximate Byzantine Consensus under a Generalized Fault Model∗ Lewis Tseng1,3, and Nitin Vaidya2,3 1 Department of Computer Science, 2...Department of Electrical and Computer Engineering, and 3 Coordinated Science Laboratory University of Illinois at Urbana-Champaign Email: {ltseng3, nhv

  19. Using Generalized Additive Models to Analyze Single-Case Designs

    ERIC Educational Resources Information Center

    Shadish, William; Sullivan, Kristynn

    2013-01-01

    Many analyses for single-case designs (SCDs)--including nearly all the effect size indicators-- currently assume no trend in the data. Regression and multilevel models allow for trend, but usually test only linear trend and have no principled way of knowing if higher order trends should be represented in the model. This paper shows how Generalized…

  20. Crystal Model Kits for Use in the General Chemistry Laboratory.

    ERIC Educational Resources Information Center

    Kildahl, Nicholas J.; And Others

    1986-01-01

    Dynamic crystal model kits are described. Laboratory experiments in which students use these kits to build models have been extremely successful in providing them with an understanding of the three-dimensional structures of the common cubic unit cells as well as hexagonal and cubic closest-packing of spheres. (JN)

  1. GeoTess: A generalized Earth model software utility

    DOE PAGES

    Ballard, Sanford; Hipp, James; Kraus, Brian; ...

    2016-03-23

    GeoTess is a model parameterization and software support library that manages the construction, population, storage, and interrogation of data stored in 2D and 3D Earth models. Here, the software is available in Java and C++, with a C interface to the C++ library.

  2. A General Multidimensional Model for the Measurement of Cultural Differences.

    ERIC Educational Resources Information Center

    Olmedo, Esteban L.; Martinez, Sergio R.

    A multidimensional model for measuring cultural differences (MCD) based on factor analytic theory and techniques is proposed. The model assumes that a cultural space may be defined by means of a relatively small number of orthogonal dimensions which are linear combinations of a much larger number of cultural variables. Once a suitable,…

  3. RxGen General Optical Model Prescription Generator

    NASA Technical Reports Server (NTRS)

    Sigrist, Norbert

    2012-01-01

    RxGen is a prescription generator for JPL's in-house optical modeling software package called MACOS (Modeling and Analysis for Controlled Optical Systems), which is an expert optical analysis software package focusing on modeling optics on dynamic structures, deformable optics, and controlled optics. The objectives of RxGen are to simplify and automate MACOS prescription generations, reducing errors associated with creating such optical prescriptions, and improving user efficiency without requiring MACOS proficiency. RxGen uses MATLAB (a high-level language and interactive environment developed by MathWorks) as the development and deployment platform, but RxGen can easily be ported to another optical modeling/analysis platform. Running RxGen within the modeling environment has the huge benefit that variations in optical models can be made an integral part of the modeling state. For instance, optical prescription parameters determined as external functional dependencies, optical variations by controlling the in-/exclusion of optical components like sub-systems, and/or controlling the state of all components. Combining the mentioned capabilities and flexibilities with RxGen's optical abstraction layer completely eliminates the hindering aspects for requiring proficiency in writing/editing MACOS prescriptions, allowing users to focus on the modeling aspects of optical systems, i.e., increasing productivity and efficiency. RxGen provides significant enhancements to MACOS and delivers a framework for fast prototyping as well as for developing very complex controlled optical systems.

  4. Anti-inflammatory effect of alpha, beta-Amyrin, a pentacyclic triterpene from Protium heptaphyllum in rat model of acute periodontitis.

    PubMed

    Holanda Pinto, S A; Pinto, L M S; Cunha, G M A; Chaves, M H; Santos, F A; Rao, V S

    2008-02-01

    This study was aimed to evaluate the anti-inflammatory potential of triterpene alpha, beta-amyrin in rats on acute phase periodontitis. Periodontitis was induced by ligature placement around the maxillary right second molar tooth. Rats (n = 8/group) were pretreated with alpha, beta-amyrin (5 and 10 mg/kg, p. o.), two hours before the induction of periodontal inflammation. Sham-operated and positive controls (lumiracoxib and dexamethasone) were included. Six hours later, plasma levels of TNF-alpha were analysed. Rats were sacrificed at 24 h, and the gingival tissue analysed for myeloperoxidase (MPO) and thiobarbituric acid-reactive substances (TBARS), as measures of neutrophil influx and lipid-peroxidation, respectively alpha, beta-Amyrin as well as dexamethasone significantly inhibited the periodontitis-associated increases of TNF-alpha, and the gingival MPO and TBARS. alpha, beta-Amyrin effect was more prominent at 5 mg/kg. Lumiracoxib manifested varied influence on the studied parameters. These results provide evidence to show that alpha, beta-Amyrin retards acute inflammation in rat model of periodontitis and warrant further study on its efficacy to prevent chronic periodontitis-associated bone loss.

  5. Highly potent and specific GSK-3beta inhibitors that block tau phosphorylation and decrease alpha-synuclein protein expression in a cellular model of Parkinson's disease.

    PubMed

    Kozikowski, Alan P; Gaisina, Irina N; Petukhov, Pavel A; Sridhar, Jayalakshmi; King, LaShaunda T; Blond, Sylvie Y; Duka, Tetyana; Rusnak, Milan; Sidhu, Anita

    2006-02-01

    Research by Klein and co-workers suggests that the inhibition of GSK-3beta by small molecules may offer an important strategy in the treatment of a number of central nervous system (CNS) disorders including Alzheimer's disease, Parkinson's disease, and bipolar disorders. Based on results from kinase-screening assays that identified a staurosporine analogue as a modest inhibitor of GSK-3beta, a series of 3-indolyl-4-indazolylmaleimides was prepared for study in both enzymatic and cell-based assays. Most strikingly, whereas we identified ligands having poor to high potency for GSK-3beta inhibition, only ligands with a Ki value of less than 8 nM, namely maleimides 18 and 22, were found to inhibit Tau phosphorylation at a GSK-3beta-specific site (Ser 396/404). Accordingly, maleimides 18 and 22 may protect neuronal cells against cell death by decreasing the level of alpha-Syn protein expression. We conclude that the GSK-3beta inhibitors described herein offer promise in defending cells against MPP+-induced neurotoxicity and that such compounds will be valuable to explore in animal models of Parkinson's disease as well as in other Tau-related neurodegenerative disease states.

  6. Regional myocardial downregulation of the inhibitory guanosine triphosphate-binding protein (Gi alpha 2) and beta-adrenergic receptors in a porcine model of chronic episodic myocardial ischemia.

    PubMed Central

    Hammond, H K; Roth, D A; McKirnan, M D; Ping, P

    1993-01-01

    Regional myocardial ischemia is associated with increased levels of adenosine and norepinephrine, factors that may alter activation of the beta-adrenergic receptor (beta AR)-G protein-adenylyl cyclase pathway in the heart. We have used the ameroid constrictor model to determine whether alterations in myocardial signal transduction through the beta AR-G protein-adenylyl cyclase pathway occur in the setting of chronic episodes of reversible ischemia. Pigs were instrumented with ameroid occluders placed around the left circumflex coronary artery. 5 wk later, after ameroid closure, flow and function were normal in the ischemic bed, but flow (P = 0.001) and function (P < 0.03) were abnormal when metabolic demands were increased. The ischemic bed showed a reduction in myocardial beta AR number (P < 0.005). Despite regional downregulation of myocardial beta AR number, adenylyl cyclase activity was similar in the ischemic and control beds. Quantitative immunoblotting showed that the cardiac inhibitory GTP-binding protein, Gi alpha 2, was decreased in the ischemic bed (P = 0.02). In contrast, the cardiac stimulatory GTP-binding protein, Gs alpha, was increased in endocardial sections from the ischemic bed (P = < 0.05). Decreased Gi alpha 2 content was associated with decreased inhibition of adenylyl cyclase. Reduced Gi alpha 2 content, in conjunction with increased Gs alpha content in the endocardium, may provide a means by which adrenergic activation is maintained in the setting of chronic episodic myocardial ischemia. Images PMID:8254020

  7. Estimation of electrokinetic and hydrodynamic global properties of relevant amyloid-beta peptides through the modeling of their effective electrophoretic mobilities and analysis of their propensities to aggregation.

    PubMed

    Deiber, Julio A; Piaggio, Maria V; Peirotti, Marta B

    2014-09-01

    Neuronal activity loss may be due to toxicity caused by amyloid-beta peptides forming soluble oligomers. Here amyloid-beta peptides (1-42, 1-40, 1-39, 1-38, and 1-37) are characterized through the modeling of their experimental effective electrophoretic mobilities determined by a capillary zone electrophoresis method as reported in the literature. The resulting electrokinetic and hydrodynamic global properties are used to evaluate amyloid-beta peptide propensities to aggregation through pair particles interaction potentials and Brownian aggregation kinetic theories. Two background electrolytes are considered at 25°C, one for pH 9 and ionic strength I = 40 mM (aggregation is inhibited through NH4OH) the other for pH 10 and I = 100 mM (without NH4OH). Physical explanations of peptide oligomerization mechanisms are provided. The effect of hydration, electrostatic, and dispersion forces in the amyloidogenic process of amyloid-beta peptides (1-40 and 1-42) are quantitatively presented. The interplay among effective charge number, hydration, and conformation of chains is described. It is shown that amyloid-beta peptides (1-40 and 1-42) at pH 10, I = 100 mM and 25°C, may form soluble oligomers, mainly of order 2 and 4, after an incubation of 48 h, which at higher times evolve and end up in complex structures (protofibrils and fibrils) found in plaques associated with Alzheimer's disease.

  8. A General Reversible Hereditary Constitutive Model. Part 1; Theoretical Developments

    NASA Technical Reports Server (NTRS)

    Saleeb, A. F.; Arnold, S. M.

    1997-01-01

    Using an internal-variable formalism as a starting point, we describe the viscoelastic extension of a previously-developed viscoplasticity formulation of the complete potential structure type. It is mainly motivated by experimental evidence for the presence of rate/time effects in the so-called quasilinear, reversible, material response range. Several possible generalizations are described, in the general format of hereditary-integral representations for non-equilibrium, stress-type, state variables, both for isotropic as well as anisotropic materials. In particular, thorough discussions are given on the important issues of thermodynamic admissibility requirements for such general descriptions, resulting in a set of explicit mathematical constraints on the associated kernel (relaxation and creep compliance) functions. In addition, a number of explicit, integrated forms are derived, under stress and strain control to facilitate the parametric and qualitative response characteristic studies reported here, as well as to help identify critical factors in the actual experimental characterizations from test data that will be reported in Part II.

  9. A generalized model for stability of trees under impact conditions

    NASA Astrophysics Data System (ADS)

    Dattola, Giuseppe; Crosta, Giovanni; Castellanza, Riccardo; di Prisco, Claudio; Canepa, Davide

    2016-04-01

    Stability of trees to external actions involve the combined effects of stem and tree root systems. A block impacting on the stem or an applied force pulling the stem can cause a tree instability involving stem bending or failure and tree root rotation. So different contributions are involved in the stability of the system. The rockfalls are common natural phenomena that can be unpredictable in terms of frequency and magnitude characteristics, and this makes difficult the estimate of potential hazard and risk for human lives and activities. In mountain areas a natural form of protection from rockfalls is provided by forest growing. The difficulties in the assessment of the real capability of this natural barrier by means of models is an open problem. Nevertheless, a large amount of experimental data are now available which provides support for the development of advanced theoretical framework and corresponding models. The aim of this contribution consists in presenting a model developed to predict the behavior of trees during a block impact. This model describes the tree stem by means of a linear elastic beam system consisting of two beams connected in series and with an equivalent geometry. The tree root system is described via an equivalent foundation, whose behavior is modelled through an elasto-plastic macro-element model. In order to calibrate the model parameters, simulations reproducing a series of winching tests, are performed. These numerical simulations confirm the capability of the model to predict the mechanical behavior of the stem-root system in terms of displacement vs force curves. Finally, numerical simulations of the impact of a boulder with a tree stem are carried out. These simulations, done under dynamic regime and with the model parameters obtained from the previous set of simulations, confirm the capability of the model to reproduce the effects on the stem-roots system generated by impulsive loads.

  10. Generating Dichotomous Item Scores with the Four-Parameter Beta Compound Binomial Model

    ERIC Educational Resources Information Center

    Monahan, Patrick O.; Lee, Won-Chan; Ankenmann, Robert D.

    2007-01-01

    A Monte Carlo simulation technique for generating dichotomous item scores is presented that implements (a) a psychometric model with different explicit assumptions than traditional parametric item response theory (IRT) models, and (b) item characteristic curves without restrictive assumptions concerning mathematical form. The four-parameter beta…

  11. General solutions of integrable cosmological models with non-minimal coupling

    NASA Astrophysics Data System (ADS)

    Kamenshchik, A. Yu.; Pozdeeva, E. O.; Tronconi, A.; Venturi, G.; Vernov, S. Yu.

    2017-03-01

    We study the integrable model with minimally and non-minimally coupled scalar fields and the correspondence of their general solutions. Using the model with a minimally coupled scalar field and a the constant potential as an example we demonstrate the difference between the general solutions of the corresponding models in the Jordan and the Einstein frames.

  12. Modified Likelihood-Based Item Fit Statistics for the Generalized Graded Unfolding Model

    ERIC Educational Resources Information Center

    Roberts, James S.

    2008-01-01

    Orlando and Thissen (2000) developed an item fit statistic for binary item response theory (IRT) models known as S-X[superscript 2]. This article generalizes their statistic to polytomous unfolding models. Four alternative formulations of S-X[superscript 2] are developed for the generalized graded unfolding model (GGUM). The GGUM is a…

  13. Monte Carlo Models for the Production of beta-delayed Gamma Rays Following Fission of Special Nuclear Materials

    SciTech Connect

    Pruet, J; Prussin, S; Descalle, M; Hall, J

    2004-02-03

    A Monte Carlo method for the estimation of {beta}-delayed {gamma}-ray spectra following fission is described that can accommodate an arbitrary time-dependent fission rate and photon collection history. The method invokes direct sampling of the independent fission yield distributions of the fissioning system, the branching ratios for decay of individual fission products and the spectral distributions for photon emission for each decay mode. Though computationally intensive, the method can provide a detailed estimate of the spectrum that would be recorded by an arbitrary spectrometer, and can prove useful in assessing the quality of evaluated data libraries, for identifying gaps in these libraries, etc. The method is illustrated by a first comparison of calculated and experimental spectra from decay of short-lived fission products following the reactions {sup 235}U(n{sub th}, f) and {sup 239}Pu(n{sub th}, f). For general purpose transport calculations, where detailed consideration of the large number of individual {gamma}-ray transitions in a spectrum may be unnecessary, it is shown that an accurate and simple parameterization of a {gamma}-ray source function can be obtained. These parametrizations should provide high-quality average spectral distributions that should prove useful in calculations describing photons escaping from thick attenuating media.

  14. Does the Interpersonal Model Generalize to Obesity Without Binge Eating?

    PubMed

    Lo Coco, Gianluca; Sutton, Rachel; Tasca, Giorgio A; Salerno, Laura; Oieni, Veronica; Compare, Angelo

    2016-09-01

    The interpersonal model has been validated for binge eating disorder (BED), but it is not yet known if the model applies to individuals who are obese but who do not binge eat. The goal of this study was to compare the validity of the interpersonal model in those with BED versus those with obesity, and normal weight samples. Data from a sample of 93 treatment-seeking women diagnosed with BED, 186 women who were obese without BED, and 100 controls who were normal weight were examined for indirect effects of interpersonal problems on binge eating psychopathology mediated through negative affect. Findings demonstrated the mediating role of negative affect for those with BED and those who were obese without BED. Testing a reverse model suggested that the interpersonal model is specific for BED but that this model may not be specific for those without BED. This is the first study to find support for the interpersonal model in a sample of women with obesity but who do not binge. However, negative affect likely plays a more complex role in determining overeating in those with obesity but who do not binge. Copyright © 2016 John Wiley & Sons, Ltd and Eating Disorders Association.

  15. GENERAL REQUIREMENTS FOR SIMULATION MODELS IN WASTE MANAGEMENT

    SciTech Connect

    Miller, Ian; Kossik, Rick; Voss, Charlie

    2003-02-27

    Most waste management activities are decided upon and carried out in a public or semi-public arena, typically involving the waste management organization, one or more regulators, and often other stakeholders and members of the public. In these environments, simulation modeling can be a powerful tool in reaching a consensus on the best path forward, but only if the models that are developed are understood and accepted by all of the parties involved. These requirements for understanding and acceptance of the models constrain the appropriate software and model development procedures that are employed. This paper discusses requirements for both simulation software and for the models that are developed using the software. Requirements for the software include transparency, accessibility, flexibility, extensibility, quality assurance, ability to do discrete and/or continuous simulation, and efficiency. Requirements for the models that are developed include traceability, transparency, credibility/validity, and quality control. The paper discusses these requirements with specific reference to the requirements for performance assessment models that are used for predicting the long-term safety of waste disposal facilities, such as the proposed Yucca Mountain repository.

  16. FBST for covariance structures of generalized Gompertz models

    NASA Astrophysics Data System (ADS)

    Maranhão, Viviane Teles de Lucca; Lauretto, Marcelo De Souza; Stern, Julio Michael

    2012-10-01

    The Gompertz distribution is commonly used in biology for modeling fatigue and mortality. This paper studies a class of models proposed by Adham and Walker, featuring a Gompertz type distribution where the dependence structure is modeled by a lognormal distribution, and develops a new multivariate formulation that facilitates several numerical and computational aspects. This paper also implements the FBST, the Full Bayesian Significance Test for pertinent sharp (precise) hypotheses on the lognormal covariance structure. The FBST's e-value, ev(H), gives the epistemic value of hypothesis, H, or the value of evidence in the observed in support of H.

  17. Computable general equilibrium model fiscal year 2014 capability development report

    SciTech Connect

    Edwards, Brian Keith; Boero, Riccardo

    2016-05-11

    This report provides an overview of the development of the NISAC CGE economic modeling capability since 2012. This capability enhances NISAC's economic modeling and analysis capabilities to answer a broader set of questions than possible with previous economic analysis capability. In particular, CGE modeling captures how the different sectors of the economy, for example, households, businesses, government, etc., interact to allocate resources in an economy and this approach captures these interactions when it is used to estimate the economic impacts of the kinds of events NISAC often analyzes.

  18. Targeting tumor-associated macrophages in an experimental glioma model with a recombinant immunotoxin to folate receptor beta.

    PubMed

    Nagai, Taku; Tanaka, Masashi; Tsuneyoshi, Yasuhiro; Xu, Baohui; Michie, Sara A; Hasui, Kazuhisa; Hirano, Hirofumi; Arita, Kazunori; Matsuyama, Takami

    2009-10-01

    Tumor-associated macrophages (TAMs) are frequently found in glioblastomas and a high degree of macrophage infiltration is associated with a poor prognosis for glioblastoma patients. However, it is unclear whether TAMs in glioblastomas promote tumor growth. In this study, we found that folate receptor beta (FR beta) was expressed on macrophages in human glioblastomas and a rat C6 glioma implanted subcutaneously in nude mice. To target FR beta-expressing TAMs, we produced a recombinant immunotoxin consisting of immunoglobulin heavy and light chain Fv portions of an anti-mouse FR beta monoclonal antibody and Pseudomonas exotoxin A. Injection of the immunotoxin into C6 glioma xenografts in nude mice significantly depleted TAMs and reduced tumor growth. The immunotoxin targeting FR beta-expressing macrophages will provide a therapeutic tool for human glioblastomas.

  19. A general method for modeling biochemical and biomedical response

    NASA Astrophysics Data System (ADS)

    Ortiz, Roberto; Lerd Ng, Jia; Hughes, Tyler; Abou Ghantous, Michel; Bouhali, Othmane; Arredouani, Abdelilah; Allen, Roland

    2012-10-01

    The impressive achievements of biomedical science have come mostly from experimental research with human subjects, animal models, and sophisticated laboratory techniques. Additionally, theoretical chemistry has been a major aid in designing new drugs. Here we introduce a method which is similar to others already well known in theoretical systems biology, but which specifically addresses biochemical changes as the human body responds to medical interventions. It is common in systems biology to use first-order differential equations to model the time evolution of various chemical concentrations, and we as physicists can make a significant impact through designing realistic models and then solving the resulting equations. Biomedical research is rapidly advancing, and the technique presented in this talk can be applied in arbitrarily large models containing tens, hundreds, or even thousands of interacting species, to determine what beneficial effects and side effects may result from pharmaceuticals or other medical interventions.

  20. The cerebellum as an adaptive filter: a general model?

    PubMed

    Dean, Paul; Porrill, John

    2010-01-01

    Many functional models of the cerebellar microcircuit are based on the adaptive-filter model first proposed by Fujita. The adaptive filter has powerful signal processing capacities that are suitable for both sensory and motor tasks, and uses a simple and intuitively plausible decorrelation learning rule that offers and account of the evolution of the inferior olive. Moreover, in those cases where the input-output transformations of cerebellar microzones have been sufficiently characterised, they appear to conform to those predicted by the adaptive-filter model. However, these cases are few in number, and comparing the model with the internal operations of the microcircuit itself has not proved straightforward. Whereas some microcircuit features appear compatible with adaptive-filter function, others such as simple granular-layer processing or Purkinje cell bistability, do not. How far these seeming incompatibilities indicate additional computational roles for the cerebellar microcircuit remains to be determined.