Modeling animal-vehicle collisions using diagonal inflated bivariate Poisson regression.

Science.gov (United States)

Lao, Yunteng; Wu, Yao-Jan; Corey, Jonathan; Wang, Yinhai

2011-01-01

Two types of animal-vehicle collision (AVC) data are commonly adopted for AVC-related risk analysis research: reported AVC data and carcass removal data. One issue with these two data sets is that they were found to have significant discrepancies by previous studies. In order to model these two types of data together and provide a better understanding of highway AVCs, this study adopts a diagonal inflated bivariate Poisson regression method, an inflated version of bivariate Poisson regression model, to fit the reported AVC and carcass removal data sets collected in Washington State during 2002-2006. The diagonal inflated bivariate Poisson model not only can model paired data with correlation, but also handle under- or over-dispersed data sets as well. Compared with three other types of models, double Poisson, bivariate Poisson, and zero-inflated double Poisson, the diagonal inflated bivariate Poisson model demonstrates its capability of fitting two data sets with remarkable overlapping portions resulting from the same stochastic process. Therefore, the diagonal inflated bivariate Poisson model provides researchers a new approach to investigating AVCs from a different perspective involving the three distribution parameters (λ(1), λ(2) and λ(3)). The modeling results show the impacts of traffic elements, geometric design and geographic characteristics on the occurrences of both reported AVC and carcass removal data. It is found that the increase of some associated factors, such as speed limit, annual average daily traffic, and shoulder width, will increase the numbers of reported AVCs and carcass removals. Conversely, the presence of some geometric factors, such as rolling and mountainous terrain, will decrease the number of reported AVCs. Published by Elsevier Ltd.

Analysis of Blood Transfusion Data Using Bivariate Zero-Inflated Poisson Model: A Bayesian Approach.

Science.gov (United States)

Mohammadi, Tayeb; Kheiri, Soleiman; Sedehi, Morteza

2016-01-01

Recognizing the factors affecting the number of blood donation and blood deferral has a major impact on blood transfusion. There is a positive correlation between the variables "number of blood donation" and "number of blood deferral": as the number of return for donation increases, so does the number of blood deferral. On the other hand, due to the fact that many donors never return to donate, there is an extra zero frequency for both of the above-mentioned variables. In this study, in order to apply the correlation and to explain the frequency of the excessive zero, the bivariate zero-inflated Poisson regression model was used for joint modeling of the number of blood donation and number of blood deferral. The data was analyzed using the Bayesian approach applying noninformative priors at the presence and absence of covariates. Estimating the parameters of the model, that is, correlation, zero-inflation parameter, and regression coefficients, was done through MCMC simulation. Eventually double-Poisson model, bivariate Poisson model, and bivariate zero-inflated Poisson model were fitted on the data and were compared using the deviance information criteria (DIC). The results showed that the bivariate zero-inflated Poisson regression model fitted the data better than the other models.

The return period analysis of natural disasters with statistical modeling of bivariate joint probability distribution.

Science.gov (United States)

Li, Ning; Liu, Xueqin; Xie, Wei; Wu, Jidong; Zhang, Peng

2013-01-01

New features of natural disasters have been observed over the last several years. The factors that influence the disasters' formation mechanisms, regularity of occurrence and main characteristics have been revealed to be more complicated and diverse in nature than previously thought. As the uncertainty involved increases, the variables need to be examined further. This article discusses the importance and the shortage of multivariate analysis of natural disasters and presents a method to estimate the joint probability of the return periods and perform a risk analysis. Severe dust storms from 1990 to 2008 in Inner Mongolia were used as a case study to test this new methodology, as they are normal and recurring climatic phenomena on Earth. Based on the 79 investigated events and according to the dust storm definition with bivariate, the joint probability distribution of severe dust storms was established using the observed data of maximum wind speed and duration. The joint return periods of severe dust storms were calculated, and the relevant risk was analyzed according to the joint probability. The copula function is able to simulate severe dust storm disasters accurately. The joint return periods generated are closer to those observed in reality than the univariate return periods and thus have more value in severe dust storm disaster mitigation, strategy making, program design, and improvement of risk management. This research may prove useful in risk-based decision making. The exploration of multivariate analysis methods can also lay the foundation for further applications in natural disaster risk analysis. © 2012 Society for Risk Analysis.

Applied Statistics: From Bivariate through Multivariate Techniques [with CD-ROM

Science.gov (United States)

Warner, Rebecca M.

2007-01-01

This book provides a clear introduction to widely used topics in bivariate and multivariate statistics, including multiple regression, discriminant analysis, MANOVA, factor analysis, and binary logistic regression. The approach is applied and does not require formal mathematics; equations are accompanied by verbal explanations. Students are asked…

Smoothing of the bivariate LOD score for non-normal quantitative traits.

Science.gov (United States)

Buil, Alfonso; Dyer, Thomas D; Almasy, Laura; Blangero, John

2005-12-30

Variance component analysis provides an efficient method for performing linkage analysis for quantitative traits. However, type I error of variance components-based likelihood ratio testing may be affected when phenotypic data are non-normally distributed (especially with high values of kurtosis). This results in inflated LOD scores when the normality assumption does not hold. Even though different solutions have been proposed to deal with this problem with univariate phenotypes, little work has been done in the multivariate case. We present an empirical approach to adjust the inflated LOD scores obtained from a bivariate phenotype that violates the assumption of normality. Using the Collaborative Study on the Genetics of Alcoholism data available for the Genetic Analysis Workshop 14, we show how bivariate linkage analysis with leptokurtotic traits gives an inflated type I error. We perform a novel correction that achieves acceptable levels of type I error.

Probability distributions with truncated, log and bivariate extensions

CERN Document Server

Thomopoulos, Nick T

2018-01-01

This volume presents a concise and practical overview of statistical methods and tables not readily available in other publications. It begins with a review of the commonly used continuous and discrete probability distributions. Several useful distributions that are not so common and less understood are described with examples and applications in full detail: discrete normal, left-partial, right-partial, left-truncated normal, right-truncated normal, lognormal, bivariate normal, and bivariate lognormal. Table values are provided with examples that enable researchers to easily apply the distributions to real applications and sample data. The left- and right-truncated normal distributions offer a wide variety of shapes in contrast to the symmetrically shaped normal distribution, and a newly developed spread ratio enables analysts to determine which of the three distributions best fits a particular set of sample data. The book will be highly useful to anyone who does statistical and probability analysis. This in...

Bivariate Kumaraswamy Models via Modified FGM Copulas: Properties and Applications

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Indranil Ghosh

2017-11-01

Full Text Available A copula is a useful tool for constructing bivariate and/or multivariate distributions. In this article, we consider a new modified class of FGM (Farlie–Gumbel–Morgenstern bivariate copula for constructing several different bivariate Kumaraswamy type copulas and discuss their structural properties, including dependence structures. It is established that construction of bivariate distributions by this method allows for greater flexibility in the values of Spearman’s correlation coefficient, ρ and Kendall’s τ .

An Affine Invariant Bivariate Version of the Sign Test.

Science.gov (United States)

1987-06-01

words: affine invariance, bivariate quantile, bivariate symmetry, model,. generalized median, influence function , permutation test, normal efficiency...calculate a bivariate version of the influence function , and the resulting form is bounded, as is the case for the univartate sign test, and shows the...terms of a blvariate analogue of IHmpel’s (1974) influence function . The latter, though usually defined as a von-Mises derivative of certain

Global assessment of predictability of water availability: A bivariate probabilistic Budyko analysis

Science.gov (United States)

Wang, Weiguang; Fu, Jianyu

2018-02-01

Estimating continental water availability is of great importance for water resources management, in terms of maintaining ecosystem integrity and sustaining society development. To more accurately quantify the predictability of water availability, on the basis of univariate probabilistic Budyko framework, a bivariate probabilistic Budyko approach was developed using copula-based joint distribution model for considering the dependence between parameter ω of Wang-Tang's equation and the Normalized Difference Vegetation Index (NDVI), and was applied globally. The results indicate the predictive performance in global water availability is conditional on the climatic condition. In comparison with simple univariate distribution, the bivariate one produces the lower interquartile range under the same global dataset, especially in the regions with higher NDVI values, highlighting the importance of developing the joint distribution by taking into account the dependence structure of parameter ω and NDVI, which can provide more accurate probabilistic evaluation of water availability.

STUDI PERBANDINGAN ANTARA ALGORITMA BIVARIATE MARGINAL DISTRIBUTION DENGAN ALGORITMA GENETIKA

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Chastine Fatichah

2006-01-01

Full Text Available Bivariate Marginal Distribution Algorithm is extended from Estimation of Distribution Algorithm. This heuristic algorithm proposes the new approach for recombination of generate new individual that without crossover and mutation process such as genetic algorithm. Bivariate Marginal Distribution Algorithm uses connectivity variable the pair gene for recombination of generate new individual. Connectivity between variable is doing along optimization process. In this research, genetic algorithm performance with one point crossover is compared with Bivariate Marginal Distribution Algorithm performance in case Onemax, De Jong F2 function, and Traveling Salesman Problem. In this research, experimental results have shown performance the both algorithm is dependence of parameter respectively and also population size that used. For Onemax case with size small problem, Genetic Algorithm perform better with small number of iteration and more fast for get optimum result. However, Bivariate Marginal Distribution Algorithm perform better of result optimization for case Onemax with huge size problem. For De Jong F2 function, Genetic Algorithm perform better from Bivariate Marginal Distribution Algorithm of a number of iteration and time. For case Traveling Salesman Problem, Bivariate Marginal Distribution Algorithm have shown perform better from Genetic Algorithm of optimization result. Abstract in Bahasa Indonesia : Bivariate Marginal Distribution Algorithm merupakan perkembangan lebih lanjut dari Estimation of Distribution Algorithm. Algoritma heuristik ini mengenalkan pendekatan baru dalam melakukan rekombinasi untuk membentuk individu baru, yaitu tidak menggunakan proses crossover dan mutasi seperti pada Genetic Algorithm. Bivariate Marginal Distribution Algorithm menggunakan keterkaitan pasangan variabel dalam melakukan rekombinasi untuk membentuk individu baru. Keterkaitan antar variabel tersebut ditemukan selama proses optimasi berlangsung. Aplikasi yang

Comparison of Model Reliabilities from Single-Step and Bivariate Blending Methods

DEFF Research Database (Denmark)

Taskinen, Matti; Mäntysaari, Esa; Lidauer, Martin

2013-01-01

Model based reliabilities in genetic evaluation are compared between three methods: animal model BLUP, single-step BLUP, and bivariate blending after genomic BLUP. The original bivariate blending is revised in this work to better account animal models. The study data is extracted from...... be calculated. Model reliabilities by the single-step and the bivariate blending methods were higher than by animal model due to genomic information. Compared to the single-step method, the bivariate blending method reliability estimates were, in general, lower. Computationally bivariate blending method was......, on the other hand, lighter than the single-step method....

Bivariate Drought Analysis Using Streamflow Reconstruction with Tree Ring Indices in the Sacramento Basin, California, USA

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Jaewon Kwak

2016-03-01

Full Text Available Long-term streamflow data are vital for analysis of hydrological droughts. Using an artificial neural network (ANN model and nine tree-ring indices, this study reconstructed the annual streamflow of the Sacramento River for the period from 1560 to 1871. Using the reconstructed streamflow data, the copula method was used for bivariate drought analysis, deriving a hydrological drought return period plot for the Sacramento River basin. Results showed strong correlation among drought characteristics, and the drought with a 20-year return period (17.2 million acre-feet (MAF per year in the Sacramento River basin could be considered a critical level of drought for water shortages.

Reliability for some bivariate beta distributions

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Nadarajah Saralees

2005-01-01

Full Text Available In the area of stress-strength models there has been a large amount of work as regards estimation of the reliability R=Pr( Xbivariate distribution with dependence between X and Y . In particular, we derive explicit expressions for R when the joint distribution is bivariate beta. The calculations involve the use of special functions.

Reliability for some bivariate gamma distributions

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Nadarajah Saralees

2005-01-01

Full Text Available In the area of stress-strength models, there has been a large amount of work as regards estimation of the reliability R=Pr( Xbivariate distribution with dependence between X and Y . In particular, we derive explicit expressions for R when the joint distribution is bivariate gamma. The calculations involve the use of special functions.

Ordinal bivariate inequality

DEFF Research Database (Denmark)

Sonne-Schmidt, Christoffer Scavenius; Tarp, Finn; Østerdal, Lars Peter Raahave

This paper introduces a concept of inequality comparisons with ordinal bivariate categorical data. In our model, one population is more unequal than another when they have common arithmetic median outcomes and the first can be obtained from the second by correlationincreasing switches and/or median......-preserving spreads. For the canonical 2x2 case (with two binary indicators), we derive a simple operational procedure for checking ordinal inequality relations in practice. As an illustration, we apply the model to childhood deprivation in Mozambique....

Ordinal Bivariate Inequality

DEFF Research Database (Denmark)

Sonne-Schmidt, Christoffer Scavenius; Tarp, Finn; Østerdal, Lars Peter Raahave

2016-01-01

This paper introduces a concept of inequality comparisons with ordinal bivariate categorical data. In our model, one population is more unequal than another when they have common arithmetic median outcomes and the first can be obtained from the second by correlation-increasing switches and....../or median-preserving spreads. For the canonical 2 × 2 case (with two binary indicators), we derive a simple operational procedure for checking ordinal inequality relations in practice. As an illustration, we apply the model to childhood deprivation in Mozambique....

Bivariate frequency analysis of rainfall intensity and duration for urban stormwater infrastructure design

Science.gov (United States)

Jun, Changhyun; Qin, Xiaosheng; Gan, Thian Yew; Tung, Yeou-Koung; De Michele, Carlo

2017-10-01

This study presents a storm-event based bivariate frequency analysis approach to determine design rainfalls in which, the number, intensity and duration of actual rainstorm events were considered. To derive more realistic design storms, the occurrence probability of an individual rainstorm event was determined from the joint distribution of storm intensity and duration through a copula model. Hourly rainfall data were used at three climate stations respectively located in Singapore, South Korea and Canada. It was found that the proposed approach could give a more realistic description of rainfall characteristics of rainstorm events and design rainfalls. As results, the design rainfall quantities from actual rainstorm events at the three studied sites are consistently lower than those obtained from the conventional rainfall depth-duration-frequency (DDF) method, especially for short-duration storms (such as 1-h). It results from occurrence probabilities of each rainstorm event and a different angle for rainfall frequency analysis, and could offer an alternative way of describing extreme rainfall properties and potentially help improve the hydrologic design of stormwater management facilities in urban areas.

Bivariate copula in fitting rainfall data

Science.gov (United States)

Yee, Kong Ching; Suhaila, Jamaludin; Yusof, Fadhilah; Mean, Foo Hui

2014-07-01

The usage of copula to determine the joint distribution between two variables is widely used in various areas. The joint distribution of rainfall characteristic obtained using the copula model is more ideal than the standard bivariate modelling where copula is belief to have overcome some limitation. Six copula models will be applied to obtain the most suitable bivariate distribution between two rain gauge stations. The copula models are Ali-Mikhail-Haq (AMH), Clayton, Frank, Galambos, Gumbel-Hoogaurd (GH) and Plackett. The rainfall data used in the study is selected from rain gauge stations which are located in the southern part of Peninsular Malaysia, during the period from 1980 to 2011. The goodness-of-fit test in this study is based on the Akaike information criterion (AIC).

Chain Plot: A Tool for Exploiting Bivariate Temporal Structures

OpenAIRE

Taylor, CC; Zempeni, A

2004-01-01

In this paper we present a graphical tool useful for visualizing the cyclic behaviour of bivariate time series. We investigate its properties and link it to the asymmetry of the two variables concerned. We also suggest adding approximate confidence bounds to the points on the plot and investigate the effect of lagging to the chain plot. We conclude our paper by some standard Fourier analysis, relating and comparing this to the chain plot.

Obtaining DDF Curves of Extreme Rainfall Data Using Bivariate Copula and Frequency Analysis

DEFF Research Database (Denmark)

Sadri, Sara; Madsen, Henrik; Mikkelsen, Peter Steen

2009-01-01

, situated near Copenhagen in Denmark. For rainfall extracted using method 2, the marginal distribution of depth was found to fit the Generalized Pareto distribution while duration was found to fit the Gamma distribution, using the method of L-moments. The volume was fit with a generalized Pareto...... with duration for a given return period and name them DDF (depth-duration-frequency) curves. The copula approach does not assume the rainfall variables are independent or jointly normally distributed. Rainfall series are extracted in three ways: (1) by maximum mean intensity; (2) by depth and duration...... distribution and the duration was fit with a Pearson type III distribution for rainfall extracted using method 3. The Clayton copula was found to be appropriate for bivariate analysis of rainfall depth and duration for both methods 2 and 3. DDF curves derived using the Clayton copula for depth and duration...

Building Bivariate Tables: The compareGroups Package for R

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Isaac Subirana

2014-05-01

Full Text Available The R package compareGroups provides functions meant to facilitate the construction of bivariate tables (descriptives of several variables for comparison between groups and generates reports in several formats (LATEX, HTML or plain text CSV. Moreover, bivariate tables can be viewed directly on the R console in a nice format. A graphical user interface (GUI has been implemented to build the bivariate tables more easily for those users who are not familiar with the R software. Some new functions and methods have been incorporated in the newest version of the compareGroups package (version 1.x to deal with time-to-event variables, stratifying tables, merging several tables, and revising the statistical methods used. The GUI interface also has been improved, making it much easier and more intuitive to set the inputs for building the bivariate tables. The ?rst version (version 0.x and this version were presented at the 2010 useR! conference (Sanz, Subirana, and Vila 2010 and the 2011 useR! conference (Sanz, Subirana, and Vila 2011, respectively. Package compareGroups is available from the Comprehensive R Archive Network at http://CRAN.R-project.org/package=compareGroups.

The relative performance of bivariate causality tests in small samples

NARCIS (Netherlands)

Bult, J..R.; Leeflang, P.S.H.; Wittink, D.R.

1997-01-01

Causality tests have been applied to establish directional effects and to reduce the set of potential predictors, For the latter type of application only bivariate tests can be used, In this study we compare bivariate causality tests. Although the problem addressed is general and could benefit

Evidence for bivariate linkage of obesity and HDL-C levels in the Framingham Heart Study.

Science.gov (United States)

Arya, Rector; Lehman, Donna; Hunt, Kelly J; Schneider, Jennifer; Almasy, Laura; Blangero, John; Stern, Michael P; Duggirala, Ravindranath

2003-12-31

Epidemiological studies have indicated that obesity and low high-density lipoprotein (HDL) levels are strong cardiovascular risk factors, and that these traits are inversely correlated. Despite the belief that these traits are correlated in part due to pleiotropy, knowledge on specific genes commonly affecting obesity and dyslipidemia is very limited. To address this issue, we first conducted univariate multipoint linkage analysis for body mass index (BMI) and HDL-C to identify loci influencing variation in these phenotypes using Framingham Heart Study data relating to 1702 subjects distributed across 330 pedigrees. Subsequently, we performed bivariate multipoint linkage analysis to detect common loci influencing covariation between these two traits. We scanned the genome and identified a major locus near marker D6S1009 influencing variation in BMI (LOD = 3.9) using the program SOLAR. We also identified a major locus for HDL-C near marker D2S1334 on chromosome 2 (LOD = 3.5) and another region near marker D6S1009 on chromosome 6 with suggestive evidence for linkage (LOD = 2.7). Since these two phenotypes have been independently mapped to the same region on chromosome 6q, we used the bivariate multipoint linkage approach using SOLAR. The bivariate linkage analysis of BMI and HDL-C implicated the genetic region near marker D6S1009 as harboring a major gene commonly influencing these phenotypes (bivariate LOD = 6.2; LODeq = 5.5) and appears to improve power to map the correlated traits to a region, precisely. We found substantial evidence for a quantitative trait locus with pleiotropic effects, which appears to influence both BMI and HDL-C phenotypes in the Framingham data.

A Bivariate return period for levee failure monitoring

Science.gov (United States)

Isola, M.; Caporali, E.

2017-12-01

Levee breaches are strongly linked with the interaction processes among water, soil and structure, thus many are the factors that affect the breach development. One of the main is the hydraulic load, characterized by intensity and duration, i.e. by the flood event hydrograph. On the magnitude of the hydraulic load is based the levee design, generally without considering the fatigue failure due to the load duration. Moreover, many are the cases in which the levee breach are characterized by flood of magnitude lower than the design one. In order to implement the strategies of flood risk management, we built here a procedure based on a multivariate statistical analysis of flood peak and volume together with the analysis of the past levee failure events. Particularly, in order to define the probability of occurrence of the hydraulic load on a levee, a bivariate copula model is used to obtain the bivariate joint distribution of flood peak and volume. Flood peak is the expression of the load magnitude, while the volume is the expression of the stress over time. We consider the annual flood peak and the relative volume. The volume is given by the hydrograph area between the beginning and the end of event. The beginning of the event is identified as an abrupt rise of the discharge by more than 20%. The end is identified as the point from which the receding limb is characterized by the baseflow, using a nonlinear reservoir algorithm as baseflow separation technique. By this, with the aim to define warning thresholds we consider the past levee failure events and the relative bivariate return period (BTr) compared with the estimation of a traditional univariate model. The discharge data of 30 hydrometric stations of Arno River in Tuscany, Italy, in the period 1995-2016 are analysed. The database of levee failure events, considering for each event the location as well as the failure mode, is also created. The events were registered in the period 2000-2014 by EEA

A dynamic bivariate Poisson model for analysing and forecasting match results in the English Premier League

NARCIS (Netherlands)

Koopman, S.J.; Lit, R.

2015-01-01

Summary: We develop a statistical model for the analysis and forecasting of football match results which assumes a bivariate Poisson distribution with intensity coefficients that change stochastically over time. The dynamic model is a novelty in the statistical time series analysis of match results

A generalized right truncated bivariate Poisson regression model with applications to health data.

Science.gov (United States)

Islam, M Ataharul; Chowdhury, Rafiqul I

2017-01-01

A generalized right truncated bivariate Poisson regression model is proposed in this paper. Estimation and tests for goodness of fit and over or under dispersion are illustrated for both untruncated and right truncated bivariate Poisson regression models using marginal-conditional approach. Estimation and test procedures are illustrated for bivariate Poisson regression models with applications to Health and Retirement Study data on number of health conditions and the number of health care services utilized. The proposed test statistics are easy to compute and it is evident from the results that the models fit the data very well. A comparison between the right truncated and untruncated bivariate Poisson regression models using the test for nonnested models clearly shows that the truncated model performs significantly better than the untruncated model.

Unadjusted Bivariate Two-Group Comparisons: When Simpler is Better.

Science.gov (United States)

Vetter, Thomas R; Mascha, Edward J

2018-01-01

Hypothesis testing involves posing both a null hypothesis and an alternative hypothesis. This basic statistical tutorial discusses the appropriate use, including their so-called assumptions, of the common unadjusted bivariate tests for hypothesis testing and thus comparing study sample data for a difference or association. The appropriate choice of a statistical test is predicated on the type of data being analyzed and compared. The unpaired or independent samples t test is used to test the null hypothesis that the 2 population means are equal, thereby accepting the alternative hypothesis that the 2 population means are not equal. The unpaired t test is intended for comparing dependent continuous (interval or ratio) data from 2 study groups. A common mistake is to apply several unpaired t tests when comparing data from 3 or more study groups. In this situation, an analysis of variance with post hoc (posttest) intragroup comparisons should instead be applied. Another common mistake is to apply a series of unpaired t tests when comparing sequentially collected data from 2 study groups. In this situation, a repeated-measures analysis of variance, with tests for group-by-time interaction, and post hoc comparisons, as appropriate, should instead be applied in analyzing data from sequential collection points. The paired t test is used to assess the difference in the means of 2 study groups when the sample observations have been obtained in pairs, often before and after an intervention in each study subject. The Pearson chi-square test is widely used to test the null hypothesis that 2 unpaired categorical variables, each with 2 or more nominal levels (values), are independent of each other. When the null hypothesis is rejected, 1 concludes that there is a probable association between the 2 unpaired categorical variables. When comparing 2 groups on an ordinal or nonnormally distributed continuous outcome variable, the 2-sample t test is usually not appropriate. The

GIS-based bivariate statistical techniques for groundwater potential analysis (an example of Iran)

Science.gov (United States)

Haghizadeh, Ali; Moghaddam, Davoud Davoudi; Pourghasemi, Hamid Reza

2017-12-01

Groundwater potential analysis prepares better comprehension of hydrological settings of different regions. This study shows the potency of two GIS-based data driven bivariate techniques namely statistical index (SI) and Dempster-Shafer theory (DST) to analyze groundwater potential in Broujerd region of Iran. The research was done using 11 groundwater conditioning factors and 496 spring positions. Based on the ground water potential maps (GPMs) of SI and DST methods, 24.22% and 23.74% of the study area is covered by poor zone of groundwater potential, and 43.93% and 36.3% of Broujerd region is covered by good and very good potential zones, respectively. The validation of outcomes displayed that area under the curve (AUC) of SI and DST techniques are 81.23% and 79.41%, respectively, which shows SI method has slightly a better performance than the DST technique. Therefore, SI and DST methods are advantageous to analyze groundwater capacity and scrutinize the complicated relation between groundwater occurrence and groundwater conditioning factors, which permits investigation of both systemic and stochastic uncertainty. Finally, it can be realized that these techniques are very beneficial for groundwater potential analyzing and can be practical for water-resource management experts.

Comparison between two bivariate Poisson distributions through the ...

African Journals Online (AJOL)

These two models express themselves by their probability mass function. ... To remedy this problem, Berkhout and Plug proposed a bivariate Poisson distribution accepting the correlation as well negative, equal to zero, that positive.

Preparation and bivariate analysis of suspensions of human chromosomes

Energy Technology Data Exchange (ETDEWEB)

van den Engh, G.J.; Trask, B.J.; Gray, J.W.; Langlois, R.G.; Yu, L.C.

1985-01-01

Chromosomes were isolated from a variety of human cell types using a HEPES-buffered hypotonic solution (pH 8.0) containing KCl, MgSO/sub 4/ dithioerythritol, and RNase. The chromosomes isolated by this procedure could be stained with a variety of fluorescent stains including propidium iodide, chromomycin A3, and Hoeschst 33258. Addition of sodium citrate to the stained chromosomes was found to improve the total fluorescence resolution. High-quality bivariate Hoeschst vs. chromomycin fluorescence distributions were obtained for chromosomes isolated from a human fibroblast cell strain, a human colon carcinoma cell line, and human peripheral blood lymphocyte cultures. Good flow karyotypes were also obtained from primary amniotic cell cultures. The Hoeschst vs. chromomycin flow karyotypes of a given cell line, made at different times and at dye concentrations varying over fourfold ranges, show little variation in the relative peak positions of the chromosomes. The size of the DNA in chromosomes isolated using this procedure ranges from 20 to 50 kilobases. The described isolation procedure is simple, it yields high-quality flow karyotypes, and it can be used to prepare chromosomes from clinical samples. 22 references, 7 figures, 1 table.

Bivariate value-at-risk

Directory of Open Access Journals (Sweden)

Giuseppe Arbia

2007-10-01

Full Text Available In this paper we extend the concept of Value-at-risk (VaR to bivariate return distributions in order to obtain measures of the market risk of an asset taking into account additional features linked to downside risk exposure. We first present a general definition of risk as the probability of an adverse event over a random distribution and we then introduce a measure of market risk (b-VaR that admits the traditional b of an asset in portfolio management as a special case when asset returns are normally distributed. Empirical evidences are provided by using Italian stock market data.

Two new bivariate zero-inflated generalized Poisson distributions with a flexible correlation structure

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Chi Zhang

2015-05-01

Full Text Available To model correlated bivariate count data with extra zero observations, this paper proposes two new bivariate zero-inflated generalized Poisson (ZIGP distributions by incorporating a multiplicative factor (or dependency parameter λ, named as Type I and Type II bivariate ZIGP distributions, respectively. The proposed distributions possess a flexible correlation structure and can be used to fit either positively or negatively correlated and either over- or under-dispersed count data, comparing to the existing models that can only fit positively correlated count data with over-dispersion. The two marginal distributions of Type I bivariate ZIGP share a common parameter of zero inflation while the two marginal distributions of Type II bivariate ZIGP have their own parameters of zero inflation, resulting in a much wider range of applications. The important distributional properties are explored and some useful statistical inference methods including maximum likelihood estimations of parameters, standard errors estimation, bootstrap confidence intervals and related testing hypotheses are developed for the two distributions. A real data are thoroughly analyzed by using the proposed distributions and statistical methods. Several simulation studies are conducted to evaluate the performance of the proposed methods.

An improved method for bivariate meta-analysis when within-study correlations are unknown.

Science.gov (United States)

Hong, Chuan; D Riley, Richard; Chen, Yong

2018-03-01

Multivariate meta-analysis, which jointly analyzes multiple and possibly correlated outcomes in a single analysis, is becoming increasingly popular in recent years. An attractive feature of the multivariate meta-analysis is its ability to account for the dependence between multiple estimates from the same study. However, standard inference procedures for multivariate meta-analysis require the knowledge of within-study correlations, which are usually unavailable. This limits standard inference approaches in practice. Riley et al proposed a working model and an overall synthesis correlation parameter to account for the marginal correlation between outcomes, where the only data needed are those required for a separate univariate random-effects meta-analysis. As within-study correlations are not required, the Riley method is applicable to a wide variety of evidence synthesis situations. However, the standard variance estimator of the Riley method is not entirely correct under many important settings. As a consequence, the coverage of a function of pooled estimates may not reach the nominal level even when the number of studies in the multivariate meta-analysis is large. In this paper, we improve the Riley method by proposing a robust variance estimator, which is asymptotically correct even when the model is misspecified (ie, when the likelihood function is incorrect). Simulation studies of a bivariate meta-analysis, in a variety of settings, show a function of pooled estimates has improved performance when using the proposed robust variance estimator. In terms of individual pooled estimates themselves, the standard variance estimator and robust variance estimator give similar results to the original method, with appropriate coverage. The proposed robust variance estimator performs well when the number of studies is relatively large. Therefore, we recommend the use of the robust method for meta-analyses with a relatively large number of studies (eg, m≥50). When the

A non-stationary cost-benefit based bivariate extreme flood estimation approach

Science.gov (United States)

Qi, Wei; Liu, Junguo

2018-02-01

Cost-benefit analysis and flood frequency analysis have been integrated into a comprehensive framework to estimate cost effective design values. However, previous cost-benefit based extreme flood estimation is based on stationary assumptions and analyze dependent flood variables separately. A Non-Stationary Cost-Benefit based bivariate design flood estimation (NSCOBE) approach is developed in this study to investigate influence of non-stationarities in both the dependence of flood variables and the marginal distributions on extreme flood estimation. The dependence is modeled utilizing copula functions. Previous design flood selection criteria are not suitable for NSCOBE since they ignore time changing dependence of flood variables. Therefore, a risk calculation approach is proposed based on non-stationarities in both marginal probability distributions and copula functions. A case study with 54-year observed data is utilized to illustrate the application of NSCOBE. Results show NSCOBE can effectively integrate non-stationarities in both copula functions and marginal distributions into cost-benefit based design flood estimation. It is also found that there is a trade-off between maximum probability of exceedance calculated from copula functions and marginal distributions. This study for the first time provides a new approach towards a better understanding of influence of non-stationarities in both copula functions and marginal distributions on extreme flood estimation, and could be beneficial to cost-benefit based non-stationary bivariate design flood estimation across the world.

Causal networks clarify productivity-richness interrelations, bivariate plots do not

Science.gov (United States)

Grace, James B.; Adler, Peter B.; Harpole, W. Stanley; Borer, Elizabeth T.; Seabloom, Eric W.

2014-01-01

Perhaps no other pair of variables in ecology has generated as much discussion as species richness and ecosystem productivity, as illustrated by the reactions by Pierce (2013) and others to Adler et al.'s (2011) report that empirical patterns are weak and inconsistent. Adler et al. (2011) argued we need to move beyond a focus on simplistic bivariate relationships and test mechanistic, multivariate causal hypotheses. We feel the continuing debate over productivity–richness relationships (PRRs) provides a focused context for illustrating the fundamental difficulties of using bivariate relationships to gain scientific understanding.

A bivariate model for analyzing recurrent multi-type automobile failures

Science.gov (United States)

Sunethra, A. A.; Sooriyarachchi, M. R.

2017-09-01

The failure mechanism in an automobile can be defined as a system of multi-type recurrent failures where failures can occur due to various multi-type failure modes and these failures are repetitive such that more than one failure can occur from each failure mode. In analysing such automobile failures, both the time and type of the failure serve as response variables. However, these two response variables are highly correlated with each other since the timing of failures has an association with the mode of the failure. When there are more than one correlated response variables, the fitting of a multivariate model is more preferable than separate univariate models. Therefore, a bivariate model of time and type of failure becomes appealing for such automobile failure data. When there are multiple failure observations pertaining to a single automobile, such data cannot be treated as independent data because failure instances of a single automobile are correlated with each other while failures among different automobiles can be treated as independent. Therefore, this study proposes a bivariate model consisting time and type of failure as responses adjusted for correlated data. The proposed model was formulated following the approaches of shared parameter models and random effects models for joining the responses and for representing the correlated data respectively. The proposed model is applied to a sample of automobile failures with three types of failure modes and up to five failure recurrences. The parametric distributions that were suitable for the two responses of time to failure and type of failure were Weibull distribution and multinomial distribution respectively. The proposed bivariate model was programmed in SAS Procedure Proc NLMIXED by user programming appropriate likelihood functions. The performance of the bivariate model was compared with separate univariate models fitted for the two responses and it was identified that better performance is secured by

Approximation of bivariate copulas by patched bivariate Fréchet copulas

KAUST Repository

Zheng, Yanting; Yang, Jingping; Huang, Jianhua Z.

2011-01-01

Bivariate Fréchet (BF) copulas characterize dependence as a mixture of three simple structures: comonotonicity, independence and countermonotonicity. They are easily interpretable but have limitations when used as approximations to general dependence structures. To improve the approximation property of the BF copulas and keep the advantage of easy interpretation, we develop a new copula approximation scheme by using BF copulas locally and patching the local pieces together. Error bounds and a probabilistic interpretation of this approximation scheme are developed. The new approximation scheme is compared with several existing copula approximations, including shuffle of min, checkmin, checkerboard and Bernstein approximations and exhibits better performance, especially in characterizing the local dependence. The utility of the new approximation scheme in insurance and finance is illustrated in the computation of the rainbow option prices and stop-loss premiums. © 2010 Elsevier B.V.

Approximation of bivariate copulas by patched bivariate Fréchet copulas

KAUST Repository

Zheng, Yanting

2011-03-01

Bivariate Fréchet (BF) copulas characterize dependence as a mixture of three simple structures: comonotonicity, independence and countermonotonicity. They are easily interpretable but have limitations when used as approximations to general dependence structures. To improve the approximation property of the BF copulas and keep the advantage of easy interpretation, we develop a new copula approximation scheme by using BF copulas locally and patching the local pieces together. Error bounds and a probabilistic interpretation of this approximation scheme are developed. The new approximation scheme is compared with several existing copula approximations, including shuffle of min, checkmin, checkerboard and Bernstein approximations and exhibits better performance, especially in characterizing the local dependence. The utility of the new approximation scheme in insurance and finance is illustrated in the computation of the rainbow option prices and stop-loss premiums. © 2010 Elsevier B.V.

A method of moments to estimate bivariate survival functions: the copula approach

Directory of Open Access Journals (Sweden)

Silvia Angela Osmetti

2013-05-01

Full Text Available In this paper we discuss the problem on parametric and non parametric estimation of the distributions generated by the Marshall-Olkin copula. This copula comes from the Marshall-Olkin bivariate exponential distribution used in reliability analysis. We generalize this model by the copula and different marginal distributions to construct several bivariate survival functions. The cumulative distribution functions are not absolutely continuous and they unknown parameters are often not be obtained in explicit form. In order to estimate the parameters we propose an easy procedure based on the moments. This method consist in two steps: in the first step we estimate only the parameters of marginal distributions and in the second step we estimate only the copula parameter. This procedure can be used to estimate the parameters of complex survival functions in which it is difficult to find an explicit expression of the mixed moments. Moreover it is preferred to the maximum likelihood one for its simplex mathematic form; in particular for distributions whose maximum likelihood parameters estimators can not be obtained in explicit form.

Application of bivariate mapping for hydrological classification and analysis of temporal change and scale effects in Switzerland

NARCIS (Netherlands)

Speich, Matthias J.R.; Bernhard, Luzi; Teuling, Ryan; Zappa, Massimiliano

2015-01-01

Hydrological classification schemes are important tools for assessing the impacts of a changing climate on the hydrology of a region. In this paper, we present bivariate mapping as a simple means of classifying hydrological data for a quantitative and qualitative assessment of temporal change.

Cost-offsets of prescription drug expenditures: data analysis via a copula-based bivariate dynamic hurdle model.

Science.gov (United States)

Deb, Partha; Trivedi, Pravin K; Zimmer, David M

2014-10-01

In this paper, we estimate a copula-based bivariate dynamic hurdle model of prescription drug and nondrug expenditures to test the cost-offset hypothesis, which posits that increased expenditures on prescription drugs are offset by reductions in other nondrug expenditures. We apply the proposed methodology to data from the Medical Expenditure Panel Survey, which have the following features: (i) the observed bivariate outcomes are a mixture of zeros and continuously measured positives; (ii) both the zero and positive outcomes show state dependence and inter-temporal interdependence; and (iii) the zeros and the positives display contemporaneous association. The point mass at zero is accommodated using a hurdle or a two-part approach. The copula-based approach to generating joint distributions is appealing because the contemporaneous association involves asymmetric dependence. The paper studies samples categorized by four health conditions: arthritis, diabetes, heart disease, and mental illness. There is evidence of greater than dollar-for-dollar cost-offsets of expenditures on prescribed drugs for relatively low levels of spending on drugs and less than dollar-for-dollar cost-offsets at higher levels of drug expenditures. Copyright © 2013 John Wiley & Sons, Ltd.

GIS-Based bivariate statistical techniques for groundwater potential ...

Indian Academy of Sciences (India)

24

This study shows the potency of two GIS-based data driven bivariate techniques namely ... In the view of these weaknesses , there is a strong requirement for reassessment of .... Font color: Text 1, Not Expanded by / Condensed by , ...... West Bengal (India) using remote sensing, geographical information system and multi-.

A Bivariate Generalized Linear Item Response Theory Modeling Framework to the Analysis of Responses and Response Times.

Science.gov (United States)

Molenaar, Dylan; Tuerlinckx, Francis; van der Maas, Han L J

2015-01-01

A generalized linear modeling framework to the analysis of responses and response times is outlined. In this framework, referred to as bivariate generalized linear item response theory (B-GLIRT), separate generalized linear measurement models are specified for the responses and the response times that are subsequently linked by cross-relations. The cross-relations can take various forms. Here, we focus on cross-relations with a linear or interaction term for ability tests, and cross-relations with a curvilinear term for personality tests. In addition, we discuss how popular existing models from the psychometric literature are special cases in the B-GLIRT framework depending on restrictions in the cross-relation. This allows us to compare existing models conceptually and empirically. We discuss various extensions of the traditional models motivated by practical problems. We also illustrate the applicability of our approach using various real data examples, including data on personality and cognitive ability.

About some properties of bivariate splines with shape parameters

Science.gov (United States)

Caliò, F.; Marchetti, E.

2017-07-01

The paper presents and proves geometrical properties of a particular bivariate function spline, built and algorithmically implemented in previous papers. The properties typical of this family of splines impact the field of computer graphics in particular that of the reverse engineering.

Optimizing an objective function under a bivariate probability model

NARCIS (Netherlands)

X. Brusset; N.M. Temme (Nico)

2007-01-01

htmlabstractThe motivation of this paper is to obtain an analytical closed form of a quadratic objective function arising from a stochastic decision process with bivariate exponential probability distribution functions that may be dependent. This method is applicable when results need to be

A New Measure Of Bivariate Asymmetry And Its Evaluation

International Nuclear Information System (INIS)

Ferreira, Flavio Henn; Kolev, Nikolai Valtchev

2008-01-01

In this paper we propose a new measure of bivariate asymmetry, based on conditional correlation coefficients. A decomposition of the Pearson correlation coefficient in terms of its conditional versions is studied and an example of application of the proposed measure is given.

Spectrum-based estimators of the bivariate Hurst exponent

Czech Academy of Sciences Publication Activity Database

Krištoufek, Ladislav

2014-01-01

Roč. 90, č. 6 (2014), art. 062802 ISSN 1539-3755 R&D Projects: GA ČR(CZ) GP14-11402P Institutional support: RVO:67985556 Keywords : bivariate Hurst exponent * power- law cross-correlations * estimation Subject RIV: AH - Economics Impact factor: 2.288, year: 2014 http://library.utia.cas.cz/separaty/2014/E/kristoufek-0436818.pdf

The Evaluation of Bivariate Mixed Models in Meta-analyses of Diagnostic Accuracy Studies with SAS, Stata and R.

Science.gov (United States)

Vogelgesang, Felicitas; Schlattmann, Peter; Dewey, Marc

2018-05-01

Meta-analyses require a thoroughly planned procedure to obtain unbiased overall estimates. From a statistical point of view not only model selection but also model implementation in the software affects the results. The present simulation study investigates the accuracy of different implementations of general and generalized bivariate mixed models in SAS (using proc mixed, proc glimmix and proc nlmixed), Stata (using gllamm, xtmelogit and midas) and R (using reitsma from package mada and glmer from package lme4). Both models incorporate the relationship between sensitivity and specificity - the two outcomes of interest in meta-analyses of diagnostic accuracy studies - utilizing random effects. Model performance is compared in nine meta-analytic scenarios reflecting the combination of three sizes for meta-analyses (89, 30 and 10 studies) with three pairs of sensitivity/specificity values (97%/87%; 85%/75%; 90%/93%). The evaluation of accuracy in terms of bias, standard error and mean squared error reveals that all implementations of the generalized bivariate model calculate sensitivity and specificity estimates with deviations less than two percentage points. proc mixed which together with reitsma implements the general bivariate mixed model proposed by Reitsma rather shows convergence problems. The random effect parameters are in general underestimated. This study shows that flexibility and simplicity of model specification together with convergence robustness should influence implementation recommendations, as the accuracy in terms of bias was acceptable in all implementations using the generalized approach. Schattauer GmbH.

Effectiveness of enforcement levels of speed limit and drink driving laws and associated factors – Exploratory empirical analysis using a bivariate ordered probit model

Directory of Open Access Journals (Sweden)

Behram Wali

2017-06-01

Full Text Available The contemporary traffic safety research comprises little information on quantifying the simultaneous association between drink driving and speeding among fatally injured drivers. Potential correlation between driver's drink driving and speeding behavior poses a substantial methodological concern which needs investigation. This study therefore focused on investigating the simultaneous impact of socioeconomic factors, fatalities, vehicle ownership, health services and highway agency road safety policies on enforcement levels of speed limit and drink driving laws. The effectiveness of enforcement levels of speed limit and drink driving laws has been investigated through development of bivariate ordered probit model using data extricated from WHO's global status report on road safety in 2013. The consistent and intuitive parameter estimates along with statistically significant correlation between response outcomes validates the statistical supremacy of bivariate ordered probit model. The results revealed that fatalities per thousand registered vehicles, hospital beds per hundred thousand population and road safety policies are associated with a likely medium or high effectiveness of enforcement levels of speed limit and drink driving laws, respectively. Also, the model encapsulates the effect of several other agency related variables and socio-economic status on the response outcomes. Marginal effects are reported for analyzing the impact of such factors on intermediate categories of response outcomes. The results of this study are expected to provide necessary insights to elemental enforcement programs. Also, marginal effects of explanatory variables may provide useful directions for formulating effective policy countermeasures for overcoming driver's speeding and drink driving behavior.

Bivariate generalized Pareto distribution for extreme atmospheric particulate matter

Science.gov (United States)

Amin, Nor Azrita Mohd; Adam, Mohd Bakri; Ibrahim, Noor Akma; Aris, Ahmad Zaharin

2015-02-01

The high particulate matter (PM10) level is the prominent issue causing various impacts to human health and seriously affecting the economics. The asymptotic theory of extreme value is apply for analyzing the relation of extreme PM10 data from two nearby air quality monitoring stations. The series of daily maxima PM10 for Johor Bahru and Pasir Gudang stations are consider for year 2001 to 2010 databases. The 85% and 95% marginal quantile apply to determine the threshold values and hence construct the series of exceedances over the chosen threshold. The logistic, asymmetric logistic, negative logistic and asymmetric negative logistic models areconsidered as the dependence function to the joint distribution of a bivariate observation. Maximum likelihood estimation is employed for parameter estimations. The best fitted model is chosen based on the Akaike Information Criterion and the quantile plots. It is found that the asymmetric logistic model gives the best fitted model for bivariate extreme PM10 data and shows the weak dependence between two stations.

Bivariate return periods of temperature and precipitation explain a large fraction of European crop yields

Science.gov (United States)

Zscheischler, Jakob; Orth, Rene; Seneviratne, Sonia I.

2017-07-01

Crops are vital for human society. Crop yields vary with climate and it is important to understand how climate and crop yields are linked to ensure future food security. Temperature and precipitation are among the key driving factors of crop yield variability. Previous studies have investigated mostly linear relationships between temperature and precipitation and crop yield variability. Other research has highlighted the adverse impacts of climate extremes, such as drought and heat waves, on crop yields. Impacts are, however, often non-linearly related to multivariate climate conditions. Here we derive bivariate return periods of climate conditions as indicators for climate variability along different temperature-precipitation gradients. We show that in Europe, linear models based on bivariate return periods of specific climate conditions explain on average significantly more crop yield variability (42 %) than models relying directly on temperature and precipitation as predictors (36 %). Our results demonstrate that most often crop yields increase along a gradient from hot and dry to cold and wet conditions, with lower yields associated with hot and dry periods. The majority of crops are most sensitive to climate conditions in summer and to maximum temperatures. The use of bivariate return periods allows the integration of non-linear impacts into climate-crop yield analysis. This offers new avenues to study the link between climate and crop yield variability and suggests that they are possibly more strongly related than what is inferred from conventional linear models.

Bivariational calculations for radiation transfer in an inhomogeneous participating media

International Nuclear Information System (INIS)

El Wakil, S.A.; Machali, H.M.; Haggag, M.H.; Attia, M.T.

1986-07-01

Equations for radiation transfer are obtained for dispersive media with space dependent albedo. Bivariational bound principle is used to calculate the reflection and transmission coefficients for such media. Numerical results are given and compared. (author)

Spectral density regression for bivariate extremes

KAUST Repository

Castro Camilo, Daniela

2016-05-11

We introduce a density regression model for the spectral density of a bivariate extreme value distribution, that allows us to assess how extremal dependence can change over a covariate. Inference is performed through a double kernel estimator, which can be seen as an extension of the Nadaraya–Watson estimator where the usual scalar responses are replaced by mean constrained densities on the unit interval. Numerical experiments with the methods illustrate their resilience in a variety of contexts of practical interest. An extreme temperature dataset is used to illustrate our methods. © 2016 Springer-Verlag Berlin Heidelberg

Using bivariate latent basis growth curve analysis to better understand treatment outcome in youth with anorexia nervosa.

Science.gov (United States)

Byrne, Catherine E; Wonderlich, Joseph A; Curby, Timothy; Fischer, Sarah; Lock, James; Le Grange, Daniel

2018-04-25

This study explored the relation between eating-related obsessionality and weight restoration utilizing bivariate latent basis growth curve modelling. Eating-related obsessionality is a moderator of treatment outcome for adolescents with anorexia nervosa (AN). This study examined the degree to which the rate of change in eating-related obsessionality was associated with the rate of change in weight over time in family-based treatment (FBT) and individual therapy for AN. Data were drawn from a 2-site randomized controlled trial that compared FBT and adolescent focused therapy for AN. Bivariate latent basis growth curves were used to examine the differences of the relations between trajectories of body weight and symptoms associated with eating and weight obsessionality. In the FBT group, the slope of eating-related obsessionality scores and the slope of weight were significantly (negatively) correlated. This finding indicates that a decrease in overall eating-relating obsessionality is significantly associated with an increase in weight for individuals who received FBT. However, there was no relation between change in obsessionality scores and change in weight in the adolescent focused therapy group. Results suggest that FBT has a specific impact on both weight gain and obsessive compulsive behaviour that is distinct from individual therapy. Copyright © 2018 John Wiley & Sons, Ltd and Eating Disorders Association.

Bivariate Rayleigh Distribution and its Properties

Directory of Open Access Journals (Sweden)

Ahmad Saeed Akhter

2007-01-01

Full Text Available Rayleigh (1880 observed that the sea waves follow no law because of the complexities of the sea, but it has been seen that the probability distributions of wave heights, wave length, wave induce pitch, wave and heave motions of the ships follow the Rayleigh distribution. At present, several different quantities are in use for describing the state of the sea; for example, the mean height of the waves, the root mean square height, the height of the “significant waves” (the mean height of the highest one-third of all the waves the maximum height over a given interval of the time, and so on. At present, the ship building industry knows less than any other construction industry about the service conditions under which it must operate. Only small efforts have been made to establish the stresses and motions and to incorporate the result of such studies in to design. This is due to the complexity of the problem caused by the extensive variability of the sea and the corresponding response of the ships. Although the problem appears feasible, yet it is possible to predict service conditions for ships in an orderly and relatively simple manner Rayleigh (1980 derived it from the amplitude of sound resulting from many independent sources. This distribution is also connected with one or two dimensions and is sometimes referred to as “random walk” frequency distribution. The Rayleigh distribution can be derived from the bivariate normal distribution when the variate are independent and random with equal variances. We try to construct bivariate Rayleigh distribution with marginal Rayleigh distribution function and discuss its fundamental properties.

Parameter estimation and statistical test of geographically weighted bivariate Poisson inverse Gaussian regression models

Science.gov (United States)

Amalia, Junita; Purhadi, Otok, Bambang Widjanarko

2017-11-01

Poisson distribution is a discrete distribution with count data as the random variables and it has one parameter defines both mean and variance. Poisson regression assumes mean and variance should be same (equidispersion). Nonetheless, some case of the count data unsatisfied this assumption because variance exceeds mean (over-dispersion). The ignorance of over-dispersion causes underestimates in standard error. Furthermore, it causes incorrect decision in the statistical test. Previously, paired count data has a correlation and it has bivariate Poisson distribution. If there is over-dispersion, modeling paired count data is not sufficient with simple bivariate Poisson regression. Bivariate Poisson Inverse Gaussian Regression (BPIGR) model is mix Poisson regression for modeling paired count data within over-dispersion. BPIGR model produces a global model for all locations. In another hand, each location has different geographic conditions, social, cultural and economic so that Geographically Weighted Regression (GWR) is needed. The weighting function of each location in GWR generates a different local model. Geographically Weighted Bivariate Poisson Inverse Gaussian Regression (GWBPIGR) model is used to solve over-dispersion and to generate local models. Parameter estimation of GWBPIGR model obtained by Maximum Likelihood Estimation (MLE) method. Meanwhile, hypothesis testing of GWBPIGR model acquired by Maximum Likelihood Ratio Test (MLRT) method.

Bivariate return periods of temperature and precipitation explain a large fraction of European crop yields

Directory of Open Access Journals (Sweden)

J. Zscheischler

2017-07-01

Full Text Available Crops are vital for human society. Crop yields vary with climate and it is important to understand how climate and crop yields are linked to ensure future food security. Temperature and precipitation are among the key driving factors of crop yield variability. Previous studies have investigated mostly linear relationships between temperature and precipitation and crop yield variability. Other research has highlighted the adverse impacts of climate extremes, such as drought and heat waves, on crop yields. Impacts are, however, often non-linearly related to multivariate climate conditions. Here we derive bivariate return periods of climate conditions as indicators for climate variability along different temperature–precipitation gradients. We show that in Europe, linear models based on bivariate return periods of specific climate conditions explain on average significantly more crop yield variability (42 % than models relying directly on temperature and precipitation as predictors (36 %. Our results demonstrate that most often crop yields increase along a gradient from hot and dry to cold and wet conditions, with lower yields associated with hot and dry periods. The majority of crops are most sensitive to climate conditions in summer and to maximum temperatures. The use of bivariate return periods allows the integration of non-linear impacts into climate–crop yield analysis. This offers new avenues to study the link between climate and crop yield variability and suggests that they are possibly more strongly related than what is inferred from conventional linear models.

Classification of Knee Joint Vibration Signals Using Bivariate Feature Distribution Estimation and Maximal Posterior Probability Decision Criterion

Directory of Open Access Journals (Sweden)

Fang Zheng

2013-04-01

Full Text Available Analysis of knee joint vibration or vibroarthrographic (VAG signals using signal processing and machine learning algorithms possesses high potential for the noninvasive detection of articular cartilage degeneration, which may reduce unnecessary exploratory surgery. Feature representation of knee joint VAG signals helps characterize the pathological condition of degenerative articular cartilages in the knee. This paper used the kernel-based probability density estimation method to model the distributions of the VAG signals recorded from healthy subjects and patients with knee joint disorders. The estimated densities of the VAG signals showed explicit distributions of the normal and abnormal signal groups, along with the corresponding contours in the bivariate feature space. The signal classifications were performed by using the Fisher’s linear discriminant analysis, support vector machine with polynomial kernels, and the maximal posterior probability decision criterion. The maximal posterior probability decision criterion was able to provide the total classification accuracy of 86.67% and the area (Az of 0.9096 under the receiver operating characteristics curve, which were superior to the results obtained by either the Fisher’s linear discriminant analysis (accuracy: 81.33%, Az: 0.8564 or the support vector machine with polynomial kernels (accuracy: 81.33%, Az: 0.8533. Such results demonstrated the merits of the bivariate feature distribution estimation and the superiority of the maximal posterior probability decision criterion for analysis of knee joint VAG signals.

Semi-automated detection of aberrant chromosomes in bivariate flow karyotypes

NARCIS (Netherlands)

Boschman, G. A.; Manders, E. M.; Rens, W.; Slater, R.; Aten, J. A.

1992-01-01

A method is described that is designed to compare, in a standardized procedure, bivariate flow karyotypes of Hoechst 33258 (HO)/Chromomycin A3 (CA) stained human chromosomes from cells with aberrations with a reference flow karyotype of normal chromosomes. In addition to uniform normalization of

On the matched pairs sign test using bivariate ranked set sampling ...

African Journals Online (AJOL)

BVRSS) is introduced and investigated. We show that this test is asymptotically more efficient than its counterpart sign test based on a bivariate simple random sample (BVSRS). The asymptotic null distribution and the efficiency of the test are derived.

Which global stock indices trigger stronger contagion risk in the Vietnamese stock market? Evidence using a bivariate analysis

OpenAIRE

Wang Kuan-Min; Lai Hung-Cheng

2013-01-01

This paper extends recent investigations into risk contagion effects on stock markets to the Vietnamese stock market. Daily data spanning October 9, 2006 to May 3, 2012 are sourced to empirically validate the contagion effects between stock markets in Vietnam, and China, Japan, Singapore, and the US. To facilitate the validation of contagion effects with market-related coefficients, this paper constructs a bivariate EGARCH model of dynamic conditional correlation coefficients. Using the...

Using bivariate signal analysis to characterize the epileptic focus: the benefit of surrogates.

Science.gov (United States)

Andrzejak, R G; Chicharro, D; Lehnertz, K; Mormann, F

2011-04-01

The disease epilepsy is related to hypersynchronous activity of networks of neurons. While acute epileptic seizures are the most extreme manifestation of this hypersynchronous activity, an elevated level of interdependence of neuronal dynamics is thought to persist also during the seizure-free interval. In multichannel recordings from brain areas involved in the epileptic process, this interdependence can be reflected in an increased linear cross correlation but also in signal properties of higher order. Bivariate time series analysis comprises a variety of approaches, each with different degrees of sensitivity and specificity for interdependencies reflected in lower- or higher-order properties of pairs of simultaneously recorded signals. Here we investigate which approach is best suited to detect putatively elevated interdependence levels in signals recorded from brain areas involved in the epileptic process. For this purpose, we use the linear cross correlation that is sensitive to lower-order signatures of interdependence, a nonlinear interdependence measure that integrates both lower- and higher-order properties, and a surrogate-corrected nonlinear interdependence measure that aims to specifically characterize higher-order properties. We analyze intracranial electroencephalographic recordings of the seizure-free interval from 29 patients with an epileptic focus located in the medial temporal lobe. Our results show that all three approaches detect higher levels of interdependence for signals recorded from the brain hemisphere containing the epileptic focus as compared to signals recorded from the opposite hemisphere. For the linear cross correlation, however, these differences are not significant. For the nonlinear interdependence measure, results are significant but only of moderate accuracy with regard to the discriminative power for the focal and nonfocal hemispheres. The highest significance and accuracy is obtained for the surrogate-corrected nonlinear

An integrated user-friendly ArcMAP tool for bivariate statistical modeling in geoscience applications

Science.gov (United States)

Jebur, M. N.; Pradhan, B.; Shafri, H. Z. M.; Yusof, Z.; Tehrany, M. S.

2014-10-01

Modeling and classification difficulties are fundamental issues in natural hazard assessment. A geographic information system (GIS) is a domain that requires users to use various tools to perform different types of spatial modeling. Bivariate statistical analysis (BSA) assists in hazard modeling. To perform this analysis, several calculations are required and the user has to transfer data from one format to another. Most researchers perform these calculations manually by using Microsoft Excel or other programs. This process is time consuming and carries a degree of uncertainty. The lack of proper tools to implement BSA in a GIS environment prompted this study. In this paper, a user-friendly tool, BSM (bivariate statistical modeler), for BSA technique is proposed. Three popular BSA techniques such as frequency ratio, weights-of-evidence, and evidential belief function models are applied in the newly proposed ArcMAP tool. This tool is programmed in Python and is created by a simple graphical user interface, which facilitates the improvement of model performance. The proposed tool implements BSA automatically, thus allowing numerous variables to be examined. To validate the capability and accuracy of this program, a pilot test area in Malaysia is selected and all three models are tested by using the proposed program. Area under curve is used to measure the success rate and prediction rate. Results demonstrate that the proposed program executes BSA with reasonable accuracy. The proposed BSA tool can be used in numerous applications, such as natural hazard, mineral potential, hydrological, and other engineering and environmental applications.

An integrated user-friendly ArcMAP tool for bivariate statistical modelling in geoscience applications

Science.gov (United States)

Jebur, M. N.; Pradhan, B.; Shafri, H. Z. M.; Yusoff, Z. M.; Tehrany, M. S.

2015-03-01

Modelling and classification difficulties are fundamental issues in natural hazard assessment. A geographic information system (GIS) is a domain that requires users to use various tools to perform different types of spatial modelling. Bivariate statistical analysis (BSA) assists in hazard modelling. To perform this analysis, several calculations are required and the user has to transfer data from one format to another. Most researchers perform these calculations manually by using Microsoft Excel or other programs. This process is time-consuming and carries a degree of uncertainty. The lack of proper tools to implement BSA in a GIS environment prompted this study. In this paper, a user-friendly tool, bivariate statistical modeler (BSM), for BSA technique is proposed. Three popular BSA techniques, such as frequency ratio, weight-of-evidence (WoE), and evidential belief function (EBF) models, are applied in the newly proposed ArcMAP tool. This tool is programmed in Python and created by a simple graphical user interface (GUI), which facilitates the improvement of model performance. The proposed tool implements BSA automatically, thus allowing numerous variables to be examined. To validate the capability and accuracy of this program, a pilot test area in Malaysia is selected and all three models are tested by using the proposed program. Area under curve (AUC) is used to measure the success rate and prediction rate. Results demonstrate that the proposed program executes BSA with reasonable accuracy. The proposed BSA tool can be used in numerous applications, such as natural hazard, mineral potential, hydrological, and other engineering and environmental applications.

A comparison of bivariate, multivariate random-effects, and Poisson correlated gamma-frailty models to meta-analyze individual patient data of ordinal scale diagnostic tests.

Science.gov (United States)

Simoneau, Gabrielle; Levis, Brooke; Cuijpers, Pim; Ioannidis, John P A; Patten, Scott B; Shrier, Ian; Bombardier, Charles H; de Lima Osório, Flavia; Fann, Jesse R; Gjerdingen, Dwenda; Lamers, Femke; Lotrakul, Manote; Löwe, Bernd; Shaaban, Juwita; Stafford, Lesley; van Weert, Henk C P M; Whooley, Mary A; Wittkampf, Karin A; Yeung, Albert S; Thombs, Brett D; Benedetti, Andrea

2017-11-01

Individual patient data (IPD) meta-analyses are increasingly common in the literature. In the context of estimating the diagnostic accuracy of ordinal or semi-continuous scale tests, sensitivity and specificity are often reported for a given threshold or a small set of thresholds, and a meta-analysis is conducted via a bivariate approach to account for their correlation. When IPD are available, sensitivity and specificity can be pooled for every possible threshold. Our objective was to compare the bivariate approach, which can be applied separately at every threshold, to two multivariate methods: the ordinal multivariate random-effects model and the Poisson correlated gamma-frailty model. Our comparison was empirical, using IPD from 13 studies that evaluated the diagnostic accuracy of the 9-item Patient Health Questionnaire depression screening tool, and included simulations. The empirical comparison showed that the implementation of the two multivariate methods is more laborious in terms of computational time and sensitivity to user-supplied values compared to the bivariate approach. Simulations showed that ignoring the within-study correlation of sensitivity and specificity across thresholds did not worsen inferences with the bivariate approach compared to the Poisson model. The ordinal approach was not suitable for simulations because the model was highly sensitive to user-supplied starting values. We tentatively recommend the bivariate approach rather than more complex multivariate methods for IPD diagnostic accuracy meta-analyses of ordinal scale tests, although the limited type of diagnostic data considered in the simulation study restricts the generalization of our findings. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Testing independence of bivariate interval-censored data using modified Kendall's tau statistic.

Science.gov (United States)

Kim, Yuneung; Lim, Johan; Park, DoHwan

2015-11-01

In this paper, we study a nonparametric procedure to test independence of bivariate interval censored data; for both current status data (case 1 interval-censored data) and case 2 interval-censored data. To do it, we propose a score-based modification of the Kendall's tau statistic for bivariate interval-censored data. Our modification defines the Kendall's tau statistic with expected numbers of concordant and disconcordant pairs of data. The performance of the modified approach is illustrated by simulation studies and application to the AIDS study. We compare our method to alternative approaches such as the two-stage estimation method by Sun et al. (Scandinavian Journal of Statistics, 2006) and the multiple imputation method by Betensky and Finkelstein (Statistics in Medicine, 1999b). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genetic relationship and diversity analysis of Clitoria ternatea ...

African Journals Online (AJOL)

use

2011-12-12

Dec 12, 2011 ... analysis, cluster analysis of 1-0 bivariate data was carried out; 100 random primers revealed a total of ... white at the base. Its flowering is from August to October. The objectives of this study were to identify the poly- morphism amongst the C. ternatea ... shape, colour, fruit, flower shape, colour, size etc.

Robust bivariate error detection in skewed data with application to historical radiosonde winds

KAUST Repository

Sun, Ying

2017-01-18

The global historical radiosonde archives date back to the 1920s and contain the only directly observed measurements of temperature, wind, and moisture in the upper atmosphere, but they contain many random errors. Most of the focus on cleaning these large datasets has been on temperatures, but winds are important inputs to climate models and in studies of wind climatology. The bivariate distribution of the wind vector does not have elliptical contours but is skewed and heavy-tailed, so we develop two methods for outlier detection based on the bivariate skew-t (BST) distribution, using either distance-based or contour-based approaches to flag observations as potential outliers. We develop a framework to robustly estimate the parameters of the BST and then show how the tuning parameter to get these estimates is chosen. In simulation, we compare our methods with one based on a bivariate normal distribution and a nonparametric approach based on the bagplot. We then apply all four methods to the winds observed for over 35,000 radiosonde launches at a single station and demonstrate differences in the number of observations flagged across eight pressure levels and through time. In this pilot study, the method based on the BST contours performs very well.

Robust bivariate error detection in skewed data with application to historical radiosonde winds

KAUST Repository

Sun, Ying; Hering, Amanda S.; Browning, Joshua M.

2017-01-01

The global historical radiosonde archives date back to the 1920s and contain the only directly observed measurements of temperature, wind, and moisture in the upper atmosphere, but they contain many random errors. Most of the focus on cleaning these large datasets has been on temperatures, but winds are important inputs to climate models and in studies of wind climatology. The bivariate distribution of the wind vector does not have elliptical contours but is skewed and heavy-tailed, so we develop two methods for outlier detection based on the bivariate skew-t (BST) distribution, using either distance-based or contour-based approaches to flag observations as potential outliers. We develop a framework to robustly estimate the parameters of the BST and then show how the tuning parameter to get these estimates is chosen. In simulation, we compare our methods with one based on a bivariate normal distribution and a nonparametric approach based on the bagplot. We then apply all four methods to the winds observed for over 35,000 radiosonde launches at a single station and demonstrate differences in the number of observations flagged across eight pressure levels and through time. In this pilot study, the method based on the BST contours performs very well.

Bivariate tensor product ( p , q $(p, q$ -analogue of Kantorovich-type Bernstein-Stancu-Schurer operators

Directory of Open Access Journals (Sweden)

Qing-Bo Cai

2017-11-01

Full Text Available Abstract In this paper, we construct a bivariate tensor product generalization of Kantorovich-type Bernstein-Stancu-Schurer operators based on the concept of ( p , q $(p, q$ -integers. We obtain moments and central moments of these operators, give the rate of convergence by using the complete modulus of continuity for the bivariate case and estimate a convergence theorem for the Lipschitz continuous functions. We also give some graphs and numerical examples to illustrate the convergence properties of these operators to certain functions.

Effect of catchment properties and flood generation regime on copula selection for bivariate flood frequency analysis

Science.gov (United States)

Filipova, Valeriya; Lawrence, Deborah; Klempe, Harald

2018-02-01

Applying copula-based bivariate flood frequency analysis is advantageous because the results provide information on both the flood peak and volume. More data are, however, required for such an analysis, and it is often the case that only data series with a limited record length are available. To overcome this issue of limited record length, data regarding climatic and geomorphological properties can be used to complement statistical methods. In this paper, we present a study of 27 catchments located throughout Norway, in which we assess whether catchment properties, flood generation processes and flood regime have an effect on the correlation between flood peak and volume and, in turn, on the selection of copulas. To achieve this, the annual maximum flood events were first classified into events generated primarily by rainfall, snowmelt or a combination of these. The catchments were then classified into flood regime, depending on the predominant flood generation process producing the annual maximum flood events. A contingency table and Fisher's exact test were used to determine the factors that affect the selection of copulas in the study area. The results show that the two-parameter copulas BB1 and BB7 are more commonly selected in catchments with high steepness, high mean annual runoff and rainfall flood regime. These findings suggest that in these types of catchments, the dependence structure between flood peak and volume is more complex and cannot be modeled effectively using a one-parameter copula. The results illustrate that by relating copula types to flood regime and catchment properties, additional information can be supplied for selecting copulas in catchments with limited data.

A simple approximation to the bivariate normal distribution with large correlation coefficient

NARCIS (Netherlands)

Albers, Willem/Wim; Kallenberg, W.C.M.

1994-01-01

The bivariate normal distribution function is approximated with emphasis on situations where the correlation coefficient is large. The high accuracy of the approximation is illustrated by numerical examples. Moreover, exact upper and lower bounds are presented as well as asymptotic results on the

Analysis of input variables of an artificial neural network using bivariate correlation and canonical correlation

Energy Technology Data Exchange (ETDEWEB)

Costa, Valter Magalhaes; Pereira, Iraci Martinez, E-mail: valter.costa@usp.b [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

2011-07-01

The monitoring of variables and diagnosis of sensor fault in nuclear power plants or processes industries is very important because a previous diagnosis allows the correction of the fault and, like this, to prevent the production stopped, improving operator's security and it's not provoking economics losses. The objective of this work is to build a set, using bivariate correlation and canonical correlation, which will be the set of input variables of an artificial neural network to monitor the greater number of variables. This methodology was applied to the IEA-R1 Research Reactor at IPEN. Initially, for the input set of neural network we selected the variables: nuclear power, primary circuit flow rate, control/safety rod position and difference in pressure in the core of the reactor, because almost whole of monitoring variables have relation with the variables early described or its effect can be result of the interaction of two or more. The nuclear power is related to the increasing and decreasing of temperatures as well as the amount radiation due fission of the uranium; the rods are controls of power and influence in the amount of radiation and increasing and decreasing of temperatures; the primary circuit flow rate has the function of energy transport by removing the nucleus heat. An artificial neural network was trained and the results were satisfactory since the IEA-R1 Data Acquisition System reactor monitors 64 variables and, with a set of 9 input variables resulting from the correlation analysis, it was possible to monitor 51 variables. (author)

Quasi-bivariate variational mode decomposition as a tool of scale analysis in wall-bounded turbulence

Science.gov (United States)

Wang, Wenkang; Pan, Chong; Wang, Jinjun

2018-01-01

The identification and separation of multi-scale coherent structures is a critical task for the study of scale interaction in wall-bounded turbulence. Here, we propose a quasi-bivariate variational mode decomposition (QB-VMD) method to extract structures with various scales from instantaneous two-dimensional (2D) velocity field which has only one primary dimension. This method is developed from the one-dimensional VMD algorithm proposed by Dragomiretskiy and Zosso (IEEE Trans Signal Process 62:531-544, 2014) to cope with a quasi-2D scenario. It poses the feature of length-scale bandwidth constraint along the decomposed dimension, together with the central frequency re-balancing along the non-decomposed dimension. The feasibility of this method is tested on both a synthetic flow field and a turbulent boundary layer at moderate Reynolds number (Re_{τ } = 3458) measured by 2D particle image velocimetry (PIV). Some other popular scale separation tools, including pseudo-bi-dimensional empirical mode decomposition (PB-EMD), bi-dimensional EMD (B-EMD) and proper orthogonal decomposition (POD), are also tested for comparison. Among all these methods, QB-VMD shows advantages in both scale characterization and energy recovery. More importantly, the mode mixing problem, which degrades the performance of EMD-based methods, is avoided or minimized in QB-VMD. Finally, QB-VMD analysis of the wall-parallel plane in the log layer (at y/δ = 0.12) of the studied turbulent boundary layer shows the coexistence of large- or very large-scale motions (LSMs or VLSMs) and inner-scaled structures, which can be fully decomposed in both physical and spectral domains.

Analysis of input variables of an artificial neural network using bivariate correlation and canonical correlation

International Nuclear Information System (INIS)

Costa, Valter Magalhaes; Pereira, Iraci Martinez

2011-01-01

The monitoring of variables and diagnosis of sensor fault in nuclear power plants or processes industries is very important because a previous diagnosis allows the correction of the fault and, like this, to prevent the production stopped, improving operator's security and it's not provoking economics losses. The objective of this work is to build a set, using bivariate correlation and canonical correlation, which will be the set of input variables of an artificial neural network to monitor the greater number of variables. This methodology was applied to the IEA-R1 Research Reactor at IPEN. Initially, for the input set of neural network we selected the variables: nuclear power, primary circuit flow rate, control/safety rod position and difference in pressure in the core of the reactor, because almost whole of monitoring variables have relation with the variables early described or its effect can be result of the interaction of two or more. The nuclear power is related to the increasing and decreasing of temperatures as well as the amount radiation due fission of the uranium; the rods are controls of power and influence in the amount of radiation and increasing and decreasing of temperatures; the primary circuit flow rate has the function of energy transport by removing the nucleus heat. An artificial neural network was trained and the results were satisfactory since the IEA-R1 Data Acquisition System reactor monitors 64 variables and, with a set of 9 input variables resulting from the correlation analysis, it was possible to monitor 51 variables. (author)

On minimum divergence adaptation of discrete bivariate distributions to given marginals

Czech Academy of Sciences Publication Activity Database

Vajda, Igor; van der Meulen, E. C.

2005-01-01

Roč. 51, č. 1 (2005), s. 313-320 ISSN 0018-9448 R&D Projects: GA ČR GA201/02/1391; GA MŠk 1M0572 Institutional research plan: CEZ:AV0Z10750506 Keywords : approximation of contingency tables * bivariate discrete distributions * minimization of divergences Subject RIV: BD - Theory of Information Impact factor: 2.183, year: 2005

A bivariate space-time downscaler under space and time misalignment.

Science.gov (United States)

Berrocal, Veronica J; Gelfand, Alan E; Holland, David M

2010-12-01

Ozone and particulate matter PM(2.5) are co-pollutants that have long been associated with increased public health risks. Information on concentration levels for both pollutants come from two sources: monitoring sites and output from complex numerical models that produce concentration surfaces over large spatial regions. In this paper, we offer a fully-model based approach for fusing these two sources of information for the pair of co-pollutants which is computationally feasible over large spatial regions and long periods of time. Due to the association between concentration levels of the two environmental contaminants, it is expected that information regarding one will help to improve prediction of the other. Misalignment is an obvious issue since the monitoring networks for the two contaminants only partly intersect and because the collection rate for PM(2.5) is typically less frequent than that for ozone.Extending previous work in Berrocal et al. (2009), we introduce a bivariate downscaler that provides a flexible class of bivariate space-time assimilation models. We discuss computational issues for model fitting and analyze a dataset for ozone and PM(2.5) for the ozone season during year 2002. We show a modest improvement in predictive performance, not surprising in a setting where we can anticipate only a small gain.

The bivariate probit model of uncomplicated control of tumor: a heuristic exposition of the methodology

International Nuclear Information System (INIS)

Herbert, Donald

1997-01-01

Purpose: To describe the concept, models, and methods for the construction of estimates of joint probability of uncomplicated control of tumors in radiation oncology. Interpolations using this model can lead to the identification of more efficient treatment regimens for an individual patient. The requirement to find the treatment regimen that will maximize the joint probability of uncomplicated control of tumors suggests a new class of evolutionary experimental designs--Response Surface Methods--for clinical trials in radiation oncology. Methods and Materials: The software developed by Lesaffre and Molenberghs is used to construct bivariate probit models of the joint probability of uncomplicated control of cancer of the oropharynx from a set of 45 patients for each of whom the presence/absence of recurrent tumor (the binary event E-bar 1 /E 1 ) and the presence/absence of necrosis (the binary event E 2 /E-bar 2 ) of the normal tissues of the target volume is recorded, together with the treatment variables dose, time, and fractionation. Results: The bivariate probit model can be used to select a treatment regime that will give a specified probability, say P(S) = 0.60, of uncomplicated control of tumor by interpolation within a set of treatment regimes with known outcomes of recurrence and necrosis. The bivariate probit model can be used to guide a sequence of clinical trials to find the maximum probability of uncomplicated control of tumor for patients in a given prognostic stratum using Response Surface methods by extrapolation from an initial set of treatment regimens. Conclusions: The design of treatments for individual patients and the design of clinical trials might be improved by use of a bivariate probit model and Response Surface Methods

A bivariate measurement error model for semicontinuous and continuous variables: Application to nutritional epidemiology.

Science.gov (United States)

Kipnis, Victor; Freedman, Laurence S; Carroll, Raymond J; Midthune, Douglas

2016-03-01

Semicontinuous data in the form of a mixture of a large portion of zero values and continuously distributed positive values frequently arise in many areas of biostatistics. This article is motivated by the analysis of relationships between disease outcomes and intakes of episodically consumed dietary components. An important aspect of studies in nutritional epidemiology is that true diet is unobservable and commonly evaluated by food frequency questionnaires with substantial measurement error. Following the regression calibration approach for measurement error correction, unknown individual intakes in the risk model are replaced by their conditional expectations given mismeasured intakes and other model covariates. Those regression calibration predictors are estimated using short-term unbiased reference measurements in a calibration substudy. Since dietary intakes are often "energy-adjusted," e.g., by using ratios of the intake of interest to total energy intake, the correct estimation of the regression calibration predictor for each energy-adjusted episodically consumed dietary component requires modeling short-term reference measurements of the component (a semicontinuous variable), and energy (a continuous variable) simultaneously in a bivariate model. In this article, we develop such a bivariate model, together with its application to regression calibration. We illustrate the new methodology using data from the NIH-AARP Diet and Health Study (Schatzkin et al., 2001, American Journal of Epidemiology 154, 1119-1125), and also evaluate its performance in a simulation study. © 2015, The International Biometric Society.

Dysconnection topography in schizophrenia revealed with state-space analysis of EEG.

Science.gov (United States)

Jalili, Mahdi; Lavoie, Suzie; Deppen, Patricia; Meuli, Reto; Do, Kim Q; Cuénod, Michel; Hasler, Martin; De Feo, Oscar; Knyazeva, Maria G

2007-10-24

The dysconnection hypothesis has been proposed to account for pathophysiological mechanisms underlying schizophrenia. Widespread structural changes suggesting abnormal connectivity in schizophrenia have been imaged. A functional counterpart of the structural maps would be the EEG synchronization maps. However, due to the limits of currently used bivariate methods, functional correlates of dysconnection are limited to the isolated measurements of synchronization between preselected pairs of EEG signals. To reveal a whole-head synchronization topography in schizophrenia, we applied a new method of multivariate synchronization analysis called S-estimator to the resting dense-array (128 channels) EEG obtained from 14 patients and 14 controls. This method determines synchronization from the embedding dimension in a state-space domain based on the theoretical consequence of the cooperative behavior of simultaneous time series-the shrinking of the state-space embedding dimension. The S-estimator imaging revealed a specific synchronization landscape in schizophrenia patients. Its main features included bilaterally increased synchronization over temporal brain regions and decreased synchronization over the postcentral/parietal region neighboring the midline. The synchronization topography was stable over the course of several months and correlated with the severity of schizophrenia symptoms. In particular, direct correlations linked positive, negative, and general psychopathological symptoms to the hyper-synchronized temporal clusters over both hemispheres. Along with these correlations, general psychopathological symptoms inversely correlated within the hypo-synchronized postcentral midline region. While being similar to the structural maps of cortical changes in schizophrenia, the S-maps go beyond the topography limits, demonstrating a novel aspect of the abnormalities of functional cooperation: namely, regionally reduced or enhanced connectivity. The new method of

Dysconnection topography in schizophrenia revealed with state-space analysis of EEG.

Directory of Open Access Journals (Sweden)

Mahdi Jalili

2007-10-01

Full Text Available The dysconnection hypothesis has been proposed to account for pathophysiological mechanisms underlying schizophrenia. Widespread structural changes suggesting abnormal connectivity in schizophrenia have been imaged. A functional counterpart of the structural maps would be the EEG synchronization maps. However, due to the limits of currently used bivariate methods, functional correlates of dysconnection are limited to the isolated measurements of synchronization between preselected pairs of EEG signals.To reveal a whole-head synchronization topography in schizophrenia, we applied a new method of multivariate synchronization analysis called S-estimator to the resting dense-array (128 channels EEG obtained from 14 patients and 14 controls. This method determines synchronization from the embedding dimension in a state-space domain based on the theoretical consequence of the cooperative behavior of simultaneous time series-the shrinking of the state-space embedding dimension. The S-estimator imaging revealed a specific synchronization landscape in schizophrenia patients. Its main features included bilaterally increased synchronization over temporal brain regions and decreased synchronization over the postcentral/parietal region neighboring the midline. The synchronization topography was stable over the course of several months and correlated with the severity of schizophrenia symptoms. In particular, direct correlations linked positive, negative, and general psychopathological symptoms to the hyper-synchronized temporal clusters over both hemispheres. Along with these correlations, general psychopathological symptoms inversely correlated within the hypo-synchronized postcentral midline region. While being similar to the structural maps of cortical changes in schizophrenia, the S-maps go beyond the topography limits, demonstrating a novel aspect of the abnormalities of functional cooperation: namely, regionally reduced or enhanced connectivity.The new

Technical note: Towards a continuous classification of climate using bivariate colour mapping

NARCIS (Netherlands)

Teuling, A.J.

2011-01-01

Climate is often defined in terms of discrete classes. Here I use bivariate colour mapping to show that the global distribution of K¨oppen-Geiger climate classes can largely be reproduced by combining the simple means of two key states of the climate system 5 (i.e., air temperature and relative

Bivariate functional data clustering: grouping streams based on a varying coefficient model of the stream water and air temperature relationship

Science.gov (United States)

H. Li; X. Deng; Andy Dolloff; E. P. Smith

2015-01-01

A novel clustering method for bivariate functional data is proposed to group streams based on their water–air temperature relationship. A distance measure is developed for bivariate curves by using a time-varying coefficient model and a weighting scheme. This distance is also adjusted by spatial correlation of streams via the variogram. Therefore, the proposed...

The Role of Wealth and Health in Insurance Choice: Bivariate Probit Analysis in China

Directory of Open Access Journals (Sweden)

Yiding Yue

2014-01-01

Full Text Available This paper captures the correlation between the choices of health insurance and pension insurance using the bivariate probit model and then studies the effect of wealth and health on insurance choice. Our empirical evidence shows that people who participate in a health care program are more likely to participate in a pension plan at the same time, while wealth and health have different effects on the choices of the health care program and the pension program. Generally, the higher an individual’s wealth level is, the more likelihood he will participate in a health care program; but wealth has no effect on the participation of pension. Health status has opposite effects on choices of health care programs and pension plans; the poorer an individual’s health is, the more likely he is to participate in health care programs, while the better health he enjoys, the more likely he is to participate in pension plans. When the investigation scope narrows down to commercial insurance, there is only a significant effect of health status on commercial health insurance. The commercial insurance choice and the insurance choice of the agricultural population are more complicated.

Computational approach to Thornley's problem by bivariate operational calculus

Science.gov (United States)

Bazhlekova, E.; Dimovski, I.

2012-10-01

Thornley's problem is an initial-boundary value problem with a nonlocal boundary condition for linear onedimensional reaction-diffusion equation, used as a mathematical model of spiral phyllotaxis in botany. Applying a bivariate operational calculus we find explicit representation of the solution, containing two convolution products of special solutions and the arbitrary initial and boundary functions. We use a non-classical convolution with respect to the space variable, extending in this way the classical Duhamel principle. The special solutions involved are represented in the form of fast convergent series. Numerical examples are considered to show the application of the present technique and to analyze the character of the solution.

Carbon and oxygen isotopic ratio bi-variate distribution for marble artifacts quarry assignment

International Nuclear Information System (INIS)

Pentia, M.

1995-01-01

Statistical description, by a Gaussian bi-variate probability distribution of 13 C/ 12 C and 18 O/ 16 O isotopic ratios in the ancient marble quarries has been done and the new method for obtaining the confidence level quarry assignment for marble artifacts has been presented. (author) 8 figs., 3 tabs., 4 refs

IDF relationships using bivariate copula for storm events in Peninsular Malaysia

Science.gov (United States)

Ariff, N. M.; Jemain, A. A.; Ibrahim, K.; Wan Zin, W. Z.

2012-11-01

SummaryIntensity-duration-frequency (IDF) curves are used in many hydrologic designs for the purpose of water managements and flood preventions. The IDF curves available in Malaysia are those obtained from univariate analysis approach which only considers the intensity of rainfalls at fixed time intervals. As several rainfall variables are correlated with each other such as intensity and duration, this paper aims to derive IDF points for storm events in Peninsular Malaysia by means of bivariate frequency analysis. This is achieved through utilizing the relationship between storm intensities and durations using the copula method. Four types of copulas; namely the Ali-Mikhail-Haq (AMH), Frank, Gaussian and Farlie-Gumbel-Morgenstern (FGM) copulas are considered because the correlation between storm intensity, I, and duration, D, are negative and these copulas are appropriate when the relationship between the variables are negative. The correlations are attained by means of Kendall's τ estimation. The analysis was performed on twenty rainfall stations with hourly data across Peninsular Malaysia. Using Akaike's Information Criteria (AIC) for testing goodness-of-fit, both Frank and Gaussian copulas are found to be suitable to represent the relationship between I and D. The IDF points found by the copula method are compared to the IDF curves yielded based on the typical IDF empirical formula of the univariate approach. This study indicates that storm intensities obtained from both methods are in agreement with each other for any given storm duration and for various return periods.

A Bivariate Mixture Model for Natural Antibody Levels to Human Papillomavirus Types 16 and 18: Baseline Estimates for Monitoring the Herd Effects of Immunization.

Directory of Open Access Journals (Sweden)

Margaretha A Vink

Full Text Available Post-vaccine monitoring programs for human papillomavirus (HPV have been introduced in many countries, but HPV serology is still an underutilized tool, partly owing to the weak antibody response to HPV infection. Changes in antibody levels among non-vaccinated individuals could be employed to monitor herd effects of immunization against HPV vaccine types 16 and 18, but inference requires an appropriate statistical model. The authors developed a four-component bivariate mixture model for jointly estimating vaccine-type seroprevalence from correlated antibody responses against HPV16 and -18 infections. This model takes account of the correlation between HPV16 and -18 antibody concentrations within subjects, caused e.g. by heterogeneity in exposure level and immune response. The model was fitted to HPV16 and -18 antibody concentrations as measured by a multiplex immunoassay in a large serological survey (3,875 females carried out in the Netherlands in 2006/2007, before the introduction of mass immunization. Parameters were estimated by Bayesian analysis. We used the deviance information criterion for model selection; performance of the preferred model was assessed through simulation. Our analysis uncovered elevated antibody concentrations in doubly as compared to singly seropositive individuals, and a strong clustering of HPV16 and -18 seropositivity, particularly around the age of sexual debut. The bivariate model resulted in a more reliable classification of singly and doubly seropositive individuals than achieved by a combination of two univariate models, and suggested a higher pre-vaccine HPV16 seroprevalence than previously estimated. The bivariate mixture model provides valuable baseline estimates of vaccine-type seroprevalence and may prove useful in seroepidemiologic assessment of the herd effects of HPV vaccination.

Diagnostic value of sTREM-1 in bronchoalveolar lavage fluid in ICU patients with bacterial lung infections: a bivariate meta-analysis.

Science.gov (United States)

Shi, Jia-Xin; Li, Jia-Shu; Hu, Rong; Li, Chun-Hua; Wen, Yan; Zheng, Hong; Zhang, Feng; Li, Qin

2013-01-01

The serum soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) is a useful biomarker in differentiating bacterial infections from others. However, the diagnostic value of sTREM-1 in bronchoalveolar lavage fluid (BALF) in lung infections has not been well established. We performed a meta-analysis to assess the accuracy of sTREM-1 in BALF for diagnosis of bacterial lung infections in intensive care unit (ICU) patients. We searched PUBMED, EMBASE and Web of Knowledge (from January 1966 to October 2012) databases for relevant studies that reported diagnostic accuracy data of BALF sTREM-1 in the diagnosis of bacterial lung infections in ICU patients. Pooled sensitivity, specificity, and positive and negative likelihood ratios were calculated by a bivariate regression analysis. Measures of accuracy and Q point value (Q*) were calculated using summary receiver operating characteristic (SROC) curve. The potential between-studies heterogeneity was explored by subgroup analysis. Nine studies were included in the present meta-analysis. Overall, the prevalence was 50.6%; the sensitivity was 0.87 (95% confidence interval (CI), 0.72-0.95); the specificity was 0.79 (95% CI, 0.56-0.92); the positive likelihood ratio (PLR) was 4.18 (95% CI, 1.78-9.86); the negative likelihood ratio (NLR) was 0.16 (95% CI, 0.07-0.36), and the diagnostic odds ratio (DOR) was 25.60 (95% CI, 7.28-89.93). The area under the SROC curve was 0.91 (95% CI, 0.88-0.93), with a Q* of 0.83. Subgroup analysis showed that the assay method and cutoff value influenced the diagnostic accuracy of sTREM-1. BALF sTREM-1 is a useful biomarker of bacterial lung infections in ICU patients. Further studies are needed to confirm the optimized cutoff value.

A COMPARISON OF SOME ROBUST BIVARIATE CONTROL CHARTS FOR INDIVIDUAL OBSERVATIONS

Directory of Open Access Journals (Sweden)

Moustafa Omar Ahmed Abu - Shawiesh

2014-06-01

Full Text Available This paper proposed and considered some bivariate control charts to monitor individual observations from a statistical process control. Usual control charts which use mean and variance-covariance estimators are sensitive to outliers. We consider the following robust alternatives to the classical Hoteling's T2: T2MedMAD, T2MCD, T2MVE a simulation study has been conducted to compare the performance of these control charts. Two real life data are analyzed to illustrate the application of these robust alternatives.

Bivariate spatial analysis of temperature and precipitation from general circulation models and observation proxies

KAUST Repository

Philbin, R.

2015-05-22

This study validates the near-surface temperature and precipitation output from decadal runs of eight atmospheric ocean general circulation models (AOGCMs) against observational proxy data from the National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) reanalysis temperatures and Global Precipitation Climatology Project (GPCP) precipitation data. We model the joint distribution of these two fields with a parsimonious bivariate Matérn spatial covariance model, accounting for the two fields\\' spatial cross-correlation as well as their own smoothnesses. We fit output from each AOGCM (30-year seasonal averages from 1981 to 2010) to a statistical model on each of 21 land regions. Both variance and smoothness values agree for both fields over all latitude bands except southern mid-latitudes. Our results imply that temperature fields have smaller smoothness coefficients than precipitation fields, while both have decreasing smoothness coefficients with increasing latitude. Models predict fields with smaller smoothness coefficients than observational proxy data for the tropics. The estimated spatial cross-correlations of these two fields, however, are quite different for most GCMs in mid-latitudes. Model correlation estimates agree well with those for observational proxy data for Australia, at high northern latitudes across North America, Europe and Asia, as well as across the Sahara, India, and Southeast Asia, but elsewhere, little consistent agreement exists.

Bivariate spatial analysis of temperature and precipitation from general circulation models and observation proxies

KAUST Repository

Philbin, R.; Jun, M.

2015-01-01

This study validates the near-surface temperature and precipitation output from decadal runs of eight atmospheric ocean general circulation models (AOGCMs) against observational proxy data from the National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) reanalysis temperatures and Global Precipitation Climatology Project (GPCP) precipitation data. We model the joint distribution of these two fields with a parsimonious bivariate Matérn spatial covariance model, accounting for the two fields' spatial cross-correlation as well as their own smoothnesses. We fit output from each AOGCM (30-year seasonal averages from 1981 to 2010) to a statistical model on each of 21 land regions. Both variance and smoothness values agree for both fields over all latitude bands except southern mid-latitudes. Our results imply that temperature fields have smaller smoothness coefficients than precipitation fields, while both have decreasing smoothness coefficients with increasing latitude. Models predict fields with smaller smoothness coefficients than observational proxy data for the tropics. The estimated spatial cross-correlations of these two fields, however, are quite different for most GCMs in mid-latitudes. Model correlation estimates agree well with those for observational proxy data for Australia, at high northern latitudes across North America, Europe and Asia, as well as across the Sahara, India, and Southeast Asia, but elsewhere, little consistent agreement exists.

Bivariate empirical mode decomposition for ECG-based biometric identification with emotional data.

Science.gov (United States)

Ferdinando, Hany; Seppanen, Tapio; Alasaarela, Esko

2017-07-01

Emotions modulate ECG signals such that they might affect ECG-based biometric identification in real life application. It motivated in finding good feature extraction methods where the emotional state of the subjects has minimum impacts. This paper evaluates feature extraction based on bivariate empirical mode decomposition (BEMD) for biometric identification when emotion is considered. Using the ECG signal from the Mahnob-HCI database for affect recognition, the features were statistical distributions of dominant frequency after applying BEMD analysis to ECG signals. The achieved accuracy was 99.5% with high consistency using kNN classifier in 10-fold cross validation to identify 26 subjects when the emotional states of the subjects were ignored. When the emotional states of the subject were considered, the proposed method also delivered high accuracy, around 99.4%. We concluded that the proposed method offers emotion-independent features for ECG-based biometric identification. The proposed method needs more evaluation related to testing with other classifier and variation in ECG signals, e.g. normal ECG vs. ECG with arrhythmias, ECG from various ages, and ECG from other affective databases.

A non-parametric conditional bivariate reference region with an application to height/weight measurements on normal girls

DEFF Research Database (Denmark)

Petersen, Jørgen Holm

2009-01-01

A conceptually simple two-dimensional conditional reference curve is described. The curve gives a decision basis for determining whether a bivariate response from an individual is "normal" or "abnormal" when taking into account that a third (conditioning) variable may influence the bivariate...... response. The reference curve is not only characterized analytically but also by geometric properties that are easily communicated to medical doctors - the users of such curves. The reference curve estimator is completely non-parametric, so no distributional assumptions are needed about the two......-dimensional response. An example that will serve to motivate and illustrate the reference is the study of the height/weight distribution of 7-8-year-old Danish school girls born in 1930, 1950, or 1970....

Comparison of Six Methods for the Detection of Causality in a Bivariate Time Series

Czech Academy of Sciences Publication Activity Database

Krakovská, A.; Jakubík, J.; Chvosteková, M.; Coufal, David; Jajcay, Nikola; Paluš, Milan

2018-01-01

Roč. 97, č. 4 (2018), č. článku 042207. ISSN 2470-0045 R&D Projects: GA MZd(CZ) NV15-33250A Institutional support: RVO:67985807 Keywords : comparative study * causality detection * bivariate models * Granger causality * transfer entropy * convergent cross mappings Impact factor: 2.366, year: 2016 https://journals.aps.org/pre/abstract/10.1103/PhysRevE.97.042207

Bivariate- distribution for transition matrix elements in Breit-Wigner to Gaussian domains of interacting particle systems.

Science.gov (United States)

Kota, V K B; Chavda, N D; Sahu, R

2006-04-01

Interacting many-particle systems with a mean-field one-body part plus a chaos generating random two-body interaction having strength lambda exhibit Poisson to Gaussian orthogonal ensemble and Breit-Wigner (BW) to Gaussian transitions in level fluctuations and strength functions with transition points marked by lambda = lambda c and lambda = lambda F, respectively; lambda F > lambda c. For these systems a theory for the matrix elements of one-body transition operators is available, as valid in the Gaussian domain, with lambda > lambda F, in terms of orbital occupation numbers, level densities, and an integral involving a bivariate Gaussian in the initial and final energies. Here we show that, using a bivariate-t distribution, the theory extends below from the Gaussian regime to the BW regime up to lambda = lambda c. This is well tested in numerical calculations for 6 spinless fermions in 12 single-particle states.

On the construction of bivariate exponential distributions with an arbitrary correlation coefficient

DEFF Research Database (Denmark)

Bladt, Mogens; Nielsen, Bo Friis

In this paper we use a concept of multivariate phase-type distributions to define a class of bivariate exponential distributions. This class has the following three appealing properties. Firstly, we may construct a pair of exponentially distributed random variables with any feasible correlation...... coefficient (also negative). Secondly, the class satisfies that any linear combination (projection) of the marginal random variables is a phase {type distributions, The latter property is potentially important for the development hypothesis testing in linear models. Thirdly, it is very easy to simulate...

Bivariate pointing movements on large touch screens: investigating the validity of a refined Fitts' Law.

Science.gov (United States)

Bützler, Jennifer; Vetter, Sebastian; Jochems, Nicole; Schlick, Christopher M

2012-01-01

On the basis of three empirical studies Fitts' Law was refined for bivariate pointing tasks on large touch screens. In the first study different target width parameters were investigated. The second study considered the effect of the motion angle. Based on the results of the two studies a refined model for movement time in human-computer interaction was formulated. A third study, which is described here in detail, concerns the validation of the refined model. For the validation study 20 subjects had to execute a bivariate pointing task on a large touch screen. In the experimental task 250 rectangular target objects were displayed at a randomly chosen position on the screen covering a broad range of ID values (ID= [1.01; 4.88]). Compared to existing refinements of Fitts' Law, the new model shows highest predictive validity. A promising field of application of the model is the ergonomic design and evaluation of project management software. By using the refined model, software designers can calculate a priori the appropriate angular position and the size of buttons, menus or icons.

A Bivariate Extension to Traditional Empirical Orthogonal Function Analysis

DEFF Research Database (Denmark)

Nielsen, Allan Aasbjerg; Hilger, Klaus Baggesen; Andersen, Ole Baltazar

2002-01-01

This paper describes the application of canonical correlations analysis to the joint analysis of global monthly mean values of 1996-1997 sea surface temperature (SST) and height (SSH) data. The SST data are considered as one set and the SSH data as another set of multivariate observations, both w...... as for example an increase in the SST will lead to an increase in the SSH. The analysis clearly shows the build-up of one of the largest El Niño events on record. Also the analysis indicates a phase lag of approximately one month between the SST and SSH fields....

Which global stock indices trigger stronger contagion risk in the Vietnamese stock market? Evidence using a bivariate analysis

Directory of Open Access Journals (Sweden)

Wang Kuan-Min

2013-01-01

Full Text Available This paper extends recent investigations into risk contagion effects on stock markets to the Vietnamese stock market. Daily data spanning October 9, 2006 to May 3, 2012 are sourced to empirically validate the contagion effects between stock markets in Vietnam, and China, Japan, Singapore, and the US. To facilitate the validation of contagion effects with market-related coefficients, this paper constructs a bivariate EGARCH model of dynamic conditional correlation coefficients. Using the correlation contagion test and Dungey et al.’s (2005 contagion test, we find contagion effects between the Vietnamese and four other stock markets, namely Japan, Singapore, China, and the US. Second, we show that the Japanese stock market causes stronger contagion risk in the Vietnamese stock market compared to the stock markets of China, Singapore, and the US. Finally, we show that the Chinese and US stock markets cause weaker contagion effects in the Vietnamese stock market because of stronger interdependence effects between the former two markets.

Selection effects in the bivariate brightness distribution for spiral galaxies

International Nuclear Information System (INIS)

Phillipps, S.; Disney, M.

1986-01-01

The joint distribution of total luminosity and characteristic surface brightness (the bivariate brightness distribution) is investigated for a complete sample of spiral galaxies in the Virgo cluster. The influence of selection and physical limits of various kinds on the apparent distribution are detailed. While the distribution of surface brightness for bright galaxies may be genuinely fairly narrow, faint galaxies exist right across the (quite small) range of accessible surface brightnesses so no statement can be made about the true extent of the distribution. The lack of high surface brightness bright galaxies in the Virgo sample relative to an overall RC2 sample (mostly field galaxies) supports the contention that the star-formation rate is reduced in the inner region of the cluster for environmental reasons. (author)

Can the bivariate Hurst exponent be higher than an average of the separate Hurst exponents?

Czech Academy of Sciences Publication Activity Database

Krištoufek, Ladislav

2015-01-01

Roč. 431, č. 1 (2015), s. 124-127 ISSN 0378-4371 R&D Projects: GA ČR(CZ) GP14-11402P Institutional support: RVO:67985556 Keywords : Correlations * Power- law cross-correlations * Bivariate Hurst exponent * Spectrum coherence Subject RIV: AH - Economics Impact factor: 1.785, year: 2015 http://library.utia.cas.cz/separaty/2015/E/kristoufek-0452314.pdf

Comparing Johnson’s SBB, Weibull and Logit-Logistic bivariate distributions for modeling tree diameters and heights using copulas

Energy Technology Data Exchange (ETDEWEB)

Cardil Forradellas, A.; Molina Terrén, D.M.; Oliveres, J.; Castellnou, M.

2016-07-01

Aim of study: In this study we compare the accuracy of three bivariate distributions: Johnson’s SBB, Weibull-2P and LL-2P functions for characterizing the joint distribution of tree diameters and heights. Area of study: North-West of Spain. Material and methods: Diameter and height measurements of 128 plots of pure and even-aged Tasmanian blue gum (Eucalyptus globulus Labill.) stands located in the North-west of Spain were considered in the present study. The SBB bivariate distribution was obtained from SB marginal distributions using a Normal Copula based on a four-parameter logistic transformation. The Plackett Copula was used to obtain the bivariate models from the Weibull and Logit-logistic univariate marginal distributions. The negative logarithm of the maximum likelihood function was used to compare the results and the Wilcoxon signed-rank test was used to compare the related samples of these logarithms calculated for each sample plot and each distribution. Main results: The best results were obtained by using the Plackett copula and the best marginal distribution was the Logit-logistic. Research highlights: The copulas used in this study have shown a good performance for modeling the joint distribution of tree diameters and heights. They could be easily extended for modelling multivariate distributions involving other tree variables, such as tree volume or biomass. (Author)

Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity

Directory of Open Access Journals (Sweden)

Songjoon Baek

2017-05-01

Full Text Available In response to activating signals, transcription factors (TFs bind DNA and regulate gene expression. TF binding can be measured by protection of the bound sequence from DNase digestion (i.e., footprint. Here, we report that 80% of TF binding motifs do not show a measurable footprint, partly because of a variable cleavage pattern within the motif sequence. To more faithfully portray the effect of TFs on chromatin, we developed an algorithm that captures two TF-dependent effects on chromatin accessibility: footprinting and motif-flanking accessibility. The algorithm, termed bivariate genomic footprinting (BaGFoot, efficiently detects TF activity. BaGFoot is robust to different accessibility assays (DNase-seq, ATAC-seq, all examined peak-calling programs, and a variety of cut bias correction approaches. BaGFoot reliably predicts TF binding and provides valuable information regarding the TFs affecting chromatin accessibility in various biological systems and following various biological events, including in cases where an absolute footprint cannot be determined.

Powerful bivariate genome-wide association analyses suggest the SOX6 gene influencing both obesity and osteoporosis phenotypes in males.

Directory of Open Access Journals (Sweden)

Yao-Zhong Liu

2009-08-01

Full Text Available Current genome-wide association studies (GWAS are normally implemented in a univariate framework and analyze different phenotypes in isolation. This univariate approach ignores the potential genetic correlation between important disease traits. Hence this approach is difficult to detect pleiotropic genes, which may exist for obesity and osteoporosis, two common diseases of major public health importance that are closely correlated genetically.To identify such pleiotropic genes and the key mechanistic links between the two diseases, we here performed the first bivariate GWAS of obesity and osteoporosis. We searched for genes underlying co-variation of the obesity phenotype, body mass index (BMI, with the osteoporosis risk phenotype, hip bone mineral density (BMD, scanning approximately 380,000 SNPs in 1,000 unrelated homogeneous Caucasians, including 499 males and 501 females. We identified in the male subjects two SNPs in intron 1 of the SOX6 (SRY-box 6 gene, rs297325 and rs4756846, which were bivariately associated with both BMI and hip BMD, achieving p values of 6.82x10(-7 and 1.47x10(-6, respectively. The two SNPs ranked at the top in significance for bivariate association with BMI and hip BMD in the male subjects among all the approximately 380,000 SNPs examined genome-wide. The two SNPs were replicated in a Framingham Heart Study (FHS cohort containing 3,355 Caucasians (1,370 males and 1,985 females from 975 families. In the FHS male subjects, the two SNPs achieved p values of 0.03 and 0.02, respectively, for bivariate association with BMI and femoral neck BMD. Interestingly, SOX6 was previously found to be essential to both cartilage formation/chondrogenesis and obesity-related insulin resistance, suggesting the gene's dual role in both bone and fat.Our findings, together with the prior biological evidence, suggest the SOX6 gene's importance in co-regulation of obesity and osteoporosis.

Powerful Bivariate Genome-Wide Association Analyses Suggest the SOX6 Gene Influencing Both Obesity and Osteoporosis Phenotypes in Males

Science.gov (United States)

Liu, Yao-Zhong; Pei, Yu-Fang; Liu, Jian-Feng; Yang, Fang; Guo, Yan; Zhang, Lei; Liu, Xiao-Gang; Yan, Han; Wang, Liang; Zhang, Yin-Ping; Levy, Shawn; Recker, Robert R.; Deng, Hong-Wen

2009-01-01

Background Current genome-wide association studies (GWAS) are normally implemented in a univariate framework and analyze different phenotypes in isolation. This univariate approach ignores the potential genetic correlation between important disease traits. Hence this approach is difficult to detect pleiotropic genes, which may exist for obesity and osteoporosis, two common diseases of major public health importance that are closely correlated genetically. Principal Findings To identify such pleiotropic genes and the key mechanistic links between the two diseases, we here performed the first bivariate GWAS of obesity and osteoporosis. We searched for genes underlying co-variation of the obesity phenotype, body mass index (BMI), with the osteoporosis risk phenotype, hip bone mineral density (BMD), scanning ∼380,000 SNPs in 1,000 unrelated homogeneous Caucasians, including 499 males and 501 females. We identified in the male subjects two SNPs in intron 1 of the SOX6 (SRY-box 6) gene, rs297325 and rs4756846, which were bivariately associated with both BMI and hip BMD, achieving p values of 6.82×10−7 and 1.47×10−6, respectively. The two SNPs ranked at the top in significance for bivariate association with BMI and hip BMD in the male subjects among all the ∼380,000 SNPs examined genome-wide. The two SNPs were replicated in a Framingham Heart Study (FHS) cohort containing 3,355 Caucasians (1,370 males and 1,985 females) from 975 families. In the FHS male subjects, the two SNPs achieved p values of 0.03 and 0.02, respectively, for bivariate association with BMI and femoral neck BMD. Interestingly, SOX6 was previously found to be essential to both cartilage formation/chondrogenesis and obesity-related insulin resistance, suggesting the gene's dual role in both bone and fat. Conclusions Our findings, together with the prior biological evidence, suggest the SOX6 gene's importance in co-regulation of obesity and osteoporosis. PMID:19714249

SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays

Directory of Open Access Journals (Sweden)

Stephen W. Erickson

2016-07-01

Full Text Available SNPMClust is an R package for genotype clustering and calling with Illumina microarrays. It was originally developed for studies using the GoldenGate custom genotyping platform but can be used with other Illumina platforms, including Infinium BeadChip. The algorithm first rescales the fluorescent signal intensity data, adds empirically derived pseudo-data to minor allele genotype clusters, then uses the package mclust for bivariate Gaussian model fitting. We compared the accuracy and sensitivity of SNPMClust to that of GenCall, Illumina's proprietary algorithm, on a data set of 94 whole-genome amplified buccal (cheek swab DNA samples. These samples were genotyped on a custom panel which included 1064 SNPs for which the true genotype was known with high confidence. SNPMClust produced uniformly lower false call rates over a wide range of overall call rates.

Collective estimation of multiple bivariate density functions with application to angular-sampling-based protein loop modeling

KAUST Repository

Maadooliat, Mehdi

2015-10-21

This paper develops a method for simultaneous estimation of density functions for a collection of populations of protein backbone angle pairs using a data-driven, shared basis that is constructed by bivariate spline functions defined on a triangulation of the bivariate domain. The circular nature of angular data is taken into account by imposing appropriate smoothness constraints across boundaries of the triangles. Maximum penalized likelihood is used to fit the model and an alternating blockwise Newton-type algorithm is developed for computation. A simulation study shows that the collective estimation approach is statistically more efficient than estimating the densities individually. The proposed method was used to estimate neighbor-dependent distributions of protein backbone dihedral angles (i.e., Ramachandran distributions). The estimated distributions were applied to protein loop modeling, one of the most challenging open problems in protein structure prediction, by feeding them into an angular-sampling-based loop structure prediction framework. Our estimated distributions compared favorably to the Ramachandran distributions estimated by fitting a hierarchical Dirichlet process model; and in particular, our distributions showed significant improvements on the hard cases where existing methods do not work well.

Collective estimation of multiple bivariate density functions with application to angular-sampling-based protein loop modeling

KAUST Repository

Maadooliat, Mehdi; Zhou, Lan; Najibi, Seyed Morteza; Gao, Xin; Huang, Jianhua Z.

2015-01-01

This paper develops a method for simultaneous estimation of density functions for a collection of populations of protein backbone angle pairs using a data-driven, shared basis that is constructed by bivariate spline functions defined on a triangulation of the bivariate domain. The circular nature of angular data is taken into account by imposing appropriate smoothness constraints across boundaries of the triangles. Maximum penalized likelihood is used to fit the model and an alternating blockwise Newton-type algorithm is developed for computation. A simulation study shows that the collective estimation approach is statistically more efficient than estimating the densities individually. The proposed method was used to estimate neighbor-dependent distributions of protein backbone dihedral angles (i.e., Ramachandran distributions). The estimated distributions were applied to protein loop modeling, one of the most challenging open problems in protein structure prediction, by feeding them into an angular-sampling-based loop structure prediction framework. Our estimated distributions compared favorably to the Ramachandran distributions estimated by fitting a hierarchical Dirichlet process model; and in particular, our distributions showed significant improvements on the hard cases where existing methods do not work well.

Efficient estimation of semiparametric copula models for bivariate survival data

KAUST Repository

Cheng, Guang

2014-01-01

A semiparametric copula model for bivariate survival data is characterized by a parametric copula model of dependence and nonparametric models of two marginal survival functions. Efficient estimation for the semiparametric copula model has been recently studied for the complete data case. When the survival data are censored, semiparametric efficient estimation has only been considered for some specific copula models such as the Gaussian copulas. In this paper, we obtain the semiparametric efficiency bound and efficient estimation for general semiparametric copula models for possibly censored data. We construct an approximate maximum likelihood estimator by approximating the log baseline hazard functions with spline functions. We show that our estimates of the copula dependence parameter and the survival functions are asymptotically normal and efficient. Simple consistent covariance estimators are also provided. Numerical results are used to illustrate the finite sample performance of the proposed estimators. © 2013 Elsevier Inc.

Geovisualization of land use and land cover using bivariate maps and Sankey flow diagrams

Science.gov (United States)

Strode, Georgianna; Mesev, Victor; Thornton, Benjamin; Jerez, Marjorie; Tricarico, Thomas; McAlear, Tyler

2018-05-01

The terms `land use' and `land cover' typically describe categories that convey information about the landscape. Despite the major difference of land use implying some degree of anthropogenic disturbance, the two terms are commonly used interchangeably, especially when anthropogenic disturbance is ambiguous, say managed forestland or abandoned agricultural fields. Cartographically, land use and land cover are also sometimes represented interchangeably within common legends, giving with the impression that the landscape is a seamless continuum of land use parcels spatially adjacent to land cover tracts. We believe this is misleading, and feel we need to reiterate the well-established symbiosis of land uses as amalgams of land covers; in other words land covers are subsets of land use. Our paper addresses this spatially complex, and frequently ambiguous relationship, and posits that bivariate cartographic techniques are an ideal vehicle for representing both land use and land cover simultaneously. In more specific terms, we explore the use of nested symbology as ways to represent graphically land use and land cover, where land cover are circles nested with land use squares. We also investigate bivariate legends for representing statistical covariance as a means for visualizing the combinations of land use and cover. Lastly, we apply Sankey flow diagrams to further illustrate the complex, multifaceted relationships between land use and land cover. Our work is demonstrated on data representing land use and cover data for the US state of Florida.

Regional Analysis of Precipitation by Means of Bivariate Distribution Adjusted by Maximum Entropy; Analisis regional de precipitacion con base en una distribucion bivariada ajustada por maxima entropia

Energy Technology Data Exchange (ETDEWEB)

Escalante Sandoval, Carlos A.; Dominguez Esquivel, Jose Y. [Universidad Nacional Autonoma de Mexico (Mexico)

2001-09-01

The principle of maximum entropy (POME) is used to derive an alternative method of parameter estimation for the bivariate Gumbel distribution. A simple algorithm for this parameter estimation technique is presented. This method is applied to analyze the precipitation in a region of Mexico. Design events are compered with those obtained by the maximum likelihood procedure. According to the results, the proposed technique is a suitable option to be considered when performing frequency analysis of precipitation with small samples. [Spanish] El principio de maxima entropia, conocido como POME, es utilizado para derivar un procedimiento alternativo de estimacion de parametros de la distribucion bivariada de valores extremos con marginales Gumbel. El modelo se aplica al analisis de la precipitacion maxima en 24 horas en una region de Mexico y los eventos de diseno obtenidos son comparados con los proporcionados por la tecnica de maxima verosimilitud. De acuerdo con los resultados obtenidos, se concluye que la tecnica propuesta representa una buena opcion, sobre todo para el caso de muestras pequenas.

Association of Supply Type with Fecal Contamination of Source Water and Household Stored Drinking Water in Developing Countries: A Bivariate Meta-analysis.

Science.gov (United States)

Shields, Katherine F; Bain, Robert E S; Cronk, Ryan; Wright, Jim A; Bartram, Jamie

2015-12-01

Access to safe drinking water is essential for health. Monitoring access to drinking water focuses on water supply type at the source, but there is limited evidence on whether quality differences at the source persist in water stored in the household. We assessed the extent of fecal contamination at the source and in household stored water (HSW) and explored the relationship between contamination at each sampling point and water supply type. We performed a bivariate random-effects meta-analysis of 45 studies, identified through a systematic review, that reported either the proportion of samples free of fecal indicator bacteria and/or individual sample bacteria counts for source and HSW, disaggregated by supply type. Water quality deteriorated substantially between source and stored water. The mean percentage of contaminated samples (noncompliance) at the source was 46% (95% CI: 33, 60%), whereas mean noncompliance in HSW was 75% (95% CI: 64, 84%). Water supply type was significantly associated with noncompliance at the source (p water (OR = 0.2; 95% CI: 0.1, 0.5) and HSW (OR = 0.3; 95% CI: 0.2, 0.8) from piped supplies had significantly lower odds of contamination compared with non-piped water, potentially due to residual chlorine. Piped water is less likely to be contaminated compared with other water supply types at both the source and in HSW. A focus on upgrading water services to piped supplies may help improve safety, including for those drinking stored water.

An efficient algorithm for generating random number pairs drawn from a bivariate normal distribution

Science.gov (United States)

Campbell, C. W.

1983-01-01

An efficient algorithm for generating random number pairs from a bivariate normal distribution was developed. Any desired value of the two means, two standard deviations, and correlation coefficient can be selected. Theoretically the technique is exact and in practice its accuracy is limited only by the quality of the uniform distribution random number generator, inaccuracies in computer function evaluation, and arithmetic. A FORTRAN routine was written to check the algorithm and good accuracy was obtained. Some small errors in the correlation coefficient were observed to vary in a surprisingly regular manner. A simple model was developed which explained the qualities aspects of the errors.

Predictors of postoperative outcomes of cubital tunnel syndrome treatments using multiple logistic regression analysis.

Science.gov (United States)

Suzuki, Taku; Iwamoto, Takuji; Shizu, Kanae; Suzuki, Katsuji; Yamada, Harumoto; Sato, Kazuki

2017-05-01

This retrospective study was designed to investigate prognostic factors for postoperative outcomes for cubital tunnel syndrome (CubTS) using multiple logistic regression analysis with a large number of patients. Eighty-three patients with CubTS who underwent surgeries were enrolled. The following potential prognostic factors for disease severity were selected according to previous reports: sex, age, type of surgery, disease duration, body mass index, cervical lesion, presence of diabetes mellitus, Workers' Compensation status, preoperative severity, and preoperative electrodiagnostic testing. Postoperative severity of disease was assessed 2 years after surgery by Messina's criteria which is an outcome measure specifically for CubTS. Bivariate analysis was performed to select candidate prognostic factors for multiple linear regression analyses. Multiple logistic regression analysis was conducted to identify the association between postoperative severity and selected prognostic factors. Both bivariate and multiple linear regression analysis revealed only preoperative severity as an independent risk factor for poor prognosis, while other factors did not show any significant association. Although conflicting results exist regarding prognosis of CubTS, this study supports evidence from previous studies and concludes early surgical intervention portends the most favorable prognosis. Copyright © 2017 The Japanese Orthopaedic Association. Published by Elsevier B.V. All rights reserved.

Investigating the relationship between costs and outcomes for English mental health providers: a bi-variate multi-level regression analysis.

Science.gov (United States)

Moran, Valerie; Jacobs, Rowena

2018-06-01

Provider payment systems for mental health care that incentivize cost control and quality improvement have been a policy focus in a number of countries. In England, a new prospective provider payment system is being introduced to mental health that should encourage providers to control costs and improve outcomes. The aim of this research is to investigate the relationship between costs and outcomes to ascertain whether there is a trade-off between controlling costs and improving outcomes. The main data source is the Mental Health Minimum Data Set (MHMDS) for the years 2011/12 and 2012/13. Costs are calculated using NHS reference cost data while outcomes are measured using the Health of the Nation Outcome Scales (HoNOS). We estimate a bivariate multi-level model with costs and outcomes simultaneously. We calculate the correlation and plot the pairwise relationship between residual costs and outcomes at the provider level. After controlling for a range of demographic, need, social, and treatment variables, residual variation in costs and outcomes remains at the provider level. The correlation between residual costs and outcomes is negative, but very small, suggesting that cost-containment efforts by providers should not undermine outcome-improving efforts under the new payment system.

Probabilistic modeling using bivariate normal distributions for identification of flow and displacement intervals in longwall overburden

Energy Technology Data Exchange (ETDEWEB)

Karacan, C.O.; Goodman, G.V.R. [NIOSH, Pittsburgh, PA (United States). Off Mine Safety & Health Research

2011-01-15

Gob gas ventholes (GGV) are used to control methane emissions in longwall mines by capturing it within the overlying fractured strata before it enters the work environment. In order for GGVs to effectively capture more methane and less mine air, the length of the slotted sections and their proximity to top of the coal bed should be designed based on the potential gas sources and their locations, as well as the displacements in the overburden that will create potential flow paths for the gas. In this paper, an approach to determine the conditional probabilities of depth-displacement, depth-flow percentage, depth-formation and depth-gas content of the formations was developed using bivariate normal distributions. The flow percentage, displacement and formation data as a function of distance from coal bed used in this study were obtained from a series of borehole experiments contracted by the former US Bureau of Mines as part of a research project. Each of these parameters was tested for normality and was modeled using bivariate normal distributions to determine all tail probabilities. In addition, the probability of coal bed gas content as a function of depth was determined using the same techniques. The tail probabilities at various depths were used to calculate conditional probabilities for each of the parameters. The conditional probabilities predicted for various values of the critical parameters can be used with the measurements of flow and methane percentage at gob gas ventholes to optimize their performance.

Xp21 contiguous gene syndromes: Deletion quantitation with bivariate flow karyotyping allows mapping of patient breakpoints

Energy Technology Data Exchange (ETDEWEB)

McCabe, E.R.B.; Towbin, J.A. (Baylor College of Medicine, Houston, TX (United States)); Engh, G. van den; Trask, B.J. (Lawrence Livermore National Lab., CA (United States))

1992-12-01

Bivariate flow karyotyping was used to estimate the deletion sizes for a series of patients with Xp21 contiguous gene syndromes. The deletion estimates were used to develop an approximate scale for the genomic map in Xp21. The bivariate flow karyotype results were compared with clinical and molecular genetic information on the extent of the patients' deletions, and these various types of data were consistent. The resulting map spans >15 Mb, from the telomeric interval between DXS41 (99-6) and DXS68 (1-4) to a position centromeric to the ornithine transcarbamylase locus. The deletion sizing was considered to be accurate to [plus minus]1 Mb. The map provides information on the relative localization of genes and markers within this region. For example, the map suggests that the adrenal hypoplasia congenita and glycerol kinase genes are physically close to each other, are within 1-2 Mb of the telomeric end of the Duchenne muscular dystrophy (DMD) gene, and are nearer to the DMD locus than to the more distal marker DXS28 (C7). Information of this type is useful in developing genomic strategies for positional cloning in Xp21. These investigations demonstrate that the DNA from patients with Xp21 contiguous gene syndromes can be valuable reagents, not only for ordering loci and markers but also for providing an approximate scale to the map of the Xp21 region surrounding DMD. 44 refs., 3 figs.

Genetic correlations between body condition scores and fertility in dairy cattle using bivariate random regression models.

Science.gov (United States)

De Haas, Y; Janss, L L G; Kadarmideen, H N

2007-10-01

Genetic correlations between body condition score (BCS) and fertility traits in dairy cattle were estimated using bivariate random regression models. BCS was recorded by the Swiss Holstein Association on 22,075 lactating heifers (primiparous cows) from 856 sires. Fertility data during first lactation were extracted for 40,736 cows. The fertility traits were days to first service (DFS), days between first and last insemination (DFLI), calving interval (CI), number of services per conception (NSPC) and conception rate to first insemination (CRFI). A bivariate model was used to estimate genetic correlations between BCS as a longitudinal trait by random regression components, and daughter's fertility at the sire level as a single lactation measurement. Heritability of BCS was 0.17, and heritabilities for fertility traits were low (0.01-0.08). Genetic correlations between BCS and fertility over the lactation varied from: -0.45 to -0.14 for DFS; -0.75 to 0.03 for DFLI; from -0.59 to -0.02 for CI; from -0.47 to 0.33 for NSPC and from 0.08 to 0.82 for CRFI. These results show (genetic) interactions between fat reserves and reproduction along the lactation trajectory of modern dairy cows, which can be useful in genetic selection as well as in management. Maximum genetic gain in fertility from indirect selection on BCS should be based on measurements taken in mid lactation when the genetic variance for BCS is largest, and the genetic correlations between BCS and fertility is strongest.

A comparison of the effect of 5-bromodeoxyuridine substitution on 33258 Hoechst- and DAPI-fluorescence of isolated chromosomes by bivariate flow karyotyping

NARCIS (Netherlands)

Buys, C. H.; Mesa, J.; van der Veen, A. Y.; Aten, J. A.

1986-01-01

Application of the fluorescent DNA-intercalator propidium iodide for stabilization of the mitotic chromosome structure during isolation of chromosomes from V79 Chinese hamster cells and subsequent staining with the fluorochromes 33258 Hoechst or DAPI allowed bivariate flow karyotyping of isolated

A bivariate contaminated binormal model for robust fitting of proper ROC curves to a pair of correlated, possibly degenerate, ROC datasets.

Science.gov (United States)

Zhai, Xuetong; Chakraborty, Dev P

2017-06-01

The objective was to design and implement a bivariate extension to the contaminated binormal model (CBM) to fit paired receiver operating characteristic (ROC) datasets-possibly degenerate-with proper ROC curves. Paired datasets yield two correlated ratings per case. Degenerate datasets have no interior operating points and proper ROC curves do not inappropriately cross the chance diagonal. The existing method, developed more than three decades ago utilizes a bivariate extension to the binormal model, implemented in CORROC2 software, which yields improper ROC curves and cannot fit degenerate datasets. CBM can fit proper ROC curves to unpaired (i.e., yielding one rating per case) and degenerate datasets, and there is a clear scientific need to extend it to handle paired datasets. In CBM, nondiseased cases are modeled by a probability density function (pdf) consisting of a unit variance peak centered at zero. Diseased cases are modeled with a mixture distribution whose pdf consists of two unit variance peaks, one centered at positive μ with integrated probability α, the mixing fraction parameter, corresponding to the fraction of diseased cases where the disease was visible to the radiologist, and one centered at zero, with integrated probability (1-α), corresponding to disease that was not visible. It is shown that: (a) for nondiseased cases the bivariate extension is a unit variances bivariate normal distribution centered at (0,0) with a specified correlation ρ 1 ; (b) for diseased cases the bivariate extension is a mixture distribution with four peaks, corresponding to disease not visible in either condition, disease visible in only one condition, contributing two peaks, and disease visible in both conditions. An expression for the likelihood function is derived. A maximum likelihood estimation (MLE) algorithm, CORCBM, was implemented in the R programming language that yields parameter estimates and the covariance matrix of the parameters, and other statistics

Depositional environment of the Fort Member of the Jurasic Jaisalmer Formation (western Rajasthan, India), as revealed from lithofacies and grain-size analysis

International Nuclear Information System (INIS)

Ahmad, F.; Quasim, M.; Ghaznavi, A.; Khan, Z.; Ahmad, A.H.M.

2017-01-01

Lithofacies and granulometric analysis were carried out to decipher the depositional environment of the Fort Member of the Jurassic Jaisalmer Formation. Based on field data nine lithofacies have been identified including trough cross-bedded sandstones, planar cross-bedded sandstones, matrix supported conglomerates, thinly bedded siltstone and sandstones, herringbone cross-bedded sandstones, wave rippled sandstones, laminated sandstones, hummocky cross-bedded sandstones, limestones and shales. Granulometric analysis of the sandstones samples has been carried out for their statistical and textural parameters. Bivariant plots of textural parameters such as graphic skewness versus graphic standard deviation and kewness versus standard deviation confirm the high energy (beach) origin of sandstones. These results suggest a wide spectrum of marine environments ranging from inner shelf to upper shoreface for the Fort Member sandstones.

A bivariate Chebyshev spectral collocation quasilinearization method for nonlinear evolution parabolic equations.

Science.gov (United States)

Motsa, S S; Magagula, V M; Sibanda, P

2014-01-01

This paper presents a new method for solving higher order nonlinear evolution partial differential equations (NPDEs). The method combines quasilinearisation, the Chebyshev spectral collocation method, and bivariate Lagrange interpolation. In this paper, we use the method to solve several nonlinear evolution equations, such as the modified KdV-Burgers equation, highly nonlinear modified KdV equation, Fisher's equation, Burgers-Fisher equation, Burgers-Huxley equation, and the Fitzhugh-Nagumo equation. The results are compared with known exact analytical solutions from literature to confirm accuracy, convergence, and effectiveness of the method. There is congruence between the numerical results and the exact solutions to a high order of accuracy. Tables were generated to present the order of accuracy of the method; convergence graphs to verify convergence of the method and error graphs are presented to show the excellent agreement between the results from this study and the known results from literature.

A Bivariate Chebyshev Spectral Collocation Quasilinearization Method for Nonlinear Evolution Parabolic Equations

Directory of Open Access Journals (Sweden)

S. S. Motsa

2014-01-01

Full Text Available This paper presents a new method for solving higher order nonlinear evolution partial differential equations (NPDEs. The method combines quasilinearisation, the Chebyshev spectral collocation method, and bivariate Lagrange interpolation. In this paper, we use the method to solve several nonlinear evolution equations, such as the modified KdV-Burgers equation, highly nonlinear modified KdV equation, Fisher's equation, Burgers-Fisher equation, Burgers-Huxley equation, and the Fitzhugh-Nagumo equation. The results are compared with known exact analytical solutions from literature to confirm accuracy, convergence, and effectiveness of the method. There is congruence between the numerical results and the exact solutions to a high order of accuracy. Tables were generated to present the order of accuracy of the method; convergence graphs to verify convergence of the method and error graphs are presented to show the excellent agreement between the results from this study and the known results from literature.

Analysis of Roman glass from Albania by PIXE–PIGE method

International Nuclear Information System (INIS)

Šmit, Ž.; Tartari, F.; Stamati, F.; Vevecka Priftaj, A.; Istenič, J.

2013-01-01

A series of 31 Roman glasses dated to the 1st–4th c. AD from the present Albania was analyzed by the combined PIXE–PIGE method. The analysis shows typical natron-based glass of the Roman period, though statistical treatment using principal component analysis and bivariate plots reveals four distinct groups, which are qualified by increased levels of potassium, magnesium and titanium–manganese–iron oxides, respectively. MgO content may exceed 2% and reach the level commonly accepted for halophytic plant-ash glass. The groups are formed on account of mineral impurities in the sand, which gives support to the thesis of multiple production centers of raw glass in the imperial age

An assessment on the use of bivariate, multivariate and soft computing techniques for collapse susceptibility in GIS environ

Science.gov (United States)

Yilmaz, Işik; Marschalko, Marian; Bednarik, Martin

2013-04-01

The paper presented herein compares and discusses the use of bivariate, multivariate and soft computing techniques for collapse susceptibility modelling. Conditional probability (CP), logistic regression (LR) and artificial neural networks (ANN) models representing the bivariate, multivariate and soft computing techniques were used in GIS based collapse susceptibility mapping in an area from Sivas basin (Turkey). Collapse-related factors, directly or indirectly related to the causes of collapse occurrence, such as distance from faults, slope angle and aspect, topographical elevation, distance from drainage, topographic wetness index (TWI), stream power index (SPI), Normalized Difference Vegetation Index (NDVI) by means of vegetation cover, distance from roads and settlements were used in the collapse susceptibility analyses. In the last stage of the analyses, collapse susceptibility maps were produced from the models, and they were then compared by means of their validations. However, Area Under Curve (AUC) values obtained from all three models showed that the map obtained from soft computing (ANN) model looks like more accurate than the other models, accuracies of all three models can be evaluated relatively similar. The results also showed that the conditional probability is an essential method in preparation of collapse susceptibility map and highly compatible with GIS operating features.

Optical Coherence Tomography Noise Reduction Using Anisotropic Local Bivariate Gaussian Mixture Prior in 3D Complex Wavelet Domain.

Science.gov (United States)

Rabbani, Hossein; Sonka, Milan; Abramoff, Michael D

2013-01-01

In this paper, MMSE estimator is employed for noise-free 3D OCT data recovery in 3D complex wavelet domain. Since the proposed distribution for noise-free data plays a key role in the performance of MMSE estimator, a priori distribution for the pdf of noise-free 3D complex wavelet coefficients is proposed which is able to model the main statistical properties of wavelets. We model the coefficients with a mixture of two bivariate Gaussian pdfs with local parameters which are able to capture the heavy-tailed property and inter- and intrascale dependencies of coefficients. In addition, based on the special structure of OCT images, we use an anisotropic windowing procedure for local parameters estimation that results in visual quality improvement. On this base, several OCT despeckling algorithms are obtained based on using Gaussian/two-sided Rayleigh noise distribution and homomorphic/nonhomomorphic model. In order to evaluate the performance of the proposed algorithm, we use 156 selected ROIs from 650 × 512 × 128 OCT dataset in the presence of wet AMD pathology. Our simulations show that the best MMSE estimator using local bivariate mixture prior is for the nonhomomorphic model in the presence of Gaussian noise which results in an improvement of 7.8 ± 1.7 in CNR.

Optical Coherence Tomography Noise Reduction Using Anisotropic Local Bivariate Gaussian Mixture Prior in 3D Complex Wavelet Domain

Directory of Open Access Journals (Sweden)

Hossein Rabbani

2013-01-01

Full Text Available In this paper, MMSE estimator is employed for noise-free 3D OCT data recovery in 3D complex wavelet domain. Since the proposed distribution for noise-free data plays a key role in the performance of MMSE estimator, a priori distribution for the pdf of noise-free 3D complex wavelet coefficients is proposed which is able to model the main statistical properties of wavelets. We model the coefficients with a mixture of two bivariate Gaussian pdfs with local parameters which are able to capture the heavy-tailed property and inter- and intrascale dependencies of coefficients. In addition, based on the special structure of OCT images, we use an anisotropic windowing procedure for local parameters estimation that results in visual quality improvement. On this base, several OCT despeckling algorithms are obtained based on using Gaussian/two-sided Rayleigh noise distribution and homomorphic/nonhomomorphic model. In order to evaluate the performance of the proposed algorithm, we use 156 selected ROIs from 650 × 512 × 128 OCT dataset in the presence of wet AMD pathology. Our simulations show that the best MMSE estimator using local bivariate mixture prior is for the nonhomomorphic model in the presence of Gaussian noise which results in an improvement of 7.8 ± 1.7 in CNR.

Male and female child murderers: an empirical analysis of U.S. arrest data.

Science.gov (United States)

Sellers, Brian G; Heide, Kathleen M

2012-08-01

Recent U.S. cases of murders by children below age 11 have captured national headlines. A review of the literature reveals that little is known about this population of juvenile homicide offenders (JHOs). Most studies on juvenile murderers have used small clinical samples, focused on adolescents, and concentrated on male offenders. Studies that have used Supplementary Homicide Report (SHR) data have found significant gender differences among juveniles below 18 years arrested for murder. This study investigated gender differences among 226 juvenile murderers ages 6 through 10 involved in single-victim incidents using bivariate and multivariate statistical techniques. Consistent with previous research, bivariate analyses revealed gender differences with respect to the type of weapon used, age of the victim, relationship to the victim, and circumstances of the crime. Logistic regression analysis identified female JHOs as more likely to use a knife, kill a family member, and kill a victim below age 5, when compared with male JHOs. From these findings, profiles of young male and female JHOs can be drawn. The article concludes with a discussion of the study's implications for prevention and treatment. The authors recommend that future research in gender differences among young children focus on examining psychological, neurological, and sociological variables not included in the SHR data set.

Applying Emax model and bivariate thin plate splines to assess drug interactions.

Science.gov (United States)

Kong, Maiying; Lee, J Jack

2010-01-01

We review the semiparametric approach previously proposed by Kong and Lee and extend it to a case in which the dose-effect curves follow the Emax model instead of the median effect equation. When the maximum effects for the investigated drugs are different, we provide a procedure to obtain the additive effect based on the Loewe additivity model. Then, we apply a bivariate thin plate spline approach to estimate the effect beyond additivity along with its 95 per cent point-wise confidence interval as well as its 95 per cent simultaneous confidence interval for any combination dose. Thus, synergy, additivity, and antagonism can be identified. The advantages of the method are that it provides an overall assessment of the combination effect on the entire two-dimensional dose space spanned by the experimental doses, and it enables us to identify complex patterns of drug interaction in combination studies. In addition, this approach is robust to outliers. To illustrate this procedure, we analyzed data from two case studies.

Characteristics of the tomato chromoplast revealed by proteomic analysis

OpenAIRE

Barsan, Cristina; Sanchez-Bel, Paloma; Rombaldi, César Valmor; Egea, Isabel; Rossignol, Michel; Kuntz, Marcel; Zouine, Mohamed; Latché, Alain; Bouzayen, Mondher; Pech, Jean-Claude

2010-01-01

Chromoplasts are non-photosynthetic specialized plastids that are important in ripening tomato fruit (Solanum lycopersicum) since, among other functions, they are the site of accumulation of coloured compounds. Analysis of the proteome of red fruit chromoplasts revealed the presence of 988 proteins corresponding to 802 Arabidopsis unigenes, among which 209 had not been listed so far in plastidial databanks. These data revealed several features of the chromoplast. Proteins of lipid metabolism ...

Asymptotics of bivariate generating functions with algebraic singularities

Science.gov (United States)

Greenwood, Torin

Flajolet and Odlyzko (1990) derived asymptotic formulae the coefficients of a class of uni- variate generating functions with algebraic singularities. Gao and Richmond (1992) and Hwang (1996, 1998) extended these results to classes of multivariate generating functions, in both cases by reducing to the univariate case. Pemantle and Wilson (2013) outlined new multivariate ana- lytic techniques and used them to analyze the coefficients of rational generating functions. After overviewing these methods, we use them to find asymptotic formulae for the coefficients of a broad class of bivariate generating functions with algebraic singularities. Beginning with the Cauchy integral formula, we explicity deform the contour of integration so that it hugs a set of critical points. The asymptotic contribution to the integral comes from analyzing the integrand near these points, leading to explicit asymptotic formulae. Next, we use this formula to analyze an example from current research. In the following chapter, we apply multivariate analytic techniques to quan- tum walks. Bressler and Pemantle (2007) found a (d + 1)-dimensional rational generating function whose coefficients described the amplitude of a particle at a position in the integer lattice after n steps. Here, the minimal critical points form a curve on the (d + 1)-dimensional unit torus. We find asymptotic formulae for the amplitude of a particle in a given position, normalized by the number of steps n, as n approaches infinity. Each critical point contributes to the asymptotics for a specific normalized position. Using Groebner bases in Maple again, we compute the explicit locations of peak amplitudes. In a scaling window of size the square root of n near the peaks, each amplitude is asymptotic to an Airy function.

The use of bivariate spatial modeling of questionnaire and parasitology data to predict the distribution of Schistosoma haematobium in Coastal Kenya.

Directory of Open Access Journals (Sweden)

Hugh J W Sturrock

Full Text Available Questionnaires of reported blood in urine (BIU distributed through the existing school system provide a rapid and reliable method to classify schools according to the prevalence of Schistosoma haematobium, thereby helping in the targeting of schistosomiasis control. However, not all schools return questionnaires and it is unclear whether treatment is warranted in such schools. This study investigates the use of bivariate spatial modelling of available and multiple data sources to predict the prevalence of S. haematobium at every school along the Kenyan coast.Data from a questionnaire survey conducted by the Kenya Ministry of Education in Coast Province in 2009 were combined with available parasitological and environmental data in a Bayesian bivariate spatial model. This modeled the relationship between BIU data and environmental covariates, as well as the relationship between BIU and S. haematobium infection prevalence, to predict S. haematobium infection prevalence at all schools in the study region. Validation procedures were implemented to assess the predictive accuracy of endemicity classification.The prevalence of BIU was negatively correlated with distance to nearest river and there was considerable residual spatial correlation at small (~15 km spatial scales. There was a predictable relationship between the prevalence of reported BIU and S. haematobium infection. The final model exhibited excellent sensitivity (0.94 but moderate specificity (0.69 in identifying low (<10% prevalence schools, and had poor performance in differentiating between moderate and high prevalence schools (sensitivity 0.5, specificity 1.Schistosomiasis is highly focal and there is a need to target treatment on a school-by-school basis. The use of bivariate spatial modelling can supplement questionnaire data to identify schools requiring mass treatment, but is unable to distinguish between moderate and high prevalence schools.

Epileptic seizure prediction based on a bivariate spectral power methodology.

Science.gov (United States)

Bandarabadi, Mojtaba; Teixeira, Cesar A; Direito, Bruno; Dourado, Antonio

2012-01-01

The spectral power of 5 frequently considered frequency bands (Alpha, Beta, Gamma, Theta and Delta) for 6 EEG channels is computed and then all the possible pairwise combinations among the 30 features set, are used to create a 435 dimensional feature space. Two new feature selection methods are introduced to choose the best candidate features among those and to reduce the dimensionality of this feature space. The selected features are then fed to Support Vector Machines (SVMs) that classify the cerebral state in preictal and non-preictal classes. The outputs of the SVM are regularized using a method that accounts for the classification dynamics of the preictal class, also known as "Firing Power" method. The results obtained using our feature selection approaches are compared with the ones obtained using minimum Redundancy Maximum Relevance (mRMR) feature selection method. The results in a group of 12 patients of the EPILEPSIAE database, containing 46 seizures and 787 hours multichannel recording for out-of-sample data, indicate the efficiency of the bivariate approach as well as the two new feature selection methods. The best results presented sensitivity of 76.09% (35 of 46 seizures predicted) and a false prediction rate of 0.15(-1).

Integrative modelling reveals mechanisms linking productivity and plant species richness.

Science.gov (United States)

Grace, James B; Anderson, T Michael; Seabloom, Eric W; Borer, Elizabeth T; Adler, Peter B; Harpole, W Stanley; Hautier, Yann; Hillebrand, Helmut; Lind, Eric M; Pärtel, Meelis; Bakker, Jonathan D; Buckley, Yvonne M; Crawley, Michael J; Damschen, Ellen I; Davies, Kendi F; Fay, Philip A; Firn, Jennifer; Gruner, Daniel S; Hector, Andy; Knops, Johannes M H; MacDougall, Andrew S; Melbourne, Brett A; Morgan, John W; Orrock, John L; Prober, Suzanne M; Smith, Melinda D

2016-01-21

How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns. Here, by integrating the predictions from multiple theories into a single model and using data from 1,126 grassland plots spanning five continents, we detect the clear signals of numerous underlying mechanisms linking productivity and richness. We find that an integrative model has substantially higher explanatory power than traditional bivariate analyses. In addition, the specific results unveil several surprising findings that conflict with classical models. These include the isolation of a strong and consistent enhancement of productivity by richness, an effect in striking contrast with superficial data patterns. Also revealed is a consistent importance of competition across the full range of productivity values, in direct conflict with some (but not all) proposed models. The promotion of local richness by macroecological gradients in climatic favourability, generally seen as a competing hypothesis, is also found to be important in our analysis. The results demonstrate that an integrative modelling approach leads to a major advance in our ability to discern the underlying processes operating in ecological systems.

A view on coupled cluster perturbation theory using a bivariational Lagrangian formulation.

Science.gov (United States)

Kristensen, Kasper; Eriksen, Janus J; Matthews, Devin A; Olsen, Jeppe; Jørgensen, Poul

2016-02-14

We consider two distinct coupled cluster (CC) perturbation series that both expand the difference between the energies of the CCSD (CC with single and double excitations) and CCSDT (CC with single, double, and triple excitations) models in orders of the Møller-Plesset fluctuation potential. We initially introduce the E-CCSD(T-n) series, in which the CCSD amplitude equations are satisfied at the expansion point, and compare it to the recently developed CCSD(T-n) series [J. J. Eriksen et al., J. Chem. Phys. 140, 064108 (2014)], in which not only the CCSD amplitude, but also the CCSD multiplier equations are satisfied at the expansion point. The computational scaling is similar for the two series, and both are term-wise size extensive with a formal convergence towards the CCSDT target energy. However, the two series are different, and the CCSD(T-n) series is found to exhibit a more rapid convergence up through the series, which we trace back to the fact that more information at the expansion point is utilized than for the E-CCSD(T-n) series. The present analysis can be generalized to any perturbation expansion representing the difference between a parent CC model and a higher-level target CC model. In general, we demonstrate that, whenever the parent parameters depend upon the perturbation operator, a perturbation expansion of the CC energy (where only parent amplitudes are used) differs from a perturbation expansion of the CC Lagrangian (where both parent amplitudes and parent multipliers are used). For the latter case, the bivariational Lagrangian formulation becomes more than a convenient mathematical tool, since it facilitates a different and faster convergent perturbation series than the simpler energy-based expansion.

A Basic Bivariate Structure of Personality Attributes Evident Across Nine Languages.

Science.gov (United States)

Saucier, Gerard; Thalmayer, Amber Gayle; Payne, Doris L; Carlson, Robert; Sanogo, Lamine; Ole-Kotikash, Leonard; Church, A Timothy; Katigbak, Marcia S; Somer, Oya; Szarota, Piotr; Szirmák, Zsofia; Zhou, Xinyue

2014-02-01

Here, two studies seek to characterize a parsimonious common-denominator personality structure with optimal cross-cultural replicability. Personality differences are observed in all human populations and cultures, but lexicons for personality attributes contain so many distinctions that parsimony is lacking. Models stipulating the most important attributes have been formulated by experts or by empirical studies drawing on experience in a very limited range of cultures. Factor analyses of personality lexicons of nine languages of diverse provenance (Chinese, Korean, Filipino, Turkish, Greek, Polish, Hungarian, Maasai, and Senoufo) were examined, and their common structure was compared to that of several prominent models in psychology. A parsimonious bivariate model showed evidence of substantial convergence and ubiquity across cultures. Analyses involving key markers of these dimensions in English indicate that they are broad dimensions involving the overlapping content of the interpersonal circumplex, models of communion and agency, and morality/warmth and competence. These "Big Two" dimensions-Social Self-Regulation and Dynamism-provide a common-denominator model involving the two most crucial axes of personality variation, ubiquitous across cultures. The Big Two might serve as an umbrella model serving to link diverse theoretical models and associated research literatures. © 2013 Wiley Periodicals, Inc.

Optical Coherence Tomography Noise Reduction Using Anisotropic Local Bivariate Gaussian Mixture Prior in 3D Complex Wavelet Domain

OpenAIRE

Rabbani, Hossein; Sonka, Milan; Abramoff, Michael D.

2013-01-01

In this paper, MMSE estimator is employed for noise-free 3D OCT data recovery in 3D complex wavelet domain. Since the proposed distribution for noise-free data plays a key role in the performance of MMSE estimator, a priori distribution for the pdf of noise-free 3D complex wavelet coefficients is proposed which is able to model the main statistical properties of wavelets. We model the coefficients with a mixture of two bivariate Gaussian pdfs with local parameters which are able to capture th...

Aquaculture in artificially developed wetlands in urban areas: an application of the bivariate relationship between soil and surface water in landscape ecology.

Science.gov (United States)

Paul, Abhijit

2011-01-01

Wetlands show a strong bivariate relationship between soil and surface water. Artificially developed wetlands help to build landscape ecology and make built environments sustainable. The bheries, wetlands of eastern Calcutta (India), utilize the city sewage to develop urban aquaculture that supports the local fish industries and opens a new frontier in sustainable environmental planning research.

A bivariate optimal replacement policy for a multistate repairable system

International Nuclear Information System (INIS)

Zhang Yuanlin; Yam, Richard C.M.; Zuo, Ming J.

2007-01-01

In this paper, a deteriorating simple repairable system with k+1 states, including k failure states and one working state, is studied. It is assumed that the system after repair is not 'as good as new' and the deterioration of the system is stochastic. We consider a bivariate replacement policy, denoted by (T,N), in which the system is replaced when its working age has reached T or the number of failures it has experienced has reached N, whichever occurs first. The objective is to determine the optimal replacement policy (T,N)* such that the long-run expected profit per unit time is maximized. The explicit expression of the long-run expected profit per unit time is derived and the corresponding optimal replacement policy can be determined analytically or numerically. We prove that the optimal policy (T,N)* is better than the optimal policy N* for a multistate simple repairable system. We also show that a general monotone process model for a multistate simple repairable system is equivalent to a geometric process model for a two-state simple repairable system in the sense that they have the same structure for the long-run expected profit (or cost) per unit time and the same optimal policy. Finally, a numerical example is given to illustrate the theoretical results

Integrating Expert Knowledge with Statistical Analysis for Landslide Susceptibility Assessment at Regional Scale

Directory of Open Access Journals (Sweden)

Christos Chalkias

2016-03-01

Full Text Available In this paper, an integration landslide susceptibility model by combining expert-based and bivariate statistical analysis (Landslide Susceptibility Index—LSI approaches is presented. Factors related with the occurrence of landslides—such as elevation, slope angle, slope aspect, lithology, land cover, Mean Annual Precipitation (MAP and Peak Ground Acceleration (PGA—were analyzed within a GIS environment. This integrated model produced a landslide susceptibility map which categorized the study area according to the probability level of landslide occurrence. The accuracy of the final map was evaluated by Receiver Operating Characteristics (ROC analysis depending on an independent (validation dataset of landslide events. The prediction ability was found to be 76% revealing that the integration of statistical analysis with human expertise can provide an acceptable landslide susceptibility assessment at regional scale.

A Vehicle for Bivariate Data Analysis

Science.gov (United States)

Roscoe, Matt B.

2016-01-01

Instead of reserving the study of probability and statistics for special fourth-year high school courses, the Common Core State Standards for Mathematics (CCSSM) takes a "statistics for all" approach. The standards recommend that students in grades 6-8 learn to summarize and describe data distributions, understand probability, draw…

New Colors for Histology: Optimized Bivariate Color Maps Increase Perceptual Contrast in Histological Images.

Science.gov (United States)

Kather, Jakob Nikolas; Weis, Cleo-Aron; Marx, Alexander; Schuster, Alexander K; Schad, Lothar R; Zöllner, Frank Gerrit

2015-01-01

Accurate evaluation of immunostained histological images is required for reproducible research in many different areas and forms the basis of many clinical decisions. The quality and efficiency of histopathological evaluation is limited by the information content of a histological image, which is primarily encoded as perceivable contrast differences between objects in the image. However, the colors of chromogen and counterstain used for histological samples are not always optimally distinguishable, even under optimal conditions. In this study, we present a method to extract the bivariate color map inherent in a given histological image and to retrospectively optimize this color map. We use a novel, unsupervised approach based on color deconvolution and principal component analysis to show that the commonly used blue and brown color hues in Hematoxylin-3,3'-Diaminobenzidine (DAB) images are poorly suited for human observers. We then demonstrate that it is possible to construct improved color maps according to objective criteria and that these color maps can be used to digitally re-stain histological images. To validate whether this procedure improves distinguishability of objects and background in histological images, we re-stain phantom images and N = 596 large histological images of immunostained samples of human solid tumors. We show that perceptual contrast is improved by a factor of 2.56 in phantom images and up to a factor of 2.17 in sets of histological tumor images. Thus, we provide an objective and reliable approach to measure object distinguishability in a given histological image and to maximize visual information available to a human observer. This method could easily be incorporated in digital pathology image viewing systems to improve accuracy and efficiency in research and diagnostics.

Magnitude and determinants of stunting in children under- five years ...

African Journals Online (AJOL)

Bernt Lindtjorn

bekates@yahoo.com; 2Unit of Applied Human Nutrition Program, University of Nairobi, ... Both bivariate analysis and multivariate analysis (logistic ... Results: The analyses revealed that 43.2 (12.0-17.6) 95% CI percent of the children under age .... reliability were maintained through close supervision of ... Statistical analysis.

THE BIVARIATE SIZE-LUMINOSITY RELATIONS FOR LYMAN BREAK GALAXIES AT z {approx} 4-5

Energy Technology Data Exchange (ETDEWEB)

Huang, Kuang-Han; Su, Jian [Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 (United States); Ferguson, Henry C. [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Ravindranath, Swara, E-mail: kuanghan@pha.jhu.edu [The Inter-University Center for Astronomy and Astrophysics, Pune University Campus, Pune 411007, Maharashtra (India)

2013-03-01

We study the bivariate size-luminosity distribution of Lyman break galaxies (LBGs) selected at redshifts around 4 and 5 in GOODS and the HUDF fields. We model the size-luminosity distribution as a combination of log-normal distribution (in size) and Schechter function (in luminosity), therefore it enables a more detailed study of the selection effects. We perform extensive simulations to quantify the dropout-selection completenesses and measurement biases and uncertainties in two-dimensional size and magnitude bins, and transform the theoretical size-luminosity distribution to the expected distribution for the observed data. Using maximum-likelihood estimator, we find that the Schechter function parameters for B {sub 435}-dropouts and are consistent with the values in the literature, but the size distributions are wider than expected from the angular momentum distribution of the underlying dark matter halos. The slope of the size-luminosity (RL) relation is similar to those found for local disk galaxies, but considerably shallower than local early-type galaxies.

THE BIVARIATE SIZE-LUMINOSITY RELATIONS FOR LYMAN BREAK GALAXIES AT z ∼ 4-5

International Nuclear Information System (INIS)

Huang, Kuang-Han; Su, Jian; Ferguson, Henry C.; Ravindranath, Swara

2013-01-01

We study the bivariate size-luminosity distribution of Lyman break galaxies (LBGs) selected at redshifts around 4 and 5 in GOODS and the HUDF fields. We model the size-luminosity distribution as a combination of log-normal distribution (in size) and Schechter function (in luminosity), therefore it enables a more detailed study of the selection effects. We perform extensive simulations to quantify the dropout-selection completenesses and measurement biases and uncertainties in two-dimensional size and magnitude bins, and transform the theoretical size-luminosity distribution to the expected distribution for the observed data. Using maximum-likelihood estimator, we find that the Schechter function parameters for B 435 -dropouts and are consistent with the values in the literature, but the size distributions are wider than expected from the angular momentum distribution of the underlying dark matter halos. The slope of the size-luminosity (RL) relation is similar to those found for local disk galaxies, but considerably shallower than local early-type galaxies.

Bivariate Gaussian bridges: directional factorization of diffusion in Brownian bridge models.

Science.gov (United States)

Kranstauber, Bart; Safi, Kamran; Bartumeus, Frederic

2014-01-01

In recent years high resolution animal tracking data has become the standard in movement ecology. The Brownian Bridge Movement Model (BBMM) is a widely adopted approach to describe animal space use from such high resolution tracks. One of the underlying assumptions of the BBMM is isotropic diffusive motion between consecutive locations, i.e. invariant with respect to the direction. Here we propose to relax this often unrealistic assumption by separating the Brownian motion variance into two directional components, one parallel and one orthogonal to the direction of the motion. Our new model, the Bivariate Gaussian bridge (BGB), tracks movement heterogeneity across time. Using the BGB and identifying directed and non-directed movement within a trajectory resulted in more accurate utilisation distributions compared to dynamic Brownian bridges, especially for trajectories with a non-isotropic diffusion, such as directed movement or Lévy like movements. We evaluated our model with simulated trajectories and observed tracks, demonstrating that the improvement of our model scales with the directional correlation of a correlated random walk. We find that many of the animal trajectories do not adhere to the assumptions of the BBMM. The proposed model improves accuracy when describing the space use both in simulated correlated random walks as well as observed animal tracks. Our novel approach is implemented and available within the "move" package for R.

Contributory fault and level of personal injury to drivers involved in head-on collisions: Application of copula-based bivariate ordinal models.

Science.gov (United States)

Wali, Behram; Khattak, Asad J; Xu, Jingjing

2018-01-01

The main objective of this study is to simultaneously investigate the degree of injury severity sustained by drivers involved in head-on collisions with respect to fault status designation. This is complicated to answer due to many issues, one of which is the potential presence of correlation between injury outcomes of drivers involved in the same head-on collision. To address this concern, we present seemingly unrelated bivariate ordered response models by analyzing the joint injury severity probability distribution of at-fault and not-at-fault drivers. Moreover, the assumption of bivariate normality of residuals and the linear form of stochastic dependence implied by such models may be unduly restrictive. To test this, Archimedean copula structures and normal mixture marginals are integrated into the joint estimation framework, which can characterize complex forms of stochastic dependencies and non-normality in residual terms. The models are estimated using 2013 Virginia police reported two-vehicle head-on collision data, where exactly one driver is at-fault. The results suggest that both at-fault and not-at-fault drivers sustained serious/fatal injuries in 8% of crashes, whereas, in 4% of the cases, the not-at-fault driver sustained a serious/fatal injury with no injury to the at-fault driver at all. Furthermore, if the at-fault driver is fatigued, apparently asleep, or has been drinking the not-at-fault driver is more likely to sustain a severe/fatal injury, controlling for other factors and potential correlations between the injury outcomes. While not-at-fault vehicle speed affects injury severity of at-fault driver, the effect is smaller than the effect of at-fault vehicle speed on at-fault injury outcome. Contrarily, and importantly, the effect of at-fault vehicle speed on injury severity of not-at-fault driver is almost equal to the effect of not-at-fault vehicle speed on injury outcome of not-at-fault driver. Compared to traditional ordered probability

Improving the modelling of redshift-space distortions - I. A bivariate Gaussian description for the galaxy pairwise velocity distributions

Science.gov (United States)

Bianchi, Davide; Chiesa, Matteo; Guzzo, Luigi

2015-01-01

As a step towards a more accurate modelling of redshift-space distortions (RSD) in galaxy surveys, we develop a general description of the probability distribution function of galaxy pairwise velocities within the framework of the so-called streaming model. For a given galaxy separation r, such function can be described as a superposition of virtually infinite local distributions. We characterize these in terms of their moments and then consider the specific case in which they are Gaussian functions, each with its own mean μ and dispersion σ. Based on physical considerations, we make the further crucial assumption that these two parameters are in turn distributed according to a bivariate Gaussian, with its own mean and covariance matrix. Tests using numerical simulations explicitly show that with this compact description one can correctly model redshift-space distortions on all scales, fully capturing the overall linear and non-linear dynamics of the galaxy flow at different separations. In particular, we naturally obtain Gaussian/exponential, skewed/unskewed distribution functions, depending on separation as observed in simulations and data. Also, the recently proposed single-Gaussian description of RSD is included in this model as a limiting case, when the bivariate Gaussian is collapsed to a two-dimensional Dirac delta function. We also show how this description naturally allows for the Taylor expansion of 1 + ξS(s) around 1 + ξR(r), which leads to the Kaiser linear formula when truncated to second order, explicating its connection with the moments of the velocity distribution functions. More work is needed, but these results indicate a very promising path to make definitive progress in our programme to improve RSD estimators.

Modelling the vicious circle between obesity and physical activity in children and adolescents using a bivariate probit model with endogenous regressors.

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Yeh, C-Y; Chen, L-J; Ku, P-W; Chen, C-M

2015-01-01

The increasing prevalence of obesity in children and adolescents has become one of the most important public health issues around the world. Lack of physical activity is a risk factor for obesity, while being obese could reduce the likelihood of participating in physical activity. Failing to account for the endogeneity between obesity and physical activity would result in biased estimation. This study investigates the relationship between overweight and physical activity by taking endogeneity into consideration. It develops an endogenous bivariate probit model estimated by the maximum likelihood method. The data included 4008 boys and 4197 girls in the 5th-9th grades in Taiwan in 2007-2008. The relationship between overweight and physical activity is significantly negative in the endogenous model, but insignificant in the comparative exogenous model. This endogenous relationship presents a vicious circle in which lower levels of physical activity lead to overweight, while those who are already overweight engage in less physical activity. The results not only reveal the importance of endogenous treatment, but also demonstrate the robust negative relationship between these two factors. An emphasis should be put on overweight and obese children and adolescents in order to break the vicious circle. Promotion of physical activity by appropriate counselling programmes and peer support could be effective in reducing the prevalence of obesity in children and adolescents.

Multifractal Cross Wavelet Analysis

Science.gov (United States)

Jiang, Zhi-Qiang; Gao, Xing-Lu; Zhou, Wei-Xing; Stanley, H. Eugene

Complex systems are composed of mutually interacting components and the output values of these components usually exhibit long-range cross-correlations. Using wavelet analysis, we propose a method of characterizing the joint multifractal nature of these long-range cross correlations, a method we call multifractal cross wavelet analysis (MFXWT). We assess the performance of the MFXWT method by performing extensive numerical experiments on the dual binomial measures with multifractal cross correlations and the bivariate fractional Brownian motions (bFBMs) with monofractal cross correlations. For binomial multifractal measures, we find the empirical joint multifractality of MFXWT to be in approximate agreement with the theoretical formula. For bFBMs, MFXWT may provide spurious multifractality because of the wide spanning range of the multifractal spectrum. We also apply the MFXWT method to stock market indices, and in pairs of index returns and volatilities we find an intriguing joint multifractal behavior. The tests on surrogate series also reveal that the cross correlation behavior, particularly the cross correlation with zero lag, is the main origin of cross multifractality.

Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development

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Yonglong Yu

2016-04-01

Full Text Available Wheat seed development is an important physiological process of seed maturation and directly affects wheat yield and quality. In this study, we performed dynamic transcriptome microarray analysis of an elite Chinese bread wheat cultivar (Jimai 20 during grain development using the GeneChip Wheat Genome Array. Grain morphology and scanning electron microscope observations showed that the period of 11–15 days post-anthesis (DPA was a key stage for the synthesis and accumulation of seed starch. Genome-wide transcriptional profiling and significance analysis of microarrays revealed that the period from 11 to 15 DPA was more important than the 15–20 DPA stage for the synthesis and accumulation of nutritive reserves. Series test of cluster analysis of differential genes revealed five statistically significant gene expression profiles. Gene ontology annotation and enrichment analysis gave further information about differentially expressed genes, and MapMan analysis revealed expression changes within functional groups during seed development. Metabolic pathway network analysis showed that major and minor metabolic pathways regulate one another to ensure regular seed development and nutritive reserve accumulation. We performed gene co-expression network analysis to identify genes that play vital roles in seed development and identified several key genes involved in important metabolic pathways. The transcriptional expression of eight key genes involved in starch and protein synthesis and stress defense was further validated by qRT-PCR. Our results provide new insight into the molecular mechanisms of wheat seed development and the determinants of yield and quality.

Anatomical analysis of human masseter using MRI

International Nuclear Information System (INIS)

Kitahara, Masaki

1990-01-01

To quantitatively elucidate individual variation in human masseter muscle, the cross sectional area of this muscle was measured in situ with MRI apparatus. The results were analyzed against age, body build and laterality in habitual mastication by bivariate correlation analysis. Materials included 52 healthy volunteers (26 males, 26 females). Right and left masseter areas and total cross sectional area of the face were measured in the same horizontal plane, and directly displayed on the console of the MRI apparatus. The areas of masseter muscles were not correlated with age or body build, but were positively correlated with the total cross sectional area of the face in the same horizontal plane. Because the left masseters tended to be larger than right, a method for evaluation of the relative size of each side of the messeters was established. This analysis revealed that the corrected dominance of the masseter corresponded, with high probability, to the habitual laterality in mastication. (author)

Anatomical analysis of human masseter using MRI

Energy Technology Data Exchange (ETDEWEB)

Kitahara, Masaki (Showa Univ., Tokyo (Japan). School of Medicine)

1990-10-01

To quantitatively elucidate individual variation in human masseter muscle, the cross sectional area of this muscle was measured in situ with MRI apparatus. The results were analyzed against age, body build and laterality in habitual mastication by bivariate correlation analysis. Materials included 52 healthy volunteers (26 males, 26 females). Right and left masseter areas and total cross sectional area of the face were measured in the same horizontal plane, and directly displayed on the console of the MRI apparatus. The areas of masseter muscles were not correlated with age or body build, but were positively correlated with the total cross sectional area of the face in the same horizontal plane. Because the left masseters tended to be larger than right, a method for evaluation of the relative size of each side of the messeters was established. This analysis revealed that the corrected dominance of the masseter corresponded, with high probability, to the habitual laterality in mastication. (author).

Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit.

Science.gov (United States)

Ashoori, Maryam; Burns, Catherine M; d'Entremont, Barbara; Momtahan, Kathryn

2014-01-01

Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamwork and leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams.

Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit

Science.gov (United States)

Ashoori, Maryam; Burns, Catherine M.; d'Entremont, Barbara; Momtahan, Kathryn

2014-01-01

Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamworkand leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. Practitioner Summary: This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams PMID:24837514

New Colors for Histology: Optimized Bivariate Color Maps Increase Perceptual Contrast in Histological Images.

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Jakob Nikolas Kather

Full Text Available Accurate evaluation of immunostained histological images is required for reproducible research in many different areas and forms the basis of many clinical decisions. The quality and efficiency of histopathological evaluation is limited by the information content of a histological image, which is primarily encoded as perceivable contrast differences between objects in the image. However, the colors of chromogen and counterstain used for histological samples are not always optimally distinguishable, even under optimal conditions.In this study, we present a method to extract the bivariate color map inherent in a given histological image and to retrospectively optimize this color map. We use a novel, unsupervised approach based on color deconvolution and principal component analysis to show that the commonly used blue and brown color hues in Hematoxylin-3,3'-Diaminobenzidine (DAB images are poorly suited for human observers. We then demonstrate that it is possible to construct improved color maps according to objective criteria and that these color maps can be used to digitally re-stain histological images.To validate whether this procedure improves distinguishability of objects and background in histological images, we re-stain phantom images and N = 596 large histological images of immunostained samples of human solid tumors. We show that perceptual contrast is improved by a factor of 2.56 in phantom images and up to a factor of 2.17 in sets of histological tumor images.Thus, we provide an objective and reliable approach to measure object distinguishability in a given histological image and to maximize visual information available to a human observer. This method could easily be incorporated in digital pathology image viewing systems to improve accuracy and efficiency in research and diagnostics.

Sequence analysis of serum albumins reveals the molecular evolution of ligand recognition properties.

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Fanali, Gabriella; Ascenzi, Paolo; Bernardi, Giorgio; Fasano, Mauro

2012-01-01

Serum albumin (SA) is a circulating protein providing a depot and carrier for many endogenous and exogenous compounds. At least seven major binding sites have been identified by structural and functional investigations mainly in human SA. SA is conserved in vertebrates, with at least 49 entries in protein sequence databases. The multiple sequence analysis of this set of entries leads to the definition of a cladistic tree for the molecular evolution of SA orthologs in vertebrates, thus showing the clustering of the considered species, with lamprey SAs (Lethenteron japonicum and Petromyzon marinus) in a separate outgroup. Sequence analysis aimed at searching conserved domains revealed that most SA sequences are made up by three repeated domains (about 600 residues), as extensively characterized for human SA. On the contrary, lamprey SAs are giant proteins (about 1400 residues) comprising seven repeated domains. The phylogenetic analysis of the SA family reveals a stringent correlation with the taxonomic classification of the species available in sequence databases. A focused inspection of the sequences of ligand binding sites in SA revealed that in all sites most residues involved in ligand binding are conserved, although the versatility towards different ligands could be peculiar of higher organisms. Moreover, the analysis of molecular links between the different sites suggests that allosteric modulation mechanisms could be restricted to higher vertebrates.

REGRES: A FORTRAN-77 program to calculate nonparametric and ``structural'' parametric solutions to bivariate regression equations

Science.gov (United States)

Rock, N. M. S.; Duffy, T. R.

REGRES allows a range of regression equations to be calculated for paired sets of data values in which both variables are subject to error (i.e. neither is the "independent" variable). Nonparametric regressions, based on medians of all possible pairwise slopes and intercepts, are treated in detail. Estimated slopes and intercepts are output, along with confidence limits, Spearman and Kendall rank correlation coefficients. Outliers can be rejected with user-determined stringency. Parametric regressions can be calculated for any value of λ (the ratio of the variances of the random errors for y and x)—including: (1) major axis ( λ = 1); (2) reduced major axis ( λ = variance of y/variance of x); (3) Y on Xλ = infinity; or (4) X on Y ( λ = 0) solutions. Pearson linear correlation coefficients also are output. REGRES provides an alternative to conventional isochron assessment techniques where bivariate normal errors cannot be assumed, or weighting methods are inappropriate.

EXPLORATORY DATA ANALYSIS AND MULTIVARIATE STRATEGIES FOR REVEALING MULTIVARIATE STRUCTURES IN CLIMATE DATA

Directory of Open Access Journals (Sweden)

2016-12-01

Full Text Available This paper is on data analysis strategy in a complex, multidimensional, and dynamic domain. The focus is on the use of data mining techniques to explore the importance of multivariate structures; using climate variables which influences climate change. Techniques involved in data mining exercise vary according to the data structures. The multivariate analysis strategy considered here involved choosing an appropriate tool to analyze a process. Factor analysis is introduced into data mining technique in order to reveal the influencing impacts of factors involved as well as solving for multicolinearity effect among the variables. The temporal nature and multidimensionality of the target variables is revealed in the model using multidimensional regression estimates. The strategy of integrating the method of several statistical techniques, using climate variables in Nigeria was employed. R2 of 0.518 was obtained from the ordinary least square regression analysis carried out and the test was not significant at 5% level of significance. However, factor analysis regression strategy gave a good fit with R2 of 0.811 and the test was significant at 5% level of significance. Based on this study, model building should go beyond the usual confirmatory data analysis (CDA, rather it should be complemented with exploratory data analysis (EDA in order to achieve a desired result.

A Hybrid Forecasting Model Based on Bivariate Division and a Backpropagation Artificial Neural Network Optimized by Chaos Particle Swarm Optimization for Day-Ahead Electricity Price

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Zhilong Wang

2014-01-01

Full Text Available In the electricity market, the electricity price plays an inevitable role. Nevertheless, accurate price forecasting, a vital factor affecting both government regulatory agencies and public power companies, remains a huge challenge and a critical problem. Determining how to address the accurate forecasting problem becomes an even more significant task in an era in which electricity is increasingly important. Based on the chaos particle swarm optimization (CPSO, the backpropagation artificial neural network (BPANN, and the idea of bivariate division, this paper proposes a bivariate division BPANN (BD-BPANN method and the CPSO-BD-BPANN method for forecasting electricity price. The former method creatively transforms the electricity demand and price to be a new variable, named DV, which is calculated using the division principle, to forecast the day-ahead electricity by multiplying the forecasted values of the DVs and forecasted values of the demand. Next, to improve the accuracy of BD-BPANN, chaos particle swarm optimization and BD-BPANN are synthesized to form a novel model, CPSO-BD-BPANN. In this study, CPSO is utilized to optimize the initial parameters of BD-BPANN to make its output more stable than the original model. Finally, two forecasting strategies are proposed regarding different situations.

Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

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Henry D Priest

Full Text Available Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

Re-Analysis of Metagenomic Sequences from Acute Flaccidmyelitis Patients Reveals Alternatives to Enterovirus D68 Infection

Science.gov (United States)

2015-07-13

caused in some cases by infection with enterovirus D68. We found that among the patients whose symptoms were previously attributed to enterovirus D68...distribution is unlimited. Re-analysis of metagenomic sequences from acute flaccidmyelitis patients reveals alternatives to enterovirus D68...Street Baltimore, MD 21218 -2685 ABSTRACT Re-analysis of metagenomic sequences from acute flaccidmyelitis patients reveals alternatives to enterovirus

Inference for the Bivariate and Multivariate Hidden Truncated Pareto(type II) and Pareto(type IV) Distribution and Some Measures of Divergence Related to Incompatibility of Probability Distribution

Science.gov (United States)

Ghosh, Indranil

2011-01-01

Consider a discrete bivariate random variable (X, Y) with possible values x[subscript 1], x[subscript 2],..., x[subscript I] for X and y[subscript 1], y[subscript 2],..., y[subscript J] for Y. Further suppose that the corresponding families of conditional distributions, for X given values of Y and of Y for given values of X are available. We…

Differential proteomic analysis reveals novel links between primary metabolism and antibiotic production in Amycolatopsis balhimycina

DEFF Research Database (Denmark)

Gallo, G.; Renzone, G.; Alduina, R.

2010-01-01

A differential proteomic analysis, based on 2-DE and MS procedures, was performed on Amycolatopsis balhimycina DSM5908, the actinomycete producing the vancomycin-like antibiotic balhimycin. A comparison of proteomic profiles before and during balhimycin production characterized differentially...... available over the World Wide Web as interactive web pages (http://www.unipa.it/ampuglia/Abal-proteome-maps). Functional clustering analysis revealed that differentially expressed proteins belong to functional groups involved in central carbon metabolism, amino acid metabolism and protein biosynthesis...... intermediates, were upregulated during antibiotic production. qRT-PCR analysis revealed that 8 out of 14 upregulated genes showed a positive correlation between changes at translational and transcriptional expression level. Furthermore, proteomic analysis of two nonproducing mutants, restricted to a sub...

Bivariate analysis of the genetic variability among some accessions of African Yam Bean (Sphenostylis stenocarpa (Hochst ex A. RichHarms

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Solomon Tayo AKINYOSOYE

2017-12-01

Full Text Available Variability is an important factor to consider in crop improvement programmes. This study was conducted in two years to assess genetic variability and determine relationship between seed yield, its components and tuber production characters among twelve accessions of African yam bean. Data collected were subjected to combined analysis of variance (ANOVA, Principal Component Analysis (PCA, hierarchical and K-means clustering analyses. Results obtained revealed that genotype by year (G × Y interaction had significant effects on some of variables measured (days to first flowering, days to 50 % flowering, number of pod per plant, pod length, seed yield and tuber yield per plant in this study.The first five principal components (PC with Eigen values greater than 1.0 accounted for about 66.70 % of the total variation, where PC1 and PC 2 accounted for 39.48 % of variation and were associated with seed and tuber yield variables. Three heterotic groups were clearly delineated among genotypes with accessions AY03 and AY10 identified for high seed yield and tuber yield respectively. Non-significant relationship that existed between tuber and seed yield per plant of these accessions was recommended for further test in various agro-ecologies for their suitability, adaptability and possible exploitation of heterosis to further improve the accessions.

Comparative analysis reveals that polyploidy does not decelerate diversification in fish.

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Zhan, S H; Glick, L; Tsigenopoulos, C S; Otto, S P; Mayrose, I

2014-02-01

While the proliferation of the species-rich teleost fish has been ascribed to an ancient genome duplication event at the base of this group, the broader impact of polyploidy on fish evolution and diversification remains poorly understood. Here, we investigate the association between polyploidy and diversification in several fish lineages: the sturgeons (Acipenseridae: Acipenseriformes), the botiid loaches (Botiidae: Cypriniformes), Cyprininae fishes (Cyprinidae: Cypriniformes) and the salmonids (Salmonidae: Salmoniformes). Using likelihood-based evolutionary methodologies, we co-estimate speciation and extinction rates associated with polyploid vs. diploid fish lineages. Family-level analysis of Acipenseridae and Botiidae revealed no significant difference in diversification rates between polyploid and diploid relatives, while analysis of the subfamily Cyprininae revealed higher polyploid diversification. Additionally, order-level analysis of the polyploid Salmoniformes and its diploid sister clade, the Esociformes, did not support a significantly different net diversification rate between the two groups. Taken together, our results suggest that polyploidy is generally not associated with decreased diversification in fish - a pattern that stands in contrast to that previously observed in plants. While there are notable differences in the time frame examined in the two studies, our results suggest that polyploidy is associated with different diversification patterns in these two major branches of the eukaryote tree of life. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Semiparametric bivariate zero-inflated Poisson models with application to studies of abundance for multiple species

Science.gov (United States)

Arab, Ali; Holan, Scott H.; Wikle, Christopher K.; Wildhaber, Mark L.

2012-01-01

Ecological studies involving counts of abundance, presence–absence or occupancy rates often produce data having a substantial proportion of zeros. Furthermore, these types of processes are typically multivariate and only adequately described by complex nonlinear relationships involving externally measured covariates. Ignoring these aspects of the data and implementing standard approaches can lead to models that fail to provide adequate scientific understanding of the underlying ecological processes, possibly resulting in a loss of inferential power. One method of dealing with data having excess zeros is to consider the class of univariate zero-inflated generalized linear models. However, this class of models fails to address the multivariate and nonlinear aspects associated with the data usually encountered in practice. Therefore, we propose a semiparametric bivariate zero-inflated Poisson model that takes into account both of these data attributes. The general modeling framework is hierarchical Bayes and is suitable for a broad range of applications. We demonstrate the effectiveness of our model through a motivating example on modeling catch per unit area for multiple species using data from the Missouri River Benthic Fishes Study, implemented by the United States Geological Survey.

Improving runoff risk estimates: Formulating runoff as a bivariate process using the SCS curve number method

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Shaw, Stephen B.; Walter, M. Todd

2009-03-01

The Soil Conservation Service curve number (SCS-CN) method is widely used to predict storm runoff for hydraulic design purposes, such as sizing culverts and detention basins. As traditionally used, the probability of calculated runoff is equated to the probability of the causative rainfall event, an assumption that fails to account for the influence of variations in soil moisture on runoff generation. We propose a modification to the SCS-CN method that explicitly incorporates rainfall return periods and the frequency of different soil moisture states to quantify storm runoff risks. Soil moisture status is assumed to be correlated to stream base flow. Fundamentally, this approach treats runoff as the outcome of a bivariate process instead of dictating a 1:1 relationship between causative rainfall and resulting runoff volumes. Using data from the Fall Creek watershed in western New York and the headwaters of the French Broad River in the mountains of North Carolina, we show that our modified SCS-CN method improves frequency discharge predictions in medium-sized watersheds in the eastern United States in comparison to the traditional application of the method.

Modeling both of the number of pausibacillary and multibacillary leprosy patients by using bivariate poisson regression

Science.gov (United States)

Winahju, W. S.; Mukarromah, A.; Putri, S.

2015-03-01

Leprosy is a chronic infectious disease caused by bacteria of leprosy (Mycobacterium leprae). Leprosy has become an important thing in Indonesia because its morbidity is quite high. Based on WHO data in 2014, in 2012 Indonesia has the highest number of new leprosy patients after India and Brazil with a contribution of 18.994 people (8.7% of the world). This number makes Indonesia automatically placed as the country with the highest number of leprosy morbidity of ASEAN countries. The province that most contributes to the number of leprosy patients in Indonesia is East Java. There are two kind of leprosy. They consist of pausibacillary and multibacillary. The morbidity of multibacillary leprosy is higher than pausibacillary leprosy. This paper will discuss modeling both of the number of multibacillary and pausibacillary leprosy patients as responses variables. These responses are count variables, so modeling will be conducted by using bivariate poisson regression method. Unit experiment used is in East Java, and predictors involved are: environment, demography, and poverty. The model uses data in 2012, and the result indicates that all predictors influence significantly.

Multifractal detrended cross-correlation analysis on gold, crude oil and foreign exchange rate time series

Science.gov (United States)

Pal, Mayukha; Madhusudana Rao, P.; Manimaran, P.

2014-12-01

We apply the recently developed multifractal detrended cross-correlation analysis method to investigate the cross-correlation behavior and fractal nature between two non-stationary time series. We analyze the daily return price of gold, West Texas Intermediate and Brent crude oil, foreign exchange rate data, over a period of 18 years. The cross correlation has been measured from the Hurst scaling exponents and the singularity spectrum quantitatively. From the results, the existence of multifractal cross-correlation between all of these time series is found. We also found that the cross correlation between gold and oil prices possess uncorrelated behavior and the remaining bivariate time series possess persistent behavior. It was observed for five bivariate series that the cross-correlation exponents are less than the calculated average generalized Hurst exponents (GHE) for q0 and for one bivariate series the cross-correlation exponent is greater than GHE for all q values.

application of multilinear regression analysis in modeling of soil

African Journals Online (AJOL)

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Accordingly [1, 3] in their work, they applied linear regression ... (MLRA) is a statistical technique that uses several explanatory ... order to check this, they adopted bivariate correlation analysis .... groups, namely A-1 through A-7, based on their relative expected ..... Multivariate Regression in Gorgan Province North of Iran” ...

Transcriptomic analysis of human retinal detachment reveals both inflammatory response and photoreceptor death.

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Marie-Noëlle Delyfer

Full Text Available BACKGROUND: Retinal detachment often leads to a severe and permanent loss of vision and its therapeutic management remains to this day exclusively surgical. We have used surgical specimens to perform a differential analysis of the transcriptome of human retinal tissues following detachment in order to identify new potential pharmacological targets that could be used in combination with surgery to further improve final outcome. METHODOLOGY/PRINCIPAL FINDINGS: Statistical analysis reveals major involvement of the immune response in the disease. Interestingly, using a novel approach relying on coordinated expression, the interindividual variation was monitored to unravel a second crucial aspect of the pathological process: the death of photoreceptor cells. Within the genes identified, the expression of the major histocompatibility complex I gene HLA-C enables diagnosis of the disease, while PKD2L1 and SLCO4A1 -which are both down-regulated- act synergistically to provide an estimate of the duration of the retinal detachment process. Our analysis thus reveals the two complementary cellular and molecular aspects linked to retinal detachment: an immune response and the degeneration of photoreceptor cells. We also reveal that the human specimens have a higher clinical value as compared to artificial models that point to IL6 and oxidative stress, not implicated in the surgical specimens studied here. CONCLUSIONS/SIGNIFICANCE: This systematic analysis confirmed the occurrence of both neurodegeneration and inflammation during retinal detachment, and further identifies precisely the modification of expression of the different genes implicated in these two phenomena. Our data henceforth give a new insight into the disease process and provide a rationale for therapeutic strategies aimed at limiting inflammation and photoreceptor damage associated with retinal detachment and, in turn, improving visual prognosis after retinal surgery.

Improving risk estimates of runoff producing areas: formulating variable source areas as a bivariate process.

Science.gov (United States)

Cheng, Xiaoya; Shaw, Stephen B; Marjerison, Rebecca D; Yearick, Christopher D; DeGloria, Stephen D; Walter, M Todd

2014-05-01

Predicting runoff producing areas and their corresponding risks of generating storm runoff is important for developing watershed management strategies to mitigate non-point source pollution. However, few methods for making these predictions have been proposed, especially operational approaches that would be useful in areas where variable source area (VSA) hydrology dominates storm runoff. The objective of this study is to develop a simple approach to estimate spatially-distributed risks of runoff production. By considering the development of overland flow as a bivariate process, we incorporated both rainfall and antecedent soil moisture conditions into a method for predicting VSAs based on the Natural Resource Conservation Service-Curve Number equation. We used base-flow immediately preceding storm events as an index of antecedent soil wetness status. Using nine sub-basins of the Upper Susquehanna River Basin, we demonstrated that our estimated runoff volumes and extent of VSAs agreed with observations. We further demonstrated a method for mapping these areas in a Geographic Information System using a Soil Topographic Index. The proposed methodology provides a new tool for watershed planners for quantifying runoff risks across watersheds, which can be used to target water quality protection strategies. Copyright © 2014 Elsevier Ltd. All rights reserved.

Revealing the equivalence of two clonal survival models by principal component analysis

International Nuclear Information System (INIS)

Lachet, Bernard; Dufour, Jacques

1976-01-01

The principal component analysis of 21 chlorella cell survival curves, adjusted by one-hit and two-hit target models, lead to quite similar projections on the principal plan: the homologous parameters of these models are linearly correlated; the reason for the statistical equivalence of these two models, in the present state of experimental inaccuracy, is revealed [fr

Changes in cod muscle proteins during frozen storage revealed by proteome analysis and multivariate data analysis

DEFF Research Database (Denmark)

Kjærsgård, Inger Vibeke Holst; Nørrelykke, M.R.; Jessen, Flemming

2006-01-01

Multivariate data analysis has been combined with proteomics to enhance the recovery of information from 2-DE of cod muscle proteins during different storage conditions. Proteins were extracted according to 11 different storage conditions and samples were resolved by 2-DE. Data generated by 2-DE...... was subjected to principal component analysis (PCA) and discriminant partial least squares regression (DPLSR). Applying PCA to 2-DE data revealed the samples to form groups according to frozen storage time, whereas differences due to different storage temperatures or chilled storage in modified atmosphere...... light chain 1, 2 and 3, triose-phosphate isomerase, glyceraldehyde-3-phosphate dehydrogenase, aldolase A and two ?-actin fragments, and a nuclease diphosphate kinase B fragment to change in concentration, during frozen storage. Application of proteomics, multivariate data analysis and MS/MS to analyse...

Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles

KAUST Repository

Maadooliat, Mehdi; Gao, Xin; Huang, Jianhua Z.

2012-01-01

Despite considerable progress in the past decades, protein structure prediction remains one of the major unsolved problems in computational biology. Angular-sampling-based methods have been extensively studied recently due to their ability to capture the continuous conformational space of protein structures. The literature has focused on using a variety of parametric models of the sequential dependencies between angle pairs along the protein chains. In this article, we present a thorough review of angular-sampling-based methods by assessing three main questions: What is the best distribution type to model the protein angles? What is a reasonable number of components in a mixture model that should be considered to accurately parameterize the joint distribution of the angles? and What is the order of the local sequence-structure dependency that should be considered by a prediction method? We assess the model fits for different methods using bivariate lag-distributions of the dihedral/planar angles. Moreover, the main information across the lags can be extracted using a technique called Lag singular value decomposition (LagSVD), which considers the joint distribution of the dihedral/planar angles over different lags using a nonparametric approach and monitors the behavior of the lag-distribution of the angles using singular value decomposition. As a result, we developed graphical tools and numerical measurements to compare and evaluate the performance of different model fits. Furthermore, we developed a web-tool (http://www.stat.tamu. edu/~madoliat/LagSVD) that can be used to produce informative animations. © The Author 2012. Published by Oxford University Press.

Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles

KAUST Repository

Maadooliat, Mehdi

2012-08-27

Despite considerable progress in the past decades, protein structure prediction remains one of the major unsolved problems in computational biology. Angular-sampling-based methods have been extensively studied recently due to their ability to capture the continuous conformational space of protein structures. The literature has focused on using a variety of parametric models of the sequential dependencies between angle pairs along the protein chains. In this article, we present a thorough review of angular-sampling-based methods by assessing three main questions: What is the best distribution type to model the protein angles? What is a reasonable number of components in a mixture model that should be considered to accurately parameterize the joint distribution of the angles? and What is the order of the local sequence-structure dependency that should be considered by a prediction method? We assess the model fits for different methods using bivariate lag-distributions of the dihedral/planar angles. Moreover, the main information across the lags can be extracted using a technique called Lag singular value decomposition (LagSVD), which considers the joint distribution of the dihedral/planar angles over different lags using a nonparametric approach and monitors the behavior of the lag-distribution of the angles using singular value decomposition. As a result, we developed graphical tools and numerical measurements to compare and evaluate the performance of different model fits. Furthermore, we developed a web-tool (http://www.stat.tamu. edu/~madoliat/LagSVD) that can be used to produce informative animations. © The Author 2012. Published by Oxford University Press.

Principal component regression analysis with SPSS.

Science.gov (United States)

Liu, R X; Kuang, J; Gong, Q; Hou, X L

2003-06-01

The paper introduces all indices of multicollinearity diagnoses, the basic principle of principal component regression and determination of 'best' equation method. The paper uses an example to describe how to do principal component regression analysis with SPSS 10.0: including all calculating processes of the principal component regression and all operations of linear regression, factor analysis, descriptives, compute variable and bivariate correlations procedures in SPSS 10.0. The principal component regression analysis can be used to overcome disturbance of the multicollinearity. The simplified, speeded up and accurate statistical effect is reached through the principal component regression analysis with SPSS.

Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

Science.gov (United States)

2013-01-01

Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also

Co-occurrence correlations of heavy metals in sediments revealed using network analysis.

Science.gov (United States)

Liu, Lili; Wang, Zhiping; Ju, Feng; Zhang, Tong

2015-01-01

In this study, the correlation-based study was used to identify the co-occurrence correlations among metals in marine sediment of Hong Kong, based on the long-term (from 1991 to 2011) temporal and spatial monitoring data. 14 stations out of the total 45 marine sediment monitoring stations were selected from three representative areas, including Deep Bay, Victoria Harbour and Mirs Bay. Firstly, Spearman's rank correlation-based network analysis was conducted as the first step to identify the co-occurrence correlations of metals from raw metadata, and then for further analysis using the normalized metadata. The correlations patterns obtained by network were consistent with those obtained by the other statistic normalization methods, including annual ratios, R-squared coefficient and Pearson correlation coefficient. Both Deep Bay and Victoria Harbour have been polluted by heavy metals, especially for Pb and Cu, which showed strong co-occurrence with other heavy metals (e.g. Cr, Ni, Zn and etc.) and little correlations with the reference parameters (Fe or Al). For Mirs Bay, which has better marine sediment quality compared with Deep Bay and Victoria Harbour, the co-occurrence patterns revealed by network analysis indicated that the metals in sediment dominantly followed the natural geography process. Besides the wide applications in biology, sociology and informatics, it is the first time to apply network analysis in the researches of environment pollutions. This study demonstrated its powerful application for revealing the co-occurrence correlations among heavy metals in marine sediments, which could be further applied for other pollutants in various environment systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evolution of association between renal and liver functions while awaiting heart transplant: An application using a bivariate multiphase nonlinear mixed effects model.

Science.gov (United States)

Rajeswaran, Jeevanantham; Blackstone, Eugene H; Barnard, John

2018-07-01

In many longitudinal follow-up studies, we observe more than one longitudinal outcome. Impaired renal and liver functions are indicators of poor clinical outcomes for patients who are on mechanical circulatory support and awaiting heart transplant. Hence, monitoring organ functions while waiting for heart transplant is an integral part of patient management. Longitudinal measurements of bilirubin can be used as a marker for liver function and glomerular filtration rate for renal function. We derive an approximation to evolution of association between these two organ functions using a bivariate nonlinear mixed effects model for continuous longitudinal measurements, where the two submodels are linked by a common distribution of time-dependent latent variables and a common distribution of measurement errors.

Data-Independent Acquisition-Based Quantitative Proteomic Analysis Reveals Potential Biomarkers of Kidney Cancer.

Science.gov (United States)

Song, Yimeng; Zhong, Lijun; Zhou, Juntuo; Lu, Min; Xing, Tianying; Ma, Lulin; Shen, Jing

2017-12-01

Renal cell carcinoma (RCC) is a malignant and metastatic cancer with 95% mortality, and clear cell RCC (ccRCC) is the most observed among the five major subtypes of RCC. Specific biomarkers that can distinguish cancer tissues from adjacent normal tissues should be developed to diagnose this disease in early stages and conduct a reliable prognostic evaluation. Data-independent acquisition (DIA) strategy has been widely employed in proteomic analysis because of various advantages, including enhanced protein coverage and reliable data acquisition. In this study, a DIA workflow is constructed on a quadrupole-Orbitrap LC-MS platform to reveal dysregulated proteins between ccRCC and adjacent normal tissues. More than 4000 proteins are identified, 436 of these proteins are dysregulated in ccRCC tissues. Bioinformatic analysis reveals that multiple pathways and Gene Ontology items are strongly associated with ccRCC. The expression levels of L-lactate dehydrogenase A chain, annexin A4, nicotinamide N-methyltransferase, and perilipin-2 examined through RT-qPCR, Western blot, and immunohistochemistry confirm the validity of the proteomic analysis results. The proposed DIA workflow yields optimum time efficiency and data reliability and provides a good choice for proteomic analysis in biological and clinical studies, and these dysregulated proteins might be potential biomarkers for ccRCC diagnosis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Flood risk analysis for flood control and sediment transportation in sandy regions: A case study in the Loess Plateau, China

Science.gov (United States)

Guo, Aijun; Chang, Jianxia; Wang, Yimin; Huang, Qiang; Zhou, Shuai

2018-05-01

Traditional flood risk analysis focuses on the probability of flood events exceeding the design flood of downstream hydraulic structures while neglecting the influence of sedimentation in river channels on regional flood control systems. This work advances traditional flood risk analysis by proposing a univariate and copula-based bivariate hydrological risk framework which incorporates both flood control and sediment transport. In developing the framework, the conditional probabilities of different flood events under various extreme precipitation scenarios are estimated by exploiting the copula-based model. Moreover, a Monte Carlo-based algorithm is designed to quantify the sampling uncertainty associated with univariate and bivariate hydrological risk analyses. Two catchments located on the Loess plateau are selected as study regions: the upper catchments of the Xianyang and Huaxian stations (denoted as UCX and UCH, respectively). The univariate and bivariate return periods, risk and reliability in the context of uncertainty for the purposes of flood control and sediment transport are assessed for the study regions. The results indicate that sedimentation triggers higher risks of damaging the safety of local flood control systems compared with the event that AMF exceeds the design flood of downstream hydraulic structures in the UCX and UCH. Moreover, there is considerable sampling uncertainty affecting the univariate and bivariate hydrologic risk evaluation, which greatly challenges measures of future flood mitigation. In addition, results also confirm that the developed framework can estimate conditional probabilities associated with different flood events under various extreme precipitation scenarios aiming for flood control and sediment transport. The proposed hydrological risk framework offers a promising technical reference for flood risk analysis in sandy regions worldwide.

High-speed image analysis reveals chaotic vibratory behaviors of pathological vocal folds

Energy Technology Data Exchange (ETDEWEB)

Zhang Yu, E-mail: yuzhang@xmu.edu.c [Key Laboratory of Underwater Acoustic Communication and Marine Information Technology of the Ministry of Education, Xiamen University, Xiamen Fujian 361005 (China); Shao Jun [Shanghai EENT Hospital of Fudan University, Shanghai (China); Krausert, Christopher R. [Department of Surgery, Division of Otolaryngology - Head and Neck Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792-7375 (United States); Zhang Sai [Key Laboratory of Underwater Acoustic Communication and Marine Information Technology of the Ministry of Education, Xiamen University, Xiamen Fujian 361005 (China); Jiang, Jack J. [Shanghai EENT Hospital of Fudan University, Shanghai (China); Department of Surgery, Division of Otolaryngology - Head and Neck Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792-7375 (United States)

2011-01-15

Research highlights: Low-dimensional human glottal area data. Evidence of chaos in human laryngeal activity from high-speed digital imaging. Traditional perturbation analysis should be cautiously applied to aperiodic high speed image signals. Nonlinear dynamic analysis may be helpful for understanding disordered behaviors in pathological laryngeal systems. - Abstract: Laryngeal pathology is usually associated with irregular dynamics of laryngeal activity. High-speed imaging facilitates direct observation and measurement of vocal fold vibrations. However, chaotic dynamic characteristics of aperiodic high-speed image data have not yet been investigated in previous studies. In this paper, we will apply nonlinear dynamic analysis and traditional perturbation methods to quantify high-speed image data from normal subjects and patients with various laryngeal pathologies including vocal fold nodules, polyps, bleeding, and polypoid degeneration. The results reveal the low-dimensional dynamic characteristics of human glottal area data. In comparison to periodic glottal area series from a normal subject, aperiodic glottal area series from pathological subjects show complex reconstructed phase space, fractal dimension, and positive Lyapunov exponents. The estimated positive Lyapunov exponents provide the direct evidence of chaos in pathological human vocal folds from high-speed digital imaging. Furthermore, significant differences between the normal and pathological groups are investigated for nonlinear dynamic and perturbation analyses. Jitter in the pathological group is significantly higher than in the normal group, but shimmer does not show such a difference. This finding suggests that the traditional perturbation analysis should be cautiously applied to high speed image signals. However, the correlation dimension and the maximal Lyapunov exponent reveal a statistically significant difference between normal and pathological groups. Nonlinear dynamic analysis is capable of

High-speed image analysis reveals chaotic vibratory behaviors of pathological vocal folds

International Nuclear Information System (INIS)

Zhang Yu; Shao Jun; Krausert, Christopher R.; Zhang Sai; Jiang, Jack J.

2011-01-01

Research highlights: → Low-dimensional human glottal area data. → Evidence of chaos in human laryngeal activity from high-speed digital imaging. → Traditional perturbation analysis should be cautiously applied to aperiodic high speed image signals. → Nonlinear dynamic analysis may be helpful for understanding disordered behaviors in pathological laryngeal systems. - Abstract: Laryngeal pathology is usually associated with irregular dynamics of laryngeal activity. High-speed imaging facilitates direct observation and measurement of vocal fold vibrations. However, chaotic dynamic characteristics of aperiodic high-speed image data have not yet been investigated in previous studies. In this paper, we will apply nonlinear dynamic analysis and traditional perturbation methods to quantify high-speed image data from normal subjects and patients with various laryngeal pathologies including vocal fold nodules, polyps, bleeding, and polypoid degeneration. The results reveal the low-dimensional dynamic characteristics of human glottal area data. In comparison to periodic glottal area series from a normal subject, aperiodic glottal area series from pathological subjects show complex reconstructed phase space, fractal dimension, and positive Lyapunov exponents. The estimated positive Lyapunov exponents provide the direct evidence of chaos in pathological human vocal folds from high-speed digital imaging. Furthermore, significant differences between the normal and pathological groups are investigated for nonlinear dynamic and perturbation analyses. Jitter in the pathological group is significantly higher than in the normal group, but shimmer does not show such a difference. This finding suggests that the traditional perturbation analysis should be cautiously applied to high speed image signals. However, the correlation dimension and the maximal Lyapunov exponent reveal a statistically significant difference between normal and pathological groups. Nonlinear dynamic

Genome-wide analysis of disease progression in age-related macular degeneration.

Science.gov (United States)

Yan, Qi; Ding, Ying; Liu, Yi; Sun, Tao; Fritsche, Lars G; Clemons, Traci; Ratnapriya, Rinki; Klein, Michael L; Cook, Richard J; Liu, Yu; Fan, Ruzong; Wei, Lai; Abecasis, Gonçalo R; Swaroop, Anand; Chew, Emily Y; Weeks, Daniel E; Chen, Wei

2018-03-01

Family- and population-based genetic studies have successfully identified multiple disease-susceptibility loci for Age-related macular degeneration (AMD), one of the first batch and most successful examples of genome-wide association study. However, most genetic studies to date have focused on case-control studies of late AMD (choroidal neovascularization or geographic atrophy). The genetic influences on disease progression are largely unexplored. We assembled unique resources to perform a genome-wide bivariate time-to-event analysis to test for association of time-to-late-AMD with ∼9 million variants on 2721 Caucasians from a large multi-center randomized clinical trial, the Age-Related Eye Disease Study. To our knowledge, this is the first genome-wide association study of disease progression (bivariate survival outcome) in AMD genetic studies, thus providing novel insights to AMD genetics. We used a robust Cox proportional hazards model to appropriately account for between-eye correlation when analyzing the progression time in the two eyes of each participant. We identified four previously reported susceptibility loci showing genome-wide significant association with AMD progression: ARMS2-HTRA1 (P = 8.1 × 10-43), CFH (P = 3.5 × 10-37), C2-CFB-SKIV2L (P = 8.1 × 10-10) and C3 (P = 1.2 × 10-9). Furthermore, we detected association of rs58978565 near TNR (P = 2.3 × 10-8), rs28368872 near ATF7IP2 (P = 2.9 × 10-8) and rs142450006 near MMP9 (P = 0.0006) with progression to choroidal neovascularization but not geographic atrophy. Secondary analysis limited to 34 reported risk variants revealed that LIPC and CTRB2-CTRB1 were also associated with AMD progression (P < 0.0015). Our genome-wide analysis thus expands the genetics in both development and progression of AMD and should assist in early identification of high risk individuals.

Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells

DEFF Research Database (Denmark)

Larsen, Sara C; Sylvestersen, Kathrine B; Mund, Andreas

2016-01-01

to the frequency of somatic mutations at arginine methylation sites throughout the proteome, we observed that somatic mutations were common at arginine methylation sites in proteins involved in mRNA splicing. Furthermore, in HeLa and U2OS cells, we found that distinct arginine methyltransferases differentially...... kidney 293 cells, indicating that the occurrence of this modification is comparable to phosphorylation and ubiquitylation. A site-level conservation analysis revealed that arginine methylation sites are less evolutionarily conserved compared to arginines that were not identified as modified...... as coactivator-associated arginine methyltransferase 1 (CARM1)] or PRMT1 increased the RNA binding function of HNRNPUL1. High-content single-cell imaging additionally revealed that knocking down CARM1 promoted the nuclear accumulation of SRSF2, independent of cell cycle phase. Collectively, the presented human...

Recent adaptive events in human brain revealed by meta-analysis of positively selected genes.

Directory of Open Access Journals (Sweden)

Yue Huang

Full Text Available BACKGROUND AND OBJECTIVES: Analysis of positively-selected genes can help us understand how human evolved, especially the evolution of highly developed cognitive functions. However, previous works have reached conflicting conclusions regarding whether human neuronal genes are over-represented among genes under positive selection. METHODS AND RESULTS: We divided positively-selected genes into four groups according to the identification approaches, compiling a comprehensive list from 27 previous studies. We showed that genes that are highly expressed in the central nervous system are enriched in recent positive selection events in human history identified by intra-species genomic scan, especially in brain regions related to cognitive functions. This pattern holds when different datasets, parameters and analysis pipelines were used. Functional category enrichment analysis supported these findings, showing that synapse-related functions are enriched in genes under recent positive selection. In contrast, immune-related functions, for instance, are enriched in genes under ancient positive selection revealed by inter-species coding region comparison. We further demonstrated that most of these patterns still hold even after controlling for genomic characteristics that might bias genome-wide identification of positively-selected genes including gene length, gene density, GC composition, and intensity of negative selection. CONCLUSION: Our rigorous analysis resolved previous conflicting conclusions and revealed recent adaptation of human brain functions.

Open abdomen management of intra-abdominal infections: analysis of a twenty-year experience.

Science.gov (United States)

Rausei, Stefano; Dionigi, Gianlorenzo; Boni, Luigi; Rovera, Francesca; Minoja, Giulio; Cuffari, Salvatore; Dionigi, Renzo

2014-06-01

No conclusive results on the efficacy and timing of open abdomen (OA) are available, particularly in the setting of intra-abdominal infections. We analyzed outcomes and risk factors retrospectively in a large series of patients managed with an OA during the past 20 y in an effort to clarify this issue. We reviewed the records of 133 patients who underwent treatment with an OA, considering factors related to patient, disease, medical management, and surgical treatment. The end points of the bi-variable analysis were 1-y mortality, calculated from the time of an initial OA procedure, and definitive fascial closure. Most patients (112/133) managed with an OA had one of several types of peritonitis. Many patients had severe clinical conditions (mean Acute Physiology and Chronic Health Evaluation [APACHE] II score was almost 9 points for the study population). With regard to surgical management, the mean (+SD) number of abdominal revisions was 5.9+9.3 during a mean duration of treatment with an OA of 14.3+11.6 d. The overall mortality in the study was 26% (35/133). Bi-variable analysis revealed factors associated with overall mortality to be age, renal and respiratory co-morbidities, edema on an initial chest radiograph, blood pressure, blood glucose and creatinine concentrations; and APACHE II score. The rate of definitive fascial closure was 75% (100/133). Factors associated negatively with fascial closure were respiratory co-morbidity, edema on a first chest radiograph, post-operative mesenteric ischemia as an indication for OA, blood glucose and creatinine concentrations, and duration of an OA. Patients' pre-operative clinical status influences strongly their response to surgical treatment. The management of OA does not affect adversely the survival of patients with intra-abdominal infections, but factors related to the management of OA (duration of OA) seem to affect the possibility of definitive fascial closure.

Analysis reveals potential rangeland impacts if Williamson Act eliminated

Directory of Open Access Journals (Sweden)

William C. Wetzel

2012-10-01

Full Text Available California budget cuts have resulted in dramatic reductions in state funding for the Williamson Act, a land protection program that reduces property taxes for the owners of 15 million acres of California farms and rangeland. With state reimbursements to counties eliminated, the decision to continue Williamson Act contracts lies with individual counties. We investigated the consequences of eliminating the Williamson Act, using a geospatial analysis and a mail questionnaire asking ranchers for plans under a hypothetical elimination scenario. The geospatial analysis revealed that 72% of rangeland parcels enrolled in Williamson Act contracts contained habitat important for statewide conservation goals. Presented with the elimination scenario, survey respondents reported an intention to sell 20% of their total 496,889 acres. The tendency of survey participants to respond that they would sell land was highest among full-time ranchers with low household incomes and without off-ranch employment. A majority (76% of the ranchers who reported that they would sell land predicted that the buyers would develop it for nonagricultural uses, suggesting substantial changes to California's landscape in a future without the Williamson Act.

Sexual Harassment Retaliation Climate DEOCS 4.1 Construct Validity Summary

Science.gov (United States)

2017-08-01

Correlations Bivariate Pearson correlation among items were examined to identify and reduce questions with overlapping content. Table 5 displays the...exploratory factor analysis, and bivariate correlations (sample 1) 2) To determine the factor structure of the remaining (final) questions via...statistics, reliability analysis, exploratory factor analysis, and bivariate correlations of the prospective Sexual Harassment Retaliation Climate

Assessing characteristics related to the use of seatbelts and cell phones by drivers: application of a bivariate probit model.

Science.gov (United States)

Russo, Brendan J; Kay, Jonathan J; Savolainen, Peter T; Gates, Timothy J

2014-06-01

The effects of cell phone use and safety belt use have been an important focus of research related to driver safety. Cell phone use has been shown to be a significant source of driver distraction contributing to substantial degradations in driver performance, while safety belts have been demonstrated to play a vital role in mitigating injuries to crash-involved occupants. This study examines the prevalence of cell phone use and safety belt non-use among the driving population through direct observation surveys. A bivariate probit model is developed to simultaneously examine the factors that affect cell phone and safety belt use among motor vehicle drivers. The results show that several factors may influence drivers' decision to use cell phones and safety belts, and that these decisions are correlated. Understanding the factors that affect both cell phone use and safety belt non-use is essential to targeting policy and programs that reduce such behavior. Copyright © 2014 Elsevier Ltd. All rights reserved.

Genomic analysis of primordial dwarfism reveals novel disease genes.

Science.gov (United States)

Shaheen, Ranad; Faqeih, Eissa; Ansari, Shinu; Abdel-Salam, Ghada; Al-Hassnan, Zuhair N; Al-Shidi, Tarfa; Alomar, Rana; Sogaty, Sameera; Alkuraya, Fowzan S

2014-02-01

Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in defining clinical subgroups. In this study, we present the results of clinical and genomic characterization of 16 new patients in whom a broad definition of PD was used (e.g., 3M syndrome was included). We report a novel PD syndrome with distinct facies in two unrelated patients, each with a different homozygous truncating mutation in CRIPT. Our analysis also reveals, in addition to mutations in known PD disease genes, the first instance of biallelic truncating BRCA2 mutation causing PD with normal bone marrow analysis. In addition, we have identified a novel locus for Seckel syndrome based on a consanguineous multiplex family and identified a homozygous truncating mutation in DNA2 as the likely cause. An additional novel PD disease candidate gene XRCC4 was identified by autozygome/exome analysis, and the knockout mouse phenotype is highly compatible with PD. Thus, we add a number of novel genes to the growing list of PD-linked genes, including one which we show to be linked to a novel PD syndrome with a distinct facial appearance. PD is extremely heterogeneous genetically and clinically, and genomic tools are often required to reach a molecular diagnosis.

Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit

OpenAIRE

Ashoori, Maryam; Burns, Catherine M.; d'Entremont, Barbara; Momtahan, Kathryn

2014-01-01

Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamworkand leverage the exis...

REVEAL - A tool for rule driven analysis of safety critical software

International Nuclear Information System (INIS)

Miedl, H.; Kersken, M.

1998-01-01

As the determination of ultrahigh reliability figures for safety critical software is hardly possible, national and international guidelines and standards give mainly requirements for the qualitative evaluation of software. An analysis whether all these requirements are fulfilled is time and effort consuming and prone to errors, if performed manually by analysts, and should instead be dedicated to tools as far as possible. There are many ''general-purpose'' software analysis tools, both static and dynamic, which help analyzing the source code. However, they are not designed to assess the adherence to specific requirements of guidelines and standards in the nuclear field. Against the background of the development of I and C systems in the nuclear field which are based on digital techniques and implemented in high level language, it is essential that the assessor or licenser has a tool with which he can automatically and uniformly qualify as many aspects as possible of the high level language software. For this purpose the software analysis tool REVEAL has been developed at ISTec and the Halden Reactor Project. (author)

Dynamic functional connectivity analysis reveals transient states of dysconnectivity in schizophrenia

Directory of Open Access Journals (Sweden)

E. Damaraju

2014-01-01

Full Text Available Schizophrenia is a psychotic disorder characterized by functional dysconnectivity or abnormal integration between distant brain regions. Recent functional imaging studies have implicated large-scale thalamo-cortical connectivity as being disrupted in patients. However, observed connectivity differences in schizophrenia have been inconsistent between studies, with reports of hyperconnectivity and hypoconnectivity between the same brain regions. Using resting state eyes-closed functional imaging and independent component analysis on a multi-site data that included 151 schizophrenia patients and 163 age- and gender matched healthy controls, we decomposed the functional brain data into 100 components and identified 47 as functionally relevant intrinsic connectivity networks. We subsequently evaluated group differences in functional network connectivity, both in a static sense, computed as the pairwise Pearson correlations between the full network time courses (5.4 minutes in length, and a dynamic sense, computed using sliding windows (44 s in length and k-means clustering to characterize five discrete functional connectivity states. Static connectivity analysis revealed that compared to healthy controls, patients show significantly stronger connectivity, i.e., hyperconnectivity, between the thalamus and sensory networks (auditory, motor and visual, as well as reduced connectivity (hypoconnectivity between sensory networks from all modalities. Dynamic analysis suggests that (1, on average, schizophrenia patients spend much less time than healthy controls in states typified by strong, large-scale connectivity, and (2, that abnormal connectivity patterns are more pronounced during these connectivity states. In particular, states exhibiting cortical–subcortical antagonism (anti-correlations and strong positive connectivity between sensory networks are those that show the group differences of thalamic hyperconnectivity and sensory hypoconnectivity

Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data.

Science.gov (United States)

Xu, Nan; Veesler, David; Doerschuk, Peter C; Johnson, John E

2018-05-01

The information content of cryo EM data sets exceeds that of the electron scattering potential (cryo EM) density initially derived for structure determination. Previously we demonstrated the power of data variance analysis for characterizing regions of cryo EM density that displayed functionally important variance anomalies associated with maturation cleavage events in Nudaurelia Omega Capensis Virus and the presence or absence of a maturation protease in bacteriophage HK97 procapsids. Here we extend the analysis in two ways. First, instead of imposing icosahedral symmetry on every particle in the data set during the variance analysis, we only assume that the data set as a whole has icosahedral symmetry. This change removes artifacts of high variance along icosahedral symmetry axes, but retains all of the features previously reported in the HK97 data set. Second we present a covariance analysis that reveals correlations in structural dynamics (variance) between the interior of the HK97 procapsid with the protease and regions of the exterior (not seen in the absence of the protease). The latter analysis corresponds well with hydrogen deuterium exchange studies previously published that reveal the same correlation. Copyright © 2018 Elsevier Inc. All rights reserved.

Bivariate quadratic method in quantifying the differential capacitance and energy capacity of supercapacitors under high current operation

Science.gov (United States)

Goh, Chin-Teng; Cruden, Andrew

2014-11-01

Capacitance and resistance are the fundamental electrical parameters used to evaluate the electrical characteristics of a supercapacitor, namely the dynamic voltage response, energy capacity, state of charge and health condition. In the British Standards EN62391 and EN62576, the constant capacitance method can be further improved with a differential capacitance that more accurately describes the dynamic voltage response of supercapacitors. This paper presents a novel bivariate quadratic based method to model the dynamic voltage response of supercapacitors under high current charge-discharge cycling, and to enable the derivation of the differential capacitance and energy capacity directly from terminal measurements, i.e. voltage and current, rather than from multiple pulsed-current or excitation signal tests across different bias levels. The estimation results the author achieves are in close agreement with experimental measurements, within a relative error of 0.2%, at various high current levels (25-200 A), more accurate than the constant capacitance method (4-7%). The archival value of this paper is the introduction of an improved quantification method for the electrical characteristics of supercapacitors, and the disclosure of the distinct properties of supercapacitors: the nonlinear capacitance-voltage characteristic, capacitance variation between charging and discharging, and distribution of energy capacity across the operating voltage window.

Multi scale habitat relationships of Martes americana in northern Idaho, U.S.A.

Science.gov (United States)

Tzeidle N. Wasserman; Samuel A. Cushman; David O. Wallin; Jim Hayden

2012-01-01

We used bivariate scaling and logistic regression to investigate multiple-scale habitat selection by American marten (Martes americana). Bivariate scaling reveals dramatic differences in the apparent nature and strength of relationships between marten occupancy and a number of habitat variables across a range of spatial scales. These differences include reversals in...

Assessing the Goodness of Fit of Phylogenetic Comparative Methods: A Meta-Analysis and Simulation Study.

Directory of Open Access Journals (Sweden)

Dwueng-Chwuan Jhwueng

Full Text Available Phylogenetic comparative methods (PCMs have been applied widely in analyzing data from related species but their fit to data is rarely assessed.Can one determine whether any particular comparative method is typically more appropriate than others by examining comparative data sets?I conducted a meta-analysis of 122 phylogenetic data sets found by searching all papers in JEB, Blackwell Synergy and JSTOR published in 2002-2005 for the purpose of assessing the fit of PCMs. The number of species in these data sets ranged from 9 to 117.I used the Akaike information criterion to compare PCMs, and then fit PCMs to bivariate data sets through REML analysis. Correlation estimates between two traits and bootstrapped confidence intervals of correlations from each model were also compared.For phylogenies of less than one hundred taxa, the Independent Contrast method and the independent, non-phylogenetic models provide the best fit.For bivariate analysis, correlations from different PCMs are qualitatively similar so that actual correlations from real data seem to be robust to the PCM chosen for the analysis. Therefore, researchers might apply the PCM they believe best describes the evolutionary mechanisms underlying their data.

Multilocus Sequence Analysis of Nectar Pseudomonads Reveals High Genetic Diversity and Contrasting Recombination Patterns

Science.gov (United States)

Álvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M.

2013-01-01

The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas ‘sensu stricto’ isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria. PMID:24116076

Multilocus sequence analysis of nectar pseudomonads reveals high genetic diversity and contrasting recombination patterns.

Science.gov (United States)

Alvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M

2013-01-01

The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas 'sensu stricto' isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria.

Diaphragm and Lung Ultrasound to Predict Weaning Outcome: Systematic Review and Meta-Analysis.

Science.gov (United States)

Llamas-Álvarez, Ana M; Tenza-Lozano, Eva M; Latour-Pérez, Jaime

2017-12-01

Deciding the optimal timing for extubation in patients who are mechanically ventilated can be challenging, and traditional weaning predictor tools are not very accurate. The aim of this systematic review and meta-analysis was to assess the accuracy of lung and diaphragm ultrasound for predicting weaning outcomes in critically ill adults. MEDLINE, the Cochrane Library, Web of Science, Scopus, LILACS, Teseo, Tesis Doctorales en Red, and OpenGrey were searched, and the bibliographies of relevant studies were reviewed. Two researchers independently selected studies that met the inclusion criteria and assessed study quality in accordance with the Quality Assessment of Diagnostic Accuracy Studies-2 tool. The summary receiver-operating characteristic curve and pooled diagnostic OR (DOR) were estimated by using a bivariate random effects analysis. Sources of heterogeneity were explored by using predefined subgroup analyses and bivariate meta-regression. Nineteen studies involving 1,071 people were included in the study. For diaphragm thickening fraction, the area under the summary receiver-operating characteristic curve was 0.87, and DOR was 21 (95% CI, 11-40). Regarding diaphragmatic excursion, pooled sensitivity was 75% (95% CI, 65-85); pooled specificity, 75% (95% CI, 60-85); and DOR, 10 (95% CI, 4-24). For lung ultrasound, the area under the summary receiver-operating characteristic curve was 0.77, and DOR was 38 (95% CI, 7-198). Based on bivariate meta-regression analysis, a significantly higher specificity for diaphragm thickening fraction and higher sensitivity for diaphragmatic excursion was detected in studies with applicability concerns. Lung and diaphragm ultrasound can help predict weaning outcome, but its accuracy may vary depending on the patient subpopulation. Copyright © 2017 American College of Chest Physicians. Published by Elsevier Inc. All rights reserved.

Bivariate genome-wide association meta-analysis of pediatric musculoskeletal traits reveals pleiotropic effects at the SREBF1/TOM1L2 locus

DEFF Research Database (Denmark)

Medina-Gomez, Carolina; Kemp, John P; Dimou, Niki L

2017-01-01

bone mineral density loci: WNT4, GALNT3, MEPE, CPED1/WNT16, TNFSF11, RIN3, and PPP6R3/LRP5. Variants in the TOM1L2/SREBF1 locus exert opposing effects TB-LM and TBLH-BMD, and have a stronger association with the former trait. We show that SREBF1 is expressed in murine and human osteoblasts, as well...

Interpreting Bivariate Regression Coefficients: Going beyond the Average

Science.gov (United States)

Halcoussis, Dennis; Phillips, G. Michael

2010-01-01

Statistics, econometrics, investment analysis, and data analysis classes often review the calculation of several types of averages, including the arithmetic mean, geometric mean, harmonic mean, and various weighted averages. This note shows how each of these can be computed using a basic regression framework. By recognizing when a regression model…

Large scale aggregate microarray analysis reveals three distinct molecular subclasses of human preeclampsia.

Science.gov (United States)

Leavey, Katherine; Bainbridge, Shannon A; Cox, Brian J

2015-01-01

Preeclampsia (PE) is a life-threatening hypertensive pathology of pregnancy affecting 3-5% of all pregnancies. To date, PE has no cure, early detection markers, or effective treatments short of the removal of what is thought to be the causative organ, the placenta, which may necessitate a preterm delivery. Additionally, numerous small placental microarray studies attempting to identify "PE-specific" genes have yielded inconsistent results. We therefore hypothesize that preeclampsia is a multifactorial disease encompassing several pathology subclasses, and that large cohort placental gene expression analysis will reveal these groups. To address our hypothesis, we utilized known bioinformatic methods to aggregate 7 microarray data sets across multiple platforms in order to generate a large data set of 173 patient samples, including 77 with preeclampsia. Unsupervised clustering of these patient samples revealed three distinct molecular subclasses of PE. This included a "canonical" PE subclass demonstrating elevated expression of known PE markers and genes associated with poor oxygenation and increased secretion, as well as two other subclasses potentially representing a poor maternal response to pregnancy and an immunological presentation of preeclampsia. Our analysis sheds new light on the heterogeneity of PE patients, and offers up additional avenues for future investigation. Hopefully, our subclassification of preeclampsia based on molecular diversity will finally lead to the development of robust diagnostics and patient-based treatments for this disorder.

Evolutionary Meta-Analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery

Science.gov (United States)

Dudley, Joel T.; Chen, Rong; Sanderford, Maxwell; Butte, Atul J.; Kumar, Sudhir

2012-01-01

Genome-wide disease association studies contrast genetic variation between disease cohorts and healthy populations to discover single nucleotide polymorphisms (SNPs) and other genetic markers revealing underlying genetic architectures of human diseases. Despite scores of efforts over the past decade, many reproducible genetic variants that explain substantial proportions of the heritable risk of common human diseases remain undiscovered. We have conducted a multispecies genomic analysis of 5,831 putative human risk variants for more than 230 disease phenotypes reported in 2,021 studies. We find that the current approaches show a propensity for discovering disease-associated SNPs (dSNPs) at conserved genomic positions because the effect size (odds ratio) and allelic P value of genetic association of an SNP relates strongly to the evolutionary conservation of their genomic position. We propose a new measure for ranking SNPs that integrates evolutionary conservation scores and the P value (E-rank). Using published data from a large case-control study, we demonstrate that E-rank method prioritizes SNPs with a greater likelihood of bona fide and reproducible genetic disease associations, many of which may explain greater proportions of genetic variance. Therefore, long-term evolutionary histories of genomic positions offer key practical utility in reassessing data from existing disease association studies, and in the design and analysis of future studies aimed at revealing the genetic basis of common human diseases. PMID:22389448

Comparative analysis reveals the underlying mechanism of vertebrate seasonal reproduction.

Science.gov (United States)

Ikegami, Keisuke; Yoshimura, Takashi

2016-02-01

Animals utilize photoperiodic changes as a calendar to regulate seasonal reproduction. Birds have highly sophisticated photoperiodic mechanisms and functional genomics analysis in quail uncovered the signal transduction pathway regulating avian seasonal reproduction. Birds detect light with deep brain photoreceptors. Long day (LD) stimulus induces secretion of thyroid-stimulating hormone (TSH) from the pars tuberalis (PT) of the pituitary gland. PT-derived TSH locally activates thyroid hormone (TH) in the hypothalamus, which induces gonadotropin-releasing hormone (GnRH) and hence gonadotropin secretion. However, during winter, low temperatures increase serum TH for adaptive thermogenesis, which accelerates germ cell apoptosis by activating the genes involved in metamorphosis. Therefore, TH has a dual role in the regulation of seasonal reproduction. Studies using TSH receptor knockout mice confirmed the involvement of PT-derived TSH in mammalian seasonal reproduction. In addition, studies in mice revealed that the tissue-specific glycosylation of TSH diversifies its function in the circulation to avoid crosstalk. In contrast to birds and mammals, one of the molecular machineries necessary for the seasonal reproduction of fish are localized in the saccus vasculosus from the photoreceptor to the neuroendocrine output. Thus, comparative analysis is a powerful tool to uncover the universality and diversity of fundamental properties in various organisms. Copyright © 2015 Elsevier Inc. All rights reserved.

Decision makers use norms, not cost-benefit analysis, when choosing to conceal or reveal unfair rewards.

Directory of Open Access Journals (Sweden)

Marco Heimann

Full Text Available We introduce the Conceal or Reveal Dilemma, in which individuals receive unfair benefits, and must decide whether to conceal or to reveal this unfair advantage. This dilemma has two important characteristics: it does not lend itself easily to cost-benefit analysis, neither to the application of any strong universal norm. As a consequence, it is ideally suited to the study of interindividual and intercultural variations in moral-economic norms. In this paper we focus on interindividual variations, and we report four studies showing that individuals cannot be swayed by financial incentives to conceal or to reveal, and follow instead fixed, idiosyncratic strategies. We discuss how this result can be extended to individual and cultural variations in the tendency to display or to hide unfair rewards.

Least-Squares Linear Regression and Schrodinger's Cat: Perspectives on the Analysis of Regression Residuals.

Science.gov (United States)

Hecht, Jeffrey B.

The analysis of regression residuals and detection of outliers are discussed, with emphasis on determining how deviant an individual data point must be to be considered an outlier and the impact that multiple suspected outlier data points have on the process of outlier determination and treatment. Only bivariate (one dependent and one independent)…

Attention deficit hyperactivity disorder in cocaine-dependent adults: a psychiatric comorbidity analysis.

Science.gov (United States)

Daigre, Constanza; Roncero, Carlos; Grau-López, Lara; Martínez-Luna, Nieves; Prat, Gemma; Valero, Sergi; Tejedor, Rosa; Ramos-Quiroga, Josep A; Casas, Miguel

2013-01-01

Attention deficit hyperactivity disorder (ADHD) is highly prevalent among drug abusers. We studied the psychiatric comorbidity and characteristics of cocaine use in relation to the presence of ADHD among patients with cocaine dependence. A total of 200 cocaine-dependent patients attending an Outpatient Drug Clinic participated in the study. A systematic evaluation of ADHD (CAADID-II), the severity of addiction (EuropASI) and other axes I and II psychiatric disorders was made (SCID-I and SCID-II). A descriptive, bivariate, and multivariate analysis of the data was performed. In the multivariate analysis, the identified risk factors for the development of ADHD were a history of behavioral disorder in childhood (OR: 3.04), a lifetime history of cannabis dependence in the course of life (OR: 2.68), and age at the start of treatment (OR: 1.08). The bivariate analysis showed ADHD to be associated with other factors such as male gender, age at start of cocaine use and dependence, the amount of cocaine consumed weekly, increased occupational alteration, alcohol consumption, general psychological discomfort, depressive disorder, and antisocial personality disorder. We conclude that ADHD is associated with increased psychiatric comorbidity and greater severity of addiction. Copyright © American Academy of Addiction Psychiatry.

Molecular analysis of sourdough reveals Lactobacillus mindensis sp. nov.

Science.gov (United States)

Ehrmann, Matthias A; Müller, Martin R A; Vogel, Rudi F

2003-01-01

Genotypic fingerprinting to analyse the bacterial flora of an industrial sourdough revealed a coherent group of strains which could not be associated with a valid species. Comparative 16S rDNA sequence analysis showed that these strains formed a homogeneous cluster distinct from their closest relatives, Lactobacillus farciminis, Lactobacillus alimentarius and Lactobacillus kimchii. To characterize them further, physiological (sugar fermentation, formation of DL-lactate, hydrolysis of arginine, growth temperature, CO2 production) and chemotaxonomic properties have been determined. The DNA G +C content was 37.5 0.2 mol%. The peptidoglycan was of the lysine-D-iso-asparagine (L-Lys-D-Asp) type. The strains were homofermentative, Gram-positive, catalase-negative, non-spore-forming, non-motile rods. They were found as a major stable component of a rye flour sourdough fermentation. Physiological, biochemical as well as genotypic data suggested them to be a new species of the genus Lactobacillus. This was confirmed by DNA-DNA hybridization of genomic DNA, and the name Lactobacillus mindensis is proposed. The type strain of this species is DSM 14500T (=LMG 21508T).

Proteomic analysis of three gonad types of swamp eel reveals genes differentially expressed during sex reversal

OpenAIRE

Sheng, Yue; Zhao, Wei; Song, Ying; Li, Zhigang; Luo, Majing; Lei, Quan; Cheng, Hanhua; Zhou, Rongjia

2015-01-01

A variety of mechanisms are engaged in sex determination in vertebrates. The teleost fish swamp eel undergoes sex reversal naturally and is an ideal model for vertebrate sexual development. However, the importance of proteome-wide scanning for gonad reversal was not previously determined. We report a 2-D electrophoresis analysis of three gonad types of proteomes during sex reversal. MS/MS analysis revealed a group of differentially expressed proteins during ovary to ovotestis to testis transf...

Longitudinal categorical data analysis

CERN Document Server

Sutradhar, Brajendra C

2014-01-01

This is the first book in longitudinal categorical data analysis with parametric correlation models developed based on dynamic relationships among repeated categorical responses. This book is a natural generalization of the longitudinal binary data analysis to the multinomial data setup with more than two categories. Thus, unlike the existing books on cross-sectional categorical data analysis using log linear models, this book uses multinomial probability models both in cross-sectional and longitudinal setups. A theoretical foundation is provided for the analysis of univariate multinomial responses, by developing models systematically for the cases with no covariates as well as categorical covariates, both in cross-sectional and longitudinal setups. In the longitudinal setup, both stationary and non-stationary covariates are considered. These models have also been extended to the bivariate multinomial setup along with suitable covariates. For the inferences, the book uses the generalized quasi-likelihood as w...

Combined Analysis of the Fruit Metabolome and Transcriptome Reveals Candidate Genes Involved in Flavonoid Biosynthesis in Actinidia arguta.

Science.gov (United States)

Li, Yukuo; Fang, Jinbao; Qi, Xiujuan; Lin, Miaomiao; Zhong, Yunpeng; Sun, Leiming; Cui, Wen

2018-05-15

To assess the interrelation between the change of metabolites and the change of fruit color, we performed a combined metabolome and transcriptome analysis of the flesh in two different Actinidia arguta cultivars: "HB" ("Hongbaoshixing") and "YF" ("Yongfengyihao") at two different fruit developmental stages: 70d (days after full bloom) and 100d (days after full bloom). Metabolite and transcript profiling was obtained by ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometer and high-throughput RNA sequencing, respectively. The identification and quantification results of metabolites showed that a total of 28,837 metabolites had been obtained, of which 13,715 were annotated. In comparison of HB100 vs. HB70, 41 metabolites were identified as being flavonoids, 7 of which, with significant difference, were identified as bracteatin, luteolin, dihydromyricetin, cyanidin, pelargonidin, delphinidin and (-)-epigallocatechin. Association analysis between metabolome and transcriptome revealed that there were two metabolic pathways presenting significant differences during fruit development, one of which was flavonoid biosynthesis, in which 14 structural genes were selected to conduct expression analysis, as well as 5 transcription factor genes obtained by transcriptome analysis. RT-qPCR results and cluster analysis revealed that AaF3H , AaLDOX , AaUFGT , AaMYB , AabHLH , and AaHB2 showed the best possibility of being candidate genes. A regulatory network of flavonoid biosynthesis was established to illustrate differentially expressed candidate genes involved in accumulation of metabolites with significant differences, inducing red coloring during fruit development. Such a regulatory network linking genes and flavonoids revealed a system involved in the pigmentation of all-red-fleshed and all-green-fleshed A. arguta , suggesting this conjunct analysis approach is not only useful in understanding the relationship between genotype and phenotype

Phenotypic analysis of prostate-infiltrating lymphocytes reveals TH17 and Treg skewing.

Science.gov (United States)

Sfanos, Karen Sandell; Bruno, Tullia C; Maris, Charles H; Xu, Lauren; Thoburn, Christopher J; DeMarzo, Angelo M; Meeker, Alan K; Isaacs, William B; Drake, Charles G

2008-06-01

Pathologic examination of prostate glands removed from patients with prostate cancer commonly reveals infiltrating CD4+ and CD8+ T cells. Little is known about the phenotype of these cells, despite accumulating evidence suggesting a potential role for chronic inflammation in the etiology of prostate cancer. We developed a technique that samples the majority of the peripheral prostate through serial needle aspirates. CD4+ prostate-infiltrating lymphocytes (PIL) were isolated using magnetic beads and analyzed for subset skewing using both flow cytometry and quantitative reverse transcription-PCR. The transcriptional profile of fluorescence-activated cell sorted prostate-infiltrating regulatory T cells (CD4+, CD25+, GITR+) was compared with naïve, peripheral blood T cells using microarray analysis. CD4+ PIL showed a paucity of TH2 (interleukin-4-secreting) cells, a surprising finding given the generally accepted association of these cells with chronic, smoldering inflammation. Instead, CD4+ PIL seemed to be skewed towards a regulatory Treg phenotype (FoxP3+) as well as towards the TH17 phenotype (interleukin-17+). We also found that a preponderance of TH17-mediated inflammation was associated with a lower pathologic Gleason score. These protein level data were reflected at the message level, as analyzed by quantitative reverse transcription-PCR. Microarray analysis of pooled prostate-infiltrating T(reg) revealed expected Treg-associated transcripts (FoxP3, CTLA-4, GITR, LAG-3) as well as a number of unique cell surface markers that may serve as additional Treg markers. Taken together, these data suggest that TH17 and/or Treg CD4+ T cells (rather than TH2 T cells) may be involved in the development or progression of prostate cancer.

Handbook of Time Series Analysis Recent Theoretical Developments and Applications

CERN Document Server

Schelter, Björn; Timmer, Jens

2006-01-01

This handbook provides an up-to-date survey of current research topics and applications of time series analysis methods written by leading experts in their fields. It covers recent developments in univariate as well as bivariate and multivariate time series analysis techniques ranging from physics' to life sciences' applications. Each chapter comprises both methodological aspects and applications to real world complex systems, such as the human brain or Earth's climate. Covering an exceptionally broad spectrum of topics, beginners, experts and practitioners who seek to understand the latest de

Metagenomic Analysis of the Sponge Discodermia Reveals the Production of the Cyanobacterial Natural Product Kasumigamide by 'Entotheonella'.

Science.gov (United States)

Nakashima, Yu; Egami, Yoko; Kimura, Miki; Wakimoto, Toshiyuki; Abe, Ikuro

2016-01-01

Sponge metagenomes are a useful platform to mine cryptic biosynthetic gene clusters responsible for production of natural products involved in the sponge-microbe association. Since numerous sponge-derived bioactive metabolites are biosynthesized by the symbiotic bacteria, this strategy may concurrently reveal sponge-symbiont produced compounds. Accordingly, a metagenomic analysis of the Japanese marine sponge Discodermia calyx has resulted in the identification of a hybrid type I polyketide synthase-nonribosomal peptide synthetase gene (kas). Bioinformatic analysis of the gene product suggested its involvement in the biosynthesis of kasumigamide, a tetrapeptide originally isolated from freshwater free-living cyanobacterium Microcystis aeruginosa NIES-87. Subsequent investigation of the sponge metabolic profile revealed the presence of kasumigamide in the sponge extract. The kasumigamide producing bacterium was identified as an 'Entotheonella' sp. Moreover, an in silico analysis of kas gene homologs uncovered the presence of kas family genes in two additional bacteria from different phyla. The production of kasumigamide by distantly related multiple bacterial strains implicates horizontal gene transfer and raises the potential for a wider distribution across other bacterial groups.

CNV-association meta-analysis in 191,161 European adults reveals new loci associated with anthropometric traits

NARCIS (Netherlands)

Macé, Aurélien; Tuke, Marcus A; Deelen, Patrick; Kristiansson, Kati; Mattsson, Hannele; Nõukas, Margit; Sapkota, Yadav; Schick, Ursula; Porcu, Eleonora; Rüeger, Sina; McDaid, Aaron F; Porteous, David; Winkler, Thomas W; Salvi, Erika; Shrine, Nick; Liu, Xueping; Ang, Wei Q; Zhang, Weihua; Feitosa, Mary F; Venturini, Cristina; van der Most, Peter J; Rosengren, Anders; Wood, Andrew R; Beaumont, Robin N; Jones, Samuel E; Ruth, Katherine S; Yaghootkar, Hanieh; Tyrrell, Jessica; Havulinna, Aki S; Boers, Harmen; Mägi, Reedik; Kriebel, Jennifer; Müller-Nurasyid, Martina; Perola, Markus; Nieminen, Markku; Lokki, Marja-Liisa; Kähönen, Mika; Viikari, Jorma S; Geller, Frank; Lahti, Jari; Palotie, Aarno; Koponen, Päivikki; Lundqvist, Annamari; Rissanen, Harri; Bottinger, Erwin P; Afaq, Saima; Wojczynski, Mary K; Lenzini, Petra; Nolte, Ilja M; Sparsø, Thomas; Schupf, Nicole; Christensen, Kaare; Perls, Thomas T; Newman, Anne B; Werge, Thomas; Snieder, Harold; Spector, Timothy D; Chambers, John C; Koskinen, Seppo; Melbye, Mads; Raitakari, Olli T; Lehtimäki, Terho; Tobin, Martin D; Wain, Louise V; Sinisalo, Juha; Peters, Annette; Meitinger, Thomas; Martin, Nicholas G; Wray, Naomi R; Montgomery, Grant W; Medland, Sarah E; Swertz, Morris A; Vartiainen, Erkki; Borodulin, Katja; Männistö, Satu; Murray, Anna; Bochud, Murielle; Jacquemont, Sébastien; Rivadeneira, Fernando; Hansen, Thomas F; Oldehinkel, Albertine J; Mangino, Massimo; Province, Michael A; Deloukas, Panos; Kooner, Jaspal S; Freathy, Rachel M; Pennell, Craig; Feenstra, Bjarke; Strachan, David P; Lettre, Guillaume; Hirschhorn, Joel; Cusi, Daniele; Heid, Iris M; Hayward, Caroline; Männik, Katrin; Beckmann, Jacques S; Loos, Ruth J F; Nyholt, Dale R; Metspalu, Andres; Eriksson, Johan G; Weedon, Michael N; Salomaa, Veikko; Franke, Lude; Reymond, Alexandre; Frayling, Timothy M; Kutalik, Zoltán

2017-01-01

There are few examples of robust associations between rare copy number variants (CNVs) and complex continuous human traits. Here we present a large-scale CNV association meta-analysis on anthropometric traits in up to 191,161 adult samples from 26 cohorts. The study reveals five CNV associations at

Ferricyanide-based analysis of aqueous lignin suspension revealed sequestration of water-soluble lignin moieties

OpenAIRE

Joshua, CJ; Simmons, BA; Singer, SW

2016-01-01

© 2016 The Royal Society of Chemistry. This study describes the application of a ferricyanide-based assay as a simple and inexpensive assay for rapid analysis of aqueous lignin samples. The assay measures the formation of Prussian blue from the redox reaction between a mixture of potassium ferricyanide and ferric chloride, and phenolic hydroxyl groups of lignin or lignin-derived phenolic moieties. This study revealed that soluble lignin moieties exhibited stronger ferricyanide reactivity than...

Diagnostic significance of microRNAs as novel biomarkers for bladder cancer: a meta-analysis of ten articles.

Science.gov (United States)

Shi, Hong-Bin; Yu, Jia-Xing; Yu, Jian-Xiu; Feng, Zheng; Zhang, Chao; Li, Guang-Yong; Zhao, Rui-Ning; Yang, Xiao-Bo

2017-08-03

Previous studies have revealed the importance of microRNAs' (miRNAs) function as biomarkers in diagnosing human bladder cancer (BC). However, the results are discordant. Consequently, the possibility of miRNAs to be BC biomarkers was summarized in this meta-analysis. In this study, the relevant articles were systematically searched from CBM, PubMed, EMBASE, and Chinese National Knowledge Infrastructure (CNKI). The bivariate model was used to calculate the pooled diagnostic parameters and summary receiver operator characteristic (SROC) curve in this meta-analysis, thereby estimating the whole predictive performance. STATA software was used during the whole analysis. Thirty-one studies from 10 articles, including 1556 cases and 1347 controls, were explored in this meta-analysis. In short, the pooled sensitivity, area under the SROC curve, specificity, positive likelihood ratio, diagnostic odds ratio, and negative likelihood ratio were 0.72 (95%CI 0.66-0.76), 0.80 (0.77-0.84), 0.76 (0.71-0.81), 3.0 (2.4-3.8), 8 (5.0-12.0), and 0.37 (0.30-0.46) respectively. Additionally, sub-group and meta-regression analyses revealed that there were significant differences between ethnicity, miRNA profiling, and specimen sub-groups. These results suggested that Asian population-based studies, multiple-miRNA profiling, and blood-based assays might yield a higher diagnostic accuracy than their counterparts. This meta-analysis demonstrated that miRNAs, particularly multiple miRNAs in the blood, might be novel, useful biomarkers with relatively high sensitivity and specificity and can be used for the diagnosis of BC. However, further prospective studies with more samples should be performed for further validation.

Integrative Analysis of Subcellular Quantitative Proteomics Studies Reveals Functional Cytoskeleton Membrane-Lipid Raft Interactions in Cancer.

Science.gov (United States)

Shah, Anup D; Inder, Kerry L; Shah, Alok K; Cristino, Alexandre S; McKie, Arthur B; Gabra, Hani; Davis, Melissa J; Hill, Michelle M

2016-10-07

Lipid rafts are dynamic membrane microdomains that orchestrate molecular interactions and are implicated in cancer development. To understand the functions of lipid rafts in cancer, we performed an integrated analysis of quantitative lipid raft proteomics data sets modeling progression in breast cancer, melanoma, and renal cell carcinoma. This analysis revealed that cancer development is associated with increased membrane raft-cytoskeleton interactions, with ∼40% of elevated lipid raft proteins being cytoskeletal components. Previous studies suggest a potential functional role for the raft-cytoskeleton in the action of the putative tumor suppressors PTRF/Cavin-1 and Merlin. To extend the observation, we examined lipid raft proteome modulation by an unrelated tumor suppressor opioid binding protein cell-adhesion molecule (OPCML) in ovarian cancer SKOV3 cells. In agreement with the other model systems, quantitative proteomics revealed that 39% of OPCML-depleted lipid raft proteins are cytoskeletal components, with microfilaments and intermediate filaments specifically down-regulated. Furthermore, protein-protein interaction network and simulation analysis showed significantly higher interactions among cancer raft proteins compared with general human raft proteins. Collectively, these results suggest increased cytoskeleton-mediated stabilization of lipid raft domains with greater molecular interactions as a common, functional, and reversible feature of cancer cells.

Complete genome sequence analysis of novel human bocavirus reveals genetic recombination between human bocavirus 2 and human bocavirus 4.

Science.gov (United States)

Khamrin, Pattara; Okitsu, Shoko; Ushijima, Hiroshi; Maneekarn, Niwat

2013-07-01

Epidemiological surveillance of human bocavirus (HBoV) was conducted on fecal specimens collected from hospitalized children with diarrhea in Chiang Mai, Thailand in 2011. By partial sequence analysis of VP1 gene, an unusual strain of HBoV (CMH-S011-11), was initially identified as HBoV4. The complete genome sequence of CMH-S011-11 was performed and analyzed further to clarify whether it was a recombinant strain or a new HBoV variant. Analysis of complete genome sequence revealed that the coding sequence starting from NS1, NP1 to VP1/VP2 was 4795 nucleotides long. Interestingly, the nucleotide sequence of NS1 gene of CMH-S011-11 was most closely related to the HBoV2 reference strains detected in Pakistan, which contradicted to the initial genotyping result of the partial VP1 region in the previous study. In addition, comparison of NP1 nucleotide sequence of CMH-S011-11 with those of other HBoV1-4 reference strains also revealed a high level of sequence identity with HBoV2. On the other hand, nucleotide sequence of VP1/VP2 gene of CMH-S011-11 was most closely related to those of HBoV4 reference strains detected in Nigeria. The overall full-length sequence analysis revealed that this CMH-S011-11 was grouped within HBoV4 species, but located in a separate branch from other HBoV4 prototype strains. Recombination analysis revealed that CMH-S011-11 was the result of recombination between HBoV2 and HBoV4 strains with the break point located near the start codon of VP2. Copyright © 2013 Elsevier B.V. All rights reserved.

Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways

Science.gov (United States)

2013-01-01

Background Analysis of global gene expression by DNA microarrays is widely used in experimental molecular biology. However, the complexity of such high-dimensional data sets makes it difficult to fully understand the underlying biological features present in the data. The aim of this study is to introduce a method for DNA microarray analysis that provides an intuitive interpretation of data through dimension reduction and pattern recognition. We present the first “Archetypal Analysis” of global gene expression. The analysis is based on microarray data from five integrated studies of Pseudomonas aeruginosa isolated from the airways of cystic fibrosis patients. Results Our analysis clustered samples into distinct groups with comprehensible characteristics since the archetypes representing the individual groups are closely related to samples present in the data set. Significant changes in gene expression between different groups identified adaptive changes of the bacteria residing in the cystic fibrosis lung. The analysis suggests a similar gene expression pattern between isolates with a high mutation rate (hypermutators) despite accumulation of different mutations for these isolates. This suggests positive selection in the cystic fibrosis lung environment, and changes in gene expression for these isolates are therefore most likely related to adaptation of the bacteria. Conclusions Archetypal analysis succeeded in identifying adaptive changes of P. aeruginosa. The combination of clustering and matrix factorization made it possible to reveal minor similarities among different groups of data, which other analytical methods failed to identify. We suggest that this analysis could be used to supplement current methods used to analyze DNA microarray data. PMID:24059747

Distribution patterns of firearm discharge residues as revealed by neutron activation analysis

International Nuclear Information System (INIS)

Pillay, K.K.S.; Driscoll, D.C.; Jester, W.A.

1975-01-01

A systematic investigation using a variety of handguns has revealed the existence of distinguisable distribution patterns of firearm discharge residues on surfaces below the flight path of a bullet. The residues are identificable even at distances of 12 meters from the gun using nondestructive neutron activation analysis. The results of these investigations show that the distribution pattern for a gun is reproducible using similar ammunition and that there exist two distinct regions to the patterns developed between the firearm and the target-one with respect to the position of the gun and the other in the vicinity of the target. The judicious applications of these findings could be of significant value in criminal investigations. (T.G.)

Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

Science.gov (United States)

2014-01-01

Abstract The version of this article published in BMC Genomics 2013, 14: 274, contains 9 unpublished genomes (Botryobasidium botryosum, Gymnopus luxurians, Hypholoma sublateritium, Jaapia argillacea, Hebeloma cylindrosporum, Conidiobolus coronatus, Laccaria amethystina, Paxillus involutus, and P. rubicundulus) downloaded from JGI website. In this correction, we removed these genomes after discussion with editors and data producers whom we should have contacted before downloading these genomes. Removing these data did not alter the principle results and conclusions of our original work. The relevant Figures 1, 2, 3, 4 and 6; and Table 1 have been revised. Additional files 1, 3, 4, and 5 were also revised. We would like to apologize for any confusion or inconvenience this may have caused. Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 94 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed

Extensão bivariada do índice de confiabilidade univariado para avaliação da estabilidade fenotípica Bivariate extension of univariate reliability index for evaluating phenotypic stability

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Suzankelly Cunha Arruda de Abreu

2004-10-01

Full Text Available Com o presente trabalho, objetiva-se realizar a derivação teórica da extensão bivariada dos métodos de Annicchiarico (1992 e Annicchiarico et al. (1995 para estudar a estabilidade fenotípica. A partir dos ensaios com genótipos em ambientes e mensurações de duas variáveis, cada genótipo teve seu valor padronizado com relação a cada variável k = 1, 2. Essa padronização foi realizada em função da média do ambiente, da seguinte forma: Wijk = Yijk/×100 ; em que Wijk representa o valor padronizado do genótipo i, no ambiente j para a variável k; representa a média observada do genótipo , no ambiente para a variável k e , a média de todos genótipos para o ambiente e variável k. Com os valores padronizados foram estimados o vetor média e a matriz de variância e covariância de cada genótipo. Foi obtida a derivação teórica da extensão bivariada do índice de risco (Ii de Annicchiarico com sucesso e foi proposto um segundo índice de risco baseado nas probabilidades bivariada (Prb i; os dois índices apresentaram grande concordância nos resultados obtidos em um exemplo ilustrativo com genótipos de melões.The objective of this work was to obtain the theoretical derivation of the bivariate extension to the methods proposed by Annicchiarico (1992 and Annicchiarico et al. (1995 for studing phenotypic stability. Considering assays with genotypes in environments and two variates, every genotype had the response of each variate (k = 1, 2 standardized. This standardization has been made using the environment means as follows: Wijk = Yijk/×100 ; where Wijk represents the ith genotype standard value in the jth environment for the kth variate; represents the observed mean of the ith genotype, in jth environment for the kth variate e the overall genotypes means for jth environment to kth variate. Considering the standardized values, the genotypes mean vector and covariance matrix were estimated. The theoretical derivation of the

Multilocus analysis reveals three candidate genes for Chinese migraine susceptibility.

Science.gov (United States)

An, X-K; Fang, J; Yu, Z-Z; Lin, Q; Lu, C-X; Qu, H-L; Ma, Q-L

2017-08-01

Several genome-wide association studies (GWASs) in Caucasian populations have identified 12 loci that are significantly associated with migraine. More evidence suggests that serotonin receptors are also involved in migraine pathophysiology. In the present study, a case-control study was conducted in a cohort of 581 migraine cases and 533 ethnically matched controls among a Chinese population. Eighteen polymorphisms from serotonin receptors and GWASs were selected, and genotyping was performed using a Sequenom MALDI-TOF mass spectrometry iPLEX platform. The genotypic and allelic distributions of MEF2D rs2274316 and ASTN2 rs6478241 were significantly different between migraine patients and controls. Univariate and multivariate analysis revealed significant associations of polymorphisms in the MEF2D and ASTN2 genes with migraine susceptibility. MEF2D, PRDM16 and ASTN2 were also found to be associated with migraine without aura (MO) and migraine with family history. And, MEF2D and ASTN2 also served as genetic risk factors for the migraine without family history. The generalized multifactor dimensionality reduction analysis identified that MEF2D and HTR2E constituted the two-factor interaction model. Our study suggests that the MEF2D, PRDM16 and ASTN2 genes from GWAS are associated with migraine susceptibility, especially MO, among Chinese patients. It appears that there is no association with serotonin receptor related genes. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Time-frequency wavelet analysis of the interrelationship between the global macro assets and the fear indexes

Science.gov (United States)

Abid, Fathi; Kaffel, Bilel

2018-01-01

Understanding the interrelationships of the global macro assets is crucial for global macro investing. This paper investigates the local variance and the interconnection between the stock, gold, oil, Forex and the implied volatility markets in the time/frequency domains using the wavelet methodology, including the wavelet power spectrum, the wavelet squared coherence and phase difference, the wavelet multiple correlation and cross-correlation. The univariate analysis reveals that, in some crisis periods, underlying asset markets present the same pattern in terms of the wavelet power spectrum indicating high volatility for the medium scale, and that for the other market stress periods, volatility behaves differently. Moreover, unlike the underlying asset markets, the implied volatility markets are characterized by high power regions across the entire period, even in the absence of economic events. Bivariate results show a bidirectional relationship between the underlying assets and their corresponding implied volatility indexes, and a steady co-movement between the stock index and its corresponding fear index. Multiple correlation analysis indicates a strong correlation between markets at high scales with evidence of a nearly perfect integration for a period longer than a year. In addition, the hedging strategies based on the volatility index lead to an increase in portfolio correlation. On the other hand, the results from multiple cross-correlations reveal that the lead-lag effect starts from the medium scale and that the VIX (stock market volatility index) index is the potential leader or follower of the other markets.

Differential RNA-seq, Multi-Network Analysis and Metabolic Regulation Analysis of Kluyveromyces marxianus Reveals a Compartmentalised Response to Xylose.

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Du Toit W P Schabort

Full Text Available We investigated the transcriptomic response of a new strain of the yeast Kluyveromyces marxianus, in glucose and xylose media using RNA-seq. The data were explored in a number of innovative ways using a variety of networks types, pathway maps, enrichment statistics, reporter metabolites and a flux simulation model, revealing different aspects of the genome-scale response in an integrative systems biology manner. The importance of the subcellular localisation in the transcriptomic response is emphasised here, revealing new insights. As was previously reported by others using a rich medium, we show that peroxisomal fatty acid catabolism was dramatically up-regulated in a defined xylose mineral medium without fatty acids, along with mechanisms to activate fatty acids and transfer products of β-oxidation to the mitochondria. Notably, we observed a strong up-regulation of the 2-methylcitrate pathway, supporting capacity for odd-chain fatty acid catabolism. Next we asked which pathways would respond to the additional requirement for NADPH for xylose utilisation, and rationalised the unexpected results using simulations with Flux Balance Analysis. On a fundamental level, we investigated the contribution of the hierarchical and metabolic regulation levels to the regulation of metabolic fluxes. Metabolic regulation analysis suggested that genetic level regulation plays a major role in regulating metabolic fluxes in adaptation to xylose, even for the high capacity reactions, which is unexpected. In addition, isozyme switching may play an important role in re-routing of metabolic fluxes in subcellular compartments in K. marxianus.

Comparative Transcriptome Analysis Reveals Different Silk Yields of Two Silkworm Strains.

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Juan Li

Full Text Available Cocoon and silk yields are the most important characteristics of sericulture. However, few studies have examined the genes that modulate these features. Further studies of these genes will be useful for improving the products of sericulture. JingSong (JS and Lan10 (L10 are two strains having significantly different cocoon and silk yields. In the current study, RNA-Seq and quantitative polymerase chain reaction (qPCR were performed on both strains in order to determine divergence of the silk gland, which controls silk biosynthesis in silkworms. Compared with L10, JS had 1375 differentially expressed genes (DEGs; 738 up-regulated genes and 673 down-regulated genes. Nine enriched gene ontology (GO terms were identified by GO enrichment analysis based on these DEGs. KEGG enrichment analysis results showed that the DEGs were enriched in three pathways, which were mainly associated with the processing and biosynthesis of proteins. The representative genes in the enrichment pathways and ten significant DEGs were further verified by qPCR, the results of which were consistent with the RNA-Seq data. Our study has revealed differences in silk glands between the two silkworm strains and provides a perspective for understanding the molecular mechanisms determining silk yield.

Metagenomic analysis reveals symbiotic relationship among bacteria in Microcystis-dominated community

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Meili eXie

2016-02-01

Full Text Available Microcystis bloom, a cyanobacterial mass occurrence often found in eutrophicated water bodies, is one of the most serious threats to freshwater ecosystems worldwide. In nature, Microcystis forms aggregates or colonies that contain heterotrophic bacteria. The Microcystis-bacteria colonies were persistent even when they were maintained in lab culture for a long period. The relationship between Microcystis and the associated bacteria was investigated by a metagenomic approach in this study. We developed a visualization-guided method of binning for genome assembly after total colony DNA sequencing. We found that the method was effective in grouping sequences and it did not require reference genome sequence. Individual genomes of the colony bacteria were obtained and they provided valuable insights into microbial community structures. Analysis of metabolic pathways based on these genomes revealed that while all heterotrophic bacteria were dependent upon Microcystis for carbon and energy, Vitamin B12 biosynthesis, which is required for growth by Microcystis, was accomplished in a cooperative fashion among the bacteria. Our analysis also suggests that individual bacteria in the colony community contributed a complete pathway for degradation of benzoate, which is inhibitory to the cyanobacterial growth, and its ecological implication for Microcystis bloom is discussed.

Revealed preferences towards the appraisal of orphan drugs in Poland - multi criteria decision analysis.

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Kolasa, Katarzyna; Zwolinski, Krzysztof Miroslaw; Zah, Vladimir; Kaló, Zoltán; Lewandowski, Tadeusz

2018-04-27

A Multi Criteria Decision Analysis (MCDA) technique was adopted to reveal the preferences of the Appraisal Body of the Polish HTA agency towards orphan drugs (OMPs). There were 34 positive and 23 negative HTA recommendations out of 54 distinctive drug-indication pairs. The MCDA matrix consisted of 13 criteria, seven of which made the most impact on the HTA process. Appraisal of clinical evidence, cost of therapy, and safety considerations were the main contributors to the HTA guidance, whilst advancement of technology and manufacturing costs made the least impact. MCDA can be regarded as a valuable tool for revealing decision makers' preferences in the healthcare sector. Given that only roughly half of all criteria included in the MCDA matrix were deemed to make an impact on the HTA process, there is certainly some room for improvement with respect to the adaptation of a new approach towards the value assessment of OMPs in Poland.

Accuracy of serum uric acid as a predictive test for maternal complications in pre-eclampsia: Bivariate meta-analysis and decision analysis

NARCIS (Netherlands)

Koopmans, Corine M.; van Pampus, Maria G.; Groen, Henk; Aarnoudse, Jan G.; van den Berg, Paul P.; Mol, Ben W. J.

2009-01-01

The aim of this study is to determine the accuracy and clinical value of serum uric acid in predicting maternal complications in women with pre-eclampsia. An existing meta-analysis on the subject was updated. The accuracy of serum uric acid for the prediction of maternal complications was assessed

Accuracy of serum uric acid as a predictive test for maternal complications in pre-eclampsia : Bivariate meta-analysis and decision analysis

NARCIS (Netherlands)

Koopmans, C.M.; van Pampus, Maria; Groen, H.; Aarnoudse, J.G.; van den Berg, P.P.; Mol, B.W.J.

The aim of this study is to determine the accuracy and clinical value of serum uric acid in predicting maternal complications in women with pre-eclampsia. An existing meta-analysis on the subject was updated. The accuracy of serum uric acid for the prediction of maternal complications was assessed

Simultaneous Analysis of the Behavioural Phenotype, Physical Factors, and Parenting Stress in People with Cornelia De Lange Syndrome

Science.gov (United States)

Wulffaert, J.; van Berckelaer-Onnes, I.; Kroonenberg, P.; Scholte, E.; Bhuiyan, Z.; Hennekam, R.

2009-01-01

Background: Studies into the phenotype of rare genetic syndromes largely rely on bivariate analysis. The aim of this study was to describe the phenotype of Cornelia de Lange syndrome (CdLS) in depth by examining a large number of variables with varying measurement levels. Virtually the only suitable multivariate technique for this is categorical…

Potential microRNA-mediated oncogenic intercellular communication revealed by pan-cancer analysis

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Li, Yue; Zhang, Zhaolei

2014-11-01

Carcinogenesis consists of oncogenesis and metastasis, and intriguingly microRNAs (miRNAs) are involved in both processes. Although aberrant miRNA activities are prevalent in diverse tumor types, the exact mechanisms for how they regulate cancerous processes are not always clear. To this end, we performed a large-scale pan-cancer analysis via a novel probabilistic approach to infer recurrent miRNA-target interactions implicated in 12 cancer types using data from The Cancer Genome Atlas. We discovered ~20,000 recurrent miRNA regulations, which are enriched for cancer-related miRNAs/genes. Notably, miRNA 200 family (miR-200/141/429) is among the most prominent miRNA regulators, which is known to be involved in metastasis. Importantly, the recurrent miRNA regulatory network is not only enriched for cancer pathways but also for extracellular matrix (ECM) organization and ECM-receptor interactions. The results suggest an intriguing cancer mechanism involving miRNA-mediated cell-to-cell communication, which possibly involves delivery of tumorigenic miRNA messengers to adjacent cells via exosomes. Finally, survival analysis revealed 414 recurrent-prognostic associations, where both gene and miRNA involved in each interaction conferred significant prognostic power in one or more cancer types. Together, our comprehensive pan-cancer analysis provided not only biological insights into metastasis but also brought to bear the clinical relevance of the proposed recurrent miRNA-gene associations.

Association genetics and transcriptome analysis reveal a gibberellin-responsive pathway involved in regulating photosynthesis.

Science.gov (United States)

Xie, Jianbo; Tian, Jiaxing; Du, Qingzhang; Chen, Jinhui; Li, Ying; Yang, Xiaohui; Li, Bailian; Zhang, Deqiang

2016-05-01

Gibberellins (GAs) regulate a wide range of important processes in plant growth and development, including photosynthesis. However, the mechanism by which GAs regulate photosynthesis remains to be understood. Here, we used multi-gene association to investigate the effect of genes in the GA-responsive pathway, as constructed by RNA sequencing, on photosynthesis, growth, and wood property traits, in a population of 435 Populus tomentosa By analyzing changes in the transcriptome following GA treatment, we identified many key photosynthetic genes, in agreement with the observed increase in measurements of photosynthesis. Regulatory motif enrichment analysis revealed that 37 differentially expressed genes related to photosynthesis shared two essential GA-related cis-regulatory elements, the GA response element and the pyrimidine box. Thus, we constructed a GA-responsive pathway consisting of 47 genes involved in regulating photosynthesis, including GID1, RGA, GID2, MYBGa, and 37 photosynthetic differentially expressed genes. Single nucleotide polymorphism (SNP)-based association analysis showed that 142 SNPs, representing 40 candidate genes in this pathway, were significantly associated with photosynthesis, growth, and wood property traits. Epistasis analysis uncovered interactions between 310 SNP-SNP pairs from 37 genes in this pathway, revealing possible genetic interactions. Moreover, a structural gene-gene matrix based on a time-course of transcript abundances provided a better understanding of the multi-gene pathway affecting photosynthesis. The results imply a functional role for these genes in mediating photosynthesis, growth, and wood properties, demonstrating the potential of combining transcriptome-based regulatory pathway construction and genetic association approaches to detect the complex genetic networks underlying quantitative traits. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights

Analysis of multi-species point patterns using multivariate log Gaussian Cox processes

DEFF Research Database (Denmark)

Waagepetersen, Rasmus; Guan, Yongtao; Jalilian, Abdollah

Multivariate log Gaussian Cox processes are flexible models for multivariate point patterns. However, they have so far only been applied in bivariate cases. In this paper we move beyond the bivariate case in order to model multi-species point patterns of tree locations. In particular we address t...... of the data. The selected number of common latent fields provides an index of complexity of the multivariate covariance structure. Hierarchical clustering is used to identify groups of species with similar patterns of dependence on the common latent fields.......Multivariate log Gaussian Cox processes are flexible models for multivariate point patterns. However, they have so far only been applied in bivariate cases. In this paper we move beyond the bivariate case in order to model multi-species point patterns of tree locations. In particular we address...... the problems of identifying parsimonious models and of extracting biologically relevant information from the fitted models. The latent multivariate Gaussian field is decomposed into components given in terms of random fields common to all species and components which are species specific. This allows...

Bivariate least squares linear regression: Towards a unified analytic formalism. I. Functional models

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Caimmi, R.

2011-08-01

Concerning bivariate least squares linear regression, the classical approach pursued for functional models in earlier attempts ( York, 1966, 1969) is reviewed using a new formalism in terms of deviation (matrix) traces which, for unweighted data, reduce to usual quantities leaving aside an unessential (but dimensional) multiplicative factor. Within the framework of classical error models, the dependent variable relates to the independent variable according to the usual additive model. The classes of linear models considered are regression lines in the general case of correlated errors in X and in Y for weighted data, and in the opposite limiting situations of (i) uncorrelated errors in X and in Y, and (ii) completely correlated errors in X and in Y. The special case of (C) generalized orthogonal regression is considered in detail together with well known subcases, namely: (Y) errors in X negligible (ideally null) with respect to errors in Y; (X) errors in Y negligible (ideally null) with respect to errors in X; (O) genuine orthogonal regression; (R) reduced major-axis regression. In the limit of unweighted data, the results determined for functional models are compared with their counterparts related to extreme structural models i.e. the instrumental scatter is negligible (ideally null) with respect to the intrinsic scatter ( Isobe et al., 1990; Feigelson and Babu, 1992). While regression line slope and intercept estimators for functional and structural models necessarily coincide, the contrary holds for related variance estimators even if the residuals obey a Gaussian distribution, with the exception of Y models. An example of astronomical application is considered, concerning the [O/H]-[Fe/H] empirical relations deduced from five samples related to different stars and/or different methods of oxygen abundance determination. For selected samples and assigned methods, different regression models yield consistent results within the errors (∓ σ) for both

Intestinal transcriptome analysis revealed differential salinity adaptation between two tilapiine species.

Science.gov (United States)

Ronkin, Dana; Seroussi, Eyal; Nitzan, Tali; Doron-Faigenboim, Adi; Cnaani, Avner

2015-03-01

Tilapias are a group of freshwater species, which vary in their ability to adapt to high salinity water. Osmotic regulation in fish is conducted mainly in the gills, kidney, and gastrointestinal tract (GIT). The mechanisms involved in ion and water transport through the GIT is not well-characterized, with only a few described complexes. Comparing the transcriptome of the anterior and posterior intestinal sections of a freshwater and saltwater adapted fish by deep-sequencing, we examined the salinity adaptation of two tilapia species: the high salinity-tolerant Oreochromis mossambicus (Mozambique tilapia), and the less salinity-tolerant Oreochromis niloticus (Nile tilapia). This comparative analysis revealed high similarity in gene expression response to salinity change between species in the posterior intestine and large differences in the anterior intestine. Furthermore, in the anterior intestine 68 genes were saltwater up-regulated in one species and down-regulated in the other species (47 genes up-regulated in O. niloticus and down-regulated in O. mossambicus, with 21 genes showing the reverse pattern). Gene ontology (GO) analysis showed a high proportion of transporter and ion channel function among these genes. The results of this study point to a group of genes that differed in their salinity-dependent regulation pattern in the anterior intestine as potentially having a role in the differential salinity tolerance of these two closely related species. Copyright © 2015 Elsevier Inc. All rights reserved.

Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis

KAUST Repository

Feng, Yitao

2016-10-13

The glutamine binding protein (GlnBP) binds l-glutamine and cooperates with its cognate transporters during glutamine uptake. Crystal structure analysis has revealed an open and a closed conformation for apo- and holo-GlnBP, respectively. However, the detailed conformational dynamics have remained unclear. Herein, we combined NMR spectroscopy, MD simulations, and single-molecule FRET techniques to decipher the conformational dynamics of apo-GlnBP. The NMR residual dipolar couplings of apo-GlnBP were in good agreement with a MD-derived structure ensemble consisting of four metastable states. The open and closed conformations are the two major states. This four-state model was further validated by smFRET experiments and suggests the conformational selection mechanism in ligand recognition of GlnBP. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis

KAUST Repository

Feng, Yitao; Zhang, Lu; Wu, Shaowen; Liu, Zhijun; Gao, Xin; Zhang, Xu; Liu, Maili; Liu, Jianwei; Huang, Xuhui; Wang, Wenning

2016-01-01

The glutamine binding protein (GlnBP) binds l-glutamine and cooperates with its cognate transporters during glutamine uptake. Crystal structure analysis has revealed an open and a closed conformation for apo- and holo-GlnBP, respectively. However, the detailed conformational dynamics have remained unclear. Herein, we combined NMR spectroscopy, MD simulations, and single-molecule FRET techniques to decipher the conformational dynamics of apo-GlnBP. The NMR residual dipolar couplings of apo-GlnBP were in good agreement with a MD-derived structure ensemble consisting of four metastable states. The open and closed conformations are the two major states. This four-state model was further validated by smFRET experiments and suggests the conformational selection mechanism in ligand recognition of GlnBP. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

Molecular evolution and diversification of snake toxin genes, revealed by analysis of intron sequences.

Science.gov (United States)

Fujimi, T J; Nakajyo, T; Nishimura, E; Ogura, E; Tsuchiya, T; Tamiya, T

2003-08-14

The genes encoding erabutoxin (short chain neurotoxin) isoforms (Ea, Eb, and Ec), LsIII (long chain neurotoxin) and a novel long chain neurotoxin pseudogene were cloned from a Laticauda semifasciata genomic library. Short and long chain neurotoxin genes were also cloned from the genome of Laticauda laticaudata, a closely related species of L. semifasciata, by PCR. A putative matrix attached region (MAR) sequence was found in the intron I of the LsIII gene. Comparative analysis of 11 structurally relevant snake toxin genes (three-finger-structure toxins) revealed the molecular evolution of these toxins. Three-finger-structure toxin genes diverged from a common ancestor through two types of evolutionary pathways (long and short types), early in the course of evolution. At a later stage of evolution in each gene, the accumulation of mutations in the exons, especially exon II, by accelerated evolution may have caused the increased diversification in their functions. It was also revealed that the putative MAR sequence found in the LsIII gene was integrated into the gene after the species-level divergence.

Network analysis of oyster transcriptome revealed a cascade of cellular responses during recovery after heat shock.

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Lingling Zhang

Full Text Available Oysters, as a major group of marine bivalves, can tolerate a wide range of natural and anthropogenic stressors including heat stress. Recent studies have shown that oysters pretreated with heat shock can result in induced heat tolerance. A systematic study of cellular recovery from heat shock may provide insights into the mechanism of acquired thermal tolerance. In this study, we performed the first network analysis of oyster transcriptome by reanalyzing microarray data from a previous study. Network analysis revealed a cascade of cellular responses during oyster recovery after heat shock and identified responsive gene modules and key genes. Our study demonstrates the power of network analysis in a non-model organism with poor gene annotations, which can lead to new discoveries that go beyond the focus on individual genes.

The Revealed Competitiveness of Major Ports in the East Asian Region: An Additive Market Share Analysis

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Tae Seung Kim

2015-12-01

Full Text Available In the single cargo market, the ordinary market share analysis method has been the representative tool for revealed competitiveness analysis. This paper develops and employs an applied market share index called the additive market share (AMS. Data are collected from 15 major container ports for the 1998-2013 period. In comparison to the results of an ordinary market share analysis, the highest AMS is observed for the Bohai Rim port cluster from 2008, not for the Yangtze River cluster or the Pearl River cluster. There are substitutable relationships between Yangtze River and non-Chinese ports and between Pearl River and Bohai Rim ports from 2001. Finally, there is an internal competition at Pearl River and Yangtze River ports, whereas Bohai Rim and non-Chinese ports show internally complementary relationships.

Assessing Trust and Effectiveness in Virtual Teams: Latent Growth Curve and Latent Change Score Models

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Michael D. Coovert

2017-08-01

Full Text Available Trust plays a central role in the effectiveness of work groups and teams. This is the case for both face-to-face and virtual teams. Yet little is known about the development of trust in virtual teams. We examined cognitive and affective trust and their relationship to team effectiveness as reflected through satisfaction with one’s team and task performance. Latent growth curve analysis reveals both trust types start at a significant level with individual differences in that initial level. Cognitive trust follows a linear growth pattern while affective trust is overall non-linear, but becomes linear once established. Latent change score models are utilized to examine change in trust and also its relationship with satisfaction with the team and team performance. In examining only change in trust and its relationship to satisfaction there appears to be a straightforward influence of trust on satisfaction and satisfaction on trust. However, when incorporated into a bivariate coupling latent change model the dynamics of the relationship are revealed. A similar pattern holds for trust and task performance; however, in the bivariate coupling change model a more parsimonious representation is preferred.

Phylogenetic analysis reveals two genotypes of the emerging fungus Mucor indicus, an opportunistic human pathogen in immunocompromised patients

NARCIS (Netherlands)

Taj-Aldeen, Saad J.; Almaslamani, Muna; Theelen, B.J.F.; Boekhout, Teun

2017-01-01

Mucormycosis is a rare fungal infection caused by Mucor indicus. Phylogenetic analysis of many M. indicus isolates, mainly sampled from different clinical and environmental specimens collected worldwide, revealed two genotypes, I and II, based on ITS and D1/D2 LSU rDNA sequences. A retrospective

RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in Maize

Science.gov (United States)

Ren, Wen; Yang, Fengling; He, Hang; Zhao, Jiuran

2015-01-01

The mitogen-activated protein kinase (MAPK) cascade is an evolutionarily conserved signal transduction pathway that is involved in plant development and stress responses. As the first component of this phosphorelay cascade, mitogen-activated protein kinase kinase kinases (MAPKKKs) act as adaptors linking upstream signaling steps to the core MAPK cascade to promote the appropriate cellular responses; however, the functions of MAPKKKs in maize are unclear. Here, we identified 71 MAPKKK genes, of which 14 were novel, based on a computational analysis of the maize (Zea mays L.) genome. Using an RNA-seq analysis in the leaf, stem and root of maize under well-watered and drought-stress conditions, we identified 5,866 differentially expressed genes (DEGs), including 8 MAPKKK genes responsive to drought stress. Many of the DEGs were enriched in processes such as drought stress, abiotic stimulus, oxidation-reduction, and metabolic processes. The other way round, DEGs involved in processes such as oxidation, photosynthesis, and starch, proline, ethylene, and salicylic acid metabolism were clearly co-expressed with the MAPKKK genes. Furthermore, a quantitative real-time PCR (qRT-PCR) analysis was performed to assess the relative expression levels of MAPKKKs. Correlation analysis revealed that there was a significant correlation between expression levels of two MAPKKKs and relative biomass responsive to drought in 8 inbred lines. Our results indicate that MAPKKKs may have important regulatory functions in drought tolerance in maize. PMID:26599013

Quantitative flux analysis reveals folate-dependent NADPH production

Science.gov (United States)

Fan, Jing; Ye, Jiangbin; Kamphorst, Jurre J.; Shlomi, Tomer; Thompson, Craig B.; Rabinowitz, Joshua D.

2014-06-01

ATP is the dominant energy source in animals for mechanical and electrical work (for example, muscle contraction or neuronal firing). For chemical work, there is an equally important role for NADPH, which powers redox defence and reductive biosynthesis. The most direct route to produce NADPH from glucose is the oxidative pentose phosphate pathway, with malic enzyme sometimes also important. Although the relative contribution of glycolysis and oxidative phosphorylation to ATP production has been extensively analysed, similar analysis of NADPH metabolism has been lacking. Here we demonstrate the ability to directly track, by liquid chromatography-mass spectrometry, the passage of deuterium from labelled substrates into NADPH, and combine this approach with carbon labelling and mathematical modelling to measure NADPH fluxes. In proliferating cells, the largest contributor to cytosolic NADPH is the oxidative pentose phosphate pathway. Surprisingly, a nearly comparable contribution comes from serine-driven one-carbon metabolism, in which oxidation of methylene tetrahydrofolate to 10-formyl-tetrahydrofolate is coupled to reduction of NADP+ to NADPH. Moreover, tracing of mitochondrial one-carbon metabolism revealed complete oxidation of 10-formyl-tetrahydrofolate to make NADPH. As folate metabolism has not previously been considered an NADPH producer, confirmation of its functional significance was undertaken through knockdown of methylenetetrahydrofolate dehydrogenase (MTHFD) genes. Depletion of either the cytosolic or mitochondrial MTHFD isozyme resulted in decreased cellular NADPH/NADP+ and reduced/oxidized glutathione ratios (GSH/GSSG) and increased cell sensitivity to oxidative stress. Thus, although the importance of folate metabolism for proliferating cells has been long recognized and attributed to its function of producing one-carbon units for nucleic acid synthesis, another crucial function of this pathway is generating reducing power.

Analysis of 16S libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria

NARCIS (Netherlands)

Salzman, NH; de Jong, H; Paterson, Y; Harmsen, HJM; Welling, GW; Bos, NA

2002-01-01

Total genomic DNA from samples of intact mouse small intestine, large intestine, caecum and faeces was used as template for PCR amplification of 16S rRNA gene sequences with conserved bacterial primers. Phylogenetic analysis of the amplification products revealed 40 unique 16S rDNA sequences. Of

Detrended partial cross-correlation analysis of two nonstationary time series influenced by common external forces

Science.gov (United States)

Qian, Xi-Yuan; Liu, Ya-Min; Jiang, Zhi-Qiang; Podobnik, Boris; Zhou, Wei-Xing; Stanley, H. Eugene

2015-06-01

When common factors strongly influence two power-law cross-correlated time series recorded in complex natural or social systems, using detrended cross-correlation analysis (DCCA) without considering these common factors will bias the results. We use detrended partial cross-correlation analysis (DPXA) to uncover the intrinsic power-law cross correlations between two simultaneously recorded time series in the presence of nonstationarity after removing the effects of other time series acting as common forces. The DPXA method is a generalization of the detrended cross-correlation analysis that takes into account partial correlation analysis. We demonstrate the method by using bivariate fractional Brownian motions contaminated with a fractional Brownian motion. We find that the DPXA is able to recover the analytical cross Hurst indices, and thus the multiscale DPXA coefficients are a viable alternative to the conventional cross-correlation coefficient. We demonstrate the advantage of the DPXA coefficients over the DCCA coefficients by analyzing contaminated bivariate fractional Brownian motions. We calculate the DPXA coefficients and use them to extract the intrinsic cross correlation between crude oil and gold futures by taking into consideration the impact of the U.S. dollar index. We develop the multifractal DPXA (MF-DPXA) method in order to generalize the DPXA method and investigate multifractal time series. We analyze multifractal binomial measures masked with strong white noises and find that the MF-DPXA method quantifies the hidden multifractal nature while the multifractal DCCA method fails.

Determination of equilibrium structures of bromothymol blue revealed by using quantum chemistry with an aid of multivariate analysis of electronic absorption spectra

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Shimada, Toru; Hasegawa, Takeshi

2017-10-01

The pH dependent chemical structures of bromothymol blue (BTB), which have long been under controversy, are determined by employing a combined technique of multivariate analysis of electronic absorption spectra and quantum chemistry. Principle component analysis (PCA) of the pH dependent spectra apparently reveals that only two chemical species are adequate to fully account for the color changes, with which the spectral decomposition is readily performed by using augmented alternative least-squares (ALS) regression analysis. The quantity variation by the ALS analysis also reveals the practical acid dissociation constant, pKa‧. The determination of pKa‧ is performed for various ionic strengths, which reveals the thermodynamic acid constant (pKa = 7.5) and the number of charge on each chemical species; the yellow form is negatively charged species of - 1 and the blue form that of - 2. On this chemical information, the quantum chemical calculation is carried out to find that BTB molecules take the pure quinoid form in an acid solution and the quinoid-phenolate form in an alkaline solution. The time-dependent density functional theory (TD-DFT) calculations for the theoretically determined chemical structures account for the peak shift of the electronic spectra. In this manner, the structures of all the chemical species appeared in equilibrium have finally been confirmed.

Genome Wide Transcriptome Analysis reveals ABA mediated response in Arabidopsis during Gold (AuCl4- treatment

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Devesh eShukla

2014-11-01

Full Text Available The unique physico-chemical properties of gold nanoparticles (AuNPs find manifold applications in diagnostics, medicine and catalysis. Chemical synthesis produces reactive AuNPs and generates hazardous by-products. Alternatively, plants can be utilized to produce AuNPs in an eco-friendly manner. To better control the biosynthesis of AuNPs, we need to first understand the detailed molecular response induced by AuCl4- In this study, we carried out global transcriptome analysis in root tissue of Arabidopsis grown for 12- hours in presence of gold solution (HAuCl4 using the novel unbiased Affymetrix exon array. Transcriptomics analysis revealed differential regulation of a total of 704 genes and 4900 exons. Of these, 492 and 212 genes were up- and downregulated, respectively. The validation of the expressed key genes, such as glutathione-S-transferases, auxin responsive genes, cytochrome P450 82C2, methyl transferases, transducin (G protein beta subunit, ERF transcription factor, ABC, and MATE transporters, was carried out through quantitative RT-PCR. These key genes demonstrated specific induction under AuCl4- treatment relative to other heavy metals, suggesting a unique plant-gold interaction. GO enrichment analysis reveals the upregulation of processes like oxidative stress, glutathione binding, metal binding, transport, and plant hormonal responses. Changes predicted in biochemical pathways indicated major modulation in glutathione mediated detoxification, flavones and derivatives, and plant hormone biosynthesis. Motif search analysis identified a highly significant enriched motif, ACGT, which is an abscisic acid responsive core element (ABRE, suggesting the possibility of ABA- mediated signaling. Identification of abscisic acid response element (ABRE points to the operation of a predominant signaling mechanism in response to AuCl4- exposure. Overall, this study presents a useful picture of plant-gold interaction with an identification of

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.

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Jiang, Yue; Xiong, Xuejian; Danska, Jayne; Parkinson, John

2016-01-12

Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. However, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. Systematic studies that compare data across microbiomes are needed to demonstrate the ability of such pipelines to deliver biologically meaningful insights on microbiome function. Here, we apply a standardized analytical pipeline to perform a comparative analysis of metatranscriptomic data from diverse microbial communities derived from mouse large intestine, cow rumen, kimchi culture, deep-sea thermal vent and permafrost. Sequence similarity searches allowed annotation of 19 to 76% of putative messenger RNA (mRNA) reads, with the highest frequency in the kimchi dataset due to its relatively low complexity and availability of closely related reference genomes. Metatranscriptomic datasets exhibited distinct taxonomic and functional signatures. From a metabolic perspective, we identified a common core of enzymes involved in amino acid, energy and nucleotide metabolism and also identified microbiome-specific pathways such as phosphonate metabolism (deep sea) and glycan degradation pathways (cow rumen). Integrating taxonomic and functional annotations within a novel visualization framework revealed the contribution of different taxa to metabolic pathways, allowing the identification of taxa that contribute unique functions. The application of a single, standard pipeline confirms that the rich taxonomic and functional diversity observed across microbiomes is not simply an artefact of different analysis pipelines but instead reflects distinct environmental influences. At the same time, our findings show how microbiome complexity and availability of

Distribution of triclosan-resistant genes in major pathogenic microorganisms revealed by metagenome and genome-wide analysis.

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Raees Khan

Full Text Available The substantial use of triclosan (TCS has been aimed to kill pathogenic bacteria, but TCS resistance seems to be prevalent in microbial species and limited knowledge exists about TCS resistance determinants in a majority of pathogenic bacteria. We aimed to evaluate the distribution of TCS resistance determinants in major pathogenic bacteria (N = 231 and to assess the enrichment of potentially pathogenic genera in TCS contaminated environments. A TCS-resistant gene (TRG database was constructed and experimentally validated to predict TCS resistance in major pathogenic bacteria. Genome-wide in silico analysis was performed to define the distribution of TCS-resistant determinants in major pathogens. Microbiome analysis of TCS contaminated soil samples was also performed to investigate the abundance of TCS-resistant pathogens. We experimentally confirmed that TCS resistance could be accurately predicted using genome-wide in silico analysis against TRG database. Predicted TCS resistant phenotypes were observed in all of the tested bacterial strains (N = 17, and heterologous expression of selected TCS resistant genes from those strains conferred expected levels of TCS resistance in an alternative host Escherichia coli. Moreover, genome-wide analysis revealed that potential TCS resistance determinants were abundant among the majority of human-associated pathogens (79% and soil-borne plant pathogenic bacteria (98%. These included a variety of enoyl-acyl carrier protein reductase (ENRs homologues, AcrB efflux pumps, and ENR substitutions. FabI ENR, which is the only known effective target for TCS, was either co-localized with other TCS resistance determinants or had TCS resistance-associated substitutions. Furthermore, microbiome analysis revealed that pathogenic genera with intrinsic TCS-resistant determinants exist in TCS contaminated environments. We conclude that TCS may not be as effective against the majority of bacterial pathogens as previously

Distribution of triclosan-resistant genes in major pathogenic microorganisms revealed by metagenome and genome-wide analysis

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Khan, Raees; Roy, Nazish; Choi, Kihyuck

2018-01-01

The substantial use of triclosan (TCS) has been aimed to kill pathogenic bacteria, but TCS resistance seems to be prevalent in microbial species and limited knowledge exists about TCS resistance determinants in a majority of pathogenic bacteria. We aimed to evaluate the distribution of TCS resistance determinants in major pathogenic bacteria (N = 231) and to assess the enrichment of potentially pathogenic genera in TCS contaminated environments. A TCS-resistant gene (TRG) database was constructed and experimentally validated to predict TCS resistance in major pathogenic bacteria. Genome-wide in silico analysis was performed to define the distribution of TCS-resistant determinants in major pathogens. Microbiome analysis of TCS contaminated soil samples was also performed to investigate the abundance of TCS-resistant pathogens. We experimentally confirmed that TCS resistance could be accurately predicted using genome-wide in silico analysis against TRG database. Predicted TCS resistant phenotypes were observed in all of the tested bacterial strains (N = 17), and heterologous expression of selected TCS resistant genes from those strains conferred expected levels of TCS resistance in an alternative host Escherichia coli. Moreover, genome-wide analysis revealed that potential TCS resistance determinants were abundant among the majority of human-associated pathogens (79%) and soil-borne plant pathogenic bacteria (98%). These included a variety of enoyl-acyl carrier protein reductase (ENRs) homologues, AcrB efflux pumps, and ENR substitutions. FabI ENR, which is the only known effective target for TCS, was either co-localized with other TCS resistance determinants or had TCS resistance-associated substitutions. Furthermore, microbiome analysis revealed that pathogenic genera with intrinsic TCS-resistant determinants exist in TCS contaminated environments. We conclude that TCS may not be as effective against the majority of bacterial pathogens as previously presumed

Central depression in nucleonic densities: Trend analysis in the nuclear density functional theory approach

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Schuetrumpf, B.; Nazarewicz, W.; Reinhard, P.-G.

2017-08-01

Background: The central depression of nucleonic density, i.e., a reduction of density in the nuclear interior, has been attributed to many factors. For instance, bubble structures in superheavy nuclei are believed to be due to the electrostatic repulsion. In light nuclei, the mechanism behind the density reduction in the interior has been discussed in terms of shell effects associated with occupations of s orbits. Purpose: The main objective of this work is to reveal mechanisms behind the formation of central depression in nucleonic densities in light and heavy nuclei. To this end, we introduce several measures of the internal nucleonic density. Through the statistical analysis, we study the information content of these measures with respect to nuclear matter properties. Method: We apply nuclear density functional theory with Skyrme functionals. Using the statistical tools of linear least square regression, we inspect correlations between various measures of central depression and model parameters, including nuclear matter properties. We study bivariate correlations with selected quantities as well as multiple correlations with groups of parameters. Detailed correlation analysis is carried out for 34Si for which a bubble structure has been reported recently, 48Ca, and N =82 , 126, and 184 isotonic chains. Results: We show that the central depression in medium-mass nuclei is very sensitive to shell effects, whereas for superheavy systems it is firmly driven by the electrostatic repulsion. An appreciable semibubble structure in proton density is predicted for 294Og, which is currently the heaviest nucleus known experimentally. Conclusion: Our correlation analysis reveals that the central density indicators in nuclei below 208Pb carry little information on parameters of nuclear matter; they are predominantly driven by shell structure. On the other hand, in the superheavy nuclei there exists a clear relationship between the central nucleonic density and symmetry energy.

Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans.

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Cenik, Can; Cenik, Elif Sarinay; Byeon, Gun W; Grubert, Fabian; Candille, Sophie I; Spacek, Damek; Alsallakh, Bilal; Tilgner, Hagen; Araya, Carlos L; Tang, Hua; Ricci, Emiliano; Snyder, Michael P

2015-11-01

Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding, and chromatin have been explored, little is known about global variation in translation and its genetic determinants. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences in RNA, translation, and protein levels suggesting diverse mechanisms of personalized gene expression control. Combined analysis of RNA expression and ribosome occupancy improves the identification of individual protein level differences. Finally, we identify genetic differences that specifically modulate ribosome occupancy--many of these differences lie close to start codons and upstream ORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation. © 2015 Cenik et al.; Published by Cold Spring Harbor Laboratory Press.

Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids.

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Schmitz, Alexander; Fischer, Sabine C; Mattheyer, Christian; Pampaloni, Francesco; Stelzer, Ernst H K

2017-03-03

Three-dimensional multicellular aggregates such as spheroids provide reliable in vitro substitutes for tissues. Quantitative characterization of spheroids at the cellular level is fundamental. We present the first pipeline that provides three-dimensional, high-quality images of intact spheroids at cellular resolution and a comprehensive image analysis that completes traditional image segmentation by algorithms from other fields. The pipeline combines light sheet-based fluorescence microscopy of optically cleared spheroids with automated nuclei segmentation (F score: 0.88) and concepts from graph analysis and computational topology. Incorporating cell graphs and alpha shapes provided more than 30 features of individual nuclei, the cellular neighborhood and the spheroid morphology. The application of our pipeline to a set of breast carcinoma spheroids revealed two concentric layers of different cell density for more than 30,000 cells. The thickness of the outer cell layer depends on a spheroid's size and varies between 50% and 75% of its radius. In differently-sized spheroids, we detected patches of different cell densities ranging from 5 × 10 5 to 1 × 10 6  cells/mm 3 . Since cell density affects cell behavior in tissues, structural heterogeneities need to be incorporated into existing models. Our image analysis pipeline provides a multiscale approach to obtain the relevant data for a system-level understanding of tissue architecture.

Evaluation of Factors Affecting E-Bike Involved Crash and E-Bike License Plate Use in China Using a Bivariate Probit Model

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Yanyong Guo

2017-01-01

Full Text Available The primary objective of this study is to evaluate factors affecting e-bike involved crash and license plate use in China. E-bike crashes data were collected from police database and completed through a telephone interview. Noncrash samples were collected by a questionnaire survey. A bivariate probit (BP model was developed to simultaneously examine the significant factors associated with e-bike involved crash and e-bike license plate and to account for the correlations between them. Marginal effects for contributory factors were calculated to quantify their impacts on the outcomes. The results show that several contributory factors, including gender, age, education level, driver license, car in household, experiences in using e-bike, law compliance, and aggressive driving behaviors, are found to have significant impacts on both e-bike involved crash and license plate use. Moreover, type of e-bike, frequency of using e-bike, impulse behavior, degree of riding experience, and risk perception scale are found to be associated with e-bike involved crash. It is also found that e-bike involved crash and e-bike license plate use are strongly correlated and are negative in direction. The result enhanced our comprehension of the factors related to e-bike involved crash and e-bike license plate use.

A vine copula mixed effect model for trivariate meta-analysis of diagnostic test accuracy studies accounting for disease prevalence.

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Nikoloulopoulos, Aristidis K

2017-10-01

A bivariate copula mixed model has been recently proposed to synthesize diagnostic test accuracy studies and it has been shown that it is superior to the standard generalized linear mixed model in this context. Here, we call trivariate vine copulas to extend the bivariate meta-analysis of diagnostic test accuracy studies by accounting for disease prevalence. Our vine copula mixed model includes the trivariate generalized linear mixed model as a special case and can also operate on the original scale of sensitivity, specificity, and disease prevalence. Our general methodology is illustrated by re-analyzing the data of two published meta-analyses. Our study suggests that there can be an improvement on trivariate generalized linear mixed model in fit to data and makes the argument for moving to vine copula random effects models especially because of their richness, including reflection asymmetric tail dependence, and computational feasibility despite their three dimensionality.

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

DEFF Research Database (Denmark)

Hoadley, Katherine A; Yau, Christina; Wolf, Denise M

2014-01-01

Recent genomic analyses of pathologically defined tumor types identify "within-a-tissue" disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform...... on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head and neck, and a subset...

CNV-association meta-analysis in 191,161 European adults reveals new loci associated with anthropometric traits

DEFF Research Database (Denmark)

Macé, Aurélien; Tuke, Marcus A; Deelen, Patrick

2017-01-01

There are few examples of robust associations between rare copy number variants (CNVs) and complex continuous human traits. Here we present a large-scale CNV association meta-analysis on anthropometric traits in up to 191,161 adult samples from 26 cohorts. The study reveals five CNV associations......-scale genome-wide meta-analysis of structural variation and find rare CNVs associated with height, weight and BMI with large effect sizes.......)). Burden analysis shows a 0.41 cm decrease in height, a 0.003 increase in waist-to-hip ratio and increase in BMI by 0.14 kg/m(2) for each Mb of total deletion burden (P = 2.5 × 10(-10), 6.0 × 10(-5), and 2.9 × 10(-3)). Our study provides evidence that the same genes (e.g., MC4R, FIBIN, and FMO5) harbor...

Sheep skeletal muscle transcriptome analysis reveals muscle growth regulatory lncRNAs.

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Chao, Tianle; Ji, Zhibin; Hou, Lei; Wang, Jin; Zhang, Chunlan; Wang, Guizhi; Wang, Jianmin

2018-01-01

As widely distributed domestic animals, sheep are an important species and the source of mutton. In this study, we aimed to evaluate the regulatory lncRNAs associated with muscle growth and development between high production mutton sheep (Dorper sheep and Qianhua Mutton Merino sheep) and low production mutton sheep (Small-tailed Han sheep). In total, 39 lncRNAs were found to be differentially expressed. Using co-expression analysis and functional annotation, 1,206 co-expression interactions were found between 32 lncRNAs and 369 genes, and 29 of these lncRNAs were found to be associated with muscle development, metabolism, cell proliferation and apoptosis. lncRNA-mRNA interactions revealed 6 lncRNAs as hub lncRNAs. Moreover, three lncRNAs and their associated co-expressed genes were demonstrated by cis-regulatory gene analyses, and we also found a potential regulatory relationship between the pseudogene lncRNA LOC101121401 and its parent gene FTH1. This study provides a genome-wide resolution of lncRNA and mRNA regulation in muscles from mutton sheep.

Applications of uncertainty analysis to visual evaluation of density in radiographs

International Nuclear Information System (INIS)

Uchida, Suguru; Ohtsuka, Akiyoshi; Fujita, Hiroshi.

1981-01-01

Uncertainty analysis, developed as a method of absolute judgment in psychology, is applied to a method of radiographic image evaluation with perceptual fluctuations and to an examination of visual evaluation of density in radiographs. Subjects are composed of three groups of four neurosurgeons, four radiologic technologists and four nonprofessionals. By using a five-category rating scale, each observer is directed to classify 255 radiographs randomly presented without feedback. Characteristics of each observer and each group can be shown quantitatively by calculated information values. It is also described that bivariate uncertainty analysis or entropy method can be used to calculate the degree of agreement of evaluation. (author)

Applications of uncertainty analysis to visual evaluation of density in radiographs

Energy Technology Data Exchange (ETDEWEB)

Uchida, S [Gifu Univ. (Japan); Ohtsuka, A; Fujita, H

1981-03-01

Uncertainty analysis, developed as a method of absolute judgment in psychology, is applied to a method of radiographic image evaluation with perceptual fluctuations and to an examination of visual evaluation of density in radiographs. Subjects are composed of three groups of four neurosurgeons, four radiologic technologists and four nonprofessionals. By using a five-category rating scale, each observer is directed to classify 255 radiographs randomly presented without feedback. Characteristics of each observer and each group can be shown quantitatively by calculated information values. It is also described that bivariate uncertainty analysis or entropy method can be used to calculate the degree of agreement of evaluation.

Genome sequencing and analysis reveals possible determinants of Staphylococcus aureus nasal carriage

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Cole Alexander M

2008-09-01

Full Text Available Abstract Background Nasal carriage of Staphylococcus aureus is a major risk factor in clinical and community settings due to the range of etiologies caused by the organism. We have identified unique immunological and ultrastructural properties associated with nasal carriage isolates denoting a role for bacterial factors in nasal carriage. However, despite extensive molecular level characterizations by several groups suggesting factors necessary for colonization on nasal epithelium, genetic determinants of nasal carriage are unknown. Herein, we have set a genomic foundation for unraveling the bacterial determinants of nasal carriage in S. aureus. Results MLST analysis revealed no lineage specific differences between carrier and non-carrier strains suggesting a role for mobile genetic elements. We completely sequenced a model carrier isolate (D30 and a model non-carrier strain (930918-3 to identify differential gene content. Comparison revealed the presence of 84 genes unique to the carrier strain and strongly suggests a role for Type VII secretion systems in nasal carriage. These genes, along with a putative pathogenicity island (SaPIBov present uniquely in the carrier strains are likely important in affecting carriage. Further, PCR-based genotyping of other clinical isolates for a specific subset of these 84 genes raise the possibility of nasal carriage being caused by multiple gene sets. Conclusion Our data suggest that carriage is likely a heterogeneic phenotypic trait and implies a role for nucleotide level polymorphism in carriage. Complete genome level analyses of multiple carriage strains of S. aureus will be important in clarifying molecular determinants of S. aureus nasal carriage.

Peptidomic analysis reveals proteolytic activity of kefir microorganisms on bovine milk proteins.

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Dallas, David C; Citerne, Florine; Tian, Tian; Silva, Vitor L M; Kalanetra, Karen M; Frese, Steven A; Robinson, Randall C; Mills, David A; Barile, Daniela

2016-04-15

The microorganisms that make up kefir grains are well known for lactose fermentation, but the extent to which they hydrolyze and consume milk proteins remains poorly understood. Peptidomics technologies were used to examine the proteolytic activity of kefir grains on bovine milk proteins. Gel electrophoresis revealed substantial digestion of milk proteins by kefir grains, with mass spectrometric analysis showing the release of 609 protein fragments and alteration of the abundance of >1500 peptides that derived from 27 milk proteins. Kefir contained 25 peptides identified from the literature as having biological activity, including those with antihypertensive, antimicrobial, immunomodulatory, opioid and anti-oxidative functions. 16S rRNA and shotgun metagenomic sequencing identified the principle taxa in the culture as Lactobacillus species. The model kefir sample contained thousands of protein fragments released in part by kefir microorganisms and in part by native milk proteases. Copyright © 2015 Elsevier Ltd. All rights reserved.

Peptidomic analysis reveals proteolytic activity of kefir microorganisms on bovine milk proteins

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Dallas, David C.; Citerne, Florine; Tian, Tian; Silva, Vitor L. M.; Kalanetra, Karen M.; Frese, Steven A.; Robinson, Randall C.; Mills, David A.; Barile, Daniela

2015-01-01

Scope The microorganisms that make up kefir grains are well known for lactose fermentation, but the extent to which they hydrolyze and consume milk proteins remains poorly understood. Peptidomics technologies were used to examine the proteolytic activity of kefir grains on bovine milk proteins. Methods and results Gel electrophoresis revealed substantial digestion of milk proteins by kefir grains, with mass spectrometric analysis showing the release of 609 protein fragments and alteration of the abundance of >1,500 peptides that derived from 27 milk proteins. Kefir contained 25 peptides identified from the literature as having biological activity, including those with antihypertensive, antimicrobial, immunomodulatory, opioid and anti-oxidative functions. 16S rRNA and shotgun metagenomic sequencing identified the principle taxa in the culture as Lactobacillus species. Conclusion The model kefir sample contained thousands of protein fragments released in part by kefir microorganisms and in part by native milk proteases. PMID:26616950

Determination of equilibrium structures of bromothymol blue revealed by using quantum chemistry with an aid of multivariate analysis of electronic absorption spectra.

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Shimada, Toru; Hasegawa, Takeshi

2017-10-05

The pH dependent chemical structures of bromothymol blue (BTB), which have long been under controversy, are determined by employing a combined technique of multivariate analysis of electronic absorption spectra and quantum chemistry. Principle component analysis (PCA) of the pH dependent spectra apparently reveals that only two chemical species are adequate to fully account for the color changes, with which the spectral decomposition is readily performed by using augmented alternative least-squares (ALS) regression analysis. The quantity variation by the ALS analysis also reveals the practical acid dissociation constant, pK a '. The determination of pK a ' is performed for various ionic strengths, which reveals the thermodynamic acid constant (pK a =7.5) and the number of charge on each chemical species; the yellow form is negatively charged species of -1 and the blue form that of -2. On this chemical information, the quantum chemical calculation is carried out to find that BTB molecules take the pure quinoid form in an acid solution and the quinoid-phenolate form in an alkaline solution. The time-dependent density functional theory (TD-DFT) calculations for the theoretically determined chemical structures account for the peak shift of the electronic spectra. In this manner, the structures of all the chemical species appeared in equilibrium have finally been confirmed. Copyright © 2017 Elsevier B.V. All rights reserved.

Glycomics meets artificial intelligence - Potential of glycan analysis for identification of seropositive and seronegative rheumatoid arthritis patients revealed.

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Chocholova, Erika; Bertok, Tomas; Jane, Eduard; Lorencova, Lenka; Holazova, Alena; Belicka, Ludmila; Belicky, Stefan; Mislovicova, Danica; Vikartovska, Alica; Imrich, Richard; Kasak, Peter; Tkac, Jan

2018-06-01

In this study, one hundred serum samples from healthy people and patients with rheumatoid arthritis (RA) were analyzed. Standard immunoassays for detection of 10 different RA markers and analysis of glycan markers on antibodies in 10 different assay formats with several lectins were applied for each serum sample. A dataset containing 2000 data points was data mined using artificial neural networks (ANN). We identified key RA markers, which can discriminate between healthy people and seropositive RA patients (serum containing autoantibodies) with accuracy of 83.3%. Combination of RA markers with glycan analysis provided much better discrimination accuracy of 92.5%. Immunoassays completely failed to identify seronegative RA patients (serum not containing autoantibodies), while glycan analysis correctly identified 43.8% of these patients. Further, we revealed other critical parameters for successful glycan analysis such as type of a sample, format of analysis and orientation of captured antibodies for glycan analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

Possible causes of quitting smoking among women in Ukraine

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Bondarenko, Ksenia

2011-05-01

Full Text Available BACKGROUND. According to the Global Adult Tobacco Survey completed in 2010 in Ukraine, 28,8% (about 11,5 million of adults aged 15 years and older are current smokers. Among women, prevalence of current smoking is 11,2%, which is considerably less than among men (50%. The goal of the study was to reveal the determinants of quitting smoking among women.METHODS. The sample included 571 women, who were current or former daily smokers. Firstly, the bivariate analysis (cross-tabulation and chi-square test was conducted. Then, the significant determinants from bivariate analysis were included to binary logistic regression. The women’s smoking status (current daily smokers vs. former daily smokers was considered an outcome measure. Independent variables included education, age, occupation, income, religion, marital status, variation in prices for tobacco products, awareness of the negative consequences of smoking, permission to smoke at home, and whether the woman received an advice to quit smoking from a health worker.RESULTS. Bivariate analysis showed that there was statistically significant relationships with age, marital status, occupation, permission to smoke at home, having received information about the dangers of smoking from the radio, newspapers, and other sources. The multivariate analysis demonstrated that the unemployed women and women from households where smoking was banned were more likely to quit smoking. Unmarried women were less likely to quit smoking than married.CONCLUSIONS. Quitting smoking among women was associated with being married, unemployed, and living in a home where smoking is banned. Major limitations of the study are the small sample size and cross-sectional nature of the study; hence, the inerrant conclusions about cause-effect relationships are not possible. So, longitudinal study with larger sample could be a better future option.

Comparative genomic analysis of Brucella abortus vaccine strain 104M reveals a set of candidate genes associated with its virulence attenuation.

Science.gov (United States)

Yu, Dong; Hui, Yiming; Zai, Xiaodong; Xu, Junjie; Liang, Long; Wang, Bingxiang; Yue, Junjie; Li, Shanhu

2015-01-01

The Brucella abortus strain 104M, a spontaneously attenuated strain, has been used as a vaccine strain in humans against brucellosis for 6 decades in China. Despite many studies, the molecular mechanisms that cause the attenuation are still unclear. Here, we determined the whole-genome sequence of 104M and conducted a comprehensive comparative analysis against the whole genome sequences of the virulent strain, A13334, and other reference strains. This analysis revealed a highly similar genome structure between 104M and A13334. The further comparative genomic analysis between 104M and A13334 revealed a set of genes missing in 104M. Some of these genes were identified to be directly or indirectly associated with virulence. Similarly, a set of mutations in the virulence-related genes was also identified, which may be related to virulence alteration. This study provides a set of candidate genes associated with virulence attenuation in B.abortus vaccine strain 104M.

Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network

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Chamovitz Daniel A

2009-09-01

Full Text Available Abstract Background Analyses of gene expression data from microarray experiments has become a central tool for identifying co-regulated, functional gene modules. A crucial aspect of such analysis is the integration of data from different experiments and different laboratories. How to weigh the contribution of different experiments is an important point influencing the final outcomes. We have developed a novel method for this integration, and applied it to genome-wide data from multiple Arabidopsis microarray experiments performed under a variety of experimental conditions. The goal of this study is to identify functional globally co-regulated gene modules in the Arabidopsis genome. Results Following the analysis of 21,000 Arabidopsis genes in 43 datasets and about 2 × 108 gene pairs, we identified a globally co-expressed gene network. We found clusters of globally co-expressed Arabidopsis genes that are enriched for known Gene Ontology annotations. Two types of modules were identified in the regulatory network that differed in their sensitivity to the node-scoring parameter; we further showed these two pertain to general and specialized modules. Some of these modules were further investigated using the Genevestigator compendium of microarray experiments. Analyses of smaller subsets of data lead to the identification of condition-specific modules. Conclusion Our method for identification of gene clusters allows the integration of diverse microarray experiments from many sources. The analysis reveals that part of the Arabidopsis transcriptome is globally co-expressed, and can be further divided into known as well as novel functional gene modules. Our methodology is general enough to apply to any set of microarray experiments, using any scoring function.

Proteome analysis of schizophrenia patients Wernicke's area reveals an energy metabolism dysregulation

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Marangoni Sérgio

2009-04-01

Full Text Available Abstract Background Schizophrenia is likely to be a consequence of DNA alterations that, together with environmental factors, will lead to protein expression differences and the ultimate establishment of the illness. The superior temporal gyrus is implicated in schizophrenia and executes functions such as the processing of speech, language skills and sound processing. Methods We performed an individual comparative proteome analysis using two-dimensional gel electrophoresis of 9 schizophrenia and 6 healthy control patients' left posterior superior temporal gyrus (Wernicke's area – BA22p identifying by mass spectrometry several protein expression alterations that could be related to the disease. Results Our analysis revealed 11 downregulated and 14 upregulated proteins, most of them related to energy metabolism. Whereas many of the identified proteins have been previously implicated in schizophrenia, such as fructose-bisphosphate aldolase C, creatine kinase and neuron-specific enolase, new putative disease markers were also identified such as dihydrolipoyl dehydrogenase, tropomyosin 3, breast cancer metastasis-suppressor 1, heterogeneous nuclear ribonucleoproteins C1/C2 and phosphate carrier protein, mitochondrial precursor. Besides, the differential expression of peroxiredoxin 6 (PRDX6 and glial fibrillary acidic protein (GFAP were confirmed by western blot in schizophrenia prefrontal cortex. Conclusion Our data supports a dysregulation of energy metabolism in schizophrenia as well as suggests new markers that may contribute to a better understanding of this complex disease.

Contrast-enhanced Ultrasound for Detection of Crohn's Disease Activity: Systematic Review and Meta-analysis.

Science.gov (United States)

Serafin, Zbigniew; Białecki, Marcin; Białecka, Agnieszka; Sconfienza, Luca Maria; Kłopocka, Maria

2016-03-01

Reports on imaging of active Crohn's disease (aCD) using contrast-enhanced ultrasound (CEUS) are encouraging. However, the statistical power of most published papers is limited due to the small size of the patient groups included. This study was performed to verify the diagnostic value of CEUS in detecting aCD. A systematic literature search was performed by two independent reviewers for articles on the test characteristics of CEUS for the identification of aCD. The quality of the analysed studies was evaluated using a quality assessment tool for diagnostic accuracy studies (QUADAS-2). Pooling was performed using a diagnostic random-effect model and bivariate analysis. Eight articles were included in the final analysis, with a total of 332 patients. There was no significant publication bias. Significant heterogeneity was found regarding CEUS methodology and sonographic definitions of aCD. In a bivariate analysis, pooled sensitivity was 0.94 (95% CI 0.87-0.97) and pooled specificity was 0.79 (95% CI 0.67-0.88). Spearman correlation statistics presented no significant diagnostic threshold effect (r = 0.12, p > 0.9). Subgroup analysis showed that relative intestine wall enhancement had the highest diagnostic value (area under the curve 94%), while the presence of enhancement and analysis of the slope were less useful (area under the curve 91 and 90%, respectively). CEUS presents good sensitivity and moderate specificity in the detection of the aCD. Large-scale randomized trials with quantitative evaluation of CEUS images are necessary to promote this technique in clinical practice. Copyright © 2015 European Crohn’s and Colitis Organisation (ECCO). Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Proteomic analysis of MG132-treated germinating pollen reveals expression signatures associated with proteasome inhibition.

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Candida Vannini

Full Text Available Chemical inhibition of the proteasome has been previously found to effectively impair pollen germination and tube growth in vitro. However, the mediators of these effects at the molecular level are unknown. By performing 2DE proteomic analysis, 24 differentially expressed protein spots, representing 14 unique candidate proteins, were identified in the pollen of kiwifruit (Actinidia deliciosa germinated in the presence of the MG132 proteasome inhibitor. qPCR analysis revealed that 11 of these proteins are not up-regulated at the mRNA level, but are most likely stabilized by proteasome inhibition. These differentially expressed proteins are predicted to function in various pathways including energy and lipid metabolism, cell wall synthesis, protein synthesis/degradation and stress responses. In line with this evidence, the MG132-induced changes in the proteome were accompanied by an increase in ATP and ROS content and by an alteration in fatty acid composition.

Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles

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Callister, S.J.; Wilkins, M.J.; Nicora, C.D.; Williams, K.H.; Banfield, J.F.; VerBerkmoes, N.C.; Hettich, R.L.; NGuessan, A.L.; Mouser, P.J.; Elifantz, H.; Smith, R.D.; Lovley, D.R.; Lipton, M.S.; Long, P.E.

2010-07-15

Stimulated by an acetate-amendment field experiment conducted in 2007, anaerobic microbial populations in the aquifer at the Rifle Integrated Field Research Challenge site in Colorado reduced mobile U(VI) to insoluble U(IV). During this experiment, planktonic biomass was sampled at various time points to quantitatively evaluate proteomes. In 2008, an acetate-amended field experiment was again conducted in a similar manner to the 2007 experiment. As there was no comprehensive metagenome sequence available for use in proteomics analysis, we systematically evaluated 12 different organism genome sequences to generate sets of aggregate genomes, or “pseudo-metagenomes”, for supplying relative quantitative peptide and protein identifications. Proteomics results support previous observations of the dominance of Geobacteraceae during biostimulation using acetate as sole electron donor, and revealed a shift from an early stage of iron reduction to a late stage of iron reduction. Additionally, a shift from iron reduction to sulfate reduction was indicated by changes in the contribution of proteome information contributed by different organism genome sequences within the aggregate set. In addition, the comparison of proteome measurements made between the 2007 field experiment and 2008 field experiment revealed differences in proteome profiles. These differences may be the result of alterations in abundance and population structure within the planktonic biomass samples collected for analysis.

Systems-level analysis of risk genes reveals the modular nature of schizophrenia.

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Liu, Jiewei; Li, Ming; Luo, Xiong-Jian; Su, Bing

2018-05-19

Schizophrenia (SCZ) is a complex mental disorder with high heritability. Genetic studies (especially recent genome-wide association studies) have identified many risk genes for schizophrenia. However, the physical interactions among the proteins encoded by schizophrenia risk genes remain elusive and it is not known whether the identified risk genes converge on common molecular networks or pathways. Here we systematically investigated the network characteristics of schizophrenia risk genes using the high-confidence protein-protein interactions (PPI) from the human interactome. We found that schizophrenia risk genes encode a densely interconnected PPI network (P = 4.15 × 10 -31 ). Compared with the background genes, the schizophrenia risk genes in the interactome have significantly higher degree (P = 5.39 × 10 -11 ), closeness centrality (P = 7.56 × 10 -11 ), betweeness centrality (P = 1.29 × 10 -11 ), clustering coefficient (P = 2.22 × 10 -2 ), and shorter average shortest path length (P = 7.56 × 10 -11 ). Based on the densely interconnected PPI network, we identified 48 hub genes and 4 modules formed by highly interconnected schizophrenia genes. We showed that the proteins encoded by schizophrenia hub genes have significantly more direct physical interactions. Gene ontology (GO) analysis revealed that cell adhesion, cell cycle, immune system response, and GABR-receptor complex categories were enriched in the modules formed by highly interconnected schizophrenia risk genes. Our study reveals that schizophrenia risk genes encode a densely interconnected molecular network and demonstrates the modular nature of schizophrenia. Copyright © 2018 Elsevier B.V. All rights reserved.

REVEAL: Software Documentation and Platform Migration

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Wilson, Michael A.; Veibell, Victoir T.; Freudinger, Lawrence C.

2008-01-01

The Research Environment for Vehicle Embedded Analysis on Linux (REVEAL) is reconfigurable data acquisition software designed for network-distributed test and measurement applications. In development since 2001, it has been successfully demonstrated in support of a number of actual missions within NASA s Suborbital Science Program. Improvements to software configuration control were needed to properly support both an ongoing transition to operational status and continued evolution of REVEAL capabilities. For this reason the project described in this report targets REVEAL software source documentation and deployment of the software on a small set of hardware platforms different from what is currently used in the baseline system implementation. This report specifically describes the actions taken over a ten week period by two undergraduate student interns and serves as a final report for that internship. The topics discussed include: the documentation of REVEAL source code; the migration of REVEAL to other platforms; and an end-to-end field test that successfully validates the efforts.

Trial sequential analysis reveals insufficient information size and potentially false positive results in many meta-analyses

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Brok, J.; Thorlund, K.; Gluud, C.

2008-01-01

in 80% (insufficient information size). TSA(15%) and TSA(LBHIS) found that 95% and 91% had absence of evidence. The remaining nonsignificant meta-analyses had evidence of lack of effect. CONCLUSION: TSA reveals insufficient information size and potentially false positive results in many meta......OBJECTIVES: To evaluate meta-analyses with trial sequential analysis (TSA). TSA adjusts for random error risk and provides the required number of participants (information size) in a meta-analysis. Meta-analyses not reaching information size are analyzed with trial sequential monitoring boundaries...... analogous to interim monitoring boundaries in a single trial. STUDY DESIGN AND SETTING: We applied TSA on meta-analyses performed in Cochrane Neonatal reviews. We calculated information sizes and monitoring boundaries with three different anticipated intervention effects of 30% relative risk reduction (TSA...

Proteomic analysis of three gonad types of swamp eel reveals genes differentially expressed during sex reversal.

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Sheng, Yue; Zhao, Wei; Song, Ying; Li, Zhigang; Luo, Majing; Lei, Quan; Cheng, Hanhua; Zhou, Rongjia

2015-05-18

A variety of mechanisms are engaged in sex determination in vertebrates. The teleost fish swamp eel undergoes sex reversal naturally and is an ideal model for vertebrate sexual development. However, the importance of proteome-wide scanning for gonad reversal was not previously determined. We report a 2-D electrophoresis analysis of three gonad types of proteomes during sex reversal. MS/MS analysis revealed a group of differentially expressed proteins during ovary to ovotestis to testis transformation. Cbx3 is up-regulated during gonad reversal and is likely to have a role in spermatogenesis. Rab37 is down-regulated during the reversal and is mainly associated with oogenesis. Both Cbx3 and Rab37 are linked up in a protein network. These datasets in gonadal proteomes provide a new resource for further studies in gonadal development.

What is associated with race performance in male 100-km ultra-marathoners--anthropometry, training or marathon best time?

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Knechtle, Beat; Knechtle, Patrizia; Rosemann, Thomas; Senn, Oliver

2011-03-01

We investigated the associations of anthropometry, training, and pre-race experience with race time in 93 recreational male ultra-marathoners (mean age 44.6 years, s = 10.0; body mass 74.0 kg, s = 9.0; height 1.77 m, s = 0.06; body mass index 23.4 kg · m(-2), s = 2.0) in a 100-km ultra-marathon using bivariate and multivariate analysis. In the bivariate analysis, body mass index (r = 0.24), the sum of eight skinfolds (r = 0.55), percent body fat (r = 0.57), weekly running hours (r = -0.29), weekly running kilometres (r = -0.49), running speed during training (r = -0.50), and personal best time in a marathon (r = 0.72) were associated with race time. Results of the multiple regression analysis revealed an independent and negative association of weekly running kilometres and average speed in training with race time, as well as a significant positive association between the sum of eight skinfold thicknesses and race time. There was a significant positive association between 100-km race time and personal best time in a marathon. We conclude that both training and anthropometry were independently associated with race performance. These characteristics remained relevant even when controlling for personal best time in a marathon.

Comparative genome analysis of Megasphaera sp. reveals niche specialization and its potential role in the human gut.

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Sudarshan Anand Shetty

Full Text Available With increasing number of novel bacteria being isolated from the human gut ecosystem, there is a greater need to study their role in the gut ecosystem and their effect on the host health. In the present study, we carried out in silico genome-wide analysis of two novel Megasphaera sp. isolates NM10 (DSM25563 and BL7 (DSM25562, isolated from feces of two healthy individuals and validated the key features by in vitro studies. The analysis revealed the general metabolic potential, adaptive features and the potential effects of these isolates on the host. The comparative genome analysis of the two human gut isolates NM10 and BL7 with ruminal isolate Megasphaera elsdenii (DSM20460 highlighted the differential adaptive features for their survival in human gut. The key findings include features like bile resistance, presence of various sensory and regulatory systems, stress response systems, membrane transporters and resistance to antibiotics. Comparison of the "glycobiome" based on the genomes of the ruminal isolate with the human gut isolates NM10 and BL revealed the presence of diverse and unique sets of Carbohydrate-Active enzymes (CAZymes amongst these isolates, with a higher collection of CAZymes in the human gut isolates. This could be attributed to the difference in host diet and thereby the environment, consequently suggesting host specific adaptation in these isolates. In silico analysis of metabolic potential predicted the ability of these isolates to produce important metabolites like short chain fatty acids (butyrate, acetate, formate, and caproate, vitamins and essential amino acids, which was further validated by in vitro experiments. The ability of these isolates to produce important metabolites advocates for a potential healthy influence on the host. Further in vivo studies including transcriptomic and proteomic analysis will be required for better understanding the role and impact of these Megasphaera sp. isolates NM10 and BL7 on the

Gene expression analysis of zebrafish melanocytes, iridophores, and retinal pigmented epithelium reveals indicators of biological function and developmental origin.

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Charles W Higdon

Full Text Available In order to facilitate understanding of pigment cell biology, we developed a method to concomitantly purify melanocytes, iridophores, and retinal pigmented epithelium from zebrafish, and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co-enrichment in melanocytes and retinal pigmented epithelium, as well as in melanocytes and iridophores. We found 214 genes co-enriched in melanocytes and retinal pigmented epithelium, indicating the shared functions of melanin-producing cells. We found 62 genes significantly co-enriched in melanocytes and iridophores, illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine-based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate-limiting substrate for purine synthesis, phosphoribosyl pyrophosphate, thus constituting a guanine cycle. The purification procedure and expression analysis described here, along with the accompanying transcriptome-wide expression data, provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types, and will be a useful resource for further studies of pigment cell biology.

Meta-Analysis of Public Microarray Datasets Reveals Voltage-Gated Calcium Gene Signatures in Clinical Cancer Patients.

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Chih-Yang Wang

Full Text Available Voltage-gated calcium channels (VGCCs are well documented to play roles in cell proliferation, migration, and apoptosis; however, whether VGCCs regulate the onset and progression of cancer is still under investigation. The VGCC family consists of five members, which are L-type, N-type, T-type, R-type and P/Q type. To date, no holistic approach has been used to screen VGCC family genes in different types of cancer. We analyzed the transcript expression of VGCCs in clinical cancer tissue samples by accessing ONCOMINE (www.oncomine.org, a web-based microarray database, to perform a systematic analysis. Every member of the VGCCs was examined across 21 different types of cancer by comparing mRNA expression in cancer to that in normal tissue. A previous study showed that altered expression of mRNA in cancer tissue may play an oncogenic role and promote tumor development; therefore, in the present findings, we focus only on the overexpression of VGCCs in different types of cancer. This bioinformatics analysis revealed that different subtypes of VGCCs (CACNA1C, CACNA1D, CACNA1B, CACNA1G, and CACNA1I are implicated in the development and progression of diverse types of cancer and show dramatic up-regulation in breast cancer. CACNA1F only showed high expression in testis cancer, whereas CACNA1A, CACNA1C, and CACNA1D were highly expressed in most types of cancer. The current analysis revealed that specific VGCCs likely play essential roles in specific types of cancer. Collectively, we identified several VGCC targets and classified them according to different cancer subtypes for prospective studies on the underlying carcinogenic mechanisms. The present findings suggest that VGCCs are possible targets for prospective investigation in cancer treatment.

Probabilistic Fracture Mechanics Analysis of the Orbiter's LH2 Feedline Flowliner

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Bonacuse, Peter J. (Technical Monitor); Hudak, Stephen J., Jr.; Huyse, Luc; Chell, Graham; Lee, Yi-Der; Riha, David S.; Thacker, Ben; McClung, Craig; Gardner, Brian; Leverant, Gerald R.;

Integrated bioinformatics analysis reveals key candidate genes and pathways in breast cancer.

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Wang, Yuzhi; Zhang, Yi; Huang, Qian; Li, Chengwen

2018-04-19

Breast cancer (BC) is the leading malignancy in women worldwide, yet relatively little is known about the genes and signaling pathways involved in BC tumorigenesis and progression. The present study aimed to elucidate potential key candidate genes and pathways in BC. Five gene expression profile data sets (GSE22035, GSE3744, GSE5764, GSE21422 and GSE26910) were downloaded from the Gene Expression Omnibus (GEO) database, which included data from 113 tumorous and 38 adjacent non‑tumorous tissue samples. Differentially expressed genes (DEGs) were identified using t‑tests in the limma R package. These DEGs were subsequently investigated by pathway enrichment analysis and a protein‑protein interaction (PPI) network was constructed. The most significant module from the PPI network was selected for pathway enrichment analysis. In total, 227 DEGs were identified, of which 82 were upregulated and 145 were downregulated. Pathway enrichment analysis results revealed that the upregulated DEGs were mainly enriched in 'cell division', the 'proteinaceous extracellular matrix (ECM)', 'ECM structural constituents' and 'ECM‑receptor interaction', whereas downregulated genes were mainly enriched in 'response to drugs', 'extracellular space', 'transcriptional activator activity' and the 'peroxisome proliferator‑activated receptor signaling pathway'. The PPI network contained 174 nodes and 1,257 edges. DNA topoisomerase 2‑a, baculoviral inhibitor of apoptosis repeat‑containing protein 5, cyclin‑dependent kinase 1, G2/mitotic‑specific cyclin‑B1 and kinetochore protein NDC80 homolog were identified as the top 5 hub genes. Furthermore, the genes in the most significant module were predominantly involved in 'mitotic nuclear division', 'mid‑body', 'protein binding' and 'cell cycle'. In conclusion, the DEGs, relative pathways and hub genes identified in the present study may aid in understanding of the molecular mechanisms underlying BC progression and provide

Bioinformatics analysis of RNA-seq data revealed critical genes in colon adenocarcinoma.

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Xi, W-D; Liu, Y-J; Sun, X-B; Shan, J; Yi, L; Zhang, T-T

2017-07-01

RNA-seq data of colon adenocarcinoma (COAD) were analyzed with bioinformatics tools to discover critical genes in the disease. Relevant small molecule drugs, transcription factors (TFs) and microRNAs (miRNAs) were also investigated. RNA-seq data of COAD were downloaded from The Cancer Genome Atlas (TCGA). Differential analysis was performed with package edgeR. False positive discovery (FDR) 1 were set as the cut-offs to screen out differentially expressed genes (DEGs). Gene coexpression network was constructed with package Ebcoexpress. GO enrichment analysis was performed for the DEGs in the gene coexpression network with DAVID. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was also performed for the genes with KOBASS 2.0. Modules were identified with MCODE of Cytoscape. Relevant small molecules drugs were predicted by Connectivity map. Relevant miRNAs and TFs were searched by WebGestalt. A total of 457 DEGs, including 255 up-regulated and 202 down-regulated genes, were identified from 437 COAD and 39 control samples. A gene coexpression network was constructed containing 40 DEGs and 101 edges. The genes were mainly associated with collagen fibril organization, extracellular matrix organization and translation. Two modules were identified from the gene coexpression network, which were implicated in muscle contraction and extracellular matrix organization, respectively. Several critical genes were disclosed, such as MYH11, COL5A2 and ribosomal proteins. Nine relevant small molecule drugs were identified, such as scriptaid and STOCK1N-35874. Accordingly, a total of 17 TFs and 10 miRNAs related to COAD were acquired, such as ETS2, NFAT, AP4, miR-124A, MiR-9, miR-96 and let-7. Several critical genes and relevant drugs, TFs and miRNAs were revealed in COAD. These findings could advance the understanding of the disease and benefit therapy development.

Bivariate Correlation Analysis of the Chemometric Profiles of Chinese Wild Salvia miltiorrhiza Based on UPLC-Qqq-MS and Antioxidant Activities

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Xiaodan Zhang

2018-02-01

Full Text Available To better understand the mechanisms underlying the pharmacological actions of Salvia miltiorrhiza, correlation between the chemical profiles and in vitro antioxidant activities in 50 batches of wild S. miltiorrhiza samples was analyzed. Our ultra-performance liquid chromatography–tandem mass spectrometry analysis detected twelve phenolic acids and five tanshinones and obtained various chemical profiles from different origins. In a principal component analysis (PCA and cluster analysis, the tanshinones cryptotanshinone, tanshinone IIA and dihydrotanshinone I exhibited higher weights in PC1, whereas the phenolic acids danshensu, salvianolic acids A and B and lithospermic acid were highly loaded in PC2. All components could be optimized as markers of different locations and might be suitable for S. miltiorrhiza quality analyses. Additionally, the DPPH and ABTS assays used to comprehensively evaluate antioxidant activities indicated large variations, with mean DPPH and ABTS scavenging potencies of 32.24 and 23.39 μg/mL, respectively, among S. miltiorrhiza extract solutions. Notably, samples that exceeded the mean IC50 values had higher phenolic acid contents. A correlation analysis indicated a strong correlation between the antioxidant activities and phenolic acid contents. Caffeic acid, danshensu, rosmarinic acid, lithospermic acid and salvianolic acid B were major contributors to antioxidant activity. In conclusion, phenolic compounds were the predominant antioxidant components in the investigated plant species. These plants may be sources of potent natural antioxidants and beneficial chemopreventive agents.

Role of Surgical Services in Profitability of Hospitals in California: An Analysis of Office of Statewide Health Planning and Development Annual Financial Data.

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Moazzez, Ashkan; de Virgilio, Christian

2016-10-01

With constant changes in health-care laws and payment methods, profitability, and financial sustainability of hospitals are of utmost importance. The purpose of this study is to determine the relationship between surgical services and hospital profitability. The Office of Statewide Health Planning and Development annual financial databases for the years 2009 to 2011 were used for this study. The hospitals' characteristics and income statement elements were extracted for statistical analysis using bivariate and multivariate linear regression. A total of 989 financial records of 339 hospitals were included. On bivariate analysis, the number of inpatient and ambulatory operating rooms (ORs), the number of cases done both as inpatient and outpatient in each OR, and the average minutes used in inpatient ORs were significantly related with the net income of the hospital. On multivariate regression analysis, when controlling for hospitals' payer mix and the study year, only the number of inpatient cases done in the inpatient ORs (β = 832, P = 0.037), and the number of ambulatory ORs (β = 1,485, 466, P = 0.001) were significantly related with the net income of the hospital. These findings suggest that hospitals can maximize their profitability by diverting and allocating outpatient surgeries to ambulatory ORs, to allow for more inpatient surgeries.

Sensitivity of human auditory cortex to rapid frequency modulation revealed by multivariate representational similarity analysis.

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Joanisse, Marc F; DeSouza, Diedre D

2014-01-01

Functional Magnetic Resonance Imaging (fMRI) was used to investigate the extent, magnitude, and pattern of brain activity in response to rapid frequency-modulated sounds. We examined this by manipulating the direction (rise vs. fall) and the rate (fast vs. slow) of the apparent pitch of iterated rippled noise (IRN) bursts. Acoustic parameters were selected to capture features used in phoneme contrasts, however the stimuli themselves were not perceived as speech per se. Participants were scanned as they passively listened to sounds in an event-related paradigm. Univariate analyses revealed a greater level and extent of activation in bilateral auditory cortex in response to frequency-modulated sweeps compared to steady-state sounds. This effect was stronger in the left hemisphere. However, no regions showed selectivity for either rate or direction of frequency modulation. In contrast, multivoxel pattern analysis (MVPA) revealed feature-specific encoding for direction of modulation in auditory cortex bilaterally. Moreover, this effect was strongest when analyses were restricted to anatomical regions lying outside Heschl's gyrus. We found no support for feature-specific encoding of frequency modulation rate. Differential findings of modulation rate and direction of modulation are discussed with respect to their relevance to phonetic discrimination.

Comparative Analysis of 35 Basidiomycete Genomes Reveals Diversity and Uniqueness of the Phylum

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Riley, Robert; Salamov, Asaf; Otillar, Robert; Fagnan, Kirsten; Boussau, Bastien; Brown, Daren; Henrissat, Bernard; Levasseur, Anthony; Held, Benjamin; Nagy, Laszlo; Floudas, Dimitris; Morin, Emmanuelle; Manning, Gerard; Baker, Scott; Martin, Francis; Blanchette, Robert; Hibbett, David; Grigoriev, Igor V.

2013-03-11

Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprobes including wood decaying fungi. To better understand the diversity of this phylum we compared the genomes of 35 basidiomycete fungi including 6 newly sequenced genomes. The genomes of basidiomycetes span extremes of genome size, gene number, and repeat content. A phylogenetic tree of Basidiomycota was generated using the Phyldog software, which uses all available protein sequence data to simultaneously infer gene and species trees. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) comprising proteins found in only one organism. Phylogenetic patterns of plant biomass-degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay among the members of Agaricomycotina subphylum. There is a correlation of the profile of certain gene families to nutritional mode in Agaricomycotina. Based on phylogenetically-informed PCA analysis of such profiles, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has liginolytic class II fungal peroxidases. Furthermore, we find that both fungi exhibit wood decay with white rot-like characteristics in growth assays. Analysis of the rate of discovery of proteins with no or few homologs suggests the high value of continued sequencing of basidiomycete fungi.

Analisis Faktor Permintaan Non Fungsional Kelompok Non-Member Terhadap Permintaan (Seri 2

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Iskandar Putong

2011-11-01

Full Text Available Factor analysis of non functional Demand Non-Member On to Demand aimed to discover whether there is significant influence of non-functional variable on demand. Three independent variables (the effect, ie, X1 for Snob Effect (Mode, X2 for the Bandwagon effect (Prestige and X3 for the Veblen Effect (Show-off and 1 dependent variable Y for Demand. The number of respondents of 50 and 22 indicators is statistically valid. Analysis tool using the Model Correlation and simple Regression (Simple/Bivariate, Correlation and Regression Simultaneously (Multiple Regression and Partial Correlation. The results of analysis proved statistically with LOC of 95%, indicating that the bivariate, partial unison and Simultaneously there is positive and significant correlation between variables X to Y, except for variable X2 (Prestige on Bivariate correlation. 

A Systems-Level Analysis Reveals Circadian Regulation of Splicing in Colorectal Cancer.

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El-Athman, Rukeia; Fuhr, Luise; Relógio, Angela

2018-06-20

Accumulating evidence points to a significant role of the circadian clock in the regulation of splicing in various organisms, including mammals. Both dysregulated circadian rhythms and aberrant pre-mRNA splicing are frequently implicated in human disease, in particular in cancer. To investigate the role of the circadian clock in the regulation of splicing in a cancer progression context at the systems-level, we conducted a genome-wide analysis and compared the rhythmic transcriptional profiles of colon carcinoma cell lines SW480 and SW620, derived from primary and metastatic sites of the same patient, respectively. We identified spliceosome components and splicing factors with cell-specific circadian expression patterns including SRSF1, HNRNPLL, ESRP1, and RBM 8A, as well as altered alternative splicing events and circadian alternative splicing patterns of output genes (e.g., VEGFA, NCAM1, FGFR2, CD44) in our cellular model. Our data reveals a remarkable interplay between the circadian clock and pre-mRNA splicing with putative consequences in tumor progression and metastasis. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Transcriptomic analysis reveals ethylene as stimulator and auxin as regulator of adventitious root formation in petunia cuttings

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Druege, Uwe; Franken, Philipp; Lischewski, Sandra; Ahkami, Amir H.; Zerche, Siegfried; Hause, Bettina; Hajirezaei, Mohammad R.

2014-01-01

Adventitious root (AR) formation in the stem base of cuttings is the basis for propagation of many plant species and petunia is used as model to study this developmental process. Following AR formation from 2 to 192 hours after excision (hpe) of cuttings, transcriptome analysis by microarray revealed a change of the character of the rooting zone from stem base to root identity. The greatest shift in the number of differentially expressed genes was observed between 24 and 72 hpe, when the cate...

Life satisfaction and perceived stress among young offenders in a residential therapeutic community: Latent change score analysis.

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Tang, Kristen N S; Chan, Christian S

2017-06-01

Recent rehabilitation frameworks underscore the importance of strength-based interventions for young offenders who may lack internal and external resources to manage their stress and plan for their life. This multi-wave longitudinal study investigated the dynamic relationship between perceived stress and life satisfaction among a group of young ex-offenders in a residential therapeutic community. Four waves of data were collected from 117 Hong Kong youths (24.0% female, mean age = 17.7) over one year. Latent change score analysis was employed to examine the univairate and bivariate changes of their perceived stress and life satisfaction. Results suggest a positive growth trajectory in life satisfaction over time. The results of perceived stress were less conclusive. Bivariate models indicated that the previous level of life satisfaction was negatively linked to the subsequent perceived stress level but not vice versa. The findings suggest that improvement in life satisfaction may reduce perceived stress in young ex-offenders. Copyright © 2017 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

Statistics and analysis of scientific data

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Bonamente, Massimiliano

2017-01-01

The revised second edition of this textbook provides the reader with a solid foundation in probability theory and statistics as applied to the physical sciences, engineering and related fields. It covers a broad range of numerical and analytical methods that are essential for the correct analysis of scientific data, including probability theory, distribution functions of statistics, fits to two-dimensional data and parameter estimation, Monte Carlo methods and Markov chains. Features new to this edition include: • a discussion of statistical techniques employed in business science, such as multiple regression analysis of multivariate datasets. • a new chapter on the various measures of the mean including logarithmic averages. • new chapters on systematic errors and intrinsic scatter, and on the fitting of data with bivariate errors. • a new case study and additional worked examples. • mathematical derivations and theoretical background material have been appropriately marked,to improve the readabili...

Decision Making and Revealed Preference

DEFF Research Database (Denmark)

de la Rosa, Leonidas Enrique

If our decision-making processes are to some extent shaped by evolutionary pressures and our environment is different from that to which we adapted, some of our choices will not be in our best interest. But revealed preference is the only tool that we have so far to conduct a normative analysis...

VNTR analysis reveals unexpected genetic diversity within Mycoplasma agalactiae, the main causative agent of contagious agalactia

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Ayling Roger D

2008-11-01

Full Text Available Abstract Background Mycoplasma agalactiae is the main cause of contagious agalactia, a serious disease of sheep and goats, which has major clinical and economic impacts. Previous studies of M. agalactiae have shown it to be unusually homogeneous and there are currently no available epidemiological techniques which enable a high degree of strain differentiation. Results We have developed variable number tandem repeat (VNTR analysis using the sequenced genome of the M. agalactiae type strain PG2. The PG2 genome was found to be replete with tandem repeat sequences and 4 were chosen for further analysis. VNTR 5 was located within the hypothetical protein MAG6170 a predicted lipoprotein. VNTR 14 was intergenic between the hypothetical protein MAG3350 and the hypothetical protein MAG3340. VNTR 17 was intergenic between the hypothetical protein MAG4060 and the hypothetical protein MAG4070 and VNTR 19 spanned the 5' end of the pseudogene for a lipoprotein MAG4310 and the 3' end of the hypothetical lipoprotein MAG4320. We have investigated the genetic diversity of 88 M. agalactiae isolates of wide geographic origin using VNTR analysis and compared it with pulsed field gel electrophoresis (PFGE and random amplified polymorphic DNA (RAPD analysis. Simpson's index of diversity was calculated to be 0.324 for PFGE and 0.574 for VNTR analysis. VNTR analysis revealed unexpected diversity within M. agalactiae with 9 different VNTR types discovered. Some correlation was found between geographical origin and the VNTR type of the isolates. Conclusion VNTR analysis represents a useful, rapid first-line test for use in molecular epidemiological analysis of M. agalactiae for outbreak tracing and control.

Phylogenetic diversity and genotypical complexity of H9N2 influenza A viruses revealed by genomic sequence analysis.

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Guoying Dong

Full Text Available H9N2 influenza A viruses have become established worldwide in terrestrial poultry and wild birds, and are occasionally transmitted to mammals including humans and pigs. To comprehensively elucidate the genetic and evolutionary characteristics of H9N2 influenza viruses, we performed a large-scale sequence analysis of 571 viral genomes from the NCBI Influenza Virus Resource Database, representing the spectrum of H9N2 influenza viruses isolated from 1966 to 2009. Our study provides a panoramic framework for better understanding the genesis and evolution of H9N2 influenza viruses, and for describing the history of H9N2 viruses circulating in diverse hosts. Panorama phylogenetic analysis of the eight viral gene segments revealed the complexity and diversity of H9N2 influenza viruses. The 571 H9N2 viral genomes were classified into 74 separate lineages, which had marked host and geographical differences in phylogeny. Panorama genotypical analysis also revealed that H9N2 viruses include at least 98 genotypes, which were further divided according to their HA lineages into seven series (A-G. Phylogenetic analysis of the internal genes showed that H9N2 viruses are closely related to H3, H4, H5, H7, H10, and H14 subtype influenza viruses. Our results indicate that H9N2 viruses have undergone extensive reassortments to generate multiple reassortants and genotypes, suggesting that the continued circulation of multiple genotypical H9N2 viruses throughout the world in diverse hosts has the potential to cause future influenza outbreaks in poultry and epidemics in humans. We propose a nomenclature system for identifying and unifying all lineages and genotypes of H9N2 influenza viruses in order to facilitate international communication on the evolution, ecology and epidemiology of H9N2 influenza viruses.

Transcriptional regulation of rod photoreceptor homeostasis revealed by in vivo NRL targetome analysis.

Directory of Open Access Journals (Sweden)

Hong Hao

Full Text Available A stringent control of homeostasis is critical for functional maintenance and survival of neurons. In the mammalian retina, the basic motif leucine zipper transcription factor NRL determines rod versus cone photoreceptor cell fate and activates the expression of many rod-specific genes. Here, we report an integrated analysis of NRL-centered gene regulatory network by coupling chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq data from Illumina and ABI platforms with global expression profiling and in vivo knockdown studies. We identified approximately 300 direct NRL target genes. Of these, 22 NRL targets are associated with human retinal dystrophies, whereas 95 mapped to regions of as yet uncloned retinal disease loci. In silico analysis of NRL ChIP-Seq peak sequences revealed an enrichment of distinct sets of transcription factor binding sites. Specifically, we discovered that genes involved in photoreceptor function include binding sites for both NRL and homeodomain protein CRX. Evaluation of 26 ChIP-Seq regions validated their enhancer functions in reporter assays. In vivo knockdown of 16 NRL target genes resulted in death or abnormal morphology of rod photoreceptors, suggesting their importance in maintaining retinal function. We also identified histone demethylase Kdm5b as a novel secondary node in NRL transcriptional hierarchy. Exon array analysis of flow-sorted photoreceptors in which Kdm5b was knocked down by shRNA indicated its role in regulating rod-expressed genes. Our studies identify candidate genes for retinal dystrophies, define cis-regulatory module(s for photoreceptor-expressed genes and provide a framework for decoding transcriptional regulatory networks that dictate rod homeostasis.

Salmon louse (Lepeophtheirus salmonis transcriptomes during post molting maturation and egg production, revealed using EST-sequencing and microarray analysis

Directory of Open Access Journals (Sweden)

Jonassen Inge

2008-03-01

Full Text Available Abstract Background Lepeophtheirus salmonis is an ectoparasitic copepod feeding on skin, mucus and blood from salmonid hosts. Initial analysis of EST sequences from pre adult and adult stages of L. salmonis revealed a large proportion of novel transcripts. In order to link unknown transcripts to biological functions we have combined EST sequencing and microarray analysis to characterize female salmon louse transcriptomes during post molting maturation and egg production. Results EST sequence analysis shows that 43% of the ESTs have no significant hits in GenBank. Sequenced ESTs assembled into 556 contigs and 1614 singletons and whenever homologous genes were identified no clear correlation with homologous genes from any specific animal group was evident. Sequence comparison of 27 L. salmonis proteins with homologous proteins in humans, zebrafish, insects and crustaceans revealed an almost identical sequence identity with all species. Microarray analysis of maturing female adult salmon lice revealed two major transcription patterns; up-regulation during the final molting followed by down regulation and female specific up regulation during post molting growth and egg production. For a third minor group of ESTs transcription decreased during molting from pre-adult II to immature adults. Genes regulated during molting typically gave hits with cuticula proteins whilst transcripts up regulated during post molting growth were female specific, including two vitellogenins. Conclusion The copepod L.salmonis contains high a level of novel genes. Among analyzed L.salmonis proteins, sequence identities with homologous proteins in crustaceans are no higher than to homologous proteins in humans. Three distinct processes, molting, post molting growth and egg production correlate with transcriptional regulation of three groups of transcripts; two including genes related to growth, one including genes related to egg production. The function of the regulated

Camelid genomes reveal evolution and adaptation to desert environments.

Science.gov (United States)

Wu, Huiguang; Guang, Xuanmin; Al-Fageeh, Mohamed B; Cao, Junwei; Pan, Shengkai; Zhou, Huanmin; Zhang, Li; Abutarboush, Mohammed H; Xing, Yanping; Xie, Zhiyuan; Alshanqeeti, Ali S; Zhang, Yanru; Yao, Qiulin; Al-Shomrani, Badr M; Zhang, Dong; Li, Jiang; Manee, Manee M; Yang, Zili; Yang, Linfeng; Liu, Yiyi; Zhang, Jilin; Altammami, Musaad A; Wang, Shenyuan; Yu, Lili; Zhang, Wenbin; Liu, Sanyang; Ba, La; Liu, Chunxia; Yang, Xukui; Meng, Fanhua; Wang, Shaowei; Li, Lu; Li, Erli; Li, Xueqiong; Wu, Kaifeng; Zhang, Shu; Wang, Junyi; Yin, Ye; Yang, Huanming; Al-Swailem, Abdulaziz M; Wang, Jun

2014-10-21

Bactrian camel (Camelus bactrianus), dromedary (Camelus dromedarius) and alpaca (Vicugna pacos) are economically important livestock. Although the Bactrian camel and dromedary are large, typically arid-desert-adapted mammals, alpacas are adapted to plateaus. Here we present high-quality genome sequences of these three species. Our analysis reveals the demographic history of these species since the Tortonian Stage of the Miocene and uncovers a striking correlation between large fluctuations in population size and geological time boundaries. Comparative genomic analysis reveals complex features related to desert adaptations, including fat and water metabolism, stress responses to heat, aridity, intense ultraviolet radiation and choking dust. Transcriptomic analysis of Bactrian camels further reveals unique osmoregulation, osmoprotection and compensatory mechanisms for water reservation underpinned by high blood glucose levels. We hypothesize that these physiological mechanisms represent kidney evolutionary adaptations to the desert environment. This study advances our understanding of camelid evolution and the adaptation of camels to arid-desert environments.

Expression analysis revealing destabilizing mutations in phosphomannomutase 2 deficiency (PMM2-CDG): expression analysis of PMM2-CDG mutations.

Science.gov (United States)

Vega, Ana Isabel; Pérez-Cerdá, Celia; Abia, David; Gámez, Alejandra; Briones, Paz; Artuch, Rafael; Desviat, Lourdes R; Ugarte, Magdalena; Pérez, Belén

2011-08-01

Deficiency of phosphomannomutase (PMM2, MIM#601785) is the most common congenital disorder of glycosylation. Herein we report the genetic analysis of 22 Spanish PMM2 deficient patients and the functional analysis of 14 nucleotide changes in a prokaryotic expression system in order to elucidate their molecular pathogenesis. PMM2 activity assay revealed the presence of six protein changes with no enzymatic activities (p.R123Q, p.R141H, p.F157S, p.P184T, p.F207S and p.D209G) and seven mild protein changes with residual activities ranging from 16 to 54% (p.L32R, p.V44A p.D65Y, p.P113L p.T118S, p.T237M and p.C241S) and also one variant change with normal activity (p.E197A). The results obtained from Western blot analysis, degradation time courses of 11 protein changes and structural analysis of the PMM2 protein, suggest that the loss-of-function of most mutant proteins is based on their increased susceptibility to degradation or aggregation compared to the wild type protein, considering PMM2 deficiency as a conformational disease. We have identified exclusively catalytic protein change (p.D209G), catalytic protein changes affecting protein stability (p.R123Q and p.R141H), two protein changes disrupting the dimer interface (p.P113L and p.T118S) and several misfolding changes (p.L32R, p.V44A, p.D65Y, p.F157S, p.P184T, p.F207S, p.T237M and p.C241S). Our current work opens a promising therapeutic option using pharmacological chaperones to revert the effect of the characterized misfolding mutations identified in a wide range of PMM2 deficient patients.

Comparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853

KAUST Repository

Cao, Huiluo

2017-06-12

Pseudomonas aeruginosa ATCC 27853 was isolated from a hospital blood specimen in 1971 and has been widely used as a model strain to survey antibiotics susceptibilities, biofilm development, and metabolic activities of Pseudomonas spp.. Although four draft genomes of P. aeruginosa ATCC 27853 have been sequenced, the complete genome of this strain is still lacking, hindering a comprehensive understanding of its physiology and functional genome.Here we sequenced and assembled the complete genome of P. aeruginosa ATCC 27853 using the Pacific Biosciences SMRT (PacBio) technology and Illumina sequencing platform. We found that accessory genes of ATCC 27853 including prophages and genomic islands (GIs) mainly contribute to the difference between P. aeruginosa ATCC 27853 and other P. aeruginosa strains. Seven prophages were identified within the genome of P. aeruginosa ATCC 27853. Of the predicted 25 GIs, three contain genes that encode monoxoygenases, dioxygenases and hydrolases that could be involved in the metabolism of aromatic compounds. Surveying virulence-related genes revealed that a series of genes that encode the B-band O-antigen of LPS are lacking in ATCC 27853. Distinctive SNPs in genes of cellular adhesion proteins such as type IV pili and flagella biosynthesis were also observed in this strain. Colony morphology analysis confirmed an enhanced biofilm formation capability of ATCC 27853 on solid agar surface compared to Pseudomonas aeruginosa PAO1. We then performed transcriptome analysis of ATCC 27853 and PAO1 using RNA-seq and compared the expression of orthologous genes to understand the functional genome and the genomic details underlying the distinctive colony morphogenesis. These analyses revealed an increased expression of genes involved in cellular adhesion and biofilm maturation such as type IV pili, exopolysaccharide and electron transport chain components in ATCC 27853 compared with PAO1. In addition, distinctive expression profiles of the

MDCT linear and volumetric analysis of adrenal glands: Normative data and multiparametric assessment

International Nuclear Information System (INIS)

Carsin-Vu, Aline; Mule, Sebastien; Janvier, Annaelle; Hoeffel, Christine; Oubaya, Nadia; Delemer, Brigitte; Soyer, Philippe

2016-01-01

To study linear and volumetric adrenal measurements, their reproducibility, and correlations between total adrenal volume (TAV) and adrenal micronodularity, age, gender, body mass index (BMI), visceral (VAAT) and subcutaneous adipose tissue volume (SAAT), presence of diabetes, chronic alcoholic abuse and chronic inflammatory disease (CID). We included 154 patients (M/F, 65/89; mean age, 57 years) undergoing abdominal multidetector row computed tomography (MDCT). Two radiologists prospectively independently performed adrenal linear and volumetric measurements with semi-automatic software. Inter-observer reliability was studied using inter-observer correlation coefficient (ICC). Relationships between TAV and associated factors were studied using bivariate and multivariable analysis. Mean TAV was 8.4 ± 2.7 cm 3 (3.3-18.7 cm 3 ). ICC was excellent for TAV (0.97; 95 % CI: 0.96-0.98) and moderate to good for linear measurements. TAV was significantly greater in men (p < 0.0001), alcoholics (p = 0.04), diabetics (p = 0.0003) and those with micronodular glands (p = 0.001). TAV was lower in CID patients (p = 0.0001). TAV correlated positively with VAAT (r = 0.53, p < 0.0001), BMI (r = 0.42, p < 0.0001), SAAT (r = 0.29, p = 0.0003) and age (r = 0.23, p = 0.005). Multivariable analysis revealed gender, micronodularity, diabetes, age and BMI as independent factors influencing TAV. Adrenal gland MDCT-based volumetric measurements are more reproducible than linear measurements. Gender, micronodularity, age, BMI and diabetes independently influence TAV. (orig.)

"Cooperative collapse" of the denatured state revealed through Clausius-Clapeyron analysis of protein denaturation phase diagrams.

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Tischer, Alexander; Machha, Venkata R; Rösgen, Jörg; Auton, Matthew

2018-02-19

Protein phase diagrams have a unique potential to identify the presence of additional thermodynamic states even when non-2-state character is not readily apparent from the experimental observables used to follow protein unfolding transitions. Two-state analysis of the von Willebrand factor A3 domain has previously revealed a discrepancy in the calorimetric enthalpy obtained from thermal unfolding transitions as compared with Gibbs-Helmholtz analysis of free energies obtained from the Linear Extrapolation Method (Tischer and Auton, Prot Sci 2013; 22(9):1147-60). We resolve this thermodynamic conundrum using a Clausius-Clapeyron analysis of the urea-temperature phase diagram that defines how ΔH and the urea m-value interconvert through the slope of c m versus T, (∂cm/∂T)=ΔH/(mT). This relationship permits the calculation of ΔH at low temperature from m-values obtained through iso-thermal urea denaturation and high temperature m-values from ΔH obtained through iso-urea thermal denaturation. Application of this equation uncovers sigmoid transitions in both cooperativity parameters as temperature is increased. Such residual thermal cooperativity of ΔH and the m-value confirms the presence of an additional state which is verified to result from a cooperative phase transition between urea-expanded and thermally-compact denatured states. Comparison of the equilibria between expanded and compact denatured ensembles of disulfide-intact and carboxyamidated A3 domains reveals that introducing a single disulfide crosslink does not affect the presence of the additional denatured state. It does, however, make a small thermodynamically favorable free energy (∼-13 ± 1 kJ/mol) contribution to the cooperative denatured state collapse transition as temperature is raised and urea concentration is lowered. The thermodynamics of this "cooperative collapse" of the denatured state retain significant compensations between the enthalpy and entropy contributions to the overall

Analysis of input variables of an artificial neural network using bivariate correlation and canonical correlation

International Nuclear Information System (INIS)

Costa, Valter Magalhaes

2011-01-01

was trained and the results were satisfactory since the IEA-R1 Data Acquisition System reactor monitors 64 variables and, with a set of 9 input variables resulting from the correlation analysis, it was possible to monitor 51 variables using neural networks. (author)

The study of gastronomic tourism in Cordoba and the association of the cuisine. An econometric analysis

OpenAIRE

Millán Vázquez de la Torre, Genoveva; Hernández Rojas, Ricardo; Navajas Romero, Virginia

2016-01-01

Purpose – As the city aspires to declare itself as a quality dinning destination, this paper aims to provide some guidelines to achieve that goal. Design – The paper aims to appraise as to what extent the gastronomic product supply of Córdoba can be considered a high quality and differentiated one, which may serve as a basis for tourism product development. Methodology – we use a univariate and bivariate analysis in order to describe the socioeconomic variables to explain the variety of...

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease*

Science.gov (United States)

Dewhurst, Henry; Sundararaman, Niveda

2016-01-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease.

Science.gov (United States)

Torres, Matthew P; Dewhurst, Henry; Sundararaman, Niveda

2016-11-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable

Analysis of Schizosaccharomyces pombe mediator reveals a set of essential subunits conserved between yeast and metazoan cells

DEFF Research Database (Denmark)

Spåhr, H; Samuelsen, C O; Baraznenok, V

2001-01-01

. cerevisiae share an essential protein module, which associates with nonessential speciesspecific subunits. In support of this view, sequence analysis of the conserved yeast Mediator components Med4 and Med8 reveals sequence homology to the metazoan Mediator components Trap36 and Arc32. Therefore, 8 of 10...... essential genes conserved between S. pombe and S. cerevisiae also have a metazoan homolog, indicating that an evolutionary conserved Mediator core is present in all eukaryotic cells. Our data suggest a closer functional relationship between yeast and metazoan Mediator than previously anticipated....

Genome-wide functional analysis of plasmodium protein phosphatases reveals key regulators of parasite development and differentiation

KAUST Repository

Guttery, David  S.; Poulin, Benoit; Ramaprasad, Abhinay; Wall, Richard  J.; Ferguson, David  J.P.; Brady, Declan; Patzewitz, Eva-Maria; Whipple, Sarah; Straschil, Ursula; Wright, Megan  H.; Mohamed, Alyaa  M.A.H.; Radhakrishnan, Anand; Arold, Stefan T.; Tate, Edward  W.; Holder, Anthony  A.; Wickstead, Bill; Pain, Arnab; Tewari, Rita

2014-01-01

Reversible protein phosphorylation regulated by kinases and phosphatases controls many cellular processes. Although essential functions for the malaria parasite kinome have been reported, the roles of most protein phosphatases (PPs) during Plasmodium development are unknown. We report a functional analysis of the Plasmodium berghei protein phosphatome, which exhibits high conservation with the P. falciparum phosphatome and comprises 30 predicted PPs with differential and distinct expression patterns during various stages of the life cycle. Gene disruption analysis of P. berghei PPs reveals that half of the genes are likely essential for asexual blood stage development, whereas six are required for sexual development/sporogony in mosquitoes. Phenotypic screening coupled with transcriptome sequencing unveiled morphological changes and altered gene expression in deletion mutants of two N-myristoylated PPs. These findings provide systematic functional analyses of PPs in Plasmodium, identify how phosphatases regulate parasite development and differentiation, and can inform the identification of drug targets for malaria. © 2014 The Authors.

Genome-wide functional analysis of plasmodium protein phosphatases reveals key regulators of parasite development and differentiation

KAUST Repository

Guttery, David S.

2014-07-09

Reversible protein phosphorylation regulated by kinases and phosphatases controls many cellular processes. Although essential functions for the malaria parasite kinome have been reported, the roles of most protein phosphatases (PPs) during Plasmodium development are unknown. We report a functional analysis of the Plasmodium berghei protein phosphatome, which exhibits high conservation with the P. falciparum phosphatome and comprises 30 predicted PPs with differential and distinct expression patterns during various stages of the life cycle. Gene disruption analysis of P. berghei PPs reveals that half of the genes are likely essential for asexual blood stage development, whereas six are required for sexual development/sporogony in mosquitoes. Phenotypic screening coupled with transcriptome sequencing unveiled morphological changes and altered gene expression in deletion mutants of two N-myristoylated PPs. These findings provide systematic functional analyses of PPs in Plasmodium, identify how phosphatases regulate parasite development and differentiation, and can inform the identification of drug targets for malaria. © 2014 The Authors.

Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets

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Max Lam

2017-11-01

Full Text Available Here, we present a large (n = 107,207 genome-wide association study (GWAS of general cognitive ability (“g”, further enhanced by combining results with a large-scale GWAS of educational attainment. We identified 70 independent genomic loci associated with general cognitive ability. Results showed significant enrichment for genes causing Mendelian disorders with an intellectual disability phenotype. Competitive pathway analysis implicated the biological processes of neurogenesis and synaptic regulation, as well as the gene targets of two pharmacologic agents: cinnarizine, a T-type calcium channel blocker, and LY97241, a potassium channel inhibitor. Transcriptome-wide and epigenome-wide analysis revealed that the implicated loci were enriched for genes expressed across all brain regions (most strongly in the cerebellum. Enrichment was exclusive to genes expressed in neurons but not oligodendrocytes or astrocytes. Finally, we report genetic correlations between cognitive ability and disparate phenotypes including psychiatric disorders, several autoimmune disorders, longevity, and maternal age at first birth.

Using means-end chain analysis to reveal consumers' motivation for buying local foods: An exploratory study

Directory of Open Access Journals (Sweden)

Poppy Arsil

2016-11-01

Full Text Available This article utilizes and discusses specific aspects of Means-End Chain (MEC analysis for understanding of the motives of Indonesian consumers who are involved in purchasing local foods. The MEC theory is used as a measure of attributes, consequences, and values of locally produced products involving specific aspects of this theory namely laddering methods of administration, content analysis procedure, constructing and interpreting Hierarchy Value Map (HVM. The results of the study indicate that MEC approach is a powerful method to reveal consumer motivation of local foods when associated with the various cultural groupings identified by the study particular between Javanese and Non-Javanese consumers. This study offers a practical implication and source of knowledge for other future studies and policies in term of (a a new approach for understanding the motives behind purchasing local foods for Indonesia consumers, and (b developing new categories of attributes, consequences and values of local foods.

Quantitative Tissue Proteomics Analysis Reveals Versican as Potential Biomarker for Early-Stage Hepatocellular Carcinoma.

Science.gov (United States)

Naboulsi, Wael; Megger, Dominik A; Bracht, Thilo; Kohl, Michael; Turewicz, Michael; Eisenacher, Martin; Voss, Don Marvin; Schlaak, Jörg F; Hoffmann, Andreas-Claudius; Weber, Frank; Baba, Hideo A; Meyer, Helmut E; Sitek, Barbara

2016-01-04

Hepatocellular carcinoma (HCC) is one of the most aggressive tumors, and the treatment outcome of this disease is improved when the cancer is diagnosed at an early stage. This requires biomarkers allowing an accurate and early tumor diagnosis. To identify potential markers for such applications, we analyzed a patient cohort consisting of 50 patients (50 HCC and 50 adjacent nontumorous tissue samples as controls) using two independent proteomics approaches. We performed label-free discovery analysis on 19 HCC and corresponding tissue samples. The data were analyzed considering events known to take place in early events of HCC development, such as abnormal regulation of Wnt/b-catenin and activation of receptor tyrosine kinases (RTKs). 31 proteins were selected for verification experiments. For this analysis, the second set of the patient cohort (31 HCC and corresponding tissue samples) was analyzed using selected (multiple) reaction monitoring (SRM/MRM). We present the overexpression of ATP-dependent RNA helicase (DDX39), Fibulin-5 (FBLN5), myristoylated alanine-rich C-kinase substrate (MARCKS), and Serpin H1 (SERPINH1) in HCC for the first time. We demonstrate Versican core protein (VCAN) to be significantly associated with well differentiated and low-stage HCC. We revealed for the first time the evidence of VCAN as a potential biomarker for early-HCC diagnosis.

Large-scale analysis by SAGE reveals new mechanisms of v-erbA oncogene action

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Faure Claudine

2007-10-01

Full Text Available Abstract Background: The v-erbA oncogene, carried by the Avian Erythroblastosis Virus, derives from the c-erbAα proto-oncogene that encodes the nuclear receptor for triiodothyronine (T3R. v-ErbA transforms erythroid progenitors in vitro by blocking their differentiation, supposedly by interference with T3R and RAR (Retinoic Acid Receptor. However, v-ErbA target genes involved in its transforming activity still remain to be identified. Results: By using Serial Analysis of Gene Expression (SAGE, we identified 110 genes deregulated by v-ErbA and potentially implicated in the transformation process. Bioinformatic analysis of promoter sequence and transcriptional assays point out a potential role of c-Myb in the v-ErbA effect. Furthermore, grouping of newly identified target genes by function revealed both expected (chromatin/transcription and unexpected (protein metabolism functions potentially deregulated by v-ErbA. We then focused our study on 15 of the new v-ErbA target genes and demonstrated by real time PCR that in majority their expression was activated neither by T3, nor RA, nor during differentiation. This was unexpected based upon the previously known role of v-ErbA. Conclusion: This paper suggests the involvement of a wealth of new unanticipated mechanisms of v-ErbA action.

Transcriptome analysis of Phytophthora litchii reveals pathogenicity arsenals and confirms taxonomic status.

Science.gov (United States)

Sun, Jinhua; Gao, Zhaoyin; Zhang, Xinchun; Zou, Xiaoxiao; Cao, Lulu; Wang, Jiabao

2017-01-01

Litchi downy blight, caused by Peronophythora litchii, is one of the major diseases of litchi and has caused severe economic losses. P. litchii has the unique ability to produce downy mildew like sporangiophores under artificial culture. The pathogen had been placed in a new family Peronophytophthoraceae by some authors. In this study, the whole transcriptome of P. litchii from mycelia, sporangia, and zoospores was sequenced for the first time. A set of 23637 transcripts with an average length of 1284 bp was assembled. Using six open reading frame (ORF) predictors, 19267 representative ORFs were identified and were annotated by searching against several public databases. There were 4666 conserved gene families and various sets of lineage-specific genes among P. litchii and other four closely related oomycetes. In silico analyses revealed 490 pathogen-related proteins including 128 RXLR and 22 CRN effector candidates. Based on the phylogenetic analysis of 164 single copy orthologs from 22 species, it is validated that P. litchii is in the genus Phytophthora. Our work provides valuable data to elucidate the pathogenicity basis and ascertain the taxonomic status of P. litchii.

A Simple Geotracer Compositional Correlation Analysis Reveals Oil Charge and Migration Pathways

Science.gov (United States)

Yang, Yunlai; Arouri, Khaled

2016-03-01

A novel approach, based on geotracer compositional correlation analysis is reported, which reveals the oil charge sequence and migration pathways for five oil fields in Saudi Arabia. The geotracers utilised are carbazoles, a family of neutral pyrrolic nitrogen compounds known to occur naturally in crude oils. The approach is based on the concept that closely related fields, with respect to filling sequence, will show a higher carbazole compositional correlation, than those fields that are less related. That is, carbazole compositional correlation coefficients can quantify the charge and filling relationships among different fields. Consequently, oil migration pathways can be defined based on the established filling relationships. The compositional correlation coefficients of isomers of C1 and C2 carbazoles, and benzo[a]carbazole for all different combination pairs of the five fields were found to vary extremely widely (0.28 to 0.94). A wide range of compositional correlation coefficients allows adequate differentiation of separate filling relationships. Based on the established filling relationships, three distinct migration pathways were inferred, with each apparently being charged from a different part of a common source kitchen. The recognition of these charge and migration pathways will greatly aid the search for new accumulations.

Phenotypic factor analysis of psychopathology reveals a new body-related transdiagnostic factor.

Science.gov (United States)

Pezzoli, Patrizia; Antfolk, Jan; Santtila, Pekka

2017-01-01

Comorbidity challenges the notion of mental disorders as discrete categories. An increasing body of literature shows that symptoms cut across traditional diagnostic boundaries and interact in shaping the latent structure of psychopathology. Using exploratory and confirmatory factor analysis, we reveal the latent sources of covariation among nine measures of psychopathological functioning in a population-based sample of 13024 Finnish twins and their siblings. By implementing unidimensional, multidimensional, second-order, and bifactor models, we illustrate the relationships between observed variables, specific, and general latent factors. We also provide the first investigation to date of measurement invariance of the bifactor model of psychopathology across gender and age groups. Our main result is the identification of a distinct "Body" factor, alongside the previously identified Internalizing and Externalizing factors. We also report relevant cross-disorder associations, especially between body-related psychopathology and trait anger, as well as substantial sex and age differences in observed and latent means. The findings expand the meta-structure of psychopathology, with implications for empirical and clinical practice, and demonstrate shared mechanisms underlying attitudes towards nutrition, self-image, sexuality and anger, with gender- and age-specific features.

A Simple Geotracer Compositional Correlation Analysis Reveals Oil Charge and Migration Pathways.

Science.gov (United States)

Yang, Yunlai; Arouri, Khaled

2016-03-11

A novel approach, based on geotracer compositional correlation analysis is reported, which reveals the oil charge sequence and migration pathways for five oil fields in Saudi Arabia. The geotracers utilised are carbazoles, a family of neutral pyrrolic nitrogen compounds known to occur naturally in crude oils. The approach is based on the concept that closely related fields, with respect to filling sequence, will show a higher carbazole compositional correlation, than those fields that are less related. That is, carbazole compositional correlation coefficients can quantify the charge and filling relationships among different fields. Consequently, oil migration pathways can be defined based on the established filling relationships. The compositional correlation coefficients of isomers of C1 and C2 carbazoles, and benzo[a]carbazole for all different combination pairs of the five fields were found to vary extremely widely (0.28 to 0.94). A wide range of compositional correlation coefficients allows adequate differentiation of separate filling relationships. Based on the established filling relationships, three distinct migration pathways were inferred, with each apparently being charged from a different part of a common source kitchen. The recognition of these charge and migration pathways will greatly aid the search for new accumulations.

Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups

Directory of Open Access Journals (Sweden)

Guillermo Nourdin-Galindo

2017-10-01

Full Text Available Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia, a disease that seriously affects the salmonid industry. Despite efforts to genomically characterize P. salmonis, functional information on the life cycle, pathogenesis mechanisms, diagnosis, treatment, and control of this fish pathogen remain lacking. To address this knowledge gap, the present study conducted an in silico pan-genome analysis of 19 P. salmonis strains from distinct geographic locations and genogroups. Results revealed an expected open pan-genome of 3,463 genes and a core-genome of 1,732 genes. Two marked genogroups were identified, as confirmed by phylogenetic and phylogenomic relationships to the LF-89 and EM-90 reference strains, as well as by assessments of genomic structures. Different structural configurations were found for the six identified copies of the ribosomal operon in the P. salmonis genome, indicating translocation throughout the genetic material. Chromosomal divergences in genomic localization and quantity of genetic cassettes were also found for the Dot/Icm type IVB secretion system. To determine divergences between core-genomes, additional pan-genome descriptions were compiled for the so-termed LF and EM genogroups. Open pan-genomes composed of 2,924 and 2,778 genes and core-genomes composed of 2,170 and 2,228 genes were respectively found for the LF and EM genogroups. The core-genomes were functionally annotated using the Gene Ontology, KEGG, and Virulence Factor databases, revealing the presence of several shared groups of genes related to basic function of intracellular survival and bacterial pathogenesis. Additionally, the specific pan-genomes for the LF and EM genogroups were defined, resulting in the identification of 148 and 273 exclusive proteins, respectively. Notably, specific virulence factors linked to adherence, colonization, invasion factors, and endotoxins were established. The obtained data suggest that these

Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters.

Science.gov (United States)

de Menezes, Alexandre B; Prendergast-Miller, Miranda T; Richardson, Alan E; Toscas, Peter; Farrell, Mark; Macdonald, Lynne M; Baker, Geoff; Wark, Tim; Thrall, Peter H

2015-08-01

Network and multivariate statistical analyses were performed to determine interactions between bacterial and fungal community terminal restriction length polymorphisms as well as soil properties in paired woodland and pasture sites. Canonical correspondence analysis (CCA) revealed that shifts in woodland community composition correlated with soil dissolved organic carbon, while changes in pasture community composition correlated with moisture, nitrogen and phosphorus. Weighted correlation network analysis detected two distinct microbial modules per land use. Bacterial and fungal ribotypes did not group separately, rather all modules comprised of both bacterial and fungal ribotypes. Woodland modules had a similar fungal : bacterial ribotype ratio, while in the pasture, one module was fungal dominated. There was no correspondence between pasture and woodland modules in their ribotype composition. The modules had different relationships to soil variables, and these contrasts were not detected without the use of network analysis. This study demonstrated that fungi and bacteria, components of the soil microbial communities usually treated as separate functional groups as in a CCA approach, were co-correlated and formed distinct associations in these adjacent habitats. Understanding these distinct modular associations may shed more light on their niche space in the soil environment, and allow a more realistic description of soil microbial ecology and function. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Differential network analysis reveals evolutionary complexity in secondary metabolism of Rauvolfia serpentina over Catharanthus roseus

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Shivalika Pathania

2016-08-01

Full Text Available Comparative co-expression analysis of multiple species using high-throughput data is an integrative approach to determine the uniformity as well as diversification in biological processes. Rauvolfia serpentina and Catharanthus roseus, both members of Apocyanacae family, are reported to have remedial properties against multiple diseases. Despite of sharing upstream of terpenoid indole alkaloid pathway, there is significant diversity in tissue-specific synthesis and accumulation of specialized metabolites in these plants. This led us to implement comparative co-expression network analysis to investigate the modules and genes responsible for differential tissue-specific expression as well as species-specific synthesis of metabolites. Towards these goals differential network analysis was implemented to identify candidate genes responsible for diversification of metabolites profile. Three genes were identified with significant difference in connectivity leading to differential regulatory behavior between these plants. These mechanisms may be responsible for diversification of secondary metabolism, and thereby for species-specific metabolite synthesis. The network robustness of R. serpentina, determined based on topological properties, was also complemented by comparison of gene-metabolite networks of both plants, and may have evolved to have complex metabolic mechanisms as compared to C. roseus under the influence of various stimuli. This study reveals evolution of complexity in secondary metabolism of Rauvolfia serpentina, and key genes that contribute towards diversification of specific metabolites.

Differential Network Analysis Reveals Evolutionary Complexity in Secondary Metabolism of Rauvolfia serpentina over Catharanthus roseus.

Science.gov (United States)

Pathania, Shivalika; Bagler, Ganesh; Ahuja, Paramvir S

2016-01-01

Comparative co-expression analysis of multiple species using high-throughput data is an integrative approach to determine the uniformity as well as diversification in biological processes. Rauvolfia serpentina and Catharanthus roseus, both members of Apocyanacae family, are reported to have remedial properties against multiple diseases. Despite of sharing upstream of terpenoid indole alkaloid pathway, there is significant diversity in tissue-specific synthesis and accumulation of specialized metabolites in these plants. This led us to implement comparative co-expression network analysis to investigate the modules and genes responsible for differential tissue-specific expression as well as species-specific synthesis of metabolites. Toward these goals differential network analysis was implemented to identify candidate genes responsible for diversification of metabolites profile. Three genes were identified with significant difference in connectivity leading to differential regulatory behavior between these plants. These genes may be responsible for diversification of secondary metabolism, and thereby for species-specific metabolite synthesis. The network robustness of R. serpentina, determined based on topological properties, was also complemented by comparison of gene-metabolite networks of both plants, and may have evolved to have complex metabolic mechanisms as compared to C. roseus under the influence of various stimuli. This study reveals evolution of complexity in secondary metabolism of R. serpentina, and key genes that contribute toward diversification of specific metabolites.

Analysis of 16S libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria.

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Salzman, Nita H; de Jong, Hendrik; Paterson, Yvonne; Harmsen, Hermie J M; Welling, Gjalt W; Bos, Nicolaas A

2002-11-01

Total genomic DNA from samples of intact mouse small intestine, large intestine, caecum and faeces was used as template for PCR amplification of 16S rRNA gene sequences with conserved bacterial primers. Phylogenetic analysis of the amplification products revealed 40 unique 16S rDNA sequences. Of these sequences, 25% (10/40) corresponded to described intestinal organisms of the mouse, including Lactobacillus spp., Helicobacter spp., segmented filamentous bacteria and members of the altered Schaedler flora (ASF360, ASF361, ASF502 and ASF519); 75% (30/40) represented novel sequences. A large number (11/40) of the novel sequences revealed a new operational taxonomic unit (OTU) belonging to the Cytophaga-Flavobacter-Bacteroides phylum, which the authors named 'mouse intestinal bacteria'. 16S rRNA probes were developed for this new OTU. Upon analysis of the novel sequences, eight were found to cluster within the Eubacterium rectale-Clostridium coccoides group and three clustered within the Bacteroides group. One of the novel sequences was distantly related to Verrucomicrobium spinosum and one was distantly related to Bacillus mycoides. Oligonucleotide probes specific for the 16S rRNA of these novel clones were generated. Using a combination of four previously described and four newly designed probes, approximately 80% of bacteria recovered from the murine large intestine and 71% of bacteria recovered from the murine caecum could be identified by fluorescence in situ hybridization (FISH).

Combined Transcriptomic Analysis Revealed AKR1B10 Played an Important Role in Psoriasis through the Dysregulated Lipid Pathway and Overproliferation of Keratinocyte

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Yunlu Gao

2017-01-01

Full Text Available RNA-seq has enabled in-depth analysis of the pathogenesis of psoriasis on the transcriptomic level, and many biomarkers have been discovered to be related to the immune response, lipid metabolism, and keratinocyte proliferation. However, few studies have combined analysis from various datasets. In this study, we integrated different psoriasis RNA-seq datasets to reveal the pathogenesis of psoriasis through the analysis of differentially expressed genes (DEGs, pathway analysis, and functional annotation. The revealed biomarkers were further validated through proliferation phenotypes. The results showed that DEGs were functionally related to lipid metabolism and keratinocyte differentiation dysregulation. The results also showed new biomarkers, such as AKR1B10 and PLA2G gene families, as well as pathways that include the PPAR signaling pathway, cytokine-cytokine receptor interaction, alpha-linoleic acid metabolism, and glycosphingolipid biosynthesis. Using siRNA knockdown assays, we further validated the role that the AKR1B10 gene plays in proliferation. Our study demonstrated not only the dysfunction of the AKR1B10 gene in lipid metabolizing but also its important role in the overproliferation and migration of keratinocyte, which provided evidence for further therapeutic uses for psoriasis.

Comparative proteomic analysis reveals heart toxicity induced by chronic arsenic exposure in rats

International Nuclear Information System (INIS)

Huang, Qingyu; Xi, Guochen; Alamdar, Ambreen; Zhang, Jie; Shen, Heqing

2017-01-01

Arsenic is a widespread metalloid in the environment, which poses a broad spectrum of adverse effects on human health. However, a global view of arsenic-induced heart toxicity is still lacking, and the underlying molecular mechanisms remain unclear. By performing a comparative quantitative proteomic analysis, the present study aims to investigate the alterations of proteome profile in rat heart after long-term exposure to arsenic. As a result, we found that the abundance of 81 proteins were significantly altered by arsenic treatment (35 up-regulated and 46 down-regulated). Among these, 33 proteins were specifically associated with cardiovascular system development and function, including heart development, heart morphology, cardiac contraction and dilation, and other cardiovascular functions. It is further proposed that the aberrant regulation of 14 proteins induced by arsenic would disturb cardiac contraction and relaxation, impair heart morphogenesis and development, and induce thrombosis in rats, which is mediated by the Akt/p38 MAPK signaling pathway. Overall, these findings will augment our knowledge of the involved mechanisms and develop useful biomarkers for cardiotoxicity induced by environmental arsenic exposure. - Highlights: • Arsenic exposure has been associated with a number of adverse health effects. • The molecular mechanisms involved in arsenic-induced cardiotoxicity remain unclear. • Differential proteins were identified in arsenic-exposed rat heart by proteomics. • Arsenic induces heart toxicity through the Akt/p38 MAPK signaling pathway. - Label-free quantitative proteomic analysis of rat heart reveals putative mechanisms and biomarkers for arsenic-induced cardiotoxicity.

REVEAL: Software Documentation and Platform Migration

Science.gov (United States)

Wilson, Michael A.; Veibell, Victoir T.

2011-01-01

The Research Environment for Vehicle Embedded Analysis on Linux (REVEAL) is reconfigurable data acquisition software designed for network-distributed test and measurement applications. In development since 2001, it has been successfully demonstrated in support of a number of actual missions within NASA's Suborbital Science Program. Improvements to software configuration control were needed to properly support both an ongoing transition to operational status and continued evolution of REVEAL capabilities. For this reason the project described in this report targets REVEAL software source documentation and deployment of the software on a small set of hardware platforms different from what is currently used in the baseline system implementation. This presentation specifically describes the actions taken over a ten week period by two undergraduate student interns and serves as an overview of the content of the final report for that internship.

Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity.

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Koen Illeghems

Full Text Available This is the first report on the phylogenetic analysis of the community diversity of a single spontaneous cocoa bean box fermentation sample through a metagenomic approach involving 454 pyrosequencing. Several sequence-based and composition-based taxonomic profiling tools were used and evaluated to avoid software-dependent results and their outcome was validated by comparison with previously obtained culture-dependent and culture-independent data. Overall, this approach revealed a wider bacterial (mainly γ-Proteobacteria and fungal diversity than previously found. Further, the use of a combination of different classification methods, in a software-independent way, helped to understand the actual composition of the microbial ecosystem under study. In addition, bacteriophage-related sequences were found. The bacterial diversity depended partially on the methods used, as composition-based methods predicted a wider diversity than sequence-based methods, and as classification methods based solely on phylogenetic marker genes predicted a more restricted diversity compared with methods that took all reads into account. The metagenomic sequencing analysis identified Hanseniaspora uvarum, Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus as the prevailing species. Also, the presence of occasional members of the cocoa bean fermentation process was revealed (such as Erwinia tasmaniensis, Lactobacillus brevis, Lactobacillus casei, Lactobacillus rhamnosus, Lactococcus lactis, Leuconostoc mesenteroides, and Oenococcus oeni. Furthermore, the sequence reads associated with viral communities were of a restricted diversity, dominated by Myoviridae and Siphoviridae, and reflecting Lactobacillus as the dominant host. To conclude, an accurate overview of all members of a cocoa bean fermentation process sample was revealed, indicating the superiority of metagenomic sequencing over previously used techniques.

Hyperconnectivity in juvenile myoclonic epilepsy: a network analysis.

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Caeyenberghs, K; Powell, H W R; Thomas, R H; Brindley, L; Church, C; Evans, J; Muthukumaraswamy, S D; Jones, D K; Hamandi, K

2015-01-01

Juvenile myoclonic epilepsy (JME) is a common idiopathic (genetic) generalized epilepsy (IGE) syndrome characterized by impairments in executive and cognitive control, affecting independent living and psychosocial functioning. There is a growing consensus that JME is associated with abnormal function of diffuse brain networks, typically affecting frontal and fronto-thalamic areas. Using diffusion MRI and a graph theoretical analysis, we examined bivariate (network-based statistic) and multivariate (global and local) properties of structural brain networks in patients with JME (N = 34) and matched controls. Neuropsychological assessment was performed in a subgroup of 14 patients. Neuropsychometry revealed impaired visual memory and naming in JME patients despite a normal full scale IQ (mean = 98.6). Both JME patients and controls exhibited a small world topology in their white matter networks, with no significant differences in the global multivariate network properties between the groups. The network-based statistic approach identified one subnetwork of hyperconnectivity in the JME group, involving primary motor, parietal and subcortical regions. Finally, there was a significant positive correlation in structural connectivity with cognitive task performance. Our findings suggest that structural changes in JME patients are distributed at a network level, beyond the frontal lobes. The identified subnetwork includes key structures in spike wave generation, along with primary motor areas, which may contribute to myoclonic jerks. We conclude that analyzing the affected subnetworks may provide new insights into understanding seizure generation, as well as the cognitive deficits observed in JME patients.

Network Analysis Reveals Putative Genes Affecting Meat Quality in Angus Cattle.

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Mateescu, Raluca G; Garrick, Dorian J; Reecy, James M

2017-01-01

Improvements in eating satisfaction will benefit consumers and should increase beef demand which is of interest to the beef industry. Tenderness, juiciness, and flavor are major determinants of the palatability of beef and are often used to reflect eating satisfaction. Carcass qualities are used as indicator traits for meat quality, with higher quality grade carcasses expected to relate to more tender and palatable meat. However, meat quality is a complex concept determined by many component traits making interpretation of genome-wide association studies (GWAS) on any one component challenging to interpret. Recent approaches combining traditional GWAS with gene network interactions theory could be more efficient in dissecting the genetic architecture of complex traits. Phenotypic measures of 23 traits reflecting carcass characteristics, components of meat quality, along with mineral and peptide concentrations were used along with Illumina 54k bovine SNP genotypes to derive an annotated gene network associated with meat quality in 2,110 Angus beef cattle. The efficient mixed model association (EMMAX) approach in combination with a genomic relationship matrix was used to directly estimate the associations between 54k SNP genotypes and each of the 23 component traits. Genomic correlated regions were identified by partial correlations which were further used along with an information theory algorithm to derive gene network clusters. Correlated SNP across 23 component traits were subjected to network scoring and visualization software to identify significant SNP. Significant pathways implicated in the meat quality complex through GO term enrichment analysis included angiogenesis, inflammation, transmembrane transporter activity, and receptor activity. These results suggest that network analysis using partial correlations and annotation of significant SNP can reveal the genetic architecture of complex traits and provide novel information regarding biological mechanisms

The Immersive Virtual Reality Experience: A Typology of Users Revealed Through Multiple Correspondence Analysis Combined with Cluster Analysis Technique.

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Rosa, Pedro J; Morais, Diogo; Gamito, Pedro; Oliveira, Jorge; Saraiva, Tomaz

2016-03-01

Immersive virtual reality is thought to be advantageous by leading to higher levels of presence. However, and despite users getting actively involved in immersive three-dimensional virtual environments that incorporate sound and motion, there are individual factors, such as age, video game knowledge, and the predisposition to immersion, that may be associated with the quality of virtual reality experience. Moreover, one particular concern for users engaged in immersive virtual reality environments (VREs) is the possibility of side effects, such as cybersickness. The literature suggests that at least 60% of virtual reality users report having felt symptoms of cybersickness, which reduces the quality of the virtual reality experience. The aim of this study was thus to profile the right user to be involved in a VRE through head-mounted display. To examine which user characteristics are associated with the most effective virtual reality experience (lower cybersickness), a multiple correspondence analysis combined with cluster analysis technique was performed. Results revealed three distinct profiles, showing that the PC gamer profile is more associated with higher levels of virtual reality effectiveness, that is, higher predisposition to be immersed and reduced cybersickness symptoms in the VRE than console gamer and nongamer. These findings can be a useful orientation in clinical practice and future research as they help identify which users are more predisposed to benefit from immersive VREs.

Analysis of an RNA-seq Strand-Specific Library from an East Timorese Cucumber Sample Reveals a Complete Cucurbit aphid-borne yellows virus Genome.

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Maina, Solomon; Edwards, Owain R; de Almeida, Luis; Ximenes, Abel; Jones, Roger A C

2017-05-11

Analysis of an RNA-seq library from cucumber leaf RNA extracted from a fast technology for analysis of nucleic acids (FTA) card revealed the first complete genome of Cucurbit aphid-borne yellows virus (CABYV) from East Timor. We compare it with 35 complete CABYV genomes from other world regions. It most resembled the genome of the South Korean isolate HD118. Copyright © 2017 Maina et al.

Combined Metabolomic Analysis of Plasma and Urine Reveals AHBA, Tryptophan and Serotonin Metabolism as Potential Risk Factors in Gestational Diabetes Mellitus (GDM

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Miriam Leitner

2017-12-01

Full Text Available Gestational diabetes mellitus during pregnancy has severe implications for the health of the mother and the fetus. Therefore, early prediction and an understanding of the physiology are an important part of prenatal care. Metabolite profiling is a long established method for the analysis and prediction of metabolic diseases. Here, we applied untargeted and targeted metabolomic protocols to analyze plasma and urine samples of pregnant women with and without GDM. Univariate and multivariate statistical analyses of metabolomic profiles revealed markers such as 2-hydroxybutanoic acid (AHBA, 3-hydroxybutanoic acid (BHBA, amino acids valine and alanine, the glucose-alanine-cycle, but also plant-derived compounds like sitosterin as different between control and GDM patients. PLS-DA and VIP analysis revealed tryptophan as a strong variable separating control and GDM. As tryptophan is biotransformed to serotonin we hypothesized whether serotonin metabolism might also be altered in GDM. To test this hypothesis we applied a method for the analysis of serotonin, metabolic intermediates and dopamine in urine by stable isotope dilution direct infusion electrospray ionization mass spectrometry (SID-MS. Indeed, serotonin and related metabolites differ significantly between control and GDM patients confirming the involvement of serotonin metabolism in GDM. Clustered correlation coefficient visualization of metabolite correlation networks revealed the different metabolic signatures between control and GDM patients. Eventually, the combination of selected blood plasma and urine sample metabolites improved the AUC prediction accuracy to 0.99. The detected GDM candidate biomarkers and the related systemic metabolic signatures are discussed in their pathophysiological context. Further studies with larger cohorts are necessary to underpin these observations.

Revealed Preference Theory, Rationality, and Neoclassical ...

African Journals Online (AJOL)

Revealed Preference Theory (Samuelson 1938) is an attempt to establish economic theory as a genuine empirical science by ridding it of nonempirical psychological concepts. Samuelson's goal was to rid economic theory of the last vestiges of utility analysis. Samuelson structured his theory on a set of preference axioms ...

Laminar and dorsoventral molecular organization of the medial entorhinal cortex revealed by large-scale anatomical analysis of gene expression.

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Helen L Ramsden

2015-01-01

Full Text Available Neural circuits in the medial entorhinal cortex (MEC encode an animal's position and orientation in space. Within the MEC spatial representations, including grid and directional firing fields, have a laminar and dorsoventral organization that corresponds to a similar topography of neuronal connectivity and cellular properties. Yet, in part due to the challenges of integrating anatomical data at the resolution of cortical layers and borders, we know little about the molecular components underlying this organization. To address this we develop a new computational pipeline for high-throughput analysis and comparison of in situ hybridization (ISH images at laminar resolution. We apply this pipeline to ISH data for over 16,000 genes in the Allen Brain Atlas and validate our analysis with RNA sequencing of MEC tissue from adult mice. We find that differential gene expression delineates the borders of the MEC with neighboring brain structures and reveals its laminar and dorsoventral organization. We propose a new molecular basis for distinguishing the deep layers of the MEC and show that their similarity to corresponding layers of neocortex is greater than that of superficial layers. Our analysis identifies ion channel-, cell adhesion- and synapse-related genes as candidates for functional differentiation of MEC layers and for encoding of spatial information at different scales along the dorsoventral axis of the MEC. We also reveal laminar organization of genes related to disease pathology and suggest that a high metabolic demand predisposes layer II to neurodegenerative pathology. In principle, our computational pipeline can be applied to high-throughput analysis of many forms of neuroanatomical data. Our results support the hypothesis that differences in gene expression contribute to functional specialization of superficial layers of the MEC and dorsoventral organization of the scale of spatial representations.

Phylogenetic analysis reveals two genotypes of the emerging fungus Mucor indicus, an opportunistic human pathogen in immunocompromised patients.

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Taj-Aldeen, Saad J; Almaslamani, Muna; Theelen, Bart; Boekhout, Teun

2017-07-12

Mucormycosis is a rare fungal infection caused by Mucor indicus. Phylogenetic analysis of many M. indicus isolates, mainly sampled from different clinical and environmental specimens collected worldwide, revealed two genotypes, I and II, based on ITS and D1/D2 LSU rDNA sequences. A retrospective review of the literature revealed 13 cases. Eight (76.9%) patients had disseminated infections, and the overall mortality rate was 30.7%. A pulmonary infection caused by M. indicus genotype I in a liver transplant recipient was disseminated to include the skin and was successfully treated with liposomal amphotericin B and aggressive surgery. M. indicus can infect a wide variety of patients with no real preference for the site of infection. We concluded that M. indicus has emerged as a significant cause of invasive mycosis in severely immunocompromised patients worldwide. Early diagnosis and initiation of appropriate therapy could enhance survival in these immunocompromised patient populations.

Acculturation and Self-Rated Mental Health Among Latino and Asian Immigrants in the United States: A Latent Class Analysis.

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Bulut, Elif; Gayman, Matthew D

2016-08-01

This study assesses variations in acculturation experiences by identifying distinct acculturation classes, and investigates the role of these acculturation classes for self-rated mental health among Latino and Asian immigrants in the United States. Using 2002-2003 the National Latino and Asian American Study, Latent Class Analysis is used to capture variations in immigrant classes (recent arrivals, separated, bicultural and assimilated), and OLS regressions are used to assess the link between acculturation classes and self-rated mental health. For both Latinos and Asians, bicultural immigrants reported the best mental health, and separated immigrants and recent arrivals reported the worst mental health. The findings also reveal group differences in acculturation classes, whereby Latino immigrants were more likely to be in the separated class and recent arrivals class relative to Asian immigrants. While there was not a significant group difference in self-rated mental health at the bivariate level, controlling for acculturation classes revealed that Latinos report better self-rated mental health than Asians. Thus, Latino immigrants would actually have better self-rated mental health than their Asian counterparts if they were not more likely to be represented in less acculturated classes (separated class and recent arrivals) and/or as likely to be in the bicultural class as their Asian counterparts. Together the findings underscore the nuanced and complex nature of the acculturation process, highlighting the importance of race differences in this process, and demonstrate the role of acculturation classes for immigrant group differences in self-rated mental health.

Cardiovascular coupling analysis with high-resolution joint symbolic dynamics in patients suffering from acute schizophrenia

International Nuclear Information System (INIS)

Schulz, Steffen; Tupaika, Nadine; Voss, Andreas; Berger, Sandy; Bär, Karl-Jürgen; Haueisen, Jens

2013-01-01

Besides the well-known cardiac risk factors for schizophrenia, increasing concerns have been raised regarding the cardiac side-effects of antipsychotic medications. A bivariate analysis of autonomic regulation, based on cardiovascular coupling, can provide additional information about heart rate (HR) and blood pressure regulatory patterns within the complex interactions of the cardiovascular system. We introduce a new high-resolution coupling analysis method (HRJSD) based on joint symbolic dynamics (JSD), which is characterized by three symbols, a threshold (individual dynamic variability, physiological) for time series transformation and eight coupling pattern families. This is based on a redundancy reduction strategy used to quantify and characterize cardiovascular couplings. In this study, short-term (30 min) HR and systolic blood pressure (SP) time series of 42 unmedicated (UNMED) and 42 medicated patients (MED) suffering from acute schizophrenia were analysed to establish the suitability of the new method for quantifying the effects of antipsychotics on cardiovascular couplings. We were able to demonstrate that HRJSD, applying the threshold based on spontaneous baroreflex sensitivity (BRS) estimation, revealed eight significant pattern families that were able to quantify the anti-cholinergic effects of antipsychotics and the related changes of cardiovascular regulation (coupling) in MED in comparison to UNMED. This was in contrast to the simple JSD, BRS (sequence method) and only partly to standard linear HR variability indices. HRJSD provides strong evidence that autonomic regulation in MED seems to be, to some extent, predominated by invariable HR responses in combination with alternating SP values in contrast to UNMED, indicating an impairment of the baroreflex control feedback loop in MED. Surrogate data analysis was applied to test for the significance and nonlinearity of cardiovascular couplings in the original data due to medical treatment with

Multifractal detrended cross-correlation analysis in the MENA area

Science.gov (United States)

El Alaoui, Marwane; Benbachir, Saâd

2013-12-01

In this paper, we investigated multifractal cross-correlations qualitatively and quantitatively using a cross-correlation test and the Multifractal detrended cross-correlation analysis method (MF-DCCA) for markets in the MENA area. We used cross-correlation coefficients to measure the level of this correlation. The analysis concerns four stock market indices of Morocco, Tunisia, Egypt and Jordan. The countries chosen are signatory of the Agadir agreement concerning the establishment of a free trade area comprising Arab Mediterranean countries. We computed the bivariate generalized Hurst exponent, Rényi exponent and spectrum of singularity for each pair of indices to measure quantitatively the cross-correlations. By analyzing the results, we found the existence of multifractal cross-correlations between all of these markets. We compared the spectrum width of these indices; we also found which pair of indices has a strong multifractal cross-correlation.

Biophysical analysis of HTLV-1 particles reveals novel insights into particle morphology and Gag stochiometry

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Fogarty Keir H

2010-09-01

Full Text Available Abstract Background Human T-lymphotropic virus type 1 (HTLV-1 is an important human retrovirus that is a cause of adult T-cell leukemia/lymphoma. While an important human pathogen, the details regarding virus replication cycle, including the nature of HTLV-1 particles, remain largely unknown due to the difficulties in propagating the virus in tissue culture. In this study, we created a codon-optimized HTLV-1 Gag fused to an EYFP reporter as a model system to quantitatively analyze HTLV-1 particles released from producer cells. Results The codon-optimized Gag led to a dramatic and highly robust level of Gag expression as well as virus-like particle (VLP production. The robust level of particle production overcomes previous technical difficulties with authentic particles and allowed for detailed analysis of particle architecture using two novel methodologies. We quantitatively measured the diameter and morphology of HTLV-1 VLPs in their native, hydrated state using cryo-transmission electron microscopy (cryo-TEM. Furthermore, we were able to determine HTLV-1 Gag stoichiometry as well as particle size with the novel biophysical technique of fluorescence fluctuation spectroscopy (FFS. The average HTLV-1 particle diameter determined by cryo-TEM and FFS was 71 ± 20 nm and 75 ± 4 nm, respectively. These values are significantly smaller than previous estimates made of HTLV-1 particles by negative staining TEM. Furthermore, cryo-TEM reveals that the majority of HTLV-1 VLPs lacks an ordered structure of the Gag lattice, suggesting that the HTLV-1 Gag shell is very likely to be organized differently compared to that observed with HIV-1 Gag in immature particles. This conclusion is supported by our observation that the average copy number of HTLV-1 Gag per particle is estimated to be 510 based on FFS, which is significantly lower than that found for HIV-1 immature virions. Conclusions In summary, our studies represent the first quantitative biophysical

Calculus of bivariant function

OpenAIRE

PTÁČNÍK, Jan

2011-01-01

This thesis deals with the introduction of function of two variables and differential calculus of this function. This work should serve as a textbook for students of elementary school's teacher. Each chapter contains a summary of basic concepts and explanations of relationships, then solved model exercises of the topic and finally the exercises, which should solve the student himself. Thesis have transmit to students basic knowledges of differential calculus of functions of two variables, inc...

Comparative genomic analysis of the microbiome [corrected] of herbivorous insects reveals eco-environmental adaptations: biotechnology applications.

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Weibing Shi

Full Text Available Metagenome analysis of the gut symbionts of three different insects was conducted as a means of comparing taxonomic and metabolic diversity of gut microbiomes to diet and life history of the insect hosts. A second goal was the discovery of novel biocatalysts for biorefinery applications. Grasshopper and cutworm gut symbionts were sequenced and compared with the previously identified metagenome of termite gut microbiota. These insect hosts represent three different insect orders and specialize on different food types. The comparative analysis revealed dramatic differences among the three insect species in the abundance and taxonomic composition of the symbiont populations present in the gut. The composition and abundance of symbionts was correlated with their previously identified capacity to degrade and utilize the different types of food consumed by their hosts. The metabolic reconstruction revealed that the gut metabolome of cutworms and grasshoppers was more enriched for genes involved in carbohydrate metabolism and transport than wood-feeding termite, whereas the termite gut metabolome was enriched for glycosyl hydrolase (GH enzymes relevant to lignocellulosic biomass degradation. Moreover, termite gut metabolome was more enriched with nitrogen fixation genes than those of grasshopper and cutworm gut, presumably due to the termite's adaptation to the high fiber and less nutritious food types. In order to evaluate and exploit the insect symbionts for biotechnology applications, we cloned and further characterized four biomass-degrading enzymes including one endoglucanase and one xylanase from both the grasshopper and cutworm gut symbionts. The results indicated that the grasshopper symbiont enzymes were generally more efficient in biomass degradation than the homologous enzymes from cutworm symbionts. Together, these results demonstrated a correlation between the composition and putative metabolic functionality of the gut microbiome and host

Grain size statistics and depositional pattern of the Ecca Group sandstones, Karoo Supergroup in the Eastern Cape Province, South Africa

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Baiyegunhi Christopher

2017-11-01

Full Text Available Grain size analysis is a vital sedimentological tool used to unravel the hydrodynamic conditions, mode of transportation and deposition of detrital sediments. In this study, detailed grain-size analysis was carried out on thirty-five sandstone samples from the Ecca Group in the Eastern Cape Province of South Africa. Grain-size statistical parameters, bivariate analysis, linear discriminate functions, Passega diagrams and log-probability curves were used to reveal the depositional processes, sedimentation mechanisms, hydrodynamic energy conditions and to discriminate different depositional environments. The grain-size parameters show that most of the sandstones are very fine to fine grained, moderately well sorted, mostly near-symmetrical and mesokurtic in nature. The abundance of very fine to fine grained sandstones indicate the dominance of low energy environment. The bivariate plots show that the samples are mostly grouped, except for the Prince Albert samples that show scattered trend, which is due to the either mixture of two modes in equal proportion in bimodal sediments or good sorting in unimodal sediments. The linear discriminant function analysis is dominantly indicative of turbidity current deposits under shallow marine environments for samples from the Prince Albert, Collingham and Ripon Formations, while those samples from the Fort Brown Formation are lacustrine or deltaic deposits. The C-M plots indicated that the sediments were deposited mainly by suspension and saltation, and graded suspension. Visher diagrams show that saltation is the major process of transportation, followed by suspension.

Grain size statistics and depositional pattern of the Ecca Group sandstones, Karoo Supergroup in the Eastern Cape Province, South Africa

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Baiyegunhi, Christopher; Liu, Kuiwu; Gwavava, Oswald

2017-11-01

Grain size analysis is a vital sedimentological tool used to unravel the hydrodynamic conditions, mode of transportation and deposition of detrital sediments. In this study, detailed grain-size analysis was carried out on thirty-five sandstone samples from the Ecca Group in the Eastern Cape Province of South Africa. Grain-size statistical parameters, bivariate analysis, linear discriminate functions, Passega diagrams and log-probability curves were used to reveal the depositional processes, sedimentation mechanisms, hydrodynamic energy conditions and to discriminate different depositional environments. The grain-size parameters show that most of the sandstones are very fine to fine grained, moderately well sorted, mostly near-symmetrical and mesokurtic in nature. The abundance of very fine to fine grained sandstones indicate the dominance of low energy environment. The bivariate plots show that the samples are mostly grouped, except for the Prince Albert samples that show scattered trend, which is due to the either mixture of two modes in equal proportion in bimodal sediments or good sorting in unimodal sediments. The linear discriminant function analysis is dominantly indicative of turbidity current deposits under shallow marine environments for samples from the Prince Albert, Collingham and Ripon Formations, while those samples from the Fort Brown Formation are lacustrine or deltaic deposits. The C-M plots indicated that the sediments were deposited mainly by suspension and saltation, and graded suspension. Visher diagrams show that saltation is the major process of transportation, followed by suspension.

Zebrafish Embryonic Lipidomic Analysis Reveals that the Yolk Cell Is Metabolically Active in Processing Lipid

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Daniel Fraher

2016-02-01

Full Text Available The role of lipids in providing energy and structural cellular components during vertebrate development is poorly understood. To elucidate these roles further, we visualized lipid deposition and examined expression of key lipid-regulating genes during zebrafish embryogenesis. We also conducted a semiquantitative analysis of lipidomic composition using liquid chromatography (LC-mass spectrometry. Finally, we analyzed processing of boron-dipyrromethene (BODIPY lipid analogs injected into the yolk using thin layer chromatography. Our data reveal that the most abundant lipids in the embryo are cholesterol, phosphatidylcholine, and triglyceride. Moreover, we demonstrate that lipids are processed within the yolk prior to mobilization to the embryonic body. Our data identify a metabolically active yolk and body resulting in a dynamic lipid composition. This provides a foundation for studying lipid biology during normal or pharmacologically compromised embryogenesis.

A points-based algorithm for prognosticating clinical outcome of Chiari malformation Type I with syringomyelia: results from a predictive model analysis of 82 surgically managed adult patients.

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Thakar, Sumit; Sivaraju, Laxminadh; Jacob, Kuruthukulangara S; Arun, Aditya Atal; Aryan, Saritha; Mohan, Dilip; Sai Kiran, Narayanam Anantha; Hegde, Alangar S

2018-01-01

OBJECTIVE Although various predictors of postoperative outcome have been previously identified in patients with Chiari malformation Type I (CMI) with syringomyelia, there is no known algorithm for predicting a multifactorial outcome measure in this widely studied disorder. Using one of the largest preoperative variable arrays used so far in CMI research, the authors attempted to generate a formula for predicting postoperative outcome. METHODS Data from the clinical records of 82 symptomatic adult patients with CMI and altered hindbrain CSF flow who were managed with foramen magnum decompression, C-1 laminectomy, and duraplasty over an 8-year period were collected and analyzed. Various preoperative clinical and radiological variables in the 57 patients who formed the study cohort were assessed in a bivariate analysis to determine their ability to predict clinical outcome (as measured on the Chicago Chiari Outcome Scale [CCOS]) and the resolution of syrinx at the last follow-up. The variables that were significant in the bivariate analysis were further analyzed in a multiple linear regression analysis. Different regression models were tested, and the model with the best prediction of CCOS was identified and internally validated in a subcohort of 25 patients. RESULTS There was no correlation between CCOS score and syrinx resolution (p = 0.24) at a mean ± SD follow-up of 40.29 ± 10.36 months. Multiple linear regression analysis revealed that the presence of gait instability, obex position, and the M-line-fourth ventricle vertex (FVV) distance correlated with CCOS score, while the presence of motor deficits was associated with poor syrinx resolution (p ≤ 0.05). The algorithm generated from the regression model demonstrated good diagnostic accuracy (area under curve 0.81), with a score of more than 128 points demonstrating 100% specificity for clinical improvement (CCOS score of 11 or greater). The model had excellent reliability (κ = 0.85) and was validated with

Correlates of susceptibility to smoking among Mexican origin youth residing in Houston, Texas: A cross-sectional analysis

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Prokhorov Alexander V

2008-09-01

Full Text Available Abstract Background Survey data suggest that in Texas Latino youth exhibit higher rates of susceptibility to smoking than youth from other ethnic groups. In this analysis we examined the relationship between susceptibility to smoking and well-known risk factors associated with smoking initiation among a cohort of 11 to 13 year old Mexican origin youth residing in Houston, Texas. Methods We analyzed cross-sectional survey data from 1,187 participants who reported they had never smoked, even a puff of a cigarette. The survey assessed peer and family social influence, school and neighborhood characteristics, level of family acculturation and socioeconomic status, and attitudes toward smoking. Bivariate associations, Student's t-tests, and logistic regression analysis were used to examine predictors of susceptibility. Results Overall, 22.1% of the never-smokers were susceptible to smoking. Boys were more likely to be susceptible than girls (25.6% vs. 18.9%, and susceptible children were slightly older than non-susceptible children (12.1 vs. 11.8 years. In addition, multivariate analyses revealed that positive expectations about smoking exerted the strongest influence on susceptibility status (odds ratio = 4.85. Multivariate analyses further revealed that compared to non-susceptible participants, susceptibles were more likely to report peer influences supportive of smoking, lower subjective social status and more detentions at school, more temptations to try smoking and to have a mother and a brother who smokes. Conclusion Our findings suggest that interventions that target positive expectations about smoking may be useful in this population. Furthermore, because youth encounter smoking-initiation risk factors in different social environments, our results underscore the continued need for both family- and school-based primary prevention programs to adequately combat their influence. The results also can be used to inform the development of culturally

Comparative proteomics and codon substitution analysis reveal mechanisms of differential resistance to hypoxia in congeneric snails

KAUST Repository

Mu, Huawei; Sun, Jin; Cheung, Siu Gin; Fang, Ling; Zhou, Haiyun; Luan, Tiangang; Zhang, Huoming; Wong, Chris K.C.; Qiu, Jian-Wen

2017-01-01

Although high-throughput proteomics has been widely applied to study mechanisms of environmental adaptation, the conclusions from studies that are based on one species can be confounded by phylogeny. We compare the freshwater snail Pomacea canaliculata (a notorious invasive species) and its congener Pomacea diffusa (a non-invasive species) to understand the molecular mechanisms of their differential resistance to hypoxia. A 72-h acute exposure experiment showed that P. canaliculata is more tolerant to hypoxia than P. diffusa. The two species were then exposed to three levels of dissolved oxygen (6.7, 2.0 and 1.0mgL−1) for 8h, and their gill proteins were analyzed using iTRAQ-coupled LC-MS/MS. The two species showed striking differences in protein expression profiles, with the more hypoxia tolerant P. canaliculata having more up-regulated proteins in signal transduction and down-regulated proteins in glycolysis and the tricarboxylic acid cycle. Evolutionary analysis revealed five orthologous genes encoding differentially expressed proteins having clear signal of positive selection, indicating selection has acted on some of the hypoxia responsive genes. Our case study has highlighted the potential of integrated proteomics and comparative evolutionary analysis for understanding the genetic basis of adaptation to global environmental change in non-model species. SignificanceRapid globalization in recent decades has greatly facilitated species introduction around the world. Successfully established introduced species, so-called invasive species, have threatened the invaded ecosystems. There has been substantial interest in studying how invasive species respond to extreme environmental conditions because the results can help not only predict their range of expansion and manage their impact, but also may reveal the adaptive mechanisms underlying their invasiveness. Our study has adopted a comparative approach to study the differential physiological and proteomic

Comparative proteomics and codon substitution analysis reveal mechanisms of differential resistance to hypoxia in congeneric snails

KAUST Repository

Mu, Huawei

2017-11-06

Although high-throughput proteomics has been widely applied to study mechanisms of environmental adaptation, the conclusions from studies that are based on one species can be confounded by phylogeny. We compare the freshwater snail Pomacea canaliculata (a notorious invasive species) and its congener Pomacea diffusa (a non-invasive species) to understand the molecular mechanisms of their differential resistance to hypoxia. A 72-h acute exposure experiment showed that P. canaliculata is more tolerant to hypoxia than P. diffusa. The two species were then exposed to three levels of dissolved oxygen (6.7, 2.0 and 1.0mgL−1) for 8h, and their gill proteins were analyzed using iTRAQ-coupled LC-MS/MS. The two species showed striking differences in protein expression profiles, with the more hypoxia tolerant P. canaliculata having more up-regulated proteins in signal transduction and down-regulated proteins in glycolysis and the tricarboxylic acid cycle. Evolutionary analysis revealed five orthologous genes encoding differentially expressed proteins having clear signal of positive selection, indicating selection has acted on some of the hypoxia responsive genes. Our case study has highlighted the potential of integrated proteomics and comparative evolutionary analysis for understanding the genetic basis of adaptation to global environmental change in non-model species. SignificanceRapid globalization in recent decades has greatly facilitated species introduction around the world. Successfully established introduced species, so-called invasive species, have threatened the invaded ecosystems. There has been substantial interest in studying how invasive species respond to extreme environmental conditions because the results can help not only predict their range of expansion and manage their impact, but also may reveal the adaptive mechanisms underlying their invasiveness. Our study has adopted a comparative approach to study the differential physiological and proteomic

PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity

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Nelson, T.A.; Holmes, S.; Alekseyenko, A.V.; Shenoy, M.; DeSantis, T.; Wu, C.H.; Andersen, G.L.; Winston, J.; Sonnenburg, J.; Pasricha, P.J.; Spormann, A.

2010-12-01

Irritable bowel syndrome (IBS) is a chronic, episodic gastrointestinal disorder that is prevalent in a significant fraction of western human populations; and changes in the microbiota of the large bowel have been implicated in the pathology of the disease. Using a novel comprehensive, high-density DNA microarray (PhyloChip) we performed a phylogenetic analysis of the microbial community of the large bowel in a rat model in which intracolonic acetic acid in neonates was used to induce long lasting colonic hypersensitivity and decreased stool water content and frequency, representing the equivalent of human constipation-predominant IBS. Our results revealed a significantly increased compositional difference in the microbial communities in rats with neonatal irritation as compared with controls. Even more striking was the dramatic change in the ratio of Firmicutes relative to Bacteroidetes, where neonatally irritated rats were enriched more with Bacteroidetes and also contained a different composition of species within this phylum. Our study also revealed differences at the level of bacterial families and species. The PhyloChip is a useful and convenient method to study enteric microflora. Further, this rat model system may be a useful experimental platform to study the causes and consequences of changes in microbial community composition associated with IBS.

Global gene expression analysis of the zoonotic parasite Trichinella spiralis revealed novel genes in host parasite interaction.

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Xiaolei Liu

Full Text Available BACKGROUND: Trichinellosis is a typical food-borne zoonotic disease which is epidemic worldwide and the nematode Trichinella spiralis is the main pathogen. The life cycle of T. spiralis contains three developmental stages, i.e. adult worms, new borne larva (new borne L1 larva and muscular larva (infective L1 larva. Stage-specific gene expression in the parasites has been investigated with various immunological and cDNA cloning approaches, whereas the genome-wide transcriptome and expression features of the parasite have been largely unknown. The availability of the genome sequence information of T. spiralis has made it possible to deeply dissect parasite biology in association with global gene expression and pathogenesis. METHODOLOGY AND PRINCIPAL FINDINGS: In this study, we analyzed the global gene expression patterns in the three developmental stages of T. spiralis using digital gene expression (DGE analysis. Almost 15 million sequence tags were generated with the Illumina RNA-seq technology, producing expression data for more than 9,000 genes, covering 65% of the genome. The transcriptome analysis revealed thousands of differentially expressed genes within the genome, and importantly, a panel of genes encoding functional proteins associated with parasite invasion and immuno-modulation were identified. More than 45% of the genes were found to be transcribed from both strands, indicating the importance of RNA-mediated gene regulation in the development of the parasite. Further, based on gene ontological analysis, over 3000 genes were functionally categorized and biological pathways in the three life cycle stage were elucidated. CONCLUSIONS AND SIGNIFICANCE: The global transcriptome of T. spiralis in three developmental stages has been profiled, and most gene activity in the genome was found to be developmentally regulated. Many metabolic and biological pathways have been revealed. The findings of the differential expression of several protein

Bach Is the Father of Harmony: Revealed by a 1/f Fluctuation Analysis across Musical Genres.

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Wu, Dan; Kendrick, Keith M; Levitin, Daniel J; Li, Chaoyi; Yao, Dezhong

2015-01-01

Harmony is a fundamental attribute of music. Close connections exist between music and mathematics since both pursue harmony and unity. In music, the consonance of notes played simultaneously partly determines our perception of harmony; associates with aesthetic responses; and influences the emotion expression. The consonance could be considered as a window to understand and analyze harmony. Here for the first time we used a 1/f fluctuation analysis to investigate whether the consonance fluctuation structure in music with a wide range of composers and genres followed the scale free pattern that has been found for pitch, melody, rhythm, human body movements, brain activity, natural images and geographical features. We then used a network graph approach to investigate which composers were the most influential both within and across genres. Our results showed that patterns of consonance in music did follow scale-free characteristics, suggesting that this feature is a universally evolved one in both music and the living world. Furthermore, our network analysis revealed that Bach's harmony patterns were having the most influence on those used by other composers, followed closely by Mozart.

Alanine Enhances Aminoglycosides-Induced ROS Production as Revealed by Proteomic Analysis

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Jin-zhou Ye

2018-01-01

Full Text Available Metabolite-enabled killing of antibiotic-resistant pathogens by antibiotics is an attractive strategy to manage antibiotic resistance. Our previous study demonstrated that alanine or/and glucose increased the killing efficacy of kanamycin on antibiotic-resistant bacteria, whose action is through up-regulating TCA cycle, increasing proton motive force and enhancing antibiotic uptake. Despite the fact that alanine altered several metabolic pathways, other mechanisms could be potentially involved in alanine-mediated kanamycin killing of bacteria which remains to be explored. In the present study, we adopted proteomic approach to analyze the proteome changes induced by exogenous alanine. Our results revealed that the expression of three outer membrane proteins was altered and the deletion of nagE and fadL decreased the intracellular kanamycin concentration, implying their possible roles in mediating kanamycin transport. More importantly, the integrated analysis of proteomic and metabolomic data pointed out that alanine metabolism could connect to riboflavin metabolism that provides the source for reactive oxygen species (ROS production. Functional studies confirmed that alanine treatment together with kanamycin could promote ROS production that in turn potentiates the killing of antibiotic-resistant bacteria. Further investigation showed that alanine repressed the transcription of antioxidant-encoding genes, and alanine metabolism to riboflavin metabolism connected with riboflavin metabolism through TCA cycle, glucogenesis pathway and pentose phosphate pathway. Our results suggest a novel mechanism by which alanine facilitates kanamycin killing of antibiotic-resistant bacteria via promoting ROS production.

[Mastitis revealing Churg-Strauss syndrome].

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Dannepond, C; Le Fourn, E; de Muret, A; Ouldamer, L; Carmier, D; Machet, L

2014-01-01

Churg-Strauss syndrome often involves the skin, and this may sometimes reveal the disease. A 25-year-old woman was referred to a gynaecologist for inflammation of the right breast with breast discharge. Cytological analysis of the liquid showed numerous inflammatory cells, particularly polymorphonuclear eosinophils and neutrophils. Ultrasound examination of the breast was consistent with galactophoritis. CRP was normal, and hypereosinophilia was seen. The patient was subsequently referred to a dermatology unit. Skin examination revealed inflammation of the entire breast, which was painful, warm and erythematous; the border was oedematous with blisters. Necrotic lesions were also present on the thumbs and knees. Skin biopsy of the breast showed a dermal infiltrate with abundant infiltrate of polymorphonuclear eosinophils, including patchy necrosis and intraepidermal vesicles. Histological examination of a biopsy sample from a thumb revealed eosinophilic granuloma and leukocytoclastic vasculitis. The patient was also presenting asthma, pulmonary infiltrates and mononeuropathy at L3, consistent with Churg-Strauss syndrome. Breast involvement in Churg-Strauss syndrome is very rare (only one other case has been reported). This is the first case in which the breast condition revealed the disease. Cutaneous involvement of the breast is, however, also compatible with Wells' cellulitis. The lesions quickly disappeared with 1mg/kg/d oral prednisolone. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Network analysis of ChIP-Seq data reveals key genes in prostate cancer.

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Zhang, Yu; Huang, Zhen; Zhu, Zhiqiang; Liu, Jianwei; Zheng, Xin; Zhang, Yuhai

2014-09-03

Prostate cancer (PC) is the second most common cancer among men in the United States, and it imposes a considerable threat to human health. A deep understanding of its underlying molecular mechanisms is the premise for developing effective targeted therapies. Recently, deep transcriptional sequencing has been used as an effective genomic assay to obtain insights into diseases and may be helpful in the study of PC. In present study, ChIP-Seq data for PC and normal samples were compared, and differential peaks identified, based upon fold changes (with P-values calculated with t-tests). Annotations of these peaks were performed. Protein-protein interaction (PPI) network analysis was performed with BioGRID and constructed with Cytoscape, following which the highly connected genes were screened. We obtained a total of 5,570 differential peaks, including 3,726 differentially enriched peaks in tumor samples and 1,844 differentially enriched peaks in normal samples. There were eight significant regions of the peaks. The intergenic region possessed the highest score (51%), followed by intronic (31%) and exonic (11%) regions. The analysis revealed the top 35 highly connected genes, which comprised 33 differential genes (such as YWHAQ, tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein and θ polypeptide) from ChIP-Seq data and 2 differential genes retrieved from the PPI network: UBA52 (ubiquitin A-52 residue ribosomal protein fusion product (1) and SUMO2 (SMT3 suppressor of mif two 3 homolog (2) . Our findings regarding potential PC-related genes increase the understanding of PC and provides direction for future research.

MRI Texture Analysis Reveals Deep Gray Nuclei Damage in Amyotrophic Lateral Sclerosis.

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de Albuquerque, Milena; Anjos, Lara G V; Maia Tavares de Andrade, Helen; de Oliveira, Márcia S; Castellano, Gabriela; Junqueira Ribeiro de Rezende, Thiago; Nucci, Anamarli; França Junior, Marcondes Cavalcante

2016-01-01

Amyotrophic Lateral Sclerosis (ALS) is characterized by extensive corticospinal damage, but extrapyramidal involvement is suggested in pathological studies. Texture analysis (TA) is an image processing technique that evaluates the distribution of gray levels between pixels in a given region of interest (ROI). It provides quantitative data and has been employed in several neurodegenerative disorders. Here, we used TA to investigate possible deep gray nuclei (DGN) abnormalities in a cohort of ALS patients. Thirty-two ALS patients and 32 healthy controls underwent MRI in a 3T scanner. The T1 volumetric sequence was used for DGN segmentation and extraction of 11 texture parameters using the MaZda software. Statistical analyses were performed using the Mann-Whitney non-parametric test, with a significance level set at α = 0.025 (FDR-corrected) for TA. Patients had significantly higher values for the parameter correlation (CO) in both thalami and in the right caudate nucleus compared to healthy controls. Also, the parameter Inverse Difference Moment or Homogeneity (IDM) presented significantly smaller values in the ALS group in both thalami. TA of T1 weighted images revealed DGN alterations in patients with ALS, namely in the thalami and caudate nuclei. Copyright © 2015 by the American Society of Neuroimaging.

Superposed ruptile deformational events revealed by field and VOM structural analysis

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Kumaira, Sissa; Guadagnin, Felipe; Keller Lautert, Maiara

2017-04-01

Virtual outcrop models (VOM) is becoming an important application in the analysis of geological structures due to the possibility of obtaining the geometry and in some cases kinematic aspects of analyzed structures in a tridimensional photorealistic space. These data are used to gain quantitative information on the deformational features which coupled with numeric models can assist in understands deformational processes. Old basement units commonly register superposed deformational events either ductile or ruptile along its evolution. The Porongos Belt, located at southern Brazil, have a complex deformational history registering at least five ductile and ruptile deformational events. In this study, we presents a structural analysis of a quarry in the Porongos Belt, coupling field and VOM structural information to understand process involved in the last two deformational events. Field information was acquired using traditional structural methods for analysis of ruptile structures, such as the descriptions, drawings, acquisition of orientation vectors and kinematic analysis. VOM was created from the image-based modeling method through photogrammetric data acquisition and orthorectification. Photogrammetric data acquisition was acquired using Sony a3500 camera and a total of 128 photographs were taken from ca. 10-20 m from the outcrop in different orientations. Thirty two control point coordinates were acquired using a combination of RTK dGPS surveying and total station work, providing a precision of few millimeters for x, y and z. Photographs were imported into the Photo Scan software to create a 3D dense point cloud from structure from-motion algorithm, which were triangulated and textured to generate the VOM. VOM was georreferenced (oriented and scaled) using the ground control points, and later analyzed in OpenPlot software to extract structural information. Data was imported in Wintensor software to obtain tensor orientations, and Move software to process and

Phosphoproteome analysis of functional mitochondria isolated from resting human muscle reveals extensive phosphorylation of inner membrane protein complexes and enzymes

DEFF Research Database (Denmark)

Zhao, Xiaolu; Leon, Ileana R; Bak, Steffen

2011-01-01

. In skeletal muscle, mitochondrial dysfunction is linked to insulin resistance in humans with obesity and type 2 diabetes. We performed a phosphoproteomic study of functional mitochondria isolated from human muscle biopsies with the aim to obtain a comprehensive overview of mitochondrial phosphoproteins...... in insulin resistance. We also assigned phosphorylation sites in mitochondrial proteins involved in amino acid degradation, importers and transporters, calcium homeostasis, and apoptosis. Bioinformatics analysis of kinase motifs revealed that many of these mitochondrial phosphoproteins are substrates....... Future comparative phosphoproteome analysis of mitochondria from healthy and diseased individuals will provide insights into the role of abnormal phosphorylation in pathologies, such as type 2 diabetes....

A Study of Effects of MultiCollinearity in the Multivariable Analysis.

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Yoo, Wonsuk; Mayberry, Robert; Bae, Sejong; Singh, Karan; Peter He, Qinghua; Lillard, James W

2014-10-01

A multivariable analysis is the most popular approach when investigating associations between risk factors and disease. However, efficiency of multivariable analysis highly depends on correlation structure among predictive variables. When the covariates in the model are not independent one another, collinearity/multicollinearity problems arise in the analysis, which leads to biased estimation. This work aims to perform a simulation study with various scenarios of different collinearity structures to investigate the effects of collinearity under various correlation structures amongst predictive and explanatory variables and to compare these results with existing guidelines to decide harmful collinearity. Three correlation scenarios among predictor variables are considered: (1) bivariate collinear structure as the most simple collinearity case, (2) multivariate collinear structure where an explanatory variable is correlated with two other covariates, (3) a more realistic scenario when an independent variable can be expressed by various functions including the other variables.

Novel phage group infecting Lactobacillus delbrueckii subsp. lactis, as revealed by genomic and proteomic analysis of bacteriophage Ldl1.

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Casey, Eoghan; Mahony, Jennifer; Neve, Horst; Noben, Jean-Paul; Dal Bello, Fabio; van Sinderen, Douwe

2015-02-01

Ldl1 is a virulent phage infecting the dairy starter Lactobacillus delbrueckii subsp. lactis LdlS. Electron microscopy analysis revealed that this phage exhibits a large head and a long tail and bears little resemblance to other characterized phages infecting Lactobacillus delbrueckii. In vitro propagation of this phage revealed a latent period of 30 to 40 min and a burst size of 59.9 +/- 1.9 phage particles. Comparative genomic and proteomic analyses showed remarkable similarity between the genome of Ldl1 and that of Lactobacillus plantarum phage ATCC 8014-B2. The genomic and proteomic characteristics of Ldl1 demonstrate that this phage does not belong to any of the four previously recognized L. delbrueckii phage groups, necessitating the creation of a new group, called group e, thus adding to the knowledge on the diversity of phages targeting strains of this industrially important lactic acid bacterial species.

Optimal Strategy Analysis of a Competing Portfolio Market with a Polyvariant Profit Function

International Nuclear Information System (INIS)

Bogolubov, Nikolai N. Jr.; Kyshakevych, Bohdan Yu.; Blackmore, Denis; Prykarpatsky, Anatoliy K.

2010-12-01

A competing market model with a polyvariant profit function that assumes 'zeitnot' stock behavior of clients is formulated within the banking portfolio medium and then analyzed from the perspective of devising optimal strategies. An associated Markov process method for finding an optimal choice strategy for monovariant and bivariant profit functions is developed. Under certain conditions on the bank 'promotional' parameter with respect to the 'fee' for a missed share package transaction and at an asymptotically large enough portfolio volume, universal transcendental equations - determining the optimal share package choice among competing strategies with monovariant and bivariant profit functions - are obtained. (author)

Impact factor analysis: combining prediction with parameter ranking to reveal the impact of behavior on health outcome

DEFF Research Database (Denmark)

Doryab, Afsaneh; Frost, Mads; Faurholt-Jepsen, Maria

2015-01-01

An increasing number of healthcare systems allow people to monitor behavior and provide feedback on health and wellness. Most applications, however, only offer feedback on behavior in form of visualization and data summaries. This paper presents a different approach—called impact factor analysis—...... in monitoring and control of mental illness, and we argue that the impact factor analysis can be useful in the design of other health and wellness systems....... ten bipolar patients, in which we were able to estimate mood values with an average mean absolute error of 0.5. This was used to rank the behavior parameters whose variations indicate changes in the mental state. The rankings acquired from our algorithms correspond to the patients’ rankings......, identifying physical activity and sleep as the highest impact parameters. These results revealed the feasibility of identifying behavioral impact factors. This data analysis motivated us to design an impact factor inference engine as part of the MONARCA system. To our knowledge, this is a novel approach...

Salivary gland proteome analysis reveals modulation of anopheline unique proteins in insensitive acetylcholinesterase resistant Anopheles gambiae mosquitoes.

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Sylvie Cornelie

Full Text Available Insensitive acetylcholinesterase resistance due to a mutation in the acetylcholinesterase (ace encoding ace-1 gene confers cross-resistance to organophosphate and carbamate insecticides in Anopheles gambiae populations from Central and West Africa. This mutation is associated with a strong genetic cost revealed through alterations of some life history traits but little is known about the physiological and behavioural changes in insects bearing the ace-1(R allele. Comparative analysis of the salivary gland contents between An. gambiae susceptible and ace-1(R resistant strains was carried out to charaterize factors that could be involved in modifications of blood meal process, trophic behaviour or pathogen interaction in the insecticide-resistant mosquitoes. Differential analysis of the salivary gland protein profiles revealed differences in abundance for several proteins, two of them showing major differences between the two strains. These two proteins identified as saglin and TRIO are salivary gland-1 related proteins, a family unique to anopheline mosquitoes, one of them playing a crucial role in salivary gland invasion by Plasmodium falciparum sporozoites. Differential expression of two other proteins previously identified in the Anopheles sialome was also observed. The differentially regulated proteins are involved in pathogen invasion, blood feeding process, and protection against oxidation, relevant steps in the outcome of malaria infection. Further functional studies and insect behaviour experiments would confirm the impact of the modification of the sialome composition on blood feeding and pathogen transmission abilities of the resistant mosquitoes. The data supports the hypothesis of alterations linked to insecticide resistance in the biology of the primary vector of human malaria in Africa.

Local fluctuations of the signed traded volumes and the dependencies of demands: a copula analysis

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Wang, Shanshan; Guhr, Thomas

2018-03-01

We investigate how the local fluctuations of the signed traded volumes affect the dependence of demands between stocks. We analyze the empirical dependence of demands using copulas and show that they are well described by a bivariate K copula density function. We find that large local fluctuations strongly increase the positive dependence but lower slightly the negative one in the copula density. This interesting feature is due to cross-correlations of volume imbalances between stocks. Also, we explore the asymmetries of tail dependencies of the copula density, which are moderate for the negative dependencies but strong for the positive ones. For the latter, we reveal that large local fluctuations of the signed traded volumes trigger stronger dependencies of demands than of supplies, probably indicating a bull market with persistent raising of prices.

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

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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.

Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements

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Ahn Jong Hwa

2011-01-01

Full Text Available Abstract Background Among the Solanaceae plants, the pepper genome is three times larger than that of tomato. Although the gene repertoire and gene order of both species are well conserved, the cause of the genome-size difference is not known. To determine the causes for the expansion of pepper euchromatic regions, we compared the pepper genome to that of tomato. Results For sequence-level analysis, we generated 35.6 Mb of pepper genomic sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative analysis of orthologous gene-rich regions between both species revealed insertion of transposons exclusively in the pepper sequences, maintaining the gene order and content. The most common type of the transposon found was the LTR retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed that two groups of Ty3/Gypsy-like elements (Tat and Athila were overly accumulated in the pepper genome. The FISH analysis of the pepper Tat elements showed a random distribution in heterochromatic and euchromatic regions, whereas the tomato Tat elements showed heterochromatin-preferential accumulation. Conclusions Compared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of Ty3/Gypsy-like elements. Our results could provide an insight on the mechanism of genome evolution in the Solanaceae family.

Analysis of the impact of crude oil price fluctuations on China's stock market in different periods-Based on time series network model

Science.gov (United States)

An, Yang; Sun, Mei; Gao, Cuixia; Han, Dun; Li, Xiuming

2018-02-01

This paper studies the influence of Brent oil price fluctuations on the stock prices of China's two distinct blocks, namely, the petrochemical block and the electric equipment and new energy block, applying the Shannon entropy of information theory. The co-movement trend of crude oil price and stock prices is divided into different fluctuation patterns with the coarse-graining method. Then, the bivariate time series network model is established for the two blocks stock in five different periods. By joint analysis of the network-oriented metrics, the key modes and underlying evolutionary mechanisms were identified. The results show that the both networks have different fluctuation characteristics in different periods. Their co-movement patterns are clustered in some key modes and conversion intermediaries. The study not only reveals the lag effect of crude oil price fluctuations on the stock in Chinese industry blocks but also verifies the necessity of research on special periods, and suggests that the government should use different energy policies to stabilize market volatility in different periods. A new way is provided to study the unidirectional influence between multiple variables or complex time series.

Possible antecedents and consequences of self-esteem in persons with multiple sclerosis: preliminary evidence from a cross-sectional analysis.

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Dlugonski, Deirdre; Motl, Robert W

2012-02-01

Persons with multiple sclerosis (MS) have consistently reported lower levels of self-esteem compared with the general population. Despite this, very little is known about the antecedents and consequences of self-esteem in persons with MS. To examine (1) physical activity and social support as potentially modifiable correlates (i.e., antecedents) of self-esteem and (2) physical and psychological health-related quality of life as possible consequences of self-esteem in persons with MS. Participants (N = 46) wore an Actigraph accelerometer for 7 days and then completed a battery of questionnaires, including the Rosenberg Self-Esteem Scale (RSES), Multiple Sclerosis Impact Scale (MSIS-29), and Social Provisions Scale (SPS). The data were analyzed using PASW Statistics 18. Bivariate correlation analysis indicated that average daily step counts (r = .298, p = .026) and social support (r = .366, p = .007) were significantly correlated with self-esteem. Multiple linear regression analysis indicated that only social support was a significant predictor of self-esteem scores (β = .411, p = .004); pedometer steps approached significance as a predictor of self-esteem (β = .178, p = .112). Bivariate correlation analysis further indicated significant negative associations between self-esteem and physical (r = -.391, p = .004) and psychological (r = -.540, p = .0001) domains of health-related quality of life (HRQOL), indicating that higher self-esteem was associated with more positive HRQOL. Social support is a potentially modifiable variable that may be important to target when designing interventions to improve self-esteem and this might have implications for improving physical and psychological HRQOL in persons with MS.

Semi-automated landmark-based 3D analysis reveals new morphometric characteristics in the trochlear dysplastic femur.

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Van Haver, Annemieke; De Roo, Karel; De Beule, Matthieu; Van Cauter, Sofie; Audenaert, Emmanuel; Claessens, Tom; Verdonk, Peter

2014-11-01

The authors hypothesise that the trochlear dysplastic distal femur is not only characterised by morphological changes to the trochlea. The purpose of this study is to describe the morphological characteristics of the trochlear dysplastic femur in and outside the trochlear region with a landmark-based 3D analysis. Arthro-CT scans of 20 trochlear dysplastic and 20 normal knees were used to generate 3D models including the cartilage. To rule out size differences, a set of landmarks were defined on the distal femur to isotropically scale the 3D models to a standard size. A predefined series of landmark-based reference planes were applied on the distal femur. With these landmarks and reference planes, a series of previously described characteristics associated with trochlear dysplasia as well as a series of morphometric characteristics were measured. For the previously described characteristics, the analysis replicated highly significant differences between trochlear dysplastic and normal knees. Furthermore, the analysis showed that, when knee size is taken into account, the cut-off values of the trochlear bump and depth would be 1 mm larger in the largest knees compared to the smallest knees. For the morphometric characteristics, the analysis revealed that the trochlear dysplastic femur is also characterised by a 10% smaller intercondylar notch, 6-8% larger posterior condyles (lateral-medial) in the anteroposterior direction and a 6% larger medial condyle in the proximodistal direction compared to a normal femur. This study shows that knee size is important in the application of absolute metric cut-off values and that the posterior femur also shows a significantly different morphology.

Degrees of Cooperation in Household Consumption Models : A Revealed Preference Analysis

NARCIS (Netherlands)

Cherchye, L.J.H.; Demuynck, T.; de Rock, B.

2009-01-01

We develop a revealed preference approach to analyze non-unitary con- sumption models with intrahousehold allocations deviating from the cooper- ative (or Pareto e¢ cient) solution. At a theoretical level, we establish re- vealed preference conditions of household consumption models with varying

Virtually naked: virtual environment reveals sex-dependent nature of skin disclosure.

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Anna M Lomanowska

Full Text Available The human tendency to reveal or cover naked skin reflects a competition between the individual propensity for social interactions related to sexual appeal and interpersonal touch versus climatic, environmental, physical, and cultural constraints. However, due to the ubiquitous nature of these constraints, isolating on a large scale the spontaneous human tendency to reveal naked skin has remained impossible. Using the online 3-dimensional virtual world of Second Life, we examined spontaneous human skin-covering behavior unhindered by real-world climatic, environmental, and physical variables. Analysis of hundreds of avatars revealed that virtual females disclose substantially more naked skin than virtual males. This phenomenon was not related to avatar hypersexualization as evaluated by measurement of sexually dimorphic body proportions. Furthermore, analysis of skin-covering behavior of a population of culturally homogeneous avatars indicated that the propensity of female avatars to reveal naked skin persisted despite explicit cultural norms promoting less revealing attire. These findings have implications for further understanding how sex-specific aspects of skin disclosure influence human social interactions in both virtual and real settings.

Comparative Analysis of WUSCHEL-Related Homeobox Genes Revealed Their Parent-of-Origin and Cell Type-Specific Expression Pattern During Early Embryogenesis in Tobacco

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Xuemei Zhou

2018-03-01

Full Text Available WUSCHEL-related homeobox (WOX gene is a plant-specific clade of homeobox transcription factors. Increasing evidences reveal that WOXs play critical roles in early embryogenesis, which involves zygote development, initiation of zygote division, and apical or basal cell lineage establishment. However, how WOXs regulate these developmental events remains largely unknown, and even detailed expression pattern in gametes and early proembryos is not yet available. Here, 13 WOX family genes were identified in Nicotiana tabacum genome. Comparative analysis of 13 WOX family genes with their homologs in Arabidopsis thaliana reveals relatively conserved expression pattern of WUS and WOX5 in shoot/root apical meristem. Whereas variations were also found, e.g., lacking homolog of WOX8 (a marker for suspensor cell in tobacco genome and the expression of WOX2/WOX9 in both apical cell and basal cell. Transient transcriptional activity analysis revealed that WOXs in WUS clade have repressive activities for their target's transcription, whereas WOXs in ancient and intermediate clade have activation activities, giving a molecular basis for the phylogenetic classification of tobacco WOXs into three major clades. Expression pattern analysis revealed that some WOXs (e.g., WOX 13a expressed in both male and female gametes and some WOXs (e.g., WOX 11 and WOX 13b displayed the characteristics of parent-of-origin genes. Interestingly, some WOXs (e.g., WOX2 and WOX9, which are essential for early embryo patterning, were de novo transcribed in zygote, indicating relevant mechanism for embryo pattern formation is only established in zygote right after fertilization and not carried in by gametes. We also found that most WOXs displayed a stage-specific and cell type-specific expression pattern. Taken together, this work provides a detailed landscape of WOXs in tobacco during fertilization and early embryogenesis, which will facilitate the understanding of their specific roles

What factors are associated with unplanned return following transurethral resection of bladder tumor? An analysis of a large single institution's experience.

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Ghali, Fady; Moses, Rachel A; Raffin, Eric; Hyams, Elias S

2016-10-01

This study sought to evaluate factors associated with unplanned hospital return (UR) following transurethral resection of bladder tumor (TURBT), the largest source of readmission among ambulatory urological procedures. A retrospective review of TURBTs at a single academic institution between April 2011 and August 2014 was performed. Demographics, comorbidities, length of stay, tumor size and multiple other factors were recorded. UR was recorded within 30 days of surgery. Bivariate and multivariable analyses were performed to determine factors associated with UR. Among 708 patients undergoing TURBT, 23.9% were female with a mean age of 70 years. The rate of UR was 10.9%. The most common cause of UR was gross hematuria, accounting for 70%. On bivariate analysis, Foley catheter placement in the operating room, non-aspirin anticoagulation and index length of stay longer than 24 h were associated with hematuria-related UR (p hematuria-related UR (p  0.05). On multivariable analysis, only Foley placement in the operating room remained associated with higher rates of hematuria-related UR, while preoperative antibiotics, female gender and aspirin therapy remained associated with a lower likelihood of this event. UR following TURBT is common and typically results from gross hematuria. Patients with postoperative Foley catheterization in the operating room may require additional counseling or supervision before discharge, and should be considered for discharge with a Foley rather than having a prompt voiding trial.

Job satisfaction and intention to quit: an empirical analysis of nurses in Turkey.

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Masum, Abdul Kadar Muhammad; Azad, Md Abul Kalam; Hoque, Kazi Enamul; Beh, Loo-See; Wanke, Peter; Arslan, Özgün

2016-01-01

The aim of this study was to identify the facets influencing job satisfaction and intention to quit of nurses employed in Turkey. Using a non-probability sampling technique, 417 nurses from six large private hospitals were surveyed from March 2014 to June 2014. The nurses' demographic data, their job-related satisfaction and turnover intentions were recorded through a self-administered questionnaire. In this study, descriptive and bivariate analyses were used to explore data, and multivariate analysis was performed using logistic regression. Nurses' job satisfaction was found at a moderate level with 61% of the nurses intended to quit. Nevertheless, nurses reported a high satisfaction level with work environment, supervisor support, and co-workers among the selected nine facets of job satisfaction. They also reported a low satisfaction level with contingent reward, fringe benefits, and pay. The impact of demographic characteristics on job satisfaction and intention to quit was also examined. The study revealed a negative relationship between job satisfaction and intention to quit the existing employment. Moreover, satisfaction with supervisor support was the only facet that significantly explained turnover intent when controlling for gender, age, marital status, education, and experience. The implications for nurse management were also described for increasing nurses' job satisfaction and retention. This study is beneficial for hospital management to ensure proper nursing care that would lead to a better quality healthcare service.

Job satisfaction and intention to quit: an empirical analysis of nurses in Turkey

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Abdul Kadar Muhammad Masum

2016-04-01

Full Text Available The aim of this study was to identify the facets influencing job satisfaction and intention to quit of nurses employed in Turkey. Using a non-probability sampling technique, 417 nurses from six large private hospitals were surveyed from March 2014 to June 2014. The nurses’ demographic data, their job-related satisfaction and turnover intentions were recorded through a self-administered questionnaire. In this study, descriptive and bivariate analyses were used to explore data, and multivariate analysis was performed using logistic regression. Nurses’ job satisfaction was found at a moderate level with 61% of the nurses intended to quit. Nevertheless, nurses reported a high satisfaction level with work environment, supervisor support, and co-workers among the selected nine facets of job satisfaction. They also reported a low satisfaction level with contingent reward, fringe benefits, and pay. The impact of demographic characteristics on job satisfaction and intention to quit was also examined. The study revealed a negative relationship between job satisfaction and intention to quit the existing employment. Moreover, satisfaction with supervisor support was the only facet that significantly explained turnover intent when controlling for gender, age, marital status, education, and experience. The implications for nurse management were also described for increasing nurses’ job satisfaction and retention. This study is beneficial for hospital management to ensure proper nursing care that would lead to a better quality healthcare service.

Job satisfaction and intention to quit: an empirical analysis of nurses in Turkey

Science.gov (United States)

Azad, Md. Abul Kalam; Hoque, Kazi Enamul; Beh, Loo-See; Wanke, Peter; Arslan, Özgün

2016-01-01

The aim of this study was to identify the facets influencing job satisfaction and intention to quit of nurses employed in Turkey. Using a non-probability sampling technique, 417 nurses from six large private hospitals were surveyed from March 2014 to June 2014. The nurses’ demographic data, their job-related satisfaction and turnover intentions were recorded through a self-administered questionnaire. In this study, descriptive and bivariate analyses were used to explore data, and multivariate analysis was performed using logistic regression. Nurses’ job satisfaction was found at a moderate level with 61% of the nurses intended to quit. Nevertheless, nurses reported a high satisfaction level with work environment, supervisor support, and co-workers among the selected nine facets of job satisfaction. They also reported a low satisfaction level with contingent reward, fringe benefits, and pay. The impact of demographic characteristics on job satisfaction and intention to quit was also examined. The study revealed a negative relationship between job satisfaction and intention to quit the existing employment. Moreover, satisfaction with supervisor support was the only facet that significantly explained turnover intent when controlling for gender, age, marital status, education, and experience. The implications for nurse management were also described for increasing nurses’ job satisfaction and retention. This study is beneficial for hospital management to ensure proper nursing care that would lead to a better quality healthcare service. PMID:27168960

Pre-2014 mudslides at Oso revealed by InSAR and multi-source DEM analysis

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Kim, J. W.; Lu, Z.; QU, F.

2014-12-01

The landslide is a process that results in the downward and outward movement of slope-reshaping materials including rocks and soils and annually causes the loss of approximately $3.5 billion and tens of casualties in the United States. The 2014 Oso mudslide was an extreme event costing nearly 40 deaths and damaging civilian properties. Landslides are often unpredictable, but in many cases, catastrophic events are repetitive. Historic record in the Oso mudslide site indicates that there have been serial events in decades, though the extent of sliding events varied from time to time. In our study, the combination of multi-source DEMs, InSAR, and time-series InSAR analysis has enabled to characterize the Oso mudslide. InSAR results from ALOS PALSAR show that there was no significant deformation between mid-2006 and 2011. The combination of time-series InSAR analysis and old-dated DEM indicated revealed topographic changes associated the 2006 sliding event, which is confirmed by the difference of multiple LiDAR DEMs. Precipitation and discharge measurements before the 2006 and 2014 landslide events did not exhibit extremely anomalous records, suggesting the precipitation is not the controlling factor in determining the sliding events at Oso. The lack of surface deformation during 2006-2011 and weak correlation between the precipitation and the sliding event, suggest other factors (such as porosity) might play a critical role on the run-away events at this Oso and other similar landslides.

Joint cross-correlation analysis reveals complex, time-dependent functional relationship between cortical neurons and arm electromyograms

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Zhuang, Katie Z.; Lebedev, Mikhail A.

2014-01-01

Correlation between cortical activity and electromyographic (EMG) activity of limb muscles has long been a subject of neurophysiological studies, especially in terms of corticospinal connectivity. Interest in this issue has recently increased due to the development of brain-machine interfaces with output signals that mimic muscle force. For this study, three monkeys were implanted with multielectrode arrays in multiple cortical areas. One monkey performed self-timed touch pad presses, whereas the other two executed arm reaching movements. We analyzed the dynamic relationship between cortical neuronal activity and arm EMGs using a joint cross-correlation (JCC) analysis that evaluated trial-by-trial correlation as a function of time intervals within a trial. JCCs revealed transient correlations between the EMGs of multiple muscles and neural activity in motor, premotor and somatosensory cortical areas. Matching results were obtained using spike-triggered averages corrected by subtracting trial-shuffled data. Compared with spike-triggered averages, JCCs more readily revealed dynamic changes in cortico-EMG correlations. JCCs showed that correlation peaks often sharpened around movement times and broadened during delay intervals. Furthermore, JCC patterns were directionally selective for the arm-reaching task. We propose that such highly dynamic, task-dependent and distributed relationships between cortical activity and EMGs should be taken into consideration for future brain-machine interfaces that generate EMG-like signals. PMID:25210153

Bivariate threshold models for genetic evaluation of susceptibility to and ability to recover from mastitis in Danish Holstein cows.

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Welderufael, B G; Janss, L L G; de Koning, D J; Sørensen, L P; Løvendahl, P; Fikse, W F

2017-06-01

Mastitis in dairy cows is an unavoidable problem and genetic variation in recovery from mastitis, in addition to susceptibility, is therefore of interest. Genetic parameters for susceptibility to and recovery from mastitis were estimated for Danish Holstein-Friesian cows using data from automatic milking systems equipped with online somatic cell count measuring units. The somatic cell count measurements were converted to elevated mastitis risk, a continuous variable [on a (0-1) scale] indicating the risk of mastitis. Risk values >0.6 were assumed to indicate that a cow had mastitis. For each cow and lactation, the sequence of health states (mastitic or healthy) was converted to a weekly transition: 0 if the cow stayed within the same state and 1 if the cow changed state. The result was 2 series of transitions: one for healthy to diseased (HD, to model mastitis susceptibility) and the other for diseased to healthy (DH, to model recovery ability). The 2 series of transitions were analyzed with bivariate threshold models, including several systematic effects and a function of time. The model included effects of herd, parity, herd-test-week, permanent environment (to account for the repetitive nature of transition records from a cow) plus two time-varying effects (lactation stage and time within episode). In early lactation, there was an increased risk of getting mastitis but the risk remained stable afterwards. Mean recovery rate was 45% per lactation. Heritabilities were 0.07 [posterior mean of standard deviations (PSD) = 0.03] for HD and 0.08 (PSD = 0.03) for DH. The genetic correlation between HD and DH has a posterior mean of -0.83 (PSD = 0.13). Although susceptibility and recovery from mastitis are strongly negatively correlated, recovery can be considered as a new trait for selection. The Authors. Published by the Federation of Animal Science Societies and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under

Bach Is the Father of Harmony: Revealed by a 1/f Fluctuation Analysis across Musical Genres.

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Dan Wu

Full Text Available Harmony is a fundamental attribute of music. Close connections exist between music and mathematics since both pursue harmony and unity. In music, the consonance of notes played simultaneously partly determines our perception of harmony; associates with aesthetic responses; and influences the emotion expression. The consonance could be considered as a window to understand and analyze harmony. Here for the first time we used a 1/f fluctuation analysis to investigate whether the consonance fluctuation structure in music with a wide range of composers and genres followed the scale free pattern that has been found for pitch, melody, rhythm, human body movements, brain activity, natural images and geographical features. We then used a network graph approach to investigate which composers were the most influential both within and across genres. Our results showed that patterns of consonance in music did follow scale-free characteristics, suggesting that this feature is a universally evolved one in both music and the living world. Furthermore, our network analysis revealed that Bach's harmony patterns were having the most influence on those used by other composers, followed closely by Mozart.

Comparative metabolome analysis of wheat embryo and endosperm reveals the dynamic changes of metabolites during seed germination.

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Han, Caixia; Zhen, Shoumin; Zhu, Gengrui; Bian, Yanwei; Yan, Yueming

2017-06-01

In this study, we performed the first comparative metabolomic analysis of the wheat embryo and endosperm during seed germination using GC-MS/MS. In total, 82 metabolites were identified in the embryo and endosperm. Principal component analysis (PCA), metabolite-metabolite correlation and hierarchical cluster analysis (HCA) revealed distinct dynamic changes in metabolites between the embryo and endosperm during seed germination. Generally, the metabolite changes in the embryo were much greater than those in the endosperm, suggesting that the embryo is more active than the endosperm during seed germination. Most amino acids were upregulated in both embryo and endosperm, while polysaccharides and organic acids associated with sugars were mainly downregulated in the embryo. Most of the sugars showed an upregulated trend in the endosperm, but significant changes in lipids occurred only in the embryo. Our results suggest that the embryo mobilises mainly protein and lipid metabolism, while the endosperm mobilises storage starch and minor protein metabolism during seed germination. The primary energy was generated mainly in the embryo by glycolysis during seed imbibition. The embryo containing most of the genetic information showed increased nucleotides during seed germination process, indicating more active transcription and translation metabolisms. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Three-dimensional Crustal Structure beneath the Tibetan Plateau Revealed by Multi-scale Gravity Analysis

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Xu, C.; Luo, Z.; Sun, R.; Li, Q.

2017-12-01

The Tibetan Plateau, the largest and highest plateau on Earth, was uplifted, shorten and thicken by the collision and continuous convergence of the Indian and Eurasian plates since 50 million years ago, the Eocene epoch. Fine three-dimensional crustal structure of the Tibetan Plateau is helpful in understanding the tectonic development. At present, the ordinary method used for revealing crustal structure is seismic method, which is inhibited by poor seismic station coverage, especially in the central and western plateau primarily due to the rugged terrain. Fortunately, with the implementation of satellite gravity missions, gravity field models have demonstrated unprecedented global-scale accuracy and spatial resolution, which can subsequently be employed to study the crustal structure of the entire Tibetan Plateau. This study inverts three-dimensional crustal density and Moho topography of the Tibetan Plateau from gravity data using multi-scale gravity analysis. The inverted results are in agreement with those provided by the previous works. Besides, they can reveal rich tectonic development of the Tibetan Plateau: (1) The low-density channel flow can be observed from the inverted crustal density; (2) The Moho depth in the west is deeper than that in the east, and the deepest Moho, which is approximately 77 km, is located beneath the western Qiangtang Block; (3) The Moho fold, the directions of which are in agreement with the results of surface movement velocities estimated from Global Positioning System, exists clearly on the Moho topography.This study is supported by the National Natural Science Foundation of China (Grant No. 41504015), the China Postdoctoral Science Foundation (Grant No. 2015M572146), and the Surveying and Mapping Basic Research Programme of the National Administration of Surveying, Mapping and Geoinformation (Grant No. 15-01-08).

Data-driven analysis of simultaneous EEG/fMRI reveals neurophysiological phenotypes of impulse control.

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Schmüser, Lena; Sebastian, Alexandra; Mobascher, Arian; Lieb, Klaus; Feige, Bernd; Tüscher, Oliver

2016-09-01

Response inhibition is the ability to suppress inadequate but prepotent or ongoing response tendencies. A fronto-striatal network is involved in these processes. Between-subject differences in the intra-individual variability have been suggested to constitute a key to pathological processes underlying impulse control disorders. Single-trial EEG/fMRI analysis allows to increase sensitivity for inter-individual differences by incorporating intra-individual variability. Thirty-eight healthy subjects performed a visual Go/Nogo task during simultaneous EEG/fMRI. Of 38 healthy subjects, 21 subjects reliably showed Nogo-related ICs (Nogo-IC-positive) while 17 subjects (Nogo-IC-negative) did not. Comparing both groups revealed differences on various levels: On trait level, Nogo-IC-negative subjects scored higher on questionnaires regarding attention deficit/hyperactivity disorder; on a behavioral level, they displayed slower response times (RT) and higher intra-individual RT variability while both groups did not differ in their inhibitory performance. On the neurophysiological level, Nogo-IC-negative subjects showed a hyperactivation of left inferior frontal cortex/insula and left putamen as well as significantly reduced P3 amplitudes. Thus, a data-driven approach for IC classification and the resulting presence or absence of early Nogo-specific ICs as criterion for group selection revealed group differences at behavioral and neurophysiological levels. This may indicate electrophysiological phenotypes characterized by inter-individual variations of neural and behavioral correlates of impulse control. We demonstrated that the inter-individual difference in an electrophysiological correlate of response inhibition is correlated with distinct, potentially compensatory neural activity. This may suggest the existence of electrophysiologically dissociable phenotypes of behavioral and neural motor response inhibition with the Nogo-IC-positive phenotype possibly providing

A survey of variable selection methods in two Chinese epidemiology journals

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Lynn Henry S

2010-09-01

Full Text Available Abstract Background Although much has been written on developing better procedures for variable selection, there is little research on how it is practiced in actual studies. This review surveys the variable selection methods reported in two high-ranking Chinese epidemiology journals. Methods Articles published in 2004, 2006, and 2008 in the Chinese Journal of Epidemiology and the Chinese Journal of Preventive Medicine were reviewed. Five categories of methods were identified whereby variables were selected using: A - bivariate analyses; B - multivariable analysis; e.g. stepwise or individual significance testing of model coefficients; C - first bivariate analyses, followed by multivariable analysis; D - bivariate analyses or multivariable analysis; and E - other criteria like prior knowledge or personal judgment. Results Among the 287 articles that reported using variable selection methods, 6%, 26%, 30%, 21%, and 17% were in categories A through E, respectively. One hundred sixty-three studies selected variables using bivariate analyses, 80% (130/163 via multiple significance testing at the 5% alpha-level. Of the 219 multivariable analyses, 97 (44% used stepwise procedures, 89 (41% tested individual regression coefficients, but 33 (15% did not mention how variables were selected. Sixty percent (58/97 of the stepwise routines also did not specify the algorithm and/or significance levels. Conclusions The variable selection methods reported in the two journals were limited in variety, and details were often missing. Many studies still relied on problematic techniques like stepwise procedures and/or multiple testing of bivariate associations at the 0.05 alpha-level. These deficiencies should be rectified to safeguard the scientific validity of articles published in Chinese epidemiology journals.

The double-edged sword of electronic health records: implications for patient disclosure.

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Campos-Castillo, Celeste; Anthony, Denise L

2015-04-01

Electronic health record (EHR) systems are linked to improvements in quality of care, yet also privacy and security risks. Results from research studies are mixed about whether patients withhold personal information from their providers to protect against the perceived EHR privacy and security risks. This study seeks to reconcile the mixed findings by focusing on whether accounting for patients' global ratings of care reveals a relationship between EHR provider-use and patient non-disclosure. A nationally representative sample from the 2012 Health Information National Trends Survey was analyzed using bivariate and multivariable logit regressions to examine whether global ratings of care suppress the relationship between EHR provider-use and patient non-disclosure. 13% of respondents reported having ever withheld information from a provider because of privacy/security concerns. Bivariate analysis showed that withholding information was unrelated to whether respondents' providers used an EHR. Multivariable analysis showed that accounting for respondents' global ratings of care revealed a positive relationship between having a provider who uses an EHR and withholding information. After accounting for global ratings of care, findings suggest that patients may non-disclose to providers to protect against the perceived EHR privacy and security risks. Despite evidence that EHRs inhibit patient disclosure, their advantages for promoting quality of care may outweigh the drawbacks. Clinicians should leverage the EHR's value in quality of care and discuss patients' privacy concerns during clinic visits, while policy makers should consider how to address the real and perceived privacy and security risks of EHRs. © The Author 2014. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Spatial structure of a natural mixed topodeme of subalpine Sorbus taxa

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Dušan Gömöry

2011-01-01

Full Text Available Spatial distribution and genetic variation of a population of Sorbus chamaemespilus (L. Crantz and putative hybrids between S. chamaemespilus, S. aria and S. aucuparia growing in the nature reserve Skalnä Alpa (central Slovakia were studied. The analysis of spatial patterns using Ripley's K-function revealed a significant clustering of the adults of both S. chamaemespilus and hybrid taxa at distances up to ~15 m and a strong affinity between both taxonomical groups, indicating similar ecological requirements. Bivariate point-pattern analysis considering cardinal direction showed that juvenile individuals of S. chamaemespilus are clustered around the adults up to the distance of ~2 m, whereas in hybrid taxa with larger and more dense crowns, juveniles are clustered at distances more than ~3 m from the adults. The analysis of genetic variation in a subset of adult shrubs using 4 nuclear microsatellite loci revealed that unlike expected, there was no variation in S. chamaemespilus but several genotypes were found in the group of hybrid taxa. Implications for the reproduction system and conservation of the investigated taxa are discussed.

In vivo transcriptional profile analysis reveals RNA splicing and chromatin remodeling as prominent processes for adult neurogenesis.

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Lim, Daniel A; Suárez-Fariñas, Mayte; Naef, Felix; Hacker, Coleen R; Menn, Benedicte; Takebayashi, Hirohide; Magnasco, Marcelo; Patil, Nila; Alvarez-Buylla, Arturo

2006-01-01

Neural stem cells and neurogenesis persist in the adult mammalian brain subventricular zone (SVZ). Cells born in the rodent SVZ migrate to the olfactory bulb (Ob) where they differentiate into interneurons. To determine the gene expression and functional profile of SVZ neurogenesis, we performed three complementary sets of transcriptional analysis experiments using Affymetrix GeneChips: (1) comparison of adult mouse SVZ and Ob gene expression profiles with those of the striatum, cerebral cortex, and hippocampus; (2) profiling of SVZ stem cells and ependyma isolated by fluorescent-activated cell sorting (FACS); and (3) analysis of gene expression changes during in vivo SVZ regeneration after anti-mitotic treatment. Gene Ontology (GO) analysis of data from these three separate approaches showed that in adult SVZ neurogenesis, RNA splicing and chromatin remodeling are biological processes as statistically significant as cell proliferation, transcription, and neurogenesis. In non-neurogenic brain regions, RNA splicing and chromatin remodeling were not prominent processes. Fourteen mRNA splicing factors including Sf3b1, Sfrs2, Lsm4, and Khdrbs1/Sam68 were detected along with 9 chromatin remodeling genes including Mll, Bmi1, Smarcad1, Baf53a, and Hat1. We validated the transcriptional profile data with Northern blot analysis and in situ hybridization. The data greatly expand the catalogue of cell cycle components, transcription factors, and migration genes for adult SVZ neurogenesis and reveal RNA splicing and chromatin remodeling as prominent biological processes for these germinal cells.

Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements.

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Voskarides, Konstantinos; Mazières, Stéphane; Hadjipanagi, Despina; Di Cristofaro, Julie; Ignatiou, Anastasia; Stefanou, Charalambos; King, Roy J; Underhill, Peter A; Chiaroni, Jacques; Deltas, Constantinos

2016-01-01

The archeological record indicates that the permanent settlement of Cyprus began with pioneering agriculturalists circa 11,000 years before present, (ca. 11,000 y BP). Subsequent colonization events followed, some recognized regionally. Here, we assess the Y-chromosome structure of Cyprus in context to regional populations and correlate it to phases of prehistoric colonization. Analysis of haplotypes from 574 samples showed that island-wide substructure was barely significant in a spatial analysis of molecular variance (SAMOVA). However, analyses of molecular variance (AMOVA) of haplogroups using 92 binary markers genotyped in 629 Cypriots revealed that the proportion of variance among the districts was irregularly distributed. Principal component analysis (PCA) revealed potential genetic associations of Greek-Cypriots with neighbor populations. Contrasting haplogroups in the PCA were used as surrogates of parental populations. Admixture analyses suggested that the majority of G2a-P15 and R1b-M269 components were contributed by Anatolia and Levant sources, respectively, while Greece Balkans supplied the majority of E-V13 and J2a-M67. Haplotype-based expansion times were at historical levels suggestive of recent demography. Analyses of Cypriot haplogroup data are consistent with two stages of prehistoric settlement. E-V13 and E-M34 are widespread, and PCA suggests sourcing them to the Balkans and Levant/Anatolia, respectively. The persistent pre-Greek component is represented by elements of G2-U5(xL30) haplogroups: U5*, PF3147, and L293. J2b-M205 may contribute also to the pre-Greek strata. The majority of R1b-Z2105 lineages occur in both the westernmost and easternmost districts. Distinctively, sub-haplogroup R1b- M589 occurs only in the east. The absence of R1b- M589 lineages in Crete and the Balkans and the presence in Asia Minor are compatible with Late Bronze Age influences from Anatolia rather than from Mycenaean Greeks.

Personality Traits as Predictors of Shopping Motivations and Behaviors: A Canonical Correlation Analysis

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Ali Gohary

2014-10-01

Full Text Available This study examines the relationship between Big Five personality traits with shopping motivation variables consisting of compulsive and impulsive buying, hedonic and utilitarian shopping values. Two hundred forty seven college students were recruited to participate in this research. Bivariate correlation demonstrates an overlap between personality traits; consequently, canonical correlation was performed to prevent this phenomenon. The results of multiple regression analysis suggested conscientiousness, neuroticism and openness as predictors of compulsive buying, impulsive buying and utilitarian shopping values. In addition, the results showed significant differences between males and females on conscientiousness, neuroticism, openness, compulsive buying and hedonic shopping value. Besides, using hierarchical regression analysis, we examined sex as moderator between Big Five personality traits and shopping variables, but we didn’t find sufficient evidence to prove it.

Differential proteomic analysis reveals sequential heat stress-responsive regulatory network in radish (Raphanus sativus L.) taproot.

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Wang, Ronghua; Mei, Yi; Xu, Liang; Zhu, Xianwen; Wang, Yan; Guo, Jun; Liu, Liwang

2018-05-01

Differential abundance protein species (DAPS) involved in reducing damage and enhancing thermotolerance in radish were firstly identified. Proteomic analysis and omics association analysis revealed a HS-responsive regulatory network in radish. Heat stress (HS) is a major destructive factor influencing radish production and supply in summer, for radish is a cool season vegetable crop being susceptible to high temperature. In this study, the proteome changes of radish taproots under 40 °C treatment at 0 h (Control), 12 h (Heat12) and 24 h (Heat24) were analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification) approach. In total, 2258 DAPS representing 1542 differentially accumulated uniprotein species which respond to HS were identified. A total of 604, 910 and 744 DAPS was detected in comparison of Control vs. Heat12, Control vs. Heat24, and Heat12 vs. Heat24, respectively. Gene ontology and pathway analysis showed that annexin, ubiquitin-conjugating enzyme, ATP synthase, heat shock protein (HSP) and other stress-related proteins were predominately enriched in signal transduction, stress and defense pathways, photosynthesis and energy metabolic pathways, working cooperatively to reduce stress-induced damage in radish. Based on iTRAQ combined with the transcriptomics analysis, a schematic model of a sequential HS-responsive regulatory network was proposed. The initial sensing of HS occurred at the plasma membrane, and then key components of stress signal transduction triggered heat-responsive genes in the plant protective metabolism to re-establish homeostasis and enhance thermotolerance. These results provide new insights into characteristics of HS-responsive DAPS and facilitate dissecting the molecular mechanisms underlying heat tolerance in radish and other root crops.

An integrative genomic and transcriptomic analysis reveals potential targets associated with cell proliferation in uterine leiomyomas.

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Priscila Daniele Ramos Cirilo

Full Text Available Uterine Leiomyomas (ULs are the most common benign tumours affecting women of reproductive age. ULs represent a major problem in public health, as they are the main indication for hysterectomy. Approximately 40-50% of ULs have non-random cytogenetic abnormalities, and half of ULs may have copy number alterations (CNAs. Gene expression microarrays studies have demonstrated that cell proliferation genes act in response to growth factors and steroids. However, only a few genes mapping to CNAs regions were found to be associated with ULs.We applied an integrative analysis using genomic and transcriptomic data to identify the pathways and molecular markers associated with ULs. Fifty-one fresh frozen specimens were evaluated by array CGH (JISTIC and gene expression microarrays (SAM. The CONEXIC algorithm was applied to integrate the data.The integrated analysis identified the top 30 significant genes (P<0.01, which comprised genes associated with cancer, whereas the protein-protein interaction analysis indicated a strong association between FANCA and BRCA1. Functional in silico analysis revealed target molecules for drugs involved in cell proliferation, including FGFR1 and IGFBP5. Transcriptional and protein analyses showed that FGFR1 (P = 0.006 and P<0.01, respectively and IGFBP5 (P = 0.0002 and P = 0.006, respectively were up-regulated in the tumours when compared with the adjacent normal myometrium.The integrative genomic and transcriptomic approach indicated that FGFR1 and IGFBP5 amplification, as well as the consequent up-regulation of the protein products, plays an important role in the aetiology of ULs and thus provides data for potential drug therapies development to target genes associated with cellular proliferation in ULs.

Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis.

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Iwata-Otsubo, Aiko; Lin, Jer-Young; Gill, Navdeep; Jackson, Scott A

2016-05-01

Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies.

Integrative testis transcriptome analysis reveals differentially expressed miRNAs and their mRNA targets during early puberty in Atlantic salmon.

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Skaftnesmo, K O; Edvardsen, R B; Furmanek, T; Crespo, D; Andersson, E; Kleppe, L; Taranger, G L; Bogerd, J; Schulz, R W; Wargelius, A

2017-10-18

Our understanding of the molecular mechanisms implementing pubertal maturation of the testis in vertebrates is incomplete. This topic is relevant in Atlantic salmon aquaculture, since precocious male puberty negatively impacts animal welfare and growth. We hypothesize that certain miRNAs modulate mRNAs relevant for the initiation of puberty. To explore which miRNAs regulate mRNAs during initiation of puberty in salmon, we performed an integrated transcriptome analysis (miRNA and mRNA-seq) of salmon testis at three stages of development: an immature, long-term quiescent stage, a prepubertal stage just before, and a pubertal stage just after the onset of single cell proliferation activity in the testis. Differentially expressed miRNAs clustered into 5 distinct expression profiles related to the immature, prepubertal and pubertal salmon testis. Potential mRNA targets of these miRNAs were predicted with miRmap and filtered for mRNAs displaying negatively correlated expression patterns. In summary, this analysis revealed miRNAs previously known to be regulated in immature vertebrate testis (miR-101, miR-137, miR-92b, miR-18a, miR-20a), but also miRNAs first reported here as regulated in the testis (miR-new289, miR-30c, miR-724, miR-26b, miR-new271, miR-217, miR-216a, miR-135a, miR-new194 and the novel predicted n268). By KEGG enrichment analysis, progesterone signaling and cell cycle pathway genes were found regulated by these differentially expressed miRNAs. During the transition into puberty we found differential expression of miRNAs previously associated (let7a/b/c), or newly associated (miR-15c, miR-2184, miR-145 and the novel predicted n7a and b) with this stage. KEGG enrichment analysis revealed that mRNAs of the Wnt, Hedgehog and Apelin signaling pathways were potential regulated targets during the transition into puberty. Likewise, several regulated miRNAs in the pubertal stage had earlier been associated (miR-20a, miR-25, miR-181a, miR-202, let7c/d/a, miR-125b

Demographic, socio-economic, and cultural factors affecting fertility differentials in Nepal

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Adhikari Ramesh

2010-04-01

Full Text Available Abstract Background Traditionally Nepalese society favors high fertility. Children are a symbol of well-being both socially and economically. Although fertility has been decreasing in Nepal since 1981, it is still high compared to many other developing countries. This paper is an attempt to examine the demographic, socio-economic, and cultural factors for fertility differentials in Nepal. Methods This paper has used data from the Nepal Demographic and Health Survey (NDHS 2006. The analysis is confined to ever married women of reproductive age (8,644. Both bivariate and multivariate analyses have been performed to describe the fertility differentials. The bivariate analysis (one-way ANOVA was applied to examine the association between children ever born and women's demographic, socio-economic, and cultural characteristics. Besides bivariate analysis, the net effect of each independent variable on the dependent variable after controlling for the effect of other predictors has also been measured through multivariate analysis (multiple linear regressions. Results The mean numbers of children ever born (CEB among married Nepali women of reproductive age and among women aged 40-49 were three and five children, respectively. There are considerable differentials in the average number of children ever born according to women's demographic, socio-economic, and cultural settings. Regression analysis revealed that age at first marriage, perceived ideal number of children, place of residence, literacy status, religion, mass media exposure, use of family planning methods, household headship, and experience of child death were the most important variables that explained the variance in fertility. Women who considered a higher number of children as ideal (β = 0.03; p Conclusion The average number of children ever born is high among women in Nepal. There are many contributing factors for the high fertility, among which are age at first marriage, perceived ideal

Demographic, socio-economic, and cultural factors affecting fertility differentials in Nepal.

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Adhikari, Ramesh

2010-04-28

Traditionally Nepalese society favors high fertility. Children are a symbol of well-being both socially and economically. Although fertility has been decreasing in Nepal since 1981, it is still high compared to many other developing countries. This paper is an attempt to examine the demographic, socio-economic, and cultural factors for fertility differentials in Nepal. This paper has used data from the Nepal Demographic and Health Survey (NDHS 2006). The analysis is confined to ever married women of reproductive age (8,644). Both bivariate and multivariate analyses have been performed to describe the fertility differentials. The bivariate analysis (one-way ANOVA) was applied to examine the association between children ever born and women's demographic, socio-economic, and cultural characteristics. Besides bivariate analysis, the net effect of each independent variable on the dependent variable after controlling for the effect of other predictors has also been measured through multivariate analysis (multiple linear regressions). The mean numbers of children ever born (CEB) among married Nepali women of reproductive age and among women aged 40-49 were three and five children, respectively. There are considerable differentials in the average number of children ever born according to women's demographic, socio-economic, and cultural settings. Regression analysis revealed that age at first marriage, perceived ideal number of children, place of residence, literacy status, religion, mass media exposure, use of family planning methods, household headship, and experience of child death were the most important variables that explained the variance in fertility. Women who considered a higher number of children as ideal (beta = 0.03; p Muslim women (beta = 0.07; p media (beta = -0.05; p women in Nepal. There are many contributing factors for the high fertility, among which are age at first marriage, perceived ideal number of children, literacy status, mass media exposure

Importance of individual analysis of environmental and climatic factors affecting the density of Leishmania vectors living in the same geographical area: the example of Phlebotomus ariasi and P. perniciosus in northeast Spain

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Cristina Ballart

2014-05-01

Full Text Available The aim of the present study was to determine the role of specific environmental and climatic factors affecting the distribution and density of Phlebotomus ariasi and P. perniciosus, the proven vectors for Leishmania infantum in Spain. An entomological study was carried out in July 2006 in the province of Lleida with sticky traps set in their diurnal resting places at altitudes ranging from 86 to 1,755 m above the mean sea level (339 sites were sampled. Bivariate analysis revealed that factors such as altitude, bioclimatic zone, temperature, precipitation, sampling site (site relative to settlement, site situation, site category, wall vegetation, particular environment (in this case a natural park, general environment, adjacent natural vegetation and land cover were significantly associated with sand fly densities. The multivariate model for P. perniciosus revealed that its density was affected by site and land cover. Specifically, paved driveways correlated negatively with vector density (Incidence Risk Ratio (IRR: 0.41 and arable land cover correlated positively (IRR: 4.59. In the case of P. ariasi, a significant correlation was observed with the altitude and bioclimatic zone, with density increasing at >800 m above the mean sea level (IRR: 3.40 and decreasing in the meso-Mediterranean bioclimatic zone (IRR: 0.08. Both species were mostly found in agricultural and forest areas far from domestic environments. However, the two species correlated differently with altitude, bio-climate, vegetation, temperature and precipitation, which emphasises the importance of their individual analysis in studies regarding risk of leishmaniasis transmission.

Genetic analysis of Aedes albopictus (Diptera, Culicidae) reveals a deep divergence in the original regions.

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Ruiling, Zhang; Tongkai, Liu; Zhendong, Huang; Guifen, Zhuang; Dezhen, Ma; Zhong, Zhang

2018-05-02

Aedes albopictus has been described as one of the 100 worst invasive species in the world. This mosquito originated from southeastern Asia and currently has a widespread presence in every continent except Antarctica. The rapid global expansion of Ae. albopictus has increased public health concerns about arbovirus-related disease threats. Adaptation, adaption to novel areas is a biological challenge for invasive species, and the underlying processes can be studied at the molecular level. In this study, genetic analysis was performed using mitochondrial gene NADH dehydrogenase subunit 5 (ND5), based on both native and invasive populations. Altogether, 38 haplotypes were detected with H1 being the dominant and widely distributed in 21 countries. Both phylogenetic and network analyses supported the existence of five clades, with only clade I being involved in the subsequent global spread of Asian tiger mosquito. The other four clades (II, III, IV and V) were restricted to their original regions, which could be ancestral populations that had diverged from clade I in the early stages of evolution. Neutrality tests suggested that most of the populations had experienced recent expansion. Analysis of molecular variance and the population-pair statistic F ST revealed that most populations lacked genetic structure, while high variability was detected within populations. Multiple and independent human-mediated introductions may explain the present results. Copyright © 2018 Elsevier B.V. All rights reserved.

Analysis of transcriptome data reveals multifactor constraint on codon usage in Taenia multiceps.

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Huang, Xing; Xu, Jing; Chen, Lin; Wang, Yu; Gu, Xiaobin; Peng, Xuerong; Yang, Guangyou

2017-04-20

Codon usage bias (CUB) is an important evolutionary feature in genomes that has been widely observed in many organisms. However, the synonymous codon usage pattern in the genome of T. multiceps remains to be clarified. In this study, we analyzed the codon usage of T. multiceps based on the transcriptome data to reveal the constraint factors and to gain an improved understanding of the mechanisms that shape synonymous CUB. Analysis of a total of 8,620 annotated mRNA sequences from T. multiceps indicated only a weak codon bias, with mean GC and GC3 content values of 49.29% and 51.43%, respectively. Our analysis indicated that nucleotide composition, mutational pressure, natural selection, gene expression level, amino acids with grand average of hydropathicity (GRAVY) and aromaticity (Aromo) and the effective selection of amino-acids all contributed to the codon usage in T. multiceps. Among these factors, natural selection was implicated as the major factor affecting the codon usage variation in T. multiceps. The codon usage of ribosome genes was affected mainly by mutations, while the essential genes were affected mainly by selection. In addition, 21codons were identified as "optimal codons". Overall, the optimal codons were GC-rich (GC:AU, 41:22), and ended with G or C (except CGU). Furthermore, different degrees of variation in codon usage were found between T. multiceps and Escherichia coli, yeast, Homo sapiens. However, little difference was found between T. multiceps and Taenia pisiformis. In this study, the codon usage pattern of T. multiceps was analyzed systematically and factors affected CUB were also identified. This is the first study of codon biology in T. multiceps. Understanding the codon usage pattern in T. multiceps can be helpful for the discovery of new genes, molecular genetic engineering and evolutionary studies.

Secretome analysis of Aspergillus fumigatus reveals Asp-hemolysin as a major secreted protein.

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Wartenberg, Dirk; Lapp, Katrin; Jacobsen, Ilse D; Dahse, Hans-Martin; Kniemeyer, Olaf; Heinekamp, Thorsten; Brakhage, Axel A

2011-11-01

Surface-associated and secreted proteins represent primarily exposed components of Aspergillus fumigatus during host infection. Several secreted proteins are known to be involved in defense mechanisms or immune evasion, thus, probably contributing to pathogenicity. Furthermore, several secreted antigens were identified as possible biomarkers for the verification of diseases caused by Aspergillus species. Nevertheless, there is only limited knowledge about the composition of the secretome and about molecular functions of particular proteins. To identify secreted proteins potentially essential for virulence, the core secretome of A. fumigatus grown in minimal medium was determined. Two-dimensional gel electrophoretic separation and subsequent MALDI-TOF-MS/MS analyses resulted in the identification of 64 different proteins. Additionally, secretome analyses of A. fumigatus utilizing elastin, collagen or keratin as main carbon and nitrogen source were performed. Thereby, the alkaline serine protease Alp1 was identified as the most abundant protein and hence presumably represents an important protease during host infection. Interestingly, the Asp-hemolysin (Asp-HS), which belongs to the protein family of aegerolysins and which was often suggested to be involved in fungal virulence, was present in the secretome under all growth conditions tested. In addition, a second, non-secreted protein with an aegerolysin domain annotated as Asp-hemolysin-like (HS-like) protein can be found to be encoded in the genome of A. fumigatus. Generation and analysis of Asp-HS and HS-like deletion strains revealed no differences in phenotype compared to the corresponding wild-type strain. Furthermore, hemolysis and cytotoxicity was not altered in both single-deletion and double-deletion mutants lacking both aegerolysin genes. All mutant strains showed no attenuation in virulence in a mouse infection model for invasive pulmonary aspergillosis. Overall, this study provides a comprehensive

Human processing of short temporal intervals as revealed by an ERP waveform analysis

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Yoshitaka eNakajima

2011-12-01

Full Text Available To clarify the time course over which the human brain processes information about durations up to ~300 ms, we reanalyzed the data that were previously reported by Mitsudo et al. (2009 using a multivariate analysis method. Event-related potentials were recorded from 19 scalp electrodes on 11 (9 original and 2 additional participants while they judged whether two neighboring empty time intervals—called t1 and t2 and marked by three tone bursts—had equal durations. There was also a control condition in which the participants were presented the same temporal patterns but without a judgment task. In the present reanalysis, we sought to visualize how the temporal patterns were represented in the brain over time. A correlation matrix across channels was calculated for each temporal pattern. Geometric separations between the correlation matrices were calculated, and subjected to multidimensional scaling. We performed such analyses for a moving 100-ms time window after the t1 presentations. In the windows centered at < 100 ms after the t2 presentation, the analyses revealed the local maxima of categorical separation between temporal patterns of perceptually equal durations versus perceptually unequal durations, both in the judgment condition and in the control condition. Such categorization of the temporal patterns was prominent only in narrow temporal regions. The analysis indicated that the participants determined whether the two neighboring time intervals were of equal duration mostly within 100 ms after the presentation of the temporal patterns. A very fast brain activity was related to the perception of elementary temporal patterns without explicit judgments. This is consistent with the findings of Mitsudo et al., and it is in line with the processing time hypothesis proposed by Nakajima et al. (2004. The validity of the correlation matrix analyses turned out to be an effective tool to grasp the overall responses of the brain to temporal

A Meta-Analysis of Social Capital and Health: A Case for Needed Research

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Gilbert, Keon L.; Quinn, Sandra C.; Goodman, Robert M.; Butler, James; Wallace, John

2014-01-01

Background Social capital refers to various levels of social relationships formed through social networks. Measurement differences have lead to imprecise measurement. Methods A meta-analysis of eligible studies assessing the bivariate association between social capital and self-reported health and all-cause mortality. Results Thirty-nine studies met inclusion criteria, showing social capital increased odds of good health by 27% (95% confidence intervals [CI] =21%, 34%). Social capital variables, reciprocity increased odds of good health by 39% (95% CI = 21%, 60%), trust by 32% (95% CI =19%, 46%). Future research suggests operationalizing measures by assessing differences by race/ethnicity, gender and socioeconomic status. PMID:23548810

Immunoglobulin G (IgG) Fab glycosylation analysis using a new mass spectrometric high-throughput profiling method reveals pregnancy-associated changes.

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Bondt, Albert; Rombouts, Yoann; Selman, Maurice H J; Hensbergen, Paul J; Reiding, Karli R; Hazes, Johanna M W; Dolhain, Radboud J E M; Wuhrer, Manfred

2014-11-01

The N-linked glycosylation of the constant fragment (Fc) of immunoglobulin G has been shown to change during pathological and physiological events and to strongly influence antibody inflammatory properties. In contrast, little is known about Fab-linked N-glycosylation, carried by ∼ 20% of IgG. Here we present a high-throughput workflow to analyze Fab and Fc glycosylation of polyclonal IgG purified from 5 μl of serum. We were able to detect and quantify 37 different N-glycans by means of MALDI-TOF-MS analysis in reflectron positive mode using a novel linkage-specific derivatization of sialic acid. This method was applied to 174 samples of a pregnancy cohort to reveal Fab glycosylation features and their change with pregnancy. Data analysis revealed marked differences between Fab and Fc glycosylation, especially in the levels of galactosylation and sialylation, incidence of bisecting GlcNAc, and presence of high mannose structures, which were all higher in the Fab portion than the Fc, whereas Fc showed higher levels of fucosylation. Additionally, we observed several changes during pregnancy and after delivery. Fab N-glycan sialylation was increased and bisection was decreased relative to postpartum time points, and nearly complete galactosylation of Fab glycans was observed throughout. Fc glycosylation changes were similar to results described before, with increased galactosylation and sialylation and decreased bisection during pregnancy. We expect that the parallel analysis of IgG Fab and Fc, as set up in this paper, will be important for unraveling roles of these glycans in (auto)immunity, which may be mediated via recognition by human lectins or modulation of antigen binding. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Immunoglobulin G (IgG) Fab Glycosylation Analysis Using a New Mass Spectrometric High-throughput Profiling Method Reveals Pregnancy-associated Changes*

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Bondt, Albert; Rombouts, Yoann; Selman, Maurice H. J.; Hensbergen, Paul J.; Reiding, Karli R.; Hazes, Johanna M. W.; Dolhain, Radboud J. E. M.; Wuhrer, Manfred

2014-01-01

The N-linked glycosylation of the constant fragment (Fc) of immunoglobulin G has been shown to change during pathological and physiological events and to strongly influence antibody inflammatory properties. In contrast, little is known about Fab-linked N-glycosylation, carried by ∼20% of IgG. Here we present a high-throughput workflow to analyze Fab and Fc glycosylation of polyclonal IgG purified from 5 μl of serum. We were able to detect and quantify 37 different N-glycans by means of MALDI-TOF-MS analysis in reflectron positive mode using a novel linkage-specific derivatization of sialic acid. This method was applied to 174 samples of a pregnancy cohort to reveal Fab glycosylation features and their change with pregnancy. Data analysis revealed marked differences between Fab and Fc glycosylation, especially in the levels of galactosylation and sialylation, incidence of bisecting GlcNAc, and presence of high mannose structures, which were all higher in the Fab portion than the Fc, whereas Fc showed higher levels of fucosylation. Additionally, we observed several changes during pregnancy and after delivery. Fab N-glycan sialylation was increased and bisection was decreased relative to postpartum time points, and nearly complete galactosylation of Fab glycans was observed throughout. Fc glycosylation changes were similar to results described before, with increased galactosylation and sialylation and decreased bisection during pregnancy. We expect that the parallel analysis of IgG Fab and Fc, as set up in this paper, will be important for unraveling roles of these glycans in (auto)immunity, which may be mediated via recognition by human lectins or modulation of antigen binding. PMID:25004930

Bayesian network analysis revealed the connectivity difference of the default mode network from the resting-state to task-state

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Wu, Xia; Yu, Xinyu; Yao, Li; Li, Rui

2014-01-01

Functional magnetic resonance imaging (fMRI) studies have converged to reveal the default mode network (DMN), a constellation of regions that display co-activation during resting-state but co-deactivation during attention-demanding tasks in the brain. Here, we employed a Bayesian network (BN) analysis method to construct a directed effective connectivity model of the DMN and compared the organizational architecture and interregional directed connections under both resting-state and task-state. The analysis results indicated that the DMN was consistently organized into two closely interacting subsystems in both resting-state and task-state. The directed connections between DMN regions, however, changed significantly from the resting-state to task-state condition. The results suggest that the DMN intrinsically maintains a relatively stable structure whether at rest or performing tasks but has different information processing mechanisms under varied states. PMID:25309414

Cumulative meta-analysis of the relationship between useful field of view and driving performance in older adults: current and future implications.

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Clay, Olivio J; Wadley, Virginia G; Edwards, Jerri D; Roth, David L; Roenker, Daniel L; Ball, Karlene K

2005-08-01

Driving is a complex behavior that requires the utilization of a wide range of individual abilities. Identifying assessments that not only capture individual differences, but also are related to older adults' driving performance would be beneficial. This investigation examines the relationship between the Useful Field of View (UFOV) assessment and objective measures of retrospective or concurrent driving performance, including state-recorded accidents, on-road driving, and driving simulator performance. The PubMed and PsycINFO databases were searched to retrieve eight studies that reported bivariate relationships between UFOV and these objective driving measures. Cumulative meta-analysis techniques were used to combine the effect sizes in an attempt to determine whether the strength of the relationship was stable across studies and to assess whether a sufficient number of studies have been conducted to validate the relationship between UFOV and driving performance. A within-group homogeneity of effect sizes test revealed that the samples could be thought of as being drawn from the same population, Q [7] = 11.29, p (one-tailed) = 0.13. Therefore, the effect sizes of eight studies were combined for the present cumulative meta-analysis. The weighted mean effect size across the studies revealed a large effect (Cohen's d = 0.945), with poorer UFOV performance associated with negative driving outcomes. This relationship was robust across multiple indices of driving performance and several research laboratories. This convergence of evidence across numerous studies using different methodologies confirms the importance of the UFOV assessment as a valid and reliable index of driving performance and safety. Recent prospective studies have confirmed a relationship between UFOV performance and future crashes, further supporting the use of this instrument as a potential screening measure for at-risk older drivers.

Isotope analysis reveals foraging area dichotomy for atlantic leatherback turtles.

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Stéphane Caut

Full Text Available BACKGROUND: The leatherback turtle (Dermochelys coriacea has undergone a dramatic decline over the last 25 years, and this is believed to be primarily the result of mortality associated with fisheries bycatch followed by egg and nesting female harvest. Atlantic leatherback turtles undertake long migrations across ocean basins from subtropical and tropical nesting beaches to productive frontal areas. Migration between two nesting seasons can last 2 or 3 years, a time period termed the remigration interval (RI. Recent satellite transmitter data revealed that Atlantic leatherbacks follow two major dispersion patterns after nesting season, through the North Gulf Stream area or more eastward across the North Equatorial Current. However, information on the whole RI is lacking, precluding the accurate identification of feeding areas where conservation measures may need to be applied. METHODOLOGY/PRINCIPAL FINDINGS: Using stable isotopes as dietary tracers we determined the characteristics of feeding grounds of leatherback females nesting in French Guiana. During migration, 3-year RI females differed from 2-year RI females in their isotope values, implying differences in their choice of feeding habitats (offshore vs. more coastal and foraging latitude (North Atlantic vs. West African coasts, respectively. Egg-yolk and blood isotope values are correlated in nesting females, indicating that egg analysis is a useful tool for assessing isotope values in these turtles, including adults when not available. CONCLUSIONS/SIGNIFICANCE: Our results complement previous data on turtle movements during the first year following the nesting season, integrating the diet consumed during the year before nesting. We suggest that the French Guiana leatherback population segregates into two distinct isotopic groupings, and highlight the urgent need to determine the feeding habitats of the turtle in the Atlantic in order to protect this species from incidental take by

[The positive psychological impact of rich childbirth experiences on child-rearing].

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Takehara, Kenji; Noguchi, Makiko; Shimane, Takuya; Misago, Chizuru

2009-05-01

The purpose of this study was to investigate the psychological implications of emotionally enriching childbirth experiences for problems such as awareness of motherhood, postnatal depression, and parenting stress among women after childbirth. All women who gave birth at five study centers (four birthing homes and one maternity hospital) during May 2002 and August 2003 were asked to participate in the cohort study. All 2314 women were approached and 1004 eligible women agreed to take part. Analyses were conducted using a baseline survey and four follow-up surveys conducted at 4 months, 9 months, 2 and a half years, and 3 years after childbirth. The questionnaire included four scales to evaluate the subjects' childbirth experiences, awareness of motherhood, postnatal depression, and parenting stress and difficulties. Data were collected via structured interviews and transcription from medical records. Bivariate and multivariate analysis indicated that women who had good childbirth experiences had positive feelings concerning motherhood and parenting stress and anxiety were lower. Bivariate analysis also indicated that childbirth experience had an inverse relationship with postnatal depression. This study revealed that having good childbirth experiences inhibits negative awareness of motherhood and abusive behavior towards children. These results show that it is important for mothers to be provided with appropriate care during pregnancy and labor for preventing child abuse and parenting stress and anxiety. More research is needed to identify the determinants of childbirth

Why are our children wasting: Determinants of wasting among under 5s in Ghana.

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Darteh, Eugene Kofuor Maafo; Acquah, Evelyn; Darteh, Florie

2017-09-01

Wasting is one of the indicators of malnutrition known to contribute to the deaths occurring from childhood malnutrition. It is the measure of body mass in relation to body length used to explain recent nutritional status. This paper examines the determinants of wasting among under 5s in Ghana. Data were drawn from the 2014 Ghana Demographic and Health Survey children's records file to examine the determinants of wasting among children. A total of 2720 children under 5 years with valid anthropometric data were used. Data on wasting were collected by measuring the weight and height of all children under 5 years of age. Bi-variate and multi-variate statistics are used to examine the determinants of wasting. The bi-variate analysis showed significant differences ( p 5s according to age of the child, region, and wealth status. On the other hand, the multi-variate analysis revealed that the odds of wasting were lower among children aged 24-35 months (Odds ratio (OR) = 0.37; p 5s. Also, efforts should be made by the relevant government agencies and other stakeholders to strengthen the socio-economic status of mothers to enable them to provide adequate nutrition and improve access to health insurance for their children in order to reduce the incidence of wasting among these children.

Childhood adversity in association with personality disorder dimensions: new findings in an old debate.

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Hengartner, M P; Ajdacic-Gross, V; Rodgers, S; Müller, M; Rössler, W

2013-10-01

Various studies have reported a positive relationship between child maltreatment and personality disorders (PDs). However, few studies included all DSM-IV PDs and even fewer adjusted for other forms of childhood adversity, e.g. bullying or family problems. We analyzed questionnaires completed by 512 participants of the ZInEP epidemiology survey, a comprehensive psychiatric survey of the general population in Zurich, Switzerland. Associations between childhood adversity and PDs were analyzed bivariately via simple regression analyses and multivariately via multiple path analysis. The bivariate analyses revealed that all PD dimensions were significantly related to various forms of family and school problems as well as child abuse. In contrast, according to the multivariate analysis only school problems and emotional abuse were associated with various PDs. Poverty was uniquely associated with schizotypal PD, conflicts with parents with obsessive-compulsive PD, physical abuse with antisocial PD, and physical neglect with narcissistic PD. Sexual abuse was statistically significantly associated with schizotypal and borderline PD, but corresponding effect sizes were small. Childhood adversity has a serious impact on PDs. Bullying and violence in schools and emotional abuse appear to be more salient markers of general personality pathology than other forms of childhood adversity. Associations with sexual abuse were negligible when adjusted for other forms of adversity. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Maternal nutritional knowledge and child nutritional status in the Volta region of Ghana.

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Appoh, Lily Yaa; Krekling, Sturla

2005-04-01

The relationship between mother's nutritional knowledge, maternal education, and child nutritional status (weight-for-age) was the subject of investigation in this study. The data were collected in Ghana on 55 well nourished and 55 malnourished mother-child pairs. A questionnaire designed to collect data on mother's knowledge and practices related to child care and nutrition was administered to the mothers. Data on mother's demographic and socio-economic characteristics as well as child anthropometric data were also collected. A nutrition knowledge score was calculated based on mother's responses to the nutrition related items. Bivariate analysis gave significant associations between child nutritional status and the following variables: time of initiating of breastfeeding, mother's knowledge of importance of colostrum and whether colostrum was given to child, age of introduction of supplementary food, and mother's knowledge about causes of kwashiorkor. The two groups also showed significant differences in their nutrition knowledge scores. Maternal formal education, and marital status were also found to be associated with child nutritional status in bivariate analyses. Further analysis with logistic regression revealed that maternal nutrition knowledge was independently associated with nutritional status after the effects of other significant variables were controlled for. Maternal education on the other hand was not found to be independently associated with nutritional status. These results imply that mother's practical knowledge about nutrition may be more important than formal maternal education for child nutrition outcome.

Statistical power to detect genetic (covariance of complex traits using SNP data in unrelated samples.

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Peter M Visscher

2014-04-01

Full Text Available We have recently developed analysis methods (GREML to estimate the genetic variance of a complex trait/disease and the genetic correlation between two complex traits/diseases using genome-wide single nucleotide polymorphism (SNP data in unrelated individuals. Here we use analytical derivations and simulations to quantify the sampling variance of the estimate of the proportion of phenotypic variance captured by all SNPs for quantitative traits and case-control studies. We also derive the approximate sampling variance of the estimate of a genetic correlation in a bivariate analysis, when two complex traits are either measured on the same or different individuals. We show that the sampling variance is inversely proportional to the number of pairwise contrasts in the analysis and to the variance in SNP-derived genetic relationships. For bivariate analysis, the sampling variance of the genetic correlation additionally depends on the harmonic mean of the proportion of variance explained by the SNPs for the two traits and the genetic correlation between the traits, and depends on the phenotypic correlation when the traits are measured on the same individuals. We provide an online tool for calculating the power of detecting genetic (covariation using genome-wide SNP data. The new theory and online tool will be helpful to plan experimental designs to estimate the missing heritability that has not yet been fully revealed through genome-wide association studies, and to estimate the genetic overlap between complex traits (diseases in particular when the traits (diseases are not measured on the same samples.

Meta-analysis reveals host-dependent nitrogen recycling as a mechanism of symbiont control in Aiptasia

KAUST Repository

Cui, Guoxin

2018-02-22

The metabolic symbiosis with photosynthetic algae of the genus Symbiodinium allows corals to thrive in the oligotrophic environments of tropical seas. Many aspects of this relationship have been investigated using transcriptomic analyses in the emerging model organism Aiptasia. However, previous studies identified thousands of putatively symbiosis-related genes, making it difficult to disentangle symbiosis-induced responses from undesired experimental parameters. Using a meta-analysis approach, we identified a core set of 731 high-confidence symbiosis-associated genes that reveal host-dependent recycling of waste ammonium and amino acid synthesis as central processes in this relationship. Combining transcriptomic and metabolomic analyses, we show that symbiont-derived carbon enables host recycling of ammonium into nonessential amino acids. We propose that this provides a regulatory mechanism to control symbiont growth through a carbon-dependent negative feedback of nitrogen availability to the symbiont. The dependence of this mechanism on symbiont-derived carbon highlights the susceptibility of this symbiosis to changes in carbon translocation, as imposed by environmental stress.

HLA-DR Genotyping and Mitochondrial DNA Analysis Reveal the Presence of Family Burials in a Fourth Century Romano-British Christian Cemetery

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Canh P. Voong

2017-12-01

Full Text Available In Colchester, Britain's oldest recorded town, during the Roman period there were areas which were clearly used solely as cemeteries. One of the most significant is at Butt Road, which includes a late Roman probable Christian cemetery with an associated building, apparently a church, that overlies and developed from a pagan inhumation cemetery. DNA was extracted from the long bones (femurs of 29 individuals, mostly from a large complex of burials centered on two timber vaults. These were thought to comprise a number of family groupings, deduced from osteological analysis, stratigraphical and other considerations. The use of a modified version of the silica-based purification method recovered nanogram quantities of DNA/gram of bone. Two-stage amplification, incorporating primer-extension preamplification-polymerase chain reaction, permitted simultaneous amplification of both mitochondrial and nuclear DNA. Sequence-specific oligonucleotide probes yielded human leukocyte antigen (HLA-DR typing of seven samples, with four revealing the infrequent HLA-DR10 genotype. Examination of the control region of mitochondrial DNA (mtDNA by direct sequencing revealed polymorphisms yet to be reported in the modern population. HLA-DRB typing and mtDNA analysis affirmatively supported kinship among some, if not all, individuals in the “vault complex” and demonstrate a continental European origin of the individuals investigated.

mRNA-seq analysis of the Gossypium arboreum transcriptome reveals tissue selective signaling in response to water stress during seedling stage.

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Xueyan Zhang

Full Text Available The cotton diploid species, Gossypium arboreum, shows important properties of stress tolerance and good genetic stability. In this study, through mRNA-seq, we de novo assembled the unigenes of multiple samples with 3h H(2O, NaCl, or PEG treatments in leaf, stem and root tissues and successfully obtained 123,579 transcripts of G. arboreum, 89,128 of which were with hits through BLAST against known cotton ESTs and draft genome of G. raimondii. About 36,961 transcripts (including 1,958 possible transcription factor members were identified with differential expression under water stresses. Principal component analysis of differential expression levels in multiple samples suggested tissue selective signalling responding to water stresses. Venn diagram analysis showed the specificity and intersection of transcripts' response to NaCl and PEG treatments in different tissues. Self-organized mapping and hierarchical cluster analysis of the data also revealed strong tissue selectivity of transcripts under salt and osmotic stresses. In addition, the enriched gene ontology (GO terms for the selected tissue groups were differed, including some unique enriched GO terms such as photosynthesis and tetrapyrrole binding only in leaf tissues, while the stem-specific genes showed unique GO terms related to plant-type cell wall biogenesis, and root-specific genes showed unique GO terms such as monooxygenase activity. Furthermore, there were multiple hormone cross-talks in response to osmotic and salt stress. In summary, our multidimensional mRNA sequencing revealed tissue selective signalling and hormone crosstalk in response to salt and osmotic stresses in G. arboreum. To our knowledge, this is the first such report of spatial resolution of transcriptome analysis in G. arboreum. Our study will potentially advance understanding of possible transcriptional networks associated with water stress in cotton and other crop species.

Acoustic Radiation Force Impulse Imaging for the Differentiation of Benign and Malignant Lymph Nodes: A Systematic Review and Meta-Analysis.

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Zhang, Peige; Zhang, Li; Zheng, Shaoping; Yu, Cheng; Xie, Mingxing; Lv, Qing

2016-01-01

To evaluate the overall performance of acoustic radiation force impulse imaging (ARFI) in differentiating between benign and malignant lymph nodes (LNs) by conducting a meta-analysis. PubMed, Embase, Web of Science, the Cochrane Library and the China National Knowledge Infrastructure were comprehensively searched for potential studies through August 13th, 2016. Studies that investigated the diagnostic power of ARFI for the differential diagnosis of benign and malignant LNs by using virtual touch tissue quantification (VTQ) or virtual touch tissue imaging quantification (VTIQ) were collected. The included articles were published in English or Chinese. Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) was used to evaluate the methodological quality. The pooled sensitivity, specificity, and the area under the summary receiver operating characteristic (SROC) curve (AUC) were calculated by means of a bivariate mixed-effects regression model. Meta-regression analysis was performed to identify the potential sources of between study heterogeneity. Fagan plot analysis was used to explore the clinical utilities. Publication bias was assessed using Deek's funnel plot. Nine studies involving 1084 LNs from 929 patients were identified to analyze in the meta-analysis. The summary sensitivity and specificity of ARFI in detecting malignant LNs were 0.87 (95% confidence interval [CI], 0.83-0.91) and 0.88 (95% CI, 0.82-0.92), respectively. The AUC was 0.93 (95% CI, 0.90-0.95). The pooled DOR was 49.59 (95% CI, 26.11-94.15). Deek's funnel plot revealed no significant publication bias. ARFI is a promising tool for the differentiation of benign and malignant LNs with high sensitivity and specificity.

Comparative genomic analysis of isoproturon-mineralizing sphingomonads reveals the isoproturon catabolic mechanism.

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Yan, Xin; Gu, Tao; Yi, Zhongquan; Huang, Junwei; Liu, Xiaowei; Zhang, Ji; Xu, Xihui; Xin, Zhihong; Hong, Qing; He, Jian; Spain, Jim C; Li, Shunpeng; Jiang, Jiandong

2016-12-01

The worldwide use of the phenylurea herbicide, isoproturon (IPU), has resulted in considerable concern about its environmental fate. Although many microbial metabolites of IPU are known and IPU-mineralizing bacteria have been isolated, the molecular mechanism of IPU catabolism has not been elucidated yet. In this study, complete genes that encode the conserved IPU catabolic pathway were revealed, based on comparative analysis of the genomes of three IPU-mineralizing sphingomonads and subsequent experimental validation. The complete genes included a novel hydrolase gene ddhA, which is responsible for the cleavage of the urea side chain of the IPU demethylated products; a distinct aniline dioxygenase gene cluster adoQTA1A2BR, which has a broad substrate range; and an inducible catechol meta-cleavage pathway gene cluster adoXEGKLIJC. Furthermore, the initial mono-N-demethylation genes pdmAB were further confirmed to be involved in the successive N-demethylation of the IPU mono-N-demethylated product. These IPU-catabolic genes were organized into four transcription units and distributed on three plasmids. They were flanked by multiple mobile genetic elements and highly conserved among IPU-mineralizing sphingomonads. The elucidation of the molecular mechanism of IPU catabolism will enhance our understanding of the microbial mineralization of IPU and provide insights into the evolutionary scenario of the conserved IPU-catabolic pathway. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Single molecule analysis of c-myb alternative splicing reveals novel classifiers for precursor B-ALL.

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Ye E Zhou

Full Text Available The c-Myb transcription factor, a key regulator of proliferation and differentiation in hematopoietic and other cell types, has an N-terminal DNA binding domain and a large C-terminal domain responsible for transcriptional activation, negative regulation and determining target gene specificity. Overexpression and rearrangement of the c-myb gene (MYB has been reported in some patients with leukemias and other types of cancers, implicating activated alleles of c-myb in the development of human tumors. Alternative RNA splicing can produce variants of c-myb with qualitatively distinct transcriptional activities that may be involved in transformation and leukemogenesis. Here, by performing a detailed, single molecule assay we found that c-myb alternative RNA splicing was elevated and much more complex in leukemia samples than in cell lines or CD34+ hematopoietic progenitor cells from normal donors. The results revealed that leukemia samples express more than 60 different c-myb splice variants, most of which have multiple alternative splicing events and were not detectable by conventional microarray or PCR approaches. For example, the single molecule assay detected 21 and 22 splice variants containing the 9B and 9S exons, respectively, most of which encoded unexpected variant forms of c-Myb protein. Furthermore, the detailed analysis identified some splice variants whose expression correlated with poor survival in a small cohort of precursor B-ALL samples. Our findings indicate that single molecule assays can reveal complexities in c-myb alternative splicing that have potential as novel biomarkers and could help explain the role of c-Myb variants in the development of human leukemia.

Metagenomic analysis of bat guano samples revealed the presence of viruses potentially carried by insects, among others by Apis mellifera in Hungary.

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Zana, Brigitta; Kemenesi, Gábor; Urbán, Péter; Földes, Fanni; Görföl, Tamás; Estók, Péter; Boldogh, Sándor; Kurucz, Kornélia; Jakab, Ferenc

2018-03-01

The predominance of dietary viruses in bat guano samples had been described recently, suggesting a new opportunity to survey the prevalence and to detect new viruses of arthropods or even plant-infecting viruses circulating locally in the ecosystem. Here we describe the diversity of viruses belonging to the order Picornavirales in Hungarian insectivorous bat guano samples. The metagenomic analysis conducted on our samples has revealed the significant predominance of aphid lethal paralysis virus (ALPV) and Big Sioux River virus (BSRV) in Hungary for the first time. Phylogenetic analysis was used to clarify the relationship to previously identified ALPV strains infecting honey bees, showing that our strain possesses a close genetic relationship with the strains that have already been described as pathogenic to honey bees. Furthermore, studies have previously confirmed the ability of these viruses to replicate in adult honey bees; however, no signs related to these viruses have been revealed yet. With the identification of two recently described possibly honey bee infecting viruses for the first time in Hungary, our results might have importance for the health conditions of Hungarian honey bee colonies in the future.

Dental Workforce Availability and Dental Services Utilization in Appalachia: A Geospatial Analysis

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Feng, Xue; Sambamoorthi, Usha; Wiener, R. Constance

2016-01-01

Objectives There is considerable variation in dental services utilization across Appalachian counties, and a plausible explanation is that individuals in some geographical areas do not utilize dental care due to dental workforce shortage. We conducted an ecological study on dental workforce availability and dental services utilization in Appalachia. Methods We derived county-level (n = 364) data on demographic, socio-economic characteristics and dental services utilization in Appalachia from the 2010 Behavioral Risk Factor Surveillance System (BRFSS) using person-level data. We obtained county-level dental workforce availability and physician-to-population ratio estimates from Area Health Resource File, and linked them to the county-level BRFSS data. The dependent variable was the proportion using dental services within the last year in each county (ranging from 16.6% to 91.0%). We described the association between dental workforce availability and dental services utilization using ordinary least squares regression and spatial regression techniques. Spatial analyses consisted of bivariate Local Indicators of Spatial Association (LISA) and geographically weighted regression (GWR). Results Bivariate LISA showed that counties in the central and southern Appalachian regions had significant (p dental workforce availability, low percent dental services utilization). GWR revealed considerable local variations in the association between dental utilization and dental workforce availability. In the multivariate GWR models, 8.5% (t-statistics >1.96) and 13.45% (t-statistics >1.96) of counties showed positive and statistically significant relationships between the dental services utilization and workforce availability of dentists and dental hygienists, respectively. Conclusions Dental workforce availability was associated with dental services utilization in the Appalachian region; however, this association was not statistically significant in all counties. The findings suggest

Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics.

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Yong Guo

Full Text Available The Dof domain protein family is a classic plant-specific zinc-finger transcription factor family involved in a variety of biological processes. There is great diversity in the number of Dof genes in different plants. However, there are only very limited reports on the characterization of Dof transcription factors in soybean (Glycine max. In the present study, 78 putative Dof genes were identified from the whole-genome sequence of soybean. The predicted GmDof genes were non-randomly distributed within and across 19 out of 20 chromosomes and 97.4% (38 pairs were preferentially retained duplicate paralogous genes located in duplicated regions of the genome. Soybean-specific segmental duplications contributed significantly to the expansion of the soybean Dof gene family. These Dof proteins were phylogenetically clustered into nine distinct subgroups among which the gene structure and motif compositions were considerably conserved. Comparative phylogenetic analysis of these Dof proteins revealed four major groups, similar to those reported for Arabidopsis and rice. Most of the GmDofs showed specific expression patterns based on RNA-seq data analyses. The expression patterns of some duplicate genes were partially redundant while others showed functional diversity, suggesting the occurrence of sub-functionalization during subsequent evolution. Comprehensive expression profile analysis also provided insights into the soybean-specific functional divergence among members of the Dof gene family. Cis-regulatory element analysis of these GmDof genes suggested diverse functions associated with different processes. Taken together, our results provide useful information for the functional characterization of soybean Dof genes by combining phylogenetic analysis with global gene-expression profiling.

Comparative transcriptomic analysis reveals similarities and dissimilarities in Saccharomyces cerevisiae wine strains response to nitrogen availability.

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Catarina Barbosa

Full Text Available Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23, under low (67 mg/L and high nitrogen (670 mg/L regimes, at three time points during fermentation (12 h, 24 h and 96 h. Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12 h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this

Comparative Transcriptomic Analysis Reveals Similarities and Dissimilarities in Saccharomyces cerevisiae Wine Strains Response to Nitrogen Availability

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Barbosa, Catarina; García-Martínez, José; Pérez-Ortín, José E.; Mendes-Ferreira, Ana

2015-01-01

Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23), under low (67 mg/L) and high nitrogen (670 mg/L) regimes, at three time points during fermentation (12h, 24h and 96h). Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this nutrient in the grape

Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR).

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Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J; Laclette, Juan P; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

2015-05-19

Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest.

Full-length VP2 gene analysis of canine parvovirus reveals emergence of newer variants in India.

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Nookala, Mangadevi; Mukhopadhyay, Hirak Kumar; Sivaprakasam, Amsaveni; Balasubramanian, Brindhalakshmi; Antony, Prabhakar Xavier; Thanislass, Jacob; Srinivas, Mouttou Vivek; Pillai, Raghavan Madhusoodanan

2016-12-01

The canine parvovirus (CPV) infection is a highly contagious and serious enteric disease of dogs with high fatality rate. The present study was taken up to characterize the full-length viral polypeptide 2 (VP2) gene of CPV of Indian origin along with the commercially available vaccines. The faecal samples from parvovirus suspected dogs were collected from various states of India for screening by PCR assay and 66.29% of samples were found positive. Six CPV-2a, three CPV-2b, and one CPV-2c types were identified by sequence analysis. Several unique and existing mutations have been noticed in CPV types analyzed indicating emergence of newer variants of CPV in India. The phylogenetic analysis revealed that all the field CPV types were grouped in different subclades within two main clades, but away from the commercial vaccine strains. CPV-2b and CPV-2c types with unique mutations were found to be establishing in India apart from the prevailing CPV-2a type. Mutations and the positive selection of the mutants were found to be the major mechanism of emergence and evolution of parvovirus. Therefore, the incorporation of local strain in the vaccine formulation may be considered for effective control of CPV infections in India.

Social phenotype extended to communities: expanded multilevel social selection analysis reveals fitness consequences of interspecific interactions.

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Campobello, Daniela; Hare, James F; Sarà, Maurizio

2015-04-01

In social species, fitness consequences are associated with both individual and social phenotypes. Social selection analysis has quantified the contribution of conspecific social traits to individual fitness. There has been no attempt, however, to apply a social selection approach to quantify the fitness implications of heterospecific social phenotypes. Here, we propose a novel social selection based approach integrating the role of all social interactions at the community level. We extended multilevel selection analysis by including a term accounting for the group phenotype of heterospecifics. We analyzed nest activity as a model social trait common to two species, the lesser kestrel (Falco naumanni) and jackdaw (Corvus monedula), nesting in either single- or mixed-species colonies. By recording reproductive outcome as a measure of relative fitness, our results reveal an asymmetric system wherein only jackdaw breeding performance was affected by the activity phenotypes of both conspecific and heterospecific neighbors. Our model incorporating heterospecific social phenotypes is applicable to animal communities where interacting species share a common social trait, thus allowing an assessment of the selection pressure imposed by interspecific interactions in nature. Finally, we discuss the potential role of ecological limitations accounting for random or preferential assortments among interspecific social phenotypes, and the implications of such processes to community evolution. © 2015 The Author(s).

Sweet Potato Value Chain Analysis Reveals Opportunities for Increased Income and Food Security in Northern Ghana

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Issah Sugri

2017-01-01

Full Text Available Sweet potato has gained prominence due to its ability to adapt to wide production ecologies and yield response to minimal external inputs. Orange-fleshed cultivars in particular have immense potential to improve household income and nutrition in sub-Saharan Africa. However, the sweet potato value chain (SPVC is not well-developed in many producing countries. The study was conducted in two regions to characterize the production operations as well as identify opportunities to propel the SPVC in Northern Ghana. Data were collected using mixed methods including structured questionnaires via face-to-face interviews. Analysis of strengths, weaknesses, opportunities, and threats (SWOT was conducted at multistakeholder platforms with different actors. Gross margin profit and benefit-cost ratios were determined by using six cost variables. Overall, the industry was largely a fresh produce market, targeting food vendors, processors, and direct selling to wholesalers, retailers, and household consumers. The SWOT analysis revealed wide-ranging opportunities including favourable production ecologies, processing options, and insatiable local and international markets. The institutional actors need to network the primary actors to synergistically operate with a collective profit motive. The most prioritized production constraints such as access to seed, cost of chemical fertilizer, short shelf-life, field pests and diseases, and declining soil fertility should be addressed.

Parametric mapping using spectral analysis for 11C-PBR28 PET reveals neuroinflammation in mild cognitive impairment subjects.

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Fan, Zhen; Dani, Melanie; Femminella, Grazia D; Wood, Melanie; Calsolaro, Valeria; Veronese, Mattia; Turkheimer, Federico; Gentleman, Steve; Brooks, David J; Hinz, Rainer; Edison, Paul

2018-07-01

Neuroinflammation and microglial activation play an important role in amnestic mild cognitive impairment (MCI) and Alzheimer's disease. In this study, we investigated the spatial distribution of neuroinflammation in MCI subjects, using spectral analysis (SA) to generate parametric maps and quantify 11 C-PBR28 PET, and compared these with compartmental and other kinetic models of quantification. Thirteen MCI and nine healthy controls were enrolled in this study. Subjects underwent 11 C-PBR28 PET scans with arterial cannulation. Spectral analysis with an arterial plasma input function was used to generate 11 C-PBR28 parametric maps. These maps were then compared with regional 11 C-PBR28 V T (volume of distribution) using a two-tissue compartment model and Logan graphic analysis. Amyloid load was also assessed with 18 F-Flutemetamol PET. With SA, three component peaks were identified in addition to blood volume. The 11 C-PBR28 impulse response function (IRF) at 90 min produced the lowest coefficient of variation. Single-subject analysis using this IRF demonstrated microglial activation in five out of seven amyloid-positive MCI subjects. IRF parametric maps of 11 C-PBR28 uptake revealed a group-wise significant increase in neuroinflammation in amyloid-positive MCI subjects versus HC in multiple cortical association areas, and particularly in the temporal lobe. Interestingly, compartmental analysis detected group-wise increase in 11 C-PBR28 binding in the thalamus of amyloid-positive MCI subjects, while Logan parametric maps did not perform well. This study demonstrates for the first time that spectral analysis can be used to generate parametric maps of 11 C-PBR28 uptake, and is able to detect microglial activation in amyloid-positive MCI subjects. IRF parametric maps of 11 C-PBR28 uptake allow voxel-wise single-subject analysis and could be used to evaluate microglial activation in individual subjects.

De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana.

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Guodong Rao

Full Text Available Salix matsudana Koidz. is a deciduous, rapidly growing, and drought resistant tree and is one of the most widely distributed and commonly cultivated willow species in China. Currently little transcriptomic and small RNAomic data are available to reveal the genes involve in the stress resistant in S. matsudana. Here, we report the RNA-seq analysis results of both transcriptome and small RNAome data using Illumina deep sequencing of shoot tips from two willow variants(Salix. matsudana and Salix matsudana Koidz. cultivar 'Tortuosa'. De novo gene assembly was used to generate the consensus transcriptome and small RNAome, which contained 106,403 unique transcripts with an average length of 944 bp and a total length of 100.45 MB, and 166 known miRNAs representing 35 miRNA families. Comparison of transcriptomes and small RNAomes combined with quantitative real-time PCR from the two Salix libraries revealed a total of 292 different expressed genes(DEGs and 36 different expressed miRNAs (DEMs. Among the DEGs and DEMs, 196 genes and 24 miRNAs were up regulated, 96 genes and 12 miRNA were down regulated in S. matsudana. Functional analysis of DEGs and miRNA targets showed that many genes were involved in stress resistance in S. matsudana. Our global gene expression profiling presents a comprehensive view of the transcriptome and small RNAome which provide valuable information and sequence resources for uncovering the stress response genes in S. matsudana. Moreover the transcriptome and small RNAome data provide a basis for future study of genetic resistance in Salix.

Analysis of the asymmetrical shortest two-server queueing model

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J.W. Cohen

1995-01-01

textabstractThis study presents the analytic solution for the asymmetrical two-server queueing model with arriving customers joining the shorter queue for the case with Poisson arrivals and negative exponentially distributed service times. The bivariate generating function of the stationary joint

Word-wide meta-analysis of Quercus forests ectomycorrhizal fungal diversity reveals southwestern Mexico as a hotspot.

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García-Guzmán, Olimpia Mariana; Garibay-Orijel, Roberto; Hernández, Edith; Arellano-Torres, Elsa; Oyama, Ken

2017-11-01

Quercus is the most diverse genus of ectomycorrhizal (ECM) host plants; it is distributed in the Northern and Southern Hemispheres, from temperate to tropical regions. However, their ECM communities have been scarcely studied in comparison to those of conifers. The objectives of this study were to determine the richness of ECM fungi associated with oak forests in the Cuitzeo basin in southwestern Mexico; and to determine the level of richness, potential endemism and species similarity among ECM fungal communities associated with natural oak forests worldwide through a meta-analysis. The ITS DNA sequences of ECM root tips from 14 studies were included in the meta-analysis. In total, 1065 species of ECM fungi have been documented worldwide; however, 812 species have been only found at one site. Oak forests in Europe contain 416 species, Mexico 307, USA 285, and China 151. Species with wider distributions are Sebacinaceae sp. SH197130, Amanita subjunquillea, Cenococcum geophilum, Cortinarius decipiens, Russula hortensis, R. risigallina, R. subrubescens, Sebacinaceae sp. SH214607, Tomentella ferruginea, and T. lapida. The meta-analysis revealed (1) that Mexico is not only a hotspot for oak species but also for their ECM mycobionts. (2) There is a particularly high diversity of ECM Pezizales in oak seasonal forests from western USA to southwestern Mexico. (3) The oak forests in southwestern Mexico have the largest number of potential endemic species. (4) Globally, there is a high turnover of ECM fungal species associated with oaks, which indicates high levels of alpha and beta diversity in these communities.

N- and O-glycosylation Analysis of Human C1-inhibitor Reveals Extensive Mucin-type O-Glycosylation.

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Stavenhagen, Kathrin; Kayili, H Mehmet; Holst, Stephanie; Koeleman, Carolien A M; Engel, Ruchira; Wouters, Diana; Zeerleder, Sacha; Salih, Bekir; Wuhrer, Manfred

2018-06-01

Human C1-inhibitor (C1-Inh) is a serine protease inhibitor and the major regulator of the contact activation pathway as well as the classical and lectin complement pathways. It is known to be a highly glycosylated plasma glycoprotein. However, both the structural features and biological role of C1-Inh glycosylation are largely unknown. Here, we performed for the first time an in-depth site-specific N - and O -glycosylation analysis of C1-Inh combining various mass spectrometric approaches, including C18-porous graphitized carbon (PGC)-LC-ESI-QTOF-MS/MS applying stepping-energy collision-induced dissociation (CID) and electron-transfer dissociation (ETD). Various proteases were applied, partly in combination with PNGase F and exoglycosidase treatment, in order to analyze the (glyco)peptides. The analysis revealed an extensively O -glycosylated N-terminal region. Five novel and five known O -glycosylation sites were identified, carrying mainly core1-type O -glycans. In addition, we detected a heavily O -glycosylated portion spanning from Thr 82 -Ser 121 with up to 16 O -glycans attached. Likewise, all known six N -glycosylation sites were covered and confirmed by this site-specific glycosylation analysis. The glycoforms were in accordance with results on released N -glycans by MALDI-TOF/TOF-MS/MS. The comprehensive characterization of C1-Inh glycosylation described in this study will form the basis for further functional studies on the role of these glycan modifications. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

QTL mapping and transcriptome analysis of cowpea reveals candidate genes for root-knot nematode resistance.

Science.gov (United States)

Santos, Jansen Rodrigo Pereira; Ndeve, Arsenio Daniel; Huynh, Bao-Lam; Matthews, William Charles; Roberts, Philip Alan

2018-01-01

Cowpea is one of the most important food and forage legumes in drier regions of the tropics and subtropics. However, cowpea yield worldwide is markedly below the known potential due to abiotic and biotic stresses, including parasitism by root-knot nematodes (Meloidogyne spp., RKN). Two resistance genes with dominant effect, Rk and Rk2, have been reported to provide resistance against RKN in cowpea. Despite their description and use in breeding for resistance to RKN and particularly genetic mapping of the Rk locus, the exact genes conferring resistance to RKN remain unknown. In the present work, QTL mapping using recombinant inbred line (RIL) population 524B x IT84S-2049 segregating for a newly mapped locus and analysis of the transcriptome changes in two cowpea near-isogenic lines (NIL) were used to identify candidate genes for Rk and the newly mapped locus. A major QTL, designated QRk-vu9.1, associated with resistance to Meloidogyne javanica reproduction, was detected and mapped on linkage group LG9 at position 13.37 cM using egg production data. Transcriptome analysis on resistant and susceptible NILs 3 and 9 days after inoculation revealed up-regulation of 109 and 98 genes and down-regulation of 110 and 89 genes, respectively, out of 19,922 unique genes mapped to the common bean reference genome. Among the differentially expressed genes, four and nine genes were found within the QRk-vu9.1 and QRk-vu11.1 QTL intervals, respectively. Six of these genes belong to the TIR-NBS-LRR family of resistance genes and three were upregulated at one or more time-points. Quantitative RT-PCR validated gene expression to be positively correlated with RNA-seq expression pattern for eight genes. Future functional analysis of these cowpea genes will enhance our understanding of Rk-mediated resistance and identify the specific gene responsible for the resistance.

Thyroid transcriptome analysis reveals different adaptive responses to cold environmental conditions between two chicken breeds.

Science.gov (United States)

Xie, Shanshan; Yang, Xukai; Wang, Dehe; Zhu, Feng; Yang, Ning; Hou, Zhuocheng; Ning, Zhonghua

2018-01-01

Selection for cold tolerance in chickens is important for improving production performance and animal welfare. The identification of chicken breeds with higher cold tolerance and production performance will help to target candidates for the selection. The thyroid gland plays important roles in thermal adaptation, and its function is influenced by breed differences and transcriptional plasticity, both of which remain largely unknown in the chicken thyroid transcriptome. In this study, we subjected Bashang Long-tail (BS) and Rhode Island Red (RIR) chickens to either cold or warm environments for 21 weeks and investigated egg production performance, body weight changes, serum thyroid hormone concentrations, and thyroid gland transcriptome profiles. RIR chickens had higher egg production than BS chickens under warm conditions, but BS chickens produced more eggs than RIRs under cold conditions. Furthermore, BS chickens showed stable body weight gain under cold conditions while RIRs did not. These results suggested that BS breed is a preferable candidate for cold-tolerance selection and that the cold adaptability of RIRs should be improved in the future. BS chickens had higher serum thyroid hormone concentrations than RIRs under both environments. RNA-Seq generated 344.3 million paired-end reads from 16 sequencing libraries, and about 90% of the processed reads were concordantly mapped to the chicken reference genome. Differential expression analysis identified 46-1,211 genes in the respective comparisons. With regard to breed differences in the thyroid transcriptome, BS chickens showed higher cell replication and development, and immune response-related activity, while RIR chickens showed higher carbohydrate and protein metabolism activity. The cold environment reduced breed differences in the thyroid transcriptome compared with the warm environment. Transcriptional plasticity analysis revealed different adaptive responses in BS and RIR chickens to cope with the cold

Joint multifractal analysis based on wavelet leaders

Science.gov (United States)

Jiang, Zhi-Qiang; Yang, Yan-Hong; Wang, Gang-Jin; Zhou, Wei-Xing

2017-12-01

Mutually interacting components form complex systems and these components usually have long-range cross-correlated outputs. Using wavelet leaders, we propose a method for characterizing the joint multifractal nature of these long-range cross correlations; we call this method joint multifractal analysis based on wavelet leaders (MF-X-WL). We test the validity of the MF-X-WL method by performing extensive numerical experiments on dual binomial measures with multifractal cross correlations and bivariate fractional Brownian motions (bFBMs) with monofractal cross correlations. Both experiments indicate that MF-X-WL is capable of detecting cross correlations in synthetic data with acceptable estimating errors. We also apply the MF-X-WL method to pairs of series from financial markets (returns and volatilities) and online worlds (online numbers of different genders and different societies) and determine intriguing joint multifractal behavior.

Performance analysis of cognitive multihop relaying with m-QAM detect-and-forward in Nakagami-m fading channels

KAUST Repository

Benjillali, Mustapha; Hyadi, Amal; Da Costa, Daniel Benevides Da; Alouini, Mohamed-Slim

2013-01-01

In this work, we investigate the performance of cognitive multihop regenerative relaying systems in the "underlay" spectrum sharing scenario. The multiple relays perform "detect-and-forward" relaying strategy to convey a message with an order m quadrature amplitude modulation (m-QAM) from the source to the destination over independent but not necessarily identical Nakagami-m fading channels. We adopt a closed-form analysis framework based on univariate and bivariate Meijer G-functions to derive the end-to-end error performance (in terms of bit and symbol error rates), the outage probability, and the ergodic capacity. Various numerical examples are presented to illustrate the results with a large combination of system and fading parameters, and simulation results confirm the accuracy of our closed-form analysis. © 2013 IEEE.

Performance analysis of cognitive multihop relaying with m-QAM detect-and-forward in Nakagami-m fading channels

KAUST Repository

Benjillali, Mustapha

2013-09-01

In this work, we investigate the performance of cognitive multihop regenerative relaying systems in the "underlay" spectrum sharing scenario. The multiple relays perform "detect-and-forward" relaying strategy to convey a message with an order m quadrature amplitude modulation (m-QAM) from the source to the destination over independent but not necessarily identical Nakagami-m fading channels. We adopt a closed-form analysis framework based on univariate and bivariate Meijer G-functions to derive the end-to-end error performance (in terms of bit and symbol error rates), the outage probability, and the ergodic capacity. Various numerical examples are presented to illustrate the results with a large combination of system and fading parameters, and simulation results confirm the accuracy of our closed-form analysis. © 2013 IEEE.

Proteomic analysis reveals the diversity and complexity of membrane proteins in chickpea (Cicer arietinum L.

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Jaiswal Dinesh Kumar

2012-10-01

Full Text Available Abstract Background Compartmentalization is a unique feature of eukaryotes that helps in maintaining cellular homeostasis not only in intra- and inter-organellar context, but also between the cells and the external environment. Plant cells are highly compartmentalized with a complex metabolic network governing various cellular events. The membranes are the most important constituents in such compartmentalization, and membrane-associated proteins play diverse roles in many cellular processes besides being part of integral component of many signaling cascades. Results To obtain valuable insight into the dynamic repertoire of membrane proteins, we have developed a proteome reference map of a grain legume, chickpea, using two-dimensional gel electrophoresis. MALDI-TOF/TOF and LC-ESI-MS/MS analysis led to the identification of 91 proteins involved in a variety of cellular functions viz., bioenergy, stress-responsive and signal transduction, metabolism, protein synthesis and degradation, among others. Significantly, 70% of the identified proteins are putative integral membrane proteins, possessing transmembrane domains. Conclusions The proteomic analysis revealed many resident integral membrane proteins as well as membrane-associated proteins including those not reported earlier. To our knowledge, this is the first report of membrane proteome from aerial tissues of a crop plant. The findings may provide a better understanding of the biochemical machinery of the plant membranes at the molecular level that might help in functional genomics studies of different developmental pathways and stress-responses.

Systematic review and meta-analysis of studies evaluating diagnostic test accuracy: A practical review for clinical researchers-Part II. general guidance and tips

International Nuclear Information System (INIS)

Kim, Kyung Won; Choi, Sang Hyun; Huh, Jimi; Park, Seong Ho; Lee, June Young

2015-01-01

Meta-analysis of diagnostic test accuracy studies differs from the usual meta-analysis of therapeutic/interventional studies in that, it is required to simultaneously analyze a pair of two outcome measures such as sensitivity and specificity, instead of a single outcome. Since sensitivity and specificity are generally inversely correlated and could be affected by a threshold effect, more sophisticated statistical methods are required for the meta-analysis of diagnostic test accuracy. Hierarchical models including the bivariate model and the hierarchical summary receiver operating characteristic model are increasingly being accepted as standard methods for meta-analysis of diagnostic test accuracy studies. We provide a conceptual review of statistical methods currently used and recommended for meta-analysis of diagnostic test accuracy studies. This article could serve as a methodological reference for those who perform systematic review and meta-analysis of diagnostic test accuracy studies

Gene array analysis of PD-1H overexpressing monocytes reveals a pro-inflammatory profile

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Preeti Bharaj

2018-02-01

Full Text Available We have previously reported that overexpression of Programmed Death -1 Homolog (PD-1H in human monocytes leads to activation and spontaneous secretion of multiple pro inflammatory cytokines. Here we evaluate changes in monocytes gene expression after enforced PD-1H expression by gene array. The results show that there are significant alterations in 51 potential candidate genes that relate to immune response, cell adhesion and metabolism. Genes corresponding to pro-inflammatory cytokines showed the highest upregulation, 7, 3.2, 3.0, 5.8, 4.4 and 3.1 fold upregulation of TNF-α, IL-1 β, IFN-α, γ, λ and IL-27 relative to vector control. The data are in agreement with cytometric bead array analysis showing induction of proinflammatory cytokines, IL-6, IL-1β and TNF-α by PD-1H. Other genes related to inflammation, include transglutaminase 2 (TG2, NF-κB (p65 and p50 and toll like receptors (TLR 3 and 4 were upregulated 5, 4.5 and 2.5 fold, respectively. Gene set enrichment analysis (GSEA also revealed that signaling pathways related to inflammatory response, such as NFκB, AT1R, PYK2, MAPK, RELA, TNFR1, MTOR and proteasomal degradation, were significantly upregulated in response to PD-1H overexpression. We validated the results utilizing a standard inflammatory sepsis model in humanized BLT mice, finding that PD-1H expression was highly correlated with proinflammatory cytokine production. We therefore conclude that PD-1H functions to enhance monocyte activation and the induction of a pro-inflammatory gene expression profile.

KHAT (CATHA EDULIS) USE IS ASSOCIATED WITH THE ...

African Journals Online (AJOL)

2014-06-01

0.05). ... data after going through training in this process. ... Bivariate analysis: Conditional Logistic Regression ... Multivariate Logistic Regression Analysis: McNemar's ...... Hosmer, D.W. and Lemeshow, S. Applied Logistic.

Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer

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Chung Jae

2009-06-01

Full Text Available Abstract Background Cisplatin and carboplatin are the primary first-line therapies for the treatment of ovarian cancer. However, resistance to these platinum-based drugs occurs in the large majority of initially responsive tumors, resulting in fully chemoresistant, fatal disease. Although the precise mechanism(s underlying the development of platinum resistance in late-stage ovarian cancer patients currently remains unknown, CpG-island (CGI methylation, a phenomenon strongly associated with aberrant gene silencing and ovarian tumorigenesis, may contribute to this devastating condition. Methods To model the onset of drug resistance, and investigate DNA methylation and gene expression alterations associated with platinum resistance, we treated clonally derived, drug-sensitive A2780 epithelial ovarian cancer cells with increasing concentrations of cisplatin. After several cycles of drug selection, the isogenic drug-sensitive and -resistant pairs were subjected to global CGI methylation and mRNA expression microarray analyses. To identify chemoresistance-associated, biological pathways likely impacted by DNA methylation, promoter CGI methylation and mRNA expression profiles were integrated and subjected to pathway enrichment analysis. Results Promoter CGI methylation revealed a positive association (Spearman correlation of 0.99 between the total number of hypermethylated CGIs and GI50 values (i.e., increased drug resistance following successive cisplatin treatment cycles. In accord with that result, chemoresistance was reversible by DNA methylation inhibitors. Pathway enrichment analysis revealed hypermethylation-mediated repression of cell adhesion and tight junction pathways and hypomethylation-mediated activation of the cell growth-promoting pathways PI3K/Akt, TGF-beta, and cell cycle progression, which may contribute to the onset of chemoresistance in ovarian cancer cells. Conclusion Selective epigenetic disruption of distinct biological

Multichannel detrended fluctuation analysis reveals synchronized patterns of spontaneous spinal activity in anesthetized cats.

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Erika E Rodríguez

Full Text Available The analysis of the interaction and synchronization of relatively large ensembles of neurons is fundamental for the understanding of complex functions of the nervous system. It is known that the temporal synchronization of neural ensembles is involved in the generation of specific motor, sensory or cognitive processes. Also, the intersegmental coherence of spinal spontaneous activity may indicate the existence of synaptic neural pathways between different pairs of lumbar segments. In this study we present a multichannel version of the detrended fluctuation analysis method (mDFA to analyze the correlation dynamics of spontaneous spinal activity (SSA from time series analysis. This method together with the classical detrended fluctuation analysis (DFA were used to find out whether the SSA recorded in one or several segments in the spinal cord of the anesthetized cat occurs either in a random or in an organized manner. Our results are consistent with a non-random organization of the sets of neurons involved in the generation of spontaneous cord dorsum potentials (CDPs recorded either from one lumbar segment (DFA-α mean = 1.04[Formula: see text]0.09 or simultaneously from several lumbar segments (mDFA-α mean = 1.01[Formula: see text]0.06, where α = 0.5 indicates randomness while α = 0.5 indicates long-term correlations. To test the sensitivity of the mDFA method we also examined the effects of small spinal lesions aimed to partially interrupt connectivity between neighboring lumbosacral segments. We found that the synchronization and correlation between the CDPs recorded from the L5 and L6 segments in both sides of the spinal cord were reduced when a lesion comprising the left dorsal quadrant was performed between the segments L5 and L6 (mDFA-[Formula: see text] = 0.992 as compared to initial conditions mDFA-α = 1.186. The synchronization and correlation were reduced even further after a similar additional right spinal lesion (mDFA-α = 0

DNA markers reveal genetic structure and localized diversity of ...

African Journals Online (AJOL)

uqhdesma

2016-10-12

Oct 12, 2016 ... STRUCTURE analysis revealed 4 clusters of genetically ..... 10000 cycles and 50000 Markov Chain Monte Carlo (MCMC) iterations and 10 replicate runs performed for each K value to ..... WL, Lee M, Porter K (2000). Genetic ...

Genome-wide analysis of gene expression in primate taste buds reveals links to diverse processes.

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Peter Hevezi

Full Text Available Efforts to unravel the mechanisms underlying taste sensation (gustation have largely focused on rodents. Here we present the first comprehensive characterization of gene expression in primate taste buds. Our findings reveal unique new insights into the biology of taste buds. We generated a taste bud gene expression database using laser capture microdissection (LCM procured fungiform (FG and circumvallate (CV taste buds from primates. We also used LCM to collect the top and bottom portions of CV taste buds. Affymetrix genome wide arrays were used to analyze gene expression in all samples. Known taste receptors are preferentially expressed in the top portion of taste buds. Genes associated with the cell cycle and stem cells are preferentially expressed in the bottom portion of taste buds, suggesting that precursor cells are located there. Several chemokines including CXCL14 and CXCL8 are among the highest expressed genes in taste buds, indicating that immune system related processes are active in taste buds. Several genes expressed specifically in endocrine glands including growth hormone releasing hormone and its receptor are also strongly expressed in taste buds, suggesting a link between metabolism and taste. Cell type-specific expression of transcription factors and signaling molecules involved in cell fate, including KIT, reveals the taste bud as an active site of cell regeneration, differentiation, and development. IKBKAP, a gene mutated in familial dysautonomia, a disease that results in loss of taste buds, is expressed in taste cells that communicate with afferent nerve fibers via synaptic transmission. This database highlights the power of LCM coupled with transcriptional profiling to dissect the molecular composition of normal tissues, represents the most comprehensive molecular analysis of primate taste buds to date, and provides a foundation for further studies in diverse aspects of taste biology.

Comparative Analysis Between Flaviviruses Reveals Specific Neural Stem Cell Tropism for Zika Virus in the Mouse Developing Neocortex

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Jean-Baptiste Brault

2016-08-01

Full Text Available The recent Zika outbreak in South America and French Polynesia was associated with an epidemic of microcephaly, a disease characterized by a reduced size of the cerebral cortex. Other members of the Flavivirus genus, including West Nile virus (WNV, can cause encephalitis but were not demonstrated to cause microcephaly. It remains unclear whether Zika virus (ZIKV and other flaviviruses may infect different cell populations in the developing neocortex and lead to distinct developmental defects. Here, we describe an assay to infect mouse E15 embryonic brain slices with ZIKV, WNV and dengue virus serotype 4 (DENV-4. We show that this tissue is able to support viral replication of ZIKV and WNV, but not DENV-4. Cell fate analysis reveals a remarkable tropism of ZIKV infection for neural stem cells. Closely related WNV displays a very different tropism of infection, with a bias towards neurons. We further show that ZIKV infection, but not WNV infection, impairs cell cycle progression of neural stem cells. Both viruses inhibited apoptosis at early stages of infection. This work establishes a powerful comparative approach to identify ZIKV-specific alterations in the developing neocortex and reveals specific preferential infection of neural stem cells by ZIKV.

Immigrants' language skills: the immigrant experience in a longitudinal survey

OpenAIRE

Barry CHISWICK; Yew LEE; Paul W. MILLER

2003-01-01

This paper is concerned with the determinants of English language proficiency among immigrants. It presents a model based on economic incentives, exposure, and efficiency in language acquisition, which it tests using the Longitudinal Survey of Immigrants to Australia. Probit and bivariate probit analyses are employed. The hypotheses are supported by the data. The bivariate probit analysis across waves indicates a "regression to the mean" in the unobserved components of English language profic...

Transcriptomic analysis of short-fruit 1 (sf1) reveals new insights into the variation of fruit-related traits in Cucumis sativus.

Science.gov (United States)

Wang, Lina; Cao, Chenxing; Zheng, Shuangshuang; Zhang, Haiyang; Liu, Panjing; Ge, Qian; Li, Jinrui; Ren, Zhonghai

2017-06-07

Fruit size is an important quality trait in different market classes of Cucumis sativus L., an economically important vegetable cultivated worldwide, but the genetic and molecular mechanisms that control fruit size are largely unknown. In this study, we isolated a natural cucumber mutant, short fruit 1 (sf1), caused by a single recessive Mendelian factor, from the North China-type inbred line CNS2. In addition to significantly decreased fruit length, other fruit-related phenotypic variations were also observed in sf1 compared to the wild-type (WT) phenotype, indicating that sf1 might have pleiotropic effects. Microscopic imaging showed that fruit cell size in sf1 was much larger than that in WT, suggesting that the short fruit phenotype in sf1 is caused by decreased cell number. Fine mapping revealed that sf1 was localized to a 174.3 kb region on chromosome 6. Similarly, SNP association analysis of bulked segregant RNA-Seq data showed increased SNP frequency in the same region of chromosome 6. In addition, transcriptomic analysis revealed that sf1 might control fruit length through the fine-tuning of cytokinin and auxin signalling, gibberellin biosynthesis and signal transduction in cucumber fruits. Overall, our results provide important information for further study of fruit length and other fruit-related features in cucumber.

Whole-Genome Analysis of Three Yeast Strains Used for Production of Sherry-Like Wines Revealed Genetic Traits Specific to Flor Yeasts

Science.gov (United States)

Eldarov, Mikhail A.; Beletsky, Alexey V.; Tanashchuk, Tatiana N.; Kishkovskaya, Svetlana A.; Ravin, Nikolai V.; Mardanov, Andrey V.

2018-01-01

Flor yeast strains represent a specialized group of Saccharomyces cerevisiae yeasts used for biological wine aging. We have sequenced the genomes of three flor strains originated from different geographic regions and used for production of sherry-like wines in Russia. According to the obtained phylogeny of 118 yeast strains, flor strains form very tight cluster adjacent to the main wine clade. SNP analysis versus available genomes of wine and flor strains revealed 2,270 genetic variants in 1,337 loci specific to flor strains. Gene ontology analysis in combination with gene content evaluation revealed a complex landscape of possibly adaptive genetic changes in flor yeast, related to genes associated with cell morphology, mitotic cell cycle, ion homeostasis, DNA repair, carbohydrate metabolism, lipid metabolism, and cell wall biogenesis. Pangenomic analysis discovered the presence of several well-known “non-reference” loci of potential industrial importance. Events of gene loss included deletions of asparaginase genes, maltose utilization locus, and FRE-FIT locus involved in iron transport. The latter in combination with a flor-yeast-specific mutation in the Aft1 transcription factor gene is likely to be responsible for the discovered phenotype of increased iron sensitivity and improved iron uptake of analyzed strains. Expansion of the coding region of the FLO11 flocullin gene and alteration of the balance between members of the FLO gene family are likely to positively affect the well-known propensity of flor strains for velum formation. Our study provides new insights in the nature of genetic variation in flor yeast strains and demonstrates that different adaptive properties of flor yeast strains could have evolved through different mechanisms of genetic variation. PMID:29867869

Cost analysis of two-dimensional warranty for products with periodic preventive maintenance

International Nuclear Information System (INIS)

Huang, Yeu-Shiang; Gau, Wei-Yo; Ho, Jyh-Wen

2015-01-01

This study uses a bivariate approach, which simultaneously considers the time and usage of a repairable product, and takes into account periodic preventive maintenance to develop a two-dimensional warranty policy for the repairable product. The proposed model is based on the bivariate Weibull process to analyze the breakdown process of a repairable product simultaneously in terms of time and usage. A repairable product may be differently utilized by various customers. We consider two types of customers: (1) customers whose product warranty is terminated because the warranty time limit has reached first; (2) customers whose product warranty is terminated because the warranty usage limit has reached first, to perform cost analyses for determining an appropriate warranty policy. However, since it is often the case that the repairable product may be equally likely purchased by the two types of customers who are equivalently important to the product manufacturer; the optimal warranty policy would thus be the equilibrium solution of the cost analyses which pay the same attention to both types of customers in order to maximize the total profit of the manufacturer. - Highlights: • We use a bivariate method to model the breakdown process. • We consider a periodic PM schedule. • We obtain an optimal two-dimensional warranty policy considering various customers. • The optimal 2D warranty is an equilibrium which satisfies both seller and buyer

The interaction properties of the human Rab GTPase family--comparative analysis reveals determinants of molecular binding selectivity.

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Matthias Stein

Full Text Available Rab GTPases constitute the largest subfamily of the Ras protein superfamily. Rab proteins regulate organelle biogenesis and transport, and display distinct binding preferences for effector and activator proteins, many of which have not been elucidated yet. The underlying molecular recognition motifs, binding partner preferences and selectivities are not well understood.Comparative analysis of the amino acid sequences and the three-dimensional electrostatic and hydrophobic molecular interaction fields of 62 human Rab proteins revealed a wide range of binding properties with large differences between some Rab proteins. This analysis assists the functional annotation of Rab proteins 12, 14, 26, 37 and 41 and provided an explanation for the shared function of Rab3 and 27. Rab7a and 7b have very different electrostatic potentials, indicating that they may bind to different effector proteins and thus, exert different functions. The subfamily V Rab GTPases which are associated with endosome differ subtly in the interaction properties of their switch regions, and this may explain exchange factor specificity and exchange kinetics.We have analysed conservation of sequence and of molecular interaction fields to cluster and annotate the human Rab proteins. The analysis of three dimensional molecular interaction fields provides detailed insight that is not available from a sequence-based approach alone. Based on our results, we predict novel functions for some Rab proteins and provide insights into their divergent functions and the determinants of their binding partner selectivity.

Analysis of Metal-Binding Features of the Wild Type and Two Domain-Truncated Mutant Variants of Littorina littorea Metallothionein Reveals Its Cd-Specific Character

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Òscar Palacios

2017-07-01

Full Text Available After the resolution of the 3D structure of the Cd9-aggregate of the Littorina littorea metallothionein (MT, we report here a detailed analysis of the metal binding capabilities of the wild type MT, LlwtMT, and of two truncated mutants lacking either the N-terminal domain, Lltr2MT, or both the N-terminal domain, plus four extra flanking residues (SSVF, Lltr1MT. The recombinant synthesis and in vitro studies of these three proteins revealed that LlwtMT forms unique M9-LlwtMT complexes with Zn(II and Cd(II, while yielding a complex mixture of heteronuclear Zn,Cu-LlwtMT species with Cu(I. As expected, the truncated mutants gave rise to unique M6-LltrMT complexes and Zn,Cu-LltrMT mixtures of lower stoichiometry with respect to LlwtMT, with the SSVF fragment having an influence on their metal binding performance. Our results also revealed a major specificity, and therefore a better metal-coordinating performance of the three proteins for Cd(II than for Zn(II, although the analysis of the Zn(II/Cd(II displacement reaction clearly demonstrates a lack of any type of cooperativity in Cd(II binding. Contrarily, the analysis of their Cu(I binding abilities revealed that every LlMT domain is prone to build Cu4-aggregates, the whole MT working by modules analogously to, as previously described, certain fungal MTs, like those of C. neoformans and T. mesenterica. It is concluded that the Littorina littorea MT is a Cd-specific protein that (beyond its extended binding capacity through an additional Cd-binding domain confers to Littorina littorea a particular adaptive advantage in its changeable marine habitat.

Integrated analysis of microRNA and gene expression profiles reveals a functional regulatory module associated with liver fibrosis.

Science.gov (United States)

Chen, Wei; Zhao, Wenshan; Yang, Aiting; Xu, Anjian; Wang, Huan; Cong, Min; Liu, Tianhui; Wang, Ping; You, Hong

2017-12-15

Liver fibrosis, characterized with the excessive accumulation of extracellular matrix (ECM) proteins, represents the final common pathway of chronic liver inflammation. Ever-increasing evidence indicates microRNAs (miRNAs) dysregulation has important implications in the different stages of liver fibrosis. However, our knowledge of miRNA-gene regulation details pertaining to such disease remains unclear. The publicly available Gene Expression Omnibus (GEO) datasets of patients suffered from cirrhosis were extracted for integrated analysis. Differentially expressed miRNAs (DEMs) and genes (DEGs) were identified using GEO2R web tool. Putative target gene prediction of DEMs was carried out using the intersection of five major algorithms: DIANA-microT, TargetScan, miRanda, PICTAR5 and miRWalk. Functional miRNA-gene regulatory network (FMGRN) was constructed based on the computational target predictions at the sequence level and the inverse expression relationships between DEMs and DEGs. DAVID web server was selected to perform KEGG pathway enrichment analysis. Functional miRNA-gene regulatory module was generated based on the biological interpretation. Internal connections among genes in liver fibrosis-related module were determined using String database. MiRNA-gene regulatory modules related to liver fibrosis were experimentally verified in recombinant human TGFβ1 stimulated and specific miRNA inhibitor treated LX-2 cells. We totally identified 85 and 923 dysregulated miRNAs and genes in liver cirrhosis biopsy samples compared to their normal controls. All evident miRNA-gene pairs were identified and assembled into FMGRN which consisted of 990 regulations between 51 miRNAs and 275 genes, forming two big sub-networks that were defined as down-network and up-network, respectively. KEGG pathway enrichment analysis revealed that up-network was prominently involved in several KEGG pathways, in which "Focal adhesion", "PI3K-Akt signaling pathway" and "ECM

Deep sequencing analysis of the developing mouse brain reveals a novel microRNA

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Piltz Sandra

2011-04-01

Full Text Available Abstract Background MicroRNAs (miRNAs are small non-coding RNAs that can exert multilevel inhibition/repression at a post-transcriptional or protein synthesis level during disease or development. Characterisation of miRNAs in adult mammalian brains by deep sequencing has been reported previously. However, to date, no small RNA profiling of the developing brain has been undertaken using this method. We have performed deep sequencing and small RNA analysis of a developing (E15.5 mouse brain. Results We identified the expression of 294 known miRNAs in the E15.5 developing mouse brain, which were mostly represented by let-7 family and other brain-specific miRNAs such as miR-9 and miR-124. We also discovered 4 putative 22-23 nt miRNAs: mm_br_e15_1181, mm_br_e15_279920, mm_br_e15_96719 and mm_br_e15_294354 each with a 70-76 nt predicted pre-miRNA. We validated the 4 putative miRNAs and further characterised one of them, mm_br_e15_1181, throughout embryogenesis. Mm_br_e15_1181 biogenesis was Dicer1-dependent and was expressed in E3.5 blastocysts and E7 whole embryos. Embryo-wide expression patterns were observed at E9.5 and E11.5 followed by a near complete loss of expression by E13.5, with expression restricted to a specialised layer of cells within the developing and early postnatal brain. Mm_br_e15_1181 was upregulated during neurodifferentiation of P19 teratocarcinoma cells. This novel miRNA has been identified as miR-3099. Conclusions We have generated and analysed the first deep sequencing dataset of small RNA sequences of the developing mouse brain. The analysis revealed a novel miRNA, miR-3099, with potential regulatory effects on early embryogenesis, and involvement in neuronal cell differentiation/function in the brain during late embryonic and early neonatal development.

Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum.

Science.gov (United States)

Kenyon, Amy; Gavriouchkina, Daria; Zorman, Jernej; Napolitani, Giorgio; Cerundolo, Vincenzo; Sauka-Spengler, Tatjana

2017-07-26

The mechanisms governing neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilise biotagging, a novel genome-wide profiling approach based on cell type-specific in vivo biotinylation in zebrafish to analyse the initial response of neutrophils to Mycobacterium marinum, a close genetic relative of M. tuberculosis used to model tuberculosis. Differential expression analysis following nuclear RNA-seq of neutrophil active transcriptomes reveals a significant upregulation in both damage-sensing and effector components of the inflammasome, including caspase b, NLRC3 ortholog (wu: fb15h11) and il1β. Crispr/Cas9-mediated knockout of caspase b, which acts by proteolytic processing of il1β, results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterial infection, thus impairing granuloma development. We also show that a number of immediate early response genes (IEGs) are responsible for orchestrating the initial neutrophil response to mycobacterial infection. Further perturbation of the IEGs exposes egr3 as a key transcriptional regulator controlling il1β transcription.

Revealing spatio-spectral electroencephalographic dynamics of musical mode and tempo perception by independent component analysis.

Science.gov (United States)

Lin, Yuan-Pin; Duann, Jeng-Ren; Feng, Wenfeng; Chen, Jyh-Horng; Jung, Tzyy-Ping

2014-02-28

Music conveys emotion by manipulating musical structures, particularly musical mode- and tempo-impact. The neural correlates of musical mode and tempo perception revealed by electroencephalography (EEG) have not been adequately addressed in the literature. This study used independent component analysis (ICA) to systematically assess spatio-spectral EEG dynamics associated with the changes of musical mode and tempo. Empirical results showed that music with major mode augmented delta-band activity over the right sensorimotor cortex, suppressed theta activity over the superior parietal cortex, and moderately suppressed beta activity over the medial frontal cortex, compared to minor-mode music, whereas fast-tempo music engaged significant alpha suppression over the right sensorimotor cortex. The resultant EEG brain sources were comparable with previous studies obtained by other neuroimaging modalities, such as functional magnetic resonance imaging (fMRI) and positron emission tomography (PET). In conjunction with advanced dry and mobile EEG technology, the EEG results might facilitate the translation from laboratory-oriented research to real-life applications for music therapy, training and entertainment in naturalistic environments.

Intensity-Curvature Measurement Approaches for the Diagnosis of Magnetic Resonance Imaging Brain Tumors

Directory of Open Access Journals (Sweden)

Carlo Ciulla

2015-11-01

Full Text Available This research presents signal-image post-processing techniques called Intensity-Curvature Measurement Approaches with application to the diagnosis of human brain tumors detected through Magnetic Resonance Imaging (MRI. Post-processing of the MRI of the human brain encompasses the following model functions: (i bivariate cubic polynomial, (ii bivariate cubic Lagrange polynomial, (iii monovariate sinc, and (iv bivariate linear. The following Intensity-Curvature Measurement Approaches were used: (i classic-curvature, (ii signal resilient to interpolation, (iii intensity-curvature measure and (iv intensity-curvature functional. The results revealed that the classic-curvature, the signal resilient to interpolation and the intensity-curvature functional are able to add additional information useful to the diagnosis carried out with MRI. The contribution to the MRI diagnosis of our study are: (i the enhanced gray level scale of the tumor mass and the well-behaved representation of the tumor provided through the signal resilient to interpolation, and (ii the visually perceptible third dimension perpendicular to the image plane provided through the classic-curvature and the intensity-curvature functional.

Network analysis reveals multiscale controls on streamwater chemistry

Science.gov (United States)

Kevin J. McGuire; Christian E. Torgersen; Gene E. Likens; Donald C. Buso; Winsor H. Lowe; Scott W. Bailey

2014-01-01

By coupling synoptic data from a basin-wide assessment of streamwater chemistry with network-based geostatistical analysis, we show that spatial processes differentially affect biogeochemical condition and pattern across a headwater stream network. We analyzed a high-resolution dataset consisting of 664 water samples collected every 100 m throughout 32 tributaries in...

A Case-Control Study and Meta-Analysis Reveal BDNF Val66Met Is a Possible Risk Factor for PTSD

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Dagmar Bruenig

2016-01-01

Full Text Available Posttraumatic stress disorder (PTSD is a debilitating condition that develops in some people after exposure to a traumatic event. Brain-derived neurotrophic factor (BDNF is highly expressed in the mammalian brain and is thought to be involved in learning and memory processes. A nonsynonymous polymorphism in the BDNF gene, rs6265 (Val66Met, has been hypothesised to be associated with PTSD. Association studies examining the Val66Met polymorphism and PTSD have been inconclusive, likely due to the variability in type of trauma exposure analysed. Vietnam veterans (n=257 screened for PTSD and controlled for trauma exposure were genotyped for BDNF Val66Met. The association was not significant so we incorporated our data into a meta-analysis to obtain greater statistical power. A comprehensive search of more than 1237 articles revealed eight additional studies suitable for meta-analysis (n=3625. A random-effects meta-analysis observed a potential protective factor of the Val/Val genotype. After removing two studies with violation of Hardy-Weinberg equilibrium, findings for the Val/Val genotype reached significance. Subgroup analyses confirmed a trend for this finding. Limitations of some studies that inform this meta-analysis include poorly screened controls and a lack of examination of population stratification. Effectively designed studies should inform this line of research in the future.

Histogram Estimators of Bivariate Densities

National Research Council Canada - National Science Library

Husemann, Joyce A

1986-01-01

One-dimensional fixed-interval histogram estimators of univariate probability density functions are less efficient than the analogous variable-interval estimators which are constructed from intervals...

BIMOND3, Monotone Bivariate Interpolation

International Nuclear Information System (INIS)

Fritsch, F.N.; Carlson, R.E.

2001-01-01

1 - Description of program or function: BIMOND is a FORTRAN-77 subroutine for piecewise bi-cubic interpolation to data on a rectangular mesh, which reproduces the monotonousness of the data. A driver program, BIMOND1, is provided which reads data, computes the interpolating surface parameters, and evaluates the function on a mesh suitable for plotting. 2 - Method of solution: Monotonic piecewise bi-cubic Hermite interpolation is used. 3 - Restrictions on the complexity of the problem: The current version of the program can treat data which are monotone in only one of the independent variables, but cannot handle piecewise monotone data

Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.

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Yanliang Jiang

Full Text Available The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied.In this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains.In this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.

Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.

Science.gov (United States)

Jiang, Yanliang; Zhang, Songhao; Xu, Jian; Feng, Jianxin; Mahboob, Shahid; Al-Ghanim, Khalid A; Sun, Xiaowen; Xu, Peng

2014-01-01

The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied. In this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains. In this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.

Proteomic analysis reveals changes in carbohydrate and protein metabolism associated with broiler breast myopathy.

Science.gov (United States)

Kuttappan, Vivek A; Bottje, Walter; Ramnathan, Ranjith; Hartson, Steven D; Coon, Craig N; Kong, Byung-Whi; Owens, Casey M; Vazquez-Añon, Mercedes; Hargis, Billy M

2017-08-01

White Striping (WS) and Woody Breast (WB) are 2 conditions that adversely affect consumer acceptance as well as quality of poultry meat and meat products. Both WS and WB are characterized with degenerative myopathic changes. Previous studies showed that WS and WB in broiler fillets could result in higher ultimate pH, increased drip loss, and decreased marinade uptake. The main objective of the present study was to compare the proteomic profiles of muscle tissue (n = 5 per group) with either NORM (no or few minor myopathic lesions) or SEV (with severe myopathic changes). Proteins were extracted from these samples and analyzed using a hybrid LTQ-OrbitrapXL mass spectrometer (LC-MS/MS). Over 800 proteins were identified in the muscle samples, among which 141 demonstrated differential (P < 0.05) expression between NORM and SEV. The set of differentially (P < 0.05) expressed proteins was uploaded to Ingenuity Pathway Analysis® (IPA) software to determine the associated biological networks and pathways. The IPA analysis showed that eukaryotic initiation factor-2 (eIF-2) signaling, mechanistic target of rapamycin (mTOR) signaling, as well as regulation of eIF4 and p70S6K signaling were the major canonical pathways up-regulated (P < 0.05) in SEV muscle compared to NORM. The up-regulation of these pathways indicate an increase in protein synthesis which could be part of the rapid growth as well as cellular stress associated with ongoing muscle degeneration and the attempt to repair tissue damage in SEV birds. Furthermore, IPA analysis revealed that glycolysis and gluconeogenesis were the major down-regulated (P < 0.05) canonical pathways in SEV with respect to NORM muscle. Down-regulation of these pathways could be the reason for higher ultimate pH seen in SEV muscle samples indicating reduced glycolytic potential. In conclusion, comparison of proteomic profiles of NORM and SEV muscle samples showed differences in protein profile which explains some of the observed

Near scale-free dynamics in neural population activity of waking/sleeping rats revealed by multiscale analysis.

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Leonid A Safonov

Full Text Available A neuron embedded in an intact brain, unlike an isolated neuron, participates in network activity at various spatial resolutions. Such multiple scale spatial dynamics is potentially reflected in multiple time scales of temporal dynamics. We identify such multiple dynamical time scales of the inter-spike interval (ISI fluctuations of neurons of waking/sleeping rats by means of multiscale analysis. The time scale of large non-Gaussianity in the ISI fluctuations, measured with the Castaing method, ranges up to several minutes, markedly escaping the low-pass filtering characteristics of neurons. A comparison between neural activity during waking and sleeping reveals that non-Gaussianity is stronger during waking than sleeping throughout the entire range of scales observed. We find a remarkable property of near scale independence of the magnitude correlations as the primary cause of persistent non-Gaussianity. Such scale-invariance of correlations is characteristic of multiplicative cascade processes and raises the possibility of the existence of a scale independent memory preserving mechanism.

Structural Analysis of Women’s Heptathlon

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Freya Gassmann

2016-02-01

Full Text Available The heptathlon comprises the results of seven single disciplines, assuming an equal influence from each discipline, depending on the measured performance. Data analysis was based on the data recorded for the individual performances of the 10 winning heptathletes in the World Athletics Championships from 1987 to 2013 and the Olympic Games from 1988 to 2012. In addition to descriptive analysis methods, correlations, bivariate and multivariate linear regressions, and panel data regressions were used. The transformation of the performances from seconds, centimeters, and meters into points showed that the individual disciplines do not equally affect the overall competition result. The currently valid conversion formula for the run, jump, and throw disciplines prefers the sprint and jump disciplines but penalizes the athletes performing in the 800 m run, javelin throw, and shotput disciplines. Furthermore, 21% to 48% of the variance of the sum of points can be attributed to the performances in the disciplines of long jump, 200 m sprint, 100 m hurdles, and high jump. To balance the effects of the single disciplines in the heptathlon, the formula to calculate points should be reevaluated.

Gene expression analysis of skin grafts and cultured keratinocytes using synthetic RNA normalization reveals insights into differentiation and growth control.

Science.gov (United States)

Katayama, Shintaro; Skoog, Tiina; Jouhilahti, Eeva-Mari; Siitonen, H Annika; Nuutila, Kristo; Tervaniemi, Mari H; Vuola, Jyrki; Johnsson, Anna; Lönnerberg, Peter; Linnarsson, Sten; Elomaa, Outi; Kankuri, Esko; Kere, Juha

2015-06-25

Keratinocytes (KCs) are the most frequent cells in the epidermis, and they are often isolated and cultured in vitro to study the molecular biology of the skin. Cultured primary cells and various immortalized cells have been frequently used as skin models but their comparability to intact skin has been questioned. Moreover, when analyzing KC transcriptomes, fluctuation of polyA+ RNA content during the KCs' lifecycle has been omitted. We performed STRT RNA sequencing on 10 ng samples of total RNA from three different sample types: i) epidermal tissue (split-thickness skin grafts), ii) cultured primary KCs, and iii) HaCaT cell line. We observed significant variation in cellular polyA+ RNA content between tissue and cell culture samples of KCs. The use of synthetic RNAs and SAMstrt in normalization enabled comparison of gene expression levels in the highly heterogenous samples and facilitated discovery of differences between the tissue samples and cultured cells. The transcriptome analysis sensitively revealed genes involved in KC differentiation in skin grafts and cell cycle regulation related genes in cultured KCs and emphasized the fluctuation of transcription factors and non-coding RNAs associated to sample types. The epidermal keratinocytes derived from tissue and cell culture samples showed highly different polyA+ RNA contents. The use of SAMstrt and synthetic RNA based normalization allowed the comparison between tissue and cell culture samples and thus proved to be valuable tools for RNA-seq analysis with translational approach. Transciptomics revealed clear difference both between tissue and cell culture samples and between primary KCs and immortalized HaCaT cells.

Spirituality/Religiosity, Life Satisfaction, and Life Meaning as Protective Factors for Nonsuicidal Self-Injury in College Students

Science.gov (United States)

Kress, Victoria E.; Newgent, Rebecca A.; Whitlock, Janis; Mease, Laura

2015-01-01

The purpose of this study was to identify factors that may protect or insulate people from engaging in nonsuicidal self-injury (NSSI). College students (N = 14,385) from 8 universities participated in a web-based survey. Results of bivariate correlations and multiple regression revealed that spirituality/religiosity, life satisfaction, and life…

Study designs, use of statistical tests, and statistical analysis software choice in 2015: Results from two Pakistani monthly Medline indexed journals.

Science.gov (United States)

Shaikh, Masood Ali

2017-09-01

Assessment of research articles in terms of study designs used, statistical tests applied and the use of statistical analysis programmes help determine research activity profile and trends in the country. In this descriptive study, all original articles published by Journal of Pakistan Medical Association (JPMA) and Journal of the College of Physicians and Surgeons Pakistan (JCPSP), in the year 2015 were reviewed in terms of study designs used, application of statistical tests, and the use of statistical analysis programmes. JPMA and JCPSP published 192 and 128 original articles, respectively, in the year 2015. Results of this study indicate that cross-sectional study design, bivariate inferential statistical analysis entailing comparison between two variables/groups, and use of statistical software programme SPSS to be the most common study design, inferential statistical analysis, and statistical analysis software programmes, respectively. These results echo previously published assessment of these two journals for the year 2014.

[Suicide -- an essay trying to reveal the theme].

Science.gov (United States)

Sampaio, M A; Boemer, M R

2000-12-01

This essay proposes to reveal facets of the suicide through the discourse of different authors treating this theme as well as through contacts that I was able to have in my nursing training, through my academic trajectory. This trajectory includes an incursion by phenomenological ideas, mainly by the ideas of Heidegger and his existential analysis of the man as being-there. In this way, the understanding of a person who decides to finalize his/her existence, can be, by the existential analysis perspective, a way to reconstruct and redimension his/her existential perspectives.

Cross wavelet analysis: significance testing and pitfalls

Directory of Open Access Journals (Sweden)

D. Maraun

2004-01-01

Full Text Available In this paper, we present a detailed evaluation of cross wavelet analysis of bivariate time series. We develop a statistical test for zero wavelet coherency based on Monte Carlo simulations. If at least one of the two processes considered is Gaussian white noise, an approximative formula for the critical value can be utilized. In a second part, typical pitfalls of wavelet cross spectra and wavelet coherency are discussed. The wavelet cross spectrum appears to be not suitable for significance testing the interrelation between two processes. Instead, one should rather apply wavelet coherency. Furthermore we investigate problems due to multiple testing. Based on these results, we show that coherency between ENSO and NAO is an artefact for most of the time from 1900 to 1995. However, during a distinct period from around 1920 to 1940, significant coherency between the two phenomena occurs.

RNA sequencing analysis reveals new findings of hyperbaric oxygen treatment on rats with acute carbon monoxide poisoning.

Science.gov (United States)

Wang, Wenlan; Xue, Li; Li, Ya; Li, Rong; Xie, Xiaoping; Bao, Junxiang; Hai, Chunxu; Li, Jinsheng

2016-01-01

To elucidate the altered gene network in the brains of carbon monoxide (CO) poisoned rats after treatment with hyperbaric oxygen (HBO₂). RNA sequencing (RNA-seq) analysis was performed to examine differentially expressed genes (DEGs) in brain tissue samples from nine male rats: a normal control group; a CO poisoning group; and an HBO₂ treatment group (three rats/group). Reverse transcription polymerase chain reaction (RT-PCR) and real-time quantitative PCR were used for validation of the DEGs in another 18 male rats (six rats/group). RNA-seq revealed that two genes were upregulated (4.18 and 8.76 log to the base 2 fold change) (p⟨0.05) in the CO-poisoned rats relative to the control rats; two genes were upregulated (3.88 and 7.69 log to the base 2 fold change); and 23 genes were downregulated (3.49-15.12 log to the base 2 fold change) (p⟨0.05) in the brains of the HBO₂-treated rats relative to the CO-poisoned rats. Target prediction of DEGs by gene network analysis and analysis of pathways affected suggested that regulation of gene expressions of dopamine metabolism and nitric oxide (NO) synthesis were significantly affected by CO poisoning and HBO₂ treatment. Results of RT-PCR and real-time quantitative PCR indicated that four genes (Pomc, GH-1, Pr1 and Fshβ) associated with hormone secretion in the hypothalamic-pituitary system have potential as markers for prognosis of CO. This study is the first RNA-seq analysis profile of HBO₂ treatment on rats with acute CO poisoning. It concludes that changes of hormone secretion in the hypothalamic-pituitary system, dopamine metabolism and NO synthesis involved in brain damage and behavior abnormalities after CO poisoning and HBO₂ therapy may regulate these changes.

Multivariate longitudinal data analysis with mixed effects hidden Markov models.

Science.gov (United States)

Raffa, Jesse D; Dubin, Joel A

2015-09-01

Multiple longitudinal responses are often collected as a means to capture relevant features of the true outcome of interest, which is often hidden and not directly measurable. We outline an approach which models these multivariate longitudinal responses as generated from a hidden disease process. We propose a class of models which uses a hidden Markov model with separate but correlated random effects between multiple longitudinal responses. This approach was motivated by a smoking cessation clinical trial, where a bivariate longitudinal response involving both a continuous and a binomial response was collected for each participant to monitor smoking behavior. A Bayesian method using Markov chain Monte Carlo is used. Comparison of separate univariate response models to the bivariate response models was undertaken. Our methods are demonstrated on the smoking cessation clinical trial dataset, and properties of our approach are examined through extensive simulation studies. © 2015, The International Biometric Society.

Detection of phase synchronization from the data: Application to physiology

Science.gov (United States)

Rosenblum, Michael G.; Pikovsky, Arkady S.; Schäfer, Carsten; Tass, Peter; Kurths, Jürgen

2000-02-01

Synchronization of coupled oscillating systems means appearance of certain relations between their phases and frequencies. Here we use this concept in order to address the inverse problem and to reveal interaction between systems from experimental data. We discuss how the phases and frequencies can be estimated from time series and present the techniques for detection and quantification of synchronization. We apply our approach to multichannel magnetoencephalography data and records of muscle activity of a Parkinsonian patient, and also use it to analyze the cardiorespiratory interaction in humans. By means of these examples we demonstrate that our method is effective for the analysis of systems interrelation from noisy nonstationary bivariate data and provides other information than traditional correlation (spectral) techniques.

Distinct Biological Potential of Streptococcus gordonii and Streptococcus sanguinis Revealed by Comparative Genome Analysis.

Science.gov (United States)

Zheng, Wenning; Tan, Mui Fern; Old, Lesley A; Paterson, Ian C; Jakubovics, Nicholas S; Choo, Siew Woh

2017-06-07

Streptococcus gordonii and Streptococcus sanguinis are pioneer colonizers of dental plaque and important agents of bacterial infective endocarditis (IE). To gain a greater understanding of these two closely related species, we performed comparative analyses on 14 new S. gordonii and 5 S. sanguinis strains using various bioinformatics approaches. We revealed S. gordonii and S. sanguinis harbor open pan-genomes and share generally high sequence homology and number of core genes including virulence genes. However, we observed subtle differences in genomic islands and prophages between the species. Comparative pathogenomics analysis identified S. sanguinis strains have genes encoding IgA proteases, mitogenic factor deoxyribonucleases, nickel/cobalt uptake and cobalamin biosynthesis. On the contrary, genomic islands of S. gordonii strains contain additional copies of comCDE quorum-sensing system components involved in genetic competence. Two distinct polysaccharide locus architectures were identified, one of which was exclusively present in S. gordonii strains. The first evidence of genes encoding the CylA and CylB system by the α-haemolytic S. gordonii is presented. This study provides new insights into the genetic distinctions between S. gordonii and S. sanguinis, which yields understanding of tooth surfaces colonization and contributions to dental plaque formation, as well as their potential roles in the pathogenesis of IE.