WorldWideScience

Sample records for cancer model fitting

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

    Science.gov (United States)

    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. PMID:25038234

  2. Model fit and model selection

    OpenAIRE

    Kocherlakota, Narayana R.

    2007-01-01

    This paper uses an example to show that a model that fits the available data perfectly may provide worse answers to policy questions than an alternative, imperfectly fitting model. The author argues that, in the context of Bayesian estimation, this result can be interpreted as being due to the use of an inappropriate prior over the parameters of shock processes. He urges the use of priors that are obtained from explicit auxiliary information, not from the desire to obtain identification.

  3. Standard Model Fits

    OpenAIRE

    Krueger, Andre

    2004-01-01

    The status of the electroweak precision measurements as of winter 2004 and the global test of the Standard Model are discussed. Important input data are the precision variables measured on the Z resonance at LEP and SLC and the measurements of the W mass at LEP~2 and Tevatron. A new combination of Tevatron experiments CDF and D0 on the top mass allows to set constraints on the radiative corrections and therefore to put improved limits on the mass of the Higgs boson. Additionally the impact of...

  4. Fitting and Interpreting Occupancy Models

    OpenAIRE

    Welsh, Alan H.; Lindenmayer, David B; Donnelly, Christine F.

    2013-01-01

    We show that occupancy models are more difficult to fit than is generally appreciated because the estimating equations often have multiple solutions, including boundary estimates which produce fitted probabilities of zero or one. The estimates are unstable when the data are sparse, making them difficult to interpret, and, even in ideal situations, highly variable. As a consequence, making accurate inference is difficult. When abundance varies over sites (which is the general rule in ecology b...

  5. Fitting and interpreting occupancy models.

    Science.gov (United States)

    Welsh, Alan H; Lindenmayer, David B; Donnelly, Christine F

    2013-01-01

    We show that occupancy models are more difficult to fit than is generally appreciated because the estimating equations often have multiple solutions, including boundary estimates which produce fitted probabilities of zero or one. The estimates are unstable when the data are sparse, making them difficult to interpret, and, even in ideal situations, highly variable. As a consequence, making accurate inference is difficult. When abundance varies over sites (which is the general rule in ecology because we expect spatial variance in abundance) and detection depends on abundance, the standard analysis suffers bias (attenuation in detection, biased estimates of occupancy and potentially finding misleading relationships between occupancy and other covariates), asymmetric sampling distributions, and slow convergence of the sampling distributions to normality. The key result of this paper is that the biases are of similar magnitude to those obtained when we ignore non-detection entirely. The fact that abundance is subject to detection error and hence is not directly observable, means that we cannot tell when bias is present (or, equivalently, how large it is) and we cannot adjust for it. This implies that we cannot tell which fit is better: the fit from the occupancy model or the fit ignoring the possibility of detection error. Therefore trying to adjust occupancy models for non-detection can be as misleading as ignoring non-detection completely. Ignoring non-detection can actually be better than trying to adjust for it. PMID:23326323

  6. Fitting and interpreting occupancy models.

    Directory of Open Access Journals (Sweden)

    Alan H Welsh

    Full Text Available We show that occupancy models are more difficult to fit than is generally appreciated because the estimating equations often have multiple solutions, including boundary estimates which produce fitted probabilities of zero or one. The estimates are unstable when the data are sparse, making them difficult to interpret, and, even in ideal situations, highly variable. As a consequence, making accurate inference is difficult. When abundance varies over sites (which is the general rule in ecology because we expect spatial variance in abundance and detection depends on abundance, the standard analysis suffers bias (attenuation in detection, biased estimates of occupancy and potentially finding misleading relationships between occupancy and other covariates, asymmetric sampling distributions, and slow convergence of the sampling distributions to normality. The key result of this paper is that the biases are of similar magnitude to those obtained when we ignore non-detection entirely. The fact that abundance is subject to detection error and hence is not directly observable, means that we cannot tell when bias is present (or, equivalently, how large it is and we cannot adjust for it. This implies that we cannot tell which fit is better: the fit from the occupancy model or the fit ignoring the possibility of detection error. Therefore trying to adjust occupancy models for non-detection can be as misleading as ignoring non-detection completely. Ignoring non-detection can actually be better than trying to adjust for it.

  7. Measured, modeled, and causal conceptions of fitness

    OpenAIRE

    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 genoty...

  8. Measured, Modeled, and Causal Conceptions of Fitness

    OpenAIRE

    Marshall eAbrams

    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 ge...

  9. The Model Characteristics of Physical Fitness in CrossFit

    Directory of Open Access Journals (Sweden)

    Vasilii V. Volkov

    2014-06-01

    Full Text Available The aim of the study is to work out the model characteristics of the physical fitness of CrossFit athletes based on laboratory functional testing (n=10. The analysis of the body composition was conducted using the dual-energy absorptiometry method. The morpho-functional characteristics of the heart were explored using a high-resolution ultrasound scanner. Oxygen consumption at the aerobic-anaerobic threshold and maximum oxygen consumption were determined in a step test on arm and leg cycle ergometers using a gas-analyzer. The level of the physical fitness of leg muscles in the males and females who took part in the study was satisfactory. However, it was considerably higher than the norm for untrained people. The level of the physical fitness of arm muscles was higher than the average and matched the Master of Sport of International Class standards. The productivity of the cardio-vascular system was much higher than in healthy males and females who do not work out and comparable to the standards for advanced soccer players.

  10. Evaluation of Model Fit in Cognitive Diagnosis Models

    Science.gov (United States)

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

    Science.gov (United States)

    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…

  12. Are Physical Education Majors Models for Fitness?

    Science.gov (United States)

    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…

  13. Contrast Gain Control Model Fits Masking Data

    Science.gov (United States)

    Watson, Andrew B.; Solomon, Joshua A.; Null, Cynthia H. (Technical Monitor)

    1994-01-01

    We studied the fit of a contrast gain control model to data of Foley (JOSA 1994), consisting of thresholds for a Gabor patch masked by gratings of various orientations, or by compounds of two orientations. Our general model includes models of Foley and Teo & Heeger (IEEE 1994). Our specific model used a bank of Gabor filters with octave bandwidths at 8 orientations. Excitatory and inhibitory nonlinearities were power functions with exponents of 2.4 and 2. Inhibitory pooling was broad in orientation, but narrow in spatial frequency and space. Minkowski pooling used an exponent of 4. All of the data for observer KMF were well fit by the model. We have developed a contrast gain control model that fits masking data. Unlike Foley's, our model accepts images as inputs. Unlike Teo & Heeger's, our model did not require multiple channels for different dynamic ranges.

  14. Fitting Neuron Models to Spike Trains

    Science.gov (United States)

    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. Screening for colorectal cancer: what fits best?

    LENUS (Irish Health Repository)

    Lee, Chun Seng

    2012-06-01

    Colorectal cancer (CRC) screening has been shown to be effective in reducing CRC incidence and mortality. There are currently a number of screening modalities available for implementation into a population-based CRC screening program. Each screening method offers different strengths but also possesses its own limitations as a population-based screening strategy. We review the current evidence base for accepted CRC screening tools and evaluate their merits alongside their challenges in fulfilling their role in the detection of CRC. We also aim to provide an outlook on the demands of a low-risk population-based CRC screening program with a view to providing insight as to which modality would best suit current and future needs.

  16. Fitness

    Science.gov (United States)

    ... gov home http://www.girlshealth.gov/ Home Fitness Fitness Want to look and feel your best? Physical ... are? Check out this info: What is physical fitness? top Physical fitness means you can do everyday ...

  17. A predictive fitness model for influenza

    Science.gov (United States)

    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.

  18. Model Fit after Pairwise Maximum Likelihood.

    Science.gov (United States)

    Barendse, M T; Ligtvoet, R; Timmerman, M E; Oort, F J

    2016-01-01

    Maximum likelihood factor analysis of discrete data within the structural equation modeling framework rests on the assumption that the observed discrete responses are manifestations of underlying continuous scores that are normally distributed. As maximizing the likelihood of multivariate response patterns is computationally very intensive, the sum of the log-likelihoods of the bivariate response patterns is maximized instead. Little is yet known about how to assess model fit when the analysis is based on such a pairwise maximum likelihood (PML) of two-way contingency tables. We propose new fit criteria for the PML method and conduct a simulation study to evaluate their performance in model selection. With large sample sizes (500 or more), PML performs as well the robust weighted least squares analysis of polychoric correlations. PMID:27148136

  19. Evaluation of model fit in nonlinear multilevel structural equation modeling

    Directory of Open Access Journals (Sweden)

    Karin eSchermelleh-Engel

    2014-03-01

    Full Text Available Evaluating model fit in nonlinear multilevel structural equation models (MSEM presents a challenge as no adequate test statistic is available. Nevertheless, using a product indicator approach a likelihood ratio test for linear models is provided which may also be useful for nonlinear MSEM. The main problem with nonlinear models is that product variables are nonnormally distributed. Although robust test statistics have been developed for linear SEM to ensure valid results under the condition of nonnormality, they were not yet investigated for nonlinear MSEM. In a Monte Carlo study, the performance of the robust likelihood ratio test was investigated for models with single-level latent interaction effects using the unconstrained product indicator approach. As overall model fit evaluation has a potential limitation in detecting the lack of fit at a single level even for linear models, level-specific model fit evaluation was also investigated using partially saturated models. Four population models were considered: a model with interaction effects at both levels, an interaction effect at the within-group level, an interaction effect at the between-group level, and a model with no interaction effects at both levels. For these models the number of groups, predictor correlation, and model misspecification was varied. The results indicate that the robust test statistic performed sufficiently well. Advantages of level-specific model fit evaluation for the detection of model misfit are demonstrated.

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

    Science.gov (United States)

    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.…

  1. Evaluating Latent Growth Curve Models Using Individual Fit Statistics

    Science.gov (United States)

    Coffman, Donna L.; Millsap, Roger E.

    2006-01-01

    The usefulness of assessing individual fit in latent growth curve models was examined. The study used simulated data based on an unconditional and a conditional latent growth curve model with a linear component and a small quadratic component and a linear model was fit to the data. Then the overall fit of linear and quadratic models to these data…

  2. Fitting and Modeling of AXAF Data with the ASC Fitting Application

    Science.gov (United States)

    Doe, S.; Ljungberg, M.; Siemiginowska, A.; Joye, W.

    The AXAF mission will provide X-ray data with unprecedented spatial and spectral resolution. Because of the high quality of these data, the AXAF Science Center will provide a new data analysis system--including a new fitting application. Our intent is to enable users to do fitting that is too awkward with, or beyond, the scope of existing astronomical fitting software. Our main goals are: 1) to take advantage of the full capabilities of the AXAF, we intend to provide a more sophisticated modeling capability (i.e., models that are $f(x,y,E,t)$, models to simulate the response of AXAF instruments, and models that enable ``joint-mode'' fitting, i.e., combined spatial-spectral or spectral-temporal fitting); and 2) to provide users with a wide variety of models, optimization methods, and fit statistics. In this paper, we discuss the use of an object-oriented approach in our implementation, the current features of the fitting application, and the features scheduled to be added in the coming year of development. Current features include: an interactive, command-line interface; a modeling language, which allows users to build models from arithmetic combinations of base functions; a suite of optimization and fit statistics; the ability to perform fits to multiple data sets simultaneously; and, an interface with SM and SAOtng to plot or image data, models, and/or residuals from a fit. We currently provide a modeling capability in one or two dimensions, and have recently made an effort to perform spectral fitting in a manner similar to XSPEC. We also allow users to dynamically link the fitting application to their own algorithms. Our goals for the coming year include incorporating the XSPEC model library as a subset of models available in the application, enabling ``joint-mode'' analysis and adding support for new algorithms.

  3. The best-fit universe. [cosmological models

    Science.gov (United States)

    Turner, Michael S.

    1991-01-01

    Inflation provides very strong motivation for a flat Universe, Harrison-Zel'dovich (constant-curvature) perturbations, and cold dark matter. However, there are a number of cosmological observations that conflict with the predictions of the simplest such model: one with zero cosmological constant. They include the age of the Universe, dynamical determinations of Omega, galaxy-number counts, and the apparent abundance of large-scale structure in the Universe. While the discrepancies are not yet serious enough to rule out the simplest and most well motivated model, the current data point to a best-fit model with the following parameters: Omega(sub B) approximately equal to 0.03, Omega(sub CDM) approximately equal to 0.17, Omega(sub Lambda) approximately equal to 0.8, and H(sub 0) approximately equal to 70 km/(sec x Mpc) which improves significantly the concordance with observations. While there is no good reason to expect such a value for the cosmological constant, there is no physical principle that would rule out such.

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

    Science.gov (United States)

    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.

  5. Cardiorespiratory Fitness in Women with and without Lymphedema following Breast Cancer Treatment

    OpenAIRE

    2012-01-01

    Following breast cancer (BC) treatment, many women develop impairments that may impact cardiorespiratory (CR) fitness. The aims of this study were to 1) evaluate CR fitness in women following BC treatment, 2) evaluate differences in CR fitness in those with and without breast cancer-related lymphedema (BCRL) and compare these to age-matched norms, and 3) evaluate the contribution of predictor variables to CR fitness. 136 women post-BC treatment completed testing: 67 with BCRL, and 69 without....

  6. Curve fitting methods for solar radiation data modeling

    Energy Technology Data Exchange (ETDEWEB)

    Karim, Samsul Ariffin Abdul, E-mail: samsul-ariffin@petronas.com.my, E-mail: balbir@petronas.com.my; Singh, Balbir Singh Mahinder, E-mail: samsul-ariffin@petronas.com.my, E-mail: balbir@petronas.com.my [Department of Fundamental and Applied Sciences, Faculty of Sciences and Information Technology, Universiti Teknologi PETRONAS, Bandar Seri Iskandar, 31750 Tronoh, Perak Darul Ridzuan (Malaysia)

    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.

  7. Curve fitting methods for solar radiation data modeling

    Science.gov (United States)

    Karim, Samsul Ariffin Abdul; Singh, Balbir Singh Mahinder

    2014-10-01

    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 R2. 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.

  8. On the Fitting of Non-Linear, Empirical Functions for the Fitting of Model Crater Ages

    Science.gov (United States)

    Weaver, B. P.; Hilbe, J. M.; Robbins, S. J.; Plesko, C. S.; Riggs, J. D.

    2015-05-01

    Fitting model crater production functions to observed crater data is considered an "art" by many, and there is no standard in the field for how best to do it. We will discuss mathematical techniques' pros and cons and make recommendations.

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

    Science.gov (United States)

    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…

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

    CERN Document Server

    Robotham, A S G

    2015-01-01

    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 (github.com/asgr/hyper.fit) and a user-friendly web interface for online fitting (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 ...

  11. Automated Model Fit Method for Diesel Engine Control Development

    NARCIS (Netherlands)

    Seykens, X.; Willems, F.P.T.; Kuijpers, B.; Rietjens, C.

    2014-01-01

    This paper presents an automated fit for a control-oriented physics-based diesel engine combustion model. This method is based on the combination of a dedicated measurement procedure and structured approach to fit the required combustion model parameters. Only a data set is required that is consider

  12. Sensitivity of Fit Indices to Misspecification in Growth Curve Models

    Science.gov (United States)

    Wu, Wei; West, Stephen G.

    2010-01-01

    This study investigated the sensitivity of fit indices to model misspecification in within-individual covariance structure, between-individual covariance structure, and marginal mean structure in growth curve models. Five commonly used fit indices were examined, including the likelihood ratio test statistic, root mean square error of…

  13. topicmodels: An R Package for Fitting Topic Models

    Directory of Open Access Journals (Sweden)

    Bettina Grun

    2011-05-01

    Full Text Available Topic models allow the probabilistic modeling of term frequency occurrences in documents. The fitted model can be used to estimate the similarity between documents as well as between a set of specified keywords using an additional layer of latent variables which are referred to as topics. The R package topicmodels provides basic infrastructure for fitting topic models based on data structures from the text mining package tm. The package includes interfaces to two algorithms for fitting topic models: the variational expectation-maximization algorithm provided by David M. Blei and co-authors and an algorithm using Gibbs sampling by Xuan-Hieu Phan and co-authors.

  14. HDFITS: Porting the FITS data model to HDF5

    Science.gov (United States)

    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.

  15. An R package for fitting age, period and cohort models

    Directory of Open Access Journals (Sweden)

    Adriano Decarli

    2014-11-01

    Full Text Available In this paper we present the R implementation of a GLIM macro which fits age-period-cohort model following Osmond and Gardner. In addition to the estimates of the corresponding model, owing to the programming capability of R as an object oriented language, methods for printing, plotting and summarizing the results are provided. Furthermore, the researcher has fully access to the output of the main function (apc which returns all the models fitted within the function. It is so possible to critically evaluate the goodness of fit of the resulting model.

  16. Person-fit to the Five Factor Model of personality

    OpenAIRE

    Allik, J.; Realo, A; Mõttus, R.; Borkenau, P.; Kuppens, P.; Hřebíčková, M.

    2012-01-01

    The Five Factor Model (FFM), a valid model of interindividual differences in the personality of a group of people, reportedly does not always provide a good fit for the individuals of that group. In addition to intraindividual variation across a considerable period of time, meaningful intraindividual variation can be observed within a single test administration. Two person-fit indices showed that the FFM is an adequate model for 95% of the 1,765 target-judge pairs in four different countries ...

  17. FITTING PHOTOIONIZATION MODELS TO PLANETARY NEBULAE

    Directory of Open Access Journals (Sweden)

    J. Bohigas

    2009-01-01

    Full Text Available Good to excellent photoionization models based on the Cloudy code were obtained for 13 out of 19 spectra of planetary nebulae. The two most important assumptions are that the photoionizing continuum is a Rauch model star, with gravity set by the condition that the stellar mass must be 1 M , and density is constant and determined from the observed [S II]6717/6731 ratio. The temperature and luminosity of the central star, the inner radius of the nebula and the abundance of carbon are treated as free parameters in each model run, destined to obtain the best possible t to the relative intensities of He II 4686, [O III]5007 and [N II]6584. Observed and modeled nebular temperatures derived from [N II] (6548+6584 /5755 agree within 10%, but models usually underestimate temperatures found from [O III] (4959+5007 /4363, more so when the slit does not cover the in-depth extent of the ionized region. Helium, nitrogen, oxygen, neon, sulfur and argon model abundances are uncertain at the 15%, 15%, 10%, 7%, 30% and 7% level. It is shown that neon abundance in PNe has been consistently overestimated, and an alternative ionization correction factor is recommended.

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

    Science.gov (United States)

    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. PMID:27189564

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

    Science.gov (United States)

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

    2016-01-01

    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. PMID:27189564

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

    Science.gov (United States)

    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.

  1. Mouse models of pancreatic cancer

    Institute of Scientific and Technical Information of China (English)

    Marta Herreros-Villanueva; Elizabeth Hijona; Angel Cosme; Luis Bujanda

    2012-01-01

    Pancreatic cancer is one of the most lethal of human malignancies ranking 4th among cancer-related death in the western world and in the United States,and potent therapeutic options are lacking.Although during the last few years there have been important advances in the understanding of the molecular events responsible for the development of pancreatic cancer,currently specific mechanisms of treatment resistance remain poorly understood and new effective systemic drugs need to be developed and probed.In vivo models to study pancreatic cancer and approach this issue remain limited and present different molecular features that must be considered in the studies depending on the purpose to fit special research themes.In the last few years,several genetically engineered mouse models of pancreatic exocrine neoplasia have been developed.These models mimic the disease as they reproduce genetic alterations implicated in the progression of pancreatic cancer.Genetic alterations such as activating mutations in KRas,or TGFb and/or inactivation of tumoral suppressors such as p53,INK4A/ARF BRCA2 and Smad4 are the most common drivers to pancreatic carcinogenesis and have been used to create transgenic mice.These mouse models have a spectrum of pathologic changes,from pancreatic intraepithelial neoplasia to lesions that progress histologically culminating in fully invasive and metastatic disease and represent the most useful preclinical model system.These models can characterize the cellular and molecular pathology of pancreatic neoplasia and cancer and constitute the best tool to investigate new therapeutic approaches,chemopreventive and/or anticancer treatments.Here,we review and update the current mouse models that reproduce different stages of human pancreatic ductal adenocarcinoma and will have clinical relevance in future pancreatic cancer developments.

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

    Science.gov (United States)

    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)

  3. Relative and Absolute Fit Evaluation in Cognitive Diagnosis Modeling

    Science.gov (United States)

    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…

  4. Fitting polytomous Rasch models in SAS

    DEFF Research Database (Denmark)

    Christensen, Karl Bang

    2006-01-01

    The item parameters of a polytomous Rasch model can be estimated using marginal and conditional approaches. This paper describes how this can be done in SAS (V8.2) for three item parameter estimation procedures: marginal maximum likelihood estimation, conditional maximum likelihood estimation, an...

  5. Goodness-of-fit methods for nonparametric IRT models

    NARCIS (Netherlands)

    K. Sijtsma; J.H. Straat; L.A. van der Ark

    2014-01-01

    This chapter has three sections. The first section introduces the unidimensionalmonotone latent variable model for data collected by means of a test or a questionnaire. The second section discusses the use of goodness-of-fit methods for statistical models, in particular, item response models such as

  6. Automatic fitting of spiking neuron models to electrophysiological recordings

    Directory of Open Access Journals (Sweden)

    Cyrille Rossant

    2010-03-01

    Full Text Available Spiking models can accurately predict the spike trains produced by cortical neurons in response to somatically injected currents. Since the specific characteristics of the model depend on the neuron, a computational method is required to fit models to electrophysiological recordings. The fitting procedure can be very time consuming both in terms of computer simulations and in terms of code writing. We present algorithms to fit spiking models to electrophysiological data (time-varying input and spike trains that can run in parallel on graphics processing units (GPUs. The model fitting library is interfaced with Brian, a neural network simulator in Python. If a GPU is present it uses just-in-time compilation to translate model equations into optimized code. Arbitrary models can then be defined at script level and run on the graphics card. This tool can be used to obtain empirically validated spiking models of neurons in various systems. We demonstrate its use on public data from the INCF Quantitative Single-Neuron Modeling 2009 competition by comparing the performance of a number of neuron spiking models.

  7. HDFITS: porting the FITS data model to HDF5

    CERN Document Server

    Price, D C; Greenhill, L J

    2015-01-01

    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...

  8. Detailed Atmosphere Model Fits to Disk-Dominated ULX Spectra

    OpenAIRE

    Hui, Y; Krolik, Julian H.

    2008-01-01

    We have chosen 6 Ultra-Luminous X-ray sources from the {\\it XMM-Newton} archive whose spectra have high signal-to-noise and can be fitted solely with a disk model without requiring any power-law component. To estimate systematic errors in the inferred parameters, we fit every spectrum to two different disk models, one based on local blackbody emission (KERRBB) and one based on detailed atmosphere modelling (BHSPEC). Both incorporate full general relativistic treatment of the disk surface brig...

  9. Fitting Equilibrium Search Models to Labour Market Data

    DEFF Research Database (Denmark)

    Bowlus, Audra J.; Kiefer, Nicholas M.; Neumann, George R.

    1996-01-01

    Specification and estimation of a Burdett-Mortensen type equilibrium search model is considered. The estimation is nonstandard. An estimation strategy asymptotically equivalent to maximum likelihood is proposed and applied. The results indicate that specifications with a small number of productiv...... of productivity types fit the data well compared to the homogeneous model....

  10. Twitter classification model: the ABC of two million fitness tweets.

    Science.gov (United States)

    Vickey, Theodore A; Ginis, Kathleen Martin; Dabrowski, Maciej

    2013-09-01

    The purpose of this project was to design and test data collection and management tools that can be used to study the use of mobile fitness applications and social networking within the context of physical activity. This project was conducted over a 6-month period and involved collecting publically shared Twitter data from five mobile fitness apps (Nike+, RunKeeper, MyFitnessPal, Endomondo, and dailymile). During that time, over 2.8 million tweets were collected, processed, and categorized using an online tweet collection application and a customized JavaScript. Using the grounded theory, a classification model was developed to categorize and understand the types of information being shared by application users. Our data show that by tracking mobile fitness app hashtags, a wealth of information can be gathered to include but not limited to daily use patterns, exercise frequency, location-based workouts, and overall workout sentiment. PMID:24073182

  11. Curve Fitting And Interpolation Model Applied In Nonel Dosage Detection

    Directory of Open Access Journals (Sweden)

    Jiuling Li

    2013-06-01

    Full Text Available The Curve Fitting and Interpolation Model are applied in Nonel dosage detection in this paper firstly, and the gray of continuous explosive in the Nonel has been forecasted. Although the traditional infrared equipment establishes the relationship of explosive dosage and light intensity, but the forecast accuracy is very low. Therefore, gray prediction models based on curve fitting and interpolation are framed separately, and the deviations from the different models are compared. Simultaneously, combining on the sample library features, the cubic polynomial fitting curve of the higher precision is used to predict grays, and 5mg-28mg Nonel gray values are calculated by MATLAB. Through the predictive values, the dosage detection operations are simplified, and the defect missing rate of the Nonel are reduced. Finally, the quality of Nonel is improved.

  12. Analysis of the American Cancer Society's Generation Fit Project

    Science.gov (United States)

    Peterson, Michael; Goodwin, Steve; Ellenberg, Deborah

    2004-01-01

    This study examined the impact of the American Cancer Society's (ACS's) media based peer education program, Message Magic: Selling Healthy Eating and Physical Activity, on participant self-reported dietary and physical activity behaviors and advocacy skill development. High school students participating in the program were required to work as a…

  13. Flexible competing risks regression modeling and goodness-of-fit

    DEFF Research Database (Denmark)

    Scheike, Thomas; Zhang, Mei-Jie

    2008-01-01

    -specific hazards. Another recent approach is to directly model the cumulative incidence by a proportional model (Fine and Gray, J Am Stat Assoc 94:496-509, 1999), and then obtain direct estimates of how covariates influences the cumulative incidence curve. We consider a simple and flexible class of regression......In this paper we consider different approaches for estimation and assessment of covariate effects for the cumulative incidence curve in the competing risks model. The classic approach is to model all cause-specific hazards and then estimate the cumulative incidence curve based on these cause...... models that is easy to fit and contains the Fine-Gray model as a special case. One advantage of this approach is that our regression modeling allows for non-proportional hazards. This leads to a new simple goodness-of-fit procedure for the proportional subdistribution hazards assumption that is very easy...

  14. Learning local objective functions for robust face model fitting.

    Science.gov (United States)

    Wimmer, Matthias; Stulp, Freek; Pietzsch, Sylvia; Radig, Bernd

    2008-08-01

    Model-based techniques have proven to be successful in interpreting the large amount of information contained in images. Associated fitting algorithms search for the global optimum of an objective function, which should correspond to the best model fit in a given image. Although fitting algorithms have been the subject of intensive research and evaluation, the objective function is usually designed ad hoc, based on implicit and domain-dependent knowledge. In this article, we address the root of the problem by learning more robust objective functions. First, we formulate a set of desirable properties for objective functions and give a concrete example function that has these properties. Then, we propose a novel approach that learns an objective function from training data generated by manual image annotations and this ideal objective function. In this approach, critical decisions such as feature selection are automated, and the remaining manual steps hardly require domain-dependent knowledge. Furthermore, an extensive empirical evaluation demonstrates that the obtained objective functions yield more robustness. Learned objective functions enable fitting algorithms to determine the best model fit more accurately than with designed objective functions. PMID:18566491

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

    International Nuclear Information System (INIS)

    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→∞ 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→0 limit

  16. Time-domain fitting of battery electrochemical impedance models

    Science.gov (United States)

    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%.

  17. Detailed Atmosphere Model Fits to Disk-Dominated ULX Spectra

    CERN Document Server

    Hui, Y

    2008-01-01

    We have chosen 6 Ultra-Luminous X-ray sources from the {\\it XMM-Newton} archive whose spectra have high signal-to-noise and can be fitted solely with a disk model without requiring any power-law component. To estimate systematic errors in the inferred parameters, we fit every spectrum to two different disk models, one based on local blackbody emission (KERRBB) and one based on detailed atmosphere modelling (BHSPEC). Both incorporate full general relativistic treatment of the disk surface brightness profile, photon Doppler shifts, and photon trajectories. We found in every case that they give almost identical fits and similar acceptable parameters. The best-fit value of the most interesting parameter, the mass of the central object, is between 23 and 73 M$_\\sun$ in 5 of the 6 examples. In every case, the best-fit inclination angle and mass are correlated, in the sense that large mass corresponds to high inclination. Even after allowing for this degeneracy, we find that, with $\\gtrsim 99.9%$ formal statistical ...

  18. Ongoing Processes in a Fitness Network Model under Restricted Resources.

    Directory of Open Access Journals (Sweden)

    Takayuki Niizato

    Full Text Available In real networks, the resources that make up the nodes and edges are finite. This constraint poses a serious problem for network modeling, namely, the compatibility between robustness and efficiency. However, these concepts are generally in conflict with each other. In this study, we propose a new fitness-driven network model for finite resources. In our model, each individual has its own fitness, which it tries to increase. The main assumption in fitness-driven networks is that incomplete estimation of fitness results in a dynamical growing network. By taking into account these internal dynamics, nodes and edges emerge as a result of exchanges between finite resources. We show that our network model exhibits exponential distributions in the in- and out-degree distributions and a power law distribution of edge weights. Furthermore, our network model resolves the trade-off relationship between robustness and efficiency. Our result suggests that growing and anti-growing networks are the result of resolving the trade-off problem itself.

  19. Assessing fit in Bayesian models for spatial processes

    KAUST Repository

    Jun, M.

    2014-09-16

    © 2014 John Wiley & Sons, Ltd. Gaussian random fields are frequently used to model spatial and spatial-temporal data, particularly in geostatistical settings. As much of the attention of the statistics community has been focused on defining and estimating the mean and covariance functions of these processes, little effort has been devoted to developing goodness-of-fit tests to allow users to assess the models\\' adequacy. We describe a general goodness-of-fit test and related graphical diagnostics for assessing the fit of Bayesian Gaussian process models using pivotal discrepancy measures. Our method is applicable for both regularly and irregularly spaced observation locations on planar and spherical domains. The essential idea behind our method is to evaluate pivotal quantities defined for a realization of a Gaussian random field at parameter values drawn from the posterior distribution. Because the nominal distribution of the resulting pivotal discrepancy measures is known, it is possible to quantitatively assess model fit directly from the output of Markov chain Monte Carlo algorithms used to sample from the posterior distribution on the parameter space. We illustrate our method in a simulation study and in two applications.

  20. The Gold Medal Fitness Program: A Model for Teacher Change

    Science.gov (United States)

    Wright, Jan; Konza, Deslea; Hearne, Doug; Okely, Tony

    2008-01-01

    Background: Following the 2000 Sydney Olympics, the NSW Premier, Mr Bob Carr, launched a school-based initiative in NSW government primary schools called the "Gold Medal Fitness Program" to encourage children to be fitter and more active. The Program was introduced into schools through a model of professional development, "Quality Teaching and…

  1. Raindrop size distribution: Fitting performance of common theoretical models

    Science.gov (United States)

    Adirosi, E.; Volpi, E.; Lombardo, F.; Baldini, L.

    2016-10-01

    Modelling raindrop size distribution (DSD) is a fundamental issue to connect remote sensing observations with reliable precipitation products for hydrological applications. To date, various standard probability distributions have been proposed to build DSD models. Relevant questions to ask indeed are how often and how good such models fit empirical data, given that the advances in both data availability and technology used to estimate DSDs have allowed many of the deficiencies of early analyses to be mitigated. Therefore, we present a comprehensive follow-up of a previous study on the comparison of statistical fitting of three common DSD models against 2D-Video Distrometer (2DVD) data, which are unique in that the size of individual drops is determined accurately. By maximum likelihood method, we fit models based on lognormal, gamma and Weibull distributions to more than 42.000 1-minute drop-by-drop data taken from the field campaigns of the NASA Ground Validation program of the Global Precipitation Measurement (GPM) mission. In order to check the adequacy between the models and the measured data, we investigate the goodness of fit of each distribution using the Kolmogorov-Smirnov test. Then, we apply a specific model selection technique to evaluate the relative quality of each model. Results show that the gamma distribution has the lowest KS rejection rate, while the Weibull distribution is the most frequently rejected. Ranking for each minute the statistical models that pass the KS test, it can be argued that the probability distributions whose tails are exponentially bounded, i.e. light-tailed distributions, seem to be adequate to model the natural variability of DSDs. However, in line with our previous study, we also found that frequency distributions of empirical DSDs could be heavy-tailed in a number of cases, which may result in severe uncertainty in estimating statistical moments and bulk variables.

  2. The global electroweak Standard Model fit after the Higgs discovery

    CERN Document Server

    Baak, Max

    2013-01-01

    We present an update of the global Standard Model (SM) fit to electroweak precision data under the assumption that the new particle discovered at the LHC is the SM Higgs boson. In this scenario all parameters entering the calculations of electroweak precision observalbes are known, allowing, for the first time, to over-constrain the SM at the electroweak scale and assert its validity. Within the SM the W boson mass and the effective weak mixing angle can be accurately predicted from the global fit. The results are compatible with, and exceed in precision, the direct measurements. An updated determination of the S, T and U parameters, which parametrize the oblique vacuum corrections, is given. The obtained values show good consistency with the SM expectation and no direct signs of new physics are seen. We conclude with an outlook to the global electroweak fit for a future e+e- collider.

  3. Cardiorespiratory fitness and digestive cancer mortality: findings from the Aerobics Center Longitudinal Study (ACLS)

    OpenAIRE

    Peel, J. Brent; Sui, Xuemei; Matthews, Charles E.; Adams, Swann A; Hébert, James R; Hardin, James W.; Timothy S Church; Blair, Steven N.

    2009-01-01

    Although higher levels of physical activity are inversely associated with risk of colon cancer, few prospective studies have evaluated overall digestive system cancer mortality in relation to cardiorespiratory fitness (CRF). The authors examined this association among 38,801 men aged 20−88 years and who performed a maximal treadmill exercise test at baseline in the Aerobics Center Longitudinal Study (Dallas, Texas) during 1974−2003. Mortality was assessed over 29 years of follow-up (1974−2003...

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

    Science.gov (United States)

    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.

  5. Error propagation with R-matrix model fitting

    Institute of Scientific and Technical Information of China (English)

    CHEN; Zhenpeng(陈振鹏); ZHANG; Rui(张瑞); SUN; Yeying(孙业英); LIU; Tingjin(刘廷进)

    2003-01-01

    The error propagation features with R-matrix model fitting 7Li, 11B and 17O systems have been researched systematically. Some laws of error propagation have been revealed, an experience formula for describing standard error propagation has been established, and the most possible error range for evaluated standard cross section of 6Li (n, α), 10B (n, α) and 10B (n, α1) has been determined.

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

    Science.gov (United States)

    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.

  7. Supersymmetry With Prejudice: Fitting the Wrong Model to LHC Data

    CERN Document Server

    Allanach, B C

    2011-01-01

    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 end-points from the golden cascade decay chain \\tilde{q}_L -> q \\chi_2^0 (-> \\tilde{l}^{\\pm} l^{\\mp} q) -> \\chi_1^0 l^+ l^- q. We assume a CMSSM point to be the `correct' one, and fit the signals instead to minimal gauge mediated supersymmetry breaking models (mGMSB) with a neutralino quasi-stable lightest supersymmetric particle, minimal anomaly mediation (mAMSB) and large volume string compactification models (LVS). mAMSB and LVS can be unambiguously discriminated against the CMSSM for the parameter point assumed and 1 inverse femtobarn of LHC data at 14 TeV. However, mGMSB would not be discriminated on the basis of the kinematic end-points alone, and would require further, more detailed investigation. The best-fit points of mGMSB and CMS...

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

    Science.gov (United States)

    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…

  9. Broadband distortion modeling in Lyman-$\\alpha$ forest BAO fitting

    CERN Document Server

    Blomqvist, Michael; Bautista, Julian E; Ariño, Andreu; Busca, Nicolás G; Miralda-Escudé, Jordi; Slosar, Anže; Font-Ribera, Andreu; Margala, Daniel; Schneider, Donald P; Vazquez, Jose A

    2015-01-01

    In recent years, the Lyman-$\\alpha$ 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-$\\alpha$ forest auto-correlation function at redshift $z\\simeq 2.3$, 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-$\\alpha$ forest spectrum. Implementing the distortion model in fits for the baryon acoustic oscillation (BAO) peak position in the Lyman-$\\alpha$ forest auto-correlation, we find that the fitting method recovers the input values of the linear bias parameter $b_{F}$ and the redshift-space distortion parameter $\\beta_{F}$ for mock dat...

  10. The effectiveness of FOBT vs. FIT: A meta-analysis on colorectal cancer screening test

    Science.gov (United States)

    Mousavinezhad, Maryam; Majdzadeh, Reza; Akbari Sari, Ali; Delavari, Alireza; Mohtasham, Farideh

    2016-01-01

    Background: After lung and prostate cancers, colorectal cancer (CRC) is the third most common cancer in men and the second most common cancer in women after breast cancer worldwide. Every year, more than one million people are diagnosed with colorectal cancer worldwide and half of these patients die from this disease, making it the fourth leading cause of death in the world. This systematic review aimed to assess the effectiveness of the two colorectal diagnostic tests of FOBT (fecal occult blood test) and FIT (fecal immunochemical test)) in terms of technical performance. Methods: To retrieve the relevant evidence, appropriate medical databases such as Cochrane library, NHSEED, Scopus and Google scholar were searched from February 2013 to July 2014, using free-texts and Mesh. In this study, inclusion/exclusion criteria of the papers, randomized controlled trials, economic evaluations, systematic reviews, meta-analyses and meta-syntheses of the effectiveness of FIT versus FOBT tests in moderate-risk populations (age: 50 to 70 years), which had reported the least of such outcomes as sensitivity, specificity and clinical outcomes were reviewed. The analyses of the effectiveness outcomes were performed in the form of meta-analysis. Results: Five papers were eligible to be included in the final phase of the study for synthesis. FIT showed a better performance in participation and positivity rate. Moreover, in terms of false positive and negative rate, FIT showed fewer rates compared to FOBT (RR:-4.06; 95% CI (-7.89-0.24), and NN-scope (Number need to scope) (2.2% vs. 1.6%), and NN-screen (Number need to screen) (84% vs. 31-49% in different cut off levels) showed significant differences in FOBT vs. FIT, respectively. Conclusion: In the five included studies (3, 11-14), the acceptability of FIT was more than FOBT. However, in our meta-analysis, no difference was found between the two tests. FIT was significant in positivity rate and had a better performance in

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

    Science.gov (United States)

    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.…

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

    Science.gov (United States)

    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. PMID:25680684

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

    Science.gov (United States)

    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.

  14. Fitting Latent Cluster Models for Networks with latentnet

    Directory of Open Access Journals (Sweden)

    Pavel N. Krivitsky

    2007-12-01

    Full Text Available latentnet is a package to fit and evaluate statistical latent position and cluster models for networks. Hoff, Raftery, and Handcock (2002 suggested an approach to modeling networks based on positing the existence of an latent space of characteristics of the actors. Relationships form as a function of distances between these characteristics as well as functions of observed dyadic level covariates. In latentnet social distances are represented in a Euclidean space. It also includes a variant of the extension of the latent position model to allow for clustering of the positions developed in Handcock, Raftery, and Tantrum (2007.The package implements Bayesian inference for the models based on an Markov chain Monte Carlo algorithm. It can also compute maximum likelihood estimates for the latent position model and a two-stage maximum likelihood method for the latent position cluster model. For latent position cluster models, the package provides a Bayesian way of assessing how many groups there are, and thus whether or not there is any clustering (since if the preferred number of groups is 1, there is little evidence for clustering. It also estimates which cluster each actor belongs to. These estimates are probabilistic, and provide the probability of each actor belonging to each cluster. It computes four types of point estimates for the coefficients and positions: maximum likelihood estimate, posterior mean, posterior mode and the estimator which minimizes Kullback-Leibler divergence from the posterior. You can assess the goodness-of-fit of the model via posterior predictive checks. It has a function to simulate networks from a latent position or latent position cluster model.

  15. Direct model fitting to combine dithered ACS images

    CERN Document Server

    Mahmoudian, Haniyeh

    2013-01-01

    The information lost in images of undersampled CCD cameras can be recovered with the technique of `dithering'. A number of subexposures is taken with sub-pixel shifts in order to record structures on scales smaller than a pixel. The standard method to combine such exposures, `Drizzle', averages after reversing the displacements, including rotations and distortions. More sophisticated methods are available to produce, e.g., Nyquist sampled representations of band-limited inputs. While the combined images produced by these methods can be of high quality, their use as input for forward-modelling techniques in gravitational lensing is still not optimal, because the residual artefacts still affect the modelling results in unpredictable ways. In this paper we argue for an overall modelling approach that takes into account the dithering and the lensing without the intermediate product of a combined image. As one building block we introduce an alternative approach to combine dithered images by direct model fitting wi...

  16. Implementation of population screening for colorectal cancer by repeated Fecal Immunochemical Test (FIT: third round

    Directory of Open Access Journals (Sweden)

    Stegeman Inge

    2012-06-01

    Full Text Available Abstract Background Colorectal cancer (CRC is the most common cancer in Europe with a mortality rate of almost 50%. The prognosis of patients is largely determined by the clinical and pathological stage at the time of diagnosis. Population screening has been shown to reduce CRC-related mortality rate. Most screening programs worldwide rely on fecal immunochemical testing (FIT. The effectiveness of a FIT screening program is not only influenced by initial participation rate, but also by program adherence during consecutive screening rounds. We aim to evaluate the participation rate in and yield of a third CRC screening round using FIT. Methods and design Four years after the first screening round and two years after the second round, a total number of approximately 11,000 average risk individuals (50 to 75 years of age will be invited to participate in a third round of FIT-based CRC screening. We will select individuals in the same target area as in the previous screening rounds, using the electronic database of the regional municipal administration registrations. We will invite all FIT-negatives and all non-participants in previous screening rounds, as well as eligible first time invitees who have moved into the area or have become 50 years of age. FITs will be analyzed in the special technique laboratory of the Academic Medical Center of the University of Amsterdam. All FIT-positives will be invited for a consultation at the outpatient clinic. In the absence of contra-indications, a colonoscopy will follow at the Academic Medical Center or at the Flevohospital. The primary outcome measures are the participation rate, defined as the proportion of invitees that return a FIT in this third round of FIT-screening, and the diagnostic yield of the program. Implications This study will provide precise data on the participation in later FIT screening rounds. This enables to estimate the effectiveness of CRC screening programs that rely on repeated

  17. Mouse models of colorectal cancer

    Institute of Scientific and Technical Information of China (English)

    Yunguang Tong; Wancai Yang; H. Phillip Koeffler

    2011-01-01

    Colorectal cancer is one of the most common malignancies in the world. Many mouse models have been developed to evaluate features of colorectal cancer in humans. These can be grouped into genetically-engineered, chemically-induced, and inoculated models. However, none recapitulates all of the characteristics of human colorectal cancer. It is critical to use a specific mouse model to address a particular research question. Here, we review commonly used mouse models for human colorectal cancer.

  18. Cardiorespiratory fitness and digestive cancer mortality: findings from the aerobics center longitudinal study.

    Science.gov (United States)

    Peel, J Brent; Sui, Xuemei; Matthews, Charles E; Adams, Swann A; Hébert, James R; Hardin, James W; Church, Timothy S; Blair, Steven N

    2009-04-01

    Although higher levels of physical activity are inversely associated with risk of colon cancer, few prospective studies have evaluated overall digestive system cancer mortality in relation to cardiorespiratory fitness (CRF). The authors examined this association among 38,801 men ages 20 to 88 years who performed a maximal treadmill exercise test at baseline in the Aerobics Center Longitudinal Study (Dallas, TX) during 1974 to 2003. Mortality was assessed over 29 years of follow-up (1974-2003). Two hundred eighty-three digestive system cancer deaths occurred during a mean 17 years of observation. Age-adjusted mortality rates per 10,000 person-years according to low, moderate, and high CRF groups were 6.8, 4.0, and 3.3 for digestive system cancer (P(trend) < 0.001). After adjustment for age, examination year, body mass index, smoking, drinking, family history of cancer, personal history of diabetes, hazard ratios (95% confidence intervals) for overall digestive cancer deaths for those in the middle and upper 40% of the distribution of CRF relative to those in the lowest 20% were 0.66 (0.49-0.88) and 0.56 (0.40-0.80), respectively. Being fit (the upper 80% of CRF) was associated with a lower risk of mortality from colon [0.61 (0.37-1.00)], colorectal [0.58 (0.37-0.92)], and liver cancer [0.28 (0.11-0.72)] compared with being unfit (the lowest 20% of CRF). These findings support a protective role of CRF against total digestive tract, colorectal, and liver cancer deaths in men. PMID:19293313

  19. Cardiorespiratory fitness and digestive cancer mortality: findings from the Aerobics Center Longitudinal Study (ACLS)

    Science.gov (United States)

    Peel, J. Brent; Sui, Xuemei; Matthews, Charles E.; Adams, Swann A.; Hébert, James R.; Hardin, James W.; Church, Timothy S.; Blair, Steven N.

    2009-01-01

    Although higher levels of physical activity are inversely associated with risk of colon cancer, few prospective studies have evaluated overall digestive system cancer mortality in relation to cardiorespiratory fitness (CRF). The authors examined this association among 38,801 men aged 20−88 years and who performed a maximal treadmill exercise test at baseline in the Aerobics Center Longitudinal Study (Dallas, Texas) during 1974−2003. Mortality was assessed over 29 years of follow-up (1974−2003). 283 digestive system cancer deaths occurred during a mean 17-year of observation. Age-adjusted mortality rates per 10,000 person-yrs according to low, moderate, and high CRF groups were 6.8, 4.0, and 3.3 for digestive system cancer (trend p < 0.001). After adjustment for age, examination year, body mass index, smoking, drinking, family history of cancer, personal history of diabetes, hazard ratios for overall digestive cancer deaths (95% confidence interval) for those in the middle and upper 40% of the distribution of CRF relative to those in the lowest 20% were 0.66 (0.49, 0.88) and 0.56 (0.40, 0.80), respectively. Being fit (the upper 80% of CRF) was associated with a lower risk of mortality from colon (0.61 [0.37, 1.00]), colorectal (0.58 [0.37, 0.92]), and liver cancer (0.28 [0.11, 0.72]), compared with being unfit (the lowest 20% of CRF). These findings support a protective role of CRF against total digestive tract, colorectal, and liver cancer deaths in men. PMID:19293313

  20. A Commentary on the Relationship between Model Fit and Saturated Path Models in Structural Equation Modeling Applications

    Science.gov (United States)

    Raykov, Tenko; Lee, Chun-Lung; Marcoulides, George A.; Chang, Chi

    2013-01-01

    The relationship between saturated path-analysis models and their fit to data is revisited. It is demonstrated that a saturated model need not fit perfectly or even well a given data set when fit to the raw data is examined, a criterion currently frequently overlooked by researchers utilizing path analysis modeling techniques. The potential of…

  1. A person-fit index for polytomous Rasch models, latent class models, and their mixture generalizations

    NARCIS (Netherlands)

    von Davier, M; Molenaar, IW

    2003-01-01

    A normally distributed person-fit index is proposed for detecting aberrant response patterns in latent class models and mixture distribution IRT models for dichotomous and polytomous data. This article extends previous work on the null distribution of person-fit indices for the dichotomous Rasch mod

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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…

  4. Cavity approach for modeling and fitting polymer stretching

    CERN Document Server

    Massucci, Francesco Alessandro; Vicente, Conrad J Pérez

    2014-01-01

    The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly studied force--elongation relation is typically hard. Here we draw from techniques developed in the context of disordered systems to solve models for single and double--stranded DNA stretching in the limit of a long polymeric chain. Since we directly derive the marginals for the molecule local orientation, our approach allows us to readily calculate the experimental elongation as well as other observables at wish. As an example, we evaluate the correlation length as a function of the stretching force. Furthermore, we are able to fit successfully our solution to real experimental data. Although the model is admittedly phenomenological, our findings are very sound. For single--stranded DNA our solution yields the correct (monomer) scale and, yet more importantly, the right pers...

  5. Empirical fitness models for hepatitis C virus immunogen design

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  8. Research on Recruitment Model Based on Person-Organization Fit

    OpenAIRE

    Zhen Cheng

    2014-01-01

    Person-organization fit is a hot problem in the study on human resource management and organizational behavior. To recruit and keep talents who fit company's development will be key to maintain sustainable development and competitiveness and origin.Traditional human resource management focus on person-position fit.People carry out a large number of person-position fit study and apply it to practice. In recent years, researchers begin to realize, in order to achieve the ideal effect, not only ...

  9. Fitting of Parametric Building Models to Oblique Aerial Images

    Science.gov (United States)

    Panday, U. S.; Gerke, M.

    2011-09-01

    In literature and in photogrammetric workstations many approaches and systems to automatically reconstruct buildings from remote sensing data are described and available. Those building models are being used for instance in city modeling or in cadastre context. If a roof overhang is present, the building walls cannot be estimated correctly from nadir-view aerial images or airborne laser scanning (ALS) data. This leads to inconsistent building outlines, which has a negative influence on visual impression, but more seriously also represents a wrong legal boundary in the cadaster. Oblique aerial images as opposed to nadir-view images reveal greater detail, enabling to see different views of an object taken from different directions. Building walls are visible from oblique images directly and those images are used for automated roof overhang estimation in this research. A fitting algorithm is employed to find roof parameters of simple buildings. It uses a least squares algorithm to fit projected wire frames to their corresponding edge lines extracted from the images. Self-occlusion is detected based on intersection result of viewing ray and the planes formed by the building whereas occlusion from other objects is detected using an ALS point cloud. Overhang and ground height are obtained by sweeping vertical and horizontal planes respectively. Experimental results are verified with high resolution ortho-images, field survey, and ALS data. Planimetric accuracy of 1cm mean and 5cm standard deviation was obtained, while buildings' orientation were accurate to mean of 0.23° and standard deviation of 0.96° with ortho-image. Overhang parameters were aligned to approximately 10cm with field survey. The ground and roof heights were accurate to mean of - 9cm and 8cm with standard deviations of 16cm and 8cm with ALS respectively. The developed approach reconstructs 3D building models well in cases of sufficient texture. More images should be acquired for completeness of

  10. Animal Models of Colorectal Cancer

    Science.gov (United States)

    Johnson, Robert L.; Fleet, James C.

    2012-01-01

    Colorectal cancer is a heterogeneous disease that afflicts a large number of people in the United States. The use of animal models has the potential to increase our understanding of carcinogenesis, tumor biology, and the impact of specific molecular events on colon biology. In addition, animal models with features of specific human colorectal cancers can be used to test strategies for cancer prevention and treatment. In this review we provide an overview of the mechanisms driving human cancer, we discuss the approaches one can take to model colon cancer in animals, and we describe a number of specific animal models that have been developed for the study of colon cancer. We believe that there are many valuable animal models to study various aspects of human colorectal cancer. However, opportunities for improving upon these models exist. PMID:23076650

  11. Engineered Swine Models of Cancer

    Directory of Open Access Journals (Sweden)

    Adrienne L. Watson

    2016-05-01

    Full Text Available Over the past decade, the technology to engineer genetically modified swine has seen many advancements, and because their physiology is remarkably similar to that of humans, swine models of cancer may be extremely valuable for preclinical safety studies as well as toxicity testing of pharmaceuticals prior to the start of human clinical trials. Hence, the benefits of using swine as a large animal model in cancer research and the potential applications and future opportunities of utilizing pigs in cancer modeling are immense. In this review, we discuss how pigs have been and can be used as a biomedical models for cancer research, with an emphasis on current technologies. We have focused on applications of precision genetics that can provide models that mimic human cancer predisposition syndromes. In particular, we describe the advantages of targeted gene-editing using custom endonucleases, specifically TALENs and CRISPRs, and transposon systems, to make novel pig models of cancer with broad preclinical applications.

  12. Engineered Swine Models of Cancer.

    Science.gov (United States)

    Watson, Adrienne L; Carlson, Daniel F; Largaespada, David A; Hackett, Perry B; Fahrenkrug, Scott C

    2016-01-01

    Over the past decade, the technology to engineer genetically modified swine has seen many advancements, and because their physiology is remarkably similar to that of humans, swine models of cancer may be extremely valuable for preclinical safety studies as well as toxicity testing of pharmaceuticals prior to the start of human clinical trials. Hence, the benefits of using swine as a large animal model in cancer research and the potential applications and future opportunities of utilizing pigs in cancer modeling are immense. In this review, we discuss how pigs have been and can be used as a biomedical models for cancer research, with an emphasis on current technologies. We have focused on applications of precision genetics that can provide models that mimic human cancer predisposition syndromes. In particular, we describe the advantages of targeted gene-editing using custom endonucleases, specifically TALENs and CRISPRs, and transposon systems, to make novel pig models of cancer with broad preclinical applications. PMID:27242889

  13. NiftyFit: a Software Package for Multi-parametric Model-Fitting of 4D Magnetic Resonance Imaging Data.

    Science.gov (United States)

    Melbourne, Andrew; Toussaint, Nicolas; Owen, David; Simpson, Ivor; Anthopoulos, Thanasis; De Vita, Enrico; Atkinson, David; Ourselin, Sebastien

    2016-07-01

    Multi-modal, multi-parametric Magnetic Resonance (MR) Imaging is becoming an increasingly sophisticated tool for neuroimaging. The relationships between parameters estimated from different individual MR modalities have the potential to transform our understanding of brain function, structure, development and disease. This article describes a new software package for such multi-contrast Magnetic Resonance Imaging that provides a unified model-fitting framework. We describe model-fitting functionality for Arterial Spin Labeled MRI, T1 Relaxometry, T2 relaxometry and Diffusion Weighted imaging, providing command line documentation to generate the figures in the manuscript. Software and data (using the nifti file format) used in this article are simultaneously provided for download. We also present some extended applications of the joint model fitting framework applied to diffusion weighted imaging and T2 relaxometry, in order to both improve parameter estimation in these models and generate new parameters that link different MR modalities. NiftyFit is intended as a clear and open-source educational release so that the user may adapt and develop their own functionality as they require. PMID:26972806

  14. Mouse models for cancer research

    Institute of Scientific and Technical Information of China (English)

    Wei Zhang; Lynette Moore; Ping Ji

    2011-01-01

    Mouse models of cancer enable researchers to leamn about tumor biology in complicated and dynamic physiological systems. Since the development of gene targeting in mice, cancer biologists have been among the most frequent users of transgenic mouse models, which have dramatically increased knowledge about how cancers form and grow. The Chinese Joumnal of Cancer will publish a series of papers reporting the use of mouse models in studying genetic events in cancer cases. This editorial is an overview of the development and applications of mouse models of cancer and directs the reader to upcoming papers describing the use of these models to be published in coming issues, beginning with three articles in the current issue.

  15. Improved physical fitness of cancer survivors : A randomised controlled trial comparing physical training with physical and cognitive-behavioural training

    NARCIS (Netherlands)

    May, Anne M.; Van Weert, Ellen; Korstjens, Irene; Hoekstra-Weebers, Josette E. H. M.; Van Der Schans, Cees P.; Zonderland, Maria L.; Mesters, Ilse; Van Den Borne, Bart; Ros, Wynand J. G.

    2008-01-01

    We compared the effect of a group-based 12-week supervised exercise programme, i.e. aerobic and resistance exercise, and group sports, with that of the same programme combined with cognitive-behavioural training on physical fitness and activity of cancer survivors. One hundred and forty seven cancer

  16. A New Finite Interval Lifetime Distribution Model for Fitting Bathtub-Shaped Failure Rate Curve

    OpenAIRE

    2015-01-01

    This paper raised a new four-parameter fitting model to describe bathtub curve, which is widely used in research on components’ life analysis, then gave explanation of model parameters, and provided parameter estimation method as well as application examples utilizing some well-known lifetime data. By comparative analysis between the new model and some existing bathtub curve fitting model, we can find that the new fitting model is very convenient and its parameters are clear; moreover, this m...

  17. Application of fit indices in testing the theoretical models in psychology: Possibilities and limitations

    OpenAIRE

    Lazarević Ljiljana

    2008-01-01

    This paper deals with the fit indices used in Structural Equation Modelling (SEM) for testing theoretical models and the difficulties that can occur during the testing of theoretical models in different fields of psychology. The paper discusses the basic assumptions of SEM and presents the indices used for assessing the fit of theoretical models. This paper also presents the procedures for calculating the basic statistic for assessing the fit of models (χ2), as well as for calculating the mos...

  18. A versatile curve-fit model for linear to deeply concave rank abundance curves

    NARCIS (Netherlands)

    Neuteboom, J.H.; Struik, P.C.

    2005-01-01

    A new, flexible curve-fit model for linear to concave rank abundance curves was conceptualized and validated using observational data. The model links the geometric-series model and log-series model and can also fit deeply concave rank abundance curves. The model is based ¿ in an unconventional way

  19. RNA virus evolution via a fitness-space model

    Energy Technology Data Exchange (ETDEWEB)

    Tsimring, L.S.; Levine, H. [Institute for Nonlinear Science, University of California, San Diego, La Jolla, California 92093-0402 (United States); Kessler, D.A. [Department of Physics, Bar-Ilan University, Ramat Gan 52900 (Israel)

    1996-06-01

    We present a mean-field theory for the evolution of RNA virus populations. The theory operates with a distribution of the population in a one-dimensional fitness space, and is valid for sufficiently smooth fitness landscapes. Our approach explains naturally the recent experimental observation [I. S. Novella {ital et} {ital al}., Proc. Natl. Acad. Sci. U.S.A. {bold 92}, 5841{endash}5844 (1995)] of two distinct stages in the growth of virus fitness. {copyright} {ital 1995 The American Physical Society.}

  20. NUTRITION AND FITNESS (PART 1: OBESITY, THE METABOLIC SYNDROME, CARDIOVASCULAR DISEASE, AND CANCER

    Directory of Open Access Journals (Sweden)

    Artemis P. Simopoulos

    2005-12-01

    Full Text Available The proceedings of the Fifth International Conference on Nutrition and Fitness held in Athens, Greece, on June 91-2, 2004 are presented in the book as the first volume of the series. The objectives of the book are to review/discuss the latest information on nutrition and fitness by taking into consideration i genetic endowment, ii adaptation to the nutritional factors and the effect of various resources of energy on exercise and performance, iii the epidemiology of obesity, iv the relationship of nutrition and fitness to chronic diseases (cardiovascular diseases, syndrome X, obesity, osteoporosis, diabetes, cancer. The book also discusses the classification system of obesity in several countries and compares the diets used in several regions/countries. FEATURES A common, uniform strategy and evidence-based approach to organizing and interpreting the literature is used in all chapters. This textbook is composed of three parts with sub-sections in three of them. The topics of the parts are: i Obesity and Metabolic Syndrome, ii Coronary Heart Disease and iii Cancer. In each specific chapter, an epidemiological picture has been systematically developed from the data available in prospective, retrospective, case-control, and cross-sectional studies. The tables and figures are numerous, helpful and very useful. AUDIENCE This book is almost a compulsory reading for anyone interested in cardiovascular system, nutrition, metabolism, social and preventive medicine, clinical nutrition, diabetics, genetics, obesity, public health, sports medicine and for those wishing to run comprehensive research in this and relevant areas. The fact that the contributors are leading international researchers in this field makes this book more welcome. ASSESSMENT This book is almost a compulsory reading for anyone interested in pediatric injuries and for those wishing to run comprehensive research in this and relevant areas. The fact that the contributors are leading

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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…

  4. Liver Cancer Risk Prediction Models

    Science.gov (United States)

    Developing statistical models that estimate the probability of developing liver cancer over a defined period of time will help clinicians identify individuals at higher risk of specific cancers, allowing for earlier or more frequent screening and counseling of behavioral changes to decrease risk.

  5. Breast Cancer Risk Prediction Models

    Science.gov (United States)

    Developing statistical models that estimate the probability of developing breast cancer over a defined period of time will help clinicians identify individuals at higher risk of specific cancers, allowing for earlier or more frequent screening and counseling of behavioral changes to decrease risk.

  6. Prostate Cancer Risk Prediction Models

    Science.gov (United States)

    Developing statistical models that estimate the probability of developing prostate cancer over a defined period of time will help clinicians identify individuals at higher risk of specific cancers, allowing for earlier or more frequent screening and counseling of behavioral changes to decrease risk.

  7. Pancreatic Cancer Risk Prediction Models

    Science.gov (United States)

    Developing statistical models that estimate the probability of developing pancreatic cancer over a defined period of time will help clinicians identify individuals at higher risk of specific cancers, allowing for earlier or more frequent screening and counseling of behavioral changes to decrease risk.

  8. Colorectal Cancer Risk Prediction Models

    Science.gov (United States)

    Developing statistical models that estimate the probability of developing colorectal cancer over a defined period of time will help clinicians identify individuals at higher risk of specific cancers, allowing for earlier or more frequent screening and counseling of behavioral changes to decrease risk.

  9. Bladder Cancer Risk Prediction Models

    Science.gov (United States)

    Developing statistical models that estimate the probability of developing bladder cancer over a defined period of time will help clinicians identify individuals at higher risk of specific cancers, allowing for earlier or more frequent screening and counseling of behavioral changes to decrease risk.

  10. Esophageal Cancer Risk Prediction Models

    Science.gov (United States)

    Developing statistical models that estimate the probability of developing esophageal cancer over a defined period of time will help clinicians identify individuals at higher risk of specific cancers, allowing for earlier or more frequent screening and counseling of behavioral changes to decrease risk.

  11. Cervical Cancer Risk Prediction Models

    Science.gov (United States)

    Developing statistical models that estimate the probability of developing cervical cancer over a defined period of time will help clinicians identify individuals at higher risk of specific cancers, allowing for earlier or more frequent screening and counseling of behavioral changes to decrease risk.

  12. Testicular Cancer Risk Prediction Models

    Science.gov (United States)

    Developing statistical models that estimate the probability of testicular cervical cancer over a defined period of time will help clinicians identify individuals at higher risk of specific cancers, allowing for earlier or more frequent screening and counseling of behavioral changes to decrease risk.

  13. Ovarian Cancer Risk Prediction Models

    Science.gov (United States)

    Developing statistical models that estimate the probability of developing ovarian cancer over a defined period of time will help clinicians identify individuals at higher risk of specific cancers, allowing for earlier or more frequent screening and counseling of behavioral changes to decrease risk.

  14. Lung Cancer Risk Prediction Models

    Science.gov (United States)

    Developing statistical models that estimate the probability of developing lung cancer over a defined period of time will help clinicians identify individuals at higher risk of specific cancers, allowing for earlier or more frequent screening and counseling of behavioral changes to decrease risk.

  15. Multiplex networks with intrinsic fitness: Modeling the merit-fame interplay via latent layers

    Science.gov (United States)

    Fotouhi, Babak; Momeni, Naghmeh

    2015-11-01

    We consider the problem of growing multiplex networks with intrinsic fitness and inter-layer coupling. The model comprises two layers; one that incorporates fitness and another in which attachments are preferential. In the first layer, attachment probabilities are proportional to fitness values, and in the second layer, proportional to the sum of degrees in both layers. We provide analytical closed-form solutions for the joint distributions of fitness and degrees. We also derive closed-form expressions for the expected value of the degree as a function of fitness. The model alleviates two shortcomings that are present in the current models of growing multiplex networks: homogeneity of connections, and homogeneity of fitness. In this paper, we posit and analyze a growth model that is heterogeneous in both senses.

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

    CERN Document Server

    Mead, Alexander; Heymans, Catherine; Joudaki, Shahab; Heavens, Alan

    2015-01-01

    We present an optimised 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 $\\Lambda$CDM and $w$CDM models the halo-model power is accurate to $\\simeq 5$ per cent for $k\\leq 10h\\,\\mathrm{Mpc}^{-1}$ and $z\\leq 2$. We compare our results with recent revisions of the popular HALOFIT model and show that our predictions are more accurate. 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 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 limi...

  17. Modelling population dynamics model formulation, fitting and assessment using state-space methods

    CERN Document Server

    Newman, K B; Morgan, B J T; King, R; Borchers, D L; Cole, D J; Besbeas, P; Gimenez, O; Thomas, L

    2014-01-01

    This book gives a unifying framework for estimating the abundance of open populations: populations subject to births, deaths and movement, given imperfect measurements or samples of the populations.  The focus is primarily on populations of vertebrates for which dynamics are typically modelled within the framework of an annual cycle, and for which stochastic variability in the demographic processes is usually modest. Discrete-time models are developed in which animals can be assigned to discrete states such as age class, gender, maturity,  population (within a metapopulation), or species (for multi-species models). The book goes well beyond estimation of abundance, allowing inference on underlying population processes such as birth or recruitment, survival and movement. This requires the formulation and fitting of population dynamics models.  The resulting fitted models yield both estimates of abundance and estimates of parameters characterizing the underlying processes.  

  18. Model-fitting approach to kinetic analysis of non-isothermal oxidation of molybdenite

    International Nuclear Information System (INIS)

    The kinetics of molybdenite oxidation was studied by non-isothermal TGA-DTA with heating rate 5degC.min-1. The model-fitting kinetic approach applied to TGA data. The Coats-Redfern method used of model fitting. The popular model-fitting gives excellent fit non-isothermal data in chemically controlled regime. The apparent activation energy was determined to be about 34.2 kcalmol-1 With pre-exponential factor about 108 sec-1 for extent of reaction less than 0.5

  19. A Gompertzian model with random effects to cervical cancer growth

    Energy Technology Data Exchange (ETDEWEB)

    Mazlan, Mazma Syahidatul Ayuni; Rosli, Norhayati [Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Pahang (Malaysia)

    2015-05-15

    In this paper, a Gompertzian model with random effects is introduced to describe the cervical cancer growth. The parameters values of the mathematical model are estimated via maximum likehood estimation. We apply 4-stage Runge-Kutta (SRK4) for solving the stochastic model numerically. The efficiency of mathematical model is measured by comparing the simulated result and the clinical data of the cervical cancer growth. Low values of root mean-square error (RMSE) of Gompertzian model with random effect indicate good fits.

  20. Gompertzian stochastic model with delay effect to cervical cancer growth

    Energy Technology Data Exchange (ETDEWEB)

    Mazlan, Mazma Syahidatul Ayuni binti; Rosli, Norhayati binti [Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Pahang (Malaysia); Bahar, Arifah [Department of Mathematical Sciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor and UTM Centre for Industrial and Applied Mathematics (UTM-CIAM), Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor (Malaysia)

    2015-02-03

    In this paper, a Gompertzian stochastic model with time delay is introduced to describe the cervical cancer growth. The parameters values of the mathematical model are estimated via Levenberg-Marquardt optimization method of non-linear least squares. We apply Milstein scheme for solving the stochastic model numerically. The efficiency of mathematical model is measured by comparing the simulated result and the clinical data of cervical cancer growth. Low values of Mean-Square Error (MSE) of Gompertzian stochastic model with delay effect indicate good fits.

  1. Engineered Swine Models of Cancer

    OpenAIRE

    Watson, Adrienne L; Carlson, Daniel F.; Largaespada, David A; Hackett, Perry B; Fahrenkrug, Scott C.

    2016-01-01

    Over the past decade, the technology to engineer genetically modified swine has seen many advancements, and because their physiology is remarkably similar to that of humans, swine models of cancer may be extremely valuable for preclinical safety studies as well as toxicity testing of pharmaceuticals prior to the start of human clinical trials. Hence, the benefits of using swine as a large animal model in cancer research and the potential applications and future opportunities of utilizing pigs...

  2. A New Finite Interval Lifetime Distribution Model for Fitting Bathtub-Shaped Failure Rate Curve

    Directory of Open Access Journals (Sweden)

    Xiaohong Wang

    2015-01-01

    Full Text Available This paper raised a new four-parameter fitting model to describe bathtub curve, which is widely used in research on components’ life analysis, then gave explanation of model parameters, and provided parameter estimation method as well as application examples utilizing some well-known lifetime data. By comparative analysis between the new model and some existing bathtub curve fitting model, we can find that the new fitting model is very convenient and its parameters are clear; moreover, this model is of universal applicability which is not only suitable for bathtub-shaped failure rate curves but also applicable for the constant, increasing, and decreasing failure rate curves.

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

    Science.gov (United States)

    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…

  4. Heuristic modeling of carcinogenesis for the population with dichotomous susceptibility to cancer: a pancreatic cancer example.

    Directory of Open Access Journals (Sweden)

    Tengiz Mdzinarishvili

    Full Text Available At present, carcinogenic models imply that all individuals in a population are susceptible to cancer. These models either ignore a fall of the cancer incidence rate at old ages, or use some poorly identifiable parameters for its accounting. In this work, a new heuristic model is proposed. The model assumes that, in a population, only a small fraction (pool of individuals is susceptible to cancer and decomposes the problem of the carcinogenic modeling on two sequentially solvable problems: (i determination of the age-specific hazard rate in individuals susceptible to cancer (individual hazard rate from the observed hazard rate in the population (population hazard rate; and (ii modelling of the individual hazard rate by a chosen "up" of the theoretical hazard function describing cancer occurrence in individuals in time (age. The model considers carcinogenesis as a failure of individuals susceptible to cancer to resist cancer occurrence in aging and uses, as the theoretical hazard function, the three-parameter Weibull hazard function, often utilized in a failure analysis. The parameters of this function, providing the best fit of the modeled and observed individual hazard rates (determined from the population hazard rates, are the outcomes of the modeling. The model was applied to the pancreatic cancer data. It was shown that, in the populations stratified by gender, race and the geographic area of living, the modeled and observed population hazard rates of pancreatic cancer occurrence have similar turnovers at old ages. The sizes of the pools of individuals susceptible to this cancer: (i depend on gender, race and the geographic area of living; (ii proportionally influence the corresponding population hazard rates; and (iii do not influence the individual hazard rates. The model should be further tested using data on other types of cancer and for the populations stratified by different categorical variables.

  5. The Model 80 face mask fit-tester

    Energy Technology Data Exchange (ETDEWEB)

    Pasternack, A.

    1978-06-01

    Leakage from a face mask can be measured quantitatively using ethylene or sulphur hexafluoride as tracer gas. Either ethylene detector tubes or a leak detector are used with a hood which fits over the head of the person tested. The tester can be used for training, to give the wearer a feeling for the correct placement of the face mask and for tightening the straps. It can also be used to check tightness when the hair-style or shape of beard is changed.

  6. Refractive Index of Humid Air in the Infrared: Model Fits

    CERN Document Server

    Mathar, R J

    2006-01-01

    The theory of summation of electromagnetic line transitions is used to tabulate the Taylor expansion of the refractive index of humid air over the basic independent parameters (temperature, pressure, humidity, wavelength) in five separate infrared regions from the H to the Q band at a fixed percentage of Carbon Dioxide. These are least-squares fits to raw, highly resolved spectra for a set of temperatures from 10 to 25 C, a set of pressures from 500 to 1023 hPa, and a set of relative humidities from 5 to 60%. These choices reflect the prospective application to characterize ambient air at mountain altitudes of astronomical telescopes.

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

    Science.gov (United States)

    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.

  8. Skin cancer prevention coverage in popular US women's health and fitness magazines: an analysis of advertisements and articles.

    Science.gov (United States)

    Basch, Corey Hannah; Ethan, Danna; Hillyer, Grace Clarke; Berdnik, Alyssa

    2014-04-02

    The desire to be tan is a phenomenon that public health researchers have investigated, as exposure to UV radiation increases the chances of developing skin cancer.  Media messages in women's magazines have been shown to contribute to this problem. Much less is known about the prevalence of skin cancer prevention messages in these magazines. This study's aim was to identify the number and type of articles and advertised products devoted to skin health (sun protection and skin cancer prevention in particular) within five popular U.S. greater than women's health and fitness magazines. We analyzed articles and advertisements over seven months of issues of the following popular women's health and fitness magazines: Fitness, Health, Self, Shape, and Women's Health, March 2013 through September 2013. Overall, 31 issues of the five magazines with a total of 780 articles and 1,986 advertisements were analyzed. Of the 780 articles, a mere 2.9% (n=23) were devoted to skin. Of the 258 skin product advertisements, less than 20% of the products contained sun protection factor (SPF). These findings suggest that women's health and fitness magazines can improve their efforts in informing women of skin cancer risks and preventive measures to minimize these risks. The role of these magazines in building health literacy among their readers is also discussed.

  9. Skin cancer prevention coverage in popular US women's health and fitness magazines: an analysis of advertisements and articles.

    Science.gov (United States)

    Basch, Corey Hannah; Ethan, Danna; Hillyer, Grace Clarke; Berdnik, Alyssa

    2014-07-01

    The desire to be tan is a phenomenon that public health researchers have investigated, as exposure to UV radiation increases the chances of developing skin cancer.  Media messages in women's magazines have been shown to contribute to this problem. Much less is known about the prevalence of skin cancer prevention messages in these magazines. This study's aim was to identify the number and type of articles and advertised products devoted to skin health (sun protection and skin cancer prevention in particular) within five popular U.S. greater than women's health and fitness magazines. We analyzed articles and advertisements over seven months of issues of the following popular women's health and fitness magazines: Fitness, Health, Self, Shape, and Women's Health, March 2013 through September 2013. Overall, 31 issues of the five magazines with a total of 780 articles and 1,986 advertisements were analyzed. Of the 780 articles, a mere 2.9% (n=23) were devoted to skin. Of the 258 skin product advertisements, less than 20% of the products contained sun protection factor (SPF). These findings suggest that women's health and fitness magazines can improve their efforts in informing women of skin cancer risks and preventive measures to minimize these risks. The role of these magazines in building health literacy among their readers is also discussed. PMID:24999136

  10. Cell Competition and Its Role in the Regulation of Cell Fitness from Development to Cancer.

    Science.gov (United States)

    Di Gregorio, Aida; Bowling, Sarah; Rodriguez, Tristan Argeo

    2016-09-26

    Cell competition is a cell fitness-sensing mechanism conserved from insects to mammals that eliminates those cells that, although viable, are less fit than their neighbors. An important implication of cell competition is that cellular fitness is not only a cell-intrinsic property but is also determined relative to the fitness of neighboring cells: a cell that is of suboptimal fitness in one context may be "super-fit" in the context of a different cell population. Here we discuss the mechanisms by which cell competition measures and communicates cell fitness levels and the implications of this mechanism for development, regeneration, and tumor progression. PMID:27676435

  11. The issue of statistical power for overall model fit in evaluating structural equation models

    Directory of Open Access Journals (Sweden)

    Richard HERMIDA

    2015-06-01

    Full Text Available Statistical power is an important concept for psychological research. However, examining the power of a structural equation model (SEM is rare in practice. This article provides an accessible review of the concept of statistical power for the Root Mean Square Error of Approximation (RMSEA index of overall model fit in structural equation modeling. By way of example, we examine the current state of power in the literature by reviewing studies in top Industrial-Organizational (I/O Psychology journals using SEMs. Results indicate that in many studies, power is very low, which implies acceptance of invalid models. Additionally, we examined methodological situations which may have an influence on statistical power of SEMs. Results showed that power varies significantly as a function of model type and whether or not the model is the main model for the study. Finally, results indicated that power is significantly related to model fit statistics used in evaluating SEMs. The results from this quantitative review imply that researchers should be more vigilant with respect to power in structural equation modeling. We therefore conclude by offering methodological best practices to increase confidence in the interpretation of structural equation modeling results with respect to statistical power issues.

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

    Science.gov (United States)

    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…

  13. Insight into model mechanisms through automatic parameter fitting: a new methodological framework for model development

    Science.gov (United States)

    2014-01-01

    Background Striking a balance between the degree of model complexity and parameter identifiability, while still producing biologically feasible simulations using modelling is a major challenge in computational biology. While these two elements of model development are closely coupled, parameter fitting from measured data and analysis of model mechanisms have traditionally been performed separately and sequentially. This process produces potential mismatches between model and data complexities that can compromise the ability of computational frameworks to reveal mechanistic insights or predict new behaviour. In this study we address this issue by presenting a generic framework for combined model parameterisation, comparison of model alternatives and analysis of model mechanisms. Results The presented methodology is based on a combination of multivariate metamodelling (statistical approximation of the input–output relationships of deterministic models) and a systematic zooming into biologically feasible regions of the parameter space by iterative generation of new experimental designs and look-up of simulations in the proximity of the measured data. The parameter fitting pipeline includes an implicit sensitivity analysis and analysis of parameter identifiability, making it suitable for testing hypotheses for model reduction. Using this approach, under-constrained model parameters, as well as the coupling between parameters within the model are identified. The methodology is demonstrated by refitting the parameters of a published model of cardiac cellular mechanics using a combination of measured data and synthetic data from an alternative model of the same system. Using this approach, reduced models with simplified expressions for the tropomyosin/crossbridge kinetics were found by identification of model components that can be omitted without affecting the fit to the parameterising data. Our analysis revealed that model parameters could be constrained to a standard

  14. Application of fit indices in testing the theoretical models in psychology: Possibilities and limitations

    Directory of Open Access Journals (Sweden)

    Lazarević Ljiljana

    2008-01-01

    Full Text Available This paper deals with the fit indices used in Structural Equation Modelling (SEM for testing theoretical models and the difficulties that can occur during the testing of theoretical models in different fields of psychology. The paper discusses the basic assumptions of SEM and presents the indices used for assessing the fit of theoretical models. This paper also presents the procedures for calculating the basic statistic for assessing the fit of models (χ2, as well as for calculating the most commonly used fit indices, in order to gain a better insight into the advantages and potential difficulties that can occur during their usage. We mention the difficulties regarding the assessment of fit of the model based on χ2 and the discussed fit indices stemming from the sample size, data distribution and assessment methods, wrong specification of model and disturbance of normality and independence of latent variables, as well as the ways in which these difficulties can be overcome. This paper provides a proposal for the approach to presenting the fit indices in reports on studies where theoretical models were tested via SEM.

  15. The Alberta moving beyond breast cancer (AMBER cohort study: a prospective study of physical activity and health-related fitness in breast cancer survivors

    Directory of Open Access Journals (Sweden)

    Courneya Kerry S

    2012-11-01

    Full Text Available Abstract Background Limited research has examined the association between physical activity, health-related fitness, and disease outcomes in breast cancer survivors. Here, we present the rationale and design of the Alberta Moving Beyond Breast Cancer (AMBER Study, a prospective cohort study designed specifically to examine the role of physical activity and health-related fitness in breast cancer survivorship from the time of diagnosis and for the balance of life. The AMBER Study will examine the role of physical activity and health-related fitness in facilitating treatment completion, alleviating treatment side effects, hastening recovery after treatments, improving long term quality of life, and reducing the risks of disease recurrence, other chronic diseases, and premature death. Methods/Design The AMBER Study will enroll 1500 newly diagnosed, incident, stage I-IIIc breast cancer survivors in Alberta, Canada over a 5 year period. Assessments will be made at baseline (within 90 days of surgery, 1 year, and 3 years consisting of objective and self-reported measurements of physical activity, health-related fitness, blood collection, lymphedema, patient-reported outcomes, and determinants of physical activity. A final assessment at 5 years will measure patient-reported data only. The cohort members will be followed for an additional 5 years for disease outcomes. Discussion The AMBER cohort will answer key questions related to physical activity and health-related fitness in breast cancer survivors including: (1 the independent and interactive associations of physical activity and health-related fitness with disease outcomes (e.g., recurrence, breast cancer-specific mortality, overall survival, treatment completion rates, symptoms and side effects (e.g., pain, lymphedema, fatigue, neuropathy, quality of life, and psychosocial functioning (e.g., anxiety, depression, self-esteem, happiness, (2 the determinants of physical activity and

  16. Diploid biological evolution models with general smooth fitness landscapes and recombination.

    Science.gov (United States)

    Saakian, David B; Kirakosyan, Zara; Hu, Chin-Kun

    2008-06-01

    Using a Hamilton-Jacobi equation approach, we obtain analytic equations for steady-state population distributions and mean fitness functions for Crow-Kimura and Eigen-type diploid biological evolution models with general smooth hypergeometric fitness landscapes. Our numerical solutions of diploid biological evolution models confirm the analytic equations obtained. We also study the parallel diploid model for the simple case of recombination and calculate the variance of distribution, which is consistent with numerical results. PMID:18643300

  17. A model for programmatic assessment fit for purpose.

    NARCIS (Netherlands)

    Vleuten, C.P.M. van der; Schuwirth, L.W.; Driessen, E.W.; Dijkstra, J.; Tigelaar, D.; Baartman, L.K.; Tartwijk, J. van

    2012-01-01

    We propose a model for programmatic assessment in action, which simultaneously optimises assessment for learning and assessment for decision making about learner progress. This model is based on a set of assessment principles that are interpreted from empirical research. It specifies cycles of train

  18. Fitting the Two-Higgs-Doublet model of type II

    CERN Document Server

    Eberhardt, Otto

    2014-01-01

    We present the current status of the Two-Higgs-Doublet model of type II. Taking into account all available relevant information, we exclude at $95$% CL sizeable deviations of the so-called alignment limit, in which all couplings of the light CP-even Higgs boson $h$ are Standard-Model-like. While we can set a lower limit of $240$ GeV on the mass of the pseudoscalar Higgs boson at $95$% CL, the mass of the heavy CP-even Higgs boson $H$ can be even lighter than $200$ GeV. The strong constraints on the model parameters also set limits on the triple Higgs couplings: the $hhh$ coupling in the Two-Higgs-Doublet model of type II cannot be larger than in the Standard Model, while the $hhH$ coupling can maximally be $2.5$ times the size of the Standard Model $hhh$ coupling, assuming an $H$ mass below $1$ TeV. The selection of benchmark scenarios which maximize specific effects within the allowed regions for further collider studies is illustrated for the $H$ branching fraction to fermions and gauge bosons. As an exampl...

  19. A versatile curve-fit model for linear to deeply concave rank abundance curves

    OpenAIRE

    Neuteboom, J.H.; Struik, P. C.

    2005-01-01

    A new, flexible curve-fit model for linear to concave rank abundance curves was conceptualized and validated using observational data. The model links the geometric-series model and log-series model and can also fit deeply concave rank abundance curves. The model is based ¿ in an unconventional way ¿ on the negative- binomial distribution and calculates (like the log-series model) a species-diversity index. The index is defined as the expected number of singleton species (species present with...

  20. Fitness model for the Italian interbank money market

    Science.gov (United States)

    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 fitness model for the Italian Interbank Money Market

    CERN Document Server

    De Masi, G; Iori, G

    2006-01-01

    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.

  2. Fitness model for the Italian interbank money market.

    Science.gov (United States)

    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.

  3. BOUSSINESQ MODELLING OF NEARSHORE WAVES UNDER BODY FITTED COORDINATE

    Institute of Scientific and Technical Information of China (English)

    FANG Ke-zhao; ZOU Zhi-li; LIU Zhong-bo; YIN Ji-wei

    2012-01-01

    A set of nonlinear Boussinesq equations with fully nonlinearity property is solved numerically in generalized coordinates,to develop a Boussinesq-type wave model in dealing with irregular computation boundaries in complex nearshore regions and to facilitate the grid refinements in simulations.The governing equations expressed in contravariant components of velocity vectors under curv ilinear coordinates are derived and a high order finite difference scheme on a staggered grid is employed for the numerical implementation.The developed model is used to simulate nearshore wave propagations under curvilinear coordinates,the numerical results are compared against analytical or experimental data with a good agreement.

  4. Fit of different linear models to the lactation curve of Italian water buffalo

    OpenAIRE

    N. P.P. Macciotta; N. Bacciu; Catillo, G; C. Dimauro

    2005-01-01

    Mathematical modelling of lactation curve by suitable functions of time, widely used in the dairy cattle industry, can represent also for buffaloes a fundamental tool for management and breeding decision, where average curves are considered, and for genetic evaluation by random regression models, where individual patterns are fitted. Average lactation curves of Italian Buffalo cows have been fitted with good results (Catillo et al., 2002) whereas there is a lack of information on ...

  5. The empirical likelihood goodness-of-fit test for regression model

    Institute of Scientific and Technical Information of China (English)

    Li-xing ZHU; Yong-song QIN; Wang-li XU

    2007-01-01

    Goodness-of-fit test for regression modes has received much attention in literature. In this paper, empirical likelihood (EL) goodness-of-fit tests for regression models including classical parametric and autoregressive (AR) time series models are proposed. Unlike the existing locally smoothing and globally smoothing methodologies, the new method has the advantage that the tests are self-scale invariant and that the asymptotic null distribution is chi-squared. Simulations are carried out to illustrate the methodology.

  6. Goodness-of-fit tests in mixed models

    KAUST Repository

    Claeskens, Gerda

    2009-05-12

    Mixed models, with both random and fixed effects, are most often estimated on the assumption that the random effects are normally distributed. In this paper we propose several formal tests of the hypothesis that the random effects and/or errors are normally distributed. Most of the proposed methods can be extended to generalized linear models where tests for non-normal distributions are of interest. Our tests are nonparametric in the sense that they are designed to detect virtually any alternative to normality. In case of rejection of the null hypothesis, the nonparametric estimation method that is used to construct a test provides an estimator of the alternative distribution. © 2009 Sociedad de Estadística e Investigación Operativa.

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

    Science.gov (United States)

    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. PMID:26186694

  8. Radiation risk models for all solid cancers other than those types of cancer requiring individual assessments after a nuclear accident.

    Science.gov (United States)

    Walsh, Linda; Zhang, Wei

    2016-03-01

    In the assessment of health risks after nuclear accidents, some health consequences require special attention. For example, in their 2013 report on health risk assessment after the Fukushima nuclear accident, the World Health Organisation (WHO) panel of experts considered risks of breast cancer, thyroid cancer and leukaemia. For these specific cancer types, use was made of already published excess relative risk (ERR) and excess absolute risk (EAR) models for radiation-related cancer incidence fitted to the epidemiological data from the Japanese A-bomb Life Span Study (LSS). However, it was also considered important to assess all other types of solid cancer together and the WHO, in their above-mentioned report, stated "No model to calculate the risk for all other solid cancer excluding breast and thyroid cancer risks is available from the LSS data". Applying the LSS models for all solid cancers along with the models for the specific sites means that some cancers have an overlap in the risk evaluations. Thus, calculating the total solid cancer risk plus the breast cancer risk plus the thyroid cancer risk can overestimate the total risk by several per cent. Therefore, the purpose of this paper was to publish the required models for all other solid cancers, i.e. all solid cancers other than those types of cancer requiring special attention after a nuclear accident. The new models presented here have been fitted to the same LSS data set from which the risks provided by the WHO were derived. Although it is known already that the EAR and ERR effect modifications by sex are statistically significant for the outcome "all solid cancer", it is shown here that sex modification is not statistically significant for the outcome "all solid cancer other than thyroid and breast cancer". It is also shown here that the sex-averaged solid cancer risks with and without the sex modification are very similar once breast and thyroid cancers are factored out. Some other notable model

  9. Radiation risk models for all solid cancers other than those types of cancer requiring individual assessments after a nuclear accident.

    Science.gov (United States)

    Walsh, Linda; Zhang, Wei

    2016-03-01

    In the assessment of health risks after nuclear accidents, some health consequences require special attention. For example, in their 2013 report on health risk assessment after the Fukushima nuclear accident, the World Health Organisation (WHO) panel of experts considered risks of breast cancer, thyroid cancer and leukaemia. For these specific cancer types, use was made of already published excess relative risk (ERR) and excess absolute risk (EAR) models for radiation-related cancer incidence fitted to the epidemiological data from the Japanese A-bomb Life Span Study (LSS). However, it was also considered important to assess all other types of solid cancer together and the WHO, in their above-mentioned report, stated "No model to calculate the risk for all other solid cancer excluding breast and thyroid cancer risks is available from the LSS data". Applying the LSS models for all solid cancers along with the models for the specific sites means that some cancers have an overlap in the risk evaluations. Thus, calculating the total solid cancer risk plus the breast cancer risk plus the thyroid cancer risk can overestimate the total risk by several per cent. Therefore, the purpose of this paper was to publish the required models for all other solid cancers, i.e. all solid cancers other than those types of cancer requiring special attention after a nuclear accident. The new models presented here have been fitted to the same LSS data set from which the risks provided by the WHO were derived. Although it is known already that the EAR and ERR effect modifications by sex are statistically significant for the outcome "all solid cancer", it is shown here that sex modification is not statistically significant for the outcome "all solid cancer other than thyroid and breast cancer". It is also shown here that the sex-averaged solid cancer risks with and without the sex modification are very similar once breast and thyroid cancers are factored out. Some other notable model

  10. Model-independent analysis of dark energy: supernova fitting result

    International Nuclear Information System (INIS)

    This paper uses supernova data to explore the property of dark energy by some model-independent methods. We first Taylor expand the scale factor a(t) and the luminosity distance dL to the fifth order to find that the deceleration parameter q0 DE0 is less than -1 almost at 1σ level from all the parametrizations used in this paper. We also find that the transition redshift from deceleration phase to acceleration phase is zT ∼ 0.3

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. ANIMAL MODELS OF CANCER: A REVIEW

    OpenAIRE

    Archana M Navale

    2013-01-01

    Cancer is the second leading cause of death worldwide. In USA three persons out of five will develop some type of cancer. Beyond these statistics of mortality, the morbidity due to cancer presents a real scary picture. Last 50 years of research has rendered some types of cancer curable, but still the major fear factor associated with this disease is unchanged. Animal models are classified according to the method of induction of cancer in the animal. Spontaneous tumor models are the most primi...

  13. Adaptation in tunably rugged fitness landscapes: the rough Mount Fuji model.

    Science.gov (United States)

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

    2014-10-01

    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.

  14. Are pollination "syndromes" predictive? Asian dalechampia fit neotropical models.

    Science.gov (United States)

    Armbruster, W Scott; Gong, Yan-Bing; Huang, Shuang-Quan

    2011-07-01

    Using pollination syndrome parameters and pollinator correlations with floral phenotype from the Neotropics, we predicted that Dalechampia bidentata Blume (Euphorbiaceae) in southern China would be pollinated by female resin-collecting bees between 12 and 20 mm in length. Observations in southwestern Yunnan Province, China, revealed pollination primarily by resin-collecting female Megachile (Callomegachile) faceta Bingham (Hymenoptera: Megachilidae). These bees, at 14 mm in length, were in the predicted size range, confirming the utility of syndromes and models developed in distant regions. Phenotypic selection analyses and estimation of adaptive surfaces and adaptive accuracies together suggest that the blossoms of D. bidentata are well adapted to pollination by their most common floral visitors. PMID:21670584

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

    Science.gov (United States)

    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. PMID:17706176

  16. Nonlinear models for fitting growth curves of Nellore cows reared in the Amazon Biome

    Directory of Open Access Journals (Sweden)

    Kedma Nayra da Silva Marinho

    2013-09-01

    Full Text Available Growth curves of Nellore cows were estimated by comparing six nonlinear models: Brody, Logistic, two alternatives by Gompertz, Richards and Von Bertalanffy. The models were fitted to weight-age data, from birth to 750 days of age of 29,221 cows, born between 1976 and 2006 in the Brazilian states of Acre, Amapá, Amazonas, Pará, Rondônia, Roraima and Tocantins. The models were fitted by the Gauss-Newton method. The goodness of fit of the models was evaluated by using mean square error, adjusted coefficient of determination, prediction error and mean absolute error. Biological interpretation of parameters was accomplished by plotting estimated weights versus the observed weight means, instantaneous growth rate, absolute maturity rate, relative instantaneous growth rate, inflection point and magnitude of the parameters A (asymptotic weight and K (maturing rate. The Brody and Von Bertalanffy models fitted the weight-age data but the other models did not. The average weight (A and growth rate (K were: 384.6±1.63 kg and 0.0022±0.00002 (Brody and 313.40±0.70 kg and 0.0045±0.00002 (Von Bertalanffy. The Brody model provides better goodness of fit than the Von Bertalanffy model.

  17. Comparative model accuracy of a data-fitted generalized Aw-Rascle-Zhang model

    CERN Document Server

    Fan, Shimao; Seibold, Benjamin

    2013-01-01

    The Aw-Rascle-Zhang (ARZ) model can be interpreted as a generalization of the Lighthill-Whitham-Richards (LWR) model, possessing a family of fundamental diagram curves, each of which represents a class of drivers with a different empty road velocity. A weakness of this approach is that different drivers possess vastly different densities at which traffic flow stagnates. This drawback can be overcome by modifying the pressure relation in the ARZ model, leading to the generalized Aw-Rascle-Zhang (GARZ) model. We present an approach to determine the parameter functions of the GARZ model from fundamental diagram measurement data. The predictive accuracy of the resulting data-fitted GARZ model is compared to other traffic models by means of a three-detector test setup, employing two types of data: vehicle trajectory data, and sensor data. This work also considers the extension of the ARZ and the GARZ models to models with a relaxation term, and conducts an investigation of the optimal relaxation time.

  18. Are Fit Indices Biased in Favor of Bi-Factor Models in Cognitive Ability Research?: A Comparison of Fit in Correlated Factors, Higher-Order, and Bi-Factor Models via Monte Carlo Simulations

    Directory of Open Access Journals (Sweden)

    Grant B. Morgan

    2015-02-01

    Full Text Available Bi-factor confirmatory factor models have been influential in research on cognitive abilities because they often better fit the data than correlated factors and higher-order models. They also instantiate a perspective that differs from that offered by other models. Motivated by previous work that hypothesized an inherent statistical bias of fit indices favoring the bi-factor model, we compared the fit of correlated factors, higher-order, and bi-factor models via Monte Carlo methods. When data were sampled from a true bi-factor structure, each of the approximate fit indices was more likely than not to identify the bi-factor solution as the best fitting. When samples were selected from a true multiple correlated factors structure, approximate fit indices were more likely overall to identify the correlated factors solution as the best fitting. In contrast, when samples were generated from a true higher-order structure, approximate fit indices tended to identify the bi-factor solution as best fitting. There was extensive overlap of fit values across the models regardless of true structure. Although one model may fit a given dataset best relative to the other models, each of the models tended to fit the data well in absolute terms. Given this variability, models must also be judged on substantive and conceptual grounds.

  19. A simple model of group selection that cannot be analyzed with inclusive fitness

    NARCIS (Netherlands)

    M. van Veelen; S. Luo; B. Simon

    2014-01-01

    A widespread claim in evolutionary theory is that every group selection model can be recast in terms of inclusive fitness. Although there are interesting classes of group selection models for which this is possible, we show that it is not true in general. With a simple set of group selection models,

  20. Asymptotic Fitness Distribution in the Bak-Sneppen Model of Biological Evolution with Four Species

    Science.gov (United States)

    Schlemm, Eckhard

    2012-08-01

    We suggest a new method to compute the asymptotic fitness distribution in the Bak-Sneppen model of biological evolution. As applications we derive the full asymptotic distribution in the four-species model, and give an explicit linear recurrence relation for a set of coefficients determining the asymptotic distribution in the five-species model.

  1. Asymptotic fitness distribution in the Bak-Sneppen model of biological evolution with four species

    OpenAIRE

    Schlemm, Eckhard

    2012-01-01

    We suggest a new method to compute the asymptotic fitness distribution in the Bak-Sneppen model of biological evolution. As applications we derive the full asymptotic distribution in the four-species model, and give an explicit linear recurrence relation for a set of coefficients determining the asymptotic distribution in the five-species model.

  2. Three dimensional fuzzy influence analysis of fitting algorithms on integrated chip topographic modeling

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Zhong Wei; Wang, Yi Jun [Guangzhou Univ., Guangzhou (China); Ye, Bang Yan [South China Univ. of Technology, Guangzhou (China); Brauwer, Richard Kars [Indian Institute of Technology, Kanpur (India)

    2012-10-15

    In inspecting the detailed performance results of surface precision modeling in different external parameter conditions, the integrated chip surfaces should be evaluated and assessed during topographic spatial modeling processes. The application of surface fitting algorithms exerts a considerable influence on topographic mathematical features. The influence mechanisms caused by different surface fitting algorithms on the integrated chip surface facilitate the quantitative analysis of different external parameter conditions. By extracting the coordinate information from the selected physical control points and using a set of precise spatial coordinate measuring apparatus, several typical surface fitting algorithms are used for constructing micro topographic models with the obtained point cloud. In computing for the newly proposed mathematical features on surface models, we construct the fuzzy evaluating data sequence and present a new three dimensional fuzzy quantitative evaluating method. Through this method, the value variation tendencies of topographic features can be clearly quantified. The fuzzy influence discipline among different surface fitting algorithms, topography spatial features, and the external science parameter conditions can be analyzed quantitatively and in detail. In addition, quantitative analysis can provide final conclusions on the inherent influence mechanism and internal mathematical relation in the performance results of different surface fitting algorithms, topographic spatial features, and their scientific parameter conditions in the case of surface micro modeling. The performance inspection of surface precision modeling will be facilitated and optimized as a new research idea for micro-surface reconstruction that will be monitored in a modeling process.

  3. 13A. Integrative Cancer Care: The Life Over Cancer Model

    OpenAIRE

    Block, Keith; Block, Penny; Gyllenhaal, Charlotte; Shoham, Jacob

    2013-01-01

    Focus Areas: Integrative Algorithms of Care Integrative cancer treatment fully blends conventional cancer treatment with integrative therapies such as diet, supplements, exercise and biobehavioral approaches. The Life Over Cancer model comprises three spheres of intervention: improving lifestyle, improving biochemical environment (terrain), and improving tolerance of conventional treatment. These levels are applied within the context of a life-affirming approach to cancer patients and treatme...

  4. Spin models inferred from patient data faithfully describe HIV fitness landscapes and enable rational vaccine design

    CERN Document Server

    Shekhar, Karthik; Ferguson, Andrew L; Barton, John P; Kardar, Mehran; Chakraborty, Arup K

    2013-01-01

    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 non-equilibrium 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 \\'{a} 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 f...

  5. Efficient Constrained Local Model Fitting for Non-Rigid Face Alignment

    OpenAIRE

    Lucey, Simon; Wang, Yang; Cox, Mark; Sridharan, Sridha; Cohn, Jeffery F.

    2009-01-01

    Active appearance models (AAMs) have demonstrated great utility when being employed for non-rigid face alignment/tracking. The “simultaneous” algorithm for fitting an AAM achieves good non-rigid face registration performance, but has poor real time performance (2-3 fps). The “project-out” algorithm for fitting an AAM achieves faster than real time performance (> 200 fps) but suffers from poor generic alignment performance. In this paper we introduce an extension to a discriminative method for...

  6. Optimisation of Ionic Models to Fit Tissue Action Potentials: Application to 3D Atrial Modelling

    Directory of Open Access Journals (Sweden)

    Amr Al Abed

    2013-01-01

    Full Text Available A 3D model of atrial electrical activity has been developed with spatially heterogeneous electrophysiological properties. The atrial geometry, reconstructed from the male Visible Human dataset, included gross anatomical features such as the central and peripheral sinoatrial node (SAN, intra-atrial connections, pulmonary veins, inferior and superior vena cava, and the coronary sinus. Membrane potentials of myocytes from spontaneously active or electrically paced in vitro rabbit cardiac tissue preparations were recorded using intracellular glass microelectrodes. Action potentials of central and peripheral SAN, right and left atrial, and pulmonary vein myocytes were each fitted using a generic ionic model having three phenomenological ionic current components: one time-dependent inward, one time-dependent outward, and one leakage current. To bridge the gap between the single-cell ionic models and the gross electrical behaviour of the 3D whole-atrial model, a simplified 2D tissue disc with heterogeneous regions was optimised to arrive at parameters for each cell type under electrotonic load. Parameters were then incorporated into the 3D atrial model, which as a result exhibited a spontaneously active SAN able to rhythmically excite the atria. The tissue-based optimisation of ionic models and the modelling process outlined are generic and applicable to image-based computer reconstruction and simulation of excitable tissue.

  7. Use of posterior predictive assessments to evaluate model fit in multilevel logistic regression

    OpenAIRE

    Green, Martin J.; Medley, Graham F; Browne, William J.

    2009-01-01

    Assessing the fit of a model is an important final step in any statistical analysis, but this is not straightforward when complex discrete response models are used. Cross validation and posterior predictions have been suggested as methods to aid model criticism. In this paper a comparison is made between four methods of model predictive assessment in the context of a three level logistic regression model for clinical mastitis in dairy cattle; cross validation, a prediction using the full post...

  8. Is Model Fitting Necessary for Model-Based fMRI?

    Science.gov (United States)

    Wilson, Robert C; Niv, Yael

    2015-06-01

    Model-based analysis of fMRI data is an important tool for investigating the computational role of different brain regions. With this method, theoretical models of behavior can be leveraged to find the brain structures underlying variables from specific algorithms, such as prediction errors in reinforcement learning. One potential weakness with this approach is that models often have free parameters and thus the results of the analysis may depend on how these free parameters are set. In this work we asked whether this hypothetical weakness is a problem in practice. We first developed general closed-form expressions for the relationship between results of fMRI analyses using different regressors, e.g., one corresponding to the true process underlying the measured data and one a model-derived approximation of the true generative regressor. Then, as a specific test case, we examined the sensitivity of model-based fMRI to the learning rate parameter in reinforcement learning, both in theory and in two previously-published datasets. We found that even gross errors in the learning rate lead to only minute changes in the neural results. Our findings thus suggest that precise model fitting is not always necessary for model-based fMRI. They also highlight the difficulty in using fMRI data for arbitrating between different models or model parameters. While these specific results pertain only to the effect of learning rate in simple reinforcement learning models, we provide a template for testing for effects of different parameters in other models. PMID:26086934

  9. Is Model Fitting Necessary for Model-Based fMRI?

    Science.gov (United States)

    Wilson, Robert C; Niv, Yael

    2015-06-01

    Model-based analysis of fMRI data is an important tool for investigating the computational role of different brain regions. With this method, theoretical models of behavior can be leveraged to find the brain structures underlying variables from specific algorithms, such as prediction errors in reinforcement learning. One potential weakness with this approach is that models often have free parameters and thus the results of the analysis may depend on how these free parameters are set. In this work we asked whether this hypothetical weakness is a problem in practice. We first developed general closed-form expressions for the relationship between results of fMRI analyses using different regressors, e.g., one corresponding to the true process underlying the measured data and one a model-derived approximation of the true generative regressor. Then, as a specific test case, we examined the sensitivity of model-based fMRI to the learning rate parameter in reinforcement learning, both in theory and in two previously-published datasets. We found that even gross errors in the learning rate lead to only minute changes in the neural results. Our findings thus suggest that precise model fitting is not always necessary for model-based fMRI. They also highlight the difficulty in using fMRI data for arbitrating between different models or model parameters. While these specific results pertain only to the effect of learning rate in simple reinforcement learning models, we provide a template for testing for effects of different parameters in other models.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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…

  12. Improved fitting of PIXE spectra: the Voigt profile and Si(Li) detector modeling

    Energy Technology Data Exchange (ETDEWEB)

    Hildner, M.L. [Sandia National Labs., Livermore, CA (United States); Antolak, A.J. [Sandia National Labs., Livermore, CA (United States); Bench, G.S. [Lawrence Livermore National Lab., CA (United States)

    1996-04-11

    The true emitted X-ray lineshape as measured by a Si(Li) detector is the convolution of the intrinsic Lorentzian X-ray lineshape and the detector response function. We demonstrate the necessity of using the Voigt profile -the convolution of a Lorentzian and a Gaussian - to fit the full-energy peak portion of directly measured X-ray lines. By incorporating the Voigtian in our PIXE spectrum fitting code, PIXEF, we have found consistent improvement in the quality of fit and calculated elemental yields. We have also found that the Voigtian fit is required to give an accurate ratio of tail to peak intensity. We attribute the tail to a surface layer of incomplete charge collection (ICC) at the front of the detector. Although this model is improved by appropriately accounting for the loss of photoelectrons that travel back to the ICC layer after being emitted from the intrinsic region, it appears to fail when the full-energy peak is fit to a Gaussian. On the other hand, excellent agreement between the improved model and experiment is found when the full-energy peak is fit to a Voigtian. (orig.).

  13. Modelling metabolic evolution on phenotypic fitness landscapes: a case study on C4 photosynthesis.

    Science.gov (United States)

    Heckmann, David

    2015-12-01

    How did the complex metabolic systems we observe today evolve through adaptive evolution? The fitness landscape is the theoretical framework to answer this question. Since experimental data on natural fitness landscapes is scarce, computational models are a valuable tool to predict landscape topologies and evolutionary trajectories. Careful assumptions about the genetic and phenotypic features of the system under study can simplify the design of such models significantly. The analysis of C4 photosynthesis evolution provides an example for accurate predictions based on the phenotypic fitness landscape of a complex metabolic trait. The C4 pathway evolved multiple times from the ancestral C3 pathway and models predict a smooth 'Mount Fuji' landscape accordingly. The modelled phenotypic landscape implies evolutionary trajectories that agree with data on modern intermediate species, indicating that evolution can be predicted based on the phenotypic fitness landscape. Future directions will have to include structural changes of metabolic fitness landscape structure with changing environments. This will not only answer important evolutionary questions about reversibility of metabolic traits, but also suggest strategies to increase crop yields by engineering the C4 pathway into C3 plants.

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

    Science.gov (United States)

    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.

  15. Does the Foreign Income Shock in a Small Open Economy DSGE Model Fit Croatian Data?

    OpenAIRE

    Arčabić, Vladimir; Globan, Tomislav; Nadoveza, Ozana; Rogić Dumančić, Lucija; Tica, Josip

    2016-01-01

    The paper compares theoretical impulse response functions from a DSGE model for a small open economy with an empirical VAR model estimated for the Croatian economy. The theoretical model fits the data well as long as monetary policy is modelled as a fixed exchange rate regime. The paper considers only a foreign output gap shock. A positive foreign shock increases domestic GDP and prices and decreases terms of trade, which is in compliance with theoretical assumptions. Interest rates behave di...

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

    Science.gov (United States)

    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

  17. Proportion cured models applied to 23 cancer sites in Norway.

    Science.gov (United States)

    Cvancarova, Milada; Aagnes, Bjarte; Fosså, Sophie D; Lambert, Paul C; Møller, Bjørn; Bray, Freddie

    2013-04-01

    Statistical cure is reached when a group of patients has the same mortality as cancer-free individuals. Cure models predict the cured proportion and the median survival of fatal cases. Cure models have seldom been applied and tested systematically across all major cancer sites. Incidence and follow-up data on 23 cancer sites recorded at the Cancer Registry of Norway 1963-2007 were obtained. Mixture cure models were fitted to obtain trends and up-to-date estimates (based on period approach) assuming cured and uncured groups exist. The model converged for cancers of the mouth and pharynx, oesophagus, stomach, colon, rectum, liver, gallbladder, pancreas, lung and trachea, ovary, kidney, bladder, CNS, non-Hodgkin lymphoma (only for males) and leukemia. The proportion of cured patients increased 1963-2002 for both sexes, with the largest changes (in percent) seen for leukemia (46.4 and 46.7) and CNS (35.9, 42.0), males given first. Median survival time for the uncured cases increased for colon and rectal cancer, and there was a three- fold increase in median survival time for patients with fatal ovarian cancers. Cancers of bladder and CNS had the highest up-to-date proportion cured (in percent), 67.4 and 64.0, respectively, pancreas and liver were amongst the lowest (5.7 and 9.9, respectively). Cure models are useful when monitoring progress in cancer care, but must be applied and interpreted with caution. The absolute estimates of the cure proportion are speculative and should not be calculated where cure is not medically anticipated. PMID:22927104

  18. Fitting and comparing competing models of the species abundance distribution: assessment and prospect

    Directory of Open Access Journals (Sweden)

    Thomas J Matthews

    2014-06-01

    Full Text Available A species abundance distribution (SAD characterises patterns in the commonness and rarity of all species within an ecological community. As such, the SAD provides the theoretical foundation for a number of other biogeographical and macroecological patterns, such as the species–area relationship, as well as being an interesting pattern in its own right. While there has been resurgence in the study of SADs in the last decade, less focus has been placed on methodology in SAD research, and few attempts have been made to synthesise the vast array of methods which have been employed in SAD model evaluation. As such, our review has two aims. First, we provide a general overview of SADs, including descriptions of the commonly used distributions, plotting methods and issues with evaluating SAD models. Second, we review a number of recent advances in SAD model fitting and comparison. We conclude by providing a list of recommendations for fitting and evaluating SAD models. We argue that it is time for SAD studies to move away from many of the traditional methods available for fitting and evaluating models, such as sole reliance on the visual examination of plots, and embrace statistically rigorous techniques. In particular, we recommend the use of both goodness-of-fit tests and model-comparison analyses because each provides unique information which one can use to draw inferences.

  19. Fitting direct covariance structures by the MSTRUCT modeling language of the CALIS procedure.

    Science.gov (United States)

    Yung, Yiu-Fai; Browne, Michael W; Zhang, Wei

    2015-02-01

    This paper demonstrates the usefulness and flexibility of the general structural equation modelling (SEM) approach to fitting direct covariance patterns or structures (as opposed to fitting implied covariance structures from functional relationships among variables). In particular, the MSTRUCT modelling language (or syntax) of the CALIS procedure (SAS/STAT version 9.22 or later: SAS Institute, 2010) is used to illustrate the SEM approach. The MSTRUCT modelling language supports a direct covariance pattern specification of each covariance element. It also supports the input of additional independent and dependent parameters. Model tests, fit statistics, estimates, and their standard errors are then produced under the general SEM framework. By using numerical and computational examples, the following tests of basic covariance patterns are illustrated: sphericity, compound symmetry, and multiple-group covariance patterns. Specification and testing of two complex correlation structures, the circumplex pattern and the composite direct product models with or without composite errors and scales, are also illustrated by the MSTRUCT syntax. It is concluded that the SEM approach offers a general and flexible modelling of direct covariance and correlation patterns. In conjunction with the use of SAS macros, the MSTRUCT syntax provides an easy-to-use interface for specifying and fitting complex covariance and correlation structures, even when the number of variables or parameters becomes large.

  20. Local and omnibus goodness-of-fit tests in classical measurement error models

    KAUST Repository

    Ma, Yanyuan

    2010-09-14

    We consider functional measurement error models, i.e. models where covariates are measured with error and yet no distributional assumptions are made about the mismeasured variable. We propose and study a score-type local test and an orthogonal series-based, omnibus goodness-of-fit test in this context, where no likelihood function is available or calculated-i.e. all the tests are proposed in the semiparametric model framework. We demonstrate that our tests have optimality properties and computational advantages that are similar to those of the classical score tests in the parametric model framework. The test procedures are applicable to several semiparametric extensions of measurement error models, including when the measurement error distribution is estimated non-parametrically as well as for generalized partially linear models. The performance of the local score-type and omnibus goodness-of-fit tests is demonstrated through simulation studies and analysis of a nutrition data set.

  1. Goodness-of- fit tests for multivariate copula-based time series models

    OpenAIRE

    Berghaus, Betina; Bücher, Axel

    2014-01-01

    In recent years, stationary time series models based on copula functions became increasingly popular in econometrics to model nonlinear temporal and cross-sectional dependencies. Within these models, we consider the problem of testing the goodness-of-fit of the parametric form of the underlying copula. Our approach is based on a dependent multiplier bootstrap and it can be applied to any stationary, strongly mixing time series. The method extends recent i.i.d. results by Koj...

  2. Study on fitness functions of genetic algorithm for dynamically correcting nuclide atmospheric diffusion model

    International Nuclear Information System (INIS)

    Background: In radioactive nuclides atmospheric diffusion models, the empirical dispersion coefficients were deduced under certain experiment conditions, whose difference with nuclear accident conditions is a source of deviation. A better estimation of the radioactive nuclide's actual dispersion process could be done by correcting dispersion coefficients with observation data, and Genetic Algorithm (GA) is an appropriate method for this correction procedure. Purpose: This study is to analyze the fitness functions' influence on the correction procedure and the forecast ability of diffusion model. Methods: GA, coupled with Lagrange dispersion model, was used in a numerical simulation to compare 4 fitness functions' impact on the correction result. Results: In the numerical simulation, the fitness function with observation deviation taken into consideration stands out when significant deviation exists in the observed data. After performing the correction procedure on the Kincaid experiment data, a significant boost was observed in the diffusion model's forecast ability. Conclusion: As the result shows, in order to improve dispersion models' forecast ability using GA, observation data should be given different weight in the fitness function corresponding to their error. (authors)

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. Fitting the linear quadratic model to detailed data sets for different dose ranges

    Science.gov (United States)

    Garcia, L. M.; Leblanc, J.; Wilkins, D.; Raaphorst, G. P.

    2006-06-01

    Survival curve behaviour and degree of correspondence between the linear-quadratic (LQ) model and experimental data in an extensive dose range for high dose rates were analysed. Detailed clonogenic assays with irradiation given in 0.5 Gy increments and a total dose range varying from 10.5 to 16 Gy were performed. The cell lines investigated were: CHOAA8 (Chinese hamster fibroblast cells), U373MG (human glioblastoma cells), CP3 and DU145 (human prostate carcinoma cell lines). The analyses were based on χ2-statistics and Monte Carlo simulation of the experiments. A decline of LQ fit quality at very low doses (<2 Gy) is observed. This result can be explained by the hypersensitive effect observed in CHOAA8, U373MG and DU145 data and an adaptive-type response in the CP3 cell line. A clear improvement of the fit is discerned by removing the low dose data points. The fit worsening at high doses also shows that LQ cannot explain this region. This shows that the LQ model fits better the middle dose region of the survival curve. The analysis conducted in our study reveals a dose dependency of the LQ fit in different cell lines.

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

    Directory of Open Access Journals (Sweden)

    Javier Macias-Guarasa

    2012-10-01

    Full Text Available 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.

  6. On Fitting Nonlinear Latent Curve Models to Multiple Variables Measured Longitudinally

    Science.gov (United States)

    Blozis, Shelley A.

    2007-01-01

    This article shows how nonlinear latent curve models may be fitted for simultaneous analysis of multiple variables measured longitudinally using Mx statistical software. Longitudinal studies often involve observation of several variables across time with interest in the associations between change characteristics of different variables measured…

  7. Small-sample robust estimators of noncentrality-based and incremental model fit

    NARCIS (Netherlands)

    Boomsma, Anne; Herzog, W.

    2009-01-01

    Traditional estimators of fit measures based on the noncentral chi-square distribution (root mean square error of approximation [RMSEA], Steiger's , etc.) tend to overreject acceptable models when the sample size is small. To handle this problem, it is proposed to employ Bartlett's (1950), Yuan's (2

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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,…

  13. Checking the Adequacy of Fit of Models from Split-Plot Designs

    DEFF Research Database (Denmark)

    Almini, A. A.; Kulahci, Murat; Montgomery, D. C.

    2009-01-01

    One of the main features that distinguish split-plot experiments from other experiments is that they involve two types of experimental errors: the whole-plot (WP) error and the subplot (SP) error. Taking this into consideration is very important when computing measures of adequacy of fit for split......-plot models. In this article, we propose the computation of two R-2, R-2-adjusted, prediction error sums of squares (PRESS), and R-2-prediction statistics to measure the adequacy of fit for the WP and the SP submodels in a split-plot design. This is complemented with the graphical analysis of the two types...... of errors to check for any violation of the underlying assumptions and the adequacy of fit of split-plot models. Using examples, we show how computing two measures of model adequacy of fit for each split-plot design model is appropriate and useful as they reveal whether the correct WP and SP effects have...

  14. Fit Gap Analysis – The Role of Business Process Reference Models

    Directory of Open Access Journals (Sweden)

    Dejan Pajk

    2013-12-01

    Full Text Available Enterprise resource planning (ERP systems support solutions for standard business processes such as financial, sales, procurement and warehouse. In order to improve the understandability and efficiency of their implementation, ERP vendors have introduced reference models that describe the processes and underlying structure of an ERP system. To select and successfully implement an ERP system, the capabilities of that system have to be compared with a company’s business needs. Based on a comparison, all of the fits and gaps must be identified and further analysed. This step usually forms part of ERP implementation methodologies and is called fit gap analysis. The paper theoretically overviews methods for applying reference models and describes fit gap analysis processes in detail. The paper’s first contribution is its presentation of a fit gap analysis using standard business process modelling notation. The second contribution is the demonstration of a process-based comparison approach between a supply chain process and an ERP system process reference model. In addition to its theoretical contributions, the results can also be practically applied to projects involving the selection and implementation of ERP systems.

  15. Bootstrapping topology and systemic risk of complex network using the fitness model

    OpenAIRE

    Musmeci N.; Battiston S.; Caldarelli G.; Puliga M.; Gabrielli A.

    2012-01-01

    We present a novel method to reconstruct complex network from partial information. We assume to know the links only for a subset of the nodes and to know some non-topological quantity (fitness) characterising every node. The missing links are generated on the basis of the latter quan- tity according to a fitness model calibrated on the subset of nodes for which links are known. We measure the quality of the reconstruction of several topological properties, such as the network density and the ...

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

    Science.gov (United States)

    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. PMID:26737125

  17. Application of log-linear models to cancer patients: a case study of data from the National Cancer Institute.

    Science.gov (United States)

    Tiensuwan, Montip; Yimprayoon, Pornpis; Lenbury, Yongwimon

    2005-09-01

    Cancer is a noninfectious disease which is on the increase throughout the world and has become a serious problem for public health in many countries, including Thailand. In Thailand, cancer has risen significantly to become a leading cause of death and most patients are admitted to the National Cancer Institute. The objective of this study is to identify the associated factors between personal, cancer/clinical variables of cancer patients using log-linear models. Tests of independence are used (chi-square and Cramer's V-value tests) to find out the relationships between any two variables. In addition two- and three-dimensional log-linear models are used to obtain estimated parameters and expected frequencies for these models. Amongst the models fitted, the best are chosen based on the analysis of deviance. The results of this study show that most paired variables of personal, cancer/clinical variables are significantly related at p-value value. Moreover, the site of cancer also affects the method of diagnostic evidence and treatment. Since the site of cancer in each sex is different, prevention for various sites of cancer should be considered for each specific sex. In addition, for male and female patients, treatment is related to the site of cancer. Consequently, physicians may consider these factors before selecting the appropriate method of treatment. PMID:16438159

  18. The mathematics of cancer: integrating quantitative models.

    Science.gov (United States)

    Altrock, Philipp M; Liu, Lin L; Michor, Franziska

    2015-12-01

    Mathematical modelling approaches have become increasingly abundant in cancer research. The complexity of cancer is well suited to quantitative approaches as it provides challenges and opportunities for new developments. In turn, mathematical modelling contributes to cancer research by helping to elucidate mechanisms and by providing quantitative predictions that can be validated. The recent expansion of quantitative models addresses many questions regarding tumour initiation, progression and metastases as well as intra-tumour heterogeneity, treatment responses and resistance. Mathematical models can complement experimental and clinical studies, but also challenge current paradigms, redefine our understanding of mechanisms driving tumorigenesis and shape future research in cancer biology.

  19. Comparison and fitting of several Global-to_beam irradiance models in Spain

    OpenAIRE

    Pagola, Íñigo; Gastón, Martín; Fernández-Peruchena, Carlos M.; Torres, Jose Luis; Silva, Manuel; Ramírez, Lourdes

    2009-01-01

    In this paper, a comparison of different global to beam irradiance models has been performed. In a first step, five global-to-beam irradiance models are compared against ground measurements from three sites in Spain. Four of these existing models have also been fitted in the selected sites, and the results are presented as well. Finally, one new model (fully described in paper 11693) is also compared with the same ground measurements. The model comparison has been made by means of first and s...

  20. A two-component model for fitting light-curves of core-collapse supernovae

    CERN Document Server

    Nagy, Andrea P

    2016-01-01

    We present an improved version of a light curve model, which is able to estimate the physical properties of different types of core-collapse supernovae having double-peaked light curves, in a quick and efficient way. The model is based on a two-component configuration consisting of a dense, inner region and an extended, low-mass envelope. Using this configuration, we estimate the initial parameters of the progenitor via fitting the shape of the quasi-bolometric light curves of 10 SNe, including Type IIP and IIb events, with model light curves. In each case we compare the fitting results with available hydrodynamic calculations, and also match the derived expansion velocities with the observed ones. Furthermore, we also compare our calculations with hydrodynamic models derived by the SNEC code, and examine the uncertainties of the estimated physical parameters caused by the assumption of constant opacity and the inaccurate knowledge of the moment of explosion.

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

    Science.gov (United States)

    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.

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

    CERN Document Server

    Juvela, M

    2013-01-01

    Sub-millimetre dust emission is an important tracer of 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. 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. 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 (MCMC) methods, comparing model predictions with observations at their native resolution. We analyse...

  3. Econometric modelling of risk adverse behaviours of entrepreneurs in the provision of house fittings in China

    Directory of Open Access Journals (Sweden)

    Rita Yi Man Li

    2012-03-01

    Full Text Available Entrepreneurs have always born the risk of running their business. They reap a profit in return for their risk taking and work. Housing developers are no different. In many countries, such as Australia, the United Kingdom and the United States, they interpret the tastes of the buyers and provide the dwellings they develop with basic fittings such as floor and wall coverings, bathroom fittings and kitchen cupboards. In mainland China, however, in most of the developments, units or houses are sold without floor or wall coverings, kitchen  or bathroom fittings. What is the motive behind this choice? This paper analyses the factors affecting housing developers’ decisions to provide fittings based on 1701 housing developments in Hangzhou, Chongqing and Hangzhou using a Probit model. The results show that developers build a higher proportion of bare units in mainland China when: 1 there is shortage of housing; 2 land costs are high so that the comparative costs of providing fittings become relatively low.

  4. Fitting the distribution of dry and wet spells with alternative probability models

    Science.gov (United States)

    Deni, Sayang Mohd; Jemain, Abdul Aziz

    2009-06-01

    The development of the rainfall occurrence model is greatly important not only for data-generation purposes, but also in providing informative resources for future advancements in water-related sectors, such as water resource management and the hydrological and agricultural sectors. Various kinds of probability models had been introduced to a sequence of dry (wet) days by previous researchers in the field. Based on the probability models developed previously, the present study is aimed to propose three types of mixture distributions, namely, the mixture of two log series distributions (LSD), the mixture of the log series Poisson distribution (MLPD), and the mixture of the log series and geometric distributions (MLGD), as the alternative probability models to describe the distribution of dry (wet) spells in daily rainfall events. In order to test the performance of the proposed new models with the other nine existing probability models, 54 data sets which had been published by several authors were reanalyzed in this study. Also, the new data sets of daily observations from the six selected rainfall stations in Peninsular Malaysia for the period 1975-2004 were used. In determining the best fitting distribution to describe the observed distribution of dry (wet) spells, a Chi-square goodness-of-fit test was considered. The results revealed that the new method proposed that MLGD and MLPD showed a better fit as more than half of the data sets successfully fitted the distribution of dry and wet spells. However, the existing models, such as the truncated negative binomial and the modified LSD, were also among the successful probability models to represent the sequence of dry (wet) days in daily rainfall occurrence.

  5. Modeling epidemics of multidrug-resistant M. tuberculosis of heterogeneous fitness

    OpenAIRE

    Cohen, Ted; Murray, Megan

    2004-01-01

    Mathematical models have recently been used to predict the future burden of multidrug-resistant tuberculosis (MDRTB)1-3. These models suggest the threat of multidrug resistance to TB control will depend on the relative ‘fitness’ of MDR strains and imply that if the average fitness of MDR strains is considerably less than that of drug-sensitive strains, the emergence of resistance will not jeopardize the success of tuberculosis control efforts. Multidrug resistance in M. tuberculosis is confer...

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

    Science.gov (United States)

    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. PMID:22624307

  7. Fitting parametric models of diffusion MRI in regions of partial volume

    Science.gov (United States)

    Eaton-Rosen, Zach; Cardoso, M. J.; Melbourne, Andrew; Orasanu, Eliza; Bainbridge, Alan; Kendall, Giles S.; Robertson, Nicola J.; Marlow, Neil; Ourselin, Sebastien

    2016-03-01

    Regional analysis is normally done by fitting models per voxel and then averaging over a region, accounting for partial volume (PV) only to some degree. In thin, folded regions such as the cerebral cortex, such methods do not work well, as the partial volume confounds parameter estimation. Instead, we propose to fit the models per region directly with explicit PV modeling. In this work we robustly estimate region-wise parameters whilst explicitly accounting for partial volume effects. We use a high-resolution segmentation from a T1 scan to assign each voxel in the diffusion image a probabilistic membership to each of k tissue classes. We rotate the DW signal at each voxel so that it aligns with the z-axis, then model the signal at each voxel as a linear superposition of a representative signal from each of the k tissue types. Fitting involves optimising these representative signals to best match the data, given the known probabilities of belonging to each tissue type that we obtained from the segmentation. We demonstrate this method improves parameter estimation in digital phantoms for the diffusion tensor (DT) and `Neurite Orientation Dispersion and Density Imaging' (NODDI) models. The method provides accurate parameter estimates even in regions where the normal approach fails completely, for example where partial volume is present in every voxel. Finally, we apply this model to brain data from preterm infants, where the thin, convoluted, maturing cortex necessitates such an approach.

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

    Directory of Open Access Journals (Sweden)

    Péter eFriedrich

    2014-07-01

    Full Text Available 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 problem 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

  9. Ensemble Modeling of Cancer Metabolism

    Directory of Open Access Journals (Sweden)

    Tahmineh eKhazaei

    2012-05-01

    Full Text Available The metabolic behaviour of cancer cells is adapted to meet their proliferative needs, with notable changes such as enhanced lactate secretion and glucose uptake rates. In this work, we use the Ensemble Modeling (EM framework to gain insight and predict potential drug targets for tumour cells. EM generates a set of models which span the space of kinetic parameters that are constrained by thermodynamics. Perturbation data based on known targets are used to screen the entire ensemble of models to obtain a sub-set, which is increasingly predictive. EM allows for incorporation of regulatory information and captures the behaviour of enzymatic reactions at the molecular level by representing reactions in the elementary reaction form. In this study, a metabolic network consisting of 58 reactions is considered and accounts for glycolysis, the pentose phosphate pathway, lipid metabolism, amino acid metabolism, and includes allosteric regulation of key enzymes. Experimentally measured intracellular and extracellular metabolite concentrations are used for developing the ensemble of models along with information on established drug targets. The resulting models predicted transaldolase (TALA and succinyl-CoA ligase (SUCOAS1m to cause a significant reduction in growth rate when repressed, relative to currently known drug targets. Furthermore, the results suggest that the synergetic repression of transaldolase and glycine hydroxymethyltransferase (GHMT2r will lead to a three-fold decrease in growth rate compared to the repression of single enzyme targets.

  10. Kompaneets Model Fitting of the Orion-Eridanus Superbubble II: Thinking Outside of Barnard's Loop

    CERN Document Server

    Pon, Andy; Alves, Joao; Bally, John; Basu, Shantanu; Tielens, Alexander G G M

    2016-01-01

    The Orion star-forming region is the nearest active high-mass star-forming region and has created a large superbubble, the Orion-Eridanus superbubble. Recent work by Ochsendorf et al. (2015) has extended the accepted boundary of the superbubble. We fit Kompaneets models of superbubbles expanding in exponential atmospheres to the new, larger shape of the Orion-Eridanus superbubble. We find that this larger morphology of the superbubble is consistent with the evolution of the superbubble being primarily controlled by expansion into the exponential Galactic disk ISM if the superbubble is oriented with the Eridanus side farther from the Sun than the Orion side. Unlike previous Kompaneets model fits that required abnormally small scale heights for the Galactic disk (<40 pc), we find morphologically consistent models with scale heights of 80 pc, similar to that expected for the Galactic disk.

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

    Energy Technology Data Exchange (ETDEWEB)

    Bailey, T.L.; Elkan, C. [Univ. of California, La Jolla, CA (United States)

    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.

  12. The Beta Problem: The Incompatibility of X-ray and Sunyaev-Zeldovich Model Fitting

    Science.gov (United States)

    Burns, Jack O.; Hallman, E.; Motl, P.; Norman, M.

    2006-12-01

    We describe an analysis of a large sample of numerically simulated clusters which demonstrates the effects of using X-ray fitted beta-model parameters with Sunyaev-Zeldovich effect (SZE) data. There is a fundamental incompatibility between beta-model fits to X-ray surface brightness profiles and those done with SZE profiles. Since observational SZE radial profiles are in short supply, the X-ray parameters are often used in SZE analysis. We show that this leads to biased estimates of the integrated Compton y-parameter inside r500 and the value of the Hubble constant calculated from clusters. We suggest a simple scaling of the X-ray beta-model parameters which brings these calculated quantities into close agreement with the true values.

  13. POLYTROPIC MODEL FITS TO THE GLOBULAR CLUSTER NGC 2419 IN MODIFIED NEWTONIAN DYNAMICS

    International Nuclear Information System (INIS)

    We present an analysis of the globular cluster NGC 2419, using a polytropic model in modified Newtonian dynamics (MOND) to reproduce recently published high-quality data on the structure and kinematics of the system. We show that a specific MOND polytropic model of NGC 2419 suggested by a previous study can be completely ruled out by the data. Furthermore, the highest likelihood fit polytrope in MOND is a substantially worse model (by a factor of ∼5000) than a Newtonian Michie model we studied previously. We conclude that the structure and dynamics of NGC 2419 favor Newtonian dynamics and do indeed challenge the MOND theory.

  14. Cancer progression modeling using static sample data.

    Science.gov (United States)

    Sun, Yijun; Yao, Jin; Nowak, Norma J; Goodison, Steve

    2014-01-01

    As molecular profiling data continues to accumulate, the design of integrative computational analyses that can provide insights into the dynamic aspects of cancer progression becomes feasible. Here, we present a novel computational method for the construction of cancer progression models based on the analysis of static tumor samples. We demonstrate the reliability of the method with simulated data, and describe the application to breast cancer data. Our findings support a linear, branching model for breast cancer progression. An interactive model facilitates the identification of key molecular events in the advance of disease to malignancy.

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

    Science.gov (United States)

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

    2016-08-01

    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 goodness-of-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

  16. Fitting a Bivariate Measurement Error Model for Episodically Consumed Dietary Components

    KAUST Repository

    Zhang, Saijuan

    2011-01-06

    There has been great public health interest in estimating usual, i.e., long-term average, intake of episodically consumed dietary components that are not consumed daily by everyone, e.g., fish, red meat and whole grains. Short-term measurements of episodically consumed dietary components have zero-inflated skewed distributions. So-called two-part models have been developed for such data in order to correct for measurement error due to within-person variation and to estimate the distribution of usual intake of the dietary component in the univariate case. However, there is arguably much greater public health interest in the usual intake of an episodically consumed dietary component adjusted for energy (caloric) intake, e.g., ounces of whole grains per 1000 kilo-calories, which reflects usual dietary composition and adjusts for different total amounts of caloric intake. Because of this public health interest, it is important to have models to fit such data, and it is important that the model-fitting methods can be applied to all episodically consumed dietary components.We have recently developed a nonlinear mixed effects model (Kipnis, et al., 2010), and have fit it by maximum likelihood using nonlinear mixed effects programs and methodology (the SAS NLMIXED procedure). Maximum likelihood fitting of such a nonlinear mixed model is generally slow because of 3-dimensional adaptive Gaussian quadrature, and there are times when the programs either fail to converge or converge to models with a singular covariance matrix. For these reasons, we develop a Monte-Carlo (MCMC) computation of fitting this model, which allows for both frequentist and Bayesian inference. There are technical challenges to developing this solution because one of the covariance matrices in the model is patterned. Our main application is to the National Institutes of Health (NIH)-AARP Diet and Health Study, where we illustrate our methods for modeling the energy-adjusted usual intake of fish and whole

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

    Science.gov (United States)

    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. PMID:26613830

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

    Science.gov (United States)

    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.

  19. Animal models of ovarian cancer

    OpenAIRE

    Shaw Tanya J; Vanderhyden Barbara C; Ethier Jean-François

    2003-01-01

    Abstract Ovarian cancer is the most lethal of all of the gynecological cancers and can arise from any cell type of the ovary, including germ cells, granulosa or stromal cells. However, the majority of ovarian cancers arise from the surface epithelium, a single layer of cells that covers the surface of the ovary. The lack of a reliable and specific method for the early detection of epithelial ovarian cancer results in diagnosis occurring most commonly at late clinical stages, when treatment is...

  20. Performance evaluation of hydrological models: Statistical significance for reducing subjectivity in goodness-of-fit assessments

    Science.gov (United States)

    Ritter, Axel; Muñoz-Carpena, Rafael

    2013-02-01

    SummarySuccess in the use of computer models for simulating environmental variables and processes requires objective model calibration and verification procedures. Several methods for quantifying the goodness-of-fit of observations against model-calculated values have been proposed but none of them is free of limitations and are often ambiguous. When a single indicator is used it may lead to incorrect verification of the model. Instead, a combination of graphical results, absolute value error statistics (i.e. root mean square error), and normalized goodness-of-fit statistics (i.e. Nash-Sutcliffe Efficiency coefficient, NSE) is currently recommended. Interpretation of NSE values is often subjective, and may be biased by the magnitude and number of data points, data outliers and repeated data. The statistical significance of the performance statistics is an aspect generally ignored that helps in reducing subjectivity in the proper interpretation of the model performance. In this work, approximated probability distributions for two common indicators (NSE and root mean square error) are derived with bootstrapping (block bootstrapping when dealing with time series), followed by bias corrected and accelerated calculation of confidence intervals. Hypothesis testing of the indicators exceeding threshold values is proposed in a unified framework for statistically accepting or rejecting the model performance. It is illustrated how model performance is not linearly related with NSE, which is critical for its proper interpretation. Additionally, the sensitivity of the indicators to model bias, outliers and repeated data is evaluated. The potential of the difference between root mean square error and mean absolute error for detecting outliers is explored, showing that this may be considered a necessary but not a sufficient condition of outlier presence. The usefulness of the approach for the evaluation of model performance is illustrated with case studies including those with

  1. Testing the goodness of fit of selected infiltration models on soils with different land use histories

    International Nuclear Information System (INIS)

    Six infiltration models, some obtained by reformulating the fitting parameters of the classical Kostiakov (1932) and Philip (1957) equations, were investigated for their ability to describe water infiltration into highly permeable sandy soils from the Nsukka plains of SE Nigeria. The models were Kostiakov, Modified Kostiakov (A), Modified Kostiakov (B), Philip, Modified Philip (A) and Modified Philip (B). Infiltration data were obtained from double ring infiltrometers on field plots established on a Knadic Paleustult (Nkpologu series) to investigate the effects of land use on soil properties and maize yield. The treatments were; (i) tilled-mulched (TM), (ii) tilled-unmulched (TU), (iii) untilled-mulched (UM), (iv) untilled-unmulched (UU) and (v) continuous pasture (CP). Cumulative infiltration was highest on the TM and lowest on the CP plots. All estimated model parameters obtained by the best fit of measured data differed significantly among the treatments. Based on the magnitude of R2 values, the Kostiakov, Modified Kostiakov (A), Philip and Modified Philip (A) models provided best predictions of cumulative infiltration as a function of time. Comparing experimental with model-predicted cumulative infiltration showed, however, that on all treatments the values predicted by the classical Kostiakov, Philip and Modified Philip (A) models deviated most from experimental data. The other models produced values that agreed very well with measured data. Considering the eases of determining the fitting parameters it is proposed that on soils with high infiltration rates, either Modified Kostiakov model (I = Kta + Ict) or Modified Philip model (I St1/2 + Ict), (where I is cumulative infiltration, K, the time coefficient, t, time elapsed, 'a' the time exponent, Ic the equilibrium infiltration rate and S, the soil water sorptivity), be used for routine characterization of the infiltration process. (author). 33 refs, 3 figs 6 tabs

  2. Efficient Constrained Local Model Fitting for Non-Rigid Face Alignment

    Science.gov (United States)

    Wang, Yang; Cox, Mark; Sridharan, Sridha; Cohn, Jeffery F.

    2009-01-01

    Active appearance models (AAMs) have demonstrated great utility when being employed for non-rigid face alignment/tracking. The “simultaneous” algorithm for fitting an AAM achieves good non-rigid face registration performance, but has poor real time performance (2-3 fps). The “project-out” algorithm for fitting an AAM achieves faster than real time performance (> 200 fps) but suffers from poor generic alignment performance. In this paper we introduce an extension to a discriminative method for non-rigid face registration/tracking referred to as a constrained local model (CLM). Our proposed method is able to achieve superior performance to the “simultaneous” AAM algorithm along with real time fitting speeds (35 fps). We improve upon the canonical CLM formulation, to gain this performance, in a number of ways by employing: (i) linear SVMs as patch-experts, (ii) a simplified optimization criteria, and (iii) a composite rather than additive warp update step. Most notably, our simplified optimization criteria for fitting the CLM divides the problem of finding a single complex registration/warp displacement into that of finding N simple warp displacements. From these N simple warp displacements, a single complex warp displacement is estimated using a weighted least-squares constraint. Another major advantage of this simplified optimization lends from its ability to be parallelized, a step which we also theoretically explore in this paper. We refer to our approach for fitting the CLM as the “exhaustive local search” (ELS) algorithm. Experiments were conducted on the CMU Multi-PIE database. PMID:20046797

  3. Efficient Constrained Local Model Fitting for Non-Rigid Face Alignment.

    Science.gov (United States)

    Lucey, Simon; Wang, Yang; Cox, Mark; Sridharan, Sridha; Cohn, Jeffery F

    2009-11-01

    Active appearance models (AAMs) have demonstrated great utility when being employed for non-rigid face alignment/tracking. The "simultaneous" algorithm for fitting an AAM achieves good non-rigid face registration performance, but has poor real time performance (2-3 fps). The "project-out" algorithm for fitting an AAM achieves faster than real time performance (> 200 fps) but suffers from poor generic alignment performance. In this paper we introduce an extension to a discriminative method for non-rigid face registration/tracking referred to as a constrained local model (CLM). Our proposed method is able to achieve superior performance to the "simultaneous" AAM algorithm along with real time fitting speeds (35 fps). We improve upon the canonical CLM formulation, to gain this performance, in a number of ways by employing: (i) linear SVMs as patch-experts, (ii) a simplified optimization criteria, and (iii) a composite rather than additive warp update step. Most notably, our simplified optimization criteria for fitting the CLM divides the problem of finding a single complex registration/warp displacement into that of finding N simple warp displacements. From these N simple warp displacements, a single complex warp displacement is estimated using a weighted least-squares constraint. Another major advantage of this simplified optimization lends from its ability to be parallelized, a step which we also theoretically explore in this paper. We refer to our approach for fitting the CLM as the "exhaustive local search" (ELS) algorithm. Experiments were conducted on the CMU Multi-PIE database. PMID:20046797

  4. Fitness, inclusive fitness, and optimization

    OpenAIRE

    Lehmann L.; Rousset F

    2014-01-01

    Individual-as-maximizing agent analogies result in a simple understanding of the functioning of the biological world. Identifying the conditions under which individuals can be regarded as fitness maximizing agents is thus of considerable interest to biologists. Here, we compare different concepts of fitness maximization, and discuss within a single framework the relationship between Hamilton's (J Theor Biol 7: 1-16, 1964) model of social interactions, Grafen's (J Evol Biol 20: 1243-1254, 2007...

  5. Tectonic plate under a localized boundary stress: fitting of a zero-range solvable model

    International Nuclear Information System (INIS)

    We suggest a method of fitting of a zero-range model of a tectonic plate under a boundary stress on the basis of comparison of the theoretical formulae for the corresponding eigenfunctions/eigenvalues with the results extraction under monitoring, in the remote zone, of non-random (regular) oscillations of the Earth with periods 0.2-6 h, on the background seismic process, in case of low seismic activity. Observations of changes of the characteristics of the oscillations (frequency, amplitude and polarization) in course of time, together with the theoretical analysis of the fitted model, would enable us to localize the stressed zone on the boundary of the plate and estimate the risk of a powerful earthquake at the zone

  6. Tectonic plate under a localized boundary stress: fitting of a zero-range solvable model

    CERN Document Server

    Petrova, L

    2008-01-01

    We suggest a method of fitting of a zero-range model of a tectonic plate under a boundary stress on the basis of comparison of the theoretical formulae for the corresponding eigenfunctions/eigenvalues with the results extraction under monitoring, in the remote zone, of non-random (regular) oscillations of the Earth with periods 0.2-6 hours, on the background seismic process, in case of low seismic activity. Observations of changes of the characteristics of the oscillations (frequency, amplitude and polarization) in course of time, together with the theoretical analysis of the fitted model, would enable us to localize the stressed zone on the boundary of the plate and estimate the risk of a powerful earthquake at the zone.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  9. Impact of Economic Development Model on the Fitting Effect of the Mathematical Model of Changes in Cultivated Land Resources

    Institute of Scientific and Technical Information of China (English)

    Xin; YAO; Min; ZHANG

    2014-01-01

    The mathematical model is often used for fitting the trend of changes in cultivated land resources in the land use planning,but the fitting effect is different in different study areas. In this paper,we take two geographically adjacent cities with great differences in the economic development model,Xinghua City and Jingjiang City,as the research object. Using logarithmic model( M1),Kuznets model( M2),logistic model( M3) and multivariate linear model( M4),we fit the process of changes in cultivated land resources during the period 1980- 2009,and compare the differences in the fitting effect between different models. In terms of the model fitting effect in Xinghua City,it is in the order of M3 > M4 > M1 > M2,which is related to the fact that the local areas lay great emphasis on agricultural development,and pay close attention to ensuring the cultivated land area; in terms of the model fitting effect in Jingjiang City,it is in the order of M1 > M3 > M4 > M2,and the deep-seated cause is that its development model is dominated by extended trade expansion,and the level of intensive land use is constantly improved. In addition,we discuss the multi-stage characteristics of changes in cultivated land resources,and propose a solution of using the same model to simulate in various phases. The research results in Jingjiang City show that the coefficient of determination in the first phase( R2=0. 958) and the standard error( SE = 0. 261) are both better than those of the original model( R2= 0. 945,SE = 0. 312); the coefficient of determination in the second phase is slightly low( R2= 0. 851),but the standard error is greatly improved( SE = 0. 137). Compared with the research conclusions of other scholars,it can be believed that this method can better solve the problems that the scatter plot of logistic model presents wave-shape and the scatter plot of Kuznets model presents " M"-shape,in order to improve the applicability of mathematical models.

  10. Avalanche dynamics in Bak-Sneppen evolution model observed with standard distribution width of fitness

    OpenAIRE

    Lee, Chaohong; Zhu, Xiwen; Gao, Kelin

    2001-01-01

    We introduce the standard distribution width of fitness to characterize the global and individual features of a ecosystem in the Bak-Sneppen evolution model. Through tracking this quantity in evolution, a different hierarchy of avalanche dynamics, $w_{0}$ avalanche is observed. The corresponding gap equation and the self-organized threshold $w_{c}$ are obtained. The critical exponents $\\tau ,$ $\\gamma $and $\\rho $, which describe the behavior of the avalanche size distribution, the average av...

  11. Convex Image Segmentation Model Based on Local and Global Intensity Fitting Energy and Split Bregman Method

    OpenAIRE

    Yunyun Yang; Boying Wu

    2012-01-01

    We propose a convex image segmentation model in a variational level set formulation. Both the local information and the global information are taken into consideration to get better segmentation results. We first propose a globally convex energy functional to combine the local and global intensity fitting terms. The proposed energy functional is then modified by adding an edge detector to force the active contour to the boundary more easily. We then apply the split Bregman method to minimize ...

  12. Goodness-of-fit test in a multivariate errors-in-variables model $AX = B$

    OpenAIRE

    Kukush, Alexander; Tsaregorodtsev, Yaroslav

    2016-01-01

    A multivariable functional errors-in-variables model $AX \\approx B$ is considered, where the data matrices $A$ and $B$ are observed with errors and a matrix parameter $X$ is to be estimated. A goodness-of-fit test is constructed based on the total least squares estimator. The proposed test is asymptotically chi-squared under null hypothesis. The power of the test under local alternatives is discussed.

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

    CERN Document Server

    Morton, R J

    2016-01-01

    {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. } {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...

  14. Liver cancer mortality rate model in Thailand

    Science.gov (United States)

    Sriwattanapongse, Wattanavadee; Prasitwattanaseree, Sukon

    2013-09-01

    Liver Cancer has been a leading cause of death in Thailand. The purpose of this study was to model and forecast liver cancer mortality rate in Thailand using death certificate reports. A retrospective analysis of the liver cancer mortality rate was conducted. Numbering of 123,280 liver cancer causes of death cases were obtained from the national vital registration database for the 10-year period from 2000 to 2009, provided by the Ministry of Interior and coded as cause-of-death using ICD-10 by the Ministry of Public Health. Multivariate regression model was used for modeling and forecasting age-specific liver cancer mortality rates in Thailand. Liver cancer mortality increased with increasing age for each sex and was also higher in the North East provinces. The trends of liver cancer mortality remained stable in most age groups with increases during ten-year period (2000 to 2009) in the Northern and Southern. Liver cancer mortality was higher in males and increase with increasing age. There is need of liver cancer control measures to remain on a sustained and long-term basis for the high liver cancer burden rate of Thailand.

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

    Science.gov (United States)

    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.

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

    Institute of Scientific and Technical Information of China (English)

    Shan-Jie Qian

    2013-01-01

    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.

  17. Role Modeling Attitudes, Physical Activity and Fitness Promoting Behaviors of Prospective Physical Education Specialists and Non-Specialists.

    Science.gov (United States)

    Cardinal, Bradley J.; Cardinal, Marita K.

    2002-01-01

    Compared the role modeling attitudes and physical activity and fitness promoting behaviors of undergraduate students majoring in physical education and in elementary education. Student teacher surveys indicated that physical education majors had more positive attitudes toward role modeling physical activity and fitness promoting behaviors and…

  18. UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions

    International Nuclear Information System (INIS)

    UROX is software designed for the interactive fitting of atomic models into electron-microscopy reconstructions. The main features of the software are presented, along with a few examples. Electron microscopy of a macromolecular structure can lead to three-dimensional reconstructions with resolutions that are typically in the 30–10 Å range and sometimes even beyond 10 Å. Fitting atomic models of the individual components of the macromolecular structure (e.g. those obtained by X-ray crystallography or nuclear magnetic resonance) into an electron-microscopy map allows the interpretation of the latter at near-atomic resolution, providing insight into the interactions between the components. Graphical software is presented that was designed for the interactive fitting and refinement of atomic models into electron-microscopy reconstructions. Several characteristics enable it to be applied over a wide range of cases and resolutions. Firstly, calculations are performed in reciprocal space, which results in fast algorithms. This allows the entire reconstruction (or at least a sizeable portion of it) to be used by taking into account the symmetry of the reconstruction both in the calculations and in the graphical display. Secondly, atomic models can be placed graphically in the map while the correlation between the model-based electron density and the electron-microscopy reconstruction is computed and displayed in real time. The positions and orientations of the models are refined by a least-squares minimization. Thirdly, normal-mode calculations can be used to simulate conformational changes between the atomic model of an individual component and its corresponding density within a macromolecular complex determined by electron microscopy. These features are illustrated using three practical cases with different symmetries and resolutions. The software, together with examples and user instructions, is available free of charge at http://mem.ibs.fr/UROX/

  19. Fitting the HIV epidemic in Zambia: a two-sex micro-simulation model.

    Directory of Open Access Journals (Sweden)

    Pauline M Leclerc

    Full Text Available BACKGROUND: In describing and understanding how the HIV epidemic spreads in African countries, previous studies have not taken into account the detailed periods at risk. This study is based on a micro-simulation model (individual-based of the spread of the HIV epidemic in the population of Zambia, where women tend to marry early and where divorces are not frequent. The main target of the model was to fit the HIV seroprevalence profiles by age and sex observed at the Demographic and Health Survey conducted in 2001. METHODS AND FINDINGS: A two-sex micro-simulation model of HIV transmission was developed. Particular attention was paid to precise age-specific estimates of exposure to risk through the modelling of the formation and dissolution of relationships: marriage (stable union, casual partnership, and commercial sex. HIV transmission was exclusively heterosexual for adults or vertical (mother-to-child for children. Three stages of HIV infection were taken into account. All parameters were derived from empirical population-based data. Results show that basic parameters could not explain the dynamics of the HIV epidemic in Zambia. In order to fit the age and sex patterns, several assumptions were made: differential susceptibility of young women to HIV infection, differential susceptibility or larger number of encounters for male clients of commercial sex workers, and higher transmission rate. The model allowed to quantify the role of each type of relationship in HIV transmission, the proportion of infections occurring at each stage of disease progression, and the net reproduction rate of the epidemic (R(0 = 1.95. CONCLUSIONS: The simulation model reproduced the dynamics of the HIV epidemic in Zambia, and fitted the age and sex pattern of HIV seroprevalence in 2001. The same model could be used to measure the effect of changing behaviour in the future.

  20. Mouse models of anemia of cancer.

    Directory of Open Access Journals (Sweden)

    Airie Kim

    Full Text Available Anemia of cancer (AC may contribute to cancer-related fatigue and impair quality of life. Improved understanding of the pathogenesis of AC could facilitate better treatment, but animal models to study AC are lacking. We characterized four syngeneic C57BL/6 mouse cancers that cause AC. Mice with two different rapidly-growing metastatic lung cancers developed the characteristic findings of anemia of inflammation (AI, with dramatically different degrees of anemia. Mice with rapidly-growing metastatic melanoma also developed a severe anemia by 14 days, with hematologic and inflammatory parameters similar to AI. Mice with a slow-growing peritoneal ovarian cancer developed an iron-deficiency anemia, likely secondary to chronically impaired nutrition and bleeding into the peritoneal cavity. Of the four models, hepcidin mRNA levels were increased only in the milder lung cancer model. Unlike in our model of systemic inflammation induced by heat-killed Brucella abortus, ablation of hepcidin in the ovarian cancer and the milder lung cancer mouse models did not affect the severity of anemia. Hepcidin-independent mechanisms play an important role in these murine models of AC.

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

    Science.gov (United States)

    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.

  2. Animal Models of Cancer Pain

    OpenAIRE

    Pacharinsak, Cholawat; Beitz, Alvin

    2008-01-01

    Modern cancer therapies have significantly increased patient survival rates in both human and veterinary medicine. Since cancer patients live longer they now face new challenges resulting from severe, chronic tumor-induced pain. Unrelieved cancer pain significantly decreases the quality of life of such patients; thus the goal of pain management is to not only to alleviate pain, but also to maintain the patient's physiological and psychological well-being. The major impediment for developing n...

  3. A NON-UNIFORM SEDIMENT TRANSPORT MODEL WITH THE BOUNDARY-FITTING ORTHOGONAL COORDINATE SYSTEM

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A 2-D non-uniform sediment mathmatical model in the boundary-fitting orthogonal coordinate system was developed in this paper. The governing equations, the numerical scheme, the boundary conditions, the movable boundary technique and the numerical solutions were presented. The model was verified by the data of the reach 25km upstream the Jialingjiang estuary and the 44km long main stream of the Chongqing reach of the Yangtze river. The calculated results show that, the water elevation, the velocity distribution and the river bed deformation are in agreement with the measured data.

  4. ANIMAL MODELS OF CANCER: A REVIEW

    Directory of Open Access Journals (Sweden)

    Archana M. Navale

    2013-01-01

    Full Text Available Cancer is the second leading cause of death worldwide. In USA three persons out of five will develop some type of cancer. Beyond these statistics of mortality, the morbidity due to cancer presents a real scary picture. Last 50 years of research has rendered some types of cancer curable, but still the major fear factor associated with this disease is unchanged. Animal models are classified according to the method of induction of cancer in the animal. Spontaneous tumor models are the most primitive models. Although these models show good resemblance to the natural disease in humans, they were not capable of keeping pace with developing experimental therapeutics programs. It has therefore been necessary to take a further step towards artificiality, away from the clinical problem in the search for satisfactory testing method. From this step, the journey of artificially induced tumor models started. It is possible to induce cancer reproducibly in animals by exposing them to various agents and now, by transplanting tumor cells or tissue. The development of Genetically Engineered Animal models has provided a great help in knowing the disease. This article takes a review of present animal models used in anti-cancer drug discovery.

  5. Testing Lack-of-fit for a Polynomial Errors-in-variables Model

    Institute of Scientific and Technical Information of China (English)

    Li-xing Zhu; Wei-xing Song; Heng-jian Gui

    2003-01-01

    When a regression model is applied as an approximation of underlying model of data, the model checking is important and relevant. In this paper, we investigate the lack-of-fit test for a polynomial errorin-variables model. As the ordinary residuals are biased when there exist measurement errors in covariables,we correct them and then construct a residual-based test of score type. The constructed test is asymptotically chi-squared under null hypotheses. Simulation study shows that the test can maintain the significance level well.The choice of weight functions involved in the test statistic and the related power study are also investigated.The application to two examples is illustrated. The approach can be readily extended to handle more general models.

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

    Science.gov (United States)

    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.

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

    OpenAIRE

    Schlemm, Eckhard

    2015-01-01

    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...

  8. The challenge of preserving cardiorespiratory fitness in physically inactive patients with colon or breast cancer during adjuvant chemotherapy: a randomised feasibility study

    DEFF Research Database (Denmark)

    Møller, Tom; Lillelund, Christian; Andersen, Christina;

    2015-01-01

    in order to support cardio-respiratory fitness and lifestyle changes in an at-risk population of pre-illness physically inactive cancer patients.Methods Patients with breast or colon cancer referred to adjuvant chemotherapy and by the oncologists pre-screening verified as physically inactive were eligible...... instrument in order to correspond with cardio-respiratory fitness (VO2 peak) proved to be an applicable method to identify pre-illness physically inactive breast and colon cancer patients. The study demonstrated convincing recruitment (67%), safety and intervention adherence among breast cancer patients...... to enter a randomised three-armed feasibility study comparing a 12-week supervised hospital-based moderate to high intensity exercise intervention or alternate an instructive home-based12-week pedometer intervention, with usual care.Results Using a recommendation based physical activity screening...

  9. Genetically engineered mouse models of prostate cancer

    NARCIS (Netherlands)

    Nawijn, Martijn C.; Bergman, Andreas M.; van der Poel, Henk G.

    2008-01-01

    Objectives: Mouse models of prostate cancer are used to test the contribution of individual genes to the transformation process, evaluate the collaboration between multiple genetic lesions observed in a single tumour, and perform preclinical intervention studies in prostate cancer research. Methods:

  10. Recapitulating Human Gastric Cancer Pathogenesis: Experimental Models of Gastric Cancer.

    Science.gov (United States)

    Ding, Lin; El Zaatari, Mohamad; Merchant, Juanita L

    2016-01-01

    This review focuses on the various experimental models to study gastric cancer pathogenesis, with the role of genetically engineered mouse models (GEMMs) used as the major examples. We review differences in human stomach anatomy compared to the stomachs of the experimental models, including the mouse and invertebrate models such as Drosophila and C. elegans. The contribution of major signaling pathways, e.g., Notch, Hedgehog, AKT/PI3K is discussed in the context of their potential contribution to foregut tumorigenesis. We critically examine the rationale behind specific GEMMs, chemical carcinogens, dietary promoters, Helicobacter infection, and direct mutagenesis of relevant oncogenes and tumor suppressor that have been developed to study gastric cancer pathogenesis. Despite species differences, more efficient and effective models to test specific genes and pathways disrupted in human gastric carcinogenesis have yet to emerge. As we better understand these species differences, "humanized" versions of mouse models will more closely approximate human gastric cancer pathogenesis. Towards that end, epigenetic marks on chromatin, the gut microbiota, and ways of manipulating the immune system will likely move center stage, permitting greater overlap between rodent and human cancer phenotypes thus providing a unified progression model. PMID:27573785

  11. Cancer Metabolism: A Modeling Perspective

    DEFF Research Database (Denmark)

    Ghaffari, Pouyan; Mardinoglu, Adil; Nielsen, Jens

    2015-01-01

    requires both the advancement of experimental technologies for more comprehensive measurement of omics as well as the advancement of robust computational methods for accurate analysis of the generated data. Here, we review cancer-associated reprogramming of metabolism and highlight the capability of genome...... suggest that utilization of amino acids and lipids contributes significantly to cancer cell metabolism. Also recent progresses in our understanding of carcinogenesis have revealed that cancer is a complex disease and cannot be understood through simple investigation of genetic mutations of cancerous cells....... Cancer cells present in complex tumor tissues communicate with the surrounding microenvironment and develop traits which promote their growth, survival, and metastasis. Decoding the full scope and targeting dysregulated metabolic pathways that support neoplastic transformations and their preservation...

  12. A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types.

    Directory of Open Access Journals (Sweden)

    Feixiong Cheng

    2015-09-01

    Full Text Available Cancer development and progression result from somatic evolution by an accumulation of genomic alterations. The effects of those alterations on the fitness of somatic cells lead to evolutionary adaptations such as increased cell proliferation, angiogenesis, and altered anticancer drug responses. However, there are few general mathematical models to quantitatively examine how perturbations of a single gene shape subsequent evolution of the cancer genome. In this study, we proposed the gene gravity model to study the evolution of cancer genomes by incorporating the genome-wide transcription and somatic mutation profiles of ~3,000 tumors across 9 cancer types from The Cancer Genome Atlas into a broad gene network. We found that somatic mutations of a cancer driver gene may drive cancer genome evolution by inducing mutations in other genes. This functional consequence is often generated by the combined effect of genetic and epigenetic (e.g., chromatin regulation alterations. By quantifying cancer genome evolution using the gene gravity model, we identified six putative cancer genes (AHNAK, COL11A1, DDX3X, FAT4, STAG2, and SYNE1. The tumor genomes harboring the nonsynonymous somatic mutations in these genes had a higher mutation density at the genome level compared to the wild-type groups. Furthermore, we provided statistical evidence that hypermutation of cancer driver genes on inactive X chromosomes is a general feature in female cancer genomes. In summary, this study sheds light on the functional consequences and evolutionary characteristics of somatic mutations during tumorigenesis by propelling adaptive cancer genome evolution, which would provide new perspectives for cancer research and therapeutics.

  13. Model-fitting of the kinematics of superluminal components in blazar 3C 279

    Institute of Scientific and Technical Information of China (English)

    Shan-Jie Qian

    2012-01-01

    A precessing jet-nozzle model with a precession period of about 25 yr has been proposed by Qian to interpret the change with time of the ejection position angle of the superluminal components observed using very long baseline interferometry (VLBI) in the blazar 3C 279.We discuss the kinematic properties of six superluminal knots (C3,C4,C7a,C8,C9 and C10) and show that their trajectory,core-distance and apparent speed,derived from VLBI observations,can be consistently well fitted by the model.Their intrinsic Lorentz factors of bulk superluminal motion are thus derived,and the evidence shows no relation between Lorentz factor and the precession phase.Interestingly,for the C7a and C8 knots,the fitted core-distance ranges from ~0.1 mas to ~0.4mas and for knots C9 and C10 from ~0.2mas to ~1.0-1.5mas.For knot C4,its trajectory and apparent velocity are well fitted in the core-distance range from ~1 mas to ~5 mas,taking into account a curvature of the trajectory at core-distance larger than ~3 mas.The consistent fitting of the kinematics of these components clearly demonstrates that the amplitude function and collimation parameter adopted in the precession model are appropriate and applicable for both the inner and outer parts of the jet in 3C 279,but in some cases the jet curvature in the outer parts (or deviation from the model trajectory) needs to be seriously taken into consideration.With the exception of C4,the ejection position angles derived from the precession model are consistent with the values measured by VLBI observations (within about 3° - 6°).Undoubtedly,the consistent interpretation of the kinematics in terms of the precession model for these superluminal components,with their ejection time spanning ~24 yr,significantly expands its applicability and implies that regular pattems of trajectories (or rotating channels) could exist in some periods.

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

    Science.gov (United States)

    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) .

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

    Science.gov (United States)

    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

  16. An improved cosmological model fitting of Planck data with a dark energy spike

    CERN Document Server

    Park, Chan-Gyung

    2015-01-01

    The $\\Lambda$ cold dark matter ($\\Lambda\\textrm{CDM}$) model is currently known as the simplest cosmology model that best describes observations with minimal number of parameters. Here we introduce a cosmology model that is preferred over the conventional $\\Lambda\\textrm{CDM}$ one by constructing dark energy as the sum of the cosmological constant $\\Lambda$ and the additional fluid that is designed to have an extremely short transient spike in energy density during the radiation-matter equality era and the 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 five times the number of additional parameters introduced and narrower constraints on matter density and Hubble constant compared with the best-fit $\\Lambda\\textrm{CDM}$ model. The...

  17. Empirical evaluation reveals best fit of a logistic mutation model for human Y-chromosomal microsatellites.

    Science.gov (United States)

    Jochens, Arne; Caliebe, Amke; Rösler, Uwe; Krawczak, Michael

    2011-12-01

    The rate of microsatellite mutation is dependent upon both the allele length and the repeat motif, but the exact nature of this relationship is still unknown. We analyzed data on the inheritance of human Y-chromosomal microsatellites in father-son duos, taken from 24 published reports and comprising 15,285 directly observable meioses. At the six microsatellites analyzed (DYS19, DYS389I, DYS390, DYS391, DYS392, and DYS393), a total of 162 mutations were observed. For each locus, we employed a maximum-likelihood approach to evaluate one of several single-step mutation models on the basis of the data. For five of the six loci considered, a novel logistic mutation model was found to provide the best fit according to Akaike's information criterion. This implies that the mutation probability at the loci increases (nonlinearly) with allele length at a rate that differs between upward and downward mutations. For DYS392, the best fit was provided by a linear model in which upward and downward mutation probabilities increase equally with allele length. This is the first study to empirically compare different microsatellite mutation models in a locus-specific fashion. PMID:21968190

  18. Maximum likelihood fitting of FROC curves under an initial-detection-and-candidate-analysis model

    International Nuclear Information System (INIS)

    We have developed a model for FROC curve fitting that relates the observer's FROC performance not to the ROC performance that would be obtained if the observer's responses were scored on a per image basis, but rather to a hypothesized ROC performance that the observer would obtain in the task of classifying a set of 'candidate detections' as positive or negative. We adopt the assumptions of the Bunch FROC model, namely that the observer's detections are all mutually independent, as well as assumptions qualitatively similar to, but different in nature from, those made by Chakraborty in his AFROC scoring methodology. Under the assumptions of our model, we show that the observer's FROC performance is a linearly scaled version of the candidate analysis ROC curve, where the scaling factors are just given by the FROC operating point coordinates for detecting initial candidates. Further, we show that the likelihood function of the model parameters given observational data takes on a simple form, and we develop a maximum likelihood method for fitting a FROC curve to this data. FROC and AFROC curves are produced for computer vision observer datasets and compared with the results of the AFROC scoring method. Although developed primarily with computer vision schemes in mind, we hope that the methodology presented here will prove worthy of further study in other applications as well

  19. Implicit Active Contour Model with Local and Global Intensity Fitting Energies

    Directory of Open Access Journals (Sweden)

    Xiaozeng Xu

    2013-01-01

    Full Text Available We propose a new active contour model which integrates a local intensity fitting (LIF energy with an auxiliary global intensity fitting (GIF energy. The LIF energy is responsible for attracting the contour toward object boundaries and is dominant near object boundaries, while the GIF energy incorporates global image information to improve the robustness to initialization of the contours. The proposed model not only can provide desirable segmentation results in the presence of intensity inhomogeneity but also allows for more flexible initialization of the contour compared to the RSF and LIF models, and we give a theoretical proof to compute a unique steady state regardless of the initialization; that is, the convergence of the zero-level line is irrespective of the initial function. This means that we can obtain the same zero-level line in the steady state, if we choose the initial function as a bounded function. In particular, our proposed model has the capability of detecting multiple objects or objects with interior holes or blurred edges.

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

    CERN Document Server

    Furlan, E; 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

    2016-01-01

    We present key results from the Herschel Orion Protostar Survey (HOPS): 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 sub-millimeter photometry from APEX, our SEDs cover 1.2-870 $\\mu$m and sample the peak of the protostellar envelope emission at ~100 $\\mu$m. 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 30400 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 cons...

  1. Systematic effects on the size-luminosity relation: dependence on model fitting and morphology

    CERN Document Server

    Bernardi, M; Vikram, V; Huertas-Company, M; Mei, S; Shankar, F; Sheth, R K

    2012-01-01

    We quantify the systematics in the size-luminosity relation of galaxies in the SDSS main sample which arise from fitting different 1- and 2-component model profiles to the images. In objects brighter than L*, fitting a single Sersic profile to what is really a two-component SerExp system leads to biases: the half-light radius is increasingly overestimated as n of the fitted single component increases; it is also overestimated at B/T ~ 0.6. However, the net effect on the R-L relation is small, except for the most luminous tail, where it curves upwards towards larger sizes. We also study how this relation depends on morphological type. Our analysis is one of the first to use Bayesian-classifier derived weights, rather than hard cuts, to define morphology. Crudely, there appear to be only two relations: one for early-types (Es, S0s and Sa's) and another for late-types (Sbs and Scds). However, closer inspection shows that within the early-type sample S0s tend to be 15% smaller than Es of the same luminosity, and,...

  2. The Shape of Dark Matter Haloes II. The Galactus HI Modelling & Fitting Tool

    CERN Document Server

    Peters, S P C; Allen, R J; Freeman, K C

    2016-01-01

    We present a new HI modelling tool called \\textsc{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 the 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 NGC2403, using both self-absorption and optically thin models, showing that self-absorption occurs even in face-on galaxies. It is shown that the maximum surface brightness plateaus seen in Paper I of this series are indeed signs of self-absorption. The apparent HI mass of an edge-on galaxy can be drastically lower compared to that same galaxy seen face-on. The Tully-Fisher relation is found to be relatively free from self-absorption issues.

  3. Fractional Differentiation-Based Active Contour Model Driven by Local Intensity Fitting Energy

    Directory of Open Access Journals (Sweden)

    Ming Gu

    2016-01-01

    Full Text Available A novel active contour model is proposed for segmentation images with inhomogeneity. Firstly, fractional order filter is defined by eight convolution masks corresponding to the image orientation in the eight compass directions. Then, the fractional order differentiation image is obtained and applied to the level set method. Secondly, we defined a new energy functional based on local image information and fractional order differentiation image; the proposed model not only can describe the input image more accurately but also can deal with intensity inhomogeneity. Local fitting term can enhance the ability of the model to deal with intensity inhomogeneity. The defined penalty term is used to reduce the occurrence of false boundaries. Finally, in order to eliminate the time-consuming step of reinitialization and ensure stable evolution of level set function, the Gaussian filtering method is used. Experiments on synthetic and real images show that the proposed model is efficient for images with intensity inhomogeneity and flexible to initial contour.

  4. Adapted strategic plannig model applied to small business: a case study in the fitness area

    Directory of Open Access Journals (Sweden)

    Eduarda Tirelli Hennig

    2012-06-01

    Full Text Available The strategic planning is an important management tool in the corporate scenario and shall not be restricted to big Companies. However, this kind of planning process in small business may need special adaptations due to their own characteristics. This paper aims to identify and adapt the existent models of strategic planning to the scenario of a small business in the fitness area. Initially, it is accomplished a comparative study among models of different authors to identify theirs phases and activities. Then, it is defined which of these phases and activities should be present in a model that will be utilized in a small business. That model was applied to a Pilates studio; it involves the establishment of an organizational identity, an environmental analysis as well as the definition of strategic goals, strategies and actions to reach them. Finally, benefits to the organization could be identified, as well as hurdles in the implementation of the tool.

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

    Science.gov (United States)

    Freeman, A.

    2007-03-01

    Two simple scattering mechanisms are f itted to polarimetric SAR observations of forests. The mechanisms are canopy scatter from a reciprocal medium with azimuthal symmetry, and a ground scatter term, which can represent double-bounce scatter from a pair of orthogonal surfaces with different d ielectric constants or Bragg scatter from a moderately rough surface, 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 NASA/JPL's 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 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 attenuation coefficient of the canopy can be obtained directly from the multi-incidence angle, polarimetric

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

    CERN Document Server

    Fuchs, J T; Clemens, J C; Meza, J A; Dennihy, E; Koester, D

    2016-01-01

    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 $\\log{g}$-$T_{\\rm eff}$ plane are consistent for these three systematics.

  7. Fitting model of ABR age dependency in a clinical population of normal hearing children

    OpenAIRE

    Coenraad, Saskia; Immerzeel, Tabitha; Hoeve, Hans; Goedegebure, Andre

    2010-01-01

    textabstractThe purpose of this study was to present a simple and powerful fitting model that describes age-dependent changes of auditory brainstem responses (ABR) in a clinical population of normal hearing children. A total of 175 children (younger than 200 weeks postconceptional age) were referred for audiologic assessment with normal ABR results. ABR parameters of normal hearing children between 2003 and 2008 were included. The results of the right ears recorded at 90 dB nHL were analyzed....

  8. Inverse problem theory methods for data fitting and model parameter estimation

    CERN Document Server

    Tarantola, A

    2002-01-01

    Inverse Problem Theory is written for physicists, geophysicists and all scientists facing the problem of quantitative interpretation of experimental data. Although it contains a lot of mathematics, it is not intended as a mathematical book, but rather tries to explain how a method of acquisition of information can be applied to the actual world.The book provides a comprehensive, up-to-date description of the methods to be used for fitting experimental data, or to estimate model parameters, and to unify these methods into the Inverse Problem Theory. The first part of the book deals wi

  9. Fitting the CDO correlation skew: a tractable structural jump-diffusion model

    DEFF Research Database (Denmark)

    Willemann, Søren

    2007-01-01

    allowing for instantaneous calibration to heterogeneous CDS curves and fast computation of CDO tranche spreads. We calibrate the model to CDX and iTraxx data from February 2007 and achieve a satisfactory fit. To price the senior tranches for both indices, we require a risk-neutral probability of a market...... crash of roughly 0.1% within five years. In the European market, the implied effect from a crash is that all companies come very close to defaulting while the implied effect in the US market is an average loss of 78% in asset value....

  10. Fitting optimum order of Markov chain models for daily rainfall occurrences in Peninsular Malaysia

    Science.gov (United States)

    Deni, Sayang Mohd; Jemain, Abdul Aziz; Ibrahim, Kamarulzaman

    2009-06-01

    The analysis of the daily rainfall occurrence behavior is becoming more important, particularly in water-related sectors. Many studies have identified a more comprehensive pattern of the daily rainfall behavior based on the Markov chain models. One of the aims in fitting the Markov chain models of various orders to the daily rainfall occurrence is to determine the optimum order. In this study, the optimum order of the Markov chain models for a 5-day sequence will be examined in each of the 18 rainfall stations in Peninsular Malaysia, which have been selected based on the availability of the data, using the Akaike’s (AIC) and Bayesian information criteria (BIC). The identification of the most appropriate order in describing the distribution of the wet (dry) spells for each of the rainfall stations is obtained using the Kolmogorov-Smirnov goodness-of-fit test. It is found that the optimum order varies according to the levels of threshold used (e.g., either 0.1 or 10.0 mm), the locations of the region and the types of monsoon seasons. At most stations, the Markov chain models of a higher order are found to be optimum for rainfall occurrence during the northeast monsoon season for both levels of threshold. However, it is generally found that regardless of the monsoon seasons, the first-order model is optimum for the northwestern and eastern regions of the peninsula when the level of thresholds of 10.0 mm is considered. The analysis indicates that the first order of the Markov chain model is found to be most appropriate for describing the distribution of wet spells, whereas the higher-order models are found to be adequate for the dry spells in most of the rainfall stations for both threshold levels and monsoon seasons.

  11. Limited-information goodness-of-fit testing of hierarchical item factor models.

    Science.gov (United States)

    Cai, Li; Hansen, Mark

    2013-05-01

    In applications of item response theory, assessment of model fit is a critical issue. Recently, limited-information goodness-of-fit testing has received increased attention in the psychometrics literature. In contrast to full-information test statistics such as Pearson's X(2) or the likelihood ratio G(2) , these limited-information tests utilize lower-order marginal tables rather than the full contingency table. A notable example is Maydeu-Olivares and colleagues'M2 family of statistics based on univariate and bivariate margins. When the contingency table is sparse, tests based on M2 retain better Type I error rate control than the full-information tests and can be more powerful. While in principle the M2 statistic can be extended to test hierarchical multidimensional item factor models (e.g., bifactor and testlet models), the computation is non-trivial. To obtain M2 , a researcher often has to obtain (many thousands of) marginal probabilities, derivatives, and weights. Each of these must be approximated with high-dimensional numerical integration. We propose a dimension reduction method that can take advantage of the hierarchical factor structure so that the integrals can be approximated far more efficiently. We also propose a new test statistic that can be substantially better calibrated and more powerful than the original M2 statistic when the test is long and the items are polytomous. We use simulations to demonstrate the performance of our new methods and illustrate their effectiveness with applications to real data. PMID:22642552

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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).

  14. Model based period analysis of absolute and relative survival with R: data preparation, model fitting and derivation of survival estimates.

    Science.gov (United States)

    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. PMID:23116692

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

    International Nuclear Information System (INIS)

    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 1o meridian arc, and the length of a pendulum beating seconds, as a function of sin2(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 its roots

  16. Bootstrapping topology and systemic risk of complex network using the fitness model

    CERN Document Server

    Musmeci, Nicoló; Caldarelli, Guido; Puliga, Michelangelo; Gabrielli, Andrea

    2012-01-01

    We present a novel method to reconstruct complex network from partial information. We assume to know the links only for a subset of the nodes and to know some non-topological quantity (fitness) characterising every node. The missing links are generated on the basis of the latter quan- tity according to a fitness model calibrated on the subset of nodes for which links are known. We measure the quality of the reconstruction of several topological properties, such as the network density and the degree distri- bution as a function of the size of the initial subset of nodes. Moreover, we also study the resilience of the network to distress propagation. We first test the method on ensembles of synthetic networks generated with the Exponential Random Graph model which allows to apply common tools from statistical mechanics. We then test it on the empirical case of the World Trade Web. In both cases, we find that a subset of 10 % of nodes is enough to reconstruct the main features of the network along with its resili...

  17. A simulation study of person-fit in the Rasch model

    Directory of Open Access Journals (Sweden)

    Richard Artner

    2016-09-01

    Full Text Available The validation of individual test scores in the Rasch model (1-PL model is of primary importance, but the decision which person-fit index to choose is still not sufficiently answered. In this work, a simulation study was conducted in order to compare five well known person-fit indices in terms of specificity and sensitivity, under different testing conditions. Furthermore, this study analyzed the decrease in specificity of Andersen´s Likelihood-Ratio test in case of person-misfit, using the median of the raw score as an internal criterion, as well as the positive effect of removing suspicious respondents with the index C*. The three non-parametric indices Ht, C* and U3 performed slightly better than the parametric indices OUTFIT and INFIT. All indices performed better with a higher number of respondents and a higher number of items. Ht, OUTFIT, and INFIT showed huge deviations between nominal and actual specificity levels. The simulation revealed that person-misfit has a huge negative impact on the specificity of Andersen´s Likelihood-Ratio test. However, the removal of suspicious respondents with C* worked quite well and the nominal specificity can be almost respected if the specificity level of C* is set to 0.95.

  18. Modeling the Time Evolution of QSH Equilibria in MST Plasmas Using V3FIT

    Science.gov (United States)

    Boguski, J.; Nornberg, M.; Munaretto, S.; Chapman, B. E.; Cianciosa, M.; Terry, P. W.; Hanson, J.

    2015-11-01

    High current and low density RFP plasmas tend towards a 3D configuration, called Quasi-Single Helicity (QSH), characterized by a dominant core helical mode. V3FIT utilizes multiple internal and edge diagnostics to reconstruct the non-axisymmetric magnetic equilibrium of the QSH state. Performing multiple reconstructions at different stages in the QSH cycle is used to learn about the time dynamics of the QSH state. Recent work on modeling a shear-suppression mechanism for QSH formation has produced a predator-prey model of the time dynamics that reproduces the observed behavior, in particular the increased persistence of the QSH state with increased plasma current. Either magnetic or flow shear can facilitate QSH formation. The magnetic shear dependence of QSH is analyzed using V3FIT reconstructions of magnetic equilibrium constrained by internal measurements of density and temperature as well as soft x-ray emission. Fluctuations in the flux surface structure are compared against the measured temperature and density fluctuations and the reconstructed temperature and density profiles are examined to look for evidence of barriers to particle and heat transport. This material is based upon work supported by the U.S. DOE.

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

    CERN Document Server

    Hong, Jie; Li, Ying; Fang, Cheng; Cao, Wenda

    2014-01-01

    We study the H$\\alpha$ and Ca II 8542 \\r{A} line spectra of four typical Ellerman bombs (EBs) in active region NOAA 11765 on 2013 June 6, observed with the Fast Imaging Solar Spectrograph installed at the 1.6 meter 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 a local heating occurs in the lower atmosphere during the appearance of EBs. We also find that...

  20. A PID Positioning Controller with a Curve Fitting Model Based on RFID Technology

    Directory of Open Access Journals (Sweden)

    Young-Long Chen

    2013-03-01

    Full Text Available The global positioning system (GPS is an important research topic to solve outdoor positioning problems, but GPSis unable to locate objects accurately and precisely indoors. Some available systems apply ultrasound or opticaltracking. This paper presents an efficient proportional-integral-derivative (PID controller with curve fitting model formobile robot localization and position estimation which adopts passive radio frequency identification (RFID tags ina space. This scheme is based on a mobile robot carries an RFID reader module which reads the installed low-costpassive tags under the floor in a grid-like pattern. The PID controllers increase the efficiency of captured RFID tagsand the curve fitting model is used to systematically identify the revolutions per minute (RPM of the motor. Wecontrol and monitor the position of the robot from a remote location through a mobile phone via Wi-Fi and Bluetoothnetwork. Experiment results present that the number of captured RFID tags of our proposed scheme outperformsthat of the previous scheme.

  1. Levy flights and self-similar exploratory behaviour of termite workers: beyond model fitting.

    Directory of Open Access Journals (Sweden)

    Octavio Miramontes

    Full Text Available 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.

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

    Directory of Open Access Journals (Sweden)

    Matthew R Nassar

    2013-04-01

    Full Text Available 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.

  3. Observations from using models to fit the gas production of varying volume test cells and landfills.

    Science.gov (United States)

    Lamborn, Julia

    2012-12-01

    Landfill operators are looking for more accurate models to predict waste degradation and landfill gas production. The simple microbial growth and decay models, whilst being easy to use, have been shown to be inaccurate. Many of the newer and more complex (component) models are highly parameter hungry and many of the required parameters have not been collected or measured at full-scale landfills. This paper compares the results of using different models (LANDGEM, HBM, and two Monod models developed by the author) to fit the gas production of laboratory scale, field test cell and full-scale landfills and discusses some observations that can be made regarding the scalability of gas generation rates. The comparison of these results show that the fast degradation rate that occurs at laboratory scale is not replicated at field-test cell and full-scale landfills. At small scale, all the models predict a slower rate of gas generation than actually occurs. At field test cell and full-scale a number of models predict a faster gas generation than actually occurs. Areas for future work have been identified, which include investigations into the capture efficiency of gas extraction systems and into the parameter sensitivity and identification of the critical parameters for field-test cell and full-scale landfill predication.

  4. Comprehensive two-dimensional river ice model based on boundary-fitted coordinate transformation method

    Directory of Open Access Journals (Sweden)

    Ze-yu MAO

    2014-01-01

    Full Text Available River ice is a natural phenomenon in cold regions, influenced by meteorology, geomorphology, and hydraulic conditions. River ice processes involve complex interactions between hydrodynamic, mechanical, and thermal processes, and they are also influenced by weather and hydrologic conditions. Because natural rivers are serpentine, with bends, narrows, and straight reaches, the commonly-used one-dimensional river ice models and two-dimensional models based on the rectangular Cartesian coordinates are incapable of simulating the physical phenomena accurately. In order to accurately simulate the complicated river geometry and overcome the difficulties of numerical simulation resulting from both complex boundaries and differences between length and width scales, a two-dimensional river ice numerical model based on a boundary-fitted coordinate transformation method was developed. The presented model considers the influence of the frazil ice accumulation under ice cover and the shape of the leading edge of ice cover during the freezing process. The model is capable of determining the velocity field, the distribution of water temperature, the concentration distribution of frazil ice, the transport of floating ice, the progression, stability, and thawing of ice cover, and the transport, accumulation, and erosion of ice under ice cover. A MacCormack scheme was used to solve the equations numerically. The model was validated with field observations from the Hequ Reach of the Yellow River. Comparison of simulation results with field data indicates that the model is capable of simulating the river ice process with high accuracy.

  5. The challenges of fitting an item response theory model to the Social Anhedonia Scale.

    Science.gov (United States)

    Reise, Steven P; Horan, William P; Blanchard, Jack J

    2011-05-01

    This study explored the application of latent variable measurement models to the Social Anhedonia Scale (SAS; Eckblad, Chapman, Chapman, & Mishlove, 1982), a widely used and influential measure in schizophrenia-related research. Specifically, we applied unidimensional and bifactor item response theory (IRT) models to data from a community sample of young adults (n = 2,227). Ordinal factor analyses revealed that identifying a coherent latent structure in the 40-item SAS data was challenging due to (a) the presence of multiple small content clusters (e.g., doublets); (b) modest relations between those clusters, which, in turn, implies a general factor of only modest strength; (c) items that shared little variance with the majority of items; and (d) cross-loadings in bifactor solutions. Consequently, we conclude that SAS responses cannot be modeled accurately by either unidimensional or bifactor IRT models. Although the application of a bifactor model to a reduced 17-item set met with better success, significant psychometric and substantive problems remained. Results highlight the challenges of applying latent variable models to scales that were not originally designed to fit these models.

  6. Modeling the Aneuploidy Control of Cancer

    Directory of Open Access Journals (Sweden)

    Wang Zhong

    2010-07-01

    Full Text Available Abstract Background Aneuploidy has long been recognized to be associated with cancer. A growing body of evidence suggests that tumorigenesis, the formation of new tumors, can be attributed to some extent to errors occurring at the mitotic checkpoint, a major cell cycle control mechanism that acts to prevent chromosome missegregation. However, so far no statistical model has been available quantify the role aneuploidy plays in determining cancer. Methods We develop a statistical model for testing the association between aneuploidy loci and cancer risk in a genome-wide association study. The model incorporates quantitative genetic principles into a mixture-model framework in which various genetic effects, including additive, dominant, imprinting, and their interactions, are estimated by implementing the EM algorithm. Results Under the new model, a series of hypotheses tests are formulated to explain the pattern of the genetic control of cancer through aneuploid loci. Simulation studies were performed to investigate the statistical behavior of the model. Conclusions The model will provide a tool for estimating the effects of genetic loci on aneuploidy abnormality in genome-wide studies of cancer cells.

  7. A Stellar Model-fitting Pipeline for Solar-like Oscillations

    CERN Document Server

    Metcalfe, T S; Christensen-Dalsgaard, J

    2009-01-01

    Over the past two decades, helioseismology has revolutionized our understanding of the interior structure and dynamics of the Sun. Asteroseismology will soon place this knowledge into a broader context by providing structural data for hundreds of Sun-like stars. Solar-like oscillations have already been detected from the ground in several stars, and NASA's Kepler mission is poised to unleash a flood of stellar pulsation data. Deriving reliable asteroseismic information from these observations demands a significant improvement in our analysis methods. We report the initial results of our efforts to develop an objective stellar model-fitting pipeline for asteroseismic data. The cornerstone of our automated approach is an optimization method using a parallel genetic algorithm. We describe the details of the pipeline and we present the initial application to Sun-as-a-star data, yielding an optimal model that accurately reproduces the known solar properties.

  8. A Stellar Model-fitting Pipeline for Asteroseismic Data from the Kepler Mission

    CERN Document Server

    Metcalfe, T S; Christensen-Dalsgaard, J

    2009-01-01

    Over the past two decades, helioseismology has revolutionized our understanding of the interior structure and dynamics of the Sun. Asteroseismology will soon place this knowledge into a broader context by providing structural data for hundreds of Sun-like stars. Solar-like oscillations have already been detected from the ground in several stars, and NASA's Kepler mission is poised to unleash a flood of stellar pulsation data. Deriving reliable asteroseismic information from these observations demands a significant improvement in our analysis methods. In this paper we report the initial results of our efforts to develop an objective stellar model-fitting pipeline for asteroseismic data. The cornerstone of our automated approach is an optimization method using a parallel genetic algorithm. We describe the details of the pipeline and we present the initial application to Sun-as-a-star data, yielding an optimal model that accurately reproduces the known solar properties.

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

    Science.gov (United States)

    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. PMID:26839880

  10. Goodness of fit assessment for a fractal model of stock markets

    International Nuclear Information System (INIS)

    An assessment of the goodness of fit of a new stochastic model of stock dynamics is investigated. The model is the multifractional Brownian motion (mBm), introduced independently by Péltier and Lévy Véhel (1995) [2] and Benassi (1997) [3]. The analysis concerns the (un)conditional distributions of log-variations of the Dow Jones Industrial Average (DJIA). By comparing the performance of mBm with respect to a Garch (1,1), we argue that the former captures the distributional features as well as the pathwise empirical ones displayed by the U.S. Dow Jones index, while the Garch (1,1) works better in global terms

  11. The use of the Levenberg-Marquardt curve-fitting algorithm in pharmacokinetic modelling of DCE-MRI data

    International Nuclear Information System (INIS)

    The use of curve-fitting and compartmental modelling for calculating physiological parameters from measured data has increased in popularity in recent years. Finding the 'best fit' of a model to data involves the minimization of a merit function. An example of a merit function is the sum of the squares of the differences between the data points and the model estimated points. This is facilitated by curve-fitting algorithms. Two curve-fitting methods, Levenberg-Marquardt and MINPACK-1, are investigated with respect to the search start points that they require and the accuracy of the returned fits. We have simulated one million dynamic contrast enhanced MRI curves using a range of parameters and investigated the use of single and multiple search starting points. We found that both algorithms, when used with a single starting point, return unreliable fits. When multiple start points are used, we found that both algorithms returned reliable parameters. However the MINPACK-1 method generally outperformed the Levenberg-Marquardt method. We conclude that the use of a single starting point when fitting compartmental modelling data such as this produces unsafe results and we recommend the use of multiple start points in order to find the global minima. (note)

  12. Public Health Action Model for Cancer Survivorship.

    Science.gov (United States)

    Moore, Angela R; Buchanan, Natasha D; Fairley, Temeika L; Lee Smith, Judith

    2015-12-01

    Long-term objectives associated with cancer survivors have been suggested by Healthy People 2020, including increasing the proportion of survivors living beyond 5 years after diagnosis and improving survivors' mental and physical health-related quality of life. Prior to reaching these objectives, several intermediate steps must be taken to improve the physical, social, emotional, and financial well-being of cancer survivors. Public health has a role in developing strategic, actionable, and measurable approaches to facilitate change at multiple levels to improve the lives of survivors and their families. The social ecological model has been used by the public health community as the foundation of multilevel intervention design and implementation, encouraging researchers and practitioners to explore methods that promote internal and external changes at the individual, interpersonal, organizational, community, and policy levels. The survivorship community, including public health professionals, providers, policymakers, survivors, advocates, and caregivers, must work collaboratively to identify, develop, and implement interventions that benefit cancer survivors. The National Action Plan for Cancer Survivorship highlights public health domains and associated strategies that can be the impetus for collaboration between and among the levels in the social ecological model and are integral to improving survivor outcomes. This paper describes the Public Health Action Model for Cancer Survivorship, an integrative framework that combines the National Action Plan for Cancer Survivorship with the social ecological model to demonstrate how interaction among the various levels may promote better outcomes for survivors. PMID:26590641

  13. Improving the Fit of a Land-Surface Model to Data Using its Adjoint

    Science.gov (United States)

    Raoult, Nina; Jupp, Tim; Cox, Peter; Luke, Catherine

    2016-04-01

    Land-surface models (LSMs) are crucial components of the Earth System Models (ESMs) which are used to make coupled climate-carbon cycle projections for the 21st century. The Joint UK Land Environment Simulator (JULES) is the land-surface model used in the climate and weather forecast models of the UK Met Office. In this study, JULES is 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. We present an introduction to the adJULES system and demonstrate its ability to improve the model-data fit using eddy covariance measurements of gross primary production (GPP) and latent heat (LE) fluxes. adJULES also has the ability to calibrate over multiple sites simultaneously. This feature is used to define new optimised parameter values for the 5 Plant Functional Types (PFTS) in JULES. The optimised PFT-specific parameters improve the performance of JULES over 90% of the FLUXNET sites used in the study. These reductions in error are shown and compared to reductions found due to site-specific optimisations. Finally, 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.

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

    Science.gov (United States)

    Rodrigue, Nicolas; Philippe, Hervé; Lartillot, Nicolas

    2010-03-01

    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

  15. Ovarian Cancer Pathogenesis: A Model in Evolution

    Directory of Open Access Journals (Sweden)

    Alison M. Karst

    2010-01-01

    Full Text Available Ovarian cancer is a deadly disease for which there is no effective means of early detection. Ovarian carcinomas comprise a diverse group of neoplasms, exhibiting a wide range of morphological characteristics, clinical manifestations, genetic alterations, and tumor behaviors. This high degree of heterogeneity presents a major clinical challenge in both diagnosing and treating ovarian cancer. Furthermore, the early events leading to ovarian carcinoma development are poorly understood, thus complicating efforts to develop screening modalities for this disease. Here, we provide an overview of the current models of ovarian cancer pathogenesis, highlighting recent findings implicating the fallopian tube fimbria as a possible site of origin of ovarian carcinomas. The ovarian cancer model will continue to evolve as we learn more about the genetics and etiology of this disease.

  16. Dynamics of the risk of smoking-induced lung cancer : A compartmental hidden markov model for longitudinal analysis

    NARCIS (Netherlands)

    Chadeau-Hyam, Marc; Tubert-Bitter, Pascale; Guihenneuc-Jouyaux, Chantal; Campanella, Gianluca; Richardson, Sylvia; Vermeulen, Roel; De Iorio, Maria; Galea, Sandro; Vineis, Paolo

    2014-01-01

    BACKGROUND:: To account for the dynamic aspects of carcinogenesis, we propose a compartmental hidden Markov model in which each person is healthy, asymptomatically affected, diagnosed, or deceased. Our model is illustrated using the example of smoking-induced lung cancer. METHODS:: The model was fit

  17. Emerging and Evolving Ovarian Cancer Animal Models

    OpenAIRE

    Bobbs, Alexander S; Jennifer M. Cole; Cowden Dahl, Karen D.

    2015-01-01

    Ovarian cancer (OC) is the leading cause of death from a gynecological malignancy in the United States. By the time a woman is diagnosed with OC, the tumor has usually metastasized. Mouse models that are used to recapitulate different aspects of human OC have been evolving for nearly 40 years. Xenograft studies in immunocompromised and immunocompetent mice have enhanced our knowledge of metastasis and immune cell involvement in cancer. Patient-derived xenografts (PDXs) can accurately reflect ...

  18. Fast fitting of non-Gaussian state-space models to animal movement data via Template Model Builder

    DEFF Research Database (Denmark)

    Albertsen, Christoffer Moesgaard; Whoriskey, Kim; Yurkowski, David;

    2015-01-01

    State-space models (SSM) are often used for analyzing complex ecological processes that are not observed directly, such as marine animal movement. When outliers are present in the measurements, special care is needed in the analysis to obtain reliable location and process estimates. Here we...... recommend using the Laplace approximation combined with automatic differentiation (as implemented in the novel R package Template Model Builder; TMB) for the fast fitting of continuous-time multivariate non-Gaussian SSMs. Through Argos satellite tracking data, we demonstrate that the use of continuous...

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

    Science.gov (United States)

    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…

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

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Jie; Ding, M. D.; Li, Ying; Fang, Cheng [School of Astronomy and Space Science, Nanjing University, Nanjing 210093 (China); Cao, Wenda, E-mail: dmd@nju.edu.cn [Big Bear Solar Observatory, New Jersey Institute of Technology, 40386 North Shore Lane, Big Bear City, CA 92314-9672 (United States)

    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.

  1. ANALYTICAL LIGHT CURVE MODELS OF SUPERLUMINOUS SUPERNOVAE: {chi}{sup 2}-MINIMIZATION OF PARAMETER FITS

    Energy Technology Data Exchange (ETDEWEB)

    Chatzopoulos, E.; Wheeler, J. Craig; Vinko, J. [Department of Astronomy, University of Texas at Austin, Austin, TX (United States); Horvath, Z. L.; Nagy, A., E-mail: manolis@astro.as.utexas.edu [Department of Optics and Quantum Electronics, University of Szeged (Hungary)

    2013-08-10

    We present fits of generalized semi-analytic supernova (SN) light curve (LC) models for a variety of power inputs including {sup 56}Ni and {sup 56}Co radioactive decay, magnetar spin-down, and forward and reverse shock heating due to supernova ejecta-circumstellar matter (CSM) interaction. We apply our models to the observed LCs of the H-rich superluminous supernovae (SLSN-II) SN 2006gy, SN 2006tf, SN 2008am, SN 2008es, CSS100217, the H-poor SLSN-I SN 2005ap, SCP06F6, SN 2007bi, SN 2010gx, and SN 2010kd, as well as to the interacting SN 2008iy and PTF 09uj. Our goal is to determine the dominant mechanism that powers the LCs of these extraordinary events and the physical conditions involved in each case. We also present a comparison of our semi-analytical results with recent results from numerical radiation hydrodynamics calculations in the particular case of SN 2006gy in order to explore the strengths and weaknesses of our models. We find that CS shock heating produced by ejecta-CSM interaction provides a better fit to the LCs of most of the events we examine. We discuss the possibility that collision of supernova ejecta with hydrogen-deficient CSM accounts for some of the hydrogen-deficient SLSNe (SLSN-I) and may be a plausible explanation for the explosion mechanism of SN 2007bi, the pair-instability supernova candidate. We characterize and discuss issues of parameter degeneracy.

  2. FIT ANALYSIS OF INDOSAT DOMPETKU BUSINESS MODEL USING A STRATEGIC DIAGNOSIS APPROACH

    Directory of Open Access Journals (Sweden)

    Fauzi Ridwansyah

    2015-09-01

    Full Text Available Mobile payment is an industry's response to global and regional technological-driven, as well as national social-economical driven in less cash society development. The purposes of this study were 1 identifying positioning of PT. Indosat in providing a response to Indonesian mobile payment market, 2 analyzing Indosat’s internal capabilities and business model fit with environment turbulence, and 3 formulating the optimum mobile payment business model development design for Indosat. The method used in this study was a combination of qualitative and quantitative analysis through in-depth interviews with purposive judgment sampling. The analysis tools used in this study were Business Model Canvas (MBC and Ansoff’s Strategic Diagnosis. The interviewees were the representatives of PT. Indosat internal management and mobile payment business value chain stakeholders. Based on BMC mapping which is then analyzed by strategic diagnosis model, a considerable gap (>1 between the current market environment and Indosat strategy of aggressiveness with the expected future of environment turbulence level was obtained. Therefore, changes in the competitive strategy that need to be conducted include 1 developing a new customer segment, 2 shifting the value proposition that leads to the extensification of mobile payment, 3 monetizing effective value proposition, and 4 integrating effective collaboration for harmonizing company’s objective with the government's vision. Keywords: business model canvas, Indosat, mobile payment, less cash society, strategic diagnosis

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

    Energy Technology Data Exchange (ETDEWEB)

    Leite, D. M. G., E-mail: dmgleite@fc.unesp.br [UNIFEI—Universidade Federal de Itajubá, Av. BPS, 1303, 37500-903 Itajubá, MG (Brazil); Batagin-Neto, A.; Nunes-Neto, O. [UNESP—Univ Estadual Paulista, POSMAT—Programa de Pós-Graduação em Ciência e Tecnologia de Materiais, Av. Eng. Luiz Edmundo Carrijo Coube, 14-01, 17033-360 Bauru, SP (Brazil); Gómez, J. A. [Departamento de Física, FFCLRP-USP, Av. Bandeirantes 3900, 14040-901 Ribeirão Preto, SP (Brazil); Graeff, C. F. O. [UNESP—Univ Estadual Paulista, POSMAT—Programa de Pós-Graduação em Ciência e Tecnologia de Materiais, Av. Eng. Luiz Edmundo Carrijo Coube, 14-01, 17033-360 Bauru, SP (Brazil); DF-FC, UNESP—Univ Estadual Paulista, Av. Eng. Luiz Edmundo Carrijo Coube, 14-01, 17033-360 Bauru, SP (Brazil)

    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.

  4. Context Sensitive Modeling of Cancer Drug Sensitivity

    Science.gov (United States)

    Chen, Bo-Juen; Litvin, Oren; Ungar, Lyle; Pe’er, Dana

    2015-01-01

    Recent screening of drug sensitivity in large panels of cancer cell lines provides a valuable resource towards developing algorithms that predict drug response. Since more samples provide increased statistical power, most approaches to prediction of drug sensitivity pool multiple cancer types together without distinction. However, pan-cancer results can be misleading due to the confounding effects of tissues or cancer subtypes. On the other hand, independent analysis for each cancer-type is hampered by small sample size. To balance this trade-off, we present CHER (Contextual Heterogeneity Enabled Regression), an algorithm that builds predictive models for drug sensitivity by selecting predictive genomic features and deciding which ones should—and should not—be shared across different cancers, tissues and drugs. CHER provides significantly more accurate models of drug sensitivity than comparable elastic-net-based models. Moreover, CHER provides better insight into the underlying biological processes by finding a sparse set of shared and type-specific genomic features. PMID:26274927

  5. Context Sensitive Modeling of Cancer Drug Sensitivity.

    Directory of Open Access Journals (Sweden)

    Bo-Juen Chen

    Full Text Available Recent screening of drug sensitivity in large panels of cancer cell lines provides a valuable resource towards developing algorithms that predict drug response. Since more samples provide increased statistical power, most approaches to prediction of drug sensitivity pool multiple cancer types together without distinction. However, pan-cancer results can be misleading due to the confounding effects of tissues or cancer subtypes. On the other hand, independent analysis for each cancer-type is hampered by small sample size. To balance this trade-off, we present CHER (Contextual Heterogeneity Enabled Regression, an algorithm that builds predictive models for drug sensitivity by selecting predictive genomic features and deciding which ones should-and should not-be shared across different cancers, tissues and drugs. CHER provides significantly more accurate models of drug sensitivity than comparable elastic-net-based models. Moreover, CHER provides better insight into the underlying biological processes by finding a sparse set of shared and type-specific genomic features.

  6. MEMLET: An Easy-to-Use Tool for Data Fitting and Model Comparison Using Maximum-Likelihood Estimation.

    Science.gov (United States)

    Woody, Michael S; Lewis, John H; Greenberg, Michael J; Goldman, Yale E; Ostap, E Michael

    2016-07-26

    We present MEMLET (MATLAB-enabled maximum-likelihood estimation tool), a simple-to-use and powerful program for utilizing maximum-likelihood estimation (MLE) for parameter estimation from data produced by single-molecule and other biophysical experiments. The program is written in MATLAB and includes a graphical user interface, making it simple to integrate into the existing workflows of many users without requiring programming knowledge. We give a comparison of MLE and other fitting techniques (e.g., histograms and cumulative frequency distributions), showing how MLE often outperforms other fitting methods. The program includes a variety of features. 1) MEMLET fits probability density functions (PDFs) for many common distributions (exponential, multiexponential, Gaussian, etc.), as well as user-specified PDFs without the need for binning. 2) It can take into account experimental limits on the size of the shortest or longest detectable event (i.e., instrument "dead time") when fitting to PDFs. The proper modification of the PDFs occurs automatically in the program and greatly increases the accuracy of fitting the rates and relative amplitudes in multicomponent exponential fits. 3) MEMLET offers model testing (i.e., single-exponential versus double-exponential) using the log-likelihood ratio technique, which shows whether additional fitting parameters are statistically justifiable. 4) Global fitting can be used to fit data sets from multiple experiments to a common model. 5) Confidence intervals can be determined via bootstrapping utilizing parallel computation to increase performance. Easy-to-follow tutorials show how these features can be used. This program packages all of these techniques into a simple-to-use and well-documented interface to increase the accessibility of MLE fitting. PMID:27463130

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

    Science.gov (United States)

    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

  8. Branching process models of cancer

    CERN Document Server

    Durrett, Richard

    2015-01-01

    This volume develops results on continuous time branching processes and applies them to study rate of tumor growth, extending classic work on the Luria-Delbruck distribution. As a consequence, the authors calculate the probability that mutations that confer resistance to treatment are present at detection and quantify the extent of tumor heterogeneity. As applications, the authors evaluate ovarian cancer screening strategies and give rigorous proofs for results of Heano and Michor concerning tumor metastasis. These notes should be accessible to students who are familiar with Poisson processes and continuous time. Richard Durrett is mathematics professor at Duke University, USA. He is the author of 8 books, over 200 journal articles, and has supervised more than 40 Ph.D. students. Most of his current research concerns the applications of probability to biology: ecology, genetics, and most recently cancer.

  9. Mathematical models of breast and ovarian cancers.

    Science.gov (United States)

    Botesteanu, Dana-Adriana; Lipkowitz, Stanley; Lee, Jung-Min; Levy, Doron

    2016-07-01

    Women constitute the majority of the aging United States (US) population, and this has substantial implications on cancer population patterns and management practices. Breast cancer is the most common women's malignancy, while ovarian cancer is the most fatal gynecological malignancy in the US. In this review, we focus on these subsets of women's cancers, seen more commonly in postmenopausal and elderly women. In order to systematically investigate the complexity of cancer progression and response to treatment in breast and ovarian malignancies, we assert that integrated mathematical modeling frameworks viewed from a systems biology perspective are needed. Such integrated frameworks could offer innovative contributions to the clinical women's cancers community, as answers to clinical questions cannot always be reached with contemporary clinical and experimental tools. Here, we recapitulate clinically known data regarding the progression and treatment of the breast and ovarian cancers. We compare and contrast the two malignancies whenever possible in order to emphasize areas where substantial contributions could be made by clinically inspired and validated mathematical modeling. We show how current paradigms in the mathematical oncology community focusing on the two malignancies do not make comprehensive use of, nor substantially reflect existing clinical data, and we highlight the modeling areas in most critical need of clinical data integration. We emphasize that the primary goal of any mathematical study of women's cancers should be to address clinically relevant questions. WIREs Syst Biol Med 2016, 8:337-362. doi: 10.1002/wsbm.1343 For further resources related to this article, please visit the WIREs website. PMID:27259061

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

    Science.gov (United States)

    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.

  11. Goodness-of-fit tests for vector autoregressive models in time series

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The paper proposes and studies some diagnostic tools for checking the goodness-of-fit of general parametric vector autoregressive models in time series. The resulted tests are asymptotically chi-squared under the null hypothesis and can detect the alternatives converging to the null at a parametric rate. The tests involve weight functions,which provides us with the flexibility to choose scores for enhancing power performance,especially under directional alternatives. When the alternatives are not directional,we construct asymptotically distribution-free maximin tests for a large class of alternatives. A possibility to construct score-based omnibus tests is discussed when the alternative is saturated. The power performance is also investigated. In addition,when the sample size is small,a nonparametric Monte Carlo test approach for dependent data is proposed to improve the performance of the tests. The algorithm is easy to implement. Simulation studies and real applications are carried out for illustration.

  12. Fast hybrid fitting energy-based active contour model for target detection

    Institute of Scientific and Technical Information of China (English)

    Dengwei Wang; Tianxu Zhang; Luxin Yan

    2011-01-01

    A novel hybrid fitting energy-based active contour model in the level set framework is proposed.The method fuses the region and boundary information of the target to achieve accurate and robust detection performance.A special extra term that penalizes the deviation of the level set function from a signed distance function is also included in our method. This term allows the time-consuming redistancing operation to be removed completely.Moreover,a fast unconditionally stable numerical scheme is introduced to solve the problem.Experimental results on real infrared images show that our method can improve target detection performance efficiently in terms of the number of iterations and the wasted central processing unit(CPU) time.

  13. Molecular mechanisms of protein aggregation from global fitting of kinetic models.

    Science.gov (United States)

    Meisl, Georg; Kirkegaard, Julius B; Arosio, Paolo; Michaels, Thomas C T; Vendruscolo, Michele; Dobson, Christopher M; Linse, Sara; Knowles, Tuomas P J

    2016-02-01

    The elucidation of the molecular mechanisms by which soluble proteins convert into their amyloid forms is a fundamental prerequisite for understanding and controlling disorders that are linked to protein aggregation, such as Alzheimer's and Parkinson's diseases. However, because of the complexity associated with aggregation reaction networks, the analysis of kinetic data of protein aggregation to obtain the underlying mechanisms represents a complex task. Here we describe a framework, using quantitative kinetic assays and global fitting, to determine and to verify a molecular mechanism for aggregation reactions that is compatible with experimental kinetic data. We implement this approach in a web-based software, AmyloFit. Our procedure starts from the results of kinetic experiments that measure the concentration of aggregate mass as a function of time. We illustrate the approach with results from the aggregation of the β-amyloid (Aβ) peptides measured using thioflavin T, but the method is suitable for data from any similar kinetic experiment measuring the accumulation of aggregate mass as a function of time; the input data are in the form of a tab-separated text file. We also outline general experimental strategies and practical considerations for obtaining kinetic data of sufficient quality to draw detailed mechanistic conclusions, and the procedure starts with instructions for extensive data quality control. For the core part of the analysis, we provide an online platform (http://www.amylofit.ch.cam.ac.uk) that enables robust global analysis of kinetic data without the need for extensive programming or detailed mathematical knowledge. The software automates repetitive tasks and guides users through the key steps of kinetic analysis: determination of constraints to be placed on the aggregation mechanism based on the concentration dependence of the aggregation reaction, choosing from several fundamental models describing assembly into linear aggregates and

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

    Science.gov (United States)

    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%…

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

    Science.gov (United States)

    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…

  16. A Cautionary Note on Using G[squared](dif) to Assess Relative Model Fit in Categorical Data Analysis

    Science.gov (United States)

    Maydeu-Olivares, Albert; Cai, Li

    2006-01-01

    The likelihood ratio test statistic G[squared](dif) is widely used for comparing the fit of nested models in categorical data analysis. In large samples, this statistic is distributed as a chi-square with degrees of freedom equal to the difference in degrees of freedom between the tested models, but only if the least restrictive model is correctly…

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

    Science.gov (United States)

    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. PMID:25571578

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

    DEFF Research Database (Denmark)

    Bolker, B.M.; Gardner, B.; Maunder, M.;

    2013-01-01

    ) to specific suggestions about how to change the mathematical description of models to make them more amenable to parameter estimation. 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...

  19. Ignoring imperfect detection in biological surveys is dangerous: a response to 'fitting and interpreting occupancy models'.

    Science.gov (United States)

    Guillera-Arroita, Gurutzeta; Lahoz-Monfort, José J; MacKenzie, Darryl I; Wintle, Brendan A; McCarthy, Michael A

    2014-01-01

    In a recent paper, Welsh, Lindenmayer and Donnelly (WLD) question the usefulness of models that estimate species occupancy while accounting for detectability. WLD claim that these models are difficult to fit and argue that disregarding detectability can be better than trying to adjust for it. We think that this conclusion and subsequent recommendations are not well founded and may negatively impact the quality of statistical inference in ecology and related management decisions. Here we respond to WLD's claims, evaluating in detail their arguments, using simulations and/or theory to support our points. In particular, WLD argue that both disregarding and accounting for imperfect detection lead to the same estimator performance regardless of sample size when detectability is a function of abundance. We show that this, the key result of their paper, only holds for cases of extreme heterogeneity like the single scenario they considered. Our results illustrate the dangers of disregarding imperfect detection. When ignored, occupancy and detection are confounded: the same naïve occupancy estimates can be obtained for very different true levels of occupancy so the size of the bias is unknowable. Hierarchical occupancy models separate occupancy and detection, and imprecise estimates simply indicate that more data are required for robust inference about the system in question. As for any statistical method, when underlying assumptions of simple hierarchical models are violated, their reliability is reduced. Resorting in those instances where hierarchical occupancy models do no perform well to the naïve occupancy estimator does not provide a satisfactory solution. The aim should instead be to achieve better estimation, by minimizing the effect of these issues during design, data collection and analysis, ensuring that the right amount of data is collected and model assumptions are met, considering model extensions where appropriate. PMID:25075615

  20. Ignoring imperfect detection in biological surveys is dangerous: a response to 'fitting and interpreting occupancy models'.

    Directory of Open Access Journals (Sweden)

    Gurutzeta Guillera-Arroita

    Full Text Available In a recent paper, Welsh, Lindenmayer and Donnelly (WLD question the usefulness of models that estimate species occupancy while accounting for detectability. WLD claim that these models are difficult to fit and argue that disregarding detectability can be better than trying to adjust for it. We think that this conclusion and subsequent recommendations are not well founded and may negatively impact the quality of statistical inference in ecology and related management decisions. Here we respond to WLD's claims, evaluating in detail their arguments, using simulations and/or theory to support our points. In particular, WLD argue that both disregarding and accounting for imperfect detection lead to the same estimator performance regardless of sample size when detectability is a function of abundance. We show that this, the key result of their paper, only holds for cases of extreme heterogeneity like the single scenario they considered. Our results illustrate the dangers of disregarding imperfect detection. When ignored, occupancy and detection are confounded: the same naïve occupancy estimates can be obtained for very different true levels of occupancy so the size of the bias is unknowable. Hierarchical occupancy models separate occupancy and detection, and imprecise estimates simply indicate that more data are required for robust inference about the system in question. As for any statistical method, when underlying assumptions of simple hierarchical models are violated, their reliability is reduced. Resorting in those instances where hierarchical occupancy models do no perform well to the naïve occupancy estimator does not provide a satisfactory solution. The aim should instead be to achieve better estimation, by minimizing the effect of these issues during design, data collection and analysis, ensuring that the right amount of data is collected and model assumptions are met, considering model extensions where appropriate.

  1. Self-organization in models of populations with two-parent reproduction on a rugged fitness landscape

    CERN Document Server

    Finjord, J

    1995-01-01

    The two-parent reproduction model of Derrida and Peliti is simulated on a rugged fitness landscape. Fixed fitness values for each possible genotype are assigned randomly, with all fit individuals having the same probability of reproduction. The previously observed transition to a self-organized state of the population with less recombinational load, implies an abrupt change of genetic overlap distributions, showing up characteristics of a phase transition. A crossover variant of the model has a smoother transition to the adapted regime, with a residual collective adaptation for small values of the threshold in fitness. When a geographical constraint (shortest possible distance) on pairwise reproduction in a population arranged one-dimensionally is imposed, a poised state results, suggestive of self-organized criticality.

  2. Effect of the choice of stagnation density in data-fitted first- and second-order traffic models

    CERN Document Server

    Fan, Shimao

    2013-01-01

    For a class of data-fitted macroscopic traffic models, the influence of the choice of the stagnation density on the model accuracy is investigated. This work builds on an established framework of data-fitted first-order Lighthill-Whitham-Richards (LWR) models and their second-order Aw-Rascle-Zhang (ARZ) generalizations. These models are systematically fitted to historic fundamental diagram data, and then their predictive accuracy is quantified via a version of the three-detector problem test, considering vehicle trajectory data and single-loop sensor data. The key outcome of this study is that with commonly suggested stagnation densities of 120 vehicles/km/lane and above, information travels backwards too slowly. It is then demonstrated that the reduction of the stagnation density to 90-100 vehicles/km/lane addresses this problem and results in a significant improvement of the predictive accuracy of the considered models.

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

    Science.gov (United States)

    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 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. PMID:24651252

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

    Directory of Open Access Journals (Sweden)

    Mónica A Silva

    Full Text Available 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.

  5. Modeling of physical fitness of young karatyst on the pre basic training

    Directory of Open Access Journals (Sweden)

    Galimskyi V.A.

    2014-05-01

    Full Text Available Purpose : to develop a program of physical fitness for the correction of the pre basic training on the basis of model performance. Material: 57 young karate sportsmen of 9-11 years old took part in the research. Results : the level of general and special physical preparedness of young karate 9-11 years old was determined. Classes in the control group occurred in the existing program for yous sports school Muay Thai (Thailand boxing. For the experimental group has developed a program of selective development of general and special physical qualities of model-based training sessions. Special program contains 6 direction: 1. Development of static and dynamic balance; 2. Development of vestibular stability (precision movements after rotation; 3. Development rate movements; 4. The development of the capacity for rapid restructuring movements; 5. Development capabilities to differentiate power and spatial parameters of movement; 6. Development of the ability to perform jumping movements of rotation. Development of special physical qualities continued to work to improve engineering complex shock motions on the place and with movement. Conclusions : the use of selective development of special physical qualities based models of training sessions has a significant performance advantage over the control group.

  6. A simple periodic-forced model for dengue fitted to incidence data in Singapore.

    Science.gov (United States)

    Andraud, Mathieu; Hens, Niel; Beutels, Philippe

    2013-07-01

    Dengue is the world's major arbovirosis and therefore an important public health concern in endemic areas. The availability of weekly reports of dengue cases in Singapore offers the opportunity to analyze the transmission dynamics and the impact of vector control strategies. Based on a previous model studying the impact of vector control strategies in Singapore during the 2005 outbreak, a simple vector-host model accounting for seasonal fluctuation in vector density was developed to estimate the parameters governing the vector population dynamics using dengue fever incidence data from August 2003 to December 2007. The impact of vector control, which consisted principally of a systematic removal of actual and potential breeding sites during a six-week period in 2005, was also investigated. Although our approach does not account for the complex life cycle of the vector, the good fit between data and model outputs showed that the impact of seasonality on the transmission dynamics is highly important. Moreover, the periodic fluctuations of the vector population were found in phase with temperature variations, suggesting a strong climate effect on the vector density and, in turn, on the transmission dynamics.

  7. Supersymmetric Fits after the Higgs Discovery and Implications for Model Building

    CERN Document Server

    Ellis, John

    2014-01-01

    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 missing transverse energy accompanied by jets, and the LHCb and CMS measurements off BR($B_s \\to \\mu^+ \\mu^-$). Results are presented from frequentist analyses of the parameter spaces of the CMSSM and NUHM1. The global $\\chi^2$ functions for the supersymmetric models vary slowly over most of the parameter spaces allowed by the Higgs mass and the missing transverse energy search, with best-fit values that are comparable to the $\\chi^2$ for the Standard Model. The $95\\%$ CL lower...

  8. Fitting density models to observational data - The local Schmidt law in molecular clouds

    CERN Document Server

    Lombardi, Marco; Alves, João

    2013-01-01

    We consider the general problem of fitting a parametric density model to discrete observations, taken to follow a non-homogeneous Poisson point process. This class of models is very common, and can be used to describe many astrophysical processes, including the distribution of protostars in molecular clouds. We give the expression for the likelihood of a given spatial density distribution of protostars and apply it to infer the most probable dependence of the protostellar surface density on the gas surface density. Finally, we apply this general technique to model the distribution of protostars in the Orion molecular cloud and robustly derive the local star formation scaling (Schmidt) law for a molecular cloud. We find that in this cloud the protostellar surface density, \\Sigma_YSO, is directly proportional to the square gas column density, here expressed as infrared extinction in the K-band, A_K: more precisely, \\Sigma_YSO = (1.65 +/- 0.19) A_K^(2.03 +/- 0.15) stars pc^-2.

  9. Minimal see-saw model predicting best fit lepton mixing angles

    Energy Technology Data Exchange (ETDEWEB)

    King, Stephen F., E-mail: king@soton.ac.uk

    2013-07-09

    We discuss a minimal predictive see-saw model in which the right-handed neutrino mainly responsible for the atmospheric neutrino mass has couplings to (ν{sub e},ν{sub μ},ν{sub τ}) proportional to (0,1,1) and the right-handed neutrino mainly responsible for the solar neutrino mass has couplings to (ν{sub e},ν{sub μ},ν{sub τ}) proportional to (1,4,2), with a relative phase η=−2π/5. We show how these patterns of couplings could arise from an A{sub 4} family symmetry model of leptons, together with Z{sub 3} and Z{sub 5} symmetries which fix η=−2π/5 up to a discrete phase choice. The PMNS matrix is then completely determined by one remaining parameter which is used to fix the neutrino mass ratio m{sub 2}/m{sub 3}. The model predicts the lepton mixing angles θ{sub 12}≈34{sup ∘},θ{sub 23}≈41{sup ∘},θ{sub 13}≈9.5{sup ∘}, which exactly coincide with the current best fit values for a normal neutrino mass hierarchy, together with the distinctive prediction for the CP violating oscillation phase δ≈106{sup ∘}.

  10. In Silico Experimental Modeling of Cancer Treatment

    OpenAIRE

    Trisilowati; D. G. Mallet

    2012-01-01

    In silico experimental modeling of cancer involves combining findings from biological literature with computer-based models of biological systems in order to conduct investigations of hypotheses entirely in the computer laboratory. In this paper, we discuss the use of in silico modeling as a precursor to traditional clinical and laboratory research, allowing researchers to refine their experimental programs with an aim to reducing costs and increasing research efficiency. We explain the metho...

  11. Poisson distribution and process as a well-fitting pattern for counting variables in biologic models

    Directory of Open Access Journals (Sweden)

    Lucietta Betti

    2012-09-01

    Full Text Available One of the major criticisms directed to basic research on high dilution effects is the lack of a steady statistical approach; therefore, it seems crucial to fix some milestones in statistical analysis of this kind of experimentation. Since plant research in homeopathy has been recently developed and one of the mostly used models is based on in vitro seed germination, here we propose a statistical approach focused on the Poisson distribution, that satisfactorily fits the number of non-germinated seeds. Poisson distribution is a discrete-valued model often used in statistics when representing the number X of specific events (telephone calls, industrial machine failures, genetic mutations etc. that occur in a fixed period of time, supposing that instant probability of occurrence of such events is constant. If we denote with λ the average number of events that occur within the fixed period, the probability of observing exactly k events is: P(k = e-λ λk /k! , k = 0, 1,2,… This distribution is commonly used when dealing with rare effects, in the sense that it has to be almost impossible to have two events at the same time. Poisson distribution is the basic model of the socalled Poisson process, which is a counting process N(t, where t is a time parameter, having these properties: -The process starts with zero: N(0 = 0; -The increments are independent; -The number of events that occur in a period of time d(t follows a Poisson distribution with parameter proportional to d(t; -The waiting time, i.e. the time between an event and another one, follows and exponential distribution. In a series of experiments performed by our research group ([1], [2]., [3], [4] we tried to apply this distribution to the number X of non-germinated seeds out of a fixed number N* of seeds in a Petri dish (usually N* = 33 or N* = 36. The goodness-of-fit was checked by different tests (Kolmogorov distance and chi-squared, as well as

  12. Preclinical fluorescent mouse models of pancreatic cancer

    Science.gov (United States)

    Bouvet, Michael; Hoffman, Robert M.

    2007-02-01

    Here we describe our cumulative experience with the development and preclinical application of several highly fluorescent, clinically-relevant, metastatic orthotopic mouse models of pancreatic cancer. These models utilize the human pancreatic cancer cell lines which have been genetically engineered to selectively express high levels of the bioluminescent green fluorescent (GFP) or red fluorescent protein (RFP). Fluorescent tumors are established subcutaneously in nude mice, and tumor fragments are then surgically transplanted onto the pancreas. Locoregional tumor growth and distant metastasis of these orthotopic implants occurs spontaneously and rapidly throughout the abdomen in a manner consistent with clinical human disease. Highly specific, high-resolution, real-time visualization of tumor growth and metastasis may be achieved in vivo without the need for contrast agents, invasive techniques, or expensive imaging equipment. We have shown a high correlation between florescent optical imaging and magnetic resonance imaging in these models. Alternatively, transplantation of RFP-expressing tumor fragments onto the pancreas of GFP-expressing transgenic mice may be used to facilitate visualization of tumor-host interaction between the pancreatic tumor fragments and host-derived stroma and vasculature. Such in vivo models have enabled us to serially visualize and acquire images of the progression of pancreatic cancer in the live animal, and to demonstrate the real-time antitumor and antimetastatic effects of several novel therapeutic strategies on pancreatic malignancy. These fluorescent models are therefore powerful and reliable tools with which to investigate human pancreatic cancer and therapeutic strategies directed against it.

  13. A clinical data validated mathematical model of prostate cancer growth under intermittent androgen suppression therapy

    Science.gov (United States)

    Portz, Travis; Kuang, Yang; Nagy, John D.

    2012-03-01

    Prostate cancer is commonly treated by a form of hormone therapy called androgen suppression. This form of treatment, while successful at reducing the cancer cell population, adversely affects quality of life and typically leads to a recurrence of the cancer in an androgen-independent form. Intermittent androgen suppression aims to alleviate some of these adverse affects by cycling the patient on and off treatment. Clinical studies have suggested that intermittent therapy is capable of maintaining androgen dependence over multiple treatment cycles while increasing quality of life during off-treatment periods. This paper presents a mathematical model of prostate cancer to study the dynamics of androgen suppression therapy and the production of prostate-specific antigen (PSA), a clinical marker for prostate cancer. Preliminary models were based on the assumption of an androgen-independent (AI) cell population with constant net growth rate. These models gave poor accuracy when fitting clinical data during simulation. The final model presented hypothesizes an AI population with increased sensitivity to low levels of androgen. It also hypothesizes that PSA production is heavily dependent on androgen. The high level of accuracy in fitting clinical data with this model appears to confirm these hypotheses, which are also consistent with biological evidence.

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

    Science.gov (United States)

    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

  15. Fitness for duty: A tried-and-true model for decision making

    International Nuclear Information System (INIS)

    The US Nuclear Regulatory Commission (NRC) rules and regulations pertaining to fitness for duty specify development of programs designed to ensure that nuclear power plant personnel are not under the influence of legal or illegal substances that cause mental or physical impairment of work performance such that public safety is compromised. These regulations specify the type of decision loop to employ in determining the employee's movement through the process of initial restriction of access to the point at which his access authorization is restores. Suggestions are also offered to determine the roles that various components of the organization should take in the decision loop. This paper discusses some implications and labor concerns arising from the suggested role of employee assistance programs (EAPs) in the decision loop for clinical assessment and return-to-work evaluation of chemical testing failures. A model for a decision loop addressing some of the issues raised is presented. The proposed model has been implemented in one nuclear facility and has withstood the scrutiny of an NRC audit

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

    Directory of Open Access Journals (Sweden)

    Barbot Jean-Pierre

    2007-01-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  18. Estimating and modelling cure in population-based cancer studies within the framework of flexible parametric survival models

    Directory of Open Access Journals (Sweden)

    Eloranta Sandra

    2011-06-01

    Full Text Available Abstract Background When the mortality among a cancer patient group returns to the same level as in the general population, that is, the patients no longer experience excess mortality, the patients still alive are considered "statistically cured". Cure models can be used to estimate the cure proportion as well as the survival function of the "uncured". One limitation of parametric cure models is that the functional form of the survival of the "uncured" has to be specified. It can sometimes be hard to find a survival function flexible enough to fit the observed data, for example, when there is high excess hazard within a few months from diagnosis, which is common among older age groups. This has led to the exclusion of older age groups in population-based cancer studies using cure models. Methods Here we have extended the flexible parametric survival model to incorporate cure as a special case to estimate the cure proportion and the survival of the "uncured". Flexible parametric survival models use splines to model the underlying hazard function, and therefore no parametric distribution has to be specified. Results We have compared the fit from standard cure models to our flexible cure model, using data on colon cancer patients in Finland. This new method gives similar results to a standard cure model, when it is reliable, and better fit when the standard cure model gives biased estimates. Conclusions Cure models within the framework of flexible parametric models enables cure modelling when standard models give biased estimates. These flexible cure models enable inclusion of older age groups and can give stage-specific estimates, which is not always possible from parametric cure models.

  19. A simulation-based goodness-of-fit test for random effects in generalized linear mixed models

    DEFF Research Database (Denmark)

    Waagepetersen, Rasmus

    2006-01-01

    The goodness-of-fit of the distribution of random effects in a generalized linear mixed model is assessed using a conditional simulation of the random effects conditional on the observations. Provided that the specified joint model for random effects and observations is correct, the marginal...

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

    Science.gov (United States)

    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. PMID:26144945

  1. Cancer immunotherapy : insights from transgenic animal models

    NARCIS (Netherlands)

    McLaughlin, PMJ; Kroesen, BJ; Harmsen, MC; de Leij, LFMH

    2001-01-01

    A wide range of strategies in cancer immunotherapy has been developed in the last decade, some of which are currently being used in clinical settings. The development of these immunotherapeutical strategies has been facilitated by the generation of relevant transgenic animal models. Since the differ

  2. Remark on statistical model fits to particle ratios in relativistic heavy ion collisions

    OpenAIRE

    Becattini, F.

    2007-01-01

    In order to determine the chemical freeze-out parameters of the hadron-emitting source in relativistic heavy ion collisions some studies in literature perform fits by using as data input a subsample of ratios calculated out of experimentally measured hadron yields instead of yields themselves. We show that this is a statistically incorrect method fit, implying a bias in the extracted parameters.

  3. Lung cancer mortality trends in Chile and six-year projections using Bayesian dynamic linear models.

    Science.gov (United States)

    Torres-Avilés, Francisco; Moraga, Tomás; Núñez, Loreto; Icaza, Gloria

    2015-09-01

    The objectives were to analyze lung cancer mortality trends in Chile from 1990 to 2009, and to project the rates six years forward. Lung cancer mortality data were obtained from the Chilean Ministry of Health. To obtain mortality rates, population projections were used, based on the 2002 National Census. Rates were adjusted using the world standard population as reference. Bayesian dynamic linear models were fitted to estimate trends from 1990 to 2009 and to obtain projections for 2010-2015. During the period under study, there was a 19.9% reduction in the lung cancer mortality rate in men. In women, there was increase of 28.4%. The second-order model showed a better fit for men, and the first-order model a better fit for women. Between 2010 and 2015 the downward trend continued in men, while a trend to stabilization was projected for lung cancer mortality in women in Chile. This analytical approach could be useful implement surveillance systems for chronic non-communicable disease and to evaluate preventive strategies. PMID:26578021

  4. Mouse models of intestinal inflammation and cancer.

    Science.gov (United States)

    Westbrook, Aya M; Szakmary, Akos; Schiestl, Robert H

    2016-09-01

    Chronic inflammation is strongly associated with approximately one-fifth of all human cancers. Arising from combinations of factors such as environmental exposures, diet, inherited gene polymorphisms, infections, or from dysfunctions of the immune response, chronic inflammation begins as an attempt of the body to remove injurious stimuli; however, over time, this results in continuous tissue destruction and promotion and maintenance of carcinogenesis. Here, we focus on intestinal inflammation and its associated cancers, a group of diseases on the rise and affecting millions of people worldwide. Intestinal inflammation can be widely grouped into inflammatory bowel diseases (ulcerative colitis and Crohn's disease) and celiac disease. Long-standing intestinal inflammation is associated with colorectal cancer and small-bowel adenocarcinoma, as well as extraintestinal manifestations, including lymphomas and autoimmune diseases. This article highlights potential mechanisms of pathogenesis in inflammatory bowel diseases and celiac disease, as well as those involved in the progression to associated cancers, most of which have been identified from studies utilizing mouse models of intestinal inflammation. Mouse models of intestinal inflammation can be widely grouped into chemically induced models; genetic models, which make up the bulk of the studied models; adoptive transfer models; and spontaneous models. Studies in these models have lead to the understanding that persistent antigen exposure in the intestinal lumen, in combination with loss of epithelial barrier function, and dysfunction and dysregulation of the innate and adaptive immune responses lead to chronic intestinal inflammation. Transcriptional changes in this environment leading to cell survival, hyperplasia, promotion of angiogenesis, persistent DNA damage, or insufficient repair of DNA damage due to an excess of proinflammatory mediators are then thought to lead to sustained malignant transformation. With

  5. Antiangiogenic cancer drug using the zebrafish model.

    Science.gov (United States)

    Santoro, Massimo M

    2014-09-01

    The process of de novo vessel formation, called angiogenesis, is essential for tumor progression and spreading. Targeting of molecular pathways involved in such tumor angiogenetic processes by using specific drugs or inhibitors is important for developing new anticancer therapies. Drug discovery remains to be the main focus for biomedical research and represents the essence of antiangiogenesis cancer research. To pursue these molecular and pharmacological goals, researchers need to use animal models that facilitate the elucidation of tumor angiogenesis mechanisms and the testing of antiangiogenic therapies. The past few years have seen the zebrafish system emerge as a valid model organism to study developmental angiogenesis and, more recently, as an alternative vertebrate model for cancer research. In this review, we will discuss why the zebrafish model system has the advantage of being a vertebrate model equipped with easy and powerful transgenesis as well as imaging tools to investigate not only physiological angiogenesis but also tumor angiogenesis. We will also highlight the potential of zebrafish for identifying antitumor angiogenesis drugs to block tumor development and progression. We foresee the zebrafish model as an important system that can possibly complement well-established mouse models in cancer research to generate novel insights into the molecular mechanism of the tumor angiogenesis. PMID:24903092

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

    Energy Technology Data Exchange (ETDEWEB)

    Ross, James C., E-mail: jross@bwh.harvard.edu [Channing Laboratory, Brigham and Women' s Hospital, Boston, Massachusetts 02215 (United States); Surgical Planning Lab, Brigham and Women' s Hospital, Boston, Massachusetts 02215 (United States); Laboratory of Mathematics in Imaging, Brigham and Women' s Hospital, Boston, Massachusetts 02126 (United States); Kindlmann, Gordon L. [Computer Science Department and Computation Institute, University of Chicago, Chicago, Illinois 60637 (United States); Okajima, Yuka; Hatabu, Hiroto [Department of Radiology, Brigham and Women' s Hospital, Boston, Massachusetts 02215 (United States); Díaz, Alejandro A. [Pulmonary and Critical Care Division, Brigham and Women' s Hospital and Harvard Medical School, Boston, Massachusetts 02215 and Department of Pulmonary Diseases, Pontificia Universidad Católica de Chile, Santiago (Chile); Silverman, Edwin K. [Channing Laboratory, Brigham and Women' s Hospital, Boston, Massachusetts 02215 and Pulmonary and Critical Care Division, Brigham and Women' s Hospital and Harvard Medical School, Boston, Massachusetts 02215 (United States); Washko, George R. [Pulmonary and Critical Care Division, Brigham and Women' s Hospital and Harvard Medical School, Boston, Massachusetts 02215 (United States); Dy, Jennifer [ECE Department, Northeastern University, Boston, Massachusetts 02115 (United States); Estépar, Raúl San José [Department of Radiology, Brigham and Women' s Hospital, Boston, Massachusetts 02215 (United States); Surgical Planning Lab, Brigham and Women' s Hospital, Boston, Massachusetts 02215 (United States); Laboratory of Mathematics in Imaging, Brigham and Women' s Hospital, Boston, Massachusetts 02126 (United States)

    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

  7. Towards a multiscale model of colorectal cancer

    Institute of Scientific and Technical Information of China (English)

    Ingeborg MM van Leeuwen; Carina M Edwards; Mohammad Ilyas; Helen M Byrne

    2007-01-01

    Colorectal cancer (CRC) is one of the best characterised cancers, with extensive data documenting the sequential gene mutations that underlie its development.Complementary datasets are also being generated describing changes in protein and RNA expression,tumour biology and clinical outcome. Both the quantity and the variety of information are inexorably increasing and there is now an accompanying need to integrate these highly disparate datasets. In this article we aim to explain why we believe that mathematical modelling represents a natural tool or language with which to integrate these data and, in so doing, to provide insight into CRC.

  8. Facultative control of matrix production optimizes competitive fitness in Pseudomonas aeruginosa PA14 biofilm models.

    Science.gov (United States)

    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.

  9. Cost-Sensitive Boosting: Fitting an Additive Asymmetric Logistic Regression Model

    Science.gov (United States)

    Li, Qiu-Jie; Mao, Yao-Bin; Wang, Zhi-Quan; Xiang, Wen-Bo

    Conventional machine learning algorithms like boosting tend to equally treat misclassification errors that are not adequate to process certain cost-sensitive classification problems such as object detection. Although many cost-sensitive extensions of boosting by directly modifying the weighting strategy of correspond original algorithms have been proposed and reported, they are heuristic in nature and only proved effective by empirical results but lack sound theoretical analysis. This paper develops a framework from a statistical insight that can embody almost all existing cost-sensitive boosting algorithms: fitting an additive asymmetric logistic regression model by stage-wise optimization of certain criterions. Four cost-sensitive versions of boosting algorithms are derived, namely CSDA, CSRA, CSGA and CSLB which respectively correspond to Discrete AdaBoost, Real AdaBoost, Gentle AdaBoost and LogitBoost. Experimental results on the application of face detection have shown the effectiveness of the proposed learning framework in the reduction of the cumulative misclassification cost.

  10. A Multivariate Fit Luminosity Function and World Model for Long GRBs

    CERN Document Server

    Shahmoradi, Amir

    2012-01-01

    It is proposed that the luminosity function, the comoving-frame spectral correlations and distributions of cosmological Long-duration Gamma-Ray Bursts (LGRBs) may be very well described as multivariate log-normal distribution. This result is based on careful selection, analysis and modeling of the spectral parameters of LGRBs in the largest catalog of Gamma-Ray Bursts available to date: 2130 BATSE GRBs, while taking into account the detection threshold and possible selection effects on observational data. Constraints on the joint quadru-variate distribution of the isotropic peak luminosity, the total isotropic emission, the comoving-frame time-integrated spectral peak energy and the comoving-frame duration of LGRBs are derived. Extensive goodness-of-fit tests are performed. The presented analysis provides evidence for a relatively large fraction of LGRBs that have been missed by BATSE detector with total isotropic emissions extending down to 10^49 [erg] and observed spectral peak energies as low as 5 [KeV]. T...

  11. The fitting of general force-of-infection models to wildlife disease prevalence data

    Science.gov (United States)

    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

  12. Modeling pancreatic cancer with organoids

    NARCIS (Netherlands)

    Baker, Lindsey A; Tiriac, Hervé; Clevers, Hans; Tuveson, David A

    2016-01-01

    Pancreatic ductal adenocarcinoma (PDA) is a highly lethal malignancy for which new treatment and diagnostic approaches are urgently needed. In order for such breakthroughs to be discovered, researchers require systems that accurately model the development and biology of PDA. While cell lines, geneti

  13. Models of breast cancer: quo vadis, animal modeling?

    International Nuclear Information System (INIS)

    Rodent models for breast cancer have for many decades provided unparalleled insights into cellular and molecular aspects of neoplastic transformation and tumorigenesis. Despite recent improvements in the fidelity of genetically engineered mice, rodent models are still being criticized by many colleagues for not being 'authentic' enough to the human disease. Motives for this criticism are manifold and range from a very general antipathy against the rodent model system to well-founded arguments that highlight physiological variations between species. Newly proposed differences in genetic pathways that cause cancer in humans and mice invigorated the ongoing discussion about the legitimacy of the murine system to model the human disease. The present commentary intends to stimulate a debate on this subject by providing the background about new developments in animal modeling, by disputing suggested limitations of genetically engineered mice, and by discussing improvements but also ambiguous expectations on the authenticity of xenograft models to faithfully mimic the human disease

  14. Skin Cancer Prevention Coverage in Popular US Women’s Health and Fitness Magazines: An Analysis of Advertisements and Articles

    OpenAIRE

    Basch, Corey Hannah; Ethan, Danna; Hillyer, Grace Clarke; Berdnik, Alyssa

    2014-01-01

    The desire to be tan is a phenomenon that public health researchers have investigated, as exposure to UV radiation increases the chances of developing skin cancer. Media messages in women’s magazines have been shown to contribute to this problem. Much less is known about the prevalence of skin cancer prevention messages in these magazines. This study’s aim was to identify the number and type of articles and advertised products devoted to skin health (sun protection and skin cancer prevention ...

  15. Promoting Fitness and Safety in Elementary Students: A Randomized Control Study of the Michigan Model for Health

    Science.gov (United States)

    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…

  16. Fit-for-purpose: species distribution model performance depends on evaluation criteria - Dutch Hoverflies as a case study.

    Directory of Open Access Journals (Sweden)

    Jesús Aguirre-Gutiérrez

    Full Text Available Understanding species distributions and the factors limiting them is an important topic in ecology and conservation, including in nature reserve selection and predicting climate change impacts. While Species Distribution Models (SDM are the main tool used for these purposes, choosing the best SDM algorithm is not straightforward as these are plentiful and can be applied in many different ways. SDM are used mainly to gain insight in 1 overall species distributions, 2 their past-present-future probability of occurrence and/or 3 to understand their ecological niche limits (also referred to as ecological niche modelling. The fact that these three aims may require different models and outputs is, however, rarely considered and has not been evaluated consistently. Here we use data from a systematically sampled set of species occurrences to specifically test the performance of Species Distribution Models across several commonly used algorithms. Species range in distribution patterns from rare to common and from local to widespread. We compare overall model fit (representing species distribution, the accuracy of the predictions at multiple spatial scales, and the consistency in selection of environmental correlations all across multiple modelling runs. As expected, the choice of modelling algorithm determines model outcome. However, model quality depends not only on the algorithm, but also on the measure of model fit used and the scale at which it is used. Although model fit was higher for the consensus approach and Maxent, Maxent and GAM models were more consistent in estimating local occurrence, while RF and GBM showed higher consistency in environmental variables selection. Model outcomes diverged more for narrowly distributed species than for widespread species. We suggest that matching study aims with modelling approach is essential in Species Distribution Models, and provide suggestions how to do this for different modelling aims and species' data

  17. The Use of the L[subscript z] and L[subscript z]* Person-Fit Statistics and Problems Derived from Model Misspecification

    Science.gov (United States)

    Meijer, Rob R.; Tendeiro, Jorge N.

    2012-01-01

    We extend a recent didactic by Magis, Raiche, and Beland on the use of the l[subscript z] and l[subscript z]* person-fit statistics. We discuss a number of possibly confusing details and show that it is important to first investigate item response theory model fit before assessing person fit. Furthermore, it is argued that appropriate…

  18. Mouse models for BRAF-induced cancers.

    Science.gov (United States)

    Pritchard, C; Carragher, L; Aldridge, V; Giblett, S; Jin, H; Foster, C; Andreadi, C; Kamata, T

    2007-11-01

    Oncogenic mutations in the BRAF gene are detected in approximately 7% of human cancer samples with a particularly high frequency of mutation in malignant melanomas. Over 40 different missense BRAF mutations have been found, but the vast majority (>90%) represent a single nucleotide change resulting in a valine-->glutamate mutation at residue 600 ((V600E)BRAF). In cells cultured in vitro, (V600E)BRAF is able to stimulate endogenous MEK [MAPK (mitogen-activated protein kinase)/ERK (extracellular-signal-regulated kinase) kinase] and ERK phosphorylation leading to an increase in cell proliferation, cell survival, transformation, tumorigenicity, invasion and vascular development. Many of these hallmarks of cancer can be reversed by treatment of cells with siRNA (small interfering RNA) to BRAF or by inhibiting MEK, indicating that BRAF and MEK are attractive therapeutic targets in cancer samples with BRAF mutations. In order to fully understand the role of oncogenic BRAF in cancer development in vivo as well as to test the in vivo efficacy of anti-BRAF or anti-MEK therapies, GEMMs (genetically engineered mouse models) have been generated in which expression of oncogenic BRaf is conditionally dependent on the Cre recombinase. The delivery/activation of the Cre recombinase can be regulated in both a temporal and spatial manner and therefore these mouse models can be used to recapitulate the somatic mutation of BRAF that occurs in different tissues in the development of human cancer. The data so far obtained following Cre-mediated activation in haemopoietic tissue and the lung indicate that (V600E)BRAF mutation can drive tumour initiation and that its primary effect is to induce high levels of cyclin D1-mediated cell proliferation. However, hallmarks of OIS (oncogene-induced senescence) are evident that restrain further development of the tumour.

  19. Formal Modeling and Analysis of Pancreatic Cancer Microenvironment

    OpenAIRE

    Wang, Qinsi; Miskov-Zivanov, Natasa; Liu, Bing; Faeder, James R.; Lotze, Michael; Clarke, Edmund M

    2016-01-01

    The focus of pancreatic cancer research has been shifted from pancreatic cancer cells towards their microenvironment, involving pancreatic stellate cells that interact with cancer cells and influence tumor progression. To quantitatively understand the pancreatic cancer microenvironment, we construct a computational model for intracellular signaling networks of cancer cells and stellate cells as well as their intercellular communication. We extend the rule-based BioNetGen language to depict in...

  20. Efficacy of multimodal exercise-based rehabilitation on physical activity, cardiorespiratory fitness, and patient-reported outcomes in cancer survivors

    DEFF Research Database (Denmark)

    Midtgaard, J; Christensen, Jesper Frank; Tolver, Anders;

    2013-01-01

    Sedentary behavior and impaired cardiovascular reserve capacity are common late effects of cancer therapy emphasizing the need for effective strategies to increase physical activity (PA) in cancer survivors. We examined the efficacy of a 12-month exercise-based rehabilitation program on self...

  1. Fast fitting of non-Gaussian state-space models to animal movement data via Template Model Builder.

    Science.gov (United States)

    Albertsen, Christoffer Moesgaard; Whoriskey, Kim; Yurkowski, David; Nielsen, Anders; Mills, Joanna

    2015-10-01

    State-space models (SSM) are often used for analyzing complex ecological processes that are not observed directly, such as marine animal movement. When outliers are present in the measurements, special care is needed in the analysis to obtain reliable location and process estimates. Here we recommend using the Laplace approximation combined with automatic differentiation (as implemented in the novel R package Template Model Builder; TMB) for the fast fitting of continuous-time multivariate non-Gaussian SSMs. Through Argos satellite tracking data, we demonstrate that the use of continuous-time t-distributed measurement errors for error-prone data is more robust to outliers and improves the location estimation compared to using discretized-time t-distributed errors (implemented with a Gibbs sampler) or using continuous-time Gaussian errors (as with the Kalman filter). Using TMB, we are able to estimate additional parameters compared to previous methods, all without requiring a substantial increase in computational time. The model implementation is made available through the R package argosTrack. PMID:26649381

  2. Fitness club

    CERN Multimedia

    Fitness club

    2011-01-01

    General fitness Classes Enrolments are open for general fitness classes at CERN taking place on Monday, Wednesday, and Friday lunchtimes in the Pump Hall (building 216). There are shower facilities for both men and women. It is possible to pay for 1, 2 or 3 classes per week for a minimum of 1 month and up to 6 months. Check out our rates and enrol at: http://cern.ch/club-fitness Hope to see you among us! CERN Fitness Club fitness.club@cern.ch  

  3. Linking the Fits, Fitting the Links: Connecting Different Types of PO Fit to Attitudinal Outcomes

    Science.gov (United States)

    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…

  4. Mouse Models of Breast Cancer: Platforms for Discovering Precision Imaging Diagnostics and Future Cancer Medicine.

    Science.gov (United States)

    Manning, H Charles; Buck, Jason R; Cook, Rebecca S

    2016-02-01

    Representing an enormous health care and socioeconomic challenge, breast cancer is the second most common cancer in the world and the second most common cause of cancer-related death. Although many of the challenges associated with preventing, treating, and ultimately curing breast cancer are addressable in the laboratory, successful translation of groundbreaking research to clinical populations remains an important barrier. Particularly when compared with research on other types of solid tumors, breast cancer research is hampered by a lack of tractable in vivo model systems that accurately recapitulate the relevant clinical features of the disease. A primary objective of this article was to provide a generalizable overview of the types of in vivo model systems, with an emphasis primarily on murine models, that are widely deployed in preclinical breast cancer research. Major opportunities to advance precision cancer medicine facilitated by molecular imaging of preclinical breast cancer models are discussed.

  5. Breast Cancer Risk Assessment SAS Macro (Gail Model)

    Science.gov (United States)

    A SAS macro (commonly referred to as the Gail Model) that projects absolute risk of invasive breast cancer according to NCI’s Breast Cancer Risk Assessment Tool (BCRAT) algorithm for specified race/ethnic groups and age intervals.

  6. Quasispecies on Fitness Landscapes.

    Science.gov (United States)

    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.

  7. Modeling relationships between physical fitness, executive functioning, and academic achievement in primary school children

    NARCIS (Netherlands)

    van der Niet, Anneke G.; Hartman, Esther; Smith, Joanne; Visscher, Chris

    2014-01-01

    Objectives: The relationship between physical fitness and academic achievement in children has received much attention, however, whether executive functioning plays a mediating role in this relationship is unclear. The aim of this study therefore was to investigate the relationships between physical

  8. Gray Matter Correlates of Fluid, Crystallized, and Spatial Intelligence: Testing the P-FIT Model

    Science.gov (United States)

    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…

  9. Testing the Youth Physical Activity Promotion Model: Fatness and Fitness as Enabling Factors

    Science.gov (United States)

    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…

  10. Using Fit Indexes to Select a Covariance Model for Longitudinal Data

    Science.gov (United States)

    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…

  11. Trend and forecasting rate of cancer deaths at a public university hospital using univariate modeling

    Science.gov (United States)

    Ismail, A.; Hassan, Noor I.

    2013-09-01

    Cancer is one of the principal causes of death in Malaysia. This study was performed to determine the pattern of rate of cancer deaths at a public hospital in Malaysia over an 11 year period from year 2001 to 2011, to determine the best fitted model of forecasting the rate of cancer deaths using Univariate Modeling and to forecast the rates for the next two years (2012 to 2013). The medical records of the death of patients with cancer admitted at this Hospital over 11 year's period were reviewed, with a total of 663 cases. The cancers were classified according to 10th Revision International Classification of Diseases (ICD-10). Data collected include socio-demographic background of patients such as registration number, age, gender, ethnicity, ward and diagnosis. Data entry and analysis was accomplished using SPSS 19.0 and Minitab 16.0. The five Univariate Models used were Naïve with Trend Model, Average Percent Change Model (ACPM), Single Exponential Smoothing, Double Exponential Smoothing and Holt's Method. The overall 11 years rate of cancer deaths showed that at this hospital, Malay patients have the highest percentage (88.10%) compared to other ethnic groups with males (51.30%) higher than females. Lung and breast cancer have the most number of cancer deaths among gender. About 29.60% of the patients who died due to cancer were aged 61 years old and above. The best Univariate Model used for forecasting the rate of cancer deaths is Single Exponential Smoothing Technique with alpha of 0.10. The forecast for the rate of cancer deaths shows a horizontally or flat value. The forecasted mortality trend remains at 6.84% from January 2012 to December 2013. All the government and private sectors and non-governmental organizations need to highlight issues on cancer especially lung and breast cancers to the public through campaigns using mass media, media electronics, posters and pamphlets in the attempt to decrease the rate of cancer deaths in Malaysia.

  12. Kompaneets Model Fitting of the Orion-Eridanus Superbubble. II. Thinking Outside of Barnard’s Loop

    Science.gov (United States)

    Pon, Andy; Ochsendorf, Bram B.; Alves, João; Bally, John; Basu, Shantanu; Tielens, Alexander G. G. M.

    2016-08-01

    The Orion star-forming region is the nearest active high-mass star-forming region and has created a large superbubble, the Orion–Eridanus superbubble. Recent work by Ochsendorf et al. has extended the accepted boundary of the superbubble. We fit Kompaneets models of superbubbles expanding in exponential atmospheres to the new larger shape of the Orion–Eridanus superbubble. We find that this larger morphology of the superbubble is consistent with the evolution of the superbubble being primarily controlled by expansion into the exponential Galactic disk ISM if the superbubble is oriented with the Eridanus side farther from the Sun than the Orion side. Unlike previous Kompaneets model fits that required abnormally small scale heights for the Galactic disk (<40 pc), we find morphologically consistent models with scale heights of 80 pc, similar to that expected for the Galactic disk.

  13. Application of 2-D Vertically Averaged Boundary-Fitted Coordinate Model of Tidal Circulation in Thale Sap Songkhla, Thailand

    Directory of Open Access Journals (Sweden)

    Somboon PORNPINATEPONG

    2006-01-01

    Full Text Available A 2-D vertically averaged boundary-fitted coordinate hydrodynamic model was employed to simulate circulation in Thale Sap Songkhla due to tides in the Gulf of Thailand. The model was calibrated against a set of current velocity data collected between June and July 1997. The best fit for observations at Ko Yo and Pak Ro was achieved. To comprehend the hydrodynamic in the lake, the current vectors were illustrated for both the flood and ebb stages. Detailed analysis indicated that there existed a turning current at the northern tip of Ko Yo Island, which induced a significant current along its northern shoreline. The calculations show the current was stronger in the deep channel north of Ko Yo than in the southern circuit. The model also predicted a gyre near the deep channel of the lake entrance, which persisted for some time during the changing direction of the flood and ebb currents.

  14. Fitting model-based psychometric functions to simultaneity and temporal-order judgment data: MATLAB and R routines.

    Science.gov (United States)

    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.

  15. Comparison of tai chi vs. strength training for fall prevention among female cancer survivors: study protocol for the GET FIT trial

    International Nuclear Information System (INIS)

    Women with cancer are significantly more likely to fall than women without cancer placing them at higher risk of fall-related fractures, other injuries and disability. Currently, no evidence-based fall prevention strategies exist that specifically target female cancer survivors. The purpose of the GET FIT (Group Exercise Training for Functional Improvement after Treatment) trial is to compare the efficacy of two distinct types of exercise, tai chi versus strength training, to prevent falls in women who have completed treatment for cancer. The specific aims of this study are to: 1) Determine and compare the efficacy of both tai chi training and strength training to reduce falls in older female cancer survivors, 2) Determine the mechanism(s) by which tai chi and strength training each reduces falls and, 3) Determine whether or not the benefits of each intervention last after structured training stops. We will conduct a three-group, single-blind, parallel design, randomized controlled trial in women, aged 50–75 years old, who have completed chemotherapy for cancer comparing 1) tai chi 2) strength training and 3) a placebo control group of seated stretching exercise. Women will participate in supervised study programs twice per week for six months and will be followed for an additional six months after formal training stops. The primary outcome in this study is falls, which will be prospectively tracked by monthly self-report. Secondary outcomes are maximal leg strength measured by isokinetic dynamometry, postural stability measured by computerized dynamic posturography and physical function measured by the Physical Performance Battery, all measured at baseline, 3, 6 and 12 months. The sample for this trial (N=429, assuming 25% attrition) will provide adequate statistical power to detect at least a 47% reduction in the fall rate over 1 year by being in either of the 2 exercise groups versus the control group. The GET FIT trial will provide important new knowledge

  16. Fitting mathematical models to lactation curves from holstein cows in the southwestern region of the state of Parana, Brazil

    Directory of Open Access Journals (Sweden)

    Abílio G.T. Ferreira

    2015-03-01

    Full Text Available 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.

  17. Spectral fits with TCAF model : A global understanding of both temporal and spectral properties of black hole sources

    Science.gov (United States)

    Debnath, Dipak; Sarathi Pal, Partha; Chakrabarti, Sandip Kumar; Mondal, Santanu; Jana, Arghajit; Chatterjee, Debjit; Molla, Aslam Ali

    2016-07-01

    There are many theoretical and phenomenological models in the literature which explain physics of accretion around black holes (BHs). Some of these models assume ad hoc components to explain different timing and spectral aspects of black hole candidates (BHCs) which no necessarily follow from physical equations. Chakrabarti and his collaborators, on the other hand claim in the last two decades that the spectral and timing properties of BHCs must not be treated separately since variation of these properties happens due to variation of two component (Keplerian and sub-Keplerian) accretion flow rates, and the Compton cloud parameters only. Recently after the inclusion of Two-component advective flow (TCAF) model in to HEASARC's spectral analysis software package XSPEC as an additive local model, we found that TCAF is quite capable to describe the underlying accretion flow dynamics around BHs with spectral fitted physical parameters. Properties of different spectral states and their transitions during an outburst of a transient BHC are more clear. A strong correlation between spectral and timing properties could also be seen in Accretion Rate Ratio Intensity Diagram (ARRID), where transitions between different spectral states are prominent. One can also predict frequency of the dominating quasi-periodic oscillation (QPO) from TCAF model fitted shock parameters and even predict the most probable mass range of an unknown BHC from TCAF fits. This gives us a confidence that the description of accretion process is more clear than ever before.

  18. Fitting mathematical models to lactation curves from Holstein cows in the southwestern region of the state of Parana, Brazil.

    Science.gov (United States)

    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.

  19. Models for prevention and treatment of cancer: problems vs promises.

    Science.gov (United States)

    Aggarwal, Bharat B; Danda, Divya; Gupta, Shan; Gehlot, Prashasnika

    2009-11-01

    Current estimates from the American Cancer Society and from the International Union Against Cancer indicate that 12 million cases of cancer were diagnosed last year, with 7 million deaths worldwide; these numbers are expected to double by 2030 (27 million cases with 17 million deaths). Despite tremendous technological developments in all areas, and President Richard Nixon's initiative in the 1974 "War against Cancer", the US cancer incidence is the highest in the world and the cancer death rate has not significantly changed in the last 50 years (193.9 per 100,000 in 1950 vs 193.4 per 100,000 in 2002). Extensive research during the same time, however, has revealed that cancer is a preventable disease that requires major changes in life style; with one third of all cancers assigned to Tobacco, one third to diet, and remaining one third to the environment. Approximately 20 billion dollars are spent annually to find a cure for cancer. We propose that our inability to find a cure to cancer lies in the models used. Whether cell culture or animal studies, no model has yet been found that can reproduce the pathogenesis of the disease in the laboratory. Mono-targeted therapies, till know in most cases, have done a little to make a difference in cancer treatment. Similarly, molecular signatures/predictors of the diagnosis of the disease and response are also lacking. This review discusses the pros and cons of current cancer models based on cancer genetics, cell culture, animal models, cancer biomarkers/signature, cancer stem cells, cancer cell signaling, targeted therapies, therapeutic targets, clinical trials, cancer prevention, personalized medicine, and off-label uses to find a cure for cancer and demonstrates an urgent need for "out of the box" approaches. PMID:19481061

  20. Models for prevention and treatment of cancer: problems vs promises.

    Science.gov (United States)

    Aggarwal, Bharat B; Danda, Divya; Gupta, Shan; Gehlot, Prashasnika

    2009-11-01

    Current estimates from the American Cancer Society and from the International Union Against Cancer indicate that 12 million cases of cancer were diagnosed last year, with 7 million deaths worldwide; these numbers are expected to double by 2030 (27 million cases with 17 million deaths). Despite tremendous technological developments in all areas, and President Richard Nixon's initiative in the 1974 "War against Cancer", the US cancer incidence is the highest in the world and the cancer death rate has not significantly changed in the last 50 years (193.9 per 100,000 in 1950 vs 193.4 per 100,000 in 2002). Extensive research during the same time, however, has revealed that cancer is a preventable disease that requires major changes in life style; with one third of all cancers assigned to Tobacco, one third to diet, and remaining one third to the environment. Approximately 20 billion dollars are spent annually to find a cure for cancer. We propose that our inability to find a cure to cancer lies in the models used. Whether cell culture or animal studies, no model has yet been found that can reproduce the pathogenesis of the disease in the laboratory. Mono-targeted therapies, till know in most cases, have done a little to make a difference in cancer treatment. Similarly, molecular signatures/predictors of the diagnosis of the disease and response are also lacking. This review discusses the pros and cons of current cancer models based on cancer genetics, cell culture, animal models, cancer biomarkers/signature, cancer stem cells, cancer cell signaling, targeted therapies, therapeutic targets, clinical trials, cancer prevention, personalized medicine, and off-label uses to find a cure for cancer and demonstrates an urgent need for "out of the box" approaches.

  1. Fitness Club

    CERN Multimedia

    Fitness Club

    2011-01-01

    The CERN Fitness Club is organising Zumba Classes on the first Wednesday of each month, starting 7 September (19.00 – 20.00). What is Zumba®? It’s an exhilarating, effective, easy-to-follow, Latin-inspired, calorie-burning dance fitness-party™ that’s moving millions of people toward joy and health. Above all it’s great fun and an excellent work out. Price: 22 CHF/person Sign-up via the following form: https://espace.cern.ch/club-fitness/Lists/Zumba%20Subscription/NewForm.aspx For more info: fitness.club@cern.ch

  2. Automated Kinematic Modelling of Warped Galaxy Discs in Large Hi Surveys: 3D Tilted Ring Fitting of HI Emission Cubes

    CERN Document Server

    Kamphuis, P; Oh, S- H; Spekkens, K; Urbancic, N; Serra, P; Koribalski, B S; Dettmar, R -J

    2015-01-01

    Kinematical parameterisations of disc galaxies, employing emission line observations, are indispensable tools for studying the formation and evolution of galaxies. Future large-scale HI surveys will resolve the discs of many thousands of galaxies, allowing a statistical analysis of their disc and halo kinematics, mass distribution and dark matter content. Here we present an automated procedure which fits tilted-ring models to Hi data cubes of individual, well-resolved galaxies. The method builds on the 3D Tilted Ring Fitting Code (TiRiFiC) and is called FAT (Fully Automated TiRiFiC). To assess the accuracy of the code we apply it to a set of 52 artificial galaxies and 25 real galaxies from the Local Volume HI Survey (LVHIS). Using LVHIS data, we compare our 3D modelling to the 2D modelling methods DiskFit and rotcur. A conservative result is that FAT accurately models the kinematics and the morphologies of galaxies with an extent of eight beams across the major axis in the inclination range 20$^{\\circ}$-90$^{...

  3. Quantum spin model fitting the Yule distribution of oligonucleotides in DNA

    CERN Document Server

    Minichini, C

    2004-01-01

    A quantum spin chain is identified by the labels of a vector state of a Kashiwara crystal basis. The intensity of the one-spin flip is assumed to depend from the variation of the labels. The rank ordered plot of the numerically computed, averaged in time, transition probabilities is nicely fitted by a Yule distribution, which is the observed distribution of the ranked short oligonucleotides frequency in DNA.

  4. Randomized controlled trial of the effects of high intensity and low-to-moderate intensity exercise on physical fitness and fatigue in cancer survivors: results of the Resistance and Endurance exercise After ChemoTherapy (REACT) study

    OpenAIRE

    Kampshoff, C.S.; Chinapaw, M.J.; Brug, J.; Twisk, J.W.R.; Schep, G.; Nijziel, M.R.; van Mechelen, W; Buffart, L.M.

    2015-01-01

    BACKGROUND: International evidence-based guidelines recommend physical exercise to form part of standard care for all cancer survivors. However, at present, the optimum exercise intensity is unclear. Therefore, we aimed to evaluate the effectiveness of a high intensity (HI) and low-to-moderate intensity (LMI) resistance and endurance exercise program compared with a wait list control (WLC) group on physical fitness and fatigue in a mixed group of cancer survivors who completed primary cancer ...

  5. Reproductive fitness and dietary choice behavior of the genetic model organism Caenorhabditis elegans under semi-natural conditions.

    Science.gov (United States)

    Freyth, Katharina; Janowitz, Tim; Nunes, Frank; Voss, Melanie; Heinick, Alexander; Bertaux, Joanne; Scheu, Stefan; Paul, Rüdiger J

    2010-10-01

    Laboratory breeding conditions of the model organism C. elegans do not correspond with the conditions in its natural soil habitat. To assess the consequences of the differences in environmental conditions, the effects of air composition, medium and bacterial food on reproductive fitness and/or dietary-choice behavior of C. elegans were investigated. The reproductive fitness of C. elegans was maximal under oxygen deficiency and not influenced by a high fractional share of carbon dioxide. In media approximating natural soil structure, reproductive fitness was much lower than in standard laboratory media. In seminatural media, the reproductive fitness of C. elegans was low with the standard laboratory food bacterium E. coli (γ-Proteobacteria), but significantly higher with C. arvensicola (Bacteroidetes) and B. tropica (β-Proteobacteria) as food. Dietary-choice experiments in semi-natural media revealed a low preference of C. elegans for E. coli but significantly higher preferences for C. arvensicola and B. tropica (among other bacteria). Dietary-choice experiments under quasi-natural conditions, which were feasible by fluorescence in situ hybridization (FISH) of bacteria, showed a high preference of C. elegans for Cytophaga-Flexibacter-Bacteroides, Firmicutes, and β-Proteobacteria, but a low preference for γ-Proteobacteria. The results show that data on C. elegans under standard laboratory conditions have to be carefully interpreted with respect to their biological significance.

  6. Clinical and multiple gene expression variables in survival analysis of breast cancer: Analysis with the hypertabastic survival model

    OpenAIRE

    Tabatabai Mohammad A; Eby Wayne M; Nimeh Nadim; Li Hong; Singh Karan P

    2012-01-01

    Abstract Background We explore the benefits of applying a new proportional hazard model to analyze survival of breast cancer patients. As a parametric model, the hypertabastic survival model offers a closer fit to experimental data than Cox regression, and furthermore provides explicit survival and hazard functions which can be used as additional tools in the survival analysis. In addition, one of our main concerns is utilization of multiple gene expression variables. Our analysis treats the ...

  7. Effect of revised $R_n$ measurements on extended Gari-Krumpelmann model fits to nucleon electromagnetic form factors

    OpenAIRE

    Lomon, Earle L.

    2006-01-01

    The extended Gari-Krumpelmann (GK) model of nucleon electromagnetic form factors, in which the $\\rho$, $\\rho'$, $\\omega$, $\\omega'$ and $\\phi$ vector meson pole contributions evolve at high momentum transfer to conform to the predictions of perturbative QCD (pQCD), was recently shown to provide a very good overall fit to all the nucleon electromagnetic form factor (emff) data, including the preliminary $R_p$ and $R_n$ polarization data available in 2002, but excluding the older $G_{Ep}$ and $...

  8. Fitness cost

    DEFF Research Database (Denmark)

    Nielsen, Karen L.; Pedersen, Thomas M.; Udekwu, Klas I.;

    2012-01-01

    of each isolate was determined in a growth competition assay with a reference isolate. Significant fitness costs of 215 were determined for the MRSA isolates studied. There was a significant negative correlation between number of antibiotic resistances and relative fitness. Multiple regression analysis...

  9. Fodbold Fitness

    DEFF Research Database (Denmark)

    Bennike, Søren

    Samfundet forandrer sig og ligeså gør danskernes idrætsmønstre. Fodbold Fitness, der er afhandlingens omdrejningspunkt, kan iagttages som en reaktion på disse forandringer. Afhandlingen ser nærmere på Fodbold Fitness og implementeringen af dette, der ingenlunde er nogen let opgave. Bennike bidrager...

  10. Evolutionary dynamics of tumor progression with random fitness values

    CERN Document Server

    Durrett, Rick; Leder, Kevin; Mayberry, John; Michor, Franziska

    2010-01-01

    Most human tumors result from the accumulation of multiple genetic and epigenetic alterations in a single cell. Mutations that confer a fitness advantage to the cell are known as driver mutations and are causally related to tumorigenesis. Other mutations, however, do not change the phenotype of the cell or even decrease cellular fitness. While much experimental effort is being devoted to the identification of the different functional effects of individual mutations, mathematical modeling of tumor progression generally considers constant fitness increments as mutations are accumulated. In this paper we study a mathematical model of tumor progression with random fitness increments. We analyze a multi-type branching process in which cells accumulate mutations whose fitness effects are chosen from a distribution. We determine the effect of the fitness distribution on the growth kinetics of the tumor. This work contributes to a quantitative understanding of the accumulation of mutations leading to cancer phenotype...

  11. Comparison of model fitting and gated integration for pulse shape discrimination and spectral estimation of digitized lanthanum halide scintillator pulses

    Science.gov (United States)

    McFee, J. E.; Mosquera, C. M.; Faust, A. A.

    2016-08-01

    An analysis of digitized pulse waveforms from experiments with LaBr3(Ce) and LaCl3(Ce) detectors is presented. Pulse waveforms from both scintillator types were captured in the presence of 22Na and 60Co sources and also background alone. Two methods to extract pulse shape discrimination (PSD) parameters and estimate energy spectra were compared. The first involved least squares fitting of the pulse waveforms to a physics-based model of one or two exponentially modified Gaussian functions. The second was the conventional gated integration method. The model fitting method produced better PSD than gated integration for LaCl3(Ce) and higher resolution energy spectra for both scintillator types. A disadvantage to the model fitting approach is that it is more computationally complex and about 5 times slower. LaBr3(Ce) waveforms had a single decay component and showed no ability for alpha/electron PSD. LaCl3(Ce) was observed to have short and long decay components and alpha/electron discrimination was observed.

  12. Using Geometry-Based Metrics as Part of Fitness-for-Purpose Evaluations of 3D City Models

    Science.gov (United States)

    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.

  13. Detecting Mixtures from Structural Model Differences Using Latent Variable Mixture Modeling: A Comparison of Relative Model Fit Statistics

    Science.gov (United States)

    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…

  14. A superstatistical model of metastasis and cancer survival

    CERN Document Server

    Chen, L Leon

    2007-01-01

    We introduce a superstatistical model for the progression statistics of malignant cancer cells. The metastatic cascade is modeled as a complex nonequilibrium system with several macroscopic pathways and inverse-chi-square distributed parameters of the underlying Poisson processes. The predictions of the model are in excellent agreement with observed survival time probability distributions of breast cancer patients.

  15. Evaluation of RGP Contact Lens Fitting in Keratoconus Patients Using Hierarchical Fuzzy Model and Genetic Algorithms.

    Science.gov (United States)

    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. PMID:27046564

  16. Mouse models for cancer stem cell research

    OpenAIRE

    Cheng, Le; Ramesh, Anirudh V.; Flesken-Nikitin, Andrea; Choi, Jinhyang; Nikitin, Alexander Yu.

    2009-01-01

    Cancer stem cell concept assumes that cancers are mainly sustained by a small pool of neoplastic cells, known as cancer stem cells or tumor initiating cells, which are able to reproduce themselves and produce phenotypically heterogeneous cells with lesser tumorigenic potential. Cancer stem cells represent an appealing target for development of more selective and efficient therapies. However, direct testing of the cancer stem cell concept and assessment of its therapeutic implications in human...

  17. Entropy, complexity, and Markov diagrams for random walk cancer models

    Science.gov (United States)

    Newton, Paul K.; Mason, Jeremy; Hurt, Brian; Bethel, Kelly; Bazhenova, Lyudmila; Nieva, Jorge; Kuhn, Peter

    2014-12-01

    The notion of entropy is used to compare the complexity associated with 12 common cancers based on metastatic tumor distribution autopsy data. We characterize power-law distributions, entropy, and Kullback-Liebler divergence associated with each primary cancer as compared with data for all cancer types aggregated. We then correlate entropy values with other measures of complexity associated with Markov chain dynamical systems models of progression. The Markov transition matrix associated with each cancer is associated with a directed graph model where nodes are anatomical locations where a metastatic tumor could develop, and edge weightings are transition probabilities of progression from site to site. The steady-state distribution corresponds to the autopsy data distribution. Entropy correlates well with the overall complexity of the reduced directed graph structure for each cancer and with a measure of systemic interconnectedness of the graph, called graph conductance. The models suggest that grouping cancers according to their entropy values, with skin, breast, kidney, and lung cancers being prototypical high entropy cancers, stomach, uterine, pancreatic and ovarian being mid-level entropy cancers, and colorectal, cervical, bladder, and prostate cancers being prototypical low entropy cancers, provides a potentially useful framework for viewing metastatic cancer in terms of predictability, complexity, and metastatic potential.

  18. The Beta-Model Problem: The Incompatibility of X-ray and Sunyaev-Zeldovich Effect Model Fitting for Galaxy Clusters

    OpenAIRE

    Hallman, Eric J.; Burns, Jack O.; Motl, Patrick M; Michael L. Norman

    2007-01-01

    We have analyzed a large sample of numerically simulated clusters to demonstrate the adverse effects resulting from use of X-ray fitted beta-model parameters with Sunyaev-Zeldovich effect (SZE) data. There is a fundamental incompatibility between model fits to X-ray surface brightness profiles and those done with SZE profiles. Since observational SZE radial profiles are in short supply, the X-ray parameters are often used in SZE analysis. We show that this leads to biased estimates of the int...

  19. Models for local implementation of comprehensive cancer control: meeting local cancer control needs through community collaboration.

    Science.gov (United States)

    Behringer, Bruce; Lofton, Staci; Knight, Margaret L

    2010-12-01

    The comprehensive cancer control approach is used by state, tribes, tribal organizations, territorial and Pacific Island Jurisdiction cancer coalitions to spur local implementation of cancer plans to reduce the burden of cancer in jurisdictions across the country. There is a rich diversity of models and approaches to the development of relationships and scope of planning for cancer control activities between coalitions and advocates in local communities. The national comprehensive cancer control philosophy provides an operational framework while support from the Centers for Disease Control and Prevention enables coalitions to act as catalysts to bring local partners together to combat cancer in communities. This manuscript describes multiple characteristics of cancer coalitions and how they are organized. Two models of how coalitions and local partners collaborate are described. A case study method was used to identify how five different state and tribal coalitions use the two models to organize their collaborations with local communities that result in local implementation of cancer plan priorities. Conclusions support the use of multiple organizing models to ensure involvement of diverse interests and sensitivity to local cancer issues that encourages implementation of cancer control activities. PMID:20938731

  20. Dynamic modeling and analysis of vortex filament motion using a novel curve-fitting method

    Directory of Open Access Journals (Sweden)

    Chang-Joo Kim

    2016-02-01

    Full Text Available Applications of a novel curve-fitting technique are presented to efficiently predict the motion of the vortex filament, which is trailed from a rigid body such as wings and rotors. The governing equations of the motion, when a Lagrangian approach with the present curve-fitting method is applied, can be transformed into an easily solvable form of the system of nonlinear ordinary differential equations. The applicability of Bézier curves, B-spline, and Lagrange interpolating polynomials is investigated. Local Lagrange interpolating polynomials with a shift operator are proposed as the best selection for applications, since it provides superior system characteristics with minimum computing time, compared to other methods. In addition, the Gauss quadrature formula with local refinement strategy has been developed for an accurate prediction of the induced velocity computed with the line integration of the Biot–Savart law. Rotary-wing problems including a vortex ring problem are analyzed to show the efficiency, accuracy, and flexibility in the applications of the proposed method.

  1. Next-to-leading order unitarity fits in Two-Higgs-Doublet models with soft $\\mathbb{Z}_2$ breaking

    CERN Document Server

    Cacchio, Vincenzo; Eberhardt, Otto; Murphy, Christopher W

    2016-01-01

    We fit the next-to-leading order unitarity conditions to the Two-Higgs-Doublet model with a softly broken $\\mathbb{Z}_2$ symmetry. In doing so, we alleviate the existing uncertainty on how to treat higher order corrections to quartic couplings of its Higgs potential. A simplified approach to implementing the next-to-leading order unitarity conditions is presented. These new bounds are then combined with all other relevant constraints, including the complete set of LHC Run I data. The upper $95\\%$ bounds we find are $4.2$ on the absolute values of the quartic couplings, and $235$ GeV ($100$ GeV) for the mass degeneracies between the heavy Higgs particles in the type I (type II) scenario. In type II, we exclude an unbroken $\\mathbb{Z}_2$ symmetry with a probability of $95\\%$. All fits are performed using the open-source code HEPfit.

  2. Genome-Enabled Modeling of Biogeochemical Processes Predicts Metabolic Dependencies that Connect the Relative Fitness of Microbial Functional Guilds

    Science.gov (United States)

    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

  3. Fitness Club

    CERN Document Server

    Fitness Club

    2012-01-01

    Open to All: http://cern.ch/club-fitness  fitness.club@cern.ch Boxing Your supervisor makes your life too tough ! You really need to release the pressure you've been building up ! Come and join the fit-boxers. We train three times a week in Bd 216, classes for beginners and advanced available. Visit our website cern.ch/Boxing General Fitness Escape from your desk with our general fitness classes, to strengthen your heart, muscles and bones, improve you stamina, balance and flexibility, achieve new goals, be more productive and experience a sense of well-being, every Monday, Wednesday and Friday lunchtime, Tuesday mornings before work and Thursday evenings after work – join us for one of our monthly fitness workshops. Nordic Walking Enjoy the great outdoors; Nordic Walking is a great way to get your whole body moving and to significantly improve the condition of your muscles, heart and lungs. It will boost your energy levels no end. Pilates A body-conditioning technique de...

  4. Extensive fitness and human cooperation.

    Science.gov (United States)

    van Hateren, J H

    2015-12-01

    Evolution depends on the fitness of organisms, the expected rate of reproducing. Directly getting offspring is the most basic form of fitness, but fitness can also be increased indirectly by helping genetically related individuals (such as kin) to increase their fitness. The combined effect is known as inclusive fitness. Here it is argued that a further elaboration of fitness has evolved, particularly in humans. It is called extensive fitness and it incorporates producing organisms that are merely similar in phenotype. The evolvability of this mechanism is illustrated by computations on a simple model combining heredity and behaviour. Phenotypes are driven into the direction of high fitness through a mechanism that involves an internal estimate of fitness, implicitly made within the organism itself. This mechanism has recently been conjectured to be responsible for producing agency and goals. In the model, inclusive and extensive fitness are both implemented by letting fitness increase nonlinearly with the size of subpopulations of similar heredity (for the indirect part of inclusive fitness) and of similar phenotype (for the phenotypic part of extensive fitness). Populations implementing extensive fitness outcompete populations implementing mere inclusive fitness. This occurs because groups with similar phenotype tend to be larger than groups with similar heredity, and fitness increases more when groups are larger. Extensive fitness has two components, a direct component where individuals compete in inducing others to become like them and an indirect component where individuals cooperate and help others who are already similar to them.

  5. Seeking for Spin-Opposite-Scaled Double-Hybrid Models Free of Fitted Parameters.

    Science.gov (United States)

    Alipour, Mojtaba

    2016-05-26

    On the basis of theoretical arguments, a new exchange-correlation energy expression free of any fitted parameter has been proposed for spin-opposite-scaled double-hybrid density functionals (SOS0-DHs). Employing the recently presented DHs, the working expressions for SOS0-DH functionals are obtained and benchmarked numerically against several standard databases. Our test calculations show that for some cases such as interaction energies and barrier heights the SOS0-DHs without dispersion corrections perform better than their non-SOS counterparts. On the other hand, for other properties like atomization energies, the conventional DHs provide reliable results. We hope that the findings of this work can excite further developments of DH functionals in the framework of SOS scheme for a wide variety of applications resolving the failures at a reasonable computational cost. It seems that a bright future lies ahead in this arena. PMID:27163506

  6. The universal Higgs fit

    OpenAIRE

    Pier Paolo Giardino; Kristjan Kannike(Scuola Normale Superiore and INFN, Piazza dei Cavalieri 7, 56126 Pisa, Italy); Isabella Masina(Dipartimento di Fisica e Scienze della Terra dell’Università di Ferrara and INFN, Italy); Martti Raidal; Alessandro Strumia(Dipartimento di Fisica, Università di Pisa and INFN, Italy)

    2014-01-01

    We perform a state-of-the-art global fit to all Higgs data. We synthesise them into a ‘universal’ form, which allows to easily test any desired model. We apply the proposed methodology to extract from data the Higgs branching ratios, production cross sections, couplings and to analyse composite Higgs models, models with extra Higgs doublets, supersymmetry, extra particles in the loops, anomalous top couplings, and invisible Higgs decays into Dark Matter. Best fit regions lie around the Standa...

  7. Three-dimensional in vitro cancer models: a short review

    International Nuclear Information System (INIS)

    The re-creation of the tumor microenvironment including tumor–stromal interactions, cell–cell adhesion and cellular signaling is essential in cancer-related studies. Traditional two-dimensional (2D) cell culture and animal models have been proven to be valid in some areas of explaining cancerous cell behavior and interpreting hypotheses of possible mechanisms. However, a well-defined three-dimensional (3D) in vitro cancer model, which mimics tumor structures found in vivo and allows cell–cell and cell–matrix interactions, has gained strong interest for a wide variety of diagnostic and therapeutic applications. This communication attempts to provide a representative overview of applying 3D in vitro biological model systems for cancer related studies. The review compares and comments on the differences in using 2D models, animal models and 3D in vitro models for cancer research. Recent technologies to construct and develop 3D in vitro cancer models are summarized in aspects of modeling design, fabrication technique and potential application to biology, pathogenesis study and drug testing. With the help of advanced engineering techniques, the development of a novel complex 3D in vitro cancer model system will provide a better opportunity to understand crucial cancer mechanisms and to develop new clinical therapies. (topical review)

  8. Use of Approximate Bayesian Computation to Assess and Fit Models of Mycobacterium leprae to Predict Outcomes of the Brazilian Control Program.

    Directory of Open Access Journals (Sweden)

    Rebecca Lee Smith

    Full Text Available Hansen's disease (leprosy elimination has proven difficult in several countries, including Brazil, and there is a need for a mathematical model that can predict control program efficacy. This study applied the Approximate Bayesian Computation algorithm to fit 6 different proposed models to each of the 5 regions of Brazil, then fitted hierarchical models based on the best-fit regional models to the entire country. The best model proposed for most regions was a simple model. Posterior checks found that the model results were more similar to the observed incidence after fitting than before, and that parameters varied slightly by region. Current control programs were predicted to require additional measures to eliminate Hansen's Disease as a public health problem in Brazil.

  9. Use of Approximate Bayesian Computation to Assess and Fit Models of Mycobacterium leprae to Predict Outcomes of the Brazilian Control Program.

    Science.gov (United States)

    Smith, Rebecca Lee; Gröhn, Yrjö Tapio

    2015-01-01

    Hansen's disease (leprosy) elimination has proven difficult in several countries, including Brazil, and there is a need for a mathematical model that can predict control program efficacy. This study applied the Approximate Bayesian Computation algorithm to fit 6 different proposed models to each of the 5 regions of Brazil, then fitted hierarchical models based on the best-fit regional models to the entire country. The best model proposed for most regions was a simple model. Posterior checks found that the model results were more similar to the observed incidence after fitting than before, and that parameters varied slightly by region. Current control programs were predicted to require additional measures to eliminate Hansen's Disease as a public health problem in Brazil. PMID:26107951

  10. A mathematical model of cancer cells with phenotypic plasticity

    Directory of Open Access Journals (Sweden)

    Da Zhou

    2015-12-01

    Full Text Available Purpose: The phenotypic plasticity of cancer cells is recently becoming a cutting-edge research area in cancer, which challenges the cellular hierarchy proposed by the conventional cancer stem cell theory. In this study, we establish a mathematical model for describing the phenotypic plasticity of cancer cells, based on which we try to find some salient features that can characterize the dynamic behavior of the phenotypic plasticity especially in comparison to the hierarchical model of cancer cells. Methods: We model cancer as population dynamics composed of different phenotypes of cancer cells. In this model, not only can cancer cells divide (symmetrically and asymmetrically and die, but they can also convert into other cellular phenotypes. According to the Law of Mass Action, the cellular processes can be captured by a system of ordinary differential equations (ODEs. On one hand, we can analyze the long-term stability of the model by applying qualitative method of ODEs. On the other hand, we are also concerned about the short-term behavior of the model by studying its transient dynamics. Meanwhile, we validate our model to the cell-state dynamics in published experimental data.Results: Our results show that the phenotypic plasticity plays important roles in both stabilizing the distribution of different phenotypic mixture and maintaining the cancer stem cells proportion. In particular, the phenotypic plasticity model shows decided advantages over the hierarchical model in predicting the phenotypic equilibrium and cancer stem cells’ overshoot reported in previous biological experiments in cancer cell lines.Conclusion: Since the validity of the phenotypic plasticity paradigm and the conventional cancer stem cell theory is still debated in experimental biology, it is worthy of theoretically searching for good indicators to distinguish the two models through quantitative methods. According to our study, the phenotypic equilibrium and overshoot

  11. Quantification of mouse pulmonary cancer models by microcomputed tomography imaging

    International Nuclear Information System (INIS)

    The advances in preclinical cancer models, including orthotopic implantation models or genetically engineered mouse models of cancer, enable pursuing the molecular mechanism of cancer disease that might mimic genetic and biological processes in humans. Lung cancer is the major cause of cancer deaths; therefore, the treatment and prevention of lung cancer are expected to be improved by a better understanding of the complex mechanism of disease. In this study, we have examined the quantification of two distinct mouse lung cancer models by utilizing imaging modalities for monitoring tumor progression and drug efficacy evaluation. The utility of microcomputed tomography (micro-CT) for real-time/non-invasive monitoring of lung cancer progression has been confirmed by combining bioluminescent imaging and histopathological analyses. Further, we have developed a more clinically relevant lung cancer model by utilizing K-rasLSL-G12D/p53LSL-R270H mutant mice. Using micro-CT imaging, we monitored the development and progression of solitary lung tumor in K-rasLSL-G12D/p53LSL-R270H mutant mouse, and further demonstrated tumor growth inhibition by anticancer drug treatment. These results clearly indicate that imaging-guided evaluation of more clinically relevant tumor models would improve the process of new drug discovery and increase the probability of success in subsequent clinical studies. (author)

  12. Exchange interactions in [2 × 2] Cu(II) grids: on the reliability of the fitting spin models.

    Science.gov (United States)

    Calzado, Carmen J; Evangelisti, Stefano

    2014-02-21

    This paper reports a theoretical analysis of the electronic structure and magnetic properties of a ferromagnetic Cu(II) [2 × 2] grid. The calculations confirm a quintet (S = 2) ground state and an energy-level distribution of the magnetic states in accordance with Heisenberg behaviour. The whole set of first- and second-neighbour magnetic coupling constants has been evaluated, all in agreement with the structure and arrangement of the Cu 3dx(2) - y(2) magnetic orbitals. The results indicate that the dominant interaction in the system is the ferromagnetic coupling between the nearest Cu sites. The calculated J values suggest a C(2v) spin-spin interaction pattern, instead of the D(4h) model employed in the magnetic data fit. However, both spin models provide similar plots of the thermal dependence of the susceptibility and magnetic moment data. This study highlights the fact that the spin models resulting from the fittings can be just effective models, capable of correctly reproducing the macroscopic properties, although not always in accordance with the microscopic interactions governing these properties.

  13. The Electroweak Fit of the Standard Model after the Discovery of a New Boson at the LHC

    CERN Document Server

    Baak, M

    2012-01-01

    In view of the discovery of a new boson by the ATLAS and CMS Collaborations at the LHC, we present an update of the global Standard Model (SM) fit to electroweak precision data. Assuming the new particle to be the SM Higgs boson, all fundamental parameters of the SM are known allowing, for the first time, to overconstrain the SM at the electroweak scale and assert its validity. Including the effects of radiative corrections and the experimental and theoretical uncertainties, the global fit exhibits a p-value of 0.07. The mass measurements by ATLAS and CMS agree within 1.3sigma with the indirect determination M_H=(94 +25 -22) GeV. Within the SM the W boson mass and the effective weak mixing angle can be accurately predicted to be M_W=(80.359 +- 0.011) GeV and sin^2(theta_eff^ell)=(0.23150 +- 0.00010) from the global fit. These results are compatible with, and exceed in precision, the direct measurements. For the indirect determination of the top quark mass we find m_t=(175.8 +2.7 -2.4) GeV, in agreement with t...

  14. Parameter estimation and optimal scheduling algorithm for a mathematical model of intermittent androgen suppression therapy for prostate cancer

    Science.gov (United States)

    Guo, Qian; Lu, Zhichang; Hirata, Yoshito; Aihara, Kazuyuki

    2013-12-01

    We propose an algorithm based on cross-entropy to determine parameters of a piecewise linear model, which describes intermittent androgen suppression therapy for prostate cancer. By comparing with clinical data, the parameter estimation for the switched system shows good fitting accuracy and efficiency. We further optimize switching time points for the piecewise linear model to obtain a feasible therapeutic schedule. The simulation results of therapeutic effect are superior to those of previous strategy.

  15. 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

    Science.gov (United States)

    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…

  16. Numerical simulation of a relaxation test designed to fit a quasi-linear viscoelastic model for temporomandibular joint discs.

    Science.gov (United States)

    Commisso, Maria S; Martínez-Reina, Javier; Mayo, Juana; Domínguez, Jaime

    2013-02-01

    The main objectives of this work are: (a) to introduce an algorithm for adjusting the quasi-linear viscoelastic model to fit a material using a stress relaxation test and (b) to validate a protocol for performing such tests in temporomandibular joint discs. This algorithm is intended for fitting the Prony series coefficients and the hyperelastic constants of the quasi-linear viscoelastic model by considering that the relaxation test is performed with an initial ramp loading at a certain rate. This algorithm was validated before being applied to achieve the second objective. Generally, the complete three-dimensional formulation of the quasi-linear viscoelastic model is very complex. Therefore, it is necessary to design an experimental test to ensure a simple stress state, such as uniaxial compression to facilitate obtaining the viscoelastic properties. This work provides some recommendations about the experimental setup, which are important to follow, as an inadequate setup could produce a stress state far from uniaxial, thus, distorting the material constants determined from the experiment. The test considered is a stress relaxation test using unconfined compression performed in cylindrical specimens extracted from temporomandibular joint discs. To validate the experimental protocol, the test was numerically simulated using finite-element modelling. The disc was arbitrarily assigned a set of quasi-linear viscoelastic constants (c1) in the finite-element model. Another set of constants (c2) was obtained by fitting the results of the simulated test with the proposed algorithm. The deviation of constants c2 from constants c1 measures how far the stresses are from the uniaxial state. The effects of the following features of the experimental setup on this deviation have been analysed: (a) the friction coefficient between the compression plates and the specimen (which should be as low as possible); (b) the portion of the specimen glued to the compression plates (smaller

  17. Review of Animal Models of Prostate Cancer Bone Metastasis

    Directory of Open Access Journals (Sweden)

    Jessica K. Simmons

    2014-06-01

    Full Text Available Prostate cancer bone metastases are associated with a poor prognosis and are considered incurable. Insight into the formation and growth of prostate cancer bone metastasis is required for development of new imaging and therapeutic strategies to combat this devastating disease. Animal models are indispensable in investigating cancer pathogenesis and evaluating therapeutics. Multiple animal models of prostate cancer bone metastasis have been developed, but few effectively model prostatic neoplasms and osteoblastic bone metastases as they occur in men. This review discusses the animal models that have been developed to investigate prostate cancer bone metastasis, with a focus on canine models and also includes human xenograft and rodent models. Adult dogs spontaneously develop benign prostatic hyperplasia and prostate cancer with osteoblastic bone metastases. Large animal models, such as dogs, are needed to develop new molecular imaging tools and effective focal intraprostatic therapy. None of the available models fully reflect the metastatic disease seen in men, although the various models have provided important insight into the metastatic process. As additional models are developed and knowledge from the different models is combined, the molecular mechanisms of prostate cancer bone metastasis can be deciphered and targeted for development of novel therapies and molecular diagnostic imaging.

  18. Fitting Proportional Odds Models to Educational Data in Ordinal Logistic Regression Using Stata, SAS and SPSS

    Science.gov (United States)

    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…

  19. Fitting Procedures for Novel Gene-by-Measured Environment Interaction Models in Behavior Genetic Designs.

    Science.gov (United States)

    Zheng, Hao; Rathouz, Paul J

    2015-07-01

    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 extant GxM models and the new non-linear models critically assume normality of all structural components, which implies continuous, but not normal, manifest response variables.

  20. A transformed coordinates shallow water model in boundary-fitted curvilinear grids for the head Bay of Bengal

    International Nuclear Information System (INIS)

    The Bay of Bengal is surrounded by the coasts from all sides except in the south where there is open sea. The coasts are curvilinear in nature and the bending is very high along the coast of Bangladesh. Moreover, there are many small and big islands in the offshore region of the Bangladesh coast. In order to incorporate the island boundaries and the coastlines properly in the numerical scheme it is necessary to consider a very fine grid resolution along the coastal belts, whereas this is unnecessary away from the coasts. Consideration of very fine resolution involves, unnecessarily, more memory and more CPU time in the solution process and invites problem of numerical instability. In hydrodynamic models for coastal seas, bays, and estuaries the use of boundary-fitted curvilinear grids not only makes the model grids fit to the coastline, but also make the finite difference scheme simple and more accurate. In this study we use the boundary-fitted curvilinear grids where the complete boundary of the analysis area is represented by four curves and they are defined by four functions. Based on them, the four boundaries of each island are represented approximately by two generalized functions. Appropriate transformations of independent coordinates are considered so that the curvilinear physical domain transforms to a square one and also each island boundary transforms to a rectangle within this square domain. The vertically integrated shallow water equations are transformed to the new space domain. In the transformed domain, the regular explicit finite difference scheme is used to solve the shallow water equations. The model is applied to compute the water levels due to astronomical tide and surges associated with a few tropical storms that hit the coast of Bangladesh. (author)

  1. Avalanche dynamics in the Bak-Sneppen evolution model observed with a standard distribution width of fitness

    Science.gov (United States)

    Lee, Chaohong; Zhu, Xiwen; Gao, Kelin

    2003-01-01

    We introduce the standard distribution width of fitness to characterize the global and individual features of an ecosystem described by the Bak-Sneppen evolution model. Through tracking this quantity in evolution, a different hierarchy of avalanche dynamics, the w0 avalanche, is observed. The corresponding gap equation and the self-organized threshold wc are obtained. The critical exponents τ, γ and ρ, which describe the behaviour of the avalanche size distribution, the average avalanche size and the relaxation to attractor, respectively, are calculated by numerical simulation. The exact master equation and γ equation are derived, and the scaling relations are established among the critical exponents of this new avalanche.

  2. Multi-reaction-channel fitting calculations in a coupled-channel model: Photoinduced strangeness production

    Indian Academy of Sciences (India)

    O Scholten; A Usov

    2010-08-01

    To describe photo- and meson-induced reactions on the nucleon, one is faced with a rather extensive coupled-channel problem. Ignoring the effects of channel coupling, as one would do in describing a certain reaction at the tree level, invariably creates a large inconsistency between the different reactions that are described. In addition, the imaginary parts of the amplitude, which are related through the optical theorem, to total cross-sections, are directly reflected in certain polarization observables. Performing a full coupled-channel calculation thus offers the possibility to implement the maximum number of constraints. The drawback one is faced with is to arrive at a simultaneous fit of a large number of reaction channels. While some of the parameters are common to many reactions, one is still faced with the challenge to optimize a large number of parameters in a highly non-linear calculation. Here we show that such an approach is possible and present some results for photoinduced strangeness production.

  3. A Hierarchical Probability Model of Colon Cancer

    CERN Document Server

    Kelly, Michael

    2010-01-01

    We consider a model of fixed size $N = 2^l$ in which there are $l$ generations of daughter cells and a stem cell. In each generation $i$ there are $2^{i-1}$ daughter cells. At each integral time unit the cells split so that the stem cell splits into a stem cell and generation 1 daughter cell and the generation $i$ daughter cells become two cells of generation $i+1$. The last generation is removed from the population. The stem cell gets first and second mutations at rates $u_1$ and $u_2$ and the daughter cells get first and second mutations at rates $v_1$ and $v_2$. We find the distribution for the time it takes to get two mutations as $N$ goes to infinity and the mutation rates go to 0. We also find the distribution for the location of the mutations. Several outcomes are possible depending on how fast the rates go to 0. The model considered has been proposed by Komarova (2007) as a model for colon cancer.

  4. Bayesian spatio-temporal modelling of tobacco-related cancer mortality in Switzerland

    Directory of Open Access Journals (Sweden)

    Verena Jürgens

    2013-05-01

    Full Text Available Tobacco smoking is a main cause of disease in Switzerland; lung cancer being the most common cancer mortality in men and the second most common in women. Although disease-specific mortality is decreasing in men, it is steadily increasing in women. The four language regions in this country might play a role in this context as they are influenced in different ways by the cultural and social behaviour of neighbouring countries. Bayesian hierarchical spatio-temporal, negative binomial models were fitted on subgroup-specific death rates indirectly standardized by national references to explore age- and gender-specific spatio-temporal patterns of mortality due to lung cancer and other tobacco-related cancers in Switzerland for the time period 1969-2002. Differences influenced by linguistic region and life in rural or urban areas were also accounted for. Male lung cancer mortality was found to be rather homogeneous in space, whereas women were confirmed to be more affected in urban regions. Compared to the German-speaking part, female mortality was higher in the French-speaking part of the country, a result contradicting other reports of similar comparisons between France and Germany. The spatio-temporal patterns of mortality were similar for lung cancer and other tobacco-related cancers. The estimated mortality maps can support the planning in health care services and evaluation of a national tobacco control programme. Better understanding of spatial and temporal variation of cancer of the lung and other tobacco-related cancers may help in allocating resources for more effective screening, diagnosis and therapy. The methodology can be applied to similar studies in other settings.

  5. How sensitive are the thermal fits to heavy-ion hadron yield data to the modeling of the eigenvolume interactions?

    CERN Document Server

    Vovchenko, Volodymyr

    2016-01-01

    The hadron-resonance gas (HRG) model with eigenvolume corrections is employed to fit the hadron yield data of the NA49 collaboration for central Pb+Pb collisions at $\\sqrt{s_{NN}}$ = 6.3, 7.6, 8.8, 12.3, and 17.3 GeV, the hadron midrapidity yield data of the STAR collaboration for Au+Au collisions at $\\sqrt{s_{NN}}$ = 200 GeV, and the hadron midrapidity yield data of the ALICE collaboration for Pb+Pb collisions at $\\sqrt{s_{NN}}$ = 2760 GeV. The influence of the EV corrections is studied within two different formulations of the EV HRG model. For the case of the point-particle HRG the extracted values of temperature and chemical potential are consistent with previous findings. The situation is very different when we apply the eigenvolume corrections with mass-proportional eigenvolumes $v_i \\sim m_i$, fixed to different values of the proton hard-core radius of $r_p$. At given bombarding energy the EV HRG model fits do not just yield a single $T-\\mu_B$ pair, but a whole range of $T-\\mu_B$ pairs. These pairs form...

  6. Does the first chaotic inflation model in supergravity provide the best fit to the Planck data?

    International Nuclear Information System (INIS)

    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 V0(1−(8/3) e−√6|ϕ|) at large values of the inflaton field. This model predicts ns=1−(2/N)≈0.967 and r=(4/(3N2))≈4×10−4, 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

  7. The PX-EM algorithm for fast stable fitting of Henderson's mixed model

    Directory of Open Access Journals (Sweden)

    Van Dyk David A

    2000-03-01

    Full Text Available Abstract This paper presents procedures for implementing the PX-EM algorithm of Liu, Rubin and Wu to compute REML estimates of variance covariance components in Henderson's linear mixed models. The class of models considered encompasses several correlated random factors having the same vector length e.g., as in random regression models for longitudinal data analysis and in sire-maternal grandsire models for genetic evaluation. Numerical examples are presented to illustrate the procedures. Much better results in terms of convergence characteristics (number of iterations and time required for convergence are obtained for PX-EM relative to the basic EM algorithm in the random regression.

  8. FITTING A THREE DIMENSIONAL PEM FUEL CELL MODEL TO MEASUREMENTS BY TUNING THE POROSITY AND

    DEFF Research Database (Denmark)

    Bang, Mads; Odgaard, Madeleine; Condra, Thomas Joseph;

    2004-01-01

    A three-dimensional, computational fluid dynamics (CFD) model of a PEM fuel cell is presented. The model consists ofstraight channels, porous gas diffusion layers, porous catalystlayers and a membrane. In this computational domain, most ofthe transport phenomena which govern the performance of thePEM...

  9. Fitting macroevolutionary models to phylogenies: an example using vertebrate body sizes

    NARCIS (Netherlands)

    Mooers, Arne Ø.; Schluter, Dolph

    1998-01-01

    How do traits change through time and with speciation? We present a simple and generally applicable method for comparing various models of the macroevolution of traits within a maximum likelihood framework. We illustrate four such models: 1) variance among species accumulates in direct proportion to

  10. Fitting multistate transition models with autoregressive logistic regression : Supervised exercise in intermittent claudication

    NARCIS (Netherlands)

    de Vries, SO; Fidler, [No Value; Kuipers, WD; Hunink, MGM

    1998-01-01

    The purpose of this study was to develop a model that predicts the outcome of supervised exercise for intermittent claudication. The authors present an example of the use of autoregressive logistic regression for modeling observed longitudinal data. Data were collected from 329 participants in a six

  11. Fitting multi-state transition models with autoregressive logistic regression : supervised exercise in intermittent claudication

    NARCIS (Netherlands)

    de Vries, S.O.; Fidler, V.; Kuipers, W.D.; Hunink, M.G.

    1998-01-01

    The purpose of this study was to develop a model that predicts the outcome of supervised exercise for intermittent claudication. The authors present an example of the use of autoregressive logistic regression for modeling observed longitudinal data. Data were collected from 329 participants in a six

  12. Practical Poissonian-Gaussian noise modeling and fitting for single-image raw-data.

    Science.gov (United States)

    Foi, Alessandro; Trimeche, Mejdi; Katkovnik, Vladimir; Egiazarian, Karen

    2008-10-01

    We present a simple and usable noise model for the raw-data of digital imaging sensors. This signal-dependent noise model, which gives the pointwise standard-deviation of the noise as a function of the expectation of the pixel raw-data output, is composed of a Poissonian part, modeling the photon sensing, and Gaussian part, for the remaining stationary disturbances in the output data. We further explicitly take into account the clipping of the data (over- and under-exposure), faithfully reproducing the nonlinear response of the sensor. We propose an algorithm for the fully automatic estimation of the model parameters given a single noisy image. Experiments with synthetic images and with real raw-data from various sensors prove the practical applicability of the method and the accuracy of the proposed model. PMID:18784024

  13. A Bayesian model for censored positive count data in evaluating breast cancer progression.

    Science.gov (United States)

    Yeh, Hung-Wen; Jiang, Yu; Garrard, Lili; Lei, Yang; Gajewski, Byron

    2013-01-01

    Basic science researchers transplant human cancer tissues from patients with ductal carcinoma in situ (DCIS) to animals and observe the progression of the disease. Successful transplants show invasion of human tissues across mammary ducts in animal fat pads and cause DCIS-like lesions in one or more ducts. In this work, we consider data from a recent publication of breast cancer research where positive counts of affected ducts may be subject to censoring. We fit the data with zero-truncated Poisson (ZTP) models with an informative prior of gamma. Due to the zero-truncation and right censoring, posterior distributions may not be conventional gamma and are estimated through Markov chain Monte Carlo and grid approximation. For each of the two cell lines, we fit a model with group-specific parameters for DCIS subtypes classified by the cell surface biomarkers, and another model with a homogeneous parameter across groups. Models are compared by the Deviance Information Criterion (DIC). For the chosen prior parameter values, Bayes estimates are comparative to the maximum likelihood estimates, and the DIC favors the simpler model in both cell lines. PMID:23997758

  14. Effects of a Three-Tiered Intervention Model on Physical Activity and Fitness Levels of Elementary School Children.

    Science.gov (United States)

    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. PMID:27059849

  15. Structural model for gamma-aminobutyric acid receptor noncompetitive antagonist binding: widely diverse structures fit the same site.

    Science.gov (United States)

    Chen, Ligong; Durkin, Kathleen A; Casida, John E

    2006-03-28

    Several major insecticides, including alpha-endosulfan, lindane, and fipronil, and the botanical picrotoxinin are noncompetitive antagonists (NCAs) for the GABA receptor. We showed earlier that human beta(3) homopentameric GABA(A) receptor recognizes all of the important GABAergic insecticides and reproduces the high insecticide sensitivity and structure-activity relationships of the native insect receptor. Despite large structural diversity, the NCAs are proposed to fit a single binding site in the chloride channel lumen lined by five transmembrane 2 segments. This hypothesis is examined with the beta(3) homopentamer by mutagenesis, pore structure studies, NCA binding, and molecular modeling. The 15 amino acids in the cytoplasmic half of the pore were mutated to cysteine, serine, or other residue for 22 mutants overall. Localization of A-1'C, A2'C, T6'C, and L9'C (index numbers for the transmembrane 2 region) in the channel lumen was established by disulfide cross-linking. Binding of two NCA radioligands [(3)H]1-(4-ethynylphenyl)-4-n-propyl-2,6,7-trioxabicyclo[2.2.2]octane and [(3)H] 3,3-bis-trifluoromethyl-bicyclo[2,2,1]heptane-2,2-dicarbonitrile was dramatically reduced with 8 of the 15 mutated positions, focusing attention on A2', T6', and L9' as proposed binding sites, consistent with earlier mutagenesis studies. The cytoplasmic half of the beta3 homopentamer pore was modeled as an alpha-helix. The six NCAs listed above plus t-butylbicyclophosphorothionate fit the 2' to 9' pore region forming hydrogen bonds with the T6' hydroxyl and hydrophobic interactions with A2', T6', and L9' alkyl substituents, thereby blocking the channel. Thus, widely diverse NCA structures fit the same GABA receptor beta subunit site with important implications for insecticide cross-resistance and selective toxicity between insects and mammals.

  16. Fitting HIV Prevalence 1981 Onwards for Three Indian States Using the Goals Model and the Estimation and Projection Package

    Science.gov (United States)

    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

  17. Establishing of the Transplanted Animal Models for Human Lung Cancer

    Institute of Scientific and Technical Information of China (English)

    Xingli Zhang; Jinchang Wu

    2009-01-01

    Lung cancer is the leading cause of cancer mortality worldwide.Even with the applications of excision,radiotherapy,chemotherapy,and gene therapy,the 5 year survival rate is only 15% in the USA.Clinically relevant laboratory animal models of the disease could greatly facilitate understanding of the pathogenesis of lung cancer,its progression,invasion and metastasis.Transplanted lung cancer models are of special interest and are widely used today.Such models are essential tools in accelerating development of new therapies for lung cancer.In this communication we will present a brief overview of the hosts,sites and pathways used to establish transplanted animal lung tumor models.

  18. “Psychosocial Interventions for Cancer Survivors, Caregivers and Family Members—One Size Does Not Fit All: My Perspective as a Young Adult Survivor, Advocate and Oncology Social Worker” a personal reflection by Mary Grace Bontempo - Office of Cancer Survivorship

    Science.gov (United States)

    “Psychosocial Interventions for Cancer Survivors, Caregivers and Family Members—One Size Does Not Fit All: My Perspective as a Young Adult Survivor, Advocate and Oncology Social Worker” a personal reflection by Mary Grace Bontempo page

  19. Model of Care for Adolescents and Young Adults with Cancer: The Youth Project in Milan.

    Science.gov (United States)

    Magni, Chiara; Veneroni, Laura; Silva, Matteo; Casanova, Michela; Chiaravalli, Stefano; Massimino, Maura; Clerici, Carlo Alfredo; Ferrari, Andrea

    2016-01-01

    Adolescents and young adults (AYA) with cancer form a particular group of patients with unique characteristics, who inhabit a so-called "no man's land" between pediatric and adult services. In the last 10 years, the scientific oncology community has started to pay attention to these patients, implementing dedicated programs. A standardized model of care directed toward patients in this age range has yet to be developed and neither the pediatric nor the adult oncologic systems perfectly fit these patients' needs. The Youth Project of the Istituto Nazionale Tumori in Milan, dedicated to AYA with pediatric-type solid tumors, can be seen as a model of care for AYA patients, with its heterogeneous multidisciplinary staff and close cooperation with adult medical oncologists and surgeons. Further progress in the care of AYA cancer patients is still needed to improve their outcomes. PMID:27606308

  20. Model of Care for Adolescents and Young Adults with Cancer: The Youth Project in Milan

    Science.gov (United States)

    Magni, Chiara; Veneroni, Laura; Silva, Matteo; Casanova, Michela; Chiaravalli, Stefano; Massimino, Maura; Clerici, Carlo Alfredo; Ferrari, Andrea

    2016-01-01

    Adolescents and young adults (AYA) with cancer form a particular group of patients with unique characteristics, who inhabit a so-called “no man’s land” between pediatric and adult services. In the last 10 years, the scientific oncology community has started to pay attention to these patients, implementing dedicated programs. A standardized model of care directed toward patients in this age range has yet to be developed and neither the pediatric nor the adult oncologic systems perfectly fit these patients’ needs. The Youth Project of the Istituto Nazionale Tumori in Milan, dedicated to AYA with pediatric-type solid tumors, can be seen as a model of care for AYA patients, with its heterogeneous multidisciplinary staff and close cooperation with adult medical oncologists and surgeons. Further progress in the care of AYA cancer patients is still needed to improve their outcomes. PMID:27606308

  1. Fitness club

    CERN Document Server

    Fitness club

    2013-01-01

      Nordic Walking Classes Come join the Nordic walking classes and outings offered by the CERN Fitness Club starting September 2013. Our licensed instructor Christine offers classes for people who’ve never tried Nordic Walking and who would like to learn the technique, and outings for people who have completed the classes and enjoy going out as a group. Course 1: Tuesdays 12:30 - 13:30 24 September, 1 October, 8 October, 15 October Course 2: Tuesdays 12:30 - 13:30 5 November, 12 November, 19 November, 26 November Outings will take place on Thursdays (12:30 to 13:30) from 12 September 2013. We meet at the CERN Club Barracks car park (close to Entrance A) 10 minutes before departure. Prices: 50 CHF for 4 classes, including the 10 CHF Club membership. Payments made directly to instructor. Renting Poles: Poles can be rented from Christine at 5 CHF / hour. Subscription: Please subscribe at: http://cern.ch/club-fitness Looking forward to seeing you among us! Fitness Club FitnessClub@c...

  2. Fitness Basics

    Science.gov (United States)

    ... that gets your heart pumping, such as dancing, running, or swimming laps. How hard you exercise matters, too. You can learn how to measure your workout to see if it is light, medium, or intense. Fitness for all Do you have an illness or ...

  3. Fitness Club

    CERN Multimedia

    Fitness Club

    2012-01-01

    Get in Shape for Summer with the CERN Fitness Club Saturday 23 June 2012 from 14:30 to 16.30 (doors open at 14.00) Germana’s Fitness Workshop. Build strength and stamina, sculpt and tone your body and get your heart pumping with Germana’s workout mixture of Cardio Attack, Power Pump, Power Step, Cardio Combat and Cross-Training. Where: 216 (Pump room – equipped with changing rooms and showers). What to wear: comfortable clothes and indoor sports shoes + bring a drink! How much: 15 chf Sign up here: https://espace.cern.ch/club-fitness/Lists/Test_Subscription/NewForm.aspx? Join the Party and dance yourself into shape at Marco + Marials Zumba Masterclass. Saturday 30 June 2012 from 15:00 to 16:30 Marco + Mariel’s Zumba Masterclass Where: 216 (Pump room – equipped with changing rooms and showers). What to wear: comfortable clothes and indoor sports shoes + bring a drink! How much: 25 chf Sign up here: https://espace.cern.ch/club-fitness/Lists/Zumba%20...

  4. Fitness Club

    CERN Multimedia

    Fitness Club

    2010-01-01

    Nordic Walking Please note that the subscriptions for the general fitness classes from July to December are open: Subscriptions general fitness classes Jul-Dec 2010 Sign-up to the Fitness Club mailing list here Nordic Walking: Sign-up to the Nordic Walking mailing list here Beginners Nordic walking lessons Monday Lunchtimes (rdv 12:20 for 12:30 departure) 13.09/20.09/27.09/04.10 11.10/18.10/08.11/15.11 22.11/29.11/06.12/20.12 Nordic walking lessons Tuesday evenings (rdv 17:50 for 18:00 departure) 07.09/14.09/21.09/28.09 05.10/12.10/19.10/26.10 Intermediate/Advanced Nordic walking outings (follow the nordic walking lessons before signing up for the outings) every Thursday from 16.09 - 16.12, excluding 28.10 and 09.12 Subscriptions and info: fitness.club@cern.ch  

  5. Fitness Club

    CERN Multimedia

    Fitness Club

    2012-01-01

      The CERN Fitness Club is pleased to announce its new early morning class which will be taking place on: Tuesdays from 24th April 07:30 to 08:15 216 (Pump Hall, close to entrance C) – Facilities include changing rooms and showers. The Classes: The early morning classes will focus on workouts which will help you build not only strength and stamina, but will also improve your balance, and coordination. Our qualified instructor Germana will accompany you throughout the workout  to ensure you stay motivated so you achieve the best results. Sign up and discover the best way to start your working day full of energy! How to subscribe? We invite you along to a FREE trial session, if you enjoy the activity, please sign up via our website: https://espace.cern.ch/club-fitness/Activities/SUBSCRIBE.aspx. * * * * * * * * Saturday 28th April Get in shape for the summer at our fitness workshop and zumba dance party: Fitness workshop with Germana 13:00 to 14:30 - 216 (Pump Hall) Price...

  6. An improved nonlinear model of HEMTs with independent transconductance tail-off fitting

    Institute of Scientific and Technical Information of China (English)

    Liu Linsheng

    2011-01-01

    We present an improved large-signal device model of GaAs/GaN HEMTs, amenable for use in commercial nonlinear simulators. The proposed model includes a new exponential function to independently control the transconductance compression/tail-offbehaviors. The main advantage of this model is to provide a simple and coherent description of the bias-dependent drain current (I-V) that is valid in all regions of operation. All aspects of the model are validated for 0.25-μm gate-length GaAs and GaN HEMT processes. The simulation results of DC/pulsed I-V, RF large-signal power and intermodulation distortion products show excellent agreement with the measured data.

  7. Some Properties of A Lack-of-Fit Test for a Linear Errors in Variables Model

    Institute of Scientific and Technical Information of China (English)

    Li-xing Zhu; Heng-jian Cui; K.W.Ng

    2004-01-01

    The relationship between the linear errors-in-variables model and the corresponding ordinary linear model in statistical inference is studied.It is shown that normality of the distribution of covariate is a necessary and su cient condition for the equivalence.Therefore,testing for lack-of-t in linear errors-in-variables model can be converted into testing for it in the corresponding ordinary linear model under normality assumption.A test of score type is constructed and the limiting chi-squared distribution is derived under the null hypothesis.Furthermore,we discuss the power of the test and the choice of the weight function involved in the test statistic.

  8. Do telemonitoring projects of heart failure fit the Chronic Care Model?

    OpenAIRE

    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...

  9. Fitted HBT radii versus space-time variances in flow-dominated models

    OpenAIRE

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

    2006-01-01

    The inability of otherwise successful dynamical models to reproduce the ``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 which can be directly computed from the emission function, without having to evaluate, at significant e...

  10. Fractional Differentiation-Based Active Contour Model Driven by Local Intensity Fitting Energy

    OpenAIRE

    Ming Gu; Renfang Wang

    2016-01-01

    A novel active contour model is proposed for segmentation images with inhomogeneity. Firstly, fractional order filter is defined by eight convolution masks corresponding to the image orientation in the eight compass directions. Then, the fractional order differentiation image is obtained and applied to the level set method. Secondly, we defined a new energy functional based on local image information and fractional order differentiation image; the proposed model not only can describe the inpu...

  11. The β-Model Problem: The Incompatibility of X-Ray and Sunyaev-Zeldovich Effect Model Fitting for Galaxy Clusters

    Science.gov (United States)

    Hallman, Eric J.; Burns, Jack O.; Motl, Patrick M.; Norman, Michael L.

    2007-08-01

    We have analyzed a large sample of numerically simulated clusters to demonstrate the adverse effects resulting from the use of X-ray-fitted β-model parameters with Sunyaev-Zeldovich effect (SZE) data. There is a fundamental incompatibility between β-model fits to X-ray surface brightness profiles and those done with SZE profiles. Since observational SZE radial profiles are in short supply, the X-ray parameters are often used in SZE analysis. We show that this leads to biased estimates of the integrated Compton y-parameter inside r500 calculated from clusters. We suggest a simple correction of the method, using a nonisothermal β-model modified by a universal temperature profile, which brings these calculated quantities into closer agreement with the true values.

  12. The Beta-Model Problem: The Incompatibility of X-ray and Sunyaev-Zeldovich Effect Model Fitting for Galaxy Clusters

    CERN Document Server

    Hallman, Eric J; Motl, Patrick M; Norman, Michael L

    2007-01-01

    We have analyzed a large sample of numerically simulated clusters to demonstrate the adverse effects resulting from use of X-ray fitted beta-model parameters with Sunyaev-Zeldovich effect (SZE) data. There is a fundamental incompatibility between model fits to X-ray surface brightness profiles and those done with SZE profiles. Since observational SZE radial profiles are in short supply, the X-ray parameters are often used in SZE analysis. We show that this leads to biased estimates of the integrated Compton y-parameter inside r_{500} calculated from clusters. We suggest a simple correction of the method, using a non-isothermal beta-model modified by a universal temperature profile, which brings these calculated quantities into closer agreement with the true values.

  13. Cognitive fitness.

    Science.gov (United States)

    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. PMID:18159786

  14. Fitting a Turbulent Cloud Model to CO Observations of Starless Bok Globules

    Science.gov (United States)

    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.

  15. Calibration Methods Used in Cancer Simulation Models and Suggested Reporting Guidelines

    Science.gov (United States)

    Stout, Natasha K.; Knudsen, Amy B.; Kong, Chung Yin (Joey); McMahon, Pamela M.; Gazelle, G. Scott

    2009-01-01

    Background Increasingly, computer simulation models are used for economic and policy evaluation in cancer prevention and control. A model’s predictions of key outcomes such as screening effectiveness depends on the values of unobservable natural history parameters. Calibration is the process of determining the values of unobservable parameters by constraining model output to replicate observed data. Because there are many approaches for model calibration and little consensus on best practices, we surveyed the literature to catalogue the use and reporting of these methods in cancer simulation models. Methods We conducted a MEDLINE search (1980 through 2006) for articles on cancer screening models and supplemented search results with articles from our personal reference databases. For each article, two authors independently abstracted pre-determined items using a standard form. Data items included cancer site, model type, methods used for determination of unobservable parameter values, and description of any calibration protocol. All authors reached consensus on items of disagreement. Reviews and non-cancer models were excluded. Articles describing analytical models which estimate parameters with statistical approaches (e.g., maximum likelihood) were catalogued separately. Models that included unobservable parameters were analyzed and classified by whether calibration methods were reported and if so, the methods used. Results The review process yielded 154 articles that met our inclusion criteria and of these, we concluded that 131 may have used calibration methods to determine model parameters. Although the term “calibration” was not always used, descriptions of calibration or “model fitting” were found in 50% (n=66) of the articles with an additional 16% (n=21) providing a reference to methods. Calibration target data were identified in nearly all of these articles. Other methodologic details such as the goodness-of-fit metric were discussed in 54% (n=47

  16. Dietary Zinc and Prostate Cancer in the TRAMP Mouse Model

    OpenAIRE

    Prasad, Ananda S; Mukhtar, Hasan; Beck, Frances W.J.; Adhami, Vaqar M.; Siddiqui, Imtiaz A.; Din, Maria; Hafeez, Bilal B.; KUCUK, Omer

    2010-01-01

    Circumstantial evidence indicates that zinc may have an important role in the prostate. Total zinc levels in the prostate are 10 times higher than in other soft tissues. Zinc concentrations in prostate epithethial cancer cells are decreased significantly. Zinc supplementation for prevention and treatment of prostate cancer in humans has yielded controversial results. No studies have been reported in animal models to show the effect of zinc supplementation on prevention of prostate cancer, thu...

  17. Interdependence in Women with Breast Cancer and Their Partners: An Interindividual Model of Distress

    Science.gov (United States)

    Dorros, Sam M.; Card, Noel A.; Segrin, Chris; Badger, Terry A.

    2010-01-01

    Objective: The aim of this investigation was to test whether interdependence in dyads living with breast cancer could account for person-partner crossover effects in distress outcomes. Method: The sample consisted of 95 dyads with early-stage breast cancer. By using reciprocal dyadic data from women with breast cancer and their partners, we fit a…

  18. Extinction Models for Cancer Stem Cell Therapy

    OpenAIRE

    Sehl, Mary; Zhou, Hua; Sinsheimer, Janet ,; Lange, Kenneth

    2009-01-01

    Cells with stem cell-like properties are now viewed as initiating and sustaining many cancers. This suggests that cancer can be cured by driving these cancer stem cells to extinction. The problem with this strategy is that ordinary stem cells are apt to be killed in the process. This paper sets bounds on the killing differential (difference between death rates of cancer stem cells and normal stem cells) that must exist for the survival of an adequate number of normal stem cells. Our main tool...

  19. Statistics of Dark Matter Substructure: I. Model and Universal Fitting Functions

    CERN Document Server

    Jiang, Fangzhou

    2014-01-01

    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. (2008) 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, and uses a simple recipe to convert subhalo mass to maximum circular velocity. The model accurately reproduces the average subhalo mass and velocity functions in numerical simulations. The inferred subhalo mass loss rates imply that an average dark matter subhalo loses in excess of 80 percent of its infall mass during its first radial orbit within the host halo. We demonstrate that the total 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 for...

  20. Calculating Model of Interference Amount for Miniaturized Gear and Shaft Shrink Fit

    Institute of Scientific and Technical Information of China (English)

    JIN Xin; ZHANG Zhi-jing; YE Xin; LI Zhong-xin

    2006-01-01

    Based on miniaturized components' characteristics, the method of assembling miniaturized gear and shaft together with corresponding calculating model of the interference amount are proposed. On the basis of main effecting factors analysis on the gear and shaft assembling interference amount, calculating formula including all factors effective on the interference amount necessary for reliable system running was built up. The methods of reverse calculating theoretical model was used to build up the equivalent simulation model of the theoretical one, together with simulation verification and case study for calculating formula. The results show that the cold assembling method is applicable for miniaturized gear and shaft, but in the assembling process,the interference amount compensating the shape error of contacting surfaces takes a large proportion, which is the main cause of stress variance on contacting surfaces.

  1. Fitting and interpreting continuous-time latent Markov models for panel data.

    Science.gov (United States)

    Lange, Jane M; Minin, Vladimir N

    2013-11-20

    Multistate models characterize disease processes within an individual. Clinical studies often observe the disease status of individuals at discrete time points, making exact times of transitions between disease states unknown. Such panel data pose considerable modeling challenges. Assuming the disease process progresses accordingly, a standard continuous-time Markov chain (CTMC) yields tractable likelihoods, but the assumption of exponential sojourn time distributions is typically unrealistic. More flexible semi-Markov models permit generic sojourn distributions yet yield intractable likelihoods for panel data in the presence of reversible transitions. One attractive alternative is to assume that the disease process is characterized by an underlying latent CTMC, with multiple latent states mapping to each disease state. These models retain analytic tractability due to the CTMC framework but allow for flexible, duration-dependent disease state sojourn distributions. We have developed a robust and efficient expectation-maximization algorithm in this context. Our complete data state space consists of the observed data and the underlying latent trajectory, yielding computationally efficient expectation and maximization steps. Our algorithm outperforms alternative methods measured in terms of time to convergence and robustness. We also examine the frequentist performance of latent CTMC point and interval estimates of disease process functionals based on simulated data. The performance of estimates depends on time, functional, and data-generating scenario. Finally, we illustrate the interpretive power of latent CTMC models for describing disease processes on a dataset of lung transplant patients. We hope our work will encourage wider use of these models in the biomedical setting. PMID:23740756

  2. Some Fast Methods for Fitting Some One-parameter Spatial Models

    Directory of Open Access Journals (Sweden)

    R. J. Martin

    2005-01-01

    Full Text Available It is common in geographic modelling to use a one-parameter spatial model to specify the inverse covariance matrix in terms of I-bW, for some known matrix W. Exact Gaussian maximum likelihood estimation of b requires evaluation of the determinant of the covariance matrix. For large data sets, this evaluation of the determinant can be slow and good approximations can be useful. Seventy regional configurations are used to consider some approximations to the determinant of I-bW that are fast to evaluate, and their usefulness is compared.

  3. Modeling and estimation of replication fitness of human immunodeficiency virus type 1 in vitro experiments by using a growth competition assay.

    Science.gov (United States)

    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.

  4. Organoids as Models for Neoplastic Transformation | Office of Cancer Genomics

    Science.gov (United States)

    Cancer models strive to recapitulate the incredible diversity inherent in human tumors. A key challenge in accurate tumor modeling lies in capturing the panoply of homo- and heterotypic cellular interactions within the context of a three-dimensional tissue microenvironment. To address this challenge, researchers have developed organotypic cancer models (organoids) that combine the 3D architecture of in vivo tissues with the experimental facility of 2D cell lines.

  5. A mathematical framework for estimating pathogen transmission fitness and inoculum size using data from a competitive mixtures animal model.

    Directory of Open Access Journals (Sweden)

    James M McCaw

    2011-04-01

    Full Text Available 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

  6. Heliospheric Propagation of Coronal Mass Ejections: Drag-Based Model Fitting

    CERN Document Server

    Žic, T; Temmer, M

    2015-01-01

    The so-called drag-based model (DBM) simulates analytically the propagation of coronal mass ejections (CMEs) in interplanetary space and allows the prediction of their arrival times and impact speeds at any point in the heliosphere ("target"). The DBM is based on the assumption that beyond a distance of about 20 solar radii from the Sun, the dominant force acting on CMEs is the "aerodynamic" drag force. In the standard form of DBM, the user provisionally chooses values for the model input parameters, by which the kinematics of the CME over the entire Sun--"target" distance range is defined. The choice of model input parameters is usually based on several previously undertaken statistical studies. In other words, the model is used by ad hoc implementation of statistics-based values of the input parameters, which are not necessarily appropriate for the CME under study. Furthermore, such a procedure lacks quantitative information on how well the simulation reproduces the coronagraphically observed kinematics of ...

  7. Fitting Social Network Models Using Varying Truncation Stochastic Approximation MCMC Algorithm

    KAUST Repository

    Jin, Ick Hoon

    2013-10-01

    The exponential random graph model (ERGM) plays a major role in social network analysis. However, parameter estimation for the ERGM is a hard problem due to the intractability of its normalizing constant and the model degeneracy. The existing algorithms, such as Monte Carlo maximum likelihood estimation (MCMLE) and stochastic approximation, often fail for this problem in the presence of model degeneracy. In this article, we introduce the varying truncation stochastic approximation Markov chain Monte Carlo (SAMCMC) algorithm to tackle this problem. The varying truncation mechanism enables the algorithm to choose an appropriate starting point and an appropriate gain factor sequence, and thus to produce a reasonable parameter estimate for the ERGM even in the presence of model degeneracy. The numerical results indicate that the varying truncation SAMCMC algorithm can significantly outperform the MCMLE and stochastic approximation algorithms: for degenerate ERGMs, MCMLE and stochastic approximation often fail to produce any reasonable parameter estimates, while SAMCMC can do; for nondegenerate ERGMs, SAMCMC can work as well as or better than MCMLE and stochastic approximation. The data and source codes used for this article are available online as supplementary materials. © 2013 American Statistical Association, Institute of Mathematical Statistics, and Interface Foundation of North America.

  8. Understanding the Listening Process: Rethinking the "One Size Fits All" Model

    Science.gov (United States)

    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…

  9. Where Does Creativity Fit into a Productivist Industrial Model of Knowledge Production?

    Science.gov (United States)

    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…

  10. Are Earth System model software engineering practices fit for purpose? A case study.

    Science.gov (United States)

    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.

  11. Fitting the Mixed Rasch Model to a Reading Comprehension Test: Identifying Reader Types

    Science.gov (United States)

    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…

  12. Using the SPSS Mixed Procedure to Fit Cross-Sectional and Longitudinal Multilevel Models

    Science.gov (United States)

    Peugh, James L.; Enders, Craig K.

    2005-01-01

    Beginning with Version 11, SPSS implemented the MIXED procedure, which is capable of performing many common hierarchical linear model analyses. The purpose of this article was to provide a tutorial for performing cross-sectional and longitudinal analyses using this popular software platform. In doing so, the authors borrowed heavily from Singer's…

  13. Do telemonitoring projects of heart failure fit the Chronic Care Model?

    Directory of Open Access Journals (Sweden)

    Evi Willemse

    2014-07-01

    Full Text Available 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.

  14. Do telemonitoring projects of heart failure fit the Chronic Care Model?

    Directory of Open Access Journals (Sweden)

    Evi Willemse

    2014-07-01

    Full Text Available 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.

  15. Risk Prediction Model for Colorectal Cancer: National Health Insurance Corporation Study, Korea

    OpenAIRE

    Aesun Shin; Jungnam Joo; Hye-Ryung Yang; Jeongin Bak; Yunjin Park; Jeongseon Kim; Jae Hwan Oh; Byung-Ho Nam

    2014-01-01

    PURPOSE: Incidence and mortality rates of colorectal cancer have been rapidly increasing in Korea during last few decades. Development of risk prediction models for colorectal cancer in Korean men and women is urgently needed to enhance its prevention and early detection. METHODS: Gender specific five-year risk prediction models were developed for overall colorectal cancer, proximal colon cancer, distal colon cancer, colon cancer and rectal cancer. The model was developed using data from a po...

  16. A CONTRASTIVE ANALYSIS OF THE FACTORIAL STRUCTURE OF THE PCL-R: WHICH MODEL FITS BEST THE DATA?

    Directory of Open Access Journals (Sweden)

    Beatriz Pérez

    2015-01-01

    Full Text Available The aim of this study was to determine which of the factorial solutions proposed for the Hare Psychopathy Checklist-Revised (PCL-R of two, three, four factors, and unidimensional fitted best the data. Two trained and experienced independent raters scored 197 prisoners from the Villabona Penitentiary (Asturias, Spain, age range 21 to 73 years (M = 36.0, SD = 9.7, of whom 60.12% were reoffenders and 73% had committed violent crimes. The results revealed that the two-factor correlational, three-factor hierarchical without testlets, four-factor correlational and hierarchical, and unidimensional models were a poor fit for the data (CFI ≤ .86, and the three-factor model with testlets was a reasonable fit for the data (CFI = .93. The scale resulting from the three-factor hierarchical model with testlets (13 items classified psychopathy significantly higher than the original 20-item scale. The results are discussed in terms of their implications for theoretical models of psychopathy, decision-making, prison classification and intervention, and prevention. Se diseñó un estudio con el objetivo de conocer cuál de las soluciones factoriales propuestas para la Hare Psychopathy Checklist-Revised (PCL-R de dos, tres y cuatro factores y unidimensional era la que presentaba mejor ajuste a los datos. Para ello, dos evaluadores entrenados y con experiencia evaluaron de forma independiente a 197 internos en la prisión Villabona (Asturias, España, con edades comprendidas entre los 21 y los 73 años (M = 36.0, DT = 9.7, de los cuales el 60.12% eran reincidentes y el 73% había cometido delitos violentos. Los resultados mostraron que los modelos unidimensional, correlacional de 2 factores, jerárquico de 3 factores sin testlest y correlacional y jerárquico de 4 factores, presentaban un pobre ajuste con los datos (CFI ≤ .86 y un ajuste razonable del modelo jerárquico de tres factores con testlets (CFI = .93. La escala resultante del modelo de tres factores

  17. Risk Prediction Models for Other Cancers or Multiple Sites

    Science.gov (United States)

    Developing statistical models that estimate the probability of developing other multiple cancers over a defined period of time will help clinicians identify individuals at higher risk of specific cancers, allowing for earlier or more frequent screening and counseling of behavioral changes to decrease risk.

  18. Fitness Club

    CERN Multimedia

    Fitness Club

    2012-01-01

    Nordic Walking Classes Sessions of four classes of one hour each are held on Tuesdays. RDV barracks parking at Entrance A, 10 minutes before class time. Session 1 =  11.09 / 18.09 / 25.09 / 02.10, 18:15 - 19:15 Session 2 = 25.09 / 02.10 / 09.10 / 16.10, 12:30 - 13:30 Session 3 = 23.10 / 30.10 / 06.11 / 13.11, 12:30 - 13:30 Session 4 = 20.11 / 27.11 / 04.12 / 11.12, 12:30 - 13:30 Prices 40 CHF per session + 10 CHF club membership 5 CHF/hour pole rental Check out our schedule and enroll at http://cern.ch/club-fitness   Hope to see you among us!  fitness.club@cern.ch In spring 2012 there was a long-awaited progress in CERN Fitness club. We have officially opened a Powerlifting @ CERN, and the number of members of the new section has been increasing since then reaching 70+ people in less than 4 months. Powerlifting is a strength sport, which is simple as 1-2-3 and efficient. The "1-2-3" are the three basic lifts (bench press...

  19. A Neuro-Fuzzy Inference Model for Breast Cancer Recognitio

    Directory of Open Access Journals (Sweden)

    Bekaddour Fatima

    2012-11-01

    Full Text Available Breast cancer is known as one of the most common cancers to afflict the female population. Computerassisted diagnosis can be helpful for doctors in detection and diagnosing of potential abnormalities.Several techniques can be useful for accomplishing this task. This paper outlines an approach forrecognizing breast cancer diagnosis using neuro-fuzzy inference technique namely ANFIS (AdaptativeNeuro-Fuzzy Inference System. Wisconsin breast cancer diagnosis (WBCDdatabase developed atUniversity of California, Irvine (UCI is used to evaluate this method. Results show that the bestperformances are obtained by our model compared to others cited in literatur (an accuracy of 98, 25 % .

  20. Modelled Group Fitted XAFS Debye-Waller factors for Zn metalloproteins

    Science.gov (United States)

    Dimakis, Nicholas; Bunker, Grant

    2003-03-01

    X-ray Absorption Fine Structure spectroscopy is one of the few direct methods for determining the structure of metalloprotein active sites that are applicable to noncrystalline proteins in solutions and membranes. Considerable progress has been made in the calculation of photoelectron scattering aspects of XAFS,but calculation of the vibrational aspects has lagged because of the difficulty of the accurate calculations. Recently we have presented initial results that enabled practical numerical evaluation of XAFS multiple scattering Debye Waller Factors (MSDWFs) of Zn ions bound to histidines in metalloproteins. Recently we have refined our Zn-histidine model to provide more accurate first shell single scattering Debye-Waller parameters, and we have developed a model for Zn-cysteine model that described the MSDWFs enabling for the first time quantitative full single- and multiple-scattering XAFS data analysis of Zn/His/Cys sites at arbitrary temperatures, without the use of ad hoc assumptions. This opens up a wide class of important Zn proteins for study by these methods. Illustrative examples will be presented.

  1. Fitting Galaxies on GPUs

    Science.gov (United States)

    Barsdell, B. R.; Barnes, D. G.; Fluke, C. J.

    2011-07-01

    Structural parameters are normally extracted from observed galaxies by fitting analytic light profiles to the observations. Obtaining accurate fits to high-resolution images is a computationally expensive task, requiring many model evaluations and convolutions with the imaging point spread function. While these algorithms contain high degrees of parallelism, current implementations do not exploit this property. With ever-growing volumes of observational data, an inability to make use of advances in computing power can act as a constraint on scientific outcomes. This is the motivation behind our work, which aims to implement the model-fitting procedure on a graphics processing unit (GPU). We begin by analysing the algorithms involved in model evaluation with respect to their suitability for modern many-core computing architectures like GPUs, finding them to be well-placed to take advantage of the high memory bandwidth offered by this hardware. Following our analysis, we briefly describe a preliminary implementation of the model fitting procedure using freely-available GPU libraries. Early results suggest a speed-up of around 10× over a CPU implementation. We discuss the opportunities such a speed-up could provide, including the ability to use more computationally expensive but better-performing fitting routines to increase the quality and robustness of fits.

  2. The Candida albicans Pho4 Transcription Factor Mediates Susceptibility to Stress and Influences Fitness in a Mouse Commensalism Model

    Science.gov (United States)

    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.

  3. A Monte Carlo-adjusted goodness-of-fit test for parametric models describing spatial point patterns

    KAUST Repository

    Dao, Ngocanh

    2014-04-03

    Assessing the goodness-of-fit (GOF) for intricate parametric spatial point process models is important for many application fields. When the probability density of the statistic of the GOF test is intractable, a commonly used procedure is the Monte Carlo GOF test. Additionally, if the data comprise a single dataset, a popular version of the test plugs a parameter estimate in the hypothesized parametric model to generate data for theMonte Carlo GOF test. In this case, the test is invalid because the resulting empirical level does not reach the nominal level. In this article, we propose a method consisting of nested Monte Carlo simulations which has the following advantages: the bias of the resulting empirical level of the test is eliminated, hence the empirical levels can always reach the nominal level, and information about inhomogeneity of the data can be provided.We theoretically justify our testing procedure using Taylor expansions and demonstrate that it is correctly sized through various simulation studies. In our first data application, we discover, in agreement with Illian et al., that Phlebocarya filifolia plants near Perth, Australia, can follow a homogeneous Poisson clustered process that provides insight into the propagation mechanism of these plants. In our second data application, we find, in contrast to Diggle, that a pairwise interaction model provides a good fit to the micro-anatomy data of amacrine cells designed for analyzing the developmental growth of immature retina cells in rabbits. This article has supplementary material online. © 2013 American Statistical Association, Institute of Mathematical Statistics, and Interface Foundation of North America.

  4. A fully Bayesian method for jointly fitting instrumental calibration and X-ray spectral models

    International Nuclear Information System (INIS)

    Owing to a lack of robust principled methods, systematic instrumental uncertainties have generally been ignored in astrophysical data analysis despite wide recognition of the importance of including them. Ignoring calibration uncertainty can cause bias in the estimation of source model parameters and can lead to underestimation of the variance of these estimates. We previously introduced a pragmatic Bayesian method to address this problem. The method is 'pragmatic' in that it introduced an ad hoc technique that simplified computation by neglecting the potential information in the data for narrowing the uncertainty for the calibration product. Following that work, we use a principal component analysis to efficiently represent the uncertainty of the effective area of an X-ray (or γ-ray) telescope. Here, however, we leverage this representation to enable a principled, fully Bayesian method that coherently accounts for the calibration uncertainty in high-energy spectral analysis. In this setting, the method is compared with standard analysis techniques and the pragmatic Bayesian method. The advantage of the fully Bayesian method is that it allows the data to provide information not only for estimation of the source parameters but also for the calibration product—here the effective area, conditional on the adopted spectral model. In this way, it can yield more accurate and efficient estimates of the source parameters along with valid estimates of their uncertainty. Provided that the source spectrum can be accurately described by a parameterized model, this method allows rigorous inference about the effective area by quantifying which possible curves are most consistent with the data.

  5. Experimentally fitted biodynamic models for pedestrian-structure interaction in walking situations

    Science.gov (United States)

    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.

  6. A Fully Bayesian Method for Jointly Fitting Instrumental Calibration and X-Ray Spectral Models

    Science.gov (United States)

    Xu, Jin; van Dyk, David A.; Kashyap, Vinay L.; Siemiginowska, Aneta; Connors, Alanna; Drake, Jeremy; Meng, Xiao-Li; Ratzlaff, Pete; Yu, Yaming

    2014-10-01

    Owing to a lack of robust principled methods, systematic instrumental uncertainties have generally been ignored in astrophysical data analysis despite wide recognition of the importance of including them. Ignoring calibration uncertainty can cause bias in the estimation of source model parameters and can lead to underestimation of the variance of these estimates. We previously introduced a pragmatic Bayesian method to address this problem. The method is "pragmatic" in that it introduced an ad hoc technique that simplified computation by neglecting the potential information in the data for narrowing the uncertainty for the calibration product. Following that work, we use a principal component analysis to efficiently represent the uncertainty of the effective area of an X-ray (or γ-ray) telescope. Here, however, we leverage this representation to enable a principled, fully Bayesian method that coherently accounts for the calibration uncertainty in high-energy spectral analysis. In this setting, the method is compared with standard analysis techniques and the pragmatic Bayesian method. The advantage of the fully Bayesian method is that it allows the data to provide information not only for estimation of the source parameters but also for the calibration product—here the effective area, conditional on the adopted spectral model. In this way, it can yield more accurate and efficient estimates of the source parameters along with valid estimates of their uncertainty. Provided that the source spectrum can be accurately described by a parameterized model, this method allows rigorous inference about the effective area by quantifying which possible curves are most consistent with the data.

  7. A fully Bayesian method for jointly fitting instrumental calibration and X-ray spectral models

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Jin; Yu, Yaming [Department of Statistics, University of California, Irvine, Irvine, CA 92697-1250 (United States); Van Dyk, David A. [Statistics Section, Imperial College London, Huxley Building, South Kensington Campus, London SW7 2AZ (United Kingdom); Kashyap, Vinay L.; Siemiginowska, Aneta; Drake, Jeremy; Ratzlaff, Pete [Smithsonian Astrophysical Observatory, 60 Garden Street, Cambridge, MA 02138 (United States); Connors, Alanna; Meng, Xiao-Li, E-mail: jinx@uci.edu, E-mail: yamingy@ics.uci.edu, E-mail: dvandyk@imperial.ac.uk, E-mail: vkashyap@cfa.harvard.edu, E-mail: asiemiginowska@cfa.harvard.edu, E-mail: jdrake@cfa.harvard.edu, E-mail: pratzlaff@cfa.harvard.edu, E-mail: meng@stat.harvard.edu [Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, MA 02138 (United States)

    2014-10-20

    Owing to a lack of robust principled methods, systematic instrumental uncertainties have generally been ignored in astrophysical data analysis despite wide recognition of the importance of including them. Ignoring calibration uncertainty can cause bias in the estimation of source model parameters and can lead to underestimation of the variance of these estimates. We previously introduced a pragmatic Bayesian method to address this problem. The method is 'pragmatic' in that it introduced an ad hoc technique that simplified computation by neglecting the potential information in the data for narrowing the uncertainty for the calibration product. Following that work, we use a principal component analysis to efficiently represent the uncertainty of the effective area of an X-ray (or γ-ray) telescope. Here, however, we leverage this representation to enable a principled, fully Bayesian method that coherently accounts for the calibration uncertainty in high-energy spectral analysis. In this setting, the method is compared with standard analysis techniques and the pragmatic Bayesian method. The advantage of the fully Bayesian method is that it allows the data to provide information not only for estimation of the source parameters but also for the calibration product—here the effective area, conditional on the adopted spectral model. In this way, it can yield more accurate and efficient estimates of the source parameters along with valid estimates of their uncertainty. Provided that the source spectrum can be accurately described by a parameterized model, this method allows rigorous inference about the effective area by quantifying which possible curves are most consistent with the data.

  8. Fitting a mixture of von Mises distributions in order to model data on wind direction in Peninsular Malaysia

    International Nuclear Information System (INIS)

    Highlights: • We suggest a simple way for wind direction modeling using the mixture of von Mises distribution. • We determine the most suitable probability model for wind direction regime in Malaysia. • We provide the circular density plots to show the most prominent directions of wind blows. - Abstract: A statistical distribution for describing wind direction provides information about the wind regime at a particular location. In addition, this information complements knowledge of wind speed, which allows researchers to draw some conclusions about the energy potential of wind and aids the development of efficient wind energy generation. This study focuses on modeling the frequency distribution of wind direction, including some characteristics of wind regime that cannot be represented by a unimodal distribution. To identify the most suitable model, a finite mixture of von Mises distributions were fitted to the average hourly wind direction data for nine wind stations located in Peninsular Malaysia. The data used were from the years 2000 to 2009. The suitability of each mixture distribution was judged based on the R2 coefficient and the histogram plot with a density line. The results showed that the finite mixture of the von Mises distribution with H number of components was the best distribution to describe the wind direction distributions in Malaysia. In addition, the circular density plots of the suitable model clearly showed the most prominent directions of wind blows than the other directions

  9. ESTIMATE OF THE HYPSOMETRIC RELATIONSHIP WITH NONLINEAR MODELS FITTED BY EMPIRICAL BAYESIAN METHODS

    Directory of Open Access Journals (Sweden)

    Monica Fabiana Bento Moreira

    2015-09-01

    Full Text Available In this paper we propose a Bayesian approach to solve the inference problem with restriction on parameters, regarding to nonlinear models used to represent the hypsometric relationship in clones of Eucalyptus sp. The Bayesian estimates are calculated using Monte Carlo Markov Chain (MCMC method. The proposed method was applied to different groups of actual data from which two were selected to show the results. These results were compared to the results achieved by the minimum square method, highlighting the superiority of the Bayesian approach, since this approach always generate the biologically consistent results for hipsometric relationship.

  10. An Orthotopic Mouse Model of Spontaneous Breast Cancer Metastasis.

    Science.gov (United States)

    Paschall, Amy V; Liu, Kebin

    2016-01-01

    Metastasis is the primary cause of mortality of breast cancer patients. The mechanism underlying cancer cell metastasis, including breast cancer metastasis, is largely unknown and is a focus in cancer research. Various breast cancer spontaneous metastasis mouse models have been established. Here, we report a simplified procedure to establish orthotopic transplanted breast cancer primary tumor and resultant spontaneous metastasis that mimic human breast cancer metastasis. Combined with the bioluminescence live tumor imaging, this mouse model allows tumor growth and progression kinetics to be monitored and quantified. In this model, a low dose (1 x 10(4) cells) of 4T1-Luc breast cancer cells was injected into BALB/c mouse mammary fat pad using a tuberculin syringe. Mice were injected with luciferin and imaged at various time points using a bioluminescent imaging system. When the primary tumors grew to the size limit as in the IACUC-approved protocol (approximately 30 days), mice were anesthetized under constant flow of 2% isoflurane and oxygen. The tumor area was sterilized with 70% ethanol. The mouse skin around the tumor was excised to expose the tumor which was removed with a pair of sterile scissors. Removal of the primary tumor extends the survival of the 4T-1 tumor-bearing mice for one month. The mice were then repeatedly imaged for metastatic tumor spreading to distant organs. Therapeutic agents can be administered to suppress tumor metastasis at this point. This model is simple and yet sensitive in quantifying breast cancer cell growth in the primary site and progression kinetics to distant organs, and thus is an excellent model for studying breast cancer growth and progression, and for testing anti-metastasis therapeutic and immunotherapeutic agents in vivo. PMID:27584043

  11. Optimization of parameters for fitting linear accelerator photon beams using a modified CBEAM model

    Energy Technology Data Exchange (ETDEWEB)

    Ayyangar, K.; Daftari, I.; Palta, J.; Suntharalingam, N. (Thomas Jefferson University Hospital, Department of Radiation Oncology and Nuclear Medicine, Philadelphia, Pennsylvania 19107 (US))

    1989-11-01

    Measured beam profiles and central-axis depth-dose data for 6- and 25-MV photon beams are used to generate a dose matrix which represents the full beam. A corresponding dose matrix is also calculated using the modified CBEAM model. The calculational model uses the usual set of three parameters to define the intensity at beam edges and the parameter that accounts for collimator transmission. An additional set of three parameters is used for the primary profile factor, expressed as a function of distance from the central axis. An optimization program has been adapted to automatically adjust these parameters to minimize the {chi}{sup 2} between the measured and calculated data. The average values of the parameters for small (6{times}6 cm{sup 2}), medium (10{times}10 cm{sup 2}), and large (20{times}20 cm{sup 2}) field sizes are found to represent the beam adequately for all field sizes. The calculated and the measured doses at any point agree to within 2% for any field size in the range 4{times}4 to 40{times}40 cm{sup 2}.

  12. Assessing the fit of biotic ligand model validation data in a risk management decision context.

    Science.gov (United States)

    McLaughlin, Douglas B

    2015-10-01

    Biotic ligand models (BLMs) have advanced the ability to predict the concentrations of metals in surface waters likely to harm aquatic organisms. BLMs have been developed for several metals including Cu, Zn, Cd, and Ag. Additionally, the US Environmental Protection Agency has published guidance on the use of a BLM to develop water quality criteria for Cu. To validate the predictive performance of many BLMs, model predictions based on test water quality have been compared with corresponding laboratory toxicity measurements. Validation results are typically described in the published literature in terms of the proportion of predicted effect concentrations that fall within a factor of 2 of measured values. In this article, an alternative is presented using a receiver operating characteristics approach and regression prediction limit analyses, quantifying the probabilities of true and false predictions of excess toxicity risk based on toxic unit calculations and a risk management threshold of 1. The approaches are applied to a published Zn BLM and 3 simulated data sets that reflect attributes of other published BLM validation data. The overall accuracy of the unified Zn BLM is estimated to be 80% to 90%, and analyses of simulated data suggest a similar level of accuracy for other published BLMs. Further application of these validation methods to other BLMs may provide more complete and transparent information on their possible predictive value when used in the management of risks due to aqueous metals. PMID:25779880

  13. A microengineered pathophysiological model of early-stage breast cancer.

    Science.gov (United States)

    Choi, Yoonseok; Hyun, Eunjeh; Seo, Jeongyun; Blundell, Cassidy; Kim, Hee Chan; Lee, Eunhee; Lee, Su Hyun; Moon, Aree; Moon, Woo Kyung; Huh, Dongeun

    2015-08-21

    A mounting body of evidence in cancer research suggests that the local microenvironment of tumor cells has a profound influence on cancer progression and metastasis. In vitro studies on the tumor microenvironment and its pharmacological modulation, however, are often hampered by the technical challenges associated with creating physiological cell culture environments that integrate cancer cells with the key components of their native niche such as neighboring cells and extracellular matrix (ECM) to mimic complex microarchitecture of cancerous tissue. Using early-stage breast cancer as a model disease, here we describe a biomimetic microengineering strategy to reconstitute three-dimensional (3D) structural organization and microenvironment of breast tumors in human cell-based in vitro models. Specifically, we developed a microsystem that enabled co-culture of breast tumor spheroids with human mammary ductal epithelial cells and mammary fibroblasts in a compartmentalized 3D microfluidic device to replicate microarchitecture of breast ductal carcinoma in situ (DCIS). We also explored the potential of this breast cancer-on-a-chip system as a drug screening platform by evaluating the efficacy and toxicity of an anticancer drug (paclitaxel). Our microengineered disease model represents the first critical step towards recapitulating pathophysiological complexity of breast cancer, and may serve as an enabling tool to systematically examine the contribution of the breast cancer microenvironment to the progression of DCIS to an invasive form of the disease. PMID:26158500

  14. STATISTICAL EVALUATION OF FITTING ACCURACY OF GLOBAL AND LOCAL DIGITAL ELEVATION MODELS IN IRAN

    Directory of Open Access Journals (Sweden)

    F. Alidoost

    2013-09-01

    Full Text Available Digital Elevation Models (DEMs are one of the most important data for various applications such as hydrological studies, topography mapping and ortho image generation. There are well-known DEMs of the whole world that represent the terrain's surface at variable resolution and they are also freely available for 99% of the globe. However, it is necessary to assess the quality of the global DEMs for the regional scale applications.These models are evaluated by differencing with other reference DEMs or ground control points (GCPs in order to estimate the quality and accuracy parameters over different land cover types. In this paper, a comparison of ASTER GDEM ver2, SRTM DEM with more than 800 reference GCPs and also with a local elevation model over the area of Iran is presented. This study investigates DEM’s characteristics such as systematic error (bias, vertical accuracy and outliers for DEMs using both the usual (Mean error, Root Mean Square Error, Standard Deviation and the robust (Median, Normalized Median Absolute Deviation, Sample Quantiles descriptors. Also, the visual assessment tools are used to illustrate the quality of DEMs, such as normalized histograms and Q-Q plots. The results of the study confirmed that there is a negative elevation bias of approximately 5 meters of GDEM ver2. The measured RMSE and NMAD for elevation differences of GDEM-GCPs are 7.1 m and 3.2 m, respectively, while these values for SRTM and GCPs are 9.0 m and 4.4 m. On the other hand, in comparison with the local DEM, GDEM ver2 exhibits the RMSE of about 6.7 m, a little higher than the RMSE of SRTM (5.1 m.The results of height difference classification and other statistical analysis of GDEM ver2-local DEM and SRTM-local DEM reveal that SRTM is slightly more accurate than GDEM ver2. Accordingly, SRTM has no noticeable bias and shift from Local DEM and they have more consistency to each other, while GDEM ver2 has always a negative bias.

  15. The conceptual basis of mathematics in cardiology IV: statistics and model fitting.

    Science.gov (United States)

    Bates, Jason H T; Sobel, Burton E

    2003-06-01

    This is the fourth in a series of four articles developed for the readers of Coronary Artery Disease. Without language ideas cannot be articulated. What may not be so immediately obvious is that they cannot be formulated either. One of the essential languages of cardiology is mathematics. Unfortunately, medical education does not emphasize, and in fact, often neglects empowering physicians to think mathematically. Reference to statistics, conditional probability, multicompartmental modeling, algebra, calculus and transforms is common but often without provision of genuine conceptual understanding. At the University of Vermont College of Medicine, Professor Bates developed a course designed to address these deficiencies. The course covered mathematical principles pertinent to clinical cardiovascular and pulmonary medicine and research. It focused on fundamental concepts to facilitate formulation and grasp of ideas. This series of four articles was developed to make the material available for a wider audience. The articles will be published sequentially in Coronary Artery Disease. Beginning with fundamental axioms and basic algebraic manipulations they address algebra, function and graph theory, real and complex numbers, calculus and differential equations, mathematical modeling, linear system theory and integral transforms and statistical theory. The principles and concepts they address provide the foundation needed for in-depth study of any of these topics. Perhaps of even more importance, they should empower cardiologists and cardiovascular researchers to utilize the language of mathematics in assessing the phenomena of immediate pertinence to diagnosis, pathophysiology and therapeutics. The presentations are interposed with queries (by Coronary Artery Disease abbreviated as CAD) simulating the nature of interactions that occurred during the course itself. Each article concludes with one or more examples illustrating application of the concepts covered to

  16. Submission Form for Peer-Reviewed Cancer Risk Prediction Models

    Science.gov (United States)

    If you have information about a peer-reviewd cancer risk prediction model that you would like to be considered for inclusion on this list, submit as much information as possible through the form on this page.

  17. Score, pseudo-score and residual diagnostics for goodness-of-fit of spatial point process models

    DEFF Research Database (Denmark)

    Baddeley, Adrian; Rubak, Ege H.; Møller, Jesper

    We develop newtools for formal inference and informalmodel validation in the analysis of spatial point pattern data. The score test is generalised to a ‘pseudo-score’ test derived from Besag’s pseudolikelihood, and to a class of diagnostics based on point process residuals. The results lend...... theoretical support to the established practice of using functional summary statistics such as Ripley’s K-function, when testing for complete spatial randomness; and they provide new tools such as the compensator of the K-function for testing other fitted models. The results also support localisation methods...... such as the scan statistic and smoothed residual plots. Software for computing the diagnostics is provided....

  18. Simultaneous estimation of plasma parameters from spectroscopic data of neutral helium using least square fitting of CR-model

    Science.gov (United States)

    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.

  19. A MULTIVARIATE FIT LUMINOSITY FUNCTION AND WORLD MODEL FOR LONG GAMMA-RAY BURSTS

    Energy Technology Data Exchange (ETDEWEB)

    Shahmoradi, Amir, E-mail: amir@physics.utexas.edu [Institute for Fusion Studies, The University of Texas at Austin, TX 78712 (United States)

    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.

  20. A Comparison of Two-Stage Approaches for Fitting Nonlinear Ordinary Differential Equation Models with Mixed Effects.

    Science.gov (United States)

    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. PMID:27391255