Impact of bootstrap current and Landau-fluid closure on ELM crashes and transport

NASA Astrophysics Data System (ADS)

Chen, J. G.; Xu, X. Q.; Ma, C. H.; Lei, Y. A.

2018-05-01

Results presented here are from 6-field Landau-Fluid simulations using shifted circular cross-section tokamak equilibria on BOUT++ framework. Linear benchmark results imply that the collisional and collisionless Landau resonance closures make a little difference on linear growth rate spectra which are quite close to the results with the flux limited Spitzer-Härm parallel flux. Both linear and nonlinear simulations show that the plasma current profile plays dual roles on the peeling-ballooning modes that it can drive the low-n peeling modes and stabilize the high-n ballooning modes. For fixed total pressure and current, as the pedestal current decreases due to the bootstrap current which becomes smaller when the density (collisionality) increases, the operational point is shifted downwards vertically in the Jped - α diagram, resulting in threshold changes of different modes. The bootstrap current can slightly increase radial turbulence spreading range and enhance the energy and particle transports by increasing the perturbed amplitude and broadening cross-phase frequency distribution.

Technology Teaching or Mediated Learning, Part II, 1990s: Literacy Linkages and Intervention Contexts.

ERIC Educational Resources Information Center

Coufal, Kathy L.

2002-01-01

Themes during the 1990s included the bootstrapping effects between oral and literate language, importance of supporting emergent literacy, parallels between oral language impairment and academic failure, and challenges in facilitating language learning. This article addresses questions posed in Part I related to use of computer technology for…

The sound symbolism bootstrapping hypothesis for language acquisition and language evolution.

PubMed

Imai, Mutsumi; Kita, Sotaro

2014-09-19

Sound symbolism is a non-arbitrary relationship between speech sounds and meaning. We review evidence that, contrary to the traditional view in linguistics, sound symbolism is an important design feature of language, which affects online processing of language, and most importantly, language acquisition. We propose the sound symbolism bootstrapping hypothesis, claiming that (i) pre-verbal infants are sensitive to sound symbolism, due to a biologically endowed ability to map and integrate multi-modal input, (ii) sound symbolism helps infants gain referential insight for speech sounds, (iii) sound symbolism helps infants and toddlers associate speech sounds with their referents to establish a lexical representation and (iv) sound symbolism helps toddlers learn words by allowing them to focus on referents embedded in a complex scene, alleviating Quine's problem. We further explore the possibility that sound symbolism is deeply related to language evolution, drawing the parallel between historical development of language across generations and ontogenetic development within individuals. Finally, we suggest that sound symbolism bootstrapping is a part of a more general phenomenon of bootstrapping by means of iconic representations, drawing on similarities and close behavioural links between sound symbolism and speech-accompanying iconic gesture. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Comparison of bootstrap approaches for estimation of uncertainties of DTI parameters.

PubMed

Chung, SungWon; Lu, Ying; Henry, Roland G

2006-11-01

Bootstrap is an empirical non-parametric statistical technique based on data resampling that has been used to quantify uncertainties of diffusion tensor MRI (DTI) parameters, useful in tractography and in assessing DTI methods. The current bootstrap method (repetition bootstrap) used for DTI analysis performs resampling within the data sharing common diffusion gradients, requiring multiple acquisitions for each diffusion gradient. Recently, wild bootstrap was proposed that can be applied without multiple acquisitions. In this paper, two new approaches are introduced called residual bootstrap and repetition bootknife. We show that repetition bootknife corrects for the large bias present in the repetition bootstrap method and, therefore, better estimates the standard errors. Like wild bootstrap, residual bootstrap is applicable to single acquisition scheme, and both are based on regression residuals (called model-based resampling). Residual bootstrap is based on the assumption that non-constant variance of measured diffusion-attenuated signals can be modeled, which is actually the assumption behind the widely used weighted least squares solution of diffusion tensor. The performances of these bootstrap approaches were compared in terms of bias, variance, and overall error of bootstrap-estimated standard error by Monte Carlo simulation. We demonstrate that residual bootstrap has smaller biases and overall errors, which enables estimation of uncertainties with higher accuracy. Understanding the properties of these bootstrap procedures will help us to choose the optimal approach for estimating uncertainties that can benefit hypothesis testing based on DTI parameters, probabilistic fiber tracking, and optimizing DTI methods.

Standard Error Estimation of 3PL IRT True Score Equating with an MCMC Method

ERIC Educational Resources Information Center

Liu, Yuming; Schulz, E. Matthew; Yu, Lei

2008-01-01

A Markov chain Monte Carlo (MCMC) method and a bootstrap method were compared in the estimation of standard errors of item response theory (IRT) true score equating. Three test form relationships were examined: parallel, tau-equivalent, and congeneric. Data were simulated based on Reading Comprehension and Vocabulary tests of the Iowa Tests of…

Non-inductive current generation in fusion plasmas with turbulence

NASA Astrophysics Data System (ADS)

Wang, Weixing; Ethier, S.; Startsev, E.; Chen, J.; Hahm, T. S.; Yoo, M. G.

2017-10-01

It is found that plasma turbulence may strongly influence non-inductive current generation. This may have radical impact on various aspects of tokamak physics. Our simulation study employs a global gyrokinetic model coupling self-consistent neoclassical and turbulent dynamics with focus on electron current. Distinct phases in electron current generation are illustrated in the initial value simulation. In the early phase before turbulence develops, the electron bootstrap current is established in a time scale of a few electron collision times, which closely agrees with the neoclassical prediction. The second phase follows when turbulence begins to saturate, during which turbulent fluctuations are found to strongly affect electron current. The profile structure, amplitude and phase space structure of electron current density are all significantly modified relative to the neoclassical bootstrap current by the presence of turbulence. Both electron parallel acceleration and parallel residual stress drive are shown to play important roles in turbulence-induced current generation. The current density profile is modified in a way that correlates with the fluctuation intensity gradient through its effect on k//-symmetry breaking in fluctuation spectrum. Turbulence is shown to deduct (enhance) plasma self-generated current in low (high) collisionality regime, and the reduction of total electron current relative to the neoclassical bootstrap current increases as collisionality decreases. The implication of this result to the fully non-inductive current operation in steady state burning plasma regime should be investigated. Finally, significant non-inductive current is observed in flat pressure region, which is a nonlocal effect and results from turbulence spreading induced current diffusion. Work supported by U.S. DOE Contract DE-AC02-09-CH11466.

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

PubMed Central

Aberer, Andre J.; Krompass, Denis; Stamatakis, Alexandros

2013-01-01

Abstract The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive webservice implementing this algorithm. Compared with our previous method, the new algorithm is up to 4 orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world data sets, we show that our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116 334 taxa each. For simulated data sets, we show that when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum-likelihood trees that are topologically closer to the respective true trees. PMID:22962004

Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice.

PubMed

Aberer, Andre J; Krompass, Denis; Stamatakis, Alexandros

2013-01-01

The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive webservice implementing this algorithm. Compared with our previous method, the new algorithm is up to 4 orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world data sets, we show that our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116 334 taxa each. For simulated data sets, we show that when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum-likelihood trees that are topologically closer to the respective true trees.

Analysis of small sample size studies using nonparametric bootstrap test with pooled resampling method.

PubMed

Dwivedi, Alok Kumar; Mallawaarachchi, Indika; Alvarado, Luis A

2017-06-30

Experimental studies in biomedical research frequently pose analytical problems related to small sample size. In such studies, there are conflicting findings regarding the choice of parametric and nonparametric analysis, especially with non-normal data. In such instances, some methodologists questioned the validity of parametric tests and suggested nonparametric tests. In contrast, other methodologists found nonparametric tests to be too conservative and less powerful and thus preferred using parametric tests. Some researchers have recommended using a bootstrap test; however, this method also has small sample size limitation. We used a pooled method in nonparametric bootstrap test that may overcome the problem related with small samples in hypothesis testing. The present study compared nonparametric bootstrap test with pooled resampling method corresponding to parametric, nonparametric, and permutation tests through extensive simulations under various conditions and using real data examples. The nonparametric pooled bootstrap t-test provided equal or greater power for comparing two means as compared with unpaired t-test, Welch t-test, Wilcoxon rank sum test, and permutation test while maintaining type I error probability for any conditions except for Cauchy and extreme variable lognormal distributions. In such cases, we suggest using an exact Wilcoxon rank sum test. Nonparametric bootstrap paired t-test also provided better performance than other alternatives. Nonparametric bootstrap test provided benefit over exact Kruskal-Wallis test. We suggest using nonparametric bootstrap test with pooled resampling method for comparing paired or unpaired means and for validating the one way analysis of variance test results for non-normal data in small sample size studies. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Bootstrap investigation of the stability of a Cox regression model.

PubMed

Altman, D G; Andersen, P K

1989-07-01

We describe a bootstrap investigation of the stability of a Cox proportional hazards regression model resulting from the analysis of a clinical trial of azathioprine versus placebo in patients with primary biliary cirrhosis. We have considered stability to refer both to the choice of variables included in the model and, more importantly, to the predictive ability of the model. In stepwise Cox regression analyses of 100 bootstrap samples using 17 candidate variables, the most frequently selected variables were those selected in the original analysis, and no other important variable was identified. Thus there was no reason to doubt the model obtained in the original analysis. For each patient in the trial, bootstrap confidence intervals were constructed for the estimated probability of surviving two years. It is shown graphically that these intervals are markedly wider than those obtained from the original model.

Turbulence Evolution and Shock Acceleration of Solar Energetic Particles

NASA Technical Reports Server (NTRS)

Chee, Ng K.

2007-01-01

We model the effects of self-excitation/damping and shock transmission of Alfven waves on solar-energetic-particle (SEP) acceleration at a coronal-mass-ejection (CME) driven parallel shock. SEP-excited outward upstream waves speedily bootstrap acceleration. Shock transmission further raises the SEP-excited wave intensities at high wavenumbers but lowers them at low wavenumbers through wavenumber shift. Downstream, SEP excitation of inward waves and damping of outward waves tend to slow acceleration. Nevertheless, > 2000 km/s parallel shocks at approx. 3.5 solar radii can accelerate SEPs to 100 MeV in < 5 minutes.

A Resampling Analysis of Federal Family Assistance Program Quality Control Data: An Application of the Bootstrap.

ERIC Educational Resources Information Center

Hand, Michael L.

1990-01-01

Use of the bootstrap resampling technique (BRT) is assessed in its application to resampling analysis associated with measurement of payment allocation errors by federally funded Family Assistance Programs. The BRT is applied to a food stamp quality control database in Oregon. This analysis highlights the outlier-sensitivity of the…

Bootstrap Confidence Intervals for Ordinary Least Squares Factor Loadings and Correlations in Exploratory Factor Analysis

ERIC Educational Resources Information Center

Zhang, Guangjian; Preacher, Kristopher J.; Luo, Shanhong

2010-01-01

This article is concerned with using the bootstrap to assign confidence intervals for rotated factor loadings and factor correlations in ordinary least squares exploratory factor analysis. Coverage performances of "SE"-based intervals, percentile intervals, bias-corrected percentile intervals, bias-corrected accelerated percentile…

How bootstrap can help in forecasting time series with more than one seasonal pattern

NASA Astrophysics Data System (ADS)

Cordeiro, Clara; Neves, M. Manuela

2012-09-01

The search for the future is an appealing challenge in time series analysis. The diversity of forecasting methodologies is inevitable and is still in expansion. Exponential smoothing methods are the launch platform for modelling and forecasting in time series analysis. Recently this methodology has been combined with bootstrapping revealing a good performance. The algorithm (Boot. EXPOS) using exponential smoothing and bootstrap methodologies, has showed promising results for forecasting time series with one seasonal pattern. In case of more than one seasonal pattern, the double seasonal Holt-Winters methods and the exponential smoothing methods were developed. A new challenge was now to combine these seasonal methods with bootstrap and carry over a similar resampling scheme used in Boot. EXPOS procedure. The performance of such partnership will be illustrated for some well-know data sets existing in software.

Bootstrap-based methods for estimating standard errors in Cox's regression analyses of clustered event times.

PubMed

Xiao, Yongling; Abrahamowicz, Michal

2010-03-30

We propose two bootstrap-based methods to correct the standard errors (SEs) from Cox's model for within-cluster correlation of right-censored event times. The cluster-bootstrap method resamples, with replacement, only the clusters, whereas the two-step bootstrap method resamples (i) the clusters, and (ii) individuals within each selected cluster, with replacement. In simulations, we evaluate both methods and compare them with the existing robust variance estimator and the shared gamma frailty model, which are available in statistical software packages. We simulate clustered event time data, with latent cluster-level random effects, which are ignored in the conventional Cox's model. For cluster-level covariates, both proposed bootstrap methods yield accurate SEs, and type I error rates, and acceptable coverage rates, regardless of the true random effects distribution, and avoid serious variance under-estimation by conventional Cox-based standard errors. However, the two-step bootstrap method over-estimates the variance for individual-level covariates. We also apply the proposed bootstrap methods to obtain confidence bands around flexible estimates of time-dependent effects in a real-life analysis of cluster event times.

A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0

PubMed Central

Bazinet, Adam L.; Zwickl, Derrick J.; Cummings, Michael P.

2014-01-01

We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum-likelihood phylogenetic analysis powered by grid computing. The gateway features a garli 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The garli web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic results. Although the garli web service has been used by the research community for over three years, here we formally announce the availability of the service, describe its capabilities, highlight new features and recent improvements, and provide details about how the grid system efficiently delivers high-quality phylogenetic results. [garli, gateway, grid computing, maximum likelihood, molecular evolution portal, phylogenetics, web service.] PMID:24789072

A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0.

PubMed

Bazinet, Adam L; Zwickl, Derrick J; Cummings, Michael P

2014-09-01

We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum-likelihood phylogenetic analysis powered by grid computing. The gateway features a garli 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The garli web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic results. Although the garli web service has been used by the research community for over three years, here we formally announce the availability of the service, describe its capabilities, highlight new features and recent improvements, and provide details about how the grid system efficiently delivers high-quality phylogenetic results. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Exploring the Replicability of a Study's Results: Bootstrap Statistics for the Multivariate Case.

ERIC Educational Resources Information Center

Thompson, Bruce

1995-01-01

Use of the bootstrap method in a canonical correlation analysis to evaluate the replicability of a study's results is illustrated. More confidence may be vested in research results that replicate. (SLD)

Probabilistic sensitivity analysis incorporating the bootstrap: an example comparing treatments for the eradication of Helicobacter pylori.

PubMed

Pasta, D J; Taylor, J L; Henning, J M

1999-01-01

Decision-analytic models are frequently used to evaluate the relative costs and benefits of alternative therapeutic strategies for health care. Various types of sensitivity analysis are used to evaluate the uncertainty inherent in the models. Although probabilistic sensitivity analysis is more difficult theoretically and computationally, the results can be much more powerful and useful than deterministic sensitivity analysis. The authors show how a Monte Carlo simulation can be implemented using standard software to perform a probabilistic sensitivity analysis incorporating the bootstrap. The method is applied to a decision-analytic model evaluating the cost-effectiveness of Helicobacter pylori eradication. The necessary steps are straightforward and are described in detail. The use of the bootstrap avoids certain difficulties encountered with theoretical distributions. The probabilistic sensitivity analysis provided insights into the decision-analytic model beyond the traditional base-case and deterministic sensitivity analyses and should become the standard method for assessing sensitivity.

A Class of Population Covariance Matrices in the Bootstrap Approach to Covariance Structure Analysis

ERIC Educational Resources Information Center

Yuan, Ke-Hai; Hayashi, Kentaro; Yanagihara, Hirokazu

2007-01-01

Model evaluation in covariance structure analysis is critical before the results can be trusted. Due to finite sample sizes and unknown distributions of real data, existing conclusions regarding a particular statistic may not be applicable in practice. The bootstrap procedure automatically takes care of the unknown distribution and, for a given…

Insight from uncertainty: bootstrap-derived diffusion metrics differentially predict memory function among older adults.

PubMed

Vorburger, Robert S; Habeck, Christian G; Narkhede, Atul; Guzman, Vanessa A; Manly, Jennifer J; Brickman, Adam M

2016-01-01

Diffusion tensor imaging suffers from an intrinsic low signal-to-noise ratio. Bootstrap algorithms have been introduced to provide a non-parametric method to estimate the uncertainty of the measured diffusion parameters. To quantify the variability of the principal diffusion direction, bootstrap-derived metrics such as the cone of uncertainty have been proposed. However, bootstrap-derived metrics are not independent of the underlying diffusion profile. A higher mean diffusivity causes a smaller signal-to-noise ratio and, thus, increases the measurement uncertainty. Moreover, the goodness of the tensor model, which relies strongly on the complexity of the underlying diffusion profile, influences bootstrap-derived metrics as well. The presented simulations clearly depict the cone of uncertainty as a function of the underlying diffusion profile. Since the relationship of the cone of uncertainty and common diffusion parameters, such as the mean diffusivity and the fractional anisotropy, is not linear, the cone of uncertainty has a different sensitivity. In vivo analysis of the fornix reveals the cone of uncertainty to be a predictor of memory function among older adults. No significant correlation occurs with the common diffusion parameters. The present work not only demonstrates the cone of uncertainty as a function of the actual diffusion profile, but also discloses the cone of uncertainty as a sensitive predictor of memory function. Future studies should incorporate bootstrap-derived metrics to provide more comprehensive analysis.

Semantic Drift in Espresso-style Bootstrapping: Graph-theoretic Analysis and Evaluation in Word Sense Disambiguation

NASA Astrophysics Data System (ADS)

Komachi, Mamoru; Kudo, Taku; Shimbo, Masashi; Matsumoto, Yuji

Bootstrapping has a tendency, called semantic drift, to select instances unrelated to the seed instances as the iteration proceeds. We demonstrate the semantic drift of Espresso-style bootstrapping has the same root as the topic drift of Kleinberg's HITS, using a simplified graph-based reformulation of bootstrapping. We confirm that two graph-based algorithms, the von Neumann kernels and the regularized Laplacian, can reduce the effect of semantic drift in the task of word sense disambiguation (WSD) on Senseval-3 English Lexical Sample Task. Proposed algorithms achieve superior performance to Espresso and previous graph-based WSD methods, even though the proposed algorithms have less parameters and are easy to calibrate.

Bootstrap Methods: A Very Leisurely Look.

ERIC Educational Resources Information Center

Hinkle, Dennis E.; Winstead, Wayland H.

The Bootstrap method, a computer-intensive statistical method of estimation, is illustrated using a simple and efficient Statistical Analysis System (SAS) routine. The utility of the method for generating unknown parameters, including standard errors for simple statistics, regression coefficients, discriminant function coefficients, and factor…

Long multiplet bootstrap

NASA Astrophysics Data System (ADS)

Cornagliotto, Martina; Lemos, Madalena; Schomerus, Volker

2017-10-01

Applications of the bootstrap program to superconformal field theories promise unique new insights into their landscape and could even lead to the discovery of new models. Most existing results of the superconformal bootstrap were obtained form correlation functions of very special fields in short (BPS) representations of the superconformal algebra. Our main goal is to initiate a superconformal bootstrap for long multiplets, one that exploits all constraints from superprimaries and their descendants. To this end, we work out the Casimir equations for four-point correlators of long multiplets of the two-dimensional global N=2 superconformal algebra. After constructing the full set of conformal blocks we discuss two different applications. The first one concerns two-dimensional (2,0) theories. The numerical bootstrap analysis we perform serves a twofold purpose, as a feasibility study of our long multiplet bootstrap and also as an exploration of (2,0) theories. A second line of applications is directed towards four-dimensional N=3 SCFTs. In this context, our results imply a new bound c≥ 13/24 for the central charge of such models, which we argue cannot be saturated by an interacting SCFT.

Measuring Efficiency of Tunisian Schools in the Presence of Quasi-Fixed Inputs: A Bootstrap Data Envelopment Analysis Approach

ERIC Educational Resources Information Center

Essid, Hedi; Ouellette, Pierre; Vigeant, Stephane

2010-01-01

The objective of this paper is to measure the efficiency of high schools in Tunisia. We use a statistical data envelopment analysis (DEA)-bootstrap approach with quasi-fixed inputs to estimate the precision of our measure. To do so, we developed a statistical model serving as the foundation of the data generation process (DGP). The DGP is…

Simulating realistic predator signatures in quantitative fatty acid signature analysis

USGS Publications Warehouse

Bromaghin, Jeffrey F.

2015-01-01

Diet estimation is an important field within quantitative ecology, providing critical insights into many aspects of ecology and community dynamics. Quantitative fatty acid signature analysis (QFASA) is a prominent method of diet estimation, particularly for marine mammal and bird species. Investigators using QFASA commonly use computer simulation to evaluate statistical characteristics of diet estimators for the populations they study. Similar computer simulations have been used to explore and compare the performance of different variations of the original QFASA diet estimator. In both cases, computer simulations involve bootstrap sampling prey signature data to construct pseudo-predator signatures with known properties. However, bootstrap sample sizes have been selected arbitrarily and pseudo-predator signatures therefore may not have realistic properties. I develop an algorithm to objectively establish bootstrap sample sizes that generates pseudo-predator signatures with realistic properties, thereby enhancing the utility of computer simulation for assessing QFASA estimator performance. The algorithm also appears to be computationally efficient, resulting in bootstrap sample sizes that are smaller than those commonly used. I illustrate the algorithm with an example using data from Chukchi Sea polar bears (Ursus maritimus) and their marine mammal prey. The concepts underlying the approach may have value in other areas of quantitative ecology in which bootstrap samples are post-processed prior to their use.

The Novaya Zemlya Event of 31 December 1992 and Seismic Identification Issues: Annual Seismic Research Symposium (15th) Held in Vail, Colorado on 8-10 September 1993

DTIC Science & Technology

1993-09-10

1993). A bootstrap generalizedlikelihood ratio test in discriminant analysis, Proc. 15th Annual Seismic Research Symposium, in press. I Hedlin, M., J... ratio indicate that the event does not belong to the first class. The bootstrap technique is used here as well to set the critical value of the test ...Methodist University. Baek, J., H. L. Gray, W. A. Woodward and M.D. Fisk (1993). A Bootstrap Generalized Likelihood Ratio Test in Discriminant

Bootsie: estimation of coefficient of variation of AFLP data by bootstrap analysis

USDA-ARS?s Scientific Manuscript database

Bootsie is an English-native replacement for ASG Coelho’s “DBOOT” utility for estimating coefficient of variation of a population of AFLP marker data using bootstrapping. Bootsie improves on DBOOT by supporting batch processing, time-to-completion estimation, built-in graphs, and a suite of export t...

Measuring and Benchmarking Technical Efficiency of Public Hospitals in Tianjin, China: A Bootstrap-Data Envelopment Analysis Approach.

PubMed

Li, Hao; Dong, Siping

2015-01-01

China has long been stuck in applying traditional data envelopment analysis (DEA) models to measure technical efficiency of public hospitals without bias correction of efficiency scores. In this article, we have introduced the Bootstrap-DEA approach from the international literature to analyze the technical efficiency of public hospitals in Tianjin (China) and tried to improve the application of this method for benchmarking and inter-organizational learning. It is found that the bias corrected efficiency scores of Bootstrap-DEA differ significantly from those of the traditional Banker, Charnes, and Cooper (BCC) model, which means that Chinese researchers need to update their DEA models for more scientific calculation of hospital efficiency scores. Our research has helped shorten the gap between China and the international world in relative efficiency measurement and improvement of hospitals. It is suggested that Bootstrap-DEA be widely applied into afterward research to measure relative efficiency and productivity of Chinese hospitals so as to better serve for efficiency improvement and related decision making. © The Author(s) 2015.

Using Cluster Bootstrapping to Analyze Nested Data With a Few Clusters.

PubMed

Huang, Francis L

2018-04-01

Cluster randomized trials involving participants nested within intact treatment and control groups are commonly performed in various educational, psychological, and biomedical studies. However, recruiting and retaining intact groups present various practical, financial, and logistical challenges to evaluators and often, cluster randomized trials are performed with a low number of clusters (~20 groups). Although multilevel models are often used to analyze nested data, researchers may be concerned of potentially biased results due to having only a few groups under study. Cluster bootstrapping has been suggested as an alternative procedure when analyzing clustered data though it has seen very little use in educational and psychological studies. Using a Monte Carlo simulation that varied the number of clusters, average cluster size, and intraclass correlations, we compared standard errors using cluster bootstrapping with those derived using ordinary least squares regression and multilevel models. Results indicate that cluster bootstrapping, though more computationally demanding, can be used as an alternative procedure for the analysis of clustered data when treatment effects at the group level are of primary interest. Supplementary material showing how to perform cluster bootstrapped regressions using R is also provided.

Linear regression in astronomy. II

NASA Technical Reports Server (NTRS)

Feigelson, Eric D.; Babu, Gutti J.

1992-01-01

A wide variety of least-squares linear regression procedures used in observational astronomy, particularly investigations of the cosmic distance scale, are presented and discussed. The classes of linear models considered are (1) unweighted regression lines, with bootstrap and jackknife resampling; (2) regression solutions when measurement error, in one or both variables, dominates the scatter; (3) methods to apply a calibration line to new data; (4) truncated regression models, which apply to flux-limited data sets; and (5) censored regression models, which apply when nondetections are present. For the calibration problem we develop two new procedures: a formula for the intercept offset between two parallel data sets, which propagates slope errors from one regression to the other; and a generalization of the Working-Hotelling confidence bands to nonstandard least-squares lines. They can provide improved error analysis for Faber-Jackson, Tully-Fisher, and similar cosmic distance scale relations.

The economics of bootstrapping space industries - Development of an analytic computer model

NASA Technical Reports Server (NTRS)

Goldberg, A. H.; Criswell, D. R.

1982-01-01

A simple economic model of 'bootstrapping' industrial growth in space and on the Moon is presented. An initial space manufacturing facility (SMF) is assumed to consume lunar materials to enlarge the productive capacity in space. After reaching a predetermined throughput, the enlarged SMF is devoted to products which generate revenue continuously in proportion to the accumulated output mass (such as space solar power stations). Present discounted value and physical estimates for the general factors of production (transport, capital efficiency, labor, etc.) are combined to explore optimum growth in terms of maximized discounted revenues. It is found that 'bootstrapping' reduces the fractional cost to a space industry of transport off-Earth, permits more efficient use of a given transport fleet. It is concluded that more attention should be given to structuring 'bootstrapping' scenarios in which 'learning while doing' can be more fully incorporated in program analysis.

Towards a bootstrap approach to higher orders of epsilon expansion

NASA Astrophysics Data System (ADS)

Dey, Parijat; Kaviraj, Apratim

2018-02-01

We employ a hybrid approach in determining the anomalous dimension and OPE coefficient of higher spin operators in the Wilson-Fisher theory. First we do a large spin analysis for CFT data where we use results obtained from the usual and the Mellin bootstrap and also from Feynman diagram literature. This gives new predictions at O( ɛ 4) and O( ɛ 5) for anomalous dimensions and OPE coefficients, and also provides a cross-check for the results from Mellin bootstrap. These higher orders get contributions from all higher spin operators in the crossed channel. We also use the bootstrap in Mellin space method for ϕ 3 in d = 6 - ɛ CFT where we calculate general higher spin OPE data. We demonstrate a higher loop order calculation in this approach by summing over contributions from higher spin operators of the crossed channel in the same spirit as before.

Three-dimensional magnetohydrodynamic equilibrium of quiescent H-modes in tokamak systems

NASA Astrophysics Data System (ADS)

Cooper, W. A.; Graves, J. P.; Duval, B. P.; Sauter, O.; Faustin, J. M.; Kleiner, A.; Lanthaler, S.; Patten, H.; Raghunathan, M.; Tran, T.-M.; Chapman, I. T.; Ham, C. J.

2016-06-01

Three dimensional free boundary magnetohydrodynamic equilibria that recover saturated ideal kink/peeling structures are obtained numerically. Simulations that model the JET tokamak at fixed < β > =1.7% with a large edge bootstrap current that flattens the q-profile near the plasma boundary demonstrate that a radial parallel current density ribbon with a dominant m /n  =  5/1 Fourier component at {{I}\\text{t}}=2.2 MA develops into a broadband spectrum when the toroidal current I t is increased to 2.5 MA.

Evaluating sufficient similarity for drinking-water disinfection by-product (DBP) mixtures with bootstrap hypothesis test procedures.

PubMed

Feder, Paul I; Ma, Zhenxu J; Bull, Richard J; Teuschler, Linda K; Rice, Glenn

2009-01-01

In chemical mixtures risk assessment, the use of dose-response data developed for one mixture to estimate risk posed by a second mixture depends on whether the two mixtures are sufficiently similar. While evaluations of similarity may be made using qualitative judgments, this article uses nonparametric statistical methods based on the "bootstrap" resampling technique to address the question of similarity among mixtures of chemical disinfectant by-products (DBP) in drinking water. The bootstrap resampling technique is a general-purpose, computer-intensive approach to statistical inference that substitutes empirical sampling for theoretically based parametric mathematical modeling. Nonparametric, bootstrap-based inference involves fewer assumptions than parametric normal theory based inference. The bootstrap procedure is appropriate, at least in an asymptotic sense, whether or not the parametric, distributional assumptions hold, even approximately. The statistical analysis procedures in this article are initially illustrated with data from 5 water treatment plants (Schenck et al., 2009), and then extended using data developed from a study of 35 drinking-water utilities (U.S. EPA/AMWA, 1989), which permits inclusion of a greater number of water constituents and increased structure in the statistical models.

A factor analysis of the SSQ (Speech, Spatial, and Qualities of Hearing Scale).

PubMed

Akeroyd, Michael A; Guy, Fiona H; Harrison, Dawn L; Suller, Sharon L

2014-02-01

The speech, spatial, and qualities of hearing questionnaire (SSQ) is a self-report test of auditory disability. The 49 items ask how well a listener would do in many complex listening situations illustrative of real life. The scores on the items are often combined into the three main sections or into 10 pragmatic subscales. We report here a factor analysis of the SSQ that we conducted to further investigate its statistical properties and to determine its structure. Statistical factor analysis of questionnaire data, using parallel analysis to determine the number of factors to retain, oblique rotation of factors, and a bootstrap method to estimate the confidence intervals. 1220 people who have attended MRC IHR over the last decade. We found three clear factors, essentially corresponding to the three main sections of the SSQ. They are termed "speech understanding", "spatial perception", and "clarity, separation, and identification". Thirty-five of the SSQ questions were included in the three factors. There was partial evidence for a fourth factor, "effort and concentration", representing two more questions. These results aid in the interpretation and application of the SSQ and indicate potential methods for generating average scores.

Closure of the operator product expansion in the non-unitary bootstrap

DOE Office of Scientific and Technical Information (OSTI.GOV)

Esterlis, Ilya; Fitzpatrick, A. Liam; Ramirez, David M.

We use the numerical conformal bootstrap in two dimensions to search for finite, closed sub-algebras of the operator product expansion (OPE), without assuming unitarity. We find the minimal models as special cases, as well as additional lines of solutions that can be understood in the Coulomb gas formalism. All the solutions we find that contain the vacuum in the operator algebra are cases where the external operators of the bootstrap equation are degenerate operators, and we argue that this follows analytically from the expressions in arXiv:1202.4698 for the crossing matrices of Virasoro conformal blocks. Our numerical analysis is a specialmore » case of the “Gliozzi” bootstrap method, and provides a simpler setting in which to study technical challenges with the method. In the supplementary material, we provide a Mathematica notebook that automates the calculation of the crossing matrices and OPE coefficients for degenerate operators using the formulae of Dotsenko and Fateev.« less

Closure of the operator product expansion in the non-unitary bootstrap

DOE PAGES

Esterlis, Ilya; Fitzpatrick, A. Liam; Ramirez, David M.

2016-11-07

We use the numerical conformal bootstrap in two dimensions to search for finite, closed sub-algebras of the operator product expansion (OPE), without assuming unitarity. We find the minimal models as special cases, as well as additional lines of solutions that can be understood in the Coulomb gas formalism. All the solutions we find that contain the vacuum in the operator algebra are cases where the external operators of the bootstrap equation are degenerate operators, and we argue that this follows analytically from the expressions in arXiv:1202.4698 for the crossing matrices of Virasoro conformal blocks. Our numerical analysis is a specialmore » case of the “Gliozzi” bootstrap method, and provides a simpler setting in which to study technical challenges with the method. In the supplementary material, we provide a Mathematica notebook that automates the calculation of the crossing matrices and OPE coefficients for degenerate operators using the formulae of Dotsenko and Fateev.« less

Trends and Correlation Estimation in Climate Sciences: Effects of Timescale Errors

NASA Astrophysics Data System (ADS)

Mudelsee, M.; Bermejo, M. A.; Bickert, T.; Chirila, D.; Fohlmeister, J.; Köhler, P.; Lohmann, G.; Olafsdottir, K.; Scholz, D.

2012-12-01

Trend describes time-dependence in the first moment of a stochastic process, and correlation measures the linear relation between two random variables. Accurately estimating the trend and correlation, including uncertainties, from climate time series data in the uni- and bivariate domain, respectively, allows first-order insights into the geophysical process that generated the data. Timescale errors, ubiquitious in paleoclimatology, where archives are sampled for proxy measurements and dated, poses a problem to the estimation. Statistical science and the various applied research fields, including geophysics, have almost completely ignored this problem due to its theoretical almost-intractability. However, computational adaptations or replacements of traditional error formulas have become technically feasible. This contribution gives a short overview of such an adaptation package, bootstrap resampling combined with parametric timescale simulation. We study linear regression, parametric change-point models and nonparametric smoothing for trend estimation. We introduce pairwise-moving block bootstrap resampling for correlation estimation. Both methods share robustness against autocorrelation and non-Gaussian distributional shape. We shortly touch computing-intensive calibration of bootstrap confidence intervals and consider options to parallelize the related computer code. Following examples serve not only to illustrate the methods but tell own climate stories: (1) the search for climate drivers of the Agulhas Current on recent timescales, (2) the comparison of three stalagmite-based proxy series of regional, western German climate over the later part of the Holocene, and (3) trends and transitions in benthic oxygen isotope time series from the Cenozoic. Financial support by Deutsche Forschungsgemeinschaft (FOR 668, FOR 1070, MU 1595/4-1) and the European Commission (MC ITN 238512, MC ITN 289447) is acknowledged.

Interpersonal and intrapersonal factors as parallel independent mediators in the association between internalized HIV stigma and ART adherence

PubMed Central

Seghatol-Eslami, Victoria C.; Dark, Heather; Raper, James L.; Mugavero, Michael J.; Turan, Janet M.; Turan, Bulent

2016-01-01

Introduction People living with HIV (PLWH) need to adhere to antiretroviral therapy (ART) to achieve optimal health. One reason for ART non-adherence is HIV-related stigma. Objectives We aimed to examine whether HIV treatment self-efficacy (an intrapersonal mechanism) mediates the stigma – adherence association. We also examined whether self-efficacy and the concern about being seen while taking HIV medication (an interpersonal mechanism) are parallel mediators independent of each other. Methods 180 PLWH self-reported internalized HIV stigma, ART adherence, HIV treatment self-efficacy, and concerns about being seen while taking HIV medication. We calculated bias-corrected 95% confidence intervals (CIs) for indirect effects using bootstrapping to conduct mediation analyses. Results Adherence self-efficacy mediated the relationship between internalized stigma and ART adherence. Additionally, self-efficacy and concern about being seen while taking HIV medication uniquely mediated and explained almost all of the stigma – adherence association in independent paths (parallel mediation). Conclusion These results can inform intervention strategies to promote ART adherence. PMID:27926668

Acculturation, Income and Vegetable Consumption Behaviors Among Latino Adults in the U.S.: A Mediation Analysis with the Bootstrapping Technique.

PubMed

López, Erick B; Yamashita, Takashi

2017-02-01

This study examined whether household income mediates the relationship between acculturation and vegetable consumption among Latino adults in the U.S. Data from the 2009 to 2010 National Health and Nutrition Examination Survey were analyzed. Vegetable consumption index was created based on the frequencies of five kinds of vegetables intake. Acculturation was measured with the degree of English language use at home. Path model with bootstrapping technique was employed for mediation analysis. A significant partial mediation relationship was identified. Greater acculturation [95 % bias corrected bootstrap confident interval (BCBCI) = (0.02, 0.33)] was associated with the higher income and in turn, greater vegetable consumption. At the same time, greater acculturation was associated with lower vegetable consumption [95 % BCBCI = (-0.88, -0.07)]. Findings regarding the income as a mediator of the acculturation-dietary behavior relationship inform unique intervention programs and policy changes to address health disparities by race/ethnicity.

Monte Carlo based statistical power analysis for mediation models: methods and software.

PubMed

Zhang, Zhiyong

2014-12-01

The existing literature on statistical power analysis for mediation models often assumes data normality and is based on a less powerful Sobel test instead of the more powerful bootstrap test. This study proposes to estimate statistical power to detect mediation effects on the basis of the bootstrap method through Monte Carlo simulation. Nonnormal data with excessive skewness and kurtosis are allowed in the proposed method. A free R package called bmem is developed to conduct the power analysis discussed in this study. Four examples, including a simple mediation model, a multiple-mediator model with a latent mediator, a multiple-group mediation model, and a longitudinal mediation model, are provided to illustrate the proposed method.

Impact of Sampling Density on the Extent of HIV Clustering

PubMed Central

Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor

2014-01-01

Abstract Identifying and monitoring HIV clusters could be useful in tracking the leading edge of HIV transmission in epidemics. Currently, greater specificity in the definition of HIV clusters is needed to reduce confusion in the interpretation of HIV clustering results. We address sampling density as one of the key aspects of HIV cluster analysis. The proportion of viral sequences in clusters was estimated at sampling densities from 1.0% to 70%. A set of 1,248 HIV-1C env gp120 V1C5 sequences from a single community in Botswana was utilized in simulation studies. Matching numbers of HIV-1C V1C5 sequences from the LANL HIV Database were used as comparators. HIV clusters were identified by phylogenetic inference under bootstrapped maximum likelihood and pairwise distance cut-offs. Sampling density below 10% was associated with stochastic HIV clustering with broad confidence intervals. HIV clustering increased linearly at sampling density >10%, and was accompanied by narrowing confidence intervals. Patterns of HIV clustering were similar at bootstrap thresholds 0.7 to 1.0, but the extent of HIV clustering decreased with higher bootstrap thresholds. The origin of sampling (local concentrated vs. scattered global) had a substantial impact on HIV clustering at sampling densities ≥10%. Pairwise distances at 10% were estimated as a threshold for cluster analysis of HIV-1 V1C5 sequences. The node bootstrap support distribution provided additional evidence for 10% sampling density as the threshold for HIV cluster analysis. The detectability of HIV clusters is substantially affected by sampling density. A minimal genotyping density of 10% and sampling density of 50–70% are suggested for HIV-1 V1C5 cluster analysis. PMID:25275430

Image analysis of representative food structures: application of the bootstrap method.

PubMed

Ramírez, Cristian; Germain, Juan C; Aguilera, José M

2009-08-01

Images (for example, photomicrographs) are routinely used as qualitative evidence of the microstructure of foods. In quantitative image analysis it is important to estimate the area (or volume) to be sampled, the field of view, and the resolution. The bootstrap method is proposed to estimate the size of the sampling area as a function of the coefficient of variation (CV(Bn)) and standard error (SE(Bn)) of the bootstrap taking sub-areas of different sizes. The bootstrap method was applied to simulated and real structures (apple tissue). For simulated structures, 10 computer-generated images were constructed containing 225 black circles (elements) and different coefficient of variation (CV(image)). For apple tissue, 8 images of apple tissue containing cellular cavities with different CV(image) were analyzed. Results confirmed that for simulated and real structures, increasing the size of the sampling area decreased the CV(Bn) and SE(Bn). Furthermore, there was a linear relationship between the CV(image) and CV(Bn) (.) For example, to obtain a CV(Bn) = 0.10 in an image with CV(image) = 0.60, a sampling area of 400 x 400 pixels (11% of whole image) was required, whereas if CV(image) = 1.46, a sampling area of 1000 x 100 pixels (69% of whole image) became necessary. This suggests that a large-size dispersion of element sizes in an image requires increasingly larger sampling areas or a larger number of images.

Combining Nordtest method and bootstrap resampling for measurement uncertainty estimation of hematology analytes in a medical laboratory.

PubMed

Cui, Ming; Xu, Lili; Wang, Huimin; Ju, Shaoqing; Xu, Shuizhu; Jing, Rongrong

2017-12-01

Measurement uncertainty (MU) is a metrological concept, which can be used for objectively estimating the quality of test results in medical laboratories. The Nordtest guide recommends an approach that uses both internal quality control (IQC) and external quality assessment (EQA) data to evaluate the MU. Bootstrap resampling is employed to simulate the unknown distribution based on the mathematical statistics method using an existing small sample of data, where the aim is to transform the small sample into a large sample. However, there have been no reports of the utilization of this method in medical laboratories. Thus, this study applied the Nordtest guide approach based on bootstrap resampling for estimating the MU. We estimated the MU for the white blood cell (WBC) count, red blood cell (RBC) count, hemoglobin (Hb), and platelets (Plt). First, we used 6months of IQC data and 12months of EQA data to calculate the MU according to the Nordtest method. Second, we combined the Nordtest method and bootstrap resampling with the quality control data and calculated the MU using MATLAB software. We then compared the MU results obtained using the two approaches. The expanded uncertainty results determined for WBC, RBC, Hb, and Plt using the bootstrap resampling method were 4.39%, 2.43%, 3.04%, and 5.92%, respectively, and 4.38%, 2.42%, 3.02%, and 6.00% with the existing quality control data (U [k=2]). For WBC, RBC, Hb, and Plt, the differences between the results obtained using the two methods were lower than 1.33%. The expanded uncertainty values were all less than the target uncertainties. The bootstrap resampling method allows the statistical analysis of the MU. Combining the Nordtest method and bootstrap resampling is considered a suitable alternative method for estimating the MU. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Governance and performance: the performance of Dutch hospitals explained by governance characteristics.

PubMed

Blank, Jos L T; van Hulst, Bart Laurents

2011-10-01

This paper describes the efficiency of Dutch hospitals using the Data Envelopment Analysis (DEA) method with bootstrapping. In particular, the analysis focuses on accounting for cost inefficiency measures on the part of hospital corporate governance. We use bootstrap techniques, as introduced by Simar and Wilson (J. Econom. 136(1):31-64, 2007), in order to obtain more efficient estimates of the effects of governance on the efficiency. The results show that part of the cost efficiency can be explained with governance. In particular we find that a higher remuneration of the board as well as a higher remuneration of the supervisory board does not implicate better performance.

Comparison of Bootstrapping and Markov Chain Monte Carlo for Copula Analysis of Hydrological Droughts

NASA Astrophysics Data System (ADS)

Yang, P.; Ng, T. L.; Yang, W.

2015-12-01

Effective water resources management depends on the reliable estimation of the uncertainty of drought events. Confidence intervals (CIs) are commonly applied to quantify this uncertainty. A CI seeks to be at the minimal length necessary to cover the true value of the estimated variable with the desired probability. In drought analysis where two or more variables (e.g., duration and severity) are often used to describe a drought, copulas have been found suitable for representing the joint probability behavior of these variables. However, the comprehensive assessment of the parameter uncertainties of copulas of droughts has been largely ignored, and the few studies that have recognized this issue have not explicitly compared the various methods to produce the best CIs. Thus, the objective of this study to compare the CIs generated using two widely applied uncertainty estimation methods, bootstrapping and Markov Chain Monte Carlo (MCMC). To achieve this objective, (1) the marginal distributions lognormal, Gamma, and Generalized Extreme Value, and the copula functions Clayton, Frank, and Plackett are selected to construct joint probability functions of two drought related variables. (2) The resulting joint functions are then fitted to 200 sets of simulated realizations of drought events with known distribution and extreme parameters and (3) from there, using bootstrapping and MCMC, CIs of the parameters are generated and compared. The effect of an informative prior on the CIs generated by MCMC is also evaluated. CIs are produced for different sample sizes (50, 100, and 200) of the simulated drought events for fitting the joint probability functions. Preliminary results assuming lognormal marginal distributions and the Clayton copula function suggest that for cases with small or medium sample sizes (~50-100), MCMC to be superior method if an informative prior exists. Where an informative prior is unavailable, for small sample sizes (~50), both bootstrapping and MCMC yield the same level of performance, and for medium sample sizes (~100), bootstrapping is better. For cases with a large sample size (~200), there is little difference between the CIs generated using bootstrapping and MCMC regardless of whether or not an informative prior exists.

A factor analysis of the SSQ (Speech, Spatial, and Qualities of Hearing Scale)

PubMed Central

2014-01-01

Objective The speech, spatial, and qualities of hearing questionnaire (SSQ) is a self-report test of auditory disability. The 49 items ask how well a listener would do in many complex listening situations illustrative of real life. The scores on the items are often combined into the three main sections or into 10 pragmatic subscales. We report here a factor analysis of the SSQ that we conducted to further investigate its statistical properties and to determine its structure. Design Statistical factor analysis of questionnaire data, using parallel analysis to determine the number of factors to retain, oblique rotation of factors, and a bootstrap method to estimate the confidence intervals. Study sample 1220 people who have attended MRC IHR over the last decade. Results We found three clear factors, essentially corresponding to the three main sections of the SSQ. They are termed “speech understanding”, “spatial perception”, and “clarity, separation, and identification”. Thirty-five of the SSQ questions were included in the three factors. There was partial evidence for a fourth factor, “effort and concentration”, representing two more questions. Conclusions These results aid in the interpretation and application of the SSQ and indicate potential methods for generating average scores. PMID:24417459

Applying causal mediation analysis to personality disorder research.

PubMed

Walters, Glenn D

2018-01-01

This article is designed to address fundamental issues in the application of causal mediation analysis to research on personality disorders. Causal mediation analysis is used to identify mechanisms of effect by testing variables as putative links between the independent and dependent variables. As such, it would appear to have relevance to personality disorder research. It is argued that proper implementation of causal mediation analysis requires that investigators take several factors into account. These factors are discussed under 5 headings: variable selection, model specification, significance evaluation, effect size estimation, and sensitivity testing. First, care must be taken when selecting the independent, dependent, mediator, and control variables for a mediation analysis. Some variables make better mediators than others and all variables should be based on reasonably reliable indicators. Second, the mediation model needs to be properly specified. This requires that the data for the analysis be prospectively or historically ordered and possess proper causal direction. Third, it is imperative that the significance of the identified pathways be established, preferably with a nonparametric bootstrap resampling approach. Fourth, effect size estimates should be computed or competing pathways compared. Finally, investigators employing the mediation method are advised to perform a sensitivity analysis. Additional topics covered in this article include parallel and serial multiple mediation designs, moderation, and the relationship between mediation and moderation. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

A comparison of bootstrap methods and an adjusted bootstrap approach for estimating the prediction error in microarray classification.

PubMed

Jiang, Wenyu; Simon, Richard

2007-12-20

This paper first provides a critical review on some existing methods for estimating the prediction error in classifying microarray data where the number of genes greatly exceeds the number of specimens. Special attention is given to the bootstrap-related methods. When the sample size n is small, we find that all the reviewed methods suffer from either substantial bias or variability. We introduce a repeated leave-one-out bootstrap (RLOOB) method that predicts for each specimen in the sample using bootstrap learning sets of size ln. We then propose an adjusted bootstrap (ABS) method that fits a learning curve to the RLOOB estimates calculated with different bootstrap learning set sizes. The ABS method is robust across the situations we investigate and provides a slightly conservative estimate for the prediction error. Even with small samples, it does not suffer from large upward bias as the leave-one-out bootstrap and the 0.632+ bootstrap, and it does not suffer from large variability as the leave-one-out cross-validation in microarray applications. Copyright (c) 2007 John Wiley & Sons, Ltd.

Kepler Planet Detection Metrics: Statistical Bootstrap Test

NASA Technical Reports Server (NTRS)

Jenkins, Jon M.; Burke, Christopher J.

2016-01-01

This document describes the data produced by the Statistical Bootstrap Test over the final three Threshold Crossing Event (TCE) deliveries to NExScI: SOC 9.1 (Q1Q16)1 (Tenenbaum et al. 2014), SOC 9.2 (Q1Q17) aka DR242 (Seader et al. 2015), and SOC 9.3 (Q1Q17) aka DR253 (Twicken et al. 2016). The last few years have seen significant improvements in the SOC science data processing pipeline, leading to higher quality light curves and more sensitive transit searches. The statistical bootstrap analysis results presented here and the numerical results archived at NASAs Exoplanet Science Institute (NExScI) bear witness to these software improvements. This document attempts to introduce and describe the main features and differences between these three data sets as a consequence of the software changes.

Speeding Up Non-Parametric Bootstrap Computations for Statistics Based on Sample Moments in Small/Moderate Sample Size Applications

PubMed Central

Chaibub Neto, Elias

2015-01-01

In this paper we propose a vectorized implementation of the non-parametric bootstrap for statistics based on sample moments. Basically, we adopt the multinomial sampling formulation of the non-parametric bootstrap, and compute bootstrap replications of sample moment statistics by simply weighting the observed data according to multinomial counts instead of evaluating the statistic on a resampled version of the observed data. Using this formulation we can generate a matrix of bootstrap weights and compute the entire vector of bootstrap replications with a few matrix multiplications. Vectorization is particularly important for matrix-oriented programming languages such as R, where matrix/vector calculations tend to be faster than scalar operations implemented in a loop. We illustrate the application of the vectorized implementation in real and simulated data sets, when bootstrapping Pearson’s sample correlation coefficient, and compared its performance against two state-of-the-art R implementations of the non-parametric bootstrap, as well as a straightforward one based on a for loop. Our investigations spanned varying sample sizes and number of bootstrap replications. The vectorized bootstrap compared favorably against the state-of-the-art implementations in all cases tested, and was remarkably/considerably faster for small/moderate sample sizes. The same results were observed in the comparison with the straightforward implementation, except for large sample sizes, where the vectorized bootstrap was slightly slower than the straightforward implementation due to increased time expenditures in the generation of weight matrices via multinomial sampling. PMID:26125965

NATbox: a network analysis toolbox in R.

PubMed

Chavan, Shweta S; Bauer, Michael A; Scutari, Marco; Nagarajan, Radhakrishnan

2009-10-08

There has been recent interest in capturing the functional relationships (FRs) from high-throughput assays using suitable computational techniques. FRs elucidate the working of genes in concert as a system as opposed to independent entities hence may provide preliminary insights into biological pathways and signalling mechanisms. Bayesian structure learning (BSL) techniques and its extensions have been used successfully for modelling FRs from expression profiles. Such techniques are especially useful in discovering undocumented FRs, investigating non-canonical signalling mechanisms and cross-talk between pathways. The objective of the present study is to develop a graphical user interface (GUI), NATbox: Network Analysis Toolbox in the language R that houses a battery of BSL algorithms in conjunction with suitable statistical tools for modelling FRs in the form of acyclic networks from gene expression profiles and their subsequent analysis. NATbox is a menu-driven open-source GUI implemented in the R statistical language for modelling and analysis of FRs from gene expression profiles. It provides options to (i) impute missing observations in the given data (ii) model FRs and network structure from gene expression profiles using a battery of BSL algorithms and identify robust dependencies using a bootstrap procedure, (iii) present the FRs in the form of acyclic graphs for visualization and investigate its topological properties using network analysis metrics, (iv) retrieve FRs of interest from published literature. Subsequently, use these FRs as structural priors in BSL (v) enhance scalability of BSL across high-dimensional data by parallelizing the bootstrap routines. NATbox provides a menu-driven GUI for modelling and analysis of FRs from gene expression profiles. By incorporating readily available functions from existing R-packages, it minimizes redundancy and improves reproducibility, transparency and sustainability, characteristic of open-source environments. NATbox is especially suited for interdisciplinary researchers and biologists with minimal programming experience and would like to use systems biology approaches without delving into the algorithmic aspects. The GUI provides appropriate parameter recommendations for the various menu options including default parameter choices for the user. NATbox can also prove to be a useful demonstration and teaching tool in graduate and undergraduate course in systems biology. It has been tested successfully under Windows and Linux operating systems. The source code along with installation instructions and accompanying tutorial can be found at http://bioinformatics.ualr.edu/natboxWiki/index.php/Main_Page.

Patient satisfaction after pulmonary resection for lung cancer: a multicenter comparative analysis.

PubMed

Pompili, Cecilia; Brunelli, Alessandro; Rocco, Gaetano; Salvi, Rosario; Xiumé, Francesco; La Rocca, Antonello; Sabbatini, Armando; Martucci, Nicola

2013-01-01

Patient satisfaction reflects the perception of the customer about the level of quality of care received during the episode of hospitalization. To compare the levels of satisfaction of patients submitted to lung resection in two different thoracic surgical units. Prospective analysis of 280 consecutive patients submitted to pulmonary resection for neoplastic disease in two centers (center A: 139 patients; center B: 141 patients; 2009-2010). Patients' satisfaction was assessed at discharge through the EORTC-InPatSat32 module, a 32-item, multi-scale self-administered anonymous questionnaire. Each scale (ranging from 0 to 100 in score) was compared between the two units. Multivariable regression and bootstrap were used to verify factors associated with the patients' general satisfaction (dependent variable). Patients from unit B reported a higher general satisfaction (91.5 vs. 88.3, p = 0.04), mainly due to a significantly higher satisfaction in the doctor-related scales (doctors' technical skill: p = 0.001; doctors' interpersonal skill: p = 0.008; doctors' availability: p = 0.005, and doctors information provision: p = 0.0006). Multivariable regression analysis and bootstrap confirmed that level of care in unit B (p = 0.006, bootstrap frequency 60%) along with lower level of education of the patient population (p = 0.02, bootstrap frequency 62%) were independent factors associated with a higher general patient satisfaction. We were able to show a different level of patient satisfaction in patients operated on in two different thoracic surgery units. A reduced level of patient satisfaction may trigger changes in the management policy of individual units in order to meet patients' expectations and improve organizational efficiency. Copyright © 2012 S. Karger AG, Basel.

An inferential study of the phenotype for the chromosome 15q24 microdeletion syndrome: a bootstrap analysis

PubMed Central

Ramírez-Prado, Dolores; Cortés, Ernesto; Aguilar-Segura, María Soledad; Gil-Guillén, Vicente Francisco

2016-01-01

In January 2012, a review of the cases of chromosome 15q24 microdeletion syndrome was published. However, this study did not include inferential statistics. The aims of the present study were to update the literature search and calculate confidence intervals for the prevalence of each phenotype using bootstrap methodology. Published case reports of patients with the syndrome that included detailed information about breakpoints and phenotype were sought and 36 were included. Deletions in megabase (Mb) pairs were determined to calculate the size of the interstitial deletion of the phenotypes studied in 2012. To determine confidence intervals for the prevalence of the phenotype and the interstitial loss, we used bootstrap methodology. Using the bootstrap percentiles method, we found wide variability in the prevalence of the different phenotypes (3–100%). The mean interstitial deletion size was 2.72 Mb (95% CI [2.35–3.10 Mb]). In comparison with our work, which expanded the literature search by 45 months, there were differences in the prevalence of 17% of the phenotypes, indicating that more studies are needed to analyze this rare disease. PMID:26925314

Transformational leadership in the consumer service workgroup: competing models of job satisfaction, change commitment, and cooperative conflict resolution.

PubMed

Yang, Yi-Feng

2014-02-01

This paper discusses the effects of transformational leadership on cooperative conflict resolution (management) by evaluating several alternative models related to the mediating role of job satisfaction and change commitment. Samples of data from customer service personnel in Taiwan were analyzed. Based on the bootstrap sample technique, an empirical study was carried out to yield the best fitting model. The procedure of hierarchical nested model analysis was used, incorporating the methods of bootstrapping mediation, PRODCLIN2, and structural equation modeling (SEM) comparison. The analysis suggests that leadership that promotes integration (change commitment) and provides inspiration and motivation (job satisfaction), in the proper order, creates the means for cooperative conflict resolution.

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

PubMed

Stamatakis, Alexandros

2006-11-01

RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively. icwww.epfl.ch/~stamatak

Coefficient Omega Bootstrap Confidence Intervals: Nonnormal Distributions

ERIC Educational Resources Information Center

Padilla, Miguel A.; Divers, Jasmin

2013-01-01

The performance of the normal theory bootstrap (NTB), the percentile bootstrap (PB), and the bias-corrected and accelerated (BCa) bootstrap confidence intervals (CIs) for coefficient omega was assessed through a Monte Carlo simulation under conditions not previously investigated. Of particular interests were nonnormal Likert-type and binary items.…

Tests of Independence for Ordinal Data Using Bootstrap.

ERIC Educational Resources Information Center

Chan, Wai; Yung, Yiu-Fai; Bentler, Peter M.; Tang, Man-Lai

1998-01-01

Two bootstrap tests are proposed to test the independence hypothesis in a two-way cross table. Monte Carlo studies are used to compare the traditional asymptotic test with these bootstrap methods, and the bootstrap methods are found superior in two ways: control of Type I error and statistical power. (SLD)

EARLY CHILDHOOD INVESTMENTS SUBSTANTIALLY BOOST ADULT HEALTH

PubMed Central

Campbell, Frances; Conti, Gabriella; Heckman, James J.; Moon, Seong Hyeok; Pinto, Rodrigo; Pungello, Elizabeth; Pan, Yi

2014-01-01

High-quality early childhood programs have been shown to have substantial benefits in reducing crime, raising earnings, and promoting education. Much less is known about their benefits for adult health. We report the long-term health impacts of one of the oldest and most heavily cited early childhood interventions with long-term follow-up evaluated by the method of randomization: the Carolina Abecedarian Project (ABC). Using recently collected biomedical data, we find that disadvantaged children randomly assigned to treatment have significantly lower prevalence of risk factors for cardiovascular and metabolic diseases in their mid-30s. The evidence is especially strong for males. The mean systolic blood pressure among the control males is 143, while only 126 among the treated. One in four males in the control group is affected by metabolic syndrome, while none in the treatment group is. To reach these conclusions, we address several statistical challenges. We use exact permutation tests to account for small sample sizes and conduct a parallel bootstrap confidence interval analysis to confirm the permutation analysis. We adjust inference to account for the multiple hypotheses tested and for nonrandom attrition. Our evidence shows the potential of early life interventions for preventing disease and promoting health. PMID:24675955

Causality constraints in conformal field theory

DOE PAGES

Hartman, Thomas; Jain, Sachin; Kundu, Sandipan

2016-05-17

Causality places nontrivial constraints on QFT in Lorentzian signature, for example fixing the signs of certain terms in the low energy Lagrangian. In d dimensional conformal field theory, we show how such constraints are encoded in crossing symmetry of Euclidean correlators, and derive analogous constraints directly from the conformal bootstrap (analytically). The bootstrap setup is a Lorentzian four-point function corresponding to propagation through a shockwave. Crossing symmetry fixes the signs of certain log terms that appear in the conformal block expansion, which constrains the interactions of low-lying operators. As an application, we use the bootstrap to rederive the well knownmore » sign constraint on the (Φ) 4 coupling in effective field theory, from a dual CFT. We also find constraints on theories with higher spin conserved currents. As a result, our analysis is restricted to scalar correlators, but we argue that similar methods should also impose nontrivial constraints on the interactions of spinning operators« less

Benchmarking the efficiency of the Chilean water and sewerage companies: a double-bootstrap approach.

PubMed

Molinos-Senante, María; Donoso, Guillermo; Sala-Garrido, Ramon; Villegas, Andrés

2018-03-01

Benchmarking the efficiency of water companies is essential to set water tariffs and to promote their sustainability. In doing so, most of the previous studies have applied conventional data envelopment analysis (DEA) models. However, it is a deterministic method that does not allow to identify environmental factors influencing efficiency scores. To overcome this limitation, this paper evaluates the efficiency of a sample of Chilean water and sewerage companies applying a double-bootstrap DEA model. Results evidenced that the ranking of water and sewerage companies changes notably whether efficiency scores are computed applying conventional or double-bootstrap DEA models. Moreover, it was found that the percentage of non-revenue water and customer density are factors influencing the efficiency of Chilean water and sewerage companies. This paper illustrates the importance of using a robust and reliable method to increase the relevance of benchmarking tools.

Relationships among genera of the Saccharomycotina from multigene sequence analysis

USDA-ARS?s Scientific Manuscript database

Most known species of the subphylum Saccharomycotina (budding ascomycetous yeasts) have now been placed in phylogenetically defined clades following multigene sequence analysis. Terminal clades, which are usually well supported from bootstrap analysis, are viewed as phylogenetically circumscribed ge...

Does Bootstrap Procedure Provide Biased Estimates? An Empirical Examination for a Case of Multiple Regression.

ERIC Educational Resources Information Center

Fan, Xitao

This paper empirically and systematically assessed the performance of bootstrap resampling procedure as it was applied to a regression model. Parameter estimates from Monte Carlo experiments (repeated sampling from population) and bootstrap experiments (repeated resampling from one original bootstrap sample) were generated and compared. Sample…

Using the Descriptive Bootstrap to Evaluate Result Replicability (Because Statistical Significance Doesn't)

ERIC Educational Resources Information Center

Spinella, Sarah

2011-01-01

As result replicability is essential to science and difficult to achieve through external replicability, the present paper notes the insufficiency of null hypothesis statistical significance testing (NHSST) and explains the bootstrap as a plausible alternative, with a heuristic example to illustrate the bootstrap method. The bootstrap relies on…

Performance of Bootstrapping Approaches To Model Test Statistics and Parameter Standard Error Estimation in Structural Equation Modeling.

ERIC Educational Resources Information Center

Nevitt, Jonathan; Hancock, Gregory R.

2001-01-01

Evaluated the bootstrap method under varying conditions of nonnormality, sample size, model specification, and number of bootstrap samples drawn from the resampling space. Results for the bootstrap suggest the resampling-based method may be conservative in its control over model rejections, thus having an impact on the statistical power associated…

Effects of magnetic islands on bootstrap current in toroidal plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong, G.; Lin, Z.

The effects of magnetic islands on electron bootstrap current in toroidal plasmas are studied using gyrokinetic simulations. The magnetic islands cause little changes of the bootstrap current level in the banana regime because of trapped electron effects. In the plateau regime, the bootstrap current is completely suppressed at the island centers due to the destruction of trapped electron orbits by collisions and the flattening of pressure profiles by the islands. In the collisional regime, small but finite bootstrap current can exist inside the islands because of the pressure gradients created by large collisional transport across the islands. Lastly, simulation resultsmore » show that the bootstrap current level increases near the island separatrix due to steeper local density gradients.« less

Effects of magnetic islands on bootstrap current in toroidal plasmas

DOE PAGES

Dong, G.; Lin, Z.

2016-12-19

The effects of magnetic islands on electron bootstrap current in toroidal plasmas are studied using gyrokinetic simulations. The magnetic islands cause little changes of the bootstrap current level in the banana regime because of trapped electron effects. In the plateau regime, the bootstrap current is completely suppressed at the island centers due to the destruction of trapped electron orbits by collisions and the flattening of pressure profiles by the islands. In the collisional regime, small but finite bootstrap current can exist inside the islands because of the pressure gradients created by large collisional transport across the islands. Lastly, simulation resultsmore » show that the bootstrap current level increases near the island separatrix due to steeper local density gradients.« less

An enhanced cluster analysis program with bootstrap significance testing for ecological community analysis

USGS Publications Warehouse

McKenna, J.E.

2003-01-01

The biosphere is filled with complex living patterns and important questions about biodiversity and community and ecosystem ecology are concerned with structure and function of multispecies systems that are responsible for those patterns. Cluster analysis identifies discrete groups within multivariate data and is an effective method of coping with these complexities, but often suffers from subjective identification of groups. The bootstrap testing method greatly improves objective significance determination for cluster analysis. The BOOTCLUS program makes cluster analysis that reliably identifies real patterns within a data set more accessible and easier to use than previously available programs. A variety of analysis options and rapid re-analysis provide a means to quickly evaluate several aspects of a data set. Interpretation is influenced by sampling design and a priori designation of samples into replicate groups, and ultimately relies on the researcher's knowledge of the organisms and their environment. However, the BOOTCLUS program provides reliable, objectively determined groupings of multivariate data.

Forecasting drought risks for a water supply storage system using bootstrap position analysis

USGS Publications Warehouse

Tasker, Gary; Dunne, Paul

1997-01-01

Forecasting the likelihood of drought conditions is an integral part of managing a water supply storage and delivery system. Position analysis uses a large number of possible flow sequences as inputs to a simulation of a water supply storage and delivery system. For a given set of operating rules and water use requirements, water managers can use such a model to forecast the likelihood of specified outcomes such as reservoir levels falling below a specified level or streamflows falling below statutory passing flows a few months ahead conditioned on the current reservoir levels and streamflows. The large number of possible flow sequences are generated using a stochastic streamflow model with a random resampling of innovations. The advantages of this resampling scheme, called bootstrap position analysis, are that it does not rely on the unverifiable assumption of normality and it allows incorporation of long-range weather forecasts into the analysis.

Bootstrap position analysis for forecasting low flow frequency

USGS Publications Warehouse

Tasker, Gary D.; Dunne, P.

1997-01-01

A method of random resampling of residuals from stochastic models is used to generate a large number of 12-month-long traces of natural monthly runoff to be used in a position analysis model for a water-supply storage and delivery system. Position analysis uses the traces to forecast the likelihood of specified outcomes such as reservoir levels falling below a specified level or streamflows falling below statutory passing flows conditioned on the current reservoir levels and streamflows. The advantages of this resampling scheme, called bootstrap position analysis, are that it does not rely on the unverifiable assumption of normality, fewer parameters need to be estimated directly from the data, and accounting for parameter uncertainty is easily done. For a given set of operating rules and water-use requirements for a system, water managers can use such a model as a decision-making tool to evaluate different operating rules. ?? ASCE,.

The R package "sperrorest" : Parallelized spatial error estimation and variable importance assessment for geospatial machine learning

NASA Astrophysics Data System (ADS)

Schratz, Patrick; Herrmann, Tobias; Brenning, Alexander

2017-04-01

Computational and statistical prediction methods such as the support vector machine have gained popularity in remote-sensing applications in recent years and are often compared to more traditional approaches like maximum-likelihood classification. However, the accuracy assessment of such predictive models in a spatial context needs to account for the presence of spatial autocorrelation in geospatial data by using spatial cross-validation and bootstrap strategies instead of their now more widely used non-spatial equivalent. The R package sperrorest by A. Brenning [IEEE International Geoscience and Remote Sensing Symposium, 1, 374 (2012)] provides a generic interface for performing (spatial) cross-validation of any statistical or machine-learning technique available in R. Since spatial statistical models as well as flexible machine-learning algorithms can be computationally expensive, parallel computing strategies are required to perform cross-validation efficiently. The most recent major release of sperrorest therefore comes with two new features (aside from improved documentation): The first one is the parallelized version of sperrorest(), parsperrorest(). This function features two parallel modes to greatly speed up cross-validation runs. Both parallel modes are platform independent and provide progress information. par.mode = 1 relies on the pbapply package and calls interactively (depending on the platform) parallel::mclapply() or parallel::parApply() in the background. While forking is used on Unix-Systems, Windows systems use a cluster approach for parallel execution. par.mode = 2 uses the foreach package to perform parallelization. This method uses a different way of cluster parallelization than the parallel package does. In summary, the robustness of parsperrorest() is increased with the implementation of two independent parallel modes. A new way of partitioning the data in sperrorest is provided by partition.factor.cv(). This function gives the user the possibility to perform cross-validation at the level of some grouping structure. As an example, in remote sensing of agricultural land uses, pixels from the same field contain nearly identical information and will thus be jointly placed in either the test set or the training set. Other spatial sampling resampling strategies are already available and can be extended by the user.

Tests of Mediation: Paradoxical Decline in Statistical Power as a Function of Mediator Collinearity

PubMed Central

Beasley, T. Mark

2013-01-01

Increasing the correlation between the independent variable and the mediator (a coefficient) increases the effect size (ab) for mediation analysis; however, increasing a by definition increases collinearity in mediation models. As a result, the standard error of product tests increase. The variance inflation due to increases in a at some point outweighs the increase of the effect size (ab) and results in a loss of statistical power. This phenomenon also occurs with nonparametric bootstrapping approaches because the variance of the bootstrap distribution of ab approximates the variance expected from normal theory. Both variances increase dramatically when a exceeds the b coefficient, thus explaining the power decline with increases in a. Implications for statistical analysis and applied researchers are discussed. PMID:24954952

The relationship between the number of loci and the statistical support for the topology of UPGMA trees obtained from genetic distance data.

PubMed

Highton, R

1993-12-01

An analysis of the relationship between the number of loci utilized in an electrophoretic study of genetic relationships and the statistical support for the topology of UPGMA trees is reported for two published data sets. These are Highton and Larson (Syst. Zool.28:579-599, 1979), an analysis of the relationships of 28 species of plethodonine salamanders, and Hedges (Syst. Zool., 35:1-21, 1986), a similar study of 30 taxa of Holarctic hylid frogs. As the number of loci increases, the statistical support for the topology at each node in UPGMA trees was determined by both the bootstrap and jackknife methods. The results show that the bootstrap and jackknife probabilities supporting the topology at some nodes of UPGMA trees increase as the number of loci utilized in a study is increased, as expected for nodes that have groupings that reflect phylogenetic relationships. The pattern of increase varies and is especially rapid in the case of groups with no close relatives. At nodes that likely do not represent correct phylogenetic relationships, the bootstrap probabilities do not increase and often decline with the addition of more loci.

Technical and scale efficiency in public and private Irish nursing homes - a bootstrap DEA approach.

PubMed

Ni Luasa, Shiovan; Dineen, Declan; Zieba, Marta

2016-10-27

This article provides methodological and empirical insights into the estimation of technical efficiency in the nursing home sector. Focusing on long-stay care and using primary data, we examine technical and scale efficiency in 39 public and 73 private Irish nursing homes by applying an input-oriented data envelopment analysis (DEA). We employ robust bootstrap methods to validate our nonparametric DEA scores and to integrate the effects of potential determinants in estimating the efficiencies. Both the homogenous and two-stage double bootstrap procedures are used to obtain confidence intervals for the bias-corrected DEA scores. Importantly, the application of the double bootstrap approach affords true DEA technical efficiency scores after adjusting for the effects of ownership, size, case-mix, and other determinants such as location, and quality. Based on our DEA results for variable returns to scale technology, the average technical efficiency score is 62 %, and the mean scale efficiency is 88 %, with nearly all units operating on the increasing returns to scale part of the production frontier. Moreover, based on the double bootstrap results, Irish nursing homes are less technically efficient, and more scale efficient than the conventional DEA estimates suggest. Regarding the efficiency determinants, in terms of ownership, we find that private facilities are less efficient than the public units. Furthermore, the size of the nursing home has a positive effect, and this reinforces our finding that Irish homes produce at increasing returns to scale. Also, notably, we find that a tendency towards quality improvements can lead to poorer technical efficiency performance.

Efficient bootstrap estimates for tail statistics

NASA Astrophysics Data System (ADS)

Breivik, Øyvind; Aarnes, Ole Johan

2017-03-01

Bootstrap resamples can be used to investigate the tail of empirical distributions as well as return value estimates from the extremal behaviour of the sample. Specifically, the confidence intervals on return value estimates or bounds on in-sample tail statistics can be obtained using bootstrap techniques. However, non-parametric bootstrapping from the entire sample is expensive. It is shown here that it suffices to bootstrap from a small subset consisting of the highest entries in the sequence to make estimates that are essentially identical to bootstraps from the entire sample. Similarly, bootstrap estimates of confidence intervals of threshold return estimates are found to be well approximated by using a subset consisting of the highest entries. This has practical consequences in fields such as meteorology, oceanography and hydrology where return values are calculated from very large gridded model integrations spanning decades at high temporal resolution or from large ensembles of independent and identically distributed model fields. In such cases the computational savings are substantial.

Detecting transitions in protein dynamics using a recurrence quantification analysis based bootstrap method.

PubMed

Karain, Wael I

2017-11-28

Proteins undergo conformational transitions over different time scales. These transitions are closely intertwined with the protein's function. Numerous standard techniques such as principal component analysis are used to detect these transitions in molecular dynamics simulations. In this work, we add a new method that has the ability to detect transitions in dynamics based on the recurrences in the dynamical system. It combines bootstrapping and recurrence quantification analysis. We start from the assumption that a protein has a "baseline" recurrence structure over a given period of time. Any statistically significant deviation from this recurrence structure, as inferred from complexity measures provided by recurrence quantification analysis, is considered a transition in the dynamics of the protein. We apply this technique to a 132 ns long molecular dynamics simulation of the β-Lactamase Inhibitory Protein BLIP. We are able to detect conformational transitions in the nanosecond range in the recurrence dynamics of the BLIP protein during the simulation. The results compare favorably to those extracted using the principal component analysis technique. The recurrence quantification analysis based bootstrap technique is able to detect transitions between different dynamics states for a protein over different time scales. It is not limited to linear dynamics regimes, and can be generalized to any time scale. It also has the potential to be used to cluster frames in molecular dynamics trajectories according to the nature of their recurrence dynamics. One shortcoming for this method is the need to have large enough time windows to insure good statistical quality for the recurrence complexity measures needed to detect the transitions.

What Teachers Should Know About the Bootstrap: Resampling in the Undergraduate Statistics Curriculum

PubMed Central

Hesterberg, Tim C.

2015-01-01

Bootstrapping has enormous potential in statistics education and practice, but there are subtle issues and ways to go wrong. For example, the common combination of nonparametric bootstrapping and bootstrap percentile confidence intervals is less accurate than using t-intervals for small samples, though more accurate for larger samples. My goals in this article are to provide a deeper understanding of bootstrap methods—how they work, when they work or not, and which methods work better—and to highlight pedagogical issues. Supplementary materials for this article are available online. [Received December 2014. Revised August 2015] PMID:27019512

Advancing theory development: exploring the leadership-climate relationship as a mechanism of the implementation of cultural competence.

PubMed

Guerrero, Erick G; Fenwick, Karissa; Kong, Yinfei

2017-11-14

Leadership style and specific organizational climates have emerged as critical mechanisms to implement targeted practices in organizations. Drawing from relevant theories, we propose that climate for implementation of cultural competence reflects how transformational leadership may enhance the organizational implementation of culturally responsive practices in health care organizations. Using multilevel data from 427 employees embedded in 112 addiction treatment programs collected in 2013, confirmatory factor analysis showed adequate fit statistics for our measure of climate for implementation of cultural competence (Cronbach's alpha = .88) and three outcomes: knowledge (Cronbach's alpha = .88), services (Cronbach's alpha = .86), and personnel (Cronbach's alpha = .86) practices. Results from multilevel path analyses indicate a positive relationship between employee perceptions of transformational leadership and climate for implementation of cultural competence (standardized indirect effect = .057, bootstrap p < .001). We also found a positive indirect effect between transformational leadership and each of the culturally competent practices: knowledge (standardized indirect effect = .006, bootstrap p = .004), services (standardized indirect effect = .019, bootstrap p < .001), and personnel (standardized indirect effect = .014, bootstrap p = .005). Findings contribute to implementation science. They build on leadership theory and offer evidence of the mediating role of climate in the implementation of cultural competence in addiction health service organizations.

Non-parametric methods for cost-effectiveness analysis: the central limit theorem and the bootstrap compared.

PubMed

Nixon, Richard M; Wonderling, David; Grieve, Richard D

2010-03-01

Cost-effectiveness analyses (CEA) alongside randomised controlled trials commonly estimate incremental net benefits (INB), with 95% confidence intervals, and compute cost-effectiveness acceptability curves and confidence ellipses. Two alternative non-parametric methods for estimating INB are to apply the central limit theorem (CLT) or to use the non-parametric bootstrap method, although it is unclear which method is preferable. This paper describes the statistical rationale underlying each of these methods and illustrates their application with a trial-based CEA. It compares the sampling uncertainty from using either technique in a Monte Carlo simulation. The experiments are repeated varying the sample size and the skewness of costs in the population. The results showed that, even when data were highly skewed, both methods accurately estimated the true standard errors (SEs) when sample sizes were moderate to large (n>50), and also gave good estimates for small data sets with low skewness. However, when sample sizes were relatively small and the data highly skewed, using the CLT rather than the bootstrap led to slightly more accurate SEs. We conclude that while in general using either method is appropriate, the CLT is easier to implement, and provides SEs that are at least as accurate as the bootstrap. (c) 2009 John Wiley & Sons, Ltd.

Frequentist and Bayesian Orbital Parameter Estimaton from Radial Velocity Data Using RVLIN, BOOTTRAN, and RUN DMC

NASA Astrophysics Data System (ADS)

Nelson, Benjamin Earl; Wright, Jason Thomas; Wang, Sharon

2015-08-01

For this hack session, we will present three tools used in analyses of radial velocity exoplanet systems. RVLIN is a set of IDL routines used to quickly fit an arbitrary number of Keplerian curves to radial velocity data to find adequate parameter point estimates. BOOTTRAN is an IDL-based extension of RVLIN to provide orbital parameter uncertainties using bootstrap based on a Keplerian model. RUN DMC is a highly parallelized Markov chain Monte Carlo algorithm that employs an n-body model, primarily used for dynamically complex or poorly constrained exoplanet systems. We will compare the performance of these tools and their applications to various exoplanet systems.

A Critical Meta-Analysis of Lens Model Studies in Human Judgment and Decision-Making

PubMed Central

Kaufmann, Esther; Reips, Ulf-Dietrich; Wittmann, Werner W.

2013-01-01

Achieving accurate judgment (‘judgmental achievement’) is of utmost importance in daily life across multiple domains. The lens model and the lens model equation provide useful frameworks for modeling components of judgmental achievement and for creating tools to help decision makers (e.g., physicians, teachers) reach better judgments (e.g., a correct diagnosis, an accurate estimation of intelligence). Previous meta-analyses of judgment and decision-making studies have attempted to evaluate overall judgmental achievement and have provided the basis for evaluating the success of bootstrapping (i.e., replacing judges by linear models that guide decision making). However, previous meta-analyses have failed to appropriately correct for a number of study design artifacts (e.g., measurement error, dichotomization), which may have potentially biased estimations (e.g., of the variability between studies) and led to erroneous interpretations (e.g., with regards to moderator variables). In the current study we therefore conduct the first psychometric meta-analysis of judgmental achievement studies that corrects for a number of study design artifacts. We identified 31 lens model studies (N = 1,151, k = 49) that met our inclusion criteria. We evaluated overall judgmental achievement as well as whether judgmental achievement depended on decision domain (e.g., medicine, education) and/or the level of expertise (expert vs. novice). We also evaluated whether using corrected estimates affected conclusions with regards to the success of bootstrapping with psychometrically-corrected models. Further, we introduce a new psychometric trim-and-fill method to estimate the effect sizes of potentially missing studies correct psychometric meta-analyses for effects of publication bias. Comparison of the results of the psychometric meta-analysis with the results of a traditional meta-analysis (which only corrected for sampling error) indicated that artifact correction leads to a) an increase in values of the lens model components, b) reduced heterogeneity between studies, and c) increases the success of bootstrapping. We argue that psychometric meta-analysis is useful for accurately evaluating human judgment and show the success of bootstrapping. PMID:24391781

A critical meta-analysis of lens model studies in human judgment and decision-making.

PubMed

Kaufmann, Esther; Reips, Ulf-Dietrich; Wittmann, Werner W

2013-01-01

Achieving accurate judgment ('judgmental achievement') is of utmost importance in daily life across multiple domains. The lens model and the lens model equation provide useful frameworks for modeling components of judgmental achievement and for creating tools to help decision makers (e.g., physicians, teachers) reach better judgments (e.g., a correct diagnosis, an accurate estimation of intelligence). Previous meta-analyses of judgment and decision-making studies have attempted to evaluate overall judgmental achievement and have provided the basis for evaluating the success of bootstrapping (i.e., replacing judges by linear models that guide decision making). However, previous meta-analyses have failed to appropriately correct for a number of study design artifacts (e.g., measurement error, dichotomization), which may have potentially biased estimations (e.g., of the variability between studies) and led to erroneous interpretations (e.g., with regards to moderator variables). In the current study we therefore conduct the first psychometric meta-analysis of judgmental achievement studies that corrects for a number of study design artifacts. We identified 31 lens model studies (N = 1,151, k = 49) that met our inclusion criteria. We evaluated overall judgmental achievement as well as whether judgmental achievement depended on decision domain (e.g., medicine, education) and/or the level of expertise (expert vs. novice). We also evaluated whether using corrected estimates affected conclusions with regards to the success of bootstrapping with psychometrically-corrected models. Further, we introduce a new psychometric trim-and-fill method to estimate the effect sizes of potentially missing studies correct psychometric meta-analyses for effects of publication bias. Comparison of the results of the psychometric meta-analysis with the results of a traditional meta-analysis (which only corrected for sampling error) indicated that artifact correction leads to a) an increase in values of the lens model components, b) reduced heterogeneity between studies, and c) increases the success of bootstrapping. We argue that psychometric meta-analysis is useful for accurately evaluating human judgment and show the success of bootstrapping.

permGPU: Using graphics processing units in RNA microarray association studies.

PubMed

Shterev, Ivo D; Jung, Sin-Ho; George, Stephen L; Owzar, Kouros

2010-06-16

Many analyses of microarray association studies involve permutation, bootstrap resampling and cross-validation, that are ideally formulated as embarrassingly parallel computing problems. Given that these analyses are computationally intensive, scalable approaches that can take advantage of multi-core processor systems need to be developed. We have developed a CUDA based implementation, permGPU, that employs graphics processing units in microarray association studies. We illustrate the performance and applicability of permGPU within the context of permutation resampling for a number of test statistics. An extensive simulation study demonstrates a dramatic increase in performance when using permGPU on an NVIDIA GTX 280 card compared to an optimized C/C++ solution running on a conventional Linux server. permGPU is available as an open-source stand-alone application and as an extension package for the R statistical environment. It provides a dramatic increase in performance for permutation resampling analysis in the context of microarray association studies. The current version offers six test statistics for carrying out permutation resampling analyses for binary, quantitative and censored time-to-event traits.

New Methods for Estimating Seasonal Potential Climate Predictability

NASA Astrophysics Data System (ADS)

Feng, Xia

This study develops two new statistical approaches to assess the seasonal potential predictability of the observed climate variables. One is the univariate analysis of covariance (ANOCOVA) model, a combination of autoregressive (AR) model and analysis of variance (ANOVA). It has the advantage of taking into account the uncertainty of the estimated parameter due to sampling errors in statistical test, which is often neglected in AR based methods, and accounting for daily autocorrelation that is not considered in traditional ANOVA. In the ANOCOVA model, the seasonal signals arising from external forcing are determined to be identical or not to assess any interannual variability that may exist is potentially predictable. The bootstrap is an attractive alternative method that requires no hypothesis model and is available no matter how mathematically complicated the parameter estimator. This method builds up the empirical distribution of the interannual variance from the resamplings drawn with replacement from the given sample, in which the only predictability in seasonal means arises from the weather noise. These two methods are applied to temperature and water cycle components including precipitation and evaporation, to measure the extent to which the interannual variance of seasonal means exceeds the unpredictable weather noise compared with the previous methods, including Leith-Shukla-Gutzler (LSG), Madden, and Katz. The potential predictability of temperature from ANOCOVA model, bootstrap, LSG and Madden exhibits a pronounced tropical-extratropical contrast with much larger predictability in the tropics dominated by El Nino/Southern Oscillation (ENSO) than in higher latitudes where strong internal variability lowers predictability. Bootstrap tends to display highest predictability of the four methods, ANOCOVA lies in the middle, while LSG and Madden appear to generate lower predictability. Seasonal precipitation from ANOCOVA, bootstrap, and Katz, resembling that for temperature, is more predictable over the tropical regions, and less predictable in extropics. Bootstrap and ANOCOVA are in good agreement with each other, both methods generating larger predictability than Katz. The seasonal predictability of evaporation over land bears considerably similarity with that of temperature using ANOCOVA, bootstrap, LSG and Madden. The remote SST forcing and soil moisture reveal substantial seasonality in their relations with the potentially predictable seasonal signals. For selected regions, either SST or soil moisture or both shows significant relationships with predictable signals, hence providing indirect insight on slowly varying boundary processes involved to enable useful seasonal climate predication. A multivariate analysis of covariance (MANOCOVA) model is established to identify distinctive predictable patterns, which are uncorrelated with each other. Generally speaking, the seasonal predictability from multivariate model is consistent with that from ANOCOVA. Besides unveiling the spatial variability of predictability, MANOCOVA model also reveals the temporal variability of each predictable pattern, which could be linked to the periodic oscillations.

Reduced ion bootstrap current drive on NTM instability

NASA Astrophysics Data System (ADS)

Qu, Hongpeng; Wang, Feng; Wang, Aike; Peng, Xiaodong; Li, Jiquan

2018-05-01

The loss of bootstrap current inside magnetic island plays a dominant role in driving the neoclassical tearing mode (NTM) instability in tokamak plasmas. In this work, we investigate the finite-banana-width (FBW) effect on the profile of ion bootstrap current in the island vicinity via an analytical approach. The results show that even if the pressure gradient vanishes inside the island, the ion bootstrap current can partly survive due to the FBW effect. The efficiency of the FBW effect is higher when the island width becomes smaller. Nevertheless, even when the island width is comparable to the ion FBW, the unperturbed ion bootstrap current inside the island cannot be largely recovered by the FBW effect, and thus the current loss still exists. This suggests that FBW effect alone cannot dramatically reduce the ion bootstrap current drive on NTMs.

The PIT-trap-A "model-free" bootstrap procedure for inference about regression models with discrete, multivariate responses.

PubMed

Warton, David I; Thibaut, Loïc; Wang, Yi Alice

2017-01-01

Bootstrap methods are widely used in statistics, and bootstrapping of residuals can be especially useful in the regression context. However, difficulties are encountered extending residual resampling to regression settings where residuals are not identically distributed (thus not amenable to bootstrapping)-common examples including logistic or Poisson regression and generalizations to handle clustered or multivariate data, such as generalised estimating equations. We propose a bootstrap method based on probability integral transform (PIT-) residuals, which we call the PIT-trap, which assumes data come from some marginal distribution F of known parametric form. This method can be understood as a type of "model-free bootstrap", adapted to the problem of discrete and highly multivariate data. PIT-residuals have the key property that they are (asymptotically) pivotal. The PIT-trap thus inherits the key property, not afforded by any other residual resampling approach, that the marginal distribution of data can be preserved under PIT-trapping. This in turn enables the derivation of some standard bootstrap properties, including second-order correctness of pivotal PIT-trap test statistics. In multivariate data, bootstrapping rows of PIT-residuals affords the property that it preserves correlation in data without the need for it to be modelled, a key point of difference as compared to a parametric bootstrap. The proposed method is illustrated on an example involving multivariate abundance data in ecology, and demonstrated via simulation to have improved properties as compared to competing resampling methods.

Bootstrap Percolation on Homogeneous Trees Has 2 Phase Transitions

NASA Astrophysics Data System (ADS)

Fontes, L. R. G.; Schonmann, R. H.

2008-09-01

We study the threshold θ bootstrap percolation model on the homogeneous tree with degree b+1, 2≤ θ≤ b, and initial density p. It is known that there exists a nontrivial critical value for p, which we call p f , such that a) for p> p f , the final bootstrapped configuration is fully occupied for almost every initial configuration, and b) if p< p f , then for almost every initial configuration, the final bootstrapped configuration has density of occupied vertices less than 1. In this paper, we establish the existence of a distinct critical value for p, p c , such that 0< p c < p f , with the following properties: 1) if p≤ p c , then for almost every initial configuration there is no infinite cluster of occupied vertices in the final bootstrapped configuration; 2) if p> p c , then for almost every initial configuration there are infinite clusters of occupied vertices in the final bootstrapped configuration. Moreover, we show that 3) for p< p c , the distribution of the occupied cluster size in the final bootstrapped configuration has an exponential tail; 4) at p= p c , the expected occupied cluster size in the final bootstrapped configuration is infinite; 5) the probability of percolation of occupied vertices in the final bootstrapped configuration is continuous on [0, p f ] and analytic on ( p c , p f ), admitting an analytic continuation from the right at p c and, only in the case θ= b, also from the left at p f .

Visuospatial bootstrapping: implicit binding of verbal working memory to visuospatial representations in children and adults.

PubMed

Darling, Stephen; Parker, Mary-Jane; Goodall, Karen E; Havelka, Jelena; Allen, Richard J

2014-03-01

When participants carry out visually presented digit serial recall, their performance is better if they are given the opportunity to encode extra visuospatial information at encoding-a phenomenon that has been termed visuospatial bootstrapping. This bootstrapping is the result of integration of information from different modality-specific short-term memory systems and visuospatial knowledge in long term memory, and it can be understood in the context of recent models of working memory that address multimodal binding (e.g., models incorporating an episodic buffer). Here we report a cross-sectional developmental study that demonstrated visuospatial bootstrapping in adults (n=18) and 9-year-old children (n=15) but not in 6-year-old children (n=18). This is the first developmental study addressing visuospatial bootstrapping, and results demonstrate that the developmental trajectory of bootstrapping is different from that of basic verbal and visuospatial working memory. This pattern suggests that bootstrapping (and hence integrative functions such as those associated with the episodic buffer) emerge independent of the development of basic working memory slave systems during childhood. Copyright © 2013 Elsevier Inc. All rights reserved.

A bootstrap based space-time surveillance model with an application to crime occurrences

NASA Astrophysics Data System (ADS)

Kim, Youngho; O'Kelly, Morton

2008-06-01

This study proposes a bootstrap-based space-time surveillance model. Designed to find emerging hotspots in near-real time, the bootstrap based model is characterized by its use of past occurrence information and bootstrap permutations. Many existing space-time surveillance methods, using population at risk data to generate expected values, have resulting hotspots bounded by administrative area units and are of limited use for near-real time applications because of the population data needed. However, this study generates expected values for local hotspots from past occurrences rather than population at risk. Also, bootstrap permutations of previous occurrences are used for significant tests. Consequently, the bootstrap-based model, without the requirement of population at risk data, (1) is free from administrative area restriction, (2) enables more frequent surveillance for continuously updated registry database, and (3) is readily applicable to criminology and epidemiology surveillance. The bootstrap-based model performs better for space-time surveillance than the space-time scan statistic. This is shown by means of simulations and an application to residential crime occurrences in Columbus, OH, year 2000.

Transport barriers in bootstrap-driven tokamaks

NASA Astrophysics Data System (ADS)

Staebler, G. M.; Garofalo, A. M.; Pan, C.; McClenaghan, J.; Van Zeeland, M. A.; Lao, L. L.

2018-05-01

Experiments have demonstrated improved energy confinement due to the spontaneous formation of an internal transport barrier in high bootstrap fraction discharges. Gyrokinetic analysis, and quasilinear predictive modeling, demonstrates that the observed transport barrier is caused by the suppression of turbulence primarily from the large Shafranov shift. It is shown that the Shafranov shift can produce a bifurcation to improved confinement in regions of positive magnetic shear or a continuous reduction in transport for weak or negative magnetic shear. Operation at high safety factor lowers the pressure gradient threshold for the Shafranov shift-driven barrier formation. Two self-organized states of the internal and edge transport barrier are observed. It is shown that these two states are controlled by the interaction of the bootstrap current with magnetic shear, and the kinetic ballooning mode instability boundary. Election scale energy transport is predicted to be dominant in the inner 60% of the profile. Evidence is presented that energetic particle-driven instabilities could be playing a role in the thermal energy transport in this region.

Exploration of the factor structure of the Kirton Adaption-Innovation Inventory using bootstrapping estimation.

PubMed

Im, Subin; Min, Soonhong

2013-04-01

Exploratory factor analyses of the Kirton Adaption-Innovation Inventory (KAI), which serves to measure individual cognitive styles, generally indicate three factors: sufficiency of originality, efficiency, and rule/group conformity. In contrast, a 2005 study by Im and Hu using confirmatory factor analysis supported a four-factor structure, dividing the sufficiency of originality dimension into two subdimensions, idea generation and preference for change. This study extends Im and Hu's (2005) study of a derived version of the KAI by providing additional evidence of the four-factor structure. Specifically, the authors test the robustness of the parameter estimates to the violation of normality assumptions in the sample using bootstrap methods. A bias-corrected confidence interval bootstrapping procedure conducted among a sample of 356 participants--members of the Arkansas Household Research Panel, with middle SES and average age of 55.6 yr. (SD = 13.9)--showed that the four-factor model with two subdimensions of sufficiency of originality fits the data significantly better than the three-factor model in non-normality conditions.

Measuring and Benchmarking Technical Efficiency of Public Hospitals in Tianjin, China

PubMed Central

Li, Hao; Dong, Siping

2015-01-01

China has long been stuck in applying traditional data envelopment analysis (DEA) models to measure technical efficiency of public hospitals without bias correction of efficiency scores. In this article, we have introduced the Bootstrap-DEA approach from the international literature to analyze the technical efficiency of public hospitals in Tianjin (China) and tried to improve the application of this method for benchmarking and inter-organizational learning. It is found that the bias corrected efficiency scores of Bootstrap-DEA differ significantly from those of the traditional Banker, Charnes, and Cooper (BCC) model, which means that Chinese researchers need to update their DEA models for more scientific calculation of hospital efficiency scores. Our research has helped shorten the gap between China and the international world in relative efficiency measurement and improvement of hospitals. It is suggested that Bootstrap-DEA be widely applied into afterward research to measure relative efficiency and productivity of Chinese hospitals so as to better serve for efficiency improvement and related decision making. PMID:26396090

An SAS Macro for Implementing the Modified Bollen-Stine Bootstrap for Missing Data: Implementing the Bootstrap Using Existing Structural Equation Modeling Software

ERIC Educational Resources Information Center

Enders, Craig K.

2005-01-01

The Bollen-Stine bootstrap can be used to correct for standard error and fit statistic bias that occurs in structural equation modeling (SEM) applications due to nonnormal data. The purpose of this article is to demonstrate the use of a custom SAS macro program that can be used to implement the Bollen-Stine bootstrap with existing SEM software.…

Coupling of PIES 3-D Equilibrium Code and NIFS Bootstrap Code with Applications to the Computation of Stellarator Equilibria

NASA Astrophysics Data System (ADS)

Monticello, D. A.; Reiman, A. H.; Watanabe, K. Y.; Nakajima, N.; Okamoto, M.

1997-11-01

The existence of bootstrap currents in both tokamaks and stellarators was confirmed, experimentally, more than ten years ago. Such currents can have significant effects on the equilibrium and stability of these MHD devices. In addition, stellarators, with the notable exception of W7-X, are predicted to have such large bootstrap currents that reliable equilibrium calculations require the self-consistent evaluation of bootstrap currents. Modeling of discharges which contain islands requires an algorithm that does not assume good surfaces. Only one of the two 3-D equilibrium codes that exist, PIES( Reiman, A. H., Greenside, H. S., Compt. Phys. Commun. 43), (1986)., can easily be modified to handle bootstrap current. Here we report on the coupling of the PIES 3-D equilibrium code and NIFS bootstrap code(Watanabe, K., et al., Nuclear Fusion 35) (1995), 335.

Power in Bayesian Mediation Analysis for Small Sample Research

PubMed Central

Miočević, Milica; MacKinnon, David P.; Levy, Roy

2018-01-01

It was suggested that Bayesian methods have potential for increasing power in mediation analysis (Koopman, Howe, Hollenbeck, & Sin, 2015; Yuan & MacKinnon, 2009). This paper compares the power of Bayesian credibility intervals for the mediated effect to the power of normal theory, distribution of the product, percentile, and bias-corrected bootstrap confidence intervals at N≤ 200. Bayesian methods with diffuse priors have power comparable to the distribution of the product and bootstrap methods, and Bayesian methods with informative priors had the most power. Varying degrees of precision of prior distributions were also examined. Increased precision led to greater power only when N≥ 100 and the effects were small, N < 60 and the effects were large, and N < 200 and the effects were medium. An empirical example from psychology illustrated a Bayesian analysis of the single mediator model from prior selection to interpreting results. PMID:29662296

Power in Bayesian Mediation Analysis for Small Sample Research.

PubMed

Miočević, Milica; MacKinnon, David P; Levy, Roy

2017-01-01

It was suggested that Bayesian methods have potential for increasing power in mediation analysis (Koopman, Howe, Hollenbeck, & Sin, 2015; Yuan & MacKinnon, 2009). This paper compares the power of Bayesian credibility intervals for the mediated effect to the power of normal theory, distribution of the product, percentile, and bias-corrected bootstrap confidence intervals at N≤ 200. Bayesian methods with diffuse priors have power comparable to the distribution of the product and bootstrap methods, and Bayesian methods with informative priors had the most power. Varying degrees of precision of prior distributions were also examined. Increased precision led to greater power only when N≥ 100 and the effects were small, N < 60 and the effects were large, and N < 200 and the effects were medium. An empirical example from psychology illustrated a Bayesian analysis of the single mediator model from prior selection to interpreting results.

Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support.

PubMed

Wilcox, Thomas P; Zwickl, Derrick J; Heath, Tracy A; Hillis, David M

2002-11-01

Four New World genera of dwarf boas (Exiliboa, Trachyboa, Tropidophis, and Ungaliophis) have been placed by many systematists in a single group (traditionally called Tropidophiidae). However, the monophyly of this group has been questioned in several studies. Moreover, the overall relationships among basal snake lineages, including the placement of the dwarf boas, are poorly understood. We obtained mtDNA sequence data for 12S, 16S, and intervening tRNA-val genes from 23 species of snakes representing most major snake lineages, including all four genera of New World dwarf boas. We then examined the phylogenetic position of these species by estimating the phylogeny of the basal snakes. Our phylogenetic analysis suggests that New World dwarf boas are not monophyletic. Instead, we find Exiliboa and Ungaliophis to be most closely related to sand boas (Erycinae), boas (Boinae), and advanced snakes (Caenophidea), whereas Tropidophis and Trachyboa form an independent clade that separated relatively early in snake radiation. Our estimate of snake phylogeny differs significantly in other ways from some previous estimates of snake phylogeny. For instance, pythons do not cluster with boas and sand boas, but instead show a strong relationship with Loxocemus and Xenopeltis. Additionally, uropeltids cluster strongly with Cylindrophis, and together are embedded in what has previously been considered the macrostomatan radiation. These relationships are supported by both bootstrapping (parametric and nonparametric approaches) and Bayesian analysis, although Bayesian support values are consistently higher than those obtained from nonparametric bootstrapping. Simulations show that Bayesian support values represent much better estimates of phylogenetic accuracy than do nonparametric bootstrap support values, at least under the conditions of our study. Copyright 2002 Elsevier Science (USA)

Sample size determination for mediation analysis of longitudinal data.

PubMed

Pan, Haitao; Liu, Suyu; Miao, Danmin; Yuan, Ying

2018-03-27

Sample size planning for longitudinal data is crucial when designing mediation studies because sufficient statistical power is not only required in grant applications and peer-reviewed publications, but is essential to reliable research results. However, sample size determination is not straightforward for mediation analysis of longitudinal design. To facilitate planning the sample size for longitudinal mediation studies with a multilevel mediation model, this article provides the sample size required to achieve 80% power by simulations under various sizes of the mediation effect, within-subject correlations and numbers of repeated measures. The sample size calculation is based on three commonly used mediation tests: Sobel's method, distribution of product method and the bootstrap method. Among the three methods of testing the mediation effects, Sobel's method required the largest sample size to achieve 80% power. Bootstrapping and the distribution of the product method performed similarly and were more powerful than Sobel's method, as reflected by the relatively smaller sample sizes. For all three methods, the sample size required to achieve 80% power depended on the value of the ICC (i.e., within-subject correlation). A larger value of ICC typically required a larger sample size to achieve 80% power. Simulation results also illustrated the advantage of the longitudinal study design. The sample size tables for most encountered scenarios in practice have also been published for convenient use. Extensive simulations study showed that the distribution of the product method and bootstrapping method have superior performance to the Sobel's method, but the product method was recommended to use in practice in terms of less computation time load compared to the bootstrapping method. A R package has been developed for the product method of sample size determination in mediation longitudinal study design.

Reliability of dose volume constraint inference from clinical data.

PubMed

Lutz, C M; Møller, D S; Hoffmann, L; Knap, M M; Alber, M

2017-04-21

Dose volume histogram points (DVHPs) frequently serve as dose constraints in radiotherapy treatment planning. An experiment was designed to investigate the reliability of DVHP inference from clinical data for multiple cohort sizes and complication incidence rates. The experimental background was radiation pneumonitis in non-small cell lung cancer and the DVHP inference method was based on logistic regression. From 102 NSCLC real-life dose distributions and a postulated DVHP model, an 'ideal' cohort was generated where the most predictive model was equal to the postulated model. A bootstrap and a Cohort Replication Monte Carlo (CoRepMC) approach were applied to create 1000 equally sized populations each. The cohorts were then analyzed to establish inference frequency distributions. This was applied to nine scenarios for cohort sizes of 102 (1), 500 (2) to 2000 (3) patients (by sampling with replacement) and three postulated DVHP models. The Bootstrap was repeated for a 'non-ideal' cohort, where the most predictive model did not coincide with the postulated model. The Bootstrap produced chaotic results for all models of cohort size 1 for both the ideal and non-ideal cohorts. For cohort size 2 and 3, the distributions for all populations were more concentrated around the postulated DVHP. For the CoRepMC, the inference frequency increased with cohort size and incidence rate. Correct inference rates  >[Formula: see text] were only achieved by cohorts with more than 500 patients. Both Bootstrap and CoRepMC indicate that inference of the correct or approximate DVHP for typical cohort sizes is highly uncertain. CoRepMC results were less spurious than Bootstrap results, demonstrating the large influence that randomness in dose-response has on the statistical analysis.

Reliability of dose volume constraint inference from clinical data

NASA Astrophysics Data System (ADS)

Lutz, C. M.; Møller, D. S.; Hoffmann, L.; Knap, M. M.; Alber, M.

2017-04-01

Dose volume histogram points (DVHPs) frequently serve as dose constraints in radiotherapy treatment planning. An experiment was designed to investigate the reliability of DVHP inference from clinical data for multiple cohort sizes and complication incidence rates. The experimental background was radiation pneumonitis in non-small cell lung cancer and the DVHP inference method was based on logistic regression. From 102 NSCLC real-life dose distributions and a postulated DVHP model, an ‘ideal’ cohort was generated where the most predictive model was equal to the postulated model. A bootstrap and a Cohort Replication Monte Carlo (CoRepMC) approach were applied to create 1000 equally sized populations each. The cohorts were then analyzed to establish inference frequency distributions. This was applied to nine scenarios for cohort sizes of 102 (1), 500 (2) to 2000 (3) patients (by sampling with replacement) and three postulated DVHP models. The Bootstrap was repeated for a ‘non-ideal’ cohort, where the most predictive model did not coincide with the postulated model. The Bootstrap produced chaotic results for all models of cohort size 1 for both the ideal and non-ideal cohorts. For cohort size 2 and 3, the distributions for all populations were more concentrated around the postulated DVHP. For the CoRepMC, the inference frequency increased with cohort size and incidence rate. Correct inference rates  >85 % were only achieved by cohorts with more than 500 patients. Both Bootstrap and CoRepMC indicate that inference of the correct or approximate DVHP for typical cohort sizes is highly uncertain. CoRepMC results were less spurious than Bootstrap results, demonstrating the large influence that randomness in dose-response has on the statistical analysis.

Detecting temporal trends in species assemblages with bootstrapping procedures and hierarchical models

USGS Publications Warehouse

Gotelli, Nicholas J.; Dorazio, Robert M.; Ellison, Aaron M.; Grossman, Gary D.

2010-01-01

Quantifying patterns of temporal trends in species assemblages is an important analytical challenge in community ecology. We describe methods of analysis that can be applied to a matrix of counts of individuals that is organized by species (rows) and time-ordered sampling periods (columns). We first developed a bootstrapping procedure to test the null hypothesis of random sampling from a stationary species abundance distribution with temporally varying sampling probabilities. This procedure can be modified to account for undetected species. We next developed a hierarchical model to estimate species-specific trends in abundance while accounting for species-specific probabilities of detection. We analysed two long-term datasets on stream fishes and grassland insects to demonstrate these methods. For both assemblages, the bootstrap test indicated that temporal trends in abundance were more heterogeneous than expected under the null model. We used the hierarchical model to estimate trends in abundance and identified sets of species in each assemblage that were steadily increasing, decreasing or remaining constant in abundance over more than a decade of standardized annual surveys. Our methods of analysis are broadly applicable to other ecological datasets, and they represent an advance over most existing procedures, which do not incorporate effects of incomplete sampling and imperfect detection.

Small sample mediation testing: misplaced confidence in bootstrapped confidence intervals.

PubMed

Koopman, Joel; Howe, Michael; Hollenbeck, John R; Sin, Hock-Peng

2015-01-01

Bootstrapping is an analytical tool commonly used in psychology to test the statistical significance of the indirect effect in mediation models. Bootstrapping proponents have particularly advocated for its use for samples of 20-80 cases. This advocacy has been heeded, especially in the Journal of Applied Psychology, as researchers are increasingly utilizing bootstrapping to test mediation with samples in this range. We discuss reasons to be concerned with this escalation, and in a simulation study focused specifically on this range of sample sizes, we demonstrate not only that bootstrapping has insufficient statistical power to provide a rigorous hypothesis test in most conditions but also that bootstrapping has a tendency to exhibit an inflated Type I error rate. We then extend our simulations to investigate an alternative empirical resampling method as well as a Bayesian approach and demonstrate that they exhibit comparable statistical power to bootstrapping in small samples without the associated inflated Type I error. Implications for researchers testing mediation hypotheses in small samples are presented. For researchers wishing to use these methods in their own research, we have provided R syntax in the online supplemental materials. (c) 2015 APA, all rights reserved.

CME Velocity and Acceleration Error Estimates Using the Bootstrap Method

NASA Technical Reports Server (NTRS)

Michalek, Grzegorz; Gopalswamy, Nat; Yashiro, Seiji

2017-01-01

The bootstrap method is used to determine errors of basic attributes of coronal mass ejections (CMEs) visually identified in images obtained by the Solar and Heliospheric Observatory (SOHO) mission's Large Angle and Spectrometric Coronagraph (LASCO) instruments. The basic parameters of CMEs are stored, among others, in a database known as the SOHO/LASCO CME catalog and are widely employed for many research studies. The basic attributes of CMEs (e.g. velocity and acceleration) are obtained from manually generated height-time plots. The subjective nature of manual measurements introduces random errors that are difficult to quantify. In many studies the impact of such measurement errors is overlooked. In this study we present a new possibility to estimate measurements errors in the basic attributes of CMEs. This approach is a computer-intensive method because it requires repeating the original data analysis procedure several times using replicate datasets. This is also commonly called the bootstrap method in the literature. We show that the bootstrap approach can be used to estimate the errors of the basic attributes of CMEs having moderately large numbers of height-time measurements. The velocity errors are in the vast majority small and depend mostly on the number of height-time points measured for a particular event. In the case of acceleration, the errors are significant, and for more than half of all CMEs, they are larger than the acceleration itself.

Overcoming confounded controls in the analysis of gene expression data from microarray experiments.

PubMed

Bhattacharya, Soumyaroop; Long, Dang; Lyons-Weiler, James

2003-01-01

A potential limitation of data from microarray experiments exists when improper control samples are used. In cancer research, comparisons of tumour expression profiles to those from normal samples is challenging due to tissue heterogeneity (mixed cell populations). A specific example exists in a published colon cancer dataset, in which tissue heterogeneity was reported among the normal samples. In this paper, we show how to overcome or avoid the problem of using normal samples that do not derive from the same tissue of origin as the tumour. We advocate an exploratory unsupervised bootstrap analysis that can reveal unexpected and undesired, but strongly supported, clusters of samples that reflect tissue differences instead of tumour versus normal differences. All of the algorithms used in the analysis, including the maximum difference subset algorithm, unsupervised bootstrap analysis, pooled variance t-test for finding differentially expressed genes and the jackknife to reduce false positives, are incorporated into our online Gene Expression Data Analyzer ( http:// bioinformatics.upmc.edu/GE2/GEDA.html ).

Bootstrap confidence levels for phylogenetic trees.

PubMed

Efron, B; Halloran, E; Holmes, S

1996-07-09

Evolutionary trees are often estimated from DNA or RNA sequence data. How much confidence should we have in the estimated trees? In 1985, Felsenstein [Felsenstein, J. (1985) Evolution 39, 783-791] suggested the use of the bootstrap to answer this question. Felsenstein's method, which in concept is a straightforward application of the bootstrap, is widely used, but has been criticized as biased in the genetics literature. This paper concerns the use of the bootstrap in the tree problem. We show that Felsenstein's method is not biased, but that it can be corrected to better agree with standard ideas of confidence levels and hypothesis testing. These corrections can be made by using the more elaborate bootstrap method presented here, at the expense of considerably more computation.

Bootstrap Standard Error Estimates in Dynamic Factor Analysis

ERIC Educational Resources Information Center

Zhang, Guangjian; Browne, Michael W.

2010-01-01

Dynamic factor analysis summarizes changes in scores on a battery of manifest variables over repeated measurements in terms of a time series in a substantially smaller number of latent factors. Algebraic formulae for standard errors of parameter estimates are more difficult to obtain than in the usual intersubject factor analysis because of the…

Coefficient Alpha Bootstrap Confidence Interval under Nonnormality

ERIC Educational Resources Information Center

Padilla, Miguel A.; Divers, Jasmin; Newton, Matthew

2012-01-01

Three different bootstrap methods for estimating confidence intervals (CIs) for coefficient alpha were investigated. In addition, the bootstrap methods were compared with the most promising coefficient alpha CI estimation methods reported in the literature. The CI methods were assessed through a Monte Carlo simulation utilizing conditions…

Pearson-type goodness-of-fit test with bootstrap maximum likelihood estimation.

PubMed

Yin, Guosheng; Ma, Yanyuan

2013-01-01

The Pearson test statistic is constructed by partitioning the data into bins and computing the difference between the observed and expected counts in these bins. If the maximum likelihood estimator (MLE) of the original data is used, the statistic generally does not follow a chi-squared distribution or any explicit distribution. We propose a bootstrap-based modification of the Pearson test statistic to recover the chi-squared distribution. We compute the observed and expected counts in the partitioned bins by using the MLE obtained from a bootstrap sample. This bootstrap-sample MLE adjusts exactly the right amount of randomness to the test statistic, and recovers the chi-squared distribution. The bootstrap chi-squared test is easy to implement, as it only requires fitting exactly the same model to the bootstrap data to obtain the corresponding MLE, and then constructs the bin counts based on the original data. We examine the test size and power of the new model diagnostic procedure using simulation studies and illustrate it with a real data set.

Dimensions of Emotional Intelligence and Online Gaming Addiction in Adolescence: The Indirect Effects of Two Facets of Perceived Stress.

PubMed

Che, Dexin; Hu, Jianping; Zhen, Shuangju; Yu, Chengfu; Li, Bin; Chang, Xi; Zhang, Wei

2017-01-01

This study tested a parallel two-mediator model in which the relationship between dimensions of emotional intelligence and online gaming addiction are mediated by perceived helplessness and perceived self-efficacy, respectively. The sample included 931 male adolescents (mean age = 16.18 years, SD = 0.95) from southern China. Data on emotional intelligence (four dimensions, including self-management of emotion, social skills, empathy and utilization of emotions), perceived stress (two facets, including perceived self-efficacy and perceived helplessness) and online gaming addiction were collected, and bootstrap methods were used to test this parallel two-mediator model. Our findings revealed that perceived self-efficacy mediated the relationship between three dimensions of emotional intelligence (i.e., self-management, social skills, and empathy) and online gaming addiction, and perceived helplessness mediated the relationship between two dimensions of emotional intelligence (i.e., self-management and emotion utilization) and online gaming addiction. These findings underscore the importance of separating the four dimensions of emotional intelligence and two facets of perceived stress to understand the complex relationship between these factors and online gaming addiction.

Dimensions of Emotional Intelligence and Online Gaming Addiction in Adolescence: The Indirect Effects of Two Facets of Perceived Stress

PubMed Central

Che, Dexin; Hu, Jianping; Zhen, Shuangju; Yu, Chengfu; Li, Bin; Chang, Xi; Zhang, Wei

2017-01-01

This study tested a parallel two-mediator model in which the relationship between dimensions of emotional intelligence and online gaming addiction are mediated by perceived helplessness and perceived self-efficacy, respectively. The sample included 931 male adolescents (mean age = 16.18 years, SD = 0.95) from southern China. Data on emotional intelligence (four dimensions, including self-management of emotion, social skills, empathy and utilization of emotions), perceived stress (two facets, including perceived self-efficacy and perceived helplessness) and online gaming addiction were collected, and bootstrap methods were used to test this parallel two-mediator model. Our findings revealed that perceived self-efficacy mediated the relationship between three dimensions of emotional intelligence (i.e., self-management, social skills, and empathy) and online gaming addiction, and perceived helplessness mediated the relationship between two dimensions of emotional intelligence (i.e., self-management and emotion utilization) and online gaming addiction. These findings underscore the importance of separating the four dimensions of emotional intelligence and two facets of perceived stress to understand the complex relationship between these factors and online gaming addiction. PMID:28751876

The PIT-trap—A “model-free” bootstrap procedure for inference about regression models with discrete, multivariate responses

PubMed Central

Thibaut, Loïc; Wang, Yi Alice

2017-01-01

Bootstrap methods are widely used in statistics, and bootstrapping of residuals can be especially useful in the regression context. However, difficulties are encountered extending residual resampling to regression settings where residuals are not identically distributed (thus not amenable to bootstrapping)—common examples including logistic or Poisson regression and generalizations to handle clustered or multivariate data, such as generalised estimating equations. We propose a bootstrap method based on probability integral transform (PIT-) residuals, which we call the PIT-trap, which assumes data come from some marginal distribution F of known parametric form. This method can be understood as a type of “model-free bootstrap”, adapted to the problem of discrete and highly multivariate data. PIT-residuals have the key property that they are (asymptotically) pivotal. The PIT-trap thus inherits the key property, not afforded by any other residual resampling approach, that the marginal distribution of data can be preserved under PIT-trapping. This in turn enables the derivation of some standard bootstrap properties, including second-order correctness of pivotal PIT-trap test statistics. In multivariate data, bootstrapping rows of PIT-residuals affords the property that it preserves correlation in data without the need for it to be modelled, a key point of difference as compared to a parametric bootstrap. The proposed method is illustrated on an example involving multivariate abundance data in ecology, and demonstrated via simulation to have improved properties as compared to competing resampling methods. PMID:28738071

Bootstrap Estimates of Standard Errors in Generalizability Theory

ERIC Educational Resources Information Center

Tong, Ye; Brennan, Robert L.

2007-01-01

Estimating standard errors of estimated variance components has long been a challenging task in generalizability theory. Researchers have speculated about the potential applicability of the bootstrap for obtaining such estimates, but they have identified problems (especially bias) in using the bootstrap. Using Brennan's bias-correcting procedures…

Problems with Multivariate Normality: Can the Multivariate Bootstrap Help?

ERIC Educational Resources Information Center

Thompson, Bruce

Multivariate normality is required for some statistical tests. This paper explores the implications of violating the assumption of multivariate normality and illustrates a graphical procedure for evaluating multivariate normality. The logic for using the multivariate bootstrap is presented. The multivariate bootstrap can be used when distribution…

Sevelamer is cost-saving vs. calcium carbonate in non-dialysis-dependent CKD patients in italy: a patient-level cost-effectiveness analysis of the INDEPENDENT study.

PubMed

Ruggeri, Matteo; Cipriani, Filippo; Bellasi, Antonio; Russo, Domenico; Di Iorio, Biagio

2014-01-01

To conduct a cost-effectiveness analysis of sevelamer versus calcium carbonate in patients with non-dialysis-dependent CKD (NDD-CKD) from the Italian NHS perspective using patient-level data from the INDEPENDENT-CKD study. Patient-level data on all-cause mortality, dialysis inception and phosphate binder dose were obtained for all 107 sevelamer and 105 calcium carbonate patients from the INDEPENDENT-CKD study. Hospitalization and frequency of dialysis data were collected post hoc for all patients via a retrospective chart review. Phosphate binder, hospitalization, and dialysis costs were expressed in 2012 euros using hospital pharmacy, Italian diagnosis-related group and ambulatory tariffs, respectively. Total life years (LYs) and costs per treatment group were calculated for the 3-year period of the study. Bootstrapping was used to estimate confidence intervals around outcomes, costs, and cost-effectiveness and to calculate the cost-effectiveness acceptability curve. A subgroup analysis of patients who did not initiate dialysis during the INDEPENDENT-CKD study was also conducted. Sevelamer was associated with 0.06 additional LYs (95% CI -0.04 to 0.16) and cost savings of EUR -5,615 (95% CI -10,066 to -1,164) per patient compared with calcium carbonate. On the basis of the bootstrap analysis, sevelamer was dominant compared to calcium carbonate in 87.1% of 10,000 bootstrap replicates. Similar results were observed in the subgroup analysis. RESULTS were driven by a significant reduction in all-cause mortality and significantly fewer hospitalizations in the sevelamer group, which offset the higher acquisition cost for sevelamer. Sevelamer provides more LYs and is less costly than calcium carbonate in patients with NDD-CKD in Italy.

Unbiased Estimates of Variance Components with Bootstrap Procedures

ERIC Educational Resources Information Center

Brennan, Robert L.

2007-01-01

This article provides general procedures for obtaining unbiased estimates of variance components for any random-model balanced design under any bootstrap sampling plan, with the focus on designs of the type typically used in generalizability theory. The results reported here are particularly helpful when the bootstrap is used to estimate standard…

Explorations in Statistics: the Bootstrap

ERIC Educational Resources Information Center

Curran-Everett, Douglas

2009-01-01

Learning about statistics is a lot like learning about science: the learning is more meaningful if you can actively explore. This fourth installment of Explorations in Statistics explores the bootstrap. The bootstrap gives us an empirical approach to estimate the theoretical variability among possible values of a sample statistic such as the…

Bootstrapping Confidence Intervals for Robust Measures of Association.

ERIC Educational Resources Information Center

King, Jason E.

A Monte Carlo simulation study was conducted to determine the bootstrap correction formula yielding the most accurate confidence intervals for robust measures of association. Confidence intervals were generated via the percentile, adjusted, BC, and BC(a) bootstrap procedures and applied to the Winsorized, percentage bend, and Pearson correlation…

Accelerating Wright–Fisher Forward Simulations on the Graphics Processing Unit

PubMed Central

Lawrie, David S.

2017-01-01

Forward Wright–Fisher simulations are powerful in their ability to model complex demography and selection scenarios, but suffer from slow execution on the Central Processor Unit (CPU), thus limiting their usefulness. However, the single-locus Wright–Fisher forward algorithm is exceedingly parallelizable, with many steps that are so-called “embarrassingly parallel,” consisting of a vast number of individual computations that are all independent of each other and thus capable of being performed concurrently. The rise of modern Graphics Processing Units (GPUs) and programming languages designed to leverage the inherent parallel nature of these processors have allowed researchers to dramatically speed up many programs that have such high arithmetic intensity and intrinsic concurrency. The presented GPU Optimized Wright–Fisher simulation, or “GO Fish” for short, can be used to simulate arbitrary selection and demographic scenarios while running over 250-fold faster than its serial counterpart on the CPU. Even modest GPU hardware can achieve an impressive speedup of over two orders of magnitude. With simulations so accelerated, one can not only do quick parametric bootstrapping of previously estimated parameters, but also use simulated results to calculate the likelihoods and summary statistics of demographic and selection models against real polymorphism data, all without restricting the demographic and selection scenarios that can be modeled or requiring approximations to the single-locus forward algorithm for efficiency. Further, as many of the parallel programming techniques used in this simulation can be applied to other computationally intensive algorithms important in population genetics, GO Fish serves as an exciting template for future research into accelerating computation in evolution. GO Fish is part of the Parallel PopGen Package available at: http://dl42.github.io/ParallelPopGen/. PMID:28768689

Bootstrap Prediction Intervals in Non-Parametric Regression with Applications to Anomaly Detection

NASA Technical Reports Server (NTRS)

Kumar, Sricharan; Srivistava, Ashok N.

2012-01-01

Prediction intervals provide a measure of the probable interval in which the outputs of a regression model can be expected to occur. Subsequently, these prediction intervals can be used to determine if the observed output is anomalous or not, conditioned on the input. In this paper, a procedure for determining prediction intervals for outputs of nonparametric regression models using bootstrap methods is proposed. Bootstrap methods allow for a non-parametric approach to computing prediction intervals with no specific assumptions about the sampling distribution of the noise or the data. The asymptotic fidelity of the proposed prediction intervals is theoretically proved. Subsequently, the validity of the bootstrap based prediction intervals is illustrated via simulations. Finally, the bootstrap prediction intervals are applied to the problem of anomaly detection on aviation data.

BOOTSTRAPPING AND MONTE CARLO METHODS OF POWER ANALYSIS USED TO ESTABLISH CONDITION CATEGORIES FOR BIOTIC INDICES

EPA Science Inventory

Biotic indices have been used ot assess biological condition by dividing index scores into condition categories. Historically the number of categories has been based on professional judgement. Alternatively, statistical methods such as power analysis can be used to determine the ...

HEXT, a software supporting tree-based screens for hybrid taxa in multilocus data sets, and an evaluation of the homoplasy excess test.

PubMed

Schneider, Kevin; Koblmüller, Stephan; Sefc, Kristina M

2015-11-11

The homoplasy excess test (HET) is a tree-based screen for hybrid taxa in multilocus nuclear phylogenies. Homoplasy between a hybrid taxon and the clades containing the parental taxa reduces bootstrap support in the tree. The HET is based on the expectation that excluding the hybrid taxon from the data set increases the bootstrap support for the parental clades, whereas excluding non-hybrid taxa has little effect on statistical node support. To carry out a HET, bootstrap trees are calculated with taxon-jackknife data sets, that is excluding one taxon (species, population) at a time. Excess increase in bootstrap support for certain nodes upon exclusion of a particular taxon indicates the hybrid (the excluded taxon) and its parents (the clades with increased support).We introduce a new software program, hext, which generates the taxon-jackknife data sets, runs the bootstrap tree calculations, and identifies excess bootstrap increases as outlier values in boxplot graphs. hext is written in r language and accepts binary data (0/1; e.g. AFLP) as well as co-dominant SNP and genotype data.We demonstrate the usefulness of hext in large SNP data sets containing putative hybrids and their parents. For instance, using published data of the genus Vitis (~6,000 SNP loci), hext output supports V. × champinii as a hybrid between V. rupestris and V. mustangensis .With simulated SNP and AFLP data sets, excess increases in bootstrap support were not always connected with the hybrid taxon (false positives), whereas the expected bootstrap signal failed to appear on several occasions (false negatives). Potential causes for both types of spurious results are discussed.With both empirical and simulated data sets, the taxon-jackknife output generated by hext provided additional signatures of hybrid taxa, including changes in tree topology across trees, consistent effects of exclusions of the hybrid and the parent taxa, and moderate (rather than excessive) increases in bootstrap support. hext significantly facilitates the taxon-jackknife approach to hybrid taxon detection, even though the simple test for excess bootstrap increase may not reliably identify hybrid taxa in all applications.

Quantification of variability and uncertainty for air toxic emission inventories with censored emission factor data.

PubMed

Frey, H Christopher; Zhao, Yuchao

2004-11-15

Probabilistic emission inventories were developed for urban air toxic emissions of benzene, formaldehyde, chromium, and arsenic for the example of Houston. Variability and uncertainty in emission factors were quantified for 71-97% of total emissions, depending upon the pollutant and data availability. Parametric distributions for interunit variability were fit using maximum likelihood estimation (MLE), and uncertainty in mean emission factors was estimated using parametric bootstrap simulation. For data sets containing one or more nondetected values, empirical bootstrap simulation was used to randomly sample detection limits for nondetected values and observations for sample values, and parametric distributions for variability were fit using MLE estimators for censored data. The goodness-of-fit for censored data was evaluated by comparison of cumulative distributions of bootstrap confidence intervals and empirical data. The emission inventory 95% uncertainty ranges are as small as -25% to +42% for chromium to as large as -75% to +224% for arsenic with correlated surrogates. Uncertainty was dominated by only a few source categories. Recommendations are made for future improvements to the analysis.

Bootstrap Estimation of Sample Statistic Bias in Structural Equation Modeling.

ERIC Educational Resources Information Center

Thompson, Bruce; Fan, Xitao

This study empirically investigated bootstrap bias estimation in the area of structural equation modeling (SEM). Three correctly specified SEM models were used under four different sample size conditions. Monte Carlo experiments were carried out to generate the criteria against which bootstrap bias estimation should be judged. For SEM fit indices,…

Epistemic uncertainty in the location and magnitude of earthquakes in Italy from Macroseismic data

USGS Publications Warehouse

Bakun, W.H.; Gomez, Capera A.; Stucchi, M.

2011-01-01

Three independent techniques (Bakun and Wentworth, 1997; Boxer from Gasperini et al., 1999; and Macroseismic Estimation of Earthquake Parameters [MEEP; see Data and Resources section, deliverable D3] from R.M.W. Musson and M.J. Jimenez) have been proposed for estimating an earthquake location and magnitude from intensity data alone. The locations and magnitudes obtained for a given set of intensity data are almost always different, and no one technique is consistently best at matching instrumental locations and magnitudes of recent well-recorded earthquakes in Italy. Rather than attempting to select one of the three solutions as best, we use all three techniques to estimate the location and the magnitude and the epistemic uncertainties among them. The estimates are calculated using bootstrap resampled data sets with Monte Carlo sampling of a decision tree. The decision-tree branch weights are based on goodness-of-fit measures of location and magnitude for recent earthquakes. The location estimates are based on the spatial distribution of locations calculated from the bootstrap resampled data. The preferred source location is the locus of the maximum bootstrap location spatial density. The location uncertainty is obtained from contours of the bootstrap spatial density: 68% of the bootstrap locations are within the 68% confidence region, and so on. For large earthquakes, our preferred location is not associated with the epicenter but with a location on the extended rupture surface. For small earthquakes, the epicenters are generally consistent with the location uncertainties inferred from the intensity data if an epicenter inaccuracy of 2-3 km is allowed. The preferred magnitude is the median of the distribution of bootstrap magnitudes. As with location uncertainties, the uncertainties in magnitude are obtained from the distribution of bootstrap magnitudes: the bounds of the 68% uncertainty range enclose 68% of the bootstrap magnitudes, and so on. The instrumental magnitudes for large and small earthquakes are generally consistent with the confidence intervals inferred from the distribution of bootstrap resampled magnitudes.

Examining Competing Models of Transformational Leadership, Leadership Trust, Change Commitment, and Job Satisfaction.

PubMed

Yang, Yi-Feng

2016-08-01

This study discusses the influence of transformational leadership on job satisfaction through assessing six alternative models related to the mediators of leadership trust and change commitment utilizing a data sample (N = 341; M age = 32.5 year, SD = 5.2) for service promotion personnel in Taiwan. The bootstrap sampling technique was used to select the better fitting model. The tool of hierarchical nested model analysis was applied, along with the approaches of bootstrapping mediation, PRODCLIN2, and structural equation modeling comparison. The results overall demonstrate that leadership is important and that leadership role identification (trust) and workgroup cohesiveness (commitment) form an ordered serial relationship. © The Author(s) 2016.

A fast Monte Carlo EM algorithm for estimation in latent class model analysis with an application to assess diagnostic accuracy for cervical neoplasia in women with AGC

PubMed Central

Kang, Le; Carter, Randy; Darcy, Kathleen; Kauderer, James; Liao, Shu-Yuan

2013-01-01

In this article we use a latent class model (LCM) with prevalence modeled as a function of covariates to assess diagnostic test accuracy in situations where the true disease status is not observed, but observations on three or more conditionally independent diagnostic tests are available. A fast Monte Carlo EM (MCEM) algorithm with binary (disease) diagnostic data is implemented to estimate parameters of interest; namely, sensitivity, specificity, and prevalence of the disease as a function of covariates. To obtain standard errors for confidence interval construction of estimated parameters, the missing information principle is applied to adjust information matrix estimates. We compare the adjusted information matrix based standard error estimates with the bootstrap standard error estimates both obtained using the fast MCEM algorithm through an extensive Monte Carlo study. Simulation demonstrates that the adjusted information matrix approach estimates the standard error similarly with the bootstrap methods under certain scenarios. The bootstrap percentile intervals have satisfactory coverage probabilities. We then apply the LCM analysis to a real data set of 122 subjects from a Gynecologic Oncology Group (GOG) study of significant cervical lesion (S-CL) diagnosis in women with atypical glandular cells of undetermined significance (AGC) to compare the diagnostic accuracy of a histology-based evaluation, a CA-IX biomarker-based test and a human papillomavirus (HPV) DNA test. PMID:24163493

Connecting the Brain to Itself through an Emulation

PubMed Central

Serruya, Mijail D.

2017-01-01

Pilot clinical trials of human patients implanted with devices that can chronically record and stimulate ensembles of hundreds to thousands of individual neurons offer the possibility of expanding the substrate of cognition. Parallel trains of firing rate activity can be delivered in real-time to an array of intermediate external modules that in turn can trigger parallel trains of stimulation back into the brain. These modules may be built in software, VLSI firmware, or biological tissue as in vitro culture preparations or in vivo ectopic construct organoids. Arrays of modules can be constructed as early stage whole brain emulators, following canonical intra- and inter-regional circuits. By using machine learning algorithms and classic tasks known to activate quasi-orthogonal functional connectivity patterns, bedside testing can rapidly identify ensemble tuning properties and in turn cycle through a sequence of external module architectures to explore which can causatively alter perception and behavior. Whole brain emulation both (1) serves to augment human neural function, compensating for disease and injury as an auxiliary parallel system, and (2) has its independent operation bootstrapped by a human-in-the-loop to identify optimal micro- and macro-architectures, update synaptic weights, and entrain behaviors. In this manner, closed-loop brain-computer interface pilot clinical trials can advance strong artificial intelligence development and forge new therapies to restore independence in children and adults with neurological conditions. PMID:28713235

Confidence Intervals for the Mean: To Bootstrap or Not to Bootstrap

ERIC Educational Resources Information Center

Calzada, Maria E.; Gardner, Holly

2011-01-01

The results of a simulation conducted by a research team involving undergraduate and high school students indicate that when data is symmetric the student's "t" confidence interval for a mean is superior to the studied non-parametric bootstrap confidence intervals. When data is skewed and for sample sizes n greater than or equal to 10,…

The Beginner's Guide to the Bootstrap Method of Resampling.

ERIC Educational Resources Information Center

Lane, Ginny G.

The bootstrap method of resampling can be useful in estimating the replicability of study results. The bootstrap procedure creates a mock population from a given sample of data from which multiple samples are then drawn. The method extends the usefulness of the jackknife procedure as it allows for computation of a given statistic across a maximal…

Application of a New Resampling Method to SEM: A Comparison of S-SMART with the Bootstrap

ERIC Educational Resources Information Center

Bai, Haiyan; Sivo, Stephen A.; Pan, Wei; Fan, Xitao

2016-01-01

Among the commonly used resampling methods of dealing with small-sample problems, the bootstrap enjoys the widest applications because it often outperforms its counterparts. However, the bootstrap still has limitations when its operations are contemplated. Therefore, the purpose of this study is to examine an alternative, new resampling method…

Stability of Nonlinear Principal Components Analysis: An Empirical Study Using the Balanced Bootstrap

ERIC Educational Resources Information Center

Linting, Marielle; Meulman, Jacqueline J.; Groenen, Patrick J. F.; van der Kooij, Anita J.

2007-01-01

Principal components analysis (PCA) is used to explore the structure of data sets containing linearly related numeric variables. Alternatively, nonlinear PCA can handle possibly nonlinearly related numeric as well as nonnumeric variables. For linear PCA, the stability of its solution can be established under the assumption of multivariate…

Designing to Support Command and Control in Urban Firefighting

DTIC Science & Technology

2008-06-01

complex human- machine systems. Keywords: Command and control, firefighting, cognitive systems engineering, cognitive task analysis 1...Elm, W. (2000). Bootstrapping multiple converging cognitive task analysis techniques for system design. In J.M.C. Schraagen, S.F. Chipman, & V.L...Shalin, (Eds.), Cognitive Task Analysis . (pp. 317-340). Mahwah, NJ: Lawrence Erlbaum. Rasmussen, J., Pejtersen, A., Goodman, L. (1994). Cognitive

Phylogenetic Analysis of Prevalent Tuberculosis and Non-Tuberculosis Mycobacteria in Isfahan, Iran, Based on a 360 bp Sequence of the rpoB Gene

PubMed Central

Nasr Esfahani, Bahram; Moghim, Sharareh; Ghasemian Safaei, Hajieh; Moghoofei, Mohsen; Sedighi, Mansour; Hadifar, Shima

2016-01-01

Background Taxonomic and phylogenetic studies of Mycobacterium species have been based around the 16sRNA gene for many years. However, due to the high strain similarity between species in the Mycobacterium genus (94.3% - 100%), defining a valid phylogenetic tree is difficult; consequently, its use in estimating the boundaries between species is limited. The sequence of the rpoB gene makes it an appropriate gene for phylogenetic analysis, especially in bacteria with limited variation. Objectives In the present study, a 360bp sequence of rpoB was used for precise classification of Mycobacterium strains isolated in Isfahan, Iran. Materials and Methods From February to October 2013, 57 clinical and environmental isolates were collected, subcultured, and identified by phenotypic methods. After DNA extraction, a 360bp fragment was PCR-amplified and sequenced. The phylogenetic tree was constructed based on consensus sequence data, using MEGA5 software. Results Slow and fast-growing groups of the Mycobacterium strains were clearly differentiated based on the constructed tree of 56 common Mycobacterium isolates. Each species with a unique title in the tree was identified; in total, 13 nods with a bootstrap value of over 50% were supported. Among the slow-growing group was Mycobacterium kansasii, with M. tuberculosis in a cluster with a bootstrap value of 98% and M. gordonae in another cluster with a bootstrap value of 90%. In the fast-growing group, one cluster with a bootstrap value of 89% was defined, including all fast-growing members present in this study. Conclusions The results suggest that only the application of the rpoB gene sequence is sufficient for taxonomic categorization and definition of a new Mycobacterium species, due to its high resolution power and proper variation in its sequence (85% - 100%); the resulting tree has high validity. PMID:27284397

Fast Computation of the Two-Point Correlation Function in the Age of Big Data

NASA Astrophysics Data System (ADS)

Pellegrino, Andrew; Timlin, John

2018-01-01

We present a new code which quickly computes the two-point correlation function for large sets of astronomical data. This code combines the ease of use of Python with the speed of parallel shared libraries written in C. We include the capability to compute the auto- and cross-correlation statistics, and allow the user to calculate the three-dimensional and angular correlation functions. Additionally, the code automatically divides the user-provided sky masks into contiguous subsamples of similar size, using the HEALPix pixelization scheme, for the purpose of resampling. Errors are computed using jackknife and bootstrap resampling in a way that adds negligible extra runtime, even with many subsamples. We demonstrate comparable speed with other clustering codes, and code accuracy compared to known and analytic results.

Comparison of Parametric and Nonparametric Bootstrap Methods for Estimating Random Error in Equipercentile Equating

ERIC Educational Resources Information Center

Cui, Zhongmin; Kolen, Michael J.

2008-01-01

This article considers two methods of estimating standard errors of equipercentile equating: the parametric bootstrap method and the nonparametric bootstrap method. Using a simulation study, these two methods are compared under three sample sizes (300, 1,000, and 3,000), for two test content areas (the Iowa Tests of Basic Skills Maps and Diagrams…

Test of bootstrap current models using high- β p EAST-demonstration plasmas on DIII-D

DOE PAGES

Ren, Qilong; Lao, Lang L.; Garofalo, Andrea M.; ...

2015-01-12

Magnetic measurements together with kinetic profile and motional Stark effect measurements are used in full kinetic equilibrium reconstructions to test the Sauter and NEO bootstrap current models in a DIII-D high-more » $${{\\beta}_{\\text{p}}}$$ EAST-demonstration experiment. This aims at developing on DIII-D a high bootstrap current scenario to be extended on EAST for a demonstration of true steady-state at high performance and uses EAST-similar operational conditions: plasma shape, plasma current, toroidal magnetic field, total heating power and current ramp-up rate. It is found that the large edge bootstrap current in these high-$${{\\beta}_{\\text{p}}}$$ plasmas allows the use of magnetic measurements to clearly distinguish the two bootstrap current models. In these high collisionality and high-$${{\\beta}_{\\text{p}}}$$ plasmas, the Sauter model overpredicts the peak of the edge current density by about 30%, while the first-principle kinetic NEO model is in close agreement with the edge current density of the reconstructed equilibrium. Furthermore, these results are consistent with recent work showing that the Sauter model largely overestimates the edge bootstrap current at high collisionality.« less

The prospects for magnetohydrodynamic stability in advanced tokamak regimes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manickam, J.; Chance, M.S.; Jardin, S.C.

1994-05-01

Stability analysis of advanced regime tokamaks is presented. Here advanced regimes are defined to include configurations where the ratio of the bootstrap current, [ital I][sub BS], to the total plasma current, [ital I][sub [ital p

Parameter uncertainty and nonstationarity in regional extreme rainfall frequency analysis in Qu River Basin, East China

NASA Astrophysics Data System (ADS)

Zhu, Q.; Xu, Y. P.; Gu, H.

2014-12-01

Traditionally, regional frequency analysis methods were developed for stationary environmental conditions. Nevertheless, recent studies have identified significant changes in hydrological records, leading to the 'death' of stationarity. Besides, uncertainty in hydrological frequency analysis is persistent. This study aims to investigate the impact of one of the most important uncertainty sources, parameter uncertainty, together with nonstationarity, on design rainfall depth in Qu River Basin, East China. A spatial bootstrap is first proposed to analyze the uncertainty of design rainfall depth estimated by regional frequency analysis based on L-moments and estimated on at-site scale. Meanwhile, a method combining the generalized additive models with 30-year moving window is employed to analyze non-stationarity existed in the extreme rainfall regime. The results show that the uncertainties of design rainfall depth with 100-year return period under stationary conditions estimated by regional spatial bootstrap can reach 15.07% and 12.22% with GEV and PE3 respectively. On at-site scale, the uncertainties can reach 17.18% and 15.44% with GEV and PE3 respectively. In non-stationary conditions, the uncertainties of maximum rainfall depth (corresponding to design rainfall depth) with 0.01 annual exceedance probability (corresponding to 100-year return period) are 23.09% and 13.83% with GEV and PE3 respectively. Comparing the 90% confidence interval, the uncertainty of design rainfall depth resulted from parameter uncertainty is less than that from non-stationarity frequency analysis with GEV, however, slightly larger with PE3. This study indicates that the spatial bootstrap can be successfully applied to analyze the uncertainty of design rainfall depth on both regional and at-site scales. And the non-stationary analysis shows that the differences between non-stationary quantiles and their stationary equivalents are important for decision makes of water resources management and risk management.

Sevelamer is cost effective versus calcium carbonate for the first-line treatment of hyperphosphatemia in new patients to hemodialysis: a patient-level economic evaluation of the INDEPENDENT-HD study.

PubMed

Ruggeri, Matteo; Bellasi, Antonio; Cipriani, Filippo; Molony, Donald; Bell, Cynthia; Russo, Domenico; Di Iorio, Biagio

2015-10-01

The recent multicenter, randomized, open-label INDEPENDENT study demonstrated that sevelamer improves survival in new to hemodialysis (HD) patients compared with calcium carbonate. The objective of this study was to determine the cost-effectiveness of sevelamer versus calcium carbonate for patients new to HD, using patient-level data from the INDEPENDENT study. Cost-effectiveness analysis. Adult patients new to HD in Italy. A patient-level cost-effectiveness analysis was conducted from the perspective of the Servizio Sanitario Nazionale, Italy's national health service. The analysis was conducted for a 3-year time horizon. The cost of dialysis was excluded from the base case analysis. Sevelamer was compared to calcium carbonate. Total life years (LYs), total costs, and the incremental cost per LY gained were calculated. Bootstrapping was used to estimate confidence intervals around LYs, costs, and cost-effectiveness and to calculate the cost-effectiveness acceptability curve. Sevelamer was associated with a gain of 0.26 in LYs compared to calcium carbonate, over the 3-year time horizon. Total drug costs were €3,282 higher for sevelamer versus calcium carbonate, while total hospitalization costs were €2,020 lower for sevelamer versus calcium carbonate. The total incremental cost of sevelamer versus calcium carbonate was €1,262, resulting in a cost per LY gained of €4,897. The bootstrap analysis demonstrated that sevelamer was cost effective compared with calcium carbonate in 99.4 % of 10,000 bootstrap replicates, assuming a willingness-to-pay threshold of €20,000 per LY gained. Data on hospitalizations was taken from a post hoc retrospective chart review of the patients included in the INDEPENDENT study. Patient quality of life or health utility was not included in the analysis. Sevelamer is a cost-effective alternative to calcium carbonate for the first-line treatment of hyperphosphatemia in new to HD patients in Italy.

Electron transport fluxes in potato plateau regime

NASA Astrophysics Data System (ADS)

Shaing, K. C.; Hazeltine, R. D.

1997-12-01

Electron transport fluxes in the potato plateau regime are calculated from the solutions of the drift kinetic equation and fluid equations. It is found that the bootstrap current density remains finite in the region close to the magnetic axis, although it decreases with increasing collision frequency. This finite amount of the bootstrap current in the relatively collisional regime is important in modeling tokamak startup with 100% bootstrap current.

Bootstrap current in a tokamak

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kessel, C.E.

1994-03-01

The bootstrap current in a tokamak is examined by implementing the Hirshman-Sigmar model and comparing the predicted current profiles with those from two popular approximations. The dependences of the bootstrap current profile on the plasma properties are illustrated. The implications for steady state tokamaks are presented through two constraints; the pressure profile must be peaked and {beta}{sub p} must be kept below a critical value.

A Statistician's View of Upcoming Grand Challenges

NASA Astrophysics Data System (ADS)

Meng, Xiao Li

2010-01-01

In this session we have seen some snapshots of the broad spectrum of challenges, in this age of huge, complex, computer-intensive models, data, instruments,and questions. These challenges bridge astronomy at many wavelengths; basic physics; machine learning; -- and statistics. At one end of our spectrum, we think of 'compressing' the data with non-parametric methods. This raises the question of creating 'pseudo-replicas' of the data for uncertainty estimates. What would be involved in, e.g. boot-strap and related methods? Somewhere in the middle are these non-parametric methods for encapsulating the uncertainty information. At the far end, we find more model-based approaches, with the physics model embedded in the likelihood and analysis. The other distinctive problem is really the 'black-box' problem, where one has a complicated e.g. fundamental physics-based computer code, or 'black box', and one needs to know how changing the parameters at input -- due to uncertainties of any kind -- will map to changing the output. All of these connect to challenges in complexity of data and computation speed. Dr. Meng will highlight ways to 'cut corners' with advanced computational techniques, such as Parallel Tempering and Equal Energy methods. As well, there are cautionary tales of running automated analysis with real data -- where "30 sigma" outliers due to data artifacts can be more common than the astrophysical event of interest.

External heating and current drive source requirements towards steady-state operation in ITER

NASA Astrophysics Data System (ADS)

Poli, F. M.; Kessel, C. E.; Bonoli, P. T.; Batchelor, D. B.; Harvey, R. W.; Snyder, P. B.

2014-07-01

Steady state scenarios envisaged for ITER aim at optimizing the bootstrap current, while maintaining sufficient confinement and stability to provide the necessary fusion yield. Non-inductive scenarios will need to operate with internal transport barriers (ITBs) in order to reach adequate fusion gain at typical currents of 9 MA. However, the large pressure gradients associated with ITBs in regions of weak or negative magnetic shear can be conducive to ideal MHD instabilities, reducing the no-wall limit. The E × B flow shear from toroidal plasma rotation is expected to be low in ITER, with a major role in the ITB dynamics being played by magnetic geometry. Combinations of heating and current drive (H/CD) sources that sustain reversed magnetic shear profiles throughout the discharge are the focus of this work. Time-dependent transport simulations indicate that a combination of electron cyclotron (EC) and lower hybrid (LH) waves is a promising route towards steady state operation in ITER. The LH forms and sustains expanded barriers and the EC deposition at mid-radius freezes the bootstrap current profile stabilizing the barrier and leading to confinement levels 50% higher than typical H-mode energy confinement times. Using LH spectra with spectrum centred on parallel refractive index of 1.75-1.85, the performance of these plasma scenarios is close to the ITER target of 9 MA non-inductive current, global confinement gain H98 = 1.6 and fusion gain Q = 5.

Mindfulness, Empathy, and Intercultural Sensitivity amongst Undergraduate Students

ERIC Educational Resources Information Center

Menardo, Dayne Arvin

2017-01-01

This study examined the relationships amongst mindfulness, empathy, and intercultural sensitivity. Non-parametric analysis were conducted through Spearman and Hayes's PROCESS bootstrapping to examine the relationship between mindfulness and intercultural sensitivity, and whether empathy mediates the relationship between mindfulness and…

Effect of non-normality on test statistics for one-way independent groups designs.

PubMed

Cribbie, Robert A; Fiksenbaum, Lisa; Keselman, H J; Wilcox, Rand R

2012-02-01

The data obtained from one-way independent groups designs is typically non-normal in form and rarely equally variable across treatment populations (i.e., population variances are heterogeneous). Consequently, the classical test statistic that is used to assess statistical significance (i.e., the analysis of variance F test) typically provides invalid results (e.g., too many Type I errors, reduced power). For this reason, there has been considerable interest in finding a test statistic that is appropriate under conditions of non-normality and variance heterogeneity. Previously recommended procedures for analysing such data include the James test, the Welch test applied either to the usual least squares estimators of central tendency and variability, or the Welch test with robust estimators (i.e., trimmed means and Winsorized variances). A new statistic proposed by Krishnamoorthy, Lu, and Mathew, intended to deal with heterogeneous variances, though not non-normality, uses a parametric bootstrap procedure. In their investigation of the parametric bootstrap test, the authors examined its operating characteristics under limited conditions and did not compare it to the Welch test based on robust estimators. Thus, we investigated how the parametric bootstrap procedure and a modified parametric bootstrap procedure based on trimmed means perform relative to previously recommended procedures when data are non-normal and heterogeneous. The results indicated that the tests based on trimmed means offer the best Type I error control and power when variances are unequal and at least some of the distribution shapes are non-normal. © 2011 The British Psychological Society.

Making Sense of Sensemaking: Requirements of a Cognitive Analysis to Support C2 Decision Support System Design

DTIC Science & Technology

2006-06-01

heart of a distinction within the CSE community with respect to the differences between Cognitive Task Analysis (CTA) and Cognitive Work Analysis...Wesley. Pirolli, P. and Card, S. (2005). The sensemaking process and leverage points for analyst technology as identified through cognitive task analysis . In...D. D., and Elm, W. C. (2000). Cognitive task analysis as bootstrapping multiple converging techniques. In Schraagen, Chipman, and Shalin (Eds

Multi-baseline bootstrapping at the Navy precision optical interferometer

NASA Astrophysics Data System (ADS)

Armstrong, J. T.; Schmitt, H. R.; Mozurkewich, D.; Jorgensen, A. M.; Muterspaugh, M. W.; Baines, E. K.; Benson, J. A.; Zavala, Robert T.; Hutter, D. J.

2014-07-01

The Navy Precision Optical Interferometer (NPOI) was designed from the beginning to support baseline boot- strapping with equally-spaced array elements. The motivation was the desire to image the surfaces of resolved stars with the maximum resolution possible with a six-element array. Bootstrapping two baselines together to track fringes on a third baseline has been used at the NPOI for many years, but the capabilities of the fringe tracking software did not permit us to bootstrap three or more baselines together. Recently, both a new backend (VISION; Tennessee State Univ.) and new hardware and firmware (AZ Embedded Systems and New Mexico Tech, respectively) for the current hybrid backend have made multi-baseline bootstrapping possible.

Bootstrap and fast wave current drive for tokamak reactors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ehst, D.A.

1991-09-01

Using the multi-species neoclassical treatment of Hirshman and Sigmar we study steady state bootstrap equilibria with seed currents provided by low frequency (ICRF) fast waves and with additional surface current density driven by lower hybrid waves. This study applies to reactor plasmas of arbitrary aspect ratio. IN one limit the bootstrap component can supply nearly the total equilibrium current with minimal driving power (< 20 MW). However, for larger total currents considerable driving power is required (for ITER: I{sub o} = 18 MA needs P{sub FW} = 15 MW, P{sub LH} = 75 MW). A computational survey of bootstrap fractionmore » and current drive efficiency is presented. 11 refs., 8 figs.« less

Comparison of mode estimation methods and application in molecular clock analysis

NASA Technical Reports Server (NTRS)

Hedges, S. Blair; Shah, Prachi

2003-01-01

BACKGROUND: Distributions of time estimates in molecular clock studies are sometimes skewed or contain outliers. In those cases, the mode is a better estimator of the overall time of divergence than the mean or median. However, different methods are available for estimating the mode. We compared these methods in simulations to determine their strengths and weaknesses and further assessed their performance when applied to real data sets from a molecular clock study. RESULTS: We found that the half-range mode and robust parametric mode methods have a lower bias than other mode methods under a diversity of conditions. However, the half-range mode suffers from a relatively high variance and the robust parametric mode is more susceptible to bias by outliers. We determined that bootstrapping reduces the variance of both mode estimators. Application of the different methods to real data sets yielded results that were concordant with the simulations. CONCLUSION: Because the half-range mode is a simple and fast method, and produced less bias overall in our simulations, we recommend the bootstrapped version of it as a general-purpose mode estimator and suggest a bootstrap method for obtaining the standard error and 95% confidence interval of the mode.

Examining Differential Item Functioning: IRT-Based Detection in the Framework of Confirmatory Factor Analysis

ERIC Educational Resources Information Center

Dimitrov, Dimiter M.

2017-01-01

This article offers an approach to examining differential item functioning (DIF) under its item response theory (IRT) treatment in the framework of confirmatory factor analysis (CFA). The approach is based on integrating IRT- and CFA-based testing of DIF and using bias-corrected bootstrap confidence intervals with a syntax code in Mplus.

A Note on Procrustean Rotation in Exploratory Factor Analysis: A Computer Intensive Approach to Goodness-of-Fit Evaluation.

ERIC Educational Resources Information Center

Raykov, Tenko; Little, Todd D.

1999-01-01

Describes a method for evaluating results of Procrustean rotation to a target factor pattern matrix in exploratory factor analysis. The approach, based on the bootstrap method, yields empirical approximations of the sampling distributions of: (1) differences between target elements and rotated factor pattern matrices; and (2) the overall…

Confidence limit calculation for antidotal potency ratio derived from lethal dose 50

PubMed Central

Manage, Ananda; Petrikovics, Ilona

2013-01-01

AIM: To describe confidence interval calculation for antidotal potency ratios using bootstrap method. METHODS: We can easily adapt the nonparametric bootstrap method which was invented by Efron to construct confidence intervals in such situations like this. The bootstrap method is a resampling method in which the bootstrap samples are obtained by resampling from the original sample. RESULTS: The described confidence interval calculation using bootstrap method does not require the sampling distribution antidotal potency ratio. This can serve as a substantial help for toxicologists, who are directed to employ the Dixon up-and-down method with the application of lower number of animals to determine lethal dose 50 values for characterizing the investigated toxic molecules and eventually for characterizing the antidotal protections by the test antidotal systems. CONCLUSION: The described method can serve as a useful tool in various other applications. Simplicity of the method makes it easier to do the calculation using most of the programming software packages. PMID:25237618

Topics in Statistical Calibration

DTIC Science & Technology

2014-03-27

on a parametric bootstrap where, instead of sampling directly from the residuals , samples are drawn from a normal distribution. This procedure will...addition to centering them (Davison and Hinkley, 1997). When there are outliers in the residuals , the bootstrap distribution of x̂0 can become skewed or...based and inversion methods using the linear mixed-effects model. Then, a simple parametric bootstrap algorithm is proposed that can be used to either

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shaing, K.C.; Hazeltine, R.D.

Electron transport fluxes in the potato plateau regime are calculated from the solutions of the drift kinetic equation and fluid equations. It is found that the bootstrap current density remains finite in the region close to the magnetic axis, although it decreases with increasing collision frequency. This finite amount of the bootstrap current in the relatively collisional regime is important in modeling tokamak startup with 100{percent} bootstrap current. {copyright} {ital 1997 American Institute of Physics.}

Variable selection under multiple imputation using the bootstrap in a prognostic study

PubMed Central

Heymans, Martijn W; van Buuren, Stef; Knol, Dirk L; van Mechelen, Willem; de Vet, Henrica CW

2007-01-01

Background Missing data is a challenging problem in many prognostic studies. Multiple imputation (MI) accounts for imputation uncertainty that allows for adequate statistical testing. We developed and tested a methodology combining MI with bootstrapping techniques for studying prognostic variable selection. Method In our prospective cohort study we merged data from three different randomized controlled trials (RCTs) to assess prognostic variables for chronicity of low back pain. Among the outcome and prognostic variables data were missing in the range of 0 and 48.1%. We used four methods to investigate the influence of respectively sampling and imputation variation: MI only, bootstrap only, and two methods that combine MI and bootstrapping. Variables were selected based on the inclusion frequency of each prognostic variable, i.e. the proportion of times that the variable appeared in the model. The discriminative and calibrative abilities of prognostic models developed by the four methods were assessed at different inclusion levels. Results We found that the effect of imputation variation on the inclusion frequency was larger than the effect of sampling variation. When MI and bootstrapping were combined at the range of 0% (full model) to 90% of variable selection, bootstrap corrected c-index values of 0.70 to 0.71 and slope values of 0.64 to 0.86 were found. Conclusion We recommend to account for both imputation and sampling variation in sets of missing data. The new procedure of combining MI with bootstrapping for variable selection, results in multivariable prognostic models with good performance and is therefore attractive to apply on data sets with missing values. PMID:17629912

Assessing uncertainties in superficial water provision by different bootstrap-based techniques

NASA Astrophysics Data System (ADS)

Rodrigues, Dulce B. B.; Gupta, Hoshin V.; Mendiondo, Eduardo Mario

2014-05-01

An assessment of water security can incorporate several water-related concepts, characterizing the interactions between societal needs, ecosystem functioning, and hydro-climatic conditions. The superficial freshwater provision level depends on the methods chosen for 'Environmental Flow Requirement' estimations, which integrate the sources of uncertainty in the understanding of how water-related threats to aquatic ecosystem security arise. Here, we develop an uncertainty assessment of superficial freshwater provision based on different bootstrap techniques (non-parametric resampling with replacement). To illustrate this approach, we use an agricultural basin (291 km2) within the Cantareira water supply system in Brazil monitored by one daily streamflow gage (24-year period). The original streamflow time series has been randomly resampled for different times or sample sizes (N = 500; ...; 1000), then applied to the conventional bootstrap approach and variations of this method, such as: 'nearest neighbor bootstrap'; and 'moving blocks bootstrap'. We have analyzed the impact of the sampling uncertainty on five Environmental Flow Requirement methods, based on: flow duration curves or probability of exceedance (Q90%, Q75% and Q50%); 7-day 10-year low-flow statistic (Q7,10); and presumptive standard (80% of the natural monthly mean ?ow). The bootstrap technique has been also used to compare those 'Environmental Flow Requirement' (EFR) methods among themselves, considering the difference between the bootstrap estimates and the "true" EFR characteristic, which has been computed averaging the EFR values of the five methods and using the entire streamflow record at monitoring station. This study evaluates the bootstrapping strategies, the representativeness of streamflow series for EFR estimates and their confidence intervals, in addition to overview of the performance differences between the EFR methods. The uncertainties arisen during EFR methods assessment will be propagated through water security indicators referring to water scarcity and vulnerability, seeking to provide meaningful support to end-users and water managers facing the incorporation of uncertainties in the decision making process.

Comparison of variance estimators for meta-analysis of instrumental variable estimates

PubMed Central

Schmidt, AF; Hingorani, AD; Jefferis, BJ; White, J; Groenwold, RHH; Dudbridge, F

2016-01-01

Abstract Background: Mendelian randomization studies perform instrumental variable (IV) analysis using genetic IVs. Results of individual Mendelian randomization studies can be pooled through meta-analysis. We explored how different variance estimators influence the meta-analysed IV estimate. Methods: Two versions of the delta method (IV before or after pooling), four bootstrap estimators, a jack-knife estimator and a heteroscedasticity-consistent (HC) variance estimator were compared using simulation. Two types of meta-analyses were compared, a two-stage meta-analysis pooling results, and a one-stage meta-analysis pooling datasets. Results: Using a two-stage meta-analysis, coverage of the point estimate using bootstrapped estimators deviated from nominal levels at weak instrument settings and/or outcome probabilities ≤ 0.10. The jack-knife estimator was the least biased resampling method, the HC estimator often failed at outcome probabilities ≤ 0.50 and overall the delta method estimators were the least biased. In the presence of between-study heterogeneity, the delta method before meta-analysis performed best. Using a one-stage meta-analysis all methods performed equally well and better than two-stage meta-analysis of greater or equal size. Conclusions: In the presence of between-study heterogeneity, two-stage meta-analyses should preferentially use the delta method before meta-analysis. Weak instrument bias can be reduced by performing a one-stage meta-analysis. PMID:27591262

Synthetic consciousness: the distributed adaptive control perspective

PubMed Central

2016-01-01

Understanding the nature of consciousness is one of the grand outstanding scientific challenges. The fundamental methodological problem is how phenomenal first person experience can be accounted for in a third person verifiable form, while the conceptual challenge is to both define its function and physical realization. The distributed adaptive control theory of consciousness (DACtoc) proposes answers to these three challenges. The methodological challenge is answered relative to the hard problem and DACtoc proposes that it can be addressed using a convergent synthetic methodology using the analysis of synthetic biologically grounded agents, or quale parsing. DACtoc hypothesizes that consciousness in both its primary and secondary forms serves the ability to deal with the hidden states of the world and emerged during the Cambrian period, affording stable multi-agent environments to emerge. The process of consciousness is an autonomous virtualization memory, which serializes and unifies the parallel and subconscious simulations of the hidden states of the world that are largely due to other agents and the self with the objective to extract norms. These norms are in turn projected as value onto the parallel simulation and control systems that are driving action. This functional hypothesis is mapped onto the brainstem, midbrain and the thalamo-cortical and cortico-cortical systems and analysed with respect to our understanding of deficits of consciousness. Subsequently, some of the implications and predictions of DACtoc are outlined, in particular, the prediction that normative bootstrapping of conscious agents is predicated on an intentionality prior. In the view advanced here, human consciousness constitutes the ultimate evolutionary transition by allowing agents to become autonomous with respect to their evolutionary priors leading to a post-biological Anthropocene. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431526

A Behavior-Based Intervention That Prevents Sexual Assault: the Results of a Matched-Pairs, Cluster-Randomized Study in Nairobi, Kenya.

PubMed

Baiocchi, Michael; Omondi, Benjamin; Langat, Nickson; Boothroyd, Derek B; Sinclair, Jake; Pavia, Lee; Mulinge, Munyae; Githua, Oscar; Golden, Neville H; Sarnquist, Clea

2017-10-01

The study's design was a cluster-randomized, matched-pairs, parallel trial of a behavior-based sexual assault prevention intervention in the informal settlements. The participants were primary school girls aged 10-16. Classroom-based interventions for girls and boys were delivered by instructors from the same settlements, at the same time, over six 2-h sessions. The girls' program had components of empowerment, gender relations, and self-defense. The boys' program promotes healthy gender norms. The control arm of the study received a health and hygiene curriculum. The primary outcome was the rate of sexual assault in the prior 12 months at the cluster level (school level). Secondary outcomes included the generalized self-efficacy scale, the distribution of number of times victims were sexually assaulted in the prior period, skills used, disclosure rates, and distribution of perpetrators. Difference-in-differences estimates are reported with bootstrapped confidence intervals. Fourteen schools with 3147 girls from the intervention group and 14 schools with 2539 girls from the control group were included in the analysis. We estimate a 3.7 % decrease, p = 0.03 and 95 % CI = (0.4, 8.0), in risk of sexual assault in the intervention group due to the intervention (initially 7.3 % at baseline). We estimate an increase in mean generalized self-efficacy score of 0.19 (baseline average 3.1, on a 1-4 scale), p = 0.0004 and 95 % CI = (0.08, 0.39). This innovative intervention that combined parallel training for young adolescent girls and boys in school settings showed significant reduction in the rate of sexual assault among girls in this population.

Synthetic consciousness: the distributed adaptive control perspective.

PubMed

Verschure, Paul F M J

2016-08-19

Understanding the nature of consciousness is one of the grand outstanding scientific challenges. The fundamental methodological problem is how phenomenal first person experience can be accounted for in a third person verifiable form, while the conceptual challenge is to both define its function and physical realization. The distributed adaptive control theory of consciousness (DACtoc) proposes answers to these three challenges. The methodological challenge is answered relative to the hard problem and DACtoc proposes that it can be addressed using a convergent synthetic methodology using the analysis of synthetic biologically grounded agents, or quale parsing. DACtoc hypothesizes that consciousness in both its primary and secondary forms serves the ability to deal with the hidden states of the world and emerged during the Cambrian period, affording stable multi-agent environments to emerge. The process of consciousness is an autonomous virtualization memory, which serializes and unifies the parallel and subconscious simulations of the hidden states of the world that are largely due to other agents and the self with the objective to extract norms. These norms are in turn projected as value onto the parallel simulation and control systems that are driving action. This functional hypothesis is mapped onto the brainstem, midbrain and the thalamo-cortical and cortico-cortical systems and analysed with respect to our understanding of deficits of consciousness. Subsequently, some of the implications and predictions of DACtoc are outlined, in particular, the prediction that normative bootstrapping of conscious agents is predicated on an intentionality prior. In the view advanced here, human consciousness constitutes the ultimate evolutionary transition by allowing agents to become autonomous with respect to their evolutionary priors leading to a post-biological Anthropocene.This article is part of the themed issue 'The major synthetic evolutionary transitions'. © 2016 The Author(s).

Quantifying Variations In Multi-parameter Models With The Photon Clean Method (PCM) And Bootstrap Methods

NASA Astrophysics Data System (ADS)

Carpenter, Matthew H.; Jernigan, J. G.

2007-05-01

We present examples of an analysis progression consisting of a synthesis of the Photon Clean Method (Carpenter, Jernigan, Brown, Beiersdorfer 2007) and bootstrap methods to quantify errors and variations in many-parameter models. The Photon Clean Method (PCM) works well for model spaces with large numbers of parameters proportional to the number of photons, therefore a Monte Carlo paradigm is a natural numerical approach. Consequently, PCM, an "inverse Monte-Carlo" method, requires a new approach for quantifying errors as compared to common analysis methods for fitting models of low dimensionality. This presentation will explore the methodology and presentation of analysis results derived from a variety of public data sets, including observations with XMM-Newton, Chandra, and other NASA missions. Special attention is given to the visualization of both data and models including dynamic interactive presentations. This work was performed under the auspices of the Department of Energy under contract No. W-7405-Eng-48. We thank Peter Beiersdorfer and Greg Brown for their support of this technical portion of a larger program related to science with the LLNL EBIT program.

Different methodologies to quantify uncertainties of air emissions.

PubMed

Romano, Daniela; Bernetti, Antonella; De Lauretis, Riccardo

2004-10-01

Characterization of the uncertainty associated with air emission estimates is of critical importance especially in the compilation of air emission inventories. In this paper, two different theories are discussed and applied to evaluate air emissions uncertainty. In addition to numerical analysis, which is also recommended in the framework of the United Nation Convention on Climate Change guidelines with reference to Monte Carlo and Bootstrap simulation models, fuzzy analysis is also proposed. The methodologies are discussed and applied to an Italian example case study. Air concentration values are measured from two electric power plants: a coal plant, consisting of two boilers and a fuel oil plant, of four boilers; the pollutants considered are sulphur dioxide (SO(2)), nitrogen oxides (NO(X)), carbon monoxide (CO) and particulate matter (PM). Monte Carlo, Bootstrap and fuzzy methods have been applied to estimate uncertainty of these data. Regarding Monte Carlo, the most accurate results apply to Gaussian distributions; a good approximation is also observed for other distributions with almost regular features either positive asymmetrical or negative asymmetrical. Bootstrap, on the other hand, gives a good uncertainty estimation for irregular and asymmetrical distributions. The logic of fuzzy analysis, where data are represented as vague and indefinite in opposition to the traditional conception of neatness, certain classification and exactness of the data, follows a different description. In addition to randomness (stochastic variability) only, fuzzy theory deals with imprecision (vagueness) of data. Fuzzy variance of the data set was calculated; the results cannot be directly compared with empirical data but the overall performance of the theory is analysed. Fuzzy theory may appear more suitable for qualitative reasoning than for a quantitative estimation of uncertainty, but it suits well when little information and few measurements are available and when distributions of data are not properly known.

Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset

PubMed Central

2011-01-01

Background The avian family Cettiidae, including the genera Cettia, Urosphena, Tesia, Abroscopus and Tickellia and Orthotomus cucullatus, has recently been proposed based on analysis of a small number of loci and species. The close relationship of most of these taxa was unexpected, and called for a comprehensive study based on multiple loci and dense taxon sampling. In the present study, we infer the relationships of all except one of the species in this family using one mitochondrial and three nuclear loci. We use traditional gene tree methods (Bayesian inference, maximum likelihood bootstrapping, parsimony bootstrapping), as well as a recently developed Bayesian species tree approach (*BEAST) that accounts for lineage sorting processes that might produce discordance between gene trees. We also analyse mitochondrial DNA for a larger sample, comprising multiple individuals and a large number of subspecies of polytypic species. Results There are many topological incongruences among the single-locus trees, although none of these is strongly supported. The multi-locus tree inferred using concatenated sequences and the species tree agree well with each other, and are overall well resolved and well supported by the data. The main discrepancy between these trees concerns the most basal split. Both methods infer the genus Cettia to be highly non-monophyletic, as it is scattered across the entire family tree. Deep intraspecific divergences are revealed, and one or two species and one subspecies are inferred to be non-monophyletic (differences between methods). Conclusions The molecular phylogeny presented here is strongly inconsistent with the traditional, morphology-based classification. The remarkably high degree of non-monophyly in the genus Cettia is likely to be one of the most extraordinary examples of misconceived relationships in an avian genus. The phylogeny suggests instances of parallel evolution, as well as highly unequal rates of morphological divergence in different lineages. This complex morphological evolution apparently misled earlier taxonomists. These results underscore the well-known but still often neglected problem of basing classifications on overall morphological similarity. Based on the molecular data, a revised taxonomy is proposed. Although the traditional and species tree methods inferred much the same tree in the present study, the assumption by species tree methods that all species are monophyletic is a limitation in these methods, as some currently recognized species might have more complex histories. PMID:22142197

Neoclassical, semi-collisional tearing mode theory in an axisymmetric torus

NASA Astrophysics Data System (ADS)

Connor, J. W.; Hastie, R. J.; Helander, P.

2017-12-01

A set of layer equations for determining the stability of semi-collisional tearing modes in an axisymmetric torus, incorporating neoclassical physics, in the small ion Larmor radius limit, is provided. These can be used as an inner layer module for inclusion in numerical codes that asymptotically match the layer to toroidal calculations of the tearing mode stability index, \\prime $ . They are more complete than in earlier work and comprise equations for the perturbed electron density and temperature, the ion temperature, Ampère's law and the vorticity equation, amounting to a twelvth-order set of radial differential equations. While the toroidal geometry is kept quite general when treating the classical and Pfirsch-Schlüter transport, parallel bootstrap current and semi-collisional physics, it is assumed that the fraction of trapped particles is small for the banana regime contribution. This is to justify the use of a model collision term when acting on the localised (in velocity space) solutions that remain after the Spitzer solutions have been exploited to account for the bulk of the passing distributions. In this respect, unlike standard neoclassical transport theory, the calculation involves the second Spitzer solution connected with a parallel temperature gradient, because this stability problem involves parallel temperature gradients that cannot occur in equilibrium toroidal transport theory. Furthermore, a calculation of the linearised neoclassical radial transport of toroidal momentum for general geometry is required to complete the vorticity equation. The solutions of the resulting set of equations do not match properly to the ideal magnetohydrodynamic (MHD) equations at large distances from the layer, and a further, intermediate layer involving ion corrections to the electrical conductivity and ion parallel thermal transport is invoked to achieve this matching and allow one to correctly calculate the layer \\prime $ .

Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti.

PubMed

Copetti, Dario; Búrquez, Alberto; Bustamante, Enriquena; Charboneau, Joseph L M; Childs, Kevin L; Eguiarte, Luis E; Lee, Seunghee; Liu, Tiffany L; McMahon, Michelle M; Whiteman, Noah K; Wing, Rod A; Wojciechowski, Martin F; Sanderson, Michael J

2017-11-07

Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus ( Carnegiea gigantea ) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae ( Pachycereus , Lophocereus , and Stenocereus ) and a more distant outgroup cactus, Pereskia We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed "hemiplasy." The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti. Published under the PNAS license.

Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti

PubMed Central

Búrquez, Alberto; Bustamante, Enriquena; Charboneau, Joseph L. M.; Childs, Kevin L.; Eguiarte, Luis E.; Lee, Seunghee; Liu, Tiffany L.; McMahon, Michelle M.; Whiteman, Noah K.; Wing, Rod A.; Wojciechowski, Martin F.; Sanderson, Michael J.

2017-01-01

Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae (Pachycereus, Lophocereus, and Stenocereus) and a more distant outgroup cactus, Pereskia. We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed “hemiplasy.” The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti. PMID:29078296

Variable Importance in Multivariate Group Comparisons.

ERIC Educational Resources Information Center

Huberty, Carl J.; Wisenbaker, Joseph M.

1992-01-01

Interpretations of relative variable importance in multivariate analysis of variance are discussed, with attention to (1) latent construct definition; (2) linear discriminant function scores; and (3) grouping variable effects. Two numerical ranking methods are proposed and compared by the bootstrap approach using two real data sets. (SLD)

Taxonomic evaluation of Streptomyces hirsutus and related species using multi-locus sequence analysis

USDA-ARS?s Scientific Manuscript database

Phylogenetic analyses of species of Streptomyces based on 16S rRNA gene sequences resulted in a statistically well-supported clade (100% bootstrap value) containing 8 species having very similar gross morphology. These species, including Streptomyces bambergiensis, Streptomyces chlorus, Streptomyces...

More accurate, calibrated bootstrap confidence intervals for correlating two autocorrelated climate time series

NASA Astrophysics Data System (ADS)

Olafsdottir, Kristin B.; Mudelsee, Manfred

2013-04-01

Estimation of the Pearson's correlation coefficient between two time series to evaluate the influences of one time depended variable on another is one of the most often used statistical method in climate sciences. Various methods are used to estimate confidence interval to support the correlation point estimate. Many of them make strong mathematical assumptions regarding distributional shape and serial correlation, which are rarely met. More robust statistical methods are needed to increase the accuracy of the confidence intervals. Bootstrap confidence intervals are estimated in the Fortran 90 program PearsonT (Mudelsee, 2003), where the main intention was to get an accurate confidence interval for correlation coefficient between two time series by taking the serial dependence of the process that generated the data into account. However, Monte Carlo experiments show that the coverage accuracy for smaller data sizes can be improved. Here we adapt the PearsonT program into a new version called PearsonT3, by calibrating the confidence interval to increase the coverage accuracy. Calibration is a bootstrap resampling technique, which basically performs a second bootstrap loop or resamples from the bootstrap resamples. It offers, like the non-calibrated bootstrap confidence intervals, robustness against the data distribution. Pairwise moving block bootstrap is used to preserve the serial correlation of both time series. The calibration is applied to standard error based bootstrap Student's t confidence intervals. The performances of the calibrated confidence intervals are examined with Monte Carlo simulations, and compared with the performances of confidence intervals without calibration, that is, PearsonT. The coverage accuracy is evidently better for the calibrated confidence intervals where the coverage error is acceptably small (i.e., within a few percentage points) already for data sizes as small as 20. One form of climate time series is output from numerical models which simulate the climate system. The method is applied to model data from the high resolution ocean model, INALT01 where the relationship between the Agulhas Leakage and the North Brazil Current is evaluated. Preliminary results show significant correlation between the two variables when there is 10 year lag between them, which is more or less the time that takes the Agulhas Leakage water to reach the North Brazil Current. Mudelsee, M., 2003. Estimating Pearson's correlation coefficient with bootstrap confidence interval from serially dependent time series. Mathematical Geology 35, 651-665.

Bootstrap rolling window estimation approach to analysis of the Environment Kuznets Curve hypothesis: evidence from the USA.

PubMed

Aslan, Alper; Destek, Mehmet Akif; Okumus, Ilyas

2018-01-01

This study aims to examine the validity of inverted U-shaped Environmental Kuznets Curve by investigating the relationship between economic growth and environmental pollution for the period from 1966 to 2013 in the USA. Previous studies based on the assumption of parameter stability and obtained parameters do not change over the full sample. This study uses bootstrap rolling window estimation method to detect the possible changes in causal relations and also obtain the parameters for sub-sample periods. The results show that the parameter of economic growth has increasing trend in 1982-1996 sub-sample periods, and it has decreasing trend in 1996-2013 sub-sample periods. Therefore, the existence of inverted U-shaped Environmental Kuznets Curve is confirmed in the USA.

Learning predictive models that use pattern discovery--a bootstrap evaluative approach applied in organ functioning sequences.

PubMed

Toma, Tudor; Bosman, Robert-Jan; Siebes, Arno; Peek, Niels; Abu-Hanna, Ameen

2010-08-01

An important problem in the Intensive Care is how to predict on a given day of stay the eventual hospital mortality for a specific patient. A recent approach to solve this problem suggested the use of frequent temporal sequences (FTSs) as predictors. Methods following this approach were evaluated in the past by inducing a model from a training set and validating the prognostic performance on an independent test set. Although this evaluative approach addresses the validity of the specific models induced in an experiment, it falls short of evaluating the inductive method itself. To achieve this, one must account for the inherent sources of variation in the experimental design. The main aim of this work is to demonstrate a procedure based on bootstrapping, specifically the .632 bootstrap procedure, for evaluating inductive methods that discover patterns, such as FTSs. A second aim is to apply this approach to find out whether a recently suggested inductive method that discovers FTSs of organ functioning status is superior over a traditional method that does not use temporal sequences when compared on each successive day of stay at the Intensive Care Unit. The use of bootstrapping with logistic regression using pre-specified covariates is known in the statistical literature. Using inductive methods of prognostic models based on temporal sequence discovery within the bootstrap procedure is however novel at least in predictive models in the Intensive Care. Our results of applying the bootstrap-based evaluative procedure demonstrate the superiority of the FTS-based inductive method over the traditional method in terms of discrimination as well as accuracy. In addition we illustrate the insights gained by the analyst into the discovered FTSs from the bootstrap samples. Copyright 2010 Elsevier Inc. All rights reserved.

Topical ketoprofen nanogel: artificial neural network optimization, clustered bootstrap validation, and in vivo activity evaluation based on longitudinal dose response modeling.

PubMed

Elkomy, Mohammed H; Elmenshawe, Shahira F; Eid, Hussein M; Ali, Ahmed M A

2016-11-01

This work aimed at investigating the potential of solid lipid nanoparticles (SLN) as carriers for topical delivery of Ketoprofen (KP); evaluating a novel technique incorporating Artificial Neural Network (ANN) and clustered bootstrap for optimization of KP-loaded SLN (KP-SLN); and demonstrating a longitudinal dose response (LDR) modeling-based approach to compare the activity of topical non-steroidal anti-inflammatory drug formulations. KP-SLN was fabricated by a modified emulsion/solvent evaporation method. Box-Behnken design was implemented to study the influence of glycerylpalmitostearate-to-KP ratio, Tween 80, and lecithin concentrations on particle size, entrapment efficiency, and amount of drug permeated through rat skin in 24 hours. Following clustered bootstrap ANN optimization, the optimized KP-SLN was incorporated into an aqueous gel and evaluated for rheology, in vitro release, permeability, skin irritation and in vivo activity using carrageenan-induced rat paw edema model and LDR mathematical model to analyze the time course of anti-inflammatory effect at various application durations. Lipid-to-drug ratio of 7.85 [bootstrap 95%CI: 7.63-8.51], Tween 80 of 1.27% [bootstrap 95%CI: 0.601-2.40%], and Lecithin of 0.263% [bootstrap 95%CI: 0.263-0.328%] were predicted to produce optimal characteristics. Compared with profenid® gel, the optimized KP-SLN gel exhibited slower release, faster permeability, better texture properties, greater efficacy, and similar potency. SLNs are safe and effective permeation enhancers. ANN coupled with clustered bootstrap is a useful method for finding optimal solutions and estimating uncertainty associated with them. LDR models allow mechanistic understanding of comparative in vivo performances of different topical formulations, and help design efficient dermatological bioequivalence assessment methods.

Lightweight CoAP-Based Bootstrapping Service for the Internet of Things.

PubMed

Garcia-Carrillo, Dan; Marin-Lopez, Rafael

2016-03-11

The Internet of Things (IoT) is becoming increasingly important in several fields of industrial applications and personal applications, such as medical e-health, smart cities, etc. The research into protocols and security aspects related to this area is continuously advancing in making these networks more reliable and secure, taking into account these aspects by design. Bootstrapping is a procedure by which a user obtains key material and configuration information, among other parameters, to operate as an authenticated party in a security domain. Until now solutions have focused on re-using security protocols that were not developed for IoT constraints. For this reason, in this work we propose a design and implementation of a lightweight bootstrapping service for IoT networks that leverages one of the application protocols used in IoT : Constrained Application Protocol (CoAP). Additionally, in order to provide flexibility, scalability, support for large scale deployment, accountability and identity federation, our design uses technologies such as the Extensible Authentication Protocol (EAP) and Authentication Authorization and Accounting (AAA). We have named this service CoAP-EAP. First, we review the state of the art in the field of bootstrapping and specifically for IoT. Second, we detail the bootstrapping service: the architecture with entities and interfaces and the flow operation. Third, we obtain performance measurements of CoAP-EAP (bootstrapping time, memory footprint, message processing time, message length and energy consumption) and compare them with PANATIKI. The most significant and constrained representative of the bootstrapping solutions related with CoAP-EAP. As we will show, our solution provides significant improvements, mainly due to an important reduction of the message length.

Lightweight CoAP-Based Bootstrapping Service for the Internet of Things

PubMed Central

Garcia-Carrillo, Dan; Marin-Lopez, Rafael

2016-01-01

The Internet of Things (IoT) is becoming increasingly important in several fields of industrial applications and personal applications, such as medical e-health, smart cities, etc. The research into protocols and security aspects related to this area is continuously advancing in making these networks more reliable and secure, taking into account these aspects by design. Bootstrapping is a procedure by which a user obtains key material and configuration information, among other parameters, to operate as an authenticated party in a security domain. Until now solutions have focused on re-using security protocols that were not developed for IoT constraints. For this reason, in this work we propose a design and implementation of a lightweight bootstrapping service for IoT networks that leverages one of the application protocols used in IoT : Constrained Application Protocol (CoAP). Additionally, in order to provide flexibility, scalability, support for large scale deployment, accountability and identity federation, our design uses technologies such as the Extensible Authentication Protocol (EAP) and Authentication Authorization and Accounting (AAA). We have named this service CoAP-EAP. First, we review the state of the art in the field of bootstrapping and specifically for IoT. Second, we detail the bootstrapping service: the architecture with entities and interfaces and the flow operation. Third, we obtain performance measurements of CoAP-EAP (bootstrapping time, memory footprint, message processing time, message length and energy consumption) and compare them with PANATIKI. The most significant and constrained representative of the bootstrapping solutions related with CoAP-EAP. As we will show, our solution provides significant improvements, mainly due to an important reduction of the message length. PMID:26978362

A neural network based reputation bootstrapping approach for service selection

NASA Astrophysics Data System (ADS)

Wu, Quanwang; Zhu, Qingsheng; Li, Peng

2015-10-01

With the concept of service-oriented computing becoming widely accepted in enterprise application integration, more and more computing resources are encapsulated as services and published online. Reputation mechanism has been studied to establish trust on prior unknown services. One of the limitations of current reputation mechanisms is that they cannot assess the reputation of newly deployed services as no record of their previous behaviours exists. Most of the current bootstrapping approaches merely assign default reputation values to newcomers. However, by this kind of methods, either newcomers or existing services will be favoured. In this paper, we present a novel reputation bootstrapping approach, where correlations between features and performance of existing services are learned through an artificial neural network (ANN) and they are then generalised to establish a tentative reputation when evaluating new and unknown services. Reputations of services published previously by the same provider are also incorporated for reputation bootstrapping if available. The proposed reputation bootstrapping approach is seamlessly embedded into an existing reputation model and implemented in the extended service-oriented architecture. Empirical studies of the proposed approach are shown at last.

Progress Toward Steady State Tokamak Operation Exploiting the high bootstrap current fraction regime

NASA Astrophysics Data System (ADS)

Ren, Q.

2015-11-01

Recent DIII-D experiments have advanced the normalized fusion performance of the high bootstrap current fraction tokamak regime toward reactor-relevant steady state operation. The experiments, conducted by a joint team of researchers from the DIII-D and EAST tokamaks, developed a fully noninductive scenario that could be extended on EAST to a demonstration of long pulse steady-state tokamak operation. Fully noninductive plasmas with extremely high values of the poloidal beta, βp >= 4 , have been sustained at βT >= 2 % for long durations with excellent energy confinement quality (H98y,2 >= 1 . 5) and internal transport barriers (ITBs) generated at large minor radius (>= 0 . 6) in all channels (Te, Ti, ne, VTf). Large bootstrap fraction (fBS ~ 80 %) has been obtained with high βp. ITBs have been shown to be compatible with steady state operation. Because of the unusually large ITB radius, normalized pressure is not limited to low βN values by internal ITB-driven modes. βN up to ~4.3 has been obtained by optimizing the plasma-wall distance. The scenario is robust against several variations, including replacing some on-axis with off-axis neutral beam injection (NBI), adding electron cyclotron (EC) heating, and reducing the NBI torque by a factor of 2. This latter observation is particularly promising for extension of the scenario to EAST, where maximum power is obtained with balanced NBI injection, and to a reactor, expected to have low rotation. However, modeling of this regime has provided new challenges to state-of-the-art modeling capabilities: quasilinear models can dramatically underpredict the electron transport, and the Sauter bootstrap current can be insufficient. The analysis shows first-principle NEO is in good agreement with experiments for the bootstrap current calculation and ETG modes with a larger saturated amplitude or EM modes may provide the missing electron transport. Work supported in part by the US DOE under DE-FC02-04ER54698, DE-AC52-07NA27344, DE-AC02-09CH11466, and the NMCFP of China under 2015GB110000 and 2015GB102000.

A risk-adjusted financial model to estimate the cost of a video-assisted thoracoscopic surgery lobectomy programme.

PubMed

Brunelli, Alessandro; Tentzeris, Vasileios; Sandri, Alberto; McKenna, Alexandra; Liew, Shan Liung; Milton, Richard; Chaudhuri, Nilanjan; Kefaloyannis, Emmanuel; Papagiannopoulos, Kostas

2016-05-01

To develop a clinically risk-adjusted financial model to estimate the cost associated with a video-assisted thoracoscopic surgery (VATS) lobectomy programme. Prospectively collected data of 236 VATS lobectomy patients (August 2012-December 2013) were analysed retrospectively. Fixed and variable intraoperative and postoperative costs were retrieved from the Hospital Accounting Department. Baseline and surgical variables were tested for a possible association with total cost using a multivariable linear regression and bootstrap analyses. Costs were calculated in GBP and expressed in Euros (EUR:GBP exchange rate 1.4). The average total cost of a VATS lobectomy was €11 368 (range €6992-€62 535). Average intraoperative (including surgical and anaesthetic time, overhead, disposable materials) and postoperative costs [including ward stay, high dependency unit (HDU) or intensive care unit (ICU) and variable costs associated with management of complications] were €8226 (range €5656-€13 296) and €3029 (range €529-€51 970), respectively. The following variables remained reliably associated with total costs after linear regression analysis and bootstrap: carbon monoxide lung diffusion capacity (DLCO) <60% predicted value (P = 0.02, bootstrap 63%) and chronic obstructive pulmonary disease (COPD; P = 0.035, bootstrap 57%). The following model was developed to estimate the total costs: 10 523 + 1894 × COPD + 2376 × DLCO < 60%. The comparison between predicted and observed costs was repeated in 1000 bootstrapped samples to verify the stability of the model. The two values were not different (P > 0.05) in 86% of the samples. A hypothetical patient with COPD and DLCO less than 60% would cost €4270 more than a patient without COPD and with higher DLCO values (€14 793 vs €10 523). Risk-adjusting financial data can help estimate the total cost associated with VATS lobectomy based on clinical factors. This model can be used to audit the internal financial performance of a VATS lobectomy programme for budgeting, planning and for appropriate bundled payment reimbursements. © The Author 2015. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Explanation of Two Anomalous Results in Statistical Mediation Analysis.

PubMed

Fritz, Matthew S; Taylor, Aaron B; Mackinnon, David P

2012-01-01

Previous studies of different methods of testing mediation models have consistently found two anomalous results. The first result is elevated Type I error rates for the bias-corrected and accelerated bias-corrected bootstrap tests not found in nonresampling tests or in resampling tests that did not include a bias correction. This is of special concern as the bias-corrected bootstrap is often recommended and used due to its higher statistical power compared with other tests. The second result is statistical power reaching an asymptote far below 1.0 and in some conditions even declining slightly as the size of the relationship between X and M , a , increased. Two computer simulations were conducted to examine these findings in greater detail. Results from the first simulation found that the increased Type I error rates for the bias-corrected and accelerated bias-corrected bootstrap are a function of an interaction between the size of the individual paths making up the mediated effect and the sample size, such that elevated Type I error rates occur when the sample size is small and the effect size of the nonzero path is medium or larger. Results from the second simulation found that stagnation and decreases in statistical power as a function of the effect size of the a path occurred primarily when the path between M and Y , b , was small. Two empirical mediation examples are provided using data from a steroid prevention and health promotion program aimed at high school football players (Athletes Training and Learning to Avoid Steroids; Goldberg et al., 1996), one to illustrate a possible Type I error for the bias-corrected bootstrap test and a second to illustrate a loss in power related to the size of a . Implications of these findings are discussed.

Classifier performance prediction for computer-aided diagnosis using a limited dataset.

PubMed

Sahiner, Berkman; Chan, Heang-Ping; Hadjiiski, Lubomir

2008-04-01

In a practical classifier design problem, the true population is generally unknown and the available sample is finite-sized. A common approach is to use a resampling technique to estimate the performance of the classifier that will be trained with the available sample. We conducted a Monte Carlo simulation study to compare the ability of the different resampling techniques in training the classifier and predicting its performance under the constraint of a finite-sized sample. The true population for the two classes was assumed to be multivariate normal distributions with known covariance matrices. Finite sets of sample vectors were drawn from the population. The true performance of the classifier is defined as the area under the receiver operating characteristic curve (AUC) when the classifier designed with the specific sample is applied to the true population. We investigated methods based on the Fukunaga-Hayes and the leave-one-out techniques, as well as three different types of bootstrap methods, namely, the ordinary, 0.632, and 0.632+ bootstrap. The Fisher's linear discriminant analysis was used as the classifier. The dimensionality of the feature space was varied from 3 to 15. The sample size n2 from the positive class was varied between 25 and 60, while the number of cases from the negative class was either equal to n2 or 3n2. Each experiment was performed with an independent dataset randomly drawn from the true population. Using a total of 1000 experiments for each simulation condition, we compared the bias, the variance, and the root-mean-squared error (RMSE) of the AUC estimated using the different resampling techniques relative to the true AUC (obtained from training on a finite dataset and testing on the population). Our results indicated that, under the study conditions, there can be a large difference in the RMSE obtained using different resampling methods, especially when the feature space dimensionality is relatively large and the sample size is small. Under this type of conditions, the 0.632 and 0.632+ bootstrap methods have the lowest RMSE, indicating that the difference between the estimated and the true performances obtained using the 0.632 and 0.632+ bootstrap will be statistically smaller than those obtained using the other three resampling methods. Of the three bootstrap methods, the 0.632+ bootstrap provides the lowest bias. Although this investigation is performed under some specific conditions, it reveals important trends for the problem of classifier performance prediction under the constraint of a limited dataset.

A Pragmatic Cognitive System Engineering Approach to Model Dynamic Human Decision-Making Activities in Intelligent and Automated Systems

DTIC Science & Technology

2003-10-01

Among the procedures developed to identify cognitive processes, there are the Cognitive Task Analysis (CTA) and the Cognitive Work Analysis (CWA...of Cognitive Task Design. [11] Potter, S.S., Roth, E.M., Woods, D.D., and Elm, W.C. (2000). Cognitive Task Analysis as Bootstrapping Multiple...Converging Techniques, In Schraagen, Chipman, and Shalin (Eds.). Cognitive Task Analysis . Mahwah, NJ: Lawrence Erlbaum Associates. [12] Roth, E.M

Bootstrapping data envelopment analysis of efficiency and productivity of county public hospitals in Eastern, Central, and Western China after the public hospital reform.

PubMed

Wang, Man-Li; Fang, Hai-Qing; Tao, Hong-Bing; Cheng, Zhao-Hui; Lin, Xiao-Jun; Cai, Miao; Xu, Chang; Jiang, Shuai

2017-10-01

China implemented the public hospital reform in 2012. This study utilized bootstrapping data envelopment analysis (DEA) to evaluate the technical efficiency (TE) and productivity of county public hospitals in Eastern, Central, and Western China after the 2012 public hospital reform. Data from 127 county public hospitals (39, 45, and 43 in Eastern, Central, and Western China, respectively) were collected during 2012-2015. Changes of TE and productivity over time were estimated by bootstrapping DEA and bootstrapping Malmquist. The disparities in TE and productivity among public hospitals in the three regions of China were compared by Kruskal-Wallis H test and Mann-Whitney U test. The average bias-corrected TE values for the four-year period were 0.6442, 0.5785, 0.6099, and 0.6094 in Eastern, Central, and Western China, and the entire country respectively, with average non-technical efficiency, low pure technical efficiency (PTE), and high scale efficiency found. Productivity increased by 8.12%, 0.25%, 12.11%, and 11.58% in China and its three regions during 2012-2015, and such increase in productivity resulted from progressive technological changes by 16.42%, 6.32%, 21.08%, and 21.42%, respectively. The TE and PTE of the county hospitals significantly differed among the three regions of China. Eastern and Western China showed significantly higher TE and PTE than Central China. More than 60% of county public hospitals in China and its three areas operated at decreasing return scales. There was a considerable space for TE improvement in county hospitals in China and its three regions. During 2012-2015, the hospitals experienced progressive productivity; however, the PTE changed adversely. Moreover, Central China continuously achieved a significantly lower efficiency score than Eastern and Western China. Decision makers and administrators in China should identify the causes of the observed inefficiencies and take appropriate measures to increase the efficiency of county public hospitals in the three areas of China, especially in Central China.

Lung cancer signature biomarkers: tissue specific semantic similarity based clustering of digital differential display (DDD) data.

PubMed

Srivastava, Mousami; Khurana, Pankaj; Sugadev, Ragumani

2012-11-02

The tissue-specific Unigene Sets derived from more than one million expressed sequence tags (ESTs) in the NCBI, GenBank database offers a platform for identifying significantly and differentially expressed tissue-specific genes by in-silico methods. Digital differential display (DDD) rapidly creates transcription profiles based on EST comparisons and numerically calculates, as a fraction of the pool of ESTs, the relative sequence abundance of known and novel genes. However, the process of identifying the most likely tissue for a specific disease in which to search for candidate genes from the pool of differentially expressed genes remains difficult. Therefore, we have used 'Gene Ontology semantic similarity score' to measure the GO similarity between gene products of lung tissue-specific candidate genes from control (normal) and disease (cancer) sets. This semantic similarity score matrix based on hierarchical clustering represents in the form of a dendrogram. The dendrogram cluster stability was assessed by multiple bootstrapping. Multiple bootstrapping also computes a p-value for each cluster and corrects the bias of the bootstrap probability. Subsequent hierarchical clustering by the multiple bootstrapping method (α = 0.95) identified seven clusters. The comparative, as well as subtractive, approach revealed a set of 38 biomarkers comprising four distinct lung cancer signature biomarker clusters (panel 1-4). Further gene enrichment analysis of the four panels revealed that each panel represents a set of lung cancer linked metastasis diagnostic biomarkers (panel 1), chemotherapy/drug resistance biomarkers (panel 2), hypoxia regulated biomarkers (panel 3) and lung extra cellular matrix biomarkers (panel 4). Expression analysis reveals that hypoxia induced lung cancer related biomarkers (panel 3), HIF and its modulating proteins (TGM2, CSNK1A1, CTNNA1, NAMPT/Visfatin, TNFRSF1A, ETS1, SRC-1, FN1, APLP2, DMBT1/SAG, AIB1 and AZIN1) are significantly down regulated. All down regulated genes in this panel were highly up regulated in most other types of cancers. These panels of proteins may represent signature biomarkers for lung cancer and will aid in lung cancer diagnosis and disease monitoring as well as in the prediction of responses to therapeutics.

Uncertainty estimation of Intensity-Duration-Frequency relationships: A regional analysis

NASA Astrophysics Data System (ADS)

Mélèse, Victor; Blanchet, Juliette; Molinié, Gilles

2018-03-01

We propose in this article a regional study of uncertainties in IDF curves derived from point-rainfall maxima. We develop two generalized extreme value models based on the simple scaling assumption, first in the frequentist framework and second in the Bayesian framework. Within the frequentist framework, uncertainties are obtained i) from the Gaussian density stemming from the asymptotic normality theorem of the maximum likelihood and ii) with a bootstrap procedure. Within the Bayesian framework, uncertainties are obtained from the posterior densities. We confront these two frameworks on the same database covering a large region of 100, 000 km2 in southern France with contrasted rainfall regime, in order to be able to draw conclusion that are not specific to the data. The two frameworks are applied to 405 hourly stations with data back to the 1980's, accumulated in the range 3 h-120 h. We show that i) the Bayesian framework is more robust than the frequentist one to the starting point of the estimation procedure, ii) the posterior and the bootstrap densities are able to better adjust uncertainty estimation to the data than the Gaussian density, and iii) the bootstrap density give unreasonable confidence intervals, in particular for return levels associated to large return period. Therefore our recommendation goes towards the use of the Bayesian framework to compute uncertainty.

A Pilot Investigation of the Relationship between Climate Variability and Milk Compounds under the Bootstrap Technique

PubMed Central

Marami Milani, Mohammad Reza; Hense, Andreas; Rahmani, Elham; Ploeger, Angelika

2015-01-01

This study analyzes the linear relationship between climate variables and milk components in Iran by applying bootstrapping to include and assess the uncertainty. The climate parameters, Temperature Humidity Index (THI) and Equivalent Temperature Index (ETI) are computed from the NASA-Modern Era Retrospective-Analysis for Research and Applications (NASA-MERRA) reanalysis (2002–2010). Milk data for fat, protein (measured on fresh matter bases), and milk yield are taken from 936,227 milk records for the same period, using cows fed by natural pasture from April to September. Confidence intervals for the regression model are calculated using the bootstrap technique. This method is applied to the original times series, generating statistically equivalent surrogate samples. As a result, despite the short time data and the related uncertainties, an interesting behavior of the relationships between milk compound and the climate parameters is visible. During spring only, a weak dependency of milk yield and climate variations is obvious, while fat and protein concentrations show reasonable correlations. In summer, milk yield shows a similar level of relationship with ETI, but not with temperature and THI. We suggest this methodology for studies in the field of the impacts of climate change and agriculture, also environment and food with short-term data. PMID:28231215

Bootstrap-based procedures for inference in nonparametric receiver-operating characteristic curve regression analysis.

PubMed

Rodríguez-Álvarez, María Xosé; Roca-Pardiñas, Javier; Cadarso-Suárez, Carmen; Tahoces, Pablo G

2018-03-01

Prior to using a diagnostic test in a routine clinical setting, the rigorous evaluation of its diagnostic accuracy is essential. The receiver-operating characteristic curve is the measure of accuracy most widely used for continuous diagnostic tests. However, the possible impact of extra information about the patient (or even the environment) on diagnostic accuracy also needs to be assessed. In this paper, we focus on an estimator for the covariate-specific receiver-operating characteristic curve based on direct regression modelling and nonparametric smoothing techniques. This approach defines the class of generalised additive models for the receiver-operating characteristic curve. The main aim of the paper is to offer new inferential procedures for testing the effect of covariates on the conditional receiver-operating characteristic curve within the above-mentioned class. Specifically, two different bootstrap-based tests are suggested to check (a) the possible effect of continuous covariates on the receiver-operating characteristic curve and (b) the presence of factor-by-curve interaction terms. The validity of the proposed bootstrap-based procedures is supported by simulations. To facilitate the application of these new procedures in practice, an R-package, known as npROCRegression, is provided and briefly described. Finally, data derived from a computer-aided diagnostic system for the automatic detection of tumour masses in breast cancer is analysed.

Bootstrap and Counter-Bootstrap approaches for formation of the cortege of Informative indicators by Results of Measurements

NASA Astrophysics Data System (ADS)

Artemenko, M. V.; Chernetskaia, I. E.; Kalugina, N. M.; Shchekina, E. N.

2018-04-01

This article describes the solution of the actual problem of the productive formation of a cortege of informative measured features of the object of observation and / or control using author's algorithms for the use of bootstraps and counter-bootstraps technologies for processing the results of measurements of various states of the object on the basis of different volumes of the training sample. The work that is presented in this paper considers aggregation by specific indicators of informative capacity by linear, majority, logical and “greedy” methods, applied both individually and integrally. The results of the computational experiment are discussed, and in conclusion is drawn that the application of the proposed methods contributes to an increase in the efficiency of classification of the states of the object from the results of measurements.

C-17 Centerlining - Analysis of Paratrooper Trajectory

DTIC Science & Technology

2005-06-01

Linear Regression Models. 4th ed. McGraw Hill, 2004. Kuntavanish, Mark. Program Engineer for C-17 System Program Office. Briefing to US Army...Airdrop Risk Assessment Using Bootstrap Sampling, MS AFIT Thesis AFIT/GOR/ENS/96D-01, Dec 1996. Kutner, Michael, C. Nachtsheim, and J. Neter. Applied

Applying the Bootstrap to Taxometric Analysis: Generating Empirical Sampling Distributions to Help Interpret Results

ERIC Educational Resources Information Center

Ruscio, John; Ruscio, Ayelet Meron; Meron, Mati

2007-01-01

Meehl's taxometric method was developed to distinguish categorical and continuous constructs. However, taxometric output can be difficult to interpret because expected results for realistic data conditions and differing procedural implementations have not been derived analytically or studied through rigorous simulations. By applying bootstrap…

How Many Subjects are Needed for a Visual Field Normative Database? A Comparison of Ground Truth and Bootstrapped Statistics.

PubMed

Phu, Jack; Bui, Bang V; Kalloniatis, Michael; Khuu, Sieu K

2018-03-01

The number of subjects needed to establish the normative limits for visual field (VF) testing is not known. Using bootstrap resampling, we determined whether the ground truth mean, distribution limits, and standard deviation (SD) could be approximated using different set size ( x ) levels, in order to provide guidance for the number of healthy subjects required to obtain robust VF normative data. We analyzed the 500 Humphrey Field Analyzer (HFA) SITA-Standard results of 116 healthy subjects and 100 HFA full threshold results of 100 psychophysically experienced healthy subjects. These VFs were resampled (bootstrapped) to determine mean sensitivity, distribution limits (5th and 95th percentiles), and SD for different ' x ' and numbers of resamples. We also used the VF results of 122 glaucoma patients to determine the performance of ground truth and bootstrapped results in identifying and quantifying VF defects. An x of 150 (for SITA-Standard) and 60 (for full threshold) produced bootstrapped descriptive statistics that were no longer different to the original distribution limits and SD. Removing outliers produced similar results. Differences between original and bootstrapped limits in detecting glaucomatous defects were minimized at x = 250. Ground truth statistics of VF sensitivities could be approximated using set sizes that are significantly smaller than the original cohort. Outlier removal facilitates the use of Gaussian statistics and does not significantly affect the distribution limits. We provide guidance for choosing the cohort size for different levels of error when performing normative comparisons with glaucoma patients.

A bootstrap estimation scheme for chemical compositional data with nondetects

USGS Publications Warehouse

Palarea-Albaladejo, J; Martín-Fernández, J.A; Olea, Ricardo A.

2014-01-01

The bootstrap method is commonly used to estimate the distribution of estimators and their associated uncertainty when explicit analytic expressions are not available or are difficult to obtain. It has been widely applied in environmental and geochemical studies, where the data generated often represent parts of whole, typically chemical concentrations. This kind of constrained data is generically called compositional data, and they require specialised statistical methods to properly account for their particular covariance structure. On the other hand, it is not unusual in practice that those data contain labels denoting nondetects, that is, concentrations falling below detection limits. Nondetects impede the implementation of the bootstrap and represent an additional source of uncertainty that must be taken into account. In this work, a bootstrap scheme is devised that handles nondetects by adding an imputation step within the resampling process and conveniently propagates their associated uncertainly. In doing so, it considers the constrained relationships between chemical concentrations originated from their compositional nature. Bootstrap estimates using a range of imputation methods, including new stochastic proposals, are compared across scenarios of increasing difficulty. They are formulated to meet compositional principles following the log-ratio approach, and an adjustment is introduced in the multivariate case to deal with nonclosed samples. Results suggest that nondetect bootstrap based on model-based imputation is generally preferable. A robust approach based on isometric log-ratio transformations appears to be particularly suited in this context. Computer routines in the R statistical programming language are provided. 

Two-condition within-participant statistical mediation analysis: A path-analytic framework.

PubMed

Montoya, Amanda K; Hayes, Andrew F

2017-03-01

Researchers interested in testing mediation often use designs where participants are measured on a dependent variable Y and a mediator M in both of 2 different circumstances. The dominant approach to assessing mediation in such a design, proposed by Judd, Kenny, and McClelland (2001), relies on a series of hypothesis tests about components of the mediation model and is not based on an estimate of or formal inference about the indirect effect. In this article we recast Judd et al.'s approach in the path-analytic framework that is now commonly used in between-participant mediation analysis. By so doing, it is apparent how to estimate the indirect effect of a within-participant manipulation on some outcome through a mediator as the product of paths of influence. This path-analytic approach eliminates the need for discrete hypothesis tests about components of the model to support a claim of mediation, as Judd et al.'s method requires, because it relies only on an inference about the product of paths-the indirect effect. We generalize methods of inference for the indirect effect widely used in between-participant designs to this within-participant version of mediation analysis, including bootstrap confidence intervals and Monte Carlo confidence intervals. Using this path-analytic approach, we extend the method to models with multiple mediators operating in parallel and serially and discuss the comparison of indirect effects in these more complex models. We offer macros and code for SPSS, SAS, and Mplus that conduct these analyses. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

A bootstrapped, low-noise, and high-gain photodetector for shot noise measurement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Haijun; Yang, Wenhai; Li, Zhixiu

2014-01-15

We presented a low-noise, high-gain photodetector based on the bootstrap structure and the L-C (inductance and capacitance) combination. Electronic characteristics of the photodetector, including electronic noise, gain and frequency response, and dynamic range, were verified through a single-frequency Nd:YVO{sub 4} laser at 1064 nm with coherent output. The measured shot noise of 50 μW laser was 13 dB above the electronic noise at the analysis frequency of 2 MHz, and 10 dB at 3 MHz. And a maximum clearance of 28 dB at 2 MHz was achieved when 1.52 mW laser was illuminated. In addition, the photodetector showed excellent linearitiesmore » for both DC and AC amplifications in the laser power range between 12.5 μW and 1.52 mW.« less

Using the Bootstrap Method to Evaluate the Critical Range of Misfit for Polytomous Rasch Fit Statistics.

PubMed

Seol, Hyunsoo

2016-06-01

The purpose of this study was to apply the bootstrap procedure to evaluate how the bootstrapped confidence intervals (CIs) for polytomous Rasch fit statistics might differ according to sample sizes and test lengths in comparison with the rule-of-thumb critical value of misfit. A total of 25 simulated data sets were generated to fit the Rasch measurement and then a total of 1,000 replications were conducted to compute the bootstrapped CIs under each of 25 testing conditions. The results showed that rule-of-thumb critical values for assessing the magnitude of misfit were not applicable because the infit and outfit mean square error statistics showed different magnitudes of variability over testing conditions and the standardized fit statistics did not exactly follow the standard normal distribution. Further, they also do not share the same critical range for the item and person misfit. Based on the results of the study, the bootstrapped CIs can be used to identify misfitting items or persons as they offer a reasonable alternative solution, especially when the distributions of the infit and outfit statistics are not well known and depend on sample size. © The Author(s) 2016.

Working together versus working autonomously: a new power-dependence perspective on the individual-level of analysis.

PubMed

de Jong, Simon B

2014-01-01

Recent studies have indicated that it is important to investigate the interaction between task interdependence and task autonomy because this interaction can affect team effectiveness. However, only a limited number of studies have been conducted and those studies focused solely on the team level of analysis. Moreover, there has also been a dearth of theoretical development. Therefore, this study develops and tests an alternative theoretical perspective in an attempt to understand if, and if so why, this interaction is important at the individual level of analysis. Based on interdependence theory and power-dependence theory, we expected that highly task-interdependent individuals who reported high task autonomy would be more powerful and better performers. In contrast, we expected that similarly high task-interdependent individuals who reported less task autonomy would be less powerful and would be weaker performers. These expectations were supported by multi-level and bootstrapping analyses performed on a multi-source dataset (self-, peer-, manager-ratings) comprised of 182 employees drawn from 37 teams. More specifically, the interaction between task interdependence and task autonomy was γ =.128, p <.05 for power and γ =.166, p <.05 for individual performance. The 95% bootstrap interval ranged from .0038 to .0686.

[Decisions in case of "problematic" cost-effectiveness ratios based on the example of a clinical trial in rehabilitation care].

PubMed

Leidl, R; Jacobi, E; Knab, J; Schweikert, B

2006-04-01

Economic assessment of an additional psychological intervention in the rehabilitation of patients with chronic low-back pain and evaluation of results by decision makers. Piggy-back cost-utility analysis of a randomised clinical trial, including a bootstrap analysis. Costs were measured by using the cost accounting systems of the rehabilitation clinics and by surveying patients. Health-related quality of life was measured using the EQ-5D. Implications of different representations of the decision problem and corresponding decision rules concerning the cost-effectiveness plane are discussed. As compared with the 126 patients of the control arm, the 98 patients in the intervention arm gained 3.5 days in perfect health on average as well as 1219 euro cost saving. However, because of the uncertainty involved, the results of a bootstrap analysis cover all quadrants of the cost-effectiveness plane. Using maximum willingness-to-pay per effect unit gained, decision rules can be defined for parts of the cost-effectiveness plane. These have to be aggregated in a further valuation step. Study results show that decisions on stochastic economic evaluation results may require an additional valuation step aggregating the various parts of the cost-effectiveness plane.

Maternal depression and trait anger as risk factors for escalated physical discipline.

PubMed

Shay, Nicole L; Knutson, John F

2008-02-01

To test the hypothesized anger-mediated relation between maternal depression and escalation of physical discipline, 122 economically disadvantaged mothers were assessed for current and lifetime diagnoses of depression using the Current Depressive Episode, Past Depression, and Dysthymia sections of the Structured Clinical Interview for DSM-IV (SCID) and a measure of current depressive symptoms, the Beck Depression Inventory-Second Edition (BDI-II). Escalation of physical discipline was assessed using a video analog parenting task; maternal anger not specific to discipline was assessed using the Spielberger Trait Anger Expression Inventory. Reports of anger were associated with the diagnosis of depression and depressive symptoms. Bootstrap analyses of indirect effects indicated that the link between depression and escalated discipline was mediated by anger. Parallel analyses based on BDI-II scores identified a marginally significant indirect effect of depression on discipline. Findings suggest that anger and irritability are central to the putative link between depression and harsh discipline.

The Role of GRAIL Orbit Determination in Preprocessing of Gravity Science Measurements

NASA Technical Reports Server (NTRS)

Kruizinga, Gerhard; Asmar, Sami; Fahnestock, Eugene; Harvey, Nate; Kahan, Daniel; Konopliv, Alex; Oudrhiri, Kamal; Paik, Meegyeong; Park, Ryan; Strekalov, Dmitry;

Point Set Denoising Using Bootstrap-Based Radial Basis Function.

PubMed

Liew, Khang Jie; Ramli, Ahmad; Abd Majid, Ahmad

2016-01-01

This paper examines the application of a bootstrap test error estimation of radial basis functions, specifically thin-plate spline fitting, in surface smoothing. The presence of noisy data is a common issue of the point set model that is generated from 3D scanning devices, and hence, point set denoising is one of the main concerns in point set modelling. Bootstrap test error estimation, which is applied when searching for the smoothing parameters of radial basis functions, is revisited. The main contribution of this paper is a smoothing algorithm that relies on a bootstrap-based radial basis function. The proposed method incorporates a k-nearest neighbour search and then projects the point set to the approximated thin-plate spline surface. Therefore, the denoising process is achieved, and the features are well preserved. A comparison of the proposed method with other smoothing methods is also carried out in this study.

Robust control charts in industrial production of olive oil

NASA Astrophysics Data System (ADS)

Grilo, Luís M.; Mateus, Dina M. R.; Alves, Ana C.; Grilo, Helena L.

2014-10-01

Acidity is one of the most important variables in the quality analysis and characterization of olive oil. During the industrial production we use individuals and moving range charts to monitor this variable, which is not always normal distributed. After a brief exploratory data analysis, where we use the bootstrap method, we construct control charts, before and after a Box-Cox transformation, and compare their robustness and performance.

Abstract: Inference and Interval Estimation for Indirect Effects With Latent Variable Models.

PubMed

Falk, Carl F; Biesanz, Jeremy C

2011-11-30

Models specifying indirect effects (or mediation) and structural equation modeling are both popular in the social sciences. Yet relatively little research has compared methods that test for indirect effects among latent variables and provided precise estimates of the effectiveness of different methods. This simulation study provides an extensive comparison of methods for constructing confidence intervals and for making inferences about indirect effects with latent variables. We compared the percentile (PC) bootstrap, bias-corrected (BC) bootstrap, bias-corrected accelerated (BC a ) bootstrap, likelihood-based confidence intervals (Neale & Miller, 1997), partial posterior predictive (Biesanz, Falk, and Savalei, 2010), and joint significance tests based on Wald tests or likelihood ratio tests. All models included three reflective latent variables representing the independent, dependent, and mediating variables. The design included the following fully crossed conditions: (a) sample size: 100, 200, and 500; (b) number of indicators per latent variable: 3 versus 5; (c) reliability per set of indicators: .7 versus .9; (d) and 16 different path combinations for the indirect effect (α = 0, .14, .39, or .59; and β = 0, .14, .39, or .59). Simulations were performed using a WestGrid cluster of 1680 3.06GHz Intel Xeon processors running R and OpenMx. Results based on 1,000 replications per cell and 2,000 resamples per bootstrap method indicated that the BC and BC a bootstrap methods have inflated Type I error rates. Likelihood-based confidence intervals and the PC bootstrap emerged as methods that adequately control Type I error and have good coverage rates.

Combining test statistics and models in bootstrapped model rejection: it is a balancing act

PubMed Central

2014-01-01

Background Model rejections lie at the heart of systems biology, since they provide conclusive statements: that the corresponding mechanistic assumptions do not serve as valid explanations for the experimental data. Rejections are usually done using e.g. the chi-square test (χ2) or the Durbin-Watson test (DW). Analytical formulas for the corresponding distributions rely on assumptions that typically are not fulfilled. This problem is partly alleviated by the usage of bootstrapping, a computationally heavy approach to calculate an empirical distribution. Bootstrapping also allows for a natural extension to estimation of joint distributions, but this feature has so far been little exploited. Results We herein show that simplistic combinations of bootstrapped tests, like the max or min of the individual p-values, give inconsistent, i.e. overly conservative or liberal, results. A new two-dimensional (2D) approach based on parametric bootstrapping, on the other hand, is found both consistent and with a higher power than the individual tests, when tested on static and dynamic examples where the truth is known. In the same examples, the most superior test is a 2D χ2vsχ2, where the second χ2-value comes from an additional help model, and its ability to describe bootstraps from the tested model. This superiority is lost if the help model is too simple, or too flexible. If a useful help model is found, the most powerful approach is the bootstrapped log-likelihood ratio (LHR). We show that this is because the LHR is one-dimensional, because the second dimension comes at a cost, and because LHR has retained most of the crucial information in the 2D distribution. These approaches statistically resolve a previously published rejection example for the first time. Conclusions We have shown how to, and how not to, combine tests in a bootstrap setting, when the combination is advantageous, and when it is advantageous to include a second model. These results also provide a deeper insight into the original motivation for formulating the LHR, for the more general setting of nonlinear and non-nested models. These insights are valuable in cases when accuracy and power, rather than computational speed, are prioritized. PMID:24742065

Explanation of Two Anomalous Results in Statistical Mediation Analysis

ERIC Educational Resources Information Center

Fritz, Matthew S.; Taylor, Aaron B.; MacKinnon, David P.

2012-01-01

Previous studies of different methods of testing mediation models have consistently found two anomalous results. The first result is elevated Type I error rates for the bias-corrected and accelerated bias-corrected bootstrap tests not found in nonresampling tests or in resampling tests that did not include a bias correction. This is of special…

Understanding a Normal Distribution of Data (Part 2).

PubMed

Maltenfort, Mitchell

2016-02-01

Completing the discussion of data normality, advanced techniques for analysis of non-normal data are discussed including data transformation, Generalized Linear Modeling, and bootstrapping. Relative strengths and weaknesses of each technique are helpful in choosing a strategy, but help from a statistician is usually necessary to analyze non-normal data using these methods.

Home-based care after a shortened hospital stay versus hospital-based care postpartum: an economic evaluation.

PubMed

Petrou, Stavros; Boulvain, Michel; Simon, Judit; Maricot, Patrice; Borst, François; Perneger, Thomas; Irion, Olivier

2004-08-01

To compare the cost effectiveness of early postnatal discharge and home midwifery support with a traditional postnatal hospital stay. Cost minimisation analysis within a pragmatic randomised controlled trial. The University Hospital of Geneva and its catchment area. Four hundred and fifty-nine deliveries of a single infant at term following an uncomplicated pregnancy. Prospective economic evaluation alongside a randomised controlled trial in which women were allocated to either early postnatal discharge combined with home midwifery support (n= 228) or a traditional postnatal hospital stay (n= 231). Costs (Swiss francs, 2000 prices) to the health service, social services, patients, carers and society accrued between delivery and 28 days postpartum. Clinical and psychosocial outcomes were similar in the two trial arms. Early postnatal discharge combined with home midwifery support resulted in a significant reduction in postnatal hospital care costs (bootstrap mean difference 1524 francs, 95% confidence interval [CI] 675 to 2403) and a significant increase in community care costs (bootstrap mean difference 295 francs, 95% CI 245 to 343). There were no significant differences in average hospital readmission, hospital outpatient care, direct non-medical and indirect costs between the two trial groups. Overall, early postnatal discharge combined with home midwifery support resulted in a significant cost saving of 1221 francs per mother-infant dyad (bootstrap mean difference 1209 francs, 95% CI 202 to 2155). This finding remained relatively robust following variations in the values of key economic parameters performed as part of a comprehensive sensitivity analysis. A policy of early postnatal discharge combined with home midwifery support exhibits weak economic dominance over traditional postnatal care, that is, it significantly reduces costs without compromising the health and wellbeing of the mother and infant.

Zero- vs. one-dimensional, parametric vs. non-parametric, and confidence interval vs. hypothesis testing procedures in one-dimensional biomechanical trajectory analysis.

PubMed

Pataky, Todd C; Vanrenterghem, Jos; Robinson, Mark A

2015-05-01

Biomechanical processes are often manifested as one-dimensional (1D) trajectories. It has been shown that 1D confidence intervals (CIs) are biased when based on 0D statistical procedures, and the non-parametric 1D bootstrap CI has emerged in the Biomechanics literature as a viable solution. The primary purpose of this paper was to clarify that, for 1D biomechanics datasets, the distinction between 0D and 1D methods is much more important than the distinction between parametric and non-parametric procedures. A secondary purpose was to demonstrate that a parametric equivalent to the 1D bootstrap exists in the form of a random field theory (RFT) correction for multiple comparisons. To emphasize these points we analyzed six datasets consisting of force and kinematic trajectories in one-sample, paired, two-sample and regression designs. Results showed, first, that the 1D bootstrap and other 1D non-parametric CIs were qualitatively identical to RFT CIs, and all were very different from 0D CIs. Second, 1D parametric and 1D non-parametric hypothesis testing results were qualitatively identical for all six datasets. Last, we highlight the limitations of 1D CIs by demonstrating that they are complex, design-dependent, and thus non-generalizable. These results suggest that (i) analyses of 1D data based on 0D models of randomness are generally biased unless one explicitly identifies 0D variables before the experiment, and (ii) parametric and non-parametric 1D hypothesis testing provide an unambiguous framework for analysis when one׳s hypothesis explicitly or implicitly pertains to whole 1D trajectories. Copyright © 2015 Elsevier Ltd. All rights reserved.

Efficiency and productivity measurement of rural township hospitals in China: a bootstrapping data envelopment analysis

PubMed Central

Cheng, Zhaohui; Cai, Miao; Tao, Hongbing; He, Zhifei; Lin, Xiaojun; Lin, Haifeng; Zuo, Yuling

2016-01-01

Objective Township hospitals (THs) are important components of the three-tier rural healthcare system of China. However, the efficiency and productivity of THs have been questioned since the healthcare reform was implemented in 2009. The objective of this study is to analyse the efficiency and productivity changes in THs before and after the reform process. Setting and participants A total of 48 sample THs were selected from the Xiaogan Prefecture in Hubei Province from 2008 to 2014. Outcome measures First, bootstrapping data envelopment analysis (DEA) was performed to estimate the technical efficiency (TE), pure technical efficiency (PTE) and scale efficiency (SE) of the sample THs during the period. Second, the bootstrapping Malmquist productivity index was used to calculate the productivity changes over time. Results The average TE, PTE and SE of the sample THs over the 7-year period were 0.5147, 0.6373 and 0.7080, respectively. The average TE and PTE increased from 2008 to 2012 but declined considerably after 2012. In general, the sample THs experienced a negative shift in productivity from 2008 to 2014. The negative change was 2.14%, which was attributed to a 23.89% decrease in technological changes (TC). The sample THs experienced a positive productivity shift from 2008 to 2012 but experienced deterioration from 2012 to 2014. Conclusions There was considerable space for TE improvement in the sample THs since the average TE was relatively low. From 2008 to 2014, the sample THs experienced a decrease in productivity, and the adverse alteration in TC should be emphasised. In the context of healthcare reform, the factors that influence TE and productivity of THs are complex. Results suggest that numerous quantitative and qualitative studies are necessary to explore the reasons for the changes in TE and productivity. PMID:27836870

A Large-Scale, Higher-Level, Molecular Phylogenetic Study of the Insect Order Lepidoptera (Moths and Butterflies)

PubMed Central

Regier, Jerome C.; Mitter, Charles; Zwick, Andreas; Bazinet, Adam L.; Cummings, Michael P.; Kawahara, Akito Y.; Sohn, Jae-Cheon; Zwickl, Derrick J.; Cho, Soowon; Davis, Donald R.; Baixeras, Joaquin; Brown, John; Parr, Cynthia; Weller, Susan; Lees, David C.; Mitter, Kim T.

2013-01-01

Background Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. We present the most comprehensive molecular analysis of lepidopteran phylogeny to date, focusing on relationships among superfamilies. Methodology / Principal Findings 483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes, from which maximum likelihood tree estimates and bootstrap percentages were obtained using GARLI. Assessment of heuristic search effectiveness showed that better trees and higher bootstrap percentages probably remain to be discovered even after 1000 or more search replicates, but further search proved impractical even with grid computing. Other analyses explored the effects of sampling nonsynonymous change only versus partitioned and unpartitioned total nucleotide change; deletion of rogue taxa; and compositional heterogeneity. Relationships among the non-ditrysian lineages previously inferred from morphology were largely confirmed, plus some new ones, with strong support. Robust support was also found for divergences among non-apoditrysian lineages of Ditrysia, but only rarely so within Apoditrysia. Paraphyly for Tineoidea is strongly supported by analysis of nonsynonymous-only signal; conflicting, strong support for tineoid monophyly when synonymous signal was added back is shown to result from compositional heterogeneity. Conclusions / Significance Support for among-superfamily relationships outside the Apoditrysia is now generally strong. Comparable support is mostly lacking within Apoditrysia, but dramatically increased bootstrap percentages for some nodes after rogue taxon removal, and concordance with other evidence, strongly suggest that our picture of apoditrysian phylogeny is approximately correct. This study highlights the challenge of finding optimal topologies when analyzing hundreds of taxa. It also shows that some nodes get strong support only when analysis is restricted to nonsynonymous change, while total change is necessary for strong support of others. Thus, multiple types of analyses will be necessary to fully resolve lepidopteran phylogeny. PMID:23554903

Quantitative determination of additive Chlorantraniliprole in Abamectin preparation: Investigation of bootstrapping soft shrinkage approach by mid-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Yan, Hong; Song, Xiangzhong; Tian, Kuangda; Chen, Yilin; Xiong, Yanmei; Min, Shungeng

2018-02-01

A novel method, mid-infrared (MIR) spectroscopy, which enables the determination of Chlorantraniliprole in Abamectin within minutes, is proposed. We further evaluate the prediction ability of four wavelength selection methods, including bootstrapping soft shrinkage approach (BOSS), Monte Carlo uninformative variable elimination (MCUVE), genetic algorithm partial least squares (GA-PLS) and competitive adaptive reweighted sampling (CARS) respectively. The results showed that BOSS method obtained the lowest root mean squared error of cross validation (RMSECV) (0.0245) and root mean squared error of prediction (RMSEP) (0.0271), as well as the highest coefficient of determination of cross-validation (Qcv2) (0.9998) and the coefficient of determination of test set (Q2test) (0.9989), which demonstrated that the mid infrared spectroscopy can be used to detect Chlorantraniliprole in Abamectin conveniently. Meanwhile, a suitable wavelength selection method (BOSS) is essential to conducting a component spectral analysis.

The efficiency of average linkage hierarchical clustering algorithm associated multi-scale bootstrap resampling in identifying homogeneous precipitation catchments

NASA Astrophysics Data System (ADS)

Chuan, Zun Liang; Ismail, Noriszura; Shinyie, Wendy Ling; Lit Ken, Tan; Fam, Soo-Fen; Senawi, Azlyna; Yusoff, Wan Nur Syahidah Wan

2018-04-01

Due to the limited of historical precipitation records, agglomerative hierarchical clustering algorithms widely used to extrapolate information from gauged to ungauged precipitation catchments in yielding a more reliable projection of extreme hydro-meteorological events such as extreme precipitation events. However, identifying the optimum number of homogeneous precipitation catchments accurately based on the dendrogram resulted using agglomerative hierarchical algorithms are very subjective. The main objective of this study is to propose an efficient regionalized algorithm to identify the homogeneous precipitation catchments for non-stationary precipitation time series. The homogeneous precipitation catchments are identified using average linkage hierarchical clustering algorithm associated multi-scale bootstrap resampling, while uncentered correlation coefficient as the similarity measure. The regionalized homogeneous precipitation is consolidated using K-sample Anderson Darling non-parametric test. The analysis result shows the proposed regionalized algorithm performed more better compared to the proposed agglomerative hierarchical clustering algorithm in previous studies.

A bootstrap method for estimating uncertainty of water quality trends

USGS Publications Warehouse

Hirsch, Robert M.; Archfield, Stacey A.; DeCicco, Laura

2015-01-01

Estimation of the direction and magnitude of trends in surface water quality remains a problem of great scientific and practical interest. The Weighted Regressions on Time, Discharge, and Season (WRTDS) method was recently introduced as an exploratory data analysis tool to provide flexible and robust estimates of water quality trends. This paper enhances the WRTDS method through the introduction of the WRTDS Bootstrap Test (WBT), an extension of WRTDS that quantifies the uncertainty in WRTDS-estimates of water quality trends and offers various ways to visualize and communicate these uncertainties. Monte Carlo experiments are applied to estimate the Type I error probabilities for this method. WBT is compared to other water-quality trend-testing methods appropriate for data sets of one to three decades in length with sampling frequencies of 6–24 observations per year. The software to conduct the test is in the EGRETci R-package.

Tests for informative cluster size using a novel balanced bootstrap scheme.

PubMed

Nevalainen, Jaakko; Oja, Hannu; Datta, Somnath

2017-07-20

Clustered data are often encountered in biomedical studies, and to date, a number of approaches have been proposed to analyze such data. However, the phenomenon of informative cluster size (ICS) is a challenging problem, and its presence has an impact on the choice of a correct analysis methodology. For example, Dutta and Datta (2015, Biometrics) presented a number of marginal distributions that could be tested. Depending on the nature and degree of informativeness of the cluster size, these marginal distributions may differ, as do the choices of the appropriate test. In particular, they applied their new test to a periodontal data set where the plausibility of the informativeness was mentioned, but no formal test for the same was conducted. We propose bootstrap tests for testing the presence of ICS. A balanced bootstrap method is developed to successfully estimate the null distribution by merging the re-sampled observations with closely matching counterparts. Relying on the assumption of exchangeability within clusters, the proposed procedure performs well in simulations even with a small number of clusters, at different distributions and against different alternative hypotheses, thus making it an omnibus test. We also explain how to extend the ICS test to a regression setting and thereby enhancing its practical utility. The methodologies are illustrated using the periodontal data set mentioned earlier. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

More N =4 superconformal bootstrap

NASA Astrophysics Data System (ADS)

Beem, Christopher; Rastelli, Leonardo; van Rees, Balt C.

2017-08-01

In this long overdue second installment, we continue to develop the conformal bootstrap program for N =4 superconformal field theories (SCFTs) in four dimensions via an analysis of the correlation function of four stress-tensor supermultiplets. We review analytic results for this correlator and make contact with the SCFT/chiral algebra correspondence of Beem et al. [Commun. Math. Phys. 336, 1359 (2015), 10.1007/s00220-014-2272-x]. We demonstrate that the constraints of unitarity and crossing symmetry require the central charge c to be greater than or equal to 3 /4 in any interacting N =4 SCFT. We apply numerical bootstrap methods to derive upper bounds on scaling dimensions and operator product expansion coefficients for several low-lying, unprotected operators as a function of the central charge. We interpret our bounds in the context of N =4 super Yang-Mills theories, formulating a series of conjectures regarding the embedding of the conformal manifold—parametrized by the complexified gauge coupling—into the space of scaling dimensions and operator product expansion coefficients. Our conjectures assign a distinguished role to points on the conformal manifold that are self-dual under a subgroup of the S -duality group. This paper contains a more detailed exposition of a number of results previously reported in Beem et al. [Phys. Rev. Lett. 111, 071601 (2013), 10.1103/PhysRevLett.111.071601] in addition to new results.

Bootstrapping of Life through Holonomy and Self-modification

NASA Astrophysics Data System (ADS)

Kazansky, Alexander B.

2010-11-01

Life on the Earth demonstrate not only adaptive, cognitive, particularly, anticipatory properties, but also active, transformative function to its local and global environment. As V. Vernadsky stated, life is a powerful geological force. Charles Darwin realized that too. In his last work [1] he proved, that earthworms through their vital activity in geological time scale are able to form and support contemporary structure of soil on the whole planet. Locally, through so-called process of niche construction [2] organisms virtually modifies abiotic and biotic factors of natural selection and thereby insert feedback loop in evolutionary process. Stigmergy [3] is one more form of indirect interaction of organisms via the environment by signs, left in local environment or just by performing working activity in swarms, leading to self-organization and coordination of actions in the process of refuges construction. In organization of life we can separate active, rigid, organism-like, autopoietic-like systems or less rigid, sympoietic, socio-biological type systems [4]. Nevertheless, all forms of life systems demonstrate so-called bootstrapping, or spontaneous process of self-organizing emergence. This process is feasible thanks to self-modification, and holonomy in their organization, or total reflexivity. Analysis of the role of indirect interactions in bootstrapping, made in this paper, is aimed at revealing relationships between concepts and making step to forming new systemic model of organization and evolution of special dual pair, biota and biosphere.

Bootstrapping Student Understanding of What Is Going on in Econometrics.

ERIC Educational Resources Information Center

Kennedy, Peter E.

2001-01-01

Explains that econometrics is an intellectual game played by rules based on the sampling distribution concept. Contains explanations for why many students are uncomfortable with econometrics. Encourages instructors to use explain-how-to-bootstrap exercises to promote student understanding. (RLH)

Systemic Console: Advanced analysis of exoplanetary data

NASA Astrophysics Data System (ADS)

Meschiari, Stefano; Wolf, Aaron S.; Rivera, Eugenio; Laughlin, Gregory; Vogt, Steve; Butler, Paul

2012-10-01

Systemic Console is a tool for advanced analysis of exoplanetary data. It comprises a graphical tool for fitting radial velocity and transits datasets and a library of routines for non-interactive calculations. Among its features are interactive plotting of RV curves and transits, combined fitting of RV and transit timing (primary and secondary), interactive periodograms and FAP estimation, and bootstrap and MCMC error estimation. The console package includes public radial velocity and transit data.

Using the bootstrap to establish statistical significance for relative validity comparisons among patient-reported outcome measures

PubMed Central

2013-01-01

Background Relative validity (RV), a ratio of ANOVA F-statistics, is often used to compare the validity of patient-reported outcome (PRO) measures. We used the bootstrap to establish the statistical significance of the RV and to identify key factors affecting its significance. Methods Based on responses from 453 chronic kidney disease (CKD) patients to 16 CKD-specific and generic PRO measures, RVs were computed to determine how well each measure discriminated across clinically-defined groups of patients compared to the most discriminating (reference) measure. Statistical significance of RV was quantified by the 95% bootstrap confidence interval. Simulations examined the effects of sample size, denominator F-statistic, correlation between comparator and reference measures, and number of bootstrap replicates. Results The statistical significance of the RV increased as the magnitude of denominator F-statistic increased or as the correlation between comparator and reference measures increased. A denominator F-statistic of 57 conveyed sufficient power (80%) to detect an RV of 0.6 for two measures correlated at r = 0.7. Larger denominator F-statistics or higher correlations provided greater power. Larger sample size with a fixed denominator F-statistic or more bootstrap replicates (beyond 500) had minimal impact. Conclusions The bootstrap is valuable for establishing the statistical significance of RV estimates. A reasonably large denominator F-statistic (F > 57) is required for adequate power when using the RV to compare the validity of measures with small or moderate correlations (r < 0.7). Substantially greater power can be achieved when comparing measures of a very high correlation (r > 0.9). PMID:23721463

Transport Barriers in Bootstrap Driven Tokamaks

NASA Astrophysics Data System (ADS)

Staebler, Gary

2017-10-01

Maximizing the bootstrap current in a tokamak, so that it drives a high fraction of the total current, reduces the external power required to drive current by other means. Improved energy confinement, relative to empirical scaling laws, enables a reactor to more fully take advantage of the bootstrap driven tokamak. Experiments have demonstrated improved energy confinement due to the spontaneous formation of an internal transport barrier in high bootstrap fraction discharges. Gyrokinetic analysis, and quasilinear predictive modeling, demonstrates that the observed transport barrier is due to the suppression of turbulence primarily due to the large Shafranov shift. ExB velocity shear does not play a significant role in the transport barrier due to the high safety factor. It will be shown, that the Shafranov shift can produce a bifurcation to improved confinement in regions of positive magnetic shear or a continuous reduction in transport for weak or negative magnetic shear. Operation at high safety factor lowers the pressure gradient threshold for the Shafranov shift driven barrier formation. The ion energy transport is reduced to neoclassical and electron energy and particle transport is reduced, but still turbulent, within the barrier. Deeper into the plasma, very large levels of electron transport are observed. The observed electron temperature profile is shown to be close to the threshold for the electron temperature gradient (ETG) mode. A large ETG driven energy transport is qualitatively consistent with recent multi-scale gyrokinetic simulations showing that reducing the ion scale turbulence can lead to large increase in the electron scale transport. A new saturation model for the quasilinear TGLF transport code, that fits these multi-scale gyrokinetic simulations, can match the data if the impact of zonal flow mixing on the ETG modes is reduced at high safety factor. This work was supported by the U.S. Department of Energy under DE-FG02-95ER54309 and DE-FC02-04ER54698.

Four Bootstrap Confidence Intervals for the Binomial-Error Model.

ERIC Educational Resources Information Center

Lin, Miao-Hsiang; Hsiung, Chao A.

1992-01-01

Four bootstrap methods are identified for constructing confidence intervals for the binomial-error model. The extent to which similar results are obtained and the theoretical foundation of each method and its relevance and ranges of modeling the true score uncertainty are discussed. (SLD)

Nonparametric Regression and the Parametric Bootstrap for Local Dependence Assessment.

ERIC Educational Resources Information Center

Habing, Brian

2001-01-01

Discusses ideas underlying nonparametric regression and the parametric bootstrap with an overview of their application to item response theory and the assessment of local dependence. Illustrates the use of the method in assessing local dependence that varies with examinee trait levels. (SLD)

Application of the Bootstrap Statistical Method in Deriving Vibroacoustic Specifications

NASA Technical Reports Server (NTRS)

Hughes, William O.; Paez, Thomas L.

2006-01-01

This paper discusses the Bootstrap Method for specification of vibroacoustic test specifications. Vibroacoustic test specifications are necessary to properly accept or qualify a spacecraft and its components for the expected acoustic, random vibration and shock environments seen on an expendable launch vehicle. Traditionally, NASA and the U.S. Air Force have employed methods of Normal Tolerance Limits to derive these test levels based upon the amount of data available, and the probability and confidence levels desired. The Normal Tolerance Limit method contains inherent assumptions about the distribution of the data. The Bootstrap is a distribution-free statistical subsampling method which uses the measured data themselves to establish estimates of statistical measures of random sources. This is achieved through the computation of large numbers of Bootstrap replicates of a data measure of interest and the use of these replicates to derive test levels consistent with the probability and confidence desired. The comparison of the results of these two methods is illustrated via an example utilizing actual spacecraft vibroacoustic data.

The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data.

PubMed

Katsura, Yukako; Stanley, Craig E; Kumar, Sudhir; Nei, Masatoshi

2017-03-01

The reliability of a phylogenetic tree obtained from empirical data is usually measured by the bootstrap probability (Pb) of interior branches of the tree. If the bootstrap probability is high for most branches, the tree is considered to be reliable. If some interior branches show relatively low bootstrap probabilities, we are not sure that the inferred tree is really reliable. Here, we propose another quantity measuring the reliability of the tree called the stability of a subtree. This quantity refers to the probability of obtaining a subtree (Ps) of an inferred tree obtained. We then show that if the tree is to be reliable, both Pb and Ps must be high. We also show that Ps is given by a bootstrap probability of the subtree with the closest outgroup sequence, and computer program RESTA for computing the Pb and Ps values will be presented. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A revisit to contingency table and tests of independence: bootstrap is preferred to Chi-square approximations as well as Fisher's exact test.

PubMed

Lin, Jyh-Jiuan; Chang, Ching-Hui; Pal, Nabendu

2015-01-01

To test the mutual independence of two qualitative variables (or attributes), it is a common practice to follow the Chi-square tests (Pearson's as well as likelihood ratio test) based on data in the form of a contingency table. However, it should be noted that these popular Chi-square tests are asymptotic in nature and are useful when the cell frequencies are "not too small." In this article, we explore the accuracy of the Chi-square tests through an extensive simulation study and then propose their bootstrap versions that appear to work better than the asymptotic Chi-square tests. The bootstrap tests are useful even for small-cell frequencies as they maintain the nominal level quite accurately. Also, the proposed bootstrap tests are more convenient than the Fisher's exact test which is often criticized for being too conservative. Finally, all test methods are applied to a few real-life datasets for demonstration purposes.

Standard Errors of Estimated Latent Variable Scores with Estimated Structural Parameters

ERIC Educational Resources Information Center

Hoshino, Takahiro; Shigemasu, Kazuo

2008-01-01

The authors propose a concise formula to evaluate the standard error of the estimated latent variable score when the true values of the structural parameters are not known and must be estimated. The formula can be applied to factor scores in factor analysis or ability parameters in item response theory, without bootstrap or Markov chain Monte…

Social Support as a Mediator between Internalized Stigma and Coping Behaviors of Individuals with Substance Abuse Issues

ERIC Educational Resources Information Center

Chou, Chih-Chin; Robb, Jayci Lynn; Clay, Matthew Christopher; Chronister, Julie Ann

2013-01-01

In this study, 51 individuals from online substance abuse support groups were surveyed to investigate the mediating role of social support on the relationship between internalized stigma and coping. Regression and bootstrapping were conducted to perform mediation analysis. Findings suggest that social support mediates the negative impact of…

Unconventional Expressions: Productive Syntax in the L2 Acquisition of Formulaic Language

ERIC Educational Resources Information Center

Bardovi-Harlig, Kathleen; Stringer, David

2017-01-01

This article presents a generative analysis of the acquisition of formulaic language as an alternative to current usage-based proposals. One influential view of the role of formulaic expressions in second language (L2) development is that they are a bootstrapping mechanism into the L2 grammar; an initial repertoire of constructions allows for…

Taxonomic evaluation of species in the Streptomyces hirsutus clade using multi-locus sequence analysis and proposals to reclassify several species in this clade

USDA-ARS?s Scientific Manuscript database

Previous phylogenetic analyses of species of Streptomyces based on 16S rRNA gene sequences resulted in a statistically well-supported clade (100% bootstrap value) containing 8 species that exhibited very similar gross morphology in producing open looped (Retinaculum-Apertum) to spiral (Spira) chains...

Confidence Interval Coverage for Cohen's Effect Size Statistic

ERIC Educational Resources Information Center

Algina, James; Keselman, H. J.; Penfield, Randall D.

2006-01-01

Kelley compared three methods for setting a confidence interval (CI) around Cohen's standardized mean difference statistic: the noncentral-"t"-based, percentile (PERC) bootstrap, and biased-corrected and accelerated (BCA) bootstrap methods under three conditions of nonnormality, eight cases of sample size, and six cases of population…

A Bootstrap Procedure of Propensity Score Estimation

ERIC Educational Resources Information Center

Bai, Haiyan

2013-01-01

Propensity score estimation plays a fundamental role in propensity score matching for reducing group selection bias in observational data. To increase the accuracy of propensity score estimation, the author developed a bootstrap propensity score. The commonly used propensity score matching methods: nearest neighbor matching, caliper matching, and…

Incorporating external evidence in trial-based cost-effectiveness analyses: the use of resampling methods

PubMed Central

2014-01-01

Background Cost-effectiveness analyses (CEAs) that use patient-specific data from a randomized controlled trial (RCT) are popular, yet such CEAs are criticized because they neglect to incorporate evidence external to the trial. A popular method for quantifying uncertainty in a RCT-based CEA is the bootstrap. The objective of the present study was to further expand the bootstrap method of RCT-based CEA for the incorporation of external evidence. Methods We utilize the Bayesian interpretation of the bootstrap and derive the distribution for the cost and effectiveness outcomes after observing the current RCT data and the external evidence. We propose simple modifications of the bootstrap for sampling from such posterior distributions. Results In a proof-of-concept case study, we use data from a clinical trial and incorporate external evidence on the effect size of treatments to illustrate the method in action. Compared to the parametric models of evidence synthesis, the proposed approach requires fewer distributional assumptions, does not require explicit modeling of the relation between external evidence and outcomes of interest, and is generally easier to implement. A drawback of this approach is potential computational inefficiency compared to the parametric Bayesian methods. Conclusions The bootstrap method of RCT-based CEA can be extended to incorporate external evidence, while preserving its appealing features such as no requirement for parametric modeling of cost and effectiveness outcomes. PMID:24888356

Incorporating external evidence in trial-based cost-effectiveness analyses: the use of resampling methods.

PubMed

Sadatsafavi, Mohsen; Marra, Carlo; Aaron, Shawn; Bryan, Stirling

2014-06-03

Cost-effectiveness analyses (CEAs) that use patient-specific data from a randomized controlled trial (RCT) are popular, yet such CEAs are criticized because they neglect to incorporate evidence external to the trial. A popular method for quantifying uncertainty in a RCT-based CEA is the bootstrap. The objective of the present study was to further expand the bootstrap method of RCT-based CEA for the incorporation of external evidence. We utilize the Bayesian interpretation of the bootstrap and derive the distribution for the cost and effectiveness outcomes after observing the current RCT data and the external evidence. We propose simple modifications of the bootstrap for sampling from such posterior distributions. In a proof-of-concept case study, we use data from a clinical trial and incorporate external evidence on the effect size of treatments to illustrate the method in action. Compared to the parametric models of evidence synthesis, the proposed approach requires fewer distributional assumptions, does not require explicit modeling of the relation between external evidence and outcomes of interest, and is generally easier to implement. A drawback of this approach is potential computational inefficiency compared to the parametric Bayesian methods. The bootstrap method of RCT-based CEA can be extended to incorporate external evidence, while preserving its appealing features such as no requirement for parametric modeling of cost and effectiveness outcomes.

Comparing Eye Tracking with Electrooculography for Measuring Individual Sentence Comprehension Duration

PubMed Central

Müller, Jana Annina; Wendt, Dorothea; Kollmeier, Birger; Brand, Thomas

2016-01-01

The aim of this study was to validate a procedure for performing the audio-visual paradigm introduced by Wendt et al. (2015) with reduced practical challenges. The original paradigm records eye fixations using an eye tracker and calculates the duration of sentence comprehension based on a bootstrap procedure. In order to reduce practical challenges, we first reduced the measurement time by evaluating a smaller measurement set with fewer trials. The results of 16 listeners showed effects comparable to those obtained when testing the original full measurement set on a different collective of listeners. Secondly, we introduced electrooculography as an alternative technique for recording eye movements. The correlation between the results of the two recording techniques (eye tracker and electrooculography) was r = 0.97, indicating that both methods are suitable for estimating the processing duration of individual participants. Similar changes in processing duration arising from sentence complexity were found using the eye tracker and the electrooculography procedure. Thirdly, the time course of eye fixations was estimated with an alternative procedure, growth curve analysis, which is more commonly used in recent studies analyzing eye tracking data. The results of the growth curve analysis were compared with the results of the bootstrap procedure. Both analysis methods show similar processing durations. PMID:27764125

Improved dynamical scaling analysis using the kernel method for nonequilibrium relaxation.

PubMed

Echinaka, Yuki; Ozeki, Yukiyasu

2016-10-01

The dynamical scaling analysis for the Kosterlitz-Thouless transition in the nonequilibrium relaxation method is improved by the use of Bayesian statistics and the kernel method. This allows data to be fitted to a scaling function without using any parametric model function, which makes the results more reliable and reproducible and enables automatic and faster parameter estimation. Applying this method, the bootstrap method is introduced and a numerical discrimination for the transition type is proposed.

Bootstrapping Methods Applied for Simulating Laboratory Works

ERIC Educational Resources Information Center

Prodan, Augustin; Campean, Remus

2005-01-01

Purpose: The aim of this work is to implement bootstrapping methods into software tools, based on Java. Design/methodology/approach: This paper presents a category of software e-tools aimed at simulating laboratory works and experiments. Findings: Both students and teaching staff use traditional statistical methods to infer the truth from sample…

Bootstrap Estimation and Testing for Variance Equality.

ERIC Educational Resources Information Center

Olejnik, Stephen; Algina, James

The purpose of this study was to develop a single procedure for comparing population variances which could be used for distribution forms. Bootstrap methodology was used to estimate the variability of the sample variance statistic when the population distribution was normal, platykurtic and leptokurtic. The data for the study were generated and…

Bootstrapping the Syntactic Bootstrapper: Probabilistic Labeling of Prosodic Phrases

ERIC Educational Resources Information Center

Gutman, Ariel; Dautriche, Isabelle; Crabbé, Benoît; Christophe, Anne

2015-01-01

The "syntactic bootstrapping" hypothesis proposes that syntactic structure provides children with cues for learning the meaning of novel words. In this article, we address the question of how children might start acquiring some aspects of syntax before they possess a sizeable lexicon. The study presents two models of early syntax…

Evaluating the Use of Random Distribution Theory to Introduce Statistical Inference Concepts to Business Students

ERIC Educational Resources Information Center

Larwin, Karen H.; Larwin, David A.

2011-01-01

Bootstrapping methods and random distribution methods are increasingly recommended as better approaches for teaching students about statistical inference in introductory-level statistics courses. The authors examined the effect of teaching undergraduate business statistics students using random distribution and bootstrapping simulations. It is the…

MSP-Tool: a VBA-based software tool for the analysis of multispecimen paleointensity data

NASA Astrophysics Data System (ADS)

Monster, Marilyn; de Groot, Lennart; Dekkers, Mark

2015-12-01

The multispecimen protocol (MSP) is a method to estimate the Earth's magnetic field's past strength from volcanic rocks or archeological materials. By reducing the amount of heating steps and aligning the specimens parallel to the applied field, thermochemical alteration and multi-domain effects are minimized. We present a new software tool, written for Microsoft Excel 2010 in Visual Basic for Applications (VBA), that evaluates paleointensity data acquired using this protocol. In addition to the three ratios (standard, fraction-corrected and domain-state-corrected) calculated following Dekkers and Böhnel (2006) and Fabian and Leonhardt (2010) and a number of other parameters proposed by Fabian and Leonhardt (2010), it also provides several reliability criteria. These include an alteration criterion, whether or not the linear regression intersects the y axis within the theoretically prescribed range, and two directional checks. Overprints and misalignment are detected by isolating the remaining natural remanent magnetization (NRM) and the partial thermoremanent magnetization (pTRM) gained and comparing their declinations and inclinations. The NRM remaining and pTRM gained are then used to calculate alignment-corrected multispecimen plots. Data are analyzed using bootstrap statistics. The program was tested on lava samples that were given a full TRM and that acquired their pTRMs at angles of 0, 15, 30 and 90° with respect to their NRMs. MSP-Tool adequately detected and largely corrected these artificial alignment errors.

Frequency Analysis Using Bootstrap Method and SIR Algorithm for Prevention of Natural Disasters

NASA Astrophysics Data System (ADS)

Kim, T.; Kim, Y. S.

2017-12-01

The frequency analysis of hydrometeorological data is one of the most important factors in response to natural disaster damage, and design standards for a disaster prevention facilities. In case of frequency analysis of hydrometeorological data, it assumes that observation data have statistical stationarity, and a parametric method considering the parameter of probability distribution is applied. For a parametric method, it is necessary to sufficiently collect reliable data; however, snowfall observations are needed to compensate for insufficient data in Korea, because of reducing the number of days for snowfall observations and mean maximum daily snowfall depth due to climate change. In this study, we conducted the frequency analysis for snowfall using the Bootstrap method and SIR algorithm which are the resampling methods that can overcome the problems of insufficient data. For the 58 meteorological stations distributed evenly in Korea, the probability of snowfall depth was estimated by non-parametric frequency analysis using the maximum daily snowfall depth data. The results show that probabilistic daily snowfall depth by frequency analysis is decreased at most stations, and most stations representing the rate of change were found to be consistent in both parametric and non-parametric frequency analysis. This study shows that the resampling methods can do the frequency analysis of the snowfall depth that has insufficient observed samples, which can be applied to interpretation of other natural disasters such as summer typhoons with seasonal characteristics. Acknowledgment.This research was supported by a grant(MPSS-NH-2015-79) from Disaster Prediction and Mitigation Technology Development Program funded by Korean Ministry of Public Safety and Security(MPSS).

An Approach to Addressing Selection Bias in Survival Analysis

PubMed Central

Carlin, Caroline S.; Solid, Craig A.

2014-01-01

This work proposes a frailty model that accounts for non-random treatment assignment in survival analysis. Using Monte Carlo simulation, we found that estimated treatment parameters from our proposed endogenous selection survival model (esSurv) closely parallel the consistent two-stage residual inclusion (2SRI) results, while offering computational and interpretive advantages. The esSurv method greatly enhances computational speed relative to 2SRI by eliminating the need for bootstrapped standard errors, and generally results in smaller standard errors than those estimated by 2SRI. In addition, esSurv explicitly estimates the correlation of unobservable factors contributing to both treatment assignment and the outcome of interest, providing an interpretive advantage over the residual parameter estimate in the 2SRI method. Comparisons with commonly used propensity score methods and with a model that does not account for non-random treatment assignment show clear bias in these methods that is not mitigated by increased sample size. We illustrate using actual dialysis patient data comparing mortality of patients with mature arteriovenous grafts for venous access to mortality of patients with grafts placed but not yet ready for use at the initiation of dialysis. We find strong evidence of endogeneity (with estimate of correlation in unobserved factors ρ̂ = 0.55), and estimate a mature-graft hazard ratio of 0.197 in our proposed method, with a similar 0.173 hazard ratio using 2SRI. The 0.630 hazard ratio from a frailty model without a correction for the non-random nature of treatment assignment illustrates the importance of accounting for endogeneity. PMID:24845211

Separation of parallel encoded complex-valued slices (SPECS) from a single complex-valued aliased coil image.

PubMed

Rowe, Daniel B; Bruce, Iain P; Nencka, Andrew S; Hyde, James S; Kociuba, Mary C

2016-04-01

Achieving a reduction in scan time with minimal inter-slice signal leakage is one of the significant obstacles in parallel MR imaging. In fMRI, multiband-imaging techniques accelerate data acquisition by simultaneously magnetizing the spatial frequency spectrum of multiple slices. The SPECS model eliminates the consequential inter-slice signal leakage from the slice unaliasing, while maintaining an optimal reduction in scan time and activation statistics in fMRI studies. When the combined k-space array is inverse Fourier reconstructed, the resulting aliased image is separated into the un-aliased slices through a least squares estimator. Without the additional spatial information from a phased array of receiver coils, slice separation in SPECS is accomplished with acquired aliased images in shifted FOV aliasing pattern, and a bootstrapping approach of incorporating reference calibration images in an orthogonal Hadamard pattern. The aliased slices are effectively separated with minimal expense to the spatial and temporal resolution. Functional activation is observed in the motor cortex, as the number of aliased slices is increased, in a bilateral finger tapping fMRI experiment. The SPECS model incorporates calibration reference images together with coefficients of orthogonal polynomials into an un-aliasing estimator to achieve separated images, with virtually no residual artifacts and functional activation detection in separated images. Copyright © 2015 Elsevier Inc. All rights reserved.

Carving out the end of the world or (superconformal bootstrap in six dimensions)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, Chi-Ming; Lin, Ying-Hsuan

We bootstrap N=(1,0) superconformal field theories in six dimensions, by analyzing the four-point function of flavor current multiplets. By assuming E 8 flavor group, we present universal bounds on the central charge C T and the flavor central charge C J. Based on the numerical data, we conjecture that the rank-one E-string theory saturates the universal lower bound on C J , and numerically determine the spectrum of long multiplets in the rank-one E-string theory. We comment on the possibility of solving the higher-rank E-string theories by bootstrap and thereby probing M-theory on AdS 7×S 4/Z 2 .

Carving out the end of the world or (superconformal bootstrap in six dimensions)

DOE PAGES

Chang, Chi-Ming; Lin, Ying-Hsuan

2017-08-29

We bootstrap N=(1,0) superconformal field theories in six dimensions, by analyzing the four-point function of flavor current multiplets. By assuming E 8 flavor group, we present universal bounds on the central charge C T and the flavor central charge C J. Based on the numerical data, we conjecture that the rank-one E-string theory saturates the universal lower bound on C J , and numerically determine the spectrum of long multiplets in the rank-one E-string theory. We comment on the possibility of solving the higher-rank E-string theories by bootstrap and thereby probing M-theory on AdS 7×S 4/Z 2 .

Bootstrapping N=2 chiral correlators

NASA Astrophysics Data System (ADS)

Lemos, Madalena; Liendo, Pedro

2016-01-01

We apply the numerical bootstrap program to chiral operators in four-dimensional N=2 SCFTs. In the first part of this work we study four-point functions in which all fields have the same conformal dimension. We give special emphasis to bootstrapping a specific theory: the simplest Argyres-Douglas fixed point with no flavor symmetry. In the second part we generalize our setup and consider correlators of fields with unequal dimension. This is an example of a mixed correlator and allows us to probe new regions in the parameter space of N=2 SCFTs. In particular, our results put constraints on relations in the Coulomb branch chiral ring and on the curvature of the Zamolodchikov metric.

Tablet potency of Tianeptine in coated tablets by near infrared spectroscopy: model optimisation, calibration transfer and confidence intervals.

PubMed

Boiret, Mathieu; Meunier, Loïc; Ginot, Yves-Michel

2011-02-20

A near infrared (NIR) method was developed for determination of tablet potency of active pharmaceutical ingredient (API) in a complex coated tablet matrix. The calibration set contained samples from laboratory and production scale batches. The reference values were obtained by high performance liquid chromatography (HPLC) and partial least squares (PLS) regression was used to establish a model. The model was challenged by calculating tablet potency of two external test sets. Root mean square errors of prediction were respectively equal to 2.0% and 2.7%. To use this model with a second spectrometer from the production field, a calibration transfer method called piecewise direct standardisation (PDS) was used. After the transfer, the root mean square error of prediction of the first test set was 2.4% compared to 4.0% without transferring the spectra. A statistical technique using bootstrap of PLS residuals was used to estimate confidence intervals of tablet potency calculations. This method requires an optimised PLS model, selection of the bootstrap number and determination of the risk. In the case of a chemical analysis, the tablet potency value will be included within the confidence interval calculated by the bootstrap method. An easy to use graphical interface was developed to easily determine if the predictions, surrounded by minimum and maximum values, are within the specifications defined by the regulatory organisation. Copyright © 2010 Elsevier B.V. All rights reserved.

An Attenuation of the "Normal" Category Effect in Patients with Alzheimer's Disease: A Review and Bootstrap Analysis

ERIC Educational Resources Information Center

Moreno-Martinez, F. Javier; Laws, Kieth R.

2007-01-01

There is a consensus that Alzheimer's disease (AD) impairs semantic information, with one of the first markers being anomia i.e. an impaired ability to name items. Doubts remain, however, about whether this naming impairment differentially affects items from the living and nonliving knowledge domains. Most studies have reported an impairment for…

Bootstrap evaluation of a young Douglas-fir height growth model for the Pacific Northwest

Treesearch

Nicholas R. Vaughn; Eric C. Turnblom; Martin W. Ritchie

2010-01-01

We evaluated the stability of a complex regression model developed to predict the annual height growth of young Douglas-fir. This model is highly nonlinear and is fit in an iterative manner for annual growth coefficients from data with multiple periodic remeasurement intervals. The traditional methods for such a sensitivity analysis either involve laborious math or...

Development of probabilistic emission inventories of air toxics for Jacksonville, Florida, USA.

PubMed

Zhao, Yuchao; Frey, H Christopher

2004-11-01

Probabilistic emission inventories were developed for 1,3-butadiene, mercury (Hg), arsenic (As), benzene, formaldehyde, and lead for Jacksonville, FL. To quantify inter-unit variability in empirical emission factor data, the Maximum Likelihood Estimation (MLE) method or the Method of Matching Moments was used to fit parametric distributions. For data sets that contain nondetected measurements, a method based upon MLE was used for parameter estimation. To quantify the uncertainty in urban air toxic emission factors, parametric bootstrap simulation and empirical bootstrap simulation were applied to uncensored and censored data, respectively. The probabilistic emission inventories were developed based on the product of the uncertainties in the emission factors and in the activity factors. The uncertainties in the urban air toxics emission inventories range from as small as -25 to +30% for Hg to as large as -83 to +243% for As. The key sources of uncertainty in the emission inventory for each toxic are identified based upon sensitivity analysis. Typically, uncertainty in the inventory of a given pollutant can be attributed primarily to a small number of source categories. Priorities for improving the inventories and for refining the probabilistic analysis are discussed.

Quantification of Uncertainty in the Flood Frequency Analysis

NASA Astrophysics Data System (ADS)

Kasiapillai Sudalaimuthu, K.; He, J.; Swami, D.

2017-12-01

Flood frequency analysis (FFA) is usually carried out for planning and designing of water resources and hydraulic structures. Owing to the existence of variability in sample representation, selection of distribution and estimation of distribution parameters, the estimation of flood quantile has been always uncertain. Hence, suitable approaches must be developed to quantify the uncertainty in the form of prediction interval as an alternate to deterministic approach. The developed framework in the present study to include uncertainty in the FFA discusses a multi-objective optimization approach to construct the prediction interval using ensemble of flood quantile. Through this approach, an optimal variability of distribution parameters is identified to carry out FFA. To demonstrate the proposed approach, annual maximum flow data from two gauge stations (Bow river at Calgary and Banff, Canada) are used. The major focus of the present study was to evaluate the changes in magnitude of flood quantiles due to the recent extreme flood event occurred during the year 2013. In addition, the efficacy of the proposed method was further verified using standard bootstrap based sampling approaches and found that the proposed method is reliable in modeling extreme floods as compared to the bootstrap methods.

Exploring the Replicability of a Study's Results: Bootstrap Statistics for the Multivariate Case.

ERIC Educational Resources Information Center

Thompson, Bruce

Conventional statistical significance tests do not inform the researcher regarding the likelihood that results will replicate. One strategy for evaluating result replication is to use a "bootstrap" resampling of a study's data so that the stability of results across numerous configurations of the subjects can be explored. This paper…

Introducing Statistical Inference to Biology Students through Bootstrapping and Randomization

ERIC Educational Resources Information Center

Lock, Robin H.; Lock, Patti Frazer

2008-01-01

Bootstrap methods and randomization tests are increasingly being used as alternatives to standard statistical procedures in biology. They also serve as an effective introduction to the key ideas of statistical inference in introductory courses for biology students. We discuss the use of such simulation based procedures in an integrated curriculum…

Computing Robust, Bootstrap-Adjusted Fit Indices for Use with Nonnormal Data

ERIC Educational Resources Information Center

Walker, David A.; Smith, Thomas J.

2017-01-01

Nonnormality of data presents unique challenges for researchers who wish to carry out structural equation modeling. The subsequent SPSS syntax program computes bootstrap-adjusted fit indices (comparative fit index, Tucker-Lewis index, incremental fit index, and root mean square error of approximation) that adjust for nonnormality, along with the…

Forgetski Vygotsky: Or, a Plea for Bootstrapping Accounts of Learning

ERIC Educational Resources Information Center

Luntley, Michael

2017-01-01

This paper argues that sociocultural accounts of learning fail to answer the key question about learning--how is it possible? Accordingly, we should adopt an individualist bootstrapping methodology in providing a theory of learning. Such a methodology takes seriously the idea that learning is staged and distinguishes between a non-comprehending…

Higher curvature gravities, unlike GR, cannot be bootstrapped from their (usual) linearizations

NASA Astrophysics Data System (ADS)

Deser, S.

2017-12-01

We show that higher curvature order gravities, in particular the propagating quadratic curvature models, cannot be derived by self-coupling from their linear, flat space, forms, except through an unphysical version of linearization; only GR can. Separately, we comment on an early version of the self-coupling bootstrap.

Methods for Estimating Uncertainty in PMF Solutions: Examples with Ambient Air and Water Quality Data and Guidance on Reporting PMF Results

EPA Science Inventory

The new version of EPA’s positive matrix factorization (EPA PMF) software, 5.0, includes three error estimation (EE) methods for analyzing factor analytic solutions: classical bootstrap (BS), displacement of factor elements (DISP), and bootstrap enhanced by displacement (BS-DISP)...

How to Bootstrap a Human Communication System

ERIC Educational Resources Information Center

Fay, Nicolas; Arbib, Michael; Garrod, Simon

2013-01-01

How might a human communication system be bootstrapped in the absence of conventional language? We argue that motivated signs play an important role (i.e., signs that are linked to meaning by structural resemblance or by natural association). An experimental study is then reported in which participants try to communicate a range of pre-specified…

Weak percolation on multiplex networks

NASA Astrophysics Data System (ADS)

Baxter, Gareth J.; Dorogovtsev, Sergey N.; Mendes, José F. F.; Cellai, Davide

2014-04-01

Bootstrap percolation is a simple but nontrivial model. It has applications in many areas of science and has been explored on random networks for several decades. In single-layer (simplex) networks, it has been recently observed that bootstrap percolation, which is defined as an incremental process, can be seen as the opposite of pruning percolation, where nodes are removed according to a connectivity rule. Here we propose models of both bootstrap and pruning percolation for multiplex networks. We collectively refer to these two models with the concept of "weak" percolation, to distinguish them from the somewhat classical concept of ordinary ("strong") percolation. While the two models coincide in simplex networks, we show that they decouple when considering multiplexes, giving rise to a wealth of critical phenomena. Our bootstrap model constitutes the simplest example of a contagion process on a multiplex network and has potential applications in critical infrastructure recovery and information security. Moreover, we show that our pruning percolation model may provide a way to diagnose missing layers in a multiplex network. Finally, our analytical approach allows us to calculate critical behavior and characterize critical clusters.

Visuospatial bootstrapping: Binding useful visuospatial information during verbal working memory encoding does not require set-shifting executive resources.

PubMed

Calia, Clara; Darling, Stephen; Havelka, Jelena; Allen, Richard J

2018-05-01

Immediate serial recall of digits is better when the digits are shown by highlighting them in a familiar array, such as a phone keypad, compared with presenting them serially in a single location, a pattern referred to as "visuospatial bootstrapping." This pattern implies the establishment of temporary links between verbal and spatial working memory, alongside access to information in long-term memory. However, the role of working memory control processes like those implied by the "Central Executive" in bootstrapping has not been directly investigated. Here, we report a study addressing this issue, focusing on executive processes of attentional shifting. Tasks in which information has to be sequenced are thought to be heavily dependent on shifting. Memory for digits presented in keypads versus single locations was assessed under two secondary task load conditions, one with and one without a sequencing requirement, and hence differing in the degree to which they invoke shifting. Results provided clear evidence that multimodal binding (visuospatial bootstrapping) can operate independently of this form of executive control process.

Bootstrap current control studies in the Wendelstein 7-X stellarator using the free-plasma-boundary version of the SIESTA MHD equilibrium code

NASA Astrophysics Data System (ADS)

Peraza-Rodriguez, H.; Reynolds-Barredo, J. M.; Sanchez, R.; Tribaldos, V.; Geiger, J.

2018-02-01

The recently developed free-plasma-boundary version of the SIESTA MHD equilibrium code (Hirshman et al 2011 Phys. Plasmas 18 062504; Peraza-Rodriguez et al 2017 Phys. Plasmas 24 082516) is used for the first time to study scenarios with considerable bootstrap currents for the Wendelstein 7-X (W7-X) stellarator. Bootstrap currents in the range of tens of kAs can lead to the formation of unwanted magnetic island chains or stochastic regions within the plasma and alter the boundary rotational transform due to the small shear in W7-X. The latter issue is of relevance since the island divertor operation of W7-X relies on a proper positioning of magnetic island chains at the plasma edge to control the particle and energy exhaust towards the divertor plates. Two scenarios are examined with the new free-plasma-boundary capabilities of SIESTA: a freely evolving bootstrap current one that illustrates the difficulties arising from the dislocation of the boundary islands, and a second one in which off-axis electron cyclotron current drive (ECCD) is applied to compensate the effects of the bootstrap current and keep the island divertor configuration intact. SIESTA finds that off-axis ECCD is indeed able to keep the location and phase of the edge magnetic island chain unchanged, but it may also lead to an undesired stochastization of parts of the confined plasma if the EC deposition radial profile becomes too narrow.

Generalized Bootstrap Method for Assessment of Uncertainty in Semivariogram Inference

USGS Publications Warehouse

Olea, R.A.; Pardo-Iguzquiza, E.

2011-01-01

The semivariogram and its related function, the covariance, play a central role in classical geostatistics for modeling the average continuity of spatially correlated attributes. Whereas all methods are formulated in terms of the true semivariogram, in practice what can be used are estimated semivariograms and models based on samples. A generalized form of the bootstrap method to properly model spatially correlated data is used to advance knowledge about the reliability of empirical semivariograms and semivariogram models based on a single sample. Among several methods available to generate spatially correlated resamples, we selected a method based on the LU decomposition and used several examples to illustrate the approach. The first one is a synthetic, isotropic, exhaustive sample following a normal distribution, the second example is also a synthetic but following a non-Gaussian random field, and a third empirical sample consists of actual raingauge measurements. Results show wider confidence intervals than those found previously by others with inadequate application of the bootstrap. Also, even for the Gaussian example, distributions for estimated semivariogram values and model parameters are positively skewed. In this sense, bootstrap percentile confidence intervals, which are not centered around the empirical semivariogram and do not require distributional assumptions for its construction, provide an achieved coverage similar to the nominal coverage. The latter cannot be achieved by symmetrical confidence intervals based on the standard error, regardless if the standard error is estimated from a parametric equation or from bootstrap. ?? 2010 International Association for Mathematical Geosciences.

Performance Analysis of Multilevel Parallel Applications on Shared Memory Architectures

NASA Technical Reports Server (NTRS)

Biegel, Bryan A. (Technical Monitor); Jost, G.; Jin, H.; Labarta J.; Gimenez, J.; Caubet, J.

2003-01-01

Parallel programming paradigms include process level parallelism, thread level parallelization, and multilevel parallelism. This viewgraph presentation describes a detailed performance analysis of these paradigms for Shared Memory Architecture (SMA). This analysis uses the Paraver Performance Analysis System. The presentation includes diagrams of a flow of useful computations.

Use of volatile organic components in scat to identify canid species

USGS Publications Warehouse

Burnham, E.; Bender, L.C.; Eiceman, G.A.; Pierce, K.M.; Prasad, S.

2008-01-01

Identification of wildlife species from indirect evidence can be an important part of wildlife management, and conventional +methods can be expensive or have high error rates. We used chemical characterization of the volatile organic constituents (VOCs) in scat as a method to identify 5 species of North American canids from multiple individuals. We sampled vapors of scats in the headspace over a sample using solid-phase microextraction and determined VOC content using gas chromatography with a flame ionization detector. We used linear discriminant analysis to develop models for differentiating species with bootstrapping to estimate accuracy. Our method correcdy classified 82.4% (bootstrapped 95% CI = 68.8-93.8%) of scat samples. Red fox (Vulpes vulpes) scat was most frequendy misclassified (25.0% of scats misclassified); red fox was also the most common destination for misclassified samples. Our findings are the first reported identification of animal species using VOCs in vapor emissions from scat and suggest that identification of wildlife species may be plausible through chemical characterization of vapor emissions of scat.

Quasi-Axially Symmetric Stellarators with 3 Field Periods

NASA Astrophysics Data System (ADS)

Garabedian, Paul; Ku, Long-Poe

1998-11-01

Compact hybrid configurations with 2 field periods have been studied recently as candidates for a proof of principle experiment at PPPL, cf. A. Reiman et al., Physics design of a high beta quasi-axially symmetric stellarator, J. Plas. Fus. Res. SERIES 1, 429(1998). This enterprise has led us to the discovery of a family of quasi-axially symmetric stellarators with 3 field periods that seem to have significant advantages, although their aspect ratios are a little larger. They have reversed shear and perform better in a local analysis of ballooning modes. Nonlinear equilibrium and stability calculations predict that the average beta limit may be as high as 6% if the bootstrap current turns out to be as big as that expected in comparable tokamaks. The concept relies on a combination of helical fields and bootstrap current to achieve adequate rotational transform at low aspect ratio. A detailed manuscript describing some of this work will be published soon, cf. P.R. Garabedian, Quasi-axially symmetric stellarators, Proc. Natl. Acad. Sci. USA 95 (1998).

Maternal Depression and Trait Anger as Risk Factors for Escalated Physical Discipline

PubMed Central

Shay, Nicole L.; Knutson, John F.

2008-01-01

To test the hypothesized anger-mediated relation between maternal depression and escalation of physical discipline, 122 economically disadvantaged mothers were assessed for current and lifetime diagnoses of depression using the Current Depressive Episode, Past Depression, and Dysthymia sections of the Structured Clinical Interview for DSM-IV (SCID) and a measure of current depressive symptoms, the Beck Depression Inventory–Second Edition (BDI-II). Escalation of physical discipline was assessed using a video analog parenting task; maternal anger not specific to discipline was assessed using the Spielberger Trait Anger Expression Inventory. Reports of anger were associated with the diagnosis of depression and depressive symptoms. Bootstrap analyses of indirect effects indicated that the link between depression and escalated discipline was mediated by anger. Parallel analyses based on BDI-II scores identified a marginally significant indirect effect of depression on discipline. Findings suggest that anger and irritability are central to the putative link between depression and harsh discipline. PMID:18174347

A line transect model for aerial surveys

USGS Publications Warehouse

Quang, Pham Xuan; Lanctot, Richard B.

1991-01-01

We employ a line transect method to estimate the density of the common and Pacific loon in the Yukon Flats National Wildlife Refuge from aerial survey data. Line transect methods have the advantage of automatically taking into account “visibility bias” due to detectability difference of animals at different distances from the transect line. However, line transect methods must overcome two difficulties when applied to inaccurate recording of sighting distances due to high travel speeds, so that in fact only a few reliable distance class counts are available. We propose a unimodal detection function that provides an estimate of the effective area lost due to the blind strip, under the assumption that a line of perfect detection exists parallel to the transect line. The unimodal detection function can also be applied when a blind strip is absent, and in certain instances when the maximum probability of detection is less than 100%. A simple bootstrap procedure to estimate standard error is illustrated. Finally, we present results from a small set of Monte Carlo experiments.

Pulling Econometrics Students up by Their Bootstraps

ERIC Educational Resources Information Center

O'Hara, Michael E.

2014-01-01

Although the concept of the sampling distribution is at the core of much of what we do in econometrics, it is a concept that is often difficult for students to grasp. The thought process behind bootstrapping provides a way for students to conceptualize the sampling distribution in a way that is intuitive and visual. However, teaching students to…

Accuracy assessment of percent canopy cover, cover type, and size class

Treesearch

H. T. Schreuder; S. Bain; R. C. Czaplewski

2003-01-01

Truth for vegetation cover percent and type is obtained from very large-scale photography (VLSP), stand structure as measured by size classes, and vegetation types from a combination of VLSP and ground sampling. We recommend using the Kappa statistic with bootstrap confidence intervals for overall accuracy, and similarly bootstrap confidence intervals for percent...

Finding One's Meaning: A Test of the Relation between Quantifiers and Integers in Language Development

ERIC Educational Resources Information Center

Barner, David; Chow, Katherine; Yang, Shu-Ju

2009-01-01

We explored children's early interpretation of numerals and linguistic number marking, in order to test the hypothesis (e.g., Carey (2004). Bootstrapping and the origin of concepts. "Daedalus", 59-68) that children's initial distinction between "one" and other numerals (i.e., "two," "three," etc.) is bootstrapped from a prior distinction between…

Calculating Confidence Intervals for Regional Economic Impacts of Recreastion by Bootstrapping Visitor Expenditures

Treesearch

Donald B.K. English

2000-01-01

In this paper I use bootstrap procedures to develop confidence intervals for estimates of total industrial output generated per thousand tourist visits. Mean expenditures from replicated visitor expenditure data included weights to correct for response bias. Impacts were estimated with IMPLAN. Ninety percent interval endpoints were 6 to 16 percent above or below the...

Comparison of Methods for Estimating Low Flow Characteristics of Streams

USGS Publications Warehouse

Tasker, Gary D.

1987-01-01

Four methods for estimating the 7-day, 10-year and 7-day, 20-year low flows for streams are compared by the bootstrap method. The bootstrap method is a Monte Carlo technique in which random samples are drawn from an unspecified sampling distribution defined from observed data. The nonparametric nature of the bootstrap makes it suitable for comparing methods based on a flow series for which the true distribution is unknown. Results show that the two methods based on hypothetical distribution (Log-Pearson III and Weibull) had lower mean square errors than did the G. E. P. Box-D. R. Cox transformation method or the Log-W. C. Boughton method which is based on a fit of plotting positions.

Spatial data analytics on heterogeneous multi- and many-core parallel architectures using python

USGS Publications Warehouse

Laura, Jason R.; Rey, Sergio J.

2017-01-01

Parallel vector spatial analysis concerns the application of parallel computational methods to facilitate vector-based spatial analysis. The history of parallel computation in spatial analysis is reviewed, and this work is placed into the broader context of high-performance computing (HPC) and parallelization research. The rise of cyber infrastructure and its manifestation in spatial analysis as CyberGIScience is seen as a main driver of renewed interest in parallel computation in the spatial sciences. Key problems in spatial analysis that have been the focus of parallel computing are covered. Chief among these are spatial optimization problems, computational geometric problems including polygonization and spatial contiguity detection, the use of Monte Carlo Markov chain simulation in spatial statistics, and parallel implementations of spatial econometric methods. Future directions for research on parallelization in computational spatial analysis are outlined.

Revisiting the southern pine growth decline: Where are we 10 years later?

Treesearch

Gary L. Gadbury; Michael S. Williams; Hans T. Schreuder

2004-01-01

This paper evaluates changes in growth of pine stands in the state of Georgia, U.S.A., using USDA Forest Service Forest Inventory and Analysis (FIA) data. In particular, data representing an additional 10-year growth cy-cle has been added to previously published results from two earlier growth cycles. A robust regression procedure is combined with a bootstrap technique...

The Relationships among Students' Future-Oriented Goals and Subgoals, Perceived Task Instrumentality, and Task-Oriented Self-Regulation Strategies in an Academic Environment

ERIC Educational Resources Information Center

Tabachnick, Sharon E.; Miller, Raymond B.; Relyea, George E.

2008-01-01

The authors performed path analysis, followed by a bootstrap procedure, to test the predictions of a model explaining the relationships among students' distal future goals (both extrinsic and intrinsic), their adoption of a middle-range subgoal, their perceptions of task instrumentality, and their proximal task-oriented self-regulation strategies.…

DNA barcoding of Arctic Ocean holozooplankton for species identification and recognition

NASA Astrophysics Data System (ADS)

Bucklin, Ann; Hopcroft, Russell R.; Kosobokova, Ksenia N.; Nigro, Lisa M.; Ortman, Brian D.; Jennings, Robert M.; Sweetman, Christopher J.

2010-01-01

Zooplankton species diversity and distribution are important measures of environmental change in the Arctic Ocean, and may serve as 'rapid-responders' of climate-induced changes in this fragile ecosystem. The scarcity of taxonomists hampers detailed and up-to-date monitoring of these patterns for the rarer and more problematic species. DNA barcodes (short DNA sequences for species recognition and discovery) provide an alternative approach to accurate identification of known species, and can speed routine analysis of zooplankton samples. During 2004-2008, zooplankton samples were collected during cruises to the central Arctic Ocean and Chukchi Sea. A ˜700 base-pair region of the mitochondrial cytochrome oxidase I (mtCOI) gene was amplified and sequenced for 82 identified specimens of 41 species, including cnidarians (six hydrozoans, one scyphozoan), arthropod crustaceans (five amphipods, 24 copepods, one decapod, and one euphausiid); two chaetognaths; and one nemertean. Phylogenetic analysis used the Neighbor-Joining algorithm with Kimura-2-Parameter (K-2-P) distances, with 1000-fold bootstrapping. K-2-P genetic distances between individuals of the same species ranged from 0.0 to 0.2; genetic distances between species ranged widely from 0.1 to 0.7. The mtCOI gene tree showed monophyly (at 100% bootstrap value) for each of the 26 species for which more than one individual was analyzed. Of seven genera for which more than one species was analyzed, four were shown to be monophyletic; three genera were not resolved. At higher taxonomic levels, only the crustacean order Copepoda was resolved, with bootstrap value of 83%. The mtCOI barcodes accurately discriminated and identified known species of 10 taxonomic groups of Arctic Ocean holozooplankton. A comprehensive DNA barcode database for the estimated 300 described species of Arctic holozooplankton will allow rapid assessment of species diversity and distribution in this climate-vulnerable ocean ecosystem.

Efficiency and productivity measurement of rural township hospitals in China: a bootstrapping data envelopment analysis.

PubMed

Cheng, Zhaohui; Cai, Miao; Tao, Hongbing; He, Zhifei; Lin, Xiaojun; Lin, Haifeng; Zuo, Yuling

2016-11-11

Township hospitals (THs) are important components of the three-tier rural healthcare system of China. However, the efficiency and productivity of THs have been questioned since the healthcare reform was implemented in 2009. The objective of this study is to analyse the efficiency and productivity changes in THs before and after the reform process. A total of 48 sample THs were selected from the Xiaogan Prefecture in Hubei Province from 2008 to 2014. First, bootstrapping data envelopment analysis (DEA) was performed to estimate the technical efficiency (TE), pure technical efficiency (PTE) and scale efficiency (SE) of the sample THs during the period. Second, the bootstrapping Malmquist productivity index was used to calculate the productivity changes over time. The average TE, PTE and SE of the sample THs over the 7-year period were 0.5147, 0.6373 and 0.7080, respectively. The average TE and PTE increased from 2008 to 2012 but declined considerably after 2012. In general, the sample THs experienced a negative shift in productivity from 2008 to 2014. The negative change was 2.14%, which was attributed to a 23.89% decrease in technological changes (TC). The sample THs experienced a positive productivity shift from 2008 to 2012 but experienced deterioration from 2012 to 2014. There was considerable space for TE improvement in the sample THs since the average TE was relatively low. From 2008 to 2014, the sample THs experienced a decrease in productivity, and the adverse alteration in TC should be emphasised. In the context of healthcare reform, the factors that influence TE and productivity of THs are complex. Results suggest that numerous quantitative and qualitative studies are necessary to explore the reasons for the changes in TE and productivity. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Assessing Uncertainties in Surface Water Security: A Probabilistic Multi-model Resampling approach

NASA Astrophysics Data System (ADS)

Rodrigues, D. B. B.

2015-12-01

Various uncertainties are involved in the representation of processes that characterize interactions between societal needs, ecosystem functioning, and hydrological conditions. Here, we develop an empirical uncertainty assessment of water security indicators that characterize scarcity and vulnerability, based on a multi-model and resampling framework. We consider several uncertainty sources including those related to: i) observed streamflow data; ii) hydrological model structure; iii) residual analysis; iv) the definition of Environmental Flow Requirement method; v) the definition of critical conditions for water provision; and vi) the critical demand imposed by human activities. We estimate the overall uncertainty coming from the hydrological model by means of a residual bootstrap resampling approach, and by uncertainty propagation through different methodological arrangements applied to a 291 km² agricultural basin within the Cantareira water supply system in Brazil. Together, the two-component hydrograph residual analysis and the block bootstrap resampling approach result in a more accurate and precise estimate of the uncertainty (95% confidence intervals) in the simulated time series. We then compare the uncertainty estimates associated with water security indicators using a multi-model framework and provided by each model uncertainty estimation approach. The method is general and can be easily extended forming the basis for meaningful support to end-users facing water resource challenges by enabling them to incorporate a viable uncertainty analysis into a robust decision making process.

Empirical single sample quantification of bias and variance in Q-ball imaging.

PubMed

Hainline, Allison E; Nath, Vishwesh; Parvathaneni, Prasanna; Blaber, Justin A; Schilling, Kurt G; Anderson, Adam W; Kang, Hakmook; Landman, Bennett A

2018-02-06

The bias and variance of high angular resolution diffusion imaging methods have not been thoroughly explored in the literature and may benefit from the simulation extrapolation (SIMEX) and bootstrap techniques to estimate bias and variance of high angular resolution diffusion imaging metrics. The SIMEX approach is well established in the statistics literature and uses simulation of increasingly noisy data to extrapolate back to a hypothetical case with no noise. The bias of calculated metrics can then be computed by subtracting the SIMEX estimate from the original pointwise measurement. The SIMEX technique has been studied in the context of diffusion imaging to accurately capture the bias in fractional anisotropy measurements in DTI. Herein, we extend the application of SIMEX and bootstrap approaches to characterize bias and variance in metrics obtained from a Q-ball imaging reconstruction of high angular resolution diffusion imaging data. The results demonstrate that SIMEX and bootstrap approaches provide consistent estimates of the bias and variance of generalized fractional anisotropy, respectively. The RMSE for the generalized fractional anisotropy estimates shows a 7% decrease in white matter and an 8% decrease in gray matter when compared with the observed generalized fractional anisotropy estimates. On average, the bootstrap technique results in SD estimates that are approximately 97% of the true variation in white matter, and 86% in gray matter. Both SIMEX and bootstrap methods are flexible, estimate population characteristics based on single scans, and may be extended for bias and variance estimation on a variety of high angular resolution diffusion imaging metrics. © 2018 International Society for Magnetic Resonance in Medicine.

Uncertainty Estimation using Bootstrapped Kriging Predictions for Precipitation Isoscapes

NASA Astrophysics Data System (ADS)

Ma, C.; Bowen, G. J.; Vander Zanden, H.; Wunder, M.

2017-12-01

Isoscapes are spatial models representing the distribution of stable isotope values across landscapes. Isoscapes of hydrogen and oxygen in precipitation are now widely used in a diversity of fields, including geology, biology, hydrology, and atmospheric science. To generate isoscapes, geostatistical methods are typically applied to extend predictions from limited data measurements. Kriging is a popular method in isoscape modeling, but quantifying the uncertainty associated with the resulting isoscapes is challenging. Applications that use precipitation isoscapes to determine sample origin require estimation of uncertainty. Here we present a simple bootstrap method (SBM) to estimate the mean and uncertainty of the krigged isoscape and compare these results with a generalized bootstrap method (GBM) applied in previous studies. We used hydrogen isotopic data from IsoMAP to explore these two approaches for estimating uncertainty. We conducted 10 simulations for each bootstrap method and found that SBM results in more kriging predictions (9/10) compared to GBM (4/10). Prediction from SBM was closer to the original prediction generated without bootstrapping and had less variance than GBM. SBM was tested on different datasets from IsoMAP with different numbers of observation sites. We determined that predictions from the datasets with fewer than 40 observation sites using SBM were more variable than the original prediction. The approaches we used for estimating uncertainty will be compiled in an R package that is under development. We expect that these robust estimates of precipitation isoscape uncertainty can be applied in diagnosing the origin of samples ranging from various type of waters to migratory animals, food products, and humans.

Bootstrapping rapidity anomalous dimensions for transverse-momentum resummation

DOE PAGES

Li, Ye; Zhu, Hua Xing

2017-01-11

Soft function relevant for transverse-momentum resummation for Drell-Yan or Higgs production at hadron colliders are computed through to three loops in the expansion of strong coupling, with the help of bootstrap technique and supersymmetric decomposition. The corresponding rapidity anomalous dimension is extracted. Furthermore, an intriguing relation between anomalous dimensions for transverse-momentum resummation and threshold resummation is found.

Reliability of confidence intervals calculated by bootstrap and classical methods using the FIA 1-ha plot design

Treesearch

H. T. Schreuder; M. S. Williams

2000-01-01

In simulation sampling from forest populations using sample sizes of 20, 40, and 60 plots respectively, confidence intervals based on the bootstrap (accelerated, percentile, and t-distribution based) were calculated and compared with those based on the classical t confidence intervals for mapped populations and subdomains within those populations. A 68.1 ha mapped...

Morphological Cues vs. Number of Nominals in Learning Verb Types in Turkish: The Syntactic Bootstrapping Mechanism Revisited

ERIC Educational Resources Information Center

Ural, A. Engin; Yuret, Deniz; Ketrez, F. Nihan; Kocbas, Dilara; Kuntay, Aylin C.

2009-01-01

The syntactic bootstrapping mechanism of verb learning was evaluated against child-directed speech in Turkish, a language with rich morphology, nominal ellipsis and free word order. Machine-learning algorithms were run on transcribed caregiver speech directed to two Turkish learners (one hour every two weeks between 0;9 to 1;10) of different…

A Comparison of the Bootstrap-F, Improved General Approximation, and Brown-Forsythe Multivariate Approaches in a Mixed Repeated Measures Design

ERIC Educational Resources Information Center

Seco, Guillermo Vallejo; Izquierdo, Marcelino Cuesta; Garcia, M. Paula Fernandez; Diez, F. Javier Herrero

2006-01-01

The authors compare the operating characteristics of the bootstrap-F approach, a direct extension of the work of Berkovits, Hancock, and Nevitt, with Huynh's improved general approximation (IGA) and the Brown-Forsythe (BF) multivariate approach in a mixed repeated measures design when normality and multisample sphericity assumptions do not hold.…

Sample-based estimation of tree species richness in a wet tropical forest compartment

Treesearch

Steen Magnussen; Raphael Pelissier

2007-01-01

Petersen's capture-recapture ratio estimator and the well-known bootstrap estimator are compared across a range of simulated low-intensity simple random sampling with fixed-area plots of 100 m? in a rich wet tropical forest compartment with 93 tree species in the Western Ghats of India. Petersen's ratio estimator was uniformly superior to the bootstrap...

Common Ground between Form and Content: The Pragmatic Solution to the Bootstrapping Problem

ERIC Educational Resources Information Center

Oller, John W.

2005-01-01

The frame of reference for this article is second or foreign language (L2 or FL) acquisition, but the pragmatic bootstrapping hypothesis applies to language processing and acquisition in any context or modality. It is relevant to teaching children to read. It shows how connections between target language surface forms and their content can be made…

The Bacterial Gene IfpA Influences the Potent Induction of Calcitonin Receptor and Osteoclast-Related Genes in Burkholderia Pseudomallei-Induced TRAP-Positive Multinucleated Giant Cells

DTIC Science & Technology

2006-06-13

with arithmetic mean ( UPGMA ) using random tie breaking and uncorrected pairwise distances in MacVector 7.0 (Oxford Molecular). Numbers on branches...denote the UPGMA bootstrap percentage using a highly stringent number (1000) of replications (Felsenstein, 1985). All bootstrap values are 50%, as shown

A Comparison of Single Sample and Bootstrap Methods to Assess Mediation in Cluster Randomized Trials

ERIC Educational Resources Information Center

Pituch, Keenan A.; Stapleton, Laura M.; Kang, Joo Youn

2006-01-01

A Monte Carlo study examined the statistical performance of single sample and bootstrap methods that can be used to test and form confidence interval estimates of indirect effects in two cluster randomized experimental designs. The designs were similar in that they featured random assignment of clusters to one of two treatment conditions and…

Multilingual Phoneme Models for Rapid Speech Processing System Development

DTIC Science & Technology

2006-09-01

processes are used to develop an Arabic speech recognition system starting from monolingual English models, In- ternational Phonetic Association (IPA...clusters. It was found that multilingual bootstrapping methods out- perform monolingual English bootstrapping methods on the Arabic evaluation data initially...International Phonetic Alphabet . . . . . . . . . 7 2.3.2 Multilingual vs. Monolingual Speech Recognition 7 2.3.3 Data-Driven Approaches

Bootstrap imputation with a disease probability model minimized bias from misclassification due to administrative database codes.

PubMed

van Walraven, Carl

2017-04-01

Diagnostic codes used in administrative databases cause bias due to misclassification of patient disease status. It is unclear which methods minimize this bias. Serum creatinine measures were used to determine severe renal failure status in 50,074 hospitalized patients. The true prevalence of severe renal failure and its association with covariates were measured. These were compared to results for which renal failure status was determined using surrogate measures including the following: (1) diagnostic codes; (2) categorization of probability estimates of renal failure determined from a previously validated model; or (3) bootstrap methods imputation of disease status using model-derived probability estimates. Bias in estimates of severe renal failure prevalence and its association with covariates were minimal when bootstrap methods were used to impute renal failure status from model-based probability estimates. In contrast, biases were extensive when renal failure status was determined using codes or methods in which model-based condition probability was categorized. Bias due to misclassification from inaccurate diagnostic codes can be minimized using bootstrap methods to impute condition status using multivariable model-derived probability estimates. Copyright © 2017 Elsevier Inc. All rights reserved.

Reference interval computation: which method (not) to choose?

PubMed

Pavlov, Igor Y; Wilson, Andrew R; Delgado, Julio C

2012-07-11

When different methods are applied to reference interval (RI) calculation the results can sometimes be substantially different, especially for small reference groups. If there are no reliable RI data available, there is no way to confirm which method generates results closest to the true RI. We randomly drawn samples obtained from a public database for 33 markers. For each sample, RIs were calculated by bootstrapping, parametric, and Box-Cox transformed parametric methods. Results were compared to the values of the population RI. For approximately half of the 33 markers, results of all 3 methods were within 3% of the true reference value. For other markers, parametric results were either unavailable or deviated considerably from the true values. The transformed parametric method was more accurate than bootstrapping for sample size of 60, very close to bootstrapping for sample size 120, but in some cases unavailable. We recommend against using parametric calculations to determine RIs. The transformed parametric method utilizing Box-Cox transformation would be preferable way of RI calculation, if it satisfies normality test. If not, the bootstrapping is always available, and is almost as accurate and precise as the transformed parametric method. Copyright © 2012 Elsevier B.V. All rights reserved.

Estimating uncertainty in respondent-driven sampling using a tree bootstrap method.

PubMed

Baraff, Aaron J; McCormick, Tyler H; Raftery, Adrian E

2016-12-20

Respondent-driven sampling (RDS) is a network-based form of chain-referral sampling used to estimate attributes of populations that are difficult to access using standard survey tools. Although it has grown quickly in popularity since its introduction, the statistical properties of RDS estimates remain elusive. In particular, the sampling variability of these estimates has been shown to be much higher than previously acknowledged, and even methods designed to account for RDS result in misleadingly narrow confidence intervals. In this paper, we introduce a tree bootstrap method for estimating uncertainty in RDS estimates based on resampling recruitment trees. We use simulations from known social networks to show that the tree bootstrap method not only outperforms existing methods but also captures the high variability of RDS, even in extreme cases with high design effects. We also apply the method to data from injecting drug users in Ukraine. Unlike other methods, the tree bootstrap depends only on the structure of the sampled recruitment trees, not on the attributes being measured on the respondents, so correlations between attributes can be estimated as well as variability. Our results suggest that it is possible to accurately assess the high level of uncertainty inherent in RDS.

Variabilities in probabilistic seismic hazard maps for natural and induced seismicity in the central and eastern United States

USGS Publications Warehouse

Mousavi, S. Mostafa; Beroza, Gregory C.; Hoover, Susan M.

2018-01-01

Probabilistic seismic hazard analysis (PSHA) characterizes ground-motion hazard from earthquakes. Typically, the time horizon of a PSHA forecast is long, but in response to induced seismicity related to hydrocarbon development, the USGS developed one-year PSHA models. In this paper, we present a display of the variability in USGS hazard curves due to epistemic uncertainty in its informed submodel using a simple bootstrapping approach. We find that variability is highest in low-seismicity areas. On the other hand, areas of high seismic hazard, such as the New Madrid seismic zone or Oklahoma, exhibit relatively lower variability simply because of more available data and a better understanding of the seismicity. Comparing areas of high hazard, New Madrid, which has a history of large naturally occurring earthquakes, has lower forecast variability than Oklahoma, where the hazard is driven mainly by suspected induced earthquakes since 2009. Overall, the mean hazard obtained from bootstrapping is close to the published model, and variability increased in the 2017 one-year model relative to the 2016 model. Comparing the relative variations caused by individual logic-tree branches, we find that the highest hazard variation (as measured by the 95% confidence interval of bootstrapping samples) in the final model is associated with different ground-motion models and maximum magnitudes used in the logic tree, while the variability due to the smoothing distance is minimal. It should be pointed out that this study is not looking at the uncertainty in the hazard in general, but only as it is represented in the USGS one-year models.

Uncovering the structure of (super)conformal field theories

NASA Astrophysics Data System (ADS)

Liendo, Pedro

Conformal field theories (CFTs) are of central importance in modern theoretical physics, with applications that range from condensed matter physics to particle theory phenomenology. In this Ph.D. thesis we study CFTs from two somehow orthogonal (but complementary) points of view. In the first approach we concentrate our efforts in two specific examples: the Veneziano limit of N = 2 and N = 1 superconformal QCD. The addition of supersymmetry makes these theories amenable to analytical analysis. In particular, we use the correspondence between single trace operators and states of a spin chain to study the integrability properties of each theory. Our results indicate that these theories are not completely integrable, but they do contain some subsectors in which integrability might hold. In the second approach, we consider the so-called "bootstrap program'', which is the ambitious idea that the restrictions imposed by conformal symmetry (crossing symmetry in particular) are so powerful that starting from a few basic assumptions one should be able to fix the form of a theory. In this thesis we apply bootstrap techniques to CFTs in the presence of a boundary. We study two-point functions using analytical and numerical methods. One-loop results were re-obtained from crossing symmetry alone and a variety of numerical bounds for conformal dimensions of operators were obtained. These bounds are quite general and valid for any CFT in the presence of a boundary, in contrast to our first approach where a specific set of theories was studied. A natural continuation of this work is to apply bootstrap techniques to supersymmetric theories. Some preliminary results along these lines are presented.

Inference With Difference-in-Differences With a Small Number of Groups: A Review, Simulation Study, and Empirical Application Using SHARE Data.

PubMed

Rokicki, Slawa; Cohen, Jessica; Fink, Günther; Salomon, Joshua A; Landrum, Mary Beth

2018-01-01

Difference-in-differences (DID) estimation has become increasingly popular as an approach to evaluate the effect of a group-level policy on individual-level outcomes. Several statistical methodologies have been proposed to correct for the within-group correlation of model errors resulting from the clustering of data. Little is known about how well these corrections perform with the often small number of groups observed in health research using longitudinal data. First, we review the most commonly used modeling solutions in DID estimation for panel data, including generalized estimating equations (GEE), permutation tests, clustered standard errors (CSE), wild cluster bootstrapping, and aggregation. Second, we compare the empirical coverage rates and power of these methods using a Monte Carlo simulation study in scenarios in which we vary the degree of error correlation, the group size balance, and the proportion of treated groups. Third, we provide an empirical example using the Survey of Health, Ageing, and Retirement in Europe. When the number of groups is small, CSE are systematically biased downwards in scenarios when data are unbalanced or when there is a low proportion of treated groups. This can result in over-rejection of the null even when data are composed of up to 50 groups. Aggregation, permutation tests, bias-adjusted GEE, and wild cluster bootstrap produce coverage rates close to the nominal rate for almost all scenarios, though GEE may suffer from low power. In DID estimation with a small number of groups, analysis using aggregation, permutation tests, wild cluster bootstrap, or bias-adjusted GEE is recommended.

A bootstrap lunar base: Preliminary design review 2

NASA Technical Reports Server (NTRS)

1987-01-01

A bootstrap lunar base is the gateway to manned solar system exploration and requires new ideas and new designs on the cutting edge of technology. A preliminary design for a Bootstrap Lunar Base, the second provided by this contractor, is presented. An overview of the work completed is discussed as well as the technical, management, and cost strategies to complete the program requirements. The lunar base design stresses the transforming capabilities of its lander vehicles to aid in base construction. The design also emphasizes modularity and expandability in the base configuration to support the long-term goals of scientific research and profitable lunar resource exploitation. To successfully construct, develop, and inhabit a permanent lunar base, however, several technological advancements must first be realized. Some of these technological advancements are also discussed.

Spheres, charges, instantons, and bootstrap: A five-dimensional odyssey

NASA Astrophysics Data System (ADS)

Chang, Chi-Ming; Fluder, Martin; Lin, Ying-Hsuan; Wang, Yifan

2018-03-01

We combine supersymmetric localization and the conformal bootstrap to study five-dimensional superconformal field theories. To begin, we classify the admissible counter-terms and derive a general relation between the five-sphere partition function and the conformal and flavor central charges. Along the way, we discover a new superconformal anomaly in five dimensions. We then propose a precise triple factorization formula for the five-sphere partition function, that incorporates instantons and is consistent with flavor symmetry enhancement. We numerically evaluate the central charges for the rank-one Seiberg and Morrison-Seiberg theories, and find strong evidence for their saturation of bootstrap bounds, thereby determining the spectra of long multiplets in these theories. Lastly, our results provide new evidence for the F-theorem and possibly a C-theorem in five-dimensional superconformal theories.

Soft-tissue anatomy of the extant hominoids: a review and phylogenetic analysis.

PubMed

Gibbs, S; Collard, M; Wood, B

2002-01-01

This paper reports the results of a literature search for information about the soft-tissue anatomy of the extant non-human hominoid genera, Pan, Gorilla, Pongo and Hylobates, together with the results of a phylogenetic analysis of these data plus comparable data for Homo. Information on the four extant non-human hominoid genera was located for 240 out of the 1783 soft-tissue structures listed in the Nomina Anatomica. Numerically these data are biased so that information about some systems (e.g. muscles) and some regions (e.g. the forelimb) are over-represented, whereas other systems and regions (e.g. the veins and the lymphatics of the vascular system, the head region) are either under-represented or not represented at all. Screening to ensure that the data were suitable for use in a phylogenetic analysis reduced the number of eligible soft-tissue structures to 171. These data, together with comparable data for modern humans, were converted into discontinuous character states suitable for phylogenetic analysis and then used to construct a taxon-by-character matrix. This matrix was used in two tests of the hypothesis that soft-tissue characters can be relied upon to reconstruct hominoid phylogenetic relationships. In the first, parsimony analysis was used to identify cladograms requiring the smallest number of character state changes. In the second, the phylogenetic bootstrap was used to determine the confidence intervals of the most parsimonious clades. The parsimony analysis yielded a single most parsimonious cladogram that matched the molecular cladogram. Similarly the bootstrap analysis yielded clades that were compatible with the molecular cladogram; a (Homo, Pan) clade was supported by 95% of the replicates, and a (Gorilla, Pan, Homo) clade by 96%. These are the first hominoid morphological data to provide statistically significant support for the clades favoured by the molecular evidence.

Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution

PubMed Central

Moretti, Stefano; van Leeuwen, Danitsja; Gmuender, Hans; Bonassi, Stefano; van Delft, Joost; Kleinjans, Jos; Patrone, Fioravante; Merlo, Domenico Franco

2008-01-01

Background In gene expression analysis, statistical tests for differential gene expression provide lists of candidate genes having, individually, a sufficiently low p-value. However, the interpretation of each single p-value within complex systems involving several interacting genes is problematic. In parallel, in the last sixty years, game theory has been applied to political and social problems to assess the power of interacting agents in forcing a decision and, more recently, to represent the relevance of genes in response to certain conditions. Results In this paper we introduce a Bootstrap procedure to test the null hypothesis that each gene has the same relevance between two conditions, where the relevance is represented by the Shapley value of a particular coalitional game defined on a microarray data-set. This method, which is called Comparative Analysis of Shapley value (shortly, CASh), is applied to data concerning the gene expression in children differentially exposed to air pollution. The results provided by CASh are compared with the results from a parametric statistical test for testing differential gene expression. Both lists of genes provided by CASh and t-test are informative enough to discriminate exposed subjects on the basis of their gene expression profiles. While many genes are selected in common by CASh and the parametric test, it turns out that the biological interpretation of the differences between these two selections is more interesting, suggesting a different interpretation of the main biological pathways in gene expression regulation for exposed individuals. A simulation study suggests that CASh offers more power than t-test for the detection of differential gene expression variability. Conclusion CASh is successfully applied to gene expression analysis of a data-set where the joint expression behavior of genes may be critical to characterize the expression response to air pollution. We demonstrate a synergistic effect between coalitional games and statistics that resulted in a selection of genes with a potential impact in the regulation of complex pathways. PMID:18764936

Self-monitoring Using Mobile Phones in the Early Stages of Adolescent Depression: Randomized Controlled Trial

PubMed Central

Reid, Sophie Caroline; Crooke, Alexander Hew Dale; Khor, Angela; Hearps, Stephen John Charles; Jorm, Anthony Francis; Sanci, Lena; Patton, George

2012-01-01

Background The stepped-care approach, where people with early symptoms of depression are stepped up from low-intensity interventions to higher-level interventions as needed, has the potential to assist many people with mild depressive symptoms. Self-monitoring techniques assist people to understand their mental health symptoms by increasing their emotional self-awareness (ESA) and can be easily distributed on mobile phones at low cost. Increasing ESA is an important first step in psychotherapy and has the potential to intervene before mild depressive symptoms progress to major depressive disorder. In this secondary analysis we examined a mobile phone self-monitoring tool used by young people experiencing mild or more depressive symptoms to investigate the relationships between self-monitoring, ESA, and depression. Objectives We tested two main hypotheses: (1) people who monitored their mood, stress, and coping strategies would have increased ESA from pretest to 6-week follow-up compared with an attention comparison group, and (2) an increase in ESA would predict a decrease in depressive symptoms. Methods We recruited patients aged 14 to 24 years from rural and metropolitan general practices. Eligible participants were identified as having mild or more mental health concerns by their general practitioner. Participants were randomly assigned to either the intervention group (where mood, stress, and daily activities were monitored) or the attention comparison group (where only daily activities were monitored), and both groups self-monitored for 2 to 4 weeks. Randomization was carried out electronically via random seed generation, by an in-house computer programmer; therefore, general practitioners, participants, and researchers were blinded to group allocation at randomization. Participants completed pretest, posttest, and 6-week follow-up measures of the Depression Anxiety Stress Scale and the ESA Scale. We estimated a parallel process latent growth curve model (LGCM) using Mplus to test the indirect effect of the intervention on depressive symptoms via the mediator ESA, and calculated 95% bias-corrected bootstrapping confidence intervals (CIs). Results Of the 163 participants assessed for eligibility, 118 were randomly assigned and 114 were included in analyses (68 in the intervention group and 46 in the comparison group). A parallel process LGCM estimated the indirect effect of the intervention on depressive symptoms via ESA and was shown to be statistically significant based on the 95% bias-corrected bootstrapping CIs not containing zero (–6.366 to –0.029). The proportion of the maximum possible indirect effect estimated was κ2 =.54 (95% CI .426–.640). Conclusions This study supported the hypothesis that self-monitoring increases ESA, which in turn decreases depressive symptoms for young people with mild or more depressive symptoms. Mobile phone self-monitoring programs are ideally suited to first-step intervention programs for depression in the stepped-care approach, particularly when ESA is targeted as a mediating factor. Trial Registration ClinicalTrials.gov NCT00794222; http://clinicaltrials.gov/ct2/show/NCT00794222 (Archived by WebCite at http://www.webcitation.org/65lldW34k) PMID:22732135

Bootstrapped Learning Analysis and Curriculum Development Environment (BLADE)

DTIC Science & Technology

2012-02-01

framework  Development of the automated teacher   The software development aspect of the BL program was conducted primarily in the Java programming...parameters are analogous to Java class data members or to fields in a C structure. Here is an example composite IL object from Blocks World, an...2 and 3, alternative methods of implementing generators were developed, first in Java , later in Ruby. Both of these alternatives lowered the

Bootstrapping Processes in the Development of Students' Commonsense Matter Theories: Using Analogical Mappings, Thought Experiments, and Learning to Measure to Promote Conceptual Restructuring

ERIC Educational Resources Information Center

Smith, Carol L.

2007-01-01

This study explores whether the development of students' understanding of matter as something that occupies space and has weight involves conceptual change and restructuring rather than only simple belief revision. Based on an analysis of how the concepts in students' initial matter theory (henceforth MT1) may differ from the concepts in the…

Using a Nonparametric Bootstrap to Obtain a Confidence Interval for Pearson's "r" with Cluster Randomized Data: A Case Study

ERIC Educational Resources Information Center

Wagstaff, David A.; Elek, Elvira; Kulis, Stephen; Marsiglia, Flavio

2009-01-01

A nonparametric bootstrap was used to obtain an interval estimate of Pearson's "r," and test the null hypothesis that there was no association between 5th grade students' positive substance use expectancies and their intentions to not use substances. The students were participating in a substance use prevention program in which the unit of…

Bootstrapping a five-loop amplitude using Steinmann relations

DOE PAGES

Caron-Huot, Simon; Dixon, Lance J.; McLeod, Andrew; ...

2016-12-05

Here, the analytic structure of scattering amplitudes is restricted by Steinmann relations, which enforce the vanishing of certain discontinuities of discontinuities. We show that these relations dramatically simplify the function space for the hexagon function bootstrap in planar maximally supersymmetric Yang-Mills theory. Armed with this simplification, along with the constraints of dual conformal symmetry and Regge exponentiation, we obtain the complete five-loop six-particle amplitude.

A Bootstrap Algorithm for Mixture Models and Interval Data in Inter-Comparisons

DTIC Science & Technology

2001-07-01

parametric bootstrap. The present algorithm will be applied to a thermometric inter-comparison, where data cannot be assumed to be normally distributed. 2 Data...experimental methods, used in each laboratory) often imply that the statistical assumptions are not satisfied, as for example in several thermometric ...triangular). Indeed, in thermometric experiments these three probabilistic models can represent several common stochastic variabilities for

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

ERIC Educational Resources Information Center

Savalei, Victoria; Yuan, Ke-Hai

2009-01-01

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

A Comparison of Kernel Equating and Traditional Equipercentile Equating Methods and the Parametric Bootstrap Methods for Estimating Standard Errors in Equipercentile Equating

ERIC Educational Resources Information Center

Choi, Sae Il

2009-01-01

This study used simulation (a) to compare the kernel equating method to traditional equipercentile equating methods under the equivalent-groups (EG) design and the nonequivalent-groups with anchor test (NEAT) design and (b) to apply the parametric bootstrap method for estimating standard errors of equating. A two-parameter logistic item response…

Emission sources estimation of size-segregated suburban aerosols measured in continental part of Balkan region using PMF5.0 multivariate receptor model

NASA Astrophysics Data System (ADS)

Petrovic, Srdjan; Đuričić-Milanković, Jelena; Anđelković, Ivan; Pantelić, Ana; Gambaro, Andrea; Đorđević, Dragana

2017-04-01

Using Low-Pressure Cascade Impactors by Dr Berner size segregated particulate matter in the size ranges: 0.27 ≤ Dp ≤ 0.53 μm, 0.53 ≤ Dp ≤ 1.06 μm, 1.06 ≤ Dp ≤ 2.09 μm, 2.09 ≤ Dp ≤ 4.11 μm, 4.11 ≤ Dp ≤ 8.11 μm and 8.11 ≤ Dp ≤ 16 μm were collected. Forty-eight-hour size segregated particulate matter samples from atmospheric aerosols in the sub-urban site of Belgrade were measured during two years (in 2012th to 2013in). ICP-MS was used to quantify next elements: Ag, Al, As, Ba, Be, Ca, Cd, Co, Cr, Cu, Fe, K, Hg, Na, Ni, Mg, Mn, Mo, Pb, Se, Sb, Ti, Tl, V and Zn. In order to examine the number of sources and their fingerprints, EPA PMF 5.0 multivariate receptor tool was used. Error estimation methods (bootstrap, displacement, and bootstrap enhanced by displacement) in the analysis of the obtained solutions have enabled proper detection of the number and types of sources. This analysis of the results indicated the existence of four main sources that contribute to air pollution in the suburban area of Belgrade.

Nomogram Prediction of Overall Survival After Curative Irradiation for Uterine Cervical Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seo, YoungSeok; Yoo, Seong Yul; Kim, Mi-Sook

Purpose: The purpose of this study was to develop a nomogram capable of predicting the probability of 5-year survival after radical radiotherapy (RT) without chemotherapy for uterine cervical cancer. Methods and Materials: We retrospectively analyzed 549 patients that underwent radical RT for uterine cervical cancer between March 1994 and April 2002 at our institution. Multivariate analysis using Cox proportional hazards regression was performed and this Cox model was used as the basis for the devised nomogram. The model was internally validated for discrimination and calibration by bootstrap resampling. Results: By multivariate regression analysis, the model showed that age, hemoglobin levelmore » before RT, Federation Internationale de Gynecologie Obstetrique (FIGO) stage, maximal tumor diameter, lymph node status, and RT dose at Point A significantly predicted overall survival. The survival prediction model demonstrated good calibration and discrimination. The bootstrap-corrected concordance index was 0.67. The predictive ability of the nomogram proved to be superior to FIGO stage (p = 0.01). Conclusions: The devised nomogram offers a significantly better level of discrimination than the FIGO staging system. In particular, it improves predictions of survival probability and could be useful for counseling patients, choosing treatment modalities and schedules, and designing clinical trials. However, before this nomogram is used clinically, it should be externally validated.« less

BootGraph: probabilistic fiber tractography using bootstrap algorithms and graph theory.

PubMed

Vorburger, Robert S; Reischauer, Carolin; Boesiger, Peter

2013-02-01

Bootstrap methods have recently been introduced to diffusion-weighted magnetic resonance imaging to estimate the measurement uncertainty of ensuing diffusion parameters directly from the acquired data without the necessity to assume a noise model. These methods have been previously combined with deterministic streamline tractography algorithms to allow for the assessment of connection probabilities in the human brain. Thereby, the local noise induced disturbance in the diffusion data is accumulated additively due to the incremental progression of streamline tractography algorithms. Graph based approaches have been proposed to overcome this drawback of streamline techniques. For this reason, the bootstrap method is in the present work incorporated into a graph setup to derive a new probabilistic fiber tractography method, called BootGraph. The acquired data set is thereby converted into a weighted, undirected graph by defining a vertex in each voxel and edges between adjacent vertices. By means of the cone of uncertainty, which is derived using the wild bootstrap, a weight is thereafter assigned to each edge. Two path finding algorithms are subsequently applied to derive connection probabilities. While the first algorithm is based on the shortest path approach, the second algorithm takes all existing paths between two vertices into consideration. Tracking results are compared to an established algorithm based on the bootstrap method in combination with streamline fiber tractography and to another graph based algorithm. The BootGraph shows a very good performance in crossing situations with respect to false negatives and permits incorporating additional constraints, such as a curvature threshold. By inheriting the advantages of the bootstrap method and graph theory, the BootGraph method provides a computationally efficient and flexible probabilistic tractography setup to compute connection probability maps and virtual fiber pathways without the drawbacks of streamline tractography algorithms or the assumption of a noise distribution. Moreover, the BootGraph can be applied to common DTI data sets without further modifications and shows a high repeatability. Thus, it is very well suited for longitudinal studies and meta-studies based on DTI. Copyright © 2012 Elsevier Inc. All rights reserved.

Non-lignified helical cell wall thickenings in root cortical cells of Aspleniaceae (Polypodiales): histology and taxonomical significance

PubMed Central

Leroux, O.; Bagniewska-Zadworna, A.; Rambe, S. K.; Knox, J. P.; Marcus, S. E.; Bellefroid, E.; Stubbe, D.; Chabbert, B.; Habrant, A.; Claeys, M.; Viane, R. L. L.

2011-01-01

Background and Aims Extraxylary helical cell wall thickenings in vascular plants are not well documented, except for those in orchid velamen tissues which have been studied extensively. Reports on their occurrence in ferns exist, but detailed information is missing. The aim of this study is to focus on the broad patterns of structure and composition and to study the taxonomic occurrence of helical cell wall thickenings in the fern family Aspleniaceae. Methods Structural and compositional aspects of roots have been examined by means of light, electron, epifluorescence and laser scanning confocal microscopy. To assess the taxonomical distribution of helical cell wall thickenings a molecular phylogenetic analysis based on rbcL sequences of 64 taxa was performed. Key Results The helical cell wall thickenings of all examined species showed considerable uniformity of design. The pattern consists of helical, regularly bifurcating and anastomosing strands. Compositionally, the cell wall thickenings were found to be rich in homogalacturonan, cellulose, mannan and xyloglucan. Thioacidolysis confirmed our negative phloroglucinol staining tests, demonstrating the absence of lignins in the root cortex. All taxa with helical cell wall thickenings formed a monophyletic group supported by a 100 % bootstrap value and composed of mainly epiphytic species. Conclusions This is the first report of non-lignified pectin-rich secondary cell walls in ferns. Based on our molecular analysis, we reject the hypothesis of parallel evolution of helical cell wall thickenings in Aspleniaceae. Helical cell wall thickenings can mechanically stabilize the cortex tissue, allowing maximal uptake of water and nutrients during rainfall events. In addition, it can also act as a boundary layer increasing the diffusive pathway towards the atmosphere, preventing desiccation of the stele of epiphytic growing species. PMID:21118842

Stressors and anxiety in dementia caregiving: multiple mediation analysis of rumination, experiential avoidance, and leisure.

PubMed

Romero-Moreno, R; Losada, A; Márquez-González, M; Mausbach, B T

2016-11-01

Despite the robust associations between stressors and anxiety in dementia caregiving, there is a lack of research examining which factors contribute to explain this relationship. This study was designed to test a multiple mediation model of behavioral and psychological symptoms of dementia (BPSD) and anxiety that proposes higher levels of rumination and experiential avoidance and lower levels of leisure satisfaction as potential mediating variables. The sample consisted of 256 family caregivers. In order to test a simultaneously parallel multiple mediation model of the BPSD to anxiety pathway, a PROCESS method was used and bias-corrected and accelerated bootstrapping method was used to test confidence intervals. Higher levels of stressors significantly predicted anxiety. Greater stressors significantly predicted higher levels of rumination and experiential avoidance, and lower levels of leisure satisfaction. These three coping variables significantly predicted anxiety. Finally, rumination, experiential avoidance, and leisure satisfaction significantly mediated the link between stressors and anxiety. The explained variance for the final model was 47.09%. Significant contrasts were found between rumination and leisure satisfaction, with rumination being a significantly higher mediator. The results suggest that caregivers' experiential avoidance, rumination, and leisure satisfaction may function as mechanisms through which BPSD influence on caregivers' anxiety. Training caregivers in reducing their levels of experiential avoidance and rumination by techniques that foster their ability of acceptance of their negative internal experiences, and increase their level of leisure satisfaction, may be helpful to reduce their anxiety symptoms developed by stressors.

Statistical inference based on the nonparametric maximum likelihood estimator under double-truncation.

PubMed

Emura, Takeshi; Konno, Yoshihiko; Michimae, Hirofumi

2015-07-01

Doubly truncated data consist of samples whose observed values fall between the right- and left- truncation limits. With such samples, the distribution function of interest is estimated using the nonparametric maximum likelihood estimator (NPMLE) that is obtained through a self-consistency algorithm. Owing to the complicated asymptotic distribution of the NPMLE, the bootstrap method has been suggested for statistical inference. This paper proposes a closed-form estimator for the asymptotic covariance function of the NPMLE, which is computationally attractive alternative to bootstrapping. Furthermore, we develop various statistical inference procedures, such as confidence interval, goodness-of-fit tests, and confidence bands to demonstrate the usefulness of the proposed covariance estimator. Simulations are performed to compare the proposed method with both the bootstrap and jackknife methods. The methods are illustrated using the childhood cancer dataset.

Model specification and bootstrapping for multiply imputed data: An application to count models for the frequency of alcohol use

PubMed Central

Comulada, W. Scott

2015-01-01

Stata’s mi commands provide powerful tools to conduct multiple imputation in the presence of ignorable missing data. In this article, I present Stata code to extend the capabilities of the mi commands to address two areas of statistical inference where results are not easily aggregated across imputed datasets. First, mi commands are restricted to covariate selection. I show how to address model fit to correctly specify a model. Second, the mi commands readily aggregate model-based standard errors. I show how standard errors can be bootstrapped for situations where model assumptions may not be met. I illustrate model specification and bootstrapping on frequency counts for the number of times that alcohol was consumed in data with missing observations from a behavioral intervention. PMID:26973439

Heptagons from the Steinmann cluster bootstrap

DOE PAGES

Dixon, Lance J.; Drummond, James; Harrington, Thomas; ...

2017-02-28

We reformulate the heptagon cluster bootstrap to take advantage of the Steinmann relations, which require certain double discontinuities of any amplitude to vanish. These constraints vastly reduce the number of functions needed to bootstrap seven-point amplitudes in planarmore » $$ \\mathcal{N} $$ = 4 supersymmetric Yang-Mills theory, making higher-loop contributions to these amplitudes more computationally accessible. In particular, dual superconformal symmetry and well-defined collinear limits suffice to determine uniquely the symbols of the three-loop NMHV and four-loop MHV seven-point amplitudes. We also show that at three loops, relaxing the dual superconformal $$\\bar{Q}$$ relations and imposing dihedral symmetry (and for NMHV the absence of spurious poles) leaves only a single ambiguity in the heptagon amplitudes. These results point to a strong tension between the collinear properties of the amplitudes and the Steinmann relations.« less

Imaging with New Classic and Vision at the NPOI

NASA Astrophysics Data System (ADS)

Jorgensen, Anders

2018-04-01

The Navy Precision Optical Interferometer (NPOI) is unique among interferometric observatories for its ability to position telescopes in an equally-spaced array configuration. This configuration is optimal for interferometric imaging because it allows the use of bootstrapping to track fringes on long baselines with signal-to-noise ratio less than one. When combined with coherent integration techniques this can produce visibilities with acceptable SNR on baselines long enough to resolve features on the surfaces of stars. The stellar surface imaging project at NPOI combines the bootstrapping array configuration of the NPOI array, real-time fringe tracking, baseline- and wavelength bootstrapping with Earth rotation to provide dense coverage in the UV plane at a wide range of spatial frequencies. In this presentation, we provide an overview of the project and an update of the latest status and results from the project.

Bootstrapping and Maintaining Trust in the Cloud

DTIC Science & Technology

2016-12-01

proliferation and popularity of infrastructure-as-a- service (IaaS) cloud computing services such as Amazon Web Services and Google Compute Engine means...IaaS trusted computing system: • Secure Bootstrapping – the system should enable the tenant to securely install an initial root secret into each cloud ...elastically instantiated and terminated. Prior cloud trusted computing solutions address a subset of these features, but none achieve all. Excalibur [31] sup

Sample Reuse in Statistical Remodeling.

DTIC Science & Technology

1987-08-01

as the jackknife and bootstrap, is an expansion of the functional, T(Fn), or of its distribution function or both. Frangos and Schucany (1987a) used...accelerated bootstrap. In the same report Frangos and Schucany demonstrated the small sample superiority of that approach over the proposals that take...higher order terms of an Edgeworth expansion into account. In a second report Frangos and Schucany (1987b) examined the small sample performance of

Innovation cascades: artefacts, organization and attributions

PubMed Central

2016-01-01

Innovation cascades inextricably link the introduction of new artefacts, transformations in social organization, and the emergence of new functionalities and new needs. This paper describes a positive feedback dynamic, exaptive bootstrapping, through which these cascades proceed, and the characteristics of the relationships in which the new attributions that drive this dynamic are generated. It concludes by arguing that the exaptive bootstrapping dynamic is the principal driver of our current Innovation Society. PMID:26926284

Bootstrapping Development of a Cloud-Based Spoken Dialog System in the Educational Domain from Scratch Using Crowdsourced Data. Research Report. ETS RR-16-16

ERIC Educational Resources Information Center

Ramanarayanan, Vikram; Suendermann-Oeft, David; Lange, Patrick; Ivanov, Alexei V.; Evanini, Keelan; Yu, Zhou; Tsuprun, Eugene; Qian, Yao

2016-01-01

We propose a crowdsourcing-based framework to iteratively and rapidly bootstrap a dialog system from scratch for a new domain. We leverage the open-source modular HALEF dialog system to deploy dialog applications. We illustrate the usefulness of this framework using four different prototype dialog items with applications in the educational domain…

A comparison of different statistical methods analyzing hypoglycemia data using bootstrap simulations.

PubMed

Jiang, Honghua; Ni, Xiao; Huster, William; Heilmann, Cory

2015-01-01

Hypoglycemia has long been recognized as a major barrier to achieving normoglycemia with intensive diabetic therapies. It is a common safety concern for the diabetes patients. Therefore, it is important to apply appropriate statistical methods when analyzing hypoglycemia data. Here, we carried out bootstrap simulations to investigate the performance of the four commonly used statistical models (Poisson, negative binomial, analysis of covariance [ANCOVA], and rank ANCOVA) based on the data from a diabetes clinical trial. Zero-inflated Poisson (ZIP) model and zero-inflated negative binomial (ZINB) model were also evaluated. Simulation results showed that Poisson model inflated type I error, while negative binomial model was overly conservative. However, after adjusting for dispersion, both Poisson and negative binomial models yielded slightly inflated type I errors, which were close to the nominal level and reasonable power. Reasonable control of type I error was associated with ANCOVA model. Rank ANCOVA model was associated with the greatest power and with reasonable control of type I error. Inflated type I error was observed with ZIP and ZINB models.

Bootstrapping under constraint for the assessment of group behavior in human contact networks

NASA Astrophysics Data System (ADS)

Tremblay, Nicolas; Barrat, Alain; Forest, Cary; Nornberg, Mark; Pinton, Jean-François; Borgnat, Pierre

2013-11-01

The increasing availability of time- and space-resolved data describing human activities and interactions gives insights into both static and dynamic properties of human behavior. In practice, nevertheless, real-world data sets can often be considered as only one realization of a particular event. This highlights a key issue in social network analysis: the statistical significance of estimated properties. In this context, we focus here on the assessment of quantitative features of specific subset of nodes in empirical networks. We present a method of statistical resampling based on bootstrapping groups of nodes under constraints within the empirical network. The method enables us to define acceptance intervals for various null hypotheses concerning relevant properties of the subset of nodes under consideration in order to characterize by a statistical test its behavior as “normal” or not. We apply this method to a high-resolution data set describing the face-to-face proximity of individuals during two colocated scientific conferences. As a case study, we show how to probe whether colocating the two conferences succeeded in bringing together the two corresponding groups of scientists.

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

PubMed

Damkliang, Kasikrit; Tandayya, Pichaya; Sangket, Unitsa; Pasomsub, Ekawat

2016-11-28

At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow's execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. All local services have been deployed at our portal http://bioservices.sci.psu.ac.th.

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

PubMed

Damkliang, Kasikrit; Tandayya, Pichaya; Sangket, Unitsa; Pasomsub, Ekawat

2016-03-01

At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow's execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. The all local services have been deployed at our portal http://bioservices.sci.psu.ac.th.

Traffic fatality indicators in Brazil: State diagnosis based on data envelopment analysis research.

PubMed

Bastos, Jorge Tiago; Shen, Yongjun; Hermans, Elke; Brijs, Tom; Wets, Geert; Ferraz, Antonio Clóvis Pinto

2015-08-01

The intense economic growth experienced by Brazil in recent decades and its consequent explosive motorization process have evidenced an undesirable impact: the increasing and unbroken trend in traffic fatality numbers. In order to contribute to road safety diagnosis on a national level, this study presents a research into two main indicators available in Brazil: mortality rate (represented by fatalities per capita) and fatality rate (represented by two sub-indicators, i.e., fatalities per vehicle and fatalities per vehicle kilometer traveled). These indicators were aggregated into a composite indicator or index through a multiple layer data envelopment analysis (DEA) composite indicator model, which looks for the optimum combination of indicators' weights for each decision-making unit, in this case 27 Brazilian states. The index score represents the road safety performance, based on which a ranking of states can be made. Since such a model has never been applied for road safety evaluation in Brazil, its parameters were calibrated based on the experience of more consolidated European Union research in ranking its member countries using DEA techniques. Secondly, cluster analysis was conducted aiming to provide more realistic performance comparisons and, finally, the sensitivity of the results was measured through a bootstrapping method application. It can be concluded that by combining fatality indicators, defining clusters and applying bootstrapping procedures a trustworthy ranking can be created, which is valuable for nationwide road safety planning. Copyright © 2015 Elsevier Ltd. All rights reserved.

Assessing uncertainties in surface water security: An empirical multimodel approach

NASA Astrophysics Data System (ADS)

Rodrigues, Dulce B. B.; Gupta, Hoshin V.; Mendiondo, Eduardo M.; Oliveira, Paulo Tarso S.

2015-11-01

Various uncertainties are involved in the representation of processes that characterize interactions among societal needs, ecosystem functioning, and hydrological conditions. Here we develop an empirical uncertainty assessment of water security indicators that characterize scarcity and vulnerability, based on a multimodel and resampling framework. We consider several uncertainty sources including those related to (i) observed streamflow data; (ii) hydrological model structure; (iii) residual analysis; (iv) the method for defining Environmental Flow Requirement; (v) the definition of critical conditions for water provision; and (vi) the critical demand imposed by human activities. We estimate the overall hydrological model uncertainty by means of a residual bootstrap resampling approach, and by uncertainty propagation through different methodological arrangements applied to a 291 km2 agricultural basin within the Cantareira water supply system in Brazil. Together, the two-component hydrograph residual analysis and the block bootstrap resampling approach result in a more accurate and precise estimate of the uncertainty (95% confidence intervals) in the simulated time series. We then compare the uncertainty estimates associated with water security indicators using a multimodel framework and the uncertainty estimates provided by each model uncertainty estimation approach. The range of values obtained for the water security indicators suggests that the models/methods are robust and performs well in a range of plausible situations. The method is general and can be easily extended, thereby forming the basis for meaningful support to end-users facing water resource challenges by enabling them to incorporate a viable uncertainty analysis into a robust decision-making process.

Modelisation de l'historique d'operation de groupes turbine-alternateur

NASA Astrophysics Data System (ADS)

Szczota, Mickael

Because of their ageing fleet, the utility managers are increasingly in needs of tools that can help them to plan efficiently maintenance operations. Hydro-Quebec started a project that aim to foresee the degradation of their hydroelectric runner, and use that information to classify the generating unit. That classification will help to know which generating unit is more at risk to undergo a major failure. Cracks linked to the fatigue phenomenon are a predominant degradation mode and the loading sequences applied to the runner is a parameter impacting the crack growth. So, the aim of this memoir is to create a generator able to generate synthetic loading sequences that are statistically equivalent to the observed history. Those simulated sequences will be used as input in a life assessment model. At first, we describe how the generating units are operated by Hydro-Quebec and analyse the available data, the analysis shows that the data are non-stationnary. Then, we review modelisation and validation methods. In the following chapter a particular attention is given to a precise description of the validation and comparison procedure. Then, we present the comparison of three kind of model : Discrete Time Markov Chains, Discrete Time Semi-Markov Chains and the Moving Block Bootstrap. For the first two models, we describe how to take account for the non-stationnarity. Finally, we show that the Markov Chain is not adapted for our case, and that the Semi-Markov chains are better when they include the non-stationnarity. The final choice between Semi-Markov Chains and the Moving Block Bootstrap depends of the user. But, with a long term vision we recommend the use of Semi-Markov chains for their flexibility. Keywords: Stochastic models, Models validation, Reliability, Semi-Markov Chains, Markov Chains, Bootstrap

Measurement Error Correction for Predicted Spatiotemporal Air Pollution Exposures.

PubMed

Keller, Joshua P; Chang, Howard H; Strickland, Matthew J; Szpiro, Adam A

2017-05-01

Air pollution cohort studies are frequently analyzed in two stages, first modeling exposure then using predicted exposures to estimate health effects in a second regression model. The difference between predicted and unobserved true exposures introduces a form of measurement error in the second stage health model. Recent methods for spatial data correct for measurement error with a bootstrap and by requiring the study design ensure spatial compatibility, that is, monitor and subject locations are drawn from the same spatial distribution. These methods have not previously been applied to spatiotemporal exposure data. We analyzed the association between fine particulate matter (PM2.5) and birth weight in the US state of Georgia using records with estimated date of conception during 2002-2005 (n = 403,881). We predicted trimester-specific PM2.5 exposure using a complex spatiotemporal exposure model. To improve spatial compatibility, we restricted to mothers residing in counties with a PM2.5 monitor (n = 180,440). We accounted for additional measurement error via a nonparametric bootstrap. Third trimester PM2.5 exposure was associated with lower birth weight in the uncorrected (-2.4 g per 1 μg/m difference in exposure; 95% confidence interval [CI]: -3.9, -0.8) and bootstrap-corrected (-2.5 g, 95% CI: -4.2, -0.8) analyses. Results for the unrestricted analysis were attenuated (-0.66 g, 95% CI: -1.7, 0.35). This study presents a novel application of measurement error correction for spatiotemporal air pollution exposures. Our results demonstrate the importance of spatial compatibility between monitor and subject locations and provide evidence of the association between air pollution exposure and birth weight.

Testing non-inferiority of a new treatment in three-arm clinical trials with binary endpoints.

PubMed

Tang, Nian-Sheng; Yu, Bin; Tang, Man-Lai

2014-12-18

A two-arm non-inferiority trial without a placebo is usually adopted to demonstrate that an experimental treatment is not worse than a reference treatment by a small pre-specified non-inferiority margin due to ethical concerns. Selection of the non-inferiority margin and establishment of assay sensitivity are two major issues in the design, analysis and interpretation for two-arm non-inferiority trials. Alternatively, a three-arm non-inferiority clinical trial including a placebo is usually conducted to assess the assay sensitivity and internal validity of a trial. Recently, some large-sample approaches have been developed to assess the non-inferiority of a new treatment based on the three-arm trial design. However, these methods behave badly with small sample sizes in the three arms. This manuscript aims to develop some reliable small-sample methods to test three-arm non-inferiority. Saddlepoint approximation, exact and approximate unconditional, and bootstrap-resampling methods are developed to calculate p-values of the Wald-type, score and likelihood ratio tests. Simulation studies are conducted to evaluate their performance in terms of type I error rate and power. Our empirical results show that the saddlepoint approximation method generally behaves better than the asymptotic method based on the Wald-type test statistic. For small sample sizes, approximate unconditional and bootstrap-resampling methods based on the score test statistic perform better in the sense that their corresponding type I error rates are generally closer to the prespecified nominal level than those of other test procedures. Both approximate unconditional and bootstrap-resampling test procedures based on the score test statistic are generally recommended for three-arm non-inferiority trials with binary outcomes.

Economic impact study: neuromuscular training reduces the burden of injuries and costs compared to standard warm-up in youth soccer.

PubMed

Marshall, Deborah A; Lopatina, Elena; Lacny, Sarah; Emery, Carolyn A

2016-11-01

There is randomised controlled trial (RCT) evidence that neuromuscular training (NMT) programmes can reduce the risk of injury in youth soccer. We evaluated the cost-effectiveness of such an NMT prevention strategy compared to a standard of practice warm-up. A cost-effectiveness analysis was conducted alongside a cluster RCT. Injury incidence rates were adjusted for cluster using Poisson regression analyses. Direct healthcare costs and injury incidence proportions were adjusted for cluster using bootstrapping. The joint uncertainty surrounding the cost and injury rate and proportion differences was estimated using bootstrapping with 10 000 replicates. Along with a 38% reduction in injury risk (rate difference=-1.27/1000 player hours (95% CI -0.33 to -2.2)), healthcare costs were reduced by 43% in the NMT group (-$689/1000 player hours (95% CI -$1741 to $234)) compared with the control group. 90% of the bootstrapped ratios were in the south-west quadrant of the cost-effectiveness plane, showing that the NMT programme was dominant (more effective and less costly) over standard warm-up. Projecting results onto 58 100 Alberta youth soccer players, an estimated 4965 injuries and over $2.7 million in healthcare costs would be conservatively avoided in one season with implementation of a neuromuscular training prevention programme. Implementation of an NMT prevention programme in youth soccer is effective in reducing the burden of injury and leads to considerable reduction in costs. These findings inform practice and policy supporting the implementation of NMT prevention strategies in youth soccer nationally and internationally. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Bootstrapping and Maintaining Trust in the Cloud

DTIC Science & Technology

2016-03-16

of infrastructure-as-a- service (IaaS) cloud computing services such as Ama- zon Web Services, Google Compute Engine, Rackspace, et. al. means that...Implementation We implemented keylime in ∼3.2k lines of Python in four components: registrar, node, CV, and tenant. The registrar offers a REST-based web ...bootstrap key K. It provides an unencrypted REST-based web service for these two functions. As described earlier, the pro- tocols for exchanging data

Reduced Power Laer Designation Systems

DTIC Science & Technology

2008-06-20

200KD, Ri = = 60Kfl, and R 2 = R4 = 2K yields an overall transimpedance gain of 200K x 30 x 30 = 180MV/A. Figure 3. Three stage photodiode amplifier ...transistor circuit for bootstrap buffering of the input stage, comparing the noise performance of the candidate amplifier designs, selecting the two...transistor bootstrap design as the circuit of choice, and comparing the performance of this circuit against that of a basic transconductance amplifier

Bootstrapping the energy flow in the beginning of life.

PubMed

Hengeveld, R; Fedonkin, M A

2007-01-01

This paper suggests that the energy flow on which all living structures depend only started up slowly, the low-energy, initial phase starting up a second, slightly more energetic phase, and so on. In this way, the build up of the energy flow follows a bootstrapping process similar to that found in the development of computers, the first generation making possible the calculations necessary for constructing the second one, etc. In the biogenetic upstart of an energy flow, non-metals in the lower periods of the Periodic Table of Elements would have constituted the most primitive systems, their operation being enhanced and later supplanted by elements in the higher periods that demand more energy. This bootstrapping process would put the development of the metabolisms based on the second period elements carbon, nitrogen and oxygen at the end of the evolutionary process rather than at, or even before, the biogenetic event.

Conformal Bootstrap in Mellin Space

NASA Astrophysics Data System (ADS)

Gopakumar, Rajesh; Kaviraj, Apratim; Sen, Kallol; Sinha, Aninda

2017-02-01

We propose a new approach towards analytically solving for the dynamical content of conformal field theories (CFTs) using the bootstrap philosophy. This combines the original bootstrap idea of Polyakov with the modern technology of the Mellin representation of CFT amplitudes. We employ exchange Witten diagrams with built-in crossing symmetry as our basic building blocks rather than the conventional conformal blocks in a particular channel. Demanding consistency with the operator product expansion (OPE) implies an infinite set of constraints on operator dimensions and OPE coefficients. We illustrate the power of this method in the ɛ expansion of the Wilson-Fisher fixed point by reproducing anomalous dimensions and, strikingly, obtaining OPE coefficients to higher orders in ɛ than currently available using other analytic techniques (including Feynman diagram calculations). Our results enable us to get a somewhat better agreement between certain observables in the 3D Ising model and the precise numerical values that have been recently obtained.

The impact of using informative priors in a Bayesian cost-effectiveness analysis: an application of endovascular versus open surgical repair for abdominal aortic aneurysms in high-risk patients.

PubMed

McCarron, C Elizabeth; Pullenayegum, Eleanor M; Thabane, Lehana; Goeree, Ron; Tarride, Jean-Eric

2013-04-01

Bayesian methods have been proposed as a way of synthesizing all available evidence to inform decision making. However, few practical applications of the use of Bayesian methods for combining patient-level data (i.e., trial) with additional evidence (e.g., literature) exist in the cost-effectiveness literature. The objective of this study was to compare a Bayesian cost-effectiveness analysis using informative priors to a standard non-Bayesian nonparametric method to assess the impact of incorporating additional information into a cost-effectiveness analysis. Patient-level data from a previously published nonrandomized study were analyzed using traditional nonparametric bootstrap techniques and bivariate normal Bayesian models with vague and informative priors. Two different types of informative priors were considered to reflect different valuations of the additional evidence relative to the patient-level data (i.e., "face value" and "skeptical"). The impact of using different distributions and valuations was assessed in a sensitivity analysis. Models were compared in terms of incremental net monetary benefit (INMB) and cost-effectiveness acceptability frontiers (CEAFs). The bootstrapping and Bayesian analyses using vague priors provided similar results. The most pronounced impact of incorporating the informative priors was the increase in estimated life years in the control arm relative to what was observed in the patient-level data alone. Consequently, the incremental difference in life years originally observed in the patient-level data was reduced, and the INMB and CEAF changed accordingly. The results of this study demonstrate the potential impact and importance of incorporating additional information into an analysis of patient-level data, suggesting this could alter decisions as to whether a treatment should be adopted and whether more information should be acquired.

Bootstrap Current for the Edge Pedestal Plasma in a Diverted Tokamak Geometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koh, S.; Chang, C. S.; Ku, S.

The edge bootstrap current plays a critical role in the equilibrium and stability of the steep edge pedestal plasma. The pedestal plasma has an unconventional and difficult neoclassical property, as compared with the core plasma. It has a narrow passing particle region in velocity space that can be easily modified or destroyed by Coulomb collisions. At the same time, the edge pedestal plasma has steep pressure and electrostatic potential gradients whose scale-lengths are comparable with the ion banana width, and includes a magnetic separatrix surface, across which the topological properties of the magnetic field and particle orbits change abruptly. Amore » driftkinetic particle code XGC0, equipped with a mass-momentum-energy conserving collision operator, is used to study the edge bootstrap current in a realistic diverted magnetic field geometry with a self-consistent radial electric field. When the edge electrons are in the weakly collisional banana regime, surprisingly, the present kinetic simulation confirms that the existing analytic expressions [represented by O. Sauter et al. , Phys. Plasmas 6 , 2834 (1999)] are still valid in this unconventional region, except in a thin radial layer in contact with the magnetic separatrix. The agreement arises from the dominance of the electron contribution to the bootstrap current compared with ion contribution and from a reasonable separation of the trapped-passing dynamics without a strong collisional mixing. However, when the pedestal electrons are in plateau-collisional regime, there is significant deviation of numerical results from the existing analytic formulas, mainly due to large effective collisionality of the passing and the boundary layer trapped particles in edge region. In a conventional aspect ratio tokamak, the edge bootstrap current from kinetic simulation can be significantly less than that from the Sauter formula if the electron collisionality is high. On the other hand, when the aspect ratio is close to unity, the collisional edge bootstrap current can be significantly greater than that from the Sauter formula. Rapid toroidal rotation of the magnetic field lines at the high field side of a tight aspect-ratio tokamak is believed to be the cause of the different behavior. A new analytic fitting formula, as a simple modification to the Sauter formula, is obtained to bring the analytic expression to a better agreement with the edge kinetic simulation results« less

Bootstrap current for the edge pedestal plasma in a diverted tokamak geometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koh, S.; Choe, W.; Chang, C. S.

The edge bootstrap current plays a critical role in the equilibrium and stability of the steep edge pedestal plasma. The pedestal plasma has an unconventional and difficult neoclassical property, as compared with the core plasma. It has a narrow passing particle region in velocity space that can be easily modified or destroyed by Coulomb collisions. At the same time, the edge pedestal plasma has steep pressure and electrostatic potential gradients whose scale-lengths are comparable with the ion banana width, and includes a magnetic separatrix surface, across which the topological properties of the magnetic field and particle orbits change abruptly. Amore » drift-kinetic particle code XGC0, equipped with a mass-momentum-energy conserving collision operator, is used to study the edge bootstrap current in a realistic diverted magnetic field geometry with a self-consistent radial electric field. When the edge electrons are in the weakly collisional banana regime, surprisingly, the present kinetic simulation confirms that the existing analytic expressions [represented by O. Sauter et al., Phys. Plasmas 6, 2834 (1999)] are still valid in this unconventional region, except in a thin radial layer in contact with the magnetic separatrix. The agreement arises from the dominance of the electron contribution to the bootstrap current compared with ion contribution and from a reasonable separation of the trapped-passing dynamics without a strong collisional mixing. However, when the pedestal electrons are in plateau-collisional regime, there is significant deviation of numerical results from the existing analytic formulas, mainly due to large effective collisionality of the passing and the boundary layer trapped particles in edge region. In a conventional aspect ratio tokamak, the edge bootstrap current from kinetic simulation can be significantly less than that from the Sauter formula if the electron collisionality is high. On the other hand, when the aspect ratio is close to unity, the collisional edge bootstrap current can be significantly greater than that from the Sauter formula. Rapid toroidal rotation of the magnetic field lines at the high field side of a tight aspect-ratio tokamak is believed to be the cause of the different behavior. A new analytic fitting formula, as a simple modification to the Sauter formula, is obtained to bring the analytic expression to a better agreement with the edge kinetic simulation results.« less

Patient-specific estimation of spatially variant image noise for a pinhole cardiac SPECT camera.

PubMed

Cuddy-Walsh, Sarah G; Wells, R Glenn

2018-05-01

New single photon emission computed tomography (SPECT) cameras using fixed pinhole collimation are increasingly popular. Pinhole collimators are known to have variable sensitivity with distance and angle from the pinhole aperture. It follows that pinhole SPECT systems will also have spatially variant sensitivity and hence spatially variant image noise. The objective of this study was to develop and validate a rapid method for analytically estimating a map of the noise magnitude in a reconstructed image using data from a single clinical acquisition. The projected voxel (PV) noise estimation method uses a modified forward projector with attenuation effects to estimate the number of photons detected from each voxel in the field-of-view. We approximate the noise for each voxel as the standard deviation of a Poisson distribution with a mean equal to the number of detected photons. An empirical formula is used to address scaling discrepancies caused by image reconstruction. Calibration coefficients are determined for the PV method by comparing it with noise measured from a nonparametrically bootstrapped set of images of a spherical uniformly filled Tc-99m water phantom. Validation studies compare PV noise estimates with bootstrapped measured noise for 31 patient images (5 min, 340 MBq, 99m Tc-tetrofosmin rest study). Bland-Altman analysis shows R 2 correlations ≥70% between the PV-estimated and -measured image noise. For the 31 patient cardiac images, the PV noise estimate has an average bias of 0.1% compared to bootstrapped noise and have a coefficient of variation (CV) ≤ 17%. The bootstrap approach to noise measurement requires 5 h of computation for each image, whereas the PV noise estimate requires only 64 s. In cardiac images, image noise due to attenuation and camera sensitivity varies on average from 4% at the apex to 9% in the basal posterior region of the heart. The standard deviation between 15 healthy patient study images (including physiological variability in the population) ranges from 6% to 16.5% over the length of the heart. The PV method provides a rapid estimate for spatially variant patient-specific image noise magnitude in a pinhole-collimated dedicated cardiac SPECT camera with a bias of -0.3% and better than 83% precision. © 2018 American Association of Physicists in Medicine.

Seasonal comparisons of sea ice concentration estimates derived from SSM/I, OKEAN, and RADARSAT data

USGS Publications Warehouse

Belchansky, Gennady I.; Douglas, David C.

2002-01-01

The Special Sensor Microwave Imager (SSM/I) microwave satellite radiometer and its predecessor SMMR are primary sources of information for global sea ice and climate studies. However, comparisons of SSM/I, Landsat, AVHRR, and ERS-1 synthetic aperture radar (SAR) have shown substantial seasonal and regional differences in their estimates of sea ice concentration. To evaluate these differences, we compared SSM/I estimates of sea ice coverage derived with the NASA Team and Bootstrap algorithms to estimates made using RADARSAT, and OKEAN-01 satellite sensor data. The study area included the Barents Sea, Kara Sea, Laptev Sea, and adjacent parts of the Arctic Ocean, during October 1995 through October 1999. Ice concentration estimates from spatially and temporally near-coincident imagery were calculated using independent algorithms for each sensor type. The OKEAN algorithm implemented the satellite's two-channel active (radar) and passive microwave data in a linear mixture model based on the measured values of brightness temperature and radar backscatter. The RADARSAT algorithm utilized a segmentation approach of the measured radar backscatter, and the SSM/I ice concentrations were derived at National Snow and Ice Data Center (NSIDC) using the NASA Team and Bootstrap algorithms. Seasonal and monthly differences between SSM/I, OKEAN, and RADARSAT ice concentrations were calculated and compared. Overall, total sea ice concentration estimates derived independently from near-coincident RADARSAT, OKEAN-01, and SSM/I satellite imagery demonstrated mean differences of less than 5.5% (S.D.<9.5%) during the winter period. Differences between the SSM/I NASA Team and the SSM/I Bootstrap concentrations were no more than 3.1% (S.D.<5.4%) during this period. RADARSAT and OKEAN-01 data both yielded higher total ice concentrations than the NASA Team and the Bootstrap algorithms. The Bootstrap algorithm yielded higher total ice concentrations than the NASA Team algorithm. Total ice concentrations derived from OKEAN-01 and SSM/I satellite imagery were highly correlated during winter, spring, and fall, with mean differences of less than 8.1% (S.D.<15%) for the NASA Team algorithm, and less than 2.8% (S.D.<13.8%) for the Bootstrap algorithm. Respective differences between SSM/I NASA Team and SSM/I Bootstrap total concentrations were less than 5.3% (S.D.<6.9%). Monthly mean differences between SSM/I and OKEAN differed annually by less than 6%, with smaller differences primarily in winter. The NASA Team and Bootstrap algorithms underestimated the total sea ice concentrations relative to the RADARSAT ScanSAR no more than 3.0% (S.D.<9%) and 1.2% (S.D.<7.5%) during cold months, and no more than 12% and 7% during summer, respectively. ScanSAR tended to estimate higher ice concentrations for ice concentrations greater than 50%, when compared to SSM/I during all months. ScanSAR underestimated total sea ice concentration by 2% compared to the OKEAN-01 algorithm during cold months, and gave an overestimation by 2% during spring and summer months. Total NASA Team and Bootstrap sea ice concentration estimates derived from coincident SSM/I and OKEAN-01 data demonstrated mean differences of no more than 5.3% (S.D.<7%), 3.1% (S.D.<5.5%), 2.0% (S.D.<5.5%), and 7.3% (S.D.<10%) for fall, winter, spring, and summer periods, respectively. Large disagreements were observed between the OKEAN and NASA Team results in spring and summer for estimates of the first-year (FY) and multiyear (MY) age classes. The OKEAN-01 algorithm and data tended to estimate, on average, lower concentrations of young or FY ice and higher concentrations of total and MY ice for all months and seasons. Our results contribute to the growing body of documentation about the levels of disparity obtained when seasonal sea ice concentrations are estimated using various types of satellite data and algorithms.

A Proposed Solution to the Problem with Using Completely Random Data to Assess the Number of Factors with Parallel Analysis

ERIC Educational Resources Information Center

Green, Samuel B.; Levy, Roy; Thompson, Marilyn S.; Lu, Min; Lo, Wen-Juo

2012-01-01

A number of psychometricians have argued for the use of parallel analysis to determine the number of factors. However, parallel analysis must be viewed at best as a heuristic approach rather than a mathematically rigorous one. The authors suggest a revision to parallel analysis that could improve its accuracy. A Monte Carlo study is conducted to…

A cluster bootstrap for two-loop MHV amplitudes

DOE PAGES

Golden, John; Spradlin, Marcus

2015-02-02

We apply a bootstrap procedure to two-loop MHV amplitudes in planar N=4 super-Yang-Mills theory. We argue that the mathematically most complicated part (the Λ 2 B 2 coproduct component) of the n-particle amplitude is uniquely determined by a simple cluster algebra property together with a few physical constraints (dihedral symmetry, analytic structure, supersymmetry, and well-defined collinear limits). Finally, we present a concise, closed-form expression which manifests these properties for all n.

Wrappers for Performance Enhancement and Oblivious Decision Graphs

DTIC Science & Technology

1995-09-01

always select all relevant features. We test di erent search engines to search the space of feature subsets and introduce compound operators to speed...distinct instances from the original dataset appearing in the test set is thus 0:632m. The 0i accuracy estimate is derived by using bootstrap sample...i for training and the rest of the instances for testing . Given a number b, the number of bootstrap samples, let 0i be the accuracy estimate for

Simplified Estimation and Testing in Unbalanced Repeated Measures Designs.

PubMed

Spiess, Martin; Jordan, Pascal; Wendt, Mike

2018-05-07

In this paper we propose a simple estimator for unbalanced repeated measures design models where each unit is observed at least once in each cell of the experimental design. The estimator does not require a model of the error covariance structure. Thus, circularity of the error covariance matrix and estimation of correlation parameters and variances are not necessary. Together with a weak assumption about the reason for the varying number of observations, the proposed estimator and its variance estimator are unbiased. As an alternative to confidence intervals based on the normality assumption, a bias-corrected and accelerated bootstrap technique is considered. We also propose the naive percentile bootstrap for Wald-type tests where the standard Wald test may break down when the number of observations is small relative to the number of parameters to be estimated. In a simulation study we illustrate the properties of the estimator and the bootstrap techniques to calculate confidence intervals and conduct hypothesis tests in small and large samples under normality and non-normality of the errors. The results imply that the simple estimator is only slightly less efficient than an estimator that correctly assumes a block structure of the error correlation matrix, a special case of which is an equi-correlation matrix. Application of the estimator and the bootstrap technique is illustrated using data from a task switch experiment based on an experimental within design with 32 cells and 33 participants.

Associations between dietary and lifestyle risk factors and colorectal cancer in the Scottish population.

PubMed

Theodoratou, Evropi; Farrington, Susan M; Tenesa, Albert; McNeill, Geraldine; Cetnarskyj, Roseanne; Korakakis, Emmanouil; Din, Farhat V N; Porteous, Mary E; Dunlop, Malcolm G; Campbell, Harry

2014-01-01

Colorectal cancer (CRC) accounts for 9.7% of all cancer cases and for 8% of all cancer-related deaths. Established risk factors include personal or family history of CRC as well as lifestyle and dietary factors. We investigated the relationship between CRC and demographic, lifestyle, food and nutrient risk factors through a case-control study that included 2062 patients and 2776 controls from Scotland. Forward and backward stepwise regression was applied and the stability of the models was assessed in 1000 bootstrap samples. The variables that were automatically selected to be included by the forward or backward stepwise regression and whose selection was verified by bootstrap sampling in the current study were family history, dietary energy, 'high-energy snack foods', eggs, juice, sugar-sweetened beverages and white fish (associated with an increased CRC risk) and NSAIDs, coffee and magnesium (associated with a decreased CRC risk). Application of forward and backward stepwise regression in this CRC study identified some already established as well as some novel potential risk factors. Bootstrap findings suggest that examination of the stability of regression models by bootstrap sampling is useful in the interpretation of study findings. 'High-energy snack foods' and high-energy drinks (including sugar-sweetened beverages and fruit juices) as risk factors for CRC have not been reported previously and merit further investigation as such snacks and beverages are important contributors in European and North American diets.

Using the Bootstrap Method for a Statistical Significance Test of Differences between Summary Histograms

NASA Technical Reports Server (NTRS)

Xu, Kuan-Man

2006-01-01

A new method is proposed to compare statistical differences between summary histograms, which are the histograms summed over a large ensemble of individual histograms. It consists of choosing a distance statistic for measuring the difference between summary histograms and using a bootstrap procedure to calculate the statistical significance level. Bootstrapping is an approach to statistical inference that makes few assumptions about the underlying probability distribution that describes the data. Three distance statistics are compared in this study. They are the Euclidean distance, the Jeffries-Matusita distance and the Kuiper distance. The data used in testing the bootstrap method are satellite measurements of cloud systems called cloud objects. Each cloud object is defined as a contiguous region/patch composed of individual footprints or fields of view. A histogram of measured values over footprints is generated for each parameter of each cloud object and then summary histograms are accumulated over all individual histograms in a given cloud-object size category. The results of statistical hypothesis tests using all three distances as test statistics are generally similar, indicating the validity of the proposed method. The Euclidean distance is determined to be most suitable after comparing the statistical tests of several parameters with distinct probability distributions among three cloud-object size categories. Impacts on the statistical significance levels resulting from differences in the total lengths of satellite footprint data between two size categories are also discussed.

Covariance Analysis of Vision Aided Navigation by Bootstrapping

DTIC Science & Technology

2012-03-22

vision aided navigation. The aircraft uses its INS estimate to geolocate ground features, track those features to aid the INS, and using that aided...development of the 2-D case, including the dynamics and measurement model development, the state space representation and the use of the Kalman filter ...reference frame. This reference frame has its origin located somewhere on an A/C. Normally the origin is set at the A/C center of gravity to allow the use

GENOME-WIDE COMPARATIVE ANALYSIS OF PHYLOGENETIC TREES: THE PROKARYOTIC FOREST OF LIFE

PubMed Central

Puigbò, Pere; Wolf, Yuri I.; Koonin, Eugene V.

2013-01-01

Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the Boot-Split Distance (BSD) method is introduced as an extension of the previously developed Split Distance (SD) method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting tree-like and net-like evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the applications methods used to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a ‘species tree’. PMID:22399455

Nomograms Predicting Progression-Free Survival, Overall Survival, and Pelvic Recurrence in Locally Advanced Cervical Cancer Developed From an Analysis of Identifiable Prognostic Factors in Patients From NRG Oncology/Gynecologic Oncology Group Randomized Trials of Chemoradiotherapy

PubMed Central

Rose, Peter G.; Java, James; Whitney, Charles W.; Stehman, Frederick B.; Lanciano, Rachelle; Thomas, Gillian M.; DiSilvestro, Paul A.

2015-01-01

Purpose To evaluate the prognostic factors in locally advanced cervical cancer limited to the pelvis and develop nomograms for 2-year progression-free survival (PFS), 5-year overall survival (OS), and pelvic recurrence. Patients and Methods We retrospectively reviewed 2,042 patients with locally advanced cervical carcinoma enrolled onto Gynecologic Oncology Group clinical trials of concurrent cisplatin-based chemotherapy and radiotherapy. Nomograms for 2-year PFS, five-year OS, and pelvic recurrence were created as visualizations of Cox proportional hazards regression models. The models were validated by bootstrap-corrected, relatively unbiased estimates of discrimination and calibration. Results Multivariable analysis identified prognostic factors including histology, race/ethnicity, performance status, tumor size, International Federation of Gynecology and Obstetrics stage, tumor grade, pelvic node status, and treatment with concurrent cisplatin-based chemotherapy. PFS, OS, and pelvic recurrence nomograms had bootstrap-corrected concordance indices of 0.62, 0.64, and 0.73, respectively, and were well calibrated. Conclusion Prognostic factors were used to develop nomograms for 2-year PFS, 5-year OS, and pelvic recurrence for locally advanced cervical cancer clinically limited to the pelvis treated with concurrent cisplatin-based chemotherapy and radiotherapy. These nomograms can be used to better estimate individual and collective outcomes. PMID:25732170

Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life.

PubMed

Puigbò, Pere; Wolf, Yuri I; Koonin, Eugene V

2012-01-01

Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article, we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the Boot-Split Distance (BSD) method is introduced as an extension of the previously developed Split Distance method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting tree-like and net-like evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the application of these methods to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a "species tree."

Resampling to Address the Winner's Curse in Genetic Association Analysis of Time to Event

PubMed Central

Poirier, Julia G.; Faye, Laura L.; Dimitromanolakis, Apostolos; Paterson, Andrew D.; Sun, Lei

2015-01-01

ABSTRACT The “winner's curse” is a subtle and difficult problem in interpretation of genetic association, in which association estimates from large‐scale gene detection studies are larger in magnitude than those from subsequent replication studies. This is practically important because use of a biased estimate from the original study will yield an underestimate of sample size requirements for replication, leaving the investigators with an underpowered study. Motivated by investigation of the genetics of type 1 diabetes complications in a longitudinal cohort of participants in the Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) Genetics Study, we apply a bootstrap resampling method in analysis of time to nephropathy under a Cox proportional hazards model, examining 1,213 single‐nucleotide polymorphisms (SNPs) in 201 candidate genes custom genotyped in 1,361 white probands. Among 15 top‐ranked SNPs, bias reduction in log hazard ratio estimates ranges from 43.1% to 80.5%. In simulation studies based on the observed DCCT/EDIC genotype data, genome‐wide bootstrap estimates for false‐positive SNPs and for true‐positive SNPs with low‐to‐moderate power are closer to the true values than uncorrected naïve estimates, but tend to overcorrect SNPs with high power. This bias‐reduction technique is generally applicable for complex trait studies including quantitative, binary, and time‐to‐event traits. PMID:26411674

Estimation of reliability of predictions and model applicability domain evaluation in the analysis of acute toxicity (LD50).

PubMed

Sazonovas, A; Japertas, P; Didziapetris, R

2010-01-01

This study presents a new type of acute toxicity (LD(50)) prediction that enables automated assessment of the reliability of predictions (which is synonymous with the assessment of the Model Applicability Domain as defined by the Organization for Economic Cooperation and Development). Analysis involved nearly 75,000 compounds from six animal systems (acute rat toxicity after oral and intraperitoneal administration; acute mouse toxicity after oral, intraperitoneal, intravenous, and subcutaneous administration). Fragmental Partial Least Squares (PLS) with 100 bootstraps yielded baseline predictions that were automatically corrected for non-linear effects in local chemical spaces--a combination called Global, Adjusted Locally According to Similarity (GALAS) modelling methodology. Each prediction obtained in this manner is provided with a reliability index value that depends on both compound's similarity to the training set (that accounts for similar trends in LD(50) variations within multiple bootstraps) and consistency of experimental results with regard to the baseline model in the local chemical environment. The actual performance of the Reliability Index (RI) was proven by its good (and uniform) correlations with Root Mean Square Error (RMSE) in all validation sets, thus providing quantitative assessment of the Model Applicability Domain. The obtained models can be used for compound screening in the early stages of drug development and prioritization for experimental in vitro testing or later in vivo animal acute toxicity studies.

Method-independent, Computationally Frugal Convergence Testing for Sensitivity Analysis Techniques

NASA Astrophysics Data System (ADS)

Mai, J.; Tolson, B.

2017-12-01

The increasing complexity and runtime of environmental models lead to the current situation that the calibration of all model parameters or the estimation of all of their uncertainty is often computationally infeasible. Hence, techniques to determine the sensitivity of model parameters are used to identify most important parameters. All subsequent model calibrations or uncertainty estimation procedures focus then only on these subsets of parameters and are hence less computational demanding. While the examination of the convergence of calibration and uncertainty methods is state-of-the-art, the convergence of the sensitivity methods is usually not checked. If any, bootstrapping of the sensitivity results is used to determine the reliability of the estimated indexes. Bootstrapping, however, might as well become computationally expensive in case of large model outputs and a high number of bootstraps. We, therefore, present a Model Variable Augmentation (MVA) approach to check the convergence of sensitivity indexes without performing any additional model run. This technique is method- and model-independent. It can be applied either during the sensitivity analysis (SA) or afterwards. The latter case enables the checking of already processed sensitivity indexes. To demonstrate the method's independency of the convergence testing method, we applied it to two widely used, global SA methods: the screening method known as Morris method or Elementary Effects (Morris 1991) and the variance-based Sobol' method (Solbol' 1993). The new convergence testing method is first scrutinized using 12 analytical benchmark functions (Cuntz & Mai et al. 2015) where the true indexes of aforementioned three methods are known. This proof of principle shows that the method reliably determines the uncertainty of the SA results when different budgets are used for the SA. The results show that the new frugal method is able to test the convergence and therefore the reliability of SA results in an efficient way. The appealing feature of this new technique is the necessity of no further model evaluation and therefore enables checking of already processed sensitivity results. This is one step towards reliable and transferable, published sensitivity results.

A combined approach of generalized additive model and bootstrap with small sample sets for fault diagnosis in fermentation process of glutamate.

PubMed

Liu, Chunbo; Pan, Feng; Li, Yun

2016-07-29

Glutamate is of great importance in food and pharmaceutical industries. There is still lack of effective statistical approaches for fault diagnosis in the fermentation process of glutamate. To date, the statistical approach based on generalized additive model (GAM) and bootstrap has not been used for fault diagnosis in fermentation processes, much less the fermentation process of glutamate with small samples sets. A combined approach of GAM and bootstrap was developed for the online fault diagnosis in the fermentation process of glutamate with small sample sets. GAM was first used to model the relationship between glutamate production and different fermentation parameters using online data from four normal fermentation experiments of glutamate. The fitted GAM with fermentation time, dissolved oxygen, oxygen uptake rate and carbon dioxide evolution rate captured 99.6 % variance of glutamate production during fermentation process. Bootstrap was then used to quantify the uncertainty of the estimated production of glutamate from the fitted GAM using 95 % confidence interval. The proposed approach was then used for the online fault diagnosis in the abnormal fermentation processes of glutamate, and a fault was defined as the estimated production of glutamate fell outside the 95 % confidence interval. The online fault diagnosis based on the proposed approach identified not only the start of the fault in the fermentation process, but also the end of the fault when the fermentation conditions were back to normal. The proposed approach only used a small sample sets from normal fermentations excitements to establish the approach, and then only required online recorded data on fermentation parameters for fault diagnosis in the fermentation process of glutamate. The proposed approach based on GAM and bootstrap provides a new and effective way for the fault diagnosis in the fermentation process of glutamate with small sample sets.

Examination of the reliability of the crash modification factors using empirical Bayes method with resampling technique.

PubMed

Wang, Jung-Han; Abdel-Aty, Mohamed; Wang, Ling

2017-07-01

There have been plenty of studies intended to use different methods, for example, empirical Bayes before-after methods, to get accurate estimation of CMFs. All of them have different assumptions toward crash count if there was no treatment. Additionally, another major assumption is that multiple sites share the same true CMF. Under this assumption, the CMF at an individual intersection is randomly drawn from a normally distributed population of CMFs at all intersections. Since CMFs are non-zero values, the population of all CMFs might not follow normal distributions, and even if it does, the true mean of CMFs at some intersections may be different from that at others. Therefore, a bootstrap method based on before-after empirical Bayes theory was proposed to estimate CMFs, but it did not make distributional assumptions. This bootstrap procedure has the added benefit of producing a measure of CMF stability. Furthermore, based on the bootstrapped CMF, a new CMF precision rating method was proposed to evaluate the reliability of CMFs. This study chose 29 urban four-legged intersections as treated sites, and their controls were changed from stop-controlled to signal-controlled. Meanwhile, 124 urban four-legged stop-controlled intersections were selected as reference sites. At first, different safety performance functions (SPFs) were applied to five crash categories, and it was found that each crash category had different optimal SPF form. Then, the CMFs of these five crash categories were estimated using the bootstrap empirical Bayes method. The results of the bootstrapped method showed that signalization significantly decreased Angle+Left-Turn crashes, and its CMF had the highest precision. While, the CMF for Rear-End crashes was unreliable. For KABCO, KABC, and KAB crashes, their CMFs were proved to be reliable for the majority of intersections, but the estimated effect of signalization may be not accurate at some sites. Copyright © 2017 Elsevier Ltd. All rights reserved.

Parallel-vector computation for linear structural analysis and non-linear unconstrained optimization problems

NASA Technical Reports Server (NTRS)

Nguyen, D. T.; Al-Nasra, M.; Zhang, Y.; Baddourah, M. A.; Agarwal, T. K.; Storaasli, O. O.; Carmona, E. A.

1991-01-01

Several parallel-vector computational improvements to the unconstrained optimization procedure are described which speed up the structural analysis-synthesis process. A fast parallel-vector Choleski-based equation solver, pvsolve, is incorporated into the well-known SAP-4 general-purpose finite-element code. The new code, denoted PV-SAP, is tested for static structural analysis. Initial results on a four processor CRAY 2 show that using pvsolve reduces the equation solution time by a factor of 14-16 over the original SAP-4 code. In addition, parallel-vector procedures for the Golden Block Search technique and the BFGS method are developed and tested for nonlinear unconstrained optimization. A parallel version of an iterative solver and the pvsolve direct solver are incorporated into the BFGS method. Preliminary results on nonlinear unconstrained optimization test problems, using pvsolve in the analysis, show excellent parallel-vector performance indicating that these parallel-vector algorithms can be used in a new generation of finite-element based structural design/analysis-synthesis codes.

Soft-tissue anatomy of the extant hominoids: a review and phylogenetic analysis

PubMed Central

Gibbs, S; Collard, M; Wood, B

2002-01-01

This paper reports the results of a literature search for information about the soft-tissue anatomy of the extant non-human hominoid genera, Pan, Gorilla, Pongo and Hylobates, together with the results of a phylogenetic analysis of these data plus comparable data for Homo. Information on the four extant non-human hominoid genera was located for 240 out of the 1783 soft-tissue structures listed in the Nomina Anatomica. Numerically these data are biased so that information about some systems (e.g. muscles) and some regions (e.g. the forelimb) are over-represented, whereas other systems and regions (e.g. the veins and the lymphatics of the vascular system, the head region) are either under-represented or not represented at all. Screening to ensure that the data were suitable for use in a phylogenetic analysis reduced the number of eligible soft-tissue structures to 171. These data, together with comparable data for modern humans, were converted into discontinuous character states suitable for phylogenetic analysis and then used to construct a taxon-by-character matrix. This matrix was used in two tests of the hypothesis that soft-tissue characters can be relied upon to reconstruct hominoid phylogenetic relationships. In the first, parsimony analysis was used to identify cladograms requiring the smallest number of character state changes. In the second, the phylogenetic bootstrap was used to determine the confidence intervals of the most parsimonious clades. The parsimony analysis yielded a single most parsimonious cladogram that matched the molecular cladogram. Similarly the bootstrap analysis yielded clades that were compatible with the molecular cladogram; a (Homo, Pan) clade was supported by 95% of the replicates, and a (Gorilla, Pan, Homo) clade by 96%. These are the first hominoid morphological data to provide statistically significant support for the clades favoured by the molecular evidence. PMID:11833653

Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering.

PubMed

Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor; Essex, M

2015-05-01

To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice.

Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering

PubMed Central

Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor

2015-01-01

Abstract To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice. PMID:25560745

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shaffer, Richard, E-mail: rickyshaffer@yahoo.co.u; Department of Clinical Oncology, Imperial College London National Health Service Trust, London; Pickles, Tom

Purpose: Prior studies have derived low values of alpha-beta ratio (a/ss) for prostate cancer of approximately 1-2 Gy. These studies used poorly matched groups, differing definitions of biochemical failure, and insufficient follow-up. Methods and Materials: National Comprehensive Cancer Network low- or low-intermediate risk prostate cancer patients, treated with external beam radiotherapy or permanent prostate brachytherapy, were matched for prostate-specific antigen, Gleason score, T-stage, percentage of positive cores, androgen deprivation therapy, and era, yielding 118 patient pairs. The Phoenix definition of biochemical failure was used. The best-fitting value for a/ss was found for up to 90-month follow-up using maximum likelihood analysis,more » and the 95% confidence interval using the profile likelihood method. Linear quadratic formalism was applied with the radiobiological parameters of relative biological effectiveness = 1.0, potential doubling time = 45 days, and repair half-time = 1 hour. Bootstrap analysis was performed to estimate uncertainties in outcomes, and hence in a/ss. Sensitivity analysis was performed by varying the values of the radiobiological parameters to extreme values. Results: The value of a/ss best fitting the outcomes data was >30 Gy, with lower 95% confidence limit of 5.2 Gy. This was confirmed on bootstrap analysis. Varying parameters to extreme values still yielded best-fit a/ss of >30 Gy, although the lower 95% confidence interval limit was reduced to 0.6 Gy. Conclusions: Using carefully matched groups, long follow-up, the Phoenix definition of biochemical failure, and well-established statistical methods, the best estimate of a/ss for low and low-tier intermediate-risk prostate cancer is likely to be higher than that of normal tissues, although a low value cannot be excluded.« less

Alvimopan, a peripherally acting μ-opioid receptor antagonist, is associated with reduced costs after radical cystectomy: economic analysis of a phase 4 randomized, controlled trial.

PubMed

Kauf, Teresa L; Svatek, Robert S; Amiel, Gilad; Beard, Timothy L; Chang, Sam S; Fergany, Amr; Karnes, R Jeffrey; Koch, Michael; O'Hara, Jerome; Lee, Cheryl T; Sexton, Wade J; Slaton, Joel W; Steinberg, Gary D; Wilson, Shandra S; Techner, Lee; Martin, Carolyn; Moreno, Jessica; Kamat, Ashish M

2014-06-01

We evaluated the effect of alvimopan treatment vs placebo on health care utilization and costs related to gastrointestinal recovery in patients treated with radical cystectomy in a randomized, phase 4 clinical trial. Resource utilization data were prospectively collected and evaluated by cost consequence analysis. Hospital costs were estimated from 2012 Medicare reimbursement rates and medication wholesale acquisition costs. Differences in base case mean costs between the study cohorts for total postoperative ileus related costs (hospital days, study drug, nasogastric tubes, postoperative ileus related concomitant medication and postoperative ileus related readmissions) and total combined costs (postoperative ileus related, laboratory, electrocardiograms, nonpostoperative ileus related concomitant medication and nonpostoperative ileus related readmission) were evaluated by probabilistic sensitivity analysis using a bootstrap approach. Mean hospital stay was 2.63 days shorter for alvimopan than placebo (mean±SD 8.44±3.05 vs 11.07±8.23 days, p=0.005). Use of medications or interventions likely intended to diagnose or manage postoperative ileus was lower for alvimopan than for placebo, eg total parenteral nutrition 10% vs 25% (p=0.001). Postoperative ileus related health care costs were $2,340 lower for alvimopan and mean total combined costs were decreased by $2,640 per patient for alvimopan vs placebo. Analysis using a 10,000-iteration bootstrap approach showed that the mean difference in postoperative ileus related costs (p=0.04) but not total combined costs (p=0.068) was significantly lower for alvimopan than for placebo. In patients treated with radical cystectomy alvimopan decreased hospitalization cost by reducing the health care services associated with postoperative ileus and decreasing the hospital stay. Copyright © 2014 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Parallel computing for probabilistic fatigue analysis

NASA Technical Reports Server (NTRS)

Sues, Robert H.; Lua, Yuan J.; Smith, Mark D.

1993-01-01

This paper presents the results of Phase I research to investigate the most effective parallel processing software strategies and hardware configurations for probabilistic structural analysis. We investigate the efficiency of both shared and distributed-memory architectures via a probabilistic fatigue life analysis problem. We also present a parallel programming approach, the virtual shared-memory paradigm, that is applicable across both types of hardware. Using this approach, problems can be solved on a variety of parallel configurations, including networks of single or multiprocessor workstations. We conclude that it is possible to effectively parallelize probabilistic fatigue analysis codes; however, special strategies will be needed to achieve large-scale parallelism to keep large number of processors busy and to treat problems with the large memory requirements encountered in practice. We also conclude that distributed-memory architecture is preferable to shared-memory for achieving large scale parallelism; however, in the future, the currently emerging hybrid-memory architectures will likely be optimal.

Detecting seasonal and cyclical trends in agricultural runoff water quality-hypothesis tests and block bootstrap power analysis.

PubMed

Uddameri, Venkatesh; Singaraju, Sreeram; Hernandez, E Annette

2018-02-21

Seasonal and cyclic trends in nutrient concentrations at four agricultural drainage ditches were assessed using a dataset generated from a multivariate, multiscale, multiyear water quality monitoring effort in the agriculturally dominant Lower Rio Grande Valley (LRGV) River Watershed in South Texas. An innovative bootstrap sampling-based power analysis procedure was developed to evaluate the ability of Mann-Whitney and Noether tests to discern trends and to guide future monitoring efforts. The Mann-Whitney U test was able to detect significant changes between summer and winter nutrient concentrations at sites with lower depths and unimpeded flows. Pollutant dilution, non-agricultural loadings, and in-channel flow structures (weirs) masked the effects of seasonality. The detection of cyclical trends using the Noether test was highest in the presence of vegetation mainly for total phosphorus and oxidized nitrogen (nitrite + nitrate) compared to dissolved phosphorus and reduced nitrogen (total Kjeldahl nitrogen-TKN). Prospective power analysis indicated that while increased monitoring can lead to higher statistical power, the effect size (i.e., the total number of trend sequences within a time-series) had a greater influence on the Noether test. Both Mann-Whitney and Noether tests provide complementary information on seasonal and cyclic behavior of pollutant concentrations and are affected by different processes. The results from these statistical tests when evaluated in the context of flow, vegetation, and in-channel hydraulic alterations can help guide future data collection and monitoring efforts. The study highlights the need for long-term monitoring of agricultural drainage ditches to properly discern seasonal and cyclical trends.

Longterm Work Productivity Costs Due to Absenteeism and Permanent Work Disability in Patients with Early Rheumatoid Arthritis: A Nationwide Register Study of 7831 Patients.

PubMed

Martikainen, Janne A; Kautiainen, Hannu; Rantalaiho, Vappu; Puolakka, Kari T

2016-12-01

To estimate the development and potential disproportional distribution of longterm productivity costs (PC) and their determinants leading to work absenteeism and permanent work disability in working-aged patients with early rheumatoid arthritis (RA). A cohort of subjects with early RA was created by identifying the new cases of RA from the national drug reimbursement register that had been granted a special reimbursement for their antirheumatic medications for RA from 2000-2007. The dataset was enriched by cross-linking with other national registries detailing work absenteeism days and permanent disability pensions. In the base case, the human capital approach was applied to estimate PC based on subjects' annual number of absenteeism days and incomes. Hurdle regression analysis was applied to study the determinants of PC. Among the 7831 subjects with early RA, the mean (bootstrapped 95% CI) annual PC per person-observation year was €4800 (4547-5070). The annual PC declined after the first year of RA diagnosis, but increased significantly in subsequent years. In addition, the PC was heavily disproportionally concentrated in a small fraction of patients with RA, because only around 20% of patients accounted for the majority of total annual PC. The initiation of active drug treatment during the first 3 months after RA diagnosis significantly reduced the cumulative PC when compared with no drug treatment. The longterm PC increased significantly in parallel with years elapsing after RA diagnosis. Further, the majority of these PC are incurred by a small proportion of patients.

Non-suicidal self-injury among Dutch and Belgian adolescents: Personality, stress and coping.

PubMed

Kiekens, G; Bruffaerts, R; Nock, M K; Van de Ven, M; Witteman, C; Mortier, P; Demyttenaere, K; Claes, L

2015-09-01

This study examines: (1) the prevalence of Non-Suicidal Self-Injury (NSSI) among Dutch and Belgian adolescents, (2) the associations between Big Five personality traits and NSSI engagement/versatility (i.e., number of NSSI methods), and (3) whether these associations are mediated by perceived stress and coping. A total of 946 Flemish (46%) and Dutch (54%) non-institutionalized adolescents (Mean age=15.52; SD=1.34, 44% females) were surveyed. Measures included the NSSI subscale of the Self-Harm-Inventory, the Dutch Quick Big Five Personality questionnaire, the Perceived Stress Scale and the Utrecht Coping List for Adolescents. Examination of zero-order correlations was used to reveal associations, and hierarchical regression analysis was used to reveal potential mediators which were further examined within parallel mediation models by using a bootstrapping-corrected procedure. Lifetime prevalence of NSSI was 24.31%. Neuroticism; perceived stress; and distractive, avoidant, depressive, and emotional coping were positively associated with NSSI engagement, whereas Agreeableness, Conscientiousness; and active, social, and optimistic coping were negatively associated with NSSI engagement. Observed relationships between personality traits and NSSI engagement were consistently explained by perceived stress and depressive coping. A higher versatility of NSSI was not associated with any Big Five personality trait, but was associated with higher scores on perceived stress and depressive coping and with lower scores on active and optimistic coping. Our study suggests that a specific personality constellation is associated with NSSI engagement via high stress levels and a typical depressive reaction pattern to handle stressful life events. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Quantitative body DW-MRI biomarkers uncertainty estimation using unscented wild-bootstrap.

PubMed

Freiman, M; Voss, S D; Mulkern, R V; Perez-Rossello, J M; Warfield, S K

2011-01-01

We present a new method for the uncertainty estimation of diffusion parameters for quantitative body DW-MRI assessment. Diffusion parameters uncertainty estimation from DW-MRI is necessary for clinical applications that use these parameters to assess pathology. However, uncertainty estimation using traditional techniques requires repeated acquisitions, which is undesirable in routine clinical use. Model-based bootstrap techniques, for example, assume an underlying linear model for residuals rescaling and cannot be utilized directly for body diffusion parameters uncertainty estimation due to the non-linearity of the body diffusion model. To offset this limitation, our method uses the Unscented transform to compute the residuals rescaling parameters from the non-linear body diffusion model, and then applies the wild-bootstrap method to infer the body diffusion parameters uncertainty. Validation through phantom and human subject experiments shows that our method identify the regions with higher uncertainty in body DWI-MRI model parameters correctly with realtive error of -36% in the uncertainty values.

Bootstrapping the (A1, A2) Argyres-Douglas theory

NASA Astrophysics Data System (ADS)

Cornagliotto, Martina; Lemos, Madalena; Liendo, Pedro

2018-03-01

We apply bootstrap techniques in order to constrain the CFT data of the ( A 1 , A 2) Argyres-Douglas theory, which is arguably the simplest of the Argyres-Douglas models. We study the four-point function of its single Coulomb branch chiral ring generator and put numerical bounds on the low-lying spectrum of the theory. Of particular interest is an infinite family of semi-short multiplets labeled by the spin ℓ. Although the conformal dimensions of these multiplets are protected, their three-point functions are not. Using the numerical bootstrap we impose rigorous upper and lower bounds on their values for spins up to ℓ = 20. Through a recently obtained inversion formula, we also estimate them for sufficiently large ℓ, and the comparison of both approaches shows consistent results. We also give a rigorous numerical range for the OPE coefficient of the next operator in the chiral ring, and estimates for the dimension of the first R-symmetry neutral non-protected multiplet for small spin.

How to bootstrap a human communication system.

PubMed

Fay, Nicolas; Arbib, Michael; Garrod, Simon

2013-01-01

How might a human communication system be bootstrapped in the absence of conventional language? We argue that motivated signs play an important role (i.e., signs that are linked to meaning by structural resemblance or by natural association). An experimental study is then reported in which participants try to communicate a range of pre-specified items to a partner using repeated non-linguistic vocalization, repeated gesture, or repeated non-linguistic vocalization plus gesture (but without using their existing language system). Gesture proved more effective (measured by communication success) and more efficient (measured by the time taken to communicate) than non-linguistic vocalization across a range of item categories (emotion, object, and action). Combining gesture and vocalization did not improve performance beyond gesture alone. We experimentally demonstrate that gesture is a more effective means of bootstrapping a human communication system. We argue that gesture outperforms non-linguistic vocalization because it lends itself more naturally to the production of motivated signs. © 2013 Cognitive Science Society, Inc.

HPCC Methodologies for Structural Design and Analysis on Parallel and Distributed Computing Platforms

NASA Technical Reports Server (NTRS)

Farhat, Charbel

1998-01-01

In this grant, we have proposed a three-year research effort focused on developing High Performance Computation and Communication (HPCC) methodologies for structural analysis on parallel processors and clusters of workstations, with emphasis on reducing the structural design cycle time. Besides consolidating and further improving the FETI solver technology to address plate and shell structures, we have proposed to tackle the following design related issues: (a) parallel coupling and assembly of independently designed and analyzed three-dimensional substructures with non-matching interfaces, (b) fast and smart parallel re-analysis of a given structure after it has undergone design modifications, (c) parallel evaluation of sensitivity operators (derivatives) for design optimization, and (d) fast parallel analysis of mildly nonlinear structures. While our proposal was accepted, support was provided only for one year.

The CUORE slow monitoring systems

NASA Astrophysics Data System (ADS)

Gladstone, L.; Biare, D.; Cappelli, L.; Cushman, J. S.; Del Corso, F.; Fujikawa, B. K.; Hickerson, K. P.; Moggi, N.; Pagliarone, C. E.; Schmidt, B.; Wagaarachchi, S. L.; Welliver, B.; Winslow, L. A.

2017-09-01

CUORE is a cryogenic experiment searching primarily for neutrinoless double decay in 130Te. It will begin data-taking operations in 2016. To monitor the cryostat and detector during commissioning and data taking, we have designed and developed Slow Monitoring systems. In addition to real-time systems using LabVIEW, we have an alarm, analysis, and archiving website that uses MongoDB, AngularJS, and Bootstrap software. These modern, state of the art software packages make the monitoring system transparent, easily maintainable, and accessible on many platforms including mobile devices.

A new parallel-vector finite element analysis software on distributed-memory computers

NASA Technical Reports Server (NTRS)

Qin, Jiangning; Nguyen, Duc T.

1993-01-01

A new parallel-vector finite element analysis software package MPFEA (Massively Parallel-vector Finite Element Analysis) is developed for large-scale structural analysis on massively parallel computers with distributed-memory. MPFEA is designed for parallel generation and assembly of the global finite element stiffness matrices as well as parallel solution of the simultaneous linear equations, since these are often the major time-consuming parts of a finite element analysis. Block-skyline storage scheme along with vector-unrolling techniques are used to enhance the vector performance. Communications among processors are carried out concurrently with arithmetic operations to reduce the total execution time. Numerical results on the Intel iPSC/860 computers (such as the Intel Gamma with 128 processors and the Intel Touchstone Delta with 512 processors) are presented, including an aircraft structure and some very large truss structures, to demonstrate the efficiency and accuracy of MPFEA.

Evaluation of Parallel Analysis Methods for Determining the Number of Factors

ERIC Educational Resources Information Center

Crawford, Aaron V.; Green, Samuel B.; Levy, Roy; Lo, Wen-Juo; Scott, Lietta; Svetina, Dubravka; Thompson, Marilyn S.

2010-01-01

Population and sample simulation approaches were used to compare the performance of parallel analysis using principal component analysis (PA-PCA) and parallel analysis using principal axis factoring (PA-PAF) to identify the number of underlying factors. Additionally, the accuracies of the mean eigenvalue and the 95th percentile eigenvalue criteria…

Using Horn's Parallel Analysis Method in Exploratory Factor Analysis for Determining the Number of Factors

ERIC Educational Resources Information Center

Çokluk, Ömay; Koçak, Duygu

2016-01-01

In this study, the number of factors obtained from parallel analysis, a method used for determining the number of factors in exploratory factor analysis, was compared to that of the factors obtained from eigenvalue and scree plot--two traditional methods for determining the number of factors--in terms of consistency. Parallel analysis is based on…

A study on the causal effect of urban population growth and international trade on environmental pollution: evidence from China.

PubMed

Boamah, Kofi Baah; Du, Jianguo; Boamah, Angela Jacinta; Appiah, Kingsley

2018-02-01

This study seeks to contribute to the recent literature by empirically investigating the causal effect of urban population growth and international trade on environmental pollution of China, for the period 1980-2014. The Johansen cointegration confirmed a long-run cointegration association among the utilised variables for the case of China. The direction of causality among the variables was, consequently, investigated using the recent bootstrapped Granger causality test. This bootstrapped Granger causality approach is preferred as it provides robust and accurate critical values for statistical inferences. The findings from the causality analysis revealed the existence of a bi-directional causality between import and urban population. The three most paramount variables that explain the environmental pollution in China, according to the impulse response function, are imports, urbanisation and energy consumption. Our study further established the presence of an N-shaped environmental Kuznets curve relationship between economic growth and environmental pollution of China. Hence, our study recommends that China should adhere to stricter environmental regulations in international trade, as well as enforce policies that promote energy efficiency in the urban residential and commercial sector, in the quest to mitigate environmental pollution issues as the economy advances.

Generating a Dynamic Synthetic Population – Using an Age-Structured Two-Sex Model for Household Dynamics

PubMed Central

Namazi-Rad, Mohammad-Reza; Mokhtarian, Payam; Perez, Pascal

2014-01-01

Generating a reliable computer-simulated synthetic population is necessary for knowledge processing and decision-making analysis in agent-based systems in order to measure, interpret and describe each target area and the human activity patterns within it. In this paper, both synthetic reconstruction (SR) and combinatorial optimisation (CO) techniques are discussed for generating a reliable synthetic population for a certain geographic region (in Australia) using aggregated- and disaggregated-level information available for such an area. A CO algorithm using the quadratic function of population estimators is presented in this paper in order to generate a synthetic population while considering a two-fold nested structure for the individuals and households within the target areas. The baseline population in this study is generated from the confidentialised unit record files (CURFs) and 2006 Australian census tables. The dynamics of the created population is then projected over five years using a dynamic micro-simulation model for individual- and household-level demographic transitions. This projection is then compared with the 2011 Australian census. A prediction interval is provided for the population estimates obtained by the bootstrapping method, by which the variability structure of a predictor can be replicated in a bootstrap distribution. PMID:24733522

Standard errors and confidence intervals for variable importance in random forest regression, classification, and survival.

PubMed

Ishwaran, Hemant; Lu, Min

2018-06-04

Random forests are a popular nonparametric tree ensemble procedure with broad applications to data analysis. While its widespread popularity stems from its prediction performance, an equally important feature is that it provides a fully nonparametric measure of variable importance (VIMP). A current limitation of VIMP, however, is that no systematic method exists for estimating its variance. As a solution, we propose a subsampling approach that can be used to estimate the variance of VIMP and for constructing confidence intervals. The method is general enough that it can be applied to many useful settings, including regression, classification, and survival problems. Using extensive simulations, we demonstrate the effectiveness of the subsampling estimator and in particular find that the delete-d jackknife variance estimator, a close cousin, is especially effective under low subsampling rates due to its bias correction properties. These 2 estimators are highly competitive when compared with the .164 bootstrap estimator, a modified bootstrap procedure designed to deal with ties in out-of-sample data. Most importantly, subsampling is computationally fast, thus making it especially attractive for big data settings. Copyright © 2018 John Wiley & Sons, Ltd.

Asymptotic confidence intervals for the Pearson correlation via skewness and kurtosis.

PubMed

Bishara, Anthony J; Li, Jiexiang; Nash, Thomas

2018-02-01

When bivariate normality is violated, the default confidence interval of the Pearson correlation can be inaccurate. Two new methods were developed based on the asymptotic sampling distribution of Fisher's z' under the general case where bivariate normality need not be assumed. In Monte Carlo simulations, the most successful of these methods relied on the (Vale & Maurelli, 1983, Psychometrika, 48, 465) family to approximate a distribution via the marginal skewness and kurtosis of the sample data. In Simulation 1, this method provided more accurate confidence intervals of the correlation in non-normal data, at least as compared to no adjustment of the Fisher z' interval, or to adjustment via the sample joint moments. In Simulation 2, this approximate distribution method performed favourably relative to common non-parametric bootstrap methods, but its performance was mixed relative to an observed imposed bootstrap and two other robust methods (PM1 and HC4). No method was completely satisfactory. An advantage of the approximate distribution method, though, is that it can be implemented even without access to raw data if sample skewness and kurtosis are reported, making the method particularly useful for meta-analysis. Supporting information includes R code. © 2017 The British Psychological Society.

Thread concept for automatic task parallelization in image analysis

NASA Astrophysics Data System (ADS)

Lueckenhaus, Maximilian; Eckstein, Wolfgang

1998-09-01

Parallel processing of image analysis tasks is an essential method to speed up image processing and helps to exploit the full capacity of distributed systems. However, writing parallel code is a difficult and time-consuming process and often leads to an architecture-dependent program that has to be re-implemented when changing the hardware. Therefore it is highly desirable to do the parallelization automatically. For this we have developed a special kind of thread concept for image analysis tasks. Threads derivated from one subtask may share objects and run in the same context but may process different threads of execution and work on different data in parallel. In this paper we describe the basics of our thread concept and show how it can be used as basis of an automatic task parallelization to speed up image processing. We further illustrate the design and implementation of an agent-based system that uses image analysis threads for generating and processing parallel programs by taking into account the available hardware. The tests made with our system prototype show that the thread concept combined with the agent paradigm is suitable to speed up image processing by an automatic parallelization of image analysis tasks.

Concept Innateness, Concept Continuity, and Bootstrapping

PubMed Central

Carey, Susan

2011-01-01

The commentators raised issues relevant to all three important theses of The Origin of Concepts (TOOC). Some questioned the very existence of innate representational primitives, and others questioned my claims about their richness and whether they should be thought of as concepts. Some questioned the existence of conceptual discontinuity in the course of knowledge acquisition and others argued that discontinuity is much more common than portrayed in TOOC. Some raised issues with my characterization of Quinian bootstrapping, and others questioned the dual factor theory of concepts motivated by my picture of conceptual development. PMID:23264705

Crossing symmetry in alpha space

NASA Astrophysics Data System (ADS)

Hogervorst, Matthijs; van Rees, Balt C.

2017-11-01

We initiate the study of the conformal bootstrap using Sturm-Liouville theory, specializing to four-point functions in one-dimensional CFTs. We do so by decomposing conformal correlators using a basis of eigenfunctions of the Casimir which are labeled by a complex number α. This leads to a systematic method for computing conformal block decompositions. Analyzing bootstrap equations in alpha space turns crossing symmetry into an eigenvalue problem for an integral operator K. The operator K is closely related to the Wilson transform, and some of its eigenfunctions can be found in closed form.

Direct measurement of fast transients by using boot-strapped waveform averaging

NASA Astrophysics Data System (ADS)

Olsson, Mattias; Edman, Fredrik; Karki, Khadga Jung

2018-03-01

An approximation to coherent sampling, also known as boot-strapped waveform averaging, is presented. The method uses digital cavities to determine the condition for coherent sampling. It can be used to increase the effective sampling rate of a repetitive signal and the signal to noise ratio simultaneously. The method is demonstrated by using it to directly measure the fluorescence lifetime from Rhodamine 6G by digitizing the signal from a fast avalanche photodiode. The obtained lifetime of 4.0 ns is in agreement with the known values.

Computational mechanics analysis tools for parallel-vector supercomputers

NASA Technical Reports Server (NTRS)

Storaasli, Olaf O.; Nguyen, Duc T.; Baddourah, Majdi; Qin, Jiangning

1993-01-01

Computational algorithms for structural analysis on parallel-vector supercomputers are reviewed. These parallel algorithms, developed by the authors, are for the assembly of structural equations, 'out-of-core' strategies for linear equation solution, massively distributed-memory equation solution, unsymmetric equation solution, general eigensolution, geometrically nonlinear finite element analysis, design sensitivity analysis for structural dynamics, optimization search analysis and domain decomposition. The source code for many of these algorithms is available.

Identification of cephalopod species from the North and Baltic Seas using morphology, COI and 18S rDNA sequences

NASA Astrophysics Data System (ADS)

Gebhardt, Katharina; Knebelsberger, Thomas

2015-09-01

We morphologically analyzed 79 cephalopod specimens from the North and Baltic Seas belonging to 13 separate species. Another 29 specimens showed morphological features of either Alloteuthis mediaor Alloteuthis subulata or were found to be in between. Reliable identification features to distinguish between A. media and A. subulata are currently not available. The analysis of the DNA barcoding region of the COI gene revealed intraspecific distances (uncorrected p) ranging from 0 to 2.13 % (average 0.1 %) and interspecific distances between 3.31 and 22 % (average 15.52 %). All species formed monophyletic clusters in a neighbor-joining analysis and were supported by bootstrap values of ≥99 %. All COI haplotypes belonging to the 29 Alloteuthis specimens were grouped in one cluster. Neither COI nor 18S rDNA sequences helped to distinguish between the different Alloteuthis morphotypes. For species identification purposes, we recommend the use of COI, as it showed higher bootstrap support of species clusters and less amplification and sequencing failure compared to 18S. Our data strongly support the assumption that the genus Alloteuthis is only represented by a single species, at least in the North Sea. It remained unclear whether this species is A. subulata or A. media. All COI sequences including important metadata were uploaded to the Barcode of Life Data Systems and can be used as reference library for the molecular identification of more than 50 % of the cephalopod fauna known from the North and Baltic Seas.

A study of hierarchical structure on South China industrial electricity-consumption correlation

NASA Astrophysics Data System (ADS)

Yao, Can-Zhong; Lin, Ji-Nan; Liu, Xiao-Feng

2016-02-01

Based on industrial electricity-consumption data of five southern provinces of China from 2005 to 2013, we study the industrial correlation mechanism with MST (minimal spanning tree) and HT (hierarchical tree) models. First, we comparatively analyze the industrial electricity-consumption correlation structure in pre-crisis and after-crisis period using MST model and Bootstrap technique of statistical reliability test of links. Results exhibit that all industrial electricity-consumption trees of five southern provinces of China in pre-crisis and after-crisis time are in formation of chain, and the "center-periphery structure" of those chain-like trees is consistent with industrial specialization in classical industrial chain theory. Additionally, the industrial structure of some provinces is reorganized and transferred in pre-crisis and after-crisis time. Further, the comparative analysis with hierarchical tree and Bootstrap technique demonstrates that as for both observations of GD and overall NF, the industrial electricity-consumption correlation is non-significant clustered in pre-crisis period, whereas it turns significant clustered in after-crisis time. Therefore we propose that in perspective of electricity-consumption, their industrial structures are directed to optimized organization and global correlation. Finally, the analysis of distance of HTs verifies that industrial reorganization and development may strengthen market integration, coordination and correlation of industrial production. Except GZ, other four provinces have a shorter distance of industrial electricity-consumption correlation in after-crisis period, revealing a better performance of regional specialization and integration.

A new framework of statistical inferences based on the valid joint sampling distribution of the observed counts in an incomplete contingency table.

PubMed

Tian, Guo-Liang; Li, Hui-Qiong

2017-08-01

Some existing confidence interval methods and hypothesis testing methods in the analysis of a contingency table with incomplete observations in both margins entirely depend on an underlying assumption that the sampling distribution of the observed counts is a product of independent multinomial/binomial distributions for complete and incomplete counts. However, it can be shown that this independency assumption is incorrect and can result in unreliable conclusions because of the under-estimation of the uncertainty. Therefore, the first objective of this paper is to derive the valid joint sampling distribution of the observed counts in a contingency table with incomplete observations in both margins. The second objective is to provide a new framework for analyzing incomplete contingency tables based on the derived joint sampling distribution of the observed counts by developing a Fisher scoring algorithm to calculate maximum likelihood estimates of parameters of interest, the bootstrap confidence interval methods, and the bootstrap testing hypothesis methods. We compare the differences between the valid sampling distribution and the sampling distribution under the independency assumption. Simulation studies showed that average/expected confidence-interval widths of parameters based on the sampling distribution under the independency assumption are shorter than those based on the new sampling distribution, yielding unrealistic results. A real data set is analyzed to illustrate the application of the new sampling distribution for incomplete contingency tables and the analysis results again confirm the conclusions obtained from the simulation studies.

Anti-inflammatory effects of salmeterol/fluticasone propionate 50/250 mcg combination therapy in Japanese patients with chronic obstructive pulmonary disease

PubMed Central

Asai, Kazuhisa; Kobayashi, Akihiro; Makihara, Yukio; Johnson, Malcolm

2015-01-01

Purpose Using sputum neutrophils as the primary measure, and other inflammation biomarkers, this study evaluated the anti-inflammatory effects of the combination salmeterol 50 mcg and fluticasone propionate 250 mcg (SFC 250) in Japanese patients with chronic obstructive pulmonary disease (COPD). Patients and methods Patients were treated in a randomized, double-blind, parallel group, placebo-controlled trial with SFC 250 twice daily (n=26) or placebo (n=26) for 12 weeks. At the start and end of treatment, inflammation biomarkers (sputum and serum), lung function, and health status (COPD Assessment Test [CAT] questionnaire) were measured. Results Although a numerical decrease in differential neutrophil count was observed from baseline, SFC 250 did not significantly reduce sputum neutrophils compared with placebo, nor were there significant changes from baseline in the other biomarkers (sputum or serum), lung function, or CAT, versus placebo. Squamous epithelial cell contamination in some sputum samples rendered them unacceptable for analysis, which reduced the sample size to n=19 (SFC 250) and n=10 (placebo). However, inclusion of contaminated samples did not affect the overall trend of the outcome. Ad hoc bootstrap statistical analysis showed a 27.9% (SFC 250) and 1.3% (placebo) decrease in sputum neutrophils. Sputum IL-8 decreased by 43.2% after SFC 250 but increased by 48.3% with placebo. Responder analyses showed 42% of patients had ≥20% decrease in neutrophils from baseline; and 47% of patients had a ≥200 pg/mL change in sputum IL-8 following SFC 250 versus 20% after placebo; both changes are considered clinically relevant. Conclusion This study provides additional information about inflammation in Japanese COPD patients and is the first to study the anti-inflammatory effects of SFC 250 in this context and population. In the primary analysis, SFC 250 did not produce significant changes from baseline in sputum neutrophil levels or other sputum or serum inflammatory markers compared with placebo. Secondary ad hoc statistical analysis showed that SFC 250 reduced the number of sputum neutrophils and IL-8 compared with placebo. PMID:25945045

Anti-inflammatory effects of salmeterol/fluticasone propionate 50/250 mcg combination therapy in Japanese patients with chronic obstructive pulmonary disease.

PubMed

Asai, Kazuhisa; Kobayashi, Akihiro; Makihara, Yukio; Johnson, Malcolm

2015-01-01

Using sputum neutrophils as the primary measure, and other inflammation biomarkers, this study evaluated the anti-inflammatory effects of the combination salmeterol 50 mcg and fluticasone propionate 250 mcg (SFC 250) in Japanese patients with chronic obstructive pulmonary disease (COPD). Patients were treated in a randomized, double-blind, parallel group, placebo-controlled trial with SFC 250 twice daily (n=26) or placebo (n=26) for 12 weeks. At the start and end of treatment, inflammation biomarkers (sputum and serum), lung function, and health status (COPD Assessment Test [CAT] questionnaire) were measured. Although a numerical decrease in differential neutrophil count was observed from baseline, SFC 250 did not significantly reduce sputum neutrophils compared with placebo, nor were there significant changes from baseline in the other biomarkers (sputum or serum), lung function, or CAT, versus placebo. Squamous epithelial cell contamination in some sputum samples rendered them unacceptable for analysis, which reduced the sample size to n=19 (SFC 250) and n=10 (placebo). However, inclusion of contaminated samples did not affect the overall trend of the outcome. Ad hoc bootstrap statistical analysis showed a 27.9% (SFC 250) and 1.3% (placebo) decrease in sputum neutrophils. Sputum IL-8 decreased by 43.2% after SFC 250 but increased by 48.3% with placebo. Responder analyses showed 42% of patients had ≥20% decrease in neutrophils from baseline; and 47% of patients had a ≥200 pg/mL change in sputum IL-8 following SFC 250 versus 20% after placebo; both changes are considered clinically relevant. This study provides additional information about inflammation in Japanese COPD patients and is the first to study the anti-inflammatory effects of SFC 250 in this context and population. In the primary analysis, SFC 250 did not produce significant changes from baseline in sputum neutrophil levels or other sputum or serum inflammatory markers compared with placebo. Secondary ad hoc statistical analysis showed that SFC 250 reduced the number of sputum neutrophils and IL-8 compared with placebo.

SRM Internal Flow Tests and Computational Fluid Dynamic Analysis. Volume 3; Titan, ASRM, and Subscale Motor Analyses

NASA Technical Reports Server (NTRS)

1995-01-01

A computational fluid dynamics (CFD) analysis has been performed on the aft slot region of the Titan 4 Solid Rocket Motor Upgrade (SRMU). This analysis was performed in conjunction with MSFC structural modeling of the propellant grain to determine if the flow field induced stresses would adversely alter the propellant geometry to the extent of causing motor failure. The results of the coupled CFD/stress analysis have shown that there is a continual increase of flow field resistance at the aft slot due to the aft segment propellant grain being progressively moved radially toward the centerline of the motor port. This 'bootstrapping' effect between grain radial movement and internal flow resistance is conducive to causing a rapid motor failure.

Parallel Algorithms for Image Analysis.

DTIC Science & Technology

1982-06-01

8217 _ _ _ _ _ _ _ 4. TITLE (aid Subtitle) S. TYPE OF REPORT & PERIOD COVERED PARALLEL ALGORITHMS FOR IMAGE ANALYSIS TECHNICAL 6. PERFORMING O4G. REPORT NUMBER TR-1180...Continue on reverse side it neceesary aid Identlfy by block number) Image processing; image analysis ; parallel processing; cellular computers. 20... IMAGE ANALYSIS TECHNICAL 6. PERFORMING ONG. REPORT NUMBER TR-1180 - 7. AUTHOR(&) S. CONTRACT OR GRANT NUMBER(s) Azriel Rosenfeld AFOSR-77-3271 9

Phylogenetic relationships among arecoid palms (Arecaceae: Arecoideae)

PubMed Central

Baker, William J.; Norup, Maria V.; Clarkson, James J.; Couvreur, Thomas L. P.; Dowe, John L.; Lewis, Carl E.; Pintaud, Jean-Christophe; Savolainen, Vincent; Wilmot, Tomas; Chase, Mark W.

2011-01-01

Background and Aims The Arecoideae is the largest and most diverse of the five subfamilies of palms (Arecaceae/Palmae), containing >50 % of the species in the family. Despite its importance, phylogenetic relationships among Arecoideae are poorly understood. Here the most densely sampled phylogenetic analysis of Arecoideae available to date is presented. The results are used to test the current classification of the subfamily and to identify priority areas for future research. Methods DNA sequence data for the low-copy nuclear genes PRK and RPB2 were collected from 190 palm species, covering 103 (96 %) genera of Arecoideae. The data were analysed using the parsimony ratchet, maximum likelihood, and both likelihood and parsimony bootstrapping. Key Results and Conclusions Despite the recovery of paralogues and pseudogenes in a small number of taxa, PRK and RPB2 were both highly informative, producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Simultaneous analyses of the combined data sets provided additional resolution and support. Two areas of incongruence between PRK and RPB2 were strongly supported by the bootstrap relating to the placement of tribes Chamaedoreeae, Iriarteeae and Reinhardtieae; the causes of this incongruence remain uncertain. The current classification within Arecoideae was strongly supported by the present data. Of the 14 tribes and 14 sub-tribes in the classification, only five sub-tribes from tribe Areceae (Basseliniinae, Linospadicinae, Oncospermatinae, Rhopalostylidinae and Verschaffeltiinae) failed to receive support. Three major higher level clades were strongly supported: (1) the RRC clade (Roystoneeae, Reinhardtieae and Cocoseae), (2) the POS clade (Podococceae, Oranieae and Sclerospermeae) and (3) the core arecoid clade (Areceae, Euterpeae, Geonomateae, Leopoldinieae, Manicarieae and Pelagodoxeae). However, new data sources are required to elucidate ambiguities that remain in phylogenetic relationships among and within the major groups of Arecoideae, as well as within the Areceae, the largest tribe in the palm family. PMID:21325340

Statistic and dosimetric criteria to assess the shift of the prescribed dose for lung radiotherapy plans when integrating point kernel models in medical physics: are we ready?

PubMed

Chaikh, Abdulhamid; Balosso, Jacques

2016-12-01

To apply the statistical bootstrap analysis and dosimetric criteria's to assess the change of prescribed dose (PD) for lung cancer to maintain the same clinical results when using new generations of dose calculation algorithms. Nine lung cancer cases were studied. For each patient, three treatment plans were generated using exactly the same beams arrangements. In plan 1, the dose was calculated using pencil beam convolution (PBC) algorithm turning on heterogeneity correction with modified batho (PBC-MB). In plan 2, the dose was calculated using anisotropic analytical algorithm (AAA) and the same PD, as plan 1. In plan 3, the dose was calculated using AAA with monitor units (MUs) obtained from PBC-MB, as input. The dosimetric criteria's include MUs, delivered dose at isocentre (Diso) and calculated dose to 95% of the target volume (D95). The bootstrap method was used to assess the significance of the dose differences and to accurately estimate the 95% confidence interval (95% CI). Wilcoxon and Spearman's rank tests were used to calculate P values and the correlation coefficient (ρ). Statistically significant for dose difference was found using point kernel model. A good correlation was observed between both algorithms types, with ρ>0.9. Using AAA instead of PBC-MB, an adjustment of the PD in the isocentre is suggested. For a given set of patients, we assessed the need to readjust the PD for lung cancer using dosimetric indices and bootstrap statistical method. Thus, if the goal is to keep on with the same clinical results, the PD for lung tumors has to be adjusted with AAA. According to our simulation we suggest to readjust the PD by 5% and an optimization for beam arrangements to better protect the organs at risks (OARs).

Performance Analysis and Optimization on the UCLA Parallel Atmospheric General Circulation Model Code

NASA Technical Reports Server (NTRS)

Lou, John; Ferraro, Robert; Farrara, John; Mechoso, Carlos

1996-01-01

An analysis is presented of several factors influencing the performance of a parallel implementation of the UCLA atmospheric general circulation model (AGCM) on massively parallel computer systems. Several modificaitons to the original parallel AGCM code aimed at improving its numerical efficiency, interprocessor communication cost, load-balance and issues affecting single-node code performance are discussed.

Gyrokinetic neoclassical study of the bootstrap current in the tokamak edge pedestal with fully non-linear Coulomb collisions

DOE PAGES

Hager, Robert; Chang, C. S.

2016-04-08

As a follow-up on the drift-kinetic study of the non-local bootstrap current in the steep edge pedestal of tokamak plasma by Koh et al. [Phys. Plasmas 19, 072505 (2012)], a gyrokinetic neoclassical study is performed with gyrokinetic ions and drift-kinetic electrons. Besides the gyrokinetic improvement of ion physics from the drift-kinetic treatment, a fully non-linear Fokker-Planck collision operator—that conserves mass, momentum, and energy—is used instead of Koh et al.'s linearized collision operator in consideration of the possibility that the ion distribution function is non-Maxwellian in the steep pedestal. An inaccuracy in Koh et al.'s result is found in the steepmore » edge pedestal that originated from a small error in the collisional momentum conservation. The present study concludes that (1) the bootstrap current in the steep edge pedestal is generally smaller than what has been predicted from the small banana-width (local) approximation [e.g., Sauter et al., Phys. Plasmas 6, 2834 (1999) and Belli et al., Plasma Phys. Controlled Fusion 50, 095010 (2008)], (2) the plasma flow evaluated from the local approximation can significantly deviate from the non-local results, and (3) the bootstrap current in the edge pedestal, where the passing particle region is small, can be dominantly carried by the trapped particles in a broad trapped boundary layer. In conclusion, a new analytic formula based on numerous gyrokinetic simulations using various magnetic equilibria and plasma profiles with self-consistent Grad-Shafranov solutions is constructed.« less

Bootstrapping language acquisition.

PubMed

Abend, Omri; Kwiatkowski, Tom; Smith, Nathaniel J; Goldwater, Sharon; Steedman, Mark

2017-07-01

The semantic bootstrapping hypothesis proposes that children acquire their native language through exposure to sentences of the language paired with structured representations of their meaning, whose component substructures can be associated with words and syntactic structures used to express these concepts. The child's task is then to learn a language-specific grammar and lexicon based on (probably contextually ambiguous, possibly somewhat noisy) pairs of sentences and their meaning representations (logical forms). Starting from these assumptions, we develop a Bayesian probabilistic account of semantically bootstrapped first-language acquisition in the child, based on techniques from computational parsing and interpretation of unrestricted text. Our learner jointly models (a) word learning: the mapping between components of the given sentential meaning and lexical words (or phrases) of the language, and (b) syntax learning: the projection of lexical elements onto sentences by universal construction-free syntactic rules. Using an incremental learning algorithm, we apply the model to a dataset of real syntactically complex child-directed utterances and (pseudo) logical forms, the latter including contextually plausible but irrelevant distractors. Taking the Eve section of the CHILDES corpus as input, the model simulates several well-documented phenomena from the developmental literature. In particular, the model exhibits syntactic bootstrapping effects (in which previously learned constructions facilitate the learning of novel words), sudden jumps in learning without explicit parameter setting, acceleration of word-learning (the "vocabulary spurt"), an initial bias favoring the learning of nouns over verbs, and one-shot learning of words and their meanings. The learner thus demonstrates how statistical learning over structured representations can provide a unified account for these seemingly disparate phenomena. Copyright © 2017 Elsevier B.V. All rights reserved.

Gyrokinetic neoclassical study of the bootstrap current in the tokamak edge pedestal with fully non-linear Coulomb collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hager, Robert; Chang, C. S.

As a follow-up on the drift-kinetic study of the non-local bootstrap current in the steep edge pedestal of tokamak plasma by Koh et al. [Phys. Plasmas 19, 072505 (2012)], a gyrokinetic neoclassical study is performed with gyrokinetic ions and drift-kinetic electrons. Besides the gyrokinetic improvement of ion physics from the drift-kinetic treatment, a fully non-linear Fokker-Planck collision operator—that conserves mass, momentum, and energy—is used instead of Koh et al.'s linearized collision operator in consideration of the possibility that the ion distribution function is non-Maxwellian in the steep pedestal. An inaccuracy in Koh et al.'s result is found in the steepmore » edge pedestal that originated from a small error in the collisional momentum conservation. The present study concludes that (1) the bootstrap current in the steep edge pedestal is generally smaller than what has been predicted from the small banana-width (local) approximation [e.g., Sauter et al., Phys. Plasmas 6, 2834 (1999) and Belli et al., Plasma Phys. Controlled Fusion 50, 095010 (2008)], (2) the plasma flow evaluated from the local approximation can significantly deviate from the non-local results, and (3) the bootstrap current in the edge pedestal, where the passing particle region is small, can be dominantly carried by the trapped particles in a broad trapped boundary layer. In conclusion, a new analytic formula based on numerous gyrokinetic simulations using various magnetic equilibria and plasma profiles with self-consistent Grad-Shafranov solutions is constructed.« less

Gyrokinetic neoclassical study of the bootstrap current in the tokamak edge pedestal with fully non-linear Coulomb collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hager, Robert, E-mail: rhager@pppl.gov; Chang, C. S., E-mail: cschang@pppl.gov

As a follow-up on the drift-kinetic study of the non-local bootstrap current in the steep edge pedestal of tokamak plasma by Koh et al. [Phys. Plasmas 19, 072505 (2012)], a gyrokinetic neoclassical study is performed with gyrokinetic ions and drift-kinetic electrons. Besides the gyrokinetic improvement of ion physics from the drift-kinetic treatment, a fully non-linear Fokker-Planck collision operator—that conserves mass, momentum, and energy—is used instead of Koh et al.'s linearized collision operator in consideration of the possibility that the ion distribution function is non-Maxwellian in the steep pedestal. An inaccuracy in Koh et al.'s result is found in the steepmore » edge pedestal that originated from a small error in the collisional momentum conservation. The present study concludes that (1) the bootstrap current in the steep edge pedestal is generally smaller than what has been predicted from the small banana-width (local) approximation [e.g., Sauter et al., Phys. Plasmas 6, 2834 (1999) and Belli et al., Plasma Phys. Controlled Fusion 50, 095010 (2008)], (2) the plasma flow evaluated from the local approximation can significantly deviate from the non-local results, and (3) the bootstrap current in the edge pedestal, where the passing particle region is small, can be dominantly carried by the trapped particles in a broad trapped boundary layer. A new analytic formula based on numerous gyrokinetic simulations using various magnetic equilibria and plasma profiles with self-consistent Grad-Shafranov solutions is constructed.« less

Risk-Stratified Imputation in Survival Analysis

PubMed Central

Kennedy, Richard E.; Adragni, Kofi P.; Tiwari, Hemant K.; Voeks, Jenifer H.; Brott, Thomas G.; Howard, George

2013-01-01

Background Censoring that is dependent on covariates associated with survival can arise in randomized trials due to changes in recruitment and eligibility criteria to minimize withdrawals, potentially leading to biased treatment effect estimates. Imputation approaches have been proposed to address censoring in survival analysis; and while these approaches may provide unbiased estimates of treatment effects, imputation of a large number of outcomes may over- or underestimate the associated variance based on the imputation pool selected. Purpose We propose an improved method, risk-stratified imputation, as an alternative to address withdrawal related to the risk of events in the context of time-to-event analyses. Methods Our algorithm performs imputation from a pool of replacement subjects with similar values of both treatment and covariate(s) of interest, that is, from a risk-stratified sample. This stratification prior to imputation addresses the requirement of time-to-event analysis that censored observations are representative of all other observations in the risk group with similar exposure variables. We compared our risk-stratified imputation to case deletion and bootstrap imputation in a simulated dataset in which the covariate of interest (study withdrawal) was related to treatment. A motivating example from a recent clinical trial is also presented to demonstrate the utility of our method. Results In our simulations, risk-stratified imputation gives estimates of treatment effect comparable to bootstrap and auxiliary variable imputation while avoiding inaccuracies of the latter two in estimating the associated variance. Similar results were obtained in analysis of clinical trial data. Limitations Risk-stratified imputation has little advantage over other imputation methods when covariates of interest are not related to treatment, although its performance is superior when covariates are related to treatment. Risk-stratified imputation is intended for categorical covariates, and may be sensitive to the width of the matching window if continuous covariates are used. Conclusions The use of the risk-stratified imputation should facilitate the analysis of many clinical trials, in which one group has a higher withdrawal rate that is related to treatment. PMID:23818434

Bootstrapping non-commutative gauge theories from L∞ algebras

NASA Astrophysics Data System (ADS)

Blumenhagen, Ralph; Brunner, Ilka; Kupriyanov, Vladislav; Lüst, Dieter

2018-05-01

Non-commutative gauge theories with a non-constant NC-parameter are investigated. As a novel approach, we propose that such theories should admit an underlying L∞ algebra, that governs not only the action of the symmetries but also the dynamics of the theory. Our approach is well motivated from string theory. We recall that such field theories arise in the context of branes in WZW models and briefly comment on its appearance for integrable deformations of AdS5 sigma models. For the SU(2) WZW model, we show that the earlier proposed matrix valued gauge theory on the fuzzy 2-sphere can be bootstrapped via an L∞ algebra. We then apply this approach to the construction of non-commutative Chern-Simons and Yang-Mills theories on flat and curved backgrounds with non-constant NC-structure. More concretely, up to the second order, we demonstrate how derivative and curvature corrections to the equations of motion can be bootstrapped in an algebraic way from the L∞ algebra. The appearance of a non-trivial A∞ algebra is discussed, as well.

A symbol of uniqueness: the cluster bootstrap for the 3-loop MHV heptagon

DOE PAGES

Drummond, J. M.; Papathanasiou, G.; Spradlin, M.

2015-03-16

Seven-particle scattering amplitudes in planar super-Yang-Mills theory are believed to belong to a special class of generalised polylogarithm functions called heptagon functions. These are functions with physical branch cuts whose symbols may be written in terms of the 42 cluster A-coordinates on Gr(4, 7). Motivated by the success of the hexagon bootstrap programme for constructing six-particle amplitudes we initiate the systematic study of the symbols of heptagon functions. We find that there is exactly one such symbol of weight six which satisfies the MHV last-entry condition and is finite in the 7 ll 6 collinear limit. This unique symbol ismore » both dihedral and parity-symmetric, and remarkably its collinear limit is exactly the symbol of the three-loop six-particle MHV amplitude, although none of these properties were assumed a priori. It must therefore be the symbol of the threeloop seven-particle MHV amplitude. The simplicity of its construction suggests that the n-gon bootstrap may be surprisingly powerful for n > 6.« less

Review of Orbital Propellant Transfer Techniques and the Feasibility of a Thermal Bootstrap Propellant Transfer Concepts

NASA Technical Reports Server (NTRS)

Yoshikawa, H. H.; Madison, I. B.

1971-01-01

This study was performed in support of the NASA Task B-2 Study Plan for Space Basing. The nature of space-based operations implies that orbital transfer of propellant is a prime consideration. The intent of this report is (1) to report on the findings and recommendations of existing literature on space-based propellant transfer techniques, and (2) to determine possible alternatives to the recommended methods. The reviewed literature recommends, in general, the use of conventional liquid transfer techniques (i.e., pumping) in conjunction with an artificially induced gravitational field. An alternate concept that was studied, the Thermal Bootstrap Transfer Process, is based on the compression of a two-phase fluid with subsequent condensation to a liquid (vapor compression/condensation). This concept utilizes the intrinsic energy capacities of the tanks and propellant by exploiting temperature differentials and available energy differences. The results indicate the thermodynamic feasibility of the Thermal Bootstrap Transfer Process for a specific range of tank sizes, temperatures, fill-factors and receiver tank heat transfer coefficients.

Rapid processing of PET list-mode data for efficient uncertainty estimation and data analysis

NASA Astrophysics Data System (ADS)

Markiewicz, P. J.; Thielemans, K.; Schott, J. M.; Atkinson, D.; Arridge, S. R.; Hutton, B. F.; Ourselin, S.

2016-07-01

In this technical note we propose a rapid and scalable software solution for the processing of PET list-mode data, which allows the efficient integration of list mode data processing into the workflow of image reconstruction and analysis. All processing is performed on the graphics processing unit (GPU), making use of streamed and concurrent kernel execution together with data transfers between disk and CPU memory as well as CPU and GPU memory. This approach leads to fast generation of multiple bootstrap realisations, and when combined with fast image reconstruction and analysis, it enables assessment of uncertainties of any image statistic and of any component of the image generation process (e.g. random correction, image processing) within reasonable time frames (e.g. within five minutes per realisation). This is of particular value when handling complex chains of image generation and processing. The software outputs the following: (1) estimate of expected random event data for noise reduction; (2) dynamic prompt and random sinograms of span-1 and span-11 and (3) variance estimates based on multiple bootstrap realisations of (1) and (2) assuming reasonable count levels for acceptable accuracy. In addition, the software produces statistics and visualisations for immediate quality control and crude motion detection, such as: (1) count rate curves; (2) centre of mass plots of the radiodistribution for motion detection; (3) video of dynamic projection views for fast visual list-mode skimming and inspection; (4) full normalisation factor sinograms. To demonstrate the software, we present an example of the above processing for fast uncertainty estimation of regional SUVR (standard uptake value ratio) calculation for a single PET scan of 18F-florbetapir using the Siemens Biograph mMR scanner.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tucker, Susan L.; Liu, H. Helen; Wang, Shulian

Purpose: The aim of this study was to investigate the effect of radiation dose distribution in the lung on the risk of postoperative pulmonary complications among esophageal cancer patients. Methods and Materials: We analyzed data from 110 patients with esophageal cancer treated with concurrent chemoradiotherapy followed by surgery at our institution from 1998 to 2003. The endpoint for analysis was postsurgical pneumonia or acute respiratory distress syndrome. Dose-volume histograms (DVHs) and dose-mass histograms (DMHs) for the whole lung were used to fit normal-tissue complication probability (NTCP) models, and the quality of fits were compared using bootstrap analysis. Results: Normal-tissue complicationmore » probability modeling identified that the risk of postoperative pulmonary complications was most significantly associated with small absolute volumes of lung spared from doses {>=}5 Gy (VS5), that is, exposed to doses <5 Gy. However, bootstrap analysis found no significant difference between the quality of this model and fits based on other dosimetric parameters, including mean lung dose, effective dose, and relative volume of lung receiving {>=}5 Gy, probably because of correlations among these factors. The choice of DVH vs. DMH or the use of fractionation correction did not significantly affect the results of the NTCP modeling. The parameter values estimated for the Lyman NTCP model were as follows (with 95% confidence intervals in parentheses): n = 1.85 (0.04, {infinity}), m = 0.55 (0.22, 1.02), and D {sub 5} = 17.5 Gy (9.4 Gy, 102 Gy). Conclusions: In this cohort of esophageal cancer patients, several dosimetric parameters including mean lung dose, effective dose, and absolute volume of lung receiving <5 Gy provided similar descriptions of the risk of postoperative pulmonary complications as a function of Radiation dose distribution in the lung.« less

Characterization of the translation elongation factor 1-α gene in a wide range of pathogenic Aspergillus species.

PubMed

Nouripour-Sisakht, Sadegh; Ahmadi, Bahram; Makimura, Koichi; Hoog, Sybren de; Umeda, Yoshiko; Alshahni, Mohamed Mahdi; Mirhendi, Hossein

2017-04-01

We aimed to evaluate the resolving power of the translation elongation factor (TEF)-1α gene for phylogenetic analysis of Aspergillus species. Sequences of 526 bp representing the coding region of the TEF-1α gene were used for the assessment of levels of intra- and inter-specific nucleotide polymorphism in 33 species of Aspergillus, including 57 reference, clinical and environmental strains. Analysis of TEF-1α sequences indicated a mean similarity of 92.6 % between the species, with inter-species diversity ranging from 0 to 70 nucleotides. The species with the closest resemblance were A. candidus/A. carneus, and A. flavus/A. oryzae/A. ochraceus, with 100 and 99.8 % identification, respectively. These species are phylogenetically very close and the TEF-1α gene appears not to have sufficient discriminatory power to differentiate them. Meanwhile, intra-species differences were found within strains of A. clavatus, A. clavatonanicus, A. candidus, A. fumigatus, A. terreus, A. alliaceus, A. flavus, Eurotium amstelodami and E. chevalieri. The tree topology with strongly supported clades (≥70 % bootstrap values) was almost compatible with the phylogeny inferred from analysis of the DNA sequences of the beta tubulin gene (BT2). However, the backbone of the tree exhibited low bootstrap values, and inter-species correlations were not obvious in some clades; for example, tree topologies based on BT2 and TEF-1α genes were incompatible for some species, such as A. deflectus, A. janus and A. penicillioides. The gene was not phylogenetically more informative than other known molecular markers. It will be necessary to test other genes or larger genomic regions to better understand the taxonomy of this important group of fungi.

Economic evaluation of a psychological intervention for high distress cancer patients and carers: costs and quality-adjusted life years.

PubMed

Chatterton, Mary Lou; Chambers, Suzanne; Occhipinti, Stefano; Girgis, Afaf; Dunn, Jeffrey; Carter, Rob; Shih, Sophy; Mihalopoulos, Cathrine

2016-07-01

This study compared the cost-effectiveness of a psychologist-led, individualised cognitive behavioural intervention (PI) to a nurse-led, minimal contact self-management condition for highly distressed cancer patients and carers. This was an economic evaluation conducted alongside a randomised trial of highly distressed adult cancer patients and carers calling cancer helplines. Services used by participants were measured using a resource use questionnaire, and quality-adjusted life years were measured using the assessment of quality of life - eight-dimension - instrument collected through a computer-assisted telephone interview. The base case analysis stratified participants based on the baseline score on the Brief Symptom Inventory. Incremental cost-effectiveness ratio confidence intervals were calculated with a nonparametric bootstrap to reflect sampling uncertainty. The results were subjected to sensitivity analysis by varying unit costs for resource use and the method for handling missing data. No significant differences were found in overall total costs or quality-adjusted life years (QALYs) between intervention groups. Bootstrapped data suggest the PI had a higher probability of lower cost and greater QALYs for both carers and patients with high distress at baseline. For patients with low levels of distress at baseline, the PI had a higher probability of greater QALYs but at additional cost. Sensitivity analysis showed the results were robust. The PI may be cost-effective compared with the nurse-led, minimal contact self-management condition for highly distressed cancer patients and carers. More intensive psychological intervention for patients with greater levels of distress appears warranted. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

A Statistical Analysis of Brain Morphology Using Wild Bootstrapping

PubMed Central

Ibrahim, Joseph G.; Tang, Niansheng; Rowe, Daniel B.; Hao, Xuejun; Bansal, Ravi; Peterson, Bradley S.

2008-01-01

Methods for the analysis of brain morphology, including voxel-based morphology and surface-based morphometries, have been used to detect associations between brain structure and covariates of interest, such as diagnosis, severity of disease, age, IQ, and genotype. The statistical analysis of morphometric measures usually involves two statistical procedures: 1) invoking a statistical model at each voxel (or point) on the surface of the brain or brain subregion, followed by mapping test statistics (e.g., t test) or their associated p values at each of those voxels; 2) correction for the multiple statistical tests conducted across all voxels on the surface of the brain region under investigation. We propose the use of new statistical methods for each of these procedures. We first use a heteroscedastic linear model to test the associations between the morphological measures at each voxel on the surface of the specified subregion (e.g., cortical or subcortical surfaces) and the covariates of interest. Moreover, we develop a robust test procedure that is based on a resampling method, called wild bootstrapping. This procedure assesses the statistical significance of the associations between a measure of given brain structure and the covariates of interest. The value of this robust test procedure lies in its computationally simplicity and in its applicability to a wide range of imaging data, including data from both anatomical and functional magnetic resonance imaging (fMRI). Simulation studies demonstrate that this robust test procedure can accurately control the family-wise error rate. We demonstrate the application of this robust test procedure to the detection of statistically significant differences in the morphology of the hippocampus over time across gender groups in a large sample of healthy subjects. PMID:17649909

Predictors of decompressive hemicraniectomy in malignant middle cerebral artery stroke.

PubMed

Kamran, Saadat; Salam, Abdul; Akhtar, Naveed; D'soza, Atlantic; Shuaib, Ashfaq

2018-04-12

Identification of factors in malignant middle cerebral artery (MMCA) stroke patients that may be useful in selecting patients for DHC. This study was a retrospective multicenter study of patients referred for DHC based on the criteria of the randomized control trials of DHC in MMCA stroke. Demographic, clinical, and radiology data were analyzed. Patients who underwent DHC were compared to those who survived without surgery. Two hundred three patients with MMCA strokes were identified: 137 underwent DHC, 47 survived without DHC, and 19 refused surgery and died. Multivariate analysis identified the following factors determining DHC in MMCA stroke: age < 55 years (OR 8.5, 95% CI 3.3-22.1, P < 0.001), MCA with involvement of additional vascular territories (anterior cerebral artery, posterior cerebral artery (OR 4.8, 95% CI 1.5-14.9, P = 0.007), septum pellucidum displacement ≥ 7.5 mm (OR 4.8, 95% CI 1.9-11.7, P = 0.001), diabetes (OR 3.7, 95% CI 1.3-10.6, P = 0.012), infarct growth rate (IGR) ml/h (OR 1.11, 95% CI 1.02-1.2, P = 0.015), and temporal lobe involvement (OR 2.5, 95% CI 1.01-6.1, P = 0.048). The internal validation of the multivariate logistic regression model using bootstrapping analysis showed marginal bias. Among patients with MMCA infarctions, an increased possibility of DHC is associated with younger age, MCA with additional infarction, septum pellucidum deviation of > 7.5 mm, diabetes, IGR, and temporal lobe involvement. The presence of these risk factors identifies those MMCA stroke patients who may require DHC. Bootstrapping analysis indicated the model is good enough to predict the outcome in general population.

Adjuvant treatment may benefit patients with high-risk upper rectal cancer: A nomogram and recursive partitioning analysis of 547 patients.

PubMed

Wang, Xin; Jin, Jing; Yang, Yong; Liu, Wen-Yang; Ren, Hua; Feng, Yan-Ru; Xiao, Qin; Li, Ning; Deng, Lei; Fang, Hui; Jing, Hao; Lu, Ning-Ning; Tang, Yu; Wang, Jian-Yang; Wang, Shu-Lian; Wang, Wei-Hu; Song, Yong-Wen; Liu, Yue-Ping; Li, Ye-Xiong

2016-10-04

The role of adjuvant chemoradiotherapy (ACRT) or adjuvant chemotherapy (ACT) in treating patients with locally advanced upper rectal cancer (URC) after total mesorectal excision (TME) surgery remains unclear. We developed a clinical nomogram and a recursive partitioning analysis (RPA)-based risk stratification system for predicting 5-year cancer-specific survival (CSS) to determine whether these individuals require ACRT or ACT. This retrospective analysis included 547 patients with primary URC. A nomogram was developed based on the Cox regression model. The performance of the model was assessed by concordance index (C-index) and calibration curve in internal validation with bootstrapping. RPA stratified patients into risk groups based on their tumor characteristics. Five independent prognostic factors (age, preoperative increased carcinoembryonic antigen and carcinoma antigen 19-9, positive lymph node [PLN] number, tumor deposit [TD], pathological T classification) were identified and entered into the predictive nomogram. The bootstrap-corrected C-index was 0.757. RPA stratification of the three prognostic groups showed obviously different prognosis. Only the high-risk group (patients with PLN ≤ 6 and TD, or PLN > 6) benefited from ACRT plus ACT when compared with surgery followed by ACRT or ACT, and surgery alone (5-year CSS: 70.8% vs. 57.8% vs. 15.6%, P < 0.001). Our nomogram predicts 5-year CSS after TME surgery for locally advanced rectal cancer and RPA-based stratification indicates that ACRT plus ACT post-surgery may be an important treatment plan with potentially ignificant survival advantages in high-risk URC. This may help to select candidates of adjuvant treatment in prospective studies.

Novel CPR system that predicts return of spontaneous circulation from amplitude spectral area before electric shock in ventricular fibrillation.

PubMed

Nakagawa, Yoshihide; Amino, Mari; Inokuchi, Sadaki; Hayashi, Satoshi; Wakabayashi, Tsutomu; Noda, Tatsuya

2017-04-01

Amplitude spectral area (AMSA), an index for analysing ventricular fibrillation (VF) waveforms, is thought to predict the return of spontaneous circulation (ROSC) after electric shocks, but its validity is unconfirmed. We developed an equation to predict ROSC, where the change in AMSA (ΔAMSA) is added to AMSA measured immediately before the first shock (AMSA1). We examine the validity of this equation by comparing it with the conventional AMSA1-only equation. We retrospectively investigated 285 VF patients given prehospital electric shocks by emergency medical services. ΔAMSA was calculated by subtracting AMSA1 from last AMSA immediately before the last prehospital electric shock. Multivariate logistic regression analysis was performed using post-shock ROSC as a dependent variable. Analysis data were subjected to receiver operating characteristic curve analysis, goodness-of-fit testing using a likelihood ratio test, and the bootstrap method. AMSA1 (odds ratio (OR) 1.151, 95% confidence interval (CI) 1.086-1.220) and ΔAMSA (OR 1.289, 95% CI 1.156-1.438) were independent factors influencing ROSC induction by electric shock. Area under the curve (AUC) for predicting ROSC was 0.851 for AMSA1-only and 0.891 for AMSA1+ΔAMSA. Compared with the AMSA1-only equation, the AMSA1+ΔAMSA equation had significantly better goodness-of-fit (likelihood ratio test P<0.001) and showed good fit in the bootstrap method. Post-shock ROSC was accurately predicted by adding ΔAMSA to AMSA1. AMSA-based ROSC prediction enables application of electric shock to only those patients with high probability of ROSC, instead of interrupting chest compressions and delivering unnecessary shocks to patients with low probability of ROSC. Copyright © 2017 Elsevier B.V. All rights reserved.

Predictive Factor Analysis of Response-Adapted Radiation Therapy for Chemotherapy-Sensitive Pediatric Hodgkin Lymphoma: Analysis of the Children's Oncology Group AHOD 0031 Trial

DOE Office of Scientific and Technical Information (OSTI.GOV)

Charpentier, Anne-Marie; Friedman, Debra L.; Wolden, Suzanne

Purpose: To evaluate whether clinical risk factors could further distinguish children with intermediate-risk Hodgkin lymphoma (HL) with rapid early and complete anatomic response (RER/CR) who benefit significantly from involved-field RT (IFRT) from those who do not, and thereby aid refinement of treatment selection. Methods and Materials: Children with intermediate-risk HL treated on the Children's Oncology Group AHOD 0031 trial who achieved RER/CR with 4 cycles of chemotherapy, and who were randomized to 21-Gy IFRT or no additional therapy (n=716) were the subject of this study. Recursive partitioning analysis was used to identify factors associated with clinically and statistically significant improvement inmore » event-free survival (EFS) after randomization to IFRT. Bootstrap sampling was used to evaluate the robustness of the findings. Result: Although most RER/CR patients did not benefit significantly from IFRT, those with a combination of anemia and bulky limited-stage disease (n=190) had significantly better 4-year EFS with the addition of IFRT (89.3% vs 77.9% without IFRT; P=.019); this benefit was consistently reproduced in bootstrap analyses and after adjusting for other prognostic factors. Conclusion: Although most patients achieving RER/CR had favorable outcomes with 4 cycles of chemotherapy alone, those children with initial bulky stage I/II disease and anemia had significantly better EFS with the addition of IFRT as part of combined-modality therapy. Further work evaluating the interaction of clinical and biologic factors and imaging response is needed to further optimize and refine treatment selection.« less

Identification of Dyslipidemic Patients Attending Primary Care Clinics Using Electronic Medical Record (EMR) Data from the Canadian Primary Care Sentinel Surveillance Network (CPCSSN) Database.

PubMed

Aref-Eshghi, Erfan; Oake, Justin; Godwin, Marshall; Aubrey-Bassler, Kris; Duke, Pauline; Mahdavian, Masoud; Asghari, Shabnam

2017-03-01

The objective of this study was to define the optimal algorithm to identify patients with dyslipidemia using electronic medical records (EMRs). EMRs of patients attending primary care clinics in St. John's, Newfoundland and Labrador (NL), Canada during 2009-2010, were studied to determine the best algorithm for identification of dyslipidemia. Six algorithms containing three components, dyslipidemia ICD coding, lipid lowering medication use, and abnormal laboratory lipid levels, were tested against a gold standard, defined as the existence of any of the three criteria. Linear discriminate analysis, and bootstrapping were performed following sensitivity/specificity testing and receiver's operating curve analysis. Two validating datasets, NL records of 2011-2014, and Canada-wide records of 2010-2012, were used to replicate the results. Relative to the gold standard, combining laboratory data together with lipid lowering medication consumption yielded the highest sensitivity (99.6%), NPV (98.1%), Kappa agreement (0.98), and area under the curve (AUC, 0.998). The linear discriminant analysis for this combination resulted in an error rate of 0.15 and an Eigenvalue of 1.99, and the bootstrapping led to AUC: 0.998, 95% confidence interval: 0.997-0.999, Kappa: 0.99. This algorithm in the first validating dataset yielded a sensitivity of 97%, Negative Predictive Value (NPV) = 83%, Kappa = 0.88, and AUC = 0.98. These figures for the second validating data set were 98%, 93%, 0.95, and 0.99, respectively. Combining laboratory data with lipid lowering medication consumption within the EMR is the best algorithm for detecting dyslipidemia. These results can generate standardized information systems for dyslipidemia and other chronic disease investigations using EMRs.

The effects of rurality on substance use disorder diagnosis: A multiple-groups latent class analysis.

PubMed

Brooks, Billy; McBee, Matthew; Pack, Robert; Alamian, Arsham

2017-05-01

Rates of accidental overdose mortality from substance use disorder (SUD) have risen dramatically in the United States since 1990. Between 1999 and 2004 alone rates increased 62% nationwide, with rural overdose mortality increasing at a rate 3 times that seen in urban populations. Cultural differences between rural and urban populations (e.g., educational attainment, unemployment rates, social characteristics, etc.) affect the nature of SUD, leading to disparate risk of overdose across these communities. Multiple-groups latent class analysis with covariates was applied to data from the 2011 and 2012 National Survey on Drug Use and Health (n=12.140) to examine potential differences in latent classifications of SUD between rural and urban adult (aged 18years and older) populations. Nine drug categories were used to identify latent classes of SUD defined by probability of diagnosis within these categories. Once the class structures were established for rural and urban samples, posterior membership probabilities were entered into a multinomial regression analysis of socio-demographic predictors' association with the likelihood of SUD latent class membership. Latent class structures differed across the sub-groups, with the rural sample fitting a 3-class structure (Bootstrap Likelihood Ratio Test P value=0.03) and the urban fitting a 6-class model (Bootstrap Likelihood Ratio Test P value<0.0001). Overall the rural class structure exhibited less diversity in class structure and lower prevalence of SUD in multiple drug categories (e.g. cocaine, hallucinogens, and stimulants). This result supports the hypothesis that different underlying elements exist in the two populations that affect SUD patterns, and thus can inform the development of surveillance instruments, clinical services, and prevention programming tailored to specific communities. Copyright © 2017 Elsevier Ltd. All rights reserved.

Overview of physics research on the TCV tokamak

NASA Astrophysics Data System (ADS)

Fasoli, A.; TCV Team

2009-10-01

The Tokamak à Configuration Variable (TCV) tokamak is equipped with high-power (4.5 MW), real-time-controllable EC systems and flexible shaping, and plays an important role in fusion research by broadening the parameter range of reactor relevant regimes, by investigating tokamak physics questions and by developing new control tools. Steady-state discharges are achieved, in which the current is entirely self-generated through the bootstrap mechanism, a fundamental ingredient for ITER steady-state operation. The discharge remains quiescent over several current redistribution times, demonstrating that a self-consistent, 'bootstrap-aligned' equilibrium state is possible. Electron internal transport barrier regimes sustained by EC current drive have also been explored. MHD activity is shown to be crucial in scenarios characterized by large and slow oscillations in plasma confinement, which in turn can be modified by small Ohmic current perturbations altering the barrier strength. In studies of the relation between anomalous transport and plasma shape, the observed dependences of the electron thermal diffusivity on triangularity (direct) and collisionality (inverse) are qualitatively reproduced by non-linear gyro-kinetic simulations and shown to be governed by TEM turbulence. Parallel SOL flows are studied for their importance for material migration. Flow profiles are measured using a reciprocating Mach probe by changing from lower to upper single-null diverted equilibria and shifting the plasmas vertically. The dominant, field-direction-dependent Pfirsch-Schlüter component is found to be in good agreement with theoretical predictions. A field-direction-independent component is identified and is consistent with flows generated by transient over-pressure due to ballooning-like interchange turbulence. Initial high-resolution infrared images confirm that ELMs have a filamentary structure, while fast, localized radiation measurements reveal that ELM activity first appears in the X-point region. Real time control techniques are currently being applied to EC multiple independent power supplies and beam launchers, e.g. to control the plasma current in fully non-inductive conditions, and the plasma elongation through current broadening by far-off-axis heating at constant shaping field.

Parallel and convergent evolution of the dim-light vision gene RH1 in bats (Order: Chiroptera).

PubMed

Shen, Yong-Yi; Liu, Jie; Irwin, David M; Zhang, Ya-Ping

2010-01-21

Rhodopsin, encoded by the gene Rhodopsin (RH1), is extremely sensitive to light, and is responsible for dim-light vision. Bats are nocturnal mammals that inhabit poor light environments. Megabats (Old-World fruit bats) generally have well-developed eyes, while microbats (insectivorous bats) have developed echolocation and in general their eyes were degraded, however, dramatic differences in the eyes, and their reliance on vision, exist in this group. In this study, we examined the rod opsin gene (RH1), and compared its evolution to that of two cone opsin genes (SWS1 and M/LWS). While phylogenetic reconstruction with the cone opsin genes SWS1 and M/LWS generated a species tree in accord with expectations, the RH1 gene tree united Pteropodidae (Old-World fruit bats) and Yangochiroptera, with very high bootstrap values, suggesting the possibility of convergent evolution. The hypothesis of convergent evolution was further supported when nonsynonymous sites or amino acid sequences were used to construct phylogenies. Reconstructed RH1 sequences at internal nodes of the bat species phylogeny showed that: (1) Old-World fruit bats share an amino acid change (S270G) with the tomb bat; (2) Miniopterus share two amino acid changes (V104I, M183L) with Rhinolophoidea; (3) the amino acid replacement I123V occurred independently on four branches, and the replacements L99M, L266V and I286V occurred each on two branches. The multiple parallel amino acid replacements that occurred in the evolution of bat RH1 suggest the possibility of multiple convergences of their ecological specialization (i.e., various photic environments) during adaptation for the nocturnal lifestyle, and suggest that further attention is needed on the study of the ecology and behavior of bats.

Parallel and Convergent Evolution of the Dim-Light Vision Gene RH1 in Bats (Order: Chiroptera)

PubMed Central

Shen, Yong-Yi; Liu, Jie; Irwin, David M.; Zhang, Ya-Ping

2010-01-01

Rhodopsin, encoded by the gene Rhodopsin (RH1), is extremely sensitive to light, and is responsible for dim-light vision. Bats are nocturnal mammals that inhabit poor light environments. Megabats (Old-World fruit bats) generally have well-developed eyes, while microbats (insectivorous bats) have developed echolocation and in general their eyes were degraded, however, dramatic differences in the eyes, and their reliance on vision, exist in this group. In this study, we examined the rod opsin gene (RH1), and compared its evolution to that of two cone opsin genes (SWS1 and M/LWS). While phylogenetic reconstruction with the cone opsin genes SWS1 and M/LWS generated a species tree in accord with expectations, the RH1 gene tree united Pteropodidae (Old-World fruit bats) and Yangochiroptera, with very high bootstrap values, suggesting the possibility of convergent evolution. The hypothesis of convergent evolution was further supported when nonsynonymous sites or amino acid sequences were used to construct phylogenies. Reconstructed RH1 sequences at internal nodes of the bat species phylogeny showed that: (1) Old-World fruit bats share an amino acid change (S270G) with the tomb bat; (2) Miniopterus share two amino acid changes (V104I, M183L) with Rhinolophoidea; (3) the amino acid replacement I123V occurred independently on four branches, and the replacements L99M, L266V and I286V occurred each on two branches. The multiple parallel amino acid replacements that occurred in the evolution of bat RH1 suggest the possibility of multiple convergences of their ecological specialization (i.e., various photic environments) during adaptation for the nocturnal lifestyle, and suggest that further attention is needed on the study of the ecology and behavior of bats. PMID:20098620

Parallel processing for nonlinear dynamics simulations of structures including rotating bladed-disk assemblies

NASA Technical Reports Server (NTRS)

Hsieh, Shang-Hsien

1993-01-01

The principal objective of this research is to develop, test, and implement coarse-grained, parallel-processing strategies for nonlinear dynamic simulations of practical structural problems. There are contributions to four main areas: finite element modeling and analysis of rotational dynamics, numerical algorithms for parallel nonlinear solutions, automatic partitioning techniques to effect load-balancing among processors, and an integrated parallel analysis system.

Method-independent, Computationally Frugal Convergence Testing for Sensitivity Analysis Techniques

NASA Astrophysics Data System (ADS)

Mai, Juliane; Tolson, Bryan

2017-04-01

The increasing complexity and runtime of environmental models lead to the current situation that the calibration of all model parameters or the estimation of all of their uncertainty is often computationally infeasible. Hence, techniques to determine the sensitivity of model parameters are used to identify most important parameters or model processes. All subsequent model calibrations or uncertainty estimation procedures focus then only on these subsets of parameters and are hence less computational demanding. While the examination of the convergence of calibration and uncertainty methods is state-of-the-art, the convergence of the sensitivity methods is usually not checked. If any, bootstrapping of the sensitivity results is used to determine the reliability of the estimated indexes. Bootstrapping, however, might as well become computationally expensive in case of large model outputs and a high number of bootstraps. We, therefore, present a Model Variable Augmentation (MVA) approach to check the convergence of sensitivity indexes without performing any additional model run. This technique is method- and model-independent. It can be applied either during the sensitivity analysis (SA) or afterwards. The latter case enables the checking of already processed sensitivity indexes. To demonstrate the method independency of the convergence testing method, we applied it to three widely used, global SA methods: the screening method known as Morris method or Elementary Effects (Morris 1991, Campolongo et al., 2000), the variance-based Sobol' method (Solbol' 1993, Saltelli et al. 2010) and a derivative-based method known as Parameter Importance index (Goehler et al. 2013). The new convergence testing method is first scrutinized using 12 analytical benchmark functions (Cuntz & Mai et al. 2015) where the true indexes of aforementioned three methods are known. This proof of principle shows that the method reliably determines the uncertainty of the SA results when different budgets are used for the SA. Subsequently, we focus on the model-independency by testing the frugal method using the hydrologic model mHM (www.ufz.de/mhm) with about 50 model parameters. The results show that the new frugal method is able to test the convergence and therefore the reliability of SA results in an efficient way. The appealing feature of this new technique is the necessity of no further model evaluation and therefore enables checking of already processed (and published) sensitivity results. This is one step towards reliable and transferable, published sensitivity results.

Exploration of high harmonic fast wave heating on the National Spherical Torus Experiment

NASA Astrophysics Data System (ADS)

Wilson, J. R.; Bell, R. E.; Bernabei, S.; Bitter, M.; Bonoli, P.; Gates, D.; Hosea, J.; LeBlanc, B.; Mau, T. K.; Medley, S.; Menard, J.; Mueller, D.; Ono, M.; Phillips, C. K.; Pinsker, R. I.; Raman, R.; Rosenberg, A.; Ryan, P.; Sabbagh, S.; Stutman, D.; Swain, D.; Takase, Y.; Wilgen, J.

2003-05-01

High harmonic fast wave (HHFW) heating has been proposed as a particularly attractive means for plasma heating and current drive in the high beta plasmas that are achievable in spherical torus (ST) devices. The National Spherical Torus Experiment (NSTX) [M. Ono, S. M. Kaye, S. Neumeyer et al., in Proceedings of the 18th IEEE/NPSS Symposium on Fusion Engineering, Albuquerque, 1999 (IEEE, Piscataway, NJ, 1999), p. 53] is such a device. An rf heating system has been installed on the NSTX to explore the physics of HHFW heating, current drive via rf waves and for use as a tool to demonstrate the attractiveness of the ST concept as a fusion device. To date, experiments have demonstrated many of the theoretical predictions for HHFW. In particular, strong wave absorption on electrons over a wide range of plasma parameters and wave parallel phase velocities, wave acceleration of energetic ions, and indications of current drive for directed wave spectra have been observed. In addition HHFW heating has been used to explore the energy transport properties of NSTX plasmas, to create H-mode discharges with a large fraction of bootstrap current and to control the plasma current profile during the early stages of the discharge.

Improved Design of Stellarator Coils for Current Carrying Plasmas

NASA Astrophysics Data System (ADS)

Drevlak, M.; Strumberger, E.; Hirshman, S.; Boozer, A.; Brooks, A.; Valanju, P.

1998-11-01

The method of automatic optimization (P. Merkel, Nucl. Fus. 27), (1987) 867; P. Merkel, M. Drevlak, Proc 25th EPS Conf. on Cont. Fus. and Plas. Phys., Prague, in print. for the design of stellarator coils consists essentially of determining filaments such that the average relative field error int dS [ (B_coil + B_j) \\cdot n]^2/B^2_coil is minimized on the prescribed plasma boundary. Bj is the magnetic field produced by the plasma currents of the given finite β fixed boundary equilibrium. For equilibria of the W7-X type, Bj can be neglected, because of the reduced parallel plasma currents. This is not true for quasi-axisymmetric stellarator (QAS) configurations (A. Reiman, et al., to be published.) with large equilibrium and net plasma (bootstrap) currents. Although the coils for QAS exhibit low values of the field error, free boundary calculations indicate that the shape of the plasma is usually not accurately reproduced , particularly when saddle coils are used. We investigate if the surface reconstruction can be improved by introducing a modified measure of the field error based on a measure of the resonant components of the normal field.

Verification of continuum drift kinetic equation solvers in NIMROD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Held, E. D.; Ji, J.-Y.; Kruger, S. E.

Verification of continuum solutions to the electron and ion drift kinetic equations (DKEs) in NIMROD [C. R. Sovinec et al., J. Comp. Phys. 195, 355 (2004)] is demonstrated through comparison with several neoclassical transport codes, most notably NEO [E. A. Belli and J. Candy, Plasma Phys. Controlled Fusion 54, 015015 (2012)]. The DKE solutions use NIMROD's spatial representation, 2D finite-elements in the poloidal plane and a 1D Fourier expansion in toroidal angle. For 2D velocity space, a novel 1D expansion in finite elements is applied for the pitch angle dependence and a collocation grid is used for the normalized speedmore » coordinate. The full, linearized Coulomb collision operator is kept and shown to be important for obtaining quantitative results. Bootstrap currents, parallel ion flows, and radial particle and heat fluxes show quantitative agreement between NIMROD and NEO for a variety of tokamak equilibria. In addition, velocity space distribution function contours for ions and electrons show nearly identical detailed structure and agree quantitatively. A Θ-centered, implicit time discretization and a block-preconditioned, iterative linear algebra solver provide efficient electron and ion DKE solutions that ultimately will be used to obtain closures for NIMROD's evolving fluid model.« less

The CUORE slow monitoring systems

DOE PAGES

Gladstone, L.; Biare, D.; Cappelli, L.; ...

2017-09-20

CUORE is a cryogenic experiment searching primarily for neutrinoless double decay inmore » $$^{130}$$Te. It will begin data-taking operations in 2016. To monitor the cryostat and detector during commissioning and data taking, we have designed and developed Slow Monitoring systems. In addition to real-time systems using LabVIEW, we have an alarm, analysis, and archiving website that uses MongoDB, AngularJS, and Bootstrap software. These modern, state of the art software packages make the monitoring system transparent, easily maintainable, and accessible on many platforms including mobile devices.« less

A Critical Examination of Figure of Merit (FOM). Assessing the Goodness-of-Fit in Gamma/X-ray Peak Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Croft, S.; Favalli, Andrea; Weaver, Brian Phillip

2015-10-06

In this paper we develop and investigate several criteria for assessing how well a proposed spectral form fits observed spectra. We consider the classical improved figure of merit (FOM) along with several modifications, as well as criteria motivated by Poisson regression from the statistical literature. We also develop a new FOM that is based on the statistical idea of the bootstrap. A spectral simulator has been developed to assess the performance of these different criteria under multiple data configurations.

The CUORE slow monitoring systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gladstone, L.; Biare, D.; Cappelli, L.

CUORE is a cryogenic experiment searching primarily for neutrinoless double decay inmore » $$^{130}$$Te. It will begin data-taking operations in 2016. To monitor the cryostat and detector during commissioning and data taking, we have designed and developed Slow Monitoring systems. In addition to real-time systems using LabVIEW, we have an alarm, analysis, and archiving website that uses MongoDB, AngularJS, and Bootstrap software. These modern, state of the art software packages make the monitoring system transparent, easily maintainable, and accessible on many platforms including mobile devices.« less

Harmony of spinning conformal blocks

NASA Astrophysics Data System (ADS)

Schomerus, Volker; Sobko, Evgeny; Isachenkov, Mikhail

2017-03-01

Conformal blocks for correlation functions of tensor operators play an increasingly important role for the conformal bootstrap programme. We develop a universal approach to such spinning blocks through the harmonic analysis of certain bundles over a coset of the conformal group. The resulting Casimir equations are given by a matrix version of the Calogero-Sutherland Hamiltonian that describes the scattering of interacting spinning particles in a 1-dimensional external potential. The approach is illustrated in several examples including fermionic seed blocks in 3D CFT where they take a very simple form.

The ABC (in any D) of logarithmic CFT

NASA Astrophysics Data System (ADS)

Hogervorst, Matthijs; Paulos, Miguel; Vichi, Alessandro

2017-10-01

Logarithmic conformal field theories have a vast range of applications, from critical percolation to systems with quenched disorder. In this paper we thoroughly examine the structure of these theories based on their symmetry properties. Our analysis is model-independent and holds for any spacetime dimension. Our results include a determination of the general form of correlation functions and conformal block decompositions, clearing the path for future bootstrap applications. Several examples are discussed in detail, including logarithmic generalized free fields, holographic models, self-avoiding random walks and critical percolation.

Unitary subsector of generalized minimal models

NASA Astrophysics Data System (ADS)

Behan, Connor

2018-05-01

We revisit the line of nonunitary theories that interpolate between the Virasoro minimal models. Numerical bootstrap applications have brought about interest in the four-point function involving the scalar primary of lowest dimension. Using recent progress in harmonic analysis on the conformal group, we prove the conjecture that global conformal blocks in this correlator appear with positive coefficients. We also compute many such coefficients in the simplest mixed correlator system. Finally, we comment on the status of using global conformal blocks to isolate the truly unitary points on this line.

Parallel processing in finite element structural analysis

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.

1987-01-01

A brief review is made of the fundamental concepts and basic issues of parallel processing. Discussion focuses on parallel numerical algorithms, performance evaluation of machines and algorithms, and parallelism in finite element computations. A computational strategy is proposed for maximizing the degree of parallelism at different levels of the finite element analysis process including: 1) formulation level (through the use of mixed finite element models); 2) analysis level (through additive decomposition of the different arrays in the governing equations into the contributions to a symmetrized response plus correction terms); 3) numerical algorithm level (through the use of operator splitting techniques and application of iterative processes); and 4) implementation level (through the effective combination of vectorization, multitasking and microtasking, whenever available).

A condition for small bootstrap current in three-dimensional toroidal configurations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mikhailov, M. I., E-mail: mikhaylov-mi@nrcki.ru; Nührenberg, J.; Zille, R.

2016-11-15

It is shown that, if the maximum of the magnetic field strength on a magnetic surface in a threedimensional magnetic confinement configuration with stellarator symmetry constitutes a line that is orthogonal to the field lines and crosses the symmetry line, then the bootstrap current density is smaller compared to that in quasi-axisymmetric (qa) [J. Nührenberg et al., in Proc. of Joint Varenna−Lausanne Int. Workshop on Theory of Fusion Plasmas, Varenna, 1994, p. 3] and quasi-helically (qh) symmetric [J. Nührenberg and R. Zille, Phys. Lett. A 129, 113 (1988)] configurations.

Three ways to solve critical ϕ4 theory on 4 ‑ 𝜖 dimensional real projective space: Perturbation, bootstrap, and Schwinger-Dyson equation

NASA Astrophysics Data System (ADS)

Hasegawa, Chika; Nakayama, Yu

2018-03-01

In this paper, we solve the two-point function of the lowest dimensional scalar operator in the critical ϕ4 theory on 4 ‑ 𝜖 dimensional real projective space in three different methods. The first is to use the conventional perturbation theory, and the second is to impose the cross-cap bootstrap equation, and the third is to solve the Schwinger-Dyson equation under the assumption of conformal invariance. We find that the three methods lead to mutually consistent results but each has its own advantage.

On critical exponents without Feynman diagrams

NASA Astrophysics Data System (ADS)

Sen, Kallol; Sinha, Aninda

2016-11-01

In order to achieve a better analytic handle on the modern conformal bootstrap program, we re-examine and extend the pioneering 1974 work of Polyakov’s, which was based on consistency between the operator product expansion and unitarity. As in the bootstrap approach, this method does not depend on evaluating Feynman diagrams. We show how this approach can be used to compute the anomalous dimensions of certain operators in the O(n) model at the Wilson-Fisher fixed point in 4-ɛ dimensions up to O({ɛ }2). AS dedicates this work to the loving memory of his mother.

Bootstrapping 3D fermions

DOE PAGES

Iliesiu, Luca; Kos, Filip; Poland, David; ...

2016-03-17

We study the conformal bootstrap for a 4-point function of fermions in 3D. We first introduce an embedding formalism for 3D spinors and compute the conformal blocks appearing in fermion 4-point functions. Using these results, we find general bounds on the dimensions of operators appearing in the ψ × ψ OPE, and also on the central charge C T. We observe features in our bounds that coincide with scaling dimensions in the GrossNeveu models at large N. Finally, we also speculate that other features could coincide with a fermionic CFT containing no relevant scalar operators.

Transmission Index Research of Parallel Manipulators Based on Matrix Orthogonal Degree

NASA Astrophysics Data System (ADS)

Shao, Zhu-Feng; Mo, Jiao; Tang, Xiao-Qiang; Wang, Li-Ping

2017-11-01

Performance index is the standard of performance evaluation, and is the foundation of both performance analysis and optimal design for the parallel manipulator. Seeking the suitable kinematic indices is always an important and challenging issue for the parallel manipulator. So far, there are extensive studies in this field, but few existing indices can meet all the requirements, such as simple, intuitive, and universal. To solve this problem, the matrix orthogonal degree is adopted, and generalized transmission indices that can evaluate motion/force transmissibility of fully parallel manipulators are proposed. Transmission performance analysis of typical branches, end effectors, and parallel manipulators is given to illustrate proposed indices and analysis methodology. Simulation and analysis results reveal that proposed transmission indices possess significant advantages, such as normalized finite (ranging from 0 to 1), dimensionally homogeneous, frame-free, intuitive and easy to calculate. Besides, proposed indices well indicate the good transmission region and relativity to the singularity with better resolution than the traditional local conditioning index, and provide a novel tool for kinematic analysis and optimal design of fully parallel manipulators.

Parallel Event Analysis Under Unix

NASA Astrophysics Data System (ADS)

Looney, S.; Nilsson, B. S.; Oest, T.; Pettersson, T.; Ranjard, F.; Thibonnier, J.-P.

The ALEPH experiment at LEP, the CERN CN division and Digital Equipment Corp. have, in a joint project, developed a parallel event analysis system. The parallel physics code is identical to ALEPH's standard analysis code, ALPHA, only the organisation of input/output is changed. The user may switch between sequential and parallel processing by simply changing one input "card". The initial implementation runs on an 8-node DEC 3000/400 farm, using the PVM software, and exhibits a near-perfect speed-up linearity, reducing the turn-around time by a factor of 8.

Type I and Type II Error Rates and Overall Accuracy of the Revised Parallel Analysis Method for Determining the Number of Factors

ERIC Educational Resources Information Center

Green, Samuel B.; Thompson, Marilyn S.; Levy, Roy; Lo, Wen-Juo

2015-01-01

Traditional parallel analysis (T-PA) estimates the number of factors by sequentially comparing sample eigenvalues with eigenvalues for randomly generated data. Revised parallel analysis (R-PA) sequentially compares the "k"th eigenvalue for sample data to the "k"th eigenvalue for generated data sets, conditioned on"k"-…

Considering Horn's Parallel Analysis from a Random Matrix Theory Point of View.

PubMed

Saccenti, Edoardo; Timmerman, Marieke E

2017-03-01

Horn's parallel analysis is a widely used method for assessing the number of principal components and common factors. We discuss the theoretical foundations of parallel analysis for principal components based on a covariance matrix by making use of arguments from random matrix theory. In particular, we show that (i) for the first component, parallel analysis is an inferential method equivalent to the Tracy-Widom test, (ii) its use to test high-order eigenvalues is equivalent to the use of the joint distribution of the eigenvalues, and thus should be discouraged, and (iii) a formal test for higher-order components can be obtained based on a Tracy-Widom approximation. We illustrate the performance of the two testing procedures using simulated data generated under both a principal component model and a common factors model. For the principal component model, the Tracy-Widom test performs consistently in all conditions, while parallel analysis shows unpredictable behavior for higher-order components. For the common factor model, including major and minor factors, both procedures are heuristic approaches, with variable performance. We conclude that the Tracy-Widom procedure is preferred over parallel analysis for statistically testing the number of principal components based on a covariance matrix.

DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution.

PubMed

Xia, Xuhua

2018-06-01

DAMBE is a comprehensive software package for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers. New functions include imputing missing distances and phylogeny simultaneously (paving the way to build large phage and transposon trees), new bootstrapping/jackknifing methods for PhyPA (phylogenetics from pairwise alignments), and an improved function for fast and accurate estimation of the shape parameter of the gamma distribution for fitting rate heterogeneity over sites. Previous method corrects multiple hits for each site independently. DAMBE's new method uses all sites simultaneously for correction. DAMBE, featuring a user-friendly graphic interface, is freely available from http://dambe.bio.uottawa.ca (last accessed, April 17, 2018).

Computational mechanics analysis tools for parallel-vector supercomputers

NASA Technical Reports Server (NTRS)

Storaasli, O. O.; Nguyen, D. T.; Baddourah, M. A.; Qin, J.

1993-01-01

Computational algorithms for structural analysis on parallel-vector supercomputers are reviewed. These parallel algorithms, developed by the authors, are for the assembly of structural equations, 'out-of-core' strategies for linear equation solution, massively distributed-memory equation solution, unsymmetric equation solution, general eigen-solution, geometrically nonlinear finite element analysis, design sensitivity analysis for structural dynamics, optimization algorithm and domain decomposition. The source code for many of these algorithms is available from NASA Langley.

Prediction of resource volumes at untested locations using simple local prediction models

USGS Publications Warehouse

Attanasi, E.D.; Coburn, T.C.; Freeman, P.A.

2006-01-01

This paper shows how local spatial nonparametric prediction models can be applied to estimate volumes of recoverable gas resources at individual undrilled sites, at multiple sites on a regional scale, and to compute confidence bounds for regional volumes based on the distribution of those estimates. An approach that combines cross-validation, the jackknife, and bootstrap procedures is used to accomplish this task. Simulation experiments show that cross-validation can be applied beneficially to select an appropriate prediction model. The cross-validation procedure worked well for a wide range of different states of nature and levels of information. Jackknife procedures are used to compute individual prediction estimation errors at undrilled locations. The jackknife replicates also are used with a bootstrap resampling procedure to compute confidence bounds for the total volume. The method was applied to data (partitioned into a training set and target set) from the Devonian Antrim Shale continuous-type gas play in the Michigan Basin in Otsego County, Michigan. The analysis showed that the model estimate of total recoverable volumes at prediction sites is within 4 percent of the total observed volume. The model predictions also provide frequency distributions of the cell volumes at the production unit scale. Such distributions are the basis for subsequent economic analyses. ?? Springer Science+Business Media, LLC 2007.

DNA-DNA hybridization-based phylogeny for "higher" nonpasserines: reevaluating a key portion of the avian family tree.

PubMed

Bleiweiss, R; Kirsch, J A; Lapointe, F J

1994-09-01

A matrix of delta T mode values for 10 birds, including 9 nonpasserines and a suboscine passerine flycatcher, was generated by DNA-DNA hybridization. Within the most derived lineages, all bootstrapped and jackknifed FITCH trees lend strong support to sister-groupings of the two swift families, of hummingbirds to swifts, and of these to a clade containing both owls and night-hawks. The outgroup duck roots the tree between the woodpecker (Piciformes) and the remaining taxa, indicating that Piciformes are among the earliest branches within nonpasserines. However, the succeeding branches to kingfisher, mousebird, and suboscine passerine flycatcher are based on short internodes that are poorly supported by bootstrapping and that give inconsistent results in jackknifing. Although these 3 orders may have arisen through rapid or near-simultaneous divergence, placement of the "advanced" Passeriformes deep within a more "primitive" radiation indicates that nonpasserines are paraphyletic, echoing the same distinction for reptiles with respect to their advanced descendants. Despite significant rate variation among different taxa, these results largely concur with those obtained with the same technique by Sibley and Ahlquist, who used the delta T50H measure and UPGMA analysis. This agreement lends credence to some of their more controversial claims.

Empirical best linear unbiased prediction method for small areas with restricted maximum likelihood and bootstrap procedure to estimate the average of household expenditure per capita in Banjar Regency

NASA Astrophysics Data System (ADS)

Aminah, Agustin Siti; Pawitan, Gandhi; Tantular, Bertho

2017-03-01

So far, most of the data published by Statistics Indonesia (BPS) as data providers for national statistics are still limited to the district level. Less sufficient sample size for smaller area levels to make the measurement of poverty indicators with direct estimation produced high standard error. Therefore, the analysis based on it is unreliable. To solve this problem, the estimation method which can provide a better accuracy by combining survey data and other auxiliary data is required. One method often used for the estimation is the Small Area Estimation (SAE). There are many methods used in SAE, one of them is Empirical Best Linear Unbiased Prediction (EBLUP). EBLUP method of maximum likelihood (ML) procedures does not consider the loss of degrees of freedom due to estimating β with β ^. This drawback motivates the use of the restricted maximum likelihood (REML) procedure. This paper proposed EBLUP with REML procedure for estimating poverty indicators by modeling the average of household expenditures per capita and implemented bootstrap procedure to calculate MSE (Mean Square Error) to compare the accuracy EBLUP method with the direct estimation method. Results show that EBLUP method reduced MSE in small area estimation.

Advances in the high bootstrap fraction regime on DIII-D towards the Q = 5 mission of ITER steady state

DOE PAGES

Qian, Jinping P.; Garofalo, Andrea M.; Gong, Xianzu Z.; ...

2017-03-20

Recent EAST/DIII-D joint experiments on the high poloidal betamore » $${{\\beta}_{\\text{P}}}$$ regime in DIII-D have extended operation with internal transport barriers (ITBs) and excellent energy confinement (H 98y2 ~ 1.6) to higher plasma current, for lower q 95 ≤ 7.0, and more balanced neutral beam injection (NBI) (torque injection < 2 Nm), for lower plasma rotation than previous results. Transport analysis and experimental measurements at low toroidal rotation suggest that the E × B shear effect is not key to the ITB formation in these high $${{\\beta}_{\\text{P}}}$$ discharges. Experiments and TGLF modeling show that the Shafranov shift has a key stabilizing effect on turbulence. Extrapolation of the DIII-D results using a 0D model shows that with the improved confinement, the high bootstrap fraction regime could achieve fusion gain Q = 5 in ITER at $${{\\beta}_{\\text{N}}}$$ ~ 2.9 and q 95 ~ 7. With the optimization of q(0), the required improved confinement is achievable when using 1.5D TGLF-SAT1 for transport simulations. Furthermore, results reported in this paper suggest that the DIII-D high $${{\\beta}_{\\text{P}}}$$ scenario could be a candidate for ITER steady state operation.« less

Parametric methods outperformed non-parametric methods in comparisons of discrete numerical variables.

PubMed

Fagerland, Morten W; Sandvik, Leiv; Mowinckel, Petter

2011-04-13

The number of events per individual is a widely reported variable in medical research papers. Such variables are the most common representation of the general variable type called discrete numerical. There is currently no consensus on how to compare and present such variables, and recommendations are lacking. The objective of this paper is to present recommendations for analysis and presentation of results for discrete numerical variables. Two simulation studies were used to investigate the performance of hypothesis tests and confidence interval methods for variables with outcomes {0, 1, 2}, {0, 1, 2, 3}, {0, 1, 2, 3, 4}, and {0, 1, 2, 3, 4, 5}, using the difference between the means as an effect measure. The Welch U test (the T test with adjustment for unequal variances) and its associated confidence interval performed well for almost all situations considered. The Brunner-Munzel test also performed well, except for small sample sizes (10 in each group). The ordinary T test, the Wilcoxon-Mann-Whitney test, the percentile bootstrap interval, and the bootstrap-t interval did not perform satisfactorily. The difference between the means is an appropriate effect measure for comparing two independent discrete numerical variables that has both lower and upper bounds. To analyze this problem, we encourage more frequent use of parametric hypothesis tests and confidence intervals.

Phylogenomics provides strong evidence for relationships of butterflies and moths

PubMed Central

Kawahara, Akito Y.; Breinholt, Jesse W.

2014-01-01

Butterflies and moths constitute some of the most popular and charismatic insects. Lepidoptera include approximately 160 000 described species, many of which are important model organisms. Previous studies on the evolution of Lepidoptera did not confidently place butterflies, and many relationships among superfamilies in the megadiverse clade Ditrysia remain largely uncertain. We generated a molecular dataset with 46 taxa, combining 33 new transcriptomes with 13 available genomes, transcriptomes and expressed sequence tags (ESTs). Using HaMStR with a Lepidoptera-specific core-orthologue set of single copy loci, we identified 2696 genes for inclusion into the phylogenomic analysis. Nucleotides and amino acids of the all-gene, all-taxon dataset yielded nearly identical, well-supported trees. Monophyly of butterflies (Papilionoidea) was strongly supported, and the group included skippers (Hesperiidae) and the enigmatic butterfly–moths (Hedylidae). Butterflies were placed sister to the remaining obtectomeran Lepidoptera, and the latter was grouped with greater than or equal to 87% bootstrap support. Establishing confident relationships among the four most diverse macroheteroceran superfamilies was previously challenging, but we recovered 100% bootstrap support for the following relationships: ((Geometroidea, Noctuoidea), (Bombycoidea, Lasiocampoidea)). We present the first robust, transcriptome-based tree of Lepidoptera that strongly contradicts historical placement of butterflies, and provide an evolutionary framework for genomic, developmental and ecological studies on this diverse insect order. PMID:24966318

Parallel Guessing: A Strategy for High-Speed Computation

DTIC Science & Technology

1984-09-19

for using additional hardware to obtain higher processing speed). In this paper we argue that parallel guessing for image analysis is a useful...from a true solution, or the correctness of a guess, can be readily checked. We review image - analysis algorithms having a parallel guessing or

Blubber Cortisol: A Potential Tool for Assessing Stress Response in Free-Ranging Dolphins without Effects due to Sampling

PubMed Central

Kellar, Nicholas M.; Catelani, Krista N.; Robbins, Michelle N.; Trego, Marisa L.; Allen, Camryn D.; Danil, Kerri; Chivers, Susan J.

2015-01-01

When paired with dart biopsying, quantifying cortisol in blubber tissue may provide an index of relative stress levels (i.e., activation of the hypothalamus-pituitary-adrenal axis) in free-ranging cetacean populations while minimizing the effects of the act of sampling. To validate this approach, cortisol was extracted from blubber samples collected from beach-stranded and bycaught short-beaked common dolphins using a modified blubber steroid isolation technique and measured via commercially available enzyme immunoassays. The measurements exhibited appropriate quality characteristics when analyzed via a bootstraped stepwise parallelism analysis (observed/expected = 1.03, 95%CI: 99.6 – 1.08) and showed no evidence of matrix interference with increasing sample size across typical biopsy tissue masses (75–150mg; r2 = 0.012, p = 0.78, slope = 0.022ngcortisol deviation/ultissue extract added). The relationships between blubber cortisol and eight potential cofactors namely, 1) fatality type (e.g., stranded or bycaught), 2) specimen condition (state of decomposition), 3) total body length, 4) sex, 5) sexual maturity state, 6) pregnancy status, 7) lactation state, and 8) adrenal mass, were assessed using a Bayesian generalized linear model averaging technique. Fatality type was the only factor correlated with blubber cortisol, and the magnitude of the effect size was substantial: beach-stranded individuals had on average 6.1-fold higher cortisol levels than those of bycaught individuals. Because of the difference in conditions surrounding these two fatality types, we interpret this relationship as evidence that blubber cortisol is indicative of stress response. We found no evidence of seasonal variation or a relationship between cortisol and the remaining cofactors. PMID:25643144

Visceral sensitivity, anxiety, and smoking among treatment-seeking smokers.

PubMed

Zvolensky, Michael J; Bakhshaie, Jafar; Norton, Peter J; Smits, Jasper A J; Buckner, Julia D; Garey, Lorra; Manning, Kara

2017-12-01

It is widely recognized that smoking is related to abdominal pain and discomfort, as well as gastrointestinal disorders. Research has shown that visceral sensitivity, experiencing anxiety around gastrointestinal sensations, is associated with poorer gastrointestinal health and related health outcomes. Visceral sensitivity also increases anxiety symptoms and mediates the relation with other risk factors, including gastrointestinal distress. No work to date, however, has evaluated visceral sensitivity in the context of smoking despite the strong association between smoking and poor physical and mental health. The current study sought to examine visceral sensitivity as a unique predictor of cigarette dependence, threat-related smoking abstinence expectancies (somatic symptoms and harmful consequences), and perceived barriers for cessation via anxiety symptoms. Eighty-four treatment seeking adult daily smokers (M age =45.1years [SD=10.4]; 71.6% male) participated in this study. There was a statistically significant indirect effect of visceral sensitivity via general anxiety symptoms on cigarette dependence (b=0.02, SE=0.01, Bootstrapped 95% CI [0.006, 0.05]), smoking abstinence somatic expectancies (b=0.10, SE=0.03, Bootstrapped 95% CI [0.03, 0.19]), smoking abstinence harmful experiences (b=0.13, SE=0.05, Bootstrapped 95% CI [0.03, 0.25]), and barriers to cessation (b=0.05, SE=0.06, Bootstrapped 95% CI [0.01, 0.13]). Overall, the present study serves as an initial investigation into the nature of the associations between visceral sensitivity, anxiety symptoms, and clinically significant smoking processes among treatment-seeking smokers. Future work is needed to explore the extent to which anxiety accounts for relations between visceral sensitivity and other smoking processes (e.g., withdrawal, cessation outcome). Copyright © 2017 Elsevier Ltd. All rights reserved.

Phylogenetic analysis of the sharpshooter genus Subrasaca Young, 1977 (Hemiptera, Cicadellidae, Cicadellini)

PubMed Central

da Silva, Roberta dos Santos; Mejdalani, Gabriel; Cavichioli, Rodney R.

2015-01-01

Abstract The South American sharpshooter genus Subrasaca comprises 14 species. Some species of this genus are quite common in the Brazilian Atlantic Rainforest. In this paper, a phylogenetic analysis of Subrasaca, based on a matrix of 20 terminal taxa and 72 morphological characters of the head, thorax, and male and female genitalia, is presented. The analysis yielded six equally most parsimonious trees (197 steps, CI = 0.6091, RI = 0.5722, and RC = 0.3486). The results suggest that Subrasaca is a monophyletic taxon, although the genus branch is not robust. The clade showing the highest bootstrap and Bremer scores is formed by species with longitudinal dark brown to black stripes on the forewings (Subrasaca bimaculata, Subrasaca constricta, Subrasaca curvovittata, and Subrasaca flavolineata), followed by Subrasaca atronasa + Subrasaca austera. PMID:25829841

Measurement of cardiac troponin I in healthy lactating dairy cows using a point of care analyzer (i-STAT-1).

PubMed

Labonté, Josiane; Roy, Jean-Philippe; Dubuc, Jocelyn; Buczinski, Sébastien

2015-06-01

Cardiac troponin I (cTnI) has been shown to be an accurate predictor of myocardial injury in cattle. The point-of-care i-STAT 1 immunoassay can be used to quantify blood cTnI in cattle. However, the cTnI reference interval in whole blood of healthy early lactating dairy cows remains unknown. To determine a blood cTnI reference interval in healthy early lactating Holstein dairy cows using the analyzer i-STAT 1. Forty healthy lactating dairy Holstein cows (0-60 days in milk) were conveniently selected from four commercial dairy farms. Each selected cow was examined by a veterinarian and transthoracic echocardiography was performed. A cow-side blood cTnI dosage was measured at the same time. A bootstrap statistical analysis method using unrestricted resampling was used to determine a reference interval for blood cTnI values. Forty healthy cows were recruited in the study. Median blood cTnI was 0.02 ng/mL (minimum: 0.00, maximum: 0.05). Based on the bootstrap analysis method with 40 cases, the 95th percentile of cTnI values in healthy cows was 0.036 ng/mL (90% CI: 0.02-0.05 ng/mL). A reference interval for blood cTnI values in healthy lactating cows was determined. Further research is needed to determine whether cTnI blood values could be used to diagnose and provide a prognosis for cardiac and noncardiac diseases in lactating dairy cows. Copyright © 2015 Elsevier B.V. All rights reserved.

Optimization of Multilocus Sequence Analysis for Identification of Species in the Genus Vibrio

PubMed Central

Gabriel, Michael W.; Matsui, George Y.; Friedman, Robert

2014-01-01

Multilocus sequence analysis (MLSA) is an important method for identification of taxa that are not well differentiated by 16S rRNA gene sequences alone. In this procedure, concatenated sequences of selected genes are constructed and then analyzed. The effects that the number and the order of genes used in MLSA have on reconstruction of phylogenetic relationships were examined. The recA, rpoA, gapA, 16S rRNA gene, gyrB, and ftsZ sequences from 56 species of the genus Vibrio were used to construct molecular phylogenies, and these were evaluated individually and using various gene combinations. Phylogenies from two-gene sequences employing recA and rpoA in both possible gene orders were different. The addition of the gapA gene sequence, producing all six possible concatenated sequences, reduced the differences in phylogenies to degrees of statistical (bootstrap) support for some nodes. The overall statistical support for the phylogenetic tree, assayed on the basis of a reliability score (calculated from the number of nodes having bootstrap values of ≥80 divided by the total number of nodes) increased with increasing numbers of genes used, up to a maximum of four. No further improvement was observed from addition of the fifth gene sequence (ftsZ), and addition of the sixth gene (gyrB) resulted in lower proportions of strongly supported nodes. Reductions in the numbers of strongly supported nodes were also observed when maximum parsimony was employed for tree construction. Use of a small number of gene sequences in MLSA resulted in accurate identification of Vibrio species. PMID:24951781

Bootstrap Signal-to-Noise Confidence Intervals: An Objective Method for Subject Exclusion and Quality Control in ERP Studies

PubMed Central

Parks, Nathan A.; Gannon, Matthew A.; Long, Stephanie M.; Young, Madeleine E.

2016-01-01

Analysis of event-related potential (ERP) data includes several steps to ensure that ERPs meet an appropriate level of signal quality. One such step, subject exclusion, rejects subject data if ERP waveforms fail to meet an appropriate level of signal quality. Subject exclusion is an important quality control step in the ERP analysis pipeline as it ensures that statistical inference is based only upon those subjects exhibiting clear evoked brain responses. This critical quality control step is most often performed simply through visual inspection of subject-level ERPs by investigators. Such an approach is qualitative, subjective, and susceptible to investigator bias, as there are no standards as to what constitutes an ERP of sufficient signal quality. Here, we describe a standardized and objective method for quantifying waveform quality in individual subjects and establishing criteria for subject exclusion. The approach uses bootstrap resampling of ERP waveforms (from a pool of all available trials) to compute a signal-to-noise ratio confidence interval (SNR-CI) for individual subject waveforms. The lower bound of this SNR-CI (SNRLB) yields an effective and objective measure of signal quality as it ensures that ERP waveforms statistically exceed a desired signal-to-noise criterion. SNRLB provides a quantifiable metric of individual subject ERP quality and eliminates the need for subjective evaluation of waveform quality by the investigator. We detail the SNR-CI methodology, establish the efficacy of employing this approach with Monte Carlo simulations, and demonstrate its utility in practice when applied to ERP datasets. PMID:26903849

Not seeing the forest for the trees: size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis.

PubMed

Teixeira, Andreia Sofia; Monteiro, Pedro T; Carriço, João A; Ramirez, Mário; Francisco, Alexandre P

2015-01-01

Trees, including minimum spanning trees (MSTs), are commonly used in phylogenetic studies. But, for the research community, it may be unclear that the presented tree is just a hypothesis, chosen from among many possible alternatives. In this scenario, it is important to quantify our confidence in both the trees and the branches/edges included in such trees. In this paper, we address this problem for MSTs by introducing a new edge betweenness metric for undirected and weighted graphs. This spanning edge betweenness metric is defined as the fraction of equivalent MSTs where a given edge is present. The metric provides a per edge statistic that is similar to that of the bootstrap approach frequently used in phylogenetics to support the grouping of taxa. We provide methods for the exact computation of this metric based on the well known Kirchhoff's matrix tree theorem. Moreover, we implement and make available a module for the PHYLOViZ software and evaluate the proposed metric concerning both effectiveness and computational performance. Analysis of trees generated using multilocus sequence typing data (MLST) and the goeBURST algorithm revealed that the space of possible MSTs in real data sets is extremely large. Selection of the edge to be represented using bootstrap could lead to unreliable results since alternative edges are present in the same fraction of equivalent MSTs. The choice of the MST to be presented, results from criteria implemented in the algorithm that must be based in biologically plausible models.

Three-dimensional quantitative structure-activity relationship studies on novel series of benzotriazine based compounds acting as Src inhibitors using CoMFA and CoMSIA.

PubMed

Gueto, Carlos; Ruiz, José L; Torres, Juan E; Méndez, Jefferson; Vivas-Reyes, Ricardo

2008-03-01

Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on a series of benzotriazine derivatives, as Src inhibitors. Ligand molecular superimposition on the template structure was performed by database alignment method. The statistically significant model was established of 72 molecules, which were validated by a test set of six compounds. The CoMFA model yielded a q(2)=0.526, non cross-validated R(2) of 0.781, F value of 88.132, bootstrapped R(2) of 0.831, standard error of prediction=0.587, and standard error of estimate=0.351 while the CoMSIA model yielded the best predictive model with a q(2)=0.647, non cross-validated R(2) of 0.895, F value of 115.906, bootstrapped R(2) of 0.953, standard error of prediction=0.519, and standard error of estimate=0.178. The contour maps obtained from 3D-QSAR studies were appraised for activity trends for the molecules analyzed. Results indicate that small steric volumes in the hydrophobic region, electron-withdrawing groups next to the aryl linker region, and atoms close to the solvent accessible region increase the Src inhibitory activity of the compounds. In fact, adding substituents at positions 5, 6, and 8 of the benzotriazine nucleus were generated new compounds having a higher predicted activity. The data generated from the present study will further help to design novel, potent, and selective Src inhibitors as anticancer therapeutic agents.

Four distinct types of E.C. 1.2.1.30 enzymes can catalyze the reduction of carboxylic acids to aldehydes.

PubMed

Stolterfoht, Holly; Schwendenwein, Daniel; Sensen, Christoph W; Rudroff, Florian; Winkler, Margit

2017-09-10

Increasing demand for chemicals from renewable resources calls for the development of new biotechnological methods for the reduction of oxidized bio-based compounds. Enzymatic carboxylate reduction is highly selective, both in terms of chemo- and product selectivity, but not many carboxylate reductase enzymes (CARs) have been identified on the sequence level to date. Thus far, their phylogeny is unexplored and very little is known about their structure-function-relationship. CARs minimally contain an adenylation domain, a phosphopantetheinylation domain and a reductase domain. We have recently identified new enzymes of fungal origin, using similarity searches against genomic sequences from organisms in which aldehydes were detected upon incubation with carboxylic acids. Analysis of sequences with known CAR functionality and CAR enzymes recently identified in our laboratory suggests that the three-domain architecture mentioned above is modular. The construction of a distance tree with a subsequent 1000-replicate bootstrap analysis showed that the CAR sequences included in our study fall into four distinct subgroups (one of bacterial origin and three of fungal origin, respectively), each with a bootstrap value of 100%. The multiple sequence alignment of all experimentally confirmed CAR protein sequences revealed fingerprint sequences of residues which are likely to be involved in substrate and co-substrate binding and one of the three catalytic substeps, respectively. The fingerprint sequences broaden our understanding of the amino acids that might be essential for the reduction of organic acids to the corresponding aldehydes in CAR proteins. Copyright © 2017 Elsevier B.V. All rights reserved.

Performance Evaluation of Parallel Branch and Bound Search with the Intel iPSC (Intel Personal SuperComputer) Hypercube Computer.

DTIC Science & Technology

1986-12-01

17 III. Analysis of Parallel Design ................................................ 18 Parallel Abstract Data ...Types ........................................... 18 Abstract Data Type .................................................. 19 Parallel ADT...22 Data -Structure Design ........................................... 23 Object-Oriented Design

Programming Probabilistic Structural Analysis for Parallel Processing Computer

NASA Technical Reports Server (NTRS)

Sues, Robert H.; Chen, Heh-Chyun; Twisdale, Lawrence A.; Chamis, Christos C.; Murthy, Pappu L. N.

1991-01-01

The ultimate goal of this research program is to make Probabilistic Structural Analysis (PSA) computationally efficient and hence practical for the design environment by achieving large scale parallelism. The paper identifies the multiple levels of parallelism in PSA, identifies methodologies for exploiting this parallelism, describes the development of a parallel stochastic finite element code, and presents results of two example applications. It is demonstrated that speeds within five percent of those theoretically possible can be achieved. A special-purpose numerical technique, the stochastic preconditioned conjugate gradient method, is also presented and demonstrated to be extremely efficient for certain classes of PSA problems.

Cost-utility analysis of a preventive home visit program for older adults in Germany.

PubMed

Brettschneider, Christian; Luck, Tobias; Fleischer, Steffen; Roling, Gudrun; Beutner, Katrin; Luppa, Melanie; Behrens, Johann; Riedel-Heller, Steffi G; König, Hans-Helmut

2015-04-03

Most older adults want to live independently in a familiar environment instead of moving to a nursing home. Preventive home visits based on multidimensional geriatric assessment can be one strategy to support this preference and might additionally reduce health care costs, due to the avoidance of costly nursing home admissions. The purpose of this study was to analyse the cost-effectiveness of preventive home visits from a societal perspective in Germany. This study is part of a multi-centre, non-blinded, randomised controlled trial aiming at the reduction of nursing home admissions. Participants were older than 80 years and living at home. Up to three home visits were conducted to identify self-care deficits and risk factors, to present recommendations and to implement solutions. The control group received usual care. A cost-utility analysis using quality-adjusted life years (QALY) based on the EQ-5D was performed. Resource utilization was assessed by means of the interview version of a patient questionnaire. A cost-effectiveness acceptability curve controlled for prognostic variables was constructed and a sensitivity analysis to control for the influence of the mode of QALY calculation was performed. 278 individuals (intervention group: 133; control group: 145) were included in the analysis. During 18 months follow-up mean adjusted total cost (mean: +4,401 EUR; bootstrapped standard error: 3,019.61 EUR) and number of QALY (mean: 0.0061 QALY; bootstrapped standard error: 0.0388 QALY) were higher in the intervention group, but differences were not significant. For preventive home visits the probability of an incremental cost-effectiveness ratio <50,000 EUR per QALY was only 15%. The results were robust with respect to the mode of QALY calculation. The evaluated preventive home visits programme is unlikely to be cost-effective. Clinical Trials.gov Identifier: NCT00644826.

Paleomagnetism.org: An online multi-platform open source environment for paleomagnetic data analysis

NASA Astrophysics Data System (ADS)

Koymans, Mathijs R.; Langereis, Cor G.; Pastor-Galán, Daniel; van Hinsbergen, Douwe J. J.

2016-08-01

This contribution provides an overview of Paleomagnetism.org, an open-source, multi-platform online environment for paleomagnetic data analysis. Paleomagnetism.org provides an interactive environment where paleomagnetic data can be interpreted, evaluated, visualized, and exported. The Paleomagnetism.org application is split in to an interpretation portal, a statistics portal, and a portal for miscellaneous paleomagnetic tools. In the interpretation portal, principle component analysis can be performed on visualized demagnetization diagrams. Interpreted directions and great circles can be combined to find great circle solutions. These directions can be used in the statistics portal, or exported as data and figures. The tools in the statistics portal cover standard Fisher statistics for directions and VGPs, including other statistical parameters used as reliability criteria. Other available tools include an eigenvector approach foldtest, two reversal test including a Monte Carlo simulation on mean directions, and a coordinate bootstrap on the original data. An implementation is included for the detection and correction of inclination shallowing in sediments following TK03.GAD. Finally we provide a module to visualize VGPs and expected paleolatitudes, declinations, and inclinations relative to widely used global apparent polar wander path models in coordinates of major continent-bearing plates. The tools in the miscellaneous portal include a net tectonic rotation (NTR) analysis to restore a body to its paleo-vertical and a bootstrapped oroclinal test using linear regressive techniques, including a modified foldtest around a vertical axis. Paleomagnetism.org provides an integrated approach for researchers to work with visualized (e.g. hemisphere projections, Zijderveld diagrams) paleomagnetic data. The application constructs a custom exportable file that can be shared freely and included in public databases. This exported file contains all data and can later be imported to the application by other researchers. The accessibility and simplicity through which paleomagnetic data can be interpreted, analyzed, visualized, and shared makes Paleomagnetism.org of interest to the community.

Motion capability analysis of a quadruped robot as a parallel manipulator

NASA Astrophysics Data System (ADS)

Yu, Jingjun; Lu, Dengfeng; Zhang, Zhongxiang; Pei, Xu

2014-12-01

This paper presents the forward and inverse displacement analysis of a quadruped robot MANA as a parallel manipulator in quadruple stance phase, which is used to obtain the workspace and control the motion of the body. The robot MANA designed on the basis of the structure of quadruped mammal is able to not only walk and turn in the uneven terrain, but also accomplish various manipulating tasks as a parallel manipulator in quadruple stance phase. The latter will be the focus of this paper, however. For this purpose, the leg kinematics is primarily analyzed, which lays the foundation on the gait planning in terms of locomotion and body kinematics analysis as a parallel manipulator. When all four feet of the robot contact on the ground, by assuming there is no slipping at the feet, each contacting point is treated as a passive spherical joint and the kinematic model of parallel manipulator is established. The method for choosing six non-redundant actuated joints for the parallel manipulator from all twelve optional joints is elaborated. The inverse and forward displacement analysis of the parallel manipulator is carried out using the method of coordinate transformation. Finally, based on the inverse and forward kinematic model, two issues on obtaining the reachable workspace of parallel manipulator and planning the motion of the body are implemented and verified by ADAMS simulation.

Why do workaholics experience depression? A study with Chinese University teachers.

PubMed

Nie, Yingzhi; Sun, Haitao

2016-10-01

This study focuses on the relationships of workaholism to job burnout and depression of university teachers. The direct and indirect (via job burnout) effects of workaholism on depression were investigated in 412 Chinese university teachers. Structural equation modeling and bootstrap method were used. Results revealed that workaholism, job burnout, and depression significantly correlated with each other. Structural equation modeling and bootstrap test indicated the partial mediation role of job burnout on the relationship between workaholism and depression. The findings shed some light on how workaholism influenced depression and provided valuable evidence for prevention of depression in work. © The Author(s) 2015.

Construction of prediction intervals for Palmer Drought Severity Index using bootstrap

NASA Astrophysics Data System (ADS)

Beyaztas, Ufuk; Bickici Arikan, Bugrayhan; Beyaztas, Beste Hamiye; Kahya, Ercan

2018-04-01

In this study, we propose an approach based on the residual-based bootstrap method to obtain valid prediction intervals using monthly, short-term (three-months) and mid-term (six-months) drought observations. The effects of North Atlantic and Arctic Oscillation indexes on the constructed prediction intervals are also examined. Performance of the proposed approach is evaluated for the Palmer Drought Severity Index (PDSI) obtained from Konya closed basin located in Central Anatolia, Turkey. The finite sample properties of the proposed method are further illustrated by an extensive simulation study. Our results revealed that the proposed approach is capable of producing valid prediction intervals for future PDSI values.

Differentiation of Trypanosoma cruzi I subgroups through characterization of cytochrome b gene sequences.

PubMed

Spotorno O, Angel E; Córdova, Luis; Solari I, Aldo

2008-12-01

To identify and characterize chilean samples of Trypanosoma cruzi and their association with hosts, the first 516 bp of the mitochondrial cytochrome b gene were sequenced from eight biological samples, and phylogenetically compared with other known 20 American sequences. The molecular characterization of these 28 sequences in a maximum likelihood phylogram (-lnL = 1255.12, tree length = 180, consistency index = 0.79) allowed the robust identification (bootstrap % > 99) of three previously known discrete typing units (DTU): DTU IIb, IIa, and I. An apparently undescribed new sequence found in four new chilean samples was detected and designated as DTU Ib; they were separated by 24.7 differences, but robustly related (bootstrap % = 97 in 500 replicates) to those of DTU I by sharing 12 substitutions, among which four were nonsynonymous ones. Such new DTU Ib was also robust (bootstrap % = 100), and characterized by 10 unambiguous substitutions, with a single nonsynonymous G to T change at site 409. The fact that two of such new sequences were found in parasites from a chilean endemic caviomorph rodent, Octodon degus, and that they were closely related to the ancient DTU I suggested old origins and a long association to caviomorph hosts.

Bootstrap percolation on spatial networks

NASA Astrophysics Data System (ADS)

Gao, Jian; Zhou, Tao; Hu, Yanqing

2015-10-01

Bootstrap percolation is a general representation of some networked activation process, which has found applications in explaining many important social phenomena, such as the propagation of information. Inspired by some recent findings on spatial structure of online social networks, here we study bootstrap percolation on undirected spatial networks, with the probability density function of long-range links’ lengths being a power law with tunable exponent. Setting the size of the giant active component as the order parameter, we find a parameter-dependent critical value for the power-law exponent, above which there is a double phase transition, mixed of a second-order phase transition and a hybrid phase transition with two varying critical points, otherwise there is only a second-order phase transition. We further find a parameter-independent critical value around -1, about which the two critical points for the double phase transition are almost constant. To our surprise, this critical value -1 is just equal or very close to the values of many real online social networks, including LiveJournal, HP Labs email network, Belgian mobile phone network, etc. This work helps us in better understanding the self-organization of spatial structure of online social networks, in terms of the effective function for information spreading.

A resampling strategy based on bootstrap to reduce the effect of large blunders in GPS absolute positioning

NASA Astrophysics Data System (ADS)

Angrisano, Antonio; Maratea, Antonio; Gaglione, Salvatore

2018-01-01

In the absence of obstacles, a GPS device is generally able to provide continuous and accurate estimates of position, while in urban scenarios buildings can generate multipath and echo-only phenomena that severely affect the continuity and the accuracy of the provided estimates. Receiver autonomous integrity monitoring (RAIM) techniques are able to reduce the negative consequences of large blunders in urban scenarios, but require both a good redundancy and a low contamination to be effective. In this paper a resampling strategy based on bootstrap is proposed as an alternative to RAIM, in order to estimate accurately position in case of low redundancy and multiple blunders: starting with the pseudorange measurement model, at each epoch the available measurements are bootstrapped—that is random sampled with replacement—and the generated a posteriori empirical distribution is exploited to derive the final position. Compared to standard bootstrap, in this paper the sampling probabilities are not uniform, but vary according to an indicator of the measurement quality. The proposed method has been compared with two different RAIM techniques on a data set collected in critical conditions, resulting in a clear improvement on all considered figures of merit.

Reanalysis of cancer mortality in Japanese A-bomb survivors exposed to low doses of radiation: bootstrap and simulation methods

PubMed Central

2009-01-01

Background The International Commission on Radiological Protection (ICRP) recommended annual occupational dose limit is 20 mSv. Cancer mortality in Japanese A-bomb survivors exposed to less than 20 mSv external radiation in 1945 was analysed previously, using a latency model with non-linear dose response. Questions were raised regarding statistical inference with this model. Methods Cancers with over 100 deaths in the 0 - 20 mSv subcohort of the 1950-1990 Life Span Study are analysed with Poisson regression models incorporating latency, allowing linear and non-linear dose response. Bootstrap percentile and Bias-corrected accelerated (BCa) methods and simulation of the Likelihood Ratio Test lead to Confidence Intervals for Excess Relative Risk (ERR) and tests against the linear model. Results The linear model shows significant large, positive values of ERR for liver and urinary cancers at latencies from 37 - 43 years. Dose response below 20 mSv is strongly non-linear at the optimal latencies for the stomach (11.89 years), liver (36.9), lung (13.6), leukaemia (23.66), and pancreas (11.86) and across broad latency ranges. Confidence Intervals for ERR are comparable using Bootstrap and Likelihood Ratio Test methods and BCa 95% Confidence Intervals are strictly positive across latency ranges for all 5 cancers. Similar risk estimates for 10 mSv (lagged dose) are obtained from the 0 - 20 mSv and 5 - 500 mSv data for the stomach, liver, lung and leukaemia. Dose response for the latter 3 cancers is significantly non-linear in the 5 - 500 mSv range. Conclusion Liver and urinary cancer mortality risk is significantly raised using a latency model with linear dose response. A non-linear model is strongly superior for the stomach, liver, lung, pancreas and leukaemia. Bootstrap and Likelihood-based confidence intervals are broadly comparable and ERR is strictly positive by bootstrap methods for all 5 cancers. Except for the pancreas, similar estimates of latency and risk from 10 mSv are obtained from the 0 - 20 mSv and 5 - 500 mSv subcohorts. Large and significant cancer risks for Japanese survivors exposed to less than 20 mSv external radiation from the atomic bombs in 1945 cast doubt on the ICRP recommended annual occupational dose limit. PMID:20003238

A Pre-Screening Questionnaire to Predict Non-24-Hour Sleep-Wake Rhythm Disorder (N24HSWD) among the Blind

PubMed Central

Flynn-Evans, Erin E.; Lockley, Steven W.

2016-01-01

Study Objectives: There is currently no questionnaire-based pre-screening tool available to detect non-24-hour sleep-wake rhythm disorder (N24HSWD) among blind patients. Our goal was to develop such a tool, derived from gold standard, objective hormonal measures of circadian entrainment status, for the detection of N24HSWD among those with visual impairment. Methods: We evaluated the contribution of 40 variables in their ability to predict N24HSWD among 127 blind women, classified using urinary 6-sulfatoxymelatonin period, an objective marker of circadian entrainment status in this population. We subjected the 40 candidate predictors to 1,000 bootstrapped iterations of a logistic regression forward selection model to predict N24HSWD, with model inclusion set at the p < 0.05 level. We removed any predictors that were not selected at least 1% of the time in the 1,000 bootstrapped models and applied a second round of 1,000 bootstrapped logistic regression forward selection models to the remaining 23 candidate predictors. We included all questions that were selected at least 10% of the time in the final model. We subjected the selected predictors to a final logistic regression model to predict N24SWD over 1,000 bootstrapped models to calculate the concordance statistic and adjusted optimism of the final model. We used this information to generate a predictive model and determined the sensitivity and specificity of the model. Finally, we applied the model to a cohort of 1,262 blind women who completed the survey, but did not collect urine samples. Results: The final model consisted of eight questions. The concordance statistic, adjusted for bootstrapping, was 0.85. The positive predictive value was 88%, the negative predictive value was 79%. Applying this model to our larger dataset of women, we found that 61% of those without light perception, and 27% with some degree of light perception, would be referred for further screening for N24HSWD. Conclusions: Our model has predictive utility sufficient to serve as a pre-screening questionnaire for N24HSWD among the blind. Citation: Flynn-Evans EE, Lockley SW. A pre-screening questionnaire to predict non-24-hour sleep-wake rhythm disorder (N24HSWD) among the blind. J Clin Sleep Med 2016;12(5):703–710. PMID:26951421

Parallel simulation today

NASA Technical Reports Server (NTRS)

Nicol, David; Fujimoto, Richard

1992-01-01

This paper surveys topics that presently define the state of the art in parallel simulation. Included in the tutorial are discussions on new protocols, mathematical performance analysis, time parallelism, hardware support for parallel simulation, load balancing algorithms, and dynamic memory management for optimistic synchronization.

Modular reweighting software for statistical mechanical analysis of biased equilibrium data

NASA Astrophysics Data System (ADS)

Sindhikara, Daniel J.

2012-07-01

Here a simple, useful, modular approach and software suite designed for statistical reweighting and analysis of equilibrium ensembles is presented. Statistical reweighting is useful and sometimes necessary for analysis of equilibrium enhanced sampling methods, such as umbrella sampling or replica exchange, and also in experimental cases where biasing factors are explicitly known. Essentially, statistical reweighting allows extrapolation of data from one or more equilibrium ensembles to another. Here, the fundamental separable steps of statistical reweighting are broken up into modules - allowing for application to the general case and avoiding the black-box nature of some “all-inclusive” reweighting programs. Additionally, the programs included are, by-design, written with little dependencies. The compilers required are either pre-installed on most systems, or freely available for download with minimal trouble. Examples of the use of this suite applied to umbrella sampling and replica exchange molecular dynamics simulations will be shown along with advice on how to apply it in the general case. New version program summaryProgram title: Modular reweighting version 2 Catalogue identifier: AEJH_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJH_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 179 118 No. of bytes in distributed program, including test data, etc.: 8 518 178 Distribution format: tar.gz Programming language: C++, Python 2.6+, Perl 5+ Computer: Any Operating system: Any RAM: 50-500 MB Supplementary material: An updated version of the original manuscript (Comput. Phys. Commun. 182 (2011) 2227) is available Classification: 4.13 Catalogue identifier of previous version: AEJH_v1_0 Journal reference of previous version: Comput. Phys. Commun. 182 (2011) 2227 Does the new version supersede the previous version?: Yes Nature of problem: While equilibrium reweighting is ubiquitous, there are no public programs available to perform the reweighting in the general case. Further, specific programs often suffer from many library dependencies and numerical instability. Solution method: This package is written in a modular format that allows for easy applicability of reweighting in the general case. Modules are small, numerically stable, and require minimal libraries. Reasons for new version: Some minor bugs, some upgrades needed, error analysis added. analyzeweight.py/analyzeweight.py2 has been replaced by “multihist.py”. This new program performs all the functions of its predecessor while being versatile enough to handle other types of histograms and probability analysis. “bootstrap.py” was added. This script performs basic bootstrap resampling allowing for error analysis of data. “avg_dev_distribution.py” was added. This program computes the averages and standard deviations of multiple distributions, making error analysis (e.g. from bootstrap resampling) easier to visualize. WRE.cpp was slightly modified purely for cosmetic reasons. The manual was updated for clarity and to reflect version updates. Examples were removed from the manual in favor of online tutorials (packaged examples remain). Examples were updated to reflect the new format. An additional example is included to demonstrate error analysis. Running time: Preprocessing scripts 1-5 minutes, WHAM engine <1 minute, postprocess script ∼1-5 minutes.

Parallel processing considerations for image recognition tasks

NASA Astrophysics Data System (ADS)

Simske, Steven J.

2011-01-01

Many image recognition tasks are well-suited to parallel processing. The most obvious example is that many imaging tasks require the analysis of multiple images. From this standpoint, then, parallel processing need be no more complicated than assigning individual images to individual processors. However, there are three less trivial categories of parallel processing that will be considered in this paper: parallel processing (1) by task; (2) by image region; and (3) by meta-algorithm. Parallel processing by task allows the assignment of multiple workflows-as diverse as optical character recognition [OCR], document classification and barcode reading-to parallel pipelines. This can substantially decrease time to completion for the document tasks. For this approach, each parallel pipeline is generally performing a different task. Parallel processing by image region allows a larger imaging task to be sub-divided into a set of parallel pipelines, each performing the same task but on a different data set. This type of image analysis is readily addressed by a map-reduce approach. Examples include document skew detection and multiple face detection and tracking. Finally, parallel processing by meta-algorithm allows different algorithms to be deployed on the same image simultaneously. This approach may result in improved accuracy.

Parallel-vector solution of large-scale structural analysis problems on supercomputers

NASA Technical Reports Server (NTRS)

Storaasli, Olaf O.; Nguyen, Duc T.; Agarwal, Tarun K.

1989-01-01

A direct linear equation solution method based on the Choleski factorization procedure is presented which exploits both parallel and vector features of supercomputers. The new equation solver is described, and its performance is evaluated by solving structural analysis problems on three high-performance computers. The method has been implemented using Force, a generic parallel FORTRAN language.

Parallel auto-correlative statistics with VTK.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pebay, Philippe Pierre; Bennett, Janine Camille

2013-08-01

This report summarizes existing statistical engines in VTK and presents both the serial and parallel auto-correlative statistics engines. It is a sequel to [PT08, BPRT09b, PT09, BPT09, PT10] which studied the parallel descriptive, correlative, multi-correlative, principal component analysis, contingency, k-means, and order statistics engines. The ease of use of the new parallel auto-correlative statistics engine is illustrated by the means of C++ code snippets and algorithm verification is provided. This report justifies the design of the statistics engines with parallel scalability in mind, and provides scalability and speed-up analysis results for the autocorrelative statistics engine.

Introducing parallelism to histogramming functions for GEM systems

NASA Astrophysics Data System (ADS)

Krawczyk, Rafał D.; Czarski, Tomasz; Kolasinski, Piotr; Pozniak, Krzysztof T.; Linczuk, Maciej; Byszuk, Adrian; Chernyshova, Maryna; Juszczyk, Bartlomiej; Kasprowicz, Grzegorz; Wojenski, Andrzej; Zabolotny, Wojciech

2015-09-01

This article is an assessment of potential parallelization of histogramming algorithms in GEM detector system. Histogramming and preprocessing algorithms in MATLAB were analyzed with regard to adding parallelism. Preliminary implementation of parallel strip histogramming resulted in speedup. Analysis of algorithms parallelizability is presented. Overview of potential hardware and software support to implement parallel algorithm is discussed.

Confirmation of Nosocomial Transmission of Hepatitis C Virus by Phylogenetic Analysis of the NS5-B Region

PubMed Central

Norder, Heléne; Bergström, Åsa; Uhnoo, Ingrid; Aldén, Jöran; Weiss, Lars; Czajkowski, Jan; Magnius, Lars

1998-01-01

Four hepatitis C virus transmission chains at three dialysis units were disclosed by limited sequencing; three of these were disclosed by analysis of the NS5-B region of the genome. Dialysis on the same shift as that during which infected patients were dialyzed was the common factor for seven patients in two chains. Two nurses exposed to needle sticks and their sources of infection constituted two other chains. The strains of three chains belonged to subtype 1a and formed clusters with an intrachain variability of 0 to 6 nucleotides compared to 8 to 37 nucleotides for unrelated strains within this subtype. The clusters were supported by bootstrap values ranging from 89 to 100%. PMID:9738071

The effect of sheared toroidal rotation on pressure driven magnetic islands in toroidal plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hegna, C. C.

2016-05-15

The impact of sheared toroidal rotation on the evolution of pressure driven magnetic islands in tokamak plasmas is investigated using a resistive magnetohydrodynamics model augmented by a neoclassical Ohm's law. Particular attention is paid to the asymptotic matching data as the Mercier indices are altered in the presence of sheared flow. Analysis of the nonlinear island Grad-Shafranov equation shows that sheared flows tend to amplify the stabilizing pressure/curvature contribution to pressure driven islands in toroidal tokamaks relative to the island bootstrap current contribution. As such, sheared toroidal rotation tends to reduce saturated magnetic island widths.

Probabilistic margin evaluation on accidental transients for the ASTRID reactor project

NASA Astrophysics Data System (ADS)

Marquès, Michel

2014-06-01

ASTRID is a technological demonstrator of Sodium cooled Fast Reactor (SFR) under development. The conceptual design studies are being conducted in accordance with the Generation IV reactor objectives, particularly in terms of improving safety. For the hypothetical events, belonging to the accidental category "severe accident prevention situations" having a very low frequency of occurrence, the safety demonstration is no more based on a deterministic demonstration with conservative assumptions on models and parameters but on a "Best-Estimate Plus Uncertainty" (BEPU) approach. This BEPU approach ispresented in this paper for an Unprotected Loss-of-Flow (ULOF) event. The Best-Estimate (BE) analysis of this ULOFt ransient is performed with the CATHARE2 code, which is the French reference system code for SFR applications. The objective of the BEPU analysis is twofold: first evaluate the safety margin to sodium boiling in taking into account the uncertainties on the input parameters of the CATHARE2 code (twenty-two uncertain input parameters have been identified, which can be classified into five groups: reactor power, accident management, pumps characteristics, reactivity coefficients, thermal parameters and head losses); secondly quantify the contribution of each input uncertainty to the overall uncertainty of the safety margins, in order to refocusing R&D efforts on the most influential factors. This paper focuses on the methodological aspects of the evaluation of the safety margin. At least for the preliminary phase of the project (conceptual design), a probabilistic criterion has been fixed in the context of this BEPU analysis; this criterion is the value of the margin to sodium boiling, which has a probability 95% to be exceeded, obtained with a confidence level of 95% (i.e. the M5,95percentile of the margin distribution). This paper presents two methods used to assess this percentile: the Wilks method and the Bootstrap method ; the effectiveness of the two methods is compared on the basis of 500 simulations performed with theCATHARE2 code. We conclude that, with only 100 simulations performed with the CATHARE2 code, which is a number of simulations workable in the conceptual design phase of the ASTRID project where the models and the hypothesis are often modified, it is best in order to evaluate the percentile M5,95 of the margin to sodium boiling to use the bootstrap method, which will provide a slightly conservative result. On the other hand, in order to obtain an accurate estimation of the percentileM5,95, for the safety report for example, it will be necessary to perform at least 300 simulations with the CATHARE2 code. In this case, both methods (Wilks and Bootstrap) would give equivalent results.

Reliability Modeling Methodology for Independent Approaches on Parallel Runways Safety Analysis

NASA Technical Reports Server (NTRS)

Babcock, P.; Schor, A.; Rosch, G.

1998-01-01

This document is an adjunct to the final report An Integrated Safety Analysis Methodology for Emerging Air Transport Technologies. That report presents the results of our analysis of the problem of simultaneous but independent, approaches of two aircraft on parallel runways (independent approaches on parallel runways, or IAPR). This introductory chapter presents a brief overview and perspective of approaches and methodologies for performing safety analyses for complex systems. Ensuing chapter provide the technical details that underlie the approach that we have taken in performing the safety analysis for the IAPR concept.

Interactive Parallel Data Analysis within Data-Centric Cluster Facilities using the IPython Notebook

NASA Astrophysics Data System (ADS)

Pascoe, S.; Lansdowne, J.; Iwi, A.; Stephens, A.; Kershaw, P.

2012-12-01

The data deluge is making traditional analysis workflows for many researchers obsolete. Support for parallelism within popular tools such as matlab, IDL and NCO is not well developed and rarely used. However parallelism is necessary for processing modern data volumes on a timescale conducive to curiosity-driven analysis. Furthermore, for peta-scale datasets such as the CMIP5 archive, it is no longer practical to bring an entire dataset to a researcher's workstation for analysis, or even to their institutional cluster. Therefore, there is an increasing need to develop new analysis platforms which both enable processing at the point of data storage and which provides parallelism. Such an environment should, where possible, maintain the convenience and familiarity of our current analysis environments to encourage curiosity-driven research. We describe how we are combining the interactive python shell (IPython) with our JASMIN data-cluster infrastructure. IPython has been specifically designed to bridge the gap between the HPC-style parallel workflows and the opportunistic curiosity-driven analysis usually carried out using domain specific languages and scriptable tools. IPython offers a web-based interactive environment, the IPython notebook, and a cluster engine for parallelism all underpinned by the well-respected Python/Scipy scientific programming stack. JASMIN is designed to support the data analysis requirements of the UK and European climate and earth system modeling community. JASMIN, with its sister facility CEMS focusing the earth observation community, has 4.5 PB of fast parallel disk storage alongside over 370 computing cores provide local computation. Through the IPython interface to JASMIN, users can make efficient use of JASMIN's multi-core virtual machines to perform interactive analysis on all cores simultaneously or can configure IPython clusters across multiple VMs. Larger-scale clusters can be provisioned through JASMIN's batch scheduling system. Outputs can be summarised and visualised using the full power of Python's many scientific tools, including Scipy, Matplotlib, Pandas and CDAT. This rich user experience is delivered through the user's web browser; maintaining the interactive feel of a workstation-based environment with the parallel power of a remote data-centric processing facility.

A simple, objective analysis scheme for scatterometer data. [Seasat A satellite observation of wind over ocean

NASA Technical Reports Server (NTRS)

Levy, G.; Brown, R. A.

1986-01-01

A simple economical objective analysis scheme is devised and tested on real scatterometer data. It is designed to treat dense data such as those of the Seasat A Satellite Scatterometer (SASS) for individual or multiple passes, and preserves subsynoptic scale features. Errors are evaluated with the aid of sampling ('bootstrap') statistical methods. In addition, sensitivity tests have been performed which establish qualitative confidence in calculated fields of divergence and vorticity. The SASS wind algorithm could be improved; however, the data at this point are limited by instrument errors rather than analysis errors. The analysis error is typically negligible in comparison with the instrument error, but amounts to 30 percent of the instrument error in areas of strong wind shear. The scheme is very economical, and thus suitable for large volumes of dense data such as SASS data.

Phylogenetic Analysis of Nuclear-Encoded RNA Maturases

PubMed Central

Malik, Sunita; Upadhyaya, KC; Khurana, SM Paul

2017-01-01

Posttranscriptional processes, such as splicing, play a crucial role in gene expression and are prevalent not only in nuclear genes but also in plant mitochondria where splicing of group II introns is catalyzed by a class of proteins termed maturases. In plant mitochondria, there are 22 mitochondrial group II introns. matR, nMAT1, nMAT2, nMAT3, and nMAT4 proteins have been shown to be required for efficient splicing of several group II introns in Arabidopsis thaliana. Nuclear maturases (nMATs) are necessary for splicing of mitochondrial genes, leading to normal oxidative phosphorylation. Sequence analysis through phylogenetic tree (including bootstrapping) revealed high homology with maturase sequences of A thaliana and other plants. This study shows the phylogenetic relationship of nMAT proteins between A thaliana and other nonredundant plant species taken from BLASTP analysis. PMID:28607538

Pitfalls in chronobiology: a suggested analysis using intrathecal bupivacaine analgesia as an example.

PubMed

Shafer, Steven L; Lemmer, Bjoern; Boselli, Emmanuel; Boiste, Fabienne; Bouvet, Lionel; Allaouchiche, Bernard; Chassard, Dominique

2010-10-01

The duration of analgesia from epidural administration of local anesthetics to parturients has been shown to follow a rhythmic pattern according to the time of drug administration. We studied whether there was a similar pattern after intrathecal administration of bupivacaine in parturients. In the course of the analysis, we came to believe that some data points coincident with provider shift changes were influenced by nonbiological, health care system factors, thus incorrectly suggesting a periodic signal in duration of labor analgesia. We developed graphical and analytical tools to help assess the influence of individual points on the chronobiological analysis. Women with singleton term pregnancies in vertex presentation, cervical dilation 3 to 5 cm, pain score >50 mm (of 100 mm), and requesting labor analgesia were enrolled in this study. Patients received 2.5 mg of intrathecal bupivacaine in 2 mL using a combined spinal-epidural technique. Analgesia duration was the time from intrathecal injection until the first request for additional analgesia. The duration of analgesia was analyzed by visual inspection of the data, application of smoothing functions (Supersmoother; LOWESS and LOESS [locally weighted scatterplot smoothing functions]), analysis of variance, Cosinor (Chronos-Fit), Excel, and NONMEM (nonlinear mixed effect modeling). Confidence intervals (CIs) were determined by bootstrap analysis (1000 replications with replacement) using PLT Tools. Eighty-two women were included in the study. Examination of the raw data using 3 smoothing functions revealed a bimodal pattern, with a peak at approximately 0630 and a subsequent peak in the afternoon or evening, depending on the smoother. Analysis of variance did not identify any statistically significant difference between the duration of analgesia when intrathecal injection was given from midnight to 0600 compared with the duration of analgesia after intrathecal injection at other times. Chronos-Fit, Excel, and NONMEM produced identical results, with a mean duration of analgesia of 38.4 minutes (95% CI: 35.4-41.6 minutes), an 8-hour periodic waveform with an amplitude of 5.8 minutes (95% CI: 2.1-10.7 minutes), and a phase offset of 6.5 hours (95% CI: 5.4-8.0 hours) relative to midnight. The 8-hour periodic model did not reach statistical significance in 40% of bootstrap analyses, implying that statistical significance of the 8-hour periodic model was dependent on a subset of the data. Two data points before the change of shift at 0700 contributed most strongly to the statistical significance of the periodic waveform. Without these data points, there was no evidence of an 8-hour periodic waveform for intrathecal bupivacaine analgesia. Chronobiology includes the influence of external daily rhythms in the environment (e.g., nursing shifts) as well as human biological rhythms. We were able to distinguish the influence of an external rhythm by combining several novel analyses: (1) graphical presentation superimposing the raw data, external rhythms (e.g., nursing and anesthesia provider shifts), and smoothing functions; (2) graphical display of the contribution of each data point to the statistical significance; and (3) bootstrap analysis to identify whether the statistical significance was highly dependent on a data subset. These approaches suggested that 2 data points were likely artifacts of the change in nursing and anesthesia shifts. When these points were removed, there was no suggestion of biological rhythm in the duration of intrathecal bupivacaine analgesia.

SOCIAL COMPETENCE AND PSYCHOLOGICAL VULNERABILITY: THE MEDIATING ROLE OF FLOURISHING.

PubMed

Uysal, Recep

2015-10-01

This study examined whether flourishing mediated the social competence and psychological vulnerability. Participants were 259 university students (147 women, 112 men; M age = 21.3 yr., SD = 1.7) who completed the Turkish versions of the Perceived Social Competence Scale, the Flourishing Scale, and the Psychological Vulnerability Scale. Mediation models were tested using the bootstrapping method to examine indirect effects. Consistent with the hypotheses, the results indicated a positive relationship between social competence and flourishing, and a negative relationship between social competence and psychological vulnerability. Results of the bootstrapping method revealed that flourishing significantly mediated the relationship between social competence and psychological vulnerability. The significance and limitations of the results were discussed.

Bootstrapping the O(N) archipelago

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kos, Filip; Poland, David; Simmons-Duffin, David

2015-11-17

We study 3d CFTs with an O(N) global symmetry using the conformal bootstrap for a system of mixed correlators. Specifically, we consider all nonvanishing scalar four-point functions containing the lowest dimension O(N) vector Φ i and the lowest dimension O(N) singlet s, assumed to be the only relevant operators in their symmetry representations. The constraints of crossing symmetry and unitarity for these four-point functions force the scaling dimensions (Δ Φ , Δ s ) to lie inside small islands. Here, we also make rigorous determinations of current two-point functions in the O(2) and O(3) models, with applications to transport inmore » condensed matter systems.« less

Assessment of predictive performance in incomplete data by combining internal validation and multiple imputation.

PubMed

Wahl, Simone; Boulesteix, Anne-Laure; Zierer, Astrid; Thorand, Barbara; van de Wiel, Mark A

2016-10-26

Missing values are a frequent issue in human studies. In many situations, multiple imputation (MI) is an appropriate missing data handling strategy, whereby missing values are imputed multiple times, the analysis is performed in every imputed data set, and the obtained estimates are pooled. If the aim is to estimate (added) predictive performance measures, such as (change in) the area under the receiver-operating characteristic curve (AUC), internal validation strategies become desirable in order to correct for optimism. It is not fully understood how internal validation should be combined with multiple imputation. In a comprehensive simulation study and in a real data set based on blood markers as predictors for mortality, we compare three combination strategies: Val-MI, internal validation followed by MI on the training and test parts separately, MI-Val, MI on the full data set followed by internal validation, and MI(-y)-Val, MI on the full data set omitting the outcome followed by internal validation. Different validation strategies, including bootstrap und cross-validation, different (added) performance measures, and various data characteristics are considered, and the strategies are evaluated with regard to bias and mean squared error of the obtained performance estimates. In addition, we elaborate on the number of resamples and imputations to be used, and adopt a strategy for confidence interval construction to incomplete data. Internal validation is essential in order to avoid optimism, with the bootstrap 0.632+ estimate representing a reliable method to correct for optimism. While estimates obtained by MI-Val are optimistically biased, those obtained by MI(-y)-Val tend to be pessimistic in the presence of a true underlying effect. Val-MI provides largely unbiased estimates, with a slight pessimistic bias with increasing true effect size, number of covariates and decreasing sample size. In Val-MI, accuracy of the estimate is more strongly improved by increasing the number of bootstrap draws rather than the number of imputations. With a simple integrated approach, valid confidence intervals for performance estimates can be obtained. When prognostic models are developed on incomplete data, Val-MI represents a valid strategy to obtain estimates of predictive performance measures.

The impact of foreign direct investment on CO2 emissions in Turkey: new evidence from cointegration and bootstrap causality analysis.

PubMed

Koçak, Emrah; Şarkgüneşi, Aykut

2018-01-01

Pollution haven hypothesis (PHH), which is defined as foreign direct investment inducing a raising impact on the pollution level in the hosting country, is lately a subject of discussion in the field of economics. This study, within the scope of related discussion, aims to look into the potential impact of foreign direct investments on CO 2 emission in Turkey in 1974-2013 period using environmental Kuznets curve (EKC) model. For this purpose, Maki (Econ Model 29(5):2011-2015, 2012) structural break cointegration test, Stock and Watson (Econometrica 61:783-820, 1993) dynamic ordinary least square estimator (DOLS), and Hacker and Hatemi-J (J Econ Stud 39(2):144-160, 2012) bootstrap test for causality method are used. Research results indicate the existence of a long-term balance relationship between FDI, economic growth, energy usage, and CO 2 emission. As per this relationship, in Turkey, (1) the potential impact of FDI on CO 2 emission is positive. This result shows that PHH is valid in Turkey. (2) Moreover, this is not a one-way relationship; the changes in CO 2 emission also affect FDI entries. (3) The results also provide evidence for the existence of the EKC hypothesis in Turkey. Within the frame of related findings, the study concludes several polities and presents various suggestions.

Practical no-gold-standard evaluation framework for quantitative imaging methods: application to lesion segmentation in positron emission tomography

PubMed Central

Jha, Abhinav K.; Mena, Esther; Caffo, Brian; Ashrafinia, Saeed; Rahmim, Arman; Frey, Eric; Subramaniam, Rathan M.

2017-01-01

Abstract. Recently, a class of no-gold-standard (NGS) techniques have been proposed to evaluate quantitative imaging methods using patient data. These techniques provide figures of merit (FoMs) quantifying the precision of the estimated quantitative value without requiring repeated measurements and without requiring a gold standard. However, applying these techniques to patient data presents several practical difficulties including assessing the underlying assumptions, accounting for patient-sampling-related uncertainty, and assessing the reliability of the estimated FoMs. To address these issues, we propose statistical tests that provide confidence in the underlying assumptions and in the reliability of the estimated FoMs. Furthermore, the NGS technique is integrated within a bootstrap-based methodology to account for patient-sampling-related uncertainty. The developed NGS framework was applied to evaluate four methods for segmenting lesions from F-Fluoro-2-deoxyglucose positron emission tomography images of patients with head-and-neck cancer on the task of precisely measuring the metabolic tumor volume. The NGS technique consistently predicted the same segmentation method as the most precise method. The proposed framework provided confidence in these results, even when gold-standard data were not available. The bootstrap-based methodology indicated improved performance of the NGS technique with larger numbers of patient studies, as was expected, and yielded consistent results as long as data from more than 80 lesions were available for the analysis. PMID:28331883