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Sample records for adequate model fit

  1. The Air Force Physical Fitness Program is it Adequate?

    DTIC Science & Technology

    1999-04-01

    20 Table 3 Cardiovascular Fitness Classifications ( American Heart Association ). ...............20 Table 4 Norms... American Heart Association ). These two factors are high blood pressure and poor blood cholesterol levels.5 A study done at Stanford University showed that...and Rhyming, defined them and table 3 shows the American Heart Association �s classifications. Table 1 Air Force Fitness Standards.6 Minimum VO2 score

  2. Adequate mathematical modelling of environmental processes

    NASA Astrophysics Data System (ADS)

    Chashechkin, Yu. D.

    2012-04-01

    In environmental observations and laboratory visualization both large scale flow components like currents, jets, vortices, waves and a fine structure are registered (different examples are given). The conventional mathematical modeling both analytical and numerical is directed mostly on description of energetically important flow components. The role of a fine structures is still remains obscured. A variety of existing models makes it difficult to choose the most adequate and to estimate mutual assessment of their degree of correspondence. The goal of the talk is to give scrutiny analysis of kinematics and dynamics of flows. A difference between the concept of "motion" as transformation of vector space into itself with a distance conservation and the concept of "flow" as displacement and rotation of deformable "fluid particles" is underlined. Basic physical quantities of the flow that are density, momentum, energy (entropy) and admixture concentration are selected as physical parameters defined by the fundamental set which includes differential D'Alembert, Navier-Stokes, Fourier's and/or Fick's equations and closing equation of state. All of them are observable and independent. Calculations of continuous Lie groups shown that only the fundamental set is characterized by the ten-parametric Galilelian groups reflecting based principles of mechanics. Presented analysis demonstrates that conventionally used approximations dramatically change the symmetries of the governing equations sets which leads to their incompatibility or even degeneration. The fundamental set is analyzed taking into account condition of compatibility. A high order of the set indicated on complex structure of complete solutions corresponding to physical structure of real flows. Analytical solutions of a number problems including flows induced by diffusion on topography, generation of the periodic internal waves a compact sources in week-dissipative media as well as numerical solutions of the same

  3. Are Physical Education Majors Models for Fitness?

    ERIC Educational Resources Information Center

    Kamla, James; Snyder, Ben; Tanner, Lori; Wash, Pamela

    2012-01-01

    The National Association of Sport and Physical Education (NASPE) (2002) has taken a firm stance on the importance of adequate fitness levels of physical education teachers stating that they have the responsibility to model an active lifestyle and to promote fitness behaviors. Since the NASPE declaration, national initiatives like Let's Move…

  4. Arabidopsis: an adequate model for dicot root systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the search for answers to pressing root developmental genetic issues, plant science has turned to a small genome dicot plant (Arabidopsis) to be used as a model to study and use to develop hypotheses for testing other species. Through out the published research only three classes of root are des...

  5. Measured, modeled, and causal conceptions of fitness.

    PubMed

    Abrams, Marshall

    2012-01-01

    THIS PAPER PROPOSES PARTIAL ANSWERS TO THE FOLLOWING QUESTIONS: in what senses can fitness differences plausibly be considered causes of evolution?What relationships are there between fitness concepts used in empirical research, modeling, and abstract theoretical proposals? How does the relevance of different fitness concepts depend on research questions and methodological constraints? The paper develops a novel taxonomy of fitness concepts, beginning with type fitness (a property of a genotype or phenotype), token fitness (a property of a particular individual), and purely mathematical fitness. Type fitness includes statistical type fitness, which can be measured from population data, and parametric type fitness, which is an underlying property estimated by statistical type fitnesses. Token fitness includes measurable token fitness, which can be measured on an individual, and tendential token fitness, which is assumed to be an underlying property of the individual in its environmental circumstances. Some of the paper's conclusions can be outlined as follows: claims that fitness differences do not cause evolution are reasonable when fitness is treated as statistical type fitness, measurable token fitness, or purely mathematical fitness. Some of the ways in which statistical methods are used in population genetics suggest that what natural selection involves are differences in parametric type fitnesses. Further, it's reasonable to think that differences in parametric type fitness can cause evolution. Tendential token fitnesses, however, are not themselves sufficient for natural selection. Though parametric type fitnesses are typically not directly measurable, they can be modeled with purely mathematical fitnesses and estimated by statistical type fitnesses, which in turn are defined in terms of measurable token fitnesses. The paper clarifies the ways in which fitnesses depend on pragmatic choices made by researchers.

  6. Total force fitness: the military family fitness model.

    PubMed

    Bowles, Stephen V; Pollock, Liz Davenport; Moore, Monique; Wadsworth, Shelley MacDermid; Cato, Colanda; Dekle, Judith Ward; Meyer, Sonia Wei; Shriver, Amber; Mueller, Bill; Stephens, Mark; Seidler, Dustin A; Sheldon, Joseph; Picano, James; Finch, Wanda; Morales, Ricardo; Blochberger, Sean; Kleiman, Matthew E; Thompson, Daniel; Bates, Mark J

    2015-03-01

    The military lifestyle can create formidable challenges for military families. This article describes the Military Family Fitness Model (MFFM), a comprehensive model aimed at enhancing family fitness and resilience across the life span. This model is intended for use by Service members, their families, leaders, and health care providers but also has broader applications for all families. The MFFM has three core components: (1) family demands, (2) resources (including individual resources, family resources, and external resources), and (3) family outcomes (including related metrics). The MFFM proposes that resources from the individual, family, and external areas promote fitness, bolster resilience, and foster well-being for the family. The MFFM highlights each resource level for the purpose of improving family fitness and resilience over time. The MFFM both builds on existing family strengths and encourages the development of new family strengths through resource-acquiring behaviors. The purpose of this article is to (1) expand the military's Total Force Fitness (TFF) intent as it relates to families and (2) offer a family fitness model. This article will summarize relevant evidence, provide supportive theory, describe the model, and proffer metrics that support the dimensions of this model.

  7. Using Multitheory Model of Health Behavior Change to Predict Adequate Sleep Behavior.

    PubMed

    Knowlden, Adam P; Sharma, Manoj; Nahar, Vinayak K

    The purpose of this article was to use the multitheory model of health behavior change in predicting adequate sleep behavior in college students. A valid and reliable survey was administered in a cross-sectional design (n = 151). For initiation of adequate sleep behavior, the construct of behavioral confidence (P < .001) was found to be significant and accounted for 24.4% of the variance. For sustenance of adequate sleep behavior, changes in social environment (P < .02), emotional transformation (P < .001), and practice for change (P < .001) were significant and accounted for 34.2% of the variance.

  8. Coaches as Fitness Role Models

    ERIC Educational Resources Information Center

    Nichols, Randall; Zillifro, Traci D.; Nichols, Ronald; Hull, Ethan E.

    2012-01-01

    The lack of physical activity, low fitness levels, and elevated obesity rates as high as 32% of today's youth are well documented. Many strategies and grants have been developed at the national, regional, and local levels to help counteract these current trends. Strategies have been developed and implemented for schools, households (parents), and…

  9. Sensitivity of Fit Indices to Model Misspecification and Model Types

    ERIC Educational Resources Information Center

    Fan, Xitao; Sivo, Stephen A.

    2007-01-01

    The search for cut-off criteria of fit indices for model fit evaluation (e.g., Hu & Bentler, 1999) assumes that these fit indices are sensitive to model misspecification, but not to different types of models. If fit indices were sensitive to different types of models that are misspecified to the same degree, it would be very difficult to establish…

  10. Evaluation of Model Fit in Cognitive Diagnosis Models

    ERIC Educational Resources Information Center

    Hu, Jinxiang; Miller, M. David; Huggins-Manley, Anne Corinne; Chen, Yi-Hsin

    2016-01-01

    Cognitive diagnosis models (CDMs) estimate student ability profiles using latent attributes. Model fit to the data needs to be ascertained in order to determine whether inferences from CDMs are valid. This study investigated the usefulness of some popular model fit statistics to detect CDM fit including relative fit indices (AIC, BIC, and CAIC),…

  11. Biomedical model fitting and error analysis.

    PubMed

    Costa, Kevin D; Kleinstein, Steven H; Hershberg, Uri

    2011-09-20

    This Teaching Resource introduces students to curve fitting and error analysis; it is the second of two lectures on developing mathematical models of biomedical systems. The first focused on identifying, extracting, and converting required constants--such as kinetic rate constants--from experimental literature. To understand how such constants are determined from experimental data, this lecture introduces the principles and practice of fitting a mathematical model to a series of measurements. We emphasize using nonlinear models for fitting nonlinear data, avoiding problems associated with linearization schemes that can distort and misrepresent the data. To help ensure proper interpretation of model parameters estimated by inverse modeling, we describe a rigorous six-step process: (i) selecting an appropriate mathematical model; (ii) defining a "figure-of-merit" function that quantifies the error between the model and data; (iii) adjusting model parameters to get a "best fit" to the data; (iv) examining the "goodness of fit" to the data; (v) determining whether a much better fit is possible; and (vi) evaluating the accuracy of the best-fit parameter values. Implementation of the computational methods is based on MATLAB, with example programs provided that can be modified for particular applications. The problem set allows students to use these programs to develop practical experience with the inverse-modeling process in the context of determining the rates of cell proliferation and death for B lymphocytes using data from BrdU-labeling experiments.

  12. Evaluating Model Fit for Growth Curve Models: Integration of Fit Indices from SEM and MLM Frameworks

    ERIC Educational Resources Information Center

    Wu, Wei; West, Stephen G.; Taylor, Aaron B.

    2009-01-01

    Evaluating overall model fit for growth curve models involves 3 challenging issues. (a) Three types of longitudinal data with different implications for model fit may be distinguished: balanced on time with complete data, balanced on time with data missing at random, and unbalanced on time. (b) Traditional work on fit from the structural equation…

  13. Matching occupation and self: does matching theory adequately model children's thinking?

    PubMed

    Watson, Mark; McMahon, Mary

    2004-10-01

    The present exploratory-descriptive cross-national study focused on the career development of 11- to 14-yr.-old children, in particular whether they can match their personal characteristics with their occupational aspirations. Further, the study explored whether their matching may be explained in terms of a fit between person and environment using Holland's theory as an example. Participants included 511 South African and 372 Australian children. Findings relate to two items of the Revised Career Awareness Survey that require children to relate personal-social knowledge to their favorite occupation. Data were analyzed in three stages using descriptive statistics, i.e., mean scores, frequencies, and percentage agreement. The study indicated that children perceived their personal characteristics to be related to their occupational aspirations. However, how this matching takes place is not adequately accounted for in terms of a career theory such as that of Holland.

  14. Fitting Neuron Models to Spike Trains

    PubMed Central

    Rossant, Cyrille; Goodman, Dan F. M.; Fontaine, Bertrand; Platkiewicz, Jonathan; Magnusson, Anna K.; Brette, Romain

    2011-01-01

    Computational modeling is increasingly used to understand the function of neural circuits in systems neuroscience. These studies require models of individual neurons with realistic input–output properties. Recently, it was found that spiking models can accurately predict the precisely timed spike trains produced by cortical neurons in response to somatically injected currents, if properly fitted. This requires fitting techniques that are efficient and flexible enough to easily test different candidate models. We present a generic solution, based on the Brian simulator (a neural network simulator in Python), which allows the user to define and fit arbitrary neuron models to electrophysiological recordings. It relies on vectorization and parallel computing techniques to achieve efficiency. We demonstrate its use on neural recordings in the barrel cortex and in the auditory brainstem, and confirm that simple adaptive spiking models can accurately predict the response of cortical neurons. Finally, we show how a complex multicompartmental model can be reduced to a simple effective spiking model. PMID:21415925

  15. Students' Models of Curve Fitting: A Models and Modeling Perspective

    ERIC Educational Resources Information Center

    Gupta, Shweta

    2010-01-01

    The Models and Modeling Perspectives (MMP) has evolved out of research that began 26 years ago. MMP researchers use Model Eliciting Activities (MEAs) to elicit students' mental models. In this study MMP was used as the conceptual framework to investigate the nature of students' models of curve fitting in a problem-solving environment consisting of…

  16. Cost Effectiveness of Screening Colonoscopy Depends on Adequate Bowel Preparation Rates – A Modeling Study

    PubMed Central

    Kingsley, James; Karanth, Siddharth; Revere, Frances Lee

    2016-01-01

    Background Inadequate bowel preparation during screening colonoscopy necessitates repeating colonoscopy. Studies suggest inadequate bowel preparation rates of 20–60%. This increases the cost of colonoscopy for our society. Aim The aim of this study is to determine the impact of inadequate bowel preparation rate on the cost effectiveness of colonoscopy compared to other screening strategies for colorectal cancer (CRC). Methods A microsimulation model of CRC screening strategies for the general population at average risk for CRC. The strategies include fecal immunochemistry test (FIT) every year, colonoscopy every ten years, sigmoidoscopy every five years, or stool DNA test every 3 years. The screening could be performed at private practice offices, outpatient hospitals, and ambulatory surgical centers. Results At the current assumed inadequate bowel preparation rate of 25%, the cost of colonoscopy as a screening strategy is above society’s willingness to pay (<$50,000/QALY). Threshold analysis demonstrated that an inadequate bowel preparation rate of 13% or less is necessary before colonoscopy is considered more cost effective than FIT. At inadequate bowel preparation rates of 25%, colonoscopy is still more cost effective compared to sigmoidoscopy and stool DNA test. Sensitivity analysis of all inputs adjusted by ±10% showed incremental cost effectiveness ratio values were influenced most by the specificity, adherence, and sensitivity of FIT and colonoscopy. Conclusions Screening colonoscopy is not a cost effective strategy when compared with fecal immunochemical test, as long as the inadequate bowel preparation rate is greater than 13%. PMID:27936028

  17. A Stepwise Fitting Procedure for automated fitting of Ecopath with Ecosim models

    NASA Astrophysics Data System (ADS)

    Scott, Erin; Serpetti, Natalia; Steenbeek, Jeroen; Heymans, Johanna Jacomina

    The Stepwise Fitting Procedure automates testing of alternative hypotheses used for fitting Ecopath with Ecosim (EwE) models to observation reference data (Mackinson et al. 2009). The calibration of EwE model predictions to observed data is important to evaluate any model that will be used for ecosystem based management. Thus far, the model fitting procedure in EwE has been carried out manually: a repetitive task involving setting > 1000 specific individual searches to find the statistically 'best fit' model. The novel fitting procedure automates the manual procedure therefore producing accurate results and lets the modeller concentrate on investigating the 'best fit' model for ecological accuracy.

  18. A predictive fitness model for influenza

    NASA Astrophysics Data System (ADS)

    Łuksza, Marta; Lässig, Michael

    2014-03-01

    The seasonal human influenza A/H3N2 virus undergoes rapid evolution, which produces significant year-to-year sequence turnover in the population of circulating strains. Adaptive mutations respond to human immune challenge and occur primarily in antigenic epitopes, the antibody-binding domains of the viral surface protein haemagglutinin. Here we develop a fitness model for haemagglutinin that predicts the evolution of the viral population from one year to the next. Two factors are shown to determine the fitness of a strain: adaptive epitope changes and deleterious mutations outside the epitopes. We infer both fitness components for the strains circulating in a given year, using population-genetic data of all previous strains. From fitness and frequency of each strain, we predict the frequency of its descendent strains in the following year. This fitness model maps the adaptive history of influenza A and suggests a principled method for vaccine selection. Our results call for a more comprehensive epidemiology of influenza and other fast-evolving pathogens that integrates antigenic phenotypes with other viral functions coupled by genetic linkage.

  19. A predictive fitness model for influenza.

    PubMed

    Luksza, Marta; Lässig, Michael

    2014-03-06

    The seasonal human influenza A/H3N2 virus undergoes rapid evolution, which produces significant year-to-year sequence turnover in the population of circulating strains. Adaptive mutations respond to human immune challenge and occur primarily in antigenic epitopes, the antibody-binding domains of the viral surface protein haemagglutinin. Here we develop a fitness model for haemagglutinin that predicts the evolution of the viral population from one year to the next. Two factors are shown to determine the fitness of a strain: adaptive epitope changes and deleterious mutations outside the epitopes. We infer both fitness components for the strains circulating in a given year, using population-genetic data of all previous strains. From fitness and frequency of each strain, we predict the frequency of its descendent strains in the following year. This fitness model maps the adaptive history of influenza A and suggests a principled method for vaccine selection. Our results call for a more comprehensive epidemiology of influenza and other fast-evolving pathogens that integrates antigenic phenotypes with other viral functions coupled by genetic linkage.

  20. Fitting models to correlated data (large samples)

    NASA Astrophysics Data System (ADS)

    Féménias, Jean-Louis

    2004-03-01

    The study of the ordered series of residuals of a fit proved to be useful in evaluating separately the pure experimental error and the model bias leading to a possible improvement of the modeling [J. Mol. Spectrosc. 217 (2003) 32]. In the present work this procedure is extended to homogeneous correlated data. This new method allows a separate estimation of pure experimental error, model bias, and data correlation; furthermore, it brings a new insight into the difference between goodness of fit and model relevance. It can be considered either as a study of 'random systematic errors' or as an extended approach of the Durbin-Watson problem [Biometrika 37 (1950) 409] taking into account the model error. In the present work an empirical approach is proposed for large samples ( n⩾500) where numerical tests are done showing the accuracy and the limits of the method.

  1. Modeling and Fitting Exoplanet Transit Light Curves

    NASA Astrophysics Data System (ADS)

    Millholland, Sarah; Ruch, G. T.

    2013-01-01

    We present a numerical model along with an original fitting routine for the analysis of transiting extra-solar planet light curves. Our light curve model is unique in several ways from other available transit models, such as the analytic eclipse formulae of Mandel & Agol (2002) and Giménez (2006), the modified Eclipsing Binary Orbit Program (EBOP) model implemented in Southworth’s JKTEBOP code (Popper & Etzel 1981; Southworth et al. 2004), or the transit model developed as a part of the EXOFAST fitting suite (Eastman et al. in prep.). Our model employs Keplerian orbital dynamics about the system’s center of mass to properly account for stellar wobble and orbital eccentricity, uses a unique analytic solution derived from Kepler’s Second Law to calculate the projected distance between the centers of the star and planet, and calculates the effect of limb darkening using a simple technique that is different from the commonly used eclipse formulae. We have also devised a unique Monte Carlo style optimization routine for fitting the light curve model to observed transits. We demonstrate that, while the effect of stellar wobble on transit light curves is generally small, it becomes significant as the planet to stellar mass ratio increases and the semi-major axes of the orbits decrease. We also illustrate the appreciable effects of orbital ellipticity on the light curve and the necessity of accounting for its impacts for accurate modeling. We show that our simple limb darkening calculations are as accurate as the analytic equations of Mandel & Agol (2002). Although our Monte Carlo fitting algorithm is not as mathematically rigorous as the Markov Chain Monte Carlo based algorithms most often used to determine exoplanetary system parameters, we show that it is straightforward and returns reliable results. Finally, we show that analyses performed with our model and optimization routine compare favorably with exoplanet characterizations published by groups such as the

  2. Model-based estimation of individual fitness

    USGS Publications Warehouse

    Link, W.A.; Cooch, E.G.; Cam, E.

    2002-01-01

    Fitness is the currency of natural selection, a measure of the propagation rate of genotypes into future generations. Its various definitions have the common feature that they are functions of survival and fertility rates. At the individual level, the operative level for natural selection, these rates must be understood as latent features, genetically determined propensities existing at birth. This conception of rates requires that individual fitness be defined and estimated by consideration of the individual in a modelled relation to a group of similar individuals; the only alternative is to consider a sample of size one, unless a clone of identical individuals is available. We present hierarchical models describing individual heterogeneity in survival and fertility rates and allowing for associations between these rates at the individual level. We apply these models to an analysis of life histories of Kittiwakes (Rissa tridactyla) observed at several colonies on the Brittany coast of France. We compare Bayesian estimation of the population distribution of individual fitness with estimation based on treating individual life histories in isolation, as samples of size one (e.g. McGraw and Caswell, 1996).

  3. Model-based estimation of individual fitness

    USGS Publications Warehouse

    Link, W.A.; Cooch, E.G.; Cam, E.

    2002-01-01

    Fitness is the currency of natural selection, a measure of the propagation rate of genotypes into future generations. Its various definitions have the common feature that they are functions of survival and fertility rates. At the individual level, the operative level for natural selection, these rates must be understood as latent features, genetically determined propensities existing at birth. This conception of rates requires that individual fitness be defined and estimated by consideration of the individual in a modelled relation to a group of similar individuals; the only alternative is to consider a sample of size one, unless a clone of identical individuals is available. We present hierarchical models describing individual heterogeneity in survival and fertility rates and allowing for associations between these rates at the individual level. We apply these models to an analysis of life histories of Kittiwakes (Rissa tridactyla ) observed at several colonies on the Brittany coast of France. We compare Bayesian estimation of the population distribution of individual fitness with estimation based on treating individual life histories in isolation, as samples of size one (e.g. McGraw & Caswell, 1996).

  4. Assessing the fit of parametric cure models.

    PubMed

    Wileyto, E Paul; Li, Yimei; Chen, Jinbo; Heitjan, Daniel F

    2013-04-01

    Survival data can contain an unknown fraction of subjects who are "cured" in the sense of not being at risk of failure. We describe such data with cure-mixture models, which separately model cure status and the hazard of failure among non-cured subjects. No diagnostic currently exists for evaluating the fit of such models; the popular Schoenfeld residual (Schoenfeld, 1982. Partial residuals for the proportional hazards regression-model. Biometrika 69, 239-241) is not applicable to data with cures. In this article, we propose a pseudo-residual, modeled on Schoenfeld's, to assess the fit of the survival regression in the non-cured fraction. Unlike Schoenfeld's approach, which tests the validity of the proportional hazards (PH) assumption, our method uses the full hazard and is thus also applicable to non-PH models. We derive the asymptotic distribution of the residuals and evaluate their performance by simulation in a range of parametric models. We apply our approach to data from a smoking cessation drug trial.

  5. Seeing Perfectly Fitting Factor Models That Are Causally Misspecified: Understanding That Close-Fitting Models Can Be Worse

    ERIC Educational Resources Information Center

    Hayduk, Leslie

    2014-01-01

    Researchers using factor analysis tend to dismiss the significant ill fit of factor models by presuming that if their factor model is close-to-fitting, it is probably close to being properly causally specified. Close fit may indeed result from a model being close to properly causally specified, but close-fitting factor models can also be seriously…

  6. An Investigation of Item Fit Statistics for Mixed IRT Models

    ERIC Educational Resources Information Center

    Chon, Kyong Hee

    2009-01-01

    The purpose of this study was to investigate procedures for assessing model fit of IRT models for mixed format data. In this study, various IRT model combinations were fitted to data containing both dichotomous and polytomous item responses, and the suitability of the chosen model mixtures was evaluated based on a number of model fit procedures.…

  7. An Investigation of Goodness of Model Data Fit

    ERIC Educational Resources Information Center

    Onder, Ismail

    2007-01-01

    IRT models' advantages can only be realized when the model fits the data set of interest. Therefore, this study aimed to investigate which IRT model will provide the best fit to the data obtained from OZDEBYR OSS 2004 D-II Exam Science Test. In goodness-of-fit analysis, first the model assumptions and then the expected model features were checked.…

  8. Effectiveness of the Sport Education Fitness Model on Fitness Levels, Knowledge, and Physical Activity

    ERIC Educational Resources Information Center

    Pritchard, Tony; Hansen, Andrew; Scarboro, Shot; Melnic, Irina

    2015-01-01

    The purpose of this study was to investigate changes in fitness levels, content knowledge, physical activity levels, and participants' perceptions following the implementation of the sport education fitness model (SEFM) at a high school. Thirty-two high school students participated in 20 lessons using the SEFM. Aerobic capacity, muscular…

  9. Epistasis and the Structure of Fitness Landscapes: Are Experimental Fitness Landscapes Compatible with Fisher's Geometric Model?

    PubMed

    Blanquart, François; Bataillon, Thomas

    2016-06-01

    The fitness landscape defines the relationship between genotypes and fitness in a given environment and underlies fundamental quantities such as the distribution of selection coefficient and the magnitude and type of epistasis. A better understanding of variation in landscape structure across species and environments is thus necessary to understand and predict how populations will adapt. An increasing number of experiments investigate the properties of fitness landscapes by identifying mutations, constructing genotypes with combinations of these mutations, and measuring the fitness of these genotypes. Yet these empirical landscapes represent a very small sample of the vast space of all possible genotypes, and this sample is often biased by the protocol used to identify mutations. Here we develop a rigorous statistical framework based on Approximate Bayesian Computation to address these concerns and use this flexible framework to fit a broad class of phenotypic fitness models (including Fisher's model) to 26 empirical landscapes representing nine diverse biological systems. Despite uncertainty owing to the small size of most published empirical landscapes, the inferred landscapes have similar structure in similar biological systems. Surprisingly, goodness-of-fit tests reveal that this class of phenotypic models, which has been successful so far in interpreting experimental data, is a plausible in only three of nine biological systems. More precisely, although Fisher's model was able to explain several statistical properties of the landscapes-including the mean and SD of selection and epistasis coefficients-it was often unable to explain the full structure of fitness landscapes.

  10. Adopting adequate leaching requirement for practical response models of basil to salinity

    NASA Astrophysics Data System (ADS)

    Babazadeh, Hossein; Tabrizi, Mahdi Sarai; Darvishi, Hossein Hassanpour

    2016-07-01

    Several mathematical models are being used for assessing plant response to salinity of the root zone. Objectives of this study included quantifying the yield salinity threshold value of basil plants to irrigation water salinity and investigating the possibilities of using irrigation water salinity instead of saturated extract salinity in the available mathematical models for estimating yield. To achieve the above objectives, an extensive greenhouse experiment was conducted with 13 irrigation water salinity levels, namely 1.175 dS m-1 (control treatment) and 1.8 to 10 dS m-1. The result indicated that, among these models, the modified discount model (one of the most famous root water uptake model which is based on statistics) produced more accurate results in simulating the basil yield reduction function using irrigation water salinities. Overall the statistical model of Steppuhn et al. on the modified discount model and the math-empirical model of van Genuchten and Hoffman provided the best results. In general, all of the statistical models produced very similar results and their results were better than math-empirical models. It was also concluded that if enough leaching was present, there was no significant difference between the soil salinity saturated extract models and the models using irrigation water salinity.

  11. Hyper-Fit: Fitting Linear Models to Multidimensional Data with Multivariate Gaussian Uncertainties

    NASA Astrophysics Data System (ADS)

    Robotham, A. S. G.; Obreschkow, D.

    2015-09-01

    Astronomical data is often uncertain with errors that are heteroscedastic (different for each data point) and covariant between different dimensions. Assuming that a set of D-dimensional data points can be described by a (D - 1)-dimensional plane with intrinsic scatter, we derive the general likelihood function to be maximised to recover the best fitting model. Alongside the mathematical description, we also release the hyper-fit package for the R statistical language (http://github.com/asgr/hyper.fit) and a user-friendly web interface for online fitting (http://hyperfit.icrar.org). The hyper-fit package offers access to a large number of fitting routines, includes visualisation tools, and is fully documented in an extensive user manual. Most of the hyper-fit functionality is accessible via the web interface. In this paper, we include applications to toy examples and to real astronomical data from the literature: the mass-size, Tully-Fisher, Fundamental Plane, and mass-spin-morphology relations. In most cases, the hyper-fit solutions are in good agreement with published values, but uncover more information regarding the fitted model.

  12. Developing an Adequately Specified Model of State Level Student Achievement with Multilevel Data.

    ERIC Educational Resources Information Center

    Bernstein, Lawrence

    Limitations of using linear, unilevel regression procedures in modeling student achievement are discussed. This study is a part of a broader study that is developing an empirically-based predictive model of variables associated with academic achievement from a multilevel perspective and examining the differences by which parameters are estimated…

  13. Curve fitting methods for solar radiation data modeling

    SciTech Connect

    Karim, Samsul Ariffin Abdul E-mail: balbir@petronas.com.my; Singh, Balbir Singh Mahinder E-mail: balbir@petronas.com.my

    2014-10-24

    This paper studies the use of several type of curve fitting method to smooth the global solar radiation data. After the data have been fitted by using curve fitting method, the mathematical model of global solar radiation will be developed. The error measurement was calculated by using goodness-fit statistics such as root mean square error (RMSE) and the value of R{sup 2}. The best fitting methods will be used as a starting point for the construction of mathematical modeling of solar radiation received in Universiti Teknologi PETRONAS (UTP) Malaysia. Numerical results indicated that Gaussian fitting and sine fitting (both with two terms) gives better results as compare with the other fitting methods.

  14. Anatomical features for the adequate choice of experimental animal models in biomedicine: I. Fishes.

    PubMed

    D'Angelo, Livia; Lossi, Laura; Merighi, Adalberto; de Girolamo, Paolo

    2016-05-01

    Fish constitute the oldest and most diverse class of vertebrates, and are widely used in basic research due to a number of advantages (e.g., rapid development ex-utero, large-scale genetic screening of human disease). They represent excellent experimental models for addressing studies on development, morphology, physiology and behavior function in other related species, as well as informative analysis of conservation and diversity. Although less complex, fish share many anatomical and physiological features with mammals, including humans, which make them an important complement to research in mammalian models. In this review we describe and compare the most relevant anatomical features of the most used teleostean species in research, to be taken into consideration when selecting an animal model: zebrafish (Danio rerio), medaka (Oryzias latypes), the turquoise killifish (Nothobranchius furzeri), and goldfish (Carassius auratus). Zebrafish and medaka are the mainstream models for genetic manipulability and studies on developmental biology; the turquoise killifish is an excellent model for aging research; goldfish has been largely employed for neuroendocrine studies.

  15. Goodness of Model-Data Fit and Invariant Measurement

    ERIC Educational Resources Information Center

    Engelhard, George, Jr.; Perkins, Aminah

    2013-01-01

    In this commentary, Englehard and Perkins remark that Maydeu-Olivares has presented a framework for evaluating the goodness of model-data fit for item response theory (IRT) models and correctly points out that overall goodness-of-fit evaluations of IRT models and data are not generally explored within most applications in educational and…

  16. A Comparison of Item Fit Statistics for Mixed IRT Models

    ERIC Educational Resources Information Center

    Chon, Kyong Hee; Lee, Won-Chan; Dunbar, Stephen B.

    2010-01-01

    In this study we examined procedures for assessing model-data fit of item response theory (IRT) models for mixed format data. The model fit indices used in this study include PARSCALE's G[superscript 2], Orlando and Thissen's S-X[superscript 2] and S-G[superscript 2], and Stone's chi[superscript 2*] and G[superscript 2*]. To investigate the…

  17. Operational Realities: Obtaining adequate drivers and inputs for radiation belt models

    NASA Astrophysics Data System (ADS)

    Friedel, R. H. W.; Chen, Y.; Tu, W.; Cunningham, G.; Reeves, G. D.; Lichtenberger, J.

    2014-12-01

    Recent developments in 3D diffusion codes for the high energy electron radiation belt have shown that the model representation of microphysical processes in terms of diffusion coefficients, capturing radial, energy and pitch-angle diffusion (including mixed diffusion terms) is quite capable of capturing the dynamics and physics of the radiation belt system, while remaining computationally tractable; making these codes an ideal candidate for operational application. However, we hold that the major obstacle to a realistic application of such codes for now- or forecasting is our insufficient knowledge of drivers and inputs to these codes - rather than any additional improved physics in the codes. These include the specification of the initial conditions, knowledge of the background plasma distribution, the global distribution of waves, the low-energy boundary condition and the outer boundary condition. In this talk we will discuss realistic and affordable strategies of specifying these inputs through the use of proxies, ground based measurement techniques and data assimilative methods; present examples of where this is already possible (outer boundary and global chorus wave and plasma density specification), and outline where additional effort is needed. Finally we present an example of using such realistic model drivers in a state-of-the-art 3D diffusion code which demonstrates a remarkable ability of such codes to reproduce the observed dynamics - by simply using the existing physics in the code but providing the "correct" drivers and boundary conditions.

  18. Resampling methods for model fitting and model selection.

    PubMed

    Babu, G Jogesh

    2011-11-01

    Resampling procedures for fitting models and model selection are considered in this article. Nonparametric goodness-of-fit statistics are generally based on the empirical distribution function. The distribution-free property of these statistics does not hold in the multivariate case or when some of the parameters are estimated. Bootstrap methods to estimate the underlying distributions are discussed in such cases. The results hold not only in the case of one-dimensional parameter space, but also for the vector parameters. Bootstrap methods for inference, when the data is from an unknown distribution that may or may not belong to a specified family of distributions, are also considered. Most of the information criteria-based model selection procedures such as the Akaike information criterion, Bayesian information criterion, and minimum description length use estimation of bias. The bias, which is inevitable in model selection problems, arises mainly from estimating the distance between the "true" model and an estimated model. A jackknife type procedure for model selection is discussed, which instead of bias estimation is based on bias reduction.

  19. HDFITS: Porting the FITS data model to HDF5

    NASA Astrophysics Data System (ADS)

    Price, D. C.; Barsdell, B. R.; Greenhill, L. J.

    2015-09-01

    The FITS (Flexible Image Transport System) data format has been the de facto data format for astronomy-related data products since its inception in the late 1970s. While the FITS file format is widely supported, it lacks many of the features of more modern data serialization, such as the Hierarchical Data Format (HDF5). The HDF5 file format offers considerable advantages over FITS, such as improved I/O speed and compression, but has yet to gain widespread adoption within astronomy. One of the major holdbacks is that HDF5 is not well supported by data reduction software packages and image viewers. Here, we present a comparison of FITS and HDF5 as a format for storage of astronomy datasets. We show that the underlying data model of FITS can be ported to HDF5 in a straightforward manner, and that by doing so the advantages of the HDF5 file format can be leveraged immediately. In addition, we present a software tool, fits2hdf, for converting between FITS and a new 'HDFITS' format, where data are stored in HDF5 in a FITS-like manner. We show that HDFITS allows faster reading of data (up to 100x of FITS in some use cases), and improved compression (higher compression ratios and higher throughput). Finally, we show that by only changing the import lines in Python-based FITS utilities, HDFITS formatted data can be presented transparently as an in-memory FITS equivalent.

  20. Consequences of Fitting Nonidentified Latent Class Models

    ERIC Educational Resources Information Center

    Abar, Beau; Loken, Eric

    2012-01-01

    Latent class models are becoming more popular in behavioral research. When models with a large number of latent classes relative to the number of manifest indicators are estimated, researchers must consider the possibility that the model is not identified. It is not enough to determine that the model has positive degrees of freedom. A well-known…

  1. Evaluating Item Fit for Multidimensional Item Response Models

    ERIC Educational Resources Information Center

    Zhang, Bo; Stone, Clement A.

    2008-01-01

    This research examines the utility of the s-x[superscript 2] statistic proposed by Orlando and Thissen (2000) in evaluating item fit for multidimensional item response models. Monte Carlo simulation was conducted to investigate both the Type I error and statistical power of this fit statistic in analyzing two kinds of multidimensional test…

  2. Assessing Fit of Unidimensional Graded Response Models Using Bayesian Methods

    ERIC Educational Resources Information Center

    Zhu, Xiaowen; Stone, Clement A.

    2011-01-01

    The posterior predictive model checking method is a flexible Bayesian model-checking tool and has recently been used to assess fit of dichotomous IRT models. This paper extended previous research to polytomous IRT models. A simulation study was conducted to explore the performance of posterior predictive model checking in evaluating different…

  3. Source localization with acoustic sensor arrays using generative model based fitting with sparse constraints.

    PubMed

    Velasco, Jose; Pizarro, Daniel; Macias-Guarasa, Javier

    2012-10-15

    This paper presents a novel approach for indoor acoustic source localization using sensor arrays. The proposed solution starts by defining a generative model, designed to explain the acoustic power maps obtained by Steered Response Power (SRP) strategies. An optimization approach is then proposed to fit the model to real input SRP data and estimate the position of the acoustic source. Adequately fitting the model to real SRP data, where noise and other unmodelled effects distort the ideal signal, is the core contribution of the paper. Two basic strategies in the optimization are proposed. First, sparse constraints in the parameters of the model are included, enforcing the number of simultaneous active sources to be limited. Second, subspace analysis is used to filter out portions of the input signal that cannot be explained by the model. Experimental results on a realistic speech database show statistically significant localization error reductions of up to 30% when compared with the SRP-PHAT strategies.

  4. Source Localization with Acoustic Sensor Arrays Using Generative Model Based Fitting with Sparse Constraints

    PubMed Central

    Velasco, Jose; Pizarro, Daniel; Macias-Guarasa, Javier

    2012-01-01

    This paper presents a novel approach for indoor acoustic source localization using sensor arrays. The proposed solution starts by defining a generative model, designed to explain the acoustic power maps obtained by Steered Response Power (SRP) strategies. An optimization approach is then proposed to fit the model to real input SRP data and estimate the position of the acoustic source. Adequately fitting the model to real SRP data, where noise and other unmodelled effects distort the ideal signal, is the core contribution of the paper. Two basic strategies in the optimization are proposed. First, sparse constraints in the parameters of the model are included, enforcing the number of simultaneous active sources to be limited. Second, subspace analysis is used to filter out portions of the input signal that cannot be explained by the model. Experimental results on a realistic speech database show statistically significant localization error reductions of up to 30% when compared with the SRP-PHAT strategies. PMID:23202021

  5. How Good Are Statistical Models at Approximating Complex Fitness Landscapes?

    PubMed

    du Plessis, Louis; Leventhal, Gabriel E; Bonhoeffer, Sebastian

    2016-09-01

    Fitness landscapes determine the course of adaptation by constraining and shaping evolutionary trajectories. Knowledge of the structure of a fitness landscape can thus predict evolutionary outcomes. Empirical fitness landscapes, however, have so far only offered limited insight into real-world questions, as the high dimensionality of sequence spaces makes it impossible to exhaustively measure the fitness of all variants of biologically meaningful sequences. We must therefore revert to statistical descriptions of fitness landscapes that are based on a sparse sample of fitness measurements. It remains unclear, however, how much data are required for such statistical descriptions to be useful. Here, we assess the ability of regression models accounting for single and pairwise mutations to correctly approximate a complex quasi-empirical fitness landscape. We compare approximations based on various sampling regimes of an RNA landscape and find that the sampling regime strongly influences the quality of the regression. On the one hand it is generally impossible to generate sufficient samples to achieve a good approximation of the complete fitness landscape, and on the other hand systematic sampling schemes can only provide a good description of the immediate neighborhood of a sequence of interest. Nevertheless, we obtain a remarkably good and unbiased fit to the local landscape when using sequences from a population that has evolved under strong selection. Thus, current statistical methods can provide a good approximation to the landscape of naturally evolving populations.

  6. MAPCLUS: A Mathematical Programming Approach to Fitting the ADCLUS Model.

    ERIC Educational Resources Information Center

    Arabie, Phipps

    1980-01-01

    A new computing algorithm, MAPCLUS (Mathematical Programming Clustering), for fitting the Shephard-Arabie ADCLUS (Additive Clustering) model is presented. Details and benefits of the algorithm are discussed. (Author/JKS)

  7. Fitting population models from field data

    USGS Publications Warehouse

    Emlen, J.M.; Freeman, D.C.; Kirchhoff, M.D.; Alados, C.L.; Escos, J.; Duda, J.J.

    2003-01-01

    The application of population and community ecology to solving real-world problems requires population and community dynamics models that reflect the myriad patterns of interaction among organisms and between the biotic and physical environments. Appropriate models are not hard to construct, but the experimental manipulations needed to evaluate their defining coefficients are often both time consuming and costly, and sometimes environmentally destructive, as well. In this paper we present an empirical approach for finding the coefficients of broadly inclusive models without the need for environmental manipulation, demonstrate the approach with both an animal and a plant example, and suggest possible applications. Software has been developed, and is available from the senior author, with a manual describing both field and analytic procedures.

  8. Relative and Absolute Fit Evaluation in Cognitive Diagnosis Modeling

    ERIC Educational Resources Information Center

    Chen, Jinsong; de la Torre, Jimmy; Zhang, Zao

    2013-01-01

    As with any psychometric models, the validity of inferences from cognitive diagnosis models (CDMs) determines the extent to which these models can be useful. For inferences from CDMs to be valid, it is crucial that the fit of the model to the data is ascertained. Based on a simulation study, this study investigated the sensitivity of various fit…

  9. Involving regional expertise in nationwide modeling for adequate prediction of climate change effects on different demands for fresh water

    NASA Astrophysics Data System (ADS)

    de Lange, W. J.

    2014-05-01

    Wim J. de Lange, Geert F. Prinsen, Jacco H. Hoogewoud, Ab A Veldhuizen, Joachim Hunink, Erik F.W. Ruijgh, Timo Kroon Nationwide modeling aims to produce a balanced distribution of climate change effects (e.g. harm on crops) and possible compensation (e.g. volume fresh water) based on consistent calculation. The present work is based on the Netherlands Hydrological Instrument (NHI, www.nhi.nu), which is a national, integrated, hydrological model that simulates distribution, flow and storage of all water in the surface water and groundwater systems. The instrument is developed to assess the impact on water use on land-surface (sprinkling crops, drinking water) and in surface water (navigation, cooling). The regional expertise involved in the development of NHI come from all parties involved in the use, production and management of water, such as waterboards, drinking water supply companies, provinces, ngo's, and so on. Adequate prediction implies that the model computes changes in the order of magnitude that is relevant to the effects. In scenarios related to drought, adequate prediction applies to the water demand and the hydrological effects during average, dry, very dry and extremely dry periods. The NHI acts as a part of the so-called Deltamodel (www.deltamodel.nl), which aims to predict effects and compensating measures of climate change both on safety against flooding and on water shortage during drought. To assess the effects, a limited number of well-defined scenarios is used within the Deltamodel. The effects on demand of fresh water consist of an increase of the demand e.g. for surface water level control to prevent dike burst, for flushing salt in ditches, for sprinkling of crops, for preserving wet nature and so on. Many of the effects are dealt with by regional and local parties. Therefore, these parties have large interest in the outcome of the scenario analyses. They are participating in the assessment of the NHI previous to the start of the analyses

  10. Involving regional expertise in nationwide modeling for adequate prediction of climate change effects on different demands for fresh water

    NASA Astrophysics Data System (ADS)

    de Lange, Wim; Prinsen, Geert.; Hoogewoud, Jacco; Veldhuizen, Ab; Ruijgh, Erik; Kroon, Timo

    2013-04-01

    Nationwide modeling aims to produce a balanced distribution of climate change effects (e.g. harm on crops) and possible compensation (e.g. volume fresh water) based on consistent calculation. The present work is based on the Netherlands Hydrological Instrument (NHI, www.nhi.nu), which is a national, integrated, hydrological model that simulates distribution, flow and storage of all water in the surface water and groundwater systems. The instrument is developed to assess the impact on water use on land-surface (sprinkling crops, drinking water) and in surface water (navigation, cooling). The regional expertise involved in the development of NHI come from all parties involved in the use, production and management of water, such as waterboards, drinking water supply companies, provinces, ngo's, and so on. Adequate prediction implies that the model computes changes in the order of magnitude that is relevant to the effects. In scenarios related to drought, adequate prediction applies to the water demand and the hydrological effects during average, dry, very dry and extremely dry periods. The NHI acts as a part of the so-called Deltamodel (www.deltamodel.nl), which aims to predict effects and compensating measures of climate change both on safety against flooding and on water shortage during drought. To assess the effects, a limited number of well-defined scenarios is used within the Deltamodel. The effects on demand of fresh water consist of an increase of the demand e.g. for surface water level control to prevent dike burst, for flushing salt in ditches, for sprinkling of crops, for preserving wet nature and so on. Many of the effects are dealt with? by regional and local parties. Therefore, these parties have large interest in the outcome of the scenario analyses. They are participating in the assessment of the NHI previous to the start of the analyses. Regional expertise is welcomed in the calibration phase of NHI. It aims to reduce uncertainties by improving the

  11. Fitting of adaptive neuron model to electrophysiological recordings using particle swarm optimization algorithm

    NASA Astrophysics Data System (ADS)

    Shan, Bonan; Wang, Jiang; Zhang, Lvxia; Deng, Bin; Wei, Xile

    2017-02-01

    In order to fit neural model’s spiking features to electrophysiological recordings, in this paper, a fitting framework based on particle swarm optimization (PSO) algorithm is proposed to estimate the model parameters in an augmented multi-timescale adaptive threshold (AugMAT) model. PSO algorithm is an advanced evolutionary calculation method based on iteration. Selecting a reasonable criterion function will ensure the effectiveness of PSO algorithm. In this work, firing rate information is used as the main spiking feature and the estimation error of firing rate is selected as the criterion for fitting. A series of simulations are presented to verify the performance of the framework. The first step is model validation; an artificial training data is introduced to test the fitting procedure. Then we talk about the suitable PSO parameters, which exhibit adequate compromise between speediness and accuracy. Lastly, this framework is used to fit the electrophysiological recordings, after three adjustment steps, the features of experimental data are translated into realistic spiking neuron model.

  12. Assessing the goodness of fit of personal risk models.

    PubMed

    Gong, Gail; Quante, Anne S; Terry, Mary Beth; Whittemore, Alice S

    2014-08-15

    We describe a flexible family of tests for evaluating the goodness of fit (calibration) of a pre-specified personal risk model to the outcomes observed in a longitudinal cohort. Such evaluation involves using the risk model to assign each subject an absolute risk of developing the outcome within a given time from cohort entry and comparing subjects' assigned risks with their observed outcomes. This comparison involves several issues. For example, subjects followed only for part of the risk period have unknown outcomes. Moreover, existing tests do not reveal the reasons for poor model fit when it occurs, which can reflect misspecification of the model's hazards for the competing risks of outcome development and death. To address these issues, we extend the model-specified hazards for outcome and death, and use score statistics to test the null hypothesis that the extensions are unnecessary. Simulated cohort data applied to risk models whose outcome and mortality hazards agreed and disagreed with those generating the data show that the tests are sensitive to poor model fit, provide insight into the reasons for poor fit, and accommodate a wide range of model misspecification. We illustrate the methods by examining the calibration of two breast cancer risk models as applied to a cohort of participants in the Breast Cancer Family Registry. The methods can be implemented using the Risk Model Assessment Program, an R package freely available at http://stanford.edu/~ggong/rmap/.

  13. Can a first-order exponential decay model fit heart rate recovery after resistance exercise?

    PubMed

    Bartels-Ferreira, Rhenan; de Sousa, Élder D; Trevizani, Gabriela A; Silva, Lilian P; Nakamura, Fábio Y; Forjaz, Cláudia L M; Lima, Jorge Roberto P; Peçanha, Tiago

    2015-03-01

    The time-constant of postexercise heart rate recovery (HRRτ ) obtained by fitting heart rate decay curve by a first-order exponential fitting has being used to assess cardiac autonomic recovery after endurance exercise. The feasibility of this model was not tested after resistance exercise (RE). The aim of this study was to test the goodness of fit of the first-order exponential decay model to fit heart rate recovery (HRR) after RE. Ten healthy subjects participated in the study. The experimental sessions occurred in two separated days and consisted of performance of 1 set of 10 repetitions at 50% or 80% of the load achieved on the one-repetition maximum test [low-intensity (LI) and high-intensity (HI) sessions, respectively]. Heart rate (HR) was continuously registered before and during exercise and also for 10 min of recovery. A monoexponential equation was used to fit the HRR curve during the postexercise period using different time windows (i.e. 30, 60, 90, … 600 s). For each time window, (i) HRRτ was calculated and (ii) variation of HR explained by the model (R(2) goodness of fit index) was assessed. The HRRτ showed stabilization from 360 and 420 s on LI and HI, respectively. Acceptable R(2) values were observed from the 360 s on LI (R(2) > 0.65) and at all tested time windows on HI (R(2) > 0.75). In conclusion, this study showed that using a minimum length of monitoring (~420 s) HRR after RE can be adequately modelled by a first-order exponential fitting.

  14. A goodness-of-fit test for occupancy models with correlated within-season revisits

    USGS Publications Warehouse

    Wright, Wilson; Irvine, Kathryn M.; Rodhouse, Thomas J.

    2016-01-01

    Occupancy modeling is important for exploring species distribution patterns and for conservation monitoring. Within this framework, explicit attention is given to species detection probabilities estimated from replicate surveys to sample units. A central assumption is that replicate surveys are independent Bernoulli trials, but this assumption becomes untenable when ecologists serially deploy remote cameras and acoustic recording devices over days and weeks to survey rare and elusive animals. Proposed solutions involve modifying the detection-level component of the model (e.g., first-order Markov covariate). Evaluating whether a model sufficiently accounts for correlation is imperative, but clear guidance for practitioners is lacking. Currently, an omnibus goodnessof- fit test using a chi-square discrepancy measure on unique detection histories is available for occupancy models (MacKenzie and Bailey, Journal of Agricultural, Biological, and Environmental Statistics, 9, 2004, 300; hereafter, MacKenzie– Bailey test). We propose a join count summary measure adapted from spatial statistics to directly assess correlation after fitting a model. We motivate our work with a dataset of multinight bat call recordings from a pilot study for the North American Bat Monitoring Program. We found in simulations that our join count test was more reliable than the MacKenzie–Bailey test for detecting inadequacy of a model that assumed independence, particularly when serial correlation was low to moderate. A model that included a Markov-structured detection-level covariate produced unbiased occupancy estimates except in the presence of strong serial correlation and a revisit design consisting only of temporal replicates. When applied to two common bat species, our approach illustrates that sophisticated models do not guarantee adequate fit to real data, underscoring the importance of model assessment. Our join count test provides a widely applicable goodness-of-fit test and

  15. Adequate immune response ensured by binary IL-2 and graded CD25 expression in a murine transfer model

    PubMed Central

    Fuhrmann, Franziska; Lischke, Timo; Gross, Fridolin; Scheel, Tobias; Bauer, Laura; Kalim, Khalid Wasim; Radbruch, Andreas; Herzel, Hanspeter; Hutloff, Andreas; Baumgrass, Ria

    2016-01-01

    The IL-2/IL-2Ralpha (CD25) axis is of central importance for the interplay of effector and regulatory T cells. Nevertheless, the question how different antigen loads are translated into appropriate IL-2 production to ensure adequate responses against pathogens remains largely unexplored. Here we find that at single cell level, IL-2 is binary (digital) and CD25 is graded expressed whereas at population level both parameters show graded expression correlating with the antigen amount. Combining in vivo data with a mathematical model we demonstrate that only this binary IL-2 expression ensures a wide linear antigen response range for Teff and Treg cells under real spatiotemporal conditions. Furthermore, at low antigen concentrations binary IL-2 expression safeguards by its spatial distribution selective STAT5 activation only of closely adjacent Treg cells regardless of their antigen specificity. These data show that the mode of IL-2 secretion is critical to tailor the adaptive immune response to the antigen amount. DOI: http://dx.doi.org/10.7554/eLife.20616.001 PMID:28035902

  16. 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.

  17. Fitting milk production curves through nonlinear mixed models.

    PubMed

    Piccardi, Monica; Macchiavelli, Raúl; Funes, Ariel Capitaine; Bó, Gabriel A; Balzarini, Mónica

    2017-03-28

    The aim of this work was to fit and compare three non-linear models (Wood, Milkbot and diphasic) to model lactation curves from two approaches: with and without cow random effect. Knowing the behaviour of lactation curves is critical for decision-making in a dairy farm. Knowledge of the model of milk production progress along each lactation is necessary not only at the mean population level (dairy farm), but also at individual level (cow-lactation). The fits were made in a group of high production and reproduction dairy farms; in first and third lactations in cool seasons. A total of 2167 complete lactations were involved, of which 984 were first-lactations and the remaining ones, third lactations (19 382 milk yield tests). PROC NLMIXED in SAS was used to make the fits and estimate the model parameters. The diphasic model resulted to be computationally complex and barely practical. Regarding the classical Wood and MilkBot models, although the information criteria suggest the selection of MilkBot, the differences in the estimation of production indicators did not show a significant improvement. The Wood model was found to be a good option for fitting the expected value of lactation curves. Furthermore, the three models fitted better when the subject (cow) random effect was considered, which is related to magnitude of production. The random effect improved the predictive potential of the models, but it did not have a significant effect on the production indicators derived from the lactation curves, such as milk yield and days in milk to peak.

  18. Effects of Sample Size, Estimation Methods, and Model Specification on Structural Equation Modeling Fit Indexes.

    ERIC Educational Resources Information Center

    Fan, Xitao; Wang, Lin; Thompson, Bruce

    1999-01-01

    A Monte Carlo simulation study investigated the effects on 10 structural equation modeling fit indexes of sample size, estimation method, and model specification. Some fit indexes did not appear to be comparable, and it was apparent that estimation method strongly influenced almost all fit indexes examined, especially for misspecified models. (SLD)

  19. Time-domain fitting of battery electrochemical impedance models

    NASA Astrophysics Data System (ADS)

    Alavi, S. M. M.; Birkl, C. R.; Howey, D. A.

    2015-08-01

    Electrochemical impedance spectroscopy (EIS) is an effective technique for diagnosing the behaviour of electrochemical devices such as batteries and fuel cells, usually by fitting data to an equivalent circuit model (ECM). The common approach in the laboratory is to measure the impedance spectrum of a cell in the frequency domain using a single sine sweep signal, then fit the ECM parameters in the frequency domain. This paper focuses instead on estimation of the ECM parameters directly from time-domain data. This may be advantageous for parameter estimation in practical applications such as automotive systems including battery-powered vehicles, where the data may be heavily corrupted by noise. The proposed methodology is based on the simplified refined instrumental variable for continuous-time fractional systems method ('srivcf'), provided by the Crone toolbox [1,2], combined with gradient-based optimisation to estimate the order of the fractional term in the ECM. The approach was tested first on synthetic data and then on real data measured from a 26650 lithium-ion iron phosphate cell with low-cost equipment. The resulting Nyquist plots from the time-domain fitted models match the impedance spectrum closely (much more accurately than when a Randles model is assumed), and the fitted parameters as separately determined through a laboratory potentiostat with frequency domain fitting match to within 13%.

  20. Evolution in random fitness landscapes: the infinite sites model

    NASA Astrophysics Data System (ADS)

    Park, Su-Chan; Krug, Joachim

    2008-04-01

    We consider the evolution of an asexually reproducing population in an uncorrelated random fitness landscape in the limit of infinite genome size, which implies that each mutation generates a new fitness value drawn from a probability distribution g(w). This is the finite population version of Kingman's house of cards model (Kingman 1978 J. Appl. Probab. 15 1). In contrast to Kingman's work, the focus here is on unbounded distributions g(w) which lead to an indefinite growth of the population fitness. The model is solved analytically in the limit of infinite population size N \\to \\infty and simulated numerically for finite N. When the genome-wide mutation probability U is small, the long-time behavior of the model reduces to a point process of fixation events, which is referred to as a diluted record process (DRP). The DRP is similar to the standard record process except that a new record candidate (a number that exceeds all previous entries in the sequence) is accepted only with a certain probability that depends on the values of the current record and the candidate. We develop a systematic analytic approximation scheme for the DRP. At finite U the fitness frequency distribution of the population decomposes into a stationary part due to mutations and a traveling wave component due to selection, which is shown to imply a reduction of the mean fitness by a factor of 1-U compared to the U \\to 0 limit.

  1. AnnAGNPS model as a potential tool for seeking adequate agriculture land management in Navarre (Spain)

    NASA Astrophysics Data System (ADS)

    Chahor, Y.; Giménez, R.; Casalí, J.

    2012-04-01

    Nowadays agricultural activities face two important challenges. They must be efficient from an economic point of view but with low environment impacts (soil erosion risk, nutrient/pesticide contamination, greenhouse gases emissions, etc.). In this context, hydrological and erosion models appear as remarkable tools when looking for the best management practices. AnnAGNPS (Annualized Agricultural Non Point Source Pollution) is a continuous simulation watershed-scale model that estimates yield and transit of surface water, sediment, nutrients, and pesticides through a watershed. This model has been successfully evaluated -in terms of annual runoff and sediment yield- in a small (around 200 ha) agricultural watershed located in central eastern part of Navarre (Spain), named Latxaga. The watershed is under a humid Sub-Mediterranean climate. It is cultivated almost entirely with winter cereals (wheat and barley) following conventional soil and tillage management practices. The remaining 15% of the watershed is covered by urban and shrub areas. The aim of this work is to evaluate in Latxga watershed the effect of potential and realistic changes in land use and management on surface runoff and sediment yield by using AnnAGNPS. Six years (2003 - 2008) of daily climate data were considered in the simulation. This dataset is the same used in the model evaluation previously made. Six different scenarios regarding soil use and management were considered: i) 60% cereals25% sunflower; ii) 60% cereals, 25% rapeseed; iii) 60% cereals, 25% legumes; iv) 60% cereals, 25% sunflower + rapeseed+ legumes, in equal parts; v) cereals, and alternatively different amount of shrubs (from 20% to 100% ); vi) only cereal but under different combinations of conventional tillage and no-tillage management. Overall, no significant differences in runoff generation were observed with the exception of scenario iii (in which legume is the main alternative crops), whit a slight increase in predicted

  2. Genome-Wide Heterogeneity of Nucleotide Substitution Model Fit

    PubMed Central

    Arbiza, Leonardo; Patricio, Mateus; Dopazo, Hernán; Posada, David

    2011-01-01

    At a genomic scale, the patterns that have shaped molecular evolution are believed to be largely heterogeneous. Consequently, comparative analyses should use appropriate probabilistic substitution models that capture the main features under which different genomic regions have evolved. While efforts have concentrated in the development and understanding of model selection techniques, no descriptions of overall relative substitution model fit at the genome level have been reported. Here, we provide a characterization of best-fit substitution models across three genomic data sets including coding regions from mammals, vertebrates, and Drosophila (24,000 alignments). According to the Akaike Information Criterion (AIC), 82 of 88 models considered were selected as best-fit models at least in one occasion, although with very different frequencies. Most parameter estimates also varied broadly among genes. Patterns found for vertebrates and Drosophila were quite similar and often more complex than those found in mammals. Phylogenetic trees derived from models in the 95% confidence interval set showed much less variance and were significantly closer to the tree estimated under the best-fit model than trees derived from models outside this interval. Although alternative criteria selected simpler models than the AIC, they suggested similar patterns. All together our results show that at a genomic scale, different gene alignments for the same set of taxa are best explained by a large variety of different substitution models and that model choice has implications on different parameter estimates including the inferred phylogenetic trees. After taking into account the differences related to sample size, our results suggest a noticeable diversity in the underlying evolutionary process. All together, we conclude that the use of model selection techniques is important to obtain consistent phylogenetic estimates from real data at a genomic scale. PMID:21824869

  3. A neutrino model fit to the CMB power spectrum

    NASA Astrophysics Data System (ADS)

    Shanks, T.; Johnson, R. W. F.; Schewtschenko, J. A.; Whitbourn, J. R.

    2014-12-01

    The standard cosmological model, Λ cold dark matter (ΛCDM), provides an excellent fit to cosmic microwave background (CMB) data. However, the model has well-known problems. For example, the cosmological constant, Λ, is fine-tuned to 1 part in 10100 and the CDM particle is not yet detected in the laboratory. Shanks previously investigated a model which assumed neither exotic particles nor a cosmological constant but instead postulated a low Hubble constant (H0) to allow a baryon density compatible with inflation and zero spatial curvature. However, recent Planck results make it more difficult to reconcile such a model with CMB power spectra. Here, we relax the previous assumptions to assess the effects of assuming three active neutrinos of mass ≈5 eV. If we assume a low H0 ≈ 45 km s-1 Mpc-1 then, compared to the previous purely baryonic model, we find a significantly improved fit to the first three peaks of the Planck power spectrum. Nevertheless, the goodness of fit is still significantly worse than for ΛCDM and would require appeal to unknown systematic effects for the fit ever to be considered acceptable. A further serious problem is that the amplitude of fluctuations is low (σ8 ≈ 0.2), making it difficult to form galaxies by the present day. This might then require seeds, perhaps from a primordial magnetic field, to be invoked for galaxy formation. These and other problems demonstrate the difficulties faced by models other than ΛCDM in fitting ever more precise cosmological data.

  4. Multidimensional Rasch Model Information-Based Fit Index Accuracy

    ERIC Educational Resources Information Center

    Harrell-Williams, Leigh M.; Wolfe, Edward W.

    2013-01-01

    Most research on confirmatory factor analysis using information-based fit indices (Akaike information criterion [AIC], Bayesian information criteria [BIC], bias-corrected AIC [AICc], and consistent AIC [CAIC]) has used a structural equation modeling framework. Minimal research has been done concerning application of these indices to item response…

  5. Assessing the fit of site-occupancy models

    USGS Publications Warehouse

    MacKenzie, D.I.; Bailey, L.L.

    2004-01-01

    Few species are likely to be so evident that they will always be detected at a site when present. Recently a model has been developed that enables estimation of the proportion of area occupied, when the target species is not detected with certainty. Here we apply this modeling approach to data collected on terrestrial salamanders in the Plethodon glutinosus complex in the Great Smoky Mountains National Park, USA, and wish to address the question 'how accurately does the fitted model represent the data?' The goodness-of-fit of the model needs to be assessed in order to make accurate inferences. This article presents a method where a simple Pearson chi-square statistic is calculated and a parametric bootstrap procedure is used to determine whether the observed statistic is unusually large. We found evidence that the most global model considered provides a poor fit to the data, hence estimated an overdispersion factor to adjust model selection procedures and inflate standard errors. Two hypothetical datasets with known assumption violations are also analyzed, illustrating that the method may be used to guide researchers to making appropriate inferences. The results of a simulation study are presented to provide a broader view of the methods properties.

  6. Survival model construction guided by fit and predictive strength.

    PubMed

    Chauvel, Cécile; O'Quigley, John

    2016-10-05

    Survival model construction can be guided by goodness-of-fit techniques as well as measures of predictive strength. Here, we aim to bring together these distinct techniques within the context of a single framework. The goal is how to best characterize and code the effects of the variables, in particular time dependencies, when taken either singly or in combination with other related covariates. Simple graphical techniques can provide an immediate visual indication as to the goodness-of-fit but, in cases of departure from model assumptions, will point in the direction of a more involved and richer alternative model. These techniques appear to be intuitive. This intuition is backed up by formal theorems that underlie the process of building richer models from simpler ones. Measures of predictive strength are used in conjunction with these goodness-of-fit techniques and, again, formal theorems show that these measures can be used to help identify models closest to the unknown non-proportional hazards mechanism that we can suppose generates the observations. Illustrations from studies in breast cancer show how these tools can be of help in guiding the practical problem of efficient model construction for survival data.

  7. Differential equation modeling of HIV viral fitness experiments: model identification, model selection, and multimodel inference.

    PubMed

    Miao, Hongyu; Dykes, Carrie; Demeter, Lisa M; Wu, Hulin

    2009-03-01

    Many biological processes and systems can be described by a set of differential equation (DE) models. However, literature in statistical inference for DE models is very sparse. We propose statistical estimation, model selection, and multimodel averaging methods for HIV viral fitness experiments in vitro that can be described by a set of nonlinear ordinary differential equations (ODE). The parameter identifiability of the ODE models is also addressed. We apply the proposed methods and techniques to experimental data of viral fitness for HIV-1 mutant 103N. We expect that the proposed modeling and inference approaches for the DE models can be widely used for a variety of biomedical studies.

  8. Limitations of model-fitting methods for lensing shear estimation

    NASA Astrophysics Data System (ADS)

    Voigt, L. M.; Bridle, S. L.

    2010-05-01

    Gravitational lensing shear has the potential to be the most powerful tool for constraining the nature of dark energy. However, accurate measurement of galaxy shear is crucial and has been shown to be non-trivial by the Shear TEsting Programme. Here, we demonstrate a fundamental limit to the accuracy achievable by model-fitting techniques, if oversimplistic models are used. We show that even if galaxies have elliptical isophotes, model-fitting methods which assume elliptical isophotes can have significant biases if they use the wrong profile. We use noise-free simulations to show that on allowing sufficient flexibility in the profile the biases can be made negligible. This is no longer the case if elliptical isophote models are used to fit galaxies made up of a bulge plus a disc, if these two components have different ellipticities. The limiting accuracy is dependent on the galaxy shape, but we find the most significant biases (~1 per cent of the shear) for simple spiral-like galaxies. The implications for a given cosmic shear survey will depend on the actual distribution of galaxy morphologies in the Universe, taking into account the survey selection function and the point spread function. However, our results suggest that the impact on cosmic shear results from current and near future surveys may be negligible. Meanwhile, these results should encourage the development of existing approaches which are less sensitive to morphology, as well as methods which use priors on galaxy shapes learnt from deep surveys.

  9. Supersymmetry with prejudice: Fitting the wrong model to LHC data

    NASA Astrophysics Data System (ADS)

    Allanach, B. C.; Dolan, Matthew J.

    2012-09-01

    We critically examine interpretations of hypothetical supersymmetric LHC signals, fitting to alternative wrong models of supersymmetry breaking. The signals we consider are some of the most constraining on the sparticle spectrum: invariant mass distributions with edges and endpoints from the golden decay chain q˜→qχ20(→l˜±l∓q)→χ10l+l-q. We assume a constrained minimal supersymmetric standard model (CMSSM) point to be the ‘correct’ one, but fit the signals instead with minimal gauge mediated supersymmetry breaking models (mGMSB) with a neutralino quasistable lightest supersymmetric particle, minimal anomaly mediation and large volume string compactification models. Minimal anomaly mediation and large volume scenario can be unambiguously discriminated against the CMSSM for the assumed signal and 1fb-1 of LHC data at s=14TeV. However, mGMSB would not be discriminated on the basis of the kinematic endpoints alone. The best-fit point spectra of mGMSB and CMSSM look remarkably similar, making experimental discrimination at the LHC based on the edges or Higgs properties difficult. However, using rate information for the golden chain should provide the additional separation required.

  10. Atmospheric Turbulence Modeling for Aerospace Vehicles: Fractional Order Fit

    NASA Technical Reports Server (NTRS)

    Kopasakis, George (Inventor)

    2015-01-01

    An improved model for simulating atmospheric disturbances is disclosed. A scale Kolmogorov spectral may be scaled to convert the Kolmogorov spectral into a finite energy von Karman spectral and a fractional order pole-zero transfer function (TF) may be derived from the von Karman spectral. Fractional order atmospheric turbulence may be approximated with an integer order pole-zero TF fit, and the approximation may be stored in memory.

  11. Epistasis and the Structure of Fitness Landscapes: Are Experimental Fitness Landscapes Compatible with Fisher’s Geometric Model?

    PubMed Central

    Blanquart, François; Bataillon, Thomas

    2016-01-01

    The fitness landscape defines the relationship between genotypes and fitness in a given environment and underlies fundamental quantities such as the distribution of selection coefficient and the magnitude and type of epistasis. A better understanding of variation in landscape structure across species and environments is thus necessary to understand and predict how populations will adapt. An increasing number of experiments investigate the properties of fitness landscapes by identifying mutations, constructing genotypes with combinations of these mutations, and measuring the fitness of these genotypes. Yet these empirical landscapes represent a very small sample of the vast space of all possible genotypes, and this sample is often biased by the protocol used to identify mutations. Here we develop a rigorous statistical framework based on Approximate Bayesian Computation to address these concerns and use this flexible framework to fit a broad class of phenotypic fitness models (including Fisher’s model) to 26 empirical landscapes representing nine diverse biological systems. Despite uncertainty owing to the small size of most published empirical landscapes, the inferred landscapes have similar structure in similar biological systems. Surprisingly, goodness-of-fit tests reveal that this class of phenotypic models, which has been successful so far in interpreting experimental data, is a plausible in only three of nine biological systems. More precisely, although Fisher’s model was able to explain several statistical properties of the landscapes—including the mean and SD of selection and epistasis coefficients—it was often unable to explain the full structure of fitness landscapes. PMID:27052568

  12. The Meaning of Goodness-of-Fit Tests: Commentary on "Goodness-of-Fit Assessment of Item Response Theory Models"

    ERIC Educational Resources Information Center

    Thissen, David

    2013-01-01

    In this commentary, David Thissen states that "Goodness-of-fit assessment for IRT models is maturing; it has come a long way from zero." Thissen then references prior works on "goodness of fit" in the index of Lord and Novick's (1968) classic text; Yen (1984); Drasgow, Levine, Tsien, Williams, and Mead (1995); Chen and…

  13. Receptor-level interrelationships of amino acids and the adequate amino acid type hormones in Tetrahymena: a receptor evolution model.

    PubMed

    Csaba, G; Darvas, Z

    1986-01-01

    Histidine stimulates the phagocytosis of Tetrahymena to the same extent as histamine, and also stimulates its division, which histamine does not. Tyrosine and diiodotyrosine equally stimulate the growth of the Tetrahymena. Both amino acids inhibit the characteristic influence of the adequate amino acid hormone when added to Tetrahymena culture 72 h in advance of it. Primary interaction with diiodotyrosine and tyrosine notably increases the cellular growth rate. Histamine has a similar, although less notable effect than histidine. In the light of these experimental observations there is reason to postulate that the receptors of the amino acid hormones have developed from amino acid receptors.

  14. Bayesian Data-Model Fit Assessment for Structural Equation Modeling

    ERIC Educational Resources Information Center

    Levy, Roy

    2011-01-01

    Bayesian approaches to modeling are receiving an increasing amount of attention in the areas of model construction and estimation in factor analysis, structural equation modeling (SEM), and related latent variable models. However, model diagnostics and model criticism remain relatively understudied aspects of Bayesian SEM. This article describes…

  15. Broadband distortion modeling in Lyman-α forest BAO fitting

    DOE PAGES

    Blomqvist, Michael; Kirkby, David; Bautista, Julian E.; ...

    2015-11-23

    Recently, the Lyman-α absorption observed in the spectra of high-redshift quasars has been used as a tracer of large-scale structure by means of the three-dimensional Lyman-α forest auto-correlation function at redshift z≃ 2.3, but the need to fit the quasar continuum in every absorption spectrum introduces a broadband distortion that is difficult to correct and causes a systematic error for measuring any broadband properties. Here, we describe a k-space model for this broadband distortion based on a multiplicative correction to the power spectrum of the transmitted flux fraction that suppresses power on scales corresponding to the typical length of amore » Lyman-α forest spectrum. In implementing the distortion model in fits for the baryon acoustic oscillation (BAO) peak position in the Lyman-α forest auto-correlation, we find that the fitting method recovers the input values of the linear bias parameter bF and the redshift-space distortion parameter βF for mock data sets with a systematic error of less than 0.5%. Applied to the auto-correlation measured for BOSS Data Release 11, our method improves on the previous treatment of broadband distortions in BAO fitting by providing a better fit to the data using fewer parameters and reducing the statistical errors on βF and the combination bF(1+βF) by more than a factor of seven. The measured values at redshift z=2.3 are βF=1.39+0.11 +0.24 +0.38-0.10 -0.19 -0.28 and bF(1+βF)=-0.374+0.007 +0.013 +0.020-0.007 -0.014 -0.022 (1σ, 2σ and 3σ statistical errors). Our fitting software and the input files needed to reproduce our main results are publicly available.« less

  16. Broadband distortion modeling in Lyman-α forest BAO fitting

    SciTech Connect

    Blomqvist, Michael; Kirkby, David; Margala, Daniel E-mail: dkirkby@uci.edu; and others

    2015-11-01

    In recent years, the Lyman-α absorption observed in the spectra of high-redshift quasars has been used as a tracer of large-scale structure by means of the three-dimensional Lyman-α forest auto-correlation function at redshift z≅ 2.3, but the need to fit the quasar continuum in every absorption spectrum introduces a broadband distortion that is difficult to correct and causes a systematic error for measuring any broadband properties. We describe a k-space model for this broadband distortion based on a multiplicative correction to the power spectrum of the transmitted flux fraction that suppresses power on scales corresponding to the typical length of a Lyman-α forest spectrum. Implementing the distortion model in fits for the baryon acoustic oscillation (BAO) peak position in the Lyman-α forest auto-correlation, we find that the fitting method recovers the input values of the linear bias parameter b{sub F} and the redshift-space distortion parameter β{sub F} for mock data sets with a systematic error of less than 0.5%. Applied to the auto-correlation measured for BOSS Data Release 11, our method improves on the previous treatment of broadband distortions in BAO fitting by providing a better fit to the data using fewer parameters and reducing the statistical errors on β{sub F} and the combination b{sub F}(1+β{sub F}) by more than a factor of seven. The measured values at redshift z=2.3 are β{sub F}=1.39{sup +0.11 +0.24 +0.38}{sub −0.10 −0.19 −0.28} and b{sub F}(1+β{sub F})=−0.374{sup +0.007 +0.013 +0.020}{sub −0.007 −0.014 −0.022} (1σ, 2σ and 3σ statistical errors). Our fitting software and the input files needed to reproduce our main results are publicly available.

  17. Broadband distortion modeling in Lyman-α forest BAO fitting

    SciTech Connect

    Blomqvist, Michael; Kirkby, David; Bautista, Julian E.; Arinyo-i-Prats, Andreu; Busca, Nicolás G.; Miralda-Escudé, Jordi; Slosar, Anže; Font-Ribera, Andreu; Margala, Daniel; Schneider, Donald P.; Vazquez, Jose A.

    2015-11-23

    Recently, the Lyman-α absorption observed in the spectra of high-redshift quasars has been used as a tracer of large-scale structure by means of the three-dimensional Lyman-α forest auto-correlation function at redshift z≃ 2.3, but the need to fit the quasar continuum in every absorption spectrum introduces a broadband distortion that is difficult to correct and causes a systematic error for measuring any broadband properties. Here, we describe a k-space model for this broadband distortion based on a multiplicative correction to the power spectrum of the transmitted flux fraction that suppresses power on scales corresponding to the typical length of a Lyman-α forest spectrum. In implementing the distortion model in fits for the baryon acoustic oscillation (BAO) peak position in the Lyman-α forest auto-correlation, we find that the fitting method recovers the input values of the linear bias parameter bF and the redshift-space distortion parameter βF for mock data sets with a systematic error of less than 0.5%. Applied to the auto-correlation measured for BOSS Data Release 11, our method improves on the previous treatment of broadband distortions in BAO fitting by providing a better fit to the data using fewer parameters and reducing the statistical errors on βF and the combination bF(1+βF) by more than a factor of seven. The measured values at redshift z=2.3 are βF=1.39+0.11 +0.24 +0.38-0.10 -0.19 -0.28 and bF(1+βF)=-0.374+0.007 +0.013 +0.020-0.007 -0.014 -0.022 (1σ, 2σ and 3σ statistical errors). Our fitting software and the input files needed to reproduce our main results are publicly available.

  18. Chempy: A flexible chemical evolution model for abundance fitting

    NASA Astrophysics Data System (ADS)

    Rybizki, J.; Just, A.; Rix, H.-W.; Fouesneau, M.

    2017-02-01

    Chempy models Galactic chemical evolution (GCE); it is a parametrized open one-zone model within a Bayesian framework. A Chempy model is specified by a set of 5-10 parameters that describe the effective galaxy evolution along with the stellar and star-formation physics: e.g. the star-formation history (SFH), the feedback efficiency, the stellar initial mass function (IMF) and the incidence of supernova of type Ia (SN Ia). Chempy can sample the posterior probability distribution in the full model parameter space and test data-model matches for different nucleosynthetic yield sets, performing essentially as a chemical evolution fitting tool. Chempy can be used to confront predictions from stellar nucleosynthesis with complex abundance data sets and to refine the physical processes governing the chemical evolution of stellar systems.

  19. Equilibrium Distribution of Mutators in the Single Fitness Peak Model

    NASA Astrophysics Data System (ADS)

    Tannenbaum, Emmanuel; Deeds, Eric J.; Shakhnovich, Eugene I.

    2003-09-01

    This Letter develops an analytically tractable model for determining the equilibrium distribution of mismatch repair deficient strains in unicellular populations. The approach is based on the single fitness peak model, which has been used in Eigen’s quasispecies equations in order to understand various aspects of evolutionary dynamics. As with the quasispecies model, our model for mutator-nonmutator equilibrium undergoes a phase transition in the limit of infinite sequence length. This “repair catas­trophe” occurs at a critical repair error probability of ɛr=Lvia/L, where Lvia denotes the length of the genome controlling viability, while L denotes the overall length of the genome. The repair catastrophe therefore occurs when the repair error probability exceeds the fraction of deleterious mutations. Our model also gives a quantitative estimate for the equilibrium fraction of mutators in Escherichia coli.

  20. When the model fits the frame: the impact of regulatory fit on efficacy appraisal and persuasion in health communication.

    PubMed

    Bosone, Lucia; Martinez, Frédéric; Kalampalikis, Nikos

    2015-04-01

    In health-promotional campaigns, positive and negative role models can be deployed to illustrate the benefits or costs of certain behaviors. The main purpose of this article is to investigate why, how, and when exposure to role models strengthens the persuasiveness of a message, according to regulatory fit theory. We argue that exposure to a positive versus a negative model activates individuals' goals toward promotion rather than prevention. By means of two experiments, we demonstrate that high levels of persuasion occur when a message advertising healthy dietary habits offers a regulatory fit between its framing and the described role model. Our data also establish that the effects of such internal regulatory fit by vicarious experience depend on individuals' perceptions of response-efficacy and self-efficacy. Our findings constitute a significant theoretical complement to previous research on regulatory fit and contain valuable practical implications for health-promotional campaigns.

  1. Fitting IRT Models to Dichotomous and Polytomous Data: Assessing the Relative Model-Data Fit of Ideal Point and Dominance Models

    ERIC Educational Resources Information Center

    Tay, Louis; Ali, Usama S.; Drasgow, Fritz; Williams, Bruce

    2011-01-01

    This study investigated the relative model-data fit of an ideal point item response theory (IRT) model (the generalized graded unfolding model [GGUM]) and dominance IRT models (e.g., the two-parameter logistic model [2PLM] and Samejima's graded response model [GRM]) to simulated dichotomous and polytomous data generated from each of these models.…

  2. Rapid world modeling: Fitting range data to geometric primitives

    SciTech Connect

    Feddema, J.; Little, C.

    1996-12-31

    For the past seven years, Sandia National Laboratories has been active in the development of robotic systems to help remediate DOE`s waste sites and decommissioned facilities. Some of these facilities have high levels of radioactivity which prevent manual clean-up. Tele-operated and autonomous robotic systems have been envisioned as the only suitable means of removing the radioactive elements. World modeling is defined as the process of creating a numerical geometric model of a real world environment or workspace. This model is often used in robotics to plan robot motions which perform a task while avoiding obstacles. In many applications where the world model does not exist ahead of time, structured lighting, laser range finders, and even acoustical sensors have been used to create three dimensional maps of the environment. These maps consist of thousands of range points which are difficult to handle and interpret. This paper presents a least squares technique for fitting range data to planar and quadric surfaces, including cylinders and ellipsoids. Once fit to these primitive surfaces, the amount of data associated with a surface is greatly reduced up to three orders of magnitude, thus allowing for more rapid handling and analysis of world data.

  3. 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.

  4. Issues in Evaluating Model Fit With Missing Data

    ERIC Educational Resources Information Center

    Davey, Adam

    2005-01-01

    Effects of incomplete data on fit indexes remain relatively unexplored. We evaluate a wide set of fit indexes (?[squared], root mean squared error of appproximation, Normed Fit Index [NFI], Tucker-Lewis Index, comparative fit index, gamma-hat, and McDonald's Centrality Index) varying conditions of sample size (100-1,000 in increments of 50),…

  5. Effect of the Number of Variables on Measures of Fit in Structural Equation Modeling.

    ERIC Educational Resources Information Center

    Kenny, David A.; McCoach, D. Betsy

    2003-01-01

    Used three approaches to understand the effect of the number of variables in the model on model fit in structural equation modeling through computer simulation. Developed a simple formula for the theoretical value of the comparative fit index. (SLD)

  6. Assessing Model Data Fit of Unidimensional Item Response Theory Models in Simulated Data

    ERIC Educational Resources Information Center

    Kose, Ibrahim Alper

    2014-01-01

    The purpose of this paper is to give an example of how to assess the model-data fit of unidimensional IRT models in simulated data. Also, the present research aims to explain the importance of fit and the consequences of misfit by using simulated data sets. Responses of 1000 examinees to a dichotomously scoring 20 item test were simulated with 25…

  7. An NCME Instructional Module on Item-Fit Statistics for Item Response Theory Models

    ERIC Educational Resources Information Center

    Ames, Allison J.; Penfield, Randall D.

    2015-01-01

    Drawing valid inferences from item response theory (IRT) models is contingent upon a good fit of the data to the model. Violations of model-data fit have numerous consequences, limiting the usefulness and applicability of the model. This instructional module provides an overview of methods used for evaluating the fit of IRT models. Upon completing…

  8. Empirical fitness models for hepatitis C virus immunogen design

    NASA Astrophysics Data System (ADS)

    Hart, Gregory R.; Ferguson, Andrew L.

    2015-12-01

    Hepatitis C virus (HCV) afflicts 170 million people worldwide, 2%-3% of the global population, and kills 350 000 each year. Prophylactic vaccination offers the most realistic and cost effective hope of controlling this epidemic in the developing world where expensive drug therapies are not available. Despite 20 years of research, the high mutability of the virus and lack of knowledge of what constitutes effective immune responses have impeded development of an effective vaccine. Coupling data mining of sequence databases with spin glass models from statistical physics, we have developed a computational approach to translate clinical sequence databases into empirical fitness landscapes quantifying the replicative capacity of the virus as a function of its amino acid sequence. These landscapes explicitly connect viral genotype to phenotypic fitness, and reveal vulnerable immunological targets within the viral proteome that can be exploited to rationally design vaccine immunogens. We have recovered the empirical fitness landscape for the HCV RNA-dependent RNA polymerase (protein NS5B) responsible for viral genome replication, and validated the predictions of our model by demonstrating excellent accord with experimental measurements and clinical observations. We have used our landscapes to perform exhaustive in silico screening of 16.8 million T-cell immunogen candidates to identify 86 optimal formulations. By reducing the search space of immunogen candidates by over five orders of magnitude, our approach can offer valuable savings in time, expense, and labor for experimental vaccine development and accelerate the search for a HCV vaccine. Abbreviations: HCV—hepatitis C virus, HLA—human leukocyte antigen, CTL—cytotoxic T lymphocyte, NS5B—nonstructural protein 5B, MSA—multiple sequence alignment, PEG-IFN—pegylated interferon.

  9. Developing of discrimination experiment to find most adequate model of plant’s multi-nutrient functional response

    NASA Astrophysics Data System (ADS)

    Saltykov, M. Yu; Bartsev, S. I.

    2017-02-01

    To create reliable Closed Ecological Life Support Systems (CELSS) it is necessary to have models which can predict CELSS dynamic with good accuracy. However it was shown that conventional ecological models cannot describe CELSS correctly if it is closed by more than one element. This problem can be solved by means more complex models than conventional ones - so called flexible metabolism models. However it is possible that CELSS also can be described correctly in “semi-conventional” framework – when only one trophic level is described by flexible metabolism model. Another problem in CELSS modeling is existence of different and incompatible hypotheses about relationships between plants growth rate and amounts of nutrients (functional responses). Difficulty of testing these hypotheses is associated with multi-nutrient dependency of growth rate and comprehensive experimental studies are expensive and time-consuming. This work is devoted to testing the hypothesis that “semi-conventional” approach is enough to describe CELSS, and to planning the discrimination experiment on selecting correct type of the plant’s functional response. To do that three different models of plants (one flexible and two conventional) were investigated both in the scope of CELSS model, and in hemostat model. Numerical simulations show that each of the models has typical patterns which can be determined in experiment with real plants.

  10. Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS

    USGS Publications Warehouse

    Bolker, Benjamin M.; Gardner, Beth; Maunder, Mark; Berg, Casper W.; Brooks, Mollie; Comita, Liza; Crone, Elizabeth; Cubaynes, Sarah; Davies, Trevor; de Valpine, Perry; Ford, Jessica; Gimenez, Olivier; Kéry, Marc; Kim, Eun Jung; Lennert-Cody, Cleridy; Magunsson, Arni; Martell, Steve; Nash, John; Nielson, Anders; Regentz, Jim; Skaug, Hans; Zipkin, Elise

    2013-01-01

    1. Ecologists often use nonlinear fitting techniques to estimate the parameters of complex ecological models, with attendant frustration. This paper compares three open-source model fitting tools and discusses general strategies for defining and fitting models. 2. R is convenient and (relatively) easy to learn, AD Model Builder is fast and robust but comes with a steep learning curve, while BUGS provides the greatest flexibility at the price of speed. 3. Our model-fitting suggestions range from general cultural advice (where possible, use the tools and models that are most common in your subfield) to specific suggestions about how to change the mathematical description of models to make them more amenable to parameter estimation. 4. A companion web site (https://groups.nceas.ucsb.edu/nonlinear-modeling/projects) presents detailed examples of application of the three tools to a variety of typical ecological estimation problems; each example links both to a detailed project report and to full source code and data.

  11. The FIT Model - Fuel-cycle Integration and Tradeoffs

    SciTech Connect

    Steven J. Piet; Nick R. Soelberg; Samuel E. Bays; Candido Pereira; Layne F. Pincock; Eric L. Shaber; Meliisa C Teague; Gregory M Teske; Kurt G Vedros

    2010-09-01

    All mass streams from fuel separation and fabrication are products that must meet some set of product criteria – fuel feedstock impurity limits, waste acceptance criteria (WAC), material storage (if any), or recycle material purity requirements such as zirconium for cladding or lanthanides for industrial use. These must be considered in a systematic and comprehensive way. The FIT model and the “system losses study” team that developed it [Shropshire2009, Piet2010] are an initial step by the FCR&D program toward a global analysis that accounts for the requirements and capabilities of each component, as well as major material flows within an integrated fuel cycle. This will help the program identify near-term R&D needs and set longer-term goals. The question originally posed to the “system losses study” was the cost of separation, fuel fabrication, waste management, etc. versus the separation efficiency. In other words, are the costs associated with marginal reductions in separations losses (or improvements in product recovery) justified by the gains in the performance of other systems? We have learned that that is the wrong question. The right question is: how does one adjust the compositions and quantities of all mass streams, given uncertain product criteria, to balance competing objectives including cost? FIT is a method to analyze different fuel cycles using common bases to determine how chemical performance changes in one part of a fuel cycle (say used fuel cooling times or separation efficiencies) affect other parts of the fuel cycle. FIT estimates impurities in fuel and waste via a rough estimate of physics and mass balance for a set of technologies. If feasibility is an issue for a set, as it is for “minimum fuel treatment” approaches such as melt refining and AIROX, it can help to make an estimate of how performances would have to change to achieve feasibility.

  12. Upper airway and abdominal motor output during sneezing: is the in vivo decererate rat an adequate model?

    PubMed

    Ono, Kenichi; Shen, Tabitha Y; Chun, Hyun Hye; Solomon, Irene C

    2010-01-01

    While numerous studies have focused on identifying and characterizing the neural mechanisms mediating upper airway defense reflexes in the anesthetized or decerebrate adult cat, little is known about these behaviors in in vivo rodent models. The current study was undertaken to investigate whether the in vivo decelerate adult rat might serve as an acceptable model for studying these behaviors. To begin to address this possibility, we examined multiple respiratory motor activities in response to mechanical stimulation of the anterior nasal cavity (sufficient to elicit fictive sneezing) in in vivo decerebrate adult rats. We found that the neural activities observed during nasal stimulation were consistent with those previously reported during fictive sneezing in the adult cat model. We suggest that the in vivo decerebrate rat is an acceptable model for studying the sneezing reflex.

  13. An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs.

    PubMed

    Bloom, Jesse D

    2014-10-01

    Phylogenetic analyses of molecular data require a quantitative model for how sequences evolve. Traditionally, the details of the site-specific selection that governs sequence evolution are not known a priori, making it challenging to create evolutionary models that adequately capture the heterogeneity of selection at different sites. However, recent advances in high-throughput experiments have made it possible to quantify the effects of all single mutations on gene function. I have previously shown that such high-throughput experiments can be combined with knowledge of underlying mutation rates to create a parameter-free evolutionary model that describes the phylogeny of influenza nucleoprotein far better than commonly used existing models. Here, I extend this work by showing that published experimental data on TEM-1 beta-lactamase (Firnberg E, Labonte JW, Gray JJ, Ostermeier M. 2014. A comprehensive, high-resolution map of a gene's fitness landscape. Mol Biol Evol. 31:1581-1592) can be combined with a few mutation rate parameters to create an evolutionary model that describes beta-lactamase phylogenies much better than most common existing models. This experimentally informed evolutionary model is superior even for homologs that are substantially diverged (about 35% divergence at the protein level) from the TEM-1 parent that was the subject of the experimental study. These results suggest that experimental measurements can inform phylogenetic evolutionary models that are applicable to homologs that span a substantial range of sequence divergence.

  14. Anatomical features for an adequate choice of experimental animal model in biomedicine: II. Small laboratory rodents, rabbit, and pig.

    PubMed

    Lossi, Laura; D'Angelo, Livia; De Girolamo, Paolo; Merighi, Adalberto

    2016-03-01

    The anatomical features distinctive to each of the very large array of species used in today's biomedical research must be born in mind when considering the correct choice of animal model(s), particularly when translational research is concerned. In this paper we take into consideration and discuss the most important anatomical and histological features of the commonest species of laboratory rodents (rat, mouse, guinea pig, hamster, and gerbil), rabbit, and pig related to their importance for applied research.

  15. Use of the MSA products as an adequate representation of the surface albedo in the ALADIN-Belgium NWP model

    NASA Astrophysics Data System (ADS)

    Bertrand, C.; Govaerts, Y.; Clerbaux, N.; Ipe, A.; Gonzalez, L.

    2003-04-01

    Land surface albedo represents the proportion of the incoming radiative flux reflected by the surface. It is highly variable in space and time over terrestrial surfaces and plays a key role in surface-atmosphere interaction processes. In particular, it is used in numerical weather forecast and climate models to parametrize surface boundary radiative conditions. Hence, the accurate knowledge of surface albedo at the appropriate time and space scales is essential in estimating radiation balance components. Unfortunately, surface albedo in numerical models is commonly prescribed from low-resolution seasonal data sets. Such data sets are often based on limited ground-based albedo observations and information on surface and vegetation types, even though such approaches do not accurately account for the actual structural effects of the underlying surface. To account for the high spatial and temporal variability of the surface albedo, the ALADIN-Belgium NWP model has been initialized with the directional hemispherical reflectance generated by the Meteosat Surface Albedo (MSA) algorithm. The MSA product is generated every 10 days with a spatial resolution close to the 7 km mesh size of ALADIN-Belgium NWP model. A number of sensitivity forecast runs using the MSA products has shown a significant improvement of the simulated radiative fluxes with respect to simulations performed with a surface albedo derived from climatological values of soil and vegetation parameters. This finding suggests that the use of the high-resolution MSA products could also be valuable for improving model temperature forecasts.

  16. Using R^2 to compare least-squares fit models: When it must fail

    Technology Transfer Automated Retrieval System (TEKTRAN)

    R^2 can be used correctly to select from among competing least-squares fit models when the data are fitted in common form and with common weighting. However, then R^2 comparisons become equivalent to comparisons of the estimated fit variance s^2 in unweighted fitting, or of the reduced chi-square in...

  17. Assessing Fit of Latent Regression Models. Research Report. ETS RR-09-50

    ERIC Educational Resources Information Center

    Sinharay, Sandip; Guo, Zhumei; von Davier, Matthias; Veldkamp, Bernard P.

    2009-01-01

    The reporting methods used in large-scale educational assessments such as the National Assessment of Educational Progress (NAEP) rely on a "latent regression model". There is a lack of research on the assessment of fit of latent regression models. This paper suggests a simulation-based model-fit technique to assess the fit of such…

  18. Methodical fitting for mathematical models of rubber-like materials

    NASA Astrophysics Data System (ADS)

    Destrade, Michel; Saccomandi, Giuseppe; Sgura, Ivonne

    2017-02-01

    A great variety of models can describe the nonlinear response of rubber to uniaxial tension. Yet an in-depth understanding of the successive stages of large extension is still lacking. We show that the response can be broken down in three steps, which we delineate by relying on a simple formatting of the data, the so-called Mooney plot transform. First, the small-to-moderate regime, where the polymeric chains unfold easily and the Mooney plot is almost linear. Second, the strain-hardening regime, where blobs of bundled chains unfold to stiffen the response in correspondence to the `upturn' of the Mooney plot. Third, the limiting-chain regime, with a sharp stiffening occurring as the chains extend towards their limit. We provide strain-energy functions with terms accounting for each stage that (i) give an accurate local and then global fitting of the data; (ii) are consistent with weak nonlinear elasticity theory and (iii) can be interpreted in the framework of statistical mechanics. We apply our method to Treloar's classical experimental data and also to some more recent data. Our method not only provides models that describe the experimental data with a very low quantitative relative error, but also shows that the theory of nonlinear elasticity is much more robust that seemed at first sight.

  19. A Comparison of Four Estimators of a Population Measure of Model Fit in Covariance Structure Analysis

    ERIC Educational Resources Information Center

    Zhang, Wei

    2008-01-01

    A major issue in the utilization of covariance structure analysis is model fit evaluation. Recent years have witnessed increasing interest in various test statistics and so-called fit indexes, most of which are actually based on or closely related to F[subscript 0], a measure of model fit in the population. This study aims to provide a systematic…

  20. Performance of the Generalized S-X[squared] Item Fit Index for the Graded Response Model

    ERIC Educational Resources Information Center

    Kang, Taehoon; Chen, Troy T.

    2011-01-01

    The utility of Orlando and Thissen's ("2000", "2003") S-X[squared] fit index was extended to the model-fit analysis of the graded response model (GRM). The performance of a modified S-X[squared] in assessing item-fit of the GRM was investigated in light of empirical Type I error rates and power with a simulation study having…

  1. Model-independent fit to Planck and BICEP2 data

    NASA Astrophysics Data System (ADS)

    Barranco, Laura; Boubekeur, Lotfi; Mena, Olga

    2014-09-01

    Inflation is the leading theory to describe elegantly the initial conditions that led to structure formation in our Universe. In this paper, we present a novel phenomenological fit to the Planck, WMAP polarization (WP) and the BICEP2 data sets using an alternative parametrization. Instead of starting from inflationary potentials and computing the inflationary observables, we use a phenomenological parametrization due to Mukhanov, describing inflation by an effective equation of state, in terms of the number of e-folds and two phenomenological parameters α and β. Within such a parametrization, which captures the different inflationary models in a model-independent way, the values of the scalar spectral index ns, its running and the tensor-to-scalar ratio r are predicted, given a set of parameters (α ,β). We perform a Markov Chain Monte Carlo analysis of these parameters, and we show that the combined analysis of Planck and WP data favors the Starobinsky and Higgs inflation scenarios. Assuming that the BICEP2 signal is not entirely due to foregrounds, the addition of this last data set prefers instead the ϕ2 chaotic models. The constraint we get from Planck and WP data alone on the derived tensor-to-scalar ratio is r <0.18 at 95% C.L., value which is consistent with the one quoted from the BICEP2 Collaboration analysis, r =0.16-0.05+0-06, after foreground subtraction. This is not necessarily at odds with the 2σ tension found between Planck and BICEP2 measurements when analyzing data in terms of the usual ns and r parameters, given that the parametrization used here, for the preferred value ns≃0.96, allows only for a restricted parameter space in the usual (ns,r) plane.

  2. A Simulated Annealing based Optimization Algorithm for Automatic Variogram Model Fitting

    NASA Astrophysics Data System (ADS)

    Soltani-Mohammadi, Saeed; Safa, Mohammad

    2016-09-01

    Fitting a theoretical model to an experimental variogram is an important issue in geostatistical studies because if the variogram model parameters are tainted with uncertainty, the latter will spread in the results of estimations and simulations. Although the most popular fitting method is fitting by eye, in some cases use is made of the automatic fitting method on the basis of putting together the geostatistical principles and optimization techniques to: 1) provide a basic model to improve fitting by eye, 2) fit a model to a large number of experimental variograms in a short time, and 3) incorporate the variogram related uncertainty in the model fitting. Effort has been made in this paper to improve the quality of the fitted model by improving the popular objective function (weighted least squares) in the automatic fitting. Also, since the variogram model function (£) and number of structures (m) too affect the model quality, a program has been provided in the MATLAB software that can present optimum nested variogram models using the simulated annealing method. Finally, to select the most desirable model from among the single/multi-structured fitted models, use has been made of the cross-validation method, and the best model has been introduced to the user as the output. In order to check the capability of the proposed objective function and the procedure, 3 case studies have been presented.

  3. A quantitative confidence signal detection model: 1. Fitting psychometric functions

    PubMed Central

    Yi, Yongwoo

    2016-01-01

    Perceptual thresholds are commonly assayed in the laboratory and clinic. When precision and accuracy are required, thresholds are quantified by fitting a psychometric function to forced-choice data. The primary shortcoming of this approach is that it typically requires 100 trials or more to yield accurate (i.e., small bias) and precise (i.e., small variance) psychometric parameter estimates. We show that confidence probability judgments combined with a model of confidence can yield psychometric parameter estimates that are markedly more precise and/or markedly more efficient than conventional methods. Specifically, both human data and simulations show that including confidence probability judgments for just 20 trials can yield psychometric parameter estimates that match the precision of those obtained from 100 trials using conventional analyses. Such an efficiency advantage would be especially beneficial for tasks (e.g., taste, smell, and vestibular assays) that require more than a few seconds for each trial, but this potential benefit could accrue for many other tasks. PMID:26763777

  4. Comparing the Fit of Item Response Theory and Factor Analysis Models

    ERIC Educational Resources Information Center

    Maydeu-Olivares, Alberto; Cai, Li; Hernandez, Adolfo

    2011-01-01

    Linear factor analysis (FA) models can be reliably tested using test statistics based on residual covariances. We show that the same statistics can be used to reliably test the fit of item response theory (IRT) models for ordinal data (under some conditions). Hence, the fit of an FA model and of an IRT model to the same data set can now be…

  5. Convergence, Admissibility, and Fit of Alternative Confirmatory Factor Analysis Models for MTMM Data

    ERIC Educational Resources Information Center

    Lance, Charles E.; Fan, Yi

    2016-01-01

    We compared six different analytic models for multitrait-multimethod (MTMM) data in terms of convergence, admissibility, and model fit to 258 samples of previously reported data. Two well-known models, the correlated trait-correlated method (CTCM) and the correlated trait-correlated uniqueness (CTCU) models, were fit for reference purposes in…

  6. An Application of M[subscript 2] Statistic to Evaluate the Fit of Cognitive Diagnostic Models

    ERIC Educational Resources Information Center

    Liu, Yanlou; Tian, Wei; Xin, Tao

    2016-01-01

    The fit of cognitive diagnostic models (CDMs) to response data needs to be evaluated, since CDMs might yield misleading results when they do not fit the data well. Limited-information statistic M[subscript 2] and the associated root mean square error of approximation (RMSEA[subscript 2]) in item factor analysis were extended to evaluate the fit of…

  7. Keratoconus, cross-link-induction, comparison between fitting exponential function and a fitting equation obtained by a mathematical model.

    PubMed

    Albanese, A; Urso, R; Bianciardi, L; Rigato, M; Battisti, E

    2009-11-01

    With reference to experimental data in the literature, we present a model consisting of two elastic elements, conceived to simulate resistance to stretching, at constant velocity of elongation, of corneal tissue affected by keratoconus, treated with riboflavin and ultraviolet irradiation to induce cross-linking. The function describing model behaviour adapted to stress and strain values. It was found that the Young's moduli of the two elastic elements increased in cross-linked tissues and that cross-linking treatment therefore increased corneal rigidity. It is recognized that this observation is substantially in line with the conclusion reported in the literature, obtained using an exponential fitting function. It is observed, however, that the latter function implies a condition of non-zero stresses without strain, and does not provide interpretative insights for lack of any biomechanical basis. Above all, the function fits a singular trend, inexplicably claimed to be viscoelastic, with surprising perfection. In any case, using the reported data, the study demonstrates that a fitting equation obtained by a modelling approach not only shows the evident efficacy of the treatment, but also provides orientations for studying modifications induced in cross-linked fibres.

  8. Regularization Methods for Fitting Linear Models with Small Sample Sizes: Fitting the Lasso Estimator Using R

    ERIC Educational Resources Information Center

    Finch, W. Holmes; Finch, Maria E. Hernandez

    2016-01-01

    Researchers and data analysts are sometimes faced with the problem of very small samples, where the number of variables approaches or exceeds the overall sample size; i.e. high dimensional data. In such cases, standard statistical models such as regression or analysis of variance cannot be used, either because the resulting parameter estimates…

  9. Percentile Analysis for Goodness-of-Fit Comparisons of Models to Data

    DTIC Science & Technology

    2014-07-01

    Science, 1, 11-38. Roberts, S., & Pashler, H. (2000). How persuasive is a good fit ? A comment on theory testing . Psychological Review, 107, 358-367...Percentile analysis for goodness -of- fit comparisons of models to data Sangeet Khemlani and J. Gregory Trafton skhemlani@gmail.com, trafton...modeling, it is routine to report a goodness -of- fit index (e.g., R2 or RMSE) between a putative model’s predictions and an observed dataset

  10. EFFICIENT MODEL-FITTING AND MODEL-COMPARISON FOR HIGH-DIMENSIONAL BAYESIAN GEOSTATISTICAL MODELS. (R826887)

    EPA Science Inventory

    Geostatistical models are appropriate for spatially distributed data measured at irregularly spaced locations. We propose an efficient Markov chain Monte Carlo (MCMC) algorithm for fitting Bayesian geostatistical models with substantial numbers of unknown parameters to sizable...

  11. A fitted neoprene garment to cover dressings in swine models.

    PubMed

    Mino, Matthew J; Mauskar, Neil A; Matt, Sara E; Pavlovich, Anna R; Prindeze, Nicholas J; Moffatt, Lauren T; Shupp, Jeffrey W

    2012-12-17

    Domesticated porcine species are commonly used in studies of wound healing, owing to similarities between porcine skin and human skin. Such studies often involve wound dressings, and keeping these dressings intact on the animal can be a challenge. The authors describe a novel and simple technique for constructing a fitted neoprene garment for pigs that covers dressings and maintains their integrity during experiments.

  12. A Comparison of Model-Data Fit for Parametric and Nonparametric Item Response Theory Models Using Ordinal-Level Ratings

    ERIC Educational Resources Information Center

    Dyehouse, Melissa A.

    2009-01-01

    This study compared the model-data fit of a parametric item response theory (PIRT) model to a nonparametric item response theory (NIRT) model to determine the best-fitting model for use with ordinal-level alternate assessment ratings. The PIRT Generalized Graded Unfolding Model (GGUM) was compared to the NIRT Mokken model. Chi-square statistics…

  13. The Search for "Optimal" Cutoff Properties: Fit Index Criteria in Structural Equation Modeling

    ERIC Educational Resources Information Center

    Sivo, Stephen A.; Xitao, Fan; Witta, E. Lea; Willse, John T.

    2006-01-01

    This study is a partial replication of L. Hu and P. M. Bentler's (1999) fit criteria work. The purpose of this study was twofold: (a) to determine whether cut-off values vary according to which model is the true population model for a dataset and (b) to identify which of 13 fit indexes behave optimally by retaining all of the correct models while…

  14. Model Fitting for Predicted Precipitation in Darwin: Some Issues with Model Choice

    ERIC Educational Resources Information Center

    Farmer, Jim

    2010-01-01

    In Volume 23(2) of the "Australian Senior Mathematics Journal," Boncek and Harden present an exercise in fitting a Markov chain model to rainfall data for Darwin Airport (Boncek & Harden, 2009). Days are subdivided into those with precipitation and precipitation-free days. The author abbreviates these labels to wet days and dry days.…

  15. A Cautionary Note on the Use of Information Fit Indexes in Covariance Structure Modeling with Means

    ERIC Educational Resources Information Center

    Wicherts, Jelte M.; Dolan, Conor V.

    2004-01-01

    Information fit indexes such as Akaike Information Criterion, Consistent Akaike Information Criterion, Bayesian Information Criterion, and the expected cross validation index can be valuable in assessing the relative fit of structural equation models that differ regarding restrictiveness. In cases in which models without mean restrictions (i.e.,…

  16. Performance of the Generalized S-X[Superscript 2] Item Fit Index for Polytomous IRT Models

    ERIC Educational Resources Information Center

    Kang, Taehoon; Chen, Troy T.

    2008-01-01

    Orlando and Thissen's S-X[superscript 2] item fit index has performed better than traditional item fit statistics such as Yen' s Q[subscript 1] and McKinley and Mill' s G[superscript 2] for dichotomous item response theory (IRT) models. This study extends the utility of S-X[superscript 2] to polytomous IRT models, including the generalized partial…

  17. Why Should We Assess the Goodness-of-Fit of IRT Models?

    ERIC Educational Resources Information Center

    Maydeu-Olivares, Alberto

    2013-01-01

    In this rejoinder, Maydeu-Olivares states that, in item response theory (IRT) measurement applications, the application of goodness-of-fit (GOF) methods informs researchers of the discrepancy between the model and the data being fitted (the room for improvement). By routinely reporting the GOF of IRT models, together with the substantive results…

  18. Residuals and the Residual-Based Statistic for Testing Goodness of Fit of Structural Equation Models

    ERIC Educational Resources Information Center

    Foldnes, Njal; Foss, Tron; Olsson, Ulf Henning

    2012-01-01

    The residuals obtained from fitting a structural equation model are crucial ingredients in obtaining chi-square goodness-of-fit statistics for the model. The authors present a didactic discussion of the residuals, obtaining a geometrical interpretation by recognizing the residuals as the result of oblique projections. This sheds light on the…

  19. A Model-Based Approach to Goodness-of-Fit Evaluation in Item Response Theory

    ERIC Educational Resources Information Center

    Oberski, Daniel L.; Vermunt, Jeroen K.

    2013-01-01

    These authors congratulate Albert Maydeu-Olivares on his lucid and timely overview of goodness-of-fit assessment in IRT models, a field to which he himself has contributed considerably in the form of limited information statistics. In this commentary, Oberski and Vermunt focus on two aspects of model fit: (1) what causes there may be of misfit;…

  20. Approximations to the Distributions of Fit Indexes for Misspecified Structural Equation Models.

    ERIC Educational Resources Information Center

    Ogasawara, Haruhiko

    2001-01-01

    Derives approximations to the distributions of goodness-of-fit indexes in structural equation modeling with the assumption of multivariate normality and slight misspecification of models. Also derives an approximation to the asymptotic covariance matrix for the fit indexes by using the delta method and develops approximations to the densities of…

  1. Fitting Multilevel Models with Ordinal Outcomes: Performance of Alternative Specifications and Methods of Estimation

    ERIC Educational Resources Information Center

    Bauer, Daniel J.; Sterba, Sonya K.

    2011-01-01

    Previous research has compared methods of estimation for fitting multilevel models to binary data, but there are reasons to believe that the results will not always generalize to the ordinal case. This article thus evaluates (a) whether and when fitting multilevel linear models to ordinal outcome data is justified and (b) which estimator to employ…

  2. Fitting the Rasch Model to Account for Variation in Item Discrimination

    ERIC Educational Resources Information Center

    Weitzman, R. A.

    2009-01-01

    Building on the Kelley and Gulliksen versions of classical test theory, this article shows that a logistic model having only a single item parameter can account for varying item discrimination, as well as difficulty, by using item-test correlations to adjust incorrect-correct (0-1) item responses prior to an initial model fit. The fit occurs…

  3. An accurate halo model for fitting non-linear cosmological power spectra and baryonic feedback models

    NASA Astrophysics Data System (ADS)

    Mead, A. J.; Peacock, J. A.; Heymans, C.; Joudaki, S.; Heavens, A. F.

    2015-12-01

    We present an optimized variant of the halo model, designed to produce accurate matter power spectra well into the non-linear regime for a wide range of cosmological models. To do this, we introduce physically motivated free parameters into the halo-model formalism and fit these to data from high-resolution N-body simulations. For a variety of Λ cold dark matter (ΛCDM) and wCDM models, the halo-model power is accurate to ≃ 5 per cent for k ≤ 10h Mpc-1 and z ≤ 2. An advantage of our new halo model is that it can be adapted to account for the effects of baryonic feedback on the power spectrum. We demonstrate this by fitting the halo model to power spectra from the OWLS (OverWhelmingly Large Simulations) hydrodynamical simulation suite via parameters that govern halo internal structure. We are able to fit all feedback models investigated at the 5 per cent level using only two free parameters, and we place limits on the range of these halo parameters for feedback models investigated by the OWLS simulations. Accurate predictions to high k are vital for weak-lensing surveys, and these halo parameters could be considered nuisance parameters to marginalize over in future analyses to mitigate uncertainty regarding the details of feedback. Finally, we investigate how lensing observables predicted by our model compare to those from simulations and from HALOFIT for a range of k-cuts and feedback models and quantify the angular scales at which these effects become important. Code to calculate power spectra from the model presented in this paper can be found at https://github.com/alexander-mead/hmcode.

  4. Aiming towards improved flood forecasting: Identification of an adequate model structure for a semi-arid and data-scarce region

    NASA Astrophysics Data System (ADS)

    Pilz, Tobias; Francke, Till; Bronstert, Axel

    2015-04-01

    A lot of effort has already been put into the development of forecasting systems to warn people of approaching flood events. Such systems, however, are influenced by various sources of uncertainty which constrain the skill of forecasts. The main goal of this study is the identification, quantification and reduction of uncertainties to provide improved early warnings with adequate lead times in a data-scarce region with strong seasonality of the hydrological regime. This includes the setup of hydrological models and post-processing of simulation results by mathematical means such as data assimilation. The focus area is the Jaguaribe watershed in northeastern Brazil. The region is characterized by a seasonal climate with strong inter-annual variation and recurrent droughts. To ensure a secure water supply also during the dry season several thousand small and some large reservoirs have been constructed. On the other hand, floods caused by heavy rain events are an issue as well. This topic, however, so far has hardly been considered by the scientific community and until today no flood forecasting system exists for that region. To identify the most appropriate model structure for the catchment the process-based hydrological model for semi-arid environments WASA was implemented into the eco-hydrological simulation environment ECHSE. The environment consists of a generic part providing data types and simulation methods, and a problem-specific part where the user can implement different model formulations. This provides the possibility to test various process realisations under consistent input and output data structures. The most appropriate model structure can then be determined by statistical means such as Bayesian model averaging. Subsequently, forecast results may be updated by post-processing and/or data assimilation. Furthermore, methods of data fusion can be used to combine measurements of different quality and resolution, such as in-situ and remotely sensed data

  5. Model fit versus biological relevance: Evaluating photosynthesis-temperature models for three tropical seagrass species

    NASA Astrophysics Data System (ADS)

    Adams, Matthew P.; Collier, Catherine J.; Uthicke, Sven; Ow, Yan X.; Langlois, Lucas; O’Brien, Katherine R.

    2017-01-01

    When several models can describe a biological process, the equation that best fits the data is typically considered the best. However, models are most useful when they also possess biologically-meaningful parameters. In particular, model parameters should be stable, physically interpretable, and transferable to other contexts, e.g. for direct indication of system state, or usage in other model types. As an example of implementing these recommended requirements for model parameters, we evaluated twelve published empirical models for temperature-dependent tropical seagrass photosynthesis, based on two criteria: (1) goodness of fit, and (2) how easily biologically-meaningful parameters can be obtained. All models were formulated in terms of parameters characterising the thermal optimum (Topt) for maximum photosynthetic rate (Pmax). These parameters indicate the upper thermal limits of seagrass photosynthetic capacity, and hence can be used to assess the vulnerability of seagrass to temperature change. Our study exemplifies an approach to model selection which optimises the usefulness of empirical models for both modellers and ecologists alike.

  6. Model fit versus biological relevance: Evaluating photosynthesis-temperature models for three tropical seagrass species

    PubMed Central

    Adams, Matthew P.; Collier, Catherine J.; Uthicke, Sven; Ow, Yan X.; Langlois, Lucas; O’Brien, Katherine R.

    2017-01-01

    When several models can describe a biological process, the equation that best fits the data is typically considered the best. However, models are most useful when they also possess biologically-meaningful parameters. In particular, model parameters should be stable, physically interpretable, and transferable to other contexts, e.g. for direct indication of system state, or usage in other model types. As an example of implementing these recommended requirements for model parameters, we evaluated twelve published empirical models for temperature-dependent tropical seagrass photosynthesis, based on two criteria: (1) goodness of fit, and (2) how easily biologically-meaningful parameters can be obtained. All models were formulated in terms of parameters characterising the thermal optimum (Topt) for maximum photosynthetic rate (Pmax). These parameters indicate the upper thermal limits of seagrass photosynthetic capacity, and hence can be used to assess the vulnerability of seagrass to temperature change. Our study exemplifies an approach to model selection which optimises the usefulness of empirical models for both modellers and ecologists alike. PMID:28051123

  7. Assessing Fit of Cognitive Diagnostic Models: A Case Study

    ERIC Educational Resources Information Center

    Sinharay, Sandip; Almond, Russell G.

    2007-01-01

    A cognitive diagnostic model uses information from educational experts to describe the relationships between item performances and posited proficiencies. When the cognitive relationships can be described using a fully Bayesian model, Bayesian model checking procedures become available. Checking models tied to cognitive theory of the domains…

  8. Moment-Based Probability Modeling and Extreme Response Estimation, The FITS Routine Version 1.2

    SciTech Connect

    MANUEL,LANCE; KASHEF,TINA; WINTERSTEIN,STEVEN R.

    1999-11-01

    This report documents the use of the FITS routine, which provides automated fits of various analytical, commonly used probability models from input data. It is intended to complement the previously distributed FITTING routine documented in RMS Report 14 (Winterstein et al., 1994), which implements relatively complex four-moment distribution models whose parameters are fit with numerical optimization routines. Although these four-moment fits can be quite useful and faithful to the observed data, their complexity can make them difficult to automate within standard fitting algorithms. In contrast, FITS provides more robust (lower moment) fits of simpler, more conventional distribution forms. For each database of interest, the routine estimates the distribution of annual maximum response based on the data values and the duration, T, over which they were recorded. To focus on the upper tails of interest, the user can also supply an arbitrary lower-bound threshold, {chi}{sub low}, above which a shifted distribution model--exponential or Weibull--is fit.

  9. On the Use of Nonparametric Item Characteristic Curve Estimation Techniques for Checking Parametric Model Fit

    ERIC Educational Resources Information Center

    Lee, Young-Sun; Wollack, James A.; Douglas, Jeffrey

    2009-01-01

    The purpose of this study was to assess the model fit of a 2PL through comparison with the nonparametric item characteristic curve (ICC) estimation procedures. Results indicate that three nonparametric procedures implemented produced ICCs that are similar to that of the 2PL for items simulated to fit the 2PL. However for misfitting items,…

  10. Goodness of Fit Confirmatory Factor Analysis: The Effects of Sample Size and Model Parsimony.

    ERIC Educational Resources Information Center

    Marsh, Herbert W.; Balla, John

    The influence of sample size (N) and model parsimony on a set of 22 goodness of fit indices was investigated, including those typically used in confirmatory factor analysis and some recently developed indices. For sample data simulated from 2 known population data structures, values for 6 of 22 fit indices were reasonably independent of N and were…

  11. Exact Person Fit Indexes for the Rasch Model for Arbitrary Alternatives.

    ERIC Educational Resources Information Center

    Ponocny, Ivo

    2000-01-01

    Introduces a new algorithm for obtaining exact person fit indexes for the Rasch model. The algorithm realizes most tests for a general family of alternative hypotheses, including tests concerning differential item functioning. The method is also used as a goodness-of-fit test in some circumstances. Simulated examples and an empirical investigation…

  12. Covariance Structure Model Fit Testing under Missing Data: An Application of the Supplemented EM Algorithm

    ERIC Educational Resources Information Center

    Cai, Li; Lee, Taehun

    2009-01-01

    We apply the Supplemented EM algorithm (Meng & Rubin, 1991) to address a chronic problem with the "two-stage" fitting of covariance structure models in the presence of ignorable missing data: the lack of an asymptotically chi-square distributed goodness-of-fit statistic. We show that the Supplemented EM algorithm provides a…

  13. An experimentally determined evolutionary model dramatically improves phylogenetic fit.

    PubMed

    Bloom, Jesse D

    2014-08-01

    All modern approaches to molecular phylogenetics require a quantitative model for how genes evolve. Unfortunately, existing evolutionary models do not realistically represent the site-heterogeneous selection that governs actual sequence change. Attempts to remedy this problem have involved augmenting these models with a burgeoning number of free parameters. Here, I demonstrate an alternative: Experimental determination of a parameter-free evolutionary model via mutagenesis, functional selection, and deep sequencing. Using this strategy, I create an evolutionary model for influenza nucleoprotein that describes the gene phylogeny far better than existing models with dozens or even hundreds of free parameters. Emerging high-throughput experimental strategies such as the one employed here provide fundamentally new information that has the potential to transform the sensitivity of phylogenetic and genetic analyses.

  14. Fitting and Testing Conditional Multinormal Partial Credit Models

    ERIC Educational Resources Information Center

    Hessen, David J.

    2012-01-01

    A multinormal partial credit model for factor analysis of polytomously scored items with ordered response categories is derived using an extension of the Dutch Identity (Holland in "Psychometrika" 55:5-18, 1990). In the model, latent variables are assumed to have a multivariate normal distribution conditional on unweighted sums of item…

  15. Atmospheric Turbulence Modeling for Aero Vehicles: Fractional Order Fits

    NASA Technical Reports Server (NTRS)

    Kopasakis, George

    2010-01-01

    Atmospheric turbulence models are necessary for the design of both inlet/engine and flight controls, as well as for studying coupling between the propulsion and the vehicle structural dynamics for supersonic vehicles. Models based on the Kolmogorov spectrum have been previously utilized to model atmospheric turbulence. In this paper, a more accurate model is developed in its representative fractional order form, typical of atmospheric disturbances. This is accomplished by first scaling the Kolmogorov spectral to convert them into finite energy von Karman forms and then by deriving an explicit fractional circuit-filter type analog for this model. This circuit model is utilized to develop a generalized formulation in frequency domain to approximate the fractional order with the products of first order transfer functions, which enables accurate time domain simulations. The objective of this work is as follows. Given the parameters describing the conditions of atmospheric disturbances, and utilizing the derived formulations, directly compute the transfer function poles and zeros describing these disturbances for acoustic velocity, temperature, pressure, and density. Time domain simulations of representative atmospheric turbulence can then be developed by utilizing these computed transfer functions together with the disturbance frequencies of interest.

  16. Atmospheric Turbulence Modeling for Aero Vehicles: Fractional Order Fits

    NASA Technical Reports Server (NTRS)

    Kopasakis, George

    2015-01-01

    Atmospheric turbulence models are necessary for the design of both inlet/engine and flight controls, as well as for studying coupling between the propulsion and the vehicle structural dynamics for supersonic vehicles. Models based on the Kolmogorov spectrum have been previously utilized to model atmospheric turbulence. In this paper, a more accurate model is developed in its representative fractional order form, typical of atmospheric disturbances. This is accomplished by first scaling the Kolmogorov spectral to convert them into finite energy von Karman forms and then by deriving an explicit fractional circuit-filter type analog for this model. This circuit model is utilized to develop a generalized formulation in frequency domain to approximate the fractional order with the products of first order transfer functions, which enables accurate time domain simulations. The objective of this work is as follows. Given the parameters describing the conditions of atmospheric disturbances, and utilizing the derived formulations, directly compute the transfer function poles and zeros describing these disturbances for acoustic velocity, temperature, pressure, and density. Time domain simulations of representative atmospheric turbulence can then be developed by utilizing these computed transfer functions together with the disturbance frequencies of interest.

  17. Revisiting the global electroweak fit of the Standard Model and beyond with Gfitter

    NASA Astrophysics Data System (ADS)

    Flächer, H.; Goebel, M.; Haller, J.; Hoecker, A.; Mönig, K.; Stelzer, J.

    2009-04-01

    The global fit of the Standard Model to electroweak precision data, routinely performed by the LEP electroweak working group and others, demonstrated impressively the predictive power of electroweak unification and quantum loop corrections. We have revisited this fit in view of (i) the development of the new generic fitting package, Gfitter, allowing for flexible and efficient model testing in high-energy physics, (ii) the insertion of constraints from direct Higgs searches at LEP and the Tevatron, and (iii) a more thorough statistical interpretation of the results. Gfitter is a modular fitting toolkit, which features predictive theoretical models as independent plug-ins, and a statistical analysis of the fit results using toy Monte Carlo techniques. The state-of-the-art electroweak Standard Model is fully implemented, as well as generic extensions to it. Theoretical uncertainties are explicitly included in the fit through scale parameters varying within given error ranges. This paper introduces the Gfitter project, and presents state-of-the-art results for the global electroweak fit in the Standard Model (SM), and for a model with an extended Higgs sector (2HDM). Numerical and graphical results for fits with and without including the constraints from the direct Higgs searches at LEP and Tevatron are given. Perspectives for future colliders are analysed and discussed. In the SM fit including the direct Higgs searches, we find M H =116.4{-1.3/+18.3} GeV, and the 2 σ and 3 σ allowed regions [114,145] GeV and [[113,168] and [180,225

  18. A stochastic carcinogenesis model incorporating multiple types of genomic instability fitted to colon cancer data.

    PubMed

    Little, Mark P; Vineis, Paolo; Li, Guangquan

    2008-09-21

    A generalization of the two-mutation stochastic carcinogenesis model of Moolgavkar, Venzon and Knudson and certain models constructed by Little [Little, M.P. (1995). Are two mutations sufficient to cause cancer? Some generalizations of the two-mutation model of carcinogenesis of Moolgavkar, Venzon, and Knudson, and of the multistage model of Armitage and Doll. Biometrics 51, 1278-1291] and Little and Wright [Little, M.P., Wright, E.G. (2003). A stochastic carcinogenesis model incorporating genomic instability fitted to colon cancer data. Math. Biosci. 183, 111-134] is developed; the model incorporates multiple types of progressive genomic instability and an arbitrary number of mutational stages. The model is fitted to US Caucasian colon cancer incidence data. On the basis of the comparison of fits to the population-based data, there is little evidence to support the hypothesis that the model with more than one type of genomic instability fits better than models with a single type of genomic instability. Given the good fit of the model to this large dataset, it is unlikely that further information on presence of genomic instability or of types of genomic instability can be extracted from age-incidence data by extensions of this model.

  19. Fitness model for the Italian interbank money market

    NASA Astrophysics Data System (ADS)

    de Masi, G.; Iori, G.; Caldarelli, G.

    2006-12-01

    We use the theory of complex networks in order to quantitatively characterize the formation of communities in a particular financial market. The system is composed by different banks exchanging on a daily basis loans and debts of liquidity. Through topological analysis and by means of a model of network growth we can determine the formation of different group of banks characterized by different business strategy. The model based on Pareto’s law makes no use of growth or preferential attachment and it reproduces correctly all the various statistical properties of the system. We believe that this network modeling of the market could be an efficient way to evaluate the impact of different policies in the market of liquidity.

  20. Fitness model for the Italian interbank money market.

    PubMed

    De Masi, G; Iori, G; Caldarelli, G

    2006-12-01

    We use the theory of complex networks in order to quantitatively characterize the formation of communities in a particular financial market. The system is composed by different banks exchanging on a daily basis loans and debts of liquidity. Through topological analysis and by means of a model of network growth we can determine the formation of different group of banks characterized by different business strategy. The model based on Pareto's law makes no use of growth or preferential attachment and it reproduces correctly all the various statistical properties of the system. We believe that this network modeling of the market could be an efficient way to evaluate the impact of different policies in the market of liquidity.

  1. A no-scale inflationary model to fit them all

    SciTech Connect

    Ellis, John; García, Marcos A.G.; Olive, Keith A.; Nanopoulos, Dimitri V. E-mail: garciagarcia@physics.umn.edu E-mail: olive@physics.umn.edu

    2014-08-01

    The magnitude of B-mode polarization in the cosmic microwave background as measured by BICEP2 favours models of chaotic inflation with a quadratic m{sup 2} φ{sup 2}/2 potential, whereas data from the Planck satellite favour a small value of the tensor-to-scalar perturbation ratio r that is highly consistent with the Starobinsky R +R{sup 2} model. Reality may lie somewhere between these two scenarios. In this paper we propose a minimal two-field no-scale supergravity model that interpolates between quadratic and Starobinsky-like inflation as limiting cases, while retaining the successful prediction n{sub s} ≅ 0.96.

  2. Using proper regression methods for fitting the Langmuir model to sorption data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Langmuir model, originally developed for the study of gas sorption to surfaces, is one of the most commonly used models for fitting phosphorus sorption data. There are good theoretical reasons, however, against applying this model to describe P sorption to soils. Nevertheless, the Langmuir model...

  3. Design of spatial experiments: Model fitting and prediction

    SciTech Connect

    Fedorov, V.V.

    1996-03-01

    The main objective of the paper is to describe and develop model oriented methods and algorithms for the design of spatial experiments. Unlike many other publications in this area, the approach proposed here is essentially based on the ideas of convex design theory.

  4. Fitting Meta-Analytic Structural Equation Models with Complex Datasets

    ERIC Educational Resources Information Center

    Wilson, Sandra Jo; Polanin, Joshua R.; Lipsey, Mark W.

    2016-01-01

    A modification of the first stage of the standard procedure for two-stage meta-analytic structural equation modeling for use with large complex datasets is presented. This modification addresses two common problems that arise in such meta-analyses: (a) primary studies that provide multiple measures of the same construct and (b) the correlation…

  5. Fitting the Balding-Nichols model to forensic databases.

    PubMed

    Rohlfs, Rori V; Aguiar, Vitor R C; Lohmueller, Kirk E; Castro, Amanda M; Ferreira, Alessandro C S; Almeida, Vanessa C O; Louro, Iuri D; Nielsen, Rasmus

    2015-11-01

    Large forensic databases provide an opportunity to compare observed empirical rates of genotype matching with those expected under forensic genetic models. A number of researchers have taken advantage of this opportunity to validate some forensic genetic approaches, particularly to ensure that estimated rates of genotype matching between unrelated individuals are indeed slight overestimates of those observed. However, these studies have also revealed systematic error trends in genotype probability estimates. In this analysis, we investigate these error trends and show how they result from inappropriate implementation of the Balding-Nichols model in the context of database-wide matching. Specifically, we show that in addition to accounting for increased allelic matching between individuals with recent shared ancestry, studies must account for relatively decreased allelic matching between individuals with more ancient shared ancestry.

  6. Mechanical Response of Polycarbonate with Strength Model Fits

    DTIC Science & Technology

    2012-02-01

    Proceedings of the Seventh International Symposium on Ballistics. The Hague (Netherlands), 1983, 541–547. 4. Zerilli, F .; Armstrong, R . A...Constitutive Model Equation for the Dynamic Deformation Behavior of Polymers. J. Material Sci. 2007, 42 (12), 4562–4574. 5. Zerilli, F .; Armstrong, R ...Polyvinylidene Diflouride. J. Polymer. 2005, 46, 12546–12555. 19. Richeton, J.; Ahzi, S.; Vecchio, K. S.; Jiang, F . C.; Adharapurapu, R . R . Influence of

  7. Parameter fitting for piano sound synthesis by physical modeling

    NASA Astrophysics Data System (ADS)

    Bensa, Julien; Gipouloux, Olivier; Kronland-Martinet, Richard

    2005-07-01

    A difficult issue in the synthesis of piano tones by physical models is to choose the values of the parameters governing the hammer-string model. In fact, these parameters are hard to estimate from static measurements, causing the synthesis sounds to be unrealistic. An original approach that estimates the parameters of a piano model, from the measurement of the string vibration, by minimizing a perceptual criterion is proposed. The minimization process that was used is a combination of a gradient method and a simulated annealing algorithm, in order to avoid convergence problems in case of multiple local minima. The criterion, based on the tristimulus concept, takes into account the spectral energy density in three bands, each allowing particular parameters to be estimated. The optimization process has been run on signals measured on an experimental setup. The parameters thus estimated provided a better sound quality than the one obtained using a global energetic criterion. Both the sound's attack and its brightness were better preserved. This quality gain was obtained for parameter values very close to the initial ones, showing that only slight deviations are necessary to make synthetic sounds closer to the real ones.

  8. On assessing model fit for distribution-free longitudinal models under missing data.

    PubMed

    Wu, P; Tu, X M; Kowalski, J

    2014-01-15

    The generalized estimating equation (GEE), a distribution-free, or semi-parametric, approach for modeling longitudinal data, is used in a wide range of behavioral, psychotherapy, pharmaceutical drug safety, and healthcare-related research studies. Most popular methods for assessing model fit are based on the likelihood function for parametric models, rendering them inappropriate for distribution-free GEE. One rare exception is a score statistic initially proposed by Tsiatis for logistic regression (1980) and later extended by Barnhart and Willamson to GEE (1998). Because GEE only provides valid inference under the missing completely at random assumption and missing values arising in most longitudinal studies do not follow such a restricted mechanism, this GEE-based score test has very limited applications in practice. We propose extensions of this goodness-of-fit test to address missing data under the missing at random assumption, a more realistic model that applies to most studies in practice. We examine the performance of the proposed tests using simulated data and demonstrate the utilities of such tests with data from a real study on geriatric depression and associated medical comorbidities.

  9. Genetic algorithm with an improved fitness function for (N)ARX modelling

    NASA Astrophysics Data System (ADS)

    Chen, Q.; Worden, K.; Peng, P.; Leung, A. Y. T.

    2007-02-01

    In this article a new fitness function is introduced in an attempt to improve the quality of the auto-regressive with exogenous inputs (ARX) model using a genetic algorithm (GA). The GA is employed to identify the coefficients and the number of time lags of the models of dynamic systems with the new fitness function which is based on the prediction error and the correlation functions between the prediction error and the input and output signals. The new fitness function provides the GA with a better performance in the evolution process. Two examples of the ARX modelling of a linear and a non-linear (NARX) simulated dynamic system are examined using the proposed fitness function.

  10. Network growth models: A behavioural basis for attachment proportional to fitness

    NASA Astrophysics Data System (ADS)

    Bell, Michael; Perera, Supun; Piraveenan, Mahendrarajah; Bliemer, Michiel; Latty, Tanya; Reid, Chris

    2017-02-01

    Several growth models have been proposed in the literature for scale-free complex networks, with a range of fitness-based attachment models gaining prominence recently. However, the processes by which such fitness-based attachment behaviour can arise are less well understood, making it difficult to compare the relative merits of such models. This paper analyses an evolutionary mechanism that would give rise to a fitness-based attachment process. In particular, it is proven by analytical and numerical methods that in homogeneous networks, the minimisation of maximum exposure to node unfitness leads to attachment probabilities that are proportional to node fitness. This result is then extended to heterogeneous networks, with supply chain networks being used as an example.

  11. Network growth models: A behavioural basis for attachment proportional to fitness

    PubMed Central

    Bell, Michael; Perera, Supun; Piraveenan, Mahendrarajah; Bliemer, Michiel; Latty, Tanya; Reid, Chris

    2017-01-01

    Several growth models have been proposed in the literature for scale-free complex networks, with a range of fitness-based attachment models gaining prominence recently. However, the processes by which such fitness-based attachment behaviour can arise are less well understood, making it difficult to compare the relative merits of such models. This paper analyses an evolutionary mechanism that would give rise to a fitness-based attachment process. In particular, it is proven by analytical and numerical methods that in homogeneous networks, the minimisation of maximum exposure to node unfitness leads to attachment probabilities that are proportional to node fitness. This result is then extended to heterogeneous networks, with supply chain networks being used as an example. PMID:28205599

  12. Variable Transformation in Nonlinear Least Squares model Fitting

    DTIC Science & Technology

    1981-07-01

    Chemistry, Vol. 10, pp. 91-104, 1973. 11. H.J. Britt and R.H. Luecke , "The Estimation of Parameters in Nonlinear, Implicit Models", Technometrics, Vol...respect to the unknown C, 6, and K. This yields the following set of normal equations. 11 H.J, Britt and H.H. Lueake, "The Estimation of...Carbide Corporation Chemicals and Plastics ATTN: H.J. Britt P.O. Box 8361 Charleston, WV 25303 California Institute of Tech Guggenheim Aeronautical

  13. CPOPT : optimization for fitting CANDECOMP/PARAFAC models.

    SciTech Connect

    Dunlavy, Daniel M.; Kolda, Tamara Gibson; Acar, Evrim

    2008-10-01

    Tensor decompositions (e.g., higher-order analogues of matrix decompositions) are powerful tools for data analysis. In particular, the CANDECOMP/PARAFAC (CP) model has proved useful in many applications such chemometrics, signal processing, and web analysis; see for details. The problem of computing the CP decomposition is typically solved using an alternating least squares (ALS) approach. We discuss the use of optimization-based algorithms for CP, including how to efficiently compute the derivatives necessary for the optimization methods. Numerical studies highlight the positive features of our CPOPT algorithms, as compared with ALS and Gauss-Newton approaches.

  14. Fitting meta-analytic structural equation models with complex datasets.

    PubMed

    Wilson, Sandra Jo; Polanin, Joshua R; Lipsey, Mark W

    2016-06-01

    A modification of the first stage of the standard procedure for two-stage meta-analytic structural equation modeling for use with large complex datasets is presented. This modification addresses two common problems that arise in such meta-analyses: (a) primary studies that provide multiple measures of the same construct and (b) the correlation coefficients that exhibit substantial heterogeneity, some of which obscures the relationships between the constructs of interest or undermines the comparability of the correlations across the cells. One component of this approach is a three-level random effects model capable of synthesizing a pooled correlation matrix with dependent correlation coefficients. Another component is a meta-regression that can be used to generate covariate-adjusted correlation coefficients that reduce the influence of selected unevenly distributed moderator variables. A non-technical presentation of these techniques is given, along with an illustration of the procedures with a meta-analytic dataset. Copyright © 2016 John Wiley & Sons, Ltd.

  15. Adaptation in Tunably Rugged Fitness Landscapes: The Rough Mount Fuji Model

    PubMed Central

    Neidhart, Johannes; Szendro, Ivan G.; Krug, Joachim

    2014-01-01

    Much of the current theory of adaptation is based on Gillespie’s mutational landscape model (MLM), which assumes that the fitness values of genotypes linked by single mutational steps are independent random variables. On the other hand, a growing body of empirical evidence shows that real fitness landscapes, while possessing a considerable amount of ruggedness, are smoother than predicted by the MLM. In the present article we propose and analyze a simple fitness landscape model with tunable ruggedness based on the rough Mount Fuji (RMF) model originally introduced by Aita et al. in the context of protein evolution. We provide a comprehensive collection of results pertaining to the topographical structure of RMF landscapes, including explicit formulas for the expected number of local fitness maxima, the location of the global peak, and the fitness correlation function. The statistics of single and multiple adaptive steps on the RMF landscape are explored mainly through simulations, and the results are compared to the known behavior in the MLM model. Finally, we show that the RMF model can explain the large number of second-step mutations observed on a highly fit first-step background in a recent evolution experiment with a microvirid bacteriophage. PMID:25123507

  16. Use of a simulated annealing algorithm to fit compartmental models with an application to fractal pharmacokinetics.

    PubMed

    Marsh, Rebeccah E; Riauka, Terence A; McQuarrie, Steve A

    2007-01-01

    Increasingly, fractals are being incorporated into pharmacokinetic models to describe transport and chemical kinetic processes occurring in confined and heterogeneous spaces. However, fractal compartmental models lead to differential equations with power-law time-dependent kinetic rate coefficients that currently are not accommodated by common commercial software programs. This paper describes a parameter optimization method for fitting individual pharmacokinetic curves based on a simulated annealing (SA) algorithm, which always converged towards the global minimum and was independent of the initial parameter values and parameter bounds. In a comparison using a classical compartmental model, similar fits by the Gauss-Newton and Nelder-Mead simplex algorithms required stringent initial estimates and ranges for the model parameters. The SA algorithm is ideal for fitting a wide variety of pharmacokinetic models to clinical data, especially those for which there is weak prior knowledge of the parameter values, such as the fractal models.

  17. 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…

  18. Hydrothermal germination models: comparison of two data-fitting approaches with probit optimization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Probit models for estimating hydrothermal germination rate yield model parameters that have been associated with specific physiological processes. The desirability of linking germination response to seed physiology must be weighed against expectations of model fit and the relative accuracy of predi...

  19. Revisiting a Statistical Shortcoming When Fitting the Langmuir Model to Sorption Data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Langmuir model is commonly used for describing sorption behavior of reactive solutes to surfaces. Fitting the Langmuir model to sorption data requires either the use of nonlinear regression or, alternatively, linear regression using one of the linearized versions of the model. Statistical limit...

  20. Development of a program to fit data to a new logistic model for microbial growth.

    PubMed

    Fujikawa, Hiroshi; Kano, Yoshihiro

    2009-06-01

    Recently we developed a mathematical model for microbial growth in food. The model successfully predicted microbial growth at various patterns of temperature. In this study, we developed a program to fit data to the model with a spread sheet program, Microsoft Excel. Users can instantly get curves fitted to the model by inputting growth data and choosing the slope portion of a curve. The program also could estimate growth parameters including the rate constant of growth and the lag period. This program would be a useful tool for analyzing growth data and further predicting microbial growth.

  1. Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

    NASA Astrophysics Data System (ADS)

    Shekhar, Karthik; Ruberman, Claire F.; Ferguson, Andrew L.; Barton, John P.; Kardar, Mehran; Chakraborty, Arup K.

    2013-12-01

    Mutational escape from vaccine-induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic sequence can enable rational design of potent vaccines, as this information can focus vaccine-induced immune responses to target mutational vulnerabilities of the virus. Spin models have been proposed as a means to infer intrinsic fitness landscapes of HIV proteins from patient-derived viral protein sequences. These sequences are the product of nonequilibrium viral evolution driven by patient-specific immune responses and are subject to phylogenetic constraints. How can such sequence data allow inference of intrinsic fitness landscapes? We combined computer simulations and variational theory á la Feynman to show that, in most circumstances, spin models inferred from patient-derived viral sequences reflect the correct rank order of the fitness of mutant viral strains. Our findings are relevant for diverse viruses.

  2. Atmospheric Properties Of T Dwarfs Inferred From Model Fits At Low Spectral Resolution

    NASA Astrophysics Data System (ADS)

    Giorla Godfrey, Paige A.; Rice, Emily L.; Filippazzo, Joseph C.; Douglas, Stephanie E.

    2016-09-01

    Brown dwarf spectral types (M, L, T, Y) correlate with spectral morphology, and generally appear to correspond with decreasing mass and effective temperature (Teff). Model fits to observed spectra suggest, however, that spectral subclasses do not share this monotonic temperature correlation, indicating that secondary parameters (gravity, metallicity, dust) significantly influence spectral morphology. We seekto disentangle the fundamental parameters that underlie the spectral type sequence of the coolest fully populated spectral class of brown dwarfs using atmosphere models. We investigate the relationship between spectral type and best fit model parameters for a sample of over 150 T dwarfs with low resolution (R 75-100) near-infrared ( 0.8-2.5 micron) SpeX Prism spectra. We use synthetic spectra from four model grids (Saumon & Marley 2008, Morley+ 2012, Saumon+ 2012, BT Settl 2013) and a Markov-Chain Monte Carlo (MCMC) analysis to determine robust best fit parameters and their uncertainties. We compare the consistency of each model grid by performing our analysis on the full spectrum and also on individual wavelength bands (Y,J,H,K). We find more consistent results between the J band and full spectrum fits and that our best fit spectral type-Teff results agree with the polynomial relationships of Stephens+2009 and Filippazzo+ 2015 using bolometric luminosities. Our analysis consists of the most extensive low resolution T dwarf model comparison to date, and lays the foundation for interpretation of cool brown dwarf and exoplanet spectra.

  3. Soft X-ray spectral fits of Geminga with model neutron star atmospheres

    NASA Technical Reports Server (NTRS)

    Meyer, R. D.; Pavlov, G. G.; Meszaros, P.

    1994-01-01

    The spectrum of the soft X-ray pulsar Geminga consists of two components, a softer one which can be interpreted as thermal-like radiation from the surface of the neutron star, and a harder one interpreted as radiation from a polar cap heated by relativistic particles. We have fitted the soft spectrum using a detailed magnetized hydrogen atmosphere model. The fitting parameters are the hydrogen column density, the effective temperature T(sub eff), the gravitational redshift z, and the distance to radius ratio, for different values of the magnetic field B. The best fits for this model are obtained when B less than or approximately 1 x 10(exp 12) G and z lies on the upper boundary of the explored range (z = 0.45). The values of T(sub eff) approximately = (2-3) x 10(exp 5) K are a factor of 2-3 times lower than the value of T(sub eff) obtained for blackbody fits with the same z. The lower T(sub eff) increases the compatibility with some proposed schemes for fast neutrino cooling of neutron stars (NSs) by the direct Urca process or by exotic matter, but conventional cooling cannot be excluded. The hydrogen atmosphere fits also imply a smaller distance to Geminga than that inferred from a blackbody fit. An accurate evaluation of the distance would require a better knowledge of the ROSAT Position Sensitive Proportional Counter (PSPC) response to the low-energy region of the incident spectrum. Our modeling of the soft component with a cooler magnetized atmosphere also implies that the hard-component fit requires a characteristic temperature which is higher (by a factor of approximately 2-3) and a surface area which is smaller (by a factor of 10(exp 3), compared to previous blackbody fits.

  4. Finite population size effects in quasispecies models with single-peak fitness landscape

    NASA Astrophysics Data System (ADS)

    Saakian, David B.; Deem, Michael W.; Hu, Chin-Kun

    2012-04-01

    We consider finite population size effects for Crow-Kimura and Eigen quasispecies models with single-peak fitness landscape. We formulate accurately the iteration procedure for the finite population models, then derive the Hamilton-Jacobi equation (HJE) to describe the dynamic of the probability distribution. The steady-state solution of HJE gives the variance of the mean fitness. Our results are useful for understanding the population sizes of viruses in which the infinite population models can give reliable results for biological evolution problems.

  5. Optimization-Based Model Fitting for Latent Class and Latent Profile Analyses

    ERIC Educational Resources Information Center

    Huang, Guan-Hua; Wang, Su-Mei; Hsu, Chung-Chu

    2011-01-01

    Statisticians typically estimate the parameters of latent class and latent profile models using the Expectation-Maximization algorithm. This paper proposes an alternative two-stage approach to model fitting. The first stage uses the modified k-means and hierarchical clustering algorithms to identify the latent classes that best satisfy the…

  6. Status Characteristics and Expectation States: Fitting and Testing a Recent Model.

    ERIC Educational Resources Information Center

    Fox, John; Moore, James C., Jr.

    1979-01-01

    Fourteen experimental studies were reviewed using linear model of Berger et al. The model fits the data from these experiments remarkably well. These results demonstrate the utility and apparent validity of this theory of status-organizing processes. (Author/RD)

  7. Genetic Model Fitting in IQ, Assortative Mating & Components of IQ Variance.

    ERIC Educational Resources Information Center

    Capron, Christiane; Vetta, Adrian R.; Vetta, Atam

    1998-01-01

    The biometrical school of scientists who fit models to IQ data traces their intellectual ancestry to R. Fisher (1918), but their genetic models have no predictive value. Fisher himself was critical of the concept of heritability, because assortative mating, such as for IQ, introduces complexities into the study of a genetic trait. (SLD)

  8. Detecting Growth Shape Misspecifications in Latent Growth Models: An Evaluation of Fit Indexes

    ERIC Educational Resources Information Center

    Leite, Walter L.; Stapleton, Laura M.

    2011-01-01

    In this study, the authors compared the likelihood ratio test and fit indexes for detection of misspecifications of growth shape in latent growth models through a simulation study and a graphical analysis. They found that the likelihood ratio test, MFI, and root mean square error of approximation performed best for detecting model misspecification…

  9. An Assessment of the Nonparametric Approach for Evaluating the Fit of Item Response Models

    ERIC Educational Resources Information Center

    Liang, Tie; Wells, Craig S.; Hambleton, Ronald K.

    2014-01-01

    As item response theory has been more widely applied, investigating the fit of a parametric model becomes an important part of the measurement process. There is a lack of promising solutions to the detection of model misfit in IRT. Douglas and Cohen introduced a general nonparametric approach, RISE (Root Integrated Squared Error), for detecting…

  10. Automated fit quantification of tibial nail designs during the insertion using computer three-dimensional modelling.

    PubMed

    Amarathunga, Jayani P; Schuetz, Michael A; Yarlagadda, Prasad Kvd; Schmutz, Beat

    2014-12-01

    Intramedullary nailing is the standard fixation method for displaced diaphyseal fractures of the tibia. An optimal nail design should both facilitate insertion and anatomically fit the bone geometry at its final position in order to reduce the risk of stress fractures and malalignments. Due to the nonexistence of suitable commercial software, we developed a software tool for the automated fit assessment of nail designs. Furthermore, we demonstrated that an optimised nail, which fits better at the final position, is also easier to insert. Three-dimensional models of two nail designs and 20 tibiae were used. The fitting was quantified in terms of surface area, maximum distance, sum of surface areas and sum of maximum distances by which the nail was protruding into the cortex. The software was programmed to insert the nail into the bone model and to quantify the fit at defined increment levels. On average, the misfit during the insertion in terms of the four fitting parameters was smaller for the Expert Tibial Nail Proximal bend (476.3 mm(2), 1.5 mm, 2029.8 mm(2), 6.5 mm) than the Expert Tibial Nail (736.7 mm(2), 2.2 mm, 2491.4 mm(2), 8.0 mm). The differences were statistically significant (p ≤ 0.05). The software could be used by nail implant manufacturers for the purpose of implant design validation.

  11. Development and design of a late-model fitness test instrument based on LabView

    NASA Astrophysics Data System (ADS)

    Xie, Ying; Wu, Feiqing

    2010-12-01

    Undergraduates are pioneers of China's modernization program and undertake the historic mission of rejuvenating our nation in the 21st century, whose physical fitness is vital. A smart fitness test system can well help them understand their fitness and health conditions, thus they can choose more suitable approaches and make practical plans for exercising according to their own situation. following the future trends, a Late-model fitness test Instrument based on LabView has been designed to remedy defects of today's instruments. The system hardware consists of fives types of sensors with their peripheral circuits, an acquisition card of NI USB-6251 and a computer, while the system software, on the basis of LabView, includes modules of user register, data acquisition, data process and display, and data storage. The system, featured by modularization and an open structure, is able to be revised according to actual needs. Tests results have verified the system's stability and reliability.

  12. Space charge modeling in electron-beam irradiated polyethylene: Fitting model and experiments

    SciTech Connect

    Le Roy, S.; Laurent, C.; Teyssedre, G.; Baudoin, F.; Griseri, V.

    2012-07-15

    A numerical model for describing charge accumulation in electron-beam irradiated low density polyethylene has been put forward recently. It encompasses the generation of positive and negative charges due to impinging electrons and their transport in the insulation. However, the model was not optimized to fit all the data available regarding space charge dynamics obtained using up-to-date pulsed electro-acoustic techniques. In the present approach, model outputs are compared with experimental space charge distribution obtained during irradiation and post-irradiation, the irradiated samples being in short circuit conditions or with the irradiated surface at a floating potential. A unique set of parameters have been used for all the simulations, and it encompasses the transport parameters already optimized for charge transport in polyethylene under an external electric field. The model evolution in itself consists in describing the recombination between positive and negative charges according to the Langevin formula, which is physically more accurate than the previous description and has the advantage of reducing the number of adjustable parameters of the model. This also provides a better description of the experimental behavior underlining the importance of recombination processes in irradiated materials.

  13. Space charge modeling in electron-beam irradiated polyethylene: Fitting model and experiments

    NASA Astrophysics Data System (ADS)

    Le Roy, S.; Baudoin, F.; Griseri, V.; Laurent, C.; Teyssèdre, G.

    2012-07-01

    A numerical model for describing charge accumulation in electron-beam irradiated low density polyethylene has been put forward recently. It encompasses the generation of positive and negative charges due to impinging electrons and their transport in the insulation. However, the model was not optimized to fit all the data available regarding space charge dynamics obtained using up-to-date pulsed electro-acoustic techniques. In the present approach, model outputs are compared with experimental space charge distribution obtained during irradiation and post-irradiation, the irradiated samples being in short circuit conditions or with the irradiated surface at a floating potential. A unique set of parameters have been used for all the simulations, and it encompasses the transport parameters already optimized for charge transport in polyethylene under an external electric field. The model evolution in itself consists in describing the recombination between positive and negative charges according to the Langevin formula, which is physically more accurate than the previous description and has the advantage of reducing the number of adjustable parameters of the model. This also provides a better description of the experimental behavior underlining the importance of recombination processes in irradiated materials.

  14. Fast and exact Newton and Bidirectional fitting of Active Appearance Models.

    PubMed

    Kossaifi, Jean; Tzimiropoulos, Yorgos; Pantic, Maja

    2016-12-21

    Active Appearance Models (AAMs) are generative models of shape and appearance that have proven very attractive for their ability to handle wide changes in illumination, pose and occlusion when trained in the wild, while not requiring large training dataset like regression-based or deep learning methods. The problem of fitting an AAM is usually formulated as a non-linear least squares one and the main way of solving it is a standard Gauss-Newton algorithm. In this paper we extend Active Appearance Models in two ways: we first extend the Gauss-Newton framework by formulating a bidirectional fitting method that deforms both the image and the template to fit a new instance. We then formulate a second order method by deriving an efficient Newton method for AAMs fitting. We derive both methods in a unified framework for two types of Active Appearance Models, holistic and part-based, and additionally show how to exploit the structure in the problem to derive fast yet exact solutions. We perform a thorough evaluation of all algorithms on three challenging and recently annotated inthe- wild datasets, and investigate fitting accuracy, convergence properties and the influence of noise in the initialisation. We compare our proposed methods to other algorithms and show that they yield state-of-the-art results, out-performing other methods while having superior convergence properties.

  15. Shot model parameters for Cygnus X-1 through phase portrait fitting

    NASA Technical Reports Server (NTRS)

    Lochner, James C.; Swank, J. H.; Szymkowiak, A. E.

    1991-01-01

    Shot models for systems having about 1/f power density spectrum are developed by utilizing a distribution of shot durations. Parameters of the distribution are determined by fitting the power spectrum either with analytic forms for the spectrum of a shot model with a given shot profile, or with the spectrum derived from numerical realizations of trial shot models. The shot fraction is specified by fitting the phase portrait, which is a plot of intensity at a given time versus intensity at a delayed time and in principle is sensitive to different shot profiles. These techniques have been extensively applied to the X-ray variability of Cygnus X-1, using HEAO 1 A-2 and an Exosat ME observation. The power spectra suggest models having characteristic shot durations lasting from milliseconds to a few seconds, while the phase portrait fits give shot fractions of about 50 percent. Best fits to the portraits are obtained if the amplitude of the shot is a power-law function of the duration of the shot. These fits prefer shots having a symmetric exponential rise and decay. Results are interpreted in terms of a distribution of magnetic flares in the accretion disk.

  16. The Predicting Model of E-commerce Site Based on the Ideas of Curve Fitting

    NASA Astrophysics Data System (ADS)

    Tao, Zhang; Li, Zhang; Dingjun, Chen

    On the basis of the idea of the second multiplication curve fitting, the number and scale of Chinese E-commerce site is analyzed. A preventing increase model is introduced in this paper, and the model parameters are solved by the software of Matlab. The validity of the preventing increase model is confirmed though the numerical experiment. The experimental results show that the precision of preventing increase model is ideal.

  17. Curve fitting toxicity test data: Which comes first, the dose response or the model?

    SciTech Connect

    Gully, J.; Baird, R.; Bottomley, J.

    1995-12-31

    The probit model frequently does not fit the concentration-response curve of NPDES toxicity test data and non-parametric models must be used instead. The non-parametric models, trimmed Spearman-Karber, IC{sub p}, and linear interpolation, all require a monotonic concentration-response. Any deviation from a monotonic response is smoothed to obtain the desired concentration-response characteristics. Inaccurate point estimates may result from such procedures and can contribute to imprecision in replicate tests. The following study analyzed reference toxicant and effluent data from giant kelp (Macrocystis pyrifera), purple sea urchin (Strongylocentrotus purpuratus), red abalone (Haliotis rufescens), and fathead minnow (Pimephales promelas) bioassays using commercially available curve fitting software. The purpose was to search for alternative parametric models which would reduce the use of non-parametric models for point estimate analysis of toxicity data. Two non-linear models, power and logistic dose-response, were selected as possible alternatives to the probit model based upon their toxicological plausibility and ability to model most data sets examined. Unlike non-parametric procedures, these and all parametric models can be statistically evaluated for fit and significance. The use of the power or logistic dose response models increased the percentage of parametric model fits for each protocol and toxicant combination examined. The precision of the selected non-linear models was also compared with the EPA recommended point estimation models at several effect.levels. In general, precision of the alternative models was equal to or better than the traditional methods. Finally, use of the alternative models usually produced more plausible point estimates in data sets where the effects of smoothing and non-parametric modeling made the point estimate results suspect.

  18. Model fit to experimental data for foam-assisted deep vadose zone remediation.

    PubMed

    Roostapour, A; Lee, G; Zhong, L; Kam, S I

    2014-01-15

    This study investigates how a foam model, developed in Roostapour and Kam [1], can be applied to make a fit to a set of existing laboratory flow experiments in an application relevant to deep vadose zone remediation. This study reveals a few important insights regarding foam-assisted deep vadose zone remediation: (i) the mathematical framework established for foam modeling can fit typical flow experiments matching wave velocities, saturation history, and pressure responses; (ii) the set of input parameters may not be unique for the fit, and therefore conducting experiments to measure basic model parameters related to relative permeability, initial and residual saturations, surfactant adsorption and so on should not be overlooked; and (iii) gas compressibility plays an important role for data analysis, thus should be handled carefully in laboratory flow experiments. Foam kinetics, causing foam texture to reach its steady-state value slowly, may impose additional complications.

  19. The disconnected values model improves mental well-being and fitness in an employee wellness program.

    PubMed

    Anshel, Mark H; Brinthaupt, Thomas M; Kang, Minsoo

    2010-01-01

    This study examined the effect of a 10-week wellness program on changes in physical fitness and mental well-being. The conceptual framework for this study was the Disconnected Values Model (DVM). According to the DVM, detecting the inconsistencies between negative habits and values (e.g., health, family, faith, character) and concluding that these "disconnects" are unacceptable promotes the need for health behavior change. Participants were 164 full-time employees at a university in the southeastern U.S. The program included fitness coaching and a 90-minute orientation based on the DVM. Multivariate Mixed Model analyses indicated significantly improved scores from pre- to post-intervention on selected measures of physical fitness and mental well-being. The results suggest that the Disconnected Values Model provides an effective cognitive-behavioral approach to generating health behavior change in a 10-week workplace wellness program.

  20. Optimization of Active Muscle Force-Length Models Using Least Squares Curve Fitting.

    PubMed

    Mohammed, Goran Abdulrahman; Hou, Ming

    2016-03-01

    The objective of this paper is to propose an asymmetric Gaussian function as an alternative to the existing active force-length models, and to optimize this model along with several other existing models by using the least squares curve fitting method. The minimal set of coefficients is identified for each of these models to facilitate the least squares curve fitting. Sarcomere simulated data and one set of rabbits extensor digitorum II experimental data are used to illustrate optimal curve fitting of the selected force-length functions. The results shows that all the curves fit reasonably well with the simulated and experimental data, while the Gordon-Huxley-Julian model and asymmetric Gaussian function are better than other functions in terms of statistical test scores root mean squared error and R-squared. However, the differences in RMSE scores are insignificant (0.3-6%) for simulated data and (0.2-5%) for experimental data. The proposed asymmetric Gaussian model and the method of parametrization of this and the other force-length models mentioned above can be used in the studies on active force-length relationships of skeletal muscles that generate forces to cause movements of human and animal bodies.

  1. Mathematical Modeling of Allelopathy. III. A Model for Curve-Fitting Allelochemical Dose Responses

    PubMed Central

    Liu, De Li; An, Min; Johnson, Ian R.; Lovett, John V.

    2003-01-01

    Bioassay techniques are often used to study the effects of allelochemicals on plant processes, and it is generally observed that the processes are stimulated at low allelochemical concentrations and inhibited as the concentrations increase. A simple empirical model is presented to analyze this type of response. The stimulation-inhibition properties of allelochemical-dose responses can be described by the parameters in the model. The indices, p% reductions, are calculated to assess the allelochemical effects. The model is compared with experimental data for the response of lettuce seedling growth to Centaurepensin, the olfactory response of weevil larvae to α-terpineol, and the responses of annual ryegrass (Lolium multiflorum Lam.), creeping red fescue (Festuca rubra L., cv. Ensylva), Kentucky bluegrass (Poa pratensis L., cv. Kenblue), perennial ryegrass (L. perenne L., cv. Manhattan), and Rebel tall fescue (F. arundinacea Schreb) seedling growth to leachates of Rebel and Kentucky 31 tall fescue. The results show that the model gives a good description to observations and can be used to fit a wide range of dose responses. Assessments of the effects of leachates of Rebel and Kentucky 31 tall fescue clearly differentiate the properties of the allelopathic sources and the relative sensitivities of indicators such as the length of root and leaf. PMID:19330111

  2. Mathematical Modeling of Allelopathy. III. A Model for Curve-Fitting Allelochemical Dose Responses.

    PubMed

    Liu, De Li; An, Min; Johnson, Ian R; Lovett, John V

    2003-01-01

    Bioassay techniques are often used to study the effects of allelochemicals on plant processes, and it is generally observed that the processes are stimulated at low allelochemical concentrations and inhibited as the concentrations increase. A simple empirical model is presented to analyze this type of response. The stimulation-inhibition properties of allelochemical-dose responses can be described by the parameters in the model. The indices, p% reductions, are calculated to assess the allelochemical effects. The model is compared with experimental data for the response of lettuce seedling growth to Centaurepensin, the olfactory response of weevil larvae to alpha-terpineol, and the responses of annual ryegrass (Lolium multiflorum Lam.), creeping red fescue (Festuca rubra L., cv. Ensylva), Kentucky bluegrass (Poa pratensis L., cv. Kenblue), perennial ryegrass (L. perenne L., cv. Manhattan), and Rebel tall fescue (F. arundinacea Schreb) seedling growth to leachates of Rebel and Kentucky 31 tall fescue. The results show that the model gives a good description to observations and can be used to fit a wide range of dose responses. Assessments of the effects of leachates of Rebel and Kentucky 31 tall fescue clearly differentiate the properties of the allelopathic sources and the relative sensitivities of indicators such as the length of root and leaf.

  3. Efficient occupancy model-fitting for extensive citizen-science data.

    PubMed

    Dennis, Emily B; Morgan, Byron J T; Freeman, Stephen N; Ridout, Martin S; Brereton, Tom M; Fox, Richard; Powney, Gary D; Roy, David B

    2017-01-01

    Appropriate large-scale citizen-science data present important new opportunities for biodiversity modelling, due in part to the wide spatial coverage of information. Recently proposed occupancy modelling approaches naturally incorporate random effects in order to account for annual variation in the composition of sites surveyed. In turn this leads to Bayesian analysis and model fitting, which are typically extremely time consuming. Motivated by presence-only records of occurrence from the UK Butterflies for the New Millennium data base, we present an alternative approach, in which site variation is described in a standard way through logistic regression on relevant environmental covariates. This allows efficient occupancy model-fitting using classical inference, which is easily achieved using standard computers. This is especially important when models need to be fitted each year, typically for many different species, as with British butterflies for example. Using both real and simulated data we demonstrate that the two approaches, with and without random effects, can result in similar conclusions regarding trends. There are many advantages to classical model-fitting, including the ability to compare a range of alternative models, identify appropriate covariates and assess model fit, using standard tools of maximum likelihood. In addition, modelling in terms of covariates provides opportunities for understanding the ecological processes that are in operation. We show that there is even greater potential; the classical approach allows us to construct regional indices simply, which indicate how changes in occupancy typically vary over a species' range. In addition we are also able to construct dynamic occupancy maps, which provide a novel, modern tool for examining temporal changes in species distribution. These new developments may be applied to a wide range of taxa, and are valuable at a time of climate change. They also have the potential to motivate citizen

  4. Efficient occupancy model-fitting for extensive citizen-science data

    PubMed Central

    Morgan, Byron J. T.; Freeman, Stephen N.; Ridout, Martin S.; Brereton, Tom M.; Fox, Richard; Powney, Gary D.; Roy, David B.

    2017-01-01

    Appropriate large-scale citizen-science data present important new opportunities for biodiversity modelling, due in part to the wide spatial coverage of information. Recently proposed occupancy modelling approaches naturally incorporate random effects in order to account for annual variation in the composition of sites surveyed. In turn this leads to Bayesian analysis and model fitting, which are typically extremely time consuming. Motivated by presence-only records of occurrence from the UK Butterflies for the New Millennium data base, we present an alternative approach, in which site variation is described in a standard way through logistic regression on relevant environmental covariates. This allows efficient occupancy model-fitting using classical inference, which is easily achieved using standard computers. This is especially important when models need to be fitted each year, typically for many different species, as with British butterflies for example. Using both real and simulated data we demonstrate that the two approaches, with and without random effects, can result in similar conclusions regarding trends. There are many advantages to classical model-fitting, including the ability to compare a range of alternative models, identify appropriate covariates and assess model fit, using standard tools of maximum likelihood. In addition, modelling in terms of covariates provides opportunities for understanding the ecological processes that are in operation. We show that there is even greater potential; the classical approach allows us to construct regional indices simply, which indicate how changes in occupancy typically vary over a species’ range. In addition we are also able to construct dynamic occupancy maps, which provide a novel, modern tool for examining temporal changes in species distribution. These new developments may be applied to a wide range of taxa, and are valuable at a time of climate change. They also have the potential to motivate citizen

  5. Estimating the pi* goodness of fit index for finite mixtures of item response models.

    PubMed

    Revuelta, Javier

    2008-05-01

    Testing the fit of finite mixture models is a difficult task, since asymptotic results on the distribution of likelihood ratio statistics do not hold; for this reason, alternative statistics are needed. This paper applies the pi* goodness of fit statistic to finite mixture item response models. The pi* statistic assumes that the population is composed of two subpopulations - those that follow a parametric model and a residual group outside the model; pi* is defined as the proportion of population in the residual group. The population was divided into two or more groups, or classes. Several groups followed an item response model and there was also a residual group. The paper presents maximum likelihood algorithms for estimating item parameters, the probabilities of the groups and pi*. The paper also includes a simulation study on goodness of recovery for the two- and three-parameter logistic models and an example with real data from a multiple choice test.

  6. Comparing PyMorph and SDSS photometry. I. Background sky and model fitting effects

    NASA Astrophysics Data System (ADS)

    Fischer, J.-L.; Bernardi, M.; Meert, A.

    2017-01-01

    A number of recent estimates of the total luminosities of galaxies in the SDSS are significantly larger than those reported by the SDSS pipeline. This is because of a combination of three effects: one is simply a matter of defining the scale out to which one integrates the fit when defining the total luminosity, and amounts on average to ≤0.1 mags even for the most luminous galaxies. The other two are less trivial and tend to be larger; they are due to differences in how the background sky is estimated and what model is fit to the surface brightness profile. We show that PyMorph sky estimates are fainter than those of the SDSS DR7 or DR9 pipelines, but are in excellent agreement with the estimates of Blanton et al. (2011). Using the SDSS sky biases luminosities by more than a few tenths of a magnitude for objects with half-light radii ≥7 arcseconds. In the SDSS main galaxy sample these are typically luminous galaxies, so they are not necessarily nearby. This bias becomes worse when allowing the model more freedom to fit the surface brightness profile. When PyMorph sky values are used, then two component Sersic-Exponential fits to E+S0s return more light than single component deVaucouleurs fits (up to ˜0.2 mag), but less light than single Sersic fits (0.1 mag). Finally, we show that PyMorph fits of Meert et al. (2015) to DR7 data remain valid for DR9 images. Our findings show that, especially at large luminosities, these PyMorph estimates should be preferred to the SDSS pipeline values.

  7. Testing the Fitness Consequences of the Thermoregulatory and Parental Care Models for the Origin of Endothermy

    PubMed Central

    Clavijo-Baque, Sabrina; Bozinovic, Francisco

    2012-01-01

    The origin of endothermy is a puzzling phenomenon in the evolution of vertebrates. To address this issue several explicative models have been proposed. The main models proposed for the origin of endothermy are the aerobic capacity, the thermoregulatory and the parental care models. Our main proposal is that to compare the alternative models, a critical aspect is to determine how strongly natural selection was influenced by body temperature, and basal and maximum metabolic rates during the evolution of endothermy. We evaluate these relationships in the context of three main hypotheses aimed at explaining the evolution of endothermy, namely the parental care hypothesis and two hypotheses related to the thermoregulatory model (thermogenic capacity and higher body temperature models). We used data on basal and maximum metabolic rates and body temperature from 17 rodent populations, and used intrinsic population growth rate (Rmax) as a global proxy of fitness. We found greater support for the thermogenic capacity model of the thermoregulatory model. In other words, greater thermogenic capacity is associated with increased fitness in rodent populations. To our knowledge, this is the first test of the fitness consequences of the thermoregulatory and parental care models for the origin of endothermy. PMID:22606328

  8. The FIT 2.0 Model - Fuel-cycle Integration and Tradeoffs

    SciTech Connect

    Steven J. Piet; Nick R. Soelberg; Layne F. Pincock; Eric L. Shaber; Gregory M Teske

    2011-06-01

    All mass streams from fuel separation and fabrication are products that must meet some set of product criteria – fuel feedstock impurity limits, waste acceptance criteria (WAC), material storage (if any), or recycle material purity requirements such as zirconium for cladding or lanthanides for industrial use. These must be considered in a systematic and comprehensive way. The FIT model and the “system losses study” team that developed it [Shropshire2009, Piet2010b] are steps by the Fuel Cycle Technology program toward an analysis that accounts for the requirements and capabilities of each fuel cycle component, as well as major material flows within an integrated fuel cycle. This will help the program identify near-term R&D needs and set longer-term goals. This report describes FIT 2, an update of the original FIT model.[Piet2010c] FIT is a method to analyze different fuel cycles; in particular, to determine how changes in one part of a fuel cycle (say, fuel burnup, cooling, or separation efficiencies) chemically affect other parts of the fuel cycle. FIT provides the following: Rough estimate of physics and mass balance feasibility of combinations of technologies. If feasibility is an issue, it provides an estimate of how performance would have to change to achieve feasibility. Estimate of impurities in fuel and impurities in waste as function of separation performance, fuel fabrication, reactor, uranium source, etc.

  9. Aeroelastic modeling for the FIT team F/A-18 simulation

    NASA Technical Reports Server (NTRS)

    Zeiler, Thomas A.; Wieseman, Carol D.

    1989-01-01

    Some details of the aeroelastic modeling of the F/A-18 aircraft done for the Functional Integration Technology (FIT) team's research in integrated dynamics modeling and how these are combined with the FIT team's integrated dynamics model are described. Also described are mean axis corrections to elastic modes, the addition of nonlinear inertial coupling terms into the equations of motion, and the calculation of internal loads time histories using the integrated dynamics model in a batch simulation program. A video tape made of a loads time history animation was included as a part of the oral presentation. Also discussed is work done in one of the areas of unsteady aerodynamic modeling identified as needing improvement, specifically, in correction factor methodologies for improving the accuracy of stability derivatives calculated with a doublet lattice code.

  10. Model fitting of the kinematics of ten superluminal components in blazar 3C 279

    NASA Astrophysics Data System (ADS)

    Qian, Shan-Jie

    2013-07-01

    The kinematics of ten superluminal components (C11- C16, C18, C20, C21 and C24) of blazar 3C 279 are studied from VLBI observations. It is shown that their initial trajectory, distance from the core and apparent speed can be well fitted by the precession model proposed by Qian. Combined with the results of the model fit for the six superluminal components (C3, C4, C7a, C8, C9 and C10) already published, the kinematics of sixteen superluminal components can now be consistently interpreted in the precession scenario with their ejection times spanning more than 25 yr (or more than one precession period). The results from model fitting show the possible existence of a common precessing trajectory for these knots within a projected core distance of ~0.2-0.4 mas. In the framework of the jet-precession scenario, we can, for the first time, identify three classes of trajectories which are characterized by their collimation parameters. These different trajectories could be related to the helical structure of magnetic fields in the jet. Through fitting the model, the bulk Lorentz factor, Doppler factor and viewing angle of these knots are derived. It is found that there is no evidence for any correlation between the bulk Lorentz factor of the components and their precession phase (or ejection time). In a companion paper, the kinematics of another seven components (C5a, C6, C7, C17, C19, C22 and C23) have been derived from model fitting, and a binary black-hole/jet scenario was envisaged. The precession model proposed by Qian would be useful for understanding the kinematics of superluminal components in blazar 3C 279 derived from VLBI observations, by disentangling different mechanisms and ingredients. More generally, it might also be helpful for studying the mechanism of jet swing (wobbling) in other blazars.

  11. Comments on Ghassib's "Where Does Creativity Fit into a Productivist Industrial Model of Knowledge Production?"

    ERIC Educational Resources Information Center

    McCluskey, Ken W.

    2010-01-01

    This article presents the author's comments on Hisham B. Ghassib's "Where Does Creativity Fit into a Productivist Industrial Model of Knowledge Production?" Ghassib's article focuses on the transformation of science from pre-modern times to the present. Ghassib (2010) notes that, unlike in an earlier era when the economy depended on static…

  12. Critique of "Where Does Creativity Fit into a Productivist Industrial Model of Knowledge Production?"

    ERIC Educational Resources Information Center

    Harris, Carole Ruth

    2010-01-01

    This article presents the author's comments on Hisham Ghassib's article entitled "Where Does Creativity Fit into a Productivist Industrial Model of Knowledge Production?" In his article, Ghassib (2010) provides an overview of the philosophical foundations that led to exact science, its role in what was later to become a driving force in the modern…

  13. Universal Screening for Emotional and Behavioral Problems: Fitting a Population-Based Model

    ERIC Educational Resources Information Center

    Schanding, G. Thomas, Jr.; Nowell, Kerri P.

    2013-01-01

    Schools have begun to adopt a population-based method to conceptualizing assessment and intervention of students; however, little empirical evidence has been gathered to support this shift in service delivery. The present study examined the fit of a population-based model in identifying students' behavioral and emotional functioning using a…

  14. Super Kids--Superfit. A Comprehensive Fitness Intervention Model for Elementary Schools.

    ERIC Educational Resources Information Center

    Virgilio, Stephen J.; Berenson, Gerald S.

    1988-01-01

    Objectives and activities of the cardiovascular (CV) fitness program Super Kids--Superfit are related in this article. This exercise program is one component of the Heart Smart Program, a CV health intervention model for elementary school students. Program evaluation, parent education, and school and community intervention strategies are…

  15. A Bayesian Approach to Person Fit Analysis in Item Response Theory Models. Research Report.

    ERIC Educational Resources Information Center

    Glas, Cees A. W.; Meijer, Rob R.

    A Bayesian approach to the evaluation of person fit in item response theory (IRT) models is presented. In a posterior predictive check, the observed value on a discrepancy variable is positioned in its posterior distribution. In a Bayesian framework, a Markov Chain Monte Carlo procedure can be used to generate samples of the posterior distribution…

  16. Assessing item fit for unidimensional item response theory models using residuals from estimated item response functions.

    PubMed

    Haberman, Shelby J; Sinharay, Sandip; Chon, Kyong Hee

    2013-07-01

    Residual analysis (e.g. Hambleton & Swaminathan, Item response theory: principles and applications, Kluwer Academic, Boston, 1985; Hambleton, Swaminathan, & Rogers, Fundamentals of item response theory, Sage, Newbury Park, 1991) is a popular method to assess fit of item response theory (IRT) models. We suggest a form of residual analysis that may be applied to assess item fit for unidimensional IRT models. The residual analysis consists of a comparison of the maximum-likelihood estimate of the item characteristic curve with an alternative ratio estimate of the item characteristic curve. The large sample distribution of the residual is proved to be standardized normal when the IRT model fits the data. We compare the performance of our suggested residual to the standardized residual of Hambleton et al. (Fundamentals of item response theory, Sage, Newbury Park, 1991) in a detailed simulation study. We then calculate our suggested residuals using data from an operational test. The residuals appear to be useful in assessing the item fit for unidimensional IRT models.

  17. Longitudinal Changes in Physical Fitness Performance in Youth: A Multilevel Latent Growth Curve Modeling Approach

    ERIC Educational Resources Information Center

    Wang, Chee Keng John; Pyun, Do Young; Liu, Woon Chia; Lim, Boon San Coral; Li, Fuzhong

    2013-01-01

    Using a multilevel latent growth curve modeling (LGCM) approach, this study examined longitudinal change in levels of physical fitness performance over time (i.e. four years) in young adolescents aged from 12-13 years. The sample consisted of 6622 students from 138 secondary schools in Singapore. Initial analyses found between-school variation on…

  18. The Fit Between Strong-Campbell Interest Inventory General Occupational Themes and Holland's Hexagonal Model.

    ERIC Educational Resources Information Center

    Rounds, James B., Jr.; And Others

    Using a multidimensional scaling procedure, this study examined the fit of Holland's RIASEC hexagon model to the internal relationships among the Strong-Campbell Interest Inventory (SCII) General Occupational Theme scales. SCII intercorrelation matrices for both sexes as reported in the SCII Manual were submitted, separately for each sex, to…

  19. Impact of Missing Data on Person-Model Fit and Person Trait Estimation

    ERIC Educational Resources Information Center

    Zhang, Bo; Walker, Cindy M.

    2008-01-01

    The purpose of this research was to examine the effects of missing data on person-model fit and person trait estimation in tests with dichotomous items. Under the missing-completely-at-random framework, four missing data treatment techniques were investigated including pairwise deletion, coding missing responses as incorrect, hotdeck imputation,…

  20. Fitting Item Response Models to the Maryland Functional Reading Test Results.

    ERIC Educational Resources Information Center

    Hambleton, Ronald K.; And Others

    The potential of item response theory (IRT) for solving a number of testing problems in the Maryland Functional Reading Program would appear to be substantial in view of the many other promising applications of the theory. But, it is well-known that the advantages derived from an IRT model cannot be achieved when the fit between an item response…

  1. Fitting Multilevel Models with Ordinal Outcomes: Performance of Alternative Specifications and Methods of Estimation

    PubMed Central

    Bauer, Daniel J.; Sterba, Sonya K.

    2011-01-01

    Previous research has compared methods of estimation for multilevel models fit to binary data but there are reasons to believe that the results will not always generalize to the ordinal case. This paper thus evaluates (a) whether and when fitting multilevel linear models to ordinal outcome data is justified and (b) which estimator to employ when instead fitting multilevel cumulative logit models to ordinal data, Maximum Likelihood (ML) or Penalized Quasi-Likelihood (PQL). ML and PQL are compared across variations in sample size, magnitude of variance components, number of outcome categories, and distribution shape. Fitting a multilevel linear model to ordinal outcomes is shown to be inferior in virtually all circumstances. PQL performance improves markedly with the number of ordinal categories, regardless of distribution shape. In contrast to binary data, PQL often performs as well as ML when used with ordinal data. Further, the performance of PQL is typically superior to ML when the data includes a small to moderate number of clusters (i.e., ≤ 50 clusters). PMID:22040372

  2. A Nonparametric Approach for Assessing Goodness-of-Fit of IRT Models in a Mixed Format Test

    ERIC Educational Resources Information Center

    Liang, Tie; Wells, Craig S.

    2015-01-01

    Investigating the fit of a parametric model plays a vital role in validating an item response theory (IRT) model. An area that has received little attention is the assessment of multiple IRT models used in a mixed-format test. The present study extends the nonparametric approach, proposed by Douglas and Cohen (2001), to assess model fit of three…

  3. Polynomial fitting model for phase reconstruction: interferograms with high fringe density

    NASA Astrophysics Data System (ADS)

    Téllez-Quiñones, Alejandro; Malacara-Doblado, Daniel; García-Márquez, Jorge

    2012-09-01

    A data fitting model is proposed to estimate phases from its cosine and sine. The a priori assumption is that the phases to be reconstructed should be expressed by polynomials. The cosine and sine of the phases are obtained from interferograms with high fringe density by generalized phase-shifting techniques The proposed method is employed for phase reconstrution by line integration of the phase gradient or any other phase-unwrapping technique and the fit is achieved by a least-squares minimization.

  4. Estimation of heart rate and heart rate variability from pulse oximeter recordings using localized model fitting.

    PubMed

    Wadehn, Federico; Carnal, David; Loeliger, Hans-Andrea

    2015-08-01

    Heart rate variability is one of the key parameters for assessing the health status of a subject's cardiovascular system. This paper presents a local model fitting algorithm used for finding single heart beats in photoplethysmogram recordings. The local fit of exponentially decaying cosines of frequencies within the physiological range is used to detect the presence of a heart beat. Using 42 subjects from the CapnoBase database, the average heart rate error was 0.16 BPM and the standard deviation of the absolute estimation error was 0.24 BPM.

  5. Modeling of pharmaceuticals mixtures toxicity with deviation ratio and best-fit functions models.

    PubMed

    Wieczerzak, Monika; Kudłak, Błażej; Yotova, Galina; Nedyalkova, Miroslava; Tsakovski, Stefan; Simeonov, Vasil; Namieśnik, Jacek

    2016-11-15

    The present study deals with assessment of ecotoxicological parameters of 9 drugs (diclofenac (sodium salt), oxytetracycline hydrochloride, fluoxetine hydrochloride, chloramphenicol, ketoprofen, progesterone, estrone, androstenedione and gemfibrozil), present in the environmental compartments at specific concentration levels, and their mutual combinations by couples against Microtox® and XenoScreen YES/YAS® bioassays. As the quantitative assessment of ecotoxicity of drug mixtures is an complex and sophisticated topic in the present study we have used two major approaches to gain specific information on the mutual impact of two separate drugs present in a mixture. The first approach is well documented in many toxicological studies and follows the procedure for assessing three types of models, namely concentration addition (CA), independent action (IA) and simple interaction (SI) by calculation of a model deviation ratio (MDR) for each one of the experiments carried out. The second approach used was based on the assumption that the mutual impact in each mixture of two drugs could be described by a best-fit model function with calculation of weight (regression coefficient or other model parameter) for each of the participants in the mixture or by correlation analysis. It was shown that the sign and the absolute value of the weight or the correlation coefficient could be a reliable measure for the impact of either drug A on drug B or, vice versa, of B on A. Results of studies justify the statement, that both of the approaches show similar assessment of the mode of mutual interaction of the drugs studied. It was found that most of the drug mixtures exhibit independent action and quite few of the mixtures show synergic or dependent action.

  6. Phylogenetic Tree Reconstruction Accuracy and Model Fit when Proportions of Variable Sites Change across the Tree

    PubMed Central

    Grievink, Liat Shavit; Penny, David; Hendy, Michael D.; Holland, Barbara R.

    2010-01-01

    Commonly used phylogenetic models assume a homogeneous process through time in all parts of the tree. However, it is known that these models can be too simplistic as they do not account for nonhomogeneous lineage-specific properties. In particular, it is now widely recognized that as constraints on sequences evolve, the proportion and positions of variable sites can vary between lineages causing heterotachy. The extent to which this model misspecification affects tree reconstruction is still unknown. Here, we evaluate the effect of changes in the proportions and positions of variable sites on model fit and tree estimation. We consider 5 current models of nucleotide sequence evolution in a Bayesian Markov chain Monte Carlo framework as well as maximum parsimony (MP). We show that for a tree with 4 lineages where 2 nonsister taxa undergo a change in the proportion of variable sites tree reconstruction under the best-fitting model, which is chosen using a relative test, often results in the wrong tree. In this case, we found that an absolute test of model fit is a better predictor of tree estimation accuracy. We also found further evidence that MP is not immune to heterotachy. In addition, we show that increased sampling of taxa that have undergone a change in proportion and positions of variable sites is critical for accurate tree reconstruction. PMID:20525636

  7. Goodness-of-fit methods for additive-risk models in tumorigenicity experiments.

    PubMed

    Ghosh, Debashis

    2003-09-01

    In tumorigenicity experiments, a complication is that the time to event is generally not observed, so that the time to tumor is subject to interval censoring. One of the goals in these studies is to properly model the effect of dose on risk. Thus, it is important to have goodness of fit procedures available for assessing the model fit. While several estimation procedures have been developed for current-status data, relatively little work has been done on model-checking techniques. In this article, we propose numerical and graphical methods for the analysis of current-status data using the additive-risk model, primarily focusing on the situation where the monitoring times are dependent. The finite-sample properties of the proposed methodology are examined through numerical studies. The methods are then illustrated with data from a tumorigenicity experiment.

  8. Automatic segmentation of vertebral arteries in CT angiography using combined circular and cylindrical model fitting

    NASA Astrophysics Data System (ADS)

    Lee, Min Jin; Hong, Helen; Chung, Jin Wook

    2014-03-01

    We propose an automatic vessel segmentation method of vertebral arteries in CT angiography using combined circular and cylindrical model fitting. First, to generate multi-segmented volumes, whole volume is automatically divided into four segments by anatomical properties of bone structures along z-axis of head and neck. To define an optimal volume circumscribing vertebral arteries, anterior-posterior bounding and side boundaries are defined as initial extracted vessel region. Second, the initial vessel candidates are tracked using circular model fitting. Since boundaries of the vertebral arteries are ambiguous in case the arteries pass through the transverse foramen in the cervical vertebra, the circle model is extended along z-axis to cylinder model for considering additional vessel information of neighboring slices. Finally, the boundaries of the vertebral arteries are detected using graph-cut optimization. From the experiments, the proposed method provides accurate results without bone artifacts and eroded vessels in the cervical vertebra.

  9. Erroneous Arrhenius: modified arrhenius model best explains the temperature dependence of ectotherm fitness.

    PubMed

    Knies, Jennifer L; Kingsolver, Joel G

    2010-08-01

    The initial rise of fitness that occurs with increasing temperature is attributed to Arrhenius kinetics, in which rates of reaction increase exponentially with increasing temperature. Models based on Arrhenius typically assume single rate-limiting reactions over some physiological temperature range for which all the rate-limiting enzymes are in 100% active conformation. We test this assumption using data sets for microbes that have measurements of fitness (intrinsic rate of population growth) at many temperatures and over a broad temperature range and for diverse ectotherms that have measurements at fewer temperatures. When measurements are available at many temperatures, strictly Arrhenius kinetics are rejected over the physiological temperature range. However, over a narrower temperature range, we cannot reject strictly Arrhenius kinetics. The temperature range also affects estimates of the temperature dependence of fitness. These results indicate that Arrhenius kinetics only apply over a narrow range of temperatures for ectotherms, complicating attempts to identify general patterns of temperature dependence.

  10. Individual and contextual determinants of adequate maternal health care services in Kenya.

    PubMed

    Achia, Thomas N O; Mageto, Lillian E

    2015-01-01

    This study aimed to examine individual and community level factors associated with adequate use of maternal antenatal health services in Kenya. Individual and community level factors associated with adequate use of maternal health care (MHC) services were obtained from the 2008-09 Kenya Demographic and Health Survey data set. Multilevel partial-proportional odds logit models were fitted using STATA 13.0 to quantify the relations of the selected covariates to adequate MHC use, defined as a three-category ordinal variable. The sample consisted of 3,621 women who had at least one live birth in the five-year period preceding this survey. Only 18 percent of the women had adequate use of MHC services. Greater educational attainment by the woman or her partner, higher socioeconomic status, access to medical insurance coverage, and greater media exposure were the individual-level factors associated with adequate use of MHC services. Greater community ethnic diversity, higher community-level socioeconomic status, and greater community-level health facility deliveries were the contextual-level factors associated with adequate use of MHC. To improve the use of MHC services in Kenya, the government needs to design and implement programs that target underlying individual and community level factors, providing focused and sustained health education to promote the use of antenatal, delivery, and postnatal care.

  11. Fitting Models of the Population Consequences of Acoustic Disturbance to Data from Marine Mammal Populations

    DTIC Science & Technology

    2011-09-30

    2011 to 00-00-2011 4 . TITLE AND SUBTITLE Fitting Models of the Population Consequences of Acoustic Disturbance to Data from Marine Mammal...and 4 ) initialize each of the MCMC chains. The Gibbs sampler allows us to factor the above high dimensional model into a series of lower dimension 4 ...at NEAq, and an example time series for one animal highlights both body fat code, and entanglement episodes (Figure 4 ). Individual health is a

  12. Fitting complex population models by combining particle filters with Markov chain Monte Carlo.

    PubMed

    Knape, Jonas; de Valpine, Perry

    2012-02-01

    We show how a recent framework combining Markov chain Monte Carlo (MCMC) with particle filters (PFMCMC) may be used to estimate population state-space models. With the purpose of utilizing the strengths of each method, PFMCMC explores hidden states by particle filters, while process and observation parameters are estimated using an MCMC algorithm. PFMCMC is exemplified by analyzing time series data on a red kangaroo (Macropus rufus) population in New South Wales, Australia, using MCMC over model parameters based on an adaptive Metropolis-Hastings algorithm. We fit three population models to these data; a density-dependent logistic diffusion model with environmental variance, an unregulated stochastic exponential growth model, and a random-walk model. Bayes factors and posterior model probabilities show that there is little support for density dependence and that the random-walk model is the most parsimonious model. The particle filter Metropolis-Hastings algorithm is a brute-force method that may be used to fit a range of complex population models. Implementation is straightforward and less involved than standard MCMC for many models, and marginal densities for model selection can be obtained with little additional effort. The cost is mainly computational, resulting in long running times that may be improved by parallelizing the algorithm.

  13. Improved cosmological model fitting of Planck data with a dark energy spike

    NASA Astrophysics Data System (ADS)

    Park, Chan-Gyung

    2015-06-01

    The Λ cold dark matter (Λ CDM ) model is currently known as the simplest cosmology model that best describes observations with a minimal number of parameters. Here we introduce a cosmology model that is preferred over the conventional Λ CDM one by constructing dark energy as the sum of the cosmological constant Λ and an additional fluid that is designed to have an extremely short transient spike in energy density during the radiation-matter equality era and an early scaling behavior with radiation and matter densities. The density parameter of the additional fluid is defined as a Gaussian function plus a constant in logarithmic scale-factor space. Searching for the best-fit cosmological parameters in the presence of such a dark energy spike gives a far smaller chi-square value by about 5 times the number of additional parameters introduced and narrower constraints on the matter density and Hubble constant compared with the best-fit Λ CDM model. The significant improvement in reducing the chi square mainly comes from the better fitting of the Planck temperature power spectrum around the third (ℓ≈800 ) and sixth (ℓ≈1800 ) acoustic peaks. The likelihood ratio test and the Akaike information criterion suggest that the model of a dark energy spike is strongly favored by the current cosmological observations over the conventional Λ CDM model. However, based on the Bayesian information criterion which penalizes models with more parameters, the strong evidence supporting the presence of a dark energy spike disappears. Our result emphasizes that the alternative cosmological parameter estimation with even better fitting of the same observational data is allowed in Einstein's gravity.

  14. A flexible, interactive software tool for fitting the parameters of neuronal models

    PubMed Central

    Friedrich, Péter; Vella, Michael; Gulyás, Attila I.; Freund, Tamás F.; Káli, Szabolcs

    2014-01-01

    The construction of biologically relevant neuronal models as well as model-based analysis of experimental data often requires the simultaneous fitting of multiple model parameters, so that the behavior of the model in a certain paradigm matches (as closely as possible) the corresponding output of a real neuron according to some predefined criterion. Although the task of model optimization is often computationally hard, and the quality of the results depends heavily on technical issues such as the appropriate choice (and implementation) of cost functions and optimization algorithms, no existing program provides access to the best available methods while also guiding the user through the process effectively. Our software, called Optimizer, implements a modular and extensible framework for the optimization of neuronal models, and also features a graphical interface which makes it easy for even non-expert users to handle many commonly occurring scenarios. Meanwhile, educated users can extend the capabilities of the program and customize it according to their needs with relatively little effort. Optimizer has been developed in Python, takes advantage of open-source Python modules for nonlinear optimization, and interfaces directly with the NEURON simulator to run the models. Other simulators are supported through an external interface. We have tested the program on several different types of problems of varying complexity, using different model classes. As targets, we used simulated traces from the same or a more complex model class, as well as experimental data. We successfully used Optimizer to determine passive parameters and conductance densities in compartmental models, and to fit simple (adaptive exponential integrate-and-fire) neuronal models to complex biological data. Our detailed comparisons show that Optimizer can handle a wider range of problems, and delivers equally good or better performance than any other existing neuronal model fitting tool. PMID

  15. A flexible, interactive software tool for fitting the parameters of neuronal models.

    PubMed

    Friedrich, Péter; Vella, Michael; Gulyás, Attila I; Freund, Tamás F; Káli, Szabolcs

    2014-01-01

    The construction of biologically relevant neuronal models as well as model-based analysis of experimental data often requires the simultaneous fitting of multiple model parameters, so that the behavior of the model in a certain paradigm matches (as closely as possible) the corresponding output of a real neuron according to some predefined criterion. Although the task of model optimization is often computationally hard, and the quality of the results depends heavily on technical issues such as the appropriate choice (and implementation) of cost functions and optimization algorithms, no existing program provides access to the best available methods while also guiding the user through the process effectively. Our software, called Optimizer, implements a modular and extensible framework for the optimization of neuronal models, and also features a graphical interface which makes it easy for even non-expert users to handle many commonly occurring scenarios. Meanwhile, educated users can extend the capabilities of the program and customize it according to their needs with relatively little effort. Optimizer has been developed in Python, takes advantage of open-source Python modules for nonlinear optimization, and interfaces directly with the NEURON simulator to run the models. Other simulators are supported through an external interface. We have tested the program on several different types of problems of varying complexity, using different model classes. As targets, we used simulated traces from the same or a more complex model class, as well as experimental data. We successfully used Optimizer to determine passive parameters and conductance densities in compartmental models, and to fit simple (adaptive exponential integrate-and-fire) neuronal models to complex biological data. Our detailed comparisons show that Optimizer can handle a wider range of problems, and delivers equally good or better performance than any other existing neuronal model fitting tool.

  16. Fitting a mixture model by expectation maximization to discover motifs in biopolymers

    SciTech Connect

    Bailey, T.L.; Elkan, C.

    1994-12-31

    The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. Multiple motifs are found by fitting a mixture model to the data, probabilistically erasing the occurrences of the motif thus found, and repeating the process to find successive motifs. The algorithm requires only a set of unaligned sequences and a number specifying the width of the motifs as input. It returns a model of each motif and a threshold which together can be used as a Bayes-optimal classifier for searching for occurrences of the motif in other databases. The algorithm estimates how many times each motif occurs in each sequence in the dataset and outputs an alignment of the occurrences of the motif. The algorithm is capable of discovering several different motifs with differing numbers of occurrences in a single dataset.

  17. Fitting Models of the Population Consequences of Acoustic Disturbance to Data from Marine Mammal Populations

    DTIC Science & Technology

    2010-09-30

    unlimited. Fitting Models of the Population Consequences of Acoustic Disturbance to Data from Marine Mammal Populations James S. Clark H.L... model  that provides daily  estimates  of lipid status, as lipid status of the mother is directly linked  to  pup survival.  This  model  will use the drift...assess the feasibility of #2. WORK COMPLETED We have completed the following tasks: 1. Built the statistical model to estimate at-sea lipid status 2

  18. The Blazar 3C 66A in 2003-2004: hadronic versus leptonic model fits

    SciTech Connect

    Reimer, A.

    2008-12-24

    The low-frequency peaked BL Lac object 3C 66A was the subject of an extensive multi-wavelength campaign from July 2003 till April 2004, which included quasi-simultaneous observations at optical, X-rays and very high energy gamma-rays. Here we apply the hadronic Synchrotron-Proton Blazar (SPB) model to the observed spectral energy distribution time-averaged over a flaring state, and compare the resulting model fits to those obtained from the application of the leptonic Synchrotron-Self-Compton (SSC) model. The results are used to identify diagnostic key predictions of the two blazar models for future multi-wavelength observations.

  19. Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

    PubMed Central

    Shekhar, Karthik; Ruberman, Claire F.; Ferguson, Andrew L.; Barton, John P.; Kardar, Mehran; Chakraborty, Arup K.

    2017-01-01

    Mutational escape from vaccine-induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus’ fitness as a function of its proteomic sequence can enable rational design of potent vaccines, as this information can focus vaccine-induced immune responses to target mutational vulnerabilities of the virus. Spin models have been proposed as a means to infer intrinsic fitness landscapes of HIV proteins from patient-derived viral protein sequences. These sequences are the product of nonequilibrium viral evolution driven by patient-specific immune responses and are subject to phylogenetic constraints. How can such sequence data allow inference of intrinsic fitness landscapes? We combined computer simulations and variational theory á la Feynman to show that, in most circumstances, spin models inferred from patient-derived viral sequences reflect the correct rank order of the fitness of mutant viral strains. Our findings are relevant for diverse viruses. PMID:24483484

  20. The Impact of Model Misspecification on Parameter Estimation and Item-Fit Assessment in Log-Linear Diagnostic Classification Models

    ERIC Educational Resources Information Center

    Kunina-Habenicht, Olga; Rupp, Andre A.; Wilhelm, Oliver

    2012-01-01

    Using a complex simulation study we investigated parameter recovery, classification accuracy, and performance of two item-fit statistics for correct and misspecified diagnostic classification models within a log-linear modeling framework. The basic manipulated test design factors included the number of respondents (1,000 vs. 10,000), attributes (3…

  1. unmarked: An R package for fitting hierarchical models of wildlife occurrence and abundance

    USGS Publications Warehouse

    Fiske, Ian J.; Chandler, Richard B.

    2011-01-01

    Ecological research uses data collection techniques that are prone to substantial and unique types of measurement error to address scientific questions about species abundance and distribution. These data collection schemes include a number of survey methods in which unmarked individuals are counted, or determined to be present, at spatially- referenced sites. Examples include site occupancy sampling, repeated counts, distance sampling, removal sampling, and double observer sampling. To appropriately analyze these data, hierarchical models have been developed to separately model explanatory variables of both a latent abundance or occurrence process and a conditional detection process. Because these models have a straightforward interpretation paralleling mechanisms under which the data arose, they have recently gained immense popularity. The common hierarchical structure of these models is well-suited for a unified modeling interface. The R package unmarked provides such a unified modeling framework, including tools for data exploration, model fitting, model criticism, post-hoc analysis, and model comparison.

  2. Double-sigmoid model for fitting fatigue profiles in mouse fast- and slow-twitch muscle.

    PubMed

    Cairns, S P; Robinson, D M; Loiselle, D S

    2008-07-01

    We present a curve-fitting approach that permits quantitative comparisons of fatigue profiles obtained with different stimulation protocols in isolated slow-twitch soleus and fast-twitch extensor digitorum longus (EDL) muscles of mice. Profiles from our usual stimulation protocol (125 Hz for 500 ms, evoked once every second for 100-300 s) could be fitted by single-term functions (sigmoids or exponentials) but not by a double exponential. A clearly superior fit, as confirmed by the Akaiki Information Criterion, was achieved using a double-sigmoid function. Fitting accuracy was exceptional; mean square errors were typically <1% and r(2) > 0.9995. The first sigmoid (early fatigue) involved approximately 10% decline of isometric force to an intermediate plateau in both muscle types; the second sigmoid (late fatigue) involved a reduction of force to a final plateau, the decline being 83% of initial force in EDL and 63% of initial force in soleus. The maximal slope of each sigmoid was seven- to eightfold greater in EDL than in soleus. The general applicability of the model was tested by fitting profiles with a severe force loss arising from repeated tetanic stimulation evoked at different frequencies or rest periods, or with excitation via nerve terminals in soleus. Late fatigue, which was absent at 30 Hz, occurred earlier and to a greater extent at 125 than 50 Hz. The model captured small changes in rate of late fatigue for nerve terminal versus sarcolemmal stimulation. We conclude that a double-sigmoid expression is a useful and accurate model to characterize fatigue in isolated muscle preparations.

  3. The Herschel Orion Protostar Survey: Spectral Energy Distributions and Fits Using a Grid of Protostellar Models

    NASA Astrophysics Data System (ADS)

    Furlan, E.; Fischer, W. J.; Ali, B.; Stutz, A. M.; Stanke, T.; Tobin, J. J.; Megeath, S. T.; Osorio, M.; Hartmann, L.; Calvet, N.; Poteet, C. A.; Booker, J.; Manoj, P.; Watson, D. M.; Allen, L.

    2016-05-01

    We present key results from the Herschel Orion Protostar Survey: spectral energy distributions (SEDs) and model fits of 330 young stellar objects, predominantly protostars, in the Orion molecular clouds. This is the largest sample of protostars studied in a single, nearby star formation complex. With near-infrared photometry from 2MASS, mid- and far-infrared data from Spitzer and Herschel, and submillimeter photometry from APEX, our SEDs cover 1.2-870 μm and sample the peak of the protostellar envelope emission at ˜100 μm. Using mid-IR spectral indices and bolometric temperatures, we classify our sample into 92 Class 0 protostars, 125 Class I protostars, 102 flat-spectrum sources, and 11 Class II pre-main-sequence stars. We implement a simple protostellar model (including a disk in an infalling envelope with outflow cavities) to generate a grid of 30,400 model SEDs and use it to determine the best-fit model parameters for each protostar. We argue that far-IR data are essential for accurate constraints on protostellar envelope properties. We find that most protostars, and in particular the flat-spectrum sources, are well fit. The median envelope density and median inclination angle decrease from Class 0 to Class I to flat-spectrum protostars, despite the broad range in best-fit parameters in each of the three categories. We also discuss degeneracies in our model parameters. Our results confirm that the different protostellar classes generally correspond to an evolutionary sequence with a decreasing envelope infall rate, but the inclination angle also plays a role in the appearance, and thus interpretation, of the SEDs.

  4. Kinetic modelling of RDF pyrolysis: Model-fitting and model-free approaches.

    PubMed

    Çepelioğullar, Özge; Haykırı-Açma, Hanzade; Yaman, Serdar

    2016-02-01

    In this study, refuse derived fuel (RDF) was selected as solid fuel and it was pyrolyzed in a thermal analyzer from room temperature to 900°C at heating rates of 5, 10, 20, and 50°C/min in N2 atmosphere. The obtained thermal data was used to calculate the kinetic parameters using Coats-Redfern, Friedman, Flylnn-Wall-Ozawa (FWO) and Kissinger-Akahira-Sunose (KAS) methods. As a result of Coats-Redfern model, decomposition process was assumed to be four independent reactions with different reaction orders. On the other hand, model free methods demonstrated that activation energy trend had similarities for the reaction progresses of 0.1, 0.2-0.7 and 0.8-0.9. The average activation energies were found between 73-161kJ/mol and it is possible to say that FWO and KAS models produced closer results to the average activation energies compared to Friedman model. Experimental studies showed that RDF may be a sustainable and promising feedstock for alternative processes in terms of waste management strategies.

  5. Energy allowances for solid fats and added sugars in nutritionally adequate U.S. diets estimated at 17-33% by a linear programming model.

    PubMed

    Maillot, Matthieu; Drewnowski, Adam

    2011-02-01

    The 2010 Dietary Guidelines Advisory Committee has recommended that no more than 5-15% of total dietary energy should be derived from solid fats and added sugars (SoFAS). The guideline was based on USDA food pattern modeling analyses that met the Dietary Reference Intake recommendations and Dietary Guidelines and followed typical American eating habits. This study recreated food intake patterns for 6 of the same gender-age groups by using USDA data sources and a mathematical optimization technique known as linear programming. The analytic process identified food consumption patterns based on 128 food categories that met the nutritional goals for 9 vitamins, 9 minerals, 8 macronutrients, and dietary fiber and minimized deviation from typical American eating habits. Linear programming Model 1 created gender- and age-specific food patterns that corresponded to energy needs for each group. Model 2 created food patterns that were iso-caloric with diets observed for that group in the 2001-2002 NHANES. The optimized food patterns were evaluated with respect to MyPyramid servings goals, energy density [kcal/g (1 kcal = 4.18 kJ)], and energy cost (US$/2000 kcal). The optimized food patterns had more servings of vegetables and fruit, lower energy density, and higher cost compared with the observed diets. All nutrient goals were met. In contrast to the much lower USDA estimates, the 2 models placed SoFAS allowances at between 17 and 33% of total energy, depending on energy needs.

  6. Aeroelastic modeling for the FIT (Functional Integration Technology) team F/A-18 simulation

    NASA Technical Reports Server (NTRS)

    Zeiler, Thomas A.; Wieseman, Carol D.

    1989-01-01

    As part of Langley Research Center's commitment to developing multidisciplinary integration methods to improve aerospace systems, the Functional Integration Technology (FIT) team was established to perform dynamics integration research using an existing aircraft configuration, the F/A-18. An essential part of this effort has been the development of a comprehensive simulation modeling capability that includes structural, control, and propulsion dynamics as well as steady and unsteady aerodynamics. The structural and unsteady aerodynamics contributions come from an aeroelastic mode. Some details of the aeroelastic modeling done for the Functional Integration Technology (FIT) team research are presented. Particular attention is given to work done in the area of correction factors to unsteady aerodynamics data.

  7. Nonlocal nonlinear refractive index of gold nanoparticles synthesized by ascorbic acid reduction: comparison of fitting models.

    PubMed

    Balbuena Ortega, A; Arroyo Carrasco, M L; Méndez Otero, M M; Gayou, V L; Delgado Macuil, R; Martínez Gutiérrez, H; Iturbe Castillo, M D

    2014-12-12

    In this paper, the nonlinear refractive index of colloidal gold nanoparticles under continuous wave illumination is investigated with the z-scan technique. Gold nanoparticles were synthesized using ascorbic acid as reductant, phosphates as stabilizer and cetyltrimethylammonium chloride (CTAC) as surfactant agent. The nanoparticle size was controlled with the CTAC concentration. Experiments changing incident power and sample concentration were done. The experimental z-scan results were fitted with three models: thermal lens, aberrant thermal lens and the nonlocal model. It is shown that the nonlocal model reproduces with exceptionally good agreement; the obtained experimental behaviour.

  8. Validation of a Best-Fit Pharmacokinetic Model for Scopolamine Disposition after Intranasal Administration

    NASA Technical Reports Server (NTRS)

    Wu, L.; Chow, D. S-L.; Tam, V.; Putcha, L.

    2015-01-01

    An intranasal gel formulation of scopolamine (INSCOP) was developed for the treatment of Motion Sickness. Bioavailability and pharmacokinetics (PK) were determined per Investigative New Drug (IND) evaluation guidance by the Food and Drug Administration. Earlier, we reported the development of a PK model that can predict the relationship between plasma, saliva and urinary scopolamine (SCOP) concentrations using data collected from an IND clinical trial with INSCOP. This data analysis project is designed to validate the reported best fit PK model for SCOP by comparing observed and model predicted SCOP concentration-time profiles after administration of INSCOP.

  9. Nonlocal nonlinear refractive index of gold nanoparticles synthesized by ascorbic acid reduction: comparison of fitting models

    PubMed Central

    Balbuena Ortega, A.; Arroyo Carrasco, M.L.; Méndez Otero, M.M.; Gayou, V.L.; Delgado Macuil, R.; Martínez Gutiérrez, H.; Iturbe Castillo, M.D.

    2014-01-01

    In this paper, the nonlinear refractive index of colloidal gold nanoparticles under continuous wave illumination is investigated with the z-scan technique. Gold nanoparticles were synthesized using ascorbic acid as reductant, phosphates as stabilizer and cetyltrimethylammonium chloride (CTAC) as surfactant agent. The nanoparticle size was controlled with the CTAC concentration. Experiments changing incident power and sample concentration were done. The experimental z-scan results were fitted with three models: thermal lens, aberrant thermal lens and the nonlocal model. It is shown that the nonlocal model reproduces with exceptionally good agreement; the obtained experimental behaviour. PMID:25705090

  10. Rainfall interception modelling: Is the wet bulb approach adequate to estimate mean evaporation rate from wet/saturated canopies in all forest types?

    NASA Astrophysics Data System (ADS)

    Pereira, F. L.; Valente, F.; David, J. S.; Jackson, N.; Minunno, F.; Gash, J. H.

    2016-03-01

    The Penman-Monteith equation has been widely used to estimate the maximum evaporation rate (E) from wet/saturated forest canopies, regardless of canopy cover fraction. Forests are then represented as a big leaf and interception loss considered essentially as a one-dimensional process. With increasing forest sparseness the assumptions behind this big leaf approach become questionable. In sparse forests it might be better to model E and interception loss at the tree level assuming that the individual tree crowns behave as wet bulbs ("wet bulb approach"). In this study, and for five different forest types and climate conditions, interception loss measurements were compared to modelled values (Gash's interception model) based on estimates of E by the Penman-Monteith and the wet bulb approaches. Results show that the wet bulb approach is a good, and less data demanding, alternative to estimate E when the forest canopy is fully ventilated (very sparse forests with a narrow canopy depth). When the canopy is not fully ventilated, the wet bulb approach requires a reduction of leaf area index to the upper, more ventilated parts of the canopy, needing data on the vertical leaf area distribution, which is seldom-available. In such cases, the Penman-Monteith approach seems preferable. Our data also show that canopy cover does not per se allow us to identify if a forest canopy is fully ventilated or not. New methodologies of sensitivity analyses applied to Gash's model showed that a correct estimate of E is critical for the proper modelling of interception loss.

  11. Effects of new mutations on fitness: insights from models and data.

    PubMed

    Bataillon, Thomas; Bailey, Susan F

    2014-07-01

    The rates and properties of new mutations affecting fitness have implications for a number of outstanding questions in evolutionary biology. Obtaining estimates of mutation rates and effects has historically been challenging, and little theory has been available for predicting the distribution of fitness effects (DFE); however, there have been recent advances on both fronts. Extreme-value theory predicts the DFE of beneficial mutations in well-adapted populations, while phenotypic fitness landscape models make predictions for the DFE of all mutations as a function of the initial level of adaptation and the strength of stabilizing selection on traits underlying fitness. Direct experimental evidence confirms predictions on the DFE of beneficial mutations and favors distributions that are roughly exponential but bounded on the right. A growing number of studies infer the DFE using genomic patterns of polymorphism and divergence, recovering a wide range of DFE. Future work should be aimed at identifying factors driving the observed variation in the DFE. We emphasize the need for further theory explicitly incorporating the effects of partial pleiotropy and heterogeneity in the environment on the expected DFE.

  12. Model Fit to Experimental Data for Foam-Assisted Deep Vadose Zone Remediation

    SciTech Connect

    Roostapour, A.; Lee, G.; Zhong, Lirong; Kam, Seung I.

    2014-01-15

    Foam has been regarded as a promising means of remeidal amendment delivery to overcome subsurface heterogeneity in subsurface remediation processes. This study investigates how a foam model, developed by Method of Characteristics and fractional flow analysis in the companion paper of Roostapour and Kam (2012), can be applied to make a fit to a set of existing laboratory flow experiments (Zhong et al., 2009) in an application relevant to deep vadose zone remediation. This study reveals a few important insights regarding foam-assisted deep vadose zone remediation: (i) the mathematical framework established for foam modeling can fit typical flow experiments matching wave velocities, saturation history , and pressure responses; (ii) the set of input parameters may not be unique for the fit, and therefore conducting experiments to measure basic model parameters related to relative permeability, initial and residual saturations, surfactant adsorption and so on should not be overlooked; and (iii) gas compressibility plays an important role for data analysis, thus should be handled carefully in laboratory flow experiments. Foam kinetics, causing foam texture to reach its steady-state value slowly, may impose additional complications.

  13. Design and verifications of an eye model fitted with contact lenses for wavefront measurement systems

    NASA Astrophysics Data System (ADS)

    Cheng, Yuan-Chieh; Chen, Jia-Hong; Chang, Rong-Jie; Wang, Chung-Yen; Hsu, Wei-Yao; Wang, Pei-Jen

    2015-09-01

    Contact lenses are typically measured by the wet-box method because of the high optical power resulting from the anterior central curvature of cornea, even though the back vertex power of the lenses are small. In this study, an optical measurement system based on the Shack-Hartmann wavefront principle was established to investigate the aberrations of soft contact lenses. Fitting conditions were micmicked to study the optical design of an eye model with various topographical shapes in the anterior cornea. Initially, the contact lenses were measured by the wet-box method, and then by fitting the various topographical shapes of cornea to the eye model. In addition, an optics simulation program was employed to determine the sources of errors and assess the accuracy of the system. Finally, samples of soft contact lenses with various Diopters were measured; and, both simulations and experimental results were compared for resolving the controversies of fitting contact lenses to an eye model for optical measurements. More importantly, the results show that the proposed system can be employed for study of primary aberrations in contact lenses.

  14. Fitting a Two-Component Scattering Model to Polarimetric SAR Data

    NASA Technical Reports Server (NTRS)

    Freeman, A.

    1998-01-01

    Classification, decomposition and modeling of polarimetric SAR data has received a great deal of attention in the recent literature. The objective behind these efforts is to better understand the scattering mechanisms which give rise to the polarimetric signatures seen in SAR image data. In this Paper an approach is described, which involves the fit of a combination of two simple scattering mechanisms to polarimetric SAR observations. The mechanisms am canopy scatter from a cloud of randomly oriented oblate spheroids, and a ground scatter term, which can represent double-bounce scatter from a pair of orthogonal surfaces with different dielectric constants or Bragg scatter from a moderately rough surface, seen through a layer of vertically oriented scatterers. An advantage of this model fit approach is that the scattering contributions from the two basic scattering mechanisms can be estimated for clusters of pixels in polarimetric SAR images. The solution involves the estimation of four parameters from four separate equations. The model fit can be applied to polarimetric AIRSAR data at C-, L- and P-Band.

  15. Efficient parallel implementation of active appearance model fitting algorithm on GPU.

    PubMed

    Wang, Jinwei; Ma, Xirong; Zhu, Yuanping; Sun, Jizhou

    2014-01-01

    The active appearance model (AAM) is one of the most powerful model-based object detecting and tracking methods which has been widely used in various situations. However, the high-dimensional texture representation causes very time-consuming computations, which makes the AAM difficult to apply to real-time systems. The emergence of modern graphics processing units (GPUs) that feature a many-core, fine-grained parallel architecture provides new and promising solutions to overcome the computational challenge. In this paper, we propose an efficient parallel implementation of the AAM fitting algorithm on GPUs. Our design idea is fine grain parallelism in which we distribute the texture data of the AAM, in pixels, to thousands of parallel GPU threads for processing, which makes the algorithm fit better into the GPU architecture. We implement our algorithm using the compute unified device architecture (CUDA) on the Nvidia's GTX 650 GPU, which has the latest Kepler architecture. To compare the performance of our algorithm with different data sizes, we built sixteen face AAM models of different dimensional textures. The experiment results show that our parallel AAM fitting algorithm can achieve real-time performance for videos even on very high-dimensional textures.

  16. Detection of implausible phylogenetic inferences using posterior predictive assessment of model fit.

    PubMed

    Brown, Jeremy M

    2014-05-01

    Systematic phylogenetic error caused by the simplifying assumptions made in models of molecular evolution may be impossible to avoid entirely when attempting to model evolution across massive, diverse data sets. However, not all deficiencies of inference models result in unreliable phylogenetic estimates. The field of phylogenetics lacks a direct method to identify cases where model specification adversely affects inferences. Posterior predictive simulation is a flexible and intuitive approach for assessing goodness-of-fit of the assumed model and priors in a Bayesian phylogenetic analysis. Here, I propose new test statistics for use in posterior predictive assessment of model fit. These test statistics compare phylogenetic inferences from posterior predictive data sets to inferences from the original data. A simulation study demonstrates the utility of these new statistics. The new tests reject the plausibility of inferred tree lengths or topologies more often when data/model combinations produce biased inferences. I also apply this approach to exemplar empirical data sets, highlighting the value of the novel assessments.

  17. A new strategy to prevent over-fitting in partial least squares models based on model population analysis.

    PubMed

    Deng, Bai-Chuan; Yun, Yong-Huan; Liang, Yi-Zeng; Cao, Dong-Sheng; Xu, Qing-Song; Yi, Lun-Zhao; Huang, Xin

    2015-06-23

    Partial least squares (PLS) is one of the most widely used methods for chemical modeling. However, like many other parameter tunable methods, it has strong tendency of over-fitting. Thus, a crucial step in PLS model building is to select the optimal number of latent variables (nLVs). Cross-validation (CV) is the most popular method for PLS model selection because it selects a model from the perspective of prediction ability. However, a clear minimum of prediction errors may not be obtained in CV which makes the model selection difficult. To solve the problem, we proposed a new strategy for PLS model selection which combines the cross-validated coefficient of determination (Qcv(2)) and model stability (S). S is defined as the stability of PLS regression vectors which is obtained using model population analysis (MPA). The results show that, when a clear maximum of Qcv(2) is not obtained, S can provide additional information of over-fitting and it helps in finding the optimal nLVs. Compared with other regression vector based indictors such as the Euclidean 2-norm (B2), the Durbin Watson statistic (DW) and the jaggedness (J), S is more sensitive to over-fitting. The model selected by our method has both good prediction ability and stability.

  18. Fitting a Two-Component Scattering Model to Polarimetric SAR Data from Forests

    NASA Technical Reports Server (NTRS)

    Freeman, Anthony

    2007-01-01

    Two simple scattering mechanisms are fitted to polarimetric synthetic aperture radar (SAR) observations of forests. The mechanisms are canopy scatter from a reciprocal medium with azimuthal symmetry and a ground scatter term that can represent double-bounce scatter from a pair of orthogonal surfaces with different dielectric constants or Bragg scatter from a moderately rough surface, which is seen through a layer of vertically oriented scatterers. The model is shown to represent the behavior of polarimetric backscatter from a tropical forest and two temperate forest sites by applying it to data from the National Aeronautic and Space Agency/Jet Propulsion Laboratory's Airborne SAR (AIRSAR) system. Scattering contributions from the two basic scattering mechanisms are estimated for clusters of pixels in polarimetric SAR images. The solution involves the estimation of four parameters from four separate equations. This model fit approach is justified as a simplification of more complicated scattering models, which require many inputs to solve the forward scattering problem. The model is used to develop an understanding of the ground-trunk double-bounce scattering that is present in the data, which is seen to vary considerably as a function of incidence angle. Two parameters in the model fit appear to exhibit sensitivity to vegetation canopy structure, which is worth further exploration. Results from the model fit for the ground scattering term are compared with estimates from a forward model and shown to be in good agreement. The behavior of the scattering from the ground-trunk interaction is consistent with the presence of a pseudo-Brewster angle effect for the air-trunk scattering interface. If the Brewster angle is known, it is possible to directly estimate the real part of the dielectric constant of the trunks, a key variable in forward modeling of backscatter from forests. It is also shown how, with a priori knowledge of the forest height, an estimate for the

  19. Do Physical Proximity and Availability of Adequate Infrastructure at Public Health Facility Increase Institutional Delivery? A Three Level Hierarchical Model Approach.

    PubMed

    Patel, Rachana; Ladusingh, Laishram

    2015-01-01

    This study aims to examine the inter-district and inter-village variation of utilization of health services for institutional births in EAG states in presence of rural health program and availability of infrastructures. District Level Household Survey-III (2007-08) data on delivery care and facility information was used for the purpose. Bivariate results examined the utilization pattern by states in presence of correlates of women related while a three-level hierarchical multilevel model illustrates the effect of accessibility, availability of health facility and community health program variables on the utilization of health services for institutional births. The study found a satisfactory improvement in state Rajasthan, Madhya Pradesh and Orissa, importantly, in Bihar and Uttaranchal. The study showed that increasing distance from health facility discouraged institutional births and there was a rapid decline of more than 50% for institutional delivery as the distance to public health facility exceeded 10 km. Additionally, skilled female health worker (ANM) and observed improved public health facility led to significantly increase the probability of utilization as compared to non-skilled ANM and not-improved health centers. Adequacy of essential equipment/laboratory services required for maternal care significantly encouraged deliveries at public health facility. District/village variables neighborhood poverty was negatively related to institutional delivery while higher education levels in the village and women's residing in more urbanized districts increased the utilization. "Inter-district" variation was 14 percent whereas "between-villages" variation for the utilization was 11 percent variation once controlled for all the three-level variables in the model. This study suggests that the mere availability of health facilities is necessary but not sufficient condition to promote utilization until the quality of service is inadequate and inaccessible considering

  20. Do Physical Proximity and Availability of Adequate Infrastructure at Public Health Facility Increase Institutional Delivery? A Three Level Hierarchical Model Approach

    PubMed Central

    Patel, Rachana; Ladusingh, Laishram

    2015-01-01

    This study aims to examine the inter-district and inter-village variation of utilization of health services for institutional births in EAG states in presence of rural health program and availability of infrastructures. District Level Household Survey-III (2007–08) data on delivery care and facility information was used for the purpose. Bivariate results examined the utilization pattern by states in presence of correlates of women related while a three-level hierarchical multilevel model illustrates the effect of accessibility, availability of health facility and community health program variables on the utilization of health services for institutional births. The study found a satisfactory improvement in state Rajasthan, Madhya Pradesh and Orissa, importantly, in Bihar and Uttaranchal. The study showed that increasing distance from health facility discouraged institutional births and there was a rapid decline of more than 50% for institutional delivery as the distance to public health facility exceeded 10 km. Additionally, skilled female health worker (ANM) and observed improved public health facility led to significantly increase the probability of utilization as compared to non-skilled ANM and not-improved health centers. Adequacy of essential equipment/laboratory services required for maternal care significantly encouraged deliveries at public health facility. District/village variables neighborhood poverty was negatively related to institutional delivery while higher education levels in the village and women’s residing in more urbanized districts increased the utilization. “Inter-district” variation was 14 percent whereas “between-villages” variation for the utilization was 11 percent variation once controlled for all the three-level variables in the model. This study suggests that the mere availability of health facilities is necessary but not sufficient condition to promote utilization until the quality of service is inadequate and inaccessible

  1. Fit for purpose application of currently existing animal models in the discovery of novel epilepsy therapies.

    PubMed

    Löscher, Wolfgang

    2016-10-01

    Animal seizure and epilepsy models continue to play an important role in the early discovery of new therapies for the symptomatic treatment of epilepsy. Since 1937, with the discovery of phenytoin, almost all anti-seizure drugs (ASDs) have been identified by their effects in animal models, and millions of patients world-wide have benefited from the successful translation of animal data into the clinic. However, several unmet clinical needs remain, including resistance to ASDs in about 30% of patients with epilepsy, adverse effects of ASDs that can reduce quality of life, and the lack of treatments that can prevent development of epilepsy in patients at risk following brain injury. The aim of this review is to critically discuss the translational value of currently used animal models of seizures and epilepsy, particularly what animal models can tell us about epilepsy therapies in patients and which limitations exist. Principles of translational medicine will be used for this discussion. An essential requirement for translational medicine to improve success in drug development is the availability of animal models with high predictive validity for a therapeutic drug response. For this requirement, the model, by definition, does not need to be a perfect replication of the clinical condition, but it is important that the validation provided for a given model is fit for purpose. The present review should guide researchers in both academia and industry what can and cannot be expected from animal models in preclinical development of epilepsy therapies, which models are best suited for which purpose, and for which aspects suitable models are as yet not available. Overall further development is needed to improve and validate animal models for the diverse areas in epilepsy research where suitable fit for purpose models are urgently needed in the search for more effective treatments.

  2. Computational Software for Fitting Seismic Data to Epidemic-Type Aftershock Sequence Models

    NASA Astrophysics Data System (ADS)

    Chu, A.

    2014-12-01

    Modern earthquake catalogs are often analyzed using spatial-temporal point process models such as the epidemic-type aftershock sequence (ETAS) models of Ogata (1998). My work introduces software to implement two of ETAS models described in Ogata (1998). To find the Maximum-Likelihood Estimates (MLEs), my software provides estimates of the homogeneous background rate parameter and the temporal and spatial parameters that govern triggering effects by applying the Expectation-Maximization (EM) algorithm introduced in Veen and Schoenberg (2008). Despite other computer programs exist for similar data modeling purpose, using EM-algorithm has the benefits of stability and robustness (Veen and Schoenberg, 2008). Spatial shapes that are very long and narrow cause difficulties in optimization convergence and problems with flat or multi-modal log-likelihood functions encounter similar issues. My program uses a robust method to preset a parameter to overcome the non-convergence computational issue. In addition to model fitting, the software is equipped with useful tools for examining modeling fitting results, for example, visualization of estimated conditional intensity, and estimation of expected number of triggered aftershocks. A simulation generator is also given with flexible spatial shapes that may be defined by the user. This open-source software has a very simple user interface. The user may execute it on a local computer, and the program also has potential to be hosted online. Java language is used for the software's core computing part and an optional interface to the statistical package R is provided.

  3. Kinetic Modeling and Fitting Software for Inter-connected Reaction Schemes: VisKin

    PubMed Central

    Zhang, Xuan; Andrews, Jared N.; Pedersen, Steen E.

    2007-01-01

    Reaction kinetics for complex, highly-interconnected kinetic schemes are modeled using analytical solutions to a system of ordinary differential equations. The algorithm employs standard linear algebra methods that are implemented using MatLab functions in a Visual Basic interface. A graphical user interface for simple entry of reaction schemes facilitates comparison of a variety of reaction schemes. To ensure microscopic balance, graph theory algorithms are used to determine violations of thermodynamic cycle constraints. Analytical solutions based on linear differential equations result in fast comparisons of first order kinetic rates and amplitudes as a function of changing ligand concentrations. For analysis of higher order kinetics, we also implemented a solution using numerical integration. In order to determine rate constants from experimental data, fitting algorithms using the Levenberg-Marquardt algorithm or using Broyden-Fletcher-Goldfarb-Shanno (BFGS) methods were implemented that adjust rate constants to fit the model to imported data. We have included the ability to carry out global fitting of data sets obtained at varying ligand concentrations. These tools are combined in a single package, which we have dubbed VisKin, to guide and analyze kinetic experiments. The software is available online for use on PCs. PMID:17207764

  4. Fitting of different models for water vapour sorption on potato starch granules

    NASA Astrophysics Data System (ADS)

    Czepirski, L.; Komorowska-Czepirska, E.; Szymońska, J.

    2002-08-01

    Water vapour adsorption isotherms for native and modified potato starch were investigated. To obtain the best fit for the experimental data several models based on the BET approach were evaluated. The hypothesis that water is adsorbed on the starch granules at the primary and secondary adsorption sites as well as a concept considering the adsorbent fractality were also tested. It was found, that the equilibrium adsorption points in the examined range of relative humidity (0.03-0.90) were most accurately predicted by using a three-parameter model proposed by Kats and Kutarov.

  5. Goodness-of-fit tests for open capture-recapture models

    USGS Publications Warehouse

    Pollock, K.H.; Hines, J.E.; Nichols, J.D.

    1985-01-01

    General goodness-of-fit tests for the Jolly-Seber model are proposed. These tests are based on conditional arguments using minimal sufficient statistics. The tests are shown to be of simple hypergeometric form so that a series of independent contingency table chi-square tests can be performed. The relationship of these tests to other proposed tests is discussed. This is followed by a simulation study of the power of the tests to detect departures from the assumptions of the Jolly-Seber model. Some meadow vole capture-recapture data are used to illustrate the testing procedure which has been implemented in a computer program available from the authors.

  6. Freeze-Dried Platelet-Rich Plasma Accelerates Bone Union with Adequate Rigidity in Posterolateral Lumbar Fusion Surgery Model in Rats

    NASA Astrophysics Data System (ADS)

    Shiga, Yasuhiro; Orita, Sumihisa; Kubota, Go; Kamoda, Hiroto; Yamashita, Masaomi; Matsuura, Yusuke; Yamauchi, Kazuyo; Eguchi, Yawara; Suzuki, Miyako; Inage, Kazuhide; Sainoh, Takeshi; Sato, Jun; Fujimoto, Kazuki; Abe, Koki; Kanamoto, Hirohito; Inoue, Masahiro; Kinoshita, Hideyuki; Aoki, Yasuchika; Toyone, Tomoaki; Furuya, Takeo; Koda, Masao; Takahashi, Kazuhisa; Ohtori, Seiji

    2016-11-01

    Fresh platelet-rich plasma (PRP) accelerates bone union in rat model. However, fresh PRP has a short half-life. We suggested freeze-dried PRP (FD-PRP) prepared in advance and investigated its efficacy in vivo. Spinal posterolateral fusion was performed on 8-week-old male Sprague-Dawley rats divided into six groups based on the graft materials (n = 10 per group): sham control, artificial bone (A hydroxyapatite–collagen composite) –alone, autologous bone, artificial bone + fresh-PRP, artificial bone + FD-PRP preserved 8 weeks, and artificial bone + human recombinant bone morphogenetic protein 2 (BMP) as a positive control. At 4 and 8 weeks after the surgery, we investigated their bone union–related characteristics including amount of bone formation, histological characteristics of trabecular bone at remodeling site, and biomechanical strength on 3-point bending. Comparable radiological bone union was confirmed at 4 weeks after surgery in 80% of the FD-PRP groups, which was earlier than in other groups (p < 0.05). Histologically, the trabecular bone had thinner and more branches in the FD-PRP. Moreover, the biomechanical strength was comparable to that of autologous bone. FD-PRP accelerated bone union at a rate comparable to that of fresh PRP and BMP by remodeling the bone with thinner, more tangled, and rigid trabecular bone.

  7. Freeze-Dried Platelet-Rich Plasma Accelerates Bone Union with Adequate Rigidity in Posterolateral Lumbar Fusion Surgery Model in Rats

    PubMed Central

    Shiga, Yasuhiro; Orita, Sumihisa; Kubota, Go; Kamoda, Hiroto; Yamashita, Masaomi; Matsuura, Yusuke; Yamauchi, Kazuyo; Eguchi, Yawara; Suzuki, Miyako; Inage, Kazuhide; Sainoh, Takeshi; Sato, Jun; Fujimoto, Kazuki; Abe, Koki; Kanamoto, Hirohito; Inoue, Masahiro; Kinoshita, Hideyuki; Aoki, Yasuchika; Toyone, Tomoaki; Furuya, Takeo; Koda, Masao; Takahashi, Kazuhisa; Ohtori, Seiji

    2016-01-01

    Fresh platelet-rich plasma (PRP) accelerates bone union in rat model. However, fresh PRP has a short half-life. We suggested freeze-dried PRP (FD-PRP) prepared in advance and investigated its efficacy in vivo. Spinal posterolateral fusion was performed on 8-week-old male Sprague-Dawley rats divided into six groups based on the graft materials (n = 10 per group): sham control, artificial bone (A hydroxyapatite–collagen composite) –alone, autologous bone, artificial bone + fresh-PRP, artificial bone + FD-PRP preserved 8 weeks, and artificial bone + human recombinant bone morphogenetic protein 2 (BMP) as a positive control. At 4 and 8 weeks after the surgery, we investigated their bone union–related characteristics including amount of bone formation, histological characteristics of trabecular bone at remodeling site, and biomechanical strength on 3-point bending. Comparable radiological bone union was confirmed at 4 weeks after surgery in 80% of the FD-PRP groups, which was earlier than in other groups (p < 0.05). Histologically, the trabecular bone had thinner and more branches in the FD-PRP. Moreover, the biomechanical strength was comparable to that of autologous bone. FD-PRP accelerated bone union at a rate comparable to that of fresh PRP and BMP by remodeling the bone with thinner, more tangled, and rigid trabecular bone. PMID:27833116

  8. Practical Person-Fit Assessment with the Linear FA Model: New Developments and a Comparative Study.

    PubMed

    Ferrando, Pere J; Vigil-Colet, Andreu; Lorenzo-Seva, Urbano

    2016-01-01

    Linear factor analysis (FA) is, possibly, the most widely used model in psychometric applications based on graded-response or more continuous items. However, in these applications consistency at the individual level (person fit) is virtually never assessed. The aim of the present study is to propose a simple and workable approach to routinely assess person fit in FA-based studies. To do so, we first consider five potentially appropriate indices, of which one is a new proposal and the other is a modification of an existing index. Next, the effectiveness of these indices is assessed by using (a) a thorough simulation study that attempts to mimic realistic conditions, and (b) an illustrative example based on real data. Results suggest that the mean-squared lico index and the personal correlation work well in conjunction and can function effectively for detecting different types of inconsistency. Finally future directions and lines of research are discussed.

  9. Practical Person-Fit Assessment with the Linear FA Model: New Developments and a Comparative Study

    PubMed Central

    Ferrando, Pere J.; Vigil-Colet, Andreu; Lorenzo-Seva, Urbano

    2016-01-01

    Linear factor analysis (FA) is, possibly, the most widely used model in psychometric applications based on graded-response or more continuous items. However, in these applications consistency at the individual level (person fit) is virtually never assessed. The aim of the present study is to propose a simple and workable approach to routinely assess person fit in FA-based studies. To do so, we first consider five potentially appropriate indices, of which one is a new proposal and the other is a modification of an existing index. Next, the effectiveness of these indices is assessed by using (a) a thorough simulation study that attempts to mimic realistic conditions, and (b) an illustrative example based on real data. Results suggest that the mean-squared lico index and the personal correlation work well in conjunction and can function effectively for detecting different types of inconsistency. Finally future directions and lines of research are discussed. PMID:28082929

  10. Fitted Hanbury-Brown-Twiss radii versus space-time variances in flow-dominated models

    SciTech Connect

    Frodermann, Evan; Heinz, Ulrich; Lisa, Michael Annan

    2006-04-15

    The inability of otherwise successful dynamical models to reproduce the Hanbury-Brown-Twiss (HBT) radii extracted from two-particle correlations measured at the Relativistic Heavy Ion Collider (RHIC) is known as the RHIC HBT Puzzle. Most comparisons between models and experiment exploit the fact that for Gaussian sources the HBT radii agree with certain combinations of the space-time widths of the source that can be directly computed from the emission function without having to evaluate, at significant expense, the two-particle correlation function. We here study the validity of this approach for realistic emission function models, some of which exhibit significant deviations from simple Gaussian behavior. By Fourier transforming the emission function, we compute the two-particle correlation function, and fit it with a Gaussian to partially mimic the procedure used for measured correlation functions. We describe a novel algorithm to perform this Gaussian fit analytically. We find that for realistic hydrodynamic models the HBT radii extracted from this procedure agree better with the data than the values previously extracted from the space-time widths of the emission function. Although serious discrepancies between the calculated and the measured HBT radii remain, we show that a more apples-to-apples comparison of models with data can play an important role in any eventually successful theoretical description of RHIC HBT data.

  11. Fitted Hanbury-Brown Twiss radii versus space-time variances in flow-dominated models

    NASA Astrophysics Data System (ADS)

    Frodermann, Evan; Heinz, Ulrich; Lisa, Michael Annan

    2006-04-01

    The inability of otherwise successful dynamical models to reproduce the Hanbury-Brown Twiss (HBT) radii extracted from two-particle correlations measured at the Relativistic Heavy Ion Collider (RHIC) is known as the RHIC HBT Puzzle. Most comparisons between models and experiment exploit the fact that for Gaussian sources the HBT radii agree with certain combinations of the space-time widths of the source that can be directly computed from the emission function without having to evaluate, at significant expense, the two-particle correlation function. We here study the validity of this approach for realistic emission function models, some of which exhibit significant deviations from simple Gaussian behavior. By Fourier transforming the emission function, we compute the two-particle correlation function, and fit it with a Gaussian to partially mimic the procedure used for measured correlation functions. We describe a novel algorithm to perform this Gaussian fit analytically. We find that for realistic hydrodynamic models the HBT radii extracted from this procedure agree better with the data than the values previously extracted from the space-time widths of the emission function. Although serious discrepancies between the calculated and the measured HBT radii remain, we show that a more apples-to-apples comparison of models with data can play an important role in any eventually successful theoretical description of RHIC HBT data.

  12. Real-time simulation of power transmission lines using Marti model with optimal fitting on dual-DSP card

    SciTech Connect

    Dufour, C.; Le-Huy, H.; El Hakimi, A.; Soumagne, J.C.

    1996-01-01

    Real-time simulation of a small power network containing a Marti modeled transmission line is made using 2 parallel DSP`s. A new fitting method is used in the modeling of the Marti line which is optimized with regards to the fitting error curve. Results are presented which show the time costs of the Marti line modeling versus constant-parameter line modeling and the time savings by using two parallel DSP`s.

  13. Model fitting of kink waves in the solar atmosphere: Gaussian damping and time-dependence

    NASA Astrophysics Data System (ADS)

    Morton, R. J.; Mooroogen, K.

    2016-09-01

    Aims: Observations of the solar atmosphere have shown that magnetohydrodynamic waves are ubiquitous throughout. Improvements in instrumentation and the techniques used for measurement of the waves now enables subtleties of competing theoretical models to be compared with the observed waves behaviour. Some studies have already begun to undertake this process. However, the techniques employed for model comparison have generally been unsuitable and can lead to erroneous conclusions about the best model. The aim here is to introduce some robust statistical techniques for model comparison to the solar waves community, drawing on the experiences from other areas of astrophysics. In the process, we also aim to investigate the physics of coronal loop oscillations. Methods: The methodology exploits least-squares fitting to compare models to observational data. We demonstrate that the residuals between the model and observations contain significant information about the ability for the model to describe the observations, and show how they can be assessed using various statistical tests. In particular we discuss the Kolmogorov-Smirnoff one and two sample tests, as well as the runs test. We also highlight the importance of including any observational trend line in the model-fitting process. Results: To demonstrate the methodology, an observation of an oscillating coronal loop undergoing standing kink motion is used. The model comparison techniques provide evidence that a Gaussian damping profile provides a better description of the observed wave attenuation than the often used exponential profile. This supports previous analysis from Pascoe et al. (2016, A&A, 585, L6). Further, we use the model comparison to provide evidence of time-dependent wave properties of a kink oscillation, attributing the behaviour to the thermodynamic evolution of the local plasma.

  14. Model Flexibility Analysis Does Not Measure the Persuasiveness of a Fit.

    PubMed

    Evans, Nathan J; Howard, Zachary L; Heathcote, Andrew; Brown, Scott D

    2017-02-02

    Recently, Veksler, Myers, and Gluck (2015) proposed model flexibility analysis as a method that "aids model evaluation by providing a metric for gauging the persuasiveness of a given fit" (p. 755) Model flexibility analysis measures the complexity of a model in terms of the proportion of all possible data patterns it can predict. We show that this measure does not provide a reliable way to gauge complexity, which prevents model flexibility analysis from fulfilling either of the 2 aims outlined by Veksler et al. (2015): absolute and relative model evaluation. We also show that model flexibility analysis can even fail to correctly quantify complexity in the most clear cut case, with nested models. We advocate for the use of well-established techniques with these characteristics, such as Bayes factors, normalized maximum likelihood, or cross-validation, and against the use of model flexibility analysis. In the discussion, we explore 2 issues relevant to the area of model evaluation: the completeness of current model selection methods and the philosophical debate of absolute versus relative model evaluation. (PsycINFO Database Record

  15. Atmospheric Properties of T Dwarfs Inferred from Model Fits at Low Spectral Resolution

    NASA Astrophysics Data System (ADS)

    Godfrey, Paige A.; Rice, Emily L.; Filippazzo, Joe; Douglas, Stephanie; BDNYC

    2016-01-01

    Brown dwarfs are substellar objects that cool over time because they are not massive enough to sustain hydrogen fusion at their cores. While spectral types (M, L, T, Y) generally correlate with decreasing temperature, spectral subclasses (T0, T1, T2, etc.) do not, suggesting that secondary parameters (gravity, metallicity, dust) play a role in the spectral type-temperature relationship. We investigate this relationship for T dwarfs, which make up the coolest fully-populated spectral class of substellar objects. Our sample consists of 154 T dwarfs with low resolution (R~75-100) near-infrared (~0.8-2.5 micron) spectra from the SpeX Prism Library and the literature. We compare each observed spectrum to synthetic spectra from four model grids using a Markov-Chain Monte Carlo analysis to determine robust best-fit parameters and uncertainties. We evaluate the best fit parameters from each model grid per object to constrain how spectral type relates to decreasing temperature and increasing surface gravity and to compare the consistency of each model grid. To test for discrepant results when fitting to relatively narrow wavelength ranges, this analysis is performed on the full spectrum of the Y, J, H, and K bands and on each band separately. New detections of cooler objects extending into the Y dwarf and exoplanet regimes motivate our model comparisons and search for trends with spectral type and other observational properties across the decreasing temperatures in order to better understand the atmospheres of substellar objects, including cool gas giant exoplanets.

  16. Blowout Jets: Hinode X-Ray Jets that Don't Fit the Standard Model

    NASA Technical Reports Server (NTRS)

    Moore, Ronald L.; Cirtain, Jonathan W.; Sterling, Alphonse C.; Falconer, David A.

    2010-01-01

    Nearly half of all H-alpha macrospicules in polar coronal holes appear to be miniature filament eruptions. This suggests that there is a large class of X-ray jets in which the jet-base magnetic arcade undergoes a blowout eruption as in a CME, instead of remaining static as in most solar X-ray jets, the standard jets that fit the model advocated by Shibata. Along with a cartoon depicting the standard model, we present a cartoon depicting the signatures expected of blowout jets in coronal X-ray images. From Hinode/XRT movies and STEREO/EUVI snapshots in polar coronal holes, we present examples of (1) X-ray jets that fit the standard model, and (2) X-ray jets that do not fit the standard model but do have features appropriate for blowout jets. These features are (1) a flare arcade inside the jet-base arcade in addition to the small flare arcade (bright point) outside that standard jets have, (2) a filament of cool (T is approximately 80,000K) plasma that erupts from the core of the jetbase arcade, and (3) an extra jet strand that should not be made by the reconnection for standard jets but could be made by reconnection between the ambient unipolar open field and the opposite-polarity leg of the filament-carrying flux-rope core field of the erupting jet-base arcade. We therefore infer that these non-standard jets are blowout jets, jets made by miniature versions of the sheared-core-arcade eruptions that make CMEs

  17. Summary goodness-of-fit statistics for binary generalized linear models with noncanonical link functions.

    PubMed

    Canary, Jana D; Blizzard, Leigh; Barry, Ronald P; Hosmer, David W; Quinn, Stephen J

    2016-05-01

    Generalized linear models (GLM) with a canonical logit link function are the primary modeling technique used to relate a binary outcome to predictor variables. However, noncanonical links can offer more flexibility, producing convenient analytical quantities (e.g., probit GLMs in toxicology) and desired measures of effect (e.g., relative risk from log GLMs). Many summary goodness-of-fit (GOF) statistics exist for logistic GLM. Their properties make the development of GOF statistics relatively straightforward, but it can be more difficult under noncanonical links. Although GOF tests for logistic GLM with continuous covariates (GLMCC) have been applied to GLMCCs with log links, we know of no GOF tests in the literature specifically developed for GLMCCs that can be applied regardless of link function chosen. We generalize the Tsiatis GOF statistic originally developed for logistic GLMCCs, (TG), so that it can be applied under any link function. Further, we show that the algebraically related Hosmer-Lemeshow (HL) and Pigeon-Heyse (J(2) ) statistics can be applied directly. In a simulation study, TG, HL, and J(2) were used to evaluate the fit of probit, log-log, complementary log-log, and log models, all calculated with a common grouping method. The TG statistic consistently maintained Type I error rates, while those of HL and J(2) were often lower than expected if terms with little influence were included. Generally, the statistics had similar power to detect an incorrect model. An exception occurred when a log GLMCC was incorrectly fit to data generated from a logistic GLMCC. In this case, TG had more power than HL or J(2) .

  18. A Parametric Model of Shoulder Articulation for Virtual Assessment of Space Suit Fit

    NASA Technical Reports Server (NTRS)

    Kim, K. Han; Young, Karen S.; Bernal, Yaritza; Boppana, Abhishektha; Vu, Linh Q.; Benson, Elizabeth A.; Jarvis, Sarah; Rajulu, Sudhakar L.

    2016-01-01

    Shoulder injury is one of the most severe risks that have the potential to impair crewmembers' performance and health in long duration space flight. Overall, 64% of crewmembers experience shoulder pain after extra-vehicular training in a space suit, and 14% of symptomatic crewmembers require surgical repair (Williams & Johnson, 2003). Suboptimal suit fit, in particular at the shoulder region, has been identified as one of the predominant risk factors. However, traditional suit fit assessments and laser scans represent only a single person's data, and thus may not be generalized across wide variations of body shapes and poses. The aim of this work is to develop a software tool based on a statistical analysis of a large dataset of crewmember body shapes. This tool can accurately predict the skin deformation and shape variations for any body size and shoulder pose for a target population, from which the geometry can be exported and evaluated against suit models in commercial CAD software. A preliminary software tool was developed by statistically analyzing 150 body shapes matched with body dimension ranges specified in the Human-Systems Integration Requirements of NASA ("baseline model"). Further, the baseline model was incorporated with shoulder joint articulation ("articulation model"), using additional subjects scanned in a variety of shoulder poses across a pre-specified range of motion. Scan data was cleaned and aligned using body landmarks. The skin deformation patterns were dimensionally reduced and the co-variation with shoulder angles was analyzed. A software tool is currently in development and will be presented in the final proceeding. This tool would allow suit engineers to parametrically generate body shapes in strategically targeted anthropometry dimensions and shoulder poses. This would also enable virtual fit assessments, with which the contact volume and clearance between the suit and body surface can be predictively quantified at reduced time and

  19. 21 CFR 1404.900 - Adequate evidence.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 9 2012-04-01 2012-04-01 false Adequate evidence. 1404.900 Section 1404.900 Food and Drugs OFFICE OF NATIONAL DRUG CONTROL POLICY GOVERNMENTWIDE DEBARMENT AND SUSPENSION (NONPROCUREMENT) Definitions § 1404.900 Adequate evidence. Adequate evidence means information sufficient...

  20. 21 CFR 1404.900 - Adequate evidence.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Adequate evidence. 1404.900 Section 1404.900 Food and Drugs OFFICE OF NATIONAL DRUG CONTROL POLICY GOVERNMENTWIDE DEBARMENT AND SUSPENSION (NONPROCUREMENT) Definitions § 1404.900 Adequate evidence. Adequate evidence means information sufficient...

  1. Finding the right fit: A comparison of process assumptions underlying popular drift-diffusion models.

    PubMed

    Ashby, Nathaniel J S; Jekel, Marc; Dickert, Stephan; Glöckner, Andreas

    2016-12-01

    Recent research makes increasing use of eye-tracking methodologies to generate and test process models. Overall, such research suggests that attention, generally indexed by fixations (gaze duration), plays a critical role in the construction of preference, although the methods used to support this supposition differ substantially. In 2 studies we empirically test prototypical versions of prominent processing assumptions against 1 another and several base models. We find that general evidence accumulation processes provide a good fit to the data. An accumulation process that assumes leakage and temporal variability in evidence weighting (i.e., a primacy effect) fits the aggregate data, both in terms of choices and decision times, and does so across varying types of choices (e.g., charitable giving and hedonic consumption) and numbers of options well. However, when comparing models on the level of the individual, for a majority of participants simpler models capture choice data better. The theoretical and practical implications of these findings are discussed. (PsycINFO Database Record

  2. Stochastic optimization algorithm selection in hydrological model calibration based on fitness landscape characterization

    NASA Astrophysics Data System (ADS)

    Arsenault, Richard; Brissette, François P.; Poulin, Annie; Côté, Pascal; Martel, Jean-Luc

    2014-05-01

    The process of hydrological model parameter calibration is routinely performed with the help of stochastic optimization algorithms. Many such algorithms have been created and they sometimes provide varying levels of performance (as measured by an efficiency metric such as Nash-Sutcliffe). This is because each algorithm is better suited for one type of optimization problem rather than another. This research project's aim was twofold. First, it was sought upon to find various features in the calibration problem fitness landscapes to map the encountered problem types to the best possible optimization algorithm. Second, the optimal number of model evaluations in order to minimize resources usage and maximize overall model quality was investigated. A total of five stochastic optimization algorithms (SCE-UA, CMAES, DDS, PSO and ASA) were used to calibrate four lumped hydrological models (GR4J, HSAMI, HMETS and MOHYSE) on 421 basins from the US MOPEX database. Each of these combinations was performed using three objective functions (Log(RMSE), NSE, and a metric combining NSE, RMSE and BIAS) to add sufficient diversity to the fitness landscapes. Each run was performed 30 times for statistical analysis. With every parameter set tested during the calibration process, the validation value was taken on a separate period. It was then possible to outline the calibration skill versus the validation skill for the different algorithms. Fitness landscapes were characterized by various metrics, such as the dispersion metric, the mean distance between random points and their respective local minima (found through simple hill-climbing algorithms) and the mean distance between the local minima and the best local optimum found. These metrics were then compared to the calibration score of the various optimization algorithms. Preliminary results tend to show that fitness landscapes presenting a globally convergent structure are more prevalent than other types of landscapes in this

  3. A gamma variate model that includes stretched exponential is a better fit for gastric emptying data from mice

    PubMed Central

    Bajzer, Željko; Gibbons, Simon J.; Coleman, Heidi D.; Linden, David R.

    2015-01-01

    Noninvasive breath tests for gastric emptying are important techniques for understanding the changes in gastric motility that occur in disease or in response to drugs. Mice are often used as an animal model; however, the gamma variate model currently used for data analysis does not always fit the data appropriately. The aim of this study was to determine appropriate mathematical models to better fit mouse gastric emptying data including when two peaks are present in the gastric emptying curve. We fitted 175 gastric emptying data sets with two standard models (gamma variate and power exponential), with a gamma variate model that includes stretched exponential and with a proposed two-component model. The appropriateness of the fit was assessed by the Akaike Information Criterion. We found that extension of the gamma variate model to include a stretched exponential improves the fit, which allows for a better estimation of T1/2 and Tlag. When two distinct peaks in gastric emptying are present, a two-component model is required for the most appropriate fit. We conclude that use of a stretched exponential gamma variate model and when appropriate a two-component model will result in a better estimate of physiologically relevant parameters when analyzing mouse gastric emptying data. PMID:26045615

  4. Crystallographic observation of 'induced fit' in a cryptophane host–guest model system

    PubMed Central

    Taratula, Olena; Hill, P. Aru; Khan, Najat S.; Carroll, Patrick J.; Dmochowski, Ivan J.

    2010-01-01

    Cryptophane-A, comprised of two cyclotriguaiacylenes joined by three ethylene linkers, is a prototypal organic host molecule that binds reversibly to neutral small molecules via London forces. Of note are trifunctionalized, water-soluble cryptophane-A derivatives, which exhibit exceptional affinity for xenon in aqueous solution. In this paper, we report high-resolution X-ray structures of cryptophane-A and trifunctionalized derivatives in crown–crown and crown–saddle conformations, as well as in complexes with water, methanol, xenon or chloroform. Cryptophane internal volume varied by more than 20% across this series, which exemplifies 'induced fit' in a model host–guest system. PMID:21266998

  5. Understanding Systematics in ZZ Ceti Model Fitting to Enable Differential Seismology

    NASA Astrophysics Data System (ADS)

    Fuchs, J. T.; Dunlap, B. H.; Clemens, J. C.; Meza, J. A.; Dennihy, E.; Koester, D.

    2017-03-01

    We are conducting a large spectroscopic survey of over 130 Southern ZZ Cetis with the Goodman Spectrograph on the SOAR Telescope. Because it employs a single instrument with high UV throughput, this survey will both improve the signal-to-noise of the sample of SDSS ZZ Cetis and provide a uniform dataset for model comparison. We are paying special attention to systematics in the spectral fitting and quantify three of those systematics here. We show that relative positions in the log g -Teff plane are consistent for these three systematics.

  6. SSC Model Fits to Simultaneous Fermi and CAO observations of Bl Lac's

    NASA Astrophysics Data System (ADS)

    Gordon, Tyler; Macomb, Daryl J.; Hand, Jared; Norris, Jay P.; Long, Min

    2016-01-01

    The Challis Astronomical Observatory (CAO) has been surveying a sample of blazar-type AGN since 2010. The CAO blazar sample includes4 3 sources - comprising 30 FSRQs, 15 BL Lacs, one radio galaxy and four unclassified sources - covering a redshift range 0.02 < z < 2. Observations are carried out in BVRI filters. Here we describe photometric results on a small sample emphasizing BL Lacs. We combine the CAO data with Fermi/LAT data and explore the suitability of fits to the data using the uniform conical jet model of Potter and Cotter (MNRAS, 2012, 423, 756-765).

  7. Fitting models to correlated data III: A comparison between residual analysis and other methods

    NASA Astrophysics Data System (ADS)

    Féménias, Jean-Louis

    2005-07-01

    Applications of the χ2 test, the F test, the Durbin-Watson d test, and the f (or Sign) test, to examples of correlated data treatment, show important drawbacks with the d test and (apparently) with the f test. An analytical approach based on residual analysis suggests an improvement in their use that leads to better results at lowest order; it also points out a distinction between goodness-of-fit tests, as the f test, and goodness-of-modeling tests, as the χ2 and F tests. The residual analysis method is applied to the same examples; it looks faster, simpler, and often more accurate than the classical ones.

  8. Trajectory fitting in function space with application to analytic modeling of surfaces

    NASA Technical Reports Server (NTRS)

    Barger, Raymond L.

    1992-01-01

    A theory for representing a parameter-dependent function as a function trajectory is described. Additionally, a theory for determining a piecewise analytic fit to the trajectory is described. An example is given that illustrates the application of the theory to generating a smooth surface through a discrete set of input cross-section shapes. A simple procedure for smoothing in the parameter direction is discussed, and a computed example is given. Application of the theory to aerodynamic surface modeling is demonstrated by applying it to a blended wing-fuselage surface.

  9. SpectrRelax: An application for Mössbauer spectra modeling and fitting

    NASA Astrophysics Data System (ADS)

    Matsnev, M. E.; Rusakov, V. S.

    2012-10-01

    The SpectrRelax application was created for analysis and fitting of absorption and emission Mossbauer spectra of isotopes with 1/2 ↔ 3/2 transitions. Available models include a single Pseudo-Voigt line, doublet, and a sextet, a number of relaxation models, and a distribution of hyperfine/relaxation parameters of any model. SpectRelax can evaluate user supplied analytical expressions of model parameters and their error estimates. Complex parameter constraints or even new models can be implemented by setting parameter values to analytical expressions. Optimal model parameters search is performed using a maximum likelihood criterion in a Levenberg-Marquardt (L-M) algorithm. In the search process, a matrix of linear correlation coefficients between model parameters is calculated along with the error estimates, which allows better understanding of the optimized results. Partial derivatives of the model functions are evaluated using a "dual numbers" algorithm, which provides exact derivatives values at any point and improves the L-M method convergence. SpectrRelax runs under Windows operating systems by Microsoft. The application has a modern graphical user interface with extensive model editing and preview capabilities.

  10. A Pearson-type goodness-of-fit test for stationary and time-continuous Markov regression models.

    PubMed

    Aguirre-Hernández, R; Farewell, V T

    2002-07-15

    Markov regression models describe the way in which a categorical response variable changes over time for subjects with different explanatory variables. Frequently it is difficult to measure the response variable on equally spaced discrete time intervals. Here we propose a Pearson-type goodness-of-fit test for stationary Markov regression models fitted to panel data. A parametric bootstrap algorithm is used to study the distribution of the test statistic. The proposed technique is applied to examine the fit of a Markov regression model used to identify markers for disease progression in psoriatic arthritis.

  11. Fitting mathematical models to describe the rheological behaviour of chocolate pastes

    NASA Astrophysics Data System (ADS)

    Barbosa, Carla; Diogo, Filipa; Alves, M. Rui

    2016-06-01

    The flow behavior is of utmost importance for the chocolate industry. The objective of this work was to study two mathematical models, Casson and Windhab models that can be used to fit chocolate rheological data and evaluate which better infers or previews the rheological behaviour of different chocolate pastes. Rheological properties (viscosity, shear stress and shear rates) were obtained with a rotational viscometer equipped with a concentric cylinder. The chocolate samples were white chocolate and chocolate with varying percentages in cacao (55%, 70% and 83%). The results showed that the Windhab model was the best to describe the flow behaviour of all the studied samples with higher determination coefficients (r2 > 0.9).

  12. Fitting response models of benthic community structure to abiotic variables in a polluted estuarine system

    NASA Astrophysics Data System (ADS)

    González-Oreja, José Antonio; Saiz-Salinas, José Ignacio

    1999-07-01

    Models of the macrozoobenthic community responses to abiotic variables measured in the polluted Bilbao estuary were obtained by multiple linear regression analyses. Total, Oligochaeta and Nematoda abundance and biomass were considered as dependent variables. Intertidal level, dissolved oxygen at the bottom of the water column (DOXB) and organic content of the sediment were selected by the analyses as the three principal explanatory variables. Goodness-of-fit of the models was high ( overlinex=71.3% ). Total abundance and biomass increased as a linear function of DOXB. The principal outcome of the vast sewage scheme currently in progress in the study area is an important contributor of increasing DOXB levels. The models exposed in this paper will serve as a tool to evaluate the expected changes in the near future.

  13. A goodness-of-fit test for capture-recapture model M(t) under closure

    USGS Publications Warehouse

    Stanley, T.R.; Burnham, K.P.

    1999-01-01

    A new, fully efficient goodness-of-fit test for the time-specific closed-population capture-recapture model M(t) is presented. This test is based on the residual distribution of the capture history data given the maximum likelihood parameter estimates under model M(t), is partitioned into informative components, and is based on chi-square statistics. Comparison of this test with Leslie's test (Leslie, 1958, Journal of Animal Ecology 27, 84- 86) for model M(t), using Monte Carlo simulations, shows the new test generally outperforms Leslie's test. The new test is frequently computable when Leslie's test is not, has Type I error rates that are closer to nominal error rates than Leslie's test, and is sensitive to behavioral variation and heterogeneity in capture probabilities. Leslie's test is not sensitive to behavioral variation in capture probabilities but, when computable, has greater power to detect heterogeneity than the new test.

  14. GRace: a MATLAB-based application for fitting the discrimination-association model.

    PubMed

    Stefanutti, Luca; Vianello, Michelangelo; Anselmi, Pasquale; Robusto, Egidio

    2014-10-28

    The Implicit Association Test (IAT) is a computerized two-choice discrimination task in which stimuli have to be categorized as belonging to target categories or attribute categories by pressing, as quickly and accurately as possible, one of two response keys. The discrimination association model has been recently proposed for the analysis of reaction time and accuracy of an individual respondent to the IAT. The model disentangles the influences of three qualitatively different components on the responses to the IAT: stimuli discrimination, automatic association, and termination criterion. The article presents General Race (GRace), a MATLAB-based application for fitting the discrimination association model to IAT data. GRace has been developed for Windows as a standalone application. It is user-friendly and does not require any programming experience. The use of GRace is illustrated on the data of a Coca Cola-Pepsi Cola IAT, and the results of the analysis are interpreted and discussed.

  15. Towards greater realism in inclusive fitness models: the case of worker reproduction in insect societies.

    PubMed

    Wenseleers, Tom; Helanterä, Heikki; Alves, Denise A; Dueñez-Guzmán, Edgar; Pamilo, Pekka

    2013-01-01

    The conflicts over sex allocation and male production in insect societies have long served as an important test bed for Hamilton's theory of inclusive fitness, but have for the most part been considered separately. Here, we develop new coevolutionary models to examine the interaction between these two conflicts and demonstrate that sex ratio and colony productivity costs of worker reproduction can lead to vastly different outcomes even in species that show no variation in their relatedness structure. Empirical data on worker-produced males in eight species of Melipona bees support the predictions from a model that takes into account the demographic details of colony growth and reproduction. Overall, these models contribute significantly to explaining behavioural variation that previous theories could not account for.

  16. A fungal growth model fitted to carbon-limited dynamics of Rhizoctonia solani.

    PubMed

    Jeger, M J; Lamour, A; Gilligan, C A; Otten, W

    2008-01-01

    Here, a quasi-steady-state approximation was used to simplify a mathematical model for fungal growth in carbon-limiting systems, and this was fitted to growth dynamics of the soil-borne plant pathogen and saprotroph Rhizoctonia solani. The model identified a criterion for invasion into carbon-limited environments with two characteristics driving fungal growth, namely the carbon decomposition rate and a measure of carbon use efficiency. The dynamics of fungal spread through a population of sites with either low (0.0074 mg) or high (0.016 mg) carbon content were well described by the simplified model with faster colonization for the carbon-rich environment. Rhizoctonia solani responded to a lower carbon availability by increasing the carbon use efficiency and the carbon decomposition rate following colonization. The results are discussed in relation to fungal invasion thresholds in terms of carbon nutrition.

  17. Goodness-of-fit measures for individual-level models of infectious disease in a Bayesian framework.

    PubMed

    Gardner, A; Deardon, R; Darlington, G

    2011-12-01

    In simple models there are a variety of tried and tested ways to assess goodness-of-fit. However, in complex non-linear models, such as spatio-temporal individual-level models, less research has been done on how best to ascertain goodness-of-fit. Often such models are fitted within a Bayesian statistical framework, since such a framework is ideally placed to account for the many areas of data uncertainty. Within a Bayesian context, a major tool for assessing goodness-of-fit is the posterior predictive distribution. That is, a distribution for a test statistic is found through simulation from the posterior distribution and then compared with the observed test statistic for the data. Here, we examine different test statistics and ascertain how well they can detect model misspecification via a simulation study.

  18. Goodness-of-fit tests and model diagnostics for negative binomial regression of RNA sequencing data.

    PubMed

    Mi, Gu; Di, Yanming; Schafer, Daniel W

    2015-01-01

    This work is about assessing model adequacy for negative binomial (NB) regression, particularly (1) assessing the adequacy of the NB assumption, and (2) assessing the appropriateness of models for NB dispersion parameters. Tools for the first are appropriate for NB regression generally; those for the second are primarily intended for RNA sequencing (RNA-Seq) data analysis. The typically small number of biological samples and large number of genes in RNA-Seq analysis motivate us to address the trade-offs between robustness and statistical power using NB regression models. One widely-used power-saving strategy, for example, is to assume some commonalities of NB dispersion parameters across genes via simple models relating them to mean expression rates, and many such models have been proposed. As RNA-Seq analysis is becoming ever more popular, it is appropriate to make more thorough investigations into power and robustness of the resulting methods, and into practical tools for model assessment. In this article, we propose simulation-based statistical tests and diagnostic graphics to address model adequacy. We provide simulated and real data examples to illustrate that our proposed methods are effective for detecting the misspecification of the NB mean-variance relationship as well as judging the adequacy of fit of several NB dispersion models.

  19. A History of Regression and Related Model-Fitting in the Earth Sciences (1636?-2000)

    SciTech Connect

    Howarth, Richard J.

    2001-12-15

    The (statistical) modeling of the behavior of a dependent variate as a function of one or more predictors provides examples of model-fitting which span the development of the earth sciences from the 17th Century to the present. The historical development of these methods and their subsequent application is reviewed. Bond's predictions (c. 1636 and 1668) of change in the magnetic declination at London may be the earliest attempt to fit such models to geophysical data. Following publication of Newton's theory of gravitation in 1726, analysis of data on the length of a 1{sup o} meridian arc, and the length of a pendulum beating seconds, as a function of sin{sup 2}(latitude), was used to determine the ellipticity of the oblate spheroid defining the Figure of the Earth. The pioneering computational methods of Mayer in 1750, Boscovich in 1755, and Lambert in 1765, and the subsequent independent discoveries of the principle of least squares by Gauss in 1799, Legendre in 1805, and Adrain in 1808, and its later substantiation on the basis of probability theory by Gauss in 1809 were all applied to the analysis of such geodetic and geophysical data. Notable later applications include: the geomagnetic survey of Ireland by Lloyd, Sabine, and Ross in 1836, Gauss's model of the terrestrial magnetic field in 1838, and Airy's 1845 analysis of the residuals from a fit to pendulum lengths, from which he recognized the anomalous character of measurements of gravitational force which had been made on islands. In the early 20th Century applications to geological topics proliferated, but the computational burden effectively held back applications of multivariate analysis. Following World War II, the arrival of digital computers in universities in the 1950s facilitated computation, and fitting linear or polynomial models as a function of geographic coordinates, trend surface analysis, became popular during the 1950-60s. The inception of geostatistics in France at this time by Matheron had

  20. 3 Neutrino mass experiments fit a strange 3 + 3 model, but will KATRIN reveal the model's unique 3-part signature?

    NASA Astrophysics Data System (ADS)

    Ehrlich, R.

    2016-12-01

    Evidence is presented in support of an unconventional 3 + 3 model of the neutrino mass eigenstates with specific m2 > 0 and m2 < 0 masses. The two large m2 > 0 masses of the model were originally suggested based on a SN 1987A analysis, and they were further supported by several dark matter fits. The new evidence for one of the m2 > 0 mass values comes from an analysis of published data from the three most precise tritium β - decay experiments. The KATRIN experiment by virtue of a unique 3-part signature should either confirm or reject the model in its entirety.

  1. Lévy Flights and Self-Similar Exploratory Behaviour of Termite Workers: Beyond Model Fitting

    PubMed Central

    Miramontes, Octavio; DeSouza, Og; Paiva, Leticia Ribeiro; Marins, Alessandra; Orozco, Sirio

    2014-01-01

    Animal movements have been related to optimal foraging strategies where self-similar trajectories are central. Most of the experimental studies done so far have focused mainly on fitting statistical models to data in order to test for movement patterns described by power-laws. Here we show by analyzing over half a million movement displacements that isolated termite workers actually exhibit a range of very interesting dynamical properties –including Lévy flights– in their exploratory behaviour. Going beyond the current trend of statistical model fitting alone, our study analyses anomalous diffusion and structure functions to estimate values of the scaling exponents describing displacement statistics. We evince the fractal nature of the movement patterns and show how the scaling exponents describing termite space exploration intriguingly comply with mathematical relations found in the physics of transport phenomena. By doing this, we rescue a rich variety of physical and biological phenomenology that can be potentially important and meaningful for the study of complex animal behavior and, in particular, for the study of how patterns of exploratory behaviour of individual social insects may impact not only their feeding demands but also nestmate encounter patterns and, hence, their dynamics at the social scale. PMID:25353958

  2. Total Force Fitness in units part 1: military demand-resource model.

    PubMed

    Bates, Mark J; Fallesen, Jon J; Huey, Wesley S; Packard, Gary A; Ryan, Diane M; Burke, C Shawn; Smith, David G; Watola, Daniel J; Pinder, Evette D; Yosick, Todd M; Estrada, Armando X; Crepeau, Loring; Bowles, Stephen V

    2013-11-01

    The military unit is a critical center of gravity in the military's efforts to enhance resilience and the health of the force. The purpose of this article is to augment the military's Total Force Fitness (TFF) guidance with a framework of TFF in units. The framework is based on a Military Demand-Resource model that highlights the dynamic interactions across demands, resources, and outcomes. A joint team of subject-matter experts identified key variables representing unit fitness demands, resources, and outcomes. The resulting framework informs and supports leaders, support agencies, and enterprise efforts to strengthen TFF in units by (1) identifying TFF unit variables aligned with current evidence and operational practices, (2) standardizing communication about TFF in units across the Department of Defense enterprise in a variety of military organizational contexts, (3) improving current resources including evidence-based actions for leaders, (4) identifying and addressing of gaps, and (5) directing future research for enhancing TFF in units. These goals are intended to inform and enhance Service efforts to develop Service-specific TFF models, as well as provide the conceptual foundation for a follow-on article about TFF metrics for units.

  3. Lifting a veil on diversity: a Bayesian approach to fitting relative-abundance models.

    PubMed

    Golicher, Duncan J; O'Hara, Robert B; Ruíz-Montoya, Lorena; Cayuela, Luis

    2006-02-01

    Bayesian methods incorporate prior knowledge into a statistical analysis. This prior knowledge is usually restricted to assumptions regarding the form of probability distributions of the parameters of interest, leaving their values to be determined mainly through the data. Here we show how a Bayesian approach can be applied to the problem of drawing inference regarding species abundance distributions and comparing diversity indices between sites. The classic log series and the lognormal models of relative- abundance distribution are apparently quite different in form. The first is a sampling distribution while the other is a model of abundance of the underlying population. Bayesian methods help unite these two models in a common framework. Markov chain Monte Carlo simulation can be used to fit both distributions as small hierarchical models with shared common assumptions. Sampling error can be assumed to follow a Poisson distribution. Species not found in a sample, but suspected to be present in the region or community of interest, can be given zero abundance. This not only simplifies the process of model fitting, but also provides a convenient way of calculating confidence intervals for diversity indices. The method is especially useful when a comparison of species diversity between sites with different sample sizes is the key motivation behind the research. We illustrate the potential of the approach using data on fruit-feeding butterflies in southern Mexico. We conclude that, once all assumptions have been made transparent, a single data set may provide support for the belief that diversity is negatively affected by anthropogenic forest disturbance. Bayesian methods help to apply theory regarding the distribution of abundance in ecological communities to applied conservation.

  4. Estimation of high-resolution dust column density maps. Empirical model fits

    NASA Astrophysics Data System (ADS)

    Juvela, M.; Montillaud, J.

    2013-09-01

    Context. Sub-millimetre dust emission is an important tracer of column density N of dense interstellar clouds. One has to combine surface brightness information at different spatial resolutions, and specific methods are needed to derive N at a resolution higher than the lowest resolution of the observations. Some methods have been discussed in the literature, including a method (in the following, method B) that constructs the N estimate in stages, where the smallest spatial scales being derived only use the shortest wavelength maps. Aims: We propose simple model fitting as a flexible way to estimate high-resolution column density maps. Our goal is to evaluate the accuracy of this procedure and to determine whether it is a viable alternative for making these maps. Methods: The new method consists of model maps of column density (or intensity at a reference wavelength) and colour temperature. The model is fitted using Markov chain Monte Carlo methods, comparing model predictions with observations at their native resolution. We analyse simulated surface brightness maps and compare its accuracy with method B and the results that would be obtained using high-resolution observations without noise. Results: The new method is able to produce reliable column density estimates at a resolution significantly higher than the lowest resolution of the input maps. Compared to method B, it is relatively resilient against the effects of noise. The method is computationally more demanding, but is feasible even in the analysis of large Herschel maps. Conclusions: The proposed empirical modelling method E is demonstrated to be a good alternative for calculating high-resolution column density maps, even with considerable super-resolution. Both methods E and B include the potential for further improvements, e.g., in the form of better a priori constraints.

  5. Testing goodness of fit in regression: a general approach for specified alternatives.

    PubMed

    Solari, Aldo; le Cessie, Saskia; Goeman, Jelle J

    2012-12-10

    When fitting generalized linear models or the Cox proportional hazards model, it is important to have tools to test for lack of fit. Because lack of fit comes in all shapes and sizes, distinguishing among different types of lack of fit is of practical importance. We argue that an adequate diagnosis of lack of fit requires a specified alternative model. Such specification identifies the type of lack of fit the test is directed against so that if we reject the null hypothesis, we know the direction of the departure from the model. The goodness-of-fit approach of this paper allows to treat different types of lack of fit within a unified general framework and to consider many existing tests as special cases. Connections with penalized likelihood and random effects are discussed, and the application of the proposed approach is illustrated with medical examples. Tailored functions for goodness-of-fit testing have been implemented in the R package global test.

  6. A healthy fear of the unknown: perspectives on the interpretation of parameter fits from computational models in neuroscience.

    PubMed

    Nassar, Matthew R; Gold, Joshua I

    2013-04-01

    Fitting models to behavior is commonly used to infer the latent computational factors responsible for generating behavior. However, the complexity of many behaviors can handicap the interpretation of such models. Here we provide perspectives on problems that can arise when interpreting parameter fits from models that provide incomplete descriptions of behavior. We illustrate these problems by fitting commonly used and neurophysiologically motivated reinforcement-learning models to simulated behavioral data sets from learning tasks. These model fits can pass a host of standard goodness-of-fit tests and other model-selection diagnostics even when the models do not provide a complete description of the behavioral data. We show that such incomplete models can be misleading by yielding biased estimates of the parameters explicitly included in the models. This problem is particularly pernicious when the neglected factors are unknown and therefore not easily identified by model comparisons and similar methods. An obvious conclusion is that a parsimonious description of behavioral data does not necessarily imply an accurate description of the underlying computations. Moreover, general goodness-of-fit measures are not a strong basis to support claims that a particular model can provide a generalized understanding of the computations that govern behavior. To help overcome these challenges, we advocate the design of tasks that provide direct reports of the computational variables of interest. Such direct reports complement model-fitting approaches by providing a more complete, albeit possibly more task-specific, representation of the factors that drive behavior. Computational models then provide a means to connect such task-specific results to a more general algorithmic understanding of the brain.

  7. Fitting a 3-D analytic model of the coronal mass ejection to observations

    NASA Technical Reports Server (NTRS)

    Gibson, S. E.; Biesecker, D.; Fisher, R.; Howard, R. A.; Thompson, B. J.

    1997-01-01

    The application of an analytic magnetohydrodynamic model is presented to observations of the time-dependent explusion of 3D coronal mass ejections (CMEs) out of the solar corona. This model relates the white-light appearance of the CME to its internal magnetic field, which takes the form of a closed bubble, filled with a partly anchored, twisted magnetic flux rope and embedded in an otherwise open background field. The density distribution frozen into the expanding CME expanding field is fully 3D, and can be integrated along the line of sight to reproduce observations of scattered white light. The model is able to reproduce the three conspicuous features often associated with CMEs as observed with white-light coronagraphs: a surrounding high-density region, an internal low-density cavity, and a high-density core. The model also describes the self-similar radial expansion of these structures. By varying the model parameters, the model can be fitted directly to observations of CMEs. It is shown how the model can quantitatively match the polarized brightness contrast of a dark cavity emerging through the lower corona as observed by the HAO Mauna Loa K-coronameter to within the noise level of the data.

  8. Tanning Shade Gradations of Models in Mainstream Fitness and Muscle Enthusiast Magazines: Implications for Skin Cancer Prevention in Men.

    PubMed

    Basch, Corey H; Hillyer, Grace Clarke; Ethan, Danna; Berdnik, Alyssa; Basch, Charles E

    2015-07-01

    Tanned skin has been associated with perceptions of fitness and social desirability. Portrayal of models in magazines may reflect and perpetuate these perceptions. Limited research has investigated tanning shade gradations of models in men's versus women's fitness and muscle enthusiast magazines. Such findings are relevant in light of increased incidence and prevalence of melanoma in the United States. This study evaluated and compared tanning shade gradations of adult Caucasian male and female model images in mainstream fitness and muscle enthusiast magazines. Sixty-nine U.S. magazine issues (spring and summer, 2013) were utilized. Two independent reviewers rated tanning shade gradations of adult Caucasian male and female model images on magazines' covers, advertisements, and feature articles. Shade gradations were assessed using stock photographs of Caucasian models with varying levels of tanned skin on an 8-shade scale. A total of 4,683 images were evaluated. Darkest tanning shades were found among males in muscle enthusiast magazines and lightest among females in women's mainstream fitness magazines. By gender, male model images were 54% more likely to portray a darker tanning shade. In this study, images in men's (vs. women's) fitness and muscle enthusiast magazines portrayed Caucasian models with darker skin shades. Despite these magazines' fitness-related messages, pro-tanning images may promote attitudes and behaviors associated with higher skin cancer risk. To date, this is the first study to explore tanning shades in men's magazines of these genres. Further research is necessary to identify effects of exposure to these images among male readers.

  9. One size does not fit all: flexible models are required to understand animal movement across scales.

    PubMed

    Yackulic, Charles B; Blake, Stephen; Deem, Sharon; Kock, Michael; Uriarte, María

    2011-09-01

    all models underestimate the frequency of reversals. 6. The single state model we introduce may be adequate to describe movement data at many resolutions and can be interpreted easily. Multiscalar analyses of movement such as the ones presented here are a useful means of identifying inconsistencies in our understanding of movement.

  10. Optimal Experiment Design for Monoexponential Model Fitting: Application to Apparent Diffusion Coefficient Imaging.

    PubMed

    Alipoor, Mohammad; Maier, Stephan E; Gu, Irene Yu-Hua; Mehnert, Andrew; Kahl, Fredrik

    2015-01-01

    The monoexponential model is widely used in quantitative biomedical imaging. Notable applications include apparent diffusion coefficient (ADC) imaging and pharmacokinetics. The application of ADC imaging to the detection of malignant tissue has in turn prompted several studies concerning optimal experiment design for monoexponential model fitting. In this paper, we propose a new experiment design method that is based on minimizing the determinant of the covariance matrix of the estimated parameters (D-optimal design). In contrast to previous methods, D-optimal design is independent of the imaged quantities. Applying this method to ADC imaging, we demonstrate its steady performance for the whole range of input variables (imaged parameters, number of measurements, and range of b-values). Using Monte Carlo simulations we show that the D-optimal design outperforms existing experiment design methods in terms of accuracy and precision of the estimated parameters.

  11. Solvable biological evolution models with general fitness functions and multiple mutations in parallel mutation-selection scheme

    NASA Astrophysics Data System (ADS)

    Saakian, David B.; Hu, Chin-Kun; Khachatryan, H.

    2004-10-01

    In a recent paper [Phys. Rev. E 69, 046121 (2004)], we used the Suzuki-Trottere formalism to study a quasispecies biological evolution model in a parallel mutation-selection scheme with a single-peak fitness function and a point mutation. In the present paper, we extend such a study to evolution models with more general fitness functions or multiple mutations in the parallel mutation-selection scheme. We give some analytical equations to define the error thresholds for some general cases of mean-field-like or symmetric mutation schemes and fitness functions. We derive some equations for the dynamics in the case of a point mutation and polynomial fitness functions. We derive exact dynamics for two-point mutations, asymmetric mutations, and the four-value spin model with a single-peak fitness function. The same method is applied for the model with a royal road fitness function. We derive the steady-state distribution for the single-peak fitness function.

  12. Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles

    PubMed Central

    Rodrigue, Nicolas; Philippe, Hervé; Lartillot, Nicolas

    2010-01-01

    Modeling the interplay between mutation and selection at the molecular level is key to evolutionary studies. To this end, codon-based evolutionary models have been proposed as pertinent means of studying long-range evolutionary patterns and are widely used. However, these approaches have not yet consolidated results from amino acid level phylogenetic studies showing that selection acting on proteins displays strong site-specific effects, which translate into heterogeneous amino acid propensities across the columns of alignments; related codon-level studies have instead focused on either modeling a single selective context for all codon columns, or a separate selective context for each codon column, with the former strategy deemed too simplistic and the latter deemed overparameterized. Here, we integrate recent developments in nonparametric statistical approaches to propose a probabilistic model that accounts for the heterogeneity of amino acid fitness profiles across the coding positions of a gene. We apply the model to a dozen real protein-coding gene alignments and find it to produce biologically plausible inferences, for instance, as pertaining to site-specific amino acid constraints, as well as distributions of scaled selection coefficients. In their account of mutational features as well as the heterogeneous regimes of selection at the amino acid level, the modeling approaches studied here can form a backdrop for several extensions, accounting for other selective features, for variable population size, or for subtleties of mutational features, all with parameterizations couched within population-genetic theory. PMID:20176949

  13. Explicit finite element modelling of the impaction of metal press-fit acetabular components.

    PubMed

    Hothi, H S; Busfield, J J C; Shelton, J C

    2011-03-01

    Metal press-fit cups and shells are widely used in hip resurfacing and total hip replacement procedures. These acetabular components are inserted into a reamed acetabula cavity by either impacting their inner polar surface (shells) or outer rim (cups). Two-dimensional explicit dynamics axisymmetric finite element models were developed to simulate these impaction methods. Greater impact velocities were needed to insert the components when the interference fit was increased; a minimum velocity of 2 m/s was required to fully seat a component with a 2 mm interference between the bone and outer diameter. Changing the component material from cobalt-chromium to titanium alloy resulted in a reduction in the number of impacts on the pole to seat it from 14 to nine. Of greatest significance, it was found that locking a rigid cap to the cup or shell rim resulted in up to nine fewer impactions being necessary to seat it than impacting directly on the polar surface or using a cap free from the rim of the component, as is the case with many commercial resurfacing cup impaction devices currently used. This is important to impactor design and could make insertion easier and also reduce acetabula bone damage.

  14. Spectral observations of Ellerman bombs and fitting with a two-cloud model

    SciTech Connect

    Hong, Jie; Ding, M. D.; Li, Ying; Fang, Cheng; Cao, Wenda

    2014-09-01

    We study the Hα and Ca II 8542 Å line spectra of four typical Ellerman bombs (EBs) in the active region NOAA 11765 on 2013 June 6, observed with the Fast Imaging Solar Spectrograph installed at the 1.6 m New Solar Telescope at Big Bear Solar Observatory. Considering that EBs may occur in a restricted region in the lower atmosphere, and that their spectral lines show particular features, we propose a two-cloud model to fit the observed line profiles. The lower cloud can account for the wing emission, and the upper cloud is mainly responsible for the absorption at line center. After choosing carefully the free parameters, we get satisfactory fitting results. As expected, the lower cloud shows an increase of the source function, corresponding to a temperature increase of 400-1000 K in EBs relative to the quiet Sun. This is consistent with previous results deduced from semi-empirical models and confirms that local heating occurs in the lower atmosphere during the appearance of EBs. We also find that the optical depths can increase to some extent in both the lower and upper clouds, which may result from either direct heating in the lower cloud, or illumination by an enhanced radiation on the upper cloud. The velocities derived from this method, however, are different from those obtained using the traditional bisector method, implying that one should be cautious when interpreting this parameter. The two-cloud model can thus be used as an efficient method to deduce the basic physical parameters of EBs.

  15. Fitting Data to Model: Structural Equation Modeling Diagnosis Using Two Scatter Plots

    ERIC Educational Resources Information Center

    Yuan, Ke-Hai; Hayashi, Kentaro

    2010-01-01

    This article introduces two simple scatter plots for model diagnosis in structural equation modeling. One plot contrasts a residual-based M-distance of the structural model with the M-distance for the factor score. It contains information on outliers, good leverage observations, bad leverage observations, and normal cases. The other plot contrasts…

  16. Optimized aerodynamic design process for subsonic transport wing fitted with winglets. [wind tunnel model

    NASA Technical Reports Server (NTRS)

    Kuhlman, J. M.

    1979-01-01

    The aerodynamic design of a wind-tunnel model of a wing representative of that of a subsonic jet transport aircraft, fitted with winglets, was performed using two recently developed optimal wing-design computer programs. Both potential flow codes use a vortex lattice representation of the near-field of the aerodynamic surfaces for determination of the required mean camber surfaces for minimum induced drag, and both codes use far-field induced drag minimization procedures to obtain the required spanloads. One code uses a discrete vortex wake model for this far-field drag computation, while the second uses a 2-D advanced panel wake model. Wing camber shapes for the two codes are very similar, but the resulting winglet camber shapes differ widely. Design techniques and considerations for these two wind-tunnel models are detailed, including a description of the necessary modifications of the design geometry to format it for use by a numerically controlled machine for the actual model construction.

  17. Electrically detected magnetic resonance modeling and fitting: An equivalent circuit approach

    SciTech Connect

    Leite, D. M. G.; Batagin-Neto, A.; Nunes-Neto, O.; Gómez, J. A.; Graeff, C. F. O.

    2014-01-21

    The physics of electrically detected magnetic resonance (EDMR) quadrature spectra is investigated. An equivalent circuit model is proposed in order to retrieve crucial information in a variety of different situations. This model allows the discrimination and determination of spectroscopic parameters associated to distinct resonant spin lines responsible for the total signal. The model considers not just the electrical response of the sample but also features of the measuring circuit and their influence on the resulting spectral lines. As a consequence, from our model, it is possible to separate different regimes, which depend basically on the modulation frequency and the RC constant of the circuit. In what is called the high frequency regime, it is shown that the sign of the signal can be determined. Recent EDMR spectra from Alq{sub 3} based organic light emitting diodes, as well as from a-Si:H reported in the literature, were successfully fitted by the model. Accurate values of g-factor and linewidth of the resonant lines were obtained.

  18. Statistics of dark matter substructure - I. Model and universal fitting functions

    NASA Astrophysics Data System (ADS)

    Jiang, Fangzhou; van den Bosch, Frank C.

    2016-05-01

    We present a new, semi-analytical model describing the evolution of dark matter subhaloes. The model uses merger trees constructed using the method of Parkinson et al. to describe the masses and redshifts of subhaloes at accretion, which are subsequently evolved using a simple model for the orbit-averaged mass-loss rates. The model is extremely fast, treats subhaloes of all orders, accounts for scatter in orbital properties and halo concentrations, uses a simple recipe to convert subhalo mass to maximum circular velocity, and considers subhalo disruption. The model is calibrated to accurately reproduce the average subhalo mass and velocity functions in numerical simulations. We demonstrate that, on average, the mass fraction in subhaloes is tightly correlated with the `dynamical age' of the host halo, defined as the number of halo dynamical times that have elapsed since its formation. Using this relation, we present universal fitting functions for the evolved and unevolved subhalo mass and velocity functions that are valid for a broad range in host halo mass, redshift and Λ cold dark matter cosmology.

  19. The shape of dark matter haloes - II. The GALACTUS H I modelling & fitting tool

    NASA Astrophysics Data System (ADS)

    Peters, S. P. C.; van der Kruit, P. C.; Allen, R. J.; Freeman, K. C.

    2017-01-01

    We present a new H I modelling tool called GALACTUS. The program has been designed to perform automated fits of disc-galaxy models to observations. It includes a treatment for the self-absorption of gas. The software has been released into the public domain. We describe the design philosophy and inner workings of the program. After this, we model the face-on galaxy NGC 2403 using both self-absorption and optically thin models, showing that self-absorption occurs even in face-on galaxies. These results are then used to model an edge-on galaxy. It is shown that the maximum surface brightness plateaus seen in Paper I of this series are indeed signs of self-absorption. The apparent H I mass of an edge-on galaxy can be drastically lower compared with that same galaxy seen face-on. The Tully-Fisher relation is found to be relatively free from self-absorption issues.

  20. Body-Fitted Detonation Shock Dynamics and the Pseudo-Reaction-Zone Energy Release Model

    NASA Astrophysics Data System (ADS)

    Meyer, Chad; Quirk, James; Short, Mark; Chqiuete, Carlos

    2016-11-01

    Programmed-burn methods are a class of models used to propagate a detonation wave, without the high resolution cost associated with a direct numerical simulation. They separate the detonation evolution calculation into two components: timing and energy release. The timing component is usually calculated with a Detonation Shock Dynamics model, a surface evolution representation that relates the normal velocity of the surface (Dn) to its local curvature. The energy release component must appropriately capture the degree of energy change associated with chemical reaction while simultaneously remaining synchronized with the timing component. The Pseudo-Reaction-Zone (PRZ) model is a reactive burn like energy release model, converting reactants into products, but with a conversion rate that is a function of the DSD surface Dn field. As such, it requires the DSD calculation produce smooth Dn fields, a challenge in complex geometries. We describe a new body-fitted approach to the Detonation Shock Dynamics calculation which produces the required smooth Dn fields, and a method for calibrating the PRZ model such that the rate of energy release remains as synced as possible with the timing component. We show results for slab, rate-stick and arc geometries.

  1. A new fit-for-purpose model testing framework: Decision Crash Tests

    NASA Astrophysics Data System (ADS)

    Tolson, Bryan; Craig, James

    2016-04-01

    Decision-makers in water resources are often burdened with selecting appropriate multi-million dollar strategies to mitigate the impacts of climate or land use change. Unfortunately, the suitability of existing hydrologic simulation models to accurately inform decision-making is in doubt because the testing procedures used to evaluate model utility (i.e., model validation) are insufficient. For example, many authors have identified that a good standard framework for model testing called the Klemes Crash Tests (KCTs), which are the classic model validation procedures from Klemeš (1986) that Andréassian et al. (2009) rename as KCTs, have yet to become common practice in hydrology. Furthermore, Andréassian et al. (2009) claim that the progression of hydrological science requires widespread use of KCT and the development of new crash tests. Existing simulation (not forecasting) model testing procedures such as KCTs look backwards (checking for consistency between simulations and past observations) rather than forwards (explicitly assessing if the model is likely to support future decisions). We propose a fundamentally different, forward-looking, decision-oriented hydrologic model testing framework based upon the concept of fit-for-purpose model testing that we call Decision Crash Tests or DCTs. Key DCT elements are i) the model purpose (i.e., decision the model is meant to support) must be identified so that model outputs can be mapped to management decisions ii) the framework evaluates not just the selected hydrologic model but the entire suite of model-building decisions associated with model discretization, calibration etc. The framework is constructed to directly and quantitatively evaluate model suitability. The DCT framework is applied to a model building case study on the Grand River in Ontario, Canada. A hypothetical binary decision scenario is analysed (upgrade or not upgrade the existing flood control structure) under two different sets of model building

  2. 5 CFR 919.900 - Adequate evidence.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Adequate evidence. 919.900 Section 919.900 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED) GOVERNMENTWIDE DEBARMENT AND SUSPENSION (NONPROCUREMENT) Definitions § 919.900 Adequate...

  3. SCAN-based hybrid and double-hybrid density functionals from models without fitted parameters

    NASA Astrophysics Data System (ADS)

    Hui, Kerwin; Chai, Jeng-Da

    2016-01-01

    By incorporating the nonempirical strongly constrained and appropriately normed (SCAN) semilocal density functional [J. Sun, A. Ruzsinszky, and J. P. Perdew, Phys. Rev. Lett. 115, 036402 (2015)] in the underlying expression of four existing hybrid and double-hybrid models, we propose one hybrid (SCAN0) and three double-hybrid (SCAN0-DH, SCAN-QIDH, and SCAN0-2) density functionals, which are free from any fitted parameters. The SCAN-based double-hybrid functionals consistently outperform their parent SCAN semilocal functional for self-interaction problems and noncovalent interactions. In particular, SCAN0-2, which includes about 79% of Hartree-Fock exchange and 50% of second-order Møller-Plesset correlation, is shown to be reliably accurate for a very diverse range of applications, such as thermochemistry, kinetics, noncovalent interactions, and self-interaction problems.

  4. Corneal modeling using conic section fits of PAR corneal topography system measurements

    NASA Astrophysics Data System (ADS)

    Zipper, Stanley; Manns, Fabrice; Fernandez, Viviana; Sandadi, Samith; Ho, Arthur; Parel, Jean-Marie A.

    2001-06-01

    The purpose of this study was to measure the average shape and variability of human corneas and to develop a tool for analyzing, height, curvature, and aberrations based on a conic section model. Fresh Eye Bank Eyes were placed in Dextran until the corneal thickness reached a physiological value. The eyes were placed in a custom made holder and measured using an intraoperative PAR Corneal Topography System (CTS) mounted on an operation microscope. Topography was measured before and after removal of the epithelium. A series of MATLAB functions were written to analyze the raw-z (height) data in polar coordinates. The functions fit conic sections to the PAR CTS data along hemi-meridians at 5 degree(s) intervals. The conic shape factor and apical radius were used to calculate and display the curvature. The dependence of these parameters with meridional position was examined.

  5. Strain estimation in 3D by fitting linear and planar data to the March model

    NASA Astrophysics Data System (ADS)

    Mulchrone, Kieran F.; Talbot, Christopher J.

    2016-08-01

    The probability density function associated with the March model is derived and used in a maximum likelihood method to estimate the best fit distribution and 3D strain parameters for a given set of linear or planar data. Typically it is assumed that in the initial state (pre-strain) linear or planar data are uniformly distributed on the sphere which means the number of strain parameters estimated needs to be reduced so that the numerical technique succeeds. Essentially this requires that the data are rotated into a suitable reference frame prior to analysis. The method has been applied to a suitable example from the Dalradian of SW Scotland and results obtained are consistent with those from an independent method of strain analysis. Despite March theory having been incorporated deep into the fabric of geological strain analysis, its full potential as a simple direct 3D strain analytical tool has not been achieved. The method developed here may help remedy this situation.

  6. Item Parameter Recovery, Standard Error Estimates, and Fit Statistics of the Winsteps Program for the Family of Rasch Models

    ERIC Educational Resources Information Center

    Wang, Wen-Chung; Chen, Cheng-Te

    2005-01-01

    This study investigates item parameter recovery, standard error estimates, and fit statistics yielded by the WINSTEPS program under the Rasch model and the rating scale model through Monte Carlo simulations. The independent variables were item response model, test length, and sample size. WINSTEPS yielded practically unbiased estimates for the…

  7. On the Model-Based Bootstrap with Missing Data: Obtaining a "P"-Value for a Test of Exact Fit

    ERIC Educational Resources Information Center

    Savalei, Victoria; Yuan, Ke-Hai

    2009-01-01

    Evaluating the fit of a structural equation model via bootstrap requires a transformation of the data so that the null hypothesis holds exactly in the sample. For complete data, such a transformation was proposed by Beran and Srivastava (1985) for general covariance structure models and applied to structural equation modeling by Bollen and Stine…

  8. Applying the Bollen-Stine Bootstrap for Goodness-of-Fit Measures to Structural Equation Models with Missing Data.

    ERIC Educational Resources Information Center

    Enders, Craig K.

    2002-01-01

    Proposed a method for extending the Bollen-Stine bootstrap model (K. Bollen and R. Stine, 1992) fit to structural equation models with missing data. Developed a Statistical Analysis System macro program to implement this procedure, and assessed its usefulness in a simulation. The new method yielded model rejection rates close to the nominal 5%…

  9. A simple algorithm for optimization and model fitting: AGA (asexual genetic algorithm)

    NASA Astrophysics Data System (ADS)

    Cantó, J.; Curiel, S.; Martínez-Gómez, E.

    2009-07-01

    Context: Mathematical optimization can be used as a computational tool to obtain the optimal solution to a given problem in a systematic and efficient way. For example, in twice-differentiable functions and problems with no constraints, the optimization consists of finding the points where the gradient of the objective function is zero and using the Hessian matrix to classify the type of each point. Sometimes, however it is impossible to compute these derivatives and other type of techniques must be employed such as the steepest descent/ascent method and more sophisticated methods such as those based on the evolutionary algorithms. Aims: We present a simple algorithm based on the idea of genetic algorithms (GA) for optimization. We refer to this algorithm as AGA (asexual genetic algorithm) and apply it to two kinds of problems: the maximization of a function where classical methods fail and model fitting in astronomy. For the latter case, we minimize the chi-square function to estimate the parameters in two examples: the orbits of exoplanets by taking a set of radial velocity data, and the spectral energy distribution (SED) observed towards a YSO (Young Stellar Object). Methods: The algorithm AGA may also be called genetic, although it differs from standard genetic algorithms in two main aspects: a) the initial population is not encoded; and b) the new generations are constructed by asexual reproduction. Results: Applying our algorithm in optimizing some complicated functions, we find the global maxima within a few iterations. For model fitting to the orbits of exoplanets and the SED of a YSO, we estimate the parameters and their associated errors.

  10. The Kunming CalFit study: modeling dietary behavioral patterns using smartphone data.

    PubMed

    Seto, Edmund; Hua, Jenna; Wu, Lemuel; Bestick, Aaron; Shia, Victor; Eom, Sue; Han, Jay; Wang, May; Li, Yan

    2014-01-01

    Human behavioral interventions aimed at improving health can benefit from objective wearable sensor data and mathematical models. Smartphone-based sensing is particularly practical for monitoring behavioral patterns because smartphones are fairly common, are carried by individuals throughout their daily lives, offer a variety of sensing modalities, and can facilitate various forms of user feedback for intervention studies. We describe our findings from a smartphone-based study, in which an Android-based application we developed called CalFit was used to collect information related to young adults' dietary behaviors. In addition to monitoring dietary patterns, we were interested in understanding contextual factors related to when and where an individual eats, as well as how their dietary intake relates to physical activity (which creates energy demand) and psychosocial stress. 12 participants were asked to use CalFit to record videos of their meals over two 1-week periods, which were translated into nutrient intake by trained dietitians. During this same period, triaxial accelerometry was used to assess each subject's energy expenditure, and GPS was used to record time-location patterns. Ecological momentary assessment was also used to prompt subjects to respond to questions on their phone about their psychological state. The GPS data were processed through a web service we developed called Foodscoremap that is based on the Google Places API to characterize food environments that subjects were exposed to, which may explain and influence dietary patterns. Furthermore, we describe a modeling framework that incorporates all of these information to dynamically infer behavioral patterns that may be used for future intervention studies.

  11. The extended Lennard-Jones potential energy function: A simpler model for direct-potential-fit analysis

    NASA Astrophysics Data System (ADS)

    Hajigeorgiou, Photos G.

    2016-12-01

    An analytical model for the diatomic potential energy function that was recently tested as a universal function (Hajigeorgiou, 2010) has been further modified and tested as a suitable model for direct-potential-fit analysis. Applications are presented for the ground electronic states of three diatomic molecules: oxygen, carbon monoxide, and hydrogen fluoride. The adjustable parameters of the extended Lennard-Jones potential model are determined through nonlinear regression by fits to calculated rovibrational energy term values or experimental spectroscopic line positions. The model is shown to lead to reliable, compact and simple representations for the potential energy functions of these systems and could therefore be classified as a suitable and attractive model for direct-potential-fit analysis.

  12. Assessing performance of Bayesian state-space models fit to Argos satellite telemetry locations processed with Kalman filtering.

    PubMed

    Silva, Mónica A; Jonsen, Ian; Russell, Deborah J F; Prieto, Rui; Thompson, Dave; Baumgartner, Mark F

    2014-01-01

    Argos recently implemented a new algorithm to calculate locations of satellite-tracked animals that uses a Kalman filter (KF). The KF algorithm is reported to increase the number and accuracy of estimated positions over the traditional Least Squares (LS) algorithm, with potential advantages to the application of state-space methods to model animal movement data. We tested the performance of two Bayesian state-space models (SSMs) fitted to satellite tracking data processed with KF algorithm. Tracks from 7 harbour seals (Phoca vitulina) tagged with ARGOS satellite transmitters equipped with Fastloc GPS loggers were used to calculate the error of locations estimated from SSMs fitted to KF and LS data, by comparing those to "true" GPS locations. Data on 6 fin whales (Balaenoptera physalus) were used to investigate consistency in movement parameters, location and behavioural states estimated by switching state-space models (SSSM) fitted to data derived from KF and LS methods. The model fit to KF locations improved the accuracy of seal trips by 27% over the LS model. 82% of locations predicted from the KF model and 73% of locations from the LS model were <5 km from the corresponding interpolated GPS position. Uncertainty in KF model estimates (5.6 ± 5.6 km) was nearly half that of LS estimates (11.6 ± 8.4 km). Accuracy of KF and LS modelled locations was sensitive to precision but not to observation frequency or temporal resolution of raw Argos data. On average, 88% of whale locations estimated by KF models fell within the 95% probability ellipse of paired locations from LS models. Precision of KF locations for whales was generally higher. Whales' behavioural mode inferred by KF models matched the classification from LS models in 94% of the cases. State-space models fit to KF data can improve spatial accuracy of location estimates over LS models and produce equally reliable behavioural estimates.

  13. Fitting data to model: structural equation modeling diagnosis using two scatter plots.

    PubMed

    Yuan, Ke-Hai; Hayashi, Kentaro

    2010-12-01

    This article introduces two simple scatter plots for model diagnosis in structural equation modeling. One plot contrasts a residual-based M-distance of the structural model with the M-distance for the factor score. It contains information on outliers, good leverage observations, bad leverage observations, and normal cases. The other plot contrasts the residual-based M-distance with the quantile of a chi distribution. It allows the researcher to visually identify clusters of potential outliers. The article further studies the effect of the potential outliers on the overall model evaluation when they are removed according to the order of the clusters exhibited in the plot. Suggestions are provided on determining the outlier status of outstanding cases in real data analysis. Recommendations are also made on the choice of robust methods and maximum likelihood following outlier removal.

  14. Simulating topological domains in human chromosomes with a fitting-free model.

    PubMed

    Brackley, C A; Michieletto, D; Mouvet, F; Johnson, J; Kelly, S; Cook, P R; Marenduzzo, D

    2016-09-02

    We discuss a polymer model for the 3D organization of human chromosomes. A chromosome is represented by a string of beads, with each bead being "colored" according to 1D bioinformatic data (e.g., chromatin state, histone modification, GC content). Individual spheres (representing bi- and multi-valent transcription factors) can bind reversibly and selectively to beads with the appropriate color. During molecular dynamics simulations, the factors bind, and the string spontaneously folds into loops, rosettes, and topologically-associating domains (TADs). This organization occurs in the absence of any specified interactions between distant DNA segments, or between transcription factors. A comparison with Hi-C data shows that simulations predict the location of most boundaries between TADs correctly. The model is "fitting-free" in the sense that it does not use Hi-C data as an input; consequently, one of its strengths is that it can - in principle - be used to predict the 3D organization of any region of interest, or whole chromosome, in a given organism, or cell line, in the absence of existing Hi-C data. We discuss how this simple model might be refined to include more transcription factors and binding sites, and to correctly predict contacts between convergent CTCF binding sites.

  15. Supersymmetric fits after the Higgs discovery and implications for model building.

    PubMed

    Ellis, John

    The data from the first run of the LHC at 7 and 8 TeV, together with the information provided by other experiments such as precision electroweak measurements, flavour measurements, the cosmological density of cold dark matter and the direct search for the scattering of dark matter particles in the LUX experiment, provide important constraints on supersymmetric models. Important information is provided by the ATLAS and CMS measurements of the mass of the Higgs boson, as well as the negative results of searches at the LHC for events with [Formula: see text] accompanied by jets, and the LHCb and CMS measurements of [Formula: see text]. Results are presented from frequentist analyses of the parameter spaces of the CMSSM and NUHM1. The global [Formula: see text] functions for the supersymmetric models vary slowly over most of the parameter spaces allowed by the Higgs mass and the [Formula: see text] search, with best-fit values that are comparable to the [Formula: see text] for the standard model. The 95 % CL lower limits on the masses of gluinos and squarks allow significant prospects for observing them during the LHC runs at higher energies.

  16. Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation.

    PubMed

    Slater, Graham J; Harmon, Luke J; Wegmann, Daniel; Joyce, Paul; Revell, Liam J; Alfaro, Michael E

    2012-03-01

    In recent years, a suite of methods has been developed to fit multiple rate models to phylogenetic comparative data. However, most methods have limited utility at broad phylogenetic scales because they typically require complete sampling of both the tree and the associated phenotypic data. Here, we develop and implement a new, tree-based method called MECCA (Modeling Evolution of Continuous Characters using ABC) that uses a hybrid likelihood/approximate Bayesian computation (ABC)-Markov-Chain Monte Carlo approach to simultaneously infer rates of diversification and trait evolution from incompletely sampled phylogenies and trait data. We demonstrate via simulation that MECCA has considerable power to choose among single versus multiple evolutionary rate models, and thus can be used to test hypotheses about changes in the rate of trait evolution across an incomplete tree of life. We finally apply MECCA to an empirical example of body size evolution in carnivores, and show that there is no evidence for an elevated rate of body size evolution in the pinnipeds relative to terrestrial carnivores. ABC approaches can provide a useful alternative set of tools for future macroevolutionary studies where likelihood-dependent approaches are lacking.

  17. 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

  18. An Approximation to the Adaptive Exponential Integrate-and-Fire Neuron Model Allows Fast and Predictive Fitting to Physiological Data

    PubMed Central

    Hertäg, Loreen; Hass, Joachim; Golovko, Tatiana; Durstewitz, Daniel

    2012-01-01

    For large-scale network simulations, it is often desirable to have computationally tractable, yet in a defined sense still physiologically valid neuron models. In particular, these models should be able to reproduce physiological measurements, ideally in a predictive sense, and under different input regimes in which neurons may operate in vivo. Here we present an approach to parameter estimation for a simple spiking neuron model mainly based on standard f–I curves obtained from in vitro recordings. Such recordings are routinely obtained in standard protocols and assess a neuron’s response under a wide range of mean-input currents. Our fitting procedure makes use of closed-form expressions for the firing rate derived from an approximation to the adaptive exponential integrate-and-fire (AdEx) model. The resulting fitting process is simple and about two orders of magnitude faster compared to methods based on numerical integration of the differential equations. We probe this method on different cell types recorded from rodent prefrontal cortex. After fitting to the f–I current-clamp data, the model cells are tested on completely different sets of recordings obtained by fluctuating (“in vivo-like”) input currents. For a wide range of different input regimes, cell types, and cortical layers, the model could predict spike times on these test traces quite accurately within the bounds of physiological reliability, although no information from these distinct test sets was used for model fitting. Further analyses delineated some of the empirical factors constraining model fitting and the model’s generalization performance. An even simpler adaptive LIF neuron was also examined in this context. Hence, we have developed a “high-throughput” model fitting procedure which is simple and fast, with good prediction performance, and which relies only on firing rate information and standard physiological data widely and easily available. PMID:22973220

  19. [A study of coordinates transform iterative fitting method to extract bio-impedance model parameters bio-impedance model parameters].

    PubMed

    Zhou, Liming; Yang, Yuxing; Yuan, Shiying

    2006-02-01

    A new algorithm, the coordinates transform iterative optimizing method based on the least square curve fitting model, is presented. This arithmetic is used for extracting the bio-impedance model parameters. It is superior to other methods, for example, its speed of the convergence is quicker, and its calculating precision is higher. The objective to extract the model parameters, such as Ri, Re, Cm and alpha, has been realized rapidly and accurately. With the aim at lowering the power consumption, decreasing the price and improving the price-to-performance ratio, a practical bio-impedance measure system with double CPUs has been built. It can be drawn from the preliminary results that the intracellular resistance Ri increased largely with an increase in working load during sitting, which reflects the ischemic change of lower limbs.

  20. On Eigen's Quasispecies Model, Two-Valued Fitness Landscapes, and Isometry Groups Acting on Finite Metric Spaces.

    PubMed

    Semenov, Yuri S; Novozhilov, Artem S

    2016-05-01

    A two-valued fitness landscape is introduced for the classical Eigen's quasispecies model. This fitness landscape can be considered as a direct generalization of the so-called single- or sharply peaked landscape. A general, non-permutation invariant quasispecies model is studied, and therefore the dimension of the problem is [Formula: see text], where N is the sequence length. It is shown that if the fitness function is equal to [Formula: see text] on a G-orbit A and is equal to w elsewhere, then the mean population fitness can be found as the largest root of an algebraic equation of degree at most [Formula: see text]. Here G is an arbitrary isometry group acting on the metric space of sequences of zeroes and ones of the length N with the Hamming distance. An explicit form of this exact algebraic equation is given in terms of the spherical growth function of the G-orbit A. Motivated by the analysis of the two-valued fitness landscapes, an abstract generalization of Eigen's model is introduced such that the sequences are identified with the points of a finite metric space X together with a group of isometries acting transitively on X. In particular, a simplicial analog of the original quasispecies model is discussed, which can be considered as a mathematical model of the switching of the antigenic variants for some bacteria.

  1. Evapotranspiration measurement and modeling without fitting parameters in high-altitude grasslands

    NASA Astrophysics Data System (ADS)

    Ferraris, Stefano; Previati, Maurizio; Canone, Davide; Dematteis, Niccolò; Boetti, Marco; Balocco, Jacopo; Bechis, Stefano

    2016-04-01

    Mountain grasslands are important, also because one sixth of the world population lives inside watershed dominated by snowmelt. Also, grasslands provide food to both domestic and selvatic animals. The global warming will probably accelerate the hydrological cycle and increase the drought risk. The combination of measurements, modeling and remote sensing can furnish knowledge in such faraway areas (e.g.: Brocca et al., 2013). A better knowledge of water balance can also allow to optimize the irrigation (e.g.: Canone et al., 2015). This work is meant to build a model of water balance in mountain grasslands, ranging between 1500 and 2300 meters asl. The main input is the Digital Terrain Model, which is more reliable in grasslands than both in the woods and in the built environment. It drives the spatial variability of shortwave solar radiation. The other atmospheric forcings are more problematic to estimate, namely air temperature, wind and longwave radiation. Ad hoc routines have been written, in order to interpolate in space the meteorological hourly time variability. The soil hydraulic properties are less variable than in the plains, but the soil depth estimation is still an open issue. The soil vertical variability has been modeled taking into account the main processes: soil evaporation, root uptake, and fractured bedrock percolation. The time variability latent heat flux and soil moisture results have been compared with the data measured in an eddy covariance station. The results are very good, given the fact that the model has no fitting parameters. The space variability results have been compared with the results of a model based on Landsat 7 and 8 data, applied over an area of about 200 square kilometers. The spatial correlation is quite in agreement between the two models. Brocca et al. (2013). "Soil moisture estimation in alpine catchments through modelling and satellite observations". Vadose Zone Journal, 12(3), 10 pp. Canone et al. (2015). "Field

  2. Fitting Cox Models with Doubly Censored Data Using Spline-Based Sieve Marginal Likelihood.

    PubMed

    Li, Zhiguo; Owzar, Kouros

    2016-06-01

    In some applications, the failure time of interest is the time from an originating event to a failure event, while both event times are interval censored. We propose fitting Cox proportional hazards models to this type of data using a spline-based sieve maximum marginal likelihood, where the time to the originating event is integrated out in the empirical likelihood function of the failure time of interest. This greatly reduces the complexity of the objective function compared with the fully semiparametric likelihood. The dependence of the time of interest on time to the originating event is induced by including the latter as a covariate in the proportional hazards model for the failure time of interest. The use of splines results in a higher rate of convergence of the estimator of the baseline hazard function compared with the usual nonparametric estimator. The computation of the estimator is facilitated by a multiple imputation approach. Asymptotic theory is established and a simulation study is conducted to assess its finite sample performance. It is also applied to analyzing a real data set on AIDS incubation time.

  3. Equilibrium Reconstructions with V3FIT and Current Evolution Modeling for 3-D Stellarator Plasmas

    NASA Astrophysics Data System (ADS)

    Schmitt, J. C.; Cianciosa, M.; Geiger, J.; Lazerson, S.

    2016-10-01

    V3FIT is a powerful equilibrium reconstruction tool for magnetic confinement fusion experiments which are inherently 3-D in nature (i.e. stellarators) or have 3-D components (tokamaks with 3-D shaping, reversed field pinches with helical states, etc). Here, we present details of the diagnostic modeling, constraints and the user interface for reconstructions of W7-X plasmas. For typical discharges during the OP1.1 run campaign of W7-X, the net toroidal current and current density profile do not reach steady-state. When modeling the current evolution in 3-D plasmas, both poloidal and toroidal currents are linked with both poloidal and toroidal fluxes. In contrast, in toroidally axisymmetric plasmas, the poloidal flux is linked only with the toroidal current and the toroidal current is linked only with the poloidal flux. Compared to an equivalently-sized axisymmetric configuration, the current diffusion in 3-D plasmas is enhanced, leading to a faster relaxation of the current profile to its steady-state. Implications for the time-evolution of the current and rotational transform profiles in stellarator plasmas are discussed. This work is supported by DoE Grant DE-SC00014529.

  4. Improved Spectral Fitting Models for the B-Stark Diagnostic at DIII-D

    NASA Astrophysics Data System (ADS)

    Pablant, N. A.; Grierson, B. A.; Burrell, K. H.; Groebner, R. J.; Kaplan, D. H.; Holcomb, C. T.

    2010-11-01

    Recent results are presented from the B-Stark diagnostic installed on the DIII-D tokamak. This diagnostic provides measurements of the magnitude and direction of the internal magnetic field. The B-Stark system is a version of a motional Stark effect (MSE) diagnostic based on the relative line intensities and spacing of the Stark split Dα emission from injected neutral beams. Improvements to the spectral fitting model are presented, including the addition of an analytical model for Dα emission from the fast-ion distribution. We discuss the accuracy of using in-situ beam-into-gas calibrations to find the beam emission line profiles, the viewing direction and the transmission properties of the collection optics. We also present results of efforts to improve the determination of the beam emission line profiles. Finally, the magnetic field measured with the B-Stark system is compared to values found from plasma equilibrium reconstructions (EFIT) and the MSE polarimetry system on DIII-D.

  5. Model Order Selection for Short Data: An Exponential Fitting Test (EFT)

    NASA Astrophysics Data System (ADS)

    Quinlan, Angela; Barbot, Jean-Pierre; Larzabal, Pascal; Haardt, Martin

    2006-12-01

    High-resolution methods for estimating signal processing parameters such as bearing angles in array processing or frequencies in spectral analysis may be hampered by the model order if poorly selected. As classical model order selection methods fail when the number of snapshots available is small, this paper proposes a method for noncoherent sources, which continues to work under such conditions, while maintaining low computational complexity. For white Gaussian noise and short data we show that the profile of the ordered noise eigenvalues is seen to approximately fit an exponential law. This fact is used to provide a recursive algorithm which detects a mismatch between the observed eigenvalue profile and the theoretical noise-only eigenvalue profile, as such a mismatch indicates the presence of a source. Moreover this proposed method allows the probability of false alarm to be controlled and predefined, which is a crucial point for systems such as RADARs. Results of simulations are provided in order to show the capabilities of the algorithm.

  6. Moment fitting for parameter inference in repeatedly and partially observed stochastic biological models.

    PubMed

    Kügler, Philipp

    2012-01-01

    The inference of reaction rate parameters in biochemical network models from time series concentration data is a central task in computational systems biology. Under the assumption of well mixed conditions the network dynamics are typically described by the chemical master equation, the Fokker Planck equation, the linear noise approximation or the macroscopic rate equation. The inverse problem of estimating the parameters of the underlying network model can be approached in deterministic and stochastic ways, and available methods often compare individual or mean concentration traces obtained from experiments with theoretical model predictions when maximizing likelihoods, minimizing regularized least squares functionals, approximating posterior distributions or sequentially processing the data. In this article we assume that the biological reaction network can be observed at least partially and repeatedly over time such that sample moments of species molecule numbers for various time points can be calculated from the data. Based on the chemical master equation we furthermore derive closed systems of parameter dependent nonlinear ordinary differential equations that predict the time evolution of the statistical moments. For inferring the reaction rate parameters we suggest to not only compare the sample mean with the theoretical mean prediction but also to take the residual of higher order moments explicitly into account. Cost functions that involve residuals of higher order moments may form landscapes in the parameter space that have more pronounced curvatures at the minimizer and hence may weaken or even overcome parameter sloppiness and uncertainty. As a consequence both deterministic and stochastic parameter inference algorithms may be improved with respect to accuracy and efficiency. We demonstrate the potential of moment fitting for parameter inference by means of illustrative stochastic biological models from the literature and address topics for future

  7. Effects of Data Nonnormality and Other Factors on Fit Indices and Parameter Estimates for True and Misspecified SEM Models.

    ERIC Educational Resources Information Center

    Fan, Xitao; And Others

    A Monte Carlo study was conducted to assess the effects of some potential confounding factors on structural equation modeling (SEM) fit indices and parameter estimates for both true and misspecified models. The factors investigated were data nonnormality, SEM estimation method, and sample size. Based on the fully crossed and balanced 3x3x4x2…

  8. A differential equation for the asymptotic fitness distribution in the Bak-Sneppen model with five species.

    PubMed

    Schlemm, Eckhard

    2015-09-01

    The Bak-Sneppen model is an abstract representation of a biological system that evolves according to the Darwinian principles of random mutation and selection. The species in the system are characterized by a numerical fitness value between zero and one. We show that in the case of five species the steady-state fitness distribution can be obtained as a solution to a linear differential equation of order five with hypergeometric coefficients. Similar representations for the asymptotic fitness distribution in larger systems may help pave the way towards a resolution of the question of whether or not, in the limit of infinitely many species, the fitness is asymptotically uniformly distributed on the interval [fc, 1] with fc ≳ 2/3.

  9. Pulmonary lobe segmentation based on ridge surface sampling and shape model fitting

    PubMed Central

    Ross, James C.; Kindlmann, Gordon L.; Okajima, Yuka; Hatabu, Hiroto; Díaz, Alejandro A.; Silverman, Edwin K.; Washko, George R.; Dy, Jennifer; Estépar, Raúl San José

    2013-01-01

    Purpose: Performing lobe-based quantitative analysis of the lung in computed tomography (CT) scans can assist in efforts to better characterize complex diseases such as chronic obstructive pulmonary disease (COPD). While airways and vessels can help to indicate the location of lobe boundaries, segmentations of these structures are not always available, so methods to define the lobes in the absence of these structures are desirable. Methods: The authors present a fully automatic lung lobe segmentation algorithm that is effective in volumetric inspiratory and expiratory computed tomography (CT) datasets. The authors rely on ridge surface image features indicating fissure locations and a novel approach to modeling shape variation in the surfaces defining the lobe boundaries. The authors employ a particle system that efficiently samples ridge surfaces in the image domain and provides a set of candidate fissure locations based on the Hessian matrix. Following this, lobe boundary shape models generated from principal component analysis (PCA) are fit to the particles data to discriminate between fissure and nonfissure candidates. The resulting set of particle points are used to fit thin plate spline (TPS) interpolating surfaces to form the final boundaries between the lung lobes. Results: The authors tested algorithm performance on 50 inspiratory and 50 expiratory CT scans taken from the COPDGene study. Results indicate that the authors' algorithm performs comparably to pulmonologist-generated lung lobe segmentations and can produce good results in cases with accessory fissures, incomplete fissures, advanced emphysema, and low dose acquisition protocols. Dice scores indicate that only 29 out of 500 (5.85%) lobes showed Dice scores lower than 0.9. Two different approaches for evaluating lobe boundary surface discrepancies were applied and indicate that algorithm boundary identification is most accurate in the vicinity of fissures detectable on CT. Conclusions: The proposed

  10. Pulmonary lobe segmentation based on ridge surface sampling and shape model fitting

    SciTech Connect

    Ross, James C.; Kindlmann, Gordon L.; Okajima, Yuka; Hatabu, Hiroto; Díaz, Alejandro A.; Silverman, Edwin K.; Washko, George R.; Dy, Jennifer; Estépar, Raúl San José

    2013-12-15

    Purpose: Performing lobe-based quantitative analysis of the lung in computed tomography (CT) scans can assist in efforts to better characterize complex diseases such as chronic obstructive pulmonary disease (COPD). While airways and vessels can help to indicate the location of lobe boundaries, segmentations of these structures are not always available, so methods to define the lobes in the absence of these structures are desirable. Methods: The authors present a fully automatic lung lobe segmentation algorithm that is effective in volumetric inspiratory and expiratory computed tomography (CT) datasets. The authors rely on ridge surface image features indicating fissure locations and a novel approach to modeling shape variation in the surfaces defining the lobe boundaries. The authors employ a particle system that efficiently samples ridge surfaces in the image domain and provides a set of candidate fissure locations based on the Hessian matrix. Following this, lobe boundary shape models generated from principal component analysis (PCA) are fit to the particles data to discriminate between fissure and nonfissure candidates. The resulting set of particle points are used to fit thin plate spline (TPS) interpolating surfaces to form the final boundaries between the lung lobes. Results: The authors tested algorithm performance on 50 inspiratory and 50 expiratory CT scans taken from the COPDGene study. Results indicate that the authors' algorithm performs comparably to pulmonologist-generated lung lobe segmentations and can produce good results in cases with accessory fissures, incomplete fissures, advanced emphysema, and low dose acquisition protocols. Dice scores indicate that only 29 out of 500 (5.85%) lobes showed Dice scores lower than 0.9. Two different approaches for evaluating lobe boundary surface discrepancies were applied and indicate that algorithm boundary identification is most accurate in the vicinity of fissures detectable on CT. Conclusions: The proposed

  11. ProFit: Bayesian galaxy fitting tool

    NASA Astrophysics Data System (ADS)

    Robotham, A. S. G.; Taranu, D.; Tobar, R.

    2016-12-01

    ProFit is a Bayesian galaxy fitting tool that uses the fast C++ image generation library libprofit (ascl:1612.003) and a flexible R interface to a large number of likelihood samplers. It offers a fully featured Bayesian interface to galaxy model fitting (also called profiling), using mostly the same standard inputs as other popular codes (e.g. GALFIT ascl:1104.010), but it is also able to use complex priors and a number of likelihoods.

  12. Predictive Models to Estimate Probabilities of Injuries, Poor Physical Fitness, and Attrition Outcomes in Australian Defense Force Army Recruit Training

    DTIC Science & Technology

    2015-11-01

    n=19,769; 7,692 [28- day reservists course]; 12,077 [80- day standard]. The 28- day incurred 17.6% injury rate, 1 stress fracture, 5.2% attrition, 30.0...fitness test failure. The 80- day : 34.3% injury rate, 44 stress fractures, 5.0% attrition, 12.1% fitness test failure. Separate models were derived to...accuracy was poor, accuracy was improved in models that included course length (28 vs. 80 day ) as a predictor; suggesting the potential for using duration

  13. Are all models created equal? A content analysis of women in advertisements of fitness versus fashion magazines.

    PubMed

    Wasylkiw, L; Emms, A A; Meuse, R; Poirier, K F

    2009-03-01

    The current study is a content analysis of women appearing in advertisements in two types of magazines: fitness/health versus fashion/beauty chosen because of their large and predominantly female readerships. Women appearing in advertisements of the June 2007 issue of five fitness/health magazines were compared to women appearing in advertisements of the June 2007 issue of five beauty/fashion magazines. Female models appearing in advertisements of both types of magazines were primarily young, thin Caucasians; however, images of models were more likely to emphasize appearance over performance when they appeared in fashion magazines. This difference in emphasis has implications for future research.

  14. Do We Need Multiple Models of Auditory Verbal Hallucinations? Examining the Phenomenological Fit of Cognitive and Neurological Models

    PubMed Central

    Jones, Simon R.

    2010-01-01

    The causes of auditory verbal hallucinations (AVHs) are still unclear. The evidence for 2 prominent cognitive models of AVHs, one based on inner speech, the other on intrusions from memory, is briefly reviewed. The fit of these models, as well as neurological models, to the phenomenology of AVHs is then critically examined. It is argued that only a minority of AVHs, such as those with content clearly relating to verbalizations experienced surrounding previous trauma, are consistent with cognitive AVHs-as-memories models. Similarly, it is argued that current neurological models are only phenomenologically consistent with a limited subset of AVHs. In contrast, the phenomenology of the majority of AVHs, which involve voices attempting to regulate the ongoing actions of the voice hearer, are argued to be more consistent with inner speech–based models. It is concluded that subcategorizations of AVHs may be necessary, with each underpinned by different neurocognitive mechanisms. The need to study what is termed the dynamic developmental progression of AVHs is also highlighted. Future empirical research is suggested in this area. PMID:18820262

  15. Murine animal models for preclinical islet transplantation: No model fits all (research purposes).

    PubMed

    Cantarelli, Elisa; Citro, Antonio; Marzorati, Simona; Melzi, Raffaella; Scavini, Marina; Piemonti, Lorenzo

    2013-01-01

    Advances in islet transplantation research have led to remarkable improvements in the outcome in humans with type 1 diabetes. However, pitfalls, mainly linked both to early liver-specific inflammatory events and to pre-existing and transplant-induced auto- and allo-specific adaptive immune responses, still remain. In this scenario research into pancreatic islet transplantation, essential to investigate new strategies to overcome open issues, needs very well-designed preclinical studies to obtain consistent and reliable results and select only promising strategies that may be translated into the clinical practice. This review discusses the main shortcomings of the mouse models currently used in islet transplantation research, outlining the main factors and variables to take into account for the design of new preclinical studies. Since several parameters concerning both the graft (i.e., islets) and the recipient (i.e., diabetic mice) may influence transplant outcome, we recommend considering several critical points in designing future bench-to-bedside islet transplantation research.

  16. Facultative control of matrix production optimizes competitive fitness in Pseudomonas aeruginosa PA14 biofilm models.

    PubMed

    Madsen, Jonas S; Lin, Yu-Cheng; Squyres, Georgia R; Price-Whelan, Alexa; de Santiago Torio, Ana; Song, Angela; Cornell, William C; Sørensen, Søren J; Xavier, Joao B; Dietrich, Lars E P

    2015-12-01

    As biofilms grow, resident cells inevitably face the challenge of resource limitation. In the opportunistic pathogen Pseudomonas aeruginosa PA14, electron acceptor availability affects matrix production and, as a result, biofilm morphogenesis. The secreted matrix polysaccharide Pel is required for pellicle formation and for colony wrinkling, two activities that promote access to O2. We examined the exploitability and evolvability of Pel production at the air-liquid interface (during pellicle formation) and on solid surfaces (during colony formation). Although Pel contributes to the developmental response to electron acceptor limitation in both biofilm formation regimes, we found variation in the exploitability of its production and necessity for competitive fitness between the two systems. The wild type showed a competitive advantage against a non-Pel-producing mutant in pellicles but no advantage in colonies. Adaptation to the pellicle environment selected for mutants with a competitive advantage against the wild type in pellicles but also caused a severe disadvantage in colonies, even in wrinkled colony centers. Evolution in the colony center produced divergent phenotypes, while adaptation to the colony edge produced mutants with clear competitive advantages against the wild type in this O2-replete niche. In general, the structurally heterogeneous colony environment promoted more diversification than the more homogeneous pellicle. These results suggest that the role of Pel in community structure formation in response to electron acceptor limitation is unique to specific biofilm models and that the facultative control of Pel production is required for PA14 to maintain optimum benefit in different types of communities.

  17. Darwinian fitness.

    PubMed

    Demetrius, Lloyd; Ziehe, Martin

    2007-11-01

    The term Darwinian fitness refers to the capacity of a variant type to invade and displace the resident population in competition for available resources. Classical models of this dynamical process claim that competitive outcome is a deterministic event which is regulated by the population growth rate, called the Malthusian parameter. Recent analytic studies of the dynamics of competition in terms of diffusion processes show that growth rate predicts invasion success only in populations of infinite size. In populations of finite size, competitive outcome is a stochastic process--contingent on resource constraints--which is determined by the rate at which a population returns to its steady state condition after a random perturbation in the individual birth and death rates. This return rate, a measure of robustness or population stability, is analytically characterized by the demographic parameter, evolutionary entropy, a measure of the uncertainty in the age of the mother of a randomly chosen newborn. This article appeals to computational and numerical methods to contrast the predictive power of the Malthusian and the entropic principles. The computational analysis rejects the Malthusian model and is consistent with of the entropic principle. These studies thus provide support for the general claim that entropy is the appropriate measure of Darwinian fitness and constitutes an evolutionary parameter with broad predictive and explanatory powers.

  18. Genetic analysis of survival and fitness in turkeys with multiple-trait animal models.

    PubMed

    Quinton, C D; Wood, B J; Miller, S P

    2011-11-01

    Genetic parameters for production, survival, and structural fitness traits recorded in pedigreed turkey sire and dam parental lines from a nucleus breeding program were estimated with multiple-trait animal models. Survival and conformation traits were scored in binary terms of health, where 0 = died or affected, and 1 = survived or healthy. Walking ability at 20 wk was subjectively scored from 1 (poor) to 6 (excellent). Body weights and egg production displayed moderate heritability (h(2) = 0.18 to 0.35). Early survival (to 3 wk) displayed low heritability (h(2) = 0.02 and 0.04 for the dam and sire lines, respectively). Late survival (3 to 23 wk) and longevity (age at death or cull) had low to moderate heritability (h(2) = 0.12 to 0.14). Walking ability had moderate heritability (h(2) = 0.26, 0.25). Leg structure health displayed low heritability (h(2) = 0.08), as did hip structure, foot, and skin health (h(2) ≤ 0.02). Crop health displayed moderate heritability (h(2) = 0.12). Walking ability, hip and leg structures, footpad, and breast skin health had negative genetic correlations with BW (r(G) = -0.50 to -0.23). Egg production had moderate positive genetic correlation with late survival (r(G) = 0.61). Genetic correlations between early and late survival were close to zero (r(G) = 0.10 and 0.03 for the dam and sire lines, respectively). Walking ability had high positive genetic correlations with late survival, longevity, hip structure, and leg structure in both lines (r(G) = 0.51 to 0.91). These genetic parameters indicate that unchecked selection for growth could decrease survival, walking ability, and hip, leg, footpad, and skin health in turkeys. However, index selection should be effective at improving fitness, survival, and growth simultaneously in commercial turkey lines. Walking ability should be a good indicator trait for selection to improve overall late survival and hip and leg health in turkeys.

  19. A Parametric Model of Shoulder Articulation for Virtual Assessment of Space Suit Fit

    NASA Technical Reports Server (NTRS)

    Kim, K. Han; Young, Karen S.; Bernal, Yaritza; Boppana, Abhishektha; Vu, Linh Q.; Benson, Elizabeth A.; Jarvis, Sarah; Rajulu, Sudhakar L.

    2016-01-01

    Suboptimal suit fit is a known risk factor for crewmember shoulder injury. Suit fit assessment is however prohibitively time consuming and cannot be generalized across wide variations of body shapes and poses. In this work, we have developed a new design tool based on the statistical analysis of body shape scans. This tool is aimed at predicting the skin deformation and shape variations for any body size and shoulder pose for a target population. This new process, when incorporated with CAD software, will enable virtual suit fit assessments, predictively quantifying the contact volume, and clearance between the suit and body surface at reduced time and cost.

  20. The fitting of general force-of-infection models to wildlife disease prevalence data

    USGS Publications Warehouse

    Heisey, D.M.; Joly, D.O.; Messier, F.

    2006-01-01

    Researchers and wildlife managers increasingly find themselves in situations where they must deal with infectious wildlife diseases such as chronic wasting disease, brucellosis, tuberculosis, and West Nile virus. Managers are often charged with designing and implementing control strategies, and researchers often seek to determine factors that influence and control the disease process. All of these activities require the ability to measure some indication of a disease's foothold in a population and evaluate factors affecting that foothold. The most common type of data available to managers and researchers is apparent prevalence data. Apparent disease prevalence, the proportion of animals in a sample that are positive for the disease, might seem like a natural measure of disease's foothold, but several properties, in particular, its dependency on age structure and the biasing effects of disease-associated mortality, make it less than ideal. In quantitative epidemiology, the a??force of infection,a?? or infection hazard, is generally the preferred parameter for measuring a disease's foothold, and it can be viewed as the most appropriate way to a??adjusta?? apparent prevalence for age structure. The typical ecology curriculum includes little exposure to quantitative epidemiological concepts such as cumulative incidence, apparent prevalence, and the force of infection. The goal of this paper is to present these basic epidemiological concepts and resulting models in an ecological context and to illustrate how they can be applied to understand and address basic epidemiological questions. We demonstrate a practical approach to solving the heretofore intractable problem of fitting general force-of-infection models to wildlife prevalence data using a generalized regression approach. We apply the procedures to Mycobacterium bovis (bovine tuberculosis) prevalence in bison (Bison bison) in Wood Buffalo National Park, Canada, and demonstrate strong age dependency in the force of

  1. Traceable Calibration of a Radiation Thermometer in the Range 100 °C to 300 °C by Model Fitting

    NASA Astrophysics Data System (ADS)

    Olsen, Åge Andreas Falnes; Bergerud, Reidun Anita

    2015-08-01

    The Norwegian Metrology Service (JV) offers calibration of blackbodies, thermal imagers, and radiation thermometers to the national clients. The temperature measurements are traceable to the ITS-90 with a set of reference blackbodies covering the range from 10 °C to 1700 °C. However, between 100 °C and 300 °C we do not have a direct measurement of the cavity temperature from a traceable sensor, and rely instead on a pyrometer to provide the reference temperature. The pyrometer is regularly calibrated externally at a handful of predefined temperatures. In this work we present a calibration scheme for the pyrometer which allows calibration at the JV premises: the pyrometer is set to record the measured radiation level at predefined temperatures below 100 °C and just above 300 °C. The calibration data are used to fit a Sakuma-Hattori model, and subsequent readings of the radiation level can be input to the model to extract the corresponding temperature. We present uncertainty budgets for the calibration data, which is subsequently used to estimate a combined uncertainty at arbitrary measured temperatures between 100 °C and 300 °C. Finally, temperatures obtained with the described scheme are compared with recent calibration values obtained externally, and we show that this is a reasonable way to achieve traceable calibration of the pyrometer with adequate precision and low uncertainty. The model fitting has the added benefit of a continuous calibration curve throughout the relevant temperature range rather than at a handful of arbitrary points.

  2. Development of a Stellar Model-Fitting Pipeline for Asteroseismic Data from the TESS Mission

    NASA Astrophysics Data System (ADS)

    Metcalfe, Travis

    The launch of NASA's Kepler space telescope in 2009 revolutionized the quality and quantity of observational data available for asteroseismic analysis. Prior to the Kepler mission, solar-like oscillations were extremely difficult to observe, and data only existed for a handful of the brightest stars in the sky. With the necessity of studying one star at a time, the traditional approach to extracting the physical properties of the star from the observations was an uncomfortably subjective process. A variety of experts could use similar tools but come up with significantly different answers. Not only did this subjectivity have the potential to undermine the credibility of the technique, it also hindered the compilation of a uniform sample that could be used to draw broader physical conclusions from the ensemble of results. During a previous award from NASA, we addressed these issues by developing an automated and objective stellar model-fitting pipeline for Kepler data, and making it available through the Asteroseismic Modeling Portal (AMP). This community modeling tool has allowed us to derive reliable asteroseismic radii, masses and ages for large samples of stars (Metcalfe et al. 2014), but the most recent observations are so precise that we are now limited by systematic uncertainties associated with our stellar models. With a huge archive of Kepler data available for model validation, and the next planet-hunting satellite already approved for an expected launch in 2017, now is the time to incorporate what we have learned into the next generation of AMP. We propose to improve the reliability of our estimates of stellar properties over the next 4 years by collaborating with two open-source development projects that will augment and ultimately replace the stellar evolution and pulsation models that we now use in AMP. Our current treatment of the oscillations does not include the effects of radiative or convective heat-exchange, nor does it account for the influence

  3. Asbestos/NESHAP adequately wet guidance

    SciTech Connect

    Shafer, R.; Throwe, S.; Salgado, O.; Garlow, C.; Hoerath, E.

    1990-12-01

    The Asbestos NESHAP requires facility owners and/or operators involved in demolition and renovation activities to control emissions of particulate asbestos to the outside air because no safe concentration of airborne asbestos has ever been established. The primary method used to control asbestos emissions is to adequately wet the Asbestos Containing Material (ACM) with a wetting agent prior to, during and after demolition/renovation activities. The purpose of the document is to provide guidance to asbestos inspectors and the regulated community on how to determine if friable ACM is adequately wet as required by the Asbestos NESHAP.

  4. Fitting-determined formulation of effective medium approximation for 3D trench structures in model-based infrared reflectrometry.

    PubMed

    Zhang, Chuanwei; Liu, Shiyuan; Shi, Tielin; Tang, Zirong

    2011-02-01

    The success of the model-based infrared reflectrometry (MBIR) technique relies heavily on accurate modeling and fast calculation of the infrared metrology process, which continues to be a challenge, especially for three-dimensional (3D) trench structures. In this paper, we present a simplified formulation for effective medium approximation (EMA), determined by a fitting-based method for the modeling of 3D trench structures. Intensive investigations have been performed with an emphasis on the generality of the fitting-determined (FD)-EMA formulation in terms of trench depth, trench pitch, and incidence angle so that its application is not limited to a particular configuration. Simulations conducted on a taper trench structure have further verified the proposed FD-EMA and demonstrated that the MBIR metrology with the FD-EMA-based model achieves an accuracy one order higher than that of the conventional zeroth-order EMA-based model.

  5. Adjusting the Adjusted X[superscript 2]/df Ratio Statistic for Dichotomous Item Response Theory Analyses: Does the Model Fit?

    ERIC Educational Resources Information Center

    Tay, Louis; Drasgow, Fritz

    2012-01-01

    Two Monte Carlo simulation studies investigated the effectiveness of the mean adjusted X[superscript 2]/df statistic proposed by Drasgow and colleagues and, because of problems with the method, a new approach for assessing the goodness of fit of an item response theory model was developed. It has been previously recommended that mean adjusted…

  6. Limited-Information Goodness-of-Fit Testing of Diagnostic Classification Item Response Theory Models. CRESST Report 840

    ERIC Educational Resources Information Center

    Hansen, Mark; Cai, Li; Monroe, Scott; Li, Zhen

    2014-01-01

    It is a well-known problem in testing the fit of models to multinomial data that the full underlying contingency table will inevitably be sparse for tests of reasonable length and for realistic sample sizes. Under such conditions, full-information test statistics such as Pearson's X[superscript 2]?? and the likelihood ratio statistic…

  7. Promoting Fitness and Safety in Elementary Students: A Randomized Control Study of the Michigan Model for Health

    ERIC Educational Resources Information Center

    O'Neill, James M.; Clark, Jeffrey K.; Jones, James A.

    2016-01-01

    Background: In elementary grades, comprehensive health education curricula have demonstrated effectiveness in addressing singular health issues. The Michigan Model for Health (MMH) was implemented and evaluated to determine its impact on nutrition, physical fitness, and safety knowledge and skills. Methods: Schools (N = 52) were randomly assigned…

  8. An Investigation of the Effect of Sample Size and Specification Error on the Fit of Structural Equation Models.

    ERIC Educational Resources Information Center

    Gallini, Joan K., Mandeville, Garrett K.

    1984-01-01

    This Monte Carlo study examined the validity of the chi-square test for model evaluation in different instances of misspecification and sample size. The usefulness of the chi-square difference statistic to compare competing structures and improvement in fit is also addressed. (Author/BS)

  9. Facultative Control of Matrix Production Optimizes Competitive Fitness in Pseudomonas aeruginosa PA14 Biofilm Models

    PubMed Central

    Madsen, Jonas S.; Lin, Yu-Cheng; Squyres, Georgia R.; Price-Whelan, Alexa; de Santiago Torio, Ana; Song, Angela; Cornell, William C.; Sørensen, Søren J.

    2015-01-01

    As biofilms grow, resident cells inevitably face the challenge of resource limitation. In the opportunistic pathogen Pseudomonas aeruginosa PA14, electron acceptor availability affects matrix production and, as a result, biofilm morphogenesis. The secreted matrix polysaccharide Pel is required for pellicle formation and for colony wrinkling, two activities that promote access to O2. We examined the exploitability and evolvability of Pel production at the air-liquid interface (during pellicle formation) and on solid surfaces (during colony formation). Although Pel contributes to the developmental response to electron acceptor limitation in both biofilm formation regimes, we found variation in the exploitability of its production and necessity for competitive fitness between the two systems. The wild type showed a competitive advantage against a non-Pel-producing mutant in pellicles but no advantage in colonies. Adaptation to the pellicle environment selected for mutants with a competitive advantage against the wild type in pellicles but also caused a severe disadvantage in colonies, even in wrinkled colony centers. Evolution in the colony center produced divergent phenotypes, while adaptation to the colony edge produced mutants with clear competitive advantages against the wild type in this O2-replete niche. In general, the structurally heterogeneous colony environment promoted more diversification than the more homogeneous pellicle. These results suggest that the role of Pel in community structure formation in response to electron acceptor limitation is unique to specific biofilm models and that the facultative control of Pel production is required for PA14 to maintain optimum benefit in different types of communities. PMID:26431965

  10. Funding the Formula Adequately in Oklahoma

    ERIC Educational Resources Information Center

    Hancock, Kenneth

    2015-01-01

    This report is a longevity, simulational study that looks at how the ratio of state support to local support effects the number of school districts that breaks the common school's funding formula which in turns effects the equity of distribution to the common schools. After nearly two decades of adequately supporting the funding formula, Oklahoma…

  11. Linking the Fits, Fitting the Links: Connecting Different Types of PO Fit to Attitudinal Outcomes

    ERIC Educational Resources Information Center

    Leung, Aegean; Chaturvedi, Sankalp

    2011-01-01

    In this paper we explore the linkages among various types of person-organization (PO) fit and their effects on employee attitudinal outcomes. We propose and test a conceptual model which links various types of fits--objective fit, perceived fit and subjective fit--in a hierarchical order of cognitive information processing and relate them to…

  12. Landscape and flow metrics affecting the distribution of a federally-threatened fish: Improving management, model fit, and model transferability

    USGS Publications Warehouse

    Brewer, Shannon K.; Worthington, Thomas A.; Zhang, Tianjioa; Logue, Daniel R.; Mittelstet, Aaron R.

    2016-01-01

    Truncated distributions of pelagophilic fishes have been observed across the Great Plains of North America, with water use and landscape fragmentation implicated as contributing factors. Developing conservation strategies for these species is hindered by the existence of multiple competing flow regime hypotheses related to species persistence. Our primary study objective was to compare the predicted distributions of one pelagophil, the Arkansas River Shiner Notropis girardi, constructed using different flow regime metrics. Further, we investigated different approaches for improving temporal transferability of the species distribution model (SDM). We compared four hypotheses: mean annual flow (a baseline), the 75th percentile of daily flow, the number of zero-flow days, and the number of days above 55th percentile flows, to examine the relative importance of flows during the spawning period. Building on an earlier SDM, we added covariates that quantified wells in each catchment, point source discharges, and non-native species presence to a structured variable framework. We assessed the effects on model transferability and fit by reducing multicollinearity using Spearman’s rank correlations, variance inflation factors, and principal component analysis, as well as altering the regularization coefficient (β) within MaxEnt. The 75th percentile of daily flow was the most important flow metric related to structuring the species distribution. The number of wells and point source discharges were also highly ranked. At the default level of β, model transferability was improved using all methods to reduce collinearity; however, at higher levels of β, the correlation method performed best. Using β = 5 provided the best model transferability, while retaining the majority of variables that contributed 95% to the model. This study provides a workflow for improving model transferability and also presents water-management options that may be considered to improve the

  13. Multicomponent phytotherapeutic approach gaining momentum: Is the "one drug to fit all" model breaking down?

    PubMed

    Rather, Manzoor A; Bhat, Bilal A; Qurishi, Mushtaq A

    2013-12-15

    Natural product based drugs constitute a substantial proportion of the pharmaceutical market particularly in the therapeutic areas of infectious diseases and oncology. The primary focus of any drug development program so far has been to design selective ligands (drugs) that act on single selective disease targets to obtain highly efficacious and safe drugs with minimal side effects. Although this approach has been successful for many diseases, yet there is a significant decline in the number of new drug candidates being introduced into clinical practice over the past few decades. This serious innovation deficit that the pharmaceutical industries are facing is due primarily to the post-marketing failures of blockbuster drugs. Many analysts believe that the current capital-intensive model-"the one drug to fit all" approach will be unsustainable in future and that a new "less investment, more drugs" model is necessary for further scientific growth. It is now well established that many diseases are multi-factorial in nature and that cellular pathways operate more like webs than highways. There are often multiple ways or alternate routes that may be switched on in response to the inhibition of a specific target. This gives rise to the resistant cells or resistant organisms under the specific pressure of a targeted agent, resulting in drug resistance and clinical failure of the drug. Drugs designed to act against individual molecular targets cannot usually combat multifactorial diseases like cancer, or diseases that affect multiple tissues or cell types such as diabetes and immunoinflammatory diseases. Combination drugs that affect multiple targets simultaneously are better at controlling complex disease systems and are less prone to drug resistance. This multicomponent therapy forms the basis of phytotherapy or phytomedicine where the holistic therapeutic effect arises as a result of complex positive (synergistic) or negative (antagonistic) interactions between

  14. LETTER: Exact solution of a model of time-dependent evolutionary dynamics in a rugged fitness landscape

    NASA Astrophysics Data System (ADS)

    Sire, Clément; Majumdar, Satya N.; Dean, David S.

    2006-07-01

    A simplified form of the time-dependent evolutionary dynamics of a quasispecies model with a rugged fitness landscape is solved via a mapping onto a random flux model whose asymptotic behaviour can be described in terms of a random walk. The statistics of the number of changes of the dominant genotype from a finite set of genotypes are exactly obtained confirming existing conjectures based on numerics.

  15. Model-based analysis of multi-shell diffusion MR data for tractography: How to get over fitting problems

    PubMed Central

    Jbabdi, Saad; Sotiropoulos, Stamatios N; Savio, Alexander M; Graña, Manuel; Behrens, Timothy EJ

    2012-01-01

    In this article, we highlight an issue that arises when using multiple b-values in a model-based analysis of diffusion MR data for tractography. The non-mono-exponential decay, commonly observed in experimental data, is shown to induce over-fitting in the distribution of fibre orientations when not considered in the model. Extra fibre orientations perpendicular to the main orientation arise to compensate for the slower apparent signal decay at higher b-values. We propose a simple extension to the ball and stick model based on a continuous Gamma distribution of diffusivities, which significantly improves the fitting and reduces the over-fitting. Using in-vivo experimental data, we show that this model outperforms a simpler, noise floor model, especially at the interfaces between brain tissues, suggesting that partial volume effects are a major cause of the observed non-mono-exponential decay. This model may be helpful for future data acquisition strategies that may attempt to combine multiple shells to improve estimates of fibre orientations in white matter and near the cortex. PMID:22334356

  16. Quasispecies on Fitness Landscapes.

    PubMed

    Schuster, Peter

    2016-01-01

    Selection-mutation dynamics is studied as adaptation and neutral drift on abstract fitness landscapes. Various models of fitness landscapes are introduced and analyzed with respect to the stationary mutant distributions adopted by populations upon them. The concept of quasispecies is introduced, and the error threshold phenomenon is analyzed. Complex fitness landscapes with large scatter of fitness values are shown to sustain error thresholds. The phenomenological theory of the quasispecies introduced in 1971 by Eigen is compared to approximation-free numerical computations. The concept of strong quasispecies understood as mutant distributions, which are especially stable against changes in mutations rates, is presented. The role of fitness neutral genotypes in quasispecies is discussed.

  17. Using Fit Indexes to Select a Covariance Model for Longitudinal Data

    ERIC Educational Resources Information Center

    Liu, Siwei; Rovine, Michael J.; Molenaar, Peter C. M.

    2012-01-01

    This study investigated the performance of fit indexes in selecting a covariance structure for longitudinal data. Data were simulated to follow a compound symmetry, first-order autoregressive, first-order moving average, or random-coefficients covariance structure. We examined the ability of the likelihood ratio test (LRT), root mean square error…

  18. Testing the Youth Physical Activity Promotion Model: Fatness and Fitness as Enabling Factors

    ERIC Educational Resources Information Center

    Chen, Senlin; Welk, Gregory J.; Joens-Matre, Roxane R.

    2014-01-01

    As the prevalence of childhood obesity increases, it is important to examine possible differences in psychosocial correlates of physical activity between normal weight and overweight children. The study examined fatness (weight status) and (aerobic) fitness as Enabling factors related to youth physical activity within the Youth Physical Activity…

  19. Work, Family, and Mental Health: Testing Different Models of Work-Family Fit.

    ERIC Educational Resources Information Center

    Grzywacz, Joseph G.; Bass, Brenda L.

    2003-01-01

    Using family resilience theory, this study examined the effects of work-family conflict and work-family facilitation on mental health among working adults to gain a better understanding of work-family fit. Results suggest that family to work facilitation is a family protective factor that offsets and buffers the deleterious effects of work-family…

  20. Gray Matter Correlates of Fluid, Crystallized, and Spatial Intelligence: Testing the P-FIT Model

    ERIC Educational Resources Information Center

    Colom, Roberto; Haier, Richard J.; Head, Kevin; Alvarez-Linera, Juan; Quiroga, Maria Angeles; Shih, Pei Chun; Jung, Rex E.

    2009-01-01

    The parieto-frontal integration theory (P-FIT) nominates several areas distributed throughout the brain as relevant for intelligence. This theory was derived from previously published studies using a variety of both imaging methods and tests of cognitive ability. Here we test this theory in a new sample of young healthy adults (N = 100) using a…

  1. Implementation of a Personal Fitness Unit Using the Personalized System of Instruction Model

    ERIC Educational Resources Information Center

    Prewitt, Steven; Hannon, James C.; Colquitt, Gavin; Brusseau, Timothy A.; Newton, Maria; Shaw, Janet

    2015-01-01

    Levels of physical activity and health-related fitness (HRF) are decreasing among adolescents in the United States. Several interventions have been implemented to reverse this downtrend. Traditionally, physical educators incorporate a direct instruction (DI) strategy, with teaching potentially leading students to disengage during class. An…

  2. CALORIMETRY OF GRB 030329: SIMULTANEOUS MODEL FITTING TO THE BROADBAND RADIO AFTERGLOW AND THE OBSERVED IMAGE EXPANSION RATE

    SciTech Connect

    Mesler, Robert A.; Pihlstroem, Ylva M.

    2013-09-01

    We perform calorimetry on the bright gamma-ray burst GRB 030329 by fitting simultaneously the broadband radio afterglow and the observed afterglow image size to a semi-analytic MHD and afterglow emission model. Our semi-analytic method is valid in both the relativistic and non-relativistic regimes, and incorporates a model of the interstellar scintillation that substantially effects the broadband afterglow below 10 GHz. The model is fitted to archival measurements of the afterglow flux from 1 day to 8.3 yr after the burst. Values for the initial burst parameters are determined and the nature of the circumburst medium is explored. Additionally, direct measurements of the lateral expansion rate of the radio afterglow image size allow us to estimate the initial Lorentz factor of the jet.

  3. Fitting model-based psychometric functions to simultaneity and temporal-order judgment data: MATLAB and R routines.

    PubMed

    Alcalá-Quintana, Rocío; García-Pérez, Miguel A

    2013-12-01

    Research on temporal-order perception uses temporal-order judgment (TOJ) tasks or synchrony judgment (SJ) tasks in their binary SJ2 or ternary SJ3 variants. In all cases, two stimuli are presented with some temporal delay, and observers judge the order of presentation. Arbitrary psychometric functions are typically fitted to obtain performance measures such as sensitivity or the point of subjective simultaneity, but the parameters of these functions are uninterpretable. We describe routines in MATLAB and R that fit model-based functions whose parameters are interpretable in terms of the processes underlying temporal-order and simultaneity judgments and responses. These functions arise from an independent-channels model assuming arrival latencies with exponential distributions and a trichotomous decision space. Different routines fit data separately for SJ2, SJ3, and TOJ tasks, jointly for any two tasks, or also jointly for the three tasks (for common cases in which two or even the three tasks were used with the same stimuli and participants). Additional routines provide bootstrap p-values and confidence intervals for estimated parameters. A further routine is included that obtains performance measures from the fitted functions. An R package for Windows and source code of the MATLAB and R routines are available as Supplementary Files.

  4. Fitting mathematical models to lactation curves from Holstein cows in the southwestern region of the state of Parana, Brazil.

    PubMed

    Ferreira, Abílio G T; Henrique, Douglas S; Vieira, Ricardo A M; Maeda, Emilyn M; Valotto, Altair A

    2015-03-01

    The objective of this study was to evaluate four mathematical models with regards to their fit to lactation curves of Holstein cows from herds raised in the southwestern region of the state of Parana, Brazil. Initially, 42,281 milk production records from 2005 to 2011 were obtained from "Associação Paranaense de Criadores de Bovinos da Raça Holandesa (APCBRH)". Data lacking dates of drying and total milk production at 305 days of lactation were excluded, resulting in a remaining 15,142 records corresponding to 2,441 Holstein cows. Data were sorted according to the parity order (ranging from one to six), and within each parity order the animals were divided into quartiles (Q25%, Q50%, Q75% and Q100%) corresponding to 305-day lactation yield. Within each parity order, for each quartile, four mathematical models were adjusted, two of which were predominantly empirical (Brody and Wood) whereas the other two presented more mechanistic characteristics (models Dijkstra and Pollott). The quality of fit was evaluated by the corrected Akaike information criterion. The Wood model showed the best fit in almost all evaluated situations and, therefore, may be considered as the most suitable model to describe, at least empirically, the lactation curves of Holstein cows raised in Southwestern Parana.

  5. Seasonality of Influenza A(H7N9) Virus in China—Fitting Simple Epidemic Models to Human Cases

    PubMed Central

    Lin, Qianying; Lin, Zhigui; Chiu, Alice P. Y.; He, Daihai

    2016-01-01

    Background Three epidemic waves of influenza A(H7N9) (hereafter ‘H7N9’) human cases have occurred between March 2013 and July 2015 in China. However, the underlying transmission mechanism remains unclear. Our main objective is to use mathematical models to study how seasonality, secular changes and environmental transmission play a role in the spread of H7N9 in China. Methods Data on human cases and chicken cases of H7N9 infection were downloaded from the EMPRES-i Global Animal Disease Information System. We modelled on chicken-to-chicken transmission, assuming a constant ratio of 10−6 human case per chicken case, and compared the model fit with the observed human cases. We developed three different modified Susceptible-Exposed-Infectious-Recovered-Susceptible models: (i) a non-periodic transmission rate model with an environmental class, (ii) a non-periodic transmission rate model without an environmental class, and (iii) a periodic transmission rate model with an environmental class. We then estimated the key epidemiological parameters and compared the model fit using Akaike Information Criterion and Bayesian Information Criterion. Results Our results showed that a non-periodic transmission rate model with an environmental class provided the best model fit to the observed human cases in China during the study period. The estimated parameter values were within biologically plausible ranges. Conclusions This study highlighted the importance of considering secular changes and environmental transmission in the modelling of human H7N9 cases. Secular changes were most likely due to control measures such as Live Poultry Markets closures that were implemented during the initial phase of the outbreaks in China. Our results suggested that environmental transmission via viral shedding of infected chickens had contributed to the spread of H7N9 human cases in China. PMID:26963937

  6. Implementation of the Iterative Proportion Fitting Algorithm for Geostatistical Facies Modeling

    SciTech Connect

    Li Yupeng Deutsch, Clayton V.

    2012-06-15

    In geostatistics, most stochastic algorithm for simulation of categorical variables such as facies or rock types require a conditional probability distribution. The multivariate probability distribution of all the grouped locations including the unsampled location permits calculation of the conditional probability directly based on its definition. In this article, the iterative proportion fitting (IPF) algorithm is implemented to infer this multivariate probability. Using the IPF algorithm, the multivariate probability is obtained by iterative modification to an initial estimated multivariate probability using lower order bivariate probabilities as constraints. The imposed bivariate marginal probabilities are inferred from profiles along drill holes or wells. In the IPF process, a sparse matrix is used to calculate the marginal probabilities from the multivariate probability, which makes the iterative fitting more tractable and practical. This algorithm can be extended to higher order marginal probability constraints as used in multiple point statistics. The theoretical framework is developed and illustrated with estimation and simulation example.

  7. Strategy for Fitting Neuronal Models to Dual Patch Data under Multiple Stimulation Protocols

    DTIC Science & Technology

    2007-11-02

    intensity of ON shock was controlled at weak, median and strong level which caused weak, median and strong excitatory post-synaptic potential ( EPSP ...known from the experiment. The equations of the glutamatergic EPSP can be found in [5]. EPSP consisted of both α -amino-3-hydroxy- 5-methyl-4-isoxazole...the 43 parameters, there were two additional unknown parameters that needed to be fit for each EPSP stimulation protocol. All the unknown parameters

  8. Measures of relative fitness of social behaviors in finite structured population models.

    PubMed

    Tarnita, Corina E; Taylor, Peter D

    2014-10-01

    How should we measure the relative selective advantage of different behavioral strategies? The various approaches to this question have fallen into one of the following categories: the fixation probability of a mutant allele in a wild type population, some measures of gene frequency and gene frequency change, and a formulation of the inclusive fitness effect. Countless theoretical studies have examined the relationship between these approaches, and it has generally been thought that, under standard simplifying assumptions, they yield equivalent results. Most of this theoretical work, however, has assumed homogeneity of the population interaction structure--that is, that all individuals are equivalent. We explore the question of selective advantage in a general (heterogeneous) population and show that, although appropriate measures of fixation probability and gene frequency change are equivalent, they are not, in general, equivalent to the inclusive fitness effect. The latter does not reflect effects of selection acting via mutation, which can arise on heterogeneous structures, even for low mutation. Our theoretical framework provides a transparent analysis of the different biological factors at work in the comparison of these fitness measures and suggests that their theoretical and empirical use needs to be revised and carefully grounded in a more general theory.

  9. An Escherichia coli asr mutant has decreased fitness during colonization in a mouse model.

    PubMed

    Armalyte, Julija; Seputiene, Vaida; Melefors, Ojar; Suziedeliene, Edita

    2008-01-01

    The Escherichia coli asr gene, like its homologues in other enterobacteria, is strongly induced by low external pH. The E. coli asr mutant shows weakened ability to adapt to acidic pH. This suggests that the asr gene product is important for enterobacterial species, both commensal and pathogenic, in overcoming acid stress in the stomach and subsequently colonizing the intestine. We examined the relative fitness of an E. coli asr mutant compared to a wild type, by feeding both strains simultaneously to mice and letting them colonize the intestine. Analysis of the bacteria after passage through the intestine showed up to five orders of magnitude less asr mutant than wild type. Transcomplementation of the asr gene on a plasmid partially restored the number of mutants. Similar competition in liquid media demonstrated that the asr mutant has reduced viability during long-term incubation in rich media, but is as fit as the wild type when bacteria are challenged in minimal medium. Competition carried out under different pH conditions proved that pH of the media was not the main determinant leading to the decreased fitness of the asr mutant. This suggests that the asr gene product is important for adaptation to stress conditions other than acidity, including long periods of starvation.

  10. Modeling and Maximum Likelihood Fitting of Gamma-Ray and Radio Light Curves of Millisecond Pulsars Detected with Fermi

    NASA Technical Reports Server (NTRS)

    Johnson, T. J.; Harding, A. K.; Venter, C.

    2012-01-01

    Pulsed gamma rays have been detected with the Fermi Large Area Telescope (LAT) from more than 20 millisecond pulsars (MSPs), some of which were discovered in radio observations of bright, unassociated LAT sources. We have fit the radio and gamma-ray light curves of 19 LAT-detected MSPs in the context of geometric, outermagnetospheric emission models assuming the retarded vacuum dipole magnetic field using a Markov chain Monte Carlo maximum likelihood technique. We find that, in many cases, the models are able to reproduce the observed light curves well and provide constraints on the viewing geometries that are in agreement with those from radio polarization measurements. Additionally, for some MSPs we constrain the altitudes of both the gamma-ray and radio emission regions. The best-fit magnetic inclination angles are found to cover a broader range than those of non-recycled gamma-ray pulsars.

  11. How Should We Assess the Fit of Rasch-Type Models? Approximating the Power of Goodness-of-Fit Statistics in Categorical Data Analysis

    ERIC Educational Resources Information Center

    Maydeu-Olivares, Alberto; Montano, Rosa

    2013-01-01

    We investigate the performance of three statistics, R [subscript 1], R [subscript 2] (Glas in "Psychometrika" 53:525-546, 1988), and M [subscript 2] (Maydeu-Olivares & Joe in "J. Am. Stat. Assoc." 100:1009-1020, 2005, "Psychometrika" 71:713-732, 2006) to assess the overall fit of a one-parameter logistic model…

  12. Fitting state-space integral projection models to size-structured time series data to estimate unknown parameters.

    PubMed

    White, J Wilson; Nickols, Kerry J; Malone, Daniel; Carr, Mark H; Starr, Richard M; Cordoleani, Flora; Baskett, Marissa L; Hastings, Alan; Botsford, Louis W

    2016-12-01

    Integral projection models (IPMs) have a number of advantages over matrix-model approaches for analyzing size-structured population dynamics, because the latter require parameter estimates for each age or stage transition. However, IPMs still require appropriate data. Typically they are parameterized using individual-scale relationships between body size and demographic rates, but these are not always available. We present an alternative approach for estimating demographic parameters from time series of size-structured survey data using a Bayesian state-space IPM (SSIPM). By fitting an IPM in a state-space framework, we estimate unknown parameters and explicitly account for process and measurement error in a dataset to estimate the underlying process model dynamics. We tested our method by fitting SSIPMs to simulated data; the model fit the simulated size distributions well and estimated unknown demographic parameters accurately. We then illustrated our method using nine years of annual surveys of the density and size distribution of two fish species (blue rockfish, Sebastes mystinus, and gopher rockfish, S. carnatus) at seven kelp forest sites in California. The SSIPM produced reasonable fits to the data, and estimated fishing rates for both species that were higher than our Bayesian prior estimates based on coast-wide stock assessment estimates of harvest. That improvement reinforces the value of being able to estimate demographic parameters from local-scale monitoring data. We highlight a number of key decision points in SSIPM development (e.g., open vs. closed demography, number of particles in the state-space filter) so that users can apply the method to their own datasets.

  13. Fitting and Calibrating a Multilevel Mixed-Effects Stem Taper Model for Maritime Pine in NW Spain.

    PubMed

    Arias-Rodil, Manuel; Castedo-Dorado, Fernando; Cámara-Obregón, Asunción; Diéguez-Aranda, Ulises

    2015-01-01

    Stem taper data are usually hierarchical (several measurements per tree, and several trees per plot), making application of a multilevel mixed-effects modelling approach essential. However, correlation between trees in the same plot/stand has often been ignored in previous studies. Fitting and calibration of a variable-exponent stem taper function were conducted using data from 420 trees felled in even-aged maritime pine (Pinus pinaster Ait.) stands in NW Spain. In the fitting step, the tree level explained much more variability than the plot level, and therefore calibration at plot level was omitted. Several stem heights were evaluated for measurement of the additional diameter needed for calibration at tree level. Calibration with an additional diameter measured at between 40 and 60% of total tree height showed the greatest improvement in volume and diameter predictions. If additional diameter measurement is not available, the fixed-effects model fitted by the ordinary least squares technique should be used. Finally, we also evaluated how the expansion of parameters with random effects affects the stem taper prediction, as we consider this a key question when applying the mixed-effects modelling approach to taper equations. The results showed that correlation between random effects should be taken into account when assessing the influence of random effects in stem taper prediction.

  14. Fitting and Calibrating a Multilevel Mixed-Effects Stem Taper Model for Maritime Pine in NW Spain

    PubMed Central

    Arias-Rodil, Manuel; Castedo-Dorado, Fernando; Cámara-Obregón, Asunción; Diéguez-Aranda, Ulises

    2015-01-01

    Stem taper data are usually hierarchical (several measurements per tree, and several trees per plot), making application of a multilevel mixed-effects modelling approach essential. However, correlation between trees in the same plot/stand has often been ignored in previous studies. Fitting and calibration of a variable-exponent stem taper function were conducted using data from 420 trees felled in even-aged maritime pine (Pinus pinaster Ait.) stands in NW Spain. In the fitting step, the tree level explained much more variability than the plot level, and therefore calibration at plot level was omitted. Several stem heights were evaluated for measurement of the additional diameter needed for calibration at tree level. Calibration with an additional diameter measured at between 40 and 60% of total tree height showed the greatest improvement in volume and diameter predictions. If additional diameter measurement is not available, the fixed-effects model fitted by the ordinary least squares technique should be used. Finally, we also evaluated how the expansion of parameters with random effects affects the stem taper prediction, as we consider this a key question when applying the mixed-effects modelling approach to taper equations. The results showed that correlation between random effects should be taken into account when assessing the influence of random effects in stem taper prediction. PMID:26630156

  15. Using Geometry-Based Metrics as Part of Fitness-for-Purpose Evaluations of 3D City Models

    NASA Astrophysics Data System (ADS)

    Wong, K.; Ellul, C.

    2016-10-01

    Three-dimensional geospatial information is being increasingly used in a range of tasks beyond visualisation. 3D datasets, however, are often being produced without exact specifications and at mixed levels of geometric complexity. This leads to variations within the models' geometric and semantic complexity as well as the degree of deviation from the corresponding real world objects. Existing descriptors and measures of 3D data such as CityGML's level of detail are perhaps only partially sufficient in communicating data quality and fitness-for-purpose. This study investigates whether alternative, automated, geometry-based metrics describing the variation of complexity within 3D datasets could provide additional relevant information as part of a process of fitness-for-purpose evaluation. The metrics include: mean vertex/edge/face counts per building; vertex/face ratio; minimum 2D footprint area and; minimum feature length. Each metric was tested on six 3D city models from international locations. The results show that geometry-based metrics can provide additional information on 3D city models as part of fitness-for-purpose evaluations. The metrics, while they cannot be used in isolation, may provide a complement to enhance existing data descriptors if backed up with local knowledge, where possible.

  16. The Impact of Intraclass Correlation on the Effectiveness of Level-Specific Fit Indices in Multilevel Structural Equation Modeling: A Monte Carlo Study

    ERIC Educational Resources Information Center

    Hsu, Hsien-Yuan; Lin, Jr-Hung; Kwok, Oi-Man; Acosta, Sandra; Willson, Victor

    2017-01-01

    Several researchers have recommended that level-specific fit indices should be applied to detect the lack of model fit at any level in multilevel structural equation models. Although we concur with their view, we note that these studies did not sufficiently consider the impact of intraclass correlation (ICC) on the performance of level-specific…

  17. Detecting Mixtures from Structural Model Differences Using Latent Variable Mixture Modeling: A Comparison of Relative Model Fit Statistics

    ERIC Educational Resources Information Center

    Henson, James M.; Reise, Steven P.; Kim, Kevin H.

    2007-01-01

    The accuracy of structural model parameter estimates in latent variable mixture modeling was explored with a 3 (sample size) [times] 3 (exogenous latent mean difference) [times] 3 (endogenous latent mean difference) [times] 3 (correlation between factors) [times] 3 (mixture proportions) factorial design. In addition, the efficacy of several…

  18. Survival analysis of clinical mastitis data using a nested frailty Cox model fit as a mixed-effects Poisson model.

    PubMed

    Elghafghuf, Adel; Dufour, Simon; Reyher, Kristen; Dohoo, Ian; Stryhn, Henrik

    2014-12-01

    Mastitis is a complex disease affecting dairy cows and is considered to be the most costly disease of dairy herds. The hazard of mastitis is a function of many factors, both managerial and environmental, making its control a difficult issue to milk producers. Observational studies of clinical mastitis (CM) often generate datasets with a number of characteristics which influence the analysis of those data: the outcome of interest may be the time to occurrence of a case of mastitis, predictors may change over time (time-dependent predictors), the effects of factors may change over time (time-dependent effects), there are usually multiple hierarchical levels, and datasets may be very large. Analysis of such data often requires expansion of the data into the counting-process format - leading to larger datasets - thus complicating the analysis and requiring excessive computing time. In this study, a nested frailty Cox model with time-dependent predictors and effects was applied to Canadian Bovine Mastitis Research Network data in which 10,831 lactations of 8035 cows from 69 herds were followed through lactation until the first occurrence of CM. The model was fit to the data as a Poisson model with nested normally distributed random effects at the cow and herd levels. Risk factors associated with the hazard of CM during the lactation were identified, such as parity, calving season, herd somatic cell score, pasture access, fore-stripping, and proportion of treated cases of CM in a herd. The analysis showed that most of the predictors had a strong effect early in lactation and also demonstrated substantial variation in the baseline hazard among cows and between herds. A small simulation study for a setting similar to the real data was conducted to evaluate the Poisson maximum likelihood estimation approach with both Gaussian quadrature method and Laplace approximation. Further, the performance of the two methods was compared with the performance of a widely used estimation

  19. A KIM-compliant potfit for fitting sloppy interatomic potentials: application to the EDIP model for silicon

    NASA Astrophysics Data System (ADS)

    Wen, Mingjian; Li, Junhao; Brommer, Peter; Elliott, Ryan S.; Sethna, James P.; Tadmor, Ellad B.

    2017-01-01

    Fitted interatomic potentials are widely used in atomistic simulations thanks to their ability to compute the energy and forces on atoms quickly. However, the simulation results crucially depend on the quality of the potential being used. Force matching is a method aimed at constructing reliable and transferable interatomic potentials by matching the forces computed by the potential as closely as possible, with those obtained from first principles calculations. The potfit program is an implementation of the force-matching method that optimizes the potential parameters using a global minimization algorithm followed by a local minimization polish. We extended potfit in two ways. First, we adapted the code to be compliant with the KIM Application Programming Interface (API) standard (part of the Knowledgebase of Interatomic Models project). This makes it possible to use potfit to fit many KIM potential models, not just those prebuilt into the potfit code. Second, we incorporated the geodesic Levenberg-Marquardt (LM) minimization algorithm into potfit as a new local minimization algorithm. The extended potfit was tested by generating a training set using the KIM environment-dependent interatomic potential (EDIP) model for silicon and using potfit to recover the potential parameters from different initial guesses. The results show that EDIP is a ‘sloppy model’ in the sense that its predictions are insensitive to some of its parameters, which makes fitting more difficult. We find that the geodesic LM algorithm is particularly efficient for this case. The extended potfit code is the first step in developing a KIM-based fitting framework for interatomic potentials for bulk and two-dimensional materials. The code is available for download via https://www.potfit.net.

  20. Evaluation of RGP Contact Lens Fitting in Keratoconus Patients Using Hierarchical Fuzzy Model and Genetic Algorithms.

    PubMed

    Falahati Marvast, Fatemeh; Arabalibeik, Hossein; Alipour, Fatemeh; Sheikhtaheri, Abbas; Nouri, Leila; Soozande, Mehdi; Yarmahmoodi, Masood

    2016-01-01

    Keratoconus is a progressive non-inflammatory disease of the cornea. Rigid gas permeable contact lenses (RGPs) are prescribed when the disease progresses. Contact lens fitting and assessment is very difficult in these patients and is a concern of ophthalmologists and optometrists. In this study, a hierarchical fuzzy system is used to capture the expertise of experienced ophthalmologists during the lens evaluation phase of prescription. The system is fine-tuned using genetic algorithms. Sensitivity, specificity and accuracy of the final system are 88.9%, 94.4% and 92.6% respectively.

  1. Genome-Enabled Modeling of Biogeochemical Processes Predicts Metabolic Dependencies that Connect the Relative Fitness of Microbial Functional Guilds

    NASA Astrophysics Data System (ADS)

    Brodie, E.; King, E.; Molins, S.; Karaoz, U.; Steefel, C. I.; Banfield, J. F.; Beller, H. R.; Anantharaman, K.; Ligocki, T. J.; Trebotich, D.

    2015-12-01

    Pore-scale processes mediated by microorganisms underlie a range of critical ecosystem services, regulating carbon stability, nutrient flux, and the purification of water. Advances in cultivation-independent approaches now provide us with the ability to reconstruct thousands of genomes from microbial populations from which functional roles may be assigned. With this capability to reveal microbial metabolic potential, the next step is to put these microbes back where they belong to interact with their natural environment, i.e. the pore scale. At this scale, microorganisms communicate, cooperate and compete across their fitness landscapes with communities emerging that feedback on the physical and chemical properties of their environment, ultimately altering the fitness landscape and selecting for new microbial communities with new properties and so on. We have developed a trait-based model of microbial activity that simulates coupled functional guilds that are parameterized with unique combinations of traits that govern fitness under dynamic conditions. Using a reactive transport framework, we simulate the thermodynamics of coupled electron donor-acceptor reactions to predict energy available for cellular maintenance, respiration, biomass development, and enzyme production. From metagenomics, we directly estimate some trait values related to growth and identify the linkage of key traits associated with respiration and fermentation, macromolecule depolymerizing enzymes, and other key functions such as nitrogen fixation. Our simulations were carried out to explore abiotic controls on community emergence such as seasonally fluctuating water table regimes across floodplain organic matter hotspots. Simulations and metagenomic/metatranscriptomic observations highlighted the many dependencies connecting the relative fitness of functional guilds and the importance of chemolithoautotrophic lifestyles. Using an X-Ray microCT-derived soil microaggregate physical model combined

  2. Assessing the viral fitness of oseltamivir-resistant influenza viruses in ferrets, using a competitive-mixtures model.

    PubMed

    Hurt, Aeron C; Nor'e, Siti Sarah; McCaw, James M; Fryer, Helen R; Mosse, Jennifer; McLean, Angela R; Barr, Ian G

    2010-09-01

    To determine the relative fitness of oseltamivir-resistant strains compared to susceptible wild-type viruses, we combined mathematical modeling and statistical techniques with a novel in vivo "competitive-mixtures" experimental model. Ferrets were coinfected with either pure populations (100% susceptible wild-type or 100% oseltamivir-resistant mutant virus) or mixed populations of wild-type and oseltamivir-resistant influenza viruses (80%:20%, 50%:50%, and 20%:80%) at equivalent infectivity titers, and the changes in the relative proportions of those two viruses were monitored over the course of the infection during within-host and over host-to-host transmission events in a ferret contact model. Coinfection of ferrets with mixtures of an oseltamivir-resistant R292K mutant A(H3N2) virus and a R292 oseltamivir-susceptible wild-type virus demonstrated that the R292K mutant virus was rapidly outgrown by the R292 wild-type virus in artificially infected donor ferrets and did not transmit to any of the recipient ferrets. The competitive-mixtures model was also used to investigate the fitness of the seasonal A(H1N1) oseltamivir-resistant H274Y mutant and showed that within infected ferrets the H274Y mutant virus was marginally outgrown by the wild-type strain but demonstrated equivalent transmissibility between ferrets. This novel in vivo experimental method and accompanying mathematical analysis provide greater insight into the relative fitness, both within the host and between hosts, of two different influenza virus strains compared to more traditional methods that infect ferrets with only pure populations of viruses. Our statistical inferences are essential for the development of the next generation of mathematical models of the emergence and spread of oseltamivir-resistant influenza in human populations.

  3. A Paradox between IRT Invariance and Model-Data Fit When Utilizing the One-Parameter and Three-Parameter Models

    ERIC Educational Resources Information Center

    Custer, Michael; Sharairi, Sid; Yamazaki, Kenji; Signatur, Diane; Swift, David; Frey, Sharon

    2008-01-01

    The present study compared item and ability invariance as well as model-data fit between the one-parameter (1PL) and three-parameter (3PL) Item Response Theory (IRT) models utilizing real data across five grades; second through sixth as well as simulated data at second, fourth and sixth grade. At each grade, the 1PL and 3PL IRT models were run…

  4. Geometric model-based fitting algorithm for orientation-selective PELDOR data

    NASA Astrophysics Data System (ADS)

    Abdullin, Dinar; Hagelueken, Gregor; Hunter, Robert I.; Smith, Graham M.; Schiemann, Olav

    2015-03-01

    Pulsed electron-electron double resonance (PELDOR or DEER) spectroscopy is frequently used to determine distances between spin centres in biomacromolecular systems. Experiments where mutual orientations of the spin pair are selectively excited provide the so-called orientation-selective PELDOR data. This data is characterised by the orientation dependence of the modulation depth parameter and of the dipolar frequencies. This dependence has to be taken into account in the data analysis in order to extract distance distributions accurately from the experimental time traces. In this work, a fitting algorithm for such data analysis is discussed. The approach is tested on PELDOR data-sets from the literature and is compared with the previous results.

  5. Unmarked: An R package for fitting hierarchical models of wildlife occurrence and abundance

    USGS Publications Warehouse

    Fiske, I.J.; Chandler, R.B.

    2011-01-01

    Ecological research uses data collection techniques that are prone to substantial and unique types of measurement error to address scientic questions about species abundance and distribution. These data collection schemes include a number of survey methods in which unmarked individuals are counted, or determined to be present, at spatially- referenced sites. Examples include site occupancy sampling, repeated counts, distance sampling, removal sampling, and double observer sampling. To appropriately analyze these data, hierarchical models have been developed to separately model explanatory variables of both a latent abundance or occurrence process and a conditional detection process. Because these models have a straightforward interpretation paralleling mecha- nisms under which the data arose, they have recently gained immense popularity. The common hierarchical structure of these models is well-suited for a unied modeling in- terface. The R package unmarked provides such a unied modeling framework, including tools for data exploration, model tting, model criticism, post-hoc analysis, and model comparison.

  6. Model-based 3D human shape estimation from silhouettes for virtual fitting

    NASA Astrophysics Data System (ADS)

    Saito, Shunta; Kouchi, Makiko; Mochimaru, Masaaki; Aoki, Yoshimitsu

    2014-03-01

    We propose a model-based 3D human shape reconstruction system from two silhouettes. Firstly, we synthesize a deformable body model from 3D human shape database consists of a hundred whole body mesh models. Each mesh model is homologous, so that it has the same topology and same number of vertices among all models. We perform principal component analysis (PCA) on the database and synthesize an Active Shape Model (ASM). ASM allows changing the body type of the model with a few parameters. The pose changing of our model can be achieved by reconstructing the skeleton structures from implanted joints of the model. By applying pose changing after body type deformation, our model can represents various body types and any pose. We apply the model to the problem of 3D human shape reconstruction from front and side silhouette. Our approach is simply comparing the contours between the model's and input silhouettes', we then use only torso part contour of the model to reconstruct whole shape. We optimize the model parameters by minimizing the difference between corresponding silhouettes by using a stochastic, derivative-free non-linear optimization method, CMA-ES.

  7. Automated quantum mechanical total line shape fitting model for quantitative NMR-based profiling of human serum metabolites.

    PubMed

    Mihaleva, Velitchka V; Korhonen, Samuli-Petrus; van Duynhoven, John; Niemitz, Mathias; Vervoort, Jacques; Jacobs, Doris M

    2014-05-01

    An automated quantum mechanical total line shape (QMTLS) fitting model was implemented for quantitative nuclear magnetic resonance (NMR)-based profiling of 42 metabolites in ultrafiltrated human serum samples. Each metabolite was described by a set of chemical shifts, J-couplings, and line widths. These parameters were optimized for each metabolite in each sample by iteratively minimizing the difference between the calculated and the experimental spectrum. In total, 92.0 to 98.1 % of the signal intensities in the experimental spectrum could be explained by the calculated spectrum. The model was validated by comparison to signal integration of metabolites with isolated signals and by means of standard additions. Metabolites present at average concentration higher than 50 μM were quantified with average absolute relative error less than 10 % when using different initial parameters for the fitting procedure. Furthermore, the biological applicability of the QMTLS model was demonstrated on 287 samples from an intervention study in 37 human volunteers undergoing an exercise challenge. Our automated QMTLS model was able to cope with the large dynamic range of metabolite concentrations in serum and proved to be suitable for high-throughput analysis.

  8. Testing evolutionary models of senescence in a natural population: age and inbreeding effects on fitness components in song sparrows.

    PubMed

    Keller, L F; Reid, J M; Arcese, P

    2008-03-22

    Mutation accumulation (MA) and antagonistic pleiotropy (AP) have each been hypothesized to explain the evolution of 'senescence' or deteriorating fitness in old age. These hypotheses make contrasting predictions concerning age dependence in inbreeding depression in traits that show senescence. Inbreeding depression is predicted to increase with age under MA but not under AP, suggesting one empirical means by which the two can be distinguished. We use pedigree and life-history data from free-living song sparrows (Melospiza melodia) to test for additive and interactive effects of age and individual inbreeding coefficient (f) on fitness components, and thereby assess the evidence for MA. Annual reproductive success (ARS) and survival (and therefore reproductive value) declined in old age in both sexes, indicating senescence in this short-lived bird. ARS declined with f in both sexes and survival declined with f in males, indicating inbreeding depression in fitness. We observed a significant agexf interaction for male ARS (reflecting increased inbreeding depression as males aged), but not for female ARS or survival in either sex. These analyses therefore provide mixed support for MA. We discuss the strengths and limitations of such analyses and therefore the value of natural pedigreed populations in testing evolutionary models of senescence.

  9. Computing confidence intervals of item fit statistics in the family of Rasch models using the bootstrap method.

    PubMed

    Su, Ya-Hui; Sheu, Ching-Fan; Wang, Wen-Chung

    2007-01-01

    The item infit and outfit mean square errors (MSE) and their t-transformed statistics are widely used to screen poorly fitting items. The t-transformed statistics, however, do not follow the standard normal distribution so that hypothesis testing of item fit based on the conventional critical values is likely to be inaccurate (Wang and Chen, 2005). The MSE statistics are effect-size measures of misfit and have an expected value of unity when the data fit the model's expectation. Unfortunately, most computer programs for item response analysis do not report confidence intervals of the item infit and outfit MSE, mainly because their sampling distributions are analytically intractable. Hence, the user is left without interval estimates of the magnitudes of misfit. In this study, we developed a FORTRAN 90 computer program in conjunction with the commercial program WINSTEPS (Linacre, 2001) that yields confidence intervals of the item infit and outfit MSE using the bootstrap method. The utility of the program is demonstrated through three illustrations of simulated data sets.

  10. Analytic solutions to modelling exponential and harmonic functions using Chebyshev polynomials: fitting frequency-domain lifetime images with photobleaching.

    PubMed

    Malachowski, George C; Clegg, Robert M; Redford, Glen I

    2007-12-01

    A novel approach is introduced for modelling linear dynamic systems composed of exponentials and harmonics. The method improves the speed of current numerical techniques up to 1000-fold for problems that have solutions of multiple exponentials plus harmonics and decaying components. Such signals are common in fluorescence microscopy experiments. Selective constraints of the parameters being fitted are allowed. This method, using discrete Chebyshev transforms, will correctly fit large volumes of data using a noniterative, single-pass routine that is fast enough to analyse images in real time. The method is applied to fluorescence lifetime imaging data in the frequency domain with varying degrees of photobleaching over the time of total data acquisition. The accuracy of the Chebyshev method is compared to a simple rapid discrete Fourier transform (equivalent to least-squares fitting) that does not take the photobleaching into account. The method can be extended to other linear systems composed of different functions. Simulations are performed and applications are described showing the utility of the method, in particular in the area of fluorescence microscopy.

  11. Serum thyroglobulin reference intervals in regions with adequate and more than adequate iodine intake.

    PubMed

    Wang, Zhaojun; Zhang, Hanyi; Zhang, Xiaowen; Sun, Jie; Han, Cheng; Li, Chenyan; Li, Yongze; Teng, Xiaochun; Fan, Chenling; Liu, Aihua; Shan, Zhongyan; Liu, Chao; Weng, Jianping; Teng, Weiping

    2016-11-01

    The purpose of this study was to establish normal thyroglobulin (Tg) reference intervals (RIs) in regions with adequate and more than adequate iodine intake according to the National Academy of Clinical Biochemistry (NACB) guidelines and to investigate the relationships between Tg and other factors.A total of 1317 thyroid disease-free adult subjects (578 men, 739 nonpregnant women) from 2 cities (Guangzhou and Nanjing) were enrolled in this retrospective, observational study. Each subject completed a questionnaire and underwent physical and ultrasonic examination. Serum Tg, thyroid-stimulating hormone (TSH), thyroid peroxidase antibody (TPOAb), Tg antibody (TgAb), and urinary iodine concentration (UIC) were measured. Reference groups were established on the basis of TSH levels: 0.5 to 2.0 and 0.27 to 4.2 mIU/L.The Tg RIs for Guangzhou and Nanjing were 1.6 to 30.0 and 1.9 to 25.8 ng/mL, respectively. No significant differences in Tg were found between genders or among different reference groups. Stepwise linear regression analyses showed that TgAb, thyroid volume, goiter, gender, age, and TSH levels were correlated with Tg.In adults from regions with adequate and more than adequate iodine intake, we found that Tg may be a suitable marker of iodine status; gender-specific Tg RI was unnecessary; there was no difference between Tg RIs in regions with adequate and more than adequate iodine intake; and the TSH criterion for selecting the Tg reference population could follow the local TSH reference rather than 0.5 to 2.0 mIU/L.

  12. Serum thyroglobulin reference intervals in regions with adequate and more than adequate iodine intake

    PubMed Central

    Wang, Zhaojun; Zhang, Hanyi; Zhang, Xiaowen; Sun, Jie; Han, Cheng; Li, Chenyan; Li, Yongze; Teng, Xiaochun; Fan, Chenling; Liu, Aihua; Shan, Zhongyan; Liu, Chao; Weng, Jianping; Teng, Weiping

    2016-01-01

    Abstract The purpose of this study was to establish normal thyroglobulin (Tg) reference intervals (RIs) in regions with adequate and more than adequate iodine intake according to the National Academy of Clinical Biochemistry (NACB) guidelines and to investigate the relationships between Tg and other factors. A total of 1317 thyroid disease-free adult subjects (578 men, 739 nonpregnant women) from 2 cities (Guangzhou and Nanjing) were enrolled in this retrospective, observational study. Each subject completed a questionnaire and underwent physical and ultrasonic examination. Serum Tg, thyroid-stimulating hormone (TSH), thyroid peroxidase antibody (TPOAb), Tg antibody (TgAb), and urinary iodine concentration (UIC) were measured. Reference groups were established on the basis of TSH levels: 0.5 to 2.0 and 0.27 to 4.2 mIU/L. The Tg RIs for Guangzhou and Nanjing were 1.6 to 30.0 and 1.9 to 25.8 ng/mL, respectively. No significant differences in Tg were found between genders or among different reference groups. Stepwise linear regression analyses showed that TgAb, thyroid volume, goiter, gender, age, and TSH levels were correlated with Tg. In adults from regions with adequate and more than adequate iodine intake, we found that Tg may be a suitable marker of iodine status; gender-specific Tg RI was unnecessary; there was no difference between Tg RIs in regions with adequate and more than adequate iodine intake; and the TSH criterion for selecting the Tg reference population could follow the local TSH reference rather than 0.5 to 2.0 mIU/L. PMID:27902589

  13. Modelling the Factors that Affect Individuals' Utilisation of Online Learning Systems: An Empirical Study Combining the Task Technology Fit Model with the Theory of Planned Behaviour

    ERIC Educational Resources Information Center

    Yu, Tai-Kuei; Yu, Tai-Yi

    2010-01-01

    Understanding learners' behaviour, perceptions and influence in terms of learner performance is crucial to predict the use of electronic learning systems. By integrating the task-technology fit (TTF) model and the theory of planned behaviour (TPB), this paper investigates the online learning utilisation of Taiwanese students. This paper provides a…

  14. Fitting Proportional Odds Models to Educational Data in Ordinal Logistic Regression Using Stata, SAS and SPSS

    ERIC Educational Resources Information Center

    Liu, Xing

    2008-01-01

    The proportional odds (PO) model, which is also called cumulative odds model (Agresti, 1996, 2002 ; Armstrong & Sloan, 1989; Long, 1997, Long & Freese, 2006; McCullagh, 1980; McCullagh & Nelder, 1989; Powers & Xie, 2000; O'Connell, 2006), is one of the most commonly used models for the analysis of ordinal categorical data and comes from the class…

  15. The Body Micropolitic: Where Do Women Educational Leaders Fit in the Easton Model of Policy Analysis?

    ERIC Educational Resources Information Center

    Raveling, Joyce S.

    This paper asks where and how women and women's styles of leadership are situated in Easton's Model of Policy Process. The Easton Model provides a means of understanding policy development from a micropolitical perspective and offers analysis of environmental influences on policy decision making and implementation, allowing the model to…

  16. Culture and Parenting: Family Models Are Not One-Size-Fits-All. FPG Snapshot #67

    ERIC Educational Resources Information Center

    FPG Child Development Institute, 2012

    2012-01-01

    Family process models guide theories and research about family functioning and child development outcomes. Theory and research, in turn, inform policies and services aimed at families. But are widely accepted models valid across cultural groups? To address these gaps, FPG researchers examined the utility of two family process models for families…

  17. Fitting the Normal-Ogive Factor Analytic Model to Scores on Tests.

    ERIC Educational Resources Information Center

    Ferrando, Pere J.; Lorenzo-Seva, Urbano

    2001-01-01

    Describes how the nonlinear factor analytic approach of R. McDonald to the normal ogive curve can be used to factor analyze test scores. Discusses the conditions in which this model is more appropriate than the linear model and illustrates the applicability of both models using an empirical example based on data from 1,769 adolescents who took the…

  18. Evaluation of five lactation curve models fitted for fat:protein ratio of milk and daily energy balance.

    PubMed

    Buttchereit, N; Stamer, E; Junge, W; Thaller, G

    2010-04-01

    Selection for milk yield increases the metabolic load of dairy cows. The fat:protein ratio of milk (FPR) could serve as a measure of the energy balance status and might be used as a selection criterion to improve metabolic stability. The fit of different fixed and random regression models describing FPR and daily energy balance was tested to establish appropriate models for further genetic analyses. In addition, the relationship between both traits was evaluated for the best fitting model. Data were collected on a dairy research farm running a bull dam performance test. Energy balance was calculated using information on milk yield, feed intake per day, and live weight. Weekly FPR measurements were available. Three data sets were created containing records of 577 primiparous cows with observations from lactation d 11 to 180 as well as records of 613 primiparous cows and 96 multiparous cows with observations from lactation d 11 to 305. Five well-established parametric functions of days in milk (Ali and Schaeffer, Guo and Swalve, Wilmink, Legendre polynomials of third and fourth degree) were chosen for modeling the lactation curves. Evaluation of goodness of fit was based on the corrected Akaike information criterion, the Bayesian information criterion, correlation between the real observation and the estimated value, and on inspection of the residuals plotted against days in milk. The best model was chosen for estimation of correlations between both traits at different lactation stages. Random regression models were superior compared with the fixed regression models. In general, the Ali and Schaeffer function appeared most suitable for modeling both the fixed and the random regression part of the mixed model. The FPR is greatest in the initial lactation period when energy deficit is most pronounced. Energy balance stabilizes at the same point as the decrease in FPR stops. The inverted patterns indicate a causal relationship between the 2 traits. A common pattern was

  19. Fitting bevacizumab aggregation kinetic data with the Finke-Watzky two-step model: Effect of thermal and mechanical stress.

    PubMed

    Oliva, Alexis; Llabrés, Matías; Fariña, José B

    2015-09-18

    Size exclusion chromatography with light scattering detection (SEC-MALLS) was assessed as a means to characterize the type of bevacizumab aggregates that form under mechanical and thermal stress, quantitatively monitoring the aggregation kinetics. The analytical method was monitored and verified during routine use at two levels: (1) the "pre-study" validation shows that the method is specific, linear, accurate, precise, robust and stability indicating; (2) the "in-study" validation was verified by inserting quality control samples and the use of control charts, indicating that the analytical method is in statistical control and stable. The aggregation kinetics data were interpreted using a modified Lumry-Eyring model, but the quality of the fit can be considered poor (R(2)>0.96), especially at higher temperatures. This indicates that the order of the reaction could not be reliably determined, suggesting a different degradation mechanism. The kinetic data set also fit the minimalistic Finke-Watzky (F-W) 2-step model, with an excellent quality of fit (R(2)>0.99), yielding the first quantitative rate constant for the steps of nucleation and growth in bevacizumab aggregation. The bevacizumab pharmaceutical preparation contains (initially) dimers, approximately 1.6% of bevacizumab total concentration, and the effect on aggregation kinetics of seeding was analyzed using the F-W 2-step model assuming [B]0≠0 (for the seeded case). The results suggested that the seeding had no impact on aggregation kinetics. Furthermore, the Arrhenius equation cannot be used to extrapolate the shelf-life since no linear temperature dependence of the rate constant was found within the temperature range. Although the real-time stability data provides the basis for determining the product shelf-life, predictive methodologies such as Vogel-Tammann-Fulcher (VFT) or the Arrhenius approach can be misleading and result in overestimates of the product shelf-life. However, they can be successfully

  20. Effects of distance from models on the fitness of floral mimics.

    PubMed

    Duffy, K J; Johnson, S D

    2017-02-01

    Rewardless plants can attract pollinators by mimicking floral traits of rewarding heterospecific plants. This should result in the pollination success of floral mimics being dependent on the relative abundance of their models, as pollinator abundance and conditioning on model signals should be higher in the vicinity of the models. However, the attraction of pollinators to signals of the models may be partially innate, such that spatial isolation of mimics from model species may not strongly affect pollination success of mimics. We tested whether pollination rates and fruit set of the rewardless orchid Disa pulchra were influenced by proximity and abundance of its rewarding model species, Watsonia lepida. Pollination success of the orchid increased with proximity to the model species, while fruit set of the orchid increased with local abundance of the model species. Orchids that were experimentally translocated outside the model population experienced reduced pollinaria removal and increased pollinator-mediated self-pollination. These results confirm predictions that the pollination success of floral mimics should be dependent on the proximity and abundance of model taxa, and thus highlight the importance of ecological facilitation among species involved in mimicry systems.

  1. Does Current Army Physical Fitness Training Doctrine Adequately Prepare Soldiers for War?

    DTIC Science & Technology

    2010-06-11

    These divisions were supported by heavy artillery that continuously shelled the American positions previously held by German infantry. Background E...spine region: Stacked Foot/Staggered Hand Push-Up, Banana Roll, Leaning Crescent, Squat Run, Sphinx Push-Up, Bow to Boat, Low Lateral Skaters...Lunge and Reach, Prison Cell Push-Up, Side Hip Raise, Squat X-Press, Plank to Chaturanga, Walking Push-Up, Superman Banana , Lunge Kickback Curl Press

  2. MODELING THE NONLINEAR CLUSTERING IN MODIFIED GRAVITY MODELS. I. A FITTING FORMULA FOR THE MATTER POWER SPECTRUM OF f(R) GRAVITY

    SciTech Connect

    Zhao, Gong-Bo

    2014-04-01

    Based on a suite of N-body simulations of the Hu-Sawicki model of f(R) gravity with different sets of model and cosmological parameters, we develop a new fitting formula with a numeric code, MGHalofit, to calculate the nonlinear matter power spectrum P(k) for the Hu-Sawicki model. We compare the MGHalofit predictions at various redshifts (z ≤ 1) to the f(R) simulations and find that the relative error of the MGHalofit fitting formula of P(k) is no larger than 6% at k ≤ 1 h Mpc{sup –1} and 12% at k in (1, 10] h Mpc{sup –1}, respectively. Based on a sensitivity study of an ongoing and a future spectroscopic survey, we estimate the detectability of a signal of modified gravity described by the Hu-Sawicki model using the power spectrum up to quasi-nonlinear scales.

  3. A basis approach to goodness-of-fit testing in recurrent event models.

    PubMed

    Agustin, Ma Zenia N; Peña, Edsel A

    2005-08-01

    A class of tests for the hypothesis that the baseline hazard function in Cox's proportional hazards model and for a general recurrent event model belongs to a parametric family C identical with {lambda(0)(.; xi): xi in Xi} is proposed. Finite properties of the tests are examined via simulations, while asymptotic properties of the tests under a contiguous sequence of local alternatives are studied theoretically. An application of the tests to the general recurrent event model, which is an extended minimal repair model admitting covariates, is demonstrated. In addition, two real data sets are used to illustrate the applicability of the proposed tests.

  4. Effects of a Three-Tiered Intervention Model on Physical Activity and Fitness Levels of Elementary School Children.

    PubMed

    Dauenhauer, Brian; Keating, Xiaofen; Lambdin, Dolly

    2016-08-01

    Response to intervention (RtI) models are frequently used in schools to tailor academic instruction to the needs of students. The purpose of this study was to examine the effects of using RtI to promote physical activity (PA) and fitness in one urban elementary school. Ninety-nine students in grades 2-5 participated in up to three tiers of intervention throughout the course of one school year. Tier one included 150 min/week of physical education (increased from 90 min/week the previous year) and coordinated efforts to improve school health. Tier two consisted of 30 min/week of small group instruction based on goal setting and social support. Tier three included an after-school program for parents and children focused on healthy living. PA, cardiovascular fitness, and body composition were assessed before and after the interventions using pedometers, a 20-m shuttle run, and height/weight measurements. From pre- to post-testing, PA remained relatively stable in tier one and increased by 2349 steps/day in tier two. Cardiovascular fitness increased in tiers one and two by 1.17 and 1.35 ml/kg/min, respectively. Although body mass index did not change, 17 of the 99 students improved their weight status over the course of the school year, resulting in an overall decline in the prevalence of overweight/obesity from 59.6 to 53.5 %. Preliminary results suggest that the RtI model can be an effective way to structure PA/health interventions in an elementary school setting.

  5. Application of boundary-fitted coordinate (BFC) transformations to groundwater flow and transport modeling

    SciTech Connect

    Lee, K.K.

    1992-01-01

    A numerical method is presented to simulate groundwater flow and transport using the Boundary-Fitted Coordinate (BFC) systems approach initially developed for aerodynamics. An irregularly-shaped physical domain is transformed to a simple computational domain with uniform grids. Governing equations defined in the physical domain are transformed into the computational domain, wherein all transformed equations are solved by the Finite Difference Method (FDM). This study developed three FORTRAN 77 computer programs: (1) BFCGW, which simulates groundwater flow and transport, (2) SEEPAGE, which simulates free-surface and seepage face, and (3) Q3D, which simulates multi-layered flow. A series of plotting programs using [open quotes]DISSPLA,[close quotes] an IBM FORTRAN graphics package, was also developed to plot grid lines, contour lines, and flow vectors in an irregularly-shaped physical domain with non-uniform grids. Each of the three programs was verified by solving an idealized problem for which the analytical solution was known and/or a realistic problem for which field measurements could be obtained. The computer program BFCGW was employed to simulate an idealized well flow in a triangular physical domain and actual groundwater flows in the area of West Lafayette, Indiana. The numerical solutions in both cases closely matched the analytical solutions and/or numerical simulations by other computer codes such as AQUA and MODFLOW. The program BFCGW performs rotation and stretching of local coordinates prior to BFC transformations to simulate heterogeneous and anisotropic groundwater flow. The rotation and stretching technique simplifies transformed governing equations of anisotropic groundwater flow. With the program BFCGW, the groundwater flow and the transport equations are solved sequentially to simulate solute concentration distributions.

  6. Growing Fit: Georgia’s model for engaging early care environments in preventing childhood obesity

    PubMed Central

    McDavid, Kelsey; Piedrahita, Catalina; Hashima, Patricia; Vall, Emily Anne; Kay, Christi; O’Connor, Jean

    2016-01-01

    Background In the United States, one in three children is overweight or obese by their fifth birthday. In Georgia, 35 percent of children are overweight or obese. Contrary to popular belief, children who are overweight or obese are likely to be the same weight status as adults, making early childhood an essential time to address weight status. An estimated 380,000 Georgia children attend early care and education environments, such as licensed child care centers, Head Start, and pre-kindergarten programs, which provide an opportunity to reach large numbers of children, including those at risk for obesity and overweight. Methods To address this opportunity, the Georgia Department of Public Health, Georgia Shape - the Governor’s Initiative to prevent childhood obesity, and HealthMPowers, Inc., created the Growing Fit training and toolkit to assist early childhood educators in creating policy, systems, and environmental changes that support good nutrition and physical activity. This report, the first related to this project, describes the training and its dissemination between January and December 2015. Results A total of 103 early childcare educators from 39 early childcare education centers (22 individual childcare systems) from 19 counties in Georgia were trained. Fifteen systems completed a pre and post-test assessment of their system, demonstrating slight improvements. Training for an additional 125 early childcare education centers is planned for 2016. Conclusions Lessons learned from the first year of the training include the need for more robust assessment of adoption and implementation of policy, systems, and environmental changes in trained centers. PMID:27331199

  7. Fitting HIV Prevalence 1981 Onwards for Three Indian States Using the Goals Model and the Estimation and Projection Package

    PubMed Central

    Bhatnagar, Tarun; Dutta, Tapati; Stover, John; Godbole, Sheela; Sahu, Damodar; Boopathi, Kangusamy; Bembalkar, Shilpa; Singh, Kh. Jitenkumar; Goyal, Rajat; Pandey, Arvind; Mehendale, Sanjay M.

    2016-01-01

    Models are designed to provide evidence for strategic program planning by examining the impact of different interventions on projected HIV incidence. We employed the Goals Model to fit the HIV epidemic curves in Andhra Pradesh, Maharashtra and Tamil Nadu states of India where HIV epidemic is considered to have matured and in a declining phase. Input data in the Goals Model consisted of demographic, epidemiological, transmission-related and risk group wise behavioral parameters. The HIV prevalence curves generated in the Goals Model for each risk group in the three states were compared with the epidemic curves generated by the Estimation and Projection Package (EPP) that the national program is routinely using. In all the three states, the HIV prevalence trends for high-risk populations simulated by the Goals Model matched well with those derived using state-level HIV surveillance data in the EPP. However, trends for the low- and medium-risk populations differed between the two models. This highlights the need to generate more representative and robust data in these sub-populations and consider some structural changes in the modeling equation and parameters in the Goals Model to effectively use it to assess the impact of future strategies of HIV control in various sub-populations in India at the sub-national level. PMID:27711212

  8. A Bayesian chi-squared goodness-of-fit test for censored data models.

    PubMed

    Cao, Jing; Moosman, Ann; Johnson, Valen E

    2010-06-01

    We propose a Bayesian chi-squared model diagnostic for analysis of data subject to censoring. The test statistic has the form of Pearson's chi-squared test statistic and is easy to calculate from standard output of Markov chain Monte Carlo algorithms. The key innovation of this diagnostic is that it is based only on observed failure times. Because it does not rely on the imputation of failure times for observations that have been censored, we show that under heavy censoring it can have higher power for detecting model departures than a comparable test based on the complete data. In a simulation study, we show that tests based on this diagnostic exhibit comparable power and better nominal Type I error rates than a commonly used alternative test proposed by Akritas (1988, Journal of the American Statistical Association 83, 222-230). An important advantage of the proposed diagnostic is that it can be applied to a broad class of censored data models, including generalized linear models and other models with nonidentically distributed and nonadditive error structures. We illustrate the proposed model diagnostic for testing the adequacy of two parametric survival models for Space Shuttle main engine failures.

  9. One size does not fit all: Adapting mark-recapture and occupancy models for state uncertainty

    USGS Publications Warehouse

    Kendall, W.L.; Thomson, David L.; Cooch, Evan G.; Conroy, Michael J.

    2009-01-01

    Multistate capture?recapture models continue to be employed with greater frequency to test hypotheses about metapopulation dynamics and life history, and more recently disease dynamics. In recent years efforts have begun to adjust these models for cases where there is uncertainty about an animal?s state upon capture. These efforts can be categorized into models that permit misclassification between two states to occur in either direction or one direction, where state is certain for a subset of individuals or is always uncertain, and where estimation is based on one sampling occasion per period of interest or multiple sampling occasions per period. State uncertainty also arises in modeling patch occupancy dynamics. I consider several case studies involving bird and marine mammal studies that illustrate how misclassified states can arise, and outline model structures for properly utilizing the data that are produced. In each case misclassification occurs in only one direction (thus there is a subset of individuals or patches where state is known with certainty), and there are multiple sampling occasions per period of interest. For the cases involving capture?recapture data I allude to a general model structure that could include each example as a special case. However, this collection of cases also illustrates how difficult it is to develop a model structure that can be directly useful for answering every ecological question of interest and account for every type of data from the field.

  10. Fitting Procedures for Novel Gene-by-Measured Environment Interaction Models in Behavior Genetic Designs

    PubMed Central

    Zheng, Hao; Rathouz, Paul J.

    2015-01-01

    For quantitative behavior genetic (e.g., twin) studies, Purcell proposed a novel model for testing gene-by-measured environment (GxM) interactions while accounting for gene-by-environment correlation. Rathouz et al. expanded this model into a broader class of non-linear biometric models for quantifying and testing such interactions. In this work, we propose a novel factorization of the likelihood for this class of models, and adopt numerical integration techniques to achieve model estimation, especially for those without close-form likelihood. The validity of our procedures is established through numerical simulation studies. The new procedures are illustrated in a twin study analysis of the moderating effect of birth weight on the genetic influences on childhood anxiety. A second example is given in an online appendix. Both the exant GxM models and the new non-linear models critically assume normality of all structural components, which implies continuous, but not normal, manifest response variables. PMID:25732055

  11. Advantages of estimating parameters of photosynthesis model by fitting A-Ci curves at multiple subsaturating light intensities

    NASA Astrophysics Data System (ADS)

    Fu, W.; Gu, L.; Hoffman, F. M.

    2013-12-01

    The photosynthesis model of Farquhar, von Caemmerer & Berry (1980) is an important tool for predicting the response of plants to climate change. So far, the critical parameters required by the model have been obtained from the leaf-level measurements of gas exchange, namely the net assimilation of CO2 against intercellular CO2 concentration (A-Ci) curves, made at saturating light conditions. With such measurements, most points are likely in the Rubisco-limited state for which the model is structurally overparameterized (the model is also overparameterized in the TPU-limited state). In order to reliably estimate photosynthetic parameters, there must be sufficient number of points in the RuBP regeneration-limited state, which has no structural over-parameterization. To improve the accuracy of A-Ci data analysis, we investigate the potential of using multiple A-Ci curves at subsaturating light intensities to generate some important parameter estimates more accurately. Using subsaturating light intensities allow more RuBp regeneration-limited points to be obtained. In this study, simulated examples are used to demonstrate how this method can eliminate the errors of conventional A-Ci curve fitting methods. Some fitted parameters like the photocompensation point and day respiration impose a significant limitation on modeling leaf CO2 exchange. The multiple A-Ci curves fitting can also improve over the so-called Laisk (1977) method, which was shown by some recent publication to produce incorrect estimates of photocompensation point and day respiration. We also test the approach with actual measurements, along with suggested measurement conditions to constrain measured A-Ci points to maximize the occurrence of RuBP regeneration-limited photosynthesis. Finally, we use our measured gas exchange datasets to quantify the magnitude of resistance of chloroplast and cell wall-plasmalemma and explore the effect of variable mesophyll conductance. The variable mesophyll conductance

  12. Cognitive fitness.

    PubMed

    Gilkey, Roderick; Kilts, Clint

    2007-11-01

    Recent neuroscientific research shows that the health of your brain isn't, as experts once thought, just the product of childhood experiences and genetics; it reflects your adult choices and experiences as well. Professors Gilkey and Kilts of Emory University's medical and business schools explain how you can strengthen your brain's anatomy, neural networks, and cognitive abilities, and prevent functions such as memory from deteriorating as you age. The brain's alertness is the result of what the authors call cognitive fitness -a state of optimized ability to reason, remember, learn, plan, and adapt. Certain attitudes, lifestyle choices, and exercises enhance cognitive fitness. Mental workouts are the key. Brain-imaging studies indicate that acquiring expertise in areas as diverse as playing a cello, juggling, speaking a foreign language, and driving a taxicab expands your neural systems and makes them more communicative. In other words, you can alter the physical makeup of your brain by learning new skills. The more cognitively fit you are, the better equipped you are to make decisions, solve problems, and deal with stress and change. Cognitive fitness will help you be more open to new ideas and alternative perspectives. It will give you the capacity to change your behavior and realize your goals. You can delay senescence for years and even enjoy a second career. Drawing from the rapidly expanding body of neuroscience research as well as from well-established research in psychology and other mental health fields, the authors have identified four steps you can take to become cognitively fit: understand how experience makes the brain grow, work hard at play, search for patterns, and seek novelty and innovation. Together these steps capture some of the key opportunities for maintaining an engaged, creative brain.

  13. Does the first chaotic inflation model in supergravity provide the best fit to the Planck data?

    SciTech Connect

    Linde, Andrei

    2015-02-23

    I describe the first model of chaotic inflation in supergravity, which was proposed by Goncharov and the present author in 1983. The inflaton potential of this model has a plateau-type behavior V{sub 0}(1−(8/3) e{sup −√6|ϕ|}) at large values of the inflaton field. This model predicts n{sub s}=1−(2/N)≈0.967 and r=(4/(3N{sup 2}))≈4×10{sup −4}, in good agreement with the Planck data. I propose a slight generalization of this model, which allows to describe not only inflation but also dark energy and supersymmetry breaking.

  14. Fitting Microphysical Observations to a Numerical Model Through AN Optimal Control Theory Technique

    NASA Astrophysics Data System (ADS)

    Verlinde, Johannes

    Rapid advances in the quality and quantity of atmospheric observations have placed a demand for the development of techniques to assimilate these data sources into numerical forecasting models. Four-dimensional variational assimilation is a promising technique that has been applied to atmospheric and oceanic dynamical models, and also to the retrieval of three-dimensional wind fields from single Doppler radar observations. This study investigates the feasibility of using four-dimensional variational assimilation for a complex discontinuous numerical model. Three test models were developed, a positive definite advection scheme, a one -dimensional liquid physics kinematic microphysical model with a positive definite advection scheme, and a two-dimensional liquid physics kinematic microphysical model. These models were used in identical twin experiments, with observations taken intermittently. Small random errors were introduced into the observations. The retrieval runs were initialized with a large perturbation of the observation run initial conditions. All the models were able to retrieve the original initial conditions to a satisfactory degree when observations of all the model prognostic variables were used. Greater overdetermination of the degrees of freedom (the initial condition being retrieved) resulted in greater improvement of the errors in the observations of the initial conditions, but at a rapid increase in computational cost. Experiments where only some of the prognostic variables were observed also improved the initial conditions, but at a greater cost. To substantially improve the first guess of the field not observed, some spot observations are needed. The proper scaling of the variables was found to be important for the rate of convergence. This study suggests that scaling factors related to the error variance of the observations give good convergence rates. To show how this technique can be used when observations are general functions of the

  15. Fitting Models of the Population Consequences of Acoustic Disturbance to Data from Marine Mammal Populations

    DTIC Science & Technology

    2012-09-30

    for understanding the at-sea health of (initially) three species of marine mammals: southern and northern elephant seals , and northern right whales...For elephant seals our goal is to build a hierarchical Bayesian model that provides daily estimates of lipid status, as lipid status of the mother...is directly linked to pup survival (McMahon et al. 2000). This model will use the drift dive behavior of elephant seals (Crocker et al. 1997) as

  16. Fitting identity in the reasoned action framework: A meta-analysis and model comparison.

    PubMed

    Paquin, Ryan S; Keating, David M

    2017-01-01

    Several competing models have been put forth regarding the role of identity in the reasoned action framework. The standard model proposes that identity is a background variable. Under a typical augmented model, identity is treated as an additional direct predictor of intention and behavior. Alternatively, it has been proposed that identity measures are inadvertent indicators of an underlying intention factor (e.g., a manifest-intention model). In order to test these competing hypotheses, we used data from 73 independent studies (total N = 23,917) to conduct a series of meta-analytic structural equation models. We also tested for moderation effects based on whether there was a match between identity constructs and the target behaviors examined (e.g., if the study examined a "smoker identity" and "smoking behavior," there would be a match; if the study examined a "health conscious identity" and "smoking behavior," there would not be a match). Average effects among primary reasoned action variables were all substantial, rs = .37-.69. Results gave evidence for the manifest-intention model over the other explanations, and a moderation effect by identity-behavior matching.

  17. Fitting dynamic models with forcing functions: application to continuous glucose monitoring in insulin therapy.

    PubMed

    Lunn, D J; Wei, C; Hovorka, R

    2011-08-15

    The artificial pancreas is an emerging technology to treat type 1 diabetes (T1D). It has the potential to revolutionize diabetes care and improve quality of life. The system requires extensive testing, however, to ensure that it is both effective and safe. Clinical studies are resource demanding and so a principle aim is to develop an in silico population of subjects with T1D on which to conduct pre-clinical testing. This paper aims to reliably characterize the relationship between blood glucose and glucose measured by subcutaneous sensor as a major step towards this goal. Blood-and sensor-glucose are related through a dynamic model, specified in terms of differential equations. Such models can present special challenges for statistical inference, however. In this paper we make use of the BUGS software, which can accommodate a limited class of dynamic models, and it is in this context that we discuss such challenges. For example, we show how dynamic models involving forcing functions can be accommodated. To account for fluctuations away from the dynamic model that are apparent in the observed data, we assume an autoregressive structure for the residual error model. This leads to some identifiability issues but gives very good predictions of virtual data. Our approach is pragmatic and we propose a method to mitigate the consequences of such identifiability issues.

  18. Fitting a Turbulent Cloud Model to CO Observations of Starless Bok Globules

    NASA Astrophysics Data System (ADS)

    Hegmann, M.; Hengel, C.; Röllig, M.; Kegel, W. H.

    We present observations of five starless Bok globules in transitions of 12CO (J=2-1 and {J=3-2}), 13CO (J=2-1), and C18O (J=2-1) which have been obtained at the Heinrich-Hertz-Telescope. For an analysis of the data we use the model of Kegel et al. (see e.g. Piehler & Kegel 1995, A&A 297, 841; Hegmann & Kegel 2000, A&A 359, 405) which describes an isothermal sphere stabilized by turbulent and thermal pressure. This approach deals with the full NLTE radiative transfer problem and accounts for a turbulent velocity field with finite correlation length. By a comparison of observed and calculated line profiles we are able not only to determine the kinetic temperature, hydrogen density and CO coloumn density of the globules, but also to study the properties of the turbulent velocity field, i.e. the variance of its one-point-distribution and its correlation length. We consider our model to be an alternative tool for the evaluation of molecular lines emitted by molecular clouds. The model assumptions are certainly closer to reality than the assumptions behind the standard evaluation models, as for example the LVG model. Our current study shows that that the results obtained from our model can differ significantly from those obtained from a LVG analysis.

  19. SDSS-II: Determination of shape and color parameter coefficients for SALT-II fit model

    SciTech Connect

    Dojcsak, L.; Marriner, J.; /Fermilab

    2010-08-01

    In this study we look at the SALT-II model of Type IA supernova analysis, which determines the distance moduli based on the known absolute standard candle magnitude of the Type IA supernovae. We take a look at the determination of the shape and color parameter coefficients, {alpha} and {beta} respectively, in the SALT-II model with the intrinsic error that is determined from the data. Using the SNANA software package provided for the analysis of Type IA supernovae, we use a standard Monte Carlo simulation to generate data with known parameters to use as a tool for analyzing the trends in the model based on certain assumptions about the intrinsic error. In order to find the best standard candle model, we try to minimize the residuals on the Hubble diagram by calculating the correct shape and color parameter coefficients. We can estimate the magnitude of the intrinsic errors required to obtain results with {chi}{sup 2}/degree of freedom = 1. We can use the simulation to estimate the amount of color smearing as indicated by the data for our model. We find that the color smearing model works as a general estimate of the color smearing, and that we are able to use the RMS distribution in the variables as one method of estimating the correct intrinsic errors needed by the data to obtain the correct results for {alpha} and {beta}. We then apply the resultant intrinsic error matrix to the real data and show our results.

  20. Heterogeneity in Genetic Diversity among Non-Coding Loci Fails to Fit Neutral Coalescent Models of Population History

    PubMed Central

    Peters, Jeffrey L.; Roberts, Trina E.; Winker, Kevin; McCracken, Kevin G.

    2012-01-01

    Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect) to test for deviations from selective neutrality in the gadwall (Anas strepera), a Holarctic duck. Nucleotide diversity among these loci varied by nearly two orders of magnitude (from 0.0004 to 0.029), and this heterogeneity could not be explained by differences in substitution rates alone. Using two different coalescent methods to infer models of population history and then simulating neutral genetic diversity under these models, we found that the observed among-locus heterogeneity in nucleotide diversity was significantly higher than expected for these simple models. Defining more complex models of population history demonstrated that a pre-divergence bottleneck was also unlikely to explain this heterogeneity. However, both selection and interspecific hybridization could account for the heterogeneity observed among loci. Regardless of the cause of the deviation, our results illustrate that violating key assumptions of coalescent models can mislead inferences of population history. PMID:22384117

  1. Improving the Fit of a Land-Surface Model to Data Using its Adjoint

    NASA Astrophysics Data System (ADS)

    Raoult, N.; Jupp, T. E.; Cox, P. M.; Luke, C.

    2015-12-01

    Land-surface models (LSMs) are of growing importance in the world of climate prediction. They are crucial components of larger Earth system models that are aimed at understanding the effects of land surface processes on the global carbon cycle. The Joint UK Land Environment Simulator (JULES) is the land-surface model used by the UK Met Office. It has been automatically differentiated using commercial software from FastOpt, resulting in an analytical gradient, or 'adjoint', of the model. Using this adjoint, the adJULES parameter estimation system has been developed, to search for locally optimum parameter sets by calibrating against observations. adJULES presents an opportunity to confront JULES with many different observations, and make improvements to the model parameterisation. In the newest version of adJULES, multiple sites can be used in the calibration, to giving a generic set of parameters that can be generalised over plant functional types. We present an introduction to the adJULES system and its applications to data from a variety of flux tower sites. We show that calculation of the 2nd derivative of JULES allows us to produce posterior probability density functions of the parameters and how knowledge of parameter values is constrained by observations.

  2. Do telemonitoring projects of heart failure fit the Chronic Care Model?

    PubMed Central

    Willemse, Evi; Adriaenssens, Jef; Dilles, Tinne; Remmen, Roy

    2014-01-01

    This study describes the characteristics of extramural and transmural telemonitoring projects on chronic heart failure in Belgium. It describes to what extent these telemonitoring projects coincide with the Chronic Care Model of Wagner. Background The Chronic Care Model describes essential components for high-quality health care. Telemonitoring can be used to optimise home care for chronic heart failure. It provides a potential prospective to change the current care organisation. Methods This qualitative study describes seven non-invasive home-care telemonitoring projects in patients with heart failure in Belgium. A qualitative design, including interviews and literature review, was used to describe the correspondence of these home-care telemonitoring projects with the dimensions of the Chronic Care Model. Results The projects were situated in primary and secondary health care. Their primary goal was to reduce the number of readmissions for chronic heart failure. None of these projects succeeded in a final implementation of telemonitoring in home care after the pilot phase. Not all the projects were initiated to accomplish all of the dimensions of the Chronic Care Model. A central role for the patient was sparse. Conclusion Limited financial resources hampered continuation after the pilot phase. Cooperation and coordination in telemonitoring appears to be major barriers but are, within primary care as well as between the lines of care, important links in follow-up. This discrepancy can be prohibitive for deployment of good chronic care. Chronic Care Model is recommended as basis for future. PMID:25114664

  3. Analysis of stellar occultation data for planetary atmospheres. I - Model fitting, with application to Pluto

    NASA Technical Reports Server (NTRS)

    Elliot, J. L.; Young, L. A.

    1992-01-01

    Consideration is given to an analytic model for a stellar-occultation light curve developed for a small, spherically symmetric planetary atmosphere that includes thermal and molecular weight gradients in a region that overlies an extinction layer. The model incorporates two equivalent sets of parameters. One set specifies the occultation light curve in terms of signal levels, times, and time intervals. The other set specifies physical parameters of the planetary atmosphere. Equations are given for the transforming between the sets of parameters, including their errors and correlation coefficients. Detailed numerical calculations are presented for a benchmark case. The results obtained are consistent with the isothermal prediction of the 'methane-thermostat' model of Pluto's atmosphere.

  4. Testing Goodness-of-Fit for the Proportional Hazards Model based on Nested Case-Control Data

    PubMed Central

    Lu, Wenbin; Liu, Mengling; Chen, Yi-Hau

    2014-01-01

    Summary Nested case-control sampling is a popular design for large epidemiological cohort studies due to its cost effectiveness. A number of methods have been developed for the estimation of the proportional hazards model with nested case-control data; however, the evaluation of modeling assumption is less attended. In this paper, we propose a class of goodness-of-fit test statistics for testing the proportional hazards assumption based on nested case-control data. The test statistics are constructed based on asymptotically mean-zero processes derived from Samuelsen’s maximum pseudo-likelihood estimation method. In addition, we develop an innovative resampling scheme to approximate the asymptotic distribution of the test statistics while accounting for the dependent sampling scheme of nested case-control design. Numerical studies are conducted to evaluate the performance of our proposed approach, and an application to the Wilms’ Tumor Study is given to illustrate the methodology. PMID:25298193

  5. Modeling and estimation of replication fitness of human immunodeficiency virus type 1 in vitro experiments by using a growth competition assay.

    PubMed

    Wu, Hulin; Huang, Yangxin; Dykes, Carrie; Liu, Dacheng; Ma, Jingming; Perelson, Alan S; Demeter, Lisa M

    2006-03-01

    Growth competition assays have been developed to quantify the relative fitnesses of human immunodeficiency virus (HIV-1) mutants. In this article we develop mathematical models to describe viral/cellular dynamic interactions in the assay experiment, from which new competitive fitness indices or parameters are defined. These indices include the log fitness ratio (LFR), the log relative fitness (LRF), and the production rate ratio (PRR). From the population genetics perspective, we clarify the confusion and correct the inconsistency in the definition of relative fitness in the literature of HIV-1 viral fitness. The LFR and LRF are easier to estimate from the experimental data than the PRR, which was misleadingly defined as the relative fitness in recent HIV-1 research literature. Calculation and estimation methods based on two data points and multiple data points were proposed and were carefully studied. In particular, we suggest using both standard linear regression (method of least squares) and a measurement error model approach for more-accurate estimates of competitive fitness parameters from multiple data points. The developed methodologies are generally applicable to any growth competition assays. A user-friendly computational tool also has been developed and is publicly available on the World Wide Web at http://www.urmc.rochester.edu/bstools/vfitness/virusfitness.htm.

  6. Group Practices and Partnerships: A traditional model that Fits Many Situations.

    PubMed

    Pickering, Stephen R

    2015-01-01

    The traditional group practice model can take many forms, including general practitioners, specialists, and combinations, as well as solo practitioners sharing space and staff, partnerships, and other legal entities. These practices may share some or all staff functions, including contracting for some functions. The essential characteristic is that those treating patients also have full control over and often direct management of the business aspects of the practice. The most important requirements for success in this model may be a common philosophy of patient care and mutual trust regarding business matters.

  7. Meaning-making and the matrix model: does one size really fit all?

    PubMed

    Neimeyer, Robert A

    2005-09-01

    Despite the multifocal complexity of the matrix model (C.R. Snyder & T.R. Elliott, this issue, pp. 1033-1054), its close correspondence with the theoretical dialectics and philosophy of clinical constructivism auger well for its capacity to articulate with existing approaches to graduate education in psychology. In this article points of contact are documented between the two approaches, and a caveat is included about the limits of the matrix model in ensuring greater relevance of clinical training to the settings in which contemporary professionals will work.

  8. A mathematical framework for estimating pathogen transmission fitness and inoculum size using data from a competitive mixtures animal model.

    PubMed

    McCaw, James M; Arinaminpathy, Nimalan; Hurt, Aeron C; McVernon, Jodie; McLean, Angela R

    2011-04-01

    We present a method to measure the relative transmissibility ("transmission fitness") of one strain of a pathogen compared to another. The model is applied to data from "competitive mixtures" experiments in which animals are co-infected with a mixture of two strains. We observe the mixture in each animal over time and over multiple generations of transmission. We use data from influenza experiments in ferrets to demonstrate the approach. Assessment of the relative transmissibility between two strains of influenza is important in at least three contexts: 1) Within the human population antigenically novel strains of influenza arise and compete for susceptible hosts. 2) During a pandemic event, a novel sub-type of influenza competes with the existing seasonal strain(s). The unfolding epidemiological dynamics are dependent upon both the population's susceptibility profile and the inherent transmissibility of the novel strain compared to the existing strain(s). 3) Neuraminidase inhibitors (NAIs), while providing significant potential to reduce transmission of influenza, exert selective pressure on the virus and so promote the emergence of drug-resistant strains. Any adverse outcome due to selection and subsequent spread of an NAI-resistant strain is exquisitely dependent upon the transmission fitness of that strain. Measurement of the transmission fitness of two competing strains of influenza is thus of critical importance in determining the likely time-course and epidemiology of an influenza outbreak, or the potential impact of an intervention measure such as NAI distribution. The mathematical framework introduced here also provides an estimate for the size of the transmitted inoculum. We demonstrate the framework's behaviour using data from ferret transmission studies, and through simulation suggest how to optimise experimental design for assessment of transmissibility. The method introduced here for assessment of mixed transmission events has applicability beyond

  9. Fitting the Mixed Rasch Model to a Reading Comprehension Test: Identifying Reader Types

    ERIC Educational Resources Information Center

    Baghaei, Purya; Carstensen, Claus H.

    2013-01-01

    Standard unidimensional Rasch models assume that persons with the same ability parameters are comparable. That is, the same interpretation applies to persons with identical ability estimates as regards the underlying mental processes triggered by the test. However, research in cognitive psychology shows that persons at the same trait level may…

  10. Assessing Fit of Item Response Models Using the Information Matrix Test

    ERIC Educational Resources Information Center

    Ranger, Jochen; Kuhn, Jorg-Tobias

    2012-01-01

    The information matrix can equivalently be determined via the expectation of the Hessian matrix or the expectation of the outer product of the score vector. The identity of these two matrices, however, is only valid in case of a correctly specified model. Therefore, differences between the two versions of the observed information matrix indicate…

  11. Understanding the Listening Process: Rethinking the "One Size Fits All" Model

    ERIC Educational Resources Information Center

    Wolvin, Andrew

    2013-01-01

    Robert Bostrom's seminal contributions to listening theory and research represent an impressive legacy and provide listening scholars with important perspectives on the complexities of listening cognition and behavior. Bostrom's work provides a solid foundation on which to build models that more realistically explain how listeners function…

  12. Finding the Right Fit: A Comparison of Process Assumptions Underlying Popular Drift-Diffusion Models

    ERIC Educational Resources Information Center

    Ashby, Nathaniel J. S.; Jekel, Marc; Dickert, Stephan; Glöckner, Andreas

    2016-01-01

    Recent research makes increasing use of eye-tracking methodologies to generate and test process models. Overall, such research suggests that attention, generally indexed by fixations (gaze duration), plays a critical role in the construction of preference, although the methods used to support this supposition differ substantially. In two studies…

  13. Are Earth System model software engineering practices fit for purpose? A case study.

    NASA Astrophysics Data System (ADS)

    Easterbrook, S. M.; Johns, T. C.

    2009-04-01

    We present some analysis and conclusions from a case study of the culture and practices of scientists at the Met Office and Hadley Centre working on the development of software for climate and Earth System models using the MetUM infrastructure. The study examined how scientists think about software correctness, prioritize their requirements in making changes, and develop a shared understanding of the resulting models. We conclude that highly customized techniques driven strongly by scientific research goals have evolved for verification and validation of such models. In a formal software engineering context these represents costly, but invaluable, software integration tests with considerable benefits. The software engineering practices seen also exhibit recognisable features of both agile and open source software development projects - self-organisation of teams consistent with a meritocracy rather than top-down organisation, extensive use of informal communication channels, and software developers who are generally also users and science domain experts. We draw some general conclusions on whether these practices work well, and what new software engineering challenges may lie ahead as Earth System models become ever more complex and petascale computing becomes the norm.

  14. Combining IRT and SEM: A Hybrid Model for Fitting Responses and Response Certainties

    ERIC Educational Resources Information Center

    Ferrando, Pere J.; Anguiano-Carrasco, Cristina; Demestre, Josep

    2013-01-01

    This article proposes a model-based procedure, intended for personality measures, for exploiting the auxiliary information provided by the certainty with which individuals answer every item (response certainty). This information is used to (a) obtain more accurate estimates of individual trait levels, and (b) provide a more detailed assessment of…

  15. Where Does Creativity Fit into a Productivist Industrial Model of Knowledge Production?

    ERIC Educational Resources Information Center

    Ghassib, Hisham B.

    2010-01-01

    The basic premise of this paper is the fact that science has become a major industry: the knowledge industry. The paper throws some light on the reasons for the transformation of science from a limited, constrained and marginal craft into a major industry. It, then, presents a productivist industrial model of knowledge production, which shows its…

  16. Fitting the Structured General Diagnostic Model to NAEP Data. Research Report. ETS RR-08-27

    ERIC Educational Resources Information Center

    Xu, Xueli; von Davier, Matthias

    2008-01-01

    Xu and von Davier (2006) demonstrated the feasibility of using the general diagnostic model (GDM) to analyze National Assessment of Educational Progress (NAEP) proficiency data. Their work showed that the GDM analysis not only led to conclusions for gender and race groups similar to those published in the NAEP Report Card, but also allowed…

  17. A Rat Model System to Study Complex Disease Risks, Fitness, Aging, and Longevity

    PubMed Central

    Koch, Lauren Gerard; Britton, Steven L.; Wisløff, Ulrik

    2012-01-01

    The association between low exercise capacity and all-cause morbidity and mortality is statistically strong yet mechanistically unresolved. By connecting clinical observation with a theoretical base, we developed a working hypothesis that variation in capacity for oxygen metabolism is the central mechanistic determinant between disease and health (aerobic hypothesis). As an unbiased test, we show that two-way artificial selective breeding of rats for low and high intrinsic endurance exercise capacity also produces rats that differ for numerous disease risks including the metabolic syndrome, cardiovascular complications, premature aging, and reduced longevity. This contrasting animal model system may prove to be translationally superior, relative to more widely-used simplistic models for understanding geriatric biology and medicine. PMID:22867966

  18. Solution focused nursing: a fitting model for mental health nurses working in a public health paradigm.

    PubMed

    McAllister, Margaret

    2010-01-01

    The Australian Federal Government health agenda is advocating an extension of public health principles across all levels of the health sector. Since mental health nurses have long been proponents of public health and health promoting behaviours, an opportunity exists for this specialty of nursing to extend their influence and contribution within health. Solution focused nursing (SFN), a model that emerged from mental health practice, offers a framework to assist mental health nurses and leaders to more clearly practise public health principles within nursing and articulate that practice - for it is in the articulation of practice that nurses and nursing is made visible and valued. This paper aims to expand on and reiterate the SFN model, showing how it connects to public health principles and develops the mental health nurse's role - particularly in those clinical areas that require more than medical management and illness stabilization.

  19. Numerical Modeling of Two-Dimensional Width-Averaged Flows using Boundary-Fitted Coordinate Systems.

    DTIC Science & Technology

    1985-08-01

    A This report should be cited as follows: Thompson , J . F ., and Bernard, R. S. 1985. "Numerical Modeling of Two...Part 1. Theory," Journal of Fluid Mechanics, Vol 65, No. 657. 8. Thompson , J . F ., ed. 1982a. Numerical Grid Generation, Proceed- ings of a Symposium on...a’ . . . . . . . . , ,- . . . . ... . . ... . • . .r, . . . 12. Thompson , J . F ., and Bernard, R. S. 1985. "WESSEL: Code for f Numerical Simulation of

  20. Properties of and Algorithms for Fitting Three-Way Component Models with Offset Terms

    ERIC Educational Resources Information Center

    Kiers, Henk A. L.

    2006-01-01

    Prior to a three-way component analysis of a three-way data set, it is customary to preprocess the data by centering and/or rescaling them. Harshman and Lundy (1984) considered that three-way data actually consist of a three-way model part, which in fact pertains to ratio scale measurements, as well as additive "offset" terms that turn the ratio…

  1. The Candida albicans Pho4 Transcription Factor Mediates Susceptibility to Stress and Influences Fitness in a Mouse Commensalism Model

    PubMed Central

    Urrialde, Verónica; Prieto, Daniel; Pla, Jesús; Alonso-Monge, Rebeca

    2016-01-01

    The Pho4 transcription factor is required for growth under low environmental phosphate concentrations in Saccharomyces cerevisiae. A characterization of Candida albicans pho4 mutants revealed that these cells are more susceptible to both osmotic and oxidative stress and that this effect is diminished in the presence of 5% CO2 or anaerobiosis, reflecting the relevance of oxygen metabolism in the Pho4-mediated response. A pho4 mutant was as virulent as wild type strain when assayed in the Galleria mellonella infection model and was even more resistant to murine macrophages in ex vivo killing assays. The lack of Pho4 neither impairs the ability to colonize the murine gut nor alters the localization in the gastrointestinal tract. However, we found that Pho4 influenced the colonization of C. albicans in the mouse gut in competition assays; pho4 mutants were unable to attain high colonization levels when inoculated simultaneously with an isogenic wild type strain. Moreover, pho4 mutants displayed a reduced adherence to the intestinal mucosa in a competitive ex vivo assays with wild type cells. In vitro competitive assays also revealed defects in fitness for this mutant compared to the wild type strain. Thus, Pho4, a transcription factor involved in phosphate metabolism, is required for adaptation to stress and fitness in C. albicans. PMID:27458452

  2. The VMC survey - XXIII. Model fitting of light and radial velocity curves of Small Magellanic Cloud classical Cepheids

    NASA Astrophysics Data System (ADS)

    Marconi, M.; Molinaro, R.; Ripepi, V.; Cioni, M.-R. L.; Clementini, G.; Moretti, M. I.; Ragosta, F.; de Grijs, R.; Groenewegen, M. A. T.; Ivanov, V. D.

    2017-04-01

    We present the results of the χ2 minimization model fitting technique applied to optical and near-infrared photometric and radial velocity data for a sample of nine fundamental and three first overtone classical Cepheids in the Small Magellanic Cloud (SMC). The near-infrared photometry (JK filters) was obtained by the European Southern Observatory (ESO) public survey 'VISTA near-infrared Y, J, Ks survey of the Magellanic Clouds system' (VMC). For each pulsator, isoperiodic model sequences have been computed by adopting a non-linear convective hydrodynamical code in order to reproduce the multifilter light and (when available) radial velocity curve amplitudes and morphological details. The inferred individual distances provide an intrinsic mean value for the SMC distance modulus of 19.01 mag and a standard deviation of 0.08 mag, in agreement with the literature. Moreover, the intrinsic masses and luminosities of the best-fitting model show that all these pulsators are brighter than the canonical evolutionary mass-luminosity relation (MLR), suggesting a significant efficiency of core overshooting and/or mass-loss. Assuming that the inferred deviation from the canonical MLR is only due to mass-loss, we derive the expected distribution of percentage mass-loss as a function of both the pulsation period and the canonical stellar mass. Finally, a good agreement is found between the predicted mean radii and current period-radius (PR) relations in the SMC available in the literature. The results of this investigation support the predictive capabilities of the adopted theoretical scenario and pave the way for the application to other extensive data bases at various chemical compositions, including the VMC Large Magellanic Cloud pulsators and Galactic Cepheids with Gaia parallaxes.

  3. Goodness-of-fit test of the stratified mark-specific proportional hazards model with continuous mark

    PubMed Central

    Sun, Yanqing; Li, Mei; Gilbert, Peter B.

    2014-01-01

    Motivated by the need to assess HIV vaccine efficacy, previous studies proposed an extension of the discrete competing risks proportional hazards model, in which the cause of failure is replaced by a continuous mark only observed at the failure time. However the model assumptions may fail in several ways, and no diagnostic testing procedure for this situation has been proposed. A goodness-of-fit test procedure for the stratified mark-specific proportional hazards model in which the regression parameters depend nonparametrically on the mark and the baseline hazards depends nonparametrically on both time and the mark is proposed. The test statistics are constructed based on the weighted cumulative mark-specific martingale residuals. The critical values of the proposed test statistics are approximated using the Gaussian multiplier method. The performance of the proposed tests are examined extensively in simulations for a variety of the models under the null hypothesis and under different types of alternative models. An analysis of the ‘Step’ HIV vaccine efficacy trial using the proposed method is presented. The analysis suggests that the HIV vaccine candidate may increase susceptibility to HIV acquisition. PMID:26461462

  4. Wind Magnetic Clouds for 2010-2012: Model Parameter Fittings, Associated Shock Waves, and Comparisons to Earlier Periods

    NASA Technical Reports Server (NTRS)

    Lepping, R. P.; Wu, C.-C.; Berdichevsky, D. B.; Szabo, A.

    2015-01-01

    We fitted the parameters of magnetic clouds (MCs) as identified in the Wind spacecraft data from early 2010 to the end of 2012 using the model of Lepping, Jones, and Burlaga (J. Geophys. Res. 95, 1195, 1990). The interval contains 48 MCs and 39 magnetic cloud-like (MCL) events. This work is a continuation of MC model fittings of the earlier Wind sets, including those in a recent publication, which covers 2007 to 2009. This period (2010 - 2012) mainly covers the maximum portion of Solar Cycle 24. Between the previous and current interval, we document 5.7 years of MCs observations. For this interval, the occurrence frequency of MCs markedly increased in the last third of the time. In addition, over approximately the last six years, the MC type (i.e. the profile of the magnetic-field direction within an MC, such as North-to-South, South-to-North, all South) dramatically evolved to mainly North-to-South types when compared to earlier years. Furthermore, this evolution of MC type is consistent with global solar magnetic-field changes predicted by Bothmer and Rust (Coronal Mass Ejections, 139, 1997). Model fit parameters for the MCs are listed for 2010 - 2012. For the 5.7 year interval, the observed MCs are found to be slower, weaker in estimated axial magnetic-field intensity, and shorter in duration than those of the earlier 12.3 years, yielding much lower axial magnetic-field fluxes. For about the first half of this 5.7 year period, i.e. up to the end of 2009, there were very few associated MC-driven shock waves (distinctly fewer than the long-term average of about 50 % of MCs). But since 2010, such driven shocks have increased markedly, reflecting similar statistics as the long-term averages. We estimate that 56 % of the total observed MCs have upstream shocks when the full interval of 1995 - 2012 is considered. However, only 28 % of the total number of MCLs have driven shocks over the same period. Some interplanetary shocks during the 2010 - 2012 interval are seen

  5. Wind Magnetic Clouds for 2010 - 2012: Model Parameter Fittings, Associated Shock Waves, and Comparisons to Earlier Periods

    NASA Astrophysics Data System (ADS)

    Lepping, R. P.; Wu, C.-C.; Berdichevsky, D. B.; Szabo, A.

    2015-08-01

    We fitted the parameters of magnetic clouds (MCs) as identified in the Wind spacecraft data from early 2010 to the end of 2012 using the model of Lepping, Jones, and Burlaga ( J. Geophys. Res. 95, 1195, 1990). The interval contains 48 MCs and 39 magnetic cloud-like (MCL) events. This work is a continuation of MC model fittings of the earlier Wind sets, including those in a recent publication, which covers 2007 to 2009. This period (2010 - 2012) mainly covers the maximum portion of Solar Cycle 24. Between the previous and current interval, we document 5.7 years of MCs observations. For this interval, the occurrence frequency of MCs markedly increased in the last third of the time. In addition, over approximately the last six years, the MC type ( i.e. the profile of the magnetic-field direction within an MC, such as North-to-South, South-to-North, all South) dramatically evolved to mainly North-to-South types when compared to earlier years. Furthermore, this evolution of MC type is consistent with global solar magnetic-field changes predicted by Bothmer and Rust ( Coronal Mass Ejections, 139, 1997). Model fit parameters for the MCs are listed for 2010 - 2012. For the 5.7 year interval, the observed MCs are found to be slower, weaker in estimated axial magnetic-field intensity, and shorter in duration than those of the earlier 12.3 years, yielding much lower axial magnetic-field fluxes. For about the first half of this 5.7 year period, i.e. up to the end of 2009, there were very few associated MC-driven shock waves (distinctly fewer than the long-term average of about 50 % of MCs). But since 2010, such driven shocks have increased markedly, reflecting similar statistics as the long-term averages. We estimate that 56 % of the total observed MCs have upstream shocks when the full interval of 1995 - 2012 is considered. However, only 28 % of the total number of MCLs have driven shocks over the same period. Some interplanetary shocks during the 2010 - 2012 interval are

  6. How Fitness Reduced, Antimicrobial Resistant Bacteria Survive and Spread: A Multiple Pig - Multiple Bacterial Strain Model

    PubMed Central

    Græsbøll, Kaare; Nielsen, Søren Saxmose; Toft, Nils; Christiansen, Lasse Engbo

    2014-01-01

    More than 30% of E. coli strains sampled from pig farms in Denmark over the last five years were resistant to the commonly used antimicrobial tetracycline. This raises a number of questions: How is this high level sustained if resistant bacteria have reduced growth rates? Given that there are multiple susceptible and resistant bacterial strains in the pig intestines, how can we describe their coexistence? To what extent does the composition of these multiple strains in individual pigs influence the total bacterial population of the pig pen? What happens to a complex population when antimicrobials are used? To investigate these questions, we created a model where multiple strains of bacteria coexist in the intestines of pigs sharing a pen, and explored the parameter limits of a stable system; both with and without an antimicrobial treatment. The approach taken is a deterministic bacterial population model with stochastic elements of bacterial distributions and transmission. The rates that govern the model are process-oriented to represent growth, excretion, and uptake from environment, independent of herd and meta-population structures. Furthermore, an entry barrier and elimination process for the individual strains in each pig were implemented. We demonstrate how competitive growth between multiple bacterial strains in individual pigs, and the transmission between pigs in a pen allow for strains of antimicrobial resistant bacteria to persist in a pig population to different extents, and how quickly they can become dominant if antimicrobial treatment is initiated. The level of spread depends in a non-linear way of the parameters that govern excretion and uptake. Furthermore, the sampling of initial distributions of strains and stochastic transmission events give rise to large variation in how homogenous and how resistant the bacterial population becomes. Most important: resistant bacteria are demonstrated to survive with a disadvantage in growth rate of well over 10

  7. Experimentally fitted biodynamic models for pedestrian-structure interaction in walking situations

    NASA Astrophysics Data System (ADS)

    Toso, Marcelo André; Gomes, Herbert Martins; da Silva, Felipe Tavares; Pimentel, Roberto Leal

    2016-05-01

    The interaction between moving humans and structures usually occurs in slender structures in which the level of vibration is potentially high. Furthermore, there is the addition of mass to the structural system due to the presence of people and an increase in damping due to the human body´s ability to absorb vibrational energy. In this paper, a test campaign is presented to obtain parameters for a single degree of freedom (SDOF) biodynamic model that represents the action of a walking pedestrian in the vertical direction. The parameters of this model are the mass (m), damping (c) and stiffness (k). The measurements were performed on a force platform, and the inputs were the spectral acceleration amplitudes of the first three harmonics at the waist level of the test subjects and the corresponding amplitudes of the first three harmonics of the vertical ground reaction force. This leads to a system of nonlinear equations that is solved using a gradient-based optimization algorithm. A set of individuals took part in the tests to ensure inter-subject variability, and, regression expressions and an artificial neural network (ANN) were used to relate the biodynamic parameters to the pacing rate and the body mass of the pedestrians. The results showed some scatter in damping and stiffness that could not be precisely correlated with the masses and pacing rates of the subjects. The use of the ANN resulted in significant improvements in the parameter expressions with a low uncertainty. Finally, the measured vertical accelerations on a prototype footbridge show the adequacy of the numerical model for the representation of the effects of walking pedestrians on a structure. The results are consistent for many crowd densities.

  8. Fitting and using model Hamiltonian in non-adiabatic molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Smale, Jonathan Ross

    In order to study computationally increasingly complex systems using theoretical methods model, Hamiltonians are required to accurately describe the potential energy surface they represent. Also ab-initio methods improve the calculation of the excited states of these complex systems becomes increasingly feasible. One such model Hamiltonian described herein, the Vibronic Coupling Hamiltonian, has previously shown its versatility and ability to describe a variety of non-adiabatic problems. This thesis describes a new method, a genetic algorithm, for the parameterisation of the Vibronic Coupling Hamiltonian to describe both previously calculated potential energy surfaces (allene and pentatetraene) and newly calculated (cyclo-butadiene and toluene) potential energy surfaces. In order to test this genetic algorithm, quantum nuclear dynamics calculations were performed using the multi-configurational time dependent Hartree method and the results compared to experiment..

  9. Hierarchical winner-take-all particle swarm optimization social network for neural model fitting.

    PubMed

    Coventry, Brandon S; Parthasarathy, Aravindakshan; Sommer, Alexandra L; Bartlett, Edward L

    2017-02-01

    Particle swarm optimization (PSO) has gained widespread use as a general mathematical programming paradigm and seen use in a wide variety of optimization and machine learning problems. In this work, we introduce a new variant on the PSO social network and apply this method to the inverse problem of input parameter selection from recorded auditory neuron tuning curves. The topology of a PSO social network is a major contributor to optimization success. Here we propose a new social network which draws influence from winner-take-all coding found in visual cortical neurons. We show that the winner-take-all network performs exceptionally well on optimization problems with greater than 5 dimensions and runs at a lower iteration count as compared to other PSO topologies. Finally we show that this variant of PSO is able to recreate auditory frequency tuning curves and modulation transfer functions, making it a potentially useful tool for computational neuroscience models.

  10. The computation of generalized cross-validation functions through householder tridiagonalization with applications to the fitting of interaction spline models

    NASA Technical Reports Server (NTRS)

    Gu, Chong; Bates, Douglas M.; Chen, Zehua; Wahba, Grace

    1989-01-01

    An efficient algorithm for computing the generalized cross-validation function for the general cross-validated regularization/smoothing problem is provided. This algorithm is appropriate for problems where no natural structure is available, and the regularization/smoothing problem is solved (exactly) in a reproducing kernel Hilbert space. It is particularly appropriate for certain multivariate smoothing problems with irregularly spaced data, and certain remote sensing problems, such as those that occur in meteorology, where the sensors are arranged irregularly. The algorithm is applied to the fitting of interaction spline models with irregularly spaced data and two smoothing parameters; favorable timing results are presented. The algorithm may be extended to the computation of certain generalized maximum likelihood (GML) functions. Application of the GML algorithm to a problem in numerical weather forecasting, and to a broad class of hypothesis testing problems, is noted.

  11. Carotid wall volume quantification from magnetic resonance images using deformable model fitting and learning-based correction of systematic errors

    NASA Astrophysics Data System (ADS)

    Hameeteman, K.; van't Klooster, R.; Selwaness, M.; van der Lugt, A.; Witteman, J. C. M.; Niessen, W. J.; Klein, S.

    2013-03-01

    We present a method for carotid vessel wall volume quantification from magnetic resonance imaging (MRI). The method combines lumen and outer wall segmentation based on deformable model fitting with a learning-based segmentation correction step. After selecting two initialization points, the vessel wall volume in a region around the bifurcation is automatically determined. The method was trained on eight datasets (16 carotids) from a population-based study in the elderly for which one observer manually annotated both the lumen and outer wall. An evaluation was carried out on a separate set of 19 datasets (38 carotids) from the same study for which two observers made annotations. Wall volume and normalized wall index measurements resulting from the manual annotations were compared to the automatic measurements. Our experiments show that the automatic method performs comparably to the manual measurements. All image data and annotations used in this study together with the measurements are made available through the website http://ergocar.bigr.nl.

  12. Simultaneous estimation of plasma parameters from spectroscopic data of neutral helium using least square fitting of CR-model

    NASA Astrophysics Data System (ADS)

    Jain, Jalaj; Prakash, Ram; Vyas, Gheesa Lal; Pal, Udit Narayan; Chowdhuri, Malay Bikas; Manchanda, Ranjana; Halder, Nilanjan; Choyal, Yaduvendra

    2015-12-01

    In the present work an effort has been made to estimate the plasma parameters simultaneously like—electron density, electron temperature, ground state atom density, ground state ion density and metastable state density from the observed visible spectra of penning plasma discharge (PPD) source using least square fitting. The analysis is performed for the prominently observed neutral helium lines. The atomic data and analysis structure (ADAS) database is used to provide the required collisional-radiative (CR) photon emissivity coefficients (PECs) values under the optical thin plasma condition in the analysis. With this condition the estimated plasma temperature from the PPD is found rather high. It is seen that the inclusion of opacity in the observed spectral lines through PECs and addition of diffusion of neutrals and metastable state species in the CR-model code analysis improves the electron temperature estimation in the simultaneous measurement.

  13. A MULTIVARIATE FIT LUMINOSITY FUNCTION AND WORLD MODEL FOR LONG GAMMA-RAY BURSTS

    SciTech Connect

    Shahmoradi, Amir

    2013-04-01

    It is proposed that the luminosity function, the rest-frame spectral correlations, and distributions of cosmological long-duration (Type-II) gamma-ray bursts (LGRBs) may be very well described as a multivariate log-normal distribution. This result is based on careful selection, analysis, and modeling of LGRBs' temporal and spectral variables in the largest catalog of GRBs available to date: 2130 BATSE GRBs, while taking into account the detection threshold and possible selection effects. Constraints on the joint rest-frame distribution of the isotropic peak luminosity (L{sub iso}), total isotropic emission (E{sub iso}), the time-integrated spectral peak energy (E{sub p,z}), and duration (T{sub 90,z}) of LGRBs are derived. The presented analysis provides evidence for a relatively large fraction of LGRBs that have been missed by the BATSE detector with E{sub iso} extending down to {approx}10{sup 49} erg and observed spectral peak energies (E{sub p} ) as low as {approx}5 keV. LGRBs with rest-frame duration T{sub 90,z} {approx}< 1 s or observer-frame duration T{sub 90} {approx}< 2 s appear to be rare events ({approx}< 0.1% chance of occurrence). The model predicts a fairly strong but highly significant correlation ({rho} = 0.58 {+-} 0.04) between E{sub iso} and E{sub p,z} of LGRBs. Also predicted are strong correlations of L{sub iso} and E{sub iso} with T{sub 90,z} and moderate correlation between L{sub iso} and E{sub p,z}. The strength and significance of the correlations found encourage the search for underlying mechanisms, though undermine their capabilities as probes of dark energy's equation of state at high redshifts. The presented analysis favors-but does not necessitate-a cosmic rate for BATSE LGRBs tracing metallicity evolution consistent with a cutoff Z/Z{sub Sun} {approx} 0.2-0.5, assuming no luminosity-redshift evolution.

  14. Global fit analysis of glucose binding curves reveals a minimal model for kinetic cooperativity in human glucokinase.

    PubMed

    Larion, Mioara; Miller, Brian G

    2010-10-19

    Human pancreatic glucokinase is a monomeric enzyme that displays kinetic cooperativity, a feature that facilitates enzyme-mediated regulation of blood glucose levels in the body. Two theoretical models have been proposed to describe the non-Michaelis-Menten behavior of human glucokinase. The mnemonic mechanism postulates the existence of one thermodynamically favored enzyme conformation in the absence of glucose, whereas the ligand-induced slow transition model (LIST) requires a preexisting equilibrium between two enzyme species that interconvert with a rate constant slower than turnover. To investigate whether either of these mechanisms is sufficient to describe glucokinase cooperativity, a transient-state kinetic analysis of glucose binding to the enzyme was undertaken. A complex, time-dependent change in enzyme intrinsic fluorescence was observed upon exposure to glucose, which is best described by an analytical solution comprised of the sum of four exponential terms. Transient-state glucose binding experiments conducted in the presence of increasing glycerol concentrations demonstrate that three of the observed rate constants decrease with increasing viscosity. Global fit analyses of experimental glucose binding curves are consistent with a kinetic model that is an extension of the LIST mechanism with a total of four glucose-bound binary complexes. The kinetic model presented herein suggests that glucokinase samples multiple conformations in the absence of ligand and that this conformational heterogeneity persists even after the enzyme associates with glucose.

  15. A Comparison of Two-Stage Approaches for Fitting Nonlinear Ordinary Differential Equation (ODE) Models with Mixed Effects

    PubMed Central

    Chow, Sy-Miin; Bendezú, Jason J.; Cole, Pamela M.; Ram, Nilam

    2016-01-01

    Several approaches currently exist for estimating the derivatives of observed data for model exploration purposes, including functional data analysis (FDA), generalized local linear approximation (GLLA), and generalized orthogonal local derivative approximation (GOLD). These derivative estimation procedures can be used in a two-stage process to fit mixed effects ordinary differential equation (ODE) models. While the performance and utility of these routines for estimating linear ODEs have been established, they have not yet been evaluated in the context of nonlinear ODEs with mixed effects. We compared properties of the GLLA and GOLD to an FDA-based two-stage approach denoted herein as functional ordinary differential equation with mixed effects (FODEmixed) in a Monte Carlo study using a nonlinear coupled oscillators model with mixed effects. Simulation results showed that overall, the FODEmixed outperformed both the GLLA and GOLD across all the embedding dimensions considered, but a novel use of a fourth-order GLLA approach combined with very high embedding dimensions yielded estimation results that almost paralleled those from the FODEmixed. We discuss the strengths and limitations of each approach and demonstrate how output from each stage of FODEmixed may be used to inform empirical modeling of young children’s self-regulation. PMID:27391255

  16. A Comparison of Two-Stage Approaches for Fitting Nonlinear Ordinary Differential Equation Models with Mixed Effects.

    PubMed

    Chow, Sy-Miin; Bendezú, Jason J; Cole, Pamela M; Ram, Nilam

    2016-01-01

    Several approaches exist for estimating the derivatives of observed data for model exploration purposes, including functional data analysis (FDA; Ramsay & Silverman, 2005 ), generalized local linear approximation (GLLA; Boker, Deboeck, Edler, & Peel, 2010 ), and generalized orthogonal local derivative approximation (GOLD; Deboeck, 2010 ). These derivative estimation procedures can be used in a two-stage process to fit mixed effects ordinary differential equation (ODE) models. While the performance and utility of these routines for estimating linear ODEs have been established, they have not yet been evaluated in the context of nonlinear ODEs with mixed effects. We compared properties of the GLLA and GOLD to an FDA-based two-stage approach denoted herein as functional ordinary differential equation with mixed effects (FODEmixed) in a Monte Carlo (MC) study using a nonlinear coupled oscillators model with mixed effects. Simulation results showed that overall, the FODEmixed outperformed both the GLLA and GOLD across all the embedding dimensions considered, but a novel use of a fourth-order GLLA approach combined with very high embedding dimensions yielded estimation results that almost paralleled those from the FODEmixed. We discuss the strengths and limitations of each approach and demonstrate how output from each stage of FODEmixed may be used to inform empirical modeling of young children's self-regulation.

  17. Fitting a linear-linear piecewise growth mixture model with unknown knots: A comparison of two common approaches to inference.

    PubMed

    Kohli, Nidhi; Hughes, John; Wang, Chun; Zopluoglu, Cengiz; Davison, Mark L

    2015-06-01

    A linear-linear piecewise growth mixture model (PGMM) is appropriate for analyzing segmented (disjointed) change in individual behavior over time, where the data come from a mixture of 2 or more latent classes, and the underlying growth trajectories in the different segments of the developmental process within each latent class are linear. A PGMM allows the knot (change point), the time of transition from 1 phase (segment) to another, to be estimated (when it is not known a priori) along with the other model parameters. To assist researchers in deciding which estimation method is most advantageous for analyzing this kind of mixture data, the current research compares 2 popular approaches to inference for PGMMs: maximum likelihood (ML) via an expectation-maximization (EM) algorithm, and Markov chain Monte Carlo (MCMC) for Bayesian inference. Monte Carlo simulations were carried out to investigate and compare the ability of the 2 approaches to recover the true parameters in linear-linear PGMMs with unknown knots. The results show that MCMC for Bayesian inference outperformed ML via EM in nearly every simulation scenario. Real data examples are also presented, and the corresponding computer codes for model fitting are provided in the Appendix to aid practitioners who wish to apply this class of models.

  18. The Model Size Effect in SEM: Inflated Goodness-of-Fit Statistics Are due to the Size of the Covariance Matrix

    ERIC Educational Resources Information Center

    Moshagen, Morten

    2012-01-01

    The size of a model has been shown to critically affect the goodness of approximation of the model fit statistic "T" to the asymptotic chi-square distribution in finite samples. It is not clear, however, whether this "model size effect" is a function of the number of manifest variables, the number of free parameters, or both. It is demonstrated by…

  19. Viral Decay Dynamics and Mathematical Modeling of Treatment Response: Evidence of Lower in vivo Fitness of HIV-1 Subtype C

    PubMed Central

    Shet, Anita; Nagaraja, Pradeep

    2016-01-01

    Background: Despite the high prevalence of HIV-1 subtype C (HIV-1C) worldwide, information on HIV-1C viral dynamics and response to antiretroviral therapy (ART) is limited. We sought to measure viral load decay dynamics during treatment and estimate the within-host basic reproductive ratio, R0, and the critical efficacy, εc, for successful treatment of HIV-1C infection. Methods: Individuals initiated on first-line ART in India and monitored for 6 months of treatment were considered. Viral load, CD4+ count, and adherence data were collected at baseline, 4, 12, 16 and 24 weeks after ART initiation. Drug resistance genotyping was performed at baseline. R0 and εc were estimated using a mathematical model. Results: Among 257 patients with complete data, mean baseline viral load was 5.7 log10 copies per milliliter and median CD4+ count was 165 cells per cubic millimeter. Primary drug resistance was present in 3.1% at baseline. At 6 months, 87.5% had undetectable viral load, indicating excellent response to ART despite high baseline viremia. After excluding those with transmitted resistance, suboptimal adherence and viral rebound, data from 112 patients were analyzed using a mathematical model. We estimated the median R0 to be 5.3. The corresponding εc was ∼0.8. Conclusions: These estimates of R0 and εc are smaller than current estimates for HIV-1B, suggesting that HIV-1C exhibits lower in vivo fitness compared with HIV-1B, which allows successful treatment despite high baseline viral loads. The lower fitness, and potentially lower virulence, together with high viral loads may underlie the heightened transmission potential of HIV-1C and its growing global spread. PMID:27273158

  20. Stress physiology in marine mammals: how well do they fit the terrestrial model?

    PubMed

    Atkinson, Shannon; Crocker, Daniel; Houser, Dorian; Mashburn, Kendall

    2015-07-01

    Stressors are commonly accepted as the causal factors, either internal or external, that evoke physiological responses to mediate the impact of the stressor. The majority of research on the physiological stress response, and costs incurred to an animal, has focused on terrestrial species. This review presents current knowledge on the physiology of the stress response in a lesser studied group of mammals, the marine mammals. Marine mammals are an artificial or pseudo grouping from a taxonomical perspective, as this group represents several distinct and diverse orders of mammals. However, they all are fully or semi-aquatic animals and have experienced selective pressures that have shaped their physiology in a manner that differs from terrestrial relatives. What these differences are and how they relate to the stress response is an efflorescent topic of study. The identification of the many facets of the stress response is critical to marine mammal management and conservation efforts. Anthropogenic stressors in marine ecosystems, including ocean noise, pollution, and fisheries interactions, are increasing and the dramatic responses of some marine mammals to these stressors have elevated concerns over the impact of human-related activities on a diverse group of animals that are difficult to monitor. This review covers the physiology of the stress response in marine mammals and places it in context of what is known from research on terrestrial mammals, particularly with respect to mediator activity that diverges from generalized terrestrial models. Challenges in conducting research on stress physiology in marine mammals are discussed and ways to overcome these challenges in the future are suggested.

  1. The role of social capital and community belongingness for exercise adherence: An exploratory study of the CrossFit gym model.

    PubMed

    Whiteman-Sandland, Jessica; Hawkins, Jemma; Clayton, Debbie

    2016-08-23

    This is the first study to measure the 'sense of community' reportedly offered by the CrossFit gym model. A cross-sectional study adapted Social Capital and General Belongingness scales to compare perceptions of a CrossFit gym and a traditional gym. CrossFit gym members reported significantly higher levels of social capital (both bridging and bonding) and community belongingness compared with traditional gym members. However, regression analysis showed neither social capital, community belongingness, nor gym type was an independent predictor of gym attendance. Exercise and health professionals may benefit from evaluating further the 'sense of community' offered by gym-based exercise programmes.

  2. Atmospheric Properties of T Dwarfs Inferred from Model Fits at Low Spectral Resolution as Exoplanet Atmosphere Analogs

    NASA Astrophysics Data System (ADS)

    Godfrey, Paige A.

    2017-01-01

    Exoplanet direct detections are reaching the temperature regime of cool brown dwarfs, motivating further understanding of the coolest substellar atmospheres. These objects, T and Y dwarfs, are numerous and isolated in the field, thus making them easier to study in detail than objects in companion systems. Brown dwarf spectral types are derived from spectral morphology and generally appear to correspond with decreasing mass and effective temperature (Teff). However, spectral subclasses of the colder objects do not share this monotonic temperature correlation, indicating that secondary parameters (gravity, metallicity, dust) significantly influence spectral morphology. These secondary atmospheric parameters can provide insight into age and formation mechanism. We seek to disentangle the fundamental parameters that underlie the spectral morphology of T dwarfs, the coolest fully populated spectral class of brown dwarfs, using comparisons to atmospheric models. We investigate the relationship between spectral type and Teff from the best fit model parameters for a sample of 152 T dwarfs with low resolution (R~75-100) near-infrared SpeX Prism spectra. We use synthetic spectra from four model grids (Saumon & Marley 2008, Morley+ 2012, Saumon+ 2012, and BT Settl 2013) and a Markov-Chain Monte Carlo (MCMC) analysis to determine robust best fit parameters with uncertainties. To evaluate the consistency of each model grid, we perform our analysis on the full spectrum and on narrower wavelength ranges where directly detected exoplanets are typically characterized. We provide foundational assessments of the factors that affect T dwarf spectral morphology to prescribe the best approach to interpreting spectra of cool substellar objects. Using T dwarfs as exoplanet analogs, we create spectral templates from observed spectra for comparison to cool companion spectra of high contrast imaged objects. Our analysis of these proof-of-concept cases provide the backbone for interpreting

  3. An Investigation of the Performance of the Generalized S-X[superscript 2] Item-Fit Index for Polytomous IRT Models. ACT Research Report Series, 2007-1

    ERIC Educational Resources Information Center

    Kang, Taehoon; Chen, Troy T.

    2007-01-01

    Orlando and Thissen (2000, 2003) proposed an item-fit index, S-X[superscript 2], for dichotomous item response theory (IRT) models, which has performed better than traditional item-fit statistics such as Yen's (1981) Q[subscript 1] and McKinley and Mill's (1985) G[superscript 2]. This study extends the utility of S-X[superscript 2] to polytomous…

  4. A global fit of the γ-ray galactic center excess within the scalar singlet Higgs portal model

    SciTech Connect

    Cuoco, Alessandro; Eiteneuer, Benedikt; Heisig, Jan; Krämer, Michael

    2016-06-28

    We analyse the excess in the γ-ray emission from the center of our galaxy observed by Fermi-LAT in terms of dark matter annihilation within the scalar Higgs portal model. In particular, we include the astrophysical uncertainties from the dark matter distribution and allow for unspecified additional dark matter components. We demonstrate through a detailed numerical fit that the strength and shape of the γ-ray spectrum can indeed be described by the model in various regions of dark matter masses and couplings. Constraints from invisible Higgs decays, direct dark matter searches, indirect searches in dwarf galaxies and for γ-ray lines, and constraints from the dark matter relic density reduce the parameter space to dark matter masses near the Higgs resonance. We find two viable regions: one where the Higgs-dark matter coupling is of O(10{sup −2}), and an additional dark matter component beyond the scalar WIMP of our model is preferred, and one region where the Higgs-dark matter coupling may be significantly smaller, but where the scalar WIMP constitutes a significant fraction or even all of dark matter. Both viable regions are hard to probe in future direct detection and collider experiments.

  5. Adipose Tissue - Adequate, Accessible Regenerative Material

    PubMed Central

    Kolaparthy, Lakshmi Kanth.; Sanivarapu, Sahitya; Moogla, Srinivas; Kutcham, Rupa Sruthi

    2015-01-01

    The potential use of stem cell based therapies for the repair and regeneration of various tissues offers a paradigm shift that may provide alternative therapeutic solutions for a number of diseases. The use of either embryonic stem cells (ESCs) or induced pluripotent stem cells in clinical situations is limited due to cell regulations and to technical and ethical considerations involved in genetic manipulation of human ESCs, even though these cells are highly beneficial. Mesenchymal stem cells seen to be an ideal population of stem cells in particular, Adipose derived stem cells (ASCs) which can be obtained in large number and easily harvested from adipose tissue. It is ubiquitously available and has several advantages compared to other sources as easily accessible in large quantities with minimal invasive harvesting procedure, and isolation of adipose derived mesenchymal stem cells yield a high amount of stem cells which is essential for stem cell based therapies and tissue engineering. Recently, periodontal tissue regeneration using ASCs has been examined in some animal models. This method has potential in the regeneration of functional periodontal tissues because various secreted growth factors from ASCs might not only promote the regeneration of periodontal tissues but also encourage neovascularization of the damaged tissues. This review summarizes the sources, isolation and characteristics of adipose derived stem cells and its potential role in periodontal regeneration is discussed. PMID:26634060

  6. A functional tonB gene is required for both virulence and competitive fitness in a chinchilla model of Haemophilus influenzae otitis media

    PubMed Central

    2012-01-01

    Background Haemophilus influenzae requires heme for aerobic growth and possesses multiple mechanisms to obtain this essential nutrient. Methods An insertional mutation in tonB was constructed and the impact of the mutation on virulence and fitness in a chinchilla model of otitis media was determined. The tonB insertion mutant strain was significantly impacted in both virulence and fitness as compared to the wildtype strain in this model. Conclusions The tonB gene of H. influenzae is required for the establishment and maintenance of middle ear infection in this chinchilla model of bacterial disease. PMID:22731867

  7. One Model Fits All: Explaining Many Aspects of Number Comparison within a Single Coherent Model-A Random Walk Account

    ERIC Educational Resources Information Center

    Reike, Dennis; Schwarz, Wolf

    2016-01-01

    The time required to determine the larger of 2 digits decreases with their numerical distance, and, for a given distance, increases with their magnitude (Moyer & Landauer, 1967). One detailed quantitative framework to account for these effects is provided by random walk models. These chronometric models describe how number-related noisy…

  8. Model based period analysis of absolute and relative survival with R: data preparation, model fitting and derivation of survival estimates.

    PubMed

    Holleczek, Bernd; Brenner, Hermann

    2013-05-01

    Period analysis is increasingly employed in analyses of long-term survival of patients with chronic diseases such as cancer, as it derives more up-to-date survival estimates than traditional cohort based approaches. It has recently been extended with regression modelling using generalized linear models, which increases the precision of the survival estimates and enables to assess and account for effects of additional covariates. This paper provides a detailed presentation how model based period analysis may be used to derive population-based absolute and relative survival estimates using the freely available R language and statistical environment and already available R programs for period analysis. After an introduction of the underlying regression model and a description of the software tools we provide a step-by-step implementation of two regression models in R and illustrate how estimates and a test for trend over time in relative survival may be derived using data from a population based cancer registry.

  9. Measuring Your Fitness Level

    MedlinePlus

    Healthy Lifestyle Fitness Ready to start a fitness program? Measure your fitness level with a few simple tests. ... 14, 2017 Original article: http://www.mayoclinic.org/healthy-lifestyle/fitness/in-depth/fitness/art-20046433 . Mayo Clinic ...

  10. Analysis of response to 20 generations of selection for body composition in mice: fit to infinitesimal model assumptions

    PubMed Central

    Martinez, Victor; Bünger, Lutz; Hill, William G

    2000-01-01

    Data were analysed from a divergent selection experiment for an indicator of body composition in the mouse, the ratio of gonadal fat pad to body weight (GFPR). Lines were selected for 20 generations for fat (F), lean (L) or were unselected (C), with three replicates of each. Selection was within full-sib families, 16 families per replicate for the first seven generations, eight subsequently. At generation 20, GFPR in the F lines was twice and in the L lines half that of C. A log transformation removed both asymmetry of response and heterogeneity of variance among lines, and so was used throughout. Estimates of genetic variance and heritability (approximately 50%) obtained using REML with an animal model were very similar, whether estimated from the first few generations of selection, or from all 20 generations, or from late generations having fitted pedigree. The estimates were also similar when estimated from selected or control lines. Estimates from REML also agreed with estimates of realised heritability. The results all accord with expectations under the infinitesimal model, despite the four-fold changes in mean. Relaxed selection lines, derived from generation 20, showed little regression in fatness after 40 generations without selection. PMID:14736404

  11. Fit of Item Response Theory Models: A Survey of Data from Several Operational Tests. Research Report. ETS RR-11-29

    ERIC Educational Resources Information Center

    Sinharay, Sandip; Haberman, Shelby J.; Jia, Helena

    2011-01-01

    Standard 3.9 of the "Standards for Educational and Psychological Testing" (American Educational Research Association, American Psychological Association, & National Council for Measurement in Education, 1999) demands evidence of model fit when an item response theory (IRT) model is used to make inferences from a data set. We applied two recently…

  12. Fitting New Measurement Models to GRE General Test Constructed-Response Item Data. GRE Board Professional Report No. 89-11P.

    ERIC Educational Resources Information Center

    Bennett, Randy Elliot; And Others

    This exploratory study applied two new cognitively sensitive measurement models to constructed-response quantitative data. The models, intended to produce qualitative characteristics of examinee performance, were fitted to algebra word problem solutions produced by 285 examinees taking the Graduate Record Examinations (GRE) General Test. The two…

  13. A Model for the Inclusion of a Physical Fitness and Health Promotion Component in a Chemical Abuse Treatment Program.

    ERIC Educational Resources Information Center

    Fridinger, Fred; Dehart, Beverly

    1993-01-01

    Describes treatment program at Charter Hospital in Fort Worth, Texas, which incorporates comprehensive medical examination, fitness and nutritional screenings, and appropriate exercise activities into alcohol and other substance abuse treatment. Notes that educational sessions are offered on health fitness, risk reduction, stress management,…

  14. [Responses to "The Congruence Myth: An Analysis of the Efficacy of the Person-Environment Fit Model."

    ERIC Educational Resources Information Center

    Dawis, Rene V.; Gati, Itamar; Hesketh, Beryl; Prediger, Dale J.; Rounds, James; McKenna, Molly C.; Hubert, Lawrence; Day, Susan X.; Tracey, Terence J. G.; Darcy, Maria; Kovalski, Theresa M.

    2000-01-01

    Includes "P-E [Person-Environment] Fit as Paradigm" (Dawis); "Pitfalls of Congruence Research" (Gati); "The Next Millennium of 'Fit' Research" (Hesketh); "Holland's Hexagon Is Alive and Well--Though Somewhat out of Shape" (Prediger); "Tinsley on Holland: A Misshapen Argument" (Rounds, McKenna,…

  15. A simple epidemiological model for populations in the wild with Allee effects and disease-modified fitness.

    PubMed

    Kang, Yun; Castillo-Chavez, Carlos

    2014-01-01

    The study of the dynamics of human infectious disease using deterministic models is typically carried out under the assumption that a critical mass of individuals is available and involved in the transmission process. However, in the study of animal disease dynamics where demographic considerations often play a significant role, this assumption must be weakened. Models of the dynamics of animal populations often naturally assume that the presence of a minimal number of individuals is essential to avoid extinction. In the ecological literature, this a priori requirement is commonly incorporated as an Allee effect. The focus here is on the study disease dynamics under the assumption that a critical mass of susceptible individuals is required to guarantee the population's survival. Specifically, the emphasis is on the study of the role of an Allee effect on a Susceptible-Infectious (SI) model where the possibility that susceptible and infected individuals reproduce, with the S-class the best fit. It is further assumed that infected individuals loose some of their ability to compete for resources, the cost imposed by the disease. These features are set in motion in as simple model as possible. They turn out to lead to a rich set of dynamical outcomes. This toy model supports the possibility of multi-stability (hysteresis), saddle node and Hopf bifurcations, and catastrophic events (disease-induced extinction). The analyses provide a full picture of the system under disease-free dynamics including disease-induced extinction and proceed to identify required conditions for disease persistence. We conclude that increases in (i) the maximum birth rate of a species, or (ii) in the relative reproductive ability of infected individuals, or (iii) in the competitive ability of a infected individuals at low density levels, or in (iv) the per-capita death rate (including disease-induced) of infected individuals, can stabilize the system (resulting in disease persistence). We

  16. A simple epidemiological model for populations in the wild with Allee effects and disease-modified fitness

    PubMed Central

    Kang, Yun; Castillo-Chavez, Carlos

    2014-01-01

    The study of the dynamics of human infectious disease using deterministic models is typically carried out under the assumption that a critical mass of individuals is available and involved in the transmission process. However, in the study of animal disease dynamics where demographic considerations often play a significant role, this assumption must be weakened. Models of the dynamics of animal populations often naturally assume that the presence of a minimal number of individuals is essential to avoid extinction. In the ecological literature, this a priori requirement is commonly incorporated as an Allee effect. The focus here is on the study disease dynamics under the assumption that a critical mass of susceptible individuals is required to guarantee the population's survival. Specifically, the emphasis is on the study of the role of an Allee effect on a Susceptible-Infectious (SI) model where the possibility that susceptible and infected individuals reproduce, with the S-class the best fit. It is further assumed that infected individuals loose some of their ability to compete for resources, the cost imposed by the disease. These features are set in motion in as simple model as possible. They turn out to lead to a rich set of dynamical outcomes. This toy model supports the possibility of multi-stability (hysteresis), saddle node and Hopf bifurcations, and catastrophic events (disease-induced extinction). The analyses provide a full picture of the system under disease-free dynamics including disease-induced extinction and proceed to identify required conditions for disease persistence. We conclude that increases in (i) the maximum birth rate of a species, or (ii) in the relative reproductive ability of infected individuals, or (iii) in the competitive ability of a infected individuals at low density levels, or in (iv) the per-capita death rate (including disease-induced) of infected individuals, can stabilize the system (resulting in disease persistence). We

  17. Automatic segmentation of the left ventricle in cardiac MRI using local binary fitting model and dynamic programming techniques.

    PubMed

    Hu, Huaifei; Gao, Zhiyong; Liu, Liman; Liu, Haihua; Gao, Junfeng; Xu, Shengzhou; Li, Wei; Huang, Lu

    2014-01-01

    Segmentation of the left ventricle is very important to quantitatively analyze global and regional cardiac function from magnetic resonance. The aim of this study is to develop a novel algorithm for segmenting left ventricle on short-axis cardiac magnetic resonance images (MRI) to improve the performance of computer-aided diagnosis (CAD) systems. In this research, an automatic segmentation method for left ventricle is proposed on the basis of local binary fitting (LBF) model and dynamic programming techniques. The validation experiments are performed on a pool of data sets of 45 cases. For both endo- and epi-cardial contours of our results, percentage of good contours is about 93.5%, the average perpendicular distance are about 2 mm. The overlapping dice metric is about 0.91. The regression and determination coefficient between the experts and our proposed method on the LV mass is 1.038 and 0.9033, respectively; they are 1.076 and 0.9386 for ejection fraction (EF). The proposed segmentation method shows the better performance and has great potential in improving the accuracy of computer-aided diagnosis systems in cardiovascular diseases.

  18. Improving amino-acid identification, fit and C(alpha) prediction using the Simplex method in automated model building.

    PubMed

    Romo, Tod D; Sacchettini, James C; Ioerger, Thomas R

    2006-11-01

    Automated methods for protein model building in X-ray crystallography typically use a two-phased approach that involves first modeling the protein backbone followed by building in the side chains. The latter phase requires the identification of the amino-acid side-chain type as well as fitting of the side-chain model into the observed electron density. While mistakes in identification of individual side chains are common for a number of reasons, sequence alignment can sometimes be used to correct errors by mapping fragments into the true (expected) amino-acid sequence and exploiting contiguity constraints among neighbors. However, side chains cannot always be confidently aligned; this depends on having sufficient accuracy in the initial calls. The recognition of amino-acid side-chains based on the surrounding pattern of electron density, whether by features, density correlation or free atoms, can be sensitive to inaccuracies in the coordinates of the predicted backbone C(alpha) atoms to which they are anchored. By incorporating a Nelder-Mead Simplex search into the side-chain identification and model-building routines of TEXTAL, it is demonstrated that this form of residue-by-residue rigid-body real-space refinement (in which the C(alpha) itself is allowed to shift) can improve the initial accuracy of side-chain selection by over 25% on average (from 25% average identity to 32% on a test set of five representative proteins, without corrections by sequence alignment). This improvement in amino-acid selection accuracy in TEXTAL is often sufficient to bring the pairwise amino-acid identity of chains in the model out of the so-called ;twilight zone' for sequence-alignment methods. When coupled with sequence alignment, use of the Simplex search yielded improvements in side-chain accuracy on average by over 13 percentage points (from 64 to 77%) and up to 38 percentage points (from 40 to 78%) in one case compared with using sequence alignment alone.

  19. A Rigorous Test of the Fit of the Circumplex Model to Big Five Personality Data: Theoretical and Methodological Issues and Two Large Sample Empirical Tests.

    PubMed

    DeGeest, David Scott; Schmidt, Frank

    2015-01-01

    Our objective was to apply the rigorous test developed by Browne (1992) to determine whether the circumplex model fits Big Five personality data. This test has yet to be applied to personality data. Another objective was to determine whether blended items explained correlations among the Big Five traits. We used two working adult samples, the Eugene-Springfield Community Sample and the Professional Worker Career Experience Survey. Fit to the circumplex was tested via Browne's (1992) procedure. Circumplexes were graphed to identify items with loadings on multiple traits (blended items), and to determine whether removing these items changed five-factor model (FFM) trait intercorrelations. In both samples, the circumplex structure fit the FFM traits well. Each sample had items with dual-factor loadings (8 items in the first sample, 21 in the second). Removing blended items had little effect on construct-level intercorrelations among FFM traits. We conclude that rigorous tests show that the fit of personality data to the circumplex model is good. This finding means the circumplex model is competitive with the factor model in understanding the organization of personality traits. The circumplex structure also provides a theoretically and empirically sound rationale for evaluating intercorrelations among FFM traits. Even after eliminating blended items, FFM personality traits remained correlated.

  20. Three- and four-element Windkessel models: assessment of their fitting performance in a large cohort of healthy middle-aged individuals.

    PubMed

    Segers, P; Rietzschel, E R; De Buyzere, M L; Stergiopulos, N; Westerhof, N; Van Bortel, L M; Gillebert, T; Verdonck, P R

    2008-05-01

    Lumped-parameter models are used to estimate the global arterial properties by fitting the model to measured (aortic) pressure and flow. Different model configurations coexist, and it is still an open question as to which model optimally reflects the arterial tree and leads to correct estimates of arterial properties. An assessment was made of the performance of (a) the three-element Windkessel model (WK3) consisting of vascular resistance R, total arterial compliance C, and characteristic impedance Zc; (b) a four-element model with an inertance element L placed in parallel with Zc (WK4-p); and (c) a four-element model with L placed in series with Zc (WK4-s). Models were fitted to data measured non-invasively in 2404 healthy subjects, aged between 35 and 55 years. It was found that model performance segregated into two groups. In a group containing 20 per cent of the dataset (characterized by low blood pressure and wave reflection) the WK4-p model outperformed the other models, with model behaviour as envisioned by its promoters. In these cases, the WK3 and WK4-s models led to increased overestimation of total arterial compliance and underestimation of characteristic impedance. However, in about 80 per cent of the cases, the WK4-p model showed a behaviour that was very similar to that of the WK3 and WK4-s models. Here, the WK4-s model yielded the best quality of fit, although model parameters reached physically impossible values for L in about 12 per cent of all cases. The debate about which lumped-parameter model is the better approximation of the arterial tree is therefore still not fully resolved.

  1. GET FiT Plus: De-risking clean energy business models in a developing country context

    SciTech Connect

    2011-04-15

    GET Fit was first conceived in January 2010 when the United Nations Secretary General's Advisory Group on Energy and Climate Change (AGECC) invited Deutsche Bank Climate Change Advisors (DBCCA) to present new concepts to drive renewable energy investment in developing regions. DBCCA responded with the Global Energy Transfer Feed-in Tariffs Program (GET FiT), a proposal to support both renewable energy scale up and energy access through the creation of new international public-private partnerships. The concept was inspired by the theory that feed-in tariffs could serve as an effective policy structure for both public and private investment and knowledge transfer from the developed world. The original GET FiT concept was designed with input from over 160 individuals from the renewable energy, financial and international development communities. The original GET FiT report was issued in April 2010. This report reflects continued engagement of stakeholders around the world. GET FiT plus is an effort to capture the key outcomes of the GET FiT consultation process and use them to catalyze ongoing dialogue and debate about the future of international support for renewable energy in developing regions. These outcomes have been translated into key research priorities. These priorities, as well as some short issue briefs are part of this report.

  2. Source apportionment for sediment PAHs from the Daliao River (China) using an extended fit measurement mode of chemical mass balance model.

    PubMed

    Chen, Hai-Yang; Teng, Yan-Guo; Wang, Jin-Sheng

    2013-02-01

    To minimize the selection uncertainties of source profiles and obtain the higher model performance, an extended fit measurement mode for chemical mass balance model (EFMM-CMB) was proposed and applied to estimate source contributions for sediment PAHs from the Daliao River around which is the important industrial bases with oil, chemical and steel factories in the northeast part of China. Based on least squares fitting method, EFMM-CMB initially calculated the fit measurement index to every one of the possible combinations that can be made from the source profiles. Any successful applications of the fitting method were ranked according to performance measures, and then determined by maximizing an overall fitting index for a unique solution. Apportionment results from two case scenarios showed that the values of performance measures for EFMM-CMB were better to that for CMB8.2 results. With species selection of high molecular weight PAHs, power plant (45.75%), biomass burning (29.34%) and traffic tunnel (10.59%) were identified as the major sources of sediment PAHs from the Daliao River region.

  3. 40 CFR 716.25 - Adequate file search.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Adequate file search. 716.25 Section 716.25 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT HEALTH AND SAFETY DATA REPORTING General Provisions § 716.25 Adequate file search. The scope of...

  4. 40 CFR 716.25 - Adequate file search.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Adequate file search. 716.25 Section 716.25 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT HEALTH AND SAFETY DATA REPORTING General Provisions § 716.25 Adequate file search. The scope of...

  5. "Something Adequate"? In Memoriam Seamus Heaney, Sister Quinlan, Nirbhaya

    ERIC Educational Resources Information Center

    Parker, Jan

    2014-01-01

    Seamus Heaney talked of poetry's responsibility to represent the "bloody miracle", the "terrible beauty" of atrocity; to create "something adequate". This article asks, what is adequate to the burning and eating of a nun and the murderous gang rape and evisceration of a medical student? It considers Njabulo Ndebele's…

  6. 40 CFR 716.25 - Adequate file search.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Adequate file search. 716.25 Section... ACT HEALTH AND SAFETY DATA REPORTING General Provisions § 716.25 Adequate file search. The scope of a person's responsibility to search records is limited to records in the location(s) where the...

  7. 40 CFR 51.354 - Adequate tools and resources.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 2 2013-07-01 2013-07-01 false Adequate tools and resources. 51.354... Requirements § 51.354 Adequate tools and resources. (a) Administrative resources. The program shall maintain the administrative resources necessary to perform all of the program functions including...

  8. 40 CFR 51.354 - Adequate tools and resources.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 2 2014-07-01 2014-07-01 false Adequate tools and resources. 51.354... Requirements § 51.354 Adequate tools and resources. (a) Administrative resources. The program shall maintain the administrative resources necessary to perform all of the program functions including...

  9. 40 CFR 51.354 - Adequate tools and resources.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 2 2010-07-01 2010-07-01 false Adequate tools and resources. 51.354... Requirements § 51.354 Adequate tools and resources. (a) Administrative resources. The program shall maintain the administrative resources necessary to perform all of the program functions including...

  10. 40 CFR 51.354 - Adequate tools and resources.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 2 2011-07-01 2011-07-01 false Adequate tools and resources. 51.354... Requirements § 51.354 Adequate tools and resources. (a) Administrative resources. The program shall maintain the administrative resources necessary to perform all of the program functions including...

  11. 40 CFR 51.354 - Adequate tools and resources.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 2 2012-07-01 2012-07-01 false Adequate tools and resources. 51.354... Requirements § 51.354 Adequate tools and resources. (a) Administrative resources. The program shall maintain the administrative resources necessary to perform all of the program functions including...

  12. 9 CFR 305.3 - Sanitation and adequate facilities.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 9 Animals and Animal Products 2 2012-01-01 2012-01-01 false Sanitation and adequate facilities. 305.3 Section 305.3 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF... OF VIOLATION § 305.3 Sanitation and adequate facilities. Inspection shall not be inaugurated if...

  13. 9 CFR 305.3 - Sanitation and adequate facilities.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 9 Animals and Animal Products 2 2011-01-01 2011-01-01 false Sanitation and adequate facilities. 305.3 Section 305.3 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF... OF VIOLATION § 305.3 Sanitation and adequate facilities. Inspection shall not be inaugurated if...

  14. 9 CFR 305.3 - Sanitation and adequate facilities.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 9 Animals and Animal Products 2 2014-01-01 2014-01-01 false Sanitation and adequate facilities. 305.3 Section 305.3 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF... OF VIOLATION § 305.3 Sanitation and adequate facilities. Inspection shall not be inaugurated if...

  15. 9 CFR 305.3 - Sanitation and adequate facilities.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Sanitation and adequate facilities. 305.3 Section 305.3 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF... OF VIOLATION § 305.3 Sanitation and adequate facilities. Inspection shall not be inaugurated if...

  16. 9 CFR 305.3 - Sanitation and adequate facilities.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 9 Animals and Animal Products 2 2013-01-01 2013-01-01 false Sanitation and adequate facilities. 305.3 Section 305.3 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF... OF VIOLATION § 305.3 Sanitation and adequate facilities. Inspection shall not be inaugurated if...

  17. 21 CFR 201.5 - Drugs; adequate directions for use.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 4 2011-04-01 2011-04-01 false Drugs; adequate directions for use. 201.5 Section 201.5 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS: GENERAL LABELING General Labeling Provisions § 201.5 Drugs; adequate directions for use....

  18. Inferential Processing among Adequate and Struggling Adolescent Comprehenders and Relations to Reading Comprehension

    PubMed Central

    Barth, Amy E.; Barnes, Marcia; Francis, David J.; Vaughn, Sharon; York, Mary

    2015-01-01

    Separate mixed model analyses of variance (ANOVA) were conducted to examine the effect of textual distance on the accuracy and speed of text consistency judgments among adequate and struggling comprehenders across grades 6–12 (n = 1203). Multiple regressions examined whether accuracy in text consistency judgments uniquely accounted for variance in comprehension. Results suggest that there is considerable growth across the middle and high school years, particularly for adequate comprehenders in those text integration processes that maintain local coherence. Accuracy in text consistency judgments accounted for significant unique variance for passage-level, but not sentence-level comprehension, particularly for adequate comprehenders. PMID:26166946

  19. An Outcome-Based Action Study on Changes in Fitness, Blood Lipids, and Exercise Adherence, Using the Disconnected Values (Intervention) Model

    ERIC Educational Resources Information Center

    Anshel, Mark H.; Kang, Minsoo

    2007-01-01

    The authors' purpose in this action study was to examine the effect of a 10-week intervention, using the Disconnected Values Model (DVM), on changes in selected measures of fitness, blood lipids, and exercise adherence among 51 university faculty (10 men and 41 women) from a school in the southeastern United States. The DVM is an intervention…

  20. Assessing Goodness of Fit in Item Response Theory with Nonparametric Models: A Comparison of Posterior Probabilities and Kernel-Smoothing Approaches

    ERIC Educational Resources Information Center

    Sueiro, Manuel J.; Abad, Francisco J.

    2011-01-01

    The distance between nonparametric and parametric item characteristic curves has been proposed as an index of goodness of fit in item response theory in the form of a root integrated squared error index. This article proposes to use the posterior distribution of the latent trait as the nonparametric model and compares the performance of an index…