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Sample records for regression analyses compared

  1. Contesting Citizenship: Comparative Analyses

    DEFF Research Database (Denmark)

    Siim, Birte; Squires, Judith

    2007-01-01

    importance of particularized experiences and multiple ineequality agendas). These developments shape the way citizenship is both practiced and analysed. Mapping neat citizenship modles onto distinct nation-states and evaluating these in relation to formal equality is no longer an adequate approach....... Comparative citizenship analyses need to be considered in relation to multipleinequalities and their intersections and to multiple governance and trans-national organisinf. This, in turn, suggests that comparative citizenship analysis needs to consider new spaces in which struggles for equal citizenship occur...

  2. Analysing and Comparing Encodability Criteria

    Directory of Open Access Journals (Sweden)

    Kirstin Peters

    2015-08-01

    Full Text Available Encodings or the proof of their absence are the main way to compare process calculi. To analyse the quality of encodings and to rule out trivial or meaningless encodings, they are augmented with quality criteria. There exists a bunch of different criteria and different variants of criteria in order to reason in different settings. This leads to incomparable results. Moreover it is not always clear whether the criteria used to obtain a result in a particular setting do indeed fit to this setting. We show how to formally reason about and compare encodability criteria by mapping them on requirements on a relation between source and target terms that is induced by the encoding function. In particular we analyse the common criteria full abstraction, operational correspondence, divergence reflection, success sensitiveness, and respect of barbs; e.g. we analyse the exact nature of the simulation relation (coupled simulation versus bisimulation that is induced by different variants of operational correspondence. This way we reduce the problem of analysing or comparing encodability criteria to the better understood problem of comparing relations on processes.

  3. Statistical power analyses using G*Power 3.1: tests for correlation and regression analyses.

    Science.gov (United States)

    Faul, Franz; Erdfelder, Edgar; Buchner, Axel; Lang, Albert-Georg

    2009-11-01

    G*Power is a free power analysis program for a variety of statistical tests. We present extensions and improvements of the version introduced by Faul, Erdfelder, Lang, and Buchner (2007) in the domain of correlation and regression analyses. In the new version, we have added procedures to analyze the power of tests based on (1) single-sample tetrachoric correlations, (2) comparisons of dependent correlations, (3) bivariate linear regression, (4) multiple linear regression based on the random predictor model, (5) logistic regression, and (6) Poisson regression. We describe these new features and provide a brief introduction to their scope and handling.

  4. Comparing parametric and nonparametric regression methods for panel data

    DEFF Research Database (Denmark)

    Czekaj, Tomasz Gerard; Henningsen, Arne

    We investigate and compare the suitability of parametric and non-parametric stochastic regression methods for analysing production technologies and the optimal firm size. Our theoretical analysis shows that the most commonly used functional forms in empirical production analysis, Cobb......-Douglas and Translog, are unsuitable for analysing the optimal firm size. We show that the Translog functional form implies an implausible linear relationship between the (logarithmic) firm size and the elasticity of scale, where the slope is artificially related to the substitutability between the inputs....... The practical applicability of the parametric and non-parametric regression methods is scrutinised and compared by an empirical example: we analyse the production technology and investigate the optimal size of Polish crop farms based on a firm-level balanced panel data set. A nonparametric specification test...

  5. Applications of MIDAS regression in analysing trends in water quality

    Science.gov (United States)

    Penev, Spiridon; Leonte, Daniela; Lazarov, Zdravetz; Mann, Rob A.

    2014-04-01

    We discuss novel statistical methods in analysing trends in water quality. Such analysis uses complex data sets of different classes of variables, including water quality, hydrological and meteorological. We analyse the effect of rainfall and flow on trends in water quality utilising a flexible model called Mixed Data Sampling (MIDAS). This model arises because of the mixed frequency in the data collection. Typically, water quality variables are sampled fortnightly, whereas the rain data is sampled daily. The advantage of using MIDAS regression is in the flexible and parsimonious modelling of the influence of the rain and flow on trends in water quality variables. We discuss the model and its implementation on a data set from the Shoalhaven Supply System and Catchments in the state of New South Wales, Australia. Information criteria indicate that MIDAS modelling improves upon simplistic approaches that do not utilise the mixed data sampling nature of the data.

  6. Multicollinearity in Regression Analyses Conducted in Epidemiologic Studies.

    Science.gov (United States)

    Vatcheva, Kristina P; Lee, MinJae; McCormick, Joseph B; Rahbar, Mohammad H

    2016-04-01

    The adverse impact of ignoring multicollinearity on findings and data interpretation in regression analysis is very well documented in the statistical literature. The failure to identify and report multicollinearity could result in misleading interpretations of the results. A review of epidemiological literature in PubMed from January 2004 to December 2013, illustrated the need for a greater attention to identifying and minimizing the effect of multicollinearity in analysis of data from epidemiologic studies. We used simulated datasets and real life data from the Cameron County Hispanic Cohort to demonstrate the adverse effects of multicollinearity in the regression analysis and encourage researchers to consider the diagnostic for multicollinearity as one of the steps in regression analysis.

  7. Statistical and regression analyses of detected extrasolar systems

    Czech Academy of Sciences Publication Activity Database

    Pintr, Pavel; Peřinová, V.; Lukš, A.; Pathak, A.

    2013-01-01

    Roč. 75, č. 1 (2013), s. 37-45 ISSN 0032-0633 Institutional support: RVO:61389021 Keywords : Exoplanets * Kepler candidates * Regression analysis Subject RIV: BN - Astronomy, Celestial Mechanics, Astrophysics Impact factor: 1.630, year: 2013 http://www.sciencedirect.com/science/article/pii/S0032063312003066

  8. Multicollinearity in Regression Analyses Conducted in Epidemiologic Studies

    OpenAIRE

    Vatcheva, Kristina P.; Lee, MinJae; McCormick, Joseph B.; Rahbar, Mohammad H.

    2016-01-01

    The adverse impact of ignoring multicollinearity on findings and data interpretation in regression analysis is very well documented in the statistical literature. The failure to identify and report multicollinearity could result in misleading interpretations of the results. A review of epidemiological literature in PubMed from January 2004 to December 2013, illustrated the need for a greater attention to identifying and minimizing the effect of multicollinearity in analysis of data from epide...

  9. Analysing inequalities in Germany a structured additive distributional regression approach

    CERN Document Server

    Silbersdorff, Alexander

    2017-01-01

    This book seeks new perspectives on the growing inequalities that our societies face, putting forward Structured Additive Distributional Regression as a means of statistical analysis that circumvents the common problem of analytical reduction to simple point estimators. This new approach allows the observed discrepancy between the individuals’ realities and the abstract representation of those realities to be explicitly taken into consideration using the arithmetic mean alone. In turn, the method is applied to the question of economic inequality in Germany.

  10. How to deal with continuous and dichotomic outcomes in epidemiological research: linear and logistic regression analyses

    NARCIS (Netherlands)

    Tripepi, Giovanni; Jager, Kitty J.; Stel, Vianda S.; Dekker, Friedo W.; Zoccali, Carmine

    2011-01-01

    Because of some limitations of stratification methods, epidemiologists frequently use multiple linear and logistic regression analyses to address specific epidemiological questions. If the dependent variable is a continuous one (for example, systolic pressure and serum creatinine), the researcher

  11. A Powerful Test for Comparing Multiple Regression Functions.

    Science.gov (United States)

    Maity, Arnab

    2012-09-01

    In this article, we address the important problem of comparison of two or more population regression functions. Recently, Pardo-Fernández, Van Keilegom and González-Manteiga (2007) developed test statistics for simple nonparametric regression models: Y(ij) = θ(j)(Z(ij)) + σ(j)(Z(ij))∊(ij), based on empirical distributions of the errors in each population j = 1, … , J. In this paper, we propose a test for equality of the θ(j)(·) based on the concept of generalized likelihood ratio type statistics. We also generalize our test for other nonparametric regression setups, e.g, nonparametric logistic regression, where the loglikelihood for population j is any general smooth function [Formula: see text]. We describe a resampling procedure to obtain the critical values of the test. In addition, we present a simulation study to evaluate the performance of the proposed test and compare our results to those in Pardo-Fernández et al. (2007).

  12. Comparing spatial regression to random forests for large ...

    Science.gov (United States)

    Environmental data may be “large” due to number of records, number of covariates, or both. Random forests has a reputation for good predictive performance when using many covariates, whereas spatial regression, when using reduced rank methods, has a reputation for good predictive performance when using many records. In this study, we compare these two techniques using a data set containing the macroinvertebrate multimetric index (MMI) at 1859 stream sites with over 200 landscape covariates. Our primary goal is predicting MMI at over 1.1 million perennial stream reaches across the USA. For spatial regression modeling, we develop two new methods to accommodate large data: (1) a procedure that estimates optimal Box-Cox transformations to linearize covariate relationships; and (2) a computationally efficient covariate selection routine that takes into account spatial autocorrelation. We show that our new methods lead to cross-validated performance similar to random forests, but that there is an advantage for spatial regression when quantifying the uncertainty of the predictions. Simulations are used to clarify advantages for each method. This research investigates different approaches for modeling and mapping national stream condition. We use MMI data from the EPA's National Rivers and Streams Assessment and predictors from StreamCat (Hill et al., 2015). Previous studies have focused on modeling the MMI condition classes (i.e., good, fair, and po

  13. Tridimensional Regression for Comparing and Mapping 3D Anatomical Structures

    Directory of Open Access Journals (Sweden)

    Kendra K. Schmid

    2012-01-01

    Full Text Available Shape analysis is useful for a wide variety of disciplines and has many applications. There are many approaches to shape analysis, one of which focuses on the analysis of shapes that are represented by the coordinates of predefined landmarks on the object. This paper discusses Tridimensional Regression, a technique that can be used for mapping images and shapes that are represented by sets of three-dimensional landmark coordinates, for comparing and mapping 3D anatomical structures. The degree of similarity between shapes can be quantified using the tridimensional coefficient of determination (2. An experiment was conducted to evaluate the effectiveness of this technique to correctly match the image of a face with another image of the same face. These results were compared to the 2 values obtained when only two dimensions are used and show that using three dimensions increases the ability to correctly match and discriminate between faces.

  14. Genetic analyses of partial egg production in Japanese quail using multi-trait random regression models.

    Science.gov (United States)

    Karami, K; Zerehdaran, S; Barzanooni, B; Lotfi, E

    2017-12-01

    1. The aim of the present study was to estimate genetic parameters for average egg weight (EW) and egg number (EN) at different ages in Japanese quail using multi-trait random regression (MTRR) models. 2. A total of 8534 records from 900 quail, hatched between 2014 and 2015, were used in the study. Average weekly egg weights and egg numbers were measured from second until sixth week of egg production. 3. Nine random regression models were compared to identify the best order of the Legendre polynomials (LP). The most optimal model was identified by the Bayesian Information Criterion. A model with second order of LP for fixed effects, second order of LP for additive genetic effects and third order of LP for permanent environmental effects (MTRR23) was found to be the best. 4. According to the MTRR23 model, direct heritability for EW increased from 0.26 in the second week to 0.53 in the sixth week of egg production, whereas the ratio of permanent environment to phenotypic variance decreased from 0.48 to 0.1. Direct heritability for EN was low, whereas the ratio of permanent environment to phenotypic variance decreased from 0.57 to 0.15 during the production period. 5. For each trait, estimated genetic correlations among weeks of egg production were high (from 0.85 to 0.98). Genetic correlations between EW and EN were low and negative for the first two weeks, but they were low and positive for the rest of the egg production period. 6. In conclusion, random regression models can be used effectively for analysing egg production traits in Japanese quail. Response to selection for increased egg weight would be higher at older ages because of its higher heritability and such a breeding program would have no negative genetic impact on egg production.

  15. USE OF THE SIMPLE LINEAR REGRESSION MODEL IN MACRO-ECONOMICAL ANALYSES

    Directory of Open Access Journals (Sweden)

    Constantin ANGHELACHE

    2011-10-01

    Full Text Available The article presents the fundamental aspects of the linear regression, as a toolbox which can be used in macroeconomic analyses. The article describes the estimation of the parameters, the statistical tests used, the homoscesasticity and heteroskedasticity. The use of econometrics instrument in macroeconomics is an important factor that guarantees the quality of the models, analyses, results and possible interpretation that can be drawn at this level.

  16. A comparative study of multiple regression analysis and back ...

    Indian Academy of Sciences (India)

    Abhijit Sarkar

    artificial neural network (ANN) models to predict weld bead geometry and HAZ width in submerged arc welding ... Keywords. Submerged arc welding (SAW); multi-regression analysis (MRA); artificial neural network ..... Degree of freedom.

  17. Comparative sequence analyses of genome and transcriptome ...

    Indian Academy of Sciences (India)

    2015-12-04

    Dec 4, 2015 ... 2011), unique vocal communication. (Payne 2003; Nair et al. ... induction of apoptosis when compared to human cells. In this study, we have .... based on calculated Pearson correlation and displayed based on centroid of the ...

  18. Comparative analyses of bidirectional promoters in vertebrates

    Directory of Open Access Journals (Sweden)

    Taylor James

    2008-05-01

    Full Text Available Abstract Background Orthologous genes with deep phylogenetic histories are likely to retain similar regulatory features. In this report we utilize orthology assignments for pairs of genes co-regulated by bidirectional promoters to map the ancestral history of the promoter regions. Results Our mapping of bidirectional promoters from humans to fish shows that many such promoters emerged after the divergence of chickens and fish. Furthermore, annotations of promoters in deep phylogenies enable detection of missing data or assembly problems present in higher vertebrates. The functional importance of bidirectional promoters is indicated by selective pressure to maintain the arrangement of genes regulated by the promoter over long evolutionary time spans. Characteristics unique to bidirectional promoters are further elucidated using a technique for unsupervised classification, known as ESPERR. Conclusion Results of these analyses will aid in our understanding of the evolution of bidirectional promoters, including whether the regulation of two genes evolved as a consequence of their proximity or if function dictated their co-regulation.

  19. International comparative analyses of healthcare risk management.

    Science.gov (United States)

    Sun, Niuyun; Wang, Li; Zhou, Jun; Yuan, Qiang; Zhang, Zongjiu; Li, Youping; Liang, Minghui; Cheng, Lan; Gao, Guangming; Cui, Xiaohui

    2011-02-01

    Interpretation of the growing body of global literature on health care risk is compromised by a lack of common understanding and language. This series of articles aims to comprehensively compare laws and regulations, institutional management, and administration of incidence reporting systems on medical risk management in the United Kingdom, the United States, Canada, Australia, and Taiwan, so as to provide evidence and recommendations for health care risk management policy in China. We searched the official websites of the healthcare risk management agencies of the four countries and one district for laws, regulatory documents, research reports, reviews and evaluation forms concerned with healthcare risk management and assessment. Descriptive comparative analysis was performed on relevant documents. A total of 146 documents were included in this study, including 2 laws (1.4%), 17 policy documents (11.6%), 41 guidance documents (28.1%), 37 reviews (25.3%), and 49 documents giving general information (33.6%). The United States government implemented one law and one rule of patient safety management, while the United Kingdom and Australia each issued professional guidances on patient safety improvement. The four countries implemented patient safety management policy on four different levels: national, state/province, hospital, and non-governmental organization. The four countries and one district adopted four levels of patient safety management, and the administration modes can be divided into an "NGO-led mode" represented by the United States and Canada and a "government-led mode" represented by the United Kingdom, Australia, and Taiwan. © 2011 Blackwell Publishing Asia Pty Ltd and Chinese Cochrane Center, West China Hospital of Sichuan University.

  20. Reducing Inter-Laboratory Differences between Semen Analyses Using Z Score and Regression Transformations

    Directory of Open Access Journals (Sweden)

    Esther Leushuis

    2016-12-01

    Full Text Available Background: Standardization of the semen analysis may improve reproducibility. We assessed variability between laboratories in semen analyses and evaluated whether a transformation using Z scores and regression statistics was able to reduce this variability. Materials and Methods: We performed a retrospective cohort study. We calculated between-laboratory coefficients of variation (CVB for sperm concentration and for morphology. Subsequently, we standardized the semen analysis results by calculating laboratory specific Z scores, and by using regression. We used analysis of variance for four semen parameters to assess systematic differences between laboratories before and after the transformations, both in the circulation samples and in the samples obtained in the prospective cohort study in the Netherlands between January 2002 and February 2004. Results: The mean CVB was 7% for sperm concentration (range 3 to 13% and 32% for sperm morphology (range 18 to 51%. The differences between the laboratories were statistically significant for all semen parameters (all P<0.001. Standardization using Z scores did not reduce the differences in semen analysis results between the laboratories (all P<0.001. Conclusion: There exists large between-laboratory variability for sperm morphology and small, but statistically significant, between-laboratory variation for sperm concentration. Standardization using Z scores does not eliminate between-laboratory variability.

  1. Correcting for multivariate measurement error by regression calibration in meta-analyses of epidemiological studies

    DEFF Research Database (Denmark)

    Tybjærg-Hansen, Anne

    2009-01-01

    Within-person variability in measured values of multiple risk factors can bias their associations with disease. The multivariate regression calibration (RC) approach can correct for such measurement error and has been applied to studies in which true values or independent repeat measurements...... of the risk factors are observed on a subsample. We extend the multivariate RC techniques to a meta-analysis framework where multiple studies provide independent repeat measurements and information on disease outcome. We consider the cases where some or all studies have repeat measurements, and compare study......-specific, averaged and empirical Bayes estimates of RC parameters. Additionally, we allow for binary covariates (e.g. smoking status) and for uncertainty and time trends in the measurement error corrections. Our methods are illustrated using a subset of individual participant data from prospective long-term studies...

  2. Logistic regression and multiple classification analyses to explore risk factors of under-5 mortality in bangladesh

    International Nuclear Information System (INIS)

    Bhowmik, K.R.; Islam, S.

    2016-01-01

    Logistic regression (LR) analysis is the most common statistical methodology to find out the determinants of childhood mortality. However, the significant predictors cannot be ranked according to their influence on the response variable. Multiple classification (MC) analysis can be applied to identify the significant predictors with a priority index which helps to rank the predictors. The main objective of the study is to find the socio-demographic determinants of childhood mortality at neonatal, post-neonatal, and post-infant period by fitting LR model as well as to rank those through MC analysis. The study is conducted using the data of Bangladesh Demographic and Health Survey 2007 where birth and death information of children were collected from their mothers. Three dichotomous response variables are constructed from children age at death to fit the LR and MC models. Socio-economic and demographic variables significantly associated with the response variables separately are considered in LR and MC analyses. Both the LR and MC models identified the same significant predictors for specific childhood mortality. For both the neonatal and child mortality, biological factors of children, regional settings, and parents socio-economic status are found as 1st, 2nd, and 3rd significant groups of predictors respectively. Mother education and household environment are detected as major significant predictors of post-neonatal mortality. This study shows that MC analysis with or without LR analysis can be applied to detect determinants with rank which help the policy makers taking initiatives on a priority basis. (author)

  3. A Monte Carlo simulation study comparing linear regression, beta regression, variable-dispersion beta regression and fractional logit regression at recovering average difference measures in a two sample design.

    Science.gov (United States)

    Meaney, Christopher; Moineddin, Rahim

    2014-01-24

    In biomedical research, response variables are often encountered which have bounded support on the open unit interval--(0,1). Traditionally, researchers have attempted to estimate covariate effects on these types of response data using linear regression. Alternative modelling strategies may include: beta regression, variable-dispersion beta regression, and fractional logit regression models. This study employs a Monte Carlo simulation design to compare the statistical properties of the linear regression model to that of the more novel beta regression, variable-dispersion beta regression, and fractional logit regression models. In the Monte Carlo experiment we assume a simple two sample design. We assume observations are realizations of independent draws from their respective probability models. The randomly simulated draws from the various probability models are chosen to emulate average proportion/percentage/rate differences of pre-specified magnitudes. Following simulation of the experimental data we estimate average proportion/percentage/rate differences. We compare the estimators in terms of bias, variance, type-1 error and power. Estimates of Monte Carlo error associated with these quantities are provided. If response data are beta distributed with constant dispersion parameters across the two samples, then all models are unbiased and have reasonable type-1 error rates and power profiles. If the response data in the two samples have different dispersion parameters, then the simple beta regression model is biased. When the sample size is small (N0 = N1 = 25) linear regression has superior type-1 error rates compared to the other models. Small sample type-1 error rates can be improved in beta regression models using bias correction/reduction methods. In the power experiments, variable-dispersion beta regression and fractional logit regression models have slightly elevated power compared to linear regression models. Similar results were observed if the

  4. Antibiotic Resistances in Livestock: A Comparative Approach to Identify an Appropriate Regression Model for Count Data

    Directory of Open Access Journals (Sweden)

    Anke Hüls

    2017-05-01

    Full Text Available Antimicrobial resistance in livestock is a matter of general concern. To develop hygiene measures and methods for resistance prevention and control, epidemiological studies on a population level are needed to detect factors associated with antimicrobial resistance in livestock holdings. In general, regression models are used to describe these relationships between environmental factors and resistance outcome. Besides the study design, the correlation structures of the different outcomes of antibiotic resistance and structural zero measurements on the resistance outcome as well as on the exposure side are challenges for the epidemiological model building process. The use of appropriate regression models that acknowledge these complexities is essential to assure valid epidemiological interpretations. The aims of this paper are (i to explain the model building process comparing several competing models for count data (negative binomial model, quasi-Poisson model, zero-inflated model, and hurdle model and (ii to compare these models using data from a cross-sectional study on antibiotic resistance in animal husbandry. These goals are essential to evaluate which model is most suitable to identify potential prevention measures. The dataset used as an example in our analyses was generated initially to study the prevalence and associated factors for the appearance of cefotaxime-resistant Escherichia coli in 48 German fattening pig farms. For each farm, the outcome was the count of samples with resistant bacteria. There was almost no overdispersion and only moderate evidence of excess zeros in the data. Our analyses show that it is essential to evaluate regression models in studies analyzing the relationship between environmental factors and antibiotic resistances in livestock. After model comparison based on evaluation of model predictions, Akaike information criterion, and Pearson residuals, here the hurdle model was judged to be the most appropriate

  5. Easy methods for extracting individual regression slopes: Comparing SPSS, R, and Excel

    Directory of Open Access Journals (Sweden)

    Roland Pfister

    2013-10-01

    Full Text Available Three different methods for extracting coefficientsof linear regression analyses are presented. The focus is on automatic and easy-to-use approaches for common statistical packages: SPSS, R, and MS Excel / LibreOffice Calc. Hands-on examples are included for each analysis, followed by a brief description of how a subsequent regression coefficient analysis is performed.

  6. The number of subjects per variable required in linear regression analyses

    NARCIS (Netherlands)

    P.C. Austin (Peter); E.W. Steyerberg (Ewout)

    2015-01-01

    textabstractObjectives To determine the number of independent variables that can be included in a linear regression model. Study Design and Setting We used a series of Monte Carlo simulations to examine the impact of the number of subjects per variable (SPV) on the accuracy of estimated regression

  7. The number of subjects per variable required in linear regression analyses.

    Science.gov (United States)

    Austin, Peter C; Steyerberg, Ewout W

    2015-06-01

    To determine the number of independent variables that can be included in a linear regression model. We used a series of Monte Carlo simulations to examine the impact of the number of subjects per variable (SPV) on the accuracy of estimated regression coefficients and standard errors, on the empirical coverage of estimated confidence intervals, and on the accuracy of the estimated R(2) of the fitted model. A minimum of approximately two SPV tended to result in estimation of regression coefficients with relative bias of less than 10%. Furthermore, with this minimum number of SPV, the standard errors of the regression coefficients were accurately estimated and estimated confidence intervals had approximately the advertised coverage rates. A much higher number of SPV were necessary to minimize bias in estimating the model R(2), although adjusted R(2) estimates behaved well. The bias in estimating the model R(2) statistic was inversely proportional to the magnitude of the proportion of variation explained by the population regression model. Linear regression models require only two SPV for adequate estimation of regression coefficients, standard errors, and confidence intervals. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  8. Correcting for multivariate measurement error by regression calibration in meta-analyses of epidemiological studies.

    NARCIS (Netherlands)

    Kromhout, D.

    2009-01-01

    Within-person variability in measured values of multiple risk factors can bias their associations with disease. The multivariate regression calibration (RC) approach can correct for such measurement error and has been applied to studies in which true values or independent repeat measurements of the

  9. Testing Mediation Using Multiple Regression and Structural Equation Modeling Analyses in Secondary Data

    Science.gov (United States)

    Li, Spencer D.

    2011-01-01

    Mediation analysis in child and adolescent development research is possible using large secondary data sets. This article provides an overview of two statistical methods commonly used to test mediated effects in secondary analysis: multiple regression and structural equation modeling (SEM). Two empirical studies are presented to illustrate the…

  10. Regression Analyses on the Butterfly Ballot Effect: A Statistical Perspective of the US 2000 Election

    Science.gov (United States)

    Wu, Dane W.

    2002-01-01

    The year 2000 US presidential election between Al Gore and George Bush has been the most intriguing and controversial one in American history. The state of Florida was the trigger for the controversy, mainly, due to the use of the misleading "butterfly ballot". Using prediction (or confidence) intervals for least squares regression lines…

  11. Alpins and thibos vectorial astigmatism analyses: proposal of a linear regression model between methods

    Directory of Open Access Journals (Sweden)

    Giuliano de Oliveira Freitas

    2013-10-01

    Full Text Available PURPOSE: To determine linear regression models between Alpins descriptive indices and Thibos astigmatic power vectors (APV, assessing the validity and strength of such correlations. METHODS: This case series prospectively assessed 62 eyes of 31 consecutive cataract patients with preoperative corneal astigmatism between 0.75 and 2.50 diopters in both eyes. Patients were randomly assorted among two phacoemulsification groups: one assigned to receive AcrySof®Toric intraocular lens (IOL in both eyes and another assigned to have AcrySof Natural IOL associated with limbal relaxing incisions, also in both eyes. All patients were reevaluated postoperatively at 6 months, when refractive astigmatism analysis was performed using both Alpins and Thibos methods. The ratio between Thibos postoperative APV and preoperative APV (APVratio and its linear regression to Alpins percentage of success of astigmatic surgery, percentage of astigmatism corrected and percentage of astigmatism reduction at the intended axis were assessed. RESULTS: Significant negative correlation between the ratio of post- and preoperative Thibos APVratio and Alpins percentage of success (%Success was found (Spearman's ρ=-0.93; linear regression is given by the following equation: %Success = (-APVratio + 1.00x100. CONCLUSION: The linear regression we found between APVratio and %Success permits a validated mathematical inference concerning the overall success of astigmatic surgery.

  12. Duloxetine compared with fluoxetine and venlafaxine: use of meta-regression analysis for indirect comparisons

    Directory of Open Access Journals (Sweden)

    Lançon Christophe

    2006-07-01

    Full Text Available Abstract Background Data comparing duloxetine with existing antidepressant treatments is limited. A comparison of duloxetine with fluoxetine has been performed but no comparison with venlafaxine, the other antidepressant in the same therapeutic class with a significant market share, has been undertaken. In the absence of relevant data to assess the place that duloxetine should occupy in the therapeutic arsenal, indirect comparisons are the most rigorous way to go. We conducted a systematic review of the efficacy of duloxetine, fluoxetine and venlafaxine versus placebo in the treatment of Major Depressive Disorder (MDD, and performed indirect comparisons through meta-regressions. Methods The bibliography of the Agency for Health Care Policy and Research and the CENTRAL, Medline, and Embase databases were interrogated using advanced search strategies based on a combination of text and index terms. The search focused on randomized placebo-controlled clinical trials involving adult patients treated for acute phase Major Depressive Disorder. All outcomes were derived to take account for varying placebo responses throughout studies. Primary outcome was treatment efficacy as measured by Hedge's g effect size. Secondary outcomes were response and dropout rates as measured by log odds ratios. Meta-regressions were run to indirectly compare the drugs. Sensitivity analysis, assessing the influence of individual studies over the results, and the influence of patients' characteristics were run. Results 22 studies involving fluoxetine, 9 involving duloxetine and 8 involving venlafaxine were selected. Using indirect comparison methodology, estimated effect sizes for efficacy compared with duloxetine were 0.11 [-0.14;0.36] for fluoxetine and 0.22 [0.06;0.38] for venlafaxine. Response log odds ratios were -0.21 [-0.44;0.03], 0.70 [0.26;1.14]. Dropout log odds ratios were -0.02 [-0.33;0.29], 0.21 [-0.13;0.55]. Sensitivity analyses showed that results were

  13. Check-all-that-apply data analysed by Partial Least Squares regression

    DEFF Research Database (Denmark)

    Rinnan, Åsmund; Giacalone, Davide; Frøst, Michael Bom

    2015-01-01

    are analysed by multivariate techniques. CATA data can be analysed both by setting the CATA as the X and the Y. The former is the PLS-Discriminant Analysis (PLS-DA) version, while the latter is the ANOVA-PLS (A-PLS) version. We investigated the difference between these two approaches, concluding...

  14. Differential item functioning (DIF) analyses of health-related quality of life instruments using logistic regression

    DEFF Research Database (Denmark)

    Scott, Neil W; Fayers, Peter M; Aaronson, Neil K

    2010-01-01

    Differential item functioning (DIF) methods can be used to determine whether different subgroups respond differently to particular items within a health-related quality of life (HRQoL) subscale, after allowing for overall subgroup differences in that scale. This article reviews issues that arise ...... when testing for DIF in HRQoL instruments. We focus on logistic regression methods, which are often used because of their efficiency, simplicity and ease of application....

  15. Analyses of Developmental Rate Isomorphy in Ectotherms: Introducing the Dirichlet Regression.

    Directory of Open Access Journals (Sweden)

    David S Boukal

    Full Text Available Temperature drives development in insects and other ectotherms because their metabolic rate and growth depends directly on thermal conditions. However, relative durations of successive ontogenetic stages often remain nearly constant across a substantial range of temperatures. This pattern, termed 'developmental rate isomorphy' (DRI in insects, appears to be widespread and reported departures from DRI are generally very small. We show that these conclusions may be due to the caveats hidden in the statistical methods currently used to study DRI. Because the DRI concept is inherently based on proportional data, we propose that Dirichlet regression applied to individual-level data is an appropriate statistical method to critically assess DRI. As a case study we analyze data on five aquatic and four terrestrial insect species. We find that results obtained by Dirichlet regression are consistent with DRI violation in at least eight of the studied species, although standard analysis detects significant departure from DRI in only four of them. Moreover, the departures from DRI detected by Dirichlet regression are consistently much larger than previously reported. The proposed framework can also be used to infer whether observed departures from DRI reflect life history adaptations to size- or stage-dependent effects of varying temperature. Our results indicate that the concept of DRI in insects and other ectotherms should be critically re-evaluated and put in a wider context, including the concept of 'equiproportional development' developed for copepods.

  16. Correlation and regression analyses of genetic effects for different types of cells in mammals under radiation and chemical treatment

    International Nuclear Information System (INIS)

    Slutskaya, N.G.; Mosseh, I.B.

    2006-01-01

    Data about genetic mutations under radiation and chemical treatment for different types of cells have been analyzed with correlation and regression analyses. Linear correlation between different genetic effects in sex cells and somatic cells have found. The results may be extrapolated on sex cells of human and mammals. (authors)

  17. Analyses of karyotypes and comparative physical locations of the ...

    African Journals Online (AJOL)

    The frequencies of signal detection of the marker, RG556 and the BAC clone, 44B4, were 8.0 and 41.3% in O. sativa, while 9.0 and 42.3% in O. officinalis, respectively. Based on a comparative RFLP map of a wild rice, O. officinalis and O. sativa, comparative analyses of karyotypes of O. officinalis were demonstrated firstly ...

  18. Comparing Methodologies for Developing an Early Warning System: Classification and Regression Tree Model versus Logistic Regression. REL 2015-077

    Science.gov (United States)

    Koon, Sharon; Petscher, Yaacov

    2015-01-01

    The purpose of this report was to explicate the use of logistic regression and classification and regression tree (CART) analysis in the development of early warning systems. It was motivated by state education leaders' interest in maintaining high classification accuracy while simultaneously improving practitioner understanding of the rules by…

  19. Is the perceived placebo effect comparable between adults and children? A meta-regression analysis.

    Science.gov (United States)

    Janiaud, Perrine; Cornu, Catherine; Lajoinie, Audrey; Djemli, Amina; Cucherat, Michel; Kassai, Behrouz

    2017-01-01

    A potential larger perceived placebo effect in children compared with adults could influence the detection of the treatment effect and the extrapolation of the treatment benefit from adults to children. This study aims to explore this potential difference, using a meta-epidemiological approach. A systematic review of the literature was done to identify trials included in meta-analyses evaluating a drug intervention with separate data for adults and children. The standardized mean change and the proportion of responders (binary outcomes) were used to calculate the perceived placebo effect. A meta-regression analysis was conducted to test for the difference between adults and children of the perceived placebo effect. For binary outcomes, the perceived placebo effect was significantly more favorable in children compared with adults (β = 0.13; P = 0.001). Parallel group trials (β = -1.83; P < 0.001), subjective outcomes (β = -0.76; P < 0.001), and the disease type significantly influenced the perceived placebo effect. The perceived placebo effect is different between adults and children for binary outcomes. This difference seems to be influenced by the design, the disease, and outcomes. Calibration of new studies for children should consider cautiously the placebo effect in children.

  20. Comparing the index-flood and multiple-regression methods using L-moments

    Science.gov (United States)

    Malekinezhad, H.; Nachtnebel, H. P.; Klik, A.

    In arid and semi-arid regions, the length of records is usually too short to ensure reliable quantile estimates. Comparing index-flood and multiple-regression analyses based on L-moments was the main objective of this study. Factor analysis was applied to determine main influencing variables on flood magnitude. Ward’s cluster and L-moments approaches were applied to several sites in the Namak-Lake basin in central Iran to delineate homogeneous regions based on site characteristics. Homogeneity test was done using L-moments-based measures. Several distributions were fitted to the regional flood data and index-flood and multiple-regression methods as two regional flood frequency methods were compared. The results of factor analysis showed that length of main waterway, compactness coefficient, mean annual precipitation, and mean annual temperature were the main variables affecting flood magnitude. The study area was divided into three regions based on the Ward’s method of clustering approach. The homogeneity test based on L-moments showed that all three regions were acceptably homogeneous. Five distributions were fitted to the annual peak flood data of three homogeneous regions. Using the L-moment ratios and the Z-statistic criteria, GEV distribution was identified as the most robust distribution among five candidate distributions for all the proposed sub-regions of the study area, and in general, it was concluded that the generalised extreme value distribution was the best-fit distribution for every three regions. The relative root mean square error (RRMSE) measure was applied for evaluating the performance of the index-flood and multiple-regression methods in comparison with the curve fitting (plotting position) method. In general, index-flood method gives more reliable estimations for various flood magnitudes of different recurrence intervals. Therefore, this method should be adopted as regional flood frequency method for the study area and the Namak-Lake basin

  1. Comparison of BEACON and COMPARE reactor cavity subcompartment analyses

    International Nuclear Information System (INIS)

    Burkett, M.W.; Idar, E.S.; Gido, R.G.; Lime, J.F.; Koestel, A.

    1984-04-01

    In this study, a more advanced best-estimate containment code, BEACON-MOD3A, was ued to calculate force and moment loads resulting from a high-energy blowdown for two reactor cavity geometries previously analyzed with the licensing computer code COMPARE-MOD1A. The BEACON force and moment loads were compared with the COMPARE results to determine the safety margins provided by the COMPARE code. The forces and moments calculated by the codes were found to be different, although not in any consistent manner, for the two reactor cavity geometries studied. Therefore, generic summary statements regarding margins cannot be made because of the effects of the detailed physical configuration. However, differences in the BEACON and COMPARE calculated forces and moments can be attributed to differences in the modeling assumptions used in the codes and the analyses

  2. Household water treatment in developing countries: comparing different intervention types using meta-regression.

    Science.gov (United States)

    Hunter, Paul R

    2009-12-01

    Household water treatment (HWT) is being widely promoted as an appropriate intervention for reducing the burden of waterborne disease in poor communities in developing countries. A recent study has raised concerns about the effectiveness of HWT, in part because of concerns over the lack of blinding and in part because of considerable heterogeneity in the reported effectiveness of randomized controlled trials. This study set out to attempt to investigate the causes of this heterogeneity and so identify factors associated with good health gains. Studies identified in an earlier systematic review and meta-analysis were supplemented with more recently published randomized controlled trials. A total of 28 separate studies of randomized controlled trials of HWT with 39 intervention arms were included in the analysis. Heterogeneity was studied using the "metareg" command in Stata. Initial analyses with single candidate predictors were undertaken and all variables significant at the P Risk and the parameter estimates from the final regression model. The overall effect size of all unblinded studies was relative risk = 0.56 (95% confidence intervals 0.51-0.63), but after adjusting for bias due to lack of blinding the effect size was much lower (RR = 0.85, 95% CI = 0.76-0.97). Four main variables were significant predictors of effectiveness of intervention in a multipredictor meta regression model: Log duration of study follow-up (regression coefficient of log effect size = 0.186, standard error (SE) = 0.072), whether or not the study was blinded (coefficient 0.251, SE 0.066) and being conducted in an emergency setting (coefficient -0.351, SE 0.076) were all significant predictors of effect size in the final model. Compared to the ceramic filter all other interventions were much less effective (Biosand 0.247, 0.073; chlorine and safe waste storage 0.295, 0.061; combined coagulant-chlorine 0.2349, 0.067; SODIS 0.302, 0.068). A Monte Carlo model predicted that over 12 months

  3. Accounting for rate variation among lineages in comparative demographic analyses

    Science.gov (United States)

    Hope, Andrew G.; Ho, Simon Y. W.; Malaney, Jason L.; Cook, Joseph A.; Talbot, Sandra L.

    2014-01-01

    Genetic analyses of contemporary populations can be used to estimate the demographic histories of species within an ecological community. Comparison of these demographic histories can shed light on community responses to past climatic events. However, species experience different rates of molecular evolution, and this presents a major obstacle to comparative demographic analyses. We address this problem by using a Bayesian relaxed-clock method to estimate the relative evolutionary rates of 22 small mammal taxa distributed across northwestern North America. We found that estimates of the relative molecular substitution rate for each taxon were consistent across the range of sampling schemes that we compared. Using three different reference rates, we rescaled the relative rates so that they could be used to estimate absolute evolutionary timescales. Accounting for rate variation among taxa led to temporal shifts in our skyline-plot estimates of demographic history, highlighting both uniform and idiosyncratic evolutionary responses to directional climate trends for distinct ecological subsets of the small mammal community. Our approach can be used in evolutionary analyses of populations from multiple species, including comparative demographic studies.

  4. Correlation, Regression and Path Analyses of Seed Yield Components in Crambe abyssinica, a Promising Industrial Oil Crop

    OpenAIRE

    Huang, Banglian; Yang, Yiming; Luo, Tingting; Wu, S.; Du, Xuezhu; Cai, Detian; Loo, van, E.N.; Huang Bangquan

    2013-01-01

    In the present study correlation, regression and path analyses were carried out to decide correlations among the agro- nomic traits and their contributions to seed yield per plant in Crambe abyssinica. Partial correlation analysis indicated that plant height (X1) was significantly correlated with branching height and the number of first branches (P <0.01); Branching height (X2) was significantly correlated with pod number of primary inflorescence (P <0.01) and number of secondary branch...

  5. Structural vascular disease in Africans: performance of ethnic-specific waist circumference cut points using logistic regression and neural network analyses: the SABPA study

    OpenAIRE

    Botha, J.; De Ridder, J.H.; Potgieter, J.C.; Steyn, H.S.; Malan, L.

    2013-01-01

    A recently proposed model for waist circumference cut points (RPWC), driven by increased blood pressure, was demonstrated in an African population. We therefore aimed to validate the RPWC by comparing the RPWC and the Joint Statement Consensus (JSC) models via Logistic Regression (LR) and Neural Networks (NN) analyses. Urban African gender groups (N=171) were stratified according to the JSC and RPWC cut point models. Ultrasound carotid intima media thickness (CIMT), blood pressure (BP) and fa...

  6. Comparative Transcriptional Analyses of Francisella tularensis and Francisella novicida.

    Directory of Open Access Journals (Sweden)

    Siva T Sarva

    Full Text Available Francisella tularensis is composed of a number of subspecies with varied geographic distribution, host ranges, and virulence. In view of these marked differences, comparative functional genomics may elucidate some of the molecular mechanism(s behind these differences. In this study a shared probe microarray was designed that could be used to compare the transcriptomes of Francisella tularensis subsp. tularensis Schu S4 (Ftt, Francisella tularensis subsp. holarctica OR960246 (Fth, Francisella tularensis subsp. holarctica LVS (LVS, and Francisella novicida U112 (Fn. To gain insight into expression differences that may be related to the differences in virulence of these subspecies, transcriptomes were measured from each strain grown in vitro under identical conditions, utilizing a shared probe microarray. The human avirulent Fn strain exhibited high levels of transcription of genes involved in general metabolism, which are pseudogenes in the human virulent Ftt and Fth strains, consistent with the process of genome decay in the virulent strains. Genes encoding an efflux system (emrA2 cluster of genes, siderophore (fsl operon, acid phosphatase, LPS synthesis, polyamine synthesis, and citrulline ureidase were all highly expressed in Ftt when compared to Fn, suggesting that some of these may contribute to the relative high virulence of Ftt. Genes expressed at a higher level in Ftt when compared to the relatively less virulent Fth included genes encoding isochorismatases, cholylglycine hydrolase, polyamine synthesis, citrulline ureidase, Type IV pilus subunit, and the Francisella Pathogenicity Island protein PdpD. Fth and LVS had very few expression differences, consistent with the derivation of LVS from Fth. This study demonstrated that a shared probe microarray designed to detect transcripts in multiple species/subspecies of Francisella enabled comparative transcriptional analyses that may highlight critical differences that underlie the relative

  7. Comparing Regression Coefficients between Nested Linear Models for Clustered Data with Generalized Estimating Equations

    Science.gov (United States)

    Yan, Jun; Aseltine, Robert H., Jr.; Harel, Ofer

    2013-01-01

    Comparing regression coefficients between models when one model is nested within another is of great practical interest when two explanations of a given phenomenon are specified as linear models. The statistical problem is whether the coefficients associated with a given set of covariates change significantly when other covariates are added into…

  8. Using ROC curves to compare neural networks and logistic regression for modeling individual noncatastrophic tree mortality

    Science.gov (United States)

    Susan L. King

    2003-01-01

    The performance of two classifiers, logistic regression and neural networks, are compared for modeling noncatastrophic individual tree mortality for 21 species of trees in West Virginia. The output of the classifier is usually a continuous number between 0 and 1. A threshold is selected between 0 and 1 and all of the trees below the threshold are classified as...

  9. Comparing treatment effects after adjustment with multivariable Cox proportional hazards regression and propensity score methods

    NARCIS (Netherlands)

    Martens, Edwin P; de Boer, Anthonius; Pestman, Wiebe R; Belitser, Svetlana V; Stricker, Bruno H Ch; Klungel, Olaf H

    PURPOSE: To compare adjusted effects of drug treatment for hypertension on the risk of stroke from propensity score (PS) methods with a multivariable Cox proportional hazards (Cox PH) regression in an observational study with censored data. METHODS: From two prospective population-based cohort

  10. Comparing Linear Discriminant Function with Logistic Regression for the Two-Group Classification Problem.

    Science.gov (United States)

    Fan, Xitao; Wang, Lin

    The Monte Carlo study compared the performance of predictive discriminant analysis (PDA) and that of logistic regression (LR) for the two-group classification problem. Prior probabilities were used for classification, but the cost of misclassification was assumed to be equal. The study used a fully crossed three-factor experimental design (with…

  11. SPSS macros to compare any two fitted values from a regression model.

    Science.gov (United States)

    Weaver, Bruce; Dubois, Sacha

    2012-12-01

    In regression models with first-order terms only, the coefficient for a given variable is typically interpreted as the change in the fitted value of Y for a one-unit increase in that variable, with all other variables held constant. Therefore, each regression coefficient represents the difference between two fitted values of Y. But the coefficients represent only a fraction of the possible fitted value comparisons that might be of interest to researchers. For many fitted value comparisons that are not captured by any of the regression coefficients, common statistical software packages do not provide the standard errors needed to compute confidence intervals or carry out statistical tests-particularly in more complex models that include interactions, polynomial terms, or regression splines. We describe two SPSS macros that implement a matrix algebra method for comparing any two fitted values from a regression model. The !OLScomp and !MLEcomp macros are for use with models fitted via ordinary least squares and maximum likelihood estimation, respectively. The output from the macros includes the standard error of the difference between the two fitted values, a 95% confidence interval for the difference, and a corresponding statistical test with its p-value.

  12. Comparative study of biodegradability prediction of chemicals using decision trees, functional trees, and logistic regression.

    Science.gov (United States)

    Chen, Guangchao; Li, Xuehua; Chen, Jingwen; Zhang, Ya-Nan; Peijnenburg, Willie J G M

    2014-12-01

    Biodegradation is the principal environmental dissipation process of chemicals. As such, it is a dominant factor determining the persistence and fate of organic chemicals in the environment, and is therefore of critical importance to chemical management and regulation. In the present study, the authors developed in silico methods assessing biodegradability based on a large heterogeneous set of 825 organic compounds, using the techniques of the C4.5 decision tree, the functional inner regression tree, and logistic regression. External validation was subsequently carried out by 2 independent test sets of 777 and 27 chemicals. As a result, the functional inner regression tree exhibited the best predictability with predictive accuracies of 81.5% and 81.0%, respectively, on the training set (825 chemicals) and test set I (777 chemicals). Performance of the developed models on the 2 test sets was subsequently compared with that of the Estimation Program Interface (EPI) Suite Biowin 5 and Biowin 6 models, which also showed a better predictability of the functional inner regression tree model. The model built in the present study exhibits a reasonable predictability compared with existing models while possessing a transparent algorithm. Interpretation of the mechanisms of biodegradation was also carried out based on the models developed. © 2014 SETAC.

  13. A computational approach to compare regression modelling strategies in prediction research.

    Science.gov (United States)

    Pajouheshnia, Romin; Pestman, Wiebe R; Teerenstra, Steven; Groenwold, Rolf H H

    2016-08-25

    It is often unclear which approach to fit, assess and adjust a model will yield the most accurate prediction model. We present an extension of an approach for comparing modelling strategies in linear regression to the setting of logistic regression and demonstrate its application in clinical prediction research. A framework for comparing logistic regression modelling strategies by their likelihoods was formulated using a wrapper approach. Five different strategies for modelling, including simple shrinkage methods, were compared in four empirical data sets to illustrate the concept of a priori strategy comparison. Simulations were performed in both randomly generated data and empirical data to investigate the influence of data characteristics on strategy performance. We applied the comparison framework in a case study setting. Optimal strategies were selected based on the results of a priori comparisons in a clinical data set and the performance of models built according to each strategy was assessed using the Brier score and calibration plots. The performance of modelling strategies was highly dependent on the characteristics of the development data in both linear and logistic regression settings. A priori comparisons in four empirical data sets found that no strategy consistently outperformed the others. The percentage of times that a model adjustment strategy outperformed a logistic model ranged from 3.9 to 94.9 %, depending on the strategy and data set. However, in our case study setting the a priori selection of optimal methods did not result in detectable improvement in model performance when assessed in an external data set. The performance of prediction modelling strategies is a data-dependent process and can be highly variable between data sets within the same clinical domain. A priori strategy comparison can be used to determine an optimal logistic regression modelling strategy for a given data set before selecting a final modelling approach.

  14. Analyses of non-fatal accidents in an opencast mine by logistic regression model - a case study.

    Science.gov (United States)

    Onder, Seyhan; Mutlu, Mert

    2017-09-01

    Accidents cause major damage for both workers and enterprises in the mining industry. To reduce the number of occupational accidents, these incidents should be properly registered and carefully analysed. This study efficiently examines the Aegean Lignite Enterprise (ELI) of Turkish Coal Enterprises (TKI) in Soma between 2006 and 2011, and opencast coal mine occupational accident records were used for statistical analyses. A total of 231 occupational accidents were analysed for this study. The accident records were categorized into seven groups: area, reason, occupation, part of body, age, shift hour and lost days. The SPSS package program was used in this study for logistic regression analyses, which predicted the probability of accidents resulting in greater or less than 3 lost workdays for non-fatal injuries. Social facilities-area of surface installations, workshops and opencast mining areas are the areas with the highest probability for accidents with greater than 3 lost workdays for non-fatal injuries, while the reasons with the highest probability for these types of accidents are transporting and manual handling. Additionally, the model was tested for such reported accidents that occurred in 2012 for the ELI in Soma and estimated the probability of exposure to accidents with lost workdays correctly by 70%.

  15. Improving validation methods for molecular diagnostics: application of Bland-Altman, Deming and simple linear regression analyses in assay comparison and evaluation for next-generation sequencing.

    Science.gov (United States)

    Misyura, Maksym; Sukhai, Mahadeo A; Kulasignam, Vathany; Zhang, Tong; Kamel-Reid, Suzanne; Stockley, Tracy L

    2018-02-01

    A standard approach in test evaluation is to compare results of the assay in validation to results from previously validated methods. For quantitative molecular diagnostic assays, comparison of test values is often performed using simple linear regression and the coefficient of determination (R 2 ), using R 2 as the primary metric of assay agreement. However, the use of R 2 alone does not adequately quantify constant or proportional errors required for optimal test evaluation. More extensive statistical approaches, such as Bland-Altman and expanded interpretation of linear regression methods, can be used to more thoroughly compare data from quantitative molecular assays. We present the application of Bland-Altman and linear regression statistical methods to evaluate quantitative outputs from next-generation sequencing assays (NGS). NGS-derived data sets from assay validation experiments were used to demonstrate the utility of the statistical methods. Both Bland-Altman and linear regression were able to detect the presence and magnitude of constant and proportional error in quantitative values of NGS data. Deming linear regression was used in the context of assay comparison studies, while simple linear regression was used to analyse serial dilution data. Bland-Altman statistical approach was also adapted to quantify assay accuracy, including constant and proportional errors, and precision where theoretical and empirical values were known. The complementary application of the statistical methods described in this manuscript enables more extensive evaluation of performance characteristics of quantitative molecular assays, prior to implementation in the clinical molecular laboratory. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  16. Comparing Kriging and Regression Approaches for Mapping Soil Clay Content in a diverse Danish Landscape

    DEFF Research Database (Denmark)

    Adhikari, Kabindra; Bou Kheir, Rania; Greve, Mette Balslev

    2013-01-01

    Information on the spatial variability of soil texture including soil clay content in a landscape is very important for agricultural and environmental use. Different prediction techniques are available to assess and map spatial variability of soil properties, but selecting the most suitable techn...... the prediction in OKst compared with that in OK, whereas RT showed the lowest performance of all (R2 = 0.52; RMSE = 0.52; and RPD = 1.17). We found RKrr to be an effective prediction method and recommend this method for any future soil mapping activities in Denmark....... technique at a given site has always been a major issue in all soil mapping applications. We studied the prediction performance of ordinary kriging (OK), stratified OK (OKst), regression trees (RT), and rule-based regression kriging (RKrr) for digital mapping of soil clay content at 30.4-m grid size using 6...

  17. Using synthetic data to evaluate multiple regression and principal component analyses for statistical modeling of daily building energy consumption

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, T.A. (Energy Systems Lab., Texas A and M Univ., College Station, TX (United States)); Claridge, D.E. (Energy Systems Lab., Texas A and M Univ., College Station, TX (United States))

    1994-01-01

    Multiple regression modeling of monitored building energy use data is often faulted as a reliable means of predicting energy use on the grounds that multicollinearity between the regressor variables can lead both to improper interpretation of the relative importance of the various physical regressor parameters and to a model with unstable regressor coefficients. Principal component analysis (PCA) has the potential to overcome such drawbacks. While a few case studies have already attempted to apply this technique to building energy data, the objectives of this study were to make a broader evaluation of PCA and multiple regression analysis (MRA) and to establish guidelines under which one approach is preferable to the other. Four geographic locations in the US with different climatic conditions were selected and synthetic data sequence representative of daily energy use in large institutional buildings were generated in each location using a linear model with outdoor temperature, outdoor specific humidity and solar radiation as the three regression variables. MRA and PCA approaches were then applied to these data sets and their relative performances were compared. Conditions under which PCA seems to perform better than MRA were identified and preliminary recommendations on the use of either modeling approach formulated. (orig.)

  18. Improved Dietary Guidelines for Vitamin D: Application of Individual Participant Data (IPD-Level Meta-Regression Analyses

    Directory of Open Access Journals (Sweden)

    Kevin D. Cashman

    2017-05-01

    Full Text Available Dietary Reference Values (DRVs for vitamin D have a key role in the prevention of vitamin D deficiency. However, despite adopting similar risk assessment protocols, estimates from authoritative agencies over the last 6 years have been diverse. This may have arisen from diverse approaches to data analysis. Modelling strategies for pooling of individual subject data from cognate vitamin D randomized controlled trials (RCTs are likely to provide the most appropriate DRV estimates. Thus, the objective of the present work was to undertake the first-ever individual participant data (IPD-level meta-regression, which is increasingly recognized as best practice, from seven winter-based RCTs (with 882 participants ranging in age from 4 to 90 years of the vitamin D intake–serum 25-hydroxyvitamin D (25(OHD dose-response. Our IPD-derived estimates of vitamin D intakes required to maintain 97.5% of 25(OHD concentrations >25, 30, and 50 nmol/L across the population are 10, 13, and 26 µg/day, respectively. In contrast, standard meta-regression analyses with aggregate data (as used by several agencies in recent years from the same RCTs estimated that a vitamin D intake requirement of 14 µg/day would maintain 97.5% of 25(OHD >50 nmol/L. These first IPD-derived estimates offer improved dietary recommendations for vitamin D because the underpinning modeling captures the between-person variability in response of serum 25(OHD to vitamin D intake.

  19. A comparative study on entrepreneurial attitudes modeled with logistic regression and Bayes nets.

    Science.gov (United States)

    López Puga, Jorge; García García, Juan

    2012-11-01

    Entrepreneurship research is receiving increasing attention in our context, as entrepreneurs are key social agents involved in economic development. We compare the success of the dichotomic logistic regression model and the Bayes simple classifier to predict entrepreneurship, after manipulating the percentage of missing data and the level of categorization in predictors. A sample of undergraduate university students (N = 1230) completed five scales (motivation, attitude towards business creation, obstacles, deficiencies, and training needs) and we found that each of them predicted different aspects of the tendency to business creation. Additionally, our results show that the receiver operating characteristic (ROC) curve is affected by the rate of missing data in both techniques, but logistic regression seems to be more vulnerable when faced with missing data, whereas Bayes nets underperform slightly when categorization has been manipulated. Our study sheds light on the potential entrepreneur profile and we propose to use Bayesian networks as an additional alternative to overcome the weaknesses of logistic regression when missing data are present in applied research.

  20. Improved Dietary Guidelines for Vitamin D: Application of Individual Participant Data (IPD)-Level Meta-Regression Analyses

    Science.gov (United States)

    Cashman, Kevin D.; Ritz, Christian; Kiely, Mairead

    2017-01-01

    Dietary Reference Values (DRVs) for vitamin D have a key role in the prevention of vitamin D deficiency. However, despite adopting similar risk assessment protocols, estimates from authoritative agencies over the last 6 years have been diverse. This may have arisen from diverse approaches to data analysis. Modelling strategies for pooling of individual subject data from cognate vitamin D randomized controlled trials (RCTs) are likely to provide the most appropriate DRV estimates. Thus, the objective of the present work was to undertake the first-ever individual participant data (IPD)-level meta-regression, which is increasingly recognized as best practice, from seven winter-based RCTs (with 882 participants ranging in age from 4 to 90 years) of the vitamin D intake–serum 25-hydroxyvitamin D (25(OH)D) dose-response. Our IPD-derived estimates of vitamin D intakes required to maintain 97.5% of 25(OH)D concentrations >25, 30, and 50 nmol/L across the population are 10, 13, and 26 µg/day, respectively. In contrast, standard meta-regression analyses with aggregate data (as used by several agencies in recent years) from the same RCTs estimated that a vitamin D intake requirement of 14 µg/day would maintain 97.5% of 25(OH)D >50 nmol/L. These first IPD-derived estimates offer improved dietary recommendations for vitamin D because the underpinning modeling captures the between-person variability in response of serum 25(OH)D to vitamin D intake. PMID:28481259

  1. Support vector regression for porosity prediction in a heterogeneous reservoir: A comparative study

    Science.gov (United States)

    Al-Anazi, A. F.; Gates, I. D.

    2010-12-01

    In wells with limited log and core data, porosity, a fundamental and essential property to characterize reservoirs, is challenging to estimate by conventional statistical methods from offset well log and core data in heterogeneous formations. Beyond simple regression, neural networks have been used to develop more accurate porosity correlations. Unfortunately, neural network-based correlations have limited generalization ability and global correlations for a field are usually less accurate compared to local correlations for a sub-region of the reservoir. In this paper, support vector machines are explored as an intelligent technique to correlate porosity to well log data. Recently, support vector regression (SVR), based on the statistical learning theory, have been proposed as a new intelligence technique for both prediction and classification tasks. The underlying formulation of support vector machines embodies the structural risk minimization (SRM) principle which has been shown to be superior to the traditional empirical risk minimization (ERM) principle employed by conventional neural networks and classical statistical methods. This new formulation uses margin-based loss functions to control model complexity independently of the dimensionality of the input space, and kernel functions to project the estimation problem to a higher dimensional space, which enables the solution of more complex nonlinear problem optimization methods to exist for a globally optimal solution. SRM minimizes an upper bound on the expected risk using a margin-based loss function ( ɛ-insensitivity loss function for regression) in contrast to ERM which minimizes the error on the training data. Unlike classical learning methods, SRM, indexed by margin-based loss function, can also control model complexity independent of dimensionality. The SRM inductive principle is designed for statistical estimation with finite data where the ERM inductive principle provides the optimal solution (the

  2. Longitudinal changes in telomere length and associated genetic parameters in dairy cattle analysed using random regression models.

    Directory of Open Access Journals (Sweden)

    Luise A Seeker

    Full Text Available Telomeres cap the ends of linear chromosomes and shorten with age in many organisms. In humans short telomeres have been linked to morbidity and mortality. With the accumulation of longitudinal datasets the focus shifts from investigating telomere length (TL to exploring TL change within individuals over time. Some studies indicate that the speed of telomere attrition is predictive of future disease. The objectives of the present study were to 1 characterize the change in bovine relative leukocyte TL (RLTL across the lifetime in Holstein Friesian dairy cattle, 2 estimate genetic parameters of RLTL over time and 3 investigate the association of differences in individual RLTL profiles with productive lifespan. RLTL measurements were analysed using Legendre polynomials in a random regression model to describe TL profiles and genetic variance over age. The analyses were based on 1,328 repeated RLTL measurements of 308 female Holstein Friesian dairy cattle. A quadratic Legendre polynomial was fitted to the fixed effect of age in months and to the random effect of the animal identity. Changes in RLTL, heritability and within-trait genetic correlation along the age trajectory were calculated and illustrated. At a population level, the relationship between RLTL and age was described by a positive quadratic function. Individuals varied significantly regarding the direction and amount of RLTL change over life. The heritability of RLTL ranged from 0.36 to 0.47 (SE = 0.05-0.08 and remained statistically unchanged over time. The genetic correlation of RLTL at birth with measurements later in life decreased with the time interval between samplings from near unity to 0.69, indicating that TL later in life might be regulated by different genes than TL early in life. Even though animals differed in their RLTL profiles significantly, those differences were not correlated with productive lifespan (p = 0.954.

  3. Comparing transfusion reaction rates for various plasma types: a systematic review and meta-analysis/regression.

    Science.gov (United States)

    Saadah, Nicholas H; van Hout, Fabienne M A; Schipperus, Martin R; le Cessie, Saskia; Middelburg, Rutger A; Wiersum-Osselton, Johanna C; van der Bom, Johanna G

    2017-09-01

    We estimated rates for common plasma-associated transfusion reactions and compared reported rates for various plasma types. We performed a systematic review and meta-analysis of peer-reviewed articles that reported plasma transfusion reaction rates. Random-effects pooled rates were calculated and compared between plasma types. Meta-regression was used to compare various plasma types with regard to their reported plasma transfusion reaction rates. Forty-eight studies reported transfusion reaction rates for fresh-frozen plasma (FFP; mixed-sex and male-only), amotosalen INTERCEPT FFP, methylene blue-treated FFP, and solvent/detergent-treated pooled plasma. Random-effects pooled average rates for FFP were: allergic reactions, 92/10 5 units transfused (95% confidence interval [CI], 46-184/10 5 units transfused); febrile nonhemolytic transfusion reactions (FNHTRs), 12/10 5 units transfused (95% CI, 7-22/10 5 units transfused); transfusion-associated circulatory overload (TACO), 6/10 5 units transfused (95% CI, 1-30/10 5 units transfused); transfusion-related acute lung injury (TRALI), 1.8/10 5 units transfused (95% CI, 1.2-2.7/10 5 units transfused); and anaphylactic reactions, 0.8/10 5 units transfused (95% CI, 0-45.7/10 5 units transfused). Risk differences between plasma types were not significant for allergic reactions, TACO, or anaphylactic reactions. Methylene blue-treated FFP led to fewer FNHTRs than FFP (risk difference = -15.3 FNHTRs/10 5 units transfused; 95% CI, -24.7 to -7.1 reactions/10 5 units transfused); and male-only FFP led to fewer cases of TRALI than mixed-sex FFP (risk difference = -0.74 TRALI/10 5 units transfused; 95% CI, -2.42 to -0.42 injuries/10 5 units transfused). Meta-regression demonstrates that the rate of FNHTRs is lower for methylene blue-treated compared with FFP, and the rate of TRALI is lower for male-only than for mixed-sex FFP; whereas no significant differences are observed between plasma types for allergic reactions, TACO

  4. Semantics bias in cross-national comparative analyses

    DEFF Research Database (Denmark)

    Schnohr, Christina W.; Gobina, Inese; Santos, Teresa

    2016-01-01

    indicates that there are what may be called semantic issues affecting comparability in international studies, since the same original word (in an English original) is interpreted differently across countries and cultures. The paper test and discuss a few possible explanations to this, however, only leaving...

  5. Comparative and Predictive Multimedia Assessments Using Monte Carlo Uncertainty Analyses

    Science.gov (United States)

    Whelan, G.

    2002-05-01

    Multiple-pathway frameworks (sometimes referred to as multimedia models) provide a platform for combining medium-specific environmental models and databases, such that they can be utilized in a more holistic assessment of contaminant fate and transport in the environment. These frameworks provide a relatively seamless transfer of information from one model to the next and from databases to models. Within these frameworks, multiple models are linked, resulting in models that consume information from upstream models and produce information to be consumed by downstream models. The Framework for Risk Analysis in Multimedia Environmental Systems (FRAMES) is an example, which allows users to link their models to other models and databases. FRAMES is an icon-driven, site-layout platform that is an open-architecture, object-oriented system that interacts with environmental databases; helps the user construct a Conceptual Site Model that is real-world based; allows the user to choose the most appropriate models to solve simulation requirements; solves the standard risk paradigm of release transport and fate; and exposure/risk assessments to people and ecology; and presents graphical packages for analyzing results. FRAMES is specifically designed allow users to link their own models into a system, which contains models developed by others. This paper will present the use of FRAMES to evaluate potential human health exposures using real site data and realistic assumptions from sources, through the vadose and saturated zones, to exposure and risk assessment at three real-world sites, using the Multimedia Environmental Pollutant Assessment System (MEPAS), which is a multimedia model contained within FRAMES. These real-world examples use predictive and comparative approaches coupled with a Monte Carlo analysis. A predictive analysis is where models are calibrated to monitored site data, prior to the assessment, and a comparative analysis is where models are not calibrated but

  6. Comparative evaluation of left ventricular mass regression after aortic valve replacement: a prospective randomized analysis

    Directory of Open Access Journals (Sweden)

    Kiessling Arndt H

    2011-10-01

    Full Text Available Abstract Background We assessed the hemodynamic performance of various prostheses and the clinical outcomes after aortic valve replacement, in different age groups. Methods One-hundred-and-twenty patients with isolated aortic valve stenosis were included in this prospective randomized randomised trial and allocated in three age-groups to receive either pulmonary autograft (PA, n = 20 or mechanical prosthesis (MP, Edwards Mira n = 20 in group 1 (age 75. Clinical outcomes and hemodynamic performance were evaluated at discharge, six months and one year. Results In group 1, patients with PA had significantly lower mean gradients than the MP (2.6 vs. 10.9 mmHg, p = 0.0005 with comparable left ventricular mass regression (LVMR. Morbidity included 1 stroke in the PA population and 1 gastrointestinal bleeding in the MP subgroup. In group 2, mean gradients did not differ significantly between both populations (7.0 vs. 8.9 mmHg, p = 0.81. The rate of LVMR and EF were comparable at 12 months; each group with one mortality. Morbidity included 1 stroke and 1 gastrointestinal bleeding in the stentless and 3 bleeding complications in the MP group. In group 3, mean gradients did not differ significantly (7.8 vs 6.5 mmHg, p = 0.06. Postoperative EF and LVMR were comparable. There were 3 deaths in the stented group and no mortality in the stentless group. Morbidity included 1 endocarditis and 1 stroke in the stentless compared to 1 endocarditis, 1 stroke and one pulmonary embolism in the stented group. Conclusions Clinical outcomes justify valve replacement with either valve substitute in the respective age groups. The PA hemodynamically outperformed the MPs. Stentless valves however, did not demonstrate significantly superior hemodynamics or outcomes in comparison to stented bioprosthesis or MPs.

  7. Comparative Analyses of Phenotypic Trait Covariation within and among Populations.

    Science.gov (United States)

    Peiman, Kathryn S; Robinson, Beren W

    2017-10-01

    Many morphological, behavioral, physiological, and life-history traits covary across the biological scales of individuals, populations, and species. However, the processes that cause traits to covary also change over these scales, challenging our ability to use patterns of trait covariance to infer process. Trait relationships are also widely assumed to have generic functional relationships with similar evolutionary potentials, and even though many different trait relationships are now identified, there is little appreciation that these may influence trait covariation and evolution in unique ways. We use a trait-performance-fitness framework to classify and organize trait relationships into three general classes, address which ones more likely generate trait covariation among individuals in a population, and review how selection shapes phenotypic covariation. We generate predictions about how trait covariance changes within and among populations as a result of trait relationships and in response to selection and consider how these can be tested with comparative data. Careful comparisons of covariation patterns can narrow the set of hypothesized processes that cause trait covariation when the form of the trait relationship and how it responds to selection yield clear predictions about patterns of trait covariation. We discuss the opportunities and limitations of comparative approaches to evaluate hypotheses about the evolutionary causes and consequences of trait covariation and highlight the importance of evaluating patterns within populations replicated in the same and in different selective environments. Explicit hypotheses about trait relationships are key to generating effective predictions about phenotype and its evolution using covariance data.

  8. Comparative analyses of industrial-scale human platelet lysate preparations.

    Science.gov (United States)

    Pierce, Jan; Benedetti, Eric; Preslar, Amber; Jacobson, Pam; Jin, Ping; Stroncek, David F; Reems, Jo-Anna

    2017-12-01

    Efforts are underway to eliminate fetal bovine serum from mammalian cell cultures for clinical use. An emerging, viable replacement option for fetal bovine serum is human platelet lysate (PL) as either a plasma-based or serum-based product. Nine industrial-scale, serum-based PL manufacturing runs (i.e., lots) were performed, consisting of an average ± standard deviation volume of 24.6 ± 2.2 liters of pooled, platelet-rich plasma units that were obtained from apheresis donors. Manufactured lots were compared by evaluating various biochemical and functional test results. Comprehensive cytokine profiles of PL lots and product stability tests were performed. Global gene expression profiles of mesenchymal stromal cells (MSCs) cultured with plasma-based or serum-based PL were compared to MSCs cultured with fetal bovine serum. Electrolyte and protein levels were relatively consistent among all serum-based PL lots, with only slight variations in glucose and calcium levels. All nine lots were as good as or better than fetal bovine serum in expanding MSCs. Serum-based PL stored at -80°C remained stable over 2 years. Quantitative cytokine arrays showed similarities as well as dissimilarities in the proteins present in serum-based PL. Greater differences in MSC gene expression profiles were attributable to the starting cell source rather than with the use of either PL or fetal bovine serum as a culture supplement. Using a large-scale, standardized method, lot-to-lot variations were noted for industrial-scale preparations of serum-based PL products. However, all lots performed as well as or better than fetal bovine serum in supporting MSC growth. Together, these data indicate that off-the-shelf PL is a feasible substitute for fetal bovine serum in MSC cultures. © 2017 AABB.

  9. A tale of two phylogenies: comparative analyses of ecological interactions.

    Science.gov (United States)

    Hadfield, Jarrod D; Krasnov, Boris R; Poulin, Robert; Nakagawa, Shinichi

    2014-02-01

    The evolution of traits involved in ecological interactions such as predator-prey, host-parasite, and plant-pollinator interactions, are likely to be shaped by the phylogenetic history of both parties. We develop generalized linear mixed-effects models (GLMM) that estimate the effect of both parties' phylogenetic history on trait evolution, both in isolation but also in terms of how the two histories interact. Using data on the incidence and abundance of 206 flea species on 121 mammal species, we illustrate our method and compare it to previously used methods for detecting host-parasite coevolution. At large spatial scales we find that the phylogenetic interaction effect was substantial, indicating that related parasite species were more likely to be found on related host species. At smaller spatial scales, and when sampling effort was not controlled for, phylogenetic effects on the number and types of parasite species harbored by hosts were found to dominate. We go on to show that in situations where these additional phylogenetic effects exist, then previous methods have very high Type I error rates when testing for the phylogenetic interaction. Our GLMM method represents a robust and reliable approach to quantify the phylogenetic effects of traits determined by, or defined by, ecological interactions and has the advantage that it can easily be extended and interpreted in a broader context than existing permutation tests.

  10. Comparative exergy analyses of gasoline and hydrogen fuelled ices

    International Nuclear Information System (INIS)

    Nieminen, J.; Dincer, I.; Yang, Y.

    2009-01-01

    Comparative exergy models for naturally aspirated gasoline and hydrogen fuelled spark ignition internal combustion engines were developed according to the second laws of thermodynamics. A thorough graphical analysis of heat transfer, work, thermo mechanical, and intake charge exergy functions was made. An irreversibility function was developed as a function of entropy generation and graphed. A second law analysis yielded a proportional exergy distribution as a fraction of the intake charge exergy. It was found that the hydrogen fuelled engine had a greater proportion of the intake charge exergy converted into work exergy, indicating a second law efficiency of 50.13% as opposed to 44.34% for a gasoline fuelled engine. The greater exergy due to heat transfer or thermal availability associated with the hydrogen fuelled engine is postulated to be a part of the reason for decreased work output of a hydrogen engine. Finally, a second law analysis of both hydrogen and gasoline combustion reactions indicate a greater combustion irreversibility associated with gasoline combustion. A percentage breakdown of the combustion irreversibilities were also constructed according to information found in literature searches. (author)

  11. Retrospective analyses versus RCTs: comparing like with like?

    Directory of Open Access Journals (Sweden)

    Baron R

    2017-03-01

    Full Text Available Ralf Baron,1 Lieven Nils Kennes,2 Christian Elling31Division of Neurological Pain Research and Therapy, Department of Neurology, University Hospital of Schleswig-Holstein, Kiel Campus, Kiel, 2Department of Economics and Business Administration, University of Applied Sciences Stralsund, Stralsund, 3Grünenthal GmbH, Medical Affairs Europe and North America, Aachen, GermanyIn their recent retrospective analysis assessing oxycodone/naloxone (OXN vs. tapentadol (TAP treatment for chronic low-back pain with a neuropathic component, Ueberall and Mueller-Schwefe1 compare their results to the findings of an earlier phase 3b/4 study.2 In our opinion, a proper comparison to the prospective, randomized, controlled, open-label study by Baron and colleagues is scientifically not appropriate. Although Ueberall and Mueller-Schwefe use the terms “prospective,” “randomly,” and “blinded” and refer to the PROBE design (prospective, randomized, open-label, blinded endpoint,3 their database study is retrospective, nonrandomized, and nonblinded with the treatment choice left to the discretion of the physicians. In this context, the use of the term “intention-to-treat (ITT population” is inappropriate because ITT is unambiguously defined as including all randomized subjects and thus inseparable from true randomization (ICH E9.4View original paper by Ueberall and Mueller-Schwefe.

  12. Forecasting production of fossil fuel sources in Turkey using a comparative regression and ARIMA model

    International Nuclear Information System (INIS)

    Ediger, Volkan S.; Akar, Sertac; Ugurlu, Berkin

    2006-01-01

    This study aims at forecasting the most possible curve for domestic fossil fuel production of Turkey to help policy makers to develop policy implications for rapidly growing dependency problem on imported fossil fuels. The fossil fuel dependency problem is international in scope and context and Turkey is a typical example for emerging energy markets of the developing world. We developed a decision support system for forecasting fossil fuel production by applying a regression, ARIMA and SARIMA method to the historical data from 1950 to 2003 in a comparative manner. The method integrates each model by using some decision parameters related to goodness-of-fit and confidence interval, behavior of the curve, and reserves. Different forecasting models are proposed for different fossil fuel types. The best result is obtained for oil since the reserve classifications used it is much better defined them for the others. Our findings show that the fossil fuel production peak has already been reached; indicating the total fossil fuel production of the country will diminish and theoretically will end in 2038. However, production is expected to end in 2019 for hard coal, in 2024 for natural gas, in 2029 for oil and 2031 for asphaltite. The gap between the fossil fuel consumption and production is growing enormously and it reaches in 2030 to approximately twice of what it is in 2000

  13. SPECIFICS OF THE APPLICATIONS OF MULTIPLE REGRESSION MODEL IN THE ANALYSES OF THE EFFECTS OF GLOBAL FINANCIAL CRISES

    Directory of Open Access Journals (Sweden)

    Željko V. Račić

    2010-12-01

    Full Text Available This paper aims to present the specifics of the application of multiple linear regression model. The economic (financial crisis is analyzed in terms of gross domestic product which is in a function of the foreign trade balance (on one hand and the credit cards, i.e. indebtedness of the population on this basis (on the other hand, in the USA (from 1999. to 2008. We used the extended application model which shows how the analyst should run the whole development process of regression model. This process began with simple statistical features and the application of regression procedures, and ended with residual analysis, intended for the study of compatibility of data and model settings. This paper also analyzes the values of some standard statistics used in the selection of appropriate regression model. Testing of the model is carried out with the use of the Statistics PASW 17 program.

  14. Next generation sequencing and comparative analyses of Xenopus mitogenomes

    Directory of Open Access Journals (Sweden)

    Lloyd Rhiannon E

    2012-09-01

    Full Text Available Abstract Background Mitochondrial genomes comprise a small but critical component of the total DNA in eukaryotic organisms. They encode several key proteins for the cell’s major energy producing apparatus, the mitochondrial respiratory chain. Additonally, their nucleotide and amino acid sequences are of great utility as markers for systematics, molecular ecology and forensics. Their characterization through nucleotide sequencing is a fundamental starting point in mitogenomics. Methods to amplify complete mitochondrial genomes rapidly and efficiently from microgram quantities of tissue of single individuals are, however, not always available. Here we validate two approaches, which combine long-PCR with Roche 454 pyrosequencing technology, to obtain two complete mitochondrial genomes from individual amphibian species. Results We obtained two new xenopus frogs (Xenopus borealis and X. victorianus complete mitochondrial genome sequences by means of long-PCR followed by 454 of individual genomes (approach 1 or of multiple pooled genomes (approach 2, the mean depth of coverage per nucleotide was 9823 and 186, respectively. We also characterised and compared the new mitogenomes against their sister taxa; X. laevis and Silurana tropicalis, two of the most intensely studied amphibians. Our results demonstrate how our approaches can be used to obtain complete amphibian mitogenomes with depths of coverage that far surpass traditional primer-walking strategies, at either the same cost or less. Our results also demonstrate: that the size, gene content and order are the same among xenopus mitogenomes and that S. tropicalis form a separate clade to the other xenopus, among which X. laevis and X. victorianus were most closely related. Nucleotide and amino acid diversity was found to vary across the xenopus mitogenomes, with the greatest diversity observed in the Complex 1 gene nad4l and the least diversity observed in Complex 4 genes (cox1-3. All protein

  15. Modeling the potential risk factors of bovine viral diarrhea prevalence in Egypt using univariable and multivariable logistic regression analyses

    Directory of Open Access Journals (Sweden)

    Abdelfattah M. Selim

    2018-03-01

    Full Text Available Aim: The present cross-sectional study was conducted to determine the seroprevalence and potential risk factors associated with Bovine viral diarrhea virus (BVDV disease in cattle and buffaloes in Egypt, to model the potential risk factors associated with the disease using logistic regression (LR models, and to fit the best predictive model for the current data. Materials and Methods: A total of 740 blood samples were collected within November 2012-March 2013 from animals aged between 6 months and 3 years. The potential risk factors studied were species, age, sex, and herd location. All serum samples were examined with indirect ELIZA test for antibody detection. Data were analyzed with different statistical approaches such as Chi-square test, odds ratios (OR, univariable, and multivariable LR models. Results: Results revealed a non-significant association between being seropositive with BVDV and all risk factors, except for species of animal. Seroprevalence percentages were 40% and 23% for cattle and buffaloes, respectively. OR for all categories were close to one with the highest OR for cattle relative to buffaloes, which was 2.237. Likelihood ratio tests showed a significant drop of the -2LL from univariable LR to multivariable LR models. Conclusion: There was an evidence of high seroprevalence of BVDV among cattle as compared with buffaloes with the possibility of infection in different age groups of animals. In addition, multivariable LR model was proved to provide more information for association and prediction purposes relative to univariable LR models and Chi-square tests if we have more than one predictor.

  16. Comparative analyses of basal rate of metabolism in mammals: data selection does matter.

    Science.gov (United States)

    Genoud, Michel; Isler, Karin; Martin, Robert D

    2018-02-01

    Basal rate of metabolism (BMR) is a physiological parameter that should be measured under strictly defined experimental conditions. In comparative analyses among mammals BMR is widely used as an index of the intensity of the metabolic machinery or as a proxy for energy expenditure. Many databases with BMR values for mammals are available, but the criteria used to select metabolic data as BMR estimates have often varied and the potential effect of this variability has rarely been questioned. We provide a new, expanded BMR database reflecting compliance with standard criteria (resting, postabsorptive state; thermal neutrality; adult, non-reproductive status for females) and examine potential effects of differential selectivity on the results of comparative analyses. The database includes 1739 different entries for 817 species of mammals, compiled from the original sources. It provides information permitting assessment of the validity of each estimate and presents the value closest to a proper BMR for each entry. Using different selection criteria, several alternative data sets were extracted and used in comparative analyses of (i) the scaling of BMR to body mass and (ii) the relationship between brain mass and BMR. It was expected that results would be especially dependent on selection criteria with small sample sizes and with relatively weak relationships. Phylogenetically informed regression (phylogenetic generalized least squares, PGLS) was applied to the alternative data sets for several different clades (Mammalia, Eutheria, Metatheria, or individual orders). For Mammalia, a 'subsampling procedure' was also applied, in which random subsamples of different sample sizes were taken from each original data set and successively analysed. In each case, two data sets with identical sample size and species, but comprising BMR data with different degrees of reliability, were compared. Selection criteria had minor effects on scaling equations computed for large clades

  17. Predictors of success of external cephalic version and cephalic presentation at birth among 1253 women with non-cephalic presentation using logistic regression and classification tree analyses.

    Science.gov (United States)

    Hutton, Eileen K; Simioni, Julia C; Thabane, Lehana

    2017-08-01

    Among women with a fetus with a non-cephalic presentation, external cephalic version (ECV) has been shown to reduce the rate of breech presentation at birth and cesarean birth. Compared with ECV at term, beginning ECV prior to 37 weeks' gestation decreases the number of infants in a non-cephalic presentation at birth. The purpose of this secondary analysis was to investigate factors associated with a successful ECV procedure and to present this in a clinically useful format. Data were collected as part of the Early ECV Pilot and Early ECV2 Trials, which randomized 1776 women with a fetus in breech presentation to either early ECV (34-36 weeks' gestation) or delayed ECV (at or after 37 weeks). The outcome of interest was successful ECV, defined as the fetus being in a cephalic presentation immediately following the procedure, as well as at the time of birth. The importance of several factors in predicting successful ECV was investigated using two statistical methods: logistic regression and classification and regression tree (CART) analyses. Among nulliparas, non-engagement of the presenting part and an easily palpable fetal head were independently associated with success. Among multiparas, non-engagement of the presenting part, gestation less than 37 weeks and an easily palpable fetal head were found to be independent predictors of success. These findings were consistent with results of the CART analyses. Regardless of parity, descent of the presenting part was the most discriminating factor in predicting successful ECV and cephalic presentation at birth. © 2017 Nordic Federation of Societies of Obstetrics and Gynecology.

  18. Regressive Imagery in Creative Problem-Solving: Comparing Verbal Protocols of Expert and Novice Visual Artists and Computer Programmers

    Science.gov (United States)

    Kozbelt, Aaron; Dexter, Scott; Dolese, Melissa; Meredith, Daniel; Ostrofsky, Justin

    2015-01-01

    We applied computer-based text analyses of regressive imagery to verbal protocols of individuals engaged in creative problem-solving in two domains: visual art (23 experts, 23 novices) and computer programming (14 experts, 14 novices). Percentages of words involving primary process and secondary process thought, plus emotion-related words, were…

  19. Comparing lagged linear correlation, lagged regression, Granger causality, and vector autoregression for uncovering associations in EHR data.

    Science.gov (United States)

    Levine, Matthew E; Albers, David J; Hripcsak, George

    2016-01-01

    Time series analysis methods have been shown to reveal clinical and biological associations in data collected in the electronic health record. We wish to develop reliable high-throughput methods for identifying adverse drug effects that are easy to implement and produce readily interpretable results. To move toward this goal, we used univariate and multivariate lagged regression models to investigate associations between twenty pairs of drug orders and laboratory measurements. Multivariate lagged regression models exhibited higher sensitivity and specificity than univariate lagged regression in the 20 examples, and incorporating autoregressive terms for labs and drugs produced more robust signals in cases of known associations among the 20 example pairings. Moreover, including inpatient admission terms in the model attenuated the signals for some cases of unlikely associations, demonstrating how multivariate lagged regression models' explicit handling of context-based variables can provide a simple way to probe for health-care processes that confound analyses of EHR data.

  20. Comparative multivariate analyses of transient otoacoustic emissions and distorsion products in normal and impaired hearing.

    Science.gov (United States)

    Stamate, Mirela Cristina; Todor, Nicolae; Cosgarea, Marcel

    2015-01-01

    The clinical utility of otoacoustic emissions as a noninvasive objective test of cochlear function has been long studied. Both transient otoacoustic emissions and distorsion products can be used to identify hearing loss, but to what extent they can be used as predictors for hearing loss is still debated. Most studies agree that multivariate analyses have better test performances than univariate analyses. The aim of the study was to determine transient otoacoustic emissions and distorsion products performance in identifying normal and impaired hearing loss, using the pure tone audiogram as a gold standard procedure and different multivariate statistical approaches. The study included 105 adult subjects with normal hearing and hearing loss who underwent the same test battery: pure-tone audiometry, tympanometry, otoacoustic emission tests. We chose to use the logistic regression as a multivariate statistical technique. Three logistic regression models were developed to characterize the relations between different risk factors (age, sex, tinnitus, demographic features, cochlear status defined by otoacoustic emissions) and hearing status defined by pure-tone audiometry. The multivariate analyses allow the calculation of the logistic score, which is a combination of the inputs, weighted by coefficients, calculated within the analyses. The accuracy of each model was assessed using receiver operating characteristics curve analysis. We used the logistic score to generate receivers operating curves and to estimate the areas under the curves in order to compare different multivariate analyses. We compared the performance of each otoacoustic emission (transient, distorsion product) using three different multivariate analyses for each ear, when multi-frequency gold standards were used. We demonstrated that all multivariate analyses provided high values of the area under the curve proving the performance of the otoacoustic emissions. Each otoacoustic emission test presented high

  1. Exploring reasons for the observed inconsistent trial reports on intra-articular injections with hyaluronic acid in the treatment of osteoarthritis: Meta-regression analyses of randomized trials.

    Science.gov (United States)

    Johansen, Mette; Bahrt, Henriette; Altman, Roy D; Bartels, Else M; Juhl, Carsten B; Bliddal, Henning; Lund, Hans; Christensen, Robin

    2016-08-01

    The aim was to identify factors explaining inconsistent observations concerning the efficacy of intra-articular hyaluronic acid compared to intra-articular sham/control, or non-intervention control, in patients with symptomatic osteoarthritis, based on randomized clinical trials (RCTs). A systematic review and meta-regression analyses of available randomized trials were conducted. The outcome, pain, was assessed according to a pre-specified hierarchy of potentially available outcomes. Hedges׳s standardized mean difference [SMD (95% CI)] served as effect size. REstricted Maximum Likelihood (REML) mixed-effects models were used to combine study results, and heterogeneity was calculated and interpreted as Tau-squared and I-squared, respectively. Overall, 99 studies (14,804 patients) met the inclusion criteria: Of these, only 71 studies (72%), including 85 comparisons (11,216 patients), had adequate data available for inclusion in the primary meta-analysis. Overall, compared with placebo, intra-articular hyaluronic acid reduced pain with an effect size of -0.39 [-0.47 to -0.31; P hyaluronic acid. Based on available trial data, intra-articular hyaluronic acid showed a better effect than intra-articular saline on pain reduction in osteoarthritis. Publication bias and the risk of selective outcome reporting suggest only small clinical effect compared to saline. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Comparing spatial regression to random forests for large environmental data sets

    Science.gov (United States)

    Environmental data may be “large” due to number of records, number of covariates, or both. Random forests has a reputation for good predictive performance when using many covariates, whereas spatial regression, when using reduced rank methods, has a reputatio...

  3. Comparative analysis of neural network and regression based condition monitoring approaches for wind turbine fault detection

    DEFF Research Database (Denmark)

    Schlechtingen, Meik; Santos, Ilmar

    2011-01-01

    This paper presents the research results of a comparison of three different model based approaches for wind turbine fault detection in online SCADA data, by applying developed models to five real measured faults and anomalies. The regression based model as the simplest approach to build a normal...

  4. A Comparative Study of Classification and Regression Algorithms for Modelling Students' Academic Performance

    Science.gov (United States)

    Strecht, Pedro; Cruz, Luís; Soares, Carlos; Mendes-Moreira, João; Abreu, Rui

    2015-01-01

    Predicting the success or failure of a student in a course or program is a problem that has recently been addressed using data mining techniques. In this paper we evaluate some of the most popular classification and regression algorithms on this problem. We address two problems: prediction of approval/failure and prediction of grade. The former is…

  5. A Comparative Study of Pairwise Learning Methods Based on Kernel Ridge Regression.

    Science.gov (United States)

    Stock, Michiel; Pahikkala, Tapio; Airola, Antti; De Baets, Bernard; Waegeman, Willem

    2018-06-12

    Many machine learning problems can be formulated as predicting labels for a pair of objects. Problems of that kind are often referred to as pairwise learning, dyadic prediction, or network inference problems. During the past decade, kernel methods have played a dominant role in pairwise learning. They still obtain a state-of-the-art predictive performance, but a theoretical analysis of their behavior has been underexplored in the machine learning literature. In this work we review and unify kernel-based algorithms that are commonly used in different pairwise learning settings, ranging from matrix filtering to zero-shot learning. To this end, we focus on closed-form efficient instantiations of Kronecker kernel ridge regression. We show that independent task kernel ridge regression, two-step kernel ridge regression, and a linear matrix filter arise naturally as a special case of Kronecker kernel ridge regression, implying that all these methods implicitly minimize a squared loss. In addition, we analyze universality, consistency, and spectral filtering properties. Our theoretical results provide valuable insights into assessing the advantages and limitations of existing pairwise learning methods.

  6. Comparative biochemical analyses of venous blood and peritoneal fluid from horses with colic using a portable analyser and an in-house analyser.

    Science.gov (United States)

    Saulez, M N; Cebra, C K; Dailey, M

    2005-08-20

    Fifty-six horses with colic were examined over a period of three months. The concentrations of glucose, lactate, sodium, potassium and chloride, and the pH of samples of blood and peritoneal fluid, were determined with a portable clinical analyser and with an in-house analyser and the results were compared. Compared with the in-house analyser, the portable analyser gave higher pH values for blood and peritoneal fluid with greater variability in the alkaline range, and lower pH values in the acidic range, lower concentrations of glucose in the range below 8.3 mmol/l, and lower concentrations of lactate in venous blood in the range below 5 mmol/l and in peritoneal fluid in the range below 2 mmol/l, with less variability. On average, the portable analyser underestimated the concentrations of lactate and glucose in peritoneal fluid in comparison with the in-house analyser. Its measurements of the concentrations of sodium and chloride in peritoneal fluid had a higher bias and were more variable than the measurements in venous blood, and its measurements of potassium in venous blood and peritoneal fluid had a smaller bias and less variability than the measurements made with the in-house analyser.

  7. Control principles of confounders in ecological comparative studies: standardization and regressive modelss

    Directory of Open Access Journals (Sweden)

    Varaksin Anatoly

    2014-03-01

    Full Text Available The methods of the analysis of research data including the concomitant variables (confounders associated with both the response and the current factor are considered. There are two usual ways to take into account such variables: the first, at the stage of planning the experiment and the second, in analyzing the received data. Despite the equal effectiveness of these approaches, there exists strong reason to restrict the usage of regression method to accounting for confounders by ANCOVA. Authors consider the standardization by stratification as a reliable method to account for the effect of confounding factors as opposed to the widely-implemented application of logistic regression and the covariance analysis. The program for the automation of standardization procedure is proposed, it is available at the site of the Institute of Industrial Ecology.

  8. SPSS and SAS programs for comparing Pearson correlations and OLS regression coefficients.

    Science.gov (United States)

    Weaver, Bruce; Wuensch, Karl L

    2013-09-01

    Several procedures that use summary data to test hypotheses about Pearson correlations and ordinary least squares regression coefficients have been described in various books and articles. To our knowledge, however, no single resource describes all of the most common tests. Furthermore, many of these tests have not yet been implemented in popular statistical software packages such as SPSS and SAS. In this article, we describe all of the most common tests and provide SPSS and SAS programs to perform them. When they are applicable, our code also computes 100 × (1 - α)% confidence intervals corresponding to the tests. For testing hypotheses about independent regression coefficients, we demonstrate one method that uses summary data and another that uses raw data (i.e., Potthoff analysis). When the raw data are available, the latter method is preferred, because use of summary data entails some loss of precision due to rounding.

  9. A modeling approach to compare ΣPCB concentrations between congener-specific analyses

    Science.gov (United States)

    Gibson, Polly P.; Mills, Marc A.; Kraus, Johanna M.; Walters, David M.

    2017-01-01

    Changes in analytical methods over time pose problems for assessing long-term trends in environmental contamination by polychlorinated biphenyls (PCBs). Congener-specific analyses vary widely in the number and identity of the 209 distinct PCB chemical configurations (congeners) that are quantified, leading to inconsistencies among summed PCB concentrations (ΣPCB) reported by different studies. Here we present a modeling approach using linear regression to compare ΣPCB concentrations derived from different congener-specific analyses measuring different co-eluting groups. The approach can be used to develop a specific conversion model between any two sets of congener-specific analytical data from similar samples (similar matrix and geographic origin). We demonstrate the method by developing a conversion model for an example data set that includes data from two different analytical methods, a low resolution method quantifying 119 congeners and a high resolution method quantifying all 209 congeners. We used the model to show that the 119-congener set captured most (93%) of the total PCB concentration (i.e., Σ209PCB) in sediment and biological samples. ΣPCB concentrations estimated using the model closely matched measured values (mean relative percent difference = 9.6). General applications of the modeling approach include (a) generating comparable ΣPCB concentrations for samples that were analyzed for different congener sets; and (b) estimating the proportional contribution of different congener sets to ΣPCB. This approach may be especially valuable for enabling comparison of long-term remediation monitoring results even as analytical methods change over time. 

  10. The N400 as a snapshot of interactive processing: evidence from regression analyses of orthographic neighbor and lexical associate effects

    Science.gov (United States)

    Laszlo, Sarah; Federmeier, Kara D.

    2010-01-01

    Linking print with meaning tends to be divided into subprocesses, such as recognition of an input's lexical entry and subsequent access of semantics. However, recent results suggest that the set of semantic features activated by an input is broader than implied by a view wherein access serially follows recognition. EEG was collected from participants who viewed items varying in number and frequency of both orthographic neighbors and lexical associates. Regression analysis of single item ERPs replicated past findings, showing that N400 amplitudes are greater for items with more neighbors, and further revealed that N400 amplitudes increase for items with more lexical associates and with higher frequency neighbors or associates. Together, the data suggest that in the N400 time window semantic features of items broadly related to inputs are active, consistent with models in which semantic access takes place in parallel with stimulus recognition. PMID:20624252

  11. Determinants and Economic Impacts of North-South and South-South FDI in ASEAN : Panel Regression Analyses

    OpenAIRE

    Peseth, Seng

    2015-01-01

    This paper uses panel data of 10 ASEAN countries from 1995 to 2008 and studies the cross-country and industrial distribution of North and South FDI, investigates host country-specific determinants of the inflows of total FDI, North FDI and South FDI, and also compares the effects of North and South FDI on economic and industrial growth in the region.

  12. Comparing Millennials With Their Predecessors Regarding Online Travel Behaviours: A Logistical Regression Modelling Approach

    OpenAIRE

    Amaro, Suzanne; Henriques, Carla; Duarte, Paulo

    2016-01-01

    Millennials, also known as Generation Y, are characterized by their use of technology, which is an integral part of their lives. Research has shown that they are different from earlier generations regarding their behaviours and attitudes. This article investigates and compares the behavior of Millennials with those of previous generations using data collected among 1,732 Worldwide Internet users. In order to understand what differentiates Millennials, this study considers several characterist...

  13. Classification and regression tree (CART) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria

    Science.gov (United States)

    Dyer, Betsey D.; Kahn, Michael J.; LeBlanc, Mark D.

    2008-01-01

    Classification and regression tree (CART) analysis was applied to genome-wide tetranucleotide frequencies (genomic signatures) of 195 archaea and bacteria. Although genomic signatures have typically been used to classify evolutionary divergence, in this study, convergent evolution was the focus. Temperature optima for most of the organisms examined could be distinguished by CART analyses of tetranucleotide frequencies. This suggests that pervasive (nonlinear) qualities of genomes may reflect certain environmental conditions (such as temperature) in which those genomes evolved. The predominant use of GAGA and AGGA as the discriminating tetramers in CART models suggests that purine-loading and codon biases of thermophiles may explain some of the results. PMID:19054742

  14. The necessity for comparative risk analyses as seen from the political point of view

    International Nuclear Information System (INIS)

    Steger, U.

    1981-01-01

    The author describes the current insufficient utilization of risk analyses in the political decision process and investigates if other technologies encounter the same difficulties of acceptance as in the nuclear energy field. This being likely he is trying to find out which contribution comparative risk analyses could make to the process of democratic will-formation so that new technologies are accepted. Firstly the author establishes theses criticizing the recent scientific efforts made in the field of risk analyses and their usability for the political decision process. He then defines the criteria risk analyses have to meet in order to serve as scientific elements for consultative political discussions. (orig./HP) [de

  15. Assessing the suitability of summary data for two-sample Mendelian randomization analyses using MR-Egger regression: the role of the I2 statistic.

    Science.gov (United States)

    Bowden, Jack; Del Greco M, Fabiola; Minelli, Cosetta; Davey Smith, George; Sheehan, Nuala A; Thompson, John R

    2016-12-01

    : MR-Egger regression has recently been proposed as a method for Mendelian randomization (MR) analyses incorporating summary data estimates of causal effect from multiple individual variants, which is robust to invalid instruments. It can be used to test for directional pleiotropy and provides an estimate of the causal effect adjusted for its presence. MR-Egger regression provides a useful additional sensitivity analysis to the standard inverse variance weighted (IVW) approach that assumes all variants are valid instruments. Both methods use weights that consider the single nucleotide polymorphism (SNP)-exposure associations to be known, rather than estimated. We call this the `NO Measurement Error' (NOME) assumption. Causal effect estimates from the IVW approach exhibit weak instrument bias whenever the genetic variants utilized violate the NOME assumption, which can be reliably measured using the F-statistic. The effect of NOME violation on MR-Egger regression has yet to be studied. An adaptation of the I2 statistic from the field of meta-analysis is proposed to quantify the strength of NOME violation for MR-Egger. It lies between 0 and 1, and indicates the expected relative bias (or dilution) of the MR-Egger causal estimate in the two-sample MR context. We call it IGX2 . The method of simulation extrapolation is also explored to counteract the dilution. Their joint utility is evaluated using simulated data and applied to a real MR example. In simulated two-sample MR analyses we show that, when a causal effect exists, the MR-Egger estimate of causal effect is biased towards the null when NOME is violated, and the stronger the violation (as indicated by lower values of IGX2 ), the stronger the dilution. When additionally all genetic variants are valid instruments, the type I error rate of the MR-Egger test for pleiotropy is inflated and the causal effect underestimated. Simulation extrapolation is shown to substantially mitigate these adverse effects. We

  16. The more total cognitive load is reduced by cues, the better retention and transfer of multimedia learning: A meta-analysis and two meta-regression analyses.

    Science.gov (United States)

    Xie, Heping; Wang, Fuxing; Hao, Yanbin; Chen, Jiaxue; An, Jing; Wang, Yuxin; Liu, Huashan

    2017-01-01

    Cueing facilitates retention and transfer of multimedia learning. From the perspective of cognitive load theory (CLT), cueing has a positive effect on learning outcomes because of the reduction in total cognitive load and avoidance of cognitive overload. However, this has not been systematically evaluated. Moreover, what remains ambiguous is the direct relationship between the cue-related cognitive load and learning outcomes. A meta-analysis and two subsequent meta-regression analyses were conducted to explore these issues. Subjective total cognitive load (SCL) and scores on a retention test and transfer test were selected as dependent variables. Through a systematic literature search, 32 eligible articles encompassing 3,597 participants were included in the SCL-related meta-analysis. Among them, 25 articles containing 2,910 participants were included in the retention-related meta-analysis and the following retention-related meta-regression, while there were 29 articles containing 3,204 participants included in the transfer-related meta-analysis and the transfer-related meta-regression. The meta-analysis revealed a statistically significant cueing effect on subjective ratings of cognitive load (d = -0.11, 95% CI = [-0.19, -0.02], p < 0.05), retention performance (d = 0.27, 95% CI = [0.08, 0.46], p < 0.01), and transfer performance (d = 0.34, 95% CI = [0.12, 0.56], p < 0.01). The subsequent meta-regression analyses showed that dSCL for cueing significantly predicted dretention for cueing (β = -0.70, 95% CI = [-1.02, -0.38], p < 0.001), as well as dtransfer for cueing (β = -0.60, 95% CI = [-0.92, -0.28], p < 0.001). Thus in line with CLT, adding cues in multimedia materials can indeed reduce SCL and promote learning outcomes, and the more SCL is reduced by cues, the better retention and transfer of multimedia learning.

  17. Prediction Model of Cutting Parameters for Turning High Strength Steel Grade-H: Comparative Study of Regression Model versus ANFIS

    Directory of Open Access Journals (Sweden)

    Adel T. Abbas

    2017-01-01

    Full Text Available The Grade-H high strength steel is used in the manufacturing of many civilian and military products. The procedures of manufacturing these parts have several turning operations. The key factors for the manufacturing of these parts are the accuracy, surface roughness (Ra, and material removal rate (MRR. The production line of these parts contains many CNC turning machines to get good accuracy and repeatability. The manufacturing engineer should fulfill the required surface roughness value according to the design drawing from first trail (otherwise these parts will be rejected as well as keeping his eye on maximum metal removal rate. The rejection of these parts at any processing stage will represent huge problems to any factory because the processing and raw material of these parts are very expensive. In this paper the artificial neural network was used for predicting the surface roughness for different cutting parameters in CNC turning operations. These parameters were investigated to get the minimum surface roughness. In addition, a mathematical model for surface roughness was obtained from the experimental data using a regression analysis method. The experimental data are then compared with both the regression analysis results and ANFIS (Adaptive Network-based Fuzzy Inference System estimations.

  18. Comparing the cancer in Ninawa during three periods (1980-1990, 1991-2000, 2001-2010 using Poisson regression

    Directory of Open Access Journals (Sweden)

    Muzahem Mohammed Yahya AL-Hashimi

    2013-01-01

    Full Text Available Background: Iraq fought three wars in three consecutive decades, Iran-Iraq war (1980-1988, Persian Gulf War in 1991, and the Iraq′s war in 2003. In the nineties of the last century and up to the present time, there have been anecdotal reports of increase in cancer in Ninawa as in all provinces of Iraq, possibly as a result of exposure to depleted uranium used by American troops in the last two wars. This paper deals with cancer incidence in Ninawa, the most importance province in Iraq, where many of her sons were soldiers in the Iraqi army, and they have participated in the wars. Materials and Methods: The data was derived from the Directorate of Health in Ninawa. The data was divided into three sub periods: 1980-1990, 1991-2000, and 2001-2010. The analyses are performed using Poisson regressions. The response variable is the cancer incidence number. Cancer cases, age, sex, and years were considered as the explanatory variables. The logarithm of the population of Ninawa is used as an offset. The aim of this paper is to model the cancer incidence data and estimate the cancer incidence rate ratio (IRR to illustrate the changes that have occurred of incidence cancer in Ninawa in these three periods. Results: There is evidence of a reduction in the cancer IRR in Ninawa in the third period as well as in the second period. Our analyses found that breast cancer remained the first common cancer; while the lung, trachea, and bronchus the second in spite of decreasing as dramatically. Modest increases in incidence of prostate, penis, and other male genitals for the duration of the study period and stability in incidence of colon in the second and third periods. Modest increases in incidence of placenta and metastatic tumors, while the highest increase was in leukemia in the third period relates to the second period but not to the first period. The cancer IRR in men was decreased from more than 33% than those of females in the first period, more than 39

  19. Comparing the cancer in Ninawa during three periods (1980-1990, 1991-2000, 2001-2010) using Poisson regression.

    Science.gov (United States)

    Al-Hashimi, Muzahem Mohammed Yahya; Wang, Xiangjun

    2013-12-01

    Iraq fought three wars in three consecutive decades, Iran-Iraq war (1980-1988), Persian Gulf War in 1991, and the Iraq's war in 2003. In the nineties of the last century and up to the present time, there have been anecdotal reports of increase in cancer in Ninawa as in all provinces of Iraq, possibly as a result of exposure to depleted uranium used by American troops in the last two wars. This paper deals with cancer incidence in Ninawa, the most importance province in Iraq, where many of her sons were soldiers in the Iraqi army, and they have participated in the wars. The data was derived from the Directorate of Health in Ninawa. The data was divided into three sub periods: 1980-1990, 1991-2000, and 2001-2010. The analyses are performed using Poisson regressions. The response variable is the cancer incidence number. Cancer cases, age, sex, and years were considered as the explanatory variables. The logarithm of the population of Ninawa is used as an offset. The aim of this paper is to model the cancer incidence data and estimate the cancer incidence rate ratio (IRR) to illustrate the changes that have occurred of incidence cancer in Ninawa in these three periods. There is evidence of a reduction in the cancer IRR in Ninawa in the third period as well as in the second period. Our analyses found that breast cancer remained the first common cancer; while the lung, trachea, and bronchus the second in spite of decreasing as dramatically. Modest increases in incidence of prostate, penis, and other male genitals for the duration of the study period and stability in incidence of colon in the second and third periods. Modest increases in incidence of placenta and metastatic tumors, while the highest increase was in leukemia in the third period relates to the second period but not to the first period. The cancer IRR in men was decreased from more than 33% than those of females in the first period, more than 39% in the second period, and regressed to 9.56% in the third

  20. Comparing Effects of Biologic Agents in Treating Patients with Rheumatoid Arthritis: A Multiple Treatment Comparison Regression Analysis.

    Directory of Open Access Journals (Sweden)

    Ingunn Fride Tvete

    Full Text Available Rheumatoid arthritis patients have been treated with disease modifying anti-rheumatic drugs (DMARDs and the newer biologic drugs. We sought to compare and rank the biologics with respect to efficacy. We performed a literature search identifying 54 publications encompassing 9 biologics. We conducted a multiple treatment comparison regression analysis letting the number experiencing a 50% improvement on the ACR score be dependent upon dose level and disease duration for assessing the comparable relative effect between biologics and placebo or DMARD. The analysis embraced all treatment and comparator arms over all publications. Hence, all measured effects of any biologic agent contributed to the comparison of all biologic agents relative to each other either given alone or combined with DMARD. We found the drug effect to be dependent on dose level, but not on disease duration, and the impact of a high versus low dose level was the same for all drugs (higher doses indicated a higher frequency of ACR50 scores. The ranking of the drugs when given without DMARD was certolizumab (ranked highest, etanercept, tocilizumab/ abatacept and adalimumab. The ranking of the drugs when given with DMARD was certolizumab (ranked highest, tocilizumab, anakinra/rituximab, golimumab/ infliximab/ abatacept, adalimumab/ etanercept [corrected]. Still, all drugs were effective. All biologic agents were effective compared to placebo, with certolizumab the most effective and adalimumab (without DMARD treatment and adalimumab/ etanercept (combined with DMARD treatment the least effective. The drugs were in general more effective, except for etanercept, when given together with DMARDs.

  1. Using poisson regression to compare rates of unsatisfactory pap smears among gynecologists and to evaluate a performance improvement plan.

    Science.gov (United States)

    Wachtel, Mitchell S; Hatley, Warren G; de Riese, Cornelia

    2009-01-01

    To evaluate impact of a performance improvement (PI) plan implemented after initial analysis, comparing 7 gynecologists working in 2 clinics. From January to October 2005, unsatisfactory rates for gynecologists and clinics were calculated. A PI plan was instituted at the end of the first quarter of 2006. Unsatisfactory rates for each quarter of 2006 and the first quarter of 2007 were calculated. Poisson regression analyzed results. A total of 100 ThinPrep Pap smears initially deemed unsatisfactory underwent reprocessing and revaluation. The study's first part evaluated 2890 smears. Clinic unsatisfactory rates, 2.7% and 2.6%, were similar (p > 0.05). Gynecologists' unsatisfactory rates were 4.8-0.6%; differences between each of the highest 2 and lowest rates were significant (p improvement. Reprocessing ThinPrep smears is an important means of reducing unsatisfactory rates but should not be a substitute for attention to quality in sampling.

  2. Comparative genomics analyses revealed two virulent Listeria monocytogenes strains isolated from ready-to-eat food.

    Science.gov (United States)

    Lim, Shu Yong; Yap, Kien-Pong; Thong, Kwai Lin

    2016-01-01

    Listeria monocytogenes is an important foodborne pathogen that causes considerable morbidity in humans with high mortality rates. In this study, we have sequenced the genomes and performed comparative genomics analyses on two strains, LM115 and LM41, isolated from ready-to-eat food in Malaysia. The genome size of LM115 and LM41 was 2,959,041 and 2,963,111 bp, respectively. These two strains shared approximately 90% homologous genes. Comparative genomics and phylogenomic analyses revealed that LM115 and LM41 were more closely related to the reference strains F2365 and EGD-e, respectively. Our virulence profiling indicated a total of 31 virulence genes shared by both analysed strains. These shared genes included those that encode for internalins and L. monocytogenes pathogenicity island 1 (LIPI-1). Both the Malaysian L. monocytogenes strains also harboured several genes associated with stress tolerance to counter the adverse conditions. Seven antibiotic and efflux pump related genes which may confer resistance against lincomycin, erythromycin, fosfomycin, quinolone, tetracycline, and penicillin, and macrolides were identified in the genomes of both strains. Whole genome sequencing and comparative genomics analyses revealed two virulent L. monocytogenes strains isolated from ready-to-eat foods in Malaysia. The identification of strains with pathogenic, persistent, and antibiotic resistant potentials from minimally processed food warrant close attention from both healthcare and food industry.

  3. Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage.

    Science.gov (United States)

    Chen, Lin-xing; Hu, Min; Huang, Li-nan; Hua, Zheng-shuang; Kuang, Jia-liang; Li, Sheng-jin; Shu, Wen-sheng

    2015-07-01

    The microbial communities in acid mine drainage have been extensively studied to reveal their roles in acid generation and adaption to this environment. Lacking, however, are integrated community- and organism-wide comparative gene transcriptional analyses that could reveal the response and adaptation mechanisms of these extraordinary microorganisms to different environmental conditions. In this study, comparative metagenomics and metatranscriptomics were performed on microbial assemblages collected from four geochemically distinct acid mine drainage (AMD) sites. Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities. Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions. Organism-wide comparative analyses of the active taxa revealed environment-dependent gene transcriptional profiles, especially the distinct strategies used by Acidithiobacillus ferrivorans and Leptospirillum ferrodiazotrophum in nutrients assimilation and energy generation for survival under different conditions. Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments.

  4. Analyses of polycyclic aromatic hydrocarbon (PAH) and chiral-PAH analogues-methyl-β-cyclodextrin guest-host inclusion complexes by fluorescence spectrophotometry and multivariate regression analysis.

    Science.gov (United States)

    Greene, LaVana; Elzey, Brianda; Franklin, Mariah; Fakayode, Sayo O

    2017-03-05

    The negative health impact of polycyclic aromatic hydrocarbons (PAHs) and differences in pharmacological activity of enantiomers of chiral molecules in humans highlights the need for analysis of PAHs and their chiral analogue molecules in humans. Herein, the first use of cyclodextrin guest-host inclusion complexation, fluorescence spectrophotometry, and chemometric approach to PAH (anthracene) and chiral-PAH analogue derivatives (1-(9-anthryl)-2,2,2-triflouroethanol (TFE)) analyses are reported. The binding constants (K b ), stoichiometry (n), and thermodynamic properties (Gibbs free energy (ΔG), enthalpy (ΔH), and entropy (ΔS)) of anthracene and enantiomers of TFE-methyl-β-cyclodextrin (Me-β-CD) guest-host complexes were also determined. Chemometric partial-least-square (PLS) regression analysis of emission spectra data of Me-β-CD-guest-host inclusion complexes was used for the determination of anthracene and TFE enantiomer concentrations in Me-β-CD-guest-host inclusion complex samples. The values of calculated K b and negative ΔG suggest the thermodynamic favorability of anthracene-Me-β-CD and enantiomeric of TFE-Me-β-CD inclusion complexation reactions. However, anthracene-Me-β-CD and enantiomer TFE-Me-β-CD inclusion complexations showed notable differences in the binding affinity behaviors and thermodynamic properties. The PLS regression analysis resulted in square-correlation-coefficients of 0.997530 or better and a low LOD of 3.81×10 -7 M for anthracene and 3.48×10 -8 M for TFE enantiomers at physiological conditions. Most importantly, PLS regression accurately determined the anthracene and TFE enantiomer concentrations with an average low error of 2.31% for anthracene, 4.44% for R-TFE and 3.60% for S-TFE. The results of the study are highly significant because of its high sensitivity and accuracy for analysis of PAH and chiral PAH analogue derivatives without the need of an expensive chiral column, enantiomeric resolution, or use of a polarized

  5. Comparing cluster-level dynamic treatment regimens using sequential, multiple assignment, randomized trials: Regression estimation and sample size considerations.

    Science.gov (United States)

    NeCamp, Timothy; Kilbourne, Amy; Almirall, Daniel

    2017-08-01

    Cluster-level dynamic treatment regimens can be used to guide sequential treatment decision-making at the cluster level in order to improve outcomes at the individual or patient-level. In a cluster-level dynamic treatment regimen, the treatment is potentially adapted and re-adapted over time based on changes in the cluster that could be impacted by prior intervention, including aggregate measures of the individuals or patients that compose it. Cluster-randomized sequential multiple assignment randomized trials can be used to answer multiple open questions preventing scientists from developing high-quality cluster-level dynamic treatment regimens. In a cluster-randomized sequential multiple assignment randomized trial, sequential randomizations occur at the cluster level and outcomes are observed at the individual level. This manuscript makes two contributions to the design and analysis of cluster-randomized sequential multiple assignment randomized trials. First, a weighted least squares regression approach is proposed for comparing the mean of a patient-level outcome between the cluster-level dynamic treatment regimens embedded in a sequential multiple assignment randomized trial. The regression approach facilitates the use of baseline covariates which is often critical in the analysis of cluster-level trials. Second, sample size calculators are derived for two common cluster-randomized sequential multiple assignment randomized trial designs for use when the primary aim is a between-dynamic treatment regimen comparison of the mean of a continuous patient-level outcome. The methods are motivated by the Adaptive Implementation of Effective Programs Trial which is, to our knowledge, the first-ever cluster-randomized sequential multiple assignment randomized trial in psychiatry.

  6. Bisphenol-A exposures and behavioural aberrations: median and linear spline and meta-regression analyses of 12 toxicity studies in rodents.

    Science.gov (United States)

    Peluso, Marco E M; Munnia, Armelle; Ceppi, Marcello

    2014-11-05

    Exposures to bisphenol-A, a weak estrogenic chemical, largely used for the production of plastic containers, can affect the rodent behaviour. Thus, we examined the relationships between bisphenol-A and the anxiety-like behaviour, spatial skills, and aggressiveness, in 12 toxicity studies of rodent offspring from females orally exposed to bisphenol-A, while pregnant and/or lactating, by median and linear splines analyses. Subsequently, the meta-regression analysis was applied to quantify the behavioural changes. U-shaped, inverted U-shaped and J-shaped dose-response curves were found to describe the relationships between bisphenol-A with the behavioural outcomes. The occurrence of anxiogenic-like effects and spatial skill changes displayed U-shaped and inverted U-shaped curves, respectively, providing examples of effects that are observed at low-doses. Conversely, a J-dose-response relationship was observed for aggressiveness. When the proportion of rodents expressing certain traits or the time that they employed to manifest an attitude was analysed, the meta-regression indicated that a borderline significant increment of anxiogenic-like effects was present at low-doses regardless of sexes (β)=-0.8%, 95% C.I. -1.7/0.1, P=0.076, at ≤120 μg bisphenol-A. Whereas, only bisphenol-A-males exhibited a significant inhibition of spatial skills (β)=0.7%, 95% C.I. 0.2/1.2, P=0.004, at ≤100 μg/day. A significant increment of aggressiveness was observed in both the sexes (β)=67.9,C.I. 3.4, 172.5, P=0.038, at >4.0 μg. Then, bisphenol-A treatments significantly abrogated spatial learning and ability in males (Pbisphenol-A, e.g. ≤120 μg/day, were associated to behavioural aberrations in offspring. Copyright © 2014. Published by Elsevier Ireland Ltd.

  7. Comparative survey of dynamic analyses of free-piston Stirling engines

    Science.gov (United States)

    Kankam, M. D.; Rauch, J. S.

    1991-01-01

    Reported dynamics analyses for evaluating the steady-state response and stability of free-piston Stirling engine (FPSE) systems are compared. Various analytical approaches are discussed to provide guidance on their salient features. Recommendations are made in the recommendations remarks for an approach which captures most of the inherent properties of the engine. Such an approach has the potential for yielding results which will closely match practical FPSE-load systems.

  8. COMPARATIVE BIOMECHANICAL ANALYSES OF SQUAT JUMP WITHOUT AND WITH FLEXION IN KNEE JOINT

    Directory of Open Access Journals (Sweden)

    Saša Bubanj

    2009-11-01

    Full Text Available In sports hall of Faculty of sports and physical education in Niš, student demon- strated technique of squat jump – without and with flexion in knee joint. Elements of technique were recorded by using one digital video camera in sagital plane. By using comparative kinematics analyses, there were establish differences in values of kinema- tics parametres of different body segments. Bigger elevation of body centre of gravity was ascertain at bounce without flexion in knee joint.

  9. Item Response Theory Modeling and Categorical Regression Analyses of the Five-Factor Model Rating Form: A Study on Italian Community-Dwelling Adolescent Participants and Adult Participants.

    Science.gov (United States)

    Fossati, Andrea; Widiger, Thomas A; Borroni, Serena; Maffei, Cesare; Somma, Antonella

    2017-06-01

    To extend the evidence on the reliability and construct validity of the Five-Factor Model Rating Form (FFMRF) in its self-report version, two independent samples of Italian participants, which were composed of 510 adolescent high school students and 457 community-dwelling adults, respectively, were administered the FFMRF in its Italian translation. Adolescent participants were also administered the Italian translation of the Borderline Personality Features Scale for Children-11 (BPFSC-11), whereas adult participants were administered the Italian translation of the Triarchic Psychopathy Measure (TriPM). Cronbach α values were consistent with previous findings; in both samples, average interitem r values indicated acceptable internal consistency for all FFMRF scales. A multidimensional graded item response theory model indicated that the majority of FFMRF items had adequate discrimination parameters; information indices supported the reliability of the FFMRF scales. Both categorical (i.e., item-level) and scale-level regression analyses suggested that the FFMRF scores may predict a nonnegligible amount of variance in the BPFSC-11 total score in adolescent participants, and in the TriPM scale scores in adult participants.

  10. Area under the curve predictions of dalbavancin, a new lipoglycopeptide agent, using the end of intravenous infusion concentration data point by regression analyses such as linear, log-linear and power models.

    Science.gov (United States)

    Bhamidipati, Ravi Kanth; Syed, Muzeeb; Mullangi, Ramesh; Srinivas, Nuggehally

    2018-02-01

    1. Dalbavancin, a lipoglycopeptide, is approved for treating gram-positive bacterial infections. Area under plasma concentration versus time curve (AUC inf ) of dalbavancin is a key parameter and AUC inf /MIC ratio is a critical pharmacodynamic marker. 2. Using end of intravenous infusion concentration (i.e. C max ) C max versus AUC inf relationship for dalbavancin was established by regression analyses (i.e. linear, log-log, log-linear and power models) using 21 pairs of subject data. 3. The predictions of the AUC inf were performed using published C max data by application of regression equations. The quotient of observed/predicted values rendered fold difference. The mean absolute error (MAE)/root mean square error (RMSE) and correlation coefficient (r) were used in the assessment. 4. MAE and RMSE values for the various models were comparable. The C max versus AUC inf exhibited excellent correlation (r > 0.9488). The internal data evaluation showed narrow confinement (0.84-1.14-fold difference) with a RMSE models predicted AUC inf with a RMSE of 3.02-27.46% with fold difference largely contained within 0.64-1.48. 5. Regardless of the regression models, a single time point strategy of using C max (i.e. end of 30-min infusion) is amenable as a prospective tool for predicting AUC inf of dalbavancin in patients.

  11. Malignant progressive tumor cell clone exhibits significant up-regulation of cofilin-2 and 27-kDa modified form of cofilin-1 compared to regressive clone.

    Science.gov (United States)

    Kuramitsu, Yasuhiro; Wang, Yufeng; Okada, Futoshi; Baron, Byron; Tokuda, Kazuhiro; Kitagawa, Takao; Akada, Junko; Nakamura, Kazuyuki

    2013-09-01

    QR-32 is a regressive murine fibrosarcoma cell clone which cannot grow when they are transplanted in mice; QRsP-11 is a progressive malignant tumor cell clone derived from QR-32 which shows strong tumorigenicity. A recent study showed there to be differentially expressed up-regulated and down-regulated proteins in these cells, which were identified by proteomic differential display analyses by using two-dimensional gel electrophoresis and mass spectrometry. Cofilins are small proteins of less than 20 kDa. Their function is the regulation of actin assembly. Cofilin-1 is a small ubiquitous protein, and regulates actin dynamics by means of binding to actin filaments. Cofilin-1 plays roles in cell migration, proliferation and phagocytosis. Cofilin-2 is also a small protein, but it is mainly expressed in skeletal and cardiac muscles. There are many reports showing the positive correlation between the level of cofilin-1 and cancer progression. We have also reported an increased expression of cofilin-1 in pancreatic cancer tissues compared to adjacent paired normal tissues. On the other hand, cofilin-2 was significantly less expressed in pancreatic cancer tissues. Therefore, the present study investigated the comparison of the levels of cofilin-1 and cofilin-2 in regressive QR-32 and progressive QRsP-11cells by western blotting. Cofilin-2 was significantly up-regulated in QRsP-11 compared to QR-32 cells (p<0.001). On the other hand, the difference of the intensities of the bands of cofilin-1 (18 kDa) in QR-32 and QRsP-11 was not significant. However, bands of 27 kDa showed a quite different intensity between QR-32 and QRsP-11, with much higher intensities in QRsP-11 compared to QR-32 (p<0.001). These results suggested that the 27-kDa protein recognized by the antibody against cofilin-1 is a possible biomarker for progressive tumor cells.

  12. Sequencing, Characterization, and Comparative Analyses of the Plastome of Caragana rosea var. rosea

    Directory of Open Access Journals (Sweden)

    Mei Jiang

    2018-05-01

    Full Text Available To exploit the drought-resistant Caragana species, we performed a comparative study of the plastomes from four species: Caragana rosea, C. microphylla, C. kozlowii, and C. Korshinskii. The complete plastome sequence of the C. rosea was obtained using the next generation DNA sequencing technology. The genome is a circular structure of 133,122 bases and it lacks inverted repeat. It contains 111 unique genes, including 76 protein-coding, 30 tRNA, and four rRNA genes. Repeat analyses obtained 239, 244, 258, and 246 simple sequence repeats in C. rosea, C. microphylla, C. kozlowii, and C. korshinskii, respectively. Analyses of sequence divergence found two intergenic regions: trnI-CAU-ycf2 and trnN-GUU-ycf1, exhibiting a high degree of variations. Phylogenetic analyses showed that the four Caragana species belong to a monophyletic clade. Analyses of Ka/Ks ratios revealed that five genes: rpl16, rpl20, rps11, rps7, and ycf1 and several sites having undergone strong positive selection in the Caragana branch. The results lay the foundation for the development of molecular markers and the understanding of the evolutionary process for drought-resistant characteristics.

  13. CrusView: a Java-based visualization platform for comparative genomics analyses in Brassicaceae species.

    Science.gov (United States)

    Chen, Hao; Wang, Xiangfeng

    2013-09-01

    In plants and animals, chromosomal breakage and fusion events based on conserved syntenic genomic blocks lead to conserved patterns of karyotype evolution among species of the same family. However, karyotype information has not been well utilized in genomic comparison studies. We present CrusView, a Java-based bioinformatic application utilizing Standard Widget Toolkit/Swing graphics libraries and a SQLite database for performing visualized analyses of comparative genomics data in Brassicaceae (crucifer) plants. Compared with similar software and databases, one of the unique features of CrusView is its integration of karyotype information when comparing two genomes. This feature allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of the Brassicaceae genomes. Additionally, CrusView is a local program, which gives its users high flexibility when analyzing unpublished genomes and allows users to upload self-defined genomic information so that they can visually study the associations between genome structural variations and genetic elements, including chromosomal rearrangements, genomic macrosynteny, gene families, high-frequency recombination sites, and tandem and segmental duplications between related species. This tool will greatly facilitate karyotype, chromosome, and genome evolution studies using visualized comparative genomics approaches in Brassicaceae species. CrusView is freely available at http://www.cmbb.arizona.edu/CrusView/.

  14. Evaluation of modulation transfer function of optical lens system by support vector regression methodologies - A comparative study

    Science.gov (United States)

    Petković, Dalibor; Shamshirband, Shahaboddin; Saboohi, Hadi; Ang, Tan Fong; Anuar, Nor Badrul; Rahman, Zulkanain Abdul; Pavlović, Nenad T.

    2014-07-01

    The quantitative assessment of image quality is an important consideration in any type of imaging system. The modulation transfer function (MTF) is a graphical description of the sharpness and contrast of an imaging system or of its individual components. The MTF is also known and spatial frequency response. The MTF curve has different meanings according to the corresponding frequency. The MTF of an optical system specifies the contrast transmitted by the system as a function of image size, and is determined by the inherent optical properties of the system. In this study, the polynomial and radial basis function (RBF) are applied as the kernel function of Support Vector Regression (SVR) to estimate and predict estimate MTF value of the actual optical system according to experimental tests. Instead of minimizing the observed training error, SVR_poly and SVR_rbf attempt to minimize the generalization error bound so as to achieve generalized performance. The experimental results show that an improvement in predictive accuracy and capability of generalization can be achieved by the SVR_rbf approach in compare to SVR_poly soft computing methodology.

  15. Effective behaviour change techniques for physical activity and healthy eating in overweight and obese adults; systematic review and meta-regression analyses.

    Science.gov (United States)

    Samdal, Gro Beate; Eide, Geir Egil; Barth, Tom; Williams, Geoffrey; Meland, Eivind

    2017-03-28

    This systematic review aims to explain the heterogeneity in results of interventions to promote physical activity and healthy eating for overweight and obese adults, by exploring the differential effects of behaviour change techniques (BCTs) and other intervention characteristics. The inclusion criteria specified RCTs with ≥ 12 weeks' duration, from January 2007 to October 2014, for adults (mean age ≥ 40 years, mean BMI ≥ 30). Primary outcomes were measures of healthy diet or physical activity. Two reviewers rated study quality, coded the BCTs, and collected outcome results at short (≤6 months) and long term (≥12 months). Meta-analyses and meta-regressions were used to estimate effect sizes (ES), heterogeneity indices (I 2 ) and regression coefficients. We included 48 studies containing a total of 82 outcome reports. The 32 long term reports had an overall ES = 0.24 with 95% confidence interval (CI): 0.15 to 0.33 and I 2  = 59.4%. The 50 short term reports had an ES = 0.37 with 95% CI: 0.26 to 0.48, and I 2  = 71.3%. The number of BCTs unique to the intervention group, and the BCTs goal setting and self-monitoring of behaviour predicted the effect at short and long term. The total number of BCTs in both intervention arms and using the BCTs goal setting of outcome, feedback on outcome of behaviour, implementing graded tasks, and adding objects to the environment, e.g. using a step counter, significantly predicted the effect at long term. Setting a goal for change; and the presence of reporting bias independently explained 58.8% of inter-study variation at short term. Autonomy supportive and person-centred methods as in Motivational Interviewing, the BCTs goal setting of behaviour, and receiving feedback on the outcome of behaviour, explained all of the between study variations in effects at long term. There are similarities, but also differences in effective BCTs promoting change in healthy eating and physical activity and

  16. Comparative chloroplast genomics: Analyses including new sequencesfrom the angiosperms Nuphar advena and Ranunculus macranthus

    Energy Technology Data Exchange (ETDEWEB)

    Raubeso, Linda A.; Peery, Rhiannon; Chumley, Timothy W.; Dziubek,Chris; Fourcade, H. Matthew; Boore, Jeffrey L.; Jansen, Robert K.

    2007-03-01

    The number of completely sequenced plastid genomes available is growing rapidly. This new array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is most useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the new genomes reported here: Nuphar advena (from a basal-most lineage) and Ranunculus macranthus (from the basal group of eudicots). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition.

  17. Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential.

    Directory of Open Access Journals (Sweden)

    Pengpeng Li

    Full Text Available S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens.

  18. Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential.

    Science.gov (United States)

    Li, Pengpeng; Kwok, Amy H Y; Jiang, Jingwei; Ran, Tingting; Xu, Dongqing; Wang, Weiwu; Leung, Frederick C

    2015-01-01

    S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs) in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens.

  19. Comparative Genome Analyses of Serratia marcescens FS14 Reveals Its High Antagonistic Potential

    Science.gov (United States)

    Li, Pengpeng; Kwok, Amy H. Y.; Jiang, Jingwei; Ran, Tingting; Xu, Dongqing; Wang, Weiwu; Leung, Frederick C.

    2015-01-01

    S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs) in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens. PMID:25856195

  20. Comparative Phenotypical and Molecular Analyses of Arabidopsis Grown under Fluorescent and LED Light

    Directory of Open Access Journals (Sweden)

    Franka Seiler

    2017-06-01

    Full Text Available Comparative analyses of phenotypic and molecular traits of Arabidopsis thaliana grown under standardised conditions is still a challenge using climatic devices supplied with common light sources. These are in most cases fluorescent lights, which have several disadvantages such as heat production at higher light intensities, an invariable spectral output, and relatively rapid “ageing”. This results in non-desired variations of growth conditions and lowers the comparability of data acquired over extended time periods. In this study, we investigated the growth behaviour of Arabidopsis Col0 under different light conditions, applying fluorescent compared to LED lamps, and we conducted physiological as well as gene expression analyses. By changing the spectral composition and/or light intensity of LEDs we can clearly influence the growth behaviour of Arabidopsis and thereby study phenotypic attributes under very specific light conditions that are stable and reproducible, which is not necessarily given for fluorescent lamps. By using LED lights, we can also roughly mimic the sun light emission spectrum, enabling us to study plant growth in a more natural-like light set-up. We observed distinct growth behaviour under the different light regimes which was reflected by physiological properties of the plants. In conclusion, LEDs provide variable emission spectra for studying plant growth under defined, stable light conditions.

  1. CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses.

    Science.gov (United States)

    Proost, Sebastian; Mutwil, Marek

    2018-05-01

    The recent accumulation of gene expression data in the form of RNA sequencing creates unprecedented opportunities to study gene regulation and function. Furthermore, comparative analysis of the expression data from multiple species can elucidate which functional gene modules are conserved across species, allowing the study of the evolution of these modules. However, performing such comparative analyses on raw data is not feasible for many biologists. Here, we present CoNekT (Co-expression Network Toolkit), an open source web server, that contains user-friendly tools and interactive visualizations for comparative analyses of gene expression data and co-expression networks. These tools allow analysis and cross-species comparison of (i) gene expression profiles; (ii) co-expression networks; (iii) co-expressed clusters involved in specific biological processes; (iv) tissue-specific gene expression; and (v) expression profiles of gene families. To demonstrate these features, we constructed CoNekT-Plants for green alga, seed plants and flowering plants (Picea abies, Chlamydomonas reinhardtii, Vitis vinifera, Arabidopsis thaliana, Oryza sativa, Zea mays and Solanum lycopersicum) and thus provide a web-tool with the broadest available collection of plant phyla. CoNekT-Plants is freely available from http://conekt.plant.tools, while the CoNekT source code and documentation can be found at https://github.molgen.mpg.de/proost/CoNekT/.

  2. THE GOAL OF VALUE-BASED MEDICINE ANALYSES: COMPARABILITY. THE CASE FOR NEOVASCULAR MACULAR DEGENERATION

    Science.gov (United States)

    Brown, Gary C.; Brown, Melissa M.; Brown, Heidi C.; Kindermann, Sylvia; Sharma, Sanjay

    2007-01-01

    Purpose To evaluate the comparability of articles in the peer-reviewed literature assessing the (1) patient value and (2) cost-utility (cost-effectiveness) associated with interventions for neovascular age-related macular degeneration (ARMD). Methods A search was performed in the National Library of Medicine database of 16 million peer-reviewed articles using the key words cost-utility, cost-effectiveness, value, verteporfin, pegaptanib, laser photocoagulation, ranibizumab, and therapy. All articles that used an outcome of quality-adjusted life-years (QALYs) were studied in regard to (1) percent improvement in quality of life, (2) utility methodology, (3) utility respondents, (4) types of costs included (eg, direct healthcare, direct nonhealthcare, indirect), (5) cost bases (eg, Medicare, National Health Service in the United Kingdom), and (6) study cost perspective (eg, government, societal, third-party insurer). To qualify as a value-based medicine analysis, the patient value had to be measured using the outcome of the QALYs conferred by respective interventions. As with value-based medicine analyses, patient-based time tradeoff utility analysis had to be utilized, patient utility respondents were necessary, and direct medical costs were used. Results Among 21 cost-utility analyses performed on interventions for neovascular macular degeneration, 15 (71%) met value-based medicine criteria. The 6 others (29%) were not comparable owing to (1) varying utility methodology, (2) varying utility respondents, (3) differing costs utilized, (4) differing cost bases, and (5) varying study perspectives. Among value-based medicine studies, laser photocoagulation confers a 4.4% value gain (improvement in quality of life) for the treatment of classic subfoveal choroidal neovascularization. Intravitreal pegaptanib confers a 5.9% value gain (improvement in quality of life) for classic, minimally classic, and occult subfoveal choroidal neovascularization, and photodynamic therapy

  3. The goal of value-based medicine analyses: comparability. The case for neovascular macular degeneration.

    Science.gov (United States)

    Brown, Gary C; Brown, Melissa M; Brown, Heidi C; Kindermann, Sylvia; Sharma, Sanjay

    2007-01-01

    To evaluate the comparability of articles in the peer-reviewed literature assessing the (1) patient value and (2) cost-utility (cost-effectiveness) associated with interventions for neovascular age-related macular degeneration (ARMD). A search was performed in the National Library of Medicine database of 16 million peer-reviewed articles using the key words cost-utility, cost-effectiveness, value, verteporfin, pegaptanib, laser photocoagulation, ranibizumab, and therapy. All articles that used an outcome of quality-adjusted life-years (QALYs) were studied in regard to (1) percent improvement in quality of life, (2) utility methodology, (3) utility respondents, (4) types of costs included (eg, direct healthcare, direct nonhealthcare, indirect), (5) cost bases (eg, Medicare, National Health Service in the United Kingdom), and (6) study cost perspective (eg, government, societal, third-party insurer). To qualify as a value-based medicine analysis, the patient value had to be measured using the outcome of the QALYs conferred by respective interventions. As with value-based medicine analyses, patient-based time tradeoff utility analysis had to be utilized, patient utility respondents were necessary, and direct medical costs were used. Among 21 cost-utility analyses performed on interventions for neovascular macular degeneration, 15 (71%) met value-based medicine criteria. The 6 others (29%) were not comparable owing to (1) varying utility methodology, (2) varying utility respondents, (3) differing costs utilized, (4) differing cost bases, and (5) varying study perspectives. Among value-based medicine studies, laser photocoagulation confers a 4.4% value gain (improvement in quality of life) for the treatment of classic subfoveal choroidal neovascularization. Intravitreal pegaptanib confers a 5.9% value gain (improvement in quality of life) for classic, minimally classic, and occult subfoveal choroidal neovascularization, and photodynamic therapy with verteporfin confers

  4. Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and mammalian lung.

    Directory of Open Access Journals (Sweden)

    Weiling Zheng

    Full Text Available The fish swimbladder is a unique organ in vertebrate evolution and it functions for regulating buoyancy in most teleost species. It has long been postulated as a homolog of the tetrapod lung, but the molecular evidence is scarce. In order to understand the molecular function of swimbladder as well as its relationship with lungs in tetrapods, transcriptomic analyses of zebrafish swimbladder were carried out by RNA-seq. Gene ontology classification showed that genes in cytoskeleton and endoplasmic reticulum were enriched in the swimbladder. Further analyses depicted gene sets and pathways closely related to cytoskeleton constitution and regulation, cell adhesion, and extracellular matrix. Several prominent transcription factor genes in the swimbladder including hoxc4a, hoxc6a, hoxc8a and foxf1 were identified and their expressions in developing swimbladder during embryogenesis were confirmed. By comparison of enriched transcripts in the swimbladder with those in human and mouse lungs, we established the resemblance of transcriptome of the zebrafish swimbladder and mammalian lungs. Based on the transcriptomic data of zebrafish swimbladder, the predominant functions of swimbladder are in its epithelial and muscular tissues. Our comparative analyses also provide molecular evidence of the relatedness of the fish swimbladder and mammalian lung.

  5. Comparing Postural Stability Entropy Analyses to Differentiate Fallers and Non-fallers.

    Science.gov (United States)

    Fino, Peter C; Mojdehi, Ahmad R; Adjerid, Khaled; Habibi, Mohammad; Lockhart, Thurmon E; Ross, Shane D

    2016-05-01

    The health and financial cost of falls has spurred research to differentiate the characteristics of fallers and non-fallers. Postural stability has received much of the attention with recent studies exploring various measures of entropy. This study compared the discriminatory ability of several entropy methods at differentiating two paradigms in the center-of-pressure of elderly individuals: (1) eyes open (EO) vs. eyes closed (EC) and (2) fallers (F) vs. non-fallers (NF). Methods were compared using the area under the curve (AUC) of the receiver-operating characteristic curves developed from logistic regression models. Overall, multiscale entropy (MSE) and composite multiscale entropy (CompMSE) performed the best with AUCs of 0.71 for EO/EC and 0.77 for F/NF. When methods were combined together to maximize the AUC, the entropy classifier had an AUC of for 0.91 the F/NF comparison. These results suggest researchers and clinicians attempting to create clinical tests to identify fallers should consider a combination of every entropy method when creating a classifying test. Additionally, MSE and CompMSE classifiers using polar coordinate data outperformed rectangular coordinate data, encouraging more research into the most appropriate time series for postural stability entropy analysis.

  6. Genome-based comparative analyses of Antarctic and temperate species of Paenibacillus.

    Directory of Open Access Journals (Sweden)

    Melissa Dsouza

    Full Text Available Antarctic soils represent a unique environment characterised by extremes of temperature, salinity, elevated UV radiation, low nutrient and low water content. Despite the harshness of this environment, members of 15 bacterial phyla have been identified in soils of the Ross Sea Region (RSR. However, the survival mechanisms and ecological roles of these phyla are largely unknown. The aim of this study was to investigate whether strains of Paenibacillus darwinianus owe their resilience to substantial genomic changes. For this, genome-based comparative analyses were performed on three P. darwinianus strains, isolated from gamma-irradiated RSR soils, together with nine temperate, soil-dwelling Paenibacillus spp. The genome of each strain was sequenced to over 1,000-fold coverage, then assembled into contigs totalling approximately 3 Mbp per genome. Based on the occurrence of essential, single-copy genes, genome completeness was estimated at approximately 88%. Genome analysis revealed between 3,043-3,091 protein-coding sequences (CDSs, primarily associated with two-component systems, sigma factors, transporters, sporulation and genes induced by cold-shock, oxidative and osmotic stresses. These comparative analyses provide an insight into the metabolic potential of P. darwinianus, revealing potential adaptive mechanisms for survival in Antarctic soils. However, a large proportion of these mechanisms were also identified in temperate Paenibacillus spp., suggesting that these mechanisms are beneficial for growth and survival in a range of soil environments. These analyses have also revealed that the P. darwinianus genomes contain significantly fewer CDSs and have a lower paralogous content. Notwithstanding the incompleteness of the assemblies, the large differences in genome sizes, determined by the number of genes in paralogous clusters and the CDS content, are indicative of genome content scaling. Finally, these sequences are a resource for further

  7. Comparative Genomic and Transcriptional Analyses of CRISPR Systems Across the Genus Pyrobaculum

    Directory of Open Access Journals (Sweden)

    David L Bernick

    2012-07-01

    Full Text Available Within the domain Archaea, the CRISPR immune system appears to be nearly ubiquitous based on computational genome analyses. Initial studies in bacteria demonstrated that the CRISPR system targets invading plasmid and viral DNA. Recent experiments in the model archaeon Pyrococcus furiosus uncovered a novel RNA-targeting variant of the CRISPR system potentially unique to archaea. Because our understanding of CRISPR system evolution in other archaea is limited, we have taken a comparative genomic and transcriptomic view of the CRISPR arrays across six diverse species within the crenarchaeal genus Pyrobaculum. We present transcriptional data from each of four species in the genus (P. aerophilum, P. islandicum, P. calidifontis, P. arsenaticum, analyzing mature CRISPR-associated small RNA abundance from over 20 arrays. Within the genus, there is remarkable conservation of CRISPR array structure, as well as unique features that are have not been studied in other archaeal systems. These unique features include: a nearly invariant CRISPR promoter, conservation of direct repeat families, the 5' polarity of CRISPR-associated small RNA abundance, and a novel CRISPR-specific association with homologues of nurA and herA. These analyses provide a genus-level evolutionary perspective on archaeal CRISPR systems, broadening our understanding beyond existing non-comparative model systems.

  8. Parametric analyses of summative scores may lead to conflicting inferences when comparing groups: A simulation study.

    Science.gov (United States)

    Khan, Asaduzzaman; Chien, Chi-Wen; Bagraith, Karl S

    2015-04-01

    To investigate whether using a parametric statistic in comparing groups leads to different conclusions when using summative scores from rating scales compared with using their corresponding Rasch-based measures. A Monte Carlo simulation study was designed to examine between-group differences in the change scores derived from summative scores from rating scales, and those derived from their corresponding Rasch-based measures, using 1-way analysis of variance. The degree of inconsistency between the 2 scoring approaches (i.e. summative and Rasch-based) was examined, using varying sample sizes, scale difficulties and person ability conditions. This simulation study revealed scaling artefacts that could arise from using summative scores rather than Rasch-based measures for determining the changes between groups. The group differences in the change scores were statistically significant for summative scores under all test conditions and sample size scenarios. However, none of the group differences in the change scores were significant when using the corresponding Rasch-based measures. This study raises questions about the validity of the inference on group differences of summative score changes in parametric analyses. Moreover, it provides a rationale for the use of Rasch-based measures, which can allow valid parametric analyses of rating scale data.

  9. Comparative Genomics and Transcriptomics Analyses Reveal Divergent Lifestyle Features of Nematode Endoparasitic Fungus Hirsutella minnesotensis

    Science.gov (United States)

    Lai, Yiling; Liu, Keke; Zhang, Xinyu; Zhang, Xiaoling; Li, Kuan; Wang, Niuniu; Shu, Chi; Wu, Yunpeng; Wang, Chengshu; Bushley, Kathryn E.; Xiang, Meichun; Liu, Xingzhong

    2014-01-01

    Hirsutella minnesotensis [Ophiocordycipitaceae (Hypocreales, Ascomycota)] is a dominant endoparasitic fungus by using conidia that adhere to and penetrate the secondary stage juveniles of soybean cyst nematode. Its genome was de novo sequenced and compared with five entomopathogenic fungi in the Hypocreales and three nematode-trapping fungi in the Orbiliales (Ascomycota). The genome of H. minnesotensis is 51.4 Mb and encodes 12,702 genes enriched with transposable elements up to 32%. Phylogenomic analysis revealed that H. minnesotensis was diverged from entomopathogenic fungi in Hypocreales. Genome of H. minnesotensis is similar to those of entomopathogenic fungi to have fewer genes encoding lectins for adhesion and glycoside hydrolases for cellulose degradation, but is different from those of nematode-trapping fungi to possess more genes for protein degradation, signal transduction, and secondary metabolism. Those results indicate that H. minnesotensis has evolved different mechanism for nematode endoparasitism compared with nematode-trapping fungi. Transcriptomics analyses for the time-scale parasitism revealed the upregulations of lectins, secreted proteases and the genes for biosynthesis of secondary metabolites that could be putatively involved in host surface adhesion, cuticle degradation, and host manipulation. Genome and transcriptome analyses provided comprehensive understanding of the evolution and lifestyle of nematode endoparasitism. PMID:25359922

  10. Dual Regression

    OpenAIRE

    Spady, Richard; Stouli, Sami

    2012-01-01

    We propose dual regression as an alternative to the quantile regression process for the global estimation of conditional distribution functions under minimal assumptions. Dual regression provides all the interpretational power of the quantile regression process while avoiding the need for repairing the intersecting conditional quantile surfaces that quantile regression often produces in practice. Our approach introduces a mathematical programming characterization of conditional distribution f...

  11. Personal, social, and game-related correlates of active and non-active gaming among dutch gaming adolescents: survey-based multivariable, multilevel logistic regression analyses.

    Science.gov (United States)

    Simons, Monique; de Vet, Emely; Chinapaw, Mai Jm; de Boer, Michiel; Seidell, Jacob C; Brug, Johannes

    2014-04-04

    Playing video games contributes substantially to sedentary behavior in youth. A new generation of video games-active games-seems to be a promising alternative to sedentary games to promote physical activity and reduce sedentary behavior. At this time, little is known about correlates of active and non-active gaming among adolescents. The objective of this study was to examine potential personal, social, and game-related correlates of both active and non-active gaming in adolescents. A survey assessing game behavior and potential personal, social, and game-related correlates was conducted among adolescents (12-16 years, N=353) recruited via schools. Multivariable, multilevel logistic regression analyses, adjusted for demographics (age, sex and educational level of adolescents), were conducted to examine personal, social, and game-related correlates of active gaming ≥1 hour per week (h/wk) and non-active gaming >7 h/wk. Active gaming ≥1 h/wk was significantly associated with a more positive attitude toward active gaming (OR 5.3, CI 2.4-11.8; Pgames (OR 0.30, CI 0.1-0.6; P=.002), a higher score on habit strength regarding gaming (OR 1.9, CI 1.2-3.2; P=.008) and having brothers/sisters (OR 6.7, CI 2.6-17.1; Pgame engagement (OR 0.95, CI 0.91-0.997; P=.04). Non-active gaming >7 h/wk was significantly associated with a more positive attitude toward non-active gaming (OR 2.6, CI 1.1-6.3; P=.035), a stronger habit regarding gaming (OR 3.0, CI 1.7-5.3; P7 h/wk. Active gaming is most strongly (negatively) associated with attitude with respect to non-active games, followed by observed active game behavior of brothers and sisters and attitude with respect to active gaming (positive associations). On the other hand, non-active gaming is most strongly associated with observed non-active game behavior of friends, habit strength regarding gaming and attitude toward non-active gaming (positive associations). Habit strength was a correlate of both active and non-active gaming

  12. Personal, Social, and Game-Related Correlates of Active and Non-Active Gaming Among Dutch Gaming Adolescents: Survey-Based Multivariable, Multilevel Logistic Regression Analyses

    Science.gov (United States)

    de Vet, Emely; Chinapaw, Mai JM; de Boer, Michiel; Seidell, Jacob C; Brug, Johannes

    2014-01-01

    Background Playing video games contributes substantially to sedentary behavior in youth. A new generation of video games—active games—seems to be a promising alternative to sedentary games to promote physical activity and reduce sedentary behavior. At this time, little is known about correlates of active and non-active gaming among adolescents. Objective The objective of this study was to examine potential personal, social, and game-related correlates of both active and non-active gaming in adolescents. Methods A survey assessing game behavior and potential personal, social, and game-related correlates was conducted among adolescents (12-16 years, N=353) recruited via schools. Multivariable, multilevel logistic regression analyses, adjusted for demographics (age, sex and educational level of adolescents), were conducted to examine personal, social, and game-related correlates of active gaming ≥1 hour per week (h/wk) and non-active gaming >7 h/wk. Results Active gaming ≥1 h/wk was significantly associated with a more positive attitude toward active gaming (OR 5.3, CI 2.4-11.8; Pgames (OR 0.30, CI 0.1-0.6; P=.002), a higher score on habit strength regarding gaming (OR 1.9, CI 1.2-3.2; P=.008) and having brothers/sisters (OR 6.7, CI 2.6-17.1; Pgame engagement (OR 0.95, CI 0.91-0.997; P=.04). Non-active gaming >7 h/wk was significantly associated with a more positive attitude toward non-active gaming (OR 2.6, CI 1.1-6.3; P=.035), a stronger habit regarding gaming (OR 3.0, CI 1.7-5.3; P7 h/wk. Active gaming is most strongly (negatively) associated with attitude with respect to non-active games, followed by observed active game behavior of brothers and sisters and attitude with respect to active gaming (positive associations). On the other hand, non-active gaming is most strongly associated with observed non-active game behavior of friends, habit strength regarding gaming and attitude toward non-active gaming (positive associations). Habit strength was a

  13. Comparative Analyses of Zebrafish Anxiety-Like Behavior Using Conflict-Based Novelty Tests.

    Science.gov (United States)

    Kysil, Elana V; Meshalkina, Darya A; Frick, Erin E; Echevarria, David J; Rosemberg, Denis B; Maximino, Caio; Lima, Monica Gomes; Abreu, Murilo S; Giacomini, Ana C; Barcellos, Leonardo J G; Song, Cai; Kalueff, Allan V

    2017-06-01

    Modeling of stress and anxiety in adult zebrafish (Danio rerio) is increasingly utilized in neuroscience research and central nervous system (CNS) drug discovery. Representing the most commonly used zebrafish anxiety models, the novel tank test (NTT) focuses on zebrafish diving in response to potentially threatening stimuli, whereas the light-dark test (LDT) is based on fish scototaxis (innate preference for dark vs. bright areas). Here, we systematically evaluate the utility of these two tests, combining meta-analyses of published literature with comparative in vivo behavioral and whole-body endocrine (cortisol) testing. Overall, the NTT and LDT behaviors demonstrate a generally good cross-test correlation in vivo, whereas meta-analyses of published literature show that both tests have similar sensitivity to zebrafish anxiety-like states. Finally, NTT evokes higher levels of cortisol, likely representing a more stressful procedure than LDT. Collectively, our study reappraises NTT and LDT for studying anxiety-like states in zebrafish, and emphasizes their developing utility for neurobehavioral research. These findings can help optimize drug screening procedures by choosing more appropriate models for testing anxiolytic or anxiogenic drugs.

  14. A comparative study between nonlinear regression and artificial neural network approaches for modelling wild oat (Avena fatua) field emergence

    Science.gov (United States)

    Non-linear regression techniques are used widely to fit weed field emergence patterns to soil microclimatic indices using S-type functions. Artificial neural networks present interesting and alternative features for such modeling purposes. In this work, a univariate hydrothermal-time based Weibull m...

  15. Comparing of Normal Stress Distribution in Static and Dynamic Soil-Structure Interaction Analyses

    International Nuclear Information System (INIS)

    Kholdebarin, Alireza; Massumi, Ali; Davoodi, Mohammad; Tabatabaiefar, Hamid Reza

    2008-01-01

    It is important to consider the vertical component of earthquake loading and inertia force in soil-structure interaction analyses. In most circumstances, design engineers are primarily concerned about the analysis of behavior of foundations subjected to earthquake-induced forces transmitted from the bedrock. In this research, a single rigid foundation with designated geometrical parameters located on sandy-clay soil has been modeled in FLAC software with Finite Different Method and subjected to three different vertical components of earthquake records. In these cases, it is important to evaluate effect of footing on underlying soil and to consider normal stress in soil with and without footing. The distribution of normal stress under the footing in static and dynamic states has been studied and compared. This Comparison indicated that, increasing in normal stress under the footing caused by vertical component of ground excitations, has decreased dynamic vertical settlement in comparison with static state

  16. Comparative multielement analyses of airborne particulate samples collected in various areas

    International Nuclear Information System (INIS)

    Mamuro, Tetsuo; Matsuda, Yatsuka; Mizohata, Akira

    1973-01-01

    In order to grasp the characteristic features of the air pollution by particulates in various areas in Japan, multielement analyses by instrumental neutron activation analysis and radioisotope energy dispersive X-ray fluorescence analysis were applied to 31 airborne particulate samples collected in 15 different areas, and the analytical results obtained were compared with one another. All the samples were collected by so-called ''10 micron cut'' samplers, the collection efficiency of which is considered to be 50% at 8μ and nearly zero beyond 10μ. Among the areas in question there are clean seaside areas, heavily industrialized areas, small cities along the Inland Sea or the Pacific Ocean around which industrialization is progressing, a small city having only a big iron work, an area famous for its ceramic industry and so on. The atmospheres over them were found to be quite different not only in pollution extent but also in pollution pattern. (auth.)

  17. Meta-regression analyses to explain statistical heterogeneity in a systematic review of strategies for guideline implementation in primary health care.

    Directory of Open Access Journals (Sweden)

    Susanne Unverzagt

    Full Text Available This study is an in-depth-analysis to explain statistical heterogeneity in a systematic review of implementation strategies to improve guideline adherence of primary care physicians in the treatment of patients with cardiovascular diseases. The systematic review included randomized controlled trials from a systematic search in MEDLINE, EMBASE, CENTRAL, conference proceedings and registers of ongoing studies. Implementation strategies were shown to be effective with substantial heterogeneity of treatment effects across all investigated strategies. Primary aim of this study was to explain different effects of eligible trials and to identify methodological and clinical effect modifiers. Random effects meta-regression models were used to simultaneously assess the influence of multimodal implementation strategies and effect modifiers on physician adherence. Effect modifiers included the staff responsible for implementation, level of prevention and definition pf the primary outcome, unit of randomization, duration of follow-up and risk of bias. Six clinical and methodological factors were investigated as potential effect modifiers of the efficacy of different implementation strategies on guideline adherence in primary care practices on the basis of information from 75 eligible trials. Five effect modifiers were able to explain a substantial amount of statistical heterogeneity. Physician adherence was improved by 62% (95% confidence interval (95% CI 29 to 104% or 29% (95% CI 5 to 60% in trials where other non-medical professionals or nurses were included in the implementation process. Improvement of physician adherence was more successful in primary and secondary prevention of cardiovascular diseases by around 30% (30%; 95% CI -2 to 71% and 31%; 95% CI 9 to 57%, respectively compared to tertiary prevention. This study aimed to identify effect modifiers of implementation strategies on physician adherence. Especially the cooperation of different health

  18. Comparative analyses on dynamic performances of photovoltaic–thermal solar collectors integrated with phase change materials

    International Nuclear Information System (INIS)

    Su, Di; Jia, Yuting; Alva, Guruprasad; Liu, Lingkun; Fang, Guiyin

    2017-01-01

    Highlights: • The dynamic model of photovoltaic–thermal collector with phase change material was developed. • The performances of photovoltaic–thermal collector are performed comparative analyses. • The performances of photovoltaic–thermal collector with phase change material were evaluated. • Upper phase change material mode can improve performances of photovoltaic–thermal collector. - Abstract: The operating conditions (especially temperature) of photovoltaic–thermal solar collectors have significant influence on dynamic performance of the hybrid photovoltaic–thermal solar collectors. Only a small percentage of incoming solar radiation can be converted into electricity, and the rest is converted into heat. This heat leads to a decrease in efficiency of the photovoltaic module. In order to improve the performance of the hybrid photovoltaic–thermal solar collector, we performed comparative analyses on a hybrid photovoltaic–thermal solar collector integrated with phase change material. Electrical and thermal parameters like solar cell temperature, outlet temperature of air, electrical power, thermal power, electrical efficiency, thermal efficiency and overall efficiency are simulated and analyzed to evaluate the dynamic performance of the hybrid photovoltaic–thermal collector. It is found that the position of phase change material layer in the photovoltaic–thermal collector has a significant effect on the performance of the photovoltaic–thermal collector. The results indicate that upper phase change material mode in the photovoltaic–thermal collector can significantly improve the thermal and electrical performance of photovoltaic–thermal collector. It is found that overall efficiency of photovoltaic–thermal collector in ‘upper phase change material’ mode is 10.7% higher than that in ‘no phase change material’ mode. Further, for a photovoltaic–thermal collector with upper phase change material, it is verified that 3 cm

  19. A comparative study of frequency ratio, weights of evidence and logistic regression methods for landslide susceptibility mapping: Sultan Mountains, SW Turkey

    Science.gov (United States)

    Ozdemir, Adnan; Altural, Tolga

    2013-03-01

    This study evaluated and compared landslide susceptibility maps produced with three different methods, frequency ratio, weights of evidence, and logistic regression, by using validation datasets. The field surveys performed as part of this investigation mapped the locations of 90 landslides that had been identified in the Sultan Mountains of south-western Turkey. The landslide influence parameters used for this study are geology, relative permeability, land use/land cover, precipitation, elevation, slope, aspect, total curvature, plan curvature, profile curvature, wetness index, stream power index, sediment transportation capacity index, distance to drainage, distance to fault, drainage density, fault density, and spring density maps. The relationships between landslide distributions and these parameters were analysed using the three methods, and the results of these methods were then used to calculate the landslide susceptibility of the entire study area. The accuracy of the final landslide susceptibility maps was evaluated based on the landslides observed during the fieldwork, and the accuracy of the models was evaluated by calculating each model's relative operating characteristic curve. The predictive capability of each model was determined from the area under the relative operating characteristic curve and the areas under the curves obtained using the frequency ratio, logistic regression, and weights of evidence methods are 0.976, 0.952, and 0.937, respectively. These results indicate that the frequency ratio and weights of evidence models are relatively good estimators of landslide susceptibility in the study area. Specifically, the results of the correlation analysis show a high correlation between the frequency ratio and weights of evidence results, and the frequency ratio and logistic regression methods exhibit correlation coefficients of 0.771 and 0.727, respectively. The frequency ratio model is simple, and its input, calculation and output processes are

  20. Comparing Machine Learning Classifiers and Linear/Logistic Regression to Explore the Relationship between Hand Dimensions and Demographic Characteristics.

    Science.gov (United States)

    Miguel-Hurtado, Oscar; Guest, Richard; Stevenage, Sarah V; Neil, Greg J; Black, Sue

    2016-01-01

    Understanding the relationship between physiological measurements from human subjects and their demographic data is important within both the biometric and forensic domains. In this paper we explore the relationship between measurements of the human hand and a range of demographic features. We assess the ability of linear regression and machine learning classifiers to predict demographics from hand features, thereby providing evidence on both the strength of relationship and the key features underpinning this relationship. Our results show that we are able to predict sex, height, weight and foot size accurately within various data-range bin sizes, with machine learning classification algorithms out-performing linear regression in most situations. In addition, we identify the features used to provide these relationships applicable across multiple applications.

  1. Breast and cervical screening by race/ethnicity: comparative analyses before and during the Great Recession.

    Science.gov (United States)

    King, Christopher J; Chen, Jie; Garza, Mary A; Thomas, Stephen B

    2014-04-01

    Traditionally, economic recessions have resulted in decreased utilization of preventive health services. To explore racial and ethnic differences in breast and cervical cancer screening rates before and during the Great Recession. The Medical Expenditure Panel was the source for identifying 10,894 women, ages 50-74 for breast screening and 19,957 women, ages 21-65 for cervical screening. Survey years included 2004-2005 and 2009-2010. Dependent variables were as follows: 1) receipt of mammogram within the past 2 years; and 2) receipt of a Pap smear within the past 3 years. The interaction of the recession and the likelihood of screening between whites and minorities was analyzed. Multivariate regressions were applied to estimate the likelihood of screening for the two time periods while controlling for a recession variable. Nationally, breast and cervical cancer screening rates dropped during the recession period; white women contributed most to the decline. However, there were significant improvements in timely screening for both cancers among Hispanics during the recession period. After controlling for the recession, African American women were more likely to have timely screenings compared to white women. Screening rates during the recession were lowest in the South, Midwest and West. There was a national reduction in the percentages of women who obtained timely breast and cervical screenings during the Great Recession. Outreach efforts are needed to ensure that women who were not screened during the recession are screened. Widespread education about the Affordable Care Act may be helpful. Copyright © 2014 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

  2. The comparative analyses of different diagnostic approaches in detection of gastroesophageal reflux disease in children.

    Science.gov (United States)

    Ristic, Nina; Milovanovic, Ivan; Radusinovic, Milica; Stevic, Marija; Ristic, Milos; Ristic, Maja; Kisic Tepavcevic, Darija; Alempijevic, Tamara

    2017-01-01

    The aim of this study was to compare the different diagnostic approaches in detection of gastroesophageal reflux disease in children presented with symptoms suggesting gastroesophageal reflux disease. The study design was cross sectional. The study retrospectively included all children who underwent combined multiple intraluminal impedance and pH (pH-MII) monitoring due to gastrointestinal and/or extraesophageal symptoms suggesting gastroesophageal reflux disease at University Children's Hospital in Belgrade, from July 2012 to July 2016. A total of 218 (117 boys/101 girls), mean age 6.7 years (range 0.06-18.0 years), met the inclusion criteria. Gastroesophageal reflux disease was found in 128 of 218 children (57.4%) by pH-MII and in 76 (34.1%) children by pH metry alone. Using pH-MII monitoring as gold standard, sensitivity of pH-metry was lowest in infants (22.9%), with tendency to increase in older age groups (reaching 76.4% in children ≥ 9 years). The sensitivity of pH-metry alone in children with extraesophageal symptoms was 38.1%, while the sensitivity of pH-metry in children with gastrointestinal symptoms was 63.8%. Reflux esophagitis was identified in 31 (26.1%) of 119 children who underwent endoscopy. Logistic regression analysis showed that best predictors of endoscopic reflux esophagitis are the longest acid episode (OR = 1.52, preflux composite score (OR = 3.31, preflux composite score ≥ 29 (AUC 0.786, CI 0.695-0.877, preflux ≥ 18 minutes (AUC 0.784, CI 0.692-0.875, pgastroesophageal reflux disease, especially in infants. Our findings also showed that pH-MII parameters correlated significantly with the endoscopically confirmed erosive esophagitis.

  3. Propensity-score matching in economic analyses: comparison with regression models, instrumental variables, residual inclusion, differences-in-differences, and decomposition methods.

    Science.gov (United States)

    Crown, William H

    2014-02-01

    This paper examines the use of propensity score matching in economic analyses of observational data. Several excellent papers have previously reviewed practical aspects of propensity score estimation and other aspects of the propensity score literature. The purpose of this paper is to compare the conceptual foundation of propensity score models with alternative estimators of treatment effects. References are provided to empirical comparisons among methods that have appeared in the literature. These comparisons are available for a subset of the methods considered in this paper. However, in some cases, no pairwise comparisons of particular methods are yet available, and there are no examples of comparisons across all of the methods surveyed here. Irrespective of the availability of empirical comparisons, the goal of this paper is to provide some intuition about the relative merits of alternative estimators in health economic evaluations where nonlinearity, sample size, availability of pre/post data, heterogeneity, and missing variables can have important implications for choice of methodology. Also considered is the potential combination of propensity score matching with alternative methods such as differences-in-differences and decomposition methods that have not yet appeared in the empirical literature.

  4. Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization

    Directory of Open Access Journals (Sweden)

    Gelfand Mikhail S

    2009-02-01

    Full Text Available Abstract Background Nickel (Ni and cobalt (Co are trace elements required for a variety of biological processes. Ni is directly coordinated by proteins, whereas Co is mainly used as a component of vitamin B12. Although a number of Ni and Co-dependent enzymes have been characterized, systematic evolutionary analyses of utilization of these metals are limited. Results We carried out comparative genomic analyses to examine occurrence and evolutionary dynamics of the use of Ni and Co at the level of (i transport systems, and (ii metalloproteomes. Our data show that both metals are widely used in bacteria and archaea. Cbi/NikMNQO is the most common prokaryotic Ni/Co transporter, while Ni-dependent urease and Ni-Fe hydrogenase, and B12-dependent methionine synthase (MetH, ribonucleotide reductase and methylmalonyl-CoA mutase are the most widespread metalloproteins for Ni and Co, respectively. Occurrence of other metalloenzymes showed a mosaic distribution and a new B12-dependent protein family was predicted. Deltaproteobacteria and Methanosarcina generally have larger Ni- and Co-dependent proteomes. On the other hand, utilization of these two metals is limited in eukaryotes, and very few of these organisms utilize both of them. The Ni-utilizing eukaryotes are mostly fungi (except saccharomycotina and plants, whereas most B12-utilizing organisms are animals. The NiCoT transporter family is the most widespread eukaryotic Ni transporter, and eukaryotic urease and MetH are the most common Ni- and B12-dependent enzymes, respectively. Finally, investigation of environmental and other conditions and identity of organisms that show dependence on Ni or Co revealed that host-associated organisms (particularly obligate intracellular parasites and endosymbionts have a tendency for loss of Ni/Co utilization. Conclusion Our data provide information on the evolutionary dynamics of Ni and Co utilization and highlight widespread use of these metals in the three

  5. Correlation of Klebsiella pneumoniae comparative genetic analyses with virulence profiles in a murine respiratory disease model.

    Directory of Open Access Journals (Sweden)

    Ramy A Fodah

    Full Text Available Klebsiella pneumoniae is a bacterial pathogen of worldwide importance and a significant contributor to multiple disease presentations associated with both nosocomial and community acquired disease. ATCC 43816 is a well-studied K. pneumoniae strain which is capable of causing an acute respiratory disease in surrogate animal models. In this study, we performed sequencing of the ATCC 43816 genome to support future efforts characterizing genetic elements required for disease. Furthermore, we performed comparative genetic analyses to the previously sequenced genomes from NTUH-K2044 and MGH 78578 to gain an understanding of the conservation of known virulence determinants amongst the three strains. We found that ATCC 43816 and NTUH-K2044 both possess the known virulence determinant for yersiniabactin, as well as a Type 4 secretion system (T4SS, CRISPR system, and an acetonin catabolism locus, all absent from MGH 78578. While both NTUH-K2044 and MGH 78578 are clinical isolates, little is known about the disease potential of these strains in cell culture and animal models. Thus, we also performed functional analyses in the murine macrophage cell lines RAW264.7 and J774A.1 and found that MGH 78578 (K52 serotype was internalized at higher levels than ATCC 43816 (K2 and NTUH-K2044 (K1, consistent with previous characterization of the antiphagocytic properties of K1 and K2 serotype capsules. We also examined the three K. pneumoniae strains in a novel BALB/c respiratory disease model and found that ATCC 43816 and NTUH-K2044 are highly virulent (LD50<100 CFU while MGH 78578 is relatively avirulent.

  6. Creating global comparative analyses of tectonic rifts, monogenetic volcanism and inverted relief

    Science.gov (United States)

    van Wyk de Vries, Benjamin

    2016-04-01

    I have been all around the world, and to other planets and have travelled from the present to the Archaean and back to seek out the most significant tectonic rifts, monogenetic volcanoes and examples of inverted relief. I have done this to provide a broad foundation of the comparative analysis for the Chaîne des Puys - Limagne fault nomination to UNESCO world Heritage. This would have been an impossible task, if not for the cooperation of the scientific community and for Google Earth, Google Maps and academic search engines. In preparing global comparisons of geological features, these quite recently developed tools provide a powerful way to find and describe geological features. The ability to do scientific crowd sourcing, rapidly discussing with colleagues about features, allows large numbers of areas to be checked and the open GIS tools (such as Google Earth) allow a standardised description. Search engines also allow the literature on areas to be checked and compared. I will present a comparative study of rifts of the world, monogenetic volcanic field and inverted relief, integrated to analyse the full geological system represented by the Chaîne des Puys - Limagne fault. The analysis confirms that the site is an exceptional example of the first steps of continental drift in a mountain rift setting, and that this is necessarily seen through the combined landscape of tectonic, volcanic and geomorphic features. The analysis goes further to deepen the understanding of geological systems and stresses the need for more study on geological heritage using such a global and broad systems approach.

  7. Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC.

    Directory of Open Access Journals (Sweden)

    Weerachai Jaratlerdsiri

    Full Text Available The major histocompatibility complex (MHC is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.

  8. The comparative analyses of different diagnostic approaches in detection of gastroesophageal reflux disease in children.

    Directory of Open Access Journals (Sweden)

    Nina Ristic

    Full Text Available The aim of this study was to compare the different diagnostic approaches in detection of gastroesophageal reflux disease in children presented with symptoms suggesting gastroesophageal reflux disease.The study design was cross sectional. The study retrospectively included all children who underwent combined multiple intraluminal impedance and pH (pH-MII monitoring due to gastrointestinal and/or extraesophageal symptoms suggesting gastroesophageal reflux disease at University Children's Hospital in Belgrade, from July 2012 to July 2016.A total of 218 (117 boys/101 girls, mean age 6.7 years (range 0.06-18.0 years, met the inclusion criteria. Gastroesophageal reflux disease was found in 128 of 218 children (57.4% by pH-MII and in 76 (34.1% children by pH metry alone. Using pH-MII monitoring as gold standard, sensitivity of pH-metry was lowest in infants (22.9%, with tendency to increase in older age groups (reaching 76.4% in children ≥ 9 years. The sensitivity of pH-metry alone in children with extraesophageal symptoms was 38.1%, while the sensitivity of pH-metry in children with gastrointestinal symptoms was 63.8%. Reflux esophagitis was identified in 31 (26.1% of 119 children who underwent endoscopy. Logistic regression analysis showed that best predictors of endoscopic reflux esophagitis are the longest acid episode (OR = 1.52, p<0.05 and DeMeester reflux composite score (OR = 3.31, p<0.05. The significant cutoff values included DeMeester reflux composite score ≥ 29 (AUC 0.786, CI 0.695-0.877, p<0.01 and duration of longest acid reflux ≥ 18 minutes (AUC 0.784, CI 0.692-0.875, p<0.01.The results of our study suggested that compared with pH-metry alone, pH-MII had significantly higher detection rate of gastroesophageal reflux disease, especially in infants. Our findings also showed that pH-MII parameters correlated significantly with the endoscopically confirmed erosive esophagitis.

  9. Characterization of Aeromonas hydrophila wound pathotypes by comparative genomic and functional analyses of virulence genes.

    Science.gov (United States)

    Grim, Christopher J; Kozlova, Elena V; Sha, Jian; Fitts, Eric C; van Lier, Christina J; Kirtley, Michelle L; Joseph, Sandeep J; Read, Timothy D; Burd, Eileen M; Tall, Ben D; Joseph, Sam W; Horneman, Amy J; Chopra, Ashok K; Shak, Joshua R

    2013-04-23

    Aeromonas hydrophila has increasingly been implicated as a virulent and antibiotic-resistant etiologic agent in various human diseases. In a previously published case report, we described a subject with a polymicrobial wound infection that included a persistent and aggressive strain of A. hydrophila (E1), as well as a more antibiotic-resistant strain of A. hydrophila (E2). To better understand the differences between pathogenic and environmental strains of A. hydrophila, we conducted comparative genomic and functional analyses of virulence-associated genes of these two wound isolates (E1 and E2), the environmental type strain A. hydrophila ATCC 7966(T), and four other isolates belonging to A. aquariorum, A. veronii, A. salmonicida, and A. caviae. Full-genome sequencing of strains E1 and E2 revealed extensive differences between the two and strain ATCC 7966(T). The more persistent wound infection strain, E1, harbored coding sequences for a cytotoxic enterotoxin (Act), a type 3 secretion system (T3SS), flagella, hemolysins, and a homolog of exotoxin A found in Pseudomonas aeruginosa. Corresponding phenotypic analyses with A. hydrophila ATCC 7966(T) and SSU as reference strains demonstrated the functionality of these virulence genes, with strain E1 displaying enhanced swimming and swarming motility, lateral flagella on electron microscopy, the presence of T3SS effector AexU, and enhanced lethality in a mouse model of Aeromonas infection. By combining sequence-based analysis and functional assays, we characterized an A. hydrophila pathotype, exemplified by strain E1, that exhibited increased virulence in a mouse model of infection, likely because of encapsulation, enhanced motility, toxin secretion, and cellular toxicity. Aeromonas hydrophila is a common aquatic bacterium that has increasingly been implicated in serious human infections. While many determinants of virulence have been identified in Aeromonas, rapid identification of pathogenic versus nonpathogenic

  10. Differentiating regressed melanoma from regressed lichenoid keratosis.

    Science.gov (United States)

    Chan, Aegean H; Shulman, Kenneth J; Lee, Bonnie A

    2017-04-01

    Distinguishing regressed lichen planus-like keratosis (LPLK) from regressed melanoma can be difficult on histopathologic examination, potentially resulting in mismanagement of patients. We aimed to identify histopathologic features by which regressed melanoma can be differentiated from regressed LPLK. Twenty actively inflamed LPLK, 12 LPLK with regression and 15 melanomas with regression were compared and evaluated by hematoxylin and eosin staining as well as Melan-A, microphthalmia transcription factor (MiTF) and cytokeratin (AE1/AE3) immunostaining. (1) A total of 40% of regressed melanomas showed complete or near complete loss of melanocytes within the epidermis with Melan-A and MiTF immunostaining, while 8% of regressed LPLK exhibited this finding. (2) Necrotic keratinocytes were seen in the epidermis in 33% regressed melanomas as opposed to all of the regressed LPLK. (3) A dense infiltrate of melanophages in the papillary dermis was seen in 40% of regressed melanomas, a feature not seen in regressed LPLK. In summary, our findings suggest that a complete or near complete loss of melanocytes within the epidermis strongly favors a regressed melanoma over a regressed LPLK. In addition, necrotic epidermal keratinocytes and the presence of a dense band-like distribution of dermal melanophages can be helpful in differentiating these lesions. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  11. Consequences of kriging and land use regression for PM2.5 predictions in epidemiologic analyses: insights into spatial variability using high-resolution satellite data.

    Science.gov (United States)

    Alexeeff, Stacey E; Schwartz, Joel; Kloog, Itai; Chudnovsky, Alexandra; Koutrakis, Petros; Coull, Brent A

    2015-01-01

    Many epidemiological studies use predicted air pollution exposures as surrogates for true air pollution levels. These predicted exposures contain exposure measurement error, yet simulation studies have typically found negligible bias in resulting health effect estimates. However, previous studies typically assumed a statistical spatial model for air pollution exposure, which may be oversimplified. We address this shortcoming by assuming a realistic, complex exposure surface derived from fine-scale (1 km × 1 km) remote-sensing satellite data. Using simulation, we evaluate the accuracy of epidemiological health effect estimates in linear and logistic regression when using spatial air pollution predictions from kriging and land use regression models. We examined chronic (long-term) and acute (short-term) exposure to air pollution. Results varied substantially across different scenarios. Exposure models with low out-of-sample R(2) yielded severe biases in the health effect estimates of some models, ranging from 60% upward bias to 70% downward bias. One land use regression exposure model with >0.9 out-of-sample R(2) yielded upward biases up to 13% for acute health effect estimates. Almost all models drastically underestimated the SEs. Land use regression models performed better in chronic effect simulations. These results can help researchers when interpreting health effect estimates in these types of studies.

  12. Comparative transcriptomic analyses of vegetable and grain pea (Pisum sativum L. seed development

    Directory of Open Access Journals (Sweden)

    Na eLiu

    2015-11-01

    Full Text Available Understanding the molecular mechanisms regulating pea seed developmental process is extremely important for pea breeding. In this study, we used high-throughput RNA-Seq and bioinformatics analyses to examine the changes in gene expression during seed development in vegetable pea and grain pea, and compare the gene expression profiles of these two pea types. RNA-Seq generated 18.7 G of raw data, which were then de novo assembled into 77,273 unigenes with a mean length of 930 bp. Our results illustrate that transcriptional control during pea seed development is a highly coordinated process. There were 459 and 801 genes differentially expressed at early and late seed maturation stages between vegetable pea and grain pea, respectively. Soluble sugar and starch metabolism related genes were significantly activated during the development of pea seeds coinciding with the onset of accumulation of sugar and starch in the seeds. A comparative analysis of genes involved in sugar and starch biosynthesis in vegetable pea (high seed soluble sugar and low starch and grain pea (high seed starch and low soluble sugar revealed that differential expression of related genes at late development stages results in a negative correlation between soluble sugar and starch biosynthetic flux in vegetable and grain pea seeds. RNA-Seq data was validated by using real-time quantitative RT-PCR analysis for 30 randomly selected genes. To our knowledge, this work represents the first report of seed development transcriptomics in pea. The obtained results provide a foundation to support future efforts to unravel the underlying mechanisms that control the developmental biology of pea seeds, and serve as a valuable resource for improving pea breeding.

  13. Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper

    Science.gov (United States)

    Yin, Wei; Wang, Zong-ji; Li, Qi-ye; Lian, Jin-ming; Zhou, Yang; Lu, Bing-zheng; Jin, Li-jun; Qiu, Peng-xin; Zhang, Pei; Zhu, Wen-bo; Wen, Bo; Huang, Yi-jun; Lin, Zhi-long; Qiu, Bi-tao; Su, Xing-wen; Yang, Huan-ming; Zhang, Guo-jie; Yan, Guang-mei; Zhou, Qi

    2016-01-01

    Snakes have numerous features distinctive from other tetrapods and a rich history of genome evolution that is still obscure. Here, we report the high-quality genome of the five-pacer viper, Deinagkistrodon acutus, and comparative analyses with other representative snake and lizard genomes. We map the evolutionary trajectories of transposable elements (TEs), developmental genes and sex chromosomes onto the snake phylogeny. TEs exhibit dynamic lineage-specific expansion, and many viper TEs show brain-specific gene expression along with their nearby genes. We detect signatures of adaptive evolution in olfactory, venom and thermal-sensing genes and also functional degeneration of genes associated with vision and hearing. Lineage-specific relaxation of functional constraints on respective Hox and Tbx limb-patterning genes supports fossil evidence for a successive loss of forelimbs then hindlimbs during snake evolution. Finally, we infer that the ZW sex chromosome pair had undergone at least three recombination suppression events in the ancestor of advanced snakes. These results altogether forge a framework for our deep understanding into snakes' history of molecular evolution. PMID:27708285

  14. Taking a comparative approach: analysing personality as a multivariate behavioural response across species.

    Directory of Open Access Journals (Sweden)

    Alecia J Carter

    Full Text Available Animal personality, repeatable behaviour through time and across contexts, is ecologically and evolutionarily important as it can account for the exhibition of sub-optimal behaviours. Interspecific comparisons have been suggested as important for understanding the evolution of animal personality; however, these are seldom accomplished due, in part, to the lack of statistical tools for quantifying differences and similarities in behaviour between groups of individuals. We used nine species of closely-related coral reef fishes to investigate the usefulness of ecological community analyses for the analysis of between-species behavioural differences and behavioural heterogeneity. We first documented behavioural carryover across species by observing the fishes' behaviour and measuring their response to a threatening stimulus to quantify boldness. Bold fish spent more time away from the reef and fed more than shy fish. We then used ecological community analysis tools (canonical variate analysis, multi-response permutation procedure, and permutational analysis of multivariate dispersion and identified four 'clusters' of behaviourally similar fishes, and found that the species differ in the behavioural variation expressed; some species are more behaviourally heterogeneous than others. We found that ecological community analysis tools are easily and fruitfully applied to comparative studies of personality and encourage their use by future studies.

  15. Comparative proteomic analyses of macular and peripheral retina of cynomolgus monkeys (Macaca fascicularis).

    Science.gov (United States)

    Okamoto, Haru; Umeda, Shinsuke; Nozawa, Takehiro; Suzuki, Michihiro T; Yoshikawa, Yasuhiro; Matsuura, Etsuko T; Iwata, Takeshi

    2010-01-01

    The central region of the primate retina is called the macula. The fovea is located at the center of the macula, where the photoreceptors are concentrated to create a neural network adapted for high visual acuity. Damage to the fovea, e.g., by macular dystrophies and age-related macular degeneration, can reduce central visual acuity. The molecular mechanisms leading to these diseases are most likely dependent on the proteins in the macula which differ from those in the peripheral retina in expression level. To investigate whether the distribution of proteins in the macula is different from the peripheral retina, proteomic analyses of tissues from these two regions of cynomolgus monkeys were compared. Two-dimensional gel electrophoresis and mass spectrometry identified 26 proteins that were present only in the macular gel spots. The expression levels of five proteins, cone photoreceptor specific arrestin-C, gamma-synuclein, epidermal fatty acid binding protein, tropomyosin 1alpha chain, and heterogeneous nuclear ribonucleoproteins A2/B1, were significantly higher in the macula than in the peripheral retina. Immunostaining of macula sections by antibodies to each identified protein revealed unique localization in the retina, retinal pigment epithelial cells and the choroidal layer. Some of these proteins were located in cells with higher densities in the macula. We suggest that it will be important to study these proteins to determine their contribution to the pathogenesis and progression of macula diseases.

  16. Systematic comparative and sensitivity analyses of additive and outranking techniques for supporting impact significance assessments

    International Nuclear Information System (INIS)

    Cloquell-Ballester, Vicente-Agustin; Monterde-Diaz, Rafael; Cloquell-Ballester, Victor-Andres; Santamarina-Siurana, Maria-Cristina

    2007-01-01

    Assessing the significance of environmental impacts is one of the most important and all together difficult processes of Environmental Impact Assessment. This is largely due to the multicriteria nature of the problem. To date, decision techniques used in the process suffer from two drawbacks, namely the problem of compensation and the problem of identification of the 'exact boundary' between sub-ranges. This article discusses these issues and proposes a methodology for determining the significance of environmental impacts based on comparative and sensitivity analyses using the Electre TRI technique. An application of the methodology for the environmental assessment of a Power Plant project within the Valencian Region (Spain) is presented, and its performance evaluated. It is concluded that contrary to other techniques, Electre TRI automatically identifies those cases where allocation of significance categories is most difficult and, when combined with sensitivity analysis, offers greatest robustness in the face of variation in weights of the significance attributes. Likewise, this research demonstrates the efficacy of systematic comparison between Electre TRI and sum-based techniques, in the solution of assignment problems. The proposed methodology can therefore be regarded as a successful aid to the decision-maker, who will ultimately take the final decision

  17. Comparative analyses of the complete mitochondrial genomes of Dosinia clams and their phylogenetic position within Veneridae.

    Science.gov (United States)

    Lv, Changda; Li, Qi; Kong, Lingfeng

    2018-01-01

    Mitochondrial genomes have proved to be a powerful tool in resolving phylogenetic relationship. In order to understand the mitogenome characteristics and phylogenetic position of the genus Dosinia, we sequenced the complete mitochondrial genomes of Dosinia altior and Dosinia troscheli (Bivalvia: Veneridae), compared them with that of Dosinia japonica and established a phylogenetic tree for Veneridae. The mitogenomes of D. altior (17,536 bp) and D. troscheli (17,229 bp) are the two smallest in Veneridae, which include 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and non-coding regions. The mitogenomes of the Dosinia species are similar in size, gene content, AT content, AT- and GC- skews, and gene arrangement. The phylogenetic relationships of family Veneridae were established based on 12 concatenated protein-coding genes using maximum likelihood and Bayesian analyses, which supported that Dosininae and Meretricinae have a closer relationship, with Tapetinae being the sister taxon. The information obtained in this study will contribute to further understanding of the molecular features of bivalve mitogenomes and the evolutionary history of the genus Dosinia.

  18. Comparative genomic analyses of Mycoplasma hyopneumoniae pathogenic 168 strain and its high-passaged attenuated strain

    Science.gov (United States)

    2013-01-01

    Background Mycoplasma hyopneumoniae is the causative agent of porcine enzootic pneumonia (EP), a mild, chronic pneumonia of swine. Despite presenting with low direct mortality, EP is responsible for major economic losses in the pig industry. To identify the virulence-associated determinants of M. hyopneumoniae, we determined the whole genome sequence of M. hyopneumoniae strain 168 and its attenuated high-passage strain 168-L and carried out comparative genomic analyses. Results We performed the first comprehensive analysis of M. hyopneumoniae strain 168 and its attenuated strain and made a preliminary survey of coding sequences (CDSs) that may be related to virulence. The 168-L genome has a highly similar gene content and order to that of 168, but is 4,483 bp smaller because there are 60 insertions and 43 deletions in 168-L. Besides these indels, 227 single nucleotide variations (SNVs) were identified. We further investigated the variants that affected CDSs, and compared them to reported virulence determinants. Notably, almost all of the reported virulence determinants are included in these variants affected CDSs. In addition to variations previously described in mycoplasma adhesins (P97, P102, P146, P159, P216, and LppT), cell envelope proteins (P95), cell surface antigens (P36), secreted proteins and chaperone protein (DnaK), mutations in genes related to metabolism and growth may also contribute to the attenuated virulence in 168-L. Furthermore, many mutations were located in the previously described repeat motif, which may be of primary importance for virulence. Conclusions We studied the virulence attenuation mechanism of M. hyopneumoniae by comparative genomic analysis of virulent strain 168 and its attenuated high-passage strain 168-L. Our findings provide a preliminary survey of CDSs that may be related to virulence. While these include reported virulence-related genes, other novel virulence determinants were also detected. This new information will form

  19. Sample Size Estimation for Negative Binomial Regression Comparing Rates of Recurrent Events with Unequal Follow-Up Time.

    Science.gov (United States)

    Tang, Yongqiang

    2015-01-01

    A sample size formula is derived for negative binomial regression for the analysis of recurrent events, in which subjects can have unequal follow-up time. We obtain sharp lower and upper bounds on the required size, which is easy to compute. The upper bound is generally only slightly larger than the required size, and hence can be used to approximate the sample size. The lower and upper size bounds can be decomposed into two terms. The first term relies on the mean number of events in each group, and the second term depends on two factors that measure, respectively, the extent of between-subject variability in event rates, and follow-up time. Simulation studies are conducted to assess the performance of the proposed method. An application of our formulae to a multiple sclerosis trial is provided.

  20. A Comparative Investigation of the Combined Effects of Pre-Processing, Wavelength Selection, and Regression Methods on Near-Infrared Calibration Model Performance.

    Science.gov (United States)

    Wan, Jian; Chen, Yi-Chieh; Morris, A Julian; Thennadil, Suresh N

    2017-07-01

    Near-infrared (NIR) spectroscopy is being widely used in various fields ranging from pharmaceutics to the food industry for analyzing chemical and physical properties of the substances concerned. Its advantages over other analytical techniques include available physical interpretation of spectral data, nondestructive nature and high speed of measurements, and little or no need for sample preparation. The successful application of NIR spectroscopy relies on three main aspects: pre-processing of spectral data to eliminate nonlinear variations due to temperature, light scattering effects and many others, selection of those wavelengths that contribute useful information, and identification of suitable calibration models using linear/nonlinear regression . Several methods have been developed for each of these three aspects and many comparative studies of different methods exist for an individual aspect or some combinations. However, there is still a lack of comparative studies for the interactions among these three aspects, which can shed light on what role each aspect plays in the calibration and how to combine various methods of each aspect together to obtain the best calibration model. This paper aims to provide such a comparative study based on four benchmark data sets using three typical pre-processing methods, namely, orthogonal signal correction (OSC), extended multiplicative signal correction (EMSC) and optical path-length estimation and correction (OPLEC); two existing wavelength selection methods, namely, stepwise forward selection (SFS) and genetic algorithm optimization combined with partial least squares regression for spectral data (GAPLSSP); four popular regression methods, namely, partial least squares (PLS), least absolute shrinkage and selection operator (LASSO), least squares support vector machine (LS-SVM), and Gaussian process regression (GPR). The comparative study indicates that, in general, pre-processing of spectral data can play a significant

  1. Comparative analyses of forest fuels in a life cycle perspective with a focus on transport systems

    Energy Technology Data Exchange (ETDEWEB)

    Eriksson, Lisa Naeslund [Ecotechnology, Department of Engineering, Physics and Mathematics, Mid Sweden University, SE-831 25 Oestersund (Sweden)

    2008-08-15

    Local, national and international transportation of forest fuels with regard to costs, primary energy use and CO{sub 2} emission was analysed. The main issue was the extent to which both mode and distance of transport affect the monetary cost, CO{sub 2} emission and primary energy use arising from the use of various types of forest residues for energy purpose. Local applications proved the most efficient options of those studied. Chipping of bundles at a terminal, for transport by rail and sea to national or international end-users, has low costs and produces only modest CO{sub 2} emissions. For the pellet options, the cost is about the same as for chipping, but require more primary energy and emit more CO{sub 2}. The traditional chipping system is more expensive than the other options. The costs of the international options over a transport distance of 1100 km vary between 21 and 28 EUR{sub 2007}/MWh, whereas pellet options cost between 22 and 25 EUR{sub 2007}/MWh. The primary energy required for transport of logging residues vis-a-vis pellets falls in the range 4-7% and 2-4%, respectively, of the bio-energy delivered. The primary energy needed to produce pellets gives them a lower fossil fuel substitution rate per hectare, compared with bundle systems. Similarly, for chip systems vis-a-vis bundle systems, the biomass delivered to the conversion plant is reduced by the greater physical dry-matter losses entailed by chipping systems in the forest-fuel chain. (author)

  2. Selective insectivory at Toro-Semliki, Uganda: comparative analyses suggest no 'savanna' chimpanzee pattern.

    Science.gov (United States)

    Webster, Timothy H; McGrew, William C; Marchant, Linda F; Payne, Charlotte L R; Hunt, Kevin D

    2014-06-01

    Chimpanzee (Pan troglodytes) insectivory across Africa is ubiquitous. Insects provide a significant nutritional payoff and may be important for chimpanzees in dry, open habitats with narrow diets. We tested this hypothesis at Semliki, Uganda, a long-term dry study site. We evaluated prospects for insectivory by measuring insect abundance along de novo transects and trails, monitoring social insect colonies, and surveying available raw materials for elementary technology. We determined the frequency and nature of insectivory through behavioral observation and fecal analysis. We then compared our results with those from 15 other long-term chimpanzee study sites using a cluster analysis. We found that Semliki chimpanzees are one of the most insectivorous populations studied to date in terms of frequency of consumption, but they are very selective in their insectivory, regularly consuming only weaver ants (Oecophylla longinoda) and honey and bees from hives of Apis mellifera. This selectivity obtains despite having a full range of typical prey species available in harvestable quantities. We suggest that Semliki chimpanzees may face ecological time constraints and therefore bias their predation toward prey taxa that can be quickly consumed. Geographical proximity correlated with the results of the cluster analysis, while rainfall, a relatively gross measure of environment, did not. Because broad taxonomic groups of insects were used in analyses, prey availability was unlikely to have a strong effect on this pattern. Instead, we suggest that transmission of cultural knowledge may play a role in determining chimpanzee prey selection across Africa. Further study is needed to test these hypotheses. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Comparative modeling analyses of Cs-137 fate in the rivers impacted by Chernobyl and Fukushima accidents

    Energy Technology Data Exchange (ETDEWEB)

    Zheleznyak, M.; Kivva, S. [Institute of Environmental Radioactivity, Fukushima University (Japan)

    2014-07-01

    The consequences of two largest nuclear accidents of the last decades - at Chernobyl Nuclear Power Plant (ChNPP) (1986) and at Fukushima Daiichi NPP (FDNPP) (2011) clearly demonstrated that radioactive contamination of water bodies in vicinity of NPP and on the waterways from it, e.g., river- reservoir water after Chernobyl accident and rivers and coastal marine waters after Fukushima accident, in the both cases have been one of the main sources of the public concerns on the accident consequences. The higher weight of water contamination in public perception of the accidents consequences in comparison with the real fraction of doses via aquatic pathways in comparison with other dose components is a specificity of public perception of environmental contamination. This psychological phenomenon that was confirmed after these accidents provides supplementary arguments that the reliable simulation and prediction of the radionuclide dynamics in water and sediments is important part of the post-accidental radioecological research. The purpose of the research is to use the experience of the modeling activities f conducted for the past more than 25 years within the Chernobyl affected Pripyat River and Dnieper River watershed as also data of the new monitoring studies in Japan of Abukuma River (largest in the region - the watershed area is 5400 km{sup 2}), Kuchibuto River, Uta River, Niita River, Natsui River, Same River, as also of the studies on the specific of the 'water-sediment' {sup 137}Cs exchanges in this area to refine the 1-D model RIVTOX and 2-D model COASTOX for the increasing of the predictive power of the modeling technologies. The results of the modeling studies are applied for more accurate prediction of water/sediment radionuclide contamination of rivers and reservoirs in the Fukushima Prefecture and for the comparative analyses of the efficiency of the of the post -accidental measures to diminish the contamination of the water bodies. Document

  4. Functional and comparative genomics analyses of pmp22 in medaka fish

    Directory of Open Access Journals (Sweden)

    Kawarabayasi Yutaka

    2009-06-01

    Full Text Available Abstract Background Pmp22, a member of the junction protein family Claudin/EMP/PMP22, plays an important role in myelin formation. Increase of pmp22 transcription causes peripheral neuropathy, Charcot-Marie-Tooth disease type1A (CMT1A. The pathophysiological phenotype of CMT1A is aberrant axonal myelination which induces a reduction in nerve conduction velocity (NCV. Several CMT1A model rodents have been established by overexpressing pmp22. Thus, it is thought that pmp22 expression must be tightly regulated for correct myelin formation in mammals. Interestingly, the myelin sheath is also present in other jawed vertebrates. The purpose of this study is to analyze the evolutionary conservation of the association between pmp22 transcription level and vertebrate myelin formation, and to find the conserved non-coding sequences for pmp22 regulation by comparative genomics analyses between jawed fishes and mammals. Results A transgenic pmp22 over-expression medaka fish line was established. The transgenic fish had approximately one fifth the peripheral NCV values of controls, and aberrant myelination of transgenic fish in the peripheral nerve system (PNS was observed. We successfully confirmed that medaka fish pmp22 has the same exon-intron structure as mammals, and identified some known conserved regulatory motifs. Furthermore, we found novel conserved sequences in the first intron and 3'UTR. Conclusion Medaka fish undergo abnormalities in the PNS when pmp22 transcription increases. This result indicates that an adequate pmp22 transcription level is necessary for correct myelination of jawed vertebrates. Comparison of pmp22 orthologs between distantly related species identifies evolutionary conserved sequences that contribute to precise regulation of pmp22 expression.

  5. Comparative analyses of plastid genomes from fourteen Cornales species: inferences for phylogenetic relationships and genome evolution.

    Science.gov (United States)

    Fu, Chao-Nan; Li, Hong-Tao; Milne, Richard; Zhang, Ting; Ma, Peng-Fei; Yang, Jing; Li, De-Zhu; Gao, Lian-Ming

    2017-12-08

    The Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species, ten genera and seven families of Cornales were newly sequenced for comparative analyses of genome features, evolution, and phylogenomics based on different partitioning schemes and filtering strategies. All plastomes of the 14 Cornales species had the typical quadripartite structure with a genome size ranging from 156,567 bp to 158,715 bp, which included two inverted repeats (25,859-26,451 bp) separated by a large single-copy region (86,089-87,835 bp) and a small single-copy region (18,250-18,856 bp) region. These plastomes encoded the same set of 114 unique genes including 31 transfer RNA, 4 ribosomal RNA and 79 coding genes, with an identical gene order across all examined Cornales species. Two genes (rpl22 and ycf15) contained premature stop codons in seven and five species respectively. The phylogenetic relationships among all sampled species were fully resolved with maximum support. Different filtering strategies (none, light and strict) of sequence alignment did not have an effect on these relationships. The topology recovered from coding and noncoding data sets was the same as for the whole plastome, regardless of filtering strategy. Moreover, mutational hotspots and highly informative regions were identified. Phylogenetic relationships among families and intergeneric relationships within family of Cornales were well resolved. Different filtering strategies and partitioning schemes do not influence the relationships. Plastid genomes have great potential to resolve deep phylogenetic relationships of plants.

  6. Comparative Proteomic and Morphological Change Analyses of Staphylococcus aureus During Resuscitation From Prolonged Freezing

    Science.gov (United States)

    Suo, Biao; Yang, Hua; Wang, Yuexia; Lv, Haipeng; Li, Zhen; Xu, Chao; Ai, Zhilu

    2018-01-01

    When frozen, Staphylococcus aureus survives in a sublethally injured state. However, S. aureus can recover at a suitable temperature, which poses a threat to food safety. To elucidate the resuscitation mechanism of freezing survived S. aureus, we used cells stored at -18°C for 90 days as controls. After resuscitating the survived cells at 37°C, the viable cell numbers were determined on tryptic soy agar with 0.6% yeast extract (TSAYE), and the non-injured-cell numbers were determined on TSAYE supplemented with 10% NaCl. The results showed that the total viable cell number did not increase within the first 3 h of resuscitation, but the osmotic regulation ability of freezing survived cells gradually recovered to the level of healthy cells, which was evidenced by the lack of difference between the two samples seen by differential cell enumeration. Scanning electron microscopy (SEM) showed that, compared to late exponential stage cells, some frozen survived cells underwent splitting and cell lysis due to deep distortion and membrane rupture. Transmission electron microscopy (TEM) showed that, in most of the frozen survived cells, the nucleoids (low electronic density area) were loose, and the cytoplasmic matrices (high electronic density area) were sparse. Additionally, a gap was seen to form between the cytoplasmic membranes and the cell walls in the frozen survived cells. The morphological changes were restored when the survived cells were resuscitated at 37°C. We also analyzed the differential proteome after resuscitation using non-labeled high-performance liquid chromatography–mass spectrometry (HPLC-MS). The results showed that, compared with freezing survived S. aureus cells, the cells resuscitated for 1 h had 45 upregulated and 73 downregulated proteins. The differentially expressed proteins were functionally categorized by gene ontology enrichment, KEGG pathway, and STRING analyses. Cell membrane synthesis-related proteins, oxidative stress resistance

  7. Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing.

    Science.gov (United States)

    Zhang, Jin; Ruhlman, Tracey A; Mower, Jeffrey P; Jansen, Robert K

    2013-12-29

    Organelle genomes of Geraniaceae exhibit several unusual evolutionary phenomena compared to other angiosperm families including accelerated nucleotide substitution rates, widespread gene loss, reduced RNA editing, and extensive genomic rearrangements. Since most organelle-encoded proteins function in multi-subunit complexes that also contain nuclear-encoded proteins, it is likely that the atypical organellar phenomena affect the evolution of nuclear genes encoding organellar proteins. To begin to unravel the complex co-evolutionary interplay between organellar and nuclear genomes in this family, we sequenced nuclear transcriptomes of two species, Geranium maderense and Pelargonium x hortorum. Normalized cDNA libraries of G. maderense and P. x hortorum were used for transcriptome sequencing. Five assemblers (MIRA, Newbler, SOAPdenovo, SOAPdenovo-trans [SOAPtrans], Trinity) and two next-generation technologies (454 and Illumina) were compared to determine the optimal transcriptome sequencing approach. Trinity provided the highest quality assembly of Illumina data with the deepest transcriptome coverage. An analysis to determine the amount of sequencing needed for de novo assembly revealed diminishing returns of coverage and quality with data sets larger than sixty million Illumina paired end reads for both species. The G. maderense and P. x hortorum transcriptomes contained fewer transcripts encoding the PLS subclass of PPR proteins relative to other angiosperms, consistent with reduced mitochondrial RNA editing activity in Geraniaceae. In addition, transcripts for all six plastid targeted sigma factors were identified in both transcriptomes, suggesting that one of the highly divergent rpoA-like ORFs in the P. x hortorum plastid genome is functional. The findings support the use of the Illumina platform and assemblers optimized for transcriptome assembly, such as Trinity or SOAPtrans, to generate high-quality de novo transcriptomes with broad coverage. In addition

  8. Measuring decision weights in recognition experiments with multiple response alternatives: comparing the correlation and multinomial-logistic-regression methods.

    Science.gov (United States)

    Dai, Huanping; Micheyl, Christophe

    2012-11-01

    Psychophysical "reverse-correlation" methods allow researchers to gain insight into the perceptual representations and decision weighting strategies of individual subjects in perceptual tasks. Although these methods have gained momentum, until recently their development was limited to experiments involving only two response categories. Recently, two approaches for estimating decision weights in m-alternative experiments have been put forward. One approach extends the two-category correlation method to m > 2 alternatives; the second uses multinomial logistic regression (MLR). In this article, the relative merits of the two methods are discussed, and the issues of convergence and statistical efficiency of the methods are evaluated quantitatively using Monte Carlo simulations. The results indicate that, for a range of values of the number of trials, the estimated weighting patterns are closer to their asymptotic values for the correlation method than for the MLR method. Moreover, for the MLR method, weight estimates for different stimulus components can exhibit strong correlations, making the analysis and interpretation of measured weighting patterns less straightforward than for the correlation method. These and other advantages of the correlation method, which include computational simplicity and a close relationship to other well-established psychophysical reverse-correlation methods, make it an attractive tool to uncover decision strategies in m-alternative experiments.

  9. Complete chloroplast genome sequence of Elodea canadensis and comparative analyses with other monocot plastid genomes.

    Science.gov (United States)

    Huotari, Tea; Korpelainen, Helena

    2012-10-15

    Elodea canadensis is an aquatic angiosperm native to North America. It has attracted great attention due to its invasive nature when transported to new areas in its non-native range. We have determined the complete nucleotide sequence of the chloroplast (cp) genome of Elodea. Taxonomically Elodea is a basal monocot, and only few monocot cp genomes representing early lineages of monocots have been sequenced so far. The genome is a circular double-stranded DNA molecule 156,700 bp in length, and has a typical structure with large (LSC 86,194 bp) and small (SSC 17,810 bp) single-copy regions separated by a pair of inverted repeats (IRs 26,348 bp each). The Elodea cp genome contains 113 unique genes and 16 duplicated genes in the IR regions. A comparative analysis showed that the gene order and organization of the Elodea cp genome is almost identical to that of Amborella trichopoda, a basal angiosperm. The structure of IRs in Elodea is unique among monocot species with the whole cp genome sequenced. In Elodea and another monocot Lemna minor the borders between IRs and LSC are located upstream of rps 19 gene and downstream of trnH-GUG gene, while in most monocots, IR has extended to include both trnH and rps 19 genes. A phylogenetic analysis conducted using Bayesian method, based on the DNA sequences of 81 chloroplast genes from 17 monocot taxa provided support for the placement of Elodea together with Lemna as a basal monocot and the next diverging lineage of monocots after Acorales. In comparison with other monocots, the Elodea cp genome has gone through only few rearrangements or gene losses. IR of Elodea has a unique structure among the monocot species studied so far as its structure is similar to that of a basal angiosperm Amborella. This result together with phylogenetic analyses supports the placement of Elodea as a basal monocot to the next diverging lineage of monocots after Acorales. So far, only few cp genomes representing early lineages of monocots have been

  10. Comparative analyses of tooth wear in free-ranging and captive wild equids.

    Science.gov (United States)

    Taylor, L A; Müller, D W H; Schwitzer, C; Kaiser, T M; Castell, J C; Clauss, M; Schulz-Kornas, E

    2016-03-01

    Captive breeding has played a crucial role in the conservation of threatened equid species. Grazing ruminants and rhinoceros in captivity have less abrasion-dominated tooth wear than their free-ranging conspecifics, with potential negative consequences for their health. However, a similar study on wild equids in captivity is missing. The aim was to establish if different tooth wear patterns are exhibited by free-ranging and captive equids. Cross-sectional study of museum specimens comparing free-ranging and captive equids. Dental casts of maxillary cheek teeth of 228 museum specimens (122 from free-ranging and 106 from captive individuals) of 7 wild equid species were analysed using the extended mesowear method. Although teeth showing specific abnormalities were not scored, the presence of focal overgrowths (hooks) of the rostral premolars (106, 206) was recorded. Captive Equus ferus przewalskii, E. grevyi, E. hemionus, E. quagga boehmi and E. zebra hartmannae have less abrasion-dominated tooth wear on their premolars than their free-ranging conspecifics (P<0.001). Fewer differences were exhibited between populations in the molars. No differences were exhibited in the distal cusp of the molars (110, 210) between populations, except in a small sample of E. kiang. Captive equids exhibited more homogeneous wear along the tooth row whereas free-ranging equids exhibited a tooth wear gradient, with more abrasion on premolars than molars. There were more rostral hooks on the premolars (106, 206) in the captive than the free-ranging population (P = 0.02). Captive equids did experience less abrasion-dominated tooth wear than their free-ranging conspecifics, but the differences in tooth wear were less pronounced than those between captive and free-ranging wild ruminant and rhinoceros species. This indicates that feeding regimes for captive equids deviate less from natural diets than those for captive ruminants and rhinoceros but that factors leading to hook

  11. Regression Phalanxes

    OpenAIRE

    Zhang, Hongyang; Welch, William J.; Zamar, Ruben H.

    2017-01-01

    Tomal et al. (2015) introduced the notion of "phalanxes" in the context of rare-class detection in two-class classification problems. A phalanx is a subset of features that work well for classification tasks. In this paper, we propose a different class of phalanxes for application in regression settings. We define a "Regression Phalanx" - a subset of features that work well together for prediction. We propose a novel algorithm which automatically chooses Regression Phalanxes from high-dimensi...

  12. Comparing the analytical performances of Micro-NIR and FT-NIR spectrometers in the evaluation of acerola fruit quality, using PLS and SVM regression algorithms.

    Science.gov (United States)

    Malegori, Cristina; Nascimento Marques, Emanuel José; de Freitas, Sergio Tonetto; Pimentel, Maria Fernanda; Pasquini, Celio; Casiraghi, Ernestina

    2017-04-01

    The main goal of this study was to investigate the analytical performances of a state-of-the-art device, one of the smallest dispersion NIR spectrometers on the market (MicroNIR 1700), making a critical comparison with a benchtop FT-NIR spectrometer in the evaluation of the prediction accuracy. In particular, the aim of this study was to estimate in a non-destructive manner, titratable acidity and ascorbic acid content in acerola fruit during ripening, in a view of direct applicability in field of this new miniaturised handheld device. Acerola (Malpighia emarginata DC.) is a super-fruit characterised by a considerable amount of ascorbic acid, ranging from 1.0% to 4.5%. However, during ripening, acerola colour changes and the fruit may lose as much as half of its ascorbic acid content. Because the variability of chemical parameters followed a non-strictly linear profile, two different regression algorithms were compared: PLS and SVM. Regression models obtained with Micro-NIR spectra give better results using SVM algorithm, for both ascorbic acid and titratable acidity estimation. FT-NIR data give comparable results using both SVM and PLS algorithms, with lower errors for SVM regression. The prediction ability of the two instruments was statistically compared using the Passing-Bablok regression algorithm; the outcomes are critically discussed together with the regression models, showing the suitability of the portable Micro-NIR for in field monitoring of chemical parameters of interest in acerola fruits. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Univariate and multiple linear regression analyses for 23 single nucleotide polymorphisms in 14 genes predisposing to chronic glomerular diseases and IgA nephropathy in Han Chinese.

    Science.gov (United States)

    Wang, Hui; Sui, Weiguo; Xue, Wen; Wu, Junyong; Chen, Jiejing; Dai, Yong

    2014-09-01

    Immunoglobulin A nephropathy (IgAN) is a complex trait regulated by the interaction among multiple physiologic regulatory systems and probably involving numerous genes, which leads to inconsistent findings in genetic studies. One possibility of failure to replicate some single-locus results is that the underlying genetics of IgAN nephropathy is based on multiple genes with minor effects. To learn the association between 23 single nucleotide polymorphisms (SNPs) in 14 genes predisposing to chronic glomerular diseases and IgAN in Han males, the 23 SNPs genotypes of 21 Han males were detected and analyzed with a BaiO gene chip, and their associations were analyzed with univariate analysis and multiple linear regression analysis. Analysis showed that CTLA4 rs231726 and CR2 rs1048971 revealed a significant association with IgAN. These findings support the multi-gene nature of the etiology of IgAN and propose a potential gene-gene interactive model for future studies.

  14. Comparative Analysis of Upper Ocean Heat Content Variability from Ensemble Operational Ocean Analyses

    Science.gov (United States)

    Xue, Yan; Balmaseda, Magdalena A.; Boyer, Tim; Ferry, Nicolas; Good, Simon; Ishikawa, Ichiro; Rienecker, Michele; Rosati, Tony; Yin, Yonghong; Kumar, Arun

    2012-01-01

    Upper ocean heat content (HC) is one of the key indicators of climate variability on many time-scales extending from seasonal to interannual to long-term climate trends. For example, HC in the tropical Pacific provides information on thermocline anomalies that is critical for the longlead forecast skill of ENSO. Since HC variability is also associated with SST variability, a better understanding and monitoring of HC variability can help us understand and forecast SST variability associated with ENSO and other modes such as Indian Ocean Dipole (IOD), Pacific Decadal Oscillation (PDO), Tropical Atlantic Variability (TAV) and Atlantic Multidecadal Oscillation (AMO). An accurate ocean initialization of HC anomalies in coupled climate models could also contribute to skill in decadal climate prediction. Errors, and/or uncertainties, in the estimation of HC variability can be affected by many factors including uncertainties in surface forcings, ocean model biases, and deficiencies in data assimilation schemes. Changes in observing systems can also leave an imprint on the estimated variability. The availability of multiple operational ocean analyses (ORA) that are routinely produced by operational and research centers around the world provides an opportunity to assess uncertainties in HC analyses, to help identify gaps in observing systems as they impact the quality of ORAs and therefore climate model forecasts. A comparison of ORAs also gives an opportunity to identify deficiencies in data assimilation schemes, and can be used as a basis for development of real-time multi-model ensemble HC monitoring products. The OceanObs09 Conference called for an intercomparison of ORAs and use of ORAs for global ocean monitoring. As a follow up, we intercompared HC variations from ten ORAs -- two objective analyses based on in-situ data only and eight model analyses based on ocean data assimilation systems. The mean, annual cycle, interannual variability and longterm trend of HC have

  15. Interpersonal trust and mutually beneficial exchanges: Measuring social capital for comparative analyses

    Czech Academy of Sciences Publication Activity Database

    Matějů, Petr; Vitásková, Anna

    2006-01-01

    Roč. 42, č. 3 (2006), s. 493-516 ISSN 0038-0288 R&D Projects: GA MPS(CZ) 1J/005/04-DP2; GA ČR(CZ) GA403/03/0340 Institutional research plan: CEZ:AV0Z70280505 Keywords : social capital * trust * komparative analyse Subject RIV: AO - Sociology, Demography Impact factor: 0.128, year: 2006

  16. Basic Diagnosis and Prediction of Persistent Contrail Occurrence using High-resolution Numerical Weather Analyses/Forecasts and Logistic Regression. Part II: Evaluation of Sample Models

    Science.gov (United States)

    Duda, David P.; Minnis, Patrick

    2009-01-01

    Previous studies have shown that probabilistic forecasting may be a useful method for predicting persistent contrail formation. A probabilistic forecast to accurately predict contrail formation over the contiguous United States (CONUS) is created by using meteorological data based on hourly meteorological analyses from the Advanced Regional Prediction System (ARPS) and from the Rapid Update Cycle (RUC) as well as GOES water vapor channel measurements, combined with surface and satellite observations of contrails. Two groups of logistic models were created. The first group of models (SURFACE models) is based on surface-based contrail observations supplemented with satellite observations of contrail occurrence. The second group of models (OUTBREAK models) is derived from a selected subgroup of satellite-based observations of widespread persistent contrails. The mean accuracies for both the SURFACE and OUTBREAK models typically exceeded 75 percent when based on the RUC or ARPS analysis data, but decreased when the logistic models were derived from ARPS forecast data.

  17. Spectral analyses of the Forel-Ule Ocean colour comparator scale

    NARCIS (Netherlands)

    Wernand, M.; van der Woerd, H.J.

    2010-01-01

    François Alphonse Forel (1890) and Willi Ule (1892) composed a colour comparator scale, with tints varying from indigo-blue to cola brown, to quantify the colour of natural waters, like seas, lakes and rivers. For each measurement, the observer compares the colour of the water above a submersed

  18. Reliability and vulnerability analyses of critical infrastructures: Comparing two approaches in the context of power systems

    International Nuclear Information System (INIS)

    Johansson, Jonas; Hassel, Henrik; Zio, Enrico

    2013-01-01

    Society depends on services provided by critical infrastructures, and hence it is important that they are reliable and robust. Two main approaches for gaining knowledge required for designing and improving critical infrastructures are reliability analysis and vulnerability analysis. The former analyses the ability of the system to perform its intended function; the latter analyses its inability to withstand strains and the effects of the consequent failures. The two approaches have similarities but also some differences with respect to what type of information they generate about the system. In this view, the main purpose of this paper is to discuss and contrast these approaches. To strengthen the discussion and exemplify its findings, a Monte Carlo-based reliability analysis and a vulnerability analysis are considered in their application to a relatively simple, but representative, system the IEEE RTS96 electric power test system. The exemplification reveals that reliability analysis provides a good picture of the system likely behaviour, but fails to capture a large portion of the high consequence scenarios, which are instead captured in the vulnerability analysis. Although these scenarios might be estimated to have small probabilities of occurrence, they should be identified, considered and treated cautiously, as probabilistic analyses should not be the only input to decision-making for the design and protection of critical infrastructures. The general conclusion that can be drawn from the findings of the example is that vulnerability analysis should be used to complement reliability studies, as well as other forms of probabilistic risk analysis. Measures should be sought for reducing both the vulnerability, i.e. improving the system ability to withstand strains and stresses, and the reliability, i.e. improving the likely behaviour

  19. Comparative analyses of seven technologies to facilitate the integration of fluctuating renewable energy sources

    DEFF Research Database (Denmark)

    Mathiesen, Brian Vad; Lund, Henrik

    2009-01-01

    An analysis of seven different technologies is presented. The technologies integrate fluctuating renewable energy sources (RES) such as wind power production into the electricity supply, and the Danish energy system is used as a case. Comprehensive hour-by-hour energy system analyses are conducted...... of a complete system meeting electricity, heat and transport demands, and including RES, power plants, and combined heat and power production (CHP) for district heating and transport technologies. In conclusion, the most fuel-efficient and least-cost technologies are identified through energy system...

  20. Implications of Interactions among Society, Education and Technology: A Comparison of Multiple Linear Regression and Multilevel Modeling in Mathematics Achievement Analyses

    Science.gov (United States)

    Deering, Pamela Rose

    2014-01-01

    This research compares and contrasts two approaches to predictive analysis of three years' of school district data to investigate relationships between student and teacher characteristics and math achievement as measured by the state-mandated Maryland School Assessment mathematics exam. The sample for the study consisted of 3,514 students taught…

  1. Basic Diagnosis and Prediction of Persistent Contrail Occurrence using High-resolution Numerical Weather Analyses/Forecasts and Logistic Regression. Part I: Effects of Random Error

    Science.gov (United States)

    Duda, David P.; Minnis, Patrick

    2009-01-01

    Straightforward application of the Schmidt-Appleman contrail formation criteria to diagnose persistent contrail occurrence from numerical weather prediction data is hindered by significant bias errors in the upper tropospheric humidity. Logistic models of contrail occurrence have been proposed to overcome this problem, but basic questions remain about how random measurement error may affect their accuracy. A set of 5000 synthetic contrail observations is created to study the effects of random error in these probabilistic models. The simulated observations are based on distributions of temperature, humidity, and vertical velocity derived from Advanced Regional Prediction System (ARPS) weather analyses. The logistic models created from the simulated observations were evaluated using two common statistical measures of model accuracy, the percent correct (PC) and the Hanssen-Kuipers discriminant (HKD). To convert the probabilistic results of the logistic models into a dichotomous yes/no choice suitable for the statistical measures, two critical probability thresholds are considered. The HKD scores are higher when the climatological frequency of contrail occurrence is used as the critical threshold, while the PC scores are higher when the critical probability threshold is 0.5. For both thresholds, typical random errors in temperature, relative humidity, and vertical velocity are found to be small enough to allow for accurate logistic models of contrail occurrence. The accuracy of the models developed from synthetic data is over 85 percent for both the prediction of contrail occurrence and non-occurrence, although in practice, larger errors would be anticipated.

  2. Regression analysis with categorized regression calibrated exposure: some interesting findings

    Directory of Open Access Journals (Sweden)

    Hjartåker Anette

    2006-07-01

    Full Text Available Abstract Background Regression calibration as a method for handling measurement error is becoming increasingly well-known and used in epidemiologic research. However, the standard version of the method is not appropriate for exposure analyzed on a categorical (e.g. quintile scale, an approach commonly used in epidemiologic studies. A tempting solution could then be to use the predicted continuous exposure obtained through the regression calibration method and treat it as an approximation to the true exposure, that is, include the categorized calibrated exposure in the main regression analysis. Methods We use semi-analytical calculations and simulations to evaluate the performance of the proposed approach compared to the naive approach of not correcting for measurement error, in situations where analyses are performed on quintile scale and when incorporating the original scale into the categorical variables, respectively. We also present analyses of real data, containing measures of folate intake and depression, from the Norwegian Women and Cancer study (NOWAC. Results In cases where extra information is available through replicated measurements and not validation data, regression calibration does not maintain important qualities of the true exposure distribution, thus estimates of variance and percentiles can be severely biased. We show that the outlined approach maintains much, in some cases all, of the misclassification found in the observed exposure. For that reason, regression analysis with the corrected variable included on a categorical scale is still biased. In some cases the corrected estimates are analytically equal to those obtained by the naive approach. Regression calibration is however vastly superior to the naive method when applying the medians of each category in the analysis. Conclusion Regression calibration in its most well-known form is not appropriate for measurement error correction when the exposure is analyzed on a

  3. Comparative analyses of chloroplast genome data representing nine green algae in Sphaeropleales (Chlorophyceae, Chlorophyta

    Directory of Open Access Journals (Sweden)

    Karolina Fučíková

    2016-06-01

    Full Text Available The chloroplast genomes of green algae are highly variable in their architecture. In this article we summarize gene content across newly obtained and published chloroplast genomes in Chlorophyceae, including new data from nine of species in Sphaeropleales (Chlorophyceae, Chlorophyta. We present genome architecture information, including genome synteny analysis across two groups of species. Also, we provide a phylogenetic tree obtained from analysis of gene order data for species in Chlorophyceae with fully sequenced chloroplast genomes. Further analyses and interpretation of the data can be found in “Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta reveal complex patterns of sequence evolution” (Fučíková et al., In review [1].

  4. Comparative Analyses of Physics Candidates Scores in West African and National Examinations Councils

    Science.gov (United States)

    Utibe, Uduak James; Agah, John Joseph

    2015-01-01

    The study is a comparative analysis of physics candidates' scores in West African and National Examinations Councils. It also investigates influence of gender. Results of 480 candidates were randomly selected form three randomly selected Senior Science Colleges using the WASSCE and NECOSSCE computer printout sent to the schools, transformed using…

  5. Comparative Factor Analyses of the Personal Attributes Questionnaire and the Bem Sex-Role Inventory.

    Science.gov (United States)

    Antill, John K.; Cunningham, John D.

    1982-01-01

    Compared the Personal Attributes Questionnaire (PAQ) and the Bem Sex Role Inventory (BSRI) as measures of androgyny. Results showed that femininty (Concern for Others) and masculinity (Dominance) accounted for most of the variance, but for PAQ, clusters of male- and female-valued items (i.e., Extroversion and Insecurity) formed subsidiary factors.…

  6. Analyse comparative entre la distribution des fréquences de ...

    African Journals Online (AJOL)

    2016 International Formulae Group. All rights reserved. Mots clés: Hydrogéochimie, conductivité électrique, diagramme de Piper, socle cristallin et cristallophyllien, Côte d'Ivoire. English Title: Comparative analysis of electrical conductivity frequencies distribution and geochemical facies of hard rock aquifers waters (Ivory ...

  7. Comparative clinical effectiveness of management strategies for sciatica: systematic review and network meta-analyses.

    Science.gov (United States)

    Lewis, Ruth A; Williams, Nefyn H; Sutton, Alex J; Burton, Kim; Din, Nafees Ud; Matar, Hosam E; Hendry, Maggie; Phillips, Ceri J; Nafees, Sadia; Fitzsimmons, Deborah; Rickard, Ian; Wilkinson, Clare

    2015-06-01

    There are numerous treatment approaches for sciatica. Previous systematic reviews have not compared all these strategies together. To compare the clinical effectiveness of different treatment strategies for sciatica simultaneously. Systematic review and network meta-analysis. We searched 28 electronic databases and online trial registries, along with bibliographies of previous reviews for comparative studies evaluating any intervention to treat sciatica in adults, with outcome data on global effect or pain intensity. Network meta-analysis methods were used to simultaneously compare all treatment strategies and allow indirect comparisons of treatments between studies. The study was funded by the UK National Institute for Health Research Health Technology Assessment program; there are no potential conflict of interests. We identified 122 relevant studies; 90 were randomized controlled trials (RCTs) or quasi-RCTs. Interventions were grouped into 21 treatment strategies. Internal and external validity of included studies was very low. For overall recovery as the outcome, compared with inactive control or conventional care, there was a statistically significant improvement following disc surgery, epidural injections, nonopioid analgesia, manipulation, and acupuncture. Traction, percutaneous discectomy, and exercise therapy were significantly inferior to epidural injections or surgery. For pain as the outcome, epidural injections and biological agents were significantly better than inactive control, but similar findings for disc surgery were not statistically significant. Biological agents were significantly better for pain reduction than bed rest, nonopioids, and opioids. Opioids, education/advice alone, bed rest, and percutaneous discectomy were inferior to most other treatment strategies; although these findings represented large effects, they were statistically equivocal. For the first time, many different treatment strategies for sciatica have been compared in the

  8. Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system.

    Science.gov (United States)

    Richter, Sandy; Helm, Conrad; Meunier, Frederic A; Hering, Lars; Campbell, Lahcen I; Drukewitz, Stephan H; Undheim, Eivind A B; Jenner, Ronald A; Schiavo, Giampietro; Bleidorn, Christoph

    2017-03-04

    We present the first molecular characterization of glycerotoxin (GLTx), a potent neurotoxin found in the venom of the bloodworm Glycera tridactyla (Glyceridae, Annelida). Within the animal kingdom, GLTx shows a unique mode of action as it can specifically up-regulate the activity of Ca v 2.2 channels (N-type) in a reversible manner. The lack of sequence information has so far hampered a detailed understanding of its mode of action. Our analyses reveal three ~3.8 kb GLTx full-length transcripts, show that GLTx represents a multigene family, and suggest it functions as a dimer. An integrative approach using transcriptomics, quantitative real-time PCR, in situ hybridization, and immunocytochemistry shows that GLTx is highly expressed exclusively in four pharyngeal lobes, a previously unrecognized part of the venom apparatus. Our results overturn a century old textbook view on the glycerid venom system, suggesting that it is anatomically and functionally much more complex than previously thought. The herein presented GLTx sequence information constitutes an important step towards the establishment of GLTx as a versatile tool to understand the mechanism of synaptic function, as well as the mode of action of this novel neurotoxin.

  9. Comparative brain transcriptomic analyses of scouting across distinct behavioural and ecological contexts in honeybees

    Science.gov (United States)

    Liang, Zhengzheng S.; Mattila, Heather R.; Rodriguez-Zas, Sandra L.; Southey, Bruce R.; Seeley, Thomas D.; Robinson, Gene E.

    2014-01-01

    Individual differences in behaviour are often consistent across time and contexts, but it is not clear whether such consistency is reflected at the molecular level. We explored this issue by studying scouting in honeybees in two different behavioural and ecological contexts: finding new sources of floral food resources and finding a new nest site. Brain gene expression profiles in food-source and nest-site scouts showed a significant overlap, despite large expression differences associated with the two different contexts. Class prediction and ‘leave-one-out’ cross-validation analyses revealed that a bee's role as a scout in either context could be predicted with 92.5% success using 89 genes at minimum. We also found that genes related to four neurotransmitter systems were part of a shared brain molecular signature in both types of scouts, and the two types of scouts were more similar for genes related to glutamate and GABA than catecholamine or acetylcholine signalling. These results indicate that consistent behavioural tendencies across different ecological contexts involve a mixture of similarities and differences in brain gene expression. PMID:25355476

  10. Le français du tourisme dans le contexte universitaire chinois : analyse comparative des besoins

    Directory of Open Access Journals (Sweden)

    LI Lu

    2016-11-01

    Full Text Available Cette recherche vise à dévoiler la situation de l’enseignement du français du tourisme dans le contexte universitaire chinois. A travers une analyse des besoins, nous tâchons de vérifier si la formation actuelle correspond aux besoins des apprenants ainsi qu’à la demande du marché du travail. Des enquêtes ont été menées auprès d’étudiants, d’enseignants et de professionnels. Les résultats montrent que les publics se diversifient avec des besoins variés et que la rupture de l’ensei gnement avec le secteur professionnel est évidente. Trois propositions sont ainsi formulées en vue de fournir des conseils à l’amélioration et à l’innovation de la formation du français du tourisme dans les universités chinoises.

  11. Comparative analyses of amplicon migration behavior in differing denaturing gradient gel electrophoresis (DGGE) systems

    Science.gov (United States)

    Thornhill, D. J.; Kemp, D. W.; Sampayo, E. M.; Schmidt, G. W.

    2010-03-01

    Denaturing gradient gel electrophoresis (DGGE) is commonly utilized to identify and quantify microbial diversity, but the conditions required for different electrophoretic systems to yield equivalent results and optimal resolution have not been assessed. Herein, the influence of different DGGE system configuration parameters on microbial diversity estimates was tested using Symbiodinium, a group of marine eukaryotic microbes that are important constituents of coral reef ecosystems. To accomplish this, bacterial clone libraries were constructed and sequenced from cultured isolates of Symbiodinium for the ribosomal DNA internal transcribed spacer 2 (ITS2) region. From these, 15 clones were subjected to PCR with a GC clamped primer set for DGGE analyses. Migration behaviors of the resulting amplicons were analyzed using a range of conditions, including variation in the composition of the denaturing gradient, electrophoresis time, and applied voltage. All tests were conducted in parallel on two commercial DGGE systems, a C.B.S. Scientific DGGE-2001, and the Bio-Rad DCode system. In this context, identical nucleotide fragments exhibited differing migration behaviors depending on the model of apparatus utilized, with fragments denaturing at a lower gradient concentration and applied voltage on the Bio-Rad DCode system than on the C.B.S. Scientific DGGE-2001 system. Although equivalent PCR-DGGE profiles could be achieved with both brands of DGGE system, the composition of the denaturing gradient and application of electrophoresis time × voltage must be appropriately optimized to achieve congruent results across platforms.

  12. Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma.

    Science.gov (United States)

    Wrzeszczynski, Kazimierz O; Frank, Mayu O; Koyama, Takahiko; Rhrissorrakrai, Kahn; Robine, Nicolas; Utro, Filippo; Emde, Anne-Katrin; Chen, Bo-Juen; Arora, Kanika; Shah, Minita; Vacic, Vladimir; Norel, Raquel; Bilal, Erhan; Bergmann, Ewa A; Moore Vogel, Julia L; Bruce, Jeffrey N; Lassman, Andrew B; Canoll, Peter; Grommes, Christian; Harvey, Steve; Parida, Laxmi; Michelini, Vanessa V; Zody, Michael C; Jobanputra, Vaidehi; Royyuru, Ajay K; Darnell, Robert B

    2017-08-01

    To analyze a glioblastoma tumor specimen with 3 different platforms and compare potentially actionable calls from each. Tumor DNA was analyzed by a commercial targeted panel. In addition, tumor-normal DNA was analyzed by whole-genome sequencing (WGS) and tumor RNA was analyzed by RNA sequencing (RNA-seq). The WGS and RNA-seq data were analyzed by a team of bioinformaticians and cancer oncologists, and separately by IBM Watson Genomic Analytics (WGA), an automated system for prioritizing somatic variants and identifying drugs. More variants were identified by WGS/RNA analysis than by targeted panels. WGA completed a comparable analysis in a fraction of the time required by the human analysts. The development of an effective human-machine interface in the analysis of deep cancer genomic datasets may provide potentially clinically actionable calls for individual patients in a more timely and efficient manner than currently possible. NCT02725684.

  13. UniPrimer: A Web-Based Primer Design Tool for Comparative Analyses of Primate Genomes

    Directory of Open Access Journals (Sweden)

    Nomin Batnyam

    2012-01-01

    Full Text Available Whole genome sequences of various primates have been released due to advanced DNA-sequencing technology. A combination of computational data mining and the polymerase chain reaction (PCR assay to validate the data is an excellent method for conducting comparative genomics. Thus, designing primers for PCR is an essential procedure for a comparative analysis of primate genomes. Here, we developed and introduced UniPrimer for use in those studies. UniPrimer is a web-based tool that designs PCR- and DNA-sequencing primers. It compares the sequences from six different primates (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque and designs primers on the conserved region across species. UniPrimer is linked to RepeatMasker, Primer3Plus, and OligoCalc softwares to produce primers with high accuracy and UCSC In-Silico PCR to confirm whether the designed primers work. To test the performance of UniPrimer, we designed primers on sample sequences using UniPrimer and manually designed primers for the same sequences. The comparison of the two processes showed that UniPrimer was more effective than manual work in terms of saving time and reducing errors.

  14. Comparative analyses of diffusion coefficients for different extraction processes from thyme

    Directory of Open Access Journals (Sweden)

    Petrovic Slobodan S.

    2012-01-01

    Full Text Available This work was aimed to analyze kinetics and mass transfer phenomena for different extraction processes from thyme (Thymus vulgaris L. leaves. Different extraction processes with ethanol were studied: Soxhlet extraction and ultrasound-assisted batch extraction on the laboratory scale as well as pilot plant batch extraction with mixing. The extraction processes with ethanol were compared to the process of supercritical carbon dioxide extraction performed at 10 MPa and 40°C. Experimental data were analyzed by mathematical model derived from the Fick’s second law to determine and compare diffusion coefficients in the periods of constant and decreasing extraction rate. In the fast extraction period, values of diffusion coefficients were one to three orders of magnitude higher compared to those determined for the period of slow extraction. The highest diffusion coefficient was reported for the fast extraction period of supercritical fluid extraction. In the case of extraction processes with ethanol, ultrasound, stirring and extraction temperature increase enhanced mass transfer rate in the washing phase. On the other hand, ultrasound contributed the most to the increase of mass transfer rate in the period of slow extraction.

  15. Full-root aortic valve replacement with stentless xenograft achieves superior regression of left ventricular hypertrophy compared to pericardial stented aortic valves.

    Science.gov (United States)

    Tavakoli, Reza; Auf der Maur, Christoph; Mueller, Xavier; Schläpfer, Reinhard; Jamshidi, Peiman; Daubeuf, François; Frossard, Nelly

    2015-02-03

    Full-root aortic valve replacement with stentless xenografts has potentially superior hemodynamic performance compared to stented valves. However, a number of cardiac surgeons are reluctant to transform a classical stented aortic valve replacement into a technically more demanding full-root stentless aortic valve replacement. Here we describe our technique of full-root stentless aortic xenograft implantation and compare the early clinical and midterm hemodynamic outcomes to those after aortic valve replacement with stented valves. We retrospectively compared the pre-operative characteristics of 180 consecutive patients who underwent full-root replacement with stentless aortic xenografts with those of 80 patients undergoing aortic valve replacement with stented valves. In subgroups presenting with aortic stenosis, we further analyzed the intra-operative data, early postoperative outcomes and mid-term regression of left ventricular mass index. Patients in the stentless group were younger (62.6 ± 13 vs. 70.3 ± 11.8 years, p regression of the left ventricular mass index in the stentless (p replacement can be performed without adversely affecting the early morbidity or mortality in patients operated on for aortic valve stenosis provided that the coronary ostia are not heavily calcified. The additional time necessary for the full-root stentless compared to the classical stented aortic valve replacement is therefore not detrimental to the early clinical outcomes and is largely rewarded in patients with aortic stenosis by lower transvalvular gradients at mid-term and a better regression of their left ventricular mass index.

  16. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients.

    Science.gov (United States)

    Fierer, Noah; Lauber, Christian L; Ramirez, Kelly S; Zaneveld, Jesse; Bradford, Mark A; Knight, Rob

    2012-05-01

    Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.

  17. Comparative analyses of reproductive structures in harvestmen (opiliones reveal multiple transitions from courtship to precopulatory antagonism.

    Directory of Open Access Journals (Sweden)

    Mercedes M Burns

    Full Text Available Explaining the rapid, species-specific diversification of reproductive structures and behaviors is a long-standing goal of evolutionary biology, with recent research tending to attribute reproductive phenotypes to the evolutionary mechanisms of female mate choice or intersexual conflict. Progress in understanding these and other possible mechanisms depends, in part, on reconstructing the direction, frequency and relative timing of phenotypic evolution of male and female structures in species-rich clades. Here we examine evolution of reproductive structures in the leiobunine harvestmen or "daddy long-legs" of eastern North America, a monophyletic group that includes species in which males court females using nuptial gifts and other species that are equipped for apparent precopulatory antagonism (i.e., males with long, hardened penes and females with sclerotized pregenital barriers. We used parsimony- and Bayesian likelihood-based analyses to reconstruct character evolution in categorical reproductive traits and found that losses of ancestral gift-bearing penile sacs are strongly associated with gains of female pregenital barriers. In most cases, both events occur on the same internal branch of the phylogeny. These coevolutionary changes occurred at least four times, resulting in clade-specific designs in the penis and pregenital barrier. The discovery of convergent origins and/or enhancements of apparent precopulatory antagonism among closely related species offers an unusual opportunity to investigate how major changes in reproductive morphology have occurred. We propose new hypotheses that attribute these enhancements to changes in ecology or life history that reduce the duration of breeding seasons, an association that is consistent with female choice, sexual conflict, and/or an alternative evolutionary mechanism.

  18. Thermo-economic analysis of recuperated Maisotsenko bottoming cycle using triplex air saturator: Comparative analyses

    International Nuclear Information System (INIS)

    Saghafifar, Mohammad; Omar, Amr; Erfanmoghaddam, Sepehr; Gadalla, Mohamed

    2017-01-01

    Highlights: • Proposing recuperated Maisotsenko bottoming cycle (RMBC) as a new combined cycle. • Introducing triplex air saturator for waste heat recovery application. • Conducting thermodynamic optimization to maximize RMBC thermal efficiency. • Conducting thermo-economic optimization to minimize RMBC cost of electricity. - Abstract: A recently recommended combined cycle power plant is to employ another gas turbine cycle for waste heat recovery as an air bottoming cycle (ABC). There are some studies conducted to improve ABC’s thermodynamic performance utilizing commonly power augmentation methods such as steam/water injection. In particular, it is proposed to employ Maisotsenko gas turbine cycle as a bottoming cycle, i.e. Maisotsenko bottoming cycle (MBC). Due to the promising performance of the MBC configuration, it is decided to investigate a recuperated MBC (RMBC) configuration by recommending the triplex air saturator. In this way, the air saturator consists of three sections. The first section is an indirect evaporative cooler while the other two sections are responsible for heat recovery from the topping and bottoming cycle turbines exhaust. In this paper, thermodynamic and thermo-economic analyses are carried out to study the main merits and demerits of RMBC against MBC configuration. Thermodynamic optimization results indicate that the maximum achievable efficiency for MBC and RMBC incorporation in a simple gas turbine power plant are 39.40% and 44.73%, respectively. Finally, thermo-economic optimization shows that the optimum levelized cost of electricity for MBC and RMBC power plants are 62.922 US$/MWh and 58.154 US$/MWh, respectively.

  19. Analysing risk factors of co-occurrence of schistosomiasis haematobium and hookworm using bivariate regression models: Case study of Chikwawa, Malawi

    Directory of Open Access Journals (Sweden)

    Bruce B.W. Phiri

    2016-06-01

    Full Text Available Schistosomiasis and soil-transmitted helminth (STH infections constitute a major public health problem in many parts of sub-Saharan Africa. In areas where prevalence of geo-helminths and schistosomes is high, co-infection with multiple parasite species is common, resulting in disproportionately elevated burden compared with single infections. Determining risk factors of co-infection intensity is important for better design of targeted interventions. In this paper, we examined risk factors of hookworm and S. haematobium co-infection intensity, in Chikwawa district, southern Malawi in 2005, using bivariate count models. Results show that hookworm and S. haematobium infections were much localised with small proportion of individuals harbouring more parasites especially among school-aged children. The risk of co-intensity with both hookworm and S. haematobium was high for all ages, although this diminished with increasing age, increased with fishing (hookworm: coefficient. = 12.29; 95% CI = 11.50–13.09; S. haematobium: 0.040; 95% CI = 0.0037, 3.832. Both infections were abundant in those with primary education (hookworm: coef. = 0.072; 95% CI = 0.056, 0.401 and S. haematobium: coef. = 0.286; 95% CI = 0.034, 0.538. However, much lower risk was observed for those who were farmers (hookworm: coef. = −0.349, 95% CI = −0.547,−0.150; S. haematobium: coef. −0.239, 95% CI = −0.406, −0.072. In conclusion, our findings suggest that efforts to control helminths infection should be co-integrated and health promotion campaigns should be aimed at school-going children and adults who are in constant contact with water.

  20. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.

    Directory of Open Access Journals (Sweden)

    Fagen Li

    Full Text Available Dense genetic maps, along with quantitative trait loci (QTLs detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR, expressed sequence tag (EST derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS, and diversity arrays technology (DArT markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age and wood density (56 months were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

  1. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus

    Science.gov (United States)

    Weng, Qijie; Li, Mei; Yu, Xiaoli; Guo, Yong; Wang, Yu; Zhang, Xiaohong; Gan, Siming

    2015-01-01

    Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10–56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa. PMID:26695430

  2. Parental conflict in birds: comparative analyses of offspring development, ecology and mating opportunities

    Science.gov (United States)

    Olson, V.A; Liker, A; Freckleton, R.P; Székely, T

    2007-01-01

    Parents often conflict over how much care to provide to their offspring. This conflict is expected to produce a negative relationship between male and female parental care, the strength of which may be mediated by both ecological and life-history variables. Previous studies have observed such trade-offs, but it is not known how generally they occur. Traditional views of sexual conflict place great importance on ecological factors in determining levels of parental care, whereas alternative views propose that the key determinant is mating opportunity. We carried out a broad-scale comparative study of parental conflict using 193 species from 41 families of birds. Using phylogenetic comparative analysis, we establish the generality of intersexual parental care conflict. We also show that parental conflict, as indicated by the disparity in care between the male and the female, depends on offspring development and mating opportunities, since in precocial species both males and females responded to increased mating opportunities. Altricial birds, however, failed to show these relationships. We also found little influence of breeding climate on parental conflict. Taken together, our results suggest that sexual conflict is a key element in the evolution of parental care systems. They also support the view that the major correlates of the intersexual conflict are mating opportunities for both sexes, rather than the breeding environment. PMID:18029303

  3. Simple Comparative Analyses of Differentially Expressed Gene Lists May Overestimate Gene Overlap.

    Science.gov (United States)

    Lawhorn, Chelsea M; Schomaker, Rachel; Rowell, Jonathan T; Rueppell, Olav

    2018-04-16

    Comparing the overlap between sets of differentially expressed genes (DEGs) within or between transcriptome studies is regularly used to infer similarities between biological processes. Significant overlap between two sets of DEGs is usually determined by a simple test. The number of potentially overlapping genes is compared to the number of genes that actually occur in both lists, treating every gene as equal. However, gene expression is controlled by transcription factors that bind to a variable number of transcription factor binding sites, leading to variation among genes in general variability of their expression. Neglecting this variability could therefore lead to inflated estimates of significant overlap between DEG lists. With computer simulations, we demonstrate that such biases arise from variation in the control of gene expression. Significant overlap commonly arises between two lists of DEGs that are randomly generated, assuming that the control of gene expression is variable among genes but consistent between corresponding experiments. More overlap is observed when transcription factors are specific to their binding sites and when the number of genes is considerably higher than the number of different transcription factors. In contrast, overlap between two DEG lists is always lower than expected when the genetic architecture of expression is independent between the two experiments. Thus, the current methods for determining significant overlap between DEGs are potentially confounding biologically meaningful overlap with overlap that arises due to variability in control of expression among genes, and more sophisticated approaches are needed.

  4. Comparing EFT and Exact One-Loop Analyses of Non-Degenerate Stops

    CERN Document Server

    Drozd, Aleksandra; Quevillon, Jeremie; You, Tevong

    2015-01-01

    We develop a universal approach to the one-loop effective field theory (EFT) using the Covariant Derivative Expansion (CDE) method. We generalise previous results to include broader classes of UV models, showing how expressions previously obtained assuming degenerate heavy-particle masses can be extended to non-degenerate cases. We apply our method to the general MSSM with non-degenerate stop squarks, illustrating our approach with calculations of the coefficients of dimension-6 operators contributing to the $hgg$ and $h\\gamma\\gamma$ couplings, and comparing with exact calculations of one-loop Feynman diagrams. We then use present and projected future sensitivities to these operator coefficients to obtain present and possible future indirect constraints on stop masses. The current sensitivity is already comparable to that of direct LHC searches, and future FCC-ee measurements could be sensitive to stop masses above a TeV. The universality of our one-loop EFT approach facilitates extending these constraints to...

  5. Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept

    Directory of Open Access Journals (Sweden)

    Melissa B. Duhaime

    2017-07-01

    considered viral niches, while host ranges and infection efficiencies are tracked as viral traits. Quantitative host range assays revealed conserved traits within virus OTUs that break down between OTUs, suggesting the defined units capture niche and fitness differentiation. Together these analyses provide a foundation for model system-based hypothesis testing that will improve our understanding of marine copiotrophs, as well as phage–host interactions on the ocean particles and aggregates where Pseudoalteromonas thrive.

  6. THE ECONOMIC STRUCTURES IN THE ROMANIAN REGIONS AND COUNTIES AND THE EU MEMBER STATES. COMPARATIVE ANALYSES.

    Directory of Open Access Journals (Sweden)

    Marioara, IORDAN

    2014-03-01

    Full Text Available Bridging the gap between countries, and thus decresing poverty, is the greatest challenge of European countries in the context of the European social cohesion. The risk of future economic difficulties caused by the size of budget deficits is beared by the funds to be allocated to social inclusion in the EU and the EU member countries. They will be concerned in the post-crisis period with aligning the requirements of progress, of poverty reduction, but also of ensuring the sustainability of public finances. For Romania, cohesion is particularly important as most regions show significant differences as compared to the EU average and the national average. This group also includes the South Muntenia Region, which has many advantages for faster progress and to be able to exploit the opportunities offered by the implementation of the Europe 2020 strategy.

  7. Comparative analyses suggest that information transfer promoted sociality in male bats in the temperate zone.

    Science.gov (United States)

    Safi, Kamran; Kerth, Gerald

    2007-09-01

    The evolution of sociality is a central theme in evolutionary biology. The vast majority of bats are social, which has been explained in terms of the benefits of communal breeding. However, the causes for segregated male groups remain unknown. In a comparative study, we tested whether diet and morphological adaptations to specific foraging styles, two factors known to influence the occurrence of information transfer, can predict male sociality. Our results suggest that the species most likely to benefit from information transfer--namely, those preying on ephemeral insects and with morphological adaptations to feeding in open habitat--are more likely to form male groups. Our findings also indicate that solitary life was the ancestral state of males and sociality evolved in several lineages. Beyond their significance for explaining the existence of male groups in bats, our findings highlight the importance of information transfer in the evolution of animal sociality.

  8. Comparative analyses of laccase-catalyzed amination reactions for production of novel β-lactam antibiotics.

    Science.gov (United States)

    Mikolasch, Annett; Manda, Katrin; Schlüter, Rabea; Lalk, Michael; Witt, Sabine; Seefeldt, Simone; Hammer, Elke; Schauer, Frieder; Jülich, Wolf-Dieter; Lindequist, Ulrike

    2012-01-01

    Seven novel β-lactam antibiotics with activities against Gram-positive bacterial strains, among them methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci, were synthesized by amination of 2,5-dihydroxyphenylacetic acid in usable yields (30-60%). These products protected mice against an infection with S. aureus lethal to the control animals. The results show the usefulness of laccase for the synthesis of potential new antibiotics, in addition to the interdependence of the laccase substrates, the amino coupling partners, and the product formation, yield, and activity. The syntheses of β-lactam antibiotics with 2,5-dihydroxyaromatic acid substructures (para-substituted) are then compared with those of 3,4-dihydroxyaromatic acid substructures (ortho-substituted). Para-substituted laccase substrates were better reaction partners in these syntheses than ortho-substituted compounds. Copyright © 2012 International Union of Biochemistry and Molecular Biology, Inc.

  9. Comparative analyses of the internal radiation exposures due to food chain pathway using food III code

    International Nuclear Information System (INIS)

    Choi, Yong Ho; Chung, Kyu Hoi; Kim, Jin Kyu; Lee, Jeong Ho

    1988-01-01

    In order to develop a food-chain computer code suitable to the environmental conditions of Korea, the FOOD III code was partially modified. The execution results for Korean male-adult were compared to those from the Canadian version of FOOD III to deduce a more realistic approach in dose assessment. The amounts of Mn-54, Co-50, Co-60, I-131 and I-132 released from Kori unit 1 in 1984 were used as the source terms for the sample calculation. The maximum atmospheric dispersion factor(X/Q) value on the site boundary was applied. Through the code modification, organ doses decreased by about 20∼70% and the effective committed dose equivalent by about 40% to be 7.935x10 -6 Sv/y which is 0.16% of the ICRP limit, 5x10 -3 Sv/y. (Author)

  10. Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires' disease.

    Science.gov (United States)

    Gomez-Valero, Laura; Rusniok, Christophe; Rolando, Monica; Neou, Mario; Dervins-Ravault, Delphine; Demirtas, Jasmin; Rouy, Zoe; Moore, Robert J; Chen, Honglei; Petty, Nicola K; Jarraud, Sophie; Etienne, Jerome; Steinert, Michael; Heuner, Klaus; Gribaldo, Simonetta; Médigue, Claudine; Glöckner, Gernot; Hartland, Elizabeth L; Buchrieser, Carmen

    2014-01-01

    The genus Legionella comprises over 60 species. However, L. pneumophila and L. longbeachae alone cause over 95% of Legionnaires’ disease. To identify the genetic bases underlying the different capacities to cause disease we sequenced and compared the genomes of L. micdadei, L. hackeliae and L. fallonii (LLAP10), which are all rarely isolated from humans. We show that these Legionella species possess different virulence capacities in amoeba and macrophages, correlating with their occurrence in humans. Our comparative analysis of 11 Legionella genomes belonging to five species reveals highly heterogeneous genome content with over 60% representing species-specific genes; these comprise a complete prophage in L. micdadei, the first ever identified in a Legionella genome. Mobile elements are abundant in Legionella genomes; many encode type IV secretion systems for conjugative transfer, pointing to their importance for adaptation of the genus. The Dot/Icm secretion system is conserved, although the core set of substrates is small, as only 24 out of over 300 described Dot/Icm effector genes are present in all Legionella species. We also identified new eukaryotic motifs including thaumatin, synaptobrevin or clathrin/coatomer adaptine like domains. Legionella genomes are highly dynamic due to a large mobilome mainly comprising type IV secretion systems, while a minority of core substrates is shared among the diverse species. Eukaryotic like proteins and motifs remain a hallmark of the genus Legionella. Key factors such as proteins involved in oxygen binding, iron storage, host membrane transport and certain Dot/Icm substrates are specific features of disease-related strains.

  11. Predictability and interpretability of hybrid link-level crash frequency models for urban arterials compared to cluster-based and general negative binomial regression models.

    Science.gov (United States)

    Najaf, Pooya; Duddu, Venkata R; Pulugurtha, Srinivas S

    2018-03-01

    Machine learning (ML) techniques have higher prediction accuracy compared to conventional statistical methods for crash frequency modelling. However, their black-box nature limits the interpretability. The objective of this research is to combine both ML and statistical methods to develop hybrid link-level crash frequency models with high predictability and interpretability. For this purpose, M5' model trees method (M5') is introduced and applied to classify the crash data and then calibrate a model for each homogenous class. The data for 1134 and 345 randomly selected links on urban arterials in the city of Charlotte, North Carolina was used to develop and validate models, respectively. The outputs from the hybrid approach are compared with the outputs from cluster-based negative binomial regression (NBR) and general NBR models. Findings indicate that M5' has high predictability and is very reliable to interpret the role of different attributes on crash frequency compared to other developed models.

  12. Estimation of perceptible water vapor of atmosphere using artificial neural network, support vector machine and multiple linear regression algorithm and their comparative study

    Science.gov (United States)

    Shastri, Niket; Pathak, Kamlesh

    2018-05-01

    The water vapor content in atmosphere plays very important role in climate. In this paper the application of GPS signal in meteorology is discussed, which is useful technique that is used to estimate the perceptible water vapor of atmosphere. In this paper various algorithms like artificial neural network, support vector machine and multiple linear regression are use to predict perceptible water vapor. The comparative studies in terms of root mean square error and mean absolute errors are also carried out for all the algorithms.

  13. Mixed Approach Retrospective Analyses of Suicide and Suicidal Ideation for Brand Compared with Generic Central Nervous System Drugs.

    Science.gov (United States)

    Cheng, Ning; Rahman, Md Motiur; Alatawi, Yasser; Qian, Jingjing; Peissig, Peggy L; Berg, Richard L; Page, C David; Hansen, Richard A

    2018-04-01

    Several different types of drugs acting on the central nervous system (CNS) have previously been associated with an increased risk of suicide and suicidal ideation (broadly referred to as suicide). However, a differential association between brand and generic CNS drugs and suicide has not been reported. This study compares suicide adverse event rates for brand versus generic CNS drugs using multiple sources of data. Selected examples of CNS drugs (sertraline, gabapentin, zolpidem, and methylphenidate) were evaluated via the US FDA Adverse Event Reporting System (FAERS) for a hypothesis-generating study, and then via administrative claims and electronic health record (EHR) data for a more rigorous retrospective cohort study. Disproportionality analyses with reporting odds ratios and 95% confidence intervals (CIs) were used in the FAERS analyses to quantify the association between each drug and reported suicide. For the cohort studies, Cox proportional hazards models were used, controlling for demographic and clinical characteristics as well as the background risk of suicide in the insured population. The FAERS analyses found significantly lower suicide reporting rates for brands compared with generics for all four studied products (Breslow-Day P brand CNS drugs in FAERS and adjusted retrospective cohort analyses remained significant only for sertraline. However, even for sertraline, temporal confounding related to the close proximity of black box warnings and generic availability is possible. Additional analyses in larger data sources with additional drugs are needed.

  14. Comparative physiological and proteomic analyses of poplar (Populus yunnanensis plantlets exposed to high temperature and drought.

    Directory of Open Access Journals (Sweden)

    Xiong Li

    Full Text Available Plantlets of Populus yunnanensis Dode were examined in a greenhouse for 48 h to analyze their physiological and proteomic responses to sustained heat, drought, and combined heat and drought. Compared with the application of a single stress, simultaneous treatment with both stresses damaged the plantlets more heavily. The plantlets experienced two apparent response stages under sustained heat and drought. During the first stage, malondialdehyde and reactive oxygen species (ROS contents were induced by heat, but many protective substances, including antioxidant enzymes, proline, abscisic acid (ABA, dehydrin, and small heat shock proteins (sHSPs, were also stimulated. The plants thus actively defended themselves against stress and exhibited few pathological morphological features, most likely because a new cellular homeostasis was established through the collaborative operation of physiological and proteomic responses. During the second stage, ROS homeostasis was overwhelmed by substantial ROS production and a sharp decline in antioxidant enzyme activities, while the synthesis of some protective elements, such as proline and ABA, was suppressed. As a result, photosynthetic levels in P. yunnanensis decreased sharply and buds began to die, despite continued accumulation of sHSPs and dehydrin. This study supplies important information about the effects of extreme abiotic environments on woody plants.

  15. Comparative analyses reveal high levels of conserved colinearity between the finger millet and rice genomes.

    Science.gov (United States)

    Srinivasachary; Dida, Mathews M; Gale, Mike D; Devos, Katrien M

    2007-08-01

    Finger millet is an allotetraploid (2n = 4x = 36) grass that belongs to the Chloridoideae subfamily. A comparative analysis has been carried out to determine the relationship of the finger millet genome with that of rice. Six of the nine finger millet homoeologous groups corresponded to a single rice chromosome each. Each of the remaining three finger millet groups were orthologous to two rice chromosomes, and in all the three cases one rice chromosome was inserted into the centromeric region of a second rice chromosome to give the finger millet chromosomal configuration. All observed rearrangements were, among the grasses, unique to finger millet and, possibly, the Chloridoideae subfamily. Gene orders between rice and finger millet were highly conserved, with rearrangements being limited largely to single marker transpositions and small putative inversions encompassing at most three markers. Only some 10% of markers mapped to non-syntenic positions in rice and finger millet and the majority of these were located in the distal 14% of chromosome arms, supporting a possible correlation between recombination and sequence evolution as has previously been observed in wheat. A comparison of the organization of finger millet, Panicoideae and Pooideae genomes relative to rice allowed us to infer putative ancestral chromosome configurations in the grasses.

  16. New perspectives on host-parasite interplay by comparative transcriptomic and proteomic analyses of Schistosoma japonicum.

    Directory of Open Access Journals (Sweden)

    Feng Liu

    2006-04-01

    Full Text Available Schistosomiasis remains a serious public health problem with an estimated 200 million people infected in 76 countries. Here we isolated ~ 8,400 potential protein-encoding cDNA contigs from Schistosoma japonicum after sequencing circa 84,000 expressed sequence tags. In tandem, we undertook a high-throughput proteomics approach to characterize the protein expression profiles of a number of developmental stages (cercariae, hepatic schistosomula, female and male adults, eggs, and miracidia and tissues at the host-parasite interface (eggshell and tegument by interrogating the protein database deduced from the contigs. Comparative analysis of these transcriptomic and proteomic data, the latter including 3,260 proteins with putative identities, revealed differential expression of genes among the various developmental stages and sexes of S. japonicum and localization of putative secretory and membrane antigens, enzymes, and other gene products on the adult tegument and eggshell, many of which displayed genetic polymorphisms. Numerous S. japonicum genes exhibited high levels of identity with those of their mammalian hosts, whereas many others appeared to be conserved only across the genus Schistosoma or Phylum Platyhelminthes. These findings are expected to provide new insights into the pathophysiology of schistosomiasis and for the development of improved interventions for disease control and will facilitate a more fundamental understanding of schistosome biology, evolution, and the host-parasite interplay.

  17. Comparative genomic analyses of transport proteins encoded within the genomes of Leptospira species.

    Science.gov (United States)

    Buyuktimkin, Bora; Saier, Milton H

    2015-11-01

    Select species of the bacterial genus Leptospira are causative agents of leptospirosis, an emerging global zoonosis affecting nearly one million people worldwide annually. We examined two Leptospira pathogens, Leptospira interrogans serovar Lai str. 56601 and Leptospira borgpetersenii serovar Hardjo-bovis str. L550, as well as the free-living leptospiral saprophyte, Leptospira biflexa serovar Patoc str. 'Patoc 1 (Ames)'. The transport proteins of these leptospires were identified and compared using bioinformatics to gain an appreciation for which proteins may be related to pathogenesis and saprophytism. L. biflexa possesses a disproportionately high number of secondary carriers for metabolite uptake and environmental adaptability as well as an increased number of inorganic cation transporters providing ionic homeostasis and effective osmoregulation in a rapidly changing environment. L. interrogans and L. borgpetersenii possess far fewer transporters, but those that they have are remarkably similar, with near-equivalent representation in most transporter families. These two Leptospira pathogens also possess intact sphingomyelinases, holins, and virulence-related outer membrane porins. These virulence-related factors, in conjunction with decreased transporter substrate versatility, indicate that pathogenicity was accompanied by progressively narrowing ecological niches and the emergence of a limited set of proteins responsible for host invasion. The variability of host tropism and mortality rates by infectious leptospires suggests that small differences in individual sets of proteins play important physiological and pathological roles. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Comparative analyses of transport proteins encoded within the genomes of Leptospira species.

    Science.gov (United States)

    Buyuktimkin, Bora; Saier, Milton H

    2016-09-01

    Select species of the bacterial genus Leptospira are causative agents of leptospirosis, an emerging global zoonosis affecting nearly one million people worldwide annually. We examined two Leptospira pathogens, Leptospira interrogans serovar Lai str. 56601 and Leptospira borgpetersenii serovar Hardjo-bovis str. L550, as well as the free-living leptospiral saprophyte, Leptospira biflexa serovar Patoc str. 'Patoc 1 (Ames)'. The transport proteins of these leptospires were identified and compared using bioinformatics to gain an appreciation for which proteins may be related to pathogenesis and saprophytism. L. biflexa possesses a disproportionately high number of secondary carriers for metabolite uptake and environmental adaptability as well as an increased number of inorganic cation transporters providing ionic homeostasis and effective osmoregulation in a rapidly changing environment. L. interrogans and L. borgpetersenii possess far fewer transporters, but those that they all have are remarkably similar, with near-equivalent representation in most transporter families. These two Leptospira pathogens also possess intact sphingomyelinases, holins, and virulence-related outer membrane porins. These virulence-related factors, in conjunction with decreased transporter substrate versatility, indicate that pathogenicity arose in Leptospira correlating to progressively narrowing ecological niches and the emergence of a limited set of proteins responsible for host invasion. The variability of host tropism and mortality rates by infectious leptospires suggests that small differences in individual sets of proteins play important physiological and pathological roles. Copyright © 2016. Published by Elsevier Ltd.

  19. Comparative Analyses on OPR1000 Steam Generator Tube Rupture Event Emergency Operational Guideline

    International Nuclear Information System (INIS)

    Lee, Sang Won; Bae, Yeon Kyoung; Kim, Hyeong Teak

    2006-01-01

    The Steam Generator Tube Rupture (SGTR) event is one of the important scenarios in respect to the radiation release to the environment. When the SGTR occurs, containment integrity is not effective because of the direct bypass of containment via the ruptured steam generator to the MSSV and MSADV. To prevent this path, the Emergency Operational Guideline of OPR1000 indicates the use of Turbine Bypass Valves (TBVs) as an effective means to depressurize the main steam line and prevent the lifting of MSSV. However, the TBVs are not operable when the offsite power is not available (LOOP). In this situation, the RCS cool-down is achieved by opening the both intact and ruptured SG MSADV. But this action causes the large amount of radiation release to the environment. To minimize the radiation release to the environment, KSNP EOG adopts the improved strategy when the SGTR concurrently with LOOP is occurred. However, these procedures show some duplicated procedure and branch line that might confusing the operator for optimal recovery action. So, in this paper, the comparative analysis on SGTR and SGTR with LOOP is performed and optimized procedure is proposed

  20. Comparative analyses of the bacterial community of hydrothermal deposits and seafloor sediments across Okinawa Trough

    Science.gov (United States)

    Wang, Long; Yu, Min; Liu, Yan; Liu, Jiwen; Wu, Yonghua; Li, Li; Liu, Jihua; Wang, Min; Zhang, Xiao-Hua

    2018-04-01

    As an ideal place to study back-arc basins and hydrothermal eco-system, Okinawa Trough has attracted the interests of scientists for decades. However, there are still no in-depth studies targeting the bacterial community of the seafloor sediments and hydrothermal deposits in Okinawa Trough. In the present study, we reported the bacterial community of the surface deposits of a newly found hydrothermal field in the southern Okinawa Trough, and the horizontal and vertical variation of bacterial communities in the sediments of the northern Okinawa Trough. The hydrothermal deposits had a relatively high 16S rRNA gene abundance but low bacterial richness and diversity. Epsilonproteobacteria and Bacteroidetes were predominant in hydrothermal deposits whereas Deltaproteobacteria, Gammaproteobacteria and Chloroflexi were abundant across all samples. The bacterial distribution in the seafloor of Okinawa Trough was significantly correlated to the content of total nitrogen, and had consistent relationship with total carbon. Gradual changes of sulfur-oxidizing bacteria were found with the distance away from hydrothermal fields, while the hydrothermal activity did not influence the distribution of the major clades of sulfate-reducing bacteria. Higher abundance of the sulfur cycle related genes (aprA and dsrB), and lower abundance of the bacterial ammonia-oxidizing related gene (amoA) were quantified in hydrothermal deposits. In addition, the present study also compared the inter-field variation of Epsilonproteobacteria among multi-types of hydrothermal vents, revealing that the proportion and diversity of this clade were quite various.

  1. Agriproteomics of Bread Wheat: Comparative Proteomics and Network Analyses of Grain Size Variation.

    Science.gov (United States)

    Dawkar, Vishal V; Dholakia, Bhushan B; Gupta, Vidya S

    2015-07-01

    Agriproteomics signifies the merging of agriculture research and proteomics systems science and is impacting plant research and societal development. Wheat is a frequently consumed foodstuff, has highly variable grain size that in effect contributes to wheat grain yield and the end-product quality. Very limited information is available on molecular basis of grain size due to complex multifactorial nature of this trait. Here, using liquid chromatography-mass spectrometry, we investigated the proteomics profiles from grains of wheat genotypes, Rye selection 111 (RS111) and Chinese spring (CS), which differ in their size. Significant differences in protein expression were found, including 33 proteins uniquely present in RS111 and 32 only in CS, while 54 proteins were expressed from both genotypes. Among differentially expressed proteins, 22 were upregulated, while 21 proteins were downregulated in RS111 compared to CS. Functional classification revealed their role in energy metabolism, seed storage, stress tolerance and transcription. Further, protein interactive network analysis was performed to predict the targets of identified proteins. Significantly different interactions patterns were observed between these genotypes with detection of proteins such as Cyp450, Sus2, and WRKY that could potentially affect seed size. The present study illustrates the potentials of agriproteomics as a veritable new frontier of plant omics research.

  2. The complete chloroplast genome sequence of Dodonaea viscosa: comparative and phylogenetic analyses.

    Science.gov (United States)

    Saina, Josphat K; Gichira, Andrew W; Li, Zhi-Zhong; Hu, Guang-Wan; Wang, Qing-Feng; Liao, Kuo

    2018-02-01

    The plant chloroplast (cp) genome is a highly conserved structure which is beneficial for evolution and systematic research. Currently, numerous complete cp genome sequences have been reported due to high throughput sequencing technology. However, there is no complete chloroplast genome of genus Dodonaea that has been reported before. To better understand the molecular basis of Dodonaea viscosa chloroplast, we used Illumina sequencing technology to sequence its complete genome. The whole length of the cp genome is 159,375 base pairs (bp), with a pair of inverted repeats (IRs) of 27,099 bp separated by a large single copy (LSC) 87,204 bp, and small single copy (SSC) 17,972 bp. The annotation analysis revealed a total of 115 unique genes of which 81 were protein coding, 30 tRNA, and four ribosomal RNA genes. Comparative genome analysis with other closely related Sapindaceae members showed conserved gene order in the inverted and single copy regions. Phylogenetic analysis clustered D. viscosa with other species of Sapindaceae with strong bootstrap support. Finally, a total of 249 SSRs were detected. Moreover, a comparison of the synonymous (Ks) and nonsynonymous (Ka) substitution rates in D. viscosa showed very low values. The availability of cp genome reported here provides a valuable genetic resource for comprehensive further studies in genetic variation, taxonomy and phylogenetic evolution of Sapindaceae family. In addition, SSR markers detected will be used in further phylogeographic and population structure studies of the species in this genus.

  3. Comparative transcriptomic analyses of differentially expressed genes in transgenic melatonin biosynthesis ovine HIOMT gene in switchgrass

    Directory of Open Access Journals (Sweden)

    Shan Yuan

    2016-11-01

    Full Text Available Melatonin serves pleiotropic functions in prompting plant growth and resistance to various stresses. The accurate biosynthetic pathway of melatonin remains elusive in plant species, while the N-acetyltransferase and O-methyltransferase were considered to be the last two key enzymes during its biosynthesis. To investigate the biosynthesis and metabolic pathway of melatonin in plants, the RNA-seq profile of overexpression of the ovine HIOMT was analyzed and compared with the previous transcriptome of transgenic oAANAT gene in switchgrass, a model plant for cellulosic ethanol production. A total of 946, 405 and 807 differentially expressed unigenes were observed in AANAT vs. control, HIOMT vs. control, and AANAT vs. HIOMT, respectively. The significantly upregulated (F-box/kelch-repeat protein, zinc finger BED domain-containing protein-3 genes were consistent with enhanced phenotypes of shoot, stem and root growth in transgenic oHIOMT switchgrass. Early flowering in overexpression of oHIOMT switchgrass involved in the regulation of flowering-time genes (APETALA2. Several stress resistant related genes (SPX domain-containing membrane protein, copper transporter 1, late blight resistance protein homolog R1A-6 OS etc. were specifically and significantly upregulated in transgenic oHIOMT only, while metabolism-related genes (phenylalanine-4-hydroxylase, tyrosine decarboxylase 1, protein disulfide-isomerase and galactinol synthase 2 etc. were significantly upregulated in transgenic oAANAT only. These results provide new sights into the biosynthetic and physiological functional networks of melatonin in plants.

  4. Comparative analyses of physiological responses of Cynodon dactylon accessions from Southwest China to sulfur dioxide toxicity.

    Science.gov (United States)

    Li, Xi; Wang, Ling; Li, Yiqiao; Sun, Lingxia; Cai, Shizhen; Huang, Zhuo

    2014-01-01

    Sulfur dioxide (SO2), a major air pollutant in developing countries, is highly toxic to plants. To achieve better air quality and landscape, planting appropriate grass species in severe SO2 polluted areas is very critical. Cynodon dactylon, a widely used warm season turfgrass species, has good SO2-tolerant ability. In this study, we selected 9 out of 38 C. dactylon accessions from Southwest China as representatives of high, intermediate SO2-tolerant and SO2-sensitive accessions to comparatively analyze their physiological differences in leaves under SO2 untreated and treated conditions. Our results revealed that SO2-tolerant C. dactylon accessions showed higher soluble sugar, proline, and chlorophyll a contents under both SO2 treated and untreated conditions; higher chlorophyll b and carotenoid under SO2 treated condition; lower reactive oxygen species (ROS) level, oxidative damages, and superoxide dismutase (SOD) activities under SO2 treated condition; and higher peroxidase (POD) activities under SO2 untreated condition. Further results indicated that SO2-tolerant C. dactylon accessions had higher sulfur contents under both SO2 treated and untreated conditions, consistent with higher SO activities under both SO2 treated and untreated conditions, and higher SiR activities under SO2 treated condition. Taken together, our results indicated that SO2 tolerance of C. dactylon might be largely related to soluble sugar, proline and chlorophyll a contents, and SO enzyme activity.

  5. Comparative analyses of longevity and senescence reveal variable survival benefits of living in zoos across mammals.

    Science.gov (United States)

    Tidière, Morgane; Gaillard, Jean-Michel; Berger, Vérane; Müller, Dennis W H; Bingaman Lackey, Laurie; Gimenez, Olivier; Clauss, Marcus; Lemaître, Jean-François

    2016-11-07

    While it is commonly believed that animals live longer in zoos than in the wild, this assumption has rarely been tested. We compared four survival metrics (longevity, baseline mortality, onset of senescence and rate of senescence) between both sexes of free-ranging and zoo populations of more than 50 mammal species. We found that mammals from zoo populations generally lived longer than their wild counterparts (84% of species). The effect was most notable in species with a faster pace of life (i.e. a short life span, high reproductive rate and high mortality in the wild) because zoos evidently offer protection against a number of relevant conditions like predation, intraspecific competition and diseases. Species with a slower pace of life (i.e. a long life span, low reproduction rate and low mortality in the wild) benefit less from captivity in terms of longevity; in such species, there is probably less potential for a reduction in mortality. These findings provide a first general explanation about the different magnitude of zoo environment benefits among mammalian species, and thereby highlight the effort that is needed to improve captive conditions for slow-living species that are particularly susceptible to extinction in the wild.

  6. Comparative and bioinformatics analyses of pathogenic bacterial secretomes identified by mass spectrometry in Burkholderia species.

    Science.gov (United States)

    Nguyen, Thao Thi; Chon, Tae-Soo; Kim, Jaehan; Seo, Young-Su; Heo, Muyoung

    2017-07-01

    Secreted proteins (secretomes) play crucial roles during bacterial pathogenesis in both plant and human hosts. The identification and characterization of secretomes in the two plant pathogens Burkholderia glumae BGR1 and B. gladioli BSR3, which cause diseases in rice such as seedling blight, panicle blight, and grain rot, are important steps to not only understand the disease-causing mechanisms but also find remedies for the diseases. Here, we identified two datasets of secretomes in B. glumae BGR1 and B. gladioli BSR3, which consist of 118 and 111 proteins, respectively, using mass spectrometry approach and literature curation. Next, we characterized the functional properties, potential secretion pathways and sequence information properties of secretomes of two plant pathogens in a comparative analysis by various computational approaches. The ratio of potential non-classically secreted proteins (NCSPs) to classically secreted proteins (CSPs) in B. glumae BGR1 was greater than that in B. gladioli BSR3. For CSPs, the putative hydrophobic regions (PHRs) which are essential for secretion process of CSPs were screened in detail at their N-terminal sequences using hidden Markov model (HMM)-based method. Total 31 pairs of homologous proteins in two bacterial secretomes were indicated based on the global alignment (identity ≥ 70%). Our results may facilitate the understanding of the species-specific features of secretomes in two plant pathogenic Burkholderia species.

  7. Autistic Regression

    Science.gov (United States)

    Matson, Johnny L.; Kozlowski, Alison M.

    2010-01-01

    Autistic regression is one of the many mysteries in the developmental course of autism and pervasive developmental disorders not otherwise specified (PDD-NOS). Various definitions of this phenomenon have been used, further clouding the study of the topic. Despite this problem, some efforts at establishing prevalence have been made. The purpose of…

  8. Comparative exergy analyses of Jatropha curcas oil extraction methods: Solvent and mechanical extraction processes

    International Nuclear Information System (INIS)

    Ofori-Boateng, Cynthia; Keat Teong, Lee; JitKang, Lim

    2012-01-01

    Highlights: ► Exergy analysis detects locations of resource degradation within a process. ► Solvent extraction is six times exergetically destructive than mechanical extraction. ► Mechanical extraction of jatropha oil is 95.93% exergetically efficient. ► Solvent extraction of jatropha oil is 79.35% exergetically efficient. ► Exergy analysis of oil extraction processes allow room for improvements. - Abstract: Vegetable oil extraction processes are found to be energy intensive. Thermodynamically, any energy intensive process is considered to degrade the most useful part of energy that is available to produce work. This study uses literature values to compare the efficiencies and degradation of the useful energy within Jatropha curcas oil during oil extraction taking into account solvent and mechanical extraction methods. According to this study, J. curcas seeds on processing into J. curcas oil is upgraded with mechanical extraction but degraded with solvent extraction processes. For mechanical extraction, the total internal exergy destroyed is 3006 MJ which is about six times less than that for solvent extraction (18,072 MJ) for 1 ton J. curcas oil produced. The pretreatment processes of the J. curcas seeds recorded a total internal exergy destructions of 5768 MJ accounting for 24% of the total internal exergy destroyed for solvent extraction processes and 66% for mechanical extraction. The exergetic efficiencies recorded are 79.35% and 95.93% for solvent and mechanical extraction processes of J. curcas oil respectively. Hence, mechanical oil extraction processes are exergetically efficient than solvent extraction processes. Possible improvement methods are also elaborated in this study.

  9. Comparative analyses of the bacterial microbiota of the human nostril and oropharynx.

    Science.gov (United States)

    Lemon, Katherine P; Klepac-Ceraj, Vanja; Schiffer, Hilary K; Brodie, Eoin L; Lynch, Susan V; Kolter, Roberto

    2010-06-22

    The nose and throat are important sites of pathogen colonization, yet the microbiota of both is relatively unexplored by culture-independent approaches. We examined the bacterial microbiota of the nostril and posterior wall of the oropharynx from seven healthy adults using two culture-independent methods, a 16S rRNA gene microarray (PhyloChip) and 16S rRNA gene clone libraries. While the bacterial microbiota of the oropharynx was richer than that of the nostril, the oropharyngeal microbiota varied less among participants than did nostril microbiota. A few phyla accounted for the majority of the bacteria detected at each site: Firmicutes and Actinobacteria in the nostril and Firmicutes, Proteobacteria, and Bacteroidetes in the oropharynx. Compared to culture-independent surveys of microbiota from other body sites, the microbiota of the nostril and oropharynx show distinct phylum-level distribution patterns, supporting niche-specific colonization at discrete anatomical sites. In the nostril, the distribution of Actinobacteria and Firmicutes was reminiscent of that of skin, though Proteobacteria were much less prevalent. The distribution of Firmicutes, Proteobacteria, and Bacteroidetes in the oropharynx was most similar to that in saliva, with more Proteobacteria than in the distal esophagus or mouth. While Firmicutes were prevalent at both sites, distinct families within this phylum dominated numerically in each. At both sites there was an inverse correlation between the prevalences of Firmicutes and another phylum: in the oropharynx, Firmicutes and Proteobacteria, and in the nostril, Firmicutes and Actinobacteria. In the nostril, this inverse correlation existed between the Firmicutes family Staphylococcaceae and Actinobacteria families, suggesting potential antagonism between these groups.

  10. Comparative Genetic Analyses of Human Rhinovirus C (HRV-C) Complete Genome from Malaysia

    Science.gov (United States)

    Khaw, Yam Sim; Chan, Yoke Fun; Jafar, Faizatul Lela; Othman, Norlijah; Chee, Hui Yee

    2016-01-01

    Human rhinovirus-C (HRV-C) has been implicated in more severe illnesses than HRV-A and HRV-B, however, the limited number of HRV-C complete genomes (complete 5′ and 3′ non-coding region and open reading frame sequences) has hindered the in-depth genetic study of this virus. This study aimed to sequence seven complete HRV-C genomes from Malaysia and compare their genetic characteristics with the 18 published HRV-Cs. Seven Malaysian HRV-C complete genomes were obtained with newly redesigned primers. The seven genomes were classified as HRV-C6, C12, C22, C23, C26, C42, and pat16 based on the VP4/VP2 and VP1 pairwise distance threshold classification. Five of the seven Malaysian isolates, namely, 3430-MY-10/C22, 8713-MY-10/C23, 8097-MY-11/C26, 1570-MY-10/C42, and 7383-MY-10/pat16 are the first newly sequenced complete HRV-C genomes. All seven Malaysian isolates genomes displayed nucleotide similarity of 63–81% among themselves and 63–96% with other HRV-Cs. Malaysian HRV-Cs had similar putative immunogenic sites, putative receptor utilization and potential antiviral sites as other HRV-Cs. The genomic features of Malaysian isolates were similar to those of other HRV-Cs. Negative selections were frequently detected in HRV-Cs complete coding sequences indicating that these sequences were under functional constraint. The present study showed that HRV-Cs from Malaysia have diverse genetic sequences but share conserved genomic features with other HRV-Cs. This genetic information could provide further aid in the understanding of HRV-C infection. PMID:27199901

  11. Comparative Transcriptome and Microscopy Analyses Provide Insights into Flat Shape Formation in Peach (Prunus persica

    Directory of Open Access Journals (Sweden)

    Jian Guo

    2018-01-01

    Full Text Available Fruit shape is an important external characteristic that consumers use to select preferred fruit cultivars. In peach, the flat fruit cultivars have become more and more popular worldwide. Genetic markers closely linking to the flat fruit trait have been identified and are useful for marker-assisted breeding. However, the cellular and genetic mechanisms underpinning flat fruit formation are still poorly understood. In this study, we have revealed the differences in fruit cell number, cell size, and in gene expression pattern between the traditional round fruit and modern flat fruit cultivars. Flat peach cultivars possessed significantly lower number of cells in the vertical axis because cell division in the vertical direction stopped early in the flat fruit cultivars at 15 DAFB (day after full bloom than in round fruit cultivars at 35 DAFB. This resulted in the reduction in vertical development in the flat fruit. Significant linear relationship was observed between fruit vertical diameter and cell number in vertical axis for the four examined peach cultivars (R2 = 0.9964 at maturation stage, and was also observed between fruit vertical diameter and fruit weight (R2 = 0.9605, which indicated that cell number in vertical direction contributed to the flat shape formation. Furthermore, in RNA-seq analysis, 4165 differentially expressed genes (DEGs were detected by comparing RNA-seq data between flat and round peach cultivars at different fruit development stages. In contrast to previous studies, we discovered 28 candidate genes potentially responsible for the flat shape formation, including 19 located in the mapping site and 9 downstream genes. Our study indicates that flat and round fruit shape in peach is primarily determined by the regulation of cell production in the vertical direction during early fruit development.

  12. Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses

    Directory of Open Access Journals (Sweden)

    Ryan Joseph F

    2011-01-01

    Full Text Available Abstract Background Mutations in the Otopetrin 1 gene (Otop1 in mice and fish produce an unusual bilateral vestibular pathology that involves the absence of otoconia without hearing impairment. The encoded protein, Otop1, is the only functionally characterized member of the Otopetrin Domain Protein (ODP family; the extended sequence and structural preservation of ODP proteins in metazoans suggest a conserved functional role. Here, we use the tools of sequence- and cytogenetic-based comparative genomics to study the Otop1 and the Otop2-Otop3 genes and to establish their genomic context in 25 vertebrates. We extend our evolutionary study to include the gene mutated in Usher syndrome (USH subtype 1G (Ush1g, both because of the head-to-tail clustering of Ush1g with Otop2 and because Otop1 and Ush1g mutations result in inner ear phenotypes. Results We established that OTOP1 is the boundary gene of an inversion polymorphism on human chromosome 4p16 that originated in the common human-chimpanzee lineage more than 6 million years ago. Other lineage-specific evolutionary events included a three-fold expansion of the Otop genes in Xenopus tropicalis and of Ush1g in teleostei fish. The tight physical linkage between Otop2 and Ush1g is conserved in all vertebrates. To further understand the functional organization of the Ushg1-Otop2 locus, we deduced a putative map of binding sites for CCCTC-binding factor (CTCF, a mammalian insulator transcription factor, from genome-wide chromatin immunoprecipitation-sequencing (ChIP-seq data in mouse and human embryonic stem (ES cells combined with detection of CTCF-binding motifs. Conclusions The results presented here clarify the evolutionary history of the vertebrate Otop and Ush1g families, and establish a framework for studying the possible interaction(s of Ush1g and Otop in developmental pathways.

  13. Comparative analyses identified species-specific functional roles in oral microbial genomes

    Science.gov (United States)

    Chen, Tsute; Gajare, Prasad; Olsen, Ingar; Dewhirst, Floyd E.

    2017-01-01

    ABSTRACT The advent of next generation sequencing is producing more genomic sequences for various strains of many human oral microbial species and allows for insightful functional comparisons at both intra- and inter-species levels. This study performed in-silico functional comparisons for currently available genomic sequences of major species associated with periodontitis including Aggregatibacter actinomycetemcomitans (AA), Porphyromonas gingivalis (PG), Treponema denticola (TD), and Tannerella forsythia (TF), as well as several cariogenic and commensal streptococcal species. Complete or draft sequences were annotated with the RAST to infer structured functional subsystems for each genome. The subsystems profiles were clustered to groups of functions with similar patterns. Functional enrichment and depletion were evaluated based on hypergeometric distribution to identify subsystems that are unique or missing between two groups of genomes. Unique or missing metabolic pathways and biological functions were identified in different species. For example, components involved in flagellar motility were found only in the motile species TD, as expected, with few exceptions scattered in several streptococcal species, likely associated with chemotaxis. Transposable elements were only found in the two Bacteroidales species PG and TF, and half of the AA genomes. Genes involved in CRISPR were prevalent in most oral species. Furthermore, prophage related subsystems were also commonly found in most species except for PG and Streptococcus mutans, in which very few genomes contain prophage components. Comparisons between pathogenic (P) and nonpathogenic (NP) genomes also identified genes potentially important for virulence. Two such comparisons were performed between AA (P) and several A. aphrophilus (NP) strains, and between S. mutans + S. sobrinus (P) and other oral streptococcal species (NP). This comparative genomics approach can be readily used to identify functions unique to

  14. Comparative analyses of olfactory systems in terrestrial crabs (Brachyura: evidence for aerial olfaction?

    Directory of Open Access Journals (Sweden)

    Jakob Krieger

    2015-12-01

    Full Text Available Adaptations to a terrestrial lifestyle occurred convergently multiple times during the evolution of the arthropods. This holds also true for the “true crabs” (Brachyura, a taxon that includes several lineages that invaded land independently. During an evolutionary transition from sea to land, animals have to develop a variety of physiological and anatomical adaptations to a terrestrial life style related to respiration, reproduction, development, circulation, ion and water balance. In addition, sensory systems that function in air instead of in water are essential for an animal’s life on land. Besides vision and mechanosensory systems, on land, the chemical senses have to be modified substantially in comparison to their function in water. Among arthropods, insects are the most successful ones to evolve aerial olfaction. Various aspects of terrestrial adaptation have also been analyzed in those crustacean lineages that evolved terrestrial representatives including the taxa Anomala, Brachyura, Amphipoda, and Isopoda. We are interested in how the chemical senses of terrestrial crustaceans are modified to function in air. Therefore, in this study, we analyzed the brains and more specifically the structure of the olfactory system of representatives of brachyuran crabs that display different degrees of terrestriality, from exclusively marine to mainly terrestrial. The methods we used included immunohistochemistry, detection of autofluorescence- and confocal microscopy, as well as three-dimensional reconstruction and morphometry. Our comparative approach shows that both the peripheral and central olfactory pathways are reduced in terrestrial members in comparison to their marine relatives, suggesting a limited function of their olfactory system on land. We conclude that for arthropod lineages that invaded land, evolving aerial olfaction is no trivial task.

  15. Regression Analysis

    CERN Document Server

    Freund, Rudolf J; Sa, Ping

    2006-01-01

    The book provides complete coverage of the classical methods of statistical analysis. It is designed to give students an understanding of the purpose of statistical analyses, to allow the student to determine, at least to some degree, the correct type of statistical analyses to be performed in a given situation, and have some appreciation of what constitutes good experimental design

  16. Comparative analyses reveal discrepancies among results of commonly used methods for Anopheles gambiaemolecular form identification

    Directory of Open Access Journals (Sweden)

    Pinto João

    2011-08-01

    Full Text Available Abstract Background Anopheles gambiae M and S molecular forms, the major malaria vectors in the Afro-tropical region, are ongoing a process of ecological diversification and adaptive lineage splitting, which is affecting malaria transmission and vector control strategies in West Africa. These two incipient species are defined on the basis of single nucleotide differences in the IGS and ITS regions of multicopy rDNA located on the X-chromosome. A number of PCR and PCR-RFLP approaches based on form-specific SNPs in the IGS region are used for M and S identification. Moreover, a PCR-method to detect the M-specific insertion of a short interspersed transposable element (SINE200 has recently been introduced as an alternative identification approach. However, a large-scale comparative analysis of four widely used PCR or PCR-RFLP genotyping methods for M and S identification was never carried out to evaluate whether they could be used interchangeably, as commonly assumed. Results The genotyping of more than 400 A. gambiae specimens from nine African countries, and the sequencing of the IGS-amplicon of 115 of them, highlighted discrepancies among results obtained by the different approaches due to different kinds of biases, which may result in an overestimation of MS putative hybrids, as follows: i incorrect match of M and S specific primers used in the allele specific-PCR approach; ii presence of polymorphisms in the recognition sequence of restriction enzymes used in the PCR-RFLP approaches; iii incomplete cleavage during the restriction reactions; iv presence of different copy numbers of M and S-specific IGS-arrays in single individuals in areas of secondary contact between the two forms. Conclusions The results reveal that the PCR and PCR-RFLP approaches most commonly utilized to identify A. gambiae M and S forms are not fully interchangeable as usually assumed, and highlight limits of the actual definition of the two molecular forms, which might

  17. Model-based analyses to compare health and economic outcomes of cancer control: inclusion of disparities.

    Science.gov (United States)

    Goldie, Sue J; Daniels, Norman

    2011-09-21

    Disease simulation models of the health and economic consequences of different prevention and treatment strategies can guide policy decisions about cancer control. However, models that also consider health disparities can identify strategies that improve both population health and its equitable distribution. We devised a typology of cancer disparities that considers types of inequalities among black, white, and Hispanic populations across different cancers and characteristics important for near-term policy discussions. We illustrated the typology in the specific example of cervical cancer using an existing disease simulation model calibrated to clinical, epidemiological, and cost data for the United States. We calculated average reduction in cancer incidence overall and for black, white, and Hispanic women under five different prevention strategies (Strategies A1, A2, A3, B, and C) and estimated average costs and life expectancy per woman, and the cost-effectiveness ratio for each strategy. Strategies that may provide greater aggregate health benefit than existing options may also exacerbate disparities. Combining human papillomavirus vaccination (Strategy A2) with current cervical cancer screening patterns (Strategy A1) resulted in an average reduction of 69% in cancer incidence overall but a 71.6% reduction for white women, 68.3% for black women, and 63.9% for Hispanic women. Other strategies targeting risk-based screening to racial and ethnic minorities reduced disparities among racial subgroups and resulted in more equitable distribution of benefits among subgroups (reduction in cervical cancer incidence, white vs. Hispanic women, 69.7% vs. 70.1%). Strategies that employ targeted risk-based screening and new screening algorithms, with or without vaccination (Strategies B and C), provide excellent value. The most effective strategy (Strategy C) had a cost-effectiveness ratio of $28,200 per year of life saved when compared with the same strategy without

  18. Comparative energy consumption analyses of an ultra high frequency induction heating system for material processing applications

    Directory of Open Access Journals (Sweden)

    Taştan, Mehmet

    2015-09-01

    Full Text Available This study compares an energy consumption results of the TI-6Al-4V based material processing under the 900 kHz induction heating for different cases. By this means, total power consumption and energy consumptions per sample and amount have been analyzed. Experiments have been conducted with 900 kHz, 2.8 kW ultra-high frequency induction system. Two cases are considered in the study. In the first case, TI-6Al-4V samples have been heated up to 900 °C with classical heating method, which is used in industrial applications, and then they have been cooled down by water. Afterwards, the samples have been heated up to 600 °C, 650 °C and 700 °C respectively and stress relieving process has been applied through natural cooling. During these processes, energy consumptions for each defined process have been measured. In the second case, unlike the first study, can be used five different samples have been heated up to the various temperatures between 600 °C and 1120 °C and energy consumptions have been measured for these processes. Thereby, the effect of temperature increase on each sample on energy cost has been analyzed. It has been seen that as a result of heating the titanium bulk materials, which have been used in the experiment, with ultra high frequency induction, temperature increase also increases the energy consumption. But it has been revealed that the increase rate in the energy consumption is more than the increase rate of the temperature.En este estudio se comparan los consumos energéticos al procesar Ti-6Al-4V por inducción a 900 kHz. Se ha analizado la potencia total consumida y la energía consumida por muestra. Los experimentos se han realizado en un sistema de inducción de ultra alta frecuencia a 900 kHz, 2,8 kW. Se han considerado dos casos, en el primero se ha calentado Ti-6Al-4V a 900 °C por el método clásico usado en la industria y enfriado en agua; posteriormente las muestras se han calentado a 600, 650 y 700 °C y

  19. Linear regression

    CERN Document Server

    Olive, David J

    2017-01-01

    This text covers both multiple linear regression and some experimental design models. The text uses the response plot to visualize the model and to detect outliers, does not assume that the error distribution has a known parametric distribution, develops prediction intervals that work when the error distribution is unknown, suggests bootstrap hypothesis tests that may be useful for inference after variable selection, and develops prediction regions and large sample theory for the multivariate linear regression model that has m response variables. A relationship between multivariate prediction regions and confidence regions provides a simple way to bootstrap confidence regions. These confidence regions often provide a practical method for testing hypotheses. There is also a chapter on generalized linear models and generalized additive models. There are many R functions to produce response and residual plots, to simulate prediction intervals and hypothesis tests, to detect outliers, and to choose response trans...

  20. Contesting Citizenship: Comparative Analyses

    DEFF Research Database (Denmark)

    Siim, Birte; Squires, Judith

    2007-01-01

    The pursuit of equal citizenship has been complicated by two recent developments: the emergence of multi-level governance (and with it the growing importance of local, regional and global levels of citizenship practices) and the emrgence of group recognition claims (which signals the growing impo...

  1. Linear support vector regression and partial least squares chemometric models for determination of Hydrochlorothiazide and Benazepril hydrochloride in presence of related impurities: A comparative study

    Science.gov (United States)

    Naguib, Ibrahim A.; Abdelaleem, Eglal A.; Draz, Mohammed E.; Zaazaa, Hala E.

    2014-09-01

    Partial least squares regression (PLSR) and support vector regression (SVR) are two popular chemometric models that are being subjected to a comparative study in the presented work. The comparison shows their characteristics via applying them to analyze Hydrochlorothiazide (HCZ) and Benazepril hydrochloride (BZ) in presence of HCZ impurities; Chlorothiazide (CT) and Salamide (DSA) as a case study. The analysis results prove to be valid for analysis of the two active ingredients in raw materials and pharmaceutical dosage form through handling UV spectral data in range (220-350 nm). For proper analysis a 4 factor 4 level experimental design was established resulting in a training set consisting of 16 mixtures containing different ratios of interfering species. An independent test set consisting of 8 mixtures was used to validate the prediction ability of the suggested models. The results presented indicate the ability of mentioned multivariate calibration models to analyze HCZ and BZ in presence of HCZ impurities CT and DSA with high selectivity and accuracy of mean percentage recoveries of (101.01 ± 0.80) and (100.01 ± 0.87) for HCZ and BZ respectively using PLSR model and of (99.78 ± 0.80) and (99.85 ± 1.08) for HCZ and BZ respectively using SVR model. The analysis results of the dosage form were statistically compared to the reference HPLC method with no significant differences regarding accuracy and precision. SVR model gives more accurate results compared to PLSR model and show high generalization ability, however, PLSR still keeps the advantage of being fast to optimize and implement.

  2. A comparative study between the use of artificial neural networks and multiple linear regression for caustic concentration prediction in a stage of alumina production

    Directory of Open Access Journals (Sweden)

    Giovanni Leopoldo Rozza

    2015-09-01

    Full Text Available With world becoming each day a global village, enterprises continuously seek to optimize their internal processes to hold or improve their competitiveness and make better use of natural resources. In this context, decision support tools are an underlying requirement. Such tools are helpful on predicting operational issues, avoiding cost risings, loss of productivity, work-related accident leaves or environmental disasters. This paper has its focus on the prediction of spent liquor caustic concentration of Bayer process for alumina production. Caustic concentration measuring is essential to keep it at expected levels, otherwise quality issues might arise. The organization requests caustic concentration by chemical analysis laboratory once a day, such information is not enough to issue preventive actions to handle process inefficiencies that will be known only after new measurement on the next day. Thereby, this paper proposes using Multiple Linear Regression and Artificial Neural Networks techniques a mathematical model to predict the spent liquor´s caustic concentration. Hence preventive actions will occur in real time. Such models were built using software tool for numerical computation (MATLAB and a statistical analysis software package (SPSS. The models output (predicted caustic concentration were compared with the real lab data. We found evidence suggesting superior results with use of Artificial Neural Networks over Multiple Linear Regression model. The results demonstrate that replacing laboratorial analysis by the forecasting model to support technical staff on decision making could be feasible.

  3. Support vector regression and artificial neural network models for stability indicating analysis of mebeverine hydrochloride and sulpiride mixtures in pharmaceutical preparation: A comparative study

    Science.gov (United States)

    Naguib, Ibrahim A.; Darwish, Hany W.

    2012-02-01

    A comparison between support vector regression (SVR) and Artificial Neural Networks (ANNs) multivariate regression methods is established showing the underlying algorithm for each and making a comparison between them to indicate the inherent advantages and limitations. In this paper we compare SVR to ANN with and without variable selection procedure (genetic algorithm (GA)). To project the comparison in a sensible way, the methods are used for the stability indicating quantitative analysis of mixtures of mebeverine hydrochloride and sulpiride in binary mixtures as a case study in presence of their reported impurities and degradation products (summing up to 6 components) in raw materials and pharmaceutical dosage form via handling the UV spectral data. For proper analysis, a 6 factor 5 level experimental design was established resulting in a training set of 25 mixtures containing different ratios of the interfering species. An independent test set consisting of 5 mixtures was used to validate the prediction ability of the suggested models. The proposed methods (linear SVR (without GA) and linear GA-ANN) were successfully applied to the analysis of pharmaceutical tablets containing mebeverine hydrochloride and sulpiride mixtures. The results manifest the problem of nonlinearity and how models like the SVR and ANN can handle it. The methods indicate the ability of the mentioned multivariate calibration models to deconvolute the highly overlapped UV spectra of the 6 components' mixtures, yet using cheap and easy to handle instruments like the UV spectrophotometer.

  4. CrusView: A Java-Based Visualization Platform for Comparative Genomics Analyses in Brassicaceae Species[OPEN

    Science.gov (United States)

    Chen, Hao; Wang, Xiangfeng

    2013-01-01

    In plants and animals, chromosomal breakage and fusion events based on conserved syntenic genomic blocks lead to conserved patterns of karyotype evolution among species of the same family. However, karyotype information has not been well utilized in genomic comparison studies. We present CrusView, a Java-based bioinformatic application utilizing Standard Widget Toolkit/Swing graphics libraries and a SQLite database for performing visualized analyses of comparative genomics data in Brassicaceae (crucifer) plants. Compared with similar software and databases, one of the unique features of CrusView is its integration of karyotype information when comparing two genomes. This feature allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of the Brassicaceae genomes. Additionally, CrusView is a local program, which gives its users high flexibility when analyzing unpublished genomes and allows users to upload self-defined genomic information so that they can visually study the associations between genome structural variations and genetic elements, including chromosomal rearrangements, genomic macrosynteny, gene families, high-frequency recombination sites, and tandem and segmental duplications between related species. This tool will greatly facilitate karyotype, chromosome, and genome evolution studies using visualized comparative genomics approaches in Brassicaceae species. CrusView is freely available at http://www.cmbb.arizona.edu/CrusView/. PMID:23898041

  5. A comparative study of artificial neural network and multivariate regression analysis to analyze optimum renal stone fragmentation by extracorporeal shock wave lithotripsy

    Directory of Open Access Journals (Sweden)

    Goyal Neeraj

    2010-01-01

    Full Text Available To compare the accuracy of artificial neural network (ANN analysis and multi-variate regression analysis (MVRA for renal stone fragmentation by extracorporeal shock wave lithotripsy (ESWL. A total of 276 patients with renal calculus were treated by ESWL during December 2001 to December 2006. Of them, the data of 196 patients were used for training the ANN. The predictability of trained ANN was tested on 80 subsequent patients. The input data include age of patient, stone size, stone burden, number of sittings and urinary pH. The output values (predicted values were number of shocks and shock power. Of these 80 patients, the input was analyzed and output was also calculated by MVRA. The output values (predicted values from both the methods were compared and the results were drawn. The predicted and observed values of shock power and number of shocks were compared using 1:1 slope line. The results were calculated as coefficient of correlation (COC (r2 . For prediction of power, the MVRA COC was 0.0195 and ANN COC was 0.8343. For prediction of number of shocks, the MVRA COC was 0.5726 and ANN COC was 0.9329. In conclusion, ANN gives better COC than MVRA, hence could be a better tool to analyze the optimum renal stone fragmentation by ESWL.

  6. A comparative study of artificial neural network and multivariate regression analysis to analyze optimum renal stone fragmentation by extracorporeal shock wave lithotripsy

    International Nuclear Information System (INIS)

    Neeraj K Goyal, Abhay Kumar; Sameer Trivedi

    2010-01-01

    To compare the accuracy of artificial neural network (ANN) analysis and multivariate regression analysis (MVRA) for renal stone fragmentation by extracorporeal shock wave lithotripsy (ESWL). A total of 276 patients with renal calculus were treated by ESWL during December 2001 to December 2006. Of them, the data of 196 patients were used for training the ANN. The predictability of trained ANN was tested on 80 subsequent patients. The input data include age of patient, stone size, stone burden, number of sittings and urinary pH. The output values (predicted values) were number of shocks and shock power. Of these 80 patients, the input was analyzed and output was also calculated by MVRA. The output values (predicted values) from both the methods were compared and the results were drawn. The predicted and observed values of shock power and number of shocks were compared using 1:1 slope line. The results were calculated as coefficient of correlation (COC) (r2 ). For prediction of power, the MVRA COC was 0.0195 and ANN COC was 0.8343. For prediction of number of shocks, the MVRA COC was 0.5726 and ANN COC was 0.9329. In conclusion, ANN gives better COC than MVRA, hence could be a better tool to analyze the optimum renal stone fragmentation by ESWL (Author).

  7. Neural networks vs Gaussian process regression for representing potential energy surfaces: A comparative study of fit quality and vibrational spectrum accuracy

    Science.gov (United States)

    Kamath, Aditya; Vargas-Hernández, Rodrigo A.; Krems, Roman V.; Carrington, Tucker; Manzhos, Sergei

    2018-06-01

    For molecules with more than three atoms, it is difficult to fit or interpolate a potential energy surface (PES) from a small number of (usually ab initio) energies at points. Many methods have been proposed in recent decades, each claiming a set of advantages. Unfortunately, there are few comparative studies. In this paper, we compare neural networks (NNs) with Gaussian process (GP) regression. We re-fit an accurate PES of formaldehyde and compare PES errors on the entire point set used to solve the vibrational Schrödinger equation, i.e., the only error that matters in quantum dynamics calculations. We also compare the vibrational spectra computed on the underlying reference PES and the NN and GP potential surfaces. The NN and GP surfaces are constructed with exactly the same points, and the corresponding spectra are computed with the same points and the same basis. The GP fitting error is lower, and the GP spectrum is more accurate. The best NN fits to 625/1250/2500 symmetry unique potential energy points have global PES root mean square errors (RMSEs) of 6.53/2.54/0.86 cm-1, whereas the best GP surfaces have RMSE values of 3.87/1.13/0.62 cm-1, respectively. When fitting 625 symmetry unique points, the error in the first 100 vibrational levels is only 0.06 cm-1 with the best GP fit, whereas the spectrum on the best NN PES has an error of 0.22 cm-1, with respect to the spectrum computed on the reference PES. This error is reduced to about 0.01 cm-1 when fitting 2500 points with either the NN or GP. We also find that the GP surface produces a relatively accurate spectrum when obtained based on as few as 313 points.

  8. [Prevalence and factors associated with intimate partner abuse in female users of public health services in Mexico: a comparative analyses].

    Science.gov (United States)

    Ávila-Burgos, Leticia; Valdez-Santiagob, Rosario; Barroso-Quiab, Abigail; Híjar, Martha; Rojas, Rosalba; Del Río-Zolezzi, Aurora

    2014-01-01

    To analyze the evolution of the prevalence in intimate partner violence during the years 2003 and 2006 in Mexico, identifying factors associated with its severity, comparing our results with findings from 2003. Data from the Encuesta Nacional de Violencia contra las Mujeres (ENVIM 2006) was used; it has urban-rural national representation of female users of Mexican public health services. A total of 22,318 women above 14 years of age were interviewed. A multinomial logistic regression model was adjusted. The dependent variable was the Index of Intimate Partner Abuse. Intimate partner abuse increased 17% in comparison to the year 2003. Women's personal history of childhood abuse (ORA= 5.12, 95% CI4.15-6.30) and rape (ORA = 3.5, 95% CI = 2.66-4.62) were the most important women's factors that were found associated with severe violence. Male partner's daily alcohol consumption increased eleven fold the possibility of severe violence; higher disagreement with traditional female gender roles and higher education of both partners were protective factors. Factors associated with violence and their severities were consistent with findings reported in 2003. Intimate partner violence is a highly prevalent social problem which requires comprehensive strategies supporting empowerment of women through higher education, early detection and care of those battered, as well as structured interventions to prevent violence in future generations.

  9. Comparing pseudo-absences generation techniques in Boosted Regression Trees models for conservation purposes: A case study on amphibians in a protected area.

    Directory of Open Access Journals (Sweden)

    Francesco Cerasoli

    Full Text Available Boosted Regression Trees (BRT is one of the modelling techniques most recently applied to biodiversity conservation and it can be implemented with presence-only data through the generation of artificial absences (pseudo-absences. In this paper, three pseudo-absences generation techniques are compared, namely the generation of pseudo-absences within target-group background (TGB, testing both the weighted (WTGB and unweighted (UTGB scheme, and the generation at random (RDM, evaluating their performance and applicability in distribution modelling and species conservation. The choice of the target group fell on amphibians, because of their rapid decline worldwide and the frequent lack of guidelines for conservation strategies and regional-scale planning, which instead could be provided through an appropriate implementation of SDMs. Bufo bufo, Salamandrina perspicillata and Triturus carnifex were considered as target species, in order to perform our analysis with species having different ecological and distributional characteristics. The study area is the "Gran Sasso-Monti della Laga" National Park, which hosts 15 Natura 2000 sites and represents one of the most important biodiversity hotspots in Europe. Our results show that the model calibration ameliorates when using the target-group based pseudo-absences compared to the random ones, especially when applying the WTGB. Contrarily, model discrimination did not significantly vary in a consistent way among the three approaches with respect to the tree target species. Both WTGB and RDM clearly isolate the highly contributing variables, supplying many relevant indications for species conservation actions. Moreover, the assessment of pairwise variable interactions and their three-dimensional visualization further increase the amount of useful information for protected areas' managers. Finally, we suggest the use of RDM as an admissible alternative when it is not possible to individuate a suitable set of

  10. Fossil-based comparative analyses reveal ancient marine ancestry erased by extinction in ray-finned fishes.

    Science.gov (United States)

    Betancur-R, Ricardo; Ortí, Guillermo; Pyron, Robert Alexander

    2015-05-01

    The marine-freshwater boundary is a major biodiversity gradient and few groups have colonised both systems successfully. Fishes have transitioned between habitats repeatedly, diversifying in rivers, lakes and oceans over evolutionary time. However, their history of habitat colonisation and diversification is unclear based on available fossil and phylogenetic data. We estimate ancestral habitats and diversification and transition rates using a large-scale phylogeny of extant fish taxa and one containing a massive number of extinct species. Extant-only phylogenetic analyses indicate freshwater ancestry, but inclusion of fossils reveal strong evidence of marine ancestry in lineages now restricted to freshwaters. Diversification and colonisation dynamics vary asymmetrically between habitats, as marine lineages colonise and flourish in rivers more frequently than the reverse. Our study highlights the importance of including fossils in comparative analyses, showing that freshwaters have played a role as refuges for ancient fish lineages, a signal erased by extinction in extant-only phylogenies. © 2015 John Wiley & Sons Ltd/CNRS.

  11. Methodology for Analysing Energy Demand in Biogas Production Plants—A Comparative Study of Two Biogas Plants

    Directory of Open Access Journals (Sweden)

    Emma Lindkvist

    2017-11-01

    Full Text Available Biogas production through anaerobic digestion may play an important role in a circular economy because of the opportunity to produce a renewable fuel from organic waste. However, the production of biogas may require energy in the form of heat and electricity. Therefore, resource-effective biogas production must consider both biological and energy performance. For the individual biogas plant to improve its energy performance, a robust methodology to analyse and evaluate the energy demand on a detailed level is needed. Moreover, to compare the energy performance of different biogas plants, a methodology with a consistent terminology, system boundary and procedure is vital. The aim of this study was to develop a methodology for analysing the energy demand in biogas plants on a detailed level. In the methodology, the energy carriers are allocated to: (1 sub-processes (e.g., pretreatment, anaerobic digestion, gas cleaning, (2 unit processes (e.g., heating, mixing, pumping, lighting and (3 a combination of these. For a thorough energy analysis, a combination of allocations is recommended. The methodology was validated by applying it to two different biogas plants. The results show that the methodology is applicable to biogas plants with different configurations of their production system.

  12. A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations.

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    Davide Michetti

    Full Text Available The psychrophilic and mesophilic endonucleases A (EndA from Aliivibrio salmonicida (VsEndA and Vibrio cholera (VcEndA have been studied experimentally in terms of the biophysical properties related to thermal adaptation. The analyses of their static X-ray structures was no sufficient to rationalize the determinants of their adaptive traits at the molecular level. Thus, we used Molecular Dynamics (MD simulations to compare the two proteins and unveil their structural and dynamical differences. Our simulations did not show a substantial increase in flexibility in the cold-adapted variant on the nanosecond time scale. The only exception is a more rigid C-terminal region in VcEndA, which is ascribable to a cluster of electrostatic interactions and hydrogen bonds, as also supported by MD simulations of the VsEndA mutant variant where the cluster of interactions was introduced. Moreover, we identified three additional amino acidic substitutions through multiple sequence alignment and the analyses of MD-based protein structure networks. In particular, T120V occurs in the proximity of the catalytic residue H80 and alters the interaction with the residue Y43, which belongs to the second coordination sphere of the Mg2+ ion. This makes T120V an amenable candidate for future experimental mutagenesis.

  13. A comparative study between xerographic, computer-assisted overlay generation and animated-superimposition methods in bite mark analyses.

    Science.gov (United States)

    Tai, Meng Wei; Chong, Zhen Feng; Asif, Muhammad Khan; Rahmat, Rabiah A; Nambiar, Phrabhakaran

    2016-09-01

    This study was to compare the suitability and precision of xerographic and computer-assisted methods for bite mark investigations. Eleven subjects were asked to bite on their forearm and the bite marks were photographically recorded. Alginate impressions of the subjects' dentition were taken and their casts were made using dental stone. The overlays generated by xerographic method were obtained by photocopying the subjects' casts and the incisal edge outlines were then transferred on a transparent sheet. The bite mark images were imported into Adobe Photoshop® software and printed to life-size. The bite mark analyses using xerographically generated overlays were done by comparing an overlay to the corresponding printed bite mark images manually. In computer-assisted method, the subjects' casts were scanned into Adobe Photoshop®. The bite mark analyses using computer-assisted overlay generation were done by matching an overlay and the corresponding bite mark images digitally using Adobe Photoshop®. Another comparison method was superimposing the cast images with corresponding bite mark images employing the Adobe Photoshop® CS6 and GIF-Animator©. A score with a range of 0-3 was given during analysis to each precision-determining criterion and the score was increased with better matching. The Kruskal Wallis H test showed significant difference between the three sets of data (H=18.761, p<0.05). In conclusion, bite mark analysis using the computer-assisted animated-superimposition method was the most accurate, followed by the computer-assisted overlay generation and lastly the xerographic method. The superior precision contributed by digital method is discernible despite the human skin being a poor recording medium of bite marks. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  14. Evaluation of the efficiency of continuous wavelet transform as processing and preprocessing algorithm for resolution of overlapped signals in univariate and multivariate regression analyses; an application to ternary and quaternary mixtures

    Science.gov (United States)

    Hegazy, Maha A.; Lotfy, Hayam M.; Mowaka, Shereen; Mohamed, Ekram Hany

    2016-07-01

    Wavelets have been adapted for a vast number of signal-processing applications due to the amount of information that can be extracted from a signal. In this work, a comparative study on the efficiency of continuous wavelet transform (CWT) as a signal processing tool in univariate regression and a pre-processing tool in multivariate analysis using partial least square (CWT-PLS) was conducted. These were applied to complex spectral signals of ternary and quaternary mixtures. CWT-PLS method succeeded in the simultaneous determination of a quaternary mixture of drotaverine (DRO), caffeine (CAF), paracetamol (PAR) and p-aminophenol (PAP, the major impurity of paracetamol). While, the univariate CWT failed to simultaneously determine the quaternary mixture components and was able to determine only PAR and PAP, the ternary mixtures of DRO, CAF, and PAR and CAF, PAR, and PAP. During the calculations of CWT, different wavelet families were tested. The univariate CWT method was validated according to the ICH guidelines. While for the development of the CWT-PLS model a calibration set was prepared by means of an orthogonal experimental design and their absorption spectra were recorded and processed by CWT. The CWT-PLS model was constructed by regression between the wavelet coefficients and concentration matrices and validation was performed by both cross validation and external validation sets. Both methods were successfully applied for determination of the studied drugs in pharmaceutical formulations.

  15. Prediction of bending moment resistance of screw connected joints in plywood members using regression models and compare with that commercial medium density fiberboard (MDF and particleboard

    Directory of Open Access Journals (Sweden)

    Sadegh Maleki

    2014-11-01

    Full Text Available The study aimed at predicting bending moment resistance plywood of screw (coarse and fine threads joints using regression models. Thickness of the member was 19mm and compared with medium density fiberboard (MDF and particleboard with 18mm thicknesses. Two types of screws including coarse and fine thread drywall screw with nominal diameters of 6, 8 and 10mm and 3.5, 4 and 5 cm length respectively and sheet metal screw with diameters of 8 and 10 and length of 4 cm were used. The results of the study have shown that bending moment resistance of screw was increased by increasing of screws diameter and penetrating depth. Screw Length was found to have a larger influence on bending moment resistance than screw diameter. Bending moment resistance with coarse thread drywall screws was higher than those of fine thread drywall screws. The highest bending moment resistance (71.76 N.m was observed in joints made with coarse screw which were 5 mm in diameter and 28 mm in depth of penetration. The lowest bending moment resistance (12.08 N.m was observed in joints having fine screw with 3.5 mm diameter and 9 mm penetrations. Furthermore, bending moment resistance in plywood was higher than those of medium density fiberboard (MDF and particleboard. Finally, it has been found that the ultimate bending moment resistance of plywood joint can be predicted following formula Wc = 0.189×D0.726×P0.577 for coarse thread drywall screws and Wf = 0.086×D0.942×P0.704 for fine ones according to diameter and penetrating depth. The analysis of variance of the experimental and predicted data showed that the developed models provide a fair approximation of actual experimental measurements.

  16. Comparative transcriptome analyses of three medicinal Forsythia species and prediction of candidate genes involved in secondary metabolisms.

    Science.gov (United States)

    Sun, Luchao; Rai, Amit; Rai, Megha; Nakamura, Michimi; Kawano, Noriaki; Yoshimatsu, Kayo; Suzuki, Hideyuki; Kawahara, Nobuo; Saito, Kazuki; Yamazaki, Mami

    2018-05-07

    The three Forsythia species, F. suspensa, F. viridissima and F. koreana, have been used as herbal medicines in China, Japan and Korea for centuries and they are known to be rich sources of numerous pharmaceutical metabolites, forsythin, forsythoside A, arctigenin, rutin and other phenolic compounds. In this study, de novo transcriptome sequencing and assembly was performed on these species. Using leaf and flower tissues of F. suspensa, F. viridissima and F. koreana, 1.28-2.45-Gbp sequences of Illumina based pair-end reads were obtained and assembled into 81,913, 88,491 and 69,458 unigenes, respectively. Classification of the annotated unigenes in gene ontology terms and KEGG pathways was used to compare the transcriptome of three Forsythia species. The expression analysis of orthologous genes across all three species showed the expression in leaf tissues being highly correlated. The candidate genes presumably involved in the biosynthetic pathway of lignans and phenylethanoid glycosides were screened as co-expressed genes. They express highly in the leaves of F. viridissima and F. koreana. Furthermore, the three unigenes annotated as acyltransferase were predicted to be associated with the biosynthesis of acteoside and forsythoside A from the expression pattern and phylogenetic analysis. This study is the first report on comparative transcriptome analyses of medicinally important Forsythia genus and will serve as an important resource to facilitate further studies on biosynthesis and regulation of therapeutic compounds in Forsythia species.

  17. Comparative analyses reveal potential uses of Brachypodium distachyon as a model for cold stress responses in temperate grasses

    Directory of Open Access Journals (Sweden)

    Li Chuan

    2012-05-01

    Full Text Available Abstract Background Little is known about the potential of Brachypodium distachyon as a model for low temperature stress responses in Pooideae. The ice recrystallization inhibition protein (IRIP genes, fructosyltransferase (FST genes, and many C-repeat binding factor (CBF genes are Pooideae specific and important in low temperature responses. Here we used comparative analyses to study conservation and evolution of these gene families in B. distachyon to better understand its potential as a model species for agriculturally important temperate grasses. Results Brachypodium distachyon contains cold responsive IRIP genes which have evolved through Brachypodium specific gene family expansions. A large cold responsive CBF3 subfamily was identified in B. distachyon, while CBF4 homologs are absent from the genome. No B. distachyon FST gene homologs encode typical core Pooideae FST-motifs and low temperature induced fructan accumulation was dramatically different in B. distachyon compared to core Pooideae species. Conclusions We conclude that B. distachyon can serve as an interesting model for specific molecular mechanisms involved in low temperature responses in core Pooideae species. However, the evolutionary history of key genes involved in low temperature responses has been different in Brachypodium and core Pooideae species. These differences limit the use of B. distachyon as a model for holistic studies relevant for agricultural core Pooideae species.

  18. A comparative study among methods used for wheat flour analysis and for measurements of gluten properties using the Wheat Gluten Quality Analyser (WGQA

    Directory of Open Access Journals (Sweden)

    Maria Cristina Ferrari

    2014-06-01

    Full Text Available This study aimed at comparing both the results of wheat flour quality assessed by the new equipment Wheat Gluten Quality Analyser (WGQA and those obtained by the extensigraph and farinograph. Fifty-nine wheat samples were evaluated for protein and gluten contents; the rheological properties of gluten and wheat flour were assessed using the WGQA and the extensigraph/farinograph methods, respectively, in addition to the baking test. Principal component analysis (PCA and linear regression were used to evaluate the results. The parameters of energy and maximum resistance to extension determined by the extensigraph and WGQA showed an acceptable level for the linear correlation within the range from 0.6071 to 0.6511. The PCA results obtained using WGQA and the other rheological apparatus showed values similar to those expected for wheat flours in the baking test. Although all equipment used was effective in assessing the behavior of strong and weak flours, the results of medium strength wheat flour varied. WGQA has shown to use less amount of sample and to be faster and easier to use in relation to the other instruments used.

  19. Characterization of Aeromonas hydrophila Wound Pathotypes by Comparative Genomic and Functional Analyses of Virulence Genes

    Science.gov (United States)

    Grim, Christopher J.; Kozlova, Elena V.; Sha, Jian; Fitts, Eric C.; van Lier, Christina J.; Kirtley, Michelle L.; Joseph, Sandeep J.; Read, Timothy D.; Burd, Eileen M.; Tall, Ben D.; Joseph, Sam W.; Horneman, Amy J.; Chopra, Ashok K.; Shak, Joshua R.

    2013-01-01

    ABSTRACT Aeromonas hydrophila has increasingly been implicated as a virulent and antibiotic-resistant etiologic agent in various human diseases. In a previously published case report, we described a subject with a polymicrobial wound infection that included a persistent and aggressive strain of A. hydrophila (E1), as well as a more antibiotic-resistant strain of A. hydrophila (E2). To better understand the differences between pathogenic and environmental strains of A. hydrophila, we conducted comparative genomic and functional analyses of virulence-associated genes of these two wound isolates (E1 and E2), the environmental type strain A. hydrophila ATCC 7966T, and four other isolates belonging to A. aquariorum, A. veronii, A. salmonicida, and A. caviae. Full-genome sequencing of strains E1 and E2 revealed extensive differences between the two and strain ATCC 7966T. The more persistent wound infection strain, E1, harbored coding sequences for a cytotoxic enterotoxin (Act), a type 3 secretion system (T3SS), flagella, hemolysins, and a homolog of exotoxin A found in Pseudomonas aeruginosa. Corresponding phenotypic analyses with A. hydrophila ATCC 7966T and SSU as reference strains demonstrated the functionality of these virulence genes, with strain E1 displaying enhanced swimming and swarming motility, lateral flagella on electron microscopy, the presence of T3SS effector AexU, and enhanced lethality in a mouse model of Aeromonas infection. By combining sequence-based analysis and functional assays, we characterized an A. hydrophila pathotype, exemplified by strain E1, that exhibited increased virulence in a mouse model of infection, likely because of encapsulation, enhanced motility, toxin secretion, and cellular toxicity. PMID:23611906

  20. Comparative Physiological and Molecular Analyses of Two Contrasting Flue-Cured Tobacco Genotypes under Progressive Drought Stress

    Directory of Open Access Journals (Sweden)

    Xinhong Su

    2017-05-01

    Full Text Available Drought is a major environmental factor that limits crop growth and productivity. Flue-cured tobacco (Nicotiana tabacum is one of the most important commercial crops worldwide and its productivity is vulnerable to drought. However, comparative analyses of physiological, biochemical and gene expression changes in flue-cured tobacco varieties differing in drought tolerance under long-term drought stress are scarce. In this study, drought stress responses of two flue-cured tobacco varieties, LJ851 and JX6007, were comparatively studied at the physiological and transcriptional levels. After exposing to progressive drought stress, the drought-tolerant LJ851 showed less growth inhibition and chlorophyll reduction than the drought-sensitive JX6007. Moreover, higher antioxidant enzyme activities and lower levels of H2O2, Malondialdehyde (MDA, and electrolyte leakage after drought stress were found in LJ851 when compared with JX6007. Further analysis showed that LJ851 plants had much less reductions than the JX6007 in the net photosynthesis rate and stomatal conductance during drought stress; indicating that LJ851 had better photosynthetic performance than JX6007 during drought. In addition, transcriptional expression analysis revealed that LJ851 exhibited significantly increased transcripts of several categories of drought-responsive genes in leaves and roots under drought conditions. Together, these results indicated that LJ851 was more drought-tolerant than JX6007 as evidenced by better photosynthetic performance, more powerful antioxidant system, and higher expression of stress defense genes during drought stress. This study will be valuable for the development of novel flue-cured tobacco varieties with improved drought tolerance by exploitation of natural genetic variations in the future.

  1. Impact of vaccine herd-protection effects in cost-effectiveness analyses of childhood vaccinations. A quantitative comparative analysis.

    Science.gov (United States)

    Holubar, Marisa; Stavroulakis, Maria Christina; Maldonado, Yvonne; Ioannidis, John P A; Contopoulos-Ioannidis, Despina

    2017-01-01

    Inclusion of vaccine herd-protection effects in cost-effectiveness analyses (CEAs) can impact the CEAs-conclusions. However, empirical epidemiologic data on the size of herd-protection effects from original studies are limited. We performed a quantitative comparative analysis of the impact of herd-protection effects in CEAs for four childhood vaccinations (pneumococcal, meningococcal, rotavirus and influenza). We considered CEAs reporting incremental-cost-effectiveness-ratios (ICERs) (per quality-adjusted-life-years [QALY] gained; per life-years [LY] gained or per disability-adjusted-life-years [DALY] avoided), both with and without herd protection, while keeping all other model parameters stable. We calculated the size of the ICER-differences without vs with-herd-protection and estimated how often inclusion of herd-protection led to crossing of the cost-effectiveness threshold (of an assumed societal-willingness-to-pay) of $50,000 for more-developed countries or X3GDP/capita (WHO-threshold) for less-developed countries. We identified 35 CEA studies (20 pneumococcal, 4 meningococcal, 8 rotavirus and 3 influenza vaccines) with 99 ICER-analyses (55 per-QALY, 27 per-LY and 17 per-DALY). The median ICER-absolute differences per QALY, LY and DALY (without minus with herd-protection) were $15,620 (IQR: $877 to $48,376); $54,871 (IQR: $787 to $115,026) and $49 (IQR: $15 to $1,636) respectively. When the target-vaccination strategy was not cost-saving without herd-protection, inclusion of herd-protection always resulted in more favorable results. In CEAs that had ICERs above the cost-effectiveness threshold without herd-protection, inclusion of herd-protection led to crossing of that threshold in 45% of the cases. This impacted only CEAs for more developed countries, as all but one CEAs for less developed countries had ICERs below the WHO-cost-effectiveness threshold even without herd-protection. In several analyses, recommendation for the adoption of the target

  2. Modified Regression Correlation Coefficient for Poisson Regression Model

    Science.gov (United States)

    Kaengthong, Nattacha; Domthong, Uthumporn

    2017-09-01

    This study gives attention to indicators in predictive power of the Generalized Linear Model (GLM) which are widely used; however, often having some restrictions. We are interested in regression correlation coefficient for a Poisson regression model. This is a measure of predictive power, and defined by the relationship between the dependent variable (Y) and the expected value of the dependent variable given the independent variables [E(Y|X)] for the Poisson regression model. The dependent variable is distributed as Poisson. The purpose of this research was modifying regression correlation coefficient for Poisson regression model. We also compare the proposed modified regression correlation coefficient with the traditional regression correlation coefficient in the case of two or more independent variables, and having multicollinearity in independent variables. The result shows that the proposed regression correlation coefficient is better than the traditional regression correlation coefficient based on Bias and the Root Mean Square Error (RMSE).

  3. Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks

    Science.gov (United States)

    Glicksberg, Benjamin S.; Li, Li; Badgeley, Marcus A.; Shameer, Khader; Kosoy, Roman; Beckmann, Noam D.; Pho, Nam; Hakenberg, Jörg; Ma, Meng; Ayers, Kristin L.; Hoffman, Gabriel E.; Dan Li, Shuyu; Schadt, Eric E.; Patel, Chirag J.; Chen, Rong; Dudley, Joel T.

    2016-01-01

    Motivation: Underrepresentation of racial groups represents an important challenge and major gap in phenomics research. Most of the current human phenomics research is based primarily on European populations; hence it is an important challenge to expand it to consider other population groups. One approach is to utilize data from EMR databases that contain patient data from diverse demographics and ancestries. The implications of this racial underrepresentation of data can be profound regarding effects on the healthcare delivery and actionability. To the best of our knowledge, our work is the first attempt to perform comparative, population-scale analyses of disease networks across three different populations, namely Caucasian (EA), African American (AA) and Hispanic/Latino (HL). Results: We compared susceptibility profiles and temporal connectivity patterns for 1988 diseases and 37 282 disease pairs represented in a clinical population of 1 025 573 patients. Accordingly, we revealed appreciable differences in disease susceptibility, temporal patterns, network structure and underlying disease connections between EA, AA and HL populations. We found 2158 significantly comorbid diseases for the EA cohort, 3265 for AA and 672 for HL. We further outlined key disease pair associations unique to each population as well as categorical enrichments of these pairs. Finally, we identified 51 key ‘hub’ diseases that are the focal points in the race-centric networks and of particular clinical importance. Incorporating race-specific disease comorbidity patterns will produce a more accurate and complete picture of the disease landscape overall and could support more precise understanding of disease relationships and patient management towards improved clinical outcomes. Contacts: rong.chen@mssm.edu or joel.dudley@mssm.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307606

  4. Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.

    Science.gov (United States)

    Glicksberg, Benjamin S; Li, Li; Badgeley, Marcus A; Shameer, Khader; Kosoy, Roman; Beckmann, Noam D; Pho, Nam; Hakenberg, Jörg; Ma, Meng; Ayers, Kristin L; Hoffman, Gabriel E; Dan Li, Shuyu; Schadt, Eric E; Patel, Chirag J; Chen, Rong; Dudley, Joel T

    2016-06-15

    Underrepresentation of racial groups represents an important challenge and major gap in phenomics research. Most of the current human phenomics research is based primarily on European populations; hence it is an important challenge to expand it to consider other population groups. One approach is to utilize data from EMR databases that contain patient data from diverse demographics and ancestries. The implications of this racial underrepresentation of data can be profound regarding effects on the healthcare delivery and actionability. To the best of our knowledge, our work is the first attempt to perform comparative, population-scale analyses of disease networks across three different populations, namely Caucasian (EA), African American (AA) and Hispanic/Latino (HL). We compared susceptibility profiles and temporal connectivity patterns for 1988 diseases and 37 282 disease pairs represented in a clinical population of 1 025 573 patients. Accordingly, we revealed appreciable differences in disease susceptibility, temporal patterns, network structure and underlying disease connections between EA, AA and HL populations. We found 2158 significantly comorbid diseases for the EA cohort, 3265 for AA and 672 for HL. We further outlined key disease pair associations unique to each population as well as categorical enrichments of these pairs. Finally, we identified 51 key 'hub' diseases that are the focal points in the race-centric networks and of particular clinical importance. Incorporating race-specific disease comorbidity patterns will produce a more accurate and complete picture of the disease landscape overall and could support more precise understanding of disease relationships and patient management towards improved clinical outcomes. rong.chen@mssm.edu or joel.dudley@mssm.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  5. Comparative analyses of plastid sequences between native and introduced populations of aquatic weeds Elodea canadensis and E. nuttallii.

    Directory of Open Access Journals (Sweden)

    Tea Huotari

    Full Text Available Non-indigenous species (NIS are species living outside their historic or native range. Invasive NIS often cause severe environmental impacts, and may have large economical and social consequences. Elodea (Hydrocharitaceae is a New World genus with at least five submerged aquatic angiosperm species living in fresh water environments. Our aim was to survey the geographical distribution of cpDNA haplotypes within the native and introduced ranges of invasive aquatic weeds Elodea canadensis and E. nuttallii and to reconstruct the spreading histories of these invasive species. In order to reveal informative chloroplast (cp genome regions for phylogeographic analyses, we compared the plastid sequences of native and introduced individuals of E. canadensis. In total, we found 235 variable sites (186 SNPs, 47 indels and two inversions between the two plastid sequences consisting of 112,193 bp and developed primers flanking the most variable genomic areas. These 29 primer pairs were used to compare the level and pattern of intraspecific variation within E. canadensis to interspecific variation between E. canadensis and E. nuttallii. Nine potentially informative primer pairs were used to analyze the phylogeographic structure of both Elodea species, based on 70 E. canadensis and 25 E. nuttallii individuals covering native and introduced distributions. On the whole, the level of variation between the two Elodea species was 53% higher than that within E. canadensis. In our phylogeographic analysis, only a single haplotype was found in the introduced range in both species. These haplotypes H1 (E. canadensis and A (E. nuttallii were also widespread in the native range, covering the majority of native populations analyzed. Therefore, we were not able to identify either the geographic origin of the introduced populations or test the hypothesis of single versus multiple introductions. The divergence between E. canadensis haplotypes was surprisingly high, and future

  6. Comparative analyses of plastid sequences between native and introduced populations of aquatic weeds Elodea canadensis and E. nuttallii.

    Science.gov (United States)

    Huotari, Tea; Korpelainen, Helena

    2013-01-01

    Non-indigenous species (NIS) are species living outside their historic or native range. Invasive NIS often cause severe environmental impacts, and may have large economical and social consequences. Elodea (Hydrocharitaceae) is a New World genus with at least five submerged aquatic angiosperm species living in fresh water environments. Our aim was to survey the geographical distribution of cpDNA haplotypes within the native and introduced ranges of invasive aquatic weeds Elodea canadensis and E. nuttallii and to reconstruct the spreading histories of these invasive species. In order to reveal informative chloroplast (cp) genome regions for phylogeographic analyses, we compared the plastid sequences of native and introduced individuals of E. canadensis. In total, we found 235 variable sites (186 SNPs, 47 indels and two inversions) between the two plastid sequences consisting of 112,193 bp and developed primers flanking the most variable genomic areas. These 29 primer pairs were used to compare the level and pattern of intraspecific variation within E. canadensis to interspecific variation between E. canadensis and E. nuttallii. Nine potentially informative primer pairs were used to analyze the phylogeographic structure of both Elodea species, based on 70 E. canadensis and 25 E. nuttallii individuals covering native and introduced distributions. On the whole, the level of variation between the two Elodea species was 53% higher than that within E. canadensis. In our phylogeographic analysis, only a single haplotype was found in the introduced range in both species. These haplotypes H1 (E. canadensis) and A (E. nuttallii) were also widespread in the native range, covering the majority of native populations analyzed. Therefore, we were not able to identify either the geographic origin of the introduced populations or test the hypothesis of single versus multiple introductions. The divergence between E. canadensis haplotypes was surprisingly high, and future research may

  7. Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

    Directory of Open Access Journals (Sweden)

    Catherine L Worth

    Full Text Available BACKGROUND: Up until recently the only available experimental (high resolution structure of a G-protein-coupled receptor (GPCR was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. METHODOLOGY: We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s for building a comparative molecular model. CONCLUSIONS: The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying

  8. Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

    Science.gov (United States)

    Worth, Catherine L; Kleinau, Gunnar; Krause, Gerd

    2009-09-16

    Up until recently the only available experimental (high resolution) structure of a G-protein-coupled receptor (GPCR) was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s) to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s) for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s) for building a comparative molecular model. The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying suitable templates for GPCR homology modelling that will

  9. The complete chloroplast genome sequences of Lychnis wilfordii and Silene capitata and comparative analyses with other Caryophyllaceae genomes.

    Science.gov (United States)

    Kang, Jong-Soo; Lee, Byoung Yoon; Kwak, Myounghai

    2017-01-01

    The complete chloroplast genomes of Lychnis wilfordii and Silene capitata were determined and compared with ten previously reported Caryophyllaceae chloroplast genomes. The chloroplast genome sequences of L. wilfordii and S. capitata contain 152,320 bp and 150,224 bp, respectively. The gene contents and orders among 12 Caryophyllaceae species are consistent, but several microstructural changes have occurred. Expansion of the inverted repeat (IR) regions at the large single copy (LSC)/IRb and small single copy (SSC)/IR boundaries led to partial or entire gene duplications. Additionally, rearrangements of the LSC region were caused by gene inversions and/or transpositions. The 18 kb inversions, which occurred three times in different lineages of tribe Sileneae, were thought to be facilitated by the intermolecular duplicated sequences. Sequence analyses of the L. wilfordii and S. capitata genomes revealed 39 and 43 repeats, respectively, including forward, palindromic, and reverse repeats. In addition, a total of 67 and 56 simple sequence repeats were discovered in the L. wilfordii and S. capitata chloroplast genomes, respectively. Finally, we constructed phylogenetic trees of the 12 Caryophyllaceae species and two Amaranthaceae species based on 73 protein-coding genes using both maximum parsimony and likelihood methods.

  10. Soil microbial community structure in diverse land use systems:A comparative study using Biolog,DGGE,and PLFA analyses

    Institute of Scientific and Technical Information of China (English)

    XUE Dong; YAO Huai-Ying; GE De-Yong; HUANG Chang-Yong

    2008-01-01

    Biolog,16S rRNA gene denaturing gradient gel electrophoresis (DGGE),and phospholipid fatty acid (PLFA) analyses were used to assess soil microbial community characteristics in a chronosequence of tea garden systems (8-,50-,and 90year-old tea gardens),an adjacent wasteland,and a 90-year-old forest.Biolog analysis showed that the average well color development (AWCD) of all carbon sources and the functional diversity based on the Shannon index decreased (P<0.05)in the following order:wasteland>forest>tea garden.For the DGGE analysis,the genetic diversity based on the Shannon index was significantly lower in the tea garden soils than in the wasteland.However,compared to the 90-year-old forest,the tea garden soils showed significantly higher genetic diversity.PLFA analysis showed that the ratio of Gram positive bacteria to Gram negative bacteria was significantly higher in the tea garden soils than in the wasteland,and the highest value was found in the 90-year-old forest.Both the fungal PLFA and the ratio of fungi to bacteria were significantly higher in the three tea garden soils than in the wasteland and forest,indicating that fungal PLFA was significantly affected by land-use change.Based on cluster analysis of the soil microbial community structure,all three analytical methods showed that land-use change had a greater effect on soil microbial community structure than tea garden age.

  11. The cost-effectiveness of rotavirus vaccination: Comparative analyses for five European countries and transferability in Europe.

    Science.gov (United States)

    Jit, Mark; Bilcke, Joke; Mangen, Marie-Josée J; Salo, Heini; Melliez, Hugues; Edmunds, W John; Yazdan, Yazdanpanah; Beutels, Philippe

    2009-10-19

    Cost-effectiveness analyses are usually not directly comparable between countries because of differences in analytical and modelling assumptions. We investigated the cost-effectiveness of rotavirus vaccination in five European Union countries (Belgium, England and Wales, Finland, France and the Netherlands) using a single model, burden of disease estimates supplied by national public health agencies and a subset of common assumptions. Under base case assumptions (vaccination with Rotarix, 3% discount rate, health care provider perspective, no herd immunity and quality of life of one caregiver affected by a rotavirus episode) and a cost-effectiveness threshold of euro30,000, vaccination is likely to be cost effective in Finland only. However, single changes to assumptions may make it cost effective in Belgium and the Netherlands. The estimated threshold price per dose for Rotarix (excluding administration costs) to be cost effective was euro41 in Belgium, euro28 in England and Wales, euro51 in Finland, euro36 in France and euro46 in the Netherlands.

  12. Completing the Remedial Sequence and College-Level Credit-Bearing Math: Comparing Binary, Cumulative, and Continuation Ratio Logistic Regression Models

    Science.gov (United States)

    Davidson, J. Cody

    2016-01-01

    Mathematics is the most common subject area of remedial need and the majority of remedial math students never pass a college-level credit-bearing math class. The majorities of studies that investigate this phenomenon are conducted at community colleges and use some type of regression model; however, none have used a continuation ratio model. The…

  13. Working regime identification for natural circulation loops by comparative thermalhydraulic analyses with three fluids under identical operating conditions

    International Nuclear Information System (INIS)

    Sarkar, Milan K.S.; Basu, Dipankar N.

    2015-01-01

    Highlights: • Thermalhydraulic analyses of NCL to justify the use of supercritical condition. • Mass flow rate of supercritical loop increases with heater power till a maxima. • Supercritical loop suffer from HTD beyond the maxima with jump in fluid temperature. • HTD is pronounced at higher sink temperatures and pressures just above critical. • Supercritical CO_2 is preferred fluid till the HTD and single-phase water afterwards. - Abstract: Computational investigation for comparative thermalhydraulic analyses of rectangular natural circulation loops is performed to propose a guideline for selecting the working fluid and nature of the loop, subcritical or supercritical, under identical levels of operating parameters like pressure, heating power and coolant temperature. A 3-d uniform-diameter loop geometry is developed with horizontal heating and cooling. Heating is provided in constant heat flux mode, whereas cooling is through a constant temperature sink. Due to favourable thermophysical properties and environmental conformity, water, CO_2 and R134a are selected as possible working fluids. Operational parameters are set so as to have sub- to supercritical condition for CO_2, supercritical for R134a and single-phase liquid for water. Mass flow rate for supercritical fluid rapidly increases with heater power, when the fluid is allowed to cross the pseudocritical point during its passage through the heater, and exhibits a maxima. Drastic fall in mass flow rate can be observed beyond the maxima, accompanied by a jump in maximum fluid temperature and a rapid decline in sink-side heat transfer coefficient. That can be identified as heat transfer deterioration in supercritical natural circulation loops, a highly undesirable situation from loop safety point of view. Allowable working range of heater power can be enhanced by increasing system pressure and decreasing sink temperature. For any specified set of operating conditions, CO_2-based supercritical loops

  14. Working regime identification for natural circulation loops by comparative thermalhydraulic analyses with three fluids under identical operating conditions

    Energy Technology Data Exchange (ETDEWEB)

    Sarkar, Milan K.S.; Basu, Dipankar N., E-mail: dipankar.n.basu@gmail.com

    2015-11-15

    Highlights: • Thermalhydraulic analyses of NCL to justify the use of supercritical condition. • Mass flow rate of supercritical loop increases with heater power till a maxima. • Supercritical loop suffer from HTD beyond the maxima with jump in fluid temperature. • HTD is pronounced at higher sink temperatures and pressures just above critical. • Supercritical CO{sub 2} is preferred fluid till the HTD and single-phase water afterwards. - Abstract: Computational investigation for comparative thermalhydraulic analyses of rectangular natural circulation loops is performed to propose a guideline for selecting the working fluid and nature of the loop, subcritical or supercritical, under identical levels of operating parameters like pressure, heating power and coolant temperature. A 3-d uniform-diameter loop geometry is developed with horizontal heating and cooling. Heating is provided in constant heat flux mode, whereas cooling is through a constant temperature sink. Due to favourable thermophysical properties and environmental conformity, water, CO{sub 2} and R134a are selected as possible working fluids. Operational parameters are set so as to have sub- to supercritical condition for CO{sub 2}, supercritical for R134a and single-phase liquid for water. Mass flow rate for supercritical fluid rapidly increases with heater power, when the fluid is allowed to cross the pseudocritical point during its passage through the heater, and exhibits a maxima. Drastic fall in mass flow rate can be observed beyond the maxima, accompanied by a jump in maximum fluid temperature and a rapid decline in sink-side heat transfer coefficient. That can be identified as heat transfer deterioration in supercritical natural circulation loops, a highly undesirable situation from loop safety point of view. Allowable working range of heater power can be enhanced by increasing system pressure and decreasing sink temperature. For any specified set of operating conditions, CO{sub 2}-based

  15. Secondary mediation and regression analyses of the PTClinResNet database: determining causal relationships among the International Classification of Functioning, Disability and Health levels for four physical therapy intervention trials.

    Science.gov (United States)

    Mulroy, Sara J; Winstein, Carolee J; Kulig, Kornelia; Beneck, George J; Fowler, Eileen G; DeMuth, Sharon K; Sullivan, Katherine J; Brown, David A; Lane, Christianne J

    2011-12-01

    Each of the 4 randomized clinical trials (RCTs) hosted by the Physical Therapy Clinical Research Network (PTClinResNet) targeted a different disability group (low back disorder in the Muscle-Specific Strength Training Effectiveness After Lumbar Microdiskectomy [MUSSEL] trial, chronic spinal cord injury in the Strengthening and Optimal Movements for Painful Shoulders in Chronic Spinal Cord Injury [STOMPS] trial, adult stroke in the Strength Training Effectiveness Post-Stroke [STEPS] trial, and pediatric cerebral palsy in the Pediatric Endurance and Limb Strengthening [PEDALS] trial for children with spastic diplegic cerebral palsy) and tested the effectiveness of a muscle-specific or functional activity-based intervention on primary outcomes that captured pain (STOMPS, MUSSEL) or locomotor function (STEPS, PEDALS). The focus of these secondary analyses was to determine causal relationships among outcomes across levels of the International Classification of Functioning, Disability and Health (ICF) framework for the 4 RCTs. With the database from PTClinResNet, we used 2 separate secondary statistical approaches-mediation analysis for the MUSSEL and STOMPS trials and regression analysis for the STEPS and PEDALS trials-to test relationships among muscle performance, primary outcomes (pain related and locomotor related), activity and participation measures, and overall quality of life. Predictive models were stronger for the 2 studies with pain-related primary outcomes. Change in muscle performance mediated or predicted reductions in pain for the MUSSEL and STOMPS trials and, to some extent, walking speed for the STEPS trial. Changes in primary outcome variables were significantly related to changes in activity and participation variables for all 4 trials. Improvement in activity and participation outcomes mediated or predicted increases in overall quality of life for the 3 trials with adult populations. Variables included in the statistical models were limited to those

  16. Comparative proteomics analyses of Kobresia pygmaea adaptation to environment along an elevational gradient on the central Tibetan Plateau.

    Directory of Open Access Journals (Sweden)

    Xiong Li

    Full Text Available Variations in elevation limit the growth and distribution of alpine plants because multiple environmental stresses impact plant growth, including sharp temperature shifts, strong ultraviolet radiation exposure, low oxygen content, etc. Alpine plants have developed special strategies to help survive the harsh environments of high mountains, but the internal mechanisms remain undefined. Kobresia pygmaea, the dominant species of alpine meadows, is widely distributed in the Southeastern Tibet Plateau, Tibet Autonomous Region, China. In this study, we mainly used comparative proteomics analyses to investigate the dynamic protein patterns for K. pygmaea located at four different elevations (4600, 4800, 4950 and 5100 m. A total of 58 differentially expressed proteins were successfully detected and functionally characterized. The proteins were divided into various functional categories, including material and energy metabolism, protein synthesis and degradation, redox process, defense response, photosynthesis, and protein kinase. Our study confirmed that increasing levels of antioxidant and heat shock proteins and the accumulation of primary metabolites, such as proline and abscisic acid, conferred K. pygmaea with tolerance to the alpine environment. In addition, the various methods K. pygmaea used to regulate material and energy metabolism played important roles in the development of tolerance to environmental stress. Our results also showed that the way in which K. pygmaea mediated stomatal characteristics and photosynthetic pigments constitutes an enhanced adaptation to alpine environmental stress. According to these findings, we concluded that K. pygmaea adapted to the high-elevation environment on the Tibetan Plateau by aggressively accumulating abiotic stress-related metabolites and proteins and by the various life events mediated by proteins. Based on the species'lexible physiological and biochemical processes, we surmised that environment change

  17. Construction and comparative analyses of highly dense linkage maps of two sweet cherry intra-specific progenies of commercial cultivars.

    Directory of Open Access Journals (Sweden)

    Carolina Klagges

    Full Text Available Despite the agronomical importance and high synteny with other Prunus species, breeding improvements for cherry have been slow compared to other temperate fruits, such as apple or peach. However, the recent release of the peach genome v1.0 by the International Peach Genome Initiative and the sequencing of cherry accessions to identify Single Nucleotide Polymorphisms (SNPs provide an excellent basis for the advancement of cherry genetic and genomic studies. The availability of dense genetic linkage maps in phenotyped segregating progenies would be a valuable tool for breeders and geneticists. Using two sweet cherry (Prunus avium L. intra-specific progenies derived from crosses between 'Black Tartarian' × 'Kordia' (BT×K and 'Regina' × 'Lapins'(R×L, high-density genetic maps of the four parental lines and the two segregating populations were constructed. For BT×K and R×L, 89 and 121 F(1 plants were used for linkage mapping, respectively. A total of 5,696 SNP markers were tested in each progeny. As a result of these analyses, 723 and 687 markers were mapped into eight linkage groups (LGs in BT×K and R×L, respectively. The resulting maps spanned 752.9 and 639.9 cM with an average distance of 1.1 and 0.9 cM between adjacent markers in BT×K and R×L, respectively. The maps displayed high synteny and co-linearity between each other, with the Prunus bin map, and with the peach genome v1.0 for all eight LGs (LG1-LG8. These maps provide a useful tool for investigating traits of interest in sweet cherry and represent a qualitative advance in the understanding of the cherry genome and its synteny with other members of the Rosaceae family.

  18. Self-sampling with HPV mRNA analyses from vagina and urine compared with cervical samples.

    Science.gov (United States)

    Asciutto, Katrin Christine; Ernstson, Avalon; Forslund, Ola; Borgfeldt, Christer

    2018-04-01

    In order to increase coverage in the organized cervical screening program, self-sampling with HPV analyses has been suggested. The aim was to compare human papillomavirus (HPV) mRNA detection in vaginal and urine self-collected samples with clinician-taken cervical samples and the corresponding clinician-taken histological specimens. Self-collected vaginal, urine and clinician-taken cervical samples were analyzed from 209 women with the Aptima mRNA assay (Hologic Inc, MA, USA). Cervical cytology, colposcopy, biopsy and/or the loop electrosurgical excision procedure (LEEP) were performed in every examination. The sensitivity of the HPV mRNA test in detecting high-grade squamous intraepithelial lesions (HSIL)/adenocarcinoma in situ (AIS)/cancer cases was as follows: for the vaginal self-samples 85.5% (95% CI; 75.0-92.8), the urinary samples 44.8% (95% CI; 32.6-57.4), and for routine cytology 81.7% (95% CI; 70.7-89.9). For the clinician-taken cervical HPV samples the sensitivity of the HPV mRNA test in detecting HSIL/AIS/cancer was 100.0% (95% CI; 94.9-100.0). The specificity of the HPV mRNA was similar for the clinician-taken cervical HPV samples and the self-samples: 49.0% vs. 48.1%. The urinary HPV samples had a specificity of 61.9% and cytology had a specificity of 93.3%. The sensitivity of the Aptima HPV mRNA test in detecting HSIL/AIS/cancer from vaginal self-samples was similar to that of routine cytology. The Aptima HPV mRNA vaginal self-sampling analysis may serve as a complement in screening programs. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. Comparative Proteomics Analyses of Kobresia pygmaea Adaptation to Environment along an Elevational Gradient on the Central Tibetan Plateau

    Science.gov (United States)

    Li, Xiong; Yang, Yunqiang; Ma, Lan; Sun, Xudong; Yang, Shihai; Kong, Xiangxiang; Hu, Xiangyang; Yang, Yongping

    2014-01-01

    Variations in elevation limit the growth and distribution of alpine plants because multiple environmental stresses impact plant growth, including sharp temperature shifts, strong ultraviolet radiation exposure, low oxygen content, etc. Alpine plants have developed special strategies to help survive the harsh environments of high mountains, but the internal mechanisms remain undefined. Kobresia pygmaea, the dominant species of alpine meadows, is widely distributed in the Southeastern Tibet Plateau, Tibet Autonomous Region, China. In this study, we mainly used comparative proteomics analyses to investigate the dynamic protein patterns for K. pygmaea located at four different elevations (4600, 4800, 4950 and 5100 m). A total of 58 differentially expressed proteins were successfully detected and functionally characterized. The proteins were divided into various functional categories, including material and energy metabolism, protein synthesis and degradation, redox process, defense response, photosynthesis, and protein kinase. Our study confirmed that increasing levels of antioxidant and heat shock proteins and the accumulation of primary metabolites, such as proline and abscisic acid, conferred K. pygmaea with tolerance to the alpine environment. In addition, the various methods K. pygmaea used to regulate material and energy metabolism played important roles in the development of tolerance to environmental stress. Our results also showed that the way in which K. pygmaea mediated stomatal characteristics and photosynthetic pigments constitutes an enhanced adaptation to alpine environmental stress. According to these findings, we concluded that K. pygmaea adapted to the high-elevation environment on the Tibetan Plateau by aggressively accumulating abiotic stress-related metabolites and proteins and by the various life events mediated by proteins. Based on the species'lexible physiological and biochemical processes, we surmised that environment change has only a slight

  20. Comparative phenotypic and genotypic analyses of Salmonella Rissen that originated from food animals in Thailand and United States.

    Science.gov (United States)

    Pornsukarom, S; Patchanee, P; Erdman, M; Cray, P F; Wittum, T; Lee, J; Gebreyes, W A

    2015-03-01

    Salmonella enterica serovar Rissen has been recognized as one of the most common serovar among humans and pork production systems in different parts of the world, especially Asia. In the United States, this serovar caused outbreaks but its epidemiologic significance remains unknown. The objectives of this study were to compare the phenotypic (antimicrobial susceptibility) and genotypic attributes of Salmonella Rissen isolated in Thailand (Thai) and the United States (US). All the Thai isolates (n = 30) were recovered from swine faecal samples. The US isolates (n = 35) were recovered from swine faecal samples (n = 29), cattle (n = 2), chicken (n = 2), dog (n = 1) and a ready-to-eat product (n = 1). The antimicrobial susceptibility of isolates was determined using the Kirby-Bauer disk diffusion method with a panel of 12 antimicrobials. Pulse-field gel electrophoresis (PFGE) was used to determine the genotypic diversity of isolates. All Thai isolates showed multidrug resistance (MDR) with the most frequent antibiotic resistance shown against ampicillin (100%), sulfisoxazole (96.7%), tetracycline (93.3%), streptomycin (90%) and chloramphenicol (30%). About half of the isolates of USA origin were pan-susceptible and roughly 30% were resistant to only tetracycline (R-type: Te). Salmonella Rissen isolated from Thailand and the USA in this study were found to be clonally unrelated. Genotypic analyses indicated that isolates were clustered primarily based on the geographic origin implying the limited clonality among the strains. Clonal relatedness among different host species within the same geography (USA) was found. We found genotypic similarity in Thai and US isolates in few instances but with no epidemiological link. Further studies to assess propensity for increased inter-regional transmission and dissemination is warranted. © 2014 Blackwell Verlag GmbH.

  1. A comparative study on generating simulated Landsat NDVI images using data fusion and regression method-the case of the Korean Peninsula.

    Science.gov (United States)

    Lee, Mi Hee; Lee, Soo Bong; Eo, Yang Dam; Kim, Sun Woong; Woo, Jung-Hun; Han, Soo Hee

    2017-07-01

    Landsat optical images have enough spatial and spectral resolution to analyze vegetation growth characteristics. But, the clouds and water vapor degrade the image quality quite often, which limits the availability of usable images for the time series vegetation vitality measurement. To overcome this shortcoming, simulated images are used as an alternative. In this study, weighted average method, spatial and temporal adaptive reflectance fusion model (STARFM) method, and multilinear regression analysis method have been tested to produce simulated Landsat normalized difference vegetation index (NDVI) images of the Korean Peninsula. The test results showed that the weighted average method produced the images most similar to the actual images, provided that the images were available within 1 month before and after the target date. The STARFM method gives good results when the input image date is close to the target date. Careful regional and seasonal consideration is required in selecting input images. During summer season, due to clouds, it is very difficult to get the images close enough to the target date. Multilinear regression analysis gives meaningful results even when the input image date is not so close to the target date. Average R 2 values for weighted average method, STARFM, and multilinear regression analysis were 0.741, 0.70, and 0.61, respectively.

  2. Subgroup analyses on return to work in sick-listed employees with low back pain in a randomised trial comparing brief and multidisciplinary intervention

    Directory of Open Access Journals (Sweden)

    Petersen Karin D

    2011-05-01

    Full Text Available Abstract Background Multidisciplinary intervention is recommended for rehabilitation of employees sick-listed for 4-12 weeks due to low back pain (LBP. However, comparison of a brief and a multidisciplinary intervention in a randomised comparative trial of sick-listed employees showed similar return to work (RTW rates in the two groups. The aim of the present study was to identify subgroups, primarily defined by work-related baseline factors that would benefit more from the multidisciplinary intervention than from the brief intervention. Methods A total of 351 employees sick-listed for 3-16 weeks due to LBP were recruited from their general practitioners. They received a brief or a multidisciplinary intervention. Both interventions comprised clinical examination and advice by a rehabilitation doctor and a physiotherapist. The multidisciplinary intervention also comprised assignment of a case manager, who made a rehabilitation plan in collaboration with the patient and a multidisciplinary team. Using data from a national database, we defined RTW as no sickness compensation benefit disbursement for four consecutive weeks within the first year after the intervention. At the first interview in the clinic, it was ensured that sick leave was primarily due to low back problems.Questionnaires were used to obtain data on health, disability, demographic and workplace-related factors. Cox hazard regression analyses were used with RTW as outcome measure and hazard rate ratios (HRR = HRmultidisciplinary/HRbrief were adjusted for demographic and health-related variables. An interaction term consisting of a baseline variable*intervention group was added to the multivariable regression model to analyse whether the effects of the interventions were moderated by the baseline factor. Subsequently, a new study was performed that included 120 patients who followed the same protocol. This group was analyzed in the same way to verify the findings from the original

  3. A comparative study of two approaches to analyse groundwater recharge, travel times and nitrate storage distribution at a regional scale

    Science.gov (United States)

    Turkeltaub, T.; Ascott, M.; Gooddy, D.; Jia, X.; Shao, M.; Binley, A. M.

    2017-12-01

    Understanding deep percolation, travel time processes and nitrate storage in the unsaturated zone at a regional scale is crucial for sustainable management of many groundwater systems. Recently, global hydrological models have been developed to quantify the water balance at such scales and beyond. However, the coarse spatial resolution of the global hydrological models can be a limiting factor when analysing regional processes. This study compares simulations of water flow and nitrate storage based on regional and global scale approaches. The first approach was applied over the Loess Plateau of China (LPC) to investigate the water fluxes and nitrate storage and travel time to the LPC groundwater system. Using raster maps of climate variables, land use data and soil parameters enabled us to determine fluxes by employing Richards' equation and the advection - dispersion equation. These calculations were conducted for each cell on the raster map in a multiple 1-D column approach. In the second approach, vadose zone travel times and nitrate storage were estimated by coupling groundwater recharge (PCR-GLOBWB) and nitrate leaching (IMAGE) models with estimates of water table depth and unsaturated zone porosity. The simulation results of the two methods indicate similar spatial groundwater recharge, nitrate storage and travel time distribution. Intensive recharge rates are located mainly at the south central and south west parts of the aquifer's outcrops. Particularly low recharge rates were simulated in the top central area of the outcrops. However, there are significant discrepancies between the simulated absolute recharge values, which might be related to the coarse scale that is used in the PCR-GLOBWB model, leading to smoothing of the recharge estimations. Both models indicated large nitrate inventories in the south central and south west parts of the aquifer's outcrops and the shortest travel times in the vadose zone are in the south central and east parts of the

  4. On groundwater flow modelling in safety analyses of spent fuel disposal. A comparative study with emphasis on boundary conditions

    Energy Technology Data Exchange (ETDEWEB)

    Jussila, P

    1999-11-01

    Modelling groundwater flow is an essential part of the safety assessment of spent fuel disposal because moving groundwater makes a physical connection between a geological repository and the biosphere. Some of the common approaches to model groundwater flow in bedrock are equivalent porous continuum (EC), stochastic continuum and various fracture network concepts. The actual flow system is complex and measuring data are limited. Multiple distinct approaches and models, alternative scenarios as well as calibration and sensitivity analyses are used to give confidence on the results of the calculations. The correctness and orders of magnitude of results of such complex research can be assessed by comparing them to the results of simplified and robust approaches. The first part of this study is a survey of the objects, contents and methods of the groundwater flow modelling performed in the safety assessment of the spent fuel disposal in Finland and Sweden. The most apparent difference of the Swedish studies compared to the Finnish ones is the approach of using more different models, which is enabled by the more resources available in Sweden. The results of more comprehensive approaches provided by international co-operation are very useful to give perspective to the results obtained in Finland. In the second part of this study, the influence of boundary conditions on the flow fields of a simple 2D model is examined. The assumptions and simplifications in this approach include e.g. the following: (1) the EC model is used, in which the 2-dimensional domain is considered a continuum of equivalent properties without fractures present, (2) the calculations are done for stationary fields, without sources or sinks present in the domain and with a constant density of the groundwater, (3) the repository is represented by an isotropic plate, the hydraulic conductivity of which is given fictitious values, (4) the hydraulic conductivity of rock is supposed to have an exponential

  5. Comparative Analysis of Logistic Regression, Support Vector Machine and Artificial Neural Network for the Differential Diagnosis of Benign and Malignant Solid Breast Tumors by the Use of Three-Dimensional Power Doppler Imaging

    International Nuclear Information System (INIS)

    Chen, Shou Tung; Hsiao, Yi Hsuan; Kuo, Shou Jen; Tseng, Hsin Shun; Wu, Hwa Koon; Chen, Dar Ren; Huang, Yu Len

    2009-01-01

    Logistic regression analysis (LRA), Support Vector Machine (SVM) and a neural network (NN) are commonly used statistical models in computeraided diagnostic (CAD) systems for breast ultrasonography (US). The aim of this study was to clarify the diagnostic ability of the use of these statistical models for future applications of CAD systems, such as three-dimensional (3D) power Doppler imaging, vascularity evaluation and the differentiation of a solid mass. A database that contained 3D power Doppler imaging pairs of non-harmonic and tissue harmonic images for 97 benign and 86 malignant solid tumors was utilized. The virtual organ computer-aided analysis-imaging program was used to analyze the stored volumes of the 183 solid breast tumors. LRA, an SVM and NN were employed in comparative analyses for the characterization of benign and malignant solid breast masses from the database. The values of area under receiver operating characteristic (ROC) curve, referred to as Az values for the use of non-harmonic 3D power Doppler US with LRA, SVM and NN were 0.9341, 0.9185 and 0.9086, respectively. The Az values for the use of harmonic 3D power Doppler US with LRA, SVM and NN were 0.9286, 0.8979 and 0.9009, respectively. The Az values of six ROC curves for the use of LRA, SVM and NN for non-harmonic or harmonic 3D power Doppler imaging were similar. The diagnostic performances of these three models (LRA, SVM and NN) are not different as demonstrated by ROC curve analysis. Depending on user emphasis for the use of ROC curve findings, the use of LRA appears to provide better sensitivity as compared to the other statistical models

  6. Comparative Analysis of A, B Type and Exchange Traded Funds Performances with Mutual Fund Performance Measures, Regression Analysis and Manova Technique.

    Directory of Open Access Journals (Sweden)

    Mehmet Arslan

    2010-06-01

    Full Text Available The objective of the study is to evaluate risk- reward relationship and relative performances of the 4 different groups of mutual funds. To this end, daily return data of these 12 mutual funds (3 type variable fund; 3 B type variable fund; 3 A type stock fund and 3 A type Exchange traded fund together with daily market index (imkb100 return and daily return of riskless rate for the period from January 2006 to Feb 2010. The 180-day maturity T-Bill has been selected to represent riskless rate. To determine performances of mutual funds; Sharpe ratio, M2 measure, Treynor index, Jensen index, Sortino ratio, T2 ratio, Valuation ratio has been applied and these indicators produced conflicting results in ranking mutual funds. Then timingand selection capability of the fund manager has been determined by applying simple regression and Quadratic regression. Interestingly all funds found to have positive coefficient, indicating positive election capability of managers; but in terms of timing capability only one fund managers showed success. Finally, to determine extent to which mean returns are differs between mutual funds, market index (imkb100 and riskless rate (180 day TBill results of the analysis revealed that mean returns of individual security returns differs at P≤0,01 level. That shows instability in returns and poor ex-ante forecast modeling capability.

  7. The importance of statistical modelling in clinical research : Comparing multidimensional Rasch-, structural equation and linear regression models for analyzing the depression of relatives of psychiatric patients.

    Science.gov (United States)

    Alexandrowicz, Rainer W; Jahn, Rebecca; Friedrich, Fabian; Unger, Anne

    2016-06-01

    Various studies have shown that caregiving relatives of schizophrenic patients are at risk of suffering from depression. These studies differ with respect to the applied statistical methods, which could influence the findings. Therefore, the present study analyzes to which extent different methods may cause differing results. The present study contrasts by means of one data set the results of three different modelling approaches, Rasch Modelling (RM), Structural Equation Modelling (SEM), and Linear Regression Modelling (LRM). The results of the three models varied considerably, reflecting the different assumptions of the respective models. Latent trait models (i. e., RM and SEM) generally provide more convincing results by correcting for measurement error and the RM specifically proves superior for it treats ordered categorical data most adequately.

  8. Regression: A Bibliography.

    Science.gov (United States)

    Pedrini, D. T.; Pedrini, Bonnie C.

    Regression, another mechanism studied by Sigmund Freud, has had much research, e.g., hypnotic regression, frustration regression, schizophrenic regression, and infra-human-animal regression (often directly related to fixation). Many investigators worked with hypnotic age regression, which has a long history, going back to Russian reflexologists.…

  9. Comparative analyses reveal different consequences of two oxidative stress inducers, gamma irradiation and potassium tellurite, in the extremophile Deinococcus radiodurans

    International Nuclear Information System (INIS)

    Narasimha, Anaganti; Basu, Bhakti; Apte, Shree Kumar

    2014-01-01

    Proteomic and mass spectrometric analyses revealed differential responses of D. radiodurans to two oxidative stressors. While both elicited oxidative stress alleviation response, major divergence was observed at the level of DNA repair, metabolic pathways and protein homeostasis. Response to gamma irradiation was focused on DNA repair and ROS scavenging but supported metabolism as well as protein homeostasis. Tellurite, induced oxidative stress alleviation but decreased reducing affected and adversely affected metabolism and protein homeostasis

  10. Comparative in silico analyses of Cannabis sativa, Prunella vulgaris and Withania somnifera compounds elucidating the medicinal properties against rheumatoid arthritis.

    Science.gov (United States)

    Zaka, Mehreen; Sehgal, Sheikh Arslan; Shafique, Shagufta; Abbasi, Bilal Haider

    2017-06-01

    From last decade, there has been progressive improvement in computational drug designing. Several diseases are being cured from different plant extracts and products. Rheumatoid Arthritis (RA) is the most shared disease among auto-inflammatory diseases. Tumour necrosis factor (TNF)-α is associated with RA pathway and has adverse effects. Extensive literature review showed that plant species under study (Cannabis sativa, Prunella vulgaris and Withania somnifera) possess anti-inflammatory, anti-arthritic and anti-rheumatic properties. 13 anti-inflammatory compounds were characterised and filtered out from medicinal plant species and analysed for RA by targeting TNF-α through in silico analyses. By using ligand based pharmacophore generation approach and virtual screening against natural products libraries we retrieved twenty unique molecules that displayed utmost binding affinity, least binding energies and effective drug properties. The docking analyses revealed that Ala-22, Glu-23, Ser-65, Gln-67, Tyr-141, Leu-142, Asp-143, Phe-144 and Ala-145 were critical interacting residues for receptor-ligand interactions. It is proposed that the RA patients should use reported compounds for the prescription of RA by targeting TNF-α. This report is opening new dimensions for designing innovative therapeutic targets to cure RA. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Comparative analyses of microbial structures and gene copy numbers in the anaerobic digestion of various types of sewage sludge.

    Science.gov (United States)

    Hidaka, Taira; Tsushima, Ikuo; Tsumori, Jun

    2018-04-01

    Anaerobic co-digestion of various sewage sludges is a promising approach for greater recovery of energy, but the process is more complicated than mono-digestion of sewage sludge. The applicability of microbial structure analyses and gene quantification to understand microbial conditions was evaluated. The results show that information from gene analyses is useful in managing anaerobic co-digestion and damaged microbes in addition to conventional parameters like total solids, pH and biogas production. Total bacterial 16S rRNA gene copy numbers are the most useful tools for evaluating unstable anaerobic digestion of sewage sludge, rather than mcrA and total archaeal 16S rRNA gene copy numbers, and high-throughput sequencing. First order decay rates of gene copy numbers during pH failure were higher than typical decay rates of microbes in stable operation. The sequencing analyses, including multidimensional scaling, showed very different microbial structure shifts, but the results were not consistent. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Cloning, characterisation, and comparative quantitative expression analyses of receptor for advanced glycation end products (RAGE) transcript forms.

    Science.gov (United States)

    Sterenczak, Katharina A; Willenbrock, Saskia; Barann, Matthias; Klemke, Markus; Soller, Jan T; Eberle, Nina; Nolte, Ingo; Bullerdiek, Jörn; Murua Escobar, Hugo

    2009-04-01

    RAGE is a member of the immunoglobulin superfamily of cell surface molecules playing key roles in pathophysiological processes, e.g. immune/inflammatory disorders, Alzheimer's disease, diabetic arteriosclerosis and tumourigenesis. In humans 19 naturally occurring RAGE splicing variants resulting in either N-terminally or C-terminally truncated proteins were identified and are lately discussed as mechanisms for receptor regulation. Accordingly, deregulation of sRAGE levels has been associated with several diseases e.g. Alzheimer's disease, Type 1 diabetes, and rheumatoid arthritis. Administration of recombinant sRAGE to animal models of cancer blocked tumour growth successfully. In spite of its obvious relationship to cancer and metastasis data focusing sRAGE deregulation and tumours is rare. In this study we screened a set of tumours, healthy tissues and various cancer cell lines for RAGE splicing variants and analysed their structure. Additionally, we analysed the ratio of the mainly found transcript variants using quantitative Real-Time PCR. In total we characterised 24 previously not described canine and 4 human RAGE splicing variants, analysed their structure, classified their characteristics, and derived their respective protein forms. Interestingly, the healthy and the neoplastic tissue samples showed in majority RAGE transcripts coding for the complete receptor and transcripts showing insertions of intron 1.

  13. Bayesian ARTMAP for regression.

    Science.gov (United States)

    Sasu, L M; Andonie, R

    2013-10-01

    Bayesian ARTMAP (BA) is a recently introduced neural architecture which uses a combination of Fuzzy ARTMAP competitive learning and Bayesian learning. Training is generally performed online, in a single-epoch. During training, BA creates input data clusters as Gaussian categories, and also infers the conditional probabilities between input patterns and categories, and between categories and classes. During prediction, BA uses Bayesian posterior probability estimation. So far, BA was used only for classification. The goal of this paper is to analyze the efficiency of BA for regression problems. Our contributions are: (i) we generalize the BA algorithm using the clustering functionality of both ART modules, and name it BA for Regression (BAR); (ii) we prove that BAR is a universal approximator with the best approximation property. In other words, BAR approximates arbitrarily well any continuous function (universal approximation) and, for every given continuous function, there is one in the set of BAR approximators situated at minimum distance (best approximation); (iii) we experimentally compare the online trained BAR with several neural models, on the following standard regression benchmarks: CPU Computer Hardware, Boston Housing, Wisconsin Breast Cancer, and Communities and Crime. Our results show that BAR is an appropriate tool for regression tasks, both for theoretical and practical reasons. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Better Autologistic Regression

    Directory of Open Access Journals (Sweden)

    Mark A. Wolters

    2017-11-01

    Full Text Available Autologistic regression is an important probability model for dichotomous random variables observed along with covariate information. It has been used in various fields for analyzing binary data possessing spatial or network structure. The model can be viewed as an extension of the autologistic model (also known as the Ising model, quadratic exponential binary distribution, or Boltzmann machine to include covariates. It can also be viewed as an extension of logistic regression to handle responses that are not independent. Not all authors use exactly the same form of the autologistic regression model. Variations of the model differ in two respects. First, the variable coding—the two numbers used to represent the two possible states of the variables—might differ. Common coding choices are (zero, one and (minus one, plus one. Second, the model might appear in either of two algebraic forms: a standard form, or a recently proposed centered form. Little attention has been paid to the effect of these differences, and the literature shows ambiguity about their importance. It is shown here that changes to either coding or centering in fact produce distinct, non-nested probability models. Theoretical results, numerical studies, and analysis of an ecological data set all show that the differences among the models can be large and practically significant. Understanding the nature of the differences and making appropriate modeling choices can lead to significantly improved autologistic regression analyses. The results strongly suggest that the standard model with plus/minus coding, which we call the symmetric autologistic model, is the most natural choice among the autologistic variants.

  15. Comparative Performance Analysis of Support Vector Machine, Random Forest, Logistic Regression and k-Nearest Neighbours in Rainbow Trout (Oncorhynchus Mykiss) Classification Using Image-Based Features.

    Science.gov (United States)

    Saberioon, Mohammadmehdi; Císař, Petr; Labbé, Laurent; Souček, Pavel; Pelissier, Pablo; Kerneis, Thierry

    2018-03-29

    The main aim of this study was to develop a new objective method for evaluating the impacts of different diets on the live fish skin using image-based features. In total, one-hundred and sixty rainbow trout ( Oncorhynchus mykiss ) were fed either a fish-meal based diet (80 fish) or a 100% plant-based diet (80 fish) and photographed using consumer-grade digital camera. Twenty-three colour features and four texture features were extracted. Four different classification methods were used to evaluate fish diets including Random forest (RF), Support vector machine (SVM), Logistic regression (LR) and k -Nearest neighbours ( k -NN). The SVM with radial based kernel provided the best classifier with correct classification rate (CCR) of 82% and Kappa coefficient of 0.65. Although the both LR and RF methods were less accurate than SVM, they achieved good classification with CCR 75% and 70% respectively. The k -NN was the least accurate (40%) classification model. Overall, it can be concluded that consumer-grade digital cameras could be employed as the fast, accurate and non-invasive sensor for classifying rainbow trout based on their diets. Furthermore, these was a close association between image-based features and fish diet received during cultivation. These procedures can be used as non-invasive, accurate and precise approaches for monitoring fish status during the cultivation by evaluating diet's effects on fish skin.

  16. Comparative Performance Analysis of Support Vector Machine, Random Forest, Logistic Regression and k-Nearest Neighbours in Rainbow Trout (Oncorhynchus Mykiss Classification Using Image-Based Features

    Directory of Open Access Journals (Sweden)

    Mohammadmehdi Saberioon

    2018-03-01

    Full Text Available The main aim of this study was to develop a new objective method for evaluating the impacts of different diets on the live fish skin using image-based features. In total, one-hundred and sixty rainbow trout (Oncorhynchus mykiss were fed either a fish-meal based diet (80 fish or a 100% plant-based diet (80 fish and photographed using consumer-grade digital camera. Twenty-three colour features and four texture features were extracted. Four different classification methods were used to evaluate fish diets including Random forest (RF, Support vector machine (SVM, Logistic regression (LR and k-Nearest neighbours (k-NN. The SVM with radial based kernel provided the best classifier with correct classification rate (CCR of 82% and Kappa coefficient of 0.65. Although the both LR and RF methods were less accurate than SVM, they achieved good classification with CCR 75% and 70% respectively. The k-NN was the least accurate (40% classification model. Overall, it can be concluded that consumer-grade digital cameras could be employed as the fast, accurate and non-invasive sensor for classifying rainbow trout based on their diets. Furthermore, these was a close association between image-based features and fish diet received during cultivation. These procedures can be used as non-invasive, accurate and precise approaches for monitoring fish status during the cultivation by evaluating diet’s effects on fish skin.

  17. Steganalysis using logistic regression

    Science.gov (United States)

    Lubenko, Ivans; Ker, Andrew D.

    2011-02-01

    We advocate Logistic Regression (LR) as an alternative to the Support Vector Machine (SVM) classifiers commonly used in steganalysis. LR offers more information than traditional SVM methods - it estimates class probabilities as well as providing a simple classification - and can be adapted more easily and efficiently for multiclass problems. Like SVM, LR can be kernelised for nonlinear classification, and it shows comparable classification accuracy to SVM methods. This work is a case study, comparing accuracy and speed of SVM and LR classifiers in detection of LSB Matching and other related spatial-domain image steganography, through the state-of-art 686-dimensional SPAM feature set, in three image sets.

  18. Switching to olanzapine long-acting injection from either oral olanzapine or any other antipsychotic: comparative post hoc analyses

    Directory of Open Access Journals (Sweden)

    Ciudad A

    2013-11-01

    Full Text Available Antonio Ciudad,1 Ernie Anand,2 Lovisa Berggren,3 Marta Casillas,4 Alexander Schacht,3 Elena Perrin5 1Department of Clinical Research and Development, Eli Lilly & Co, Madrid, Spain; 2Neuroscience Medical Affairs – EU, Lilly Research Centre, Windlesham, Surrey, UK; 3Global Statistical Sciences, Eli Lilly & Co, Bad Homburg, Germany; 4European Scientific Communications, Eli Lilly & Co, Madrid, Spain; 5Medical Department, Eli Lilly & Co, Suresnes, Paris, France Background: A considerable proportion of patients suffering from schizophrenia show suboptimal responses to oral antipsychotics due to inadequate adherence. Hence, they are likely to benefit from switching to a long-acting injectable formulation. These post hoc analyses assessed the clinical effects of switching to olanzapine long-acting injection (OLAI from either oral olanzapine (OLZ or other antipsychotics (non-OLZ. Methods: Post hoc analyses were done based on two randomized studies (one short-term, one long-term conducted in patients suffering from schizophrenia and treated with OLAI. The short-term study was an 8-week placebo-controlled, double-blind trial in acute patients, and the long-term study was a 2-year, oral olanzapine-controlled, open-label, follow-up of stabilized outpatients. Results: These analyses used data from 62 OLAI-treated patients (12 switched from OLZ, 50 from non-OLZ from the short-term study and 190 OLAI-treated patients (56 switched from OLZ, 134 from non-OLZ from the long-term study. Kaplan–Meier survival analyses of time to all-cause discontinuation of OLAI treatment did not differ significantly between OLZ and non-OLZ patients in the short-term study (P=0.209 or long-term study (P=0.448. Similarly, the proportions of OLZ and non-OLZ patients that discontinued OLAI were not statistically different in the short-term (16.7% versus 36.0%, respectively; P=0.198 or long-term (57.1% versus 47.8% respectively; P=0.238 studies. In the short-term study, no

  19. Ridge Regression Signal Processing

    Science.gov (United States)

    Kuhl, Mark R.

    1990-01-01

    The introduction of the Global Positioning System (GPS) into the National Airspace System (NAS) necessitates the development of Receiver Autonomous Integrity Monitoring (RAIM) techniques. In order to guarantee a certain level of integrity, a thorough understanding of modern estimation techniques applied to navigational problems is required. The extended Kalman filter (EKF) is derived and analyzed under poor geometry conditions. It was found that the performance of the EKF is difficult to predict, since the EKF is designed for a Gaussian environment. A novel approach is implemented which incorporates ridge regression to explain the behavior of an EKF in the presence of dynamics under poor geometry conditions. The basic principles of ridge regression theory are presented, followed by the derivation of a linearized recursive ridge estimator. Computer simulations are performed to confirm the underlying theory and to provide a comparative analysis of the EKF and the recursive ridge estimator.

  20. Price promotions on healthier compared with less healthy foods: a hierarchical regression analysis of the impact on sales and social patterning of responses to promotions in Great Britain.

    Science.gov (United States)

    Nakamura, Ryota; Suhrcke, Marc; Jebb, Susan A; Pechey, Rachel; Almiron-Roig, Eva; Marteau, Theresa M

    2015-04-01

    There is a growing concern, but limited evidence, that price promotions contribute to a poor diet and the social patterning of diet-related disease. We examined the following questions: 1) Are less-healthy foods more likely to be promoted than healthier foods? 2) Are consumers more responsive to promotions on less-healthy products? 3) Are there socioeconomic differences in food purchases in response to price promotions? With the use of hierarchical regression, we analyzed data on purchases of 11,323 products within 135 food and beverage categories from 26,986 households in Great Britain during 2010. Major supermarkets operated the same price promotions in all branches. The number of stores that offered price promotions on each product for each week was used to measure the frequency of price promotions. We assessed the healthiness of each product by using a nutrient profiling (NP) model. A total of 6788 products (60%) were in healthier categories and 4535 products (40%) were in less-healthy categories. There was no significant gap in the frequency of promotion by the healthiness of products neither within nor between categories. However, after we controlled for the reference price, price discount rate, and brand-specific effects, the sales uplift arising from price promotions was larger in less-healthy than in healthier categories; a 1-SD point increase in the category mean NP score, implying the category becomes less healthy, was associated with an additional 7.7-percentage point increase in sales (from 27.3% to 35.0%; P sales uplift from promotions was larger for higher-socioeconomic status (SES) groups than for lower ones (34.6% for the high-SES group, 28.1% for the middle-SES group, and 23.1% for the low-SES group). Finally, there was no significant SES gap in the absolute volume of purchases of less-healthy foods made on promotion. Attempts to limit promotions on less-healthy foods could improve the population diet but would be unlikely to reduce health

  1. Biofilm-Growing Bacteria Involved in the Corrosion of Concrete Wastewater Pipes: Protocols for Comparative Metagenomic Analyses

    Science.gov (United States)

    Advances in high-throughput next-generation sequencing (NGS) technology for direct sequencing of environmental DNA (i.e. shotgun metagenomics) is transforming the field of microbiology. NGS technologies are now regularly being applied in comparative metagenomic studies, which pr...

  2. Characterizing Design Cognition of High School Students: Initial Analyses Comparing Those with and without Pre-Engineering Experiences

    Science.gov (United States)

    Wells, John; Lammi, Matthew; Gero, John; Grubbs, Michael E.; Paretti, Marie; Williams, Christopher

    2016-01-01

    Reported in this article are initial results from of a longitudinal study to characterize the design cognition and cognitive design styles of high school students with and without pre-engineering course experience over a 2-year period, and to compare them with undergraduate engineering students. The research followed a verbal protocol analysis…

  3. Application of IBA in the comparative analyses of fish scales used as biomonitors in the Matola River, Mozambique

    International Nuclear Information System (INIS)

    Guambe, J.F.; Mars, J.A.; Day, J.

    2013-01-01

    Full text: Many natural resources are invariably contaminated by industries located on the periphery of the resources. More so, fish found in the resources are used as dietary supplements, especially by individual that reside near the natural resources. The scale offish have been proven to be applicable in monitoring contamination of the natural resources. However, the morphology and chemical composition of the scale of various species differ to a significant degree. Consequently, the incorporation of contaminants into the scale structure will be different. There is a need of pilot for contaminants which can harm the biota. The composition of the fish scales is different. To quantify the degree of incorporation onto the scale matrix we have analysed, using PIXE, RBS and SEM, the scale of four types of fish scales, that is, Pomadasys kaakan the javelin grunter; Luljanus gibbus the humpback red snapper; Pinjalo pinjalo the pinjalo and Uthognathus mormyrus the sand streenbras. In this work we report on the viability of using various fish scales as monitors of natural resource contamination. (author)

  4. Application of IBA in the comparative analyses of fish scales used as biomonitors in the Matola River, Mozambique

    Energy Technology Data Exchange (ETDEWEB)

    Guambe, J.F. [Freshwater Research Unit, Department of Zoology, University of Cape Town, Private Bag, Rondebosch, 7701 (South Africa); Physics Department, Eduardo Mondlane Universily, PO Box 257, Maputo (Mozambique); Materials Research Department, iThemba LABS, PO Box 722, Somerset West, 7129 (South Africa); Mars, J.A. [Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535 (South Africa); Day, J. [Freshwater Research Unit, Department of Zoology, University of Cape Town, Private Bag, Rondebosch, 7701 (South Africa)

    2013-07-01

    Full text: Many natural resources are invariably contaminated by industries located on the periphery of the resources. More so, fish found in the resources are used as dietary supplements, especially by individual that reside near the natural resources. The scale offish have been proven to be applicable in monitoring contamination of the natural resources. However, the morphology and chemical composition of the scale of various species differ to a significant degree. Consequently, the incorporation of contaminants into the scale structure will be different. There is a need of pilot for contaminants which can harm the biota. The composition of the fish scales is different. To quantify the degree of incorporation onto the scale matrix we have analysed, using PIXE, RBS and SEM, the scale of four types of fish scales, that is, Pomadasys kaakan the javelin grunter; Luljanus gibbus the humpback red snapper; Pinjalo pinjalo the pinjalo and Uthognathus mormyrus the sand streenbras. In this work we report on the viability of using various fish scales as monitors of natural resource contamination. (author)

  5. Compare and analyse marketing strategies using consumer focused studies. The case of TomTom vs. Garmin

    OpenAIRE

    Stefanova, Antonia

    2014-01-01

    The following dissertation paper focuses on a central research question that is to compare and appraise strategic marketing activities of a first mover navigation organisation, TomTom B.V., to its most prominent competitor Garmin Ltd, a successful follower. The intense situation in the global positioning systems market provides a great possibility of investigating the two giant organisations' internal environment, competitive environment and customers' purchase behaviour. In this regard, mark...

  6. Comparative Metabolomic Analyses of Ipomoea lacunosa Biotypes with Contrasting Glyphosate Tolerance Captures Herbicide-Induced Differential Perturbations in Cellular Physiology.

    Science.gov (United States)

    Maroli, Amith S; Nandula, Vijay K; Duke, Stephen O; Gerard, Patrick; Tharayil, Nishanth

    2018-02-28

    Glyphosate-tolerant Ipomoea lacunosa is emerging as a problematic weed in the southeastern United States. Metabolomic profiling was conducted to examine the innate physiology and the glyphosate induced perturbations in two biotypes of I. lacunosa (WAS and QUI) that had contrasting glyphosate tolerance. Compared to the less tolerant QUI-biotype, the innate metabolism of the more tolerant WAS-biotype was characterized by a higher abundance of amino acids, and pyruvate; whereas the sugar profile of the QUI biotype was dominated by the transport sugar sucrose. Glyphosate application (80 g ae/ha) caused similar shikimate accumulation in both biotypes. Compared to QUI, in WAS, the content of aromatic amino acids was less affected by glyphosate treatment, and the content of Ala, Val, Ile, and Pro increased. However, the total sugars decreased by ∼75% in WAS, compared to ∼50% decrease in QUI. The innate, higher proportional abundance, of the transport-sugar sucrose in QUI coud partly explain the higher translocation and greater sensitivity of this biotype to glyphosate. The decrease in sugars, accompanied by an increase in amino acids could delay feedback regulation of upstream enzymes of the shikimate acid pathway in WAS, which could contribute to a greater glyphosate tolerance. Our study, through a metabolomics approach, provides complementary data that elucidates the cellular physiology of herbicide tolerance in Ipomoea lacunosa biotypes.

  7. Comparative energy input–output and financial analyses of greenhouse and open field vegetables production in West Java, Indonesia

    International Nuclear Information System (INIS)

    Kuswardhani, Nita; Soni, Peeyush; Shivakoti, Ganesh P.

    2013-01-01

    This paper estimates energy consumption per unit floor area of greenhouse and open field for tomato, chili and lettuce production. Primary data were collected from 530 vegetable farmers during Jan–Dec, 2010 in West Java, Indonesia. Energy estimates were calculated from actual amount of inputs and outputs and corresponding conversion factors. Results reveal that the total input energy used in greenhouse (GH) production of tomato, chili (medium and high land) and lettuce were 47.62, 41.55, 58.84, and 24.54 GJ/ha respectively. Whereas, the requirement of total input energy for open field (OF) production of tomato, chili (medium and high land) and lettuce were 49.01, 41.04, 57.94 and 23.87 GJ/ha, respectively. The ratio of output to input energy was higher in greenhouse production (0.85, 0.45 and 0.49) than open field vegetable production (0.52, 0.175 and 0.186) for tomato, chili medium land and chili highland, respectively, but output–input ratio of lettuce open field production was twice as that of greenhouse vegetable production. Financial analysis revealed higher mean net returns from greenhouse vegetable production as 7043 $/ha (922–15,299 $/ha) when compared to 571 $/ha (44–1172 $/ha) from open field vegetable production. Among the greenhouse vegetables, tomato cultivation was the most profitable in terms of energy efficiency and financial productivity. - Highlights: ► Energy input–output analysis is carried out to compare vegetables production in greenhouse and open field. ► Tomato, Chili and Lettuce production in West Java, Indonesia. ► Economic analysis is conducted to compare the two production systems

  8. Comparative Anatomical Analyses of the Forearm Muscles of Cebus libidinosus (Rylands et al. 2000): Manipulatory Behavior and Tool Use

    Science.gov (United States)

    Aversi-Ferreira, Tales Alexandre; Maior, Rafael Souto; Carneiro-e-Silva, Frederico O.; Aversi-Ferreira, Roqueline A. G. M. F.; Tavares, Maria Clotilde; Nishijo, Hisao; Tomaz, Carlos

    2011-01-01

    The present study describes the flexor and extensor muscles in Cebus libidinosus' forearm and compares them with those from humans, chimpanzees and baboons. The data is presented in quantitative anatomical indices for similarity. The capuchin forearm muscles showed important similarities with chimpanzees and humans, particularly those that act on thumb motion and allow certain degree of independence from other hand structures, even though their configuration does not enable a true opposable thumb. The characteristics of Cebus' forearm muscles corroborate the evolutionary convergence towards an adaptive behavior (tool use) between Cebus genus and apes. PMID:21789230

  9. Productivité du Capital Humain dans les Pays de l’UEMOA et de la CEMAC : Une Analyse Comparative

    OpenAIRE

    Élisé Wendlassida Miningou

    2012-01-01

    La présente étude pose le problème de la productivité du capital humain dans les pays de l’UEMOA et de la CEMAC. Dans ce papier, nous mesurons l’efficience avec laquelle le capital humain est mis à contribution dans la production. Pour ce faire, nous appliquons la méthode du Data Envelopment Analysis (DEA) pour mesurer et comparer la productivité du capital humain entre ces deux ensembles de pays. Nos résultats montrent que le capital humain dans la zone UEMOA a été moins productif ...

  10. riskRegression

    DEFF Research Database (Denmark)

    Ozenne, Brice; Sørensen, Anne Lyngholm; Scheike, Thomas

    2017-01-01

    In the presence of competing risks a prediction of the time-dynamic absolute risk of an event can be based on cause-specific Cox regression models for the event and the competing risks (Benichou and Gail, 1990). We present computationally fast and memory optimized C++ functions with an R interface......-product we obtain fast access to the baseline hazards (compared to survival::basehaz()) and predictions of survival probabilities, their confidence intervals and confidence bands. Confidence intervals and confidence bands are based on point-wise asymptotic expansions of the corresponding statistical...

  11. Comparative genomic and functional analyses: unearthing the diversity and specificity of nematicidal factors in Pseudomonas putida strain 1A00316

    Science.gov (United States)

    Guo, Jing; Jing, Xueping; Peng, Wen-Lei; Nie, Qiyu; Zhai, Yile; Shao, Zongze; Zheng, Longyu; Cai, Minmin; Li, Guangyu; Zuo, Huaiyu; Zhang, Zhitao; Wang, Rui-Ru; Huang, Dian; Cheng, Wanli; Yu, Ziniu; Chen, Ling-Ling; Zhang, Jibin

    2016-01-01

    We isolated Pseudomonas putida (P. putida) strain 1A00316 from Antarctica. This bacterium has a high efficiency against Meloidogyne incognita (M. incognita) in vitro and under greenhouse conditions. The complete genome of P. putida 1A00316 was sequenced using PacBio single molecule real-time (SMRT) technology. A comparative genomic analysis of 16 Pseudomonas strains revealed that although P. putida 1A00316 belonged to P. putida, it was phenotypically more similar to nematicidal Pseudomonas fluorescens (P. fluorescens) strains. We characterized the diversity and specificity of nematicidal factors in P. putida 1A00316 with comparative genomics and functional analysis, and found that P. putida 1A00316 has diverse nematicidal factors including protein alkaline metalloproteinase AprA and two secondary metabolites, hydrogen cyanide and cyclo-(l-isoleucyl-l-proline). We show for the first time that cyclo-(l-isoleucyl-l-proline) exhibit nematicidal activity in P. putida. Interestingly, our study had not detected common nematicidal factors such as 2,4-diacetylphloroglucinol (2,4-DAPG) and pyrrolnitrin in P. putida 1A00316. The results of the present study reveal the diversity and specificity of nematicidal factors in P. putida strain 1A00316. PMID:27384076

  12. Spectroscopic, thermogravimetric and structural characterization analyses for comparing Municipal Solid Waste composts and vermicomposts stability and maturity.

    Science.gov (United States)

    Soobhany, Nuhaa; Gunasee, Sanjana; Rago, Yogeshwari Pooja; Joyram, Hashita; Raghoo, Pravesh; Mohee, Romeela; Garg, Vinod Kumar

    2017-07-01

    This is the first-ever study of its kind for an extensive assessment and comparison of maturity indexes between compost and vermicompost that have been derived from Municipal Solid Waste (MSW). The spectroscopic (Fourier transform infrared spectroscopy: FT-IR), thermogravimetric analysis (TG), differential scanning calorimetry (DSC) and structural characterization (scanning electron microscope: SEM) were recorded. FT-IR spectra showed an increase in conversion of polysaccharides species and aliphatic methylene groups in vermicompost compared to compost as depicted from the variation of the intensity of the peaks. TG curves of final vermicompost showed a much lower mass loss when compared to compost, indicating higher stability in feedstock. SEM micrographs of the vermicompost reflected strong fragmentation of material than composts which revealed the extent of intra-structural degradation of MSW. These findings elucidate on a clear comparison between composts and vermicomposts in terms of maturity indexes for soil enhancement and in agriculture as organic fertilizer. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Comparative Transcriptomic Analyses by RNA-seq to Elucidate Differentially Expressed Genes in the Muscle of Korean Thoroughbred Horses.

    Science.gov (United States)

    Ghosh, Mrinmoy; Cho, Hyun-Woo; Park, Jeong-Woong; Choi, Jae-Young; Chung, Young-Hwa; Sharma, Neelesh; Singh, Amit Kumar; Kim, Nam Eun; Mongre, Raj Kumar; Huynh, Do; Jiao, Zhang Jiao; Do, Kyoung Tag; Lee, Hak-Kyo; Song, Ki-Duk; Cho, Byung-Wook; Jeong, DongKee

    2016-10-01

    The athletic abilities of the horse serve as a valuable model to understand the physiology and molecular mechanisms of adaptive responses to exercise. We analyzed differentially expressed genes in triceps brachii muscle tissues collected from Eonjena Taeyang and Jigusang Seryeok Thoroughbred horses and their co-expression networks in a large-scale RNA-sequence dataset comparing expression before and after exercise. High-quality horse transcriptome data were generated, with over 22 million 90-bp pair-end reads. By comparing the annotations, we found that MYH3, MPZ, and PDE8B genes in Eonjena Taeyang and PDE8B and KIF18A genes in Jigusang Seryeok were upregulated before exercise. Notably further, we observed that PPP1R27, NDUFA3, TNC, and ANK1 in Eonjena Taeyang and HIF1A, BDNF, ADRB2, OBSCN, and PER3 in Jigusang Seryeok have shown upregulation at the postexercise period. This investigation suggested that genes responsible for metabolism and oxidative phosphorylations associated with endurance and resistance exercise were highly expressed, whereas genes encoding structural proteins were generally suppressed. The expression profile of racehorses at pre- and postexercise will provide credible reference for further studies on biological effects such as responses to stress and adaption of other Thoroughbred horse, which might be useful for selective breeding for improvement of traits in commercial production.

  14. Four pathways in the analysis of adult development and aging: comparing analyses of reasoning about personal-life dilemmas.

    Science.gov (United States)

    Pratt, M W; Diessner, R; Hunsberger, B; Pancer, S M; Savoy, K

    1991-12-01

    Four systems for analyzing thinking about 2 personal-life dilemmas, as discussed by 29 men and 35 women (ages 35-85), were compared. Kohlberg's (1976) moral judgment stages, Kegan's (1982) ego-development stages, Gilligan's (1982) moral orientation system, and Suedfeld and Tetlock's (1977) integrative complexity scoring were used. Subjects completed Kohlberg's (Colby & Kohlberg, 1987) standard moral judgment measure, a self-concept description, and several questionnaires. The Kohlberg, Kegan, and integrative complexity codings of the dilemmas were positively related to each other and to the standard Kohlberg moral stage scores. There were no age-group differences and few gender differences on the measures. However, education, role-taking skills, and greater sensitivity to age changes in the self positively predicted higher stage scores across maturity.

  15. Methods and theory in bone modeling drift: comparing spatial analyses of primary bone distributions in the human humerus.

    Science.gov (United States)

    Maggiano, Corey M; Maggiano, Isabel S; Tiesler, Vera G; Chi-Keb, Julio R; Stout, Sam D

    2016-01-01

    This study compares two novel methods quantifying bone shaft tissue distributions, and relates observations on human humeral growth patterns for applications in anthropological and anatomical research. Microstructural variation in compact bone occurs due to developmental and mechanically adaptive circumstances that are 'recorded' by forming bone and are important for interpretations of growth, health, physical activity, adaptation, and identity in the past and present. Those interpretations hinge on a detailed understanding of the modeling process by which bones achieve their diametric shape, diaphyseal curvature, and general position relative to other elements. Bone modeling is a complex aspect of growth, potentially causing the shaft to drift transversely through formation and resorption on opposing cortices. Unfortunately, the specifics of modeling drift are largely unknown for most skeletal elements. Moreover, bone modeling has seen little quantitative methodological development compared with secondary bone processes, such as intracortical remodeling. The techniques proposed here, starburst point-count and 45° cross-polarization hand-drawn histomorphometry, permit the statistical and populational analysis of human primary tissue distributions and provide similar results despite being suitable for different applications. This analysis of a pooled archaeological and modern skeletal sample confirms the importance of extreme asymmetry in bone modeling as a major determinant of microstructural variation in diaphyses. Specifically, humeral drift is posteromedial in the human humerus, accompanied by a significant rotational trend. In general, results encourage the usage of endocortical primary bone distributions as an indicator and summary of bone modeling drift, enabling quantitative analysis by direction and proportion in other elements and populations. © 2015 Anatomical Society.

  16. Core Genome Multilocus Sequence Typing Scheme for Stable, Comparative Analyses of Campylobacter jejuni and C. coli Human Disease Isolates.

    Science.gov (United States)

    Cody, Alison J; Bray, James E; Jolley, Keith A; McCarthy, Noel D; Maiden, Martin C J

    2017-07-01

    Human campylobacteriosis, caused by Campylobacter jejuni and C. coli , remains a leading cause of bacterial gastroenteritis in many countries, but the epidemiology of campylobacteriosis outbreaks remains poorly defined, largely due to limitations in the resolution and comparability of isolate characterization methods. Whole-genome sequencing (WGS) data enable the improvement of sequence-based typing approaches, such as multilocus sequence typing (MLST), by substantially increasing the number of loci examined. A core genome MLST (cgMLST) scheme defines a comprehensive set of those loci present in most members of a bacterial group, balancing very high resolution with comparability across the diversity of the group. Here we propose a set of 1,343 loci as a human campylobacteriosis cgMLST scheme (v1.0), the allelic profiles of which can be assigned to core genome sequence types. The 1,343 loci chosen were a subset of the 1,643 loci identified in the reannotation of the genome sequence of C. jejuni isolate NCTC 11168, chosen as being present in >95% of draft genomes of 2,472 representative United Kingdom campylobacteriosis isolates, comprising 2,207 (89.3%) C. jejuni isolates and 265 (10.7%) C. coli isolates. Validation of the cgMLST scheme was undertaken with 1,478 further high-quality draft genomes, containing 150 or fewer contiguous sequences, from disease isolate collections: 99.5% of these isolates contained ≥95% of the 1,343 cgMLST loci. In addition to the rapid and effective high-resolution analysis of large numbers of diverse isolates, the cgMLST scheme enabled the efficient identification of very closely related isolates from a well-defined single-source campylobacteriosis outbreak. Copyright © 2017 Cody et al.

  17. Quantile Regression With Measurement Error

    KAUST Repository

    Wei, Ying; Carroll, Raymond J.

    2009-01-01

    . The finite sample performance of the proposed method is investigated in a simulation study, and compared to the standard regression calibration approach. Finally, we apply our methodology to part of the National Collaborative Perinatal Project growth data, a

  18. Comparative analyses of hydrological responses of two adjacent watersheds to climate variability and change using the SWAT model

    Science.gov (United States)

    Lee, Sangchul; Yeo, In-Young; Sadeghi, Ali M.; McCarty, Gregory W.; Hively, Wells; Lang, Megan W.; Sharifi, Amir

    2018-01-01

    Water quality problems in the Chesapeake Bay Watershed (CBW) are expected to be exacerbated by climate variability and change. However, climate impacts on agricultural lands and resultant nutrient loads into surface water resources are largely unknown. This study evaluated the impacts of climate variability and change on two adjacent watersheds in the Coastal Plain of the CBW, using the Soil and Water Assessment Tool (SWAT) model. We prepared six climate sensitivity scenarios to assess the individual impacts of variations in CO2concentration (590 and 850 ppm), precipitation increase (11 and 21 %), and temperature increase (2.9 and 5.0 °C), based on regional general circulation model (GCM) projections. Further, we considered the ensemble of five GCM projections (2085–2098) under the Representative Concentration Pathway (RCP) 8.5 scenario to evaluate simultaneous changes in CO2, precipitation, and temperature. Using SWAT model simulations from 2001 to 2014 as a baseline scenario, predicted hydrologic outputs (water and nitrate budgets) and crop growth were analyzed. Compared to the baseline scenario, a precipitation increase of 21 % and elevated CO2 concentration of 850 ppm significantly increased streamflow and nitrate loads by 50 and 52 %, respectively, while a temperature increase of 5.0 °C reduced streamflow and nitrate loads by 12 and 13 %, respectively. Crop biomass increased with elevated CO2 concentrations due to enhanced radiation- and water-use efficiency, while it decreased with precipitation and temperature increases. Over the GCM ensemble mean, annual streamflow and nitrate loads showed an increase of  ∼  70 % relative to the baseline scenario, due to elevated CO2 concentrations and precipitation increase. Different hydrological responses to climate change were observed from the two watersheds, due to contrasting land use and soil characteristics. The watershed with a larger percent of croplands demonstrated a greater

  19. Comparative analyses of hydrological responses of two adjacent watersheds to climate variability and change using the SWAT model

    Science.gov (United States)

    Lee, Sangchul; Yeo, In-Young; Sadeghi, Ali M.; McCarty, Gregory W.; Hively, Wells D.; Lang, Megan W.; Sharifi, Amir

    2018-01-01

    Water quality problems in the Chesapeake Bay Watershed (CBW) are expected to be exacerbated by climate variability and change. However, climate impacts on agricultural lands and resultant nutrient loads into surface water resources are largely unknown. This study evaluated the impacts of climate variability and change on two adjacent watersheds in the Coastal Plain of the CBW, using the Soil and Water Assessment Tool (SWAT) model. We prepared six climate sensitivity scenarios to assess the individual impacts of variations in CO2 concentration (590 and 850 ppm), precipitation increase (11 and 21 %), and temperature increase (2.9 and 5.0 °C), based on regional general circulation model (GCM) projections. Further, we considered the ensemble of five GCM projections (2085-2098) under the Representative Concentration Pathway (RCP) 8.5 scenario to evaluate simultaneous changes in CO2, precipitation, and temperature. Using SWAT model simulations from 2001 to 2014 as a baseline scenario, predicted hydrologic outputs (water and nitrate budgets) and crop growth were analyzed. Compared to the baseline scenario, a precipitation increase of 21 % and elevated CO2 concentration of 850 ppm significantly increased streamflow and nitrate loads by 50 and 52 %, respectively, while a temperature increase of 5.0 °C reduced streamflow and nitrate loads by 12 and 13 %, respectively. Crop biomass increased with elevated CO2 concentrations due to enhanced radiation- and water-use efficiency, while it decreased with precipitation and temperature increases. Over the GCM ensemble mean, annual streamflow and nitrate loads showed an increase of ˜ 70 % relative to the baseline scenario, due to elevated CO2 concentrations and precipitation increase. Different hydrological responses to climate change were observed from the two watersheds, due to contrasting land use and soil characteristics. The watershed with a larger percent of croplands demonstrated a greater increased rate of 5.2 kg N ha-1 in

  20. Reduced Rank Regression

    DEFF Research Database (Denmark)

    Johansen, Søren

    2008-01-01

    The reduced rank regression model is a multivariate regression model with a coefficient matrix with reduced rank. The reduced rank regression algorithm is an estimation procedure, which estimates the reduced rank regression model. It is related to canonical correlations and involves calculating...

  1. Comparative Transcriptomic and Proteomic Analyses Reveal a FluG-Mediated Signaling Pathway Relating to Asexual Sporulation of Antrodia camphorata.

    Science.gov (United States)

    Li, Hua-Xiang; Lu, Zhen-Ming; Zhu, Qing; Gong, Jin-Song; Geng, Yan; Shi, Jin-Song; Xu, Zheng-Hong; Ma, Yan-He

    2017-09-01

    Medicinal mushroom Antrodia camphorata sporulate large numbers of arthroconidia in submerged fermentation, which is rarely reported in basidiomycetous fungi. Nevertheless, the molecular mechanisms underlying this asexual sporulation (conidiation) remain unclear. Here, we used comparative transcriptomic and proteomic approaches to elucidate possible signaling pathway relating to the asexual sporulation of A. camphorata. First, 104 differentially expressed proteins and 2586 differential cDNA sequences during the culture process of A. camphorata were identified by 2DE and RNA-seq, respectively. By applying bioinformatics analysis, a total of 67 genes which might play roles in the sporulation were obtained, and 18 of these genes, including fluG, sfgA, SfaD, flbA, flbB, flbC, flbD, nsdD, brlA, abaA, wetA, ganB, fadA, PkaA, veA, velB, vosA, and stuA might be involved in a potential FluG-mediated signaling pathway. Furthermore, the mRNA expression levels of the 18 genes in the proposed FluG-mediated signaling pathway were analyzed by quantitative real-time PCR. In summary, our study helps elucidate the molecular mechanisms underlying the asexual sporulation of A. camphorata, and provides also useful transcripts and proteome for further bioinformatics study of this valuable medicinal mushroom. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Comparative genomic characterization of three Streptococcus parauberis strains in fish pathogen, as assessed by wide-genome analyses.

    Directory of Open Access Journals (Sweden)

    Seong-Won Nho

    Full Text Available Streptococcus parauberis, which is the main causative agent of streptococcosis among olive flounder (Paralichthys olivaceus in northeast Asia, can be distinctly divided into two groups (type I and type II by an agglutination test. Here, the whole genome sequences of two Japanese strains (KRS-02083 and KRS-02109 were determined and compared with the previously determined genome of a Korean strain (KCTC 11537. The genomes of S. parauberis are intermediate in size and have lower GC contents than those of other streptococci. We annotated 2,236 and 2,048 genes in KRS-02083 and KRS-02109, respectively. Our results revealed that the three S. parauberis strains contain different genomic insertions and deletions. In particular, the genomes of Korean and Japanese strains encode different factors for sugar utilization; the former encodes the phosphotransferase system (PTS for sorbose, whereas the latter encodes proteins for lactose hydrolysis, respectively. And the KRS-02109 strain, specifically, was the type II strain found to be able to resist phage infection through the clustered regularly interspaced short palindromic repeats (CRISPR/Cas system and which might contribute valuably to serologically distribution. Thus, our genome-wide association study shows that polymorphisms can affect pathogen responses, providing insight into biological/biochemical pathways and phylogenetic diversity.

  3. Comparative proteomic analyses reveal the proteome response to short-term drought in Italian ryegrass (Lolium multiflorum.

    Directory of Open Access Journals (Sweden)

    Ling Pan

    Full Text Available Drought is a major abiotic stress that impairs growth and productivity of Italian ryegrass. Comparative analysis of drought responsive proteins will provide insight into molecular mechanism in Lolium multiflorum drought tolerance. Using the iTRAQ-based approach, proteomic changes in tolerant and susceptible lines were examined in response to drought condition. A total of 950 differentially accumulated proteins was found to be involved in carbohydrate metabolism, amino acid metabolism, biosynthesis of secondary metabolites, and signal transduction pathway, such as β-D-xylosidase, β-D-glucan glucohydrolase, glycerate dehydrogenase, Cobalamin-independent methionine synthase, glutamine synthetase 1a, Farnesyl pyrophosphate synthase, diacylglycerol, and inositol 1, 4, 5-trisphosphate, which might contributed to enhance drought tolerance or adaption in Lolium multiflorum. Interestingly, the two specific metabolic pathways, arachidonic acid and inositol phosphate metabolism including differentially accumulated proteins, were observed only in the tolerant lines. Cysteine protease cathepsin B, Cysteine proteinase, lipid transfer protein and Aquaporin were observed as drought-regulated proteins participating in hydrolysis and transmembrane transport. The activities of phospholipid hydroperoxide glutathione peroxidase, peroxiredoxin, dehydroascorbate reductase, peroxisomal ascorbate peroxidase and monodehydroascorbate reductase associated with alleviating the accumulation of reactive oxygen species in stress inducing environments. Our results showed that drought-responsive proteins were closely related to metabolic processes including signal transduction, antioxidant defenses, hydrolysis, and transmembrane transport.

  4. Genome-Wide Comparative Functional Analyses Reveal Adaptations of Salmonella sv. Newport to a Plant Colonization Lifestyle

    Directory of Open Access Journals (Sweden)

    Marcos H. de Moraes

    2018-05-01

    Full Text Available Outbreaks of salmonellosis linked to the consumption of vegetables have been disproportionately associated with strains of serovar Newport. We tested the hypothesis that strains of sv. Newport have evolved unique adaptations to persistence in plants that are not shared by strains of other Salmonella serovars. We used a genome-wide mutant screen to compare growth in tomato fruit of a sv. Newport strain from an outbreak traced to tomatoes, and a sv. Typhimurium strain from animals. Most genes in the sv. Newport strain that were selected during persistence in tomatoes were shared with, and similarly selected in, the sv. Typhimurium strain. Many of their functions are linked to central metabolism, including amino acid biosynthetic pathways, iron acquisition, and maintenance of cell structure. One exception was a greater need for the core genes involved in purine metabolism in sv. Typhimurium than in sv. Newport. We discovered a gene, papA, that was unique to sv. Newport and contributed to the strain’s fitness in tomatoes. The papA gene was present in about 25% of sv. Newport Group III genomes and generally absent from other Salmonella genomes. Homologs of papA were detected in the genomes of Pantoea, Dickeya, and Pectobacterium, members of the Enterobacteriacea family that can colonize both plants and animals.

  5. Comparative analyses of the neuron numbers and volumes of the amygdaloid complex in old and new world primates.

    Science.gov (United States)

    Carlo, C N; Stefanacci, L; Semendeferi, K; Stevens, C F

    2010-04-15

    The amygdaloid complex (AC), a key component of the limbic system, is a brain region critical for the detection and interpretation of emotionally salient information. Therefore, changes in its structure and function are likely to provide correlates of mood and emotion disorders, diseases that afflict a large portion of the human population. Previous gross comparisons of the AC in control and diseased individuals have, however, mainly failed to discover these expected correlations with diseases. We have characterized AC nuclei in different nonhuman primate species to establish a baseline for more refined comparisons between the normal and the diseased amygdala. AC nuclei volume and neuron number in 19 subdivisions are reported from 13 Old and New World primate brains, spanning five primate species, and compared with corresponding data from humans. Analysis of the four largest AC nuclei revealed that volume and neuron number of one component, the central nucleus, has a negative allometric relationship with total amygdala volume and neuron number, which is in contrast with the isometric relationship found in the other AC nuclei (for both neuron number and volume). Neuron density decreases across all four nuclei according to a single power law with an exponent of about minus one-half. Because we have included quantitative comparisons with great apes and humans, our conclusions apply to human brains, and our scaling laws can potentially be used to study the anatomical correlates of the amygdala in disorders involving pathological emotion processing. (c) 2009 Wiley-Liss, Inc.

  6. A Comparative Analyses of Granulometry, Mineral Composition and Major and Trace Element Concentrations in Soils Commonly Ingested by Humans

    Directory of Open Access Journals (Sweden)

    Veronica M. Ngole-Jeme

    2015-07-01

    Full Text Available This study compared the granulometric properties, mineralogical composition and concentrations of major and trace element oxides of commonly ingested soils (geophagic soil collected from different countries with a view of understanding how varied they may be in these properties and to understand the possible health implications of ingesting them. Soil samples were collected from three different countries (South Africa, Swaziland and Democratic Republic of Congo (DRC and their granulometric properties, concentrations of major and trace element oxides as well as mineralogical composition determined. Differences were observed in the granulometric properties of geophagic soil from the three different countries with most of them having <20% clay content. The soils also showed varied degrees of weathering with values of Chemical Index of Alteration (CIA and Chemical Index of Weathering (CIW being between 60% and 99.9% respectively. The mineral assemblages of the soils from South Africa and Swaziland were dominated by the primary minerals quartz and feldspar whereas soils from DRC had more of kaolinite, a secondary mineral than primary minerals. Soils from DRC were associated with silt, clay, Al2O3, and CIA unlike most samples from South Africa which were associated with SiO2, sand, K2O, CaO, and MgO. The soils from Swaziland were closely associated with silt, H2O and Fe2O3(t. These associations reflect the mineralogy of the samples. These soils are not likely to serve as nutrient supplements because of the low concentrations of the nutrient elements contained. The coarse texture of the samples may also result in dental destruction during mastication. Sieving of the soils before ingestion to remove coarse particles is recommended to reduce the potential health threat associated with the ingestion of coarse-textured soils.

  7. A genetic linkage map of sole (Solea solea: a tool for evolutionary and comparative analyses of exploited (flatfishes.

    Directory of Open Access Journals (Sweden)

    Eveline Diopere

    Full Text Available Linkage maps based on markers derived from genes are essential evolutionary tools for commercial marine fish to help identify genomic regions associated with complex traits and subject to selective forces at play during exploitation or selective breeding. Additionally, they allow the use of genomic information from other related species for which more detailed information is available. Sole (solea solea L. is a commercially important flatfish species in the North Sea, subject to overexploitation and showing evidence of fisheries-induced evolutionary changes in growth- and maturation-related traits. Sole would definitely benefit from a linkage map to better understand how evolution has shaped its genome structure. This study presents a linkage map of sole based on 423 single nucleotide polymorphisms derived from expressed sequence tags and 8 neutral microsatellite markers. The total map length is 1233.8 cM and consists of 38 linkage groups with a size varying between 0 to 92.1 cM. Being derived from expressed sequence tags allowed us to align the map with the genome of four model fish species, namely medaka (Oryzias latipes, Nile tilapia (Oreochromis niloticus, three-spined stickleback (Gasterosteus aculeatus and green spotted pufferfish (Tetraodon nigroviridis. This comparison revealed multiple conserved syntenic regions with all four species, and suggested that the linkage groups represent 21 putative sole chromosomes. The map was also compared to the linkage map of turbot (Scophthalmus maximus, another commercially important flatfish species and closely related to sole. For all putative sole chromosomes (except one a turbot homolog was detected, confirming the even higher degree of synteny between these two flatfish species.

  8. A Comparative Analyses of Granulometry, Mineral Composition and Major and Trace Element Concentrations in Soils Commonly Ingested by Humans

    Science.gov (United States)

    Ngole-Jeme, Veronica M.; Ekosse, Georges-Ivo E.

    2015-01-01

    This study compared the granulometric properties, mineralogical composition and concentrations of major and trace element oxides of commonly ingested soils (geophagic soil) collected from different countries with a view of understanding how varied they may be in these properties and to understand the possible health implications of ingesting them. Soil samples were collected from three different countries (South Africa, Swaziland and Democratic Republic of Congo (DRC)) and their granulometric properties, concentrations of major and trace element oxides as well as mineralogical composition determined. Differences were observed in the granulometric properties of geophagic soil from the three different countries with most of them having soils also showed varied degrees of weathering with values of Chemical Index of Alteration (CIA) and Chemical Index of Weathering (CIW) being between 60% and 99.9% respectively. The mineral assemblages of the soils from South Africa and Swaziland were dominated by the primary minerals quartz and feldspar whereas soils from DRC had more of kaolinite, a secondary mineral than primary minerals. Soils from DRC were associated with silt, clay, Al2O3, and CIA unlike most samples from South Africa which were associated with SiO2, sand, K2O, CaO, and MgO. The soils from Swaziland were closely associated with silt, H2O and Fe2O3(t). These associations reflect the mineralogy of the samples. These soils are not likely to serve as nutrient supplements because of the low concentrations of the nutrient elements contained. The coarse texture of the samples may also result in dental destruction during mastication. Sieving of the soils before ingestion to remove coarse particles is recommended to reduce the potential health threat associated with the ingestion of coarse-textured soils. PMID:26264010

  9. Comparative analyses of gene copy number and mRNA expression in GBM tumors and GBM xenografts

    Energy Technology Data Exchange (ETDEWEB)

    Hodgson, J. Graeme; Yeh, Ru-Fang; Ray, Amrita; Wang, Nicholas J.; Smirnov, Ivan; Yu, Mamie; Hariono, Sujatmi; Silber, Joachim; Feiler, Heidi S.; Gray, Joe W.; Spellman, Paul T.; Vandenberg, Scott R.; Berger, Mitchel S.; James, C. David

    2009-04-03

    Development of model systems that recapitulate the molecular heterogeneity observed among glioblastoma multiforme (GBM) tumors will expedite the testing of targeted molecular therapeutic strategies for GBM treatment. In this study, we profiled DNA copy number and mRNA expression in 21 independent GBM tumor lines maintained as subcutaneous xenografts (GBMX), and compared GBMX molecular signatures to those observed in GBM clinical specimens derived from the Cancer Genome Atlas (TCGA). The predominant copy number signature in both tumor groups was defined by chromosome-7 gain/chromosome-10 loss, a poor-prognosis genetic signature. We also observed, at frequencies similar to that detected in TCGA GBM tumors, genomic amplification and overexpression of known GBM oncogenes, such as EGFR, MDM2, CDK6, and MYCN, and novel genes, including NUP107, SLC35E3, MMP1, MMP13, and DDX1. The transcriptional signature of GBMX tumors, which was stable over multiple subcutaneous passages, was defined by overexpression of genes involved in M phase, DNA replication, and chromosome organization (MRC) and was highly similar to the poor-prognosis mitosis and cell-cycle module (MCM) in GBM. Assessment of gene expression in TCGA-derived GBMs revealed overexpression of MRC cancer genes AURKB, BIRC5, CCNB1, CCNB2, CDC2, CDK2, and FOXM1, which form a transcriptional network important for G2/M progression and/or checkpoint activation. Our study supports propagation of GBM tumors as subcutaneous xenografts as a useful approach for sustaining key molecular characteristics of patient tumors, and highlights therapeutic opportunities conferred by this GBMX tumor panel for testing targeted therapeutic strategies for GBM treatment.

  10. Vanadium NMR Chemical Shifts of (Imido)vanadium(V) Dichloride Complexes with Imidazolin-2-iminato and Imidazolidin-2-iminato Ligands: Cooperation with Quantum-Chemical Calculations and Multiple Linear Regression Analyses.

    Science.gov (United States)

    Yi, Jun; Yang, Wenhong; Sun, Wen-Hua; Nomura, Kotohiro; Hada, Masahiko

    2017-11-30

    The NMR chemical shifts of vanadium ( 51 V) in (imido)vanadium(V) dichloride complexes with imidazolin-2-iminato and imidazolidin-2-iminato ligands were calculated by the density functional theory (DFT) method with GIAO. The calculated 51 V NMR chemical shifts were analyzed by the multiple linear regression (MLR) analysis (MLRA) method with a series of calculated molecular properties. Some of calculated NMR chemical shifts were incorrect using the optimized molecular geometries of the X-ray structures. After the global minimum geometries of all of the molecules were determined, the trend of the observed chemical shifts was well reproduced by the present DFT method. The MLRA method was performed to investigate the correlation between the 51 V NMR chemical shift and the natural charge, band energy gap, and Wiberg bond index of the V═N bond. The 51 V NMR chemical shifts obtained with the present MLR model were well reproduced with a correlation coefficient of 0.97.

  11. Cost Analyses in the US and Japan: A Cross-Country Comparative Analysis Applied to the PRONOUNCE Trial in Non-Squamous Non-Small Cell Lung Cancer.

    Science.gov (United States)

    Hess, Lisa M; Rajan, Narayan; Winfree, Katherine; Davey, Peter; Ball, Mark; Knox, Hediyyih; Graham, Christopher

    2015-12-01

    Health technology assessment is not required for regulatory submission or approval in either the United States (US) or Japan. This study was designed as a cross-country evaluation of cost analyses conducted in the US and Japan based on the PRONOUNCE phase III lung cancer trial, which compared pemetrexed plus carboplatin followed by pemetrexed (PemC) versus paclitaxel plus carboplatin plus bevacizumab followed by bevacizumab (PCB). Two cost analyses were conducted in accordance with International Society For Pharmacoeconomics and Outcomes Research good research practice standards. Costs were obtained based on local pricing structures; outcomes were considered equivalent based on the PRONOUNCE trial results. Other inputs were included from the trial data (e.g., toxicity rates) or from local practice sources (e.g., toxicity management). The models were compared across key input and transferability factors. Despite differences in local input data, both models demonstrated a similar direction, with the cost of PemC being consistently lower than the cost of PCB. The variation in individual input parameters did affect some of the specific categories, such as toxicity, and impacted sensitivity analyses, with the cost differential between comparators being greater in Japan than in the US. When economic models are based on clinical trial data, many inputs and outcomes are held consistent. The alterable inputs were not in and of themselves large enough to significantly impact the results between countries, which were directionally consistent with greater variation seen in sensitivity analyses. The factors that vary across jurisdictions, even when minor, can have an impact on trial-based economic analyses. Eli Lilly and Company.

  12. Regression analysis by example

    CERN Document Server

    Chatterjee, Samprit

    2012-01-01

    Praise for the Fourth Edition: ""This book is . . . an excellent source of examples for regression analysis. It has been and still is readily readable and understandable."" -Journal of the American Statistical Association Regression analysis is a conceptually simple method for investigating relationships among variables. Carrying out a successful application of regression analysis, however, requires a balance of theoretical results, empirical rules, and subjective judgment. Regression Analysis by Example, Fifth Edition has been expanded

  13. From Rasch scores to regression

    DEFF Research Database (Denmark)

    Christensen, Karl Bang

    2006-01-01

    Rasch models provide a framework for measurement and modelling latent variables. Having measured a latent variable in a population a comparison of groups will often be of interest. For this purpose the use of observed raw scores will often be inadequate because these lack interval scale propertie....... This paper compares two approaches to group comparison: linear regression models using estimated person locations as outcome variables and latent regression models based on the distribution of the score....

  14. Quantile Regression Methods

    DEFF Research Database (Denmark)

    Fitzenberger, Bernd; Wilke, Ralf Andreas

    2015-01-01

    if the mean regression model does not. We provide a short informal introduction into the principle of quantile regression which includes an illustrative application from empirical labor market research. This is followed by briefly sketching the underlying statistical model for linear quantile regression based......Quantile regression is emerging as a popular statistical approach, which complements the estimation of conditional mean models. While the latter only focuses on one aspect of the conditional distribution of the dependent variable, the mean, quantile regression provides more detailed insights...... by modeling conditional quantiles. Quantile regression can therefore detect whether the partial effect of a regressor on the conditional quantiles is the same for all quantiles or differs across quantiles. Quantile regression can provide evidence for a statistical relationship between two variables even...

  15. Regression to Causality : Regression-style presentation influences causal attribution

    DEFF Research Database (Denmark)

    Bordacconi, Mats Joe; Larsen, Martin Vinæs

    2014-01-01

    of equivalent results presented as either regression models or as a test of two sample means. Our experiment shows that the subjects who were presented with results as estimates from a regression model were more inclined to interpret these results causally. Our experiment implies that scholars using regression...... models – one of the primary vehicles for analyzing statistical results in political science – encourage causal interpretation. Specifically, we demonstrate that presenting observational results in a regression model, rather than as a simple comparison of means, makes causal interpretation of the results...... more likely. Our experiment drew on a sample of 235 university students from three different social science degree programs (political science, sociology and economics), all of whom had received substantial training in statistics. The subjects were asked to compare and evaluate the validity...

  16. Comparative physical-chemical characterization of encapsulated lipid-based isotretinoin products assessed by particle size distribution and thermal behavior analyses

    Energy Technology Data Exchange (ETDEWEB)

    Guimaraes, Carla Aiolfi, E-mail: carlaaiolfi@usp.br [Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, SP 05508-000 (Brazil); Menaa, Farid [Department of Dermatology, School of Medicine Wuerzburg, Wuerzburg 97080 (Germany); Fluorotronics, Inc., 1425 Russ Bvld, San Diego Technology Incubator, San Diego, CA 92101 (United States); Menaa, Bouzid, E-mail: bouzid.menaa@gmail.com [Fluorotronics, Inc., 1425 Russ Bvld, San Diego Technology Incubator, San Diego, CA 92101 (United States); Quenca-Guillen, Joyce S. [Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, SP 05508-000 (Brazil); Matos, Jivaldo do Rosario [Department of Fundamental Chemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, SP 05508-000 (Brazil); Mercuri, Lucildes Pita [Department of Exact and Earth Sciences, Federal University of Sao Paulo, Diadema, SP 09972-270 (Brazil); Braz, Andre Borges [Department of Engineering of Mines and Oil, Polytechnical School, University of Sao Paulo, SP 05508-900 (Brazil); Rossetti, Fabia Cristina [Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, SP 14015-120 (Brazil); Kedor-Hackmann, Erika Rosa Maria; Santoro, Maria Ines Rocha Miritello [Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, SP 05508-000 (Brazil)

    2010-06-10

    Isotretinoin is the drug of choice for the management of severe recalcitrant nodular acne. Nevertheless, some of its physical-chemical properties are still poorly known. Hence, the aim of our study consisted to comparatively evaluate the particle size distribution (PSD) and characterize the thermal behavior of the three encapsulated isotretinoin products in oil suspension (one reference and two generics) commercialized in Brazil. Here, we show that the PSD, estimated by laser diffraction and by polarized light microscopy, differed between the generics and the reference product. However, the thermal behavior of the three products, determined by thermogravimetry (TGA), differential thermal (DTA) analyses and differential scanning calorimetry (DSC), displayed no significant changes and were more thermostable than the isotretinoin standard used as internal control. Thus, our study suggests that PSD analyses in isotretinoin lipid-based formulations should be routinely performed in order to improve their quality and bioavailability.

  17. Localisation of nursery areas based on comparative analyses of the horizontal and vertical distribution patterns of juvenile Baltic cod (Gadus morhua)

    DEFF Research Database (Denmark)

    Nielsen, J. Rasmus; Lundgren, Bo; Kristensen, Kasper

    2013-01-01

    Baltic cod are determined, and their nursery areas are localised according to the environmental factors affecting them. Comparative statistical analyses of biological, hydrographic and hydroacoustic data are carried out based on standard ICES demersal trawl surveys and special integrated trawl...... and acoustic research surveys. Horizontal distribution maps for the 2001–2010 cohorts of juvenile cod are further generated by applying a statistical log-Gaussian Cox process model to the standard trawl survey data. The analyses indicate size-dependent horizontal and distinct vertical and diurnal distribution...... in deep sea localities down to a 100 m depth and at oxygen concentrations between 2–4 ml O2.l−1. The vertical, diurnally stratified and repeated trawling and hydroacoustic target strength-depth distributions obtained from the special surveys show juvenile cod concentrations in frontal zone water layers...

  18. Understanding logistic regression analysis

    OpenAIRE

    Sperandei, Sandro

    2014-01-01

    Logistic regression is used to obtain odds ratio in the presence of more than one explanatory variable. The procedure is quite similar to multiple linear regression, with the exception that the response variable is binomial. The result is the impact of each variable on the odds ratio of the observed event of interest. The main advantage is to avoid confounding effects by analyzing the association of all variables together. In this article, we explain the logistic regression procedure using ex...

  19. Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae Using a modification of the finite supragenome model

    Directory of Open Access Journals (Sweden)

    Yu Susan

    2011-04-01

    Full Text Available Abstract Background Staphylococcus aureus is associated with a spectrum of symbiotic relationships with its human host from carriage to sepsis and is frequently associated with nosocomial and community-acquired infections, thus the differential gene content among strains is of interest. Results We sequenced three clinical strains and combined these data with 13 publically available human isolates and one bovine strain for comparative genomic analyses. All genomes were annotated using RAST, and then their gene similarities and differences were delineated. Gene clustering yielded 3,155 orthologous gene clusters, of which 2,266 were core, 755 were distributed, and 134 were unique. Individual genomes contained between 2,524 and 2,648 genes. Gene-content comparisons among all possible S. aureus strain pairs (n = 136 revealed a mean difference of 296 genes and a maximum difference of 476 genes. We developed a revised version of our finite supragenome model to estimate the size of the S. aureus supragenome (3,221 genes, with 2,245 core genes, and compared it with those of Haemophilus influenzae and Streptococcus pneumoniae. There was excellent agreement between RAST's annotations and our CDS clustering procedure providing for high fidelity metabolomic subsystem analyses to extend our comparative genomic characterization of these strains. Conclusions Using a multi-species comparative supragenomic analysis enabled by an improved version of our finite supragenome model we provide data and an interpretation explaining the relatively larger core genome of S. aureus compared to other opportunistic nasopharyngeal pathogens. In addition, we provide independent validation for the efficiency and effectiveness of our orthologous gene clustering algorithm.

  20. Introduction to regression graphics

    CERN Document Server

    Cook, R Dennis

    2009-01-01

    Covers the use of dynamic and interactive computer graphics in linear regression analysis, focusing on analytical graphics. Features new techniques like plot rotation. The authors have composed their own regression code, using Xlisp-Stat language called R-code, which is a nearly complete system for linear regression analysis and can be utilized as the main computer program in a linear regression course. The accompanying disks, for both Macintosh and Windows computers, contain the R-code and Xlisp-Stat. An Instructor's Manual presenting detailed solutions to all the problems in the book is ava

  1. Alternative Methods of Regression

    CERN Document Server

    Birkes, David

    2011-01-01

    Of related interest. Nonlinear Regression Analysis and its Applications Douglas M. Bates and Donald G. Watts ".an extraordinary presentation of concepts and methods concerning the use and analysis of nonlinear regression models.highly recommend[ed].for anyone needing to use and/or understand issues concerning the analysis of nonlinear regression models." --Technometrics This book provides a balance between theory and practice supported by extensive displays of instructive geometrical constructs. Numerous in-depth case studies illustrate the use of nonlinear regression analysis--with all data s

  2. Comparing near-infrared conventional diffuse reflectance spectroscopy and hyperspectral imaging for determination of the bulk properties of solid samples by multivariate regression: determination of Mooney viscosity and plasticity indices of natural rubber.

    Science.gov (United States)

    Juliano da Silva, Carlos; Pasquini, Celio

    2015-01-21

    Conventional reflectance spectroscopy (NIRS) and hyperspectral imaging (HI) in the near-infrared region (1000-2500 nm) are evaluated and compared, using, as the case study, the determination of relevant properties related to the quality of natural rubber. Mooney viscosity (MV) and plasticity indices (PI) (PI0 - original plasticity, PI30 - plasticity after accelerated aging, and PRI - the plasticity retention index after accelerated aging) of rubber were determined using multivariate regression models. Two hundred and eighty six samples of rubber were measured using conventional and hyperspectral near-infrared imaging reflectance instruments in the range of 1000-2500 nm. The sample set was split into regression (n = 191) and external validation (n = 95) sub-sets. Three instruments were employed for data acquisition: a line scanning hyperspectral camera and two conventional FT-NIR spectrometers. Sample heterogeneity was evaluated using hyperspectral images obtained with a resolution of 150 × 150 μm and principal component analysis. The probed sample area (5 cm(2); 24,000 pixels) to achieve representativeness was found to be equivalent to the average of 6 spectra for a 1 cm diameter probing circular window of one FT-NIR instrument. The other spectrophotometer can probe the whole sample in only one measurement. The results show that the rubber properties can be determined with very similar accuracy and precision by Partial Least Square (PLS) regression models regardless of whether HI-NIR or conventional FT-NIR produce the spectral datasets. The best Root Mean Square Errors of Prediction (RMSEPs) of external validation for MV, PI0, PI30, and PRI were 4.3, 1.8, 3.4, and 5.3%, respectively. Though the quantitative results provided by the three instruments can be considered equivalent, the hyperspectral imaging instrument presents a number of advantages, being about 6 times faster than conventional bulk spectrometers, producing robust spectral data by ensuring sample

  3. Genome-wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants

    Directory of Open Access Journals (Sweden)

    Eunyoung Seo

    2016-08-01

    Full Text Available Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR immune receptors are known play critical roles in effector-triggered immunity (ETI plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes of pepper, tomato, and potato using fixed criteria. We then compared genomic duplication and evolution features. We identified intact 267, 443, and 755 NLR-encoding genes in tomato, potato, and pepper genomes, respectively. Phylogenetic analyses and classification of Solanaceae NLRs revealed that the majority of NLR super family members fell into 14 subgroups, including a TIR-NLR (TNL subgroup and 13 non-TNL subgroups. Specific subgroups have expanded in each genome, with the expansion in pepper showing subgroup-specific physical clusters. Comparative analysis of duplications showed distinct duplication patterns within pepper and among Solanaceae plants suggesting subgroup- or species-specific gene duplication events after speciation, resulting in divergent evolution. Taken together, genome-wide analyses of NLR family members provide insights into their evolutionary history in Solanaceae. These findings also provide important foundational knowledge for understanding NLR evolution and will empower broader characterization of disease resistance genes to be used for crop breeding.

  4. COMPAR

    International Nuclear Information System (INIS)

    Kuefner, K.

    1976-01-01

    COMPAR works on FORTRAN arrays with four indices: A = A(i,j,k,l) where, for each fixed k 0 ,l 0 , only the 'plane' [A(i,j,k 0 ,l 0 ), i = 1, isub(max), j = 1, jsub(max)] is held in fast memory. Given two arrays A, B of this type COMPAR has the capability to 1) re-norm A and B ind different ways; 2) calculate the deviations epsilon defined as epsilon(i,j,k,l): =[A(i,j,k,l) - B(i,j,k,l)] / GEW(i,j,k,l) where GEW (i,j,k,l) may be chosen in three different ways; 3) calculate mean, standard deviation and maximum in the array epsilon (by several intermediate stages); 4) determine traverses in the array epsilon; 5) plot these traverses by a printer; 6) simplify plots of these traverses by the PLOTEASY-system by creating input data blocks for this system. The main application of COMPAR is given (so far) by the comparison of two- and three-dimensional multigroup neutron flux-fields. (orig.) [de

  5. Equações de regressão para estimar valores energéticos do grão de trigo e seus subprodutos para frangos de corte, a partir de análises químicas Regression equations to evaluate the energy values of wheat grain and its by-products for broiler chickens from chemical analyses

    Directory of Open Access Journals (Sweden)

    F.M.O. Borges

    2003-12-01

    que significou pouca influência da metodologia sobre essa medida. A FDN não mostrou ser melhor preditor de EM do que a FB.One experiment was run with broiler chickens, to obtain prediction equations for metabolizable energy (ME based on feedstuffs chemical analyses, and determined ME of wheat grain and its by-products, using four different methodologies. Seven wheat grain by-products were used in five treatments: wheat grain, wheat germ, white wheat flour, dark wheat flour, wheat bran for human use, wheat bran for animal use and rough wheat bran. Based on chemical analyses of crude fiber (CF, ether extract (EE, crude protein (CP, ash (AS and starch (ST of the feeds and the determined values of apparent energy (MEA, true energy (MEV, apparent corrected energy (MEAn and true energy corrected by nitrogen balance (MEVn in five treatments, prediction equations were obtained using the stepwise procedure. CF showed the best relationship with metabolizable energy values, however, this variable alone was not enough for a good estimate of the energy values (R² below 0.80. When EE and CP were included in the equations, R² increased to 0.90 or higher in most estimates. When the equations were calculated with all treatments, the equation for MEA were less precise and R² decreased. When ME data of the traditional or force-feeding methods were used separately, the precision of the equations increases (R² higher than 0.85. For MEV and MEVn values, the best multiple linear equations included CF, EE and CP (R²>0.90, independently of using all experimental data or separating by methodology. The estimates of MEVn values showed high precision and the linear coefficients (a of the equations were similar for all treatments or methodologies. Therefore, it explains the small influence of the different methodologies on this parameter. NDF was not a better predictor of ME than CF.

  6. The analysis of nonstationary time series using regression, correlation and cointegration

    DEFF Research Database (Denmark)

    Johansen, Søren

    2012-01-01

    There are simple well-known conditions for the validity of regression and correlation as statistical tools. We analyse by examples the effect of nonstationarity on inference using these methods and compare them to model based inference using the cointegrated vector autoregressive model. Finally we...... analyse some monthly data from US on interest rates as an illustration of the methods...

  7. The Analysis of Nonstationary Time Series Using Regression, Correlation and Cointegration

    Directory of Open Access Journals (Sweden)

    Søren Johansen

    2012-06-01

    Full Text Available There are simple well-known conditions for the validity of regression and correlation as statistical tools. We analyse by examples the effect of nonstationarity on inference using these methods and compare them to model based inference using the cointegrated vector autoregressive model. Finally we analyse some monthly data from US on interest rates as an illustration of the methods.

  8. A Simulation Investigation of Principal Component Regression.

    Science.gov (United States)

    Allen, David E.

    Regression analysis is one of the more common analytic tools used by researchers. However, multicollinearity between the predictor variables can cause problems in using the results of regression analyses. Problems associated with multicollinearity include entanglement of relative influences of variables due to reduced precision of estimation,…

  9. Boosted beta regression.

    Directory of Open Access Journals (Sweden)

    Matthias Schmid

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

  10. Understanding logistic regression analysis.

    Science.gov (United States)

    Sperandei, Sandro

    2014-01-01

    Logistic regression is used to obtain odds ratio in the presence of more than one explanatory variable. The procedure is quite similar to multiple linear regression, with the exception that the response variable is binomial. The result is the impact of each variable on the odds ratio of the observed event of interest. The main advantage is to avoid confounding effects by analyzing the association of all variables together. In this article, we explain the logistic regression procedure using examples to make it as simple as possible. After definition of the technique, the basic interpretation of the results is highlighted and then some special issues are discussed.

  11. Applied linear regression

    CERN Document Server

    Weisberg, Sanford

    2013-01-01

    Praise for the Third Edition ""...this is an excellent book which could easily be used as a course text...""-International Statistical Institute The Fourth Edition of Applied Linear Regression provides a thorough update of the basic theory and methodology of linear regression modeling. Demonstrating the practical applications of linear regression analysis techniques, the Fourth Edition uses interesting, real-world exercises and examples. Stressing central concepts such as model building, understanding parameters, assessing fit and reliability, and drawing conclusions, the new edition illus

  12. Applied logistic regression

    CERN Document Server

    Hosmer, David W; Sturdivant, Rodney X

    2013-01-01

     A new edition of the definitive guide to logistic regression modeling for health science and other applications This thoroughly expanded Third Edition provides an easily accessible introduction to the logistic regression (LR) model and highlights the power of this model by examining the relationship between a dichotomous outcome and a set of covariables. Applied Logistic Regression, Third Edition emphasizes applications in the health sciences and handpicks topics that best suit the use of modern statistical software. The book provides readers with state-of-

  13. Anti-Vascular Endothelial Growth Factor Comparative Effectiveness Trial for Diabetic Macular Edema: Additional Efficacy Post Hoc Analyses of a Randomized Clinical Trial.

    Science.gov (United States)

    Jampol, Lee M; Glassman, Adam R; Bressler, Neil M; Wells, John A; Ayala, Allison R

    2016-12-01

    Post hoc analyses from the Diabetic Retinopathy Clinical Research Network randomized clinical trial comparing aflibercept, bevacizumab, and ranibizumab for diabetic macular edema (DME) might influence interpretation of study results. To provide additional outcomes comparing 3 anti-vascular endothelial growth factor (VEGF) agents for DME. Post hoc analyses performed from May 3, 2016, to June 21, 2016, of a randomized clinical trial performed from August 22, 2012, to September 23, 2015, of 660 participants comparing 3 anti-VEGF treatments in eyes with center-involved DME causing vision impairment. Randomization to intravitreous aflibercept (2.0 mg), bevacizumab (1.25 mg), or ranibizumab (0.3 mg) administered up to monthly based on a structured retreatment regimen. Focal/grid laser treatment was added after 6 months for the treatment of persistent DME. Change in visual acuity (VA) area under the curve and change in central subfield thickness (CST) within subgroups based on whether an eye received laser treatment for DME during the study. Post hoc analyses were performed for 660 participants (mean [SD] age, 61 [10] years; 47% female, 65% white, 16% black or African American, 16% Hispanic, and 3% other). For eyes with an initial VA of 20/50 or worse, VA improvement was greater with aflibercept than the other agents at 1 year but superior only to bevacizumab at 2 years. Mean (SD) letter change in VA over 2 years (area under curve) was greater with aflibercept (+17.1 [9.7]) than with bevacizumab (+12.1 [9.4]; 95% CI, +1.6 to +7.3; P grid laser treatment was performed for DME, the only participants to have a substantial reduction in mean CST between 1 and 2 years were those with a baseline VA of 20/50 or worse receiving bevacizumab and laser treatment (mean [SD], -55 [108] µm; 95% CI, -82 to -28 µm; P grid laser treatment, ceiling and floor effects, or both may account for mean thickness reductions noted only in bevacizumab-treated eyes between 1 and 2 years

  14. Efficacy and tolerability of naproxen/esomeprazole magnesium tablets compared with non-specific NSAIDs and COX-2 inhibitors: a systematic review and network analyses

    Directory of Open Access Journals (Sweden)

    Datto C

    2013-02-01

    Full Text Available Catherine Datto,1 Richard Hellmund,1 Mohd Kashif Siddiqui21AstraZeneca Pharmaceuticals LP, Wilmington, DE, USA; 2HERON PVT India, Chandigarh, UT, IndiaAbstract: Non-steroidal anti-inflammatory drugs (NSAIDs, such as non-selective NSAIDs (nsNSAIDs or selective cyclooxygenase-2 (COX-2 inhibitors, are commonly prescribed for arthritic pain relief in patients with osteoarthritis (OA, rheumatoid arthritis (RA, or ankylosing spondylitis (AS. Treatment guidelines for chronic NSAID therapy include the consideration for gastroprotection for those at risk of gastric ulcers (GUs associated with the chronic NSAID therapy. The United States Food and Drug Administration has approved naproxen/esomeprazole magnesium tablets for the relief of signs and symptoms of OA, RA, and AS, and to decrease the risk of developing GUs in patients at risk of developing NSAID-associated GUs. The European Medical Association has approved this therapy for the symptomatic treatment of OA, RA, and AS in patients who are at risk of developing NSAID-associated GUs and/or duodenal ulcers, for whom treatment with lower doses of naproxen or other NSAIDs is not considered sufficient. Naproxen/esomeprazole magnesium tablets have been compared with naproxen and celecoxib for these indications in head-to-head trials. This systematic literature review and network meta-analyses of data from randomized controlled trials was performed to compare naproxen/esomeprazole magnesium tablets with a number of additional relevant comparators. For this study, an original review examined MEDLINE®, Embase®, and the Cochrane Controlled Trials Register from database start to April 14, 2009. Using the same methodology, a review update was conducted to December 21, 2009. The systematic review and network analyses showed naproxen/esomeprazole magnesium tablets have an improved upper gastrointestinal tolerability profile (dyspepsia and gastric or gastroduodenal ulcers over several active comparators (naproxen

  15. Independent contrasts and PGLS regression estimators are equivalent.

    Science.gov (United States)

    Blomberg, Simon P; Lefevre, James G; Wells, Jessie A; Waterhouse, Mary

    2012-05-01

    We prove that the slope parameter of the ordinary least squares regression of phylogenetically independent contrasts (PICs) conducted through the origin is identical to the slope parameter of the method of generalized least squares (GLSs) regression under a Brownian motion model of evolution. This equivalence has several implications: 1. Understanding the structure of the linear model for GLS regression provides insight into when and why phylogeny is important in comparative studies. 2. The limitations of the PIC regression analysis are the same as the limitations of the GLS model. In particular, phylogenetic covariance applies only to the response variable in the regression and the explanatory variable should be regarded as fixed. Calculation of PICs for explanatory variables should be treated as a mathematical idiosyncrasy of the PIC regression algorithm. 3. Since the GLS estimator is the best linear unbiased estimator (BLUE), the slope parameter estimated using PICs is also BLUE. 4. If the slope is estimated using different branch lengths for the explanatory and response variables in the PIC algorithm, the estimator is no longer the BLUE, so this is not recommended. Finally, we discuss whether or not and how to accommodate phylogenetic covariance in regression analyses, particularly in relation to the problem of phylogenetic uncertainty. This discussion is from both frequentist and Bayesian perspectives.

  16. Multilingual speaker age recognition: regression analyses on the Lwazi corpus

    CSIR Research Space (South Africa)

    Feld, M

    2009-12-01

    Full Text Available Multilinguality represents an area of significant opportunities for automatic speech-processing systems: whereas multilingual societies are commonplace, the majority of speechprocessing systems are developed with a single language in mind. As a step...

  17. Correlation and simple linear regression.

    Science.gov (United States)

    Zou, Kelly H; Tuncali, Kemal; Silverman, Stuart G

    2003-06-01

    In this tutorial article, the concepts of correlation and regression are reviewed and demonstrated. The authors review and compare two correlation coefficients, the Pearson correlation coefficient and the Spearman rho, for measuring linear and nonlinear relationships between two continuous variables. In the case of measuring the linear relationship between a predictor and an outcome variable, simple linear regression analysis is conducted. These statistical concepts are illustrated by using a data set from published literature to assess a computed tomography-guided interventional technique. These statistical methods are important for exploring the relationships between variables and can be applied to many radiologic studies.

  18. Understanding poisson regression.

    Science.gov (United States)

    Hayat, Matthew J; Higgins, Melinda

    2014-04-01

    Nurse investigators often collect study data in the form of counts. Traditional methods of data analysis have historically approached analysis of count data either as if the count data were continuous and normally distributed or with dichotomization of the counts into the categories of occurred or did not occur. These outdated methods for analyzing count data have been replaced with more appropriate statistical methods that make use of the Poisson probability distribution, which is useful for analyzing count data. The purpose of this article is to provide an overview of the Poisson distribution and its use in Poisson regression. Assumption violations for the standard Poisson regression model are addressed with alternative approaches, including addition of an overdispersion parameter or negative binomial regression. An illustrative example is presented with an application from the ENSPIRE study, and regression modeling of comorbidity data is included for illustrative purposes. Copyright 2014, SLACK Incorporated.

  19. Comparative study of reference points by dosimetric analyses for late complications after uniform external radiotherapy and high-dose-rate brachytherapy for cervical cancer

    International Nuclear Information System (INIS)

    Chen, S.-W.; Liang, J.-A.; Yeh, L.-S.; Yang, S.-N.; Shiau, A.-C.; Lin, F.-J.

    2004-01-01

    Purpose: This study aimed to correlate and compare the predictive values of rectal and bladder reference doses of uniform external beam radiotherapy without shielding and high-dose-rate intracavitary brachytherapy (HDRICB) with late sequelae in patients with uterine cervical cancer. Methods and materials: Between September 1992 and December 1998, 154 patients who survived more than 12 months after treatment were studied. Initially, they were treated with 10-MV X-rays (44 to 45 Gy/22 to 25 fractions over 4 to 5 weeks) to the whole pelvis, after which HDRICB was performed using 192 Ir remote afterloading at 1-week intervals for 4 weeks. The standard prescribed dose for each HDRICB was 6.0 Gy to point A. Patient- and treatment-related-factors were evaluated for late rectal complications using logistic regression modeling. Results: The probability of rectal complications showed better correlation of dose-response with increasing total ICRU (International Committee on Radiotherapy Units and Measurements) rectal dose. Multivariate logistic regression demonstrated a high risk of late rectal sequelae in patients who developed rectal complications (p 0.0001;relative risk, 15.06;95% CI, 2.89∼43.7) and total ICRU rectal dose greater than 16 Gy (p = 0.02;relative risk, 2.07;95% CI, 1.13∼4.55). The high risk factors for bladder complications were seen in patients who developed rectal complications (p = 0.0001;relative risk, 15.2;95% CI, 2.81∼44.9) and total ICRU bladder dose greater than 24 Gy (p = 0.02;relative risk, 8.93;95% CI, 1.79∼33.1). Conclusion: This study demonstrated the predictive value of ICRU rectal and bladder reference dosing in HDRICB for patients receiving uniform external beam radiation therapy without central shielding. Patients who had a total ICRU rectal dose greater than 16 Gy, or a total ICRU bladder dose over 24 Gy, were at risk of late sequelae

  20. How narrow-band and broad-band uvb irradiation influences the immunohistochemistry analyses of experimental animals’ skin – a comparative study. Part II

    Directory of Open Access Journals (Sweden)

    Katarzyna Borowska

    2017-09-01

    Full Text Available This is the second part of the artcle series impact narrow-band UVB radiation (NB-UVB and broad-band UVB radiation (BB-UVB on experimental animals’ skin (white Wistar female rats. The aim of this comparative study was immunohistochemistry analyses containing expression of p53 protein. Expression of p53 protein was performed on two experimental groups. One – exposed to NB-UVB; the other – exposed to BB-UVB radiation. The results indicate that p53 protein takes an active part in the process of apoptosis that is induced by both NB-UVB and BB-UVB. The results showed an increase in p53 expressing cells following BB-UVB than NB-UVB phototherapy.

  1. Should processed or raw image data be used in mammographic image quality analyses? A comparative study of three full-field digital mammography systems

    International Nuclear Information System (INIS)

    Borg, Mark; Badr, Ishmail; Royle, Gary

    2015-01-01

    The purpose of this study is to compare a number of measured image quality parameters using processed and unprocessed or raw images in two full-field direct digital units and one computed radiography mammography system. This study shows that the difference between raw and processed image data is system specific. The results have shown that there are no significant differences between raw and processed data in the mean threshold contrast values using the contrast-detail mammography phantom in all the systems investigated; however, these results cannot be generalised to all available systems. Notable differences were noted in contrast-to-noise ratios and in other tests including: response function, modulation transfer function, noise equivalent quanta, normalised noise power spectra and detective quantum efficiency as specified in IEC 62220-1-2. Consequently, the authors strongly recommend the use of raw data for all image quality analyses in digital mammography. (authors)

  2. Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses.

    Science.gov (United States)

    Rutter, William B; Salcedo, Andres; Akhunova, Alina; He, Fei; Wang, Shichen; Liang, Hanquan; Bowden, Robert L; Akhunov, Eduard

    2017-04-12

    Two opposing evolutionary constraints exert pressure on plant pathogens: one to diversify virulence factors in order to evade plant defenses, and the other to retain virulence factors critical for maintaining a compatible interaction with the plant host. To better understand how the diversified arsenals of fungal genes promote interaction with the same compatible wheat line, we performed a comparative genomic analysis of two North American isolates of Puccinia graminis f. sp. tritici (Pgt). The patterns of inter-isolate divergence in the secreted candidate effector genes were compared with the levels of conservation and divergence of plant-pathogen gene co-expression networks (GCN) developed for each isolate. Comprative genomic analyses revealed substantial level of interisolate divergence in effector gene complement and sequence divergence. Gene Ontology (GO) analyses of the conserved and unique parts of the isolate-specific GCNs identified a number of conserved host pathways targeted by both isolates. Interestingly, the degree of inter-isolate sub-network conservation varied widely for the different host pathways and was positively associated with the proportion of conserved effector candidates associated with each sub-network. While different Pgt isolates tended to exploit similar wheat pathways for infection, the mode of plant-pathogen interaction varied for different pathways with some pathways being associated with the conserved set of effectors and others being linked with the diverged or isolate-specific effectors. Our data suggest that at the intra-species level pathogen populations likely maintain divergent sets of effectors capable of targeting the same plant host pathways. This functional redundancy may play an important role in the dynamic of the "arms-race" between host and pathogen serving as the basis for diverse virulence strategies and creating conditions where mutations in certain effector groups will not have a major effect on the pathogen

  3. Comparative Analyses of Nonpathogenic, Opportunistic, and Totally Pathogenic Mycobacteria Reveal Genomic and Biochemical Variabilities and Highlight the Survival Attributes of Mycobacterium tuberculosis

    Science.gov (United States)

    Singh, Yadvir; Kohli, Sakshi; Ahmad, Javeed; Ehtesham, Nasreen Z.; Tyagi, Anil K.

    2014-01-01

    ABSTRACT Mycobacterial evolution involves various processes, such as genome reduction, gene cooption, and critical gene acquisition. Our comparative genome size analysis of 44 mycobacterial genomes revealed that the nonpathogenic (NP) genomes were bigger than those of opportunistic (OP) or totally pathogenic (TP) mycobacteria, with the TP genomes being smaller yet variable in size—their genomic plasticity reflected their ability to evolve and survive under various environmental conditions. From the 44 mycobacterial species, 13 species, representing TP, OP, and NP, were selected for genomic-relatedness analyses. Analysis of homologous protein-coding genes shared between Mycobacterium indicus pranii (NP), Mycobacterium intracellulare ATCC 13950 (OP), and Mycobacterium tuberculosis H37Rv (TP) revealed that 4,995 (i.e., ~95%) M. indicaus pranii proteins have homology with M. intracellulare, whereas the homologies among M. indicus pranii, M. intracellulare ATCC 13950, and M. tuberculosis H37Rv were significantly lower. A total of 4,153 (~79%) M. indicus pranii proteins and 4,093 (~79%) M. intracellulare ATCC 13950 proteins exhibited homology with the M. tuberculosis H37Rv proteome, while 3,301 (~82%) and 3,295 (~82%) M. tuberculosis H37Rv proteins showed homology with M. indicus pranii and M. intracellulare ATCC 13950 proteomes, respectively. Comparative metabolic pathway analyses of TP/OP/NP mycobacteria showed enzymatic plasticity between M. indicus pranii (NP) and M. intracellulare ATCC 13950 (OP), Mycobacterium avium 104 (OP), and M. tuberculosis H37Rv (TP). Mycobacterium tuberculosis seems to have acquired novel alternate pathways with possible roles in metabolism, host-pathogen interactions, virulence, and intracellular survival, and by implication some of these could be potential drug targets. PMID:25370496

  4. Comparative accident analyses for a KONVOI-type PWR using the integral codes ASTEC V1.33 and MELCOR 1.8.6

    International Nuclear Information System (INIS)

    Reinke, Nils; Erdmann, Walter; Nowack, Holger; Sonnenkalb, Martin

    2010-08-01

    In the frame of the project RS1180 funded by the German Federal Ministry for Economics and Technology (BMWi) calculations have been carried out with the integral code ASTEC V1.33 p3 developed by GRS for two postulated accidents in a nuclear power plant with KONVOI type a pressurized water reactor and compared to calculations with MELCOR 1.8.6 YU. Major objective was to assess the capability of ASTEC for application in level 2 probabilistic safety analyses (PSA). In particular, it was investigated to which extent ASTEC is able to perform such integral calculations meeting criteria with regard to both reasonable calculation time and specific boundary conditions necessary for PSA analyses. Two exemplary accidents were selected: - A transient with loss of steam generator feed water, - A small break loss of coolant accident (50 cm 2 ) in the cold leg of the coolant line connected to the pressurizer. In principle, the results demonstrate the capability of ASTEC V1.33 to carry out such PSA level 2 calculations. In addition, it has to be noted that for both ASTEC and MELCOR the requirements in view of the quality of the results leads to prolonged calculation times due to more detailed nodalisations of the whole plant. This is valid for the core region as well as for the primary circuit and for the containment. Consequently, calculation times in the order of one day to two weeks are accomplished, thereby excluding extensive parameter analyses in order to assess the sensitivity of the calculation results. Concerning the quality of the results a good agreement can be stated between ASTEC and MELCOR results in terms of global data. In detail some results are sensitive to user effects. Here, the nodalisation seems to be of major influence besides differences in modeling specific phenomena. The comparison suggests that in particular the influence of the nodalisation defined by the user and depending on the user's experience should be carefully evaluated. Since some

  5. Comparative genomic and proteomic analyses of Clostridium acetobutylicum Rh8 and its parent strain DSM 1731 revealed new understandings on butanol tolerance

    International Nuclear Information System (INIS)

    Bao, Guanhui; Dong, Hongjun; Zhu, Yan; Mao, Shaoming; Zhang, Tianrui; Zhang, Yanping; Chen, Zugen; Li, Yin

    2014-01-01

    Highlights: • Genomes of a butanol tolerant strain and its parent strain were deciphered. • Comparative genomic and proteomic was applied to understand butanol tolerance. • None differentially expressed proteins have mutations in its corresponding genes. • Mutations in ribosome might be responsible for the global difference of proteomics. - Abstract: Clostridium acetobutylicum strain Rh8 is a butanol-tolerant mutant which can tolerate up to 19 g/L butanol, 46% higher than that of its parent strain DSM 1731. We previously performed comparative cytoplasm- and membrane-proteomic analyses to understand the mechanism underlying the improved butanol tolerance of strain Rh8. In this work, we further extended this comparison to the genomic level. Compared with the genome of the parent strain DSM 1731, two insertion sites, four deletion sites, and 67 single nucleotide variations (SNVs) are distributed throughout the genome of strain Rh8. Among the 67 SNVs, 16 SNVs are located in the predicted promoters and intergenic regions; while 29 SNVs are located in the coding sequence, affecting a total of 21 proteins involved in transport, cell structure, DNA replication, and protein translation. The remaining 22 SNVs are located in the ribosomal genes, affecting a total of 12 rRNA genes in different operons. Analysis of previous comparative proteomic data indicated that none of the differentially expressed proteins have mutations in its corresponding genes. Rchange Algorithms analysis indicated that the mutations occurred in the ribosomal genes might change the ribosome RNA thermodynamic characteristics, thus affect the translation strength of these proteins. Take together, the improved butanol tolerance of C. acetobutylicum strain Rh8 might be acquired through regulating the translational process to achieve different expression strength of genes involved in butanol tolerance

  6. Comparative genomic and proteomic analyses of Clostridium acetobutylicum Rh8 and its parent strain DSM 1731 revealed new understandings on butanol tolerance

    Energy Technology Data Exchange (ETDEWEB)

    Bao, Guanhui [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China); University of Chinese Academy of Sciences, Beijing (China); Dong, Hongjun; Zhu, Yan; Mao, Shaoming [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China); Zhang, Tianrui [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China); Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin (China); Zhang, Yanping [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China); Chen, Zugen [Department of Human Genetics, School of Medicine, University of California, Los Angeles, CA 90095 (United States); Li, Yin, E-mail: yli@im.ac.cn [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China)

    2014-08-08

    Highlights: • Genomes of a butanol tolerant strain and its parent strain were deciphered. • Comparative genomic and proteomic was applied to understand butanol tolerance. • None differentially expressed proteins have mutations in its corresponding genes. • Mutations in ribosome might be responsible for the global difference of proteomics. - Abstract: Clostridium acetobutylicum strain Rh8 is a butanol-tolerant mutant which can tolerate up to 19 g/L butanol, 46% higher than that of its parent strain DSM 1731. We previously performed comparative cytoplasm- and membrane-proteomic analyses to understand the mechanism underlying the improved butanol tolerance of strain Rh8. In this work, we further extended this comparison to the genomic level. Compared with the genome of the parent strain DSM 1731, two insertion sites, four deletion sites, and 67 single nucleotide variations (SNVs) are distributed throughout the genome of strain Rh8. Among the 67 SNVs, 16 SNVs are located in the predicted promoters and intergenic regions; while 29 SNVs are located in the coding sequence, affecting a total of 21 proteins involved in transport, cell structure, DNA replication, and protein translation. The remaining 22 SNVs are located in the ribosomal genes, affecting a total of 12 rRNA genes in different operons. Analysis of previous comparative proteomic data indicated that none of the differentially expressed proteins have mutations in its corresponding genes. Rchange Algorithms analysis indicated that the mutations occurred in the ribosomal genes might change the ribosome RNA thermodynamic characteristics, thus affect the translation strength of these proteins. Take together, the improved butanol tolerance of C. acetobutylicum strain Rh8 might be acquired through regulating the translational process to achieve different expression strength of genes involved in butanol tolerance.

  7. Comparative Analyses between Skeletal Muscle miRNAomes from Large White and Min Pigs Revealed MicroRNAs Associated with Postnatal Muscle Hypertrophy.

    Science.gov (United States)

    Sheng, Xihui; Wang, Ligang; Ni, Hemin; Wang, Lixian; Qi, Xiaolong; Xing, Shuhan; Guo, Yong

    2016-01-01

    The molecular mechanism regulated by microRNAs (miRNAs) that underlies postnatal hypertrophy of skeletal muscle is complex and remains unclear. Here, the miRNAomes of longissimus dorsi muscle collected at five postnatal stages (60, 120, 150, 180, and 210 days after birth) from Large White (commercial breed) and Min pigs (indigenous breed of China) were analyzed by Illumina sequencing. We identified 734 miRNAs comprising 308 annotated miRNAs and 426 novel miRNAs, of which 307 could be considered pig-specific. Comparative analysis between two breeds suggested that 60 and 120 days after birth were important stages for skeletal muscle hypertrophy and intramuscular fat accumulation. A total of 263 miRNAs were significantly differentially expressed between two breeds at one or more developmental stages. In addition, the differentially expressed miRNAs between every two adjacent developmental stages in each breed were determined. Notably, ssc-miR-204 was significantly more highly expressed in Min pig skeletal muscle at all postnatal stages compared with its expression in Large White pig skeletal muscle. Based on gene ontology and KEGG pathway analyses of its predicted target genes, we concluded that ssc-miR-204 may exert an impact on postnatal hypertrophy of skeletal muscle by regulating myoblast proliferation. The results of this study will help in elucidating the mechanism underlying postnatal hypertrophy of skeletal muscle modulated by miRNAs, which could provide valuable information for improvement of pork quality and human myopathy.

  8. Vector regression introduced

    Directory of Open Access Journals (Sweden)

    Mok Tik

    2014-06-01

    Full Text Available This study formulates regression of vector data that will enable statistical analysis of various geodetic phenomena such as, polar motion, ocean currents, typhoon/hurricane tracking, crustal deformations, and precursory earthquake signals. The observed vector variable of an event (dependent vector variable is expressed as a function of a number of hypothesized phenomena realized also as vector variables (independent vector variables and/or scalar variables that are likely to impact the dependent vector variable. The proposed representation has the unique property of solving the coefficients of independent vector variables (explanatory variables also as vectors, hence it supersedes multivariate multiple regression models, in which the unknown coefficients are scalar quantities. For the solution, complex numbers are used to rep- resent vector information, and the method of least squares is deployed to estimate the vector model parameters after transforming the complex vector regression model into a real vector regression model through isomorphism. Various operational statistics for testing the predictive significance of the estimated vector parameter coefficients are also derived. A simple numerical example demonstrates the use of the proposed vector regression analysis in modeling typhoon paths.

  9. Antimicrobial efficacy of Curcuma zedoaria extract as assessed by linear regression compared with commercial mouthrinses Eficácia antimicrobiana do extrato de Curcuma zedoaria avaliada por regressão linear comparada com anti-sépticos bucais comerciais

    Directory of Open Access Journals (Sweden)

    Adriana Bugno

    2007-09-01

    Full Text Available The antimicrobial activity of Curcuma zedoaria (Christm Roscoe extract against some oral microorganisms was compared with the antimicrobial activity of five commercial mouthrinses in order to evaluate the potential of the plant extract to be incorporated into formulas for improving or creating antiseptic activity. The in vitro antimicrobial efficacy of plant extracts and commercial products were evaluated against Streptococcus mutans, Enterococcus faecalis, Staphylococcus aureus and Candida albicans using a linear regression method to evaluate the microbial reduction obtained in function of the exposure time, considering as effectiveness a 99.999% reduction in count of standardized microbial populations within 60 seconds. The results showed that the antimicrobial efficacy of Curcuma zedoaria (Christm Roscoe extract was similar to that of commercial products, and its incorporation into a mouthrinse could be an alternative for improving the antimicrobial efficacy of the oral product.A atividade antimicrobiana do extrato de Curcuma zedoaria (Christm Roscoe contra algumas bactérias da microbiota bucal foi comparada com a atividade antimicrobiana de cinco anti-sépticos comerciais, a fim de avaliar o potencial do extrato vegetal de ser incorporado em formulações com a finalidade de melhorar ou conferir atividade anti-séptica. A eficácia antimicrobiana in vitro do extrato vegetal e produtos comerciais foi avaliada frente a Streptococcus mutans,Enterococcus faecalis,Staphylococcus aureus e Candida albicans, utilizando o método de regressão linear para avaliar a redução microbiana obtida em função do tempo de exposição, considerando como eficácia a redução de 99,999% na contagem de população microbiana padronizada em 60 segundos. Os resultados demonstraram que a eficácia antimicrobiana do extrato de Curcuma zedoaria (Christm Roscoe foi similar a de produtos comerciais e que sua incorporação em anti-sépticos bucais pode ser uma

  10. Multicollinearity and Regression Analysis

    Science.gov (United States)

    Daoud, Jamal I.

    2017-12-01

    In regression analysis it is obvious to have a correlation between the response and predictor(s), but having correlation among predictors is something undesired. The number of predictors included in the regression model depends on many factors among which, historical data, experience, etc. At the end selection of most important predictors is something objective due to the researcher. Multicollinearity is a phenomena when two or more predictors are correlated, if this happens, the standard error of the coefficients will increase [8]. Increased standard errors means that the coefficients for some or all independent variables may be found to be significantly different from In other words, by overinflating the standard errors, multicollinearity makes some variables statistically insignificant when they should be significant. In this paper we focus on the multicollinearity, reasons and consequences on the reliability of the regression model.

  11. Minimax Regression Quantiles

    DEFF Research Database (Denmark)

    Bache, Stefan Holst

    A new and alternative quantile regression estimator is developed and it is shown that the estimator is root n-consistent and asymptotically normal. The estimator is based on a minimax ‘deviance function’ and has asymptotically equivalent properties to the usual quantile regression estimator. It is......, however, a different and therefore new estimator. It allows for both linear- and nonlinear model specifications. A simple algorithm for computing the estimates is proposed. It seems to work quite well in practice but whether it has theoretical justification is still an open question....

  12. riskRegression

    DEFF Research Database (Denmark)

    Ozenne, Brice; Sørensen, Anne Lyngholm; Scheike, Thomas

    2017-01-01

    In the presence of competing risks a prediction of the time-dynamic absolute risk of an event can be based on cause-specific Cox regression models for the event and the competing risks (Benichou and Gail, 1990). We present computationally fast and memory optimized C++ functions with an R interface...... for predicting the covariate specific absolute risks, their confidence intervals, and their confidence bands based on right censored time to event data. We provide explicit formulas for our implementation of the estimator of the (stratified) baseline hazard function in the presence of tied event times. As a by...... functionals. The software presented here is implemented in the riskRegression package....

  13. Linear regression metamodeling as a tool to summarize and present simulation model results.

    Science.gov (United States)

    Jalal, Hawre; Dowd, Bryan; Sainfort, François; Kuntz, Karen M

    2013-10-01

    Modelers lack a tool to systematically and clearly present complex model results, including those from sensitivity analyses. The objective was to propose linear regression metamodeling as a tool to increase transparency of decision analytic models and better communicate their results. We used a simplified cancer cure model to demonstrate our approach. The model computed the lifetime cost and benefit of 3 treatment options for cancer patients. We simulated 10,000 cohorts in a probabilistic sensitivity analysis (PSA) and regressed the model outcomes on the standardized input parameter values in a set of regression analyses. We used the regression coefficients to describe measures of sensitivity analyses, including threshold and parameter sensitivity analyses. We also compared the results of the PSA to deterministic full-factorial and one-factor-at-a-time designs. The regression intercept represented the estimated base-case outcome, and the other coefficients described the relative parameter uncertainty in the model. We defined simple relationships that compute the average and incremental net benefit of each intervention. Metamodeling produced outputs similar to traditional deterministic 1-way or 2-way sensitivity analyses but was more reliable since it used all parameter values. Linear regression metamodeling is a simple, yet powerful, tool that can assist modelers in communicating model characteristics and sensitivity analyses.

  14. A Combined Comparative Transcriptomic, Metabolomic, and Anatomical Analyses of Two Key Domestication Traits: Pod Dehiscence and Seed Dormancy in Pea (Pisum sp.

    Directory of Open Access Journals (Sweden)

    Petr Smýkal

    2017-04-01

    Full Text Available The origin of the agriculture was one of the turning points in human history, and a central part of this was the evolution of new plant forms, domesticated crops. Seed dispersal and germination are two key traits which have been selected to facilitate cultivation and harvesting of crops. The objective of this study was to analyze anatomical structure of seed coat and pod, identify metabolic compounds associated with water-impermeable seed coat and differentially expressed genes involved in pea seed dormancy and pod dehiscence. Comparative anatomical, metabolomics, and transcriptomic analyses were carried out on wild dormant, dehiscent Pisum elatius (JI64, VIR320 and cultivated, indehiscent Pisum sativum non-dormant (JI92, Cameor and recombinant inbred lines (RILs. Considerable differences were found in texture of testa surface, length of macrosclereids, and seed coat thickness. Histochemical and biochemical analyses indicated genotype related variation in composition and heterogeneity of seed coat cell walls within macrosclereids. Liquid chromatography–electrospray ionization/mass spectrometry and Laser desorption/ionization–mass spectrometry of separated seed coats revealed significantly higher contents of proanthocyanidins (dimer and trimer of gallocatechin, quercetin, and myricetin rhamnosides and hydroxylated fatty acids in dormant compared to non-dormant genotypes. Bulk Segregant Analysis coupled to high throughput RNA sequencing resulted in identification of 770 and 148 differentially expressed genes between dormant and non-dormant seeds or dehiscent and indehiscent pods, respectively. The expression of 14 selected dormancy-related genes was studied by qRT-PCR. Of these, expression pattern of four genes: porin (MACE-S082, peroxisomal membrane PEX14-like protein (MACE-S108, 4-coumarate CoA ligase (MACE-S131, and UDP-glucosyl transferase (MACE-S139 was in agreement in all four genotypes with Massive analysis of cDNA Ends (MACE data. In

  15. Prediction, Regression and Critical Realism

    DEFF Research Database (Denmark)

    Næss, Petter

    2004-01-01

    This paper considers the possibility of prediction in land use planning, and the use of statistical research methods in analyses of relationships between urban form and travel behaviour. Influential writers within the tradition of critical realism reject the possibility of predicting social...... phenomena. This position is fundamentally problematic to public planning. Without at least some ability to predict the likely consequences of different proposals, the justification for public sector intervention into market mechanisms will be frail. Statistical methods like regression analyses are commonly...... seen as necessary in order to identify aggregate level effects of policy measures, but are questioned by many advocates of critical realist ontology. Using research into the relationship between urban structure and travel as an example, the paper discusses relevant research methods and the kinds...

  16. Multiple linear regression analysis

    Science.gov (United States)

    Edwards, T. R.

    1980-01-01

    Program rapidly selects best-suited set of coefficients. User supplies only vectors of independent and dependent data and specifies confidence level required. Program uses stepwise statistical procedure for relating minimal set of variables to set of observations; final regression contains only most statistically significant coefficients. Program is written in FORTRAN IV for batch execution and has been implemented on NOVA 1200.

  17. Bayesian logistic regression analysis

    NARCIS (Netherlands)

    Van Erp, H.R.N.; Van Gelder, P.H.A.J.M.

    2012-01-01

    In this paper we present a Bayesian logistic regression analysis. It is found that if one wishes to derive the posterior distribution of the probability of some event, then, together with the traditional Bayes Theorem and the integrating out of nuissance parameters, the Jacobian transformation is an

  18. Linear Regression Analysis

    CERN Document Server

    Seber, George A F

    2012-01-01

    Concise, mathematically clear, and comprehensive treatment of the subject.* Expanded coverage of diagnostics and methods of model fitting.* Requires no specialized knowledge beyond a good grasp of matrix algebra and some acquaintance with straight-line regression and simple analysis of variance models.* More than 200 problems throughout the book plus outline solutions for the exercises.* This revision has been extensively class-tested.

  19. Nonlinear Regression with R

    CERN Document Server

    Ritz, Christian; Parmigiani, Giovanni

    2009-01-01

    R is a rapidly evolving lingua franca of graphical display and statistical analysis of experiments from the applied sciences. This book provides a coherent treatment of nonlinear regression with R by means of examples from a diversity of applied sciences such as biology, chemistry, engineering, medicine and toxicology.

  20. Bounded Gaussian process regression

    DEFF Research Database (Denmark)

    Jensen, Bjørn Sand; Nielsen, Jens Brehm; Larsen, Jan

    2013-01-01

    We extend the Gaussian process (GP) framework for bounded regression by introducing two bounded likelihood functions that model the noise on the dependent variable explicitly. This is fundamentally different from the implicit noise assumption in the previously suggested warped GP framework. We...... with the proposed explicit noise-model extension....

  1. and Multinomial Logistic Regression

    African Journals Online (AJOL)

    This work presented the results of an experimental comparison of two models: Multinomial Logistic Regression (MLR) and Artificial Neural Network (ANN) for classifying students based on their academic performance. The predictive accuracy for each model was measured by their average Classification Correct Rate (CCR).

  2. Mechanisms of neuroblastoma regression

    Science.gov (United States)

    Brodeur, Garrett M.; Bagatell, Rochelle

    2014-01-01

    Recent genomic and biological studies of neuroblastoma have shed light on the dramatic heterogeneity in the clinical behaviour of this disease, which spans from spontaneous regression or differentiation in some patients, to relentless disease progression in others, despite intensive multimodality therapy. This evidence also suggests several possible mechanisms to explain the phenomena of spontaneous regression in neuroblastomas, including neurotrophin deprivation, humoral or cellular immunity, loss of telomerase activity and alterations in epigenetic regulation. A better understanding of the mechanisms of spontaneous regression might help to identify optimal therapeutic approaches for patients with these tumours. Currently, the most druggable mechanism is the delayed activation of developmentally programmed cell death regulated by the tropomyosin receptor kinase A pathway. Indeed, targeted therapy aimed at inhibiting neurotrophin receptors might be used in lieu of conventional chemotherapy or radiation in infants with biologically favourable tumours that require treatment. Alternative approaches consist of breaking immune tolerance to tumour antigens or activating neurotrophin receptor pathways to induce neuronal differentiation. These approaches are likely to be most effective against biologically favourable tumours, but they might also provide insights into treatment of biologically unfavourable tumours. We describe the different mechanisms of spontaneous neuroblastoma regression and the consequent therapeutic approaches. PMID:25331179

  3. Analysing the Advantages of High Temporal Resolution Geostationary MSG SEVIRI Data Compared to Polar Operational Environmental Satellite Data for Land Surface Monitoring in Africa

    Science.gov (United States)

    Fensholt, R.; Anyamba, A.; Huber, S.; Proud, S. R.; Tucker, C. J.; Small, J.; Pak, E.; Rasmussen, M. O.; Sandholt, I.; Shisanya, C.

    2011-01-01

    Since 1972, satellite remote sensing of the environment has been dominated by polar-orbiting sensors providing useful data for monitoring the earth s natural resources. However their observation and monitoring capacity are inhibited by daily to monthly looks for any given ground surface which often is obscured by frequent and persistent cloud cover creating large gaps in time series measurements. The launch of the Meteosat Second Generation (MSG) satellite into geostationary orbit has opened new opportunities for land surface monitoring. The Spinning Enhanced Visible and Infrared Imager (SEVIRI) instrument on-board MSG with an imaging capability every 15 minutes which is substantially greater than any temporal resolution that can be obtained from existing polar operational environmental satellites (POES) systems currently in use for environmental monitoring. Different areas of the African continent were affected by droughts and floods in 2008 caused by periods of abnormally low and high rainfall, respectively. Based on the effectiveness of monitoring these events from Earth Observation (EO) data the current analyses show that the new generation of geostationary remote sensing data can provide higher temporal resolution cloud-free (less than 5 days) measurements of the environment as compared to existing POES systems. SEVIRI MSG 5-day continental scale composites will enable rapid assessment of environmental conditions and improved early warning of disasters for the African continent such as flooding or droughts. The high temporal resolution geostationary data will complement existing higher spatial resolution polar-orbiting satellite data for various dynamic environmental and natural resource applications of terrestrial ecosystems.

  4. Comparative proteomic and metabolomic analyses reveal mechanisms of improved cold stress tolerance in bermudagrass (Cynodon dactylon (L.) Pers.) by exogenous calcium.

    Science.gov (United States)

    Shi, Haitao; Ye, Tiantian; Zhong, Bao; Liu, Xun; Chan, Zhulong

    2014-11-01

    As an important second messenger, calcium is involved in plant cold stress response, including chilling (Cynodon dactylon (L.) Pers.). Physiological analyses showed that CaCl2 treatment alleviated the reactive oxygen species (ROS) burst and cell damage triggered by chilling stress, via activating antioxidant enzymes, non-enzymatic glutathione antioxidant pool, while EGTA treatment had the opposite effects. Additionally, comparative proteomic analysis identified 51 differentially expressed proteins that were enriched in redox, tricarboxylicacid cycle, glycolysis, photosynthesis, oxidative pentose phosphate pathway, and amino acid metabolisms. Consistently, 42 metabolites including amino acids, organic acids, sugars, and sugar alcohols were regulated by CaCl2 treatment under control and cold stress conditions, further confirming the common modulation of CaCl2 treatment in carbon metabolites and amino acid metabolism. Taken together, this study reported first evidence of the essential and protective roles of endogenous and exogenous calcium in bermudagrass response to cold stress, partially via activation of the antioxidants and modulation of several differentially expressed proteins and metabolic homeostasis in the process of cold acclimation. © 2014 Institute of Botany, Chinese Academy of Sciences.

  5. Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation

    Science.gov (United States)

    Wisniewski-Dyé, Florence; Lozano, Luis; Acosta-Cruz, Erika; Borland, Stéphanie; Drogue, Benoît; Prigent-Combaret, Claire; Rouy, Zoé; Barbe, Valérie; Mendoza Herrera, Alberto; González, Victor; Mavingui, Patrick

    2012-01-01

    Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. In this study, an additional genome of an A. brasilense strain, isolated from maize grown on an alkaline soil in the northeast of Mexico, strain CBG497, was obtained. Comparative genomic analyses were performed on this new genome and three other genomes (A. brasilense Sp245, A. lipoferum 4B and Azospirillum sp. B510). The Azospirillum core genome was established and consists of 2,328 proteins, representing between 30% to 38% of the total encoded proteins within a genome. It is mainly chromosomally-encoded and contains 74% of genes of ancestral origin shared with some aquatic relatives. The non-ancestral part of the core genome is enriched in genes involved in signal transduction, in transport and in metabolism of carbohydrates and amino-acids, and in surface properties features linked to adaptation in fluctuating environments, such as soil and rhizosphere. Many genes involved in colonization of plant roots, plant-growth promotion (such as those involved in phytohormone biosynthesis), and properties involved in rhizosphere adaptation (such as catabolism of phenolic compounds, uptake of iron) are restricted to a particular strain and/or species, strongly suggesting niche-specific adaptation. PMID:24705077

  6. Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation

    Directory of Open Access Journals (Sweden)

    Victor González

    2012-09-01

    Full Text Available Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. In this study, an additional genome of an A. brasilense strain, isolated from maize grown on an alkaline soil in the northeast of Mexico, strain CBG497, was obtained. Comparative genomic analyses were performed on this new genome and three other genomes (A. brasilense Sp245, A. lipoferum 4B and Azospirillum sp. B510. The Azospirillum core genome was established and consists of 2,328 proteins, representing between 30% to 38% of the total encoded proteins within a genome. It is mainly chromosomally-encoded and contains 74% of genes of ancestral origin shared with some aquatic relatives. The non-ancestral part of the core genome is enriched in genes involved in signal transduction, in transport and in metabolism of carbohydrates and amino-acids, and in surface properties features linked to adaptation in fluctuating environments, such as soil and rhizosphere. Many genes involved in colonization of plant roots, plant-growth promotion (such as those involved in phytohormone biosynthesis, and properties involved in rhizosphere adaptation (such as catabolism of phenolic compounds, uptake of iron are restricted to a particular strain and/or species, strongly suggesting niche-specific adaptation.

  7. Analyses of the probiotic property and stress resistance-related genes of Lactococcus lactis subsp. lactis NCDO 2118 through comparative genomics and in vitro assays.

    Science.gov (United States)

    Oliveira, Letícia C; Saraiva, Tessália D L; Silva, Wanderson M; Pereira, Ulisses P; Campos, Bruno C; Benevides, Leandro J; Rocha, Flávia S; Figueiredo, Henrique C P; Azevedo, Vasco; Soares, Siomar C

    2017-01-01

    Lactococcus lactis subsp. lactis NCDO 2118 was recently reported to alleviate colitis symptoms via its anti-inflammatory and immunomodulatory activities, which are exerted by exported proteins that are not produced by L. lactis subsp. lactis IL1403. Here, we used in vitro and in silico approaches to characterize the genomic structure, the safety aspects, and the immunomodulatory activity of this strain. Through comparative genomics, we identified genomic islands, phage regions, bile salt and acid stress resistance genes, bacteriocins, adhesion-related and antibiotic resistance genes, and genes encoding proteins that are putatively secreted, expressed in vitro and absent from IL1403. The high degree of similarity between all Lactococcus suggests that the Symbiotic Islands commonly shared by both NCDO 2118 and KF147 may be responsible for their close relationship and their adaptation to plants. The predicted bacteriocins may play an important role against the invasion of competing strains. The genes related to the acid and bile salt stresses may play important roles in gastrointestinal tract survival, whereas the adhesion proteins are important for persistence in the gut, culminating in the competitive exclusion of other bacteria. Finally, the five secreted and expressed proteins may be important targets for studies of new anti-inflammatory and immunomodulatory proteins. Altogether, the analyses performed here highlight the potential use of this strain as a target for the future development of probiotic foods.

  8. Subset selection in regression

    CERN Document Server

    Miller, Alan

    2002-01-01

    Originally published in 1990, the first edition of Subset Selection in Regression filled a significant gap in the literature, and its critical and popular success has continued for more than a decade. Thoroughly revised to reflect progress in theory, methods, and computing power, the second edition promises to continue that tradition. The author has thoroughly updated each chapter, incorporated new material on recent developments, and included more examples and references. New in the Second Edition:A separate chapter on Bayesian methodsComplete revision of the chapter on estimationA major example from the field of near infrared spectroscopyMore emphasis on cross-validationGreater focus on bootstrappingStochastic algorithms for finding good subsets from large numbers of predictors when an exhaustive search is not feasible Software available on the Internet for implementing many of the algorithms presentedMore examplesSubset Selection in Regression, Second Edition remains dedicated to the techniques for fitting...

  9. Regression in organizational leadership.

    Science.gov (United States)

    Kernberg, O F

    1979-02-01

    The choice of good leaders is a major task for all organizations. Inforamtion regarding the prospective administrator's personality should complement questions regarding his previous experience, his general conceptual skills, his technical knowledge, and the specific skills in the area for which he is being selected. The growing psychoanalytic knowledge about the crucial importance of internal, in contrast to external, object relations, and about the mutual relationships of regression in individuals and in groups, constitutes an important practical tool for the selection of leaders.

  10. Classification and regression trees

    CERN Document Server

    Breiman, Leo; Olshen, Richard A; Stone, Charles J

    1984-01-01

    The methodology used to construct tree structured rules is the focus of this monograph. Unlike many other statistical procedures, which moved from pencil and paper to calculators, this text's use of trees was unthinkable before computers. Both the practical and theoretical sides have been developed in the authors' study of tree methods. Classification and Regression Trees reflects these two sides, covering the use of trees as a data analysis method, and in a more mathematical framework, proving some of their fundamental properties.

  11. Comparison of Classical Linear Regression and Orthogonal Regression According to the Sum of Squares Perpendicular Distances

    OpenAIRE

    KELEŞ, Taliha; ALTUN, Murat

    2016-01-01

    Regression analysis is a statistical technique for investigating and modeling the relationship between variables. The purpose of this study was the trivial presentation of the equation for orthogonal regression (OR) and the comparison of classical linear regression (CLR) and OR techniques with respect to the sum of squared perpendicular distances. For that purpose, the analyses were shown by an example. It was found that the sum of squared perpendicular distances of OR is smaller. Thus, it wa...

  12. Logistic regression models

    CERN Document Server

    Hilbe, Joseph M

    2009-01-01

    This book really does cover everything you ever wanted to know about logistic regression … with updates available on the author's website. Hilbe, a former national athletics champion, philosopher, and expert in astronomy, is a master at explaining statistical concepts and methods. Readers familiar with his other expository work will know what to expect-great clarity.The book provides considerable detail about all facets of logistic regression. No step of an argument is omitted so that the book will meet the needs of the reader who likes to see everything spelt out, while a person familiar with some of the topics has the option to skip "obvious" sections. The material has been thoroughly road-tested through classroom and web-based teaching. … The focus is on helping the reader to learn and understand logistic regression. The audience is not just students meeting the topic for the first time, but also experienced users. I believe the book really does meet the author's goal … .-Annette J. Dobson, Biometric...

  13. Comparative Analyses of Tomato yellow leaf curl virus C4 Protein-Interacting Host Proteins in Healthy and Infected Tomato Tissues

    Directory of Open Access Journals (Sweden)

    Namgyu Kim

    2016-10-01

    Full Text Available Tomato yellow leaf curl virus (TYLCV, a member of the genus Begomovirus, is one of the most important viruses of cultivated tomatoes worldwide, mainly causing yellowing and curling of leaves with stunting in plants. TYLCV causes severe problems in sub-tropical and tropical countries, as well as in Korea. However, the mechanism of TYLCV infection remains unclear, although the function of each viral component has been identified. TYLCV C4 codes for a small protein involved in various cellular functions, including symptom determination, gene silencing, viral movement, and induction of the plant defense response. In this study, through yeast-two hybrid screenings, we identified TYLCV C4-interacting host proteins from both healthy and symptom-exhibiting tomato tissues, to determine the role of TYLCV C4 proteins in the infection processes. Comparative analyses of 28 proteins from healthy tissues and 36 from infected tissues showing interactions with TYLCV C4 indicated that TYLCV C4 mainly interacts with host proteins involved in translation, ubiquitination, and plant defense, and most interacting proteins differed between the two tissues but belong to similar molecular functional categories. Four proteins—two ribosomal proteins, S-adenosyl-L-homocysteine hydrolase, and 14-3-3 family protein—were detected in both tissues. Furthermore, the identified proteins in symptom-exhibiting tissues showed greater involvement in plant defenses. Some are key regulators, such as receptor-like kinases and pathogenesis-related proteins, of plant defenses. Thus, TYLCV C4 may contribute to the suppression of host defense during TYLCV infection and be involved in ubiquitination for viral infection.

  14. Comparative live-cell imaging analyses of SPA-2, BUD-6 and BNI-1 in Neurospora crassa reveal novel features of the filamentous fungal polarisome.

    Directory of Open Access Journals (Sweden)

    Alexander Lichius

    Full Text Available A key multiprotein complex involved in regulating the actin cytoskeleton and secretory machinery required for polarized growth in fungi, is the polarisome. Recognized core constituents in budding yeast are the proteins Spa2, Pea2, Aip3/Bud6, and the key effector Bni1. Multicellular fungi display a more complex polarized morphogenesis than yeasts, suggesting that the filamentous fungal polarisome might fulfill additional functions. In this study, we compared the subcellular organization and dynamics of the putative polarisome components BUD-6 and BNI-1 with those of the bona fide polarisome marker SPA-2 at various developmental stages of Neurospora crassa. All three proteins exhibited a yeast-like polarisome configuration during polarized germ tube growth, cell fusion, septal pore plugging and tip repolarization. However, the localization patterns of all three proteins showed spatiotemporally distinct characteristics during the establishment of new polar axes, septum formation and cytokinesis, and maintained hyphal tip growth. Most notably, in vegetative hyphal tips BUD-6 accumulated as a subapical cloud excluded from the Spitzenkörper (Spk, whereas BNI-1 and SPA-2 partially colocalized with the Spk and the tip apex. Novel roles during septal plugging and cytokinesis, connected to the reinitiation of tip growth upon physical injury and conidial maturation, were identified for BUD-6 and BNI-1, respectively. Phenotypic analyses of gene deletion mutants revealed additional functions for BUD-6 and BNI-1 in cell fusion regulation, and the maintenance of Spk integrity. Considered together, our findings reveal novel polarisome-independent functions of BUD-6 and BNI-1 in Neurospora, but also suggest that all three proteins cooperate at plugged septal pores, and their complex arrangement within the apical dome of mature hypha might represent a novel aspect of filamentous fungal polarisome architecture.

  15. Quantile Regression With Measurement Error

    KAUST Repository

    Wei, Ying

    2009-08-27

    Regression quantiles can be substantially biased when the covariates are measured with error. In this paper we propose a new method that produces consistent linear quantile estimation in the presence of covariate measurement error. The method corrects the measurement error induced bias by constructing joint estimating equations that simultaneously hold for all the quantile levels. An iterative EM-type estimation algorithm to obtain the solutions to such joint estimation equations is provided. The finite sample performance of the proposed method is investigated in a simulation study, and compared to the standard regression calibration approach. Finally, we apply our methodology to part of the National Collaborative Perinatal Project growth data, a longitudinal study with an unusual measurement error structure. © 2009 American Statistical Association.

  16. Evaluation of Linear Regression Simultaneous Myoelectric Control Using Intramuscular EMG.

    Science.gov (United States)

    Smith, Lauren H; Kuiken, Todd A; Hargrove, Levi J

    2016-04-01

    The objective of this study was to evaluate the ability of linear regression models to decode patterns of muscle coactivation from intramuscular electromyogram (EMG) and provide simultaneous myoelectric control of a virtual 3-DOF wrist/hand system. Performance was compared to the simultaneous control of conventional myoelectric prosthesis methods using intramuscular EMG (parallel dual-site control)-an approach that requires users to independently modulate individual muscles in the residual limb, which can be challenging for amputees. Linear regression control was evaluated in eight able-bodied subjects during a virtual Fitts' law task and was compared to performance of eight subjects using parallel dual-site control. An offline analysis also evaluated how different types of training data affected prediction accuracy of linear regression control. The two control systems demonstrated similar overall performance; however, the linear regression method demonstrated improved performance for targets requiring use of all three DOFs, whereas parallel dual-site control demonstrated improved performance for targets that required use of only one DOF. Subjects using linear regression control could more easily activate multiple DOFs simultaneously, but often experienced unintended movements when trying to isolate individual DOFs. Offline analyses also suggested that the method used to train linear regression systems may influence controllability. Linear regression myoelectric control using intramuscular EMG provided an alternative to parallel dual-site control for 3-DOF simultaneous control at the wrist and hand. The two methods demonstrated different strengths in controllability, highlighting the tradeoff between providing simultaneous control and the ability to isolate individual DOFs when desired.

  17. SEPARATION PHENOMENA LOGISTIC REGRESSION

    Directory of Open Access Journals (Sweden)

    Ikaro Daniel de Carvalho Barreto

    2014-03-01

    Full Text Available This paper proposes an application of concepts about the maximum likelihood estimation of the binomial logistic regression model to the separation phenomena. It generates bias in the estimation and provides different interpretations of the estimates on the different statistical tests (Wald, Likelihood Ratio and Score and provides different estimates on the different iterative methods (Newton-Raphson and Fisher Score. It also presents an example that demonstrates the direct implications for the validation of the model and validation of variables, the implications for estimates of odds ratios and confidence intervals, generated from the Wald statistics. Furthermore, we present, briefly, the Firth correction to circumvent the phenomena of separation.

  18. Adaptive metric kernel regression

    DEFF Research Database (Denmark)

    Goutte, Cyril; Larsen, Jan

    2000-01-01

    Kernel smoothing is a widely used non-parametric pattern recognition technique. By nature, it suffers from the curse of dimensionality and is usually difficult to apply to high input dimensions. In this contribution, we propose an algorithm that adapts the input metric used in multivariate...... regression by minimising a cross-validation estimate of the generalisation error. This allows to automatically adjust the importance of different dimensions. The improvement in terms of modelling performance is illustrated on a variable selection task where the adaptive metric kernel clearly outperforms...

  19. Adaptive Metric Kernel Regression

    DEFF Research Database (Denmark)

    Goutte, Cyril; Larsen, Jan

    1998-01-01

    Kernel smoothing is a widely used nonparametric pattern recognition technique. By nature, it suffers from the curse of dimensionality and is usually difficult to apply to high input dimensions. In this paper, we propose an algorithm that adapts the input metric used in multivariate regression...... by minimising a cross-validation estimate of the generalisation error. This allows one to automatically adjust the importance of different dimensions. The improvement in terms of modelling performance is illustrated on a variable selection task where the adaptive metric kernel clearly outperforms the standard...

  20. Aid and growth regressions

    DEFF Research Database (Denmark)

    Hansen, Henrik; Tarp, Finn

    2001-01-01

    This paper examines the relationship between foreign aid and growth in real GDP per capita as it emerges from simple augmentations of popular cross country growth specifications. It is shown that aid in all likelihood increases the growth rate, and this result is not conditional on ‘good’ policy....... investment. We conclude by stressing the need for more theoretical work before this kind of cross-country regressions are used for policy purposes.......This paper examines the relationship between foreign aid and growth in real GDP per capita as it emerges from simple augmentations of popular cross country growth specifications. It is shown that aid in all likelihood increases the growth rate, and this result is not conditional on ‘good’ policy...

  1. A comparative study of first and all-author co-citation counting, and two different matrix generation approaches applied for author co-citation analyses

    DEFF Research Database (Denmark)

    Schneider, Jesper Wiborg; Larsen, Birger; Ingwersen, Peter

    2009-01-01

    XML documents extracted from the IEEE collection. These data allow the construction of ad-hoc citation indexes, which enables us to carry out the hitherto largest all-author co-citation study. Four ACA are made, combining the different units of analyses with the different matrix generation approaches...

  2. Prediction of radiation levels in residences: A methodological comparison of CART [Classification and Regression Tree Analysis] and conventional regression

    International Nuclear Information System (INIS)

    Janssen, I.; Stebbings, J.H.

    1990-01-01

    In environmental epidemiology, trace and toxic substance concentrations frequently have very highly skewed distributions ranging over one or more orders of magnitude, and prediction by conventional regression is often poor. Classification and Regression Tree Analysis (CART) is an alternative in such contexts. To compare the techniques, two Pennsylvania data sets and three independent variables are used: house radon progeny (RnD) and gamma levels as predicted by construction characteristics in 1330 houses; and ∼200 house radon (Rn) measurements as predicted by topographic parameters. CART may identify structural variables of interest not identified by conventional regression, and vice versa, but in general the regression models are similar. CART has major advantages in dealing with other common characteristics of environmental data sets, such as missing values, continuous variables requiring transformations, and large sets of potential independent variables. CART is most useful in the identification and screening of independent variables, greatly reducing the need for cross-tabulations and nested breakdown analyses. There is no need to discard cases with missing values for the independent variables because surrogate variables are intrinsic to CART. The tree-structured approach is also independent of the scale on which the independent variables are measured, so that transformations are unnecessary. CART identifies important interactions as well as main effects. The major advantages of CART appear to be in exploring data. Once the important variables are identified, conventional regressions seem to lead to results similar but more interpretable by most audiences. 12 refs., 8 figs., 10 tabs

  3. Use of probabilistic weights to enhance linear regression myoelectric control

    Science.gov (United States)

    Smith, Lauren H.; Kuiken, Todd A.; Hargrove, Levi J.

    2015-12-01

    Objective. Clinically available prostheses for transradial amputees do not allow simultaneous myoelectric control of degrees of freedom (DOFs). Linear regression methods can provide simultaneous myoelectric control, but frequently also result in difficulty with isolating individual DOFs when desired. This study evaluated the potential of using probabilistic estimates of categories of gross prosthesis movement, which are commonly used in classification-based myoelectric control, to enhance linear regression myoelectric control. Approach. Gaussian models were fit to electromyogram (EMG) feature distributions for three movement classes at each DOF (no movement, or movement in either direction) and used to weight the output of linear regression models by the probability that the user intended the movement. Eight able-bodied and two transradial amputee subjects worked in a virtual Fitts’ law task to evaluate differences in controllability between linear regression and probability-weighted regression for an intramuscular EMG-based three-DOF wrist and hand system. Main results. Real-time and offline analyses in able-bodied subjects demonstrated that probability weighting improved performance during single-DOF tasks (p < 0.05) by preventing extraneous movement at additional DOFs. Similar results were seen in experiments with two transradial amputees. Though goodness-of-fit evaluations suggested that the EMG feature distributions showed some deviations from the Gaussian, equal-covariance assumptions used in this experiment, the assumptions were sufficiently met to provide improved performance compared to linear regression control. Significance. Use of probability weights can improve the ability to isolate individual during linear regression myoelectric control, while maintaining the ability to simultaneously control multiple DOFs.

  4. Fédéralisme et droits des LGBT aux États-Unis et au Canada : analyse comparatives des politiques

    Directory of Open Access Journals (Sweden)

    Miriam Smith

    2014-12-01

    Full Text Available L’article examine le militantisme LGBT et les résultats des politiques en matière de droit pénal et du mariage entre personnes de même sexe de 1969 à aujourd’hui, dans le cadre d’une analyse comparée du fédéralisme aux États-Unis et au Canada. Nous soutiendrons que le fédéralisme a grandement façonné les politiques publiques relatives aux droits des LGBT. Dans le régime américain, le potentiel d’expansion du fédéralisme a favorisé les changements graduels de politiques dans les États et, parallèlement, les multiples points de véto créés par le système de séparation des pouvoirs conjugués aux compétences conférés aux États dans d’importants domaines de politiques ont entravé ces changements de politiques. Dans le régime canadien, la centralisation des mécanismes de protection des droits de la personne dans la Charte de même que la dynamique descendante de l’exercice du pouvoir dans le régime parlementaire de type Westminster ont facilité les changements de politiques. Le fédéralisme est souvent perçu comme un obstacle à l’adoption de politiques progressistes. La répartition des pouvoirs entrave l’élaboration de politiques cohérentes et prête le flanc à la prolifération de vétos dont peuvent se prévaloir des groupes influents pour freiner le changement. Les critiques de cette perspective arguent depuis longtemps que, même si le fédéralisme multiplie les points de véto, il présente aussi de nombreuses possibilités d’innovation. Ils font valoir que les groupes ont plus de poids dans les régimes fédéraux puisqu’ils peuvent exercer leur influence à deux paliers de gouvernement plutôt qu’à un. Ainsi, un groupe qui ne réussit pas à se faire entendre à l’un des paliers pourra tenter sa chance au second et pourra même dresser un palier contre l’autre pour atteindre ses objectifs stratégiques.

  5. The Application of Classical and Neural Regression Models for the Valuation of Residential Real Estate

    Directory of Open Access Journals (Sweden)

    Mach Łukasz

    2017-06-01

    Full Text Available The research process aimed at building regression models, which helps to valuate residential real estate, is presented in the following article. Two widely used computational tools i.e. the classical multiple regression and regression models of artificial neural networks were used in order to build models. An attempt to define the utilitarian usefulness of the above-mentioned tools and comparative analysis of them is the aim of the conducted research. Data used for conducting analyses refers to the secondary transactional residential real estate market.

  6. Comparative proteomic analyses reveal that FlbA down-regulates gliT expression and SOD activity in Aspergillus fumigatus.

    Science.gov (United States)

    Shin, Kwang-Soo; Park, Hee-Soo; Kim, Young-Hwan; Yu, Jae-Hyuk

    2013-07-11

    FlbA is a regulator of G-protein signaling protein that plays a central role in attenuating heterotrimeric G-protein mediated vegetative growth signaling in Aspergillus. The deletion of flbA (∆flbA) in the opportunistic human pathogen Aspergillus fumigatus results in accelerated cell death and autolysis in submerged culture. To further investigate the effects of ∆flbA on intracellular protein levels we carried out 2-D proteome analyses of 2-day old submerged cultures of ∆flbA and wild type (WT) strains and observed 160 differentially expressed proteins. Via nano-LC-ESI-MS/MS analyses, we revealed the identity of 10 and 2 proteins exhibiting high and low level accumulation, respectively, in ∆flbA strain. Notably, the GliT protein is accumulated at about 1800-fold higher levels in ∆flbA than WT. Moreover, GliT is secreted at high levels from ∆flbA strain, whereas Sod1 (superoxide dismutase) is secreted at a higher level in WT. Northern blot analyses reveal that ∆flbA results in elevated accumulation of gliT mRNA. Consequently, ∆flbA strain exhibits enhanced tolerance to gliotoxin toxicity. Finally, ∆flbA strain displayed enhanced SOD activity and elevated resistance to menadione and paraquat. In summary, FlbA-mediated signaling control negatively affects cellular responses associated with detoxification of reactive oxygen species and of exogenous gliotoxin in A. fumigatus. Regulator of G protein Signaling (RGS) proteins play crucial roles in fundamental biological processes in filamentous fungi. FlbA is the first studied filamentous fungal RGS protein, yet much remains to be understood about its roles in the opportunistic human pathogen Aspergillus fumigatus. In the present study, we examined the effects of the deletion of flbA using comprehensive analyses of the intra- and extracellular proteomes of A. fumigatus wild type and the flbA deletion mutant. Via MS analyses, we identified 10 proteins exhibiting high level accumulation in the flbA deletion

  7. Measurement Error in Education and Growth Regressions

    NARCIS (Netherlands)

    Portela, M.; Teulings, C.N.; Alessie, R.

    The perpetual inventory method used for the construction of education data per country leads to systematic measurement error. This paper analyses the effect of this measurement error on GDP regressions. There is a systematic difference in the education level between census data and observations

  8. Measurement error in education and growth regressions

    NARCIS (Netherlands)

    Portela, Miguel; Teulings, Coen; Alessie, R.

    2004-01-01

    The perpetual inventory method used for the construction of education data per country leads to systematic measurement error. This paper analyses the effect of this measurement error on GDP regressions. There is a systematic difference in the education level between census data and observations

  9. Panel data specifications in nonparametric kernel regression

    DEFF Research Database (Denmark)

    Czekaj, Tomasz Gerard; Henningsen, Arne

    parametric panel data estimators to analyse the production technology of Polish crop farms. The results of our nonparametric kernel regressions generally differ from the estimates of the parametric models but they only slightly depend on the choice of the kernel functions. Based on economic reasoning, we...

  10. A comparison of Cox and logistic regression for use in genome-wide association studies of cohort and case-cohort design.

    Science.gov (United States)

    Staley, James R; Jones, Edmund; Kaptoge, Stephen; Butterworth, Adam S; Sweeting, Michael J; Wood, Angela M; Howson, Joanna M M

    2017-06-01

    Logistic regression is often used instead of Cox regression to analyse genome-wide association studies (GWAS) of single-nucleotide polymorphisms (SNPs) and disease outcomes with cohort and case-cohort designs, as it is less computationally expensive. Although Cox and logistic regression models have been compared previously in cohort studies, this work does not completely cover the GWAS setting nor extend to the case-cohort study design. Here, we evaluated Cox and logistic regression applied to cohort and case-cohort genetic association studies using simulated data and genetic data from the EPIC-CVD study. In the cohort setting, there was a modest improvement in power to detect SNP-disease associations using Cox regression compared with logistic regression, which increased as the disease incidence increased. In contrast, logistic regression had more power than (Prentice weighted) Cox regression in the case-cohort setting. Logistic regression yielded inflated effect estimates (assuming the hazard ratio is the underlying measure of association) for both study designs, especially for SNPs with greater effect on disease. Given logistic regression is substantially more computationally efficient than Cox regression in both settings, we propose a two-step approach to GWAS in cohort and case-cohort studies. First to analyse all SNPs with logistic regression to identify associated variants below a pre-defined P-value threshold, and second to fit Cox regression (appropriately weighted in case-cohort studies) to those identified SNPs to ensure accurate estimation of association with disease.

  11. Canonical variate regression.

    Science.gov (United States)

    Luo, Chongliang; Liu, Jin; Dey, Dipak K; Chen, Kun

    2016-07-01

    In many fields, multi-view datasets, measuring multiple distinct but interrelated sets of characteristics on the same set of subjects, together with data on certain outcomes or phenotypes, are routinely collected. The objective in such a problem is often two-fold: both to explore the association structures of multiple sets of measurements and to develop a parsimonious model for predicting the future outcomes. We study a unified canonical variate regression framework to tackle the two problems simultaneously. The proposed criterion integrates multiple canonical correlation analysis with predictive modeling, balancing between the association strength of the canonical variates and their joint predictive power on the outcomes. Moreover, the proposed criterion seeks multiple sets of canonical variates simultaneously to enable the examination of their joint effects on the outcomes, and is able to handle multivariate and non-Gaussian outcomes. An efficient algorithm based on variable splitting and Lagrangian multipliers is proposed. Simulation studies show the superior performance of the proposed approach. We demonstrate the effectiveness of the proposed approach in an [Formula: see text] intercross mice study and an alcohol dependence study. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Detecting overdispersion in count data: A zero-inflated Poisson regression analysis

    Science.gov (United States)

    Afiqah Muhamad Jamil, Siti; Asrul Affendi Abdullah, M.; Kek, Sie Long; Nor, Maria Elena; Mohamed, Maryati; Ismail, Norradihah

    2017-09-01

    This study focusing on analysing count data of butterflies communities in Jasin, Melaka. In analysing count dependent variable, the Poisson regression model has been known as a benchmark model for regression analysis. Continuing from the previous literature that used Poisson regression analysis, this study comprising the used of zero-inflated Poisson (ZIP) regression analysis to gain acute precision on analysing the count data of butterfly communities in Jasin, Melaka. On the other hands, Poisson regression should be abandoned in the favour of count data models, which are capable of taking into account the extra zeros explicitly. By far, one of the most popular models include ZIP regression model. The data of butterfly communities which had been called as the number of subjects in this study had been taken in Jasin, Melaka and consisted of 131 number of subjects visits Jasin, Melaka. Since the researchers are considering the number of subjects, this data set consists of five families of butterfly and represent the five variables involve in the analysis which are the types of subjects. Besides, the analysis of ZIP used the SAS procedure of overdispersion in analysing zeros value and the main purpose of continuing the previous study is to compare which models would be better than when exists zero values for the observation of the count data. The analysis used AIC, BIC and Voung test of 5% level significance in order to achieve the objectives. The finding indicates that there is a presence of over-dispersion in analysing zero value. The ZIP regression model is better than Poisson regression model when zero values exist.

  13. Regression analysis of growth responses to water depth in three wetland plant species

    DEFF Research Database (Denmark)

    Sorrell, Brian K; Tanner, Chris C; Brix, Hans

    2012-01-01

    depths from 0 – 0.5 m. Morphological and growth responses to depth were followed for 54 days before harvest, and then analysed by repeated measures analysis of covariance, and non-linear and quantile regression analysis (QRA), to compare flooding tolerances. Principal results Growth responses to depth...

  14. The best of both worlds: Phylogenetic eigenvector regression and mapping

    Directory of Open Access Journals (Sweden)

    José Alexandre Felizola Diniz Filho

    2015-09-01

    Full Text Available Eigenfunction analyses have been widely used to model patterns of autocorrelation in time, space and phylogeny. In a phylogenetic context, Diniz-Filho et al. (1998 proposed what they called Phylogenetic Eigenvector Regression (PVR, in which pairwise phylogenetic distances among species are submitted to a Principal Coordinate Analysis, and eigenvectors are then used as explanatory variables in regression, correlation or ANOVAs. More recently, a new approach called Phylogenetic Eigenvector Mapping (PEM was proposed, with the main advantage of explicitly incorporating a model-based warping in phylogenetic distance in which an Ornstein-Uhlenbeck (O-U process is fitted to data before eigenvector extraction. Here we compared PVR and PEM in respect to estimated phylogenetic signal, correlated evolution under alternative evolutionary models and phylogenetic imputation, using simulated data. Despite similarity between the two approaches, PEM has a slightly higher prediction ability and is more general than the original PVR. Even so, in a conceptual sense, PEM may provide a technique in the best of both worlds, combining the flexibility of data-driven and empirical eigenfunction analyses and the sounding insights provided by evolutionary models well known in comparative analyses.

  15. Comparative physiological, metabolomic, and transcriptomic analyses reveal mechanisms of improved abiotic stress resistance in bermudagrass [Cynodon dactylon (L). Pers.] by exogenous melatonin

    Science.gov (United States)

    Shi, Haitao; Jiang, Chuan; Ye, Tiantian; Tan, Dun-xian; Reiter, Russel J.; Zhang, Heng; Liu, Renyi; Chan, Zhulong

    2015-01-01

    Melatonin (N-acetyl-5-methoxytryptamine), a well-known animal hormone, is also involved in plant development and abiotic stress responses. In this study, it is shown that exogenous application of melatonin conferred improved salt, drought, and cold stress resistances in bermudagrass. Moreover, exogenous melatonin treatment alleviated reactive oxygen species (ROS) burst and cell damage induced by abiotic stress; this involved activation of several antioxidants. Additionally, melatonin-pre-treated plants exhibited higher concentrations of 54 metabolites, including amino acids, organic acids, sugars, and sugar alcohols, than non-treated plants under abiotic stress conditions. Genome-wide transcriptomic profiling identified 3933 transcripts (2361 up-regulated and 1572 down-regulated) that were differentially expressed in melatonin-treated plants versus controls. Pathway and gene ontology (GO) term enrichment analyses revealed that genes involved in nitrogen metabolism, major carbohydrate metabolism, tricarboxylic acid (TCA)/org transformation, transport, hormone metabolism, metal handling, redox, and secondary metabolism were over-represented after melatonin pre-treatment. Taken together, this study provides the first evidence of the protective roles of exogenous melatonin in the bermudagrass response to abiotic stresses, partially via activation of antioxidants and modulation of metabolic homeostasis. Notably, metabolic and transcriptomic analyses showed that the underlying mechanisms of melatonin could involve major reorientation of photorespiratory and carbohydrate and nitrogen metabolism. PMID:25225478

  16. Comparative CO{sub 2} flux measurements by eddy covariance technique using open- and closed-path gas analysers over the equatorial Pacific Ocean

    Energy Technology Data Exchange (ETDEWEB)

    Kondo, Fumiyoshi (Graduate School of Natural Science and Technology, Okayama Univ., Okayama (Japan); Atmosphere and Ocean Research Inst., Univ. of Tokyo, Tokyo (Japan)), Email: fkondo@aori.u-tokyo.ac.jp; Tsukamoto, Osamu (Graduate School of Natural Science and Technology, Okayama Univ., Okayama (Japan))

    2012-04-15

    Direct comparison of airsea CO{sub 2} fluxes by open-path eddy covariance (OPEC) and closed-path eddy covariance (CPEC) techniques was carried out over the equatorial Pacific Ocean. Previous studies over oceans have shown that the CO{sub 2} flux by OPEC was larger than the bulk CO{sub 2} flux using the gas transfer velocity estimated by the mass balance technique, while the CO{sub 2} flux by CPEC agreed with the bulk CO{sub 2} flux. We investigated a traditional conflict between the CO{sub 2} flux by the eddy covariance technique and the bulk CO{sub 2} flux, and whether the CO{sub 2} fluctuation attenuated using the closed-path analyser can be measured with sufficient time responses to resolve small CO{sub 2} flux over oceans. Our results showed that the closed-path analyser using a short sampling tube and a high volume air pump can be used to measure the small CO{sub 2} fluctuation over the ocean. Further, the underestimated CO{sub 2} flux by CPEC due to the attenuated fluctuation can be corrected by the bandpass covariance method; its contribution was almost identical to that of H{sub 2}O flux. The CO{sub 2} flux by CPEC agreed with the total CO{sub 2} flux by OPEC with density correction; however, both of them are one order of magnitude larger than the bulk CO{sub 2} flux

  17. Comparative CO2 flux measurements by eddy covariance technique using open- and closed-path gas analysers over the equatorial Pacific Ocean

    Directory of Open Access Journals (Sweden)

    Fumiyoshi Kondo

    2012-04-01

    Full Text Available Direct comparison of air–sea CO2 fluxes by open-path eddy covariance (OPEC and closed-path eddy covariance (CPEC techniques was carried out over the equatorial Pacific Ocean. Previous studies over oceans have shown that the CO2 flux by OPEC was larger than the bulk CO2 flux using the gas transfer velocity estimated by the mass balance technique, while the CO2 flux by CPEC agreed with the bulk CO2 flux. We investigated a traditional conflict between the CO2 flux by the eddy covariance technique and the bulk CO2 flux, and whether the CO2 fluctuation attenuated using the closed-path analyser can be measured with sufficient time responses to resolve small CO2 flux over oceans. Our results showed that the closed-path analyser using a short sampling tube and a high volume air pump can be used to measure the small CO2 fluctuation over the ocean. Further, the underestimated CO2 flux by CPEC due to the attenuated fluctuation can be corrected by the bandpass covariance method; its contribution was almost identical to that of H2O flux. The CO2 flux by CPEC agreed with the total CO2 flux by OPEC with density correction; however, both of them are one order of magnitude larger than the bulk CO2 flux.

  18. Comparative physiological, metabolomic, and transcriptomic analyses reveal mechanisms of improved abiotic stress resistance in bermudagrass [Cynodon dactylon (L). Pers.] by exogenous melatonin.

    Science.gov (United States)

    Shi, Haitao; Jiang, Chuan; Ye, Tiantian; Tan, Dun-Xian; Reiter, Russel J; Zhang, Heng; Liu, Renyi; Chan, Zhulong

    2015-02-01

    Melatonin (N-acetyl-5-methoxytryptamine), a well-known animal hormone, is also involved in plant development and abiotic stress responses. In this study, it is shown that exogenous application of melatonin conferred improved salt, drought, and cold stress resistances in bermudagrass. Moreover, exogenous melatonin treatment alleviated reactive oxygen species (ROS) burst and cell damage induced by abiotic stress; this involved activation of several antioxidants. Additionally, melatonin-pre-treated plants exhibited higher concentrations of 54 metabolites, including amino acids, organic acids, sugars, and sugar alcohols, than non-treated plants under abiotic stress conditions. Genome-wide transcriptomic profiling identified 3933 transcripts (2361 up-regulated and 1572 down-regulated) that were differentially expressed in melatonin-treated plants versus controls. Pathway and gene ontology (GO) term enrichment analyses revealed that genes involved in nitrogen metabolism, major carbohydrate metabolism, tricarboxylic acid (TCA)/org transformation, transport, hormone metabolism, metal handling, redox, and secondary metabolism were over-represented after melatonin pre-treatment. Taken together, this study provides the first evidence of the protective roles of exogenous melatonin in the bermudagrass response to abiotic stresses, partially via activation of antioxidants and modulation of metabolic homeostasis. Notably, metabolic and transcriptomic analyses showed that the underlying mechanisms of melatonin could involve major reorientation of photorespiratory and carbohydrate and nitrogen metabolism. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  19. Polynomial regression analysis and significance test of the regression function

    International Nuclear Information System (INIS)

    Gao Zhengming; Zhao Juan; He Shengping

    2012-01-01

    In order to analyze the decay heating power of a certain radioactive isotope per kilogram with polynomial regression method, the paper firstly demonstrated the broad usage of polynomial function and deduced its parameters with ordinary least squares estimate. Then significance test method of polynomial regression function is derived considering the similarity between the polynomial regression model and the multivariable linear regression model. Finally, polynomial regression analysis and significance test of the polynomial function are done to the decay heating power of the iso tope per kilogram in accord with the authors' real work. (authors)

  20. Recursive Algorithm For Linear Regression

    Science.gov (United States)

    Varanasi, S. V.

    1988-01-01

    Order of model determined easily. Linear-regression algorithhm includes recursive equations for coefficients of model of increased order. Algorithm eliminates duplicative calculations, facilitates search for minimum order of linear-regression model fitting set of data satisfactory.

  1. Analysing the advantages of high temporal resolution geostationary MSG SEVIRI data compared to Polar operational environmental satellite data for land surface monitoring in Africa

    DEFF Research Database (Denmark)

    Fensholt, Rasmus; Anyamba, Assaf; Huber Gharib, Silvia

    2011-01-01

    Since 1972, satellite remote sensing of the environment has been dominated by polar-orbiting sensors providing useful data for monitoring the earth’s natural resources. However their observation and monitoring capacity are inhibited by daily to monthly looks for any given ground surface which often...... is obscured by frequent and persistent cloud cover creating large gaps in time series measurements. The launch of the Meteosat Second Generation (MSG) satellite into geostationary orbit has opened new opportunities for land surface monitoring. The Spinning Enhanced Visible and Infrared Imager (SEVIRI...... affected by droughts and floods in 2008 caused by periods of abnormally low and high rainfall, respectively. Based on the effectiveness of monitoring these events from Earth Observation (EO) data the current analyses show that the new generation of geostationary remote sensing data can provide higher...

  2. Comparative Analyses of the Teaching Methods and Evaluation Practices in English Subject at Secondary School Certificate (SSC) and General Certificate of Education (GCE O-Level) in Pakistan

    Science.gov (United States)

    Behlol, Malik Ghulam; Anwar, Mohammad

    2011-01-01

    The study was conducted to compare the teaching methods and evaluation practices in English subject at secondary school certificate (SSC) and general certificate of education GCE-O-level in Pakistan. The population of the study was students, teachers and experts at SSC and 0-level in the Punjab province. Purposive and random sampling techniques…

  3. Analyses adjusting for selective crossover show improved overall survival with adjuvant letrozole compared with tamoxifen in the BIG 1-98 study

    DEFF Research Database (Denmark)

    Colleoni, Marco; Giobbie-Hurder, Anita; Regan, Meredith M

    2011-01-01

    Among postmenopausal women with endocrine-responsive breast cancer, the aromatase inhibitor letrozole, when compared with tamoxifen, has been shown to significantly improve disease-free survival (DFS) and time to distant recurrence (TDR). We investigated whether letrozole monotherapy prolonged ov...

  4. L`ANALYSE COMPARATIVE DES FUSIONS-ACQUISITIONS AVEC LES AUTRES FORMES DE CROISSANCE DES ENTREPRISES (II- FUSIONS- ACQUISITIONS VS. ALLIANCES

    Directory of Open Access Journals (Sweden)

    Vancea Mariana

    2010-12-01

    Full Text Available Development through mergers and acquisitions is a companys external growth strategy, as well as business alliances, but these options can not be mistaken, because the characteristics, stakes and risks are fundamentally different nature. In this paper we intent to analyze mergers and acquisitions compared with other ways of the companys external growth, by presenting the main similarities and differences between them.

  5. Energy management as a factor of success. International comparative analysis of energy management systems standards; Energiemanagement als Erfolgsfaktor. International vergleichende Analyse von Energiemanagementnormen

    Energy Technology Data Exchange (ETDEWEB)

    Kahlenborn, Walter; Knopf, Jutta; Richter, Ina [adelphi research, Berlin (Germany)

    2010-11-15

    This report outlines the current state of standardised energy management systems (EnMSs) worldwide whose aim is to promote energy efficiency in the industrial sector. The core intention of the study is to identify the potential of EnMSs for German energy efficiency policy. The study examines the experiences of countries that can be defined as front runners in this context, such as the Netherlands, Denmark, Sweden, Ireland and the USA. Further input was taken from recently completed, and still ongoing, development processes of national standards. Data were generated from an intensive literature review as well as interviews with experts. Central to the analysis are questions of characteristics as well as the effectiveness of national energy management standards. In addition, political frameworks (i.e. voluntary agreements), financial tools (i.e. subsidies) and other measures of assistance (i.e. capacity building) supporting the implementation of an EnMS were analysed. The study concludes with a comparison of findings from the country-by-country analysis and provides recommendations for the effective implementation of EnMS in Germany. As part of the entire project adelphi produced a manual on the use of EN 16001 which has been published by BMU/UBA. (orig.)

  6. Combining Alphas via Bounded Regression

    Directory of Open Access Journals (Sweden)

    Zura Kakushadze

    2015-11-01

    Full Text Available We give an explicit algorithm and source code for combining alpha streams via bounded regression. In practical applications, typically, there is insufficient history to compute a sample covariance matrix (SCM for a large number of alphas. To compute alpha allocation weights, one then resorts to (weighted regression over SCM principal components. Regression often produces alpha weights with insufficient diversification and/or skewed distribution against, e.g., turnover. This can be rectified by imposing bounds on alpha weights within the regression procedure. Bounded regression can also be applied to stock and other asset portfolio construction. We discuss illustrative examples.

  7. Regression in autistic spectrum disorders.

    Science.gov (United States)

    Stefanatos, Gerry A

    2008-12-01

    A significant proportion of children diagnosed with Autistic Spectrum Disorder experience a developmental regression characterized by a loss of previously-acquired skills. This may involve a loss of speech or social responsitivity, but often entails both. This paper critically reviews the phenomena of regression in autistic spectrum disorders, highlighting the characteristics of regression, age of onset, temporal course, and long-term outcome. Important considerations for diagnosis are discussed and multiple etiological factors currently hypothesized to underlie the phenomenon are reviewed. It is argued that regressive autistic spectrum disorders can be conceptualized on a spectrum with other regressive disorders that may share common pathophysiological features. The implications of this viewpoint are discussed.

  8. Comparative analyses of DHA-Phosphatidylcholine and recombination of DHA-Triglyceride with Egg-Phosphatidylcholine or Glycerylphosphorylcholine on DHA repletion in n-3 deficient mice

    OpenAIRE

    Wu, Fang; Wang, Dan-dan; Wen, Min; Che, Hong-xia; Xue, Chang-hu; Yanagita, Teruyoshi; Zhang, Tian-tian; Wang, Yu-ming

    2017-01-01

    Background Docosahexaenoic acid (DHA) is important for optimal neurodevelopment and brain function during the childhood when the brain is still under development. Methods The effects of DHA-Phosphatidylcholine (DHA-PC) and the recombination of DHA-Triglyceride with egg PC (DHA-TG + PC) or α-Glycerylphosphorylcholine (DHA-TG + α-GPC) were comparatively analyzed on DHA recovery and the DHA accumulation kinetics in tissues including cerebral cortex, erythrocyte, liver, and testis were evaluated ...

  9. Linear regression in astronomy. I

    Science.gov (United States)

    Isobe, Takashi; Feigelson, Eric D.; Akritas, Michael G.; Babu, Gutti Jogesh

    1990-01-01

    Five methods for obtaining linear regression fits to bivariate data with unknown or insignificant measurement errors are discussed: ordinary least-squares (OLS) regression of Y on X, OLS regression of X on Y, the bisector of the two OLS lines, orthogonal regression, and 'reduced major-axis' regression. These methods have been used by various researchers in observational astronomy, most importantly in cosmic distance scale applications. Formulas for calculating the slope and intercept coefficients and their uncertainties are given for all the methods, including a new general form of the OLS variance estimates. The accuracy of the formulas was confirmed using numerical simulations. The applicability of the procedures is discussed with respect to their mathematical properties, the nature of the astronomical data under consideration, and the scientific purpose of the regression. It is found that, for problems needing symmetrical treatment of the variables, the OLS bisector performs significantly better than orthogonal or reduced major-axis regression.

  10. Comparing 1.5D ONETWO and 2D SOLPS analyses of inter-ELM H-mode plasma in DIII-D

    International Nuclear Information System (INIS)

    Owen, Larry W.; Canik, John; Groebner, R.; Callen, J.D.; Bonnin, X.; Osborne, T.H.

    2010-01-01

    A DIII-D inter-ELM H-mode plasma that is in approximate transport equilibrium is analysed with the 1.5D ONETWO core code and the 2D SOLPS code. In order to investigate the importance of core-edge coupling and 2D effects, including divertor fuelling across the X-point and poloidal asymmetries that are not explicitly included in ONETWO, the domain of SOLPS is extended to very near the magnetic axis. Two principal objectives are (1) to determine whether poloidal asymmetries in the plasma distributions are large enough to vitiate a core-type interpretive plasma transport analysis and (2) to determine whether the interpretive transport coefficients and neutral beam power and particle sources from ONETWO, when used in 2D SOLPS full plasma simulations, yield the same quality fits to the measured upstream density and temperature profiles as obtained with ONETWO. Results show that only a small increase in the separatrix value of the particle diffusion coefficient, and no change in the thermal diffusivities from ONETWO was needed to get excellent agreement of the upstream SOLPS density and temperature profiles and the Thomson scattering and CER data. Good agreement of the ONETWO and SOLPS flux surface averaged distributions of the core electron and D+ densities and temperatures are also obtained. Likewise the C6+ density, with a simple chemical sputtering model based on a constant fraction of the divertor D+ flux, the core heat and particle fluxes and the neutral density reveal no 2D effects in the core/pedestal region that would vitiate a 1.5D treatment of the inter-ELM H-mode plasma.

  11. Honeybee glucose oxidase—its expression in honeybee workers and comparative analyses of its content and H2O2-mediated antibacterial activity in natural honeys

    Science.gov (United States)

    Bucekova, Marcela; Valachova, Ivana; Kohutova, Lenka; Prochazka, Emanuel; Klaudiny, Jaroslav; Majtan, Juraj

    2014-08-01

    Antibacterial properties of honey largely depend on the accumulation of hydrogen peroxide (H2O2), which is generated by glucose oxidase (GOX)-mediated conversion of glucose in diluted honey. However, honeys exhibit considerable variation in their antibacterial activity. Therefore, the aim of the study was to identify the mechanism behind the variation in this activity and in the H2O2 content in honeys associated with the role of GOX in this process. Immunoblots and in situ hybridization analyses demonstrated that gox is solely expressed in the hypopharyngeal glands of worker bees performing various tasks and not in other glands or tissues. Real-time PCR with reference genes selected for worker heads shows that the gox expression progressively increases with ageing of the youngest bees and nurses and reached the highest values in processor bees. Immunoblot analysis of honey samples revealed that GOX is a regular honey component but its content significantly varied among honeys. Neither botanical source nor geographical origin of honeys affected the level of GOX suggesting that some other factors such as honeybee nutrition and/or genetic/epigenetic factors may take part in the observed variation. A strong correlation was found between the content of GOX and the level of generated H2O2 in honeys except honeydew honeys. Total antibacterial activity of most honey samples against Pseudomonas aeruginosa isolate significantly correlated with the H2O2 content. These results demonstrate that the level of GOX can significantly affect the total antibacterial activity of honey. They also support an idea that breeding of novel honeybee lines expressing higher amounts of GOX could help to increase the antibacterial efficacy of the hypopharyngeal gland secretion that could have positive influence on a resistance of colonies against bacterial pathogens.

  12. Lactococcus lactis Diversity in Undefined Mixed Dairy Starter Cultures as Revealed by Comparative Genome Analyses and Targeted Amplicon Sequencing of epsD.

    Science.gov (United States)

    Frantzen, Cyril A; Kleppen, Hans Petter; Holo, Helge

    2018-02-01

    Undefined mesophilic mixed (DL) starter cultures are used in the production of continental cheeses and contain unknown strain mixtures of Lactococcus lactis and leuconostocs. The choice of starter culture affects the taste, aroma, and quality of the final product. To gain insight into the diversity of Lactococcus lactis strains in starter cultures, we whole-genome sequenced 95 isolates from three different starter cultures. Pan-genomic analyses, which included 30 publically available complete genomes, grouped the strains into 21 L. lactis subsp . lactis and 28 L. lactis subsp. cremoris lineages. Only one of the 95 isolates grouped with previously sequenced strains, and the three starter cultures showed no overlap in lineage distributions. The culture diversity was assessed by targeted amplicon sequencing using purR , a core gene, and epsD , present in 93 of the 95 starter culture isolates but absent in most of the reference strains. This enabled an unprecedented discrimination of starter culture Lactococcus lactis and revealed substantial differences between the three starter cultures and compositional shifts during the cultivation of cultures in milk. IMPORTANCE In contemporary cheese production, standardized frozen seed stock starter cultures are used to ensure production stability, reproducibility, and quality control of the product. The dairy industry experiences significant disruptions of cheese production due to phage attacks, and one commonly used countermeasure to phage attack is to employ a starter rotation strategy, in which two or more starters with minimal overlap in phage sensitivity are used alternately. A culture-independent analysis of the lactococcal diversity in complex undefined starter cultures revealed large differences between the three starter cultures and temporal shifts in lactococcal composition during the production of bulk starters. A better understanding of the lactococcal diversity in starter cultures will enable the development of

  13. Advanced statistics: linear regression, part I: simple linear regression.

    Science.gov (United States)

    Marill, Keith A

    2004-01-01

    Simple linear regression is a mathematical technique used to model the relationship between a single independent predictor variable and a single dependent outcome variable. In this, the first of a two-part series exploring concepts in linear regression analysis, the four fundamental assumptions and the mechanics of simple linear regression are reviewed. The most common technique used to derive the regression line, the method of least squares, is described. The reader will be acquainted with other important concepts in simple linear regression, including: variable transformations, dummy variables, relationship to inference testing, and leverage. Simplified clinical examples with small datasets and graphic models are used to illustrate the points. This will provide a foundation for the second article in this series: a discussion of multiple linear regression, in which there are multiple predictor variables.

  14. Analyse comparative de la rentabilité des systèmes de production de coton biologique, conventionnel et transgénique au Burkina Faso

    Directory of Open Access Journals (Sweden)

    Vognan, G.

    2017-01-01

    Full Text Available Comparative Analysis of the Profitability of Organic, Conventional, and Transgenic Cotton Farming Systems in Burkina Faso. This research aimed to compare the profitability of cotton cropping systems (cotton and rotation crops according to three production modes: organic, conventional, and transgenic. The study was conducted in Burkina Faso on a sample of 180 households of which 60 households from organic cotton system, 60 households from conventional cotton system, and 60 households from transgenic cotton system. It came out that the production costs of the various crops in the transgenic and conventional systems are higher than those of the organic system. The differences in the production costs for the three modes of production are highly significant especially for cotton, corn, sorghum and groundnut. In terms of profitability, there's no significant difference in the margins generated by the different modes of cotton production. On the other hand, the sensitivity analysis revealed that organic cotton is financially more resilient to cotton price fluctuation and chemical inputs cost. Actually, organic cotton production seems to be a viable option to alleviate poverty in the present context of climate change.

  15. Comparative Transcriptome Analyses Reveal Potential Mechanisms of Enhanced Drought Tolerance in Transgenic Salvia Miltiorrhiza Plants Expressing AtDREB1A from Arabidopsis.

    Science.gov (United States)

    Wei, Tao; Deng, Kejun; Wang, Hongbin; Zhang, Lipeng; Wang, Chunguo; Song, Wenqin; Zhang, Yong; Chen, Chengbin

    2018-03-12

    In our previous study, drought-resistant transgenic plants of Salvia miltiorrhiza were produced via overexpression of the transcription factor AtDREB1A. To unravel the molecular mechanisms underpinning elevated drought tolerance in transgenic plants, in the present study we compared the global transcriptional profiles of wild-type (WT) and AtDREB1A -expressing transgenic plants using RNA-sequencing (RNA-seq). Using cluster analysis, we identified 3904 differentially expressed genes (DEGs). Compared with WT plants, 423 unigenes were up-regulated in pRD29A::AtDREB1A-31 before drought treatment, while 936 were down-regulated and 1580 and 1313 unigenes were up- and down-regulated after six days of drought. COG analysis revealed that the 'signal transduction mechanisms' category was highly enriched among these DEGs both before and after drought stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation, DEGs associated with "ribosome", "plant hormone signal transduction", photosynthesis", "plant-pathogen interaction", "glycolysis/gluconeogenesis" and "carbon fixation" are hypothesized to perform major functions in drought resistance in AtDREB1A -expressing transgenic plants. Furthermore, the number of DEGs associated with different transcription factors increased significantly after drought stress, especially the AP2/ERF, bZIP and MYB protein families. Taken together, this study substantially expands the transcriptomic information for S. miltiorrhiza and provides valuable clues for elucidating the mechanism of AtDREB1A-mediated drought tolerance in transgenic plants.

  16. Phylogenetic reconstruction of Mycobacterium tuberculosis within four settings of the Caribbean region: tree comparative analyse and first appraisal on their phylogeography.

    Science.gov (United States)

    Duchêne, Véronique; Ferdinand, Séverine; Filliol, Ingrid; Guégan, Jean François; Rastogi, Nalin; Sola, Christophe

    2004-03-01

    In order to compare phylogenetic methods and to reconstruct the evolutionary history of the tubercle bacilli, a set of macro-array-based genotyping data of Mycobacterium tuberculosis clinical isolates (called spoligotyping for spacer oligonucleotide typing, which assays the variability of the Direct Repeat -DR- locus), was analyzed in four settings of the Caribbean region (Guadeloupe, Martinique, Cuba and Haiti). A set of 47 alleles, split into 26 shared and 21 unique alleles) representative of 321 individual M. tuberculosis clinical isolates from patients residing in the above regions was studied. The following methods (and software in brackets) were investigated: numerical taxonomy distance methods (TAXOTRON), maximum parsimony procedure (PAUP), median-joining networks (NETWORK), and nested clade analysis (GEODIS). Results using these methods were analyzed, compared and discussed. The latter method (GEODIS) was investigated in detail by introducing geographical data together with genetic variability results to detect a link between population structure and population history, and to test the null hypothesis of no association between geography and genotypes. Irrespective of the methods used, our findings demonstrate that a core structure of four families (or clades) of M. tuberculosis strains is highly prevalent within the islands studied, indirectly reflecting passed colonization history of these different settings. Specificity of M. tuberculosis genotypes in each of the islands is discussed in the light of their respective colonial and contemporary histories.

  17. Performance of the fully automated progesterone assays on the Abbott AxSYM and the Technicon Immuno 1 Analyser compared with the radioimmunoassay progesterone MAIA

    International Nuclear Information System (INIS)

    Reinsberg, J.; Jost, E.; Van der Ven, H.

    1997-01-01

    Test performance of two automated progesterone assays available on the immunoassay analysers Abbott AxSYM and Technicon Immuno 1, respectively, was evaluated in comparison with the radioimmunoassay Progesterone MAIA. For assessment of test performance imprecision, functional sensitivity and linearity of dilution was examined. Correlation with the manual radioimmunoassay was assessed using 122 serum samples over the range 0-110 nmol/L. Imprecision studies revealed for the AxSYM Progesterone within-run CV's of 1.8-6.4% and day-to-day CV's of 3.5-9.7% (concentration range 2.3-75 nmol/L); Immuno 1 Progesterone: within-run CV's 1.0-7.3%, day-to-day CV's 2.3-7.7% (concentration range 1.2-60 nmol/L). The functional sensitivity was <1.7 nmol/L for the AxSYM Progesterone and <1.1 nmol/L for the Immuno 1 Progesterone. With the AxSYM Progesterone the mean recovery after dilution from five samples was 102% (89-107%), from one sample only 69-80% was recovered; with the Immuno 1 Progesterone the mean recovery was 95% (80-105%). Despite of a quite good overall correlation (coefficients 0.972 and 0.981) the relationship of both assays to the Progesterone MAIA significantly deviate from linearity with a considerably higher slope within the lower concentration range. The relationship between the automated assays was linear over the entire concentration range (Immuno = 1.207 * AxSYM + 1; r = 0.986). The time to first result was 20 min for the AxSYM Progesterone, 45 min for the Immuno 1 Progesterone and 90 min for the Progesterone MAIA. The evaluated progesterone assays both exhibit an excellent precision and a high degree of sensitivity. They offer a rapid and flexible method for progesterone determination which may be especially useful for the monitoring of ovarian stimulation during in-vitro fertilization. (author)

  18. Comparative analyses of pandemic H1N1 and seasonal H1N1, H3N2, and influenza B infections depict distinct clinical pictures in ferrets.

    Directory of Open Access Journals (Sweden)

    Stephen S H Huang

    Full Text Available Influenza A and B infections are a worldwide health concern to both humans and animals. High genetic evolution rates of the influenza virus allow the constant emergence of new strains and cause illness variation. Since human influenza infections are often complicated by secondary factors such as age and underlying medical conditions, strain or subtype specific clinical features are difficult to assess. Here we infected ferrets with 13 currently circulating influenza strains (including strains of pandemic 2009 H1N1 [H1N1pdm] and seasonal A/H1N1, A/H3N2, and B viruses. The clinical parameters were measured daily for 14 days in stable environmental conditions to compare clinical characteristics. We found that H1N1pdm strains had a more severe physiological impact than all season strains where pandemic A/California/07/2009 was the most clinically pathogenic pandemic strain. The most serious illness among seasonal A/H1N1 and A/H3N2 groups was caused by A/Solomon Islands/03/2006 and A/Perth/16/2009, respectively. Among the 13 studied strains, B/Hubei-Wujiagang/158/2009 presented the mildest clinical symptoms. We have also discovered that disease severity (by clinical illness and histopathology correlated with influenza specific antibody response but not viral replication in the upper respiratory tract. H1N1pdm induced the highest and most rapid antibody response followed by seasonal A/H3N2, seasonal A/H1N1 and seasonal influenza B (with B/Hubei-Wujiagang/158/2009 inducing the weakest response. Our study is the first to compare the clinical features of multiple circulating influenza strains in ferrets. These findings will help to characterize the clinical pictures of specific influenza strains as well as give insights into the development and administration of appropriate influenza therapeutics.

  19. Genetic, comparative genomic, and expression analyses of the Mc1r locus in the polychromatic Midas cichlid fish (Teleostei, Cichlidae Amphilophus sp.) species group.

    Science.gov (United States)

    Henning, Frederico; Renz, Adina Josepha; Fukamachi, Shoji; Meyer, Axel

    2010-05-01

    Natural populations of the Midas cichlid species in several different crater lakes in Nicaragua exhibit a conspicuous color polymorphism. Most individuals are dark and the remaining have a gold coloration. The color morphs mate assortatively and sympatric population differentiation has been shown based on neutral molecular data. We investigated the color polymorphism using segregation analysis and a candidate gene approach. The segregation patterns observed in a mapping cross between a gold and a dark individual were consistent with a single dominant gene as a cause of the gold phenotype. This suggests that a simple genetic architecture underlies some of the speciation events in the Midas cichlids. We compared the expression levels of several candidate color genes Mc1r, Ednrb1, Slc45a2, and Tfap1a between the color morphs. Mc1r was found to be up regulated in the gold morph. Given its widespread association in color evolution and role on melanin synthesis, the Mc1r locus was further investigated using sequences derived from a genomic library. Comparative analysis revealed conserved synteny in relation to the majority of teleosts and highlighted several previously unidentified conserved non-coding elements (CNEs) in the upstream and downstream regions in the vicinity of Mc1r. The identification of the CNEs regions allowed the comparison of sequences from gold and dark specimens of natural populations. No polymorphisms were found between in the population sample and Mc1r showed no linkage to the gold phenotype in the mapping cross, demonstrating that it is not causally related to the color polymorphism in the Midas cichlid.

  20. Comparative sequence, structure and redox analyses of Klebsiella pneumoniae DsbA show that anti-virulence target DsbA enzymes fall into distinct classes.

    Directory of Open Access Journals (Sweden)

    Fabian Kurth

    Full Text Available Bacterial DsbA enzymes catalyze oxidative folding of virulence factors, and have been identified as targets for antivirulence drugs. However, DsbA enzymes characterized to date exhibit a wide spectrum of redox properties and divergent structural features compared to the prototypical DsbA enzyme of Escherichia coli DsbA (EcDsbA. Nonetheless, sequence analysis shows that DsbAs are more highly conserved than their known substrate virulence factors, highlighting the potential to inhibit virulence across a range of organisms by targeting DsbA. For example, Salmonella enterica typhimurium (SeDsbA, 86 % sequence identity to EcDsbA shares almost identical structural, surface and redox properties. Using comparative sequence and structure analysis we predicted that five other bacterial DsbAs would share these properties. To confirm this, we characterized Klebsiella pneumoniae DsbA (KpDsbA, 81 % identity to EcDsbA. As expected, the redox properties, structure and surface features (from crystal and NMR data of KpDsbA were almost identical to those of EcDsbA and SeDsbA. Moreover, KpDsbA and EcDsbA bind peptides derived from their respective DsbBs with almost equal affinity, supporting the notion that compounds designed to inhibit EcDsbA will also inhibit KpDsbA. Taken together, our data show that DsbAs fall into different classes; that DsbAs within a class may be predicted by sequence analysis of binding loops; that DsbAs within a class are able to complement one another in vivo and that compounds designed to inhibit EcDsbA are likely to inhibit DsbAs within the same class.

  1. Comparative Transcriptome Analyses Reveal Potential Mechanisms of Enhanced Drought Tolerance in Transgenic Salvia Miltiorrhiza Plants Expressing AtDREB1A from Arabidopsis

    Directory of Open Access Journals (Sweden)

    Tao Wei

    2018-03-01

    Full Text Available In our previous study, drought-resistant transgenic plants of Salvia miltiorrhiza were produced via overexpression of the transcription factor AtDREB1A. To unravel the molecular mechanisms underpinning elevated drought tolerance in transgenic plants, in the present study we compared the global transcriptional profiles of wild-type (WT and AtDREB1A-expressing transgenic plants using RNA-sequencing (RNA-seq. Using cluster analysis, we identified 3904 differentially expressed genes (DEGs. Compared with WT plants, 423 unigenes were up-regulated in pRD29A::AtDREB1A-31 before drought treatment, while 936 were down-regulated and 1580 and 1313 unigenes were up- and down-regulated after six days of drought. COG analysis revealed that the ‘signal transduction mechanisms’ category was highly enriched among these DEGs both before and after drought stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG annotation, DEGs associated with “ribosome”, “plant hormone signal transduction”, photosynthesis”, “plant-pathogen interaction”, “glycolysis/gluconeogenesis” and “carbon fixation” are hypothesized to perform major functions in drought resistance in AtDREB1A-expressing transgenic plants. Furthermore, the number of DEGs associated with different transcription factors increased significantly after drought stress, especially the AP2/ERF, bZIP and MYB protein families. Taken together, this study substantially expands the transcriptomic information for S. miltiorrhiza and provides valuable clues for elucidating the mechanism of AtDREB1A-mediated drought tolerance in transgenic plants.

  2. Comparative Analyses of Immunosuppressive Characteristics of Bone-Marrow, Wharton’s Jelly, and Adipose Tissue-Derived Human Mesenchymal Stem Cells

    Directory of Open Access Journals (Sweden)

    Erdal Karaöz

    2017-09-01

    Full Text Available Objective: Mesenchymal stem cells (MSCs, which possess immunosuppressive characteristics on induced T-cells, were shown to be applicable in prevention and treatment of graft-versus-host disease. However, knowledge of effective cell sources is still limited. In this study, MSCs from different human tissues, i.e. bone marrow (BM, Wharton’s jelly (WJ, and adipose tissue, were isolated, and the immune suppression of stimulated T cells was analyzed comparatively. Materials and Methods: MSCs were co-cultured with phytohemagglutinin-induced T-cells with co-culture techniques with and without cell-to-cell contact. After co-culture for 24 and 96 h, the proliferation rate of T cells was estimated by carboxyfluorescein succinimidyl ester and apoptosis by annexin V/PI methods. Both T cells and MSCs were analyzed with respect to gene expressions by real-time polymerase chain reaction and their specific protein levels by ELISA. Results: The results showed that all three MSC lines significantly suppressed T-cell proliferation; BM-MSCs were most effective. Similarly, T-cell apoptosis was induced most strongly by BM-MSCs in indirect culture. In T cells, the genes in NFkB and tumor necrosis factor pathways were silenced and the caspase pathway was induced after co-culture. These results were confirmed with the measurement of protein levels, like transforming growth factor β1, IL-6, interferon-γ, interleukin (IL-2, and tumor necrosis factor-α. Additionally, IL-17A was detected in high levels in WJ-MSC co-cultures. We showed that IL-17A-producing Tregs are the key mediators in the treatment of graft-versus-host disease. Conclusion: BM-MSCs, which have been used in clinical applications for a while, showed the greatest immunosuppressive effect compared to other MSCs. However, a promising cell source could also be WJ, which is also effective in suppression with fewer ethical concerns. We described the molecular mechanism of WJ-MSCs in allogenic transplants for

  3. RETURNS OF PRIVATE EQUITY COMPARATIVE ANALYSES OF THE RETURNS OF VENTURE CAPITAL AND BUYOUT FUNDS IN EUROPE AND IN THE US

    Directory of Open Access Journals (Sweden)

    Becsky-Nagy Patrícia

    2014-07-01

    Full Text Available This paper focuses on the returns of two segments of Private Equity (PE market in Europe and in the US; Venture Capital (VC and Buyout (BO. Contrary to the publicly traded stocks where information about the trade of securities is public, the measuring of the returns of these asset classes is not unambiguous. The returns of PE investments are considered as confidential information therefore we only have estimations about the real characteristics of the financial performance of the PE industry. Although it is impossible to observe the whole industry it is important to chart its performance because PE plays an essential role in the financing of firms, especially firms at special stages of their lives and the more information the investors and companies have, the more effective PE market can be therefore it can contribute to economic growth, employment, innovation etc. In the literature PE, VC and BO are not distinguished properly and they are often used as synonyms. Despite their similarities, there are significant differences in the features of these types of investments. In this paper the authors present the return characteristics of the PE industry of Europe and the US with regard to the stage-focus of PE funds. The key findings of this paper are that in average the returns of BO funds exceeded the returns of VC funds in the US as well as in Europe. Not just according to the absolute value of the returns, but also according to its risk-return tradeoff BO seems to be a preferable investment. The same statements can be made in case of the European market. The US returns are higher than European VC returns, because compared to the US VC industry the European is undeveloped. On the other hand the gap between the performances of BO funds is not as significant as the difference of VC funds. While in the 90’s US BO funds outperformed the European ones, after the millennia European BO returns were higher. The analysis of returns reveals the

  4. Linear regression in astronomy. II

    Science.gov (United States)

    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.

  5. Time-adaptive quantile regression

    DEFF Research Database (Denmark)

    Møller, Jan Kloppenborg; Nielsen, Henrik Aalborg; Madsen, Henrik

    2008-01-01

    and an updating procedure are combined into a new algorithm for time-adaptive quantile regression, which generates new solutions on the basis of the old solution, leading to savings in computation time. The suggested algorithm is tested against a static quantile regression model on a data set with wind power......An algorithm for time-adaptive quantile regression is presented. The algorithm is based on the simplex algorithm, and the linear optimization formulation of the quantile regression problem is given. The observations have been split to allow a direct use of the simplex algorithm. The simplex method...... production, where the models combine splines and quantile regression. The comparison indicates superior performance for the time-adaptive quantile regression in all the performance parameters considered....

  6. Comparative analyses of genetic/epigenetic diversities and structures in a wild barley species (Hordeum brevisubulatum) using MSAP, SSAP and AFLP.

    Science.gov (United States)

    Shan, X H; Li, Y D; Liu, X M; Wu, Y; Zhang, M Z; Guo, W L; Liu, B; Yuan, Y P

    2012-08-17

    We analyzed genetic diversity and population genetic structure of four artificial populations of wild barley (Hordeum brevisubulatum); 96 plants collected from the Songnen Prairie in northeastern China were analyzed using amplified fragment length polymorphism (AFLP), specific-sequence amplified polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) markers. Indices of (epi-)genetic diversity, (epi-)genetic distance, gene flow, genotype frequency, cluster analysis, PCA analysis and AMOVA analysis generated from MSAP, AFLP and SSAP markers had the same trend. We found a high level of correlation in the artificial populations between MSAP, SSAP and AFLP markers by the Mantel test (r > 0.8). This is incongruent with previous findings showing that there is virtually no correlation between DNA methylation polymorphism and classical genetic variation; the high level of genetic polymorphism could be a result of epigenetic regulation. We compared our results with data from natural populations. The population diversity of the artificial populations was lower. However, different from what was found using AFLP and SSAP, based on MSAP results the methylation polymorphism of the artificial populations was not significantly reduced. This leads us to suggest that the DNA methylation pattern change in H. brevisubulatum populations is not only related to DNA sequence variation, but is also regulated by other controlling systems.

  7. Changes of electrocardiogram and hemodynamics in response to dipyridamole: In vivo comparative analyses using anesthetized beagle dogs and microminipigs.

    Science.gov (United States)

    Ando, Kentaro; Takahara, Akira; Nakamura, Yuji; Wada, Takeshi; Chiba, Koki; Goto, Ai; Lubna, Nur Jaharat; Hagiwara-Nagasawa, Mihoko; Izumi-Nakaseko, Hiroko; Hoshiai, Kiyotaka; Akie, Yasuki; Naito, Atsuhiko T; Sugiyama, Atsushi

    2018-02-01

    Microminipigs are expected as a novel animal model for cardiovascular pharmacological experiments. Since inherent vulnerability of coronary circulation of microminipigs has not been characterized, we performed dipyridamole-stress test to both microminipigs and beagle dogs, and compared the results. Dipyridamole in doses of 0.056 and 0.56 mg/kg were intravenously infused over 10 min (n = 4 for each animal). Dipyridamole decreased the systolic/diastolic blood pressures and double product in dogs as well as in microminipigs; but it did not significantly alter the heart rate or the global balance between the myocardial oxygen demand and supply in either animal. While organic coronary arterial stenosis was not detected in either animal, dogs have well-developed epicardial intracoronary networks unlike microminipigs. Like in humans, dipyridamole did not affect the ST segment of microminipigs, whereas it substantially depressed that in dogs. The results indicate the onset of subendocardial ischemia by dipyridamole in dogs may be partly associated with their well-developed native coronary collateral channels. Microminipigs would be more useful to evaluate the drugs which may affect the coronary circulation in the pre-clinical study than dogs. Copyright © 2018 The Authors. Production and hosting by Elsevier B.V. All rights reserved.

  8. Analyses of Genotypes and Phenotypes of Ten Chinese Patients with Wolf-Hirschhorn Syndrome by Multiplex Ligation-dependent Probe Amplification and Array Comparative Genomic Hybridization.

    Science.gov (United States)

    Yang, Wen-Xu; Pan, Hong; Li, Lin; Wu, Hai-Rong; Wang, Song-Tao; Bao, Xin-Hua; Jiang, Yu-Wu; Qi, Yu

    2016-03-20

    Wolf-Hirschhorn syndrome (WHS) is a contiguous gene syndrome that is typically caused by a deletion of the distal portion of the short arm of chromosome 4. However, there are few reports about the features of Chinese WHS patients. This study aimed to characterize the clinical and molecular cytogenetic features of Chinese WHS patients using the combination of multiplex ligation-dependent probe amplification (MLPA) and array comparative genomic hybridization (array CGH). Clinical information was collected from ten patients with WHS. Genomic DNA was extracted from the peripheral blood of the patients. The deletions were analyzed by MLPA and array CGH. All patients exhibited the core clinical symptoms of WHS, including severe growth delay, a Greek warrior helmet facial appearance, differing degrees of intellectual disability, and epilepsy or electroencephalogram anomalies. The 4p deletions ranged from 2.62 Mb to 17.25 Mb in size and included LETM1, WHSC1, and FGFR3. The combined use of MLPA and array CGH is an effective and specific means to diagnose WHS and allows for the precise identification of the breakpoints and sizes of deletions. The deletion of genes in the WHS candidate region is closely correlated with the core WHS phenotype.

  9. Comparative proteomic and physiological analyses reveal the protective effect of exogenous polyamines in the bermudagrass (Cynodon dactylon) response to salt and drought stresses.

    Science.gov (United States)

    Shi, Haitao; Ye, Tiantian; Chan, Zhulong

    2013-11-01

    Polyamines conferred enhanced abiotic stress tolerance in multiple plant species. However, the effect of polyamines on abiotic stress and physiological change in bermudagrass, the most widely used warm-season turfgrasses, are unknown. In this study, pretreatment of exogenous polyamine conferred increased salt and drought tolerances in bermudagrass. Comparative proteomic analysis was performed to further investigate polyamines mediated responses, and 36 commonly regulated proteins by at least two types of polyamines in bermudagrass were successfully identified, including 12 proteins with increased level, 20 proteins with decreased level and other 4 specifically expressed proteins. Among them, proteins involved in electron transport and energy pathways were largely enriched, and nucleoside diphosphate kinase (NDPK) and three antioxidant enzymes were extensively regulated by polyamines. Dissection of reactive oxygen species (ROS) levels indicated that polyamine-derived H2O2 production might play dual roles under abiotic stress conditions. Moreover, accumulation of osmolytes was also observed after application of exogenous polyamines, which is consistent with proteomics results that several proteins involved in carbon fixation pathway were mediated commonly by polyamines pretreatment. Taken together, we proposed that polyamines could activate multiple pathways that enhance bermudagrass adaption to salt and drought stresses. These findings might be applicable for genetically engineering of grasses and crops to improve stress tolerance.

  10. Retro-regression--another important multivariate regression improvement.

    Science.gov (United States)

    Randić, M

    2001-01-01

    We review the serious problem associated with instabilities of the coefficients of regression equations, referred to as the MRA (multivariate regression analysis) "nightmare of the first kind". This is manifested when in a stepwise regression a descriptor is included or excluded from a regression. The consequence is an unpredictable change of the coefficients of the descriptors that remain in the regression equation. We follow with consideration of an even more serious problem, referred to as the MRA "nightmare of the second kind", arising when optimal descriptors are selected from a large pool of descriptors. This process typically causes at different steps of the stepwise regression a replacement of several previously used descriptors by new ones. We describe a procedure that resolves these difficulties. The approach is illustrated on boiling points of nonanes which are considered (1) by using an ordered connectivity basis; (2) by using an ordering resulting from application of greedy algorithm; and (3) by using an ordering derived from an exhaustive search for optimal descriptors. A novel variant of multiple regression analysis, called retro-regression (RR), is outlined showing how it resolves the ambiguities associated with both "nightmares" of the first and the second kind of MRA.

  11. Citation analytics: Data exploration and comparative analyses of CiteScores of Open Access and Subscription-Based publications indexed in Scopus (2014-2016).

    Science.gov (United States)

    Atayero, Aderemi A; Popoola, Segun I; Egeonu, Jesse; Oludayo, Olumuyiwa

    2018-08-01

    Citation is one of the important metrics that are used in measuring the relevance and the impact of research publications. The potentials of citation analytics may be exploited to understand the gains of publishing scholarly peer-reviewed research outputs in either Open Access (OA) sources or Subscription-Based (SB) sources in the bid to increase citation impact. However, relevant data required for such comparative analysis must be freely accessible for evidence-based findings and conclusions. In this data article, citation scores ( CiteScores ) of 2542 OA sources and 15,040 SB sources indexed in Scopus from 2014 to 2016 were presented and analyzed based on a set of five inclusion criteria. A robust dataset, which contains the CiteScores of OA and SB publication sources included, is attached as supplementary material to this data article to facilitate further reuse. Descriptive statistics and frequency distributions of OA CiteScores and SB CiteScores are presented in tables. Boxplot representations and scatter plots are provided to show the statistical distributions of OA CiteScores and SB CiteScores across the three sub-categories (Book Series, Journal, and Trade Journal). Correlation coefficient and p-value matrices are made available within the data article. In addition, Probability Density Functions (PDFs) and Cumulative Distribution Functions (CDFs) of OA CiteScores and SB CiteScores are computed and the results are presented using tables and graphs. Furthermore, Analysis of Variance (ANOVA) and multiple comparison post-hoc tests are conducted to understand the statistical difference (and its significance, if any) in the citation impact of OA publication sources and SB publication source based on CiteScore . In the long run, the data provided in this article will help policy makers and researchers in Higher Education Institutions (HEIs) to identify the appropriate publication source type and category for dissemination of scholarly research findings with

  12. Characterization and comparative analyses of transcriptomes for in vivo and in vitro produced peri-implantation conceptuses and endometria from sheep.

    Science.gov (United States)

    Wei, Xia; Xiaoling, Zhang; Kai, Miao; Rui, Wang; Jing, Xu; Min, Guo; Zhonghong, Wu; Jianhui, Tian; Xinyu, Zhang; Lei, An

    2016-06-17

    An increasing number of reports indicate that in vitro fertilization (IVF) is highly associated with long‑term side effects on embryonic and postnatal development, and can sometimes result in embryonic implant failure. While high‑throughput gene expression analysis has been used to explore the mechanisms underlying IVF-induced side effects on embryonic development, little is known about the effects of IVF on conceptus-endometrial interactions during the peri-implantation period. Using sheep as a model, we performed a comparative transcriptome analysis between in vivo (IVO; in vivo fertilized followed by further development in the uterus) and in vitro produced (IVP; IVF with further culture in the incubator) conceptuses, and the caruncular and intercaruncular areas of the ovine endometrium. We identified several genes that were differentially expressed between the IVO and IVP groups on day 17, when adhesion between the trophoblast and the uterine luminal epithelium begins in sheep. By performing Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, we found that, in the conceptus, differentially expressed genes (DEGs) were associated mainly with functions relating to cell binding and the cell cycle. In the endometrial caruncular area, DEGs were involved in cell adhesion/migration and apoptosis, and in the intercaruncular area, they were significantly enriched in pathways of signal transduction and transport. Thus, these DEGs are potential candidates for further exploring the mechanism underlying IVF/IVP-induced embryonic implant failure that occurs due to a loss of interaction between the conceptus and endometrium during the peri-implantation period.

  13. Comparative Analyses of Proteome Complement Between Worker Bee Larvae of High Royal Jelly Producing Bees (A. m. ligustica) and Carniolian Bees (A. m. carnica)

    Institute of Scientific and Technical Information of China (English)

    CHEN Jian; LI Jian-ke

    2009-01-01

    This study is to compare the protein composition of the high royal jelly producing bee (A. m. ligustica) with that of Carniolian bee (A. m. carnica) during their worker larval developmental stage. The experiment was carried out by two-dimensional gel electrophoresis. The results showed that significant higher numbers of total proteins (283) were detected in larvae of high royal jelly producing bees (Jelly bee) than those of Camiolian bees (152) on 2-d-old larvae. Among them, 110 proteins were presented on both strains of bee larvae, whereas 173 proteins were specific to larvae of Jelly bees, and 42 proteins were exclusive to Carniolian larvae. However, on the 4th d, a significant higher number of total proteins (290) were detected in larvae of Jelly bees than those of Camiolian bees (240), 163 proteins resolved to both bee larvae, and 127 proteins were specific to Jelly bees and 77 proteins to Camiolian bees. Until the 6th d, also a significant higher number of total proteins (236) were detected in larvae of Jelly bees than those of Carniolian bees (180), 132 proteins were constantly expressed in two bee larvae, whereas 104 and 48 proteins are unique to Jelly bee and Camiolian bee larvae, respectively. We tentatively concluded that the metabolic rate and gene expression of Jelly bees larvae is higher than those of Carniolian bees based proteins detected as total proteins and proteins specific to each stage of two strains of bee larvae. Proteins constantly expressed on 3 stages of larval development with some significant differences between two bee strains, and proteins unique to each stage expressed differences in term of quality and quantity, indicating that larval development needed house keeping and specific proteins to regulate its growth at different development phage, but the expression mold is different between two strains of larval development.

  14. Comparative Analyses of Three Chlorella Species in Response to Light and Sugar Reveal Distinctive Lipid Accumulation Patterns in the Microalga C. sorokiniana

    Science.gov (United States)

    Barnes, Austin; Noel, Eric A.; Betenbaugh, Michael J.; Oyler, George A.

    2014-01-01

    While photosynthetic microalgae, such as Chlorella, serve as feedstocks for nutritional oils and biofuels, heterotrophic cultivation can augment growth rates, support high cell densities, and increase triacylglycerol (TAG) lipid content. However, these species differ significantly in their photoautotrophic and heterotrophic characteristics. In this study, the phylogeny of thirty Chlorella strains was determined in order to inform bioprospecting efforts and detailed physiological assessment of three species. The growth kinetics and lipid biochemistry of C. protothecoides UTEX 411, C. vulgaris UTEX 265, and C. sorokiniana UTEX 1230 were quantified during photoautotrophy in Bold's basal medium (BBM) and heterotrophy in BBM supplemented with glucose (10 g L−1). Heterotrophic growth rates of UTEX 411, 265, and 1230 were found to be 1.5-, 3.7-, and 5-fold higher than their respective autotrophic rates. With a rapid nine-hour heterotrophic doubling time, Chlorella sorokiniana UTEX 1230 maximally accumulated 39% total lipids by dry weight during heterotrophy compared to 18% autotrophically. Furthermore, the discrete fatty acid composition of each strain was examined in order to elucidate lipid accumulation patterns under the two trophic conditions. In both modes of growth, UTEX 411 and 265 produced 18∶1 as the principal fatty acid while UTEX 1230 exhibited a 2.5-fold enrichment in 18∶2 relative to 18∶1. Although the total lipid content was highest in UTEX 411 during heterotrophy, UTEX 1230 demonstrated a two-fold increase in its heterotrophic TAG fraction at a rate of 28.9 mg L−1 d−1 to reach 22% of the biomass, corresponding to as much as 90% of its total lipids. Interestingly, UTEX 1230 growth was restricted during mixotrophy and its TAG production rate was suppressed to 18.2 mg L−1 d−1. This constraint on carbon flow raises intriguing questions about the impact of sugar and light on the metabolic regulation of microalgal lipid biosynthesis. PMID:24699196

  15. Comparative analyses of three Chlorella species in response to light and sugar reveal distinctive lipid accumulation patterns in the Microalga C. sorokiniana.

    Directory of Open Access Journals (Sweden)

    Julian N Rosenberg

    Full Text Available While photosynthetic microalgae, such as Chlorella, serve as feedstocks for nutritional oils and biofuels, heterotrophic cultivation can augment growth rates, support high cell densities, and increase triacylglycerol (TAG lipid content. However, these species differ significantly in their photoautotrophic and heterotrophic characteristics. In this study, the phylogeny of thirty Chlorella strains was determined in order to inform bioprospecting efforts and detailed physiological assessment of three species. The growth kinetics and lipid biochemistry of C. protothecoides UTEX 411, C. vulgaris UTEX 265, and C. sorokiniana UTEX 1230 were quantified during photoautotrophy in Bold's basal medium (BBM and heterotrophy in BBM supplemented with glucose (10 g L-1. Heterotrophic growth rates of UTEX 411, 265, and 1230 were found to be 1.5-, 3.7-, and 5-fold higher than their respective autotrophic rates. With a rapid nine-hour heterotrophic doubling time, Chlorella sorokiniana UTEX 1230 maximally accumulated 39% total lipids by dry weight during heterotrophy compared to 18% autotrophically. Furthermore, the discrete fatty acid composition of each strain was examined in order to elucidate lipid accumulation patterns under the two trophic conditions. In both modes of growth, UTEX 411 and 265 produced 18:1 as the principal fatty acid while UTEX 1230 exhibited a 2.5-fold enrichment in 18:2 relative to 18:1. Although the total lipid content was highest in UTEX 411 during heterotrophy, UTEX 1230 demonstrated a two-fold increase in its heterotrophic TAG fraction at a rate of 28.9 mg L(-1 d(-1 to reach 22% of the biomass, corresponding to as much as 90% of its total lipids. Interestingly, UTEX 1230 growth was restricted during mixotrophy and its TAG production rate was suppressed to 18.2 mg L-1 d-1. This constraint on carbon flow raises intriguing questions about the impact of sugar and light on the metabolic regulation of microalgal lipid biosynthesis.

  16. Comparative molecular analyses of select pH- and osmoregulatory genes in three freshwater crayfish Cherax quadricarinatus, C. destructor and C. cainii

    Directory of Open Access Journals (Sweden)

    Muhammad Y. Ali

    2017-08-01

    Full Text Available Systemic acid-base balance and osmotic/ionic regulation in decapod crustaceans are in part maintained by a set of transport-related enzymes such as carbonic anhydrase (CA, Na+/K+-ATPase (NKA, H+-ATPase (HAT, Na+/K+/2Cl− cotransporter (NKCC, Na+/Cl−/HCO ${}_{3}^{-}$ 3 − cotransporter (NBC, Na+/H+ exchanger (NHE, Arginine kinase (AK, Sarcoplasmic Ca+2-ATPase (SERCA and Calreticulin (CRT. We carried out a comparative molecular analysis of these genes in three commercially important yet eco-physiologically distinct freshwater crayfish, Cherax quadricarinatus, C. destructor and C. cainii, with the aim to identify mutations in these genes and determine if observed patterns of mutations were consistent with the action of natural selection. We also conducted a tissue-specific expression analysis of these genes across seven different organs, including gills, hepatopancreas, heart, kidney, liver, nerve and testes using NGS transcriptome data. The molecular analysis of the candidate genes revealed a high level of sequence conservation across the three Cherax sp. Hyphy analysis revealed that all candidate genes showed patterns of molecular variation consistent with neutral evolution. The tissue-specific expression analysis showed that 46% of candidate genes were expressed in all tissue types examined, while approximately 10% of candidate genes were only expressed in a single tissue type. The largest number of genes was observed in nerve (84% and gills (78% and the lowest in testes (66%. The tissue-specific expression analysis also revealed that most of the master genes regulating pH and osmoregulation (CA, NKA, HAT, NKCC, NBC, NHE were expressed in all tissue types indicating an important physiological role for these genes outside of osmoregulation in other tissue types. The high level of sequence conservation observed in the candidate genes may be explained by the important role of these genes as well as potentially having a number of other basic

  17. Comparative molecular analyses of select pH- and osmoregulatory genes in three freshwater crayfish Cherax quadricarinatus, C. destructor and C. cainii.

    Science.gov (United States)

    Ali, Muhammad Y; Pavasovic, Ana; Dammannagoda, Lalith K; Mather, Peter B; Prentis, Peter J

    2017-01-01

    Systemic acid-base balance and osmotic/ionic regulation in decapod crustaceans are in part maintained by a set of transport-related enzymes such as carbonic anhydrase (CA), Na + /K + -ATPase (NKA), H + -ATPase (HAT), Na + /K + /2Cl - cotransporter (NKCC), Na + /Cl - /HCO[Formula: see text] cotransporter (NBC), Na + /H + exchanger (NHE), Arginine kinase (AK), Sarcoplasmic Ca +2 -ATPase (SERCA) and Calreticulin (CRT). We carried out a comparative molecular analysis of these genes in three commercially important yet eco-physiologically distinct freshwater crayfish , Cherax quadricarinatus, C. destructor and C. cainii , with the aim to identify mutations in these genes and determine if observed patterns of mutations were consistent with the action of natural selection. We also conducted a tissue-specific expression analysis of these genes across seven different organs, including gills, hepatopancreas, heart, kidney, liver, nerve and testes using NGS transcriptome data. The molecular analysis of the candidate genes revealed a high level of sequence conservation across the three Cherax sp. Hyphy analysis revealed that all candidate genes showed patterns of molecular variation consistent with neutral evolution. The tissue-specific expression analysis showed that 46% of candidate genes were expressed in all tissue types examined, while approximately 10% of candidate genes were only expressed in a single tissue type. The largest number of genes was observed in nerve (84%) and gills (78%) and the lowest in testes (66%). The tissue-specific expression analysis also revealed that most of the master genes regulating pH and osmoregulation (CA, NKA, HAT, NKCC, NBC, NHE) were expressed in all tissue types indicating an important physiological role for these genes outside of osmoregulation in other tissue types. The high level of sequence conservation observed in the candidate genes may be explained by the important role of these genes as well as potentially having a number of

  18. Proteomic and Metabolomic Analyses Reveal Contrasting Anti-Inflammatory Effects of an Extract of Mucor Racemosus Secondary Metabolites Compared to Dexamethasone.

    Science.gov (United States)

    Meier, Samuel M; Muqaku, Besnik; Ullmann, Ronald; Bileck, Andrea; Kreutz, Dominique; Mader, Johanna C; Knasmüller, Siegfried; Gerner, Christopher

    2015-01-01

    Classical drug assays are often confined to single molecules and targeting single pathways. However, it is also desirable to investigate the effects of complex mixtures on complex systems such as living cells including the natural multitude of signalling pathways. Evidence based on herbal medicine has motivated us to investigate potential beneficial health effects of Mucor racemosus (M rac) extracts. Secondary metabolites of M rac were collected using a good-manufacturing process (GMP) approved production line and a validated manufacturing process, in order to obtain a stable product termed SyCircue (National Drug Code USA: 10424-102). Toxicological studies confirmed that this product does not contain mycotoxins and is non-genotoxic. Potential effects on inflammatory processes were investigated by treating stimulated cells with M rac extracts and the effects were compared to the standard anti-inflammatory drug dexamethasone on the levels of the proteome and metabolome. Using 2D-PAGE, slight anti-inflammatory effects were observed in primary white blood mononuclear cells, which were more pronounced in primary human umbilical vein endothelial cells (HUVECs). Proteome profiling based on nLC-MS/MS analysis of tryptic digests revealed inhibitory effects of M rac extracts on pro-inflammatory cytoplasmic mediators and secreted cytokines and chemokines in these endothelial cells. This finding was confirmed using targeted proteomics, here treatment of stimulated cells with M rac extracts down-regulated the secretion of IL-6, IL-8, CXCL5 and GROA significantly. Finally, the modulating effects of M rac on HUVECs were also confirmed on the level of the metabolome. Several metabolites displayed significant concentration changes upon treatment of inflammatory activated HUVECs with the M rac extract, including spermine and lysophosphatidylcholine acyl C18:0 and sphingomyelin C26:1, while the bulk of measured metabolites remained unaffected. Interestingly, the effects of M rac

  19. Comparative proteomic analyses reveal that the regulators of G-protein signaling proteins regulate amino acid metabolism of the rice blast fungus Magnaporthe oryzae.

    Science.gov (United States)

    Zhang, Haifeng; Ma, Hongyu; Xie, Xin; Ji, Jun; Dong, Yanhan; Du, Yan; Tang, Wei; Zheng, Xiaobo; Wang, Ping; Zhang, Zhengguang

    2014-11-01

    The rice blast fungus Magnaporthe oryzae encodes eight regulators of G-protein (GTP-binding protein) signaling (RGS) proteins MoRgs1-MoRgs8 that orchestrate the growth, asexual/sexual production, appressorium differentiation, and pathogenicity. To address the mechanisms by which MoRgs proteins function, we conducted a 2DE proteome study and identified 82 differentially expressed proteins by comparing five ∆Morgs mutants with wild-type Guy11 strain. We found that the abundances of eight amino acid (AA) biosynthesis or degradation associated proteins were markedly altered in five ∆Morgs mutants, indicating one of the main collective roles for the MoRgs proteins is to influence AA metabolism. We showed that MoRgs proteins have distinct roles in AA metabolism and nutrient responses from growth assays. In addition, we characterized MoLys20 (Lys is lysine), a homocitrate synthase, whose abundance was significantly decreased in the ∆Morgs mutants. The ∆Molys20 mutant is auxotrophic for lys and exogenous lys could partially rescue its auxotrophic defects. Deletion of MoLYS20 resulted in defects in conidiation and infection, as well as pathogenicity on rice. Overall, our results indicate that one of the critical roles for MoRgs proteins is to regulate AA metabolism, and that MoLys20 may be directly or indirectly regulated by MoRgs and participated in lys biosynthesis, thereby affecting fungal development and pathogenicity. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods.

    Science.gov (United States)

    Baa-Puyoulet, Patrice; Parisot, Nicolas; Febvay, Gérard; Huerta-Cepas, Jaime; Vellozo, Augusto F; Gabaldón, Toni; Calevro, Federica; Charles, Hubert; Colella, Stefano

    2016-01-01

    Arthropods interact with humans at different levels with highly beneficial roles (e.g. as pollinators), as well as with a negative impact for example as vectors of human or animal diseases, or as agricultural pests. Several arthropod genomes are available at present and many others will be sequenced in the near future in the context of the i5K initiative, offering opportunities for reconstructing, modelling and comparing their metabolic networks. In-depth analysis of these genomic data through metabolism reconstruction is expected to contribute to a better understanding of the biology of arthropods, thereby allowing the development of new strategies to control harmful species. In this context, we present here ArthropodaCyc, a dedicated BioCyc collection of databases using the Cyc annotation database system (CycADS), allowing researchers to perform reliable metabolism comparisons of fully sequenced arthropods genomes. Since the annotation quality is a key factor when performing such global genome comparisons, all proteins from the genomes included in the ArthropodaCyc database were re-annotated using several annotation tools and orthology information. All functional/domain annotation results and their sources were integrated in the databases for user access. Currently, ArthropodaCyc offers a centralized repository of metabolic pathways, protein sequence domains, Gene Ontology annotations as well as evolutionary information for 28 arthropod species. Such database collection allows metabolism analysis both with integrated tools and through extraction of data in formats suitable for systems biology studies.Database URL: http://arthropodacyc.cycadsys.org/. © The Author(s) 2016. Published by Oxford University Press.

  1. Quantile regression theory and applications

    CERN Document Server

    Davino, Cristina; Vistocco, Domenico

    2013-01-01

    A guide to the implementation and interpretation of Quantile Regression models This book explores the theory and numerous applications of quantile regression, offering empirical data analysis as well as the software tools to implement the methods. The main focus of this book is to provide the reader with a comprehensivedescription of the main issues concerning quantile regression; these include basic modeling, geometrical interpretation, estimation and inference for quantile regression, as well as issues on validity of the model, diagnostic tools. Each methodological aspect is explored and

  2. Circular job-related spatial mobility in Germany:Comparative analyses of two representative surveys on the forms, prevalence and relevance in the context of partnership and family development

    Directory of Open Access Journals (Sweden)

    Heiko Rüger

    2012-01-01

    In this regard, the present article aims at achieving three essential objectives. First, we will introduce a common indicator for circular job mobility patterns found in the two surveys. On the basis of this common indicator, we will comparatively analyse the prevalence of different mobility forms and their composition according to key socio-demographic characteristics. In addition, we will use multivariate analyses to illustrate the relevance of job mobility for partnership and family development. Results suggest mobility patterns to be an important individual context factor when explaining processes relevant to partnerships and family. In particular, women who exhibit some degree of job mobility are less often married and rarely have children.

  3. The regulation mechanisms of soluble starch and glycerol for production of azaphilone pigments in Monascus purpureus FAFU618 as revealed by comparative proteomic and transcriptional analyses.

    Science.gov (United States)

    Huang, Zi-Rui; Zhou, Wen-Bin; Yang, Xue-Ling; Tong, Ai-Jun; Hong, Jia-Li; Guo, Wei-Ling; Li, Tian-Tian; Jia, Rui-Bo; Pan, Yu-Yang; Lin, Jun; Lv, Xu-Cong; Liu, Bin

    2018-04-01

    Monascus spp. have been used for thousands of years as a traditional food additive in China. This mold can produce many different types of commercially valuable secondary metabolites of biological activity. Soluble starch and glycerol are the two principal carbon sources universally utilized by Monascus for the production of beneficial metabolites. In this study, the effects and regulation mechanisms of soluble starch and glycerol for M. purpureus FAFU618 on Monascus azaphilone pigments (MonAzPs) were investigated through ultra-performance liquid chromatography quadrupole time of flight mass spectrometry (UPLC-QTOF-MS/MS), comparative proteomics and quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR). The production of intracellular and extracellular pigments was significantly different between the soluble starch group (SSG) and glycerol group (GCG). Additionally, the components of intracellular pigments revealed by UPLC-QTOF-MS/MS showed that Monascin and Ankaflavin increased significantly in the GCG, while Rubropunctatin and Monascorubrin increased in the SSG. Differentially expressed proteins of mycelia between SSG and GCG were analyzed by two-dimensional gel electrophoresis (2-DE) and MALDI-TOF/TOF MS. We identified 27 proteins with statistically altered expression, of which 18 proteins associated with the EMP (glycolytic pathway), translation, energy generation, proteolysis, etc. were up-regulated, and 9 proteins, including ribosomal proteins, heat shock proteins (HSPs) and others, were down-regulated in GCG. Meanwhile, the expression levels of MonAzP biosynthetic genes were also analyzed by RT-qPCR, and the results showed that mppA, mppC, mppR1 and mppR2 were down-regulated, whereas genes MpPKS5, MpFasA2, MpFasB2, mppB, mppD and mppE were up-regulated. Collectively, these findings illustrate that the regulation of MonAzPs is not only closely related to the expression levels of certain proteins in the polyketide synthesis pathway

  4. Pre-service Teachers’ Comparative Analyses of Teacher-/Parent- Child Talk: Making Literacy Teaching Explicit and Children’s Literacy Learning Visible

    Directory of Open Access Journals (Sweden)

    Deborah Geoghegan

    2012-06-01

    Full Text Available This paper reports on the results of a meta-analysis of first year pre-service teachers’ investigations of two transcripts of teacher/student talk. The first is set in the home environment and the second in the classroom. Working with specific tools of analysis and knowledge of the role of talk in literate, cultural and social practices they identified evidence of effective literacy pedagogy. They presented their findings in the genre of a written comparative analysis. The results showed the discourse analysis task helped them understand the vital role of the adult’s talk in scaffolding children’s learning in each context and raised awareness of how the adults’ cognitive “moves” impacted on the scaffolding of literacy learning. Outcomes highlighted the need for teacher preparation courses to focus on the way classroom discourse relates to pedagogy and children’s literacy learning by providing exemplary teaching episodes, and studying the pedagogical language competencies involved.Este artículo presenta los resultados de un meta-análisis de dos investigaciones sobre la función comunicativa profesor/alumno realizadas por docentes en su primer año de pre-servicio. La primera en el entorno doméstico y la segunda en el aula. Utilizándose instrumentos de análisis y sus conocimientos de la función comunicativa en las prácticas de alfabetización cultural y social, los docentes encontraron evidencia de una pedagogía eficaz de alfabetización. Las conclusiones en el género de análisis comparativo muestran como el ejercicio de análisis de la conversación ayuda a entender la función vital de la comunicación del adulto en el aprendizaje de los niños en cada contexto y concientizó como las decisiones cognoscitivas de los adultos influyen en la pedagogía de alfabetización. Los resultados recalcan la necesidad de formaciones para docentes en la comunicación en clase y como se relaciona con la pedagogía y alfabetización de

  5. Comparative analyses of two thermophilic enzymes exhibiting both beta-1,4 mannosidic and beta-1,4 glucosidic cleavage activities from Caldanaerobius polysaccharolyticus.

    Science.gov (United States)

    Han, Yejun; Dodd, Dylan; Hespen, Charles W; Ohene-Adjei, Samuel; Schroeder, Charles M; Mackie, Roderick I; Cann, Isaac K O

    2010-08-01

    The hydrolysis of polysaccharides containing mannan requires endo-1,4-beta-mannanase and 1,4-beta-mannosidase activities. In the current report, the biochemical properties of two endo-beta-1,4-mannanases (Man5A and Man5B) from Caldanaerobius polysaccharolyticus were studied. Man5A is composed of an N-terminal signal peptide (SP), a catalytic domain, two carbohydrate-binding modules (CBMs), and three surface layer homology (SLH) repeats, whereas Man5B lacks the SP, CBMs, and SLH repeats. To gain insights into how the two glycoside hydrolase family 5 (GH5) enzymes may aid the bacterium in energy acquisition and also the potential application of the two enzymes in the biofuel industry, two derivatives of Man5A (Man5A-TM1 [TM1 stands for truncational mutant 1], which lacks the SP and SLH repeats, and Man5A-TM2, which lacks the SP, CBMs, and SLH repeats) and the wild-type Man5B were biochemically analyzed. The Man5A derivatives displayed endo-1,4-beta-mannanase and endo-1,4-beta-glucanase activities and hydrolyzed oligosaccharides with a degree of polymerization (DP) of 4 or higher. Man5B exhibited endo-1,4-beta-mannanase activity and little endo-1,4-beta-glucanase activity; however, this enzyme also exhibited 1,4-beta-mannosidase and cellodextrinase activities. Man5A-TM1, compared to either Man5A-TM2 or Man5B, had higher catalytic activity with soluble and insoluble polysaccharides, indicating that the CBMs enhance catalysis of Man5A. Furthermore, Man5A-TM1 acted synergistically with Man5B in the hydrolysis of beta-mannan and carboxymethyl cellulose. The versatility of the two enzymes, therefore, makes them a resource for depolymerization of mannan-containing polysaccharides in the biofuel industry. Furthermore, on the basis of the biochemical and genomic data, a molecular mechanism for utilization of mannan-containing nutrients by C. polysaccharolyticus is proposed.

  6. Logistic regression applied to natural hazards: rare event logistic regression with replications

    Directory of Open Access Journals (Sweden)

    M. Guns

    2012-06-01

    Full Text Available Statistical analysis of natural hazards needs particular attention, as most of these phenomena are rare events. This study shows that the ordinary rare event logistic regression, as it is now commonly used in geomorphologic studies, does not always lead to a robust detection of controlling factors, as the results can be strongly sample-dependent. In this paper, we introduce some concepts of Monte Carlo simulations in rare event logistic regression. This technique, so-called rare event logistic regression with replications, combines the strength of probabilistic and statistical methods, and allows overcoming some of the limitations of previous developments through robust variable selection. This technique was here developed for the analyses of landslide controlling factors, but the concept is widely applicable for statistical analyses of natural hazards.

  7. Logistic regression applied to natural hazards: rare event logistic regression with replications

    Science.gov (United States)

    Guns, M.; Vanacker, V.

    2012-06-01

    Statistical analysis of natural hazards needs particular attention, as most of these phenomena are rare events. This study shows that the ordinary rare event logistic regression, as it is now commonly used in geomorphologic studies, does not always lead to a robust detection of controlling factors, as the results can be strongly sample-dependent. In this paper, we introduce some concepts of Monte Carlo simulations in rare event logistic regression. This technique, so-called rare event logistic regression with replications, combines the strength of probabilistic and statistical methods, and allows overcoming some of the limitations of previous developments through robust variable selection. This technique was here developed for the analyses of landslide controlling factors, but the concept is widely applicable for statistical analyses of natural hazards.

  8. Price promotions on healthier compared with less healthy foods: a hierarchical regression analysis of the impact on sales and social patterning of responses to promotions in Great Britain12345

    Science.gov (United States)

    Nakamura, Ryota; Suhrcke, Marc; Jebb, Susan A; Pechey, Rachel; Almiron-Roig, Eva; Marteau, Theresa M

    2015-01-01

    Background: There is a growing concern, but limited evidence, that price promotions contribute to a poor diet and the social patterning of diet-related disease. Objective: We examined the following questions: 1) Are less-healthy foods more likely to be promoted than healthier foods? 2) Are consumers more responsive to promotions on less-healthy products? 3) Are there socioeconomic differences in food purchases in response to price promotions? Design: With the use of hierarchical regression, we analyzed data on purchases of 11,323 products within 135 food and beverage categories from 26,986 households in Great Britain during 2010. Major supermarkets operated the same price promotions in all branches. The number of stores that offered price promotions on each product for each week was used to measure the frequency of price promotions. We assessed the healthiness of each product by using a nutrient profiling (NP) model. Results: A total of 6788 products (60%) were in healthier categories and 4535 products (40%) were in less-healthy categories. There was no significant gap in the frequency of promotion by the healthiness of products neither within nor between categories. However, after we controlled for the reference price, price discount rate, and brand-specific effects, the sales uplift arising from price promotions was larger in less-healthy than in healthier categories; a 1-SD point increase in the category mean NP score, implying the category becomes less healthy, was associated with an additional 7.7–percentage point increase in sales (from 27.3% to 35.0%; P sales uplift from promotions was larger for higher–socioeconomic status (SES) groups than for lower ones (34.6% for the high-SES group, 28.1% for the middle-SES group, and 23.1% for the low-SES group). Finally, there was no significant SES gap in the absolute volume of purchases of less-healthy foods made on promotion. Conclusion: Attempts to limit promotions on less-healthy foods could improve the

  9. Panel Smooth Transition Regression Models

    DEFF Research Database (Denmark)

    González, Andrés; Terasvirta, Timo; Dijk, Dick van

    We introduce the panel smooth transition regression model. This new model is intended for characterizing heterogeneous panels, allowing the regression coefficients to vary both across individuals and over time. Specifically, heterogeneity is allowed for by assuming that these coefficients are bou...

  10. Testing discontinuities in nonparametric regression

    KAUST Repository

    Dai, Wenlin

    2017-01-19

    In nonparametric regression, it is often needed to detect whether there are jump discontinuities in the mean function. In this paper, we revisit the difference-based method in [13 H.-G. Müller and U. Stadtmüller, Discontinuous versus smooth regression, Ann. Stat. 27 (1999), pp. 299–337. doi: 10.1214/aos/1018031100

  11. Testing discontinuities in nonparametric regression

    KAUST Repository

    Dai, Wenlin; Zhou, Yuejin; Tong, Tiejun

    2017-01-01

    In nonparametric regression, it is often needed to detect whether there are jump discontinuities in the mean function. In this paper, we revisit the difference-based method in [13 H.-G. Müller and U. Stadtmüller, Discontinuous versus smooth regression, Ann. Stat. 27 (1999), pp. 299–337. doi: 10.1214/aos/1018031100

  12. Logistic Regression: Concept and Application

    Science.gov (United States)

    Cokluk, Omay

    2010-01-01

    The main focus of logistic regression analysis is classification of individuals in different groups. The aim of the present study is to explain basic concepts and processes of binary logistic regression analysis intended to determine the combination of independent variables which best explain the membership in certain groups called dichotomous…

  13. Fungible weights in logistic regression.

    Science.gov (United States)

    Jones, Jeff A; Waller, Niels G

    2016-06-01

    In this article we develop methods for assessing parameter sensitivity in logistic regression models. To set the stage for this work, we first review Waller's (2008) equations for computing fungible weights in linear regression. Next, we describe 2 methods for computing fungible weights in logistic regression. To demonstrate the utility of these methods, we compute fungible logistic regression weights using data from the Centers for Disease Control and Prevention's (2010) Youth Risk Behavior Surveillance Survey, and we illustrate how these alternate weights can be used to evaluate parameter sensitivity. To make our work accessible to the research community, we provide R code (R Core Team, 2015) that will generate both kinds of fungible logistic regression weights. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  14. Ordinary least square regression, orthogonal regression, geometric mean regression and their applications in aerosol science

    International Nuclear Information System (INIS)

    Leng Ling; Zhang Tianyi; Kleinman, Lawrence; Zhu Wei

    2007-01-01

    Regression analysis, especially the ordinary least squares method which assumes that errors are confined to the dependent variable, has seen a fair share of its applications in aerosol science. The ordinary least squares approach, however, could be problematic due to the fact that atmospheric data often does not lend itself to calling one variable independent and the other dependent. Errors often exist for both measurements. In this work, we examine two regression approaches available to accommodate this situation. They are orthogonal regression and geometric mean regression. Comparisons are made theoretically as well as numerically through an aerosol study examining whether the ratio of organic aerosol to CO would change with age

  15. Post-processing through linear regression

    Science.gov (United States)

    van Schaeybroeck, B.; Vannitsem, S.

    2011-03-01

    Various post-processing techniques are compared for both deterministic and ensemble forecasts, all based on linear regression between forecast data and observations. In order to evaluate the quality of the regression methods, three criteria are proposed, related to the effective correction of forecast error, the optimal variability of the corrected forecast and multicollinearity. The regression schemes under consideration include the ordinary least-square (OLS) method, a new time-dependent Tikhonov regularization (TDTR) method, the total least-square method, a new geometric-mean regression (GM), a recently introduced error-in-variables (EVMOS) method and, finally, a "best member" OLS method. The advantages and drawbacks of each method are clarified. These techniques are applied in the context of the 63 Lorenz system, whose model version is affected by both initial condition and model errors. For short forecast lead times, the number and choice of predictors plays an important role. Contrarily to the other techniques, GM degrades when the number of predictors increases. At intermediate lead times, linear regression is unable to provide corrections to the forecast and can sometimes degrade the performance (GM and the best member OLS with noise). At long lead times the regression schemes (EVMOS, TDTR) which yield the correct variability and the largest correlation between ensemble error and spread, should be preferred.

  16. Post-processing through linear regression

    Directory of Open Access Journals (Sweden)

    B. Van Schaeybroeck

    2011-03-01

    Full Text Available Various post-processing techniques are compared for both deterministic and ensemble forecasts, all based on linear regression between forecast data and observations. In order to evaluate the quality of the regression methods, three criteria are proposed, related to the effective correction of forecast error, the optimal variability of the corrected forecast and multicollinearity. The regression schemes under consideration include the ordinary least-square (OLS method, a new time-dependent Tikhonov regularization (TDTR method, the total least-square method, a new geometric-mean regression (GM, a recently introduced error-in-variables (EVMOS method and, finally, a "best member" OLS method. The advantages and drawbacks of each method are clarified.

    These techniques are applied in the context of the 63 Lorenz system, whose model version is affected by both initial condition and model errors. For short forecast lead times, the number and choice of predictors plays an important role. Contrarily to the other techniques, GM degrades when the number of predictors increases. At intermediate lead times, linear regression is unable to provide corrections to the forecast and can sometimes degrade the performance (GM and the best member OLS with noise. At long lead times the regression schemes (EVMOS, TDTR which yield the correct variability and the largest correlation between ensemble error and spread, should be preferred.

  17. Tumor regression patterns in retinoblastoma

    International Nuclear Information System (INIS)

    Zafar, S.N.; Siddique, S.N.; Zaheer, N.

    2016-01-01

    To observe the types of tumor regression after treatment, and identify the common pattern of regression in our patients. Study Design: Descriptive study. Place and Duration of Study: Department of Pediatric Ophthalmology and Strabismus, Al-Shifa Trust Eye Hospital, Rawalpindi, Pakistan, from October 2011 to October 2014. Methodology: Children with unilateral and bilateral retinoblastoma were included in the study. Patients were referred to Pakistan Institute of Medical Sciences, Islamabad, for chemotherapy. After every cycle of chemotherapy, dilated funds examination under anesthesia was performed to record response of the treatment. Regression patterns were recorded on RetCam II. Results: Seventy-four tumors were included in the study. Out of 74 tumors, 3 were ICRB group A tumors, 43 were ICRB group B tumors, 14 tumors belonged to ICRB group C, and remaining 14 were ICRB group D tumors. Type IV regression was seen in 39.1% (n=29) tumors, type II in 29.7% (n=22), type III in 25.6% (n=19), and type I in 5.4% (n=4). All group A tumors (100%) showed type IV regression. Seventeen (39.5%) group B tumors showed type IV regression. In group C, 5 tumors (35.7%) showed type II regression and 5 tumors (35.7%) showed type IV regression. In group D, 6 tumors (42.9%) regressed to type II non-calcified remnants. Conclusion: The response and success of the focal and systemic treatment, as judged by the appearance of different patterns of tumor regression, varies with the ICRB grouping of the tumor. (author)

  18. Discriminative Elastic-Net Regularized Linear Regression.

    Science.gov (United States)

    Zhang, Zheng; Lai, Zhihui; Xu, Yong; Shao, Ling; Wu, Jian; Xie, Guo-Sen

    2017-03-01

    In this paper, we aim at learning compact and discriminative linear regression models. Linear regression has been widely used in different problems. However, most of the existing linear regression methods exploit the conventional zero-one matrix as the regression targets, which greatly narrows the flexibility of the regression model. Another major limitation of these methods is that the learned projection matrix fails to precisely project the image features to the target space due to their weak discriminative capability. To this end, we present an elastic-net regularized linear regression (ENLR) framework, and develop two robust linear regression models which possess the following special characteristics. First, our methods exploit two particular strategies to enlarge the margins of different classes by relaxing the strict binary targets into a more feasible variable matrix. Second, a robust elastic-net regularization of singular values is introduced to enhance the compactness and effectiveness of the learned projection matrix. Third, the resulting optimization problem of ENLR has a closed-form solution in each iteration, which can be solved efficiently. Finally, rather than directly exploiting the projection matrix for recognition, our methods employ the transformed features as the new discriminate representations to make final image classification. Compared with the traditional linear regression model and some of its variants, our method is much more accurate in image classification. Extensive experiments conducted on publicly available data sets well demonstrate that the proposed framework can outperform the state-of-the-art methods. The MATLAB codes of our methods can be available at http://www.yongxu.org/lunwen.html.

  19. Regression Models and Fuzzy Logic Prediction of TBM Penetration Rate

    Directory of Open Access Journals (Sweden)

    Minh Vu Trieu

    2017-03-01

    Full Text Available This paper presents statistical analyses of rock engineering properties and the measured penetration rate of tunnel boring machine (TBM based on the data of an actual project. The aim of this study is to analyze the influence of rock engineering properties including uniaxial compressive strength (UCS, Brazilian tensile strength (BTS, rock brittleness index (BI, the distance between planes of weakness (DPW, and the alpha angle (Alpha between the tunnel axis and the planes of weakness on the TBM rate of penetration (ROP. Four (4 statistical regression models (two linear and two nonlinear are built to predict the ROP of TBM. Finally a fuzzy logic model is developed as an alternative method and compared to the four statistical regression models. Results show that the fuzzy logic model provides better estimations a