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Sample records for randomly selected population-based

  1. Applications of random forest feature selection for fine-scale genetic population assignment.

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    Sylvester, Emma V A; Bentzen, Paul; Bradbury, Ian R; Clément, Marie; Pearce, Jon; Horne, John; Beiko, Robert G

    2018-02-01

    Genetic population assignment used to inform wildlife management and conservation efforts requires panels of highly informative genetic markers and sensitive assignment tests. We explored the utility of machine-learning algorithms (random forest, regularized random forest and guided regularized random forest) compared with F ST ranking for selection of single nucleotide polymorphisms (SNP) for fine-scale population assignment. We applied these methods to an unpublished SNP data set for Atlantic salmon ( Salmo salar ) and a published SNP data set for Alaskan Chinook salmon ( Oncorhynchus tshawytscha ). In each species, we identified the minimum panel size required to obtain a self-assignment accuracy of at least 90% using each method to create panels of 50-700 markers Panels of SNPs identified using random forest-based methods performed up to 7.8 and 11.2 percentage points better than F ST -selected panels of similar size for the Atlantic salmon and Chinook salmon data, respectively. Self-assignment accuracy ≥90% was obtained with panels of 670 and 384 SNPs for each data set, respectively, a level of accuracy never reached for these species using F ST -selected panels. Our results demonstrate a role for machine-learning approaches in marker selection across large genomic data sets to improve assignment for management and conservation of exploited populations.

  2. Selection for altruism through random drift in variable size populations

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    Houchmandzadeh Bahram

    2012-05-01

    Full Text Available Abstract Background Altruistic behavior is defined as helping others at a cost to oneself and a lowered fitness. The lower fitness implies that altruists should be selected against, which is in contradiction with their widespread presence is nature. Present models of selection for altruism (kin or multilevel show that altruistic behaviors can have ‘hidden’ advantages if the ‘common good’ produced by altruists is restricted to some related or unrelated groups. These models are mostly deterministic, or assume a frequency dependent fitness. Results Evolutionary dynamics is a competition between deterministic selection pressure and stochastic events due to random sampling from one generation to the next. We show here that an altruistic allele extending the carrying capacity of the habitat can win by increasing the random drift of “selfish” alleles. In other terms, the fixation probability of altruistic genes can be higher than those of a selfish ones, even though altruists have a smaller fitness. Moreover when populations are geographically structured, the altruists advantage can be highly amplified and the fixation probability of selfish genes can tend toward zero. The above results are obtained both by numerical and analytical calculations. Analytical results are obtained in the limit of large populations. Conclusions The theory we present does not involve kin or multilevel selection, but is based on the existence of random drift in variable size populations. The model is a generalization of the original Fisher-Wright and Moran models where the carrying capacity depends on the number of altruists.

  3. A Bayesian random effects discrete-choice model for resource selection: Population-level selection inference

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    Thomas, D.L.; Johnson, D.; Griffith, B.

    2006-01-01

    Modeling the probability of use of land units characterized by discrete and continuous measures, we present a Bayesian random-effects model to assess resource selection. This model provides simultaneous estimation of both individual- and population-level selection. Deviance information criterion (DIC), a Bayesian alternative to AIC that is sample-size specific, is used for model selection. Aerial radiolocation data from 76 adult female caribou (Rangifer tarandus) and calf pairs during 1 year on an Arctic coastal plain calving ground were used to illustrate models and assess population-level selection of landscape attributes, as well as individual heterogeneity of selection. Landscape attributes included elevation, NDVI (a measure of forage greenness), and land cover-type classification. Results from the first of a 2-stage model-selection procedure indicated that there is substantial heterogeneity among cow-calf pairs with respect to selection of the landscape attributes. In the second stage, selection of models with heterogeneity included indicated that at the population-level, NDVI and land cover class were significant attributes for selection of different landscapes by pairs on the calving ground. Population-level selection coefficients indicate that the pairs generally select landscapes with higher levels of NDVI, but the relationship is quadratic. The highest rate of selection occurs at values of NDVI less than the maximum observed. Results for land cover-class selections coefficients indicate that wet sedge, moist sedge, herbaceous tussock tundra, and shrub tussock tundra are selected at approximately the same rate, while alpine and sparsely vegetated landscapes are selected at a lower rate. Furthermore, the variability in selection by individual caribou for moist sedge and sparsely vegetated landscapes is large relative to the variability in selection of other land cover types. The example analysis illustrates that, while sometimes computationally intense, a

  4. SELECTION OF FISÁLIS POPULATIONS FOR HIBRIDIZATIONS, BASED ON FRUIT TRAITS

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    NICOLE TREVISANI

    2016-01-01

    Full Text Available ABSTRACT The objective of this study was to characterize the genetic variability in fisális populations and select promising parents based on fruit traits. The experimental design consisted of randomized blocks, with six populations. Five plants per treatment were sampled. The evaluated traits were fruit weight, capsule weight, 1000- seed weight and fruit diameter. The data were subjected to multivariate analysis of variance with error specification between and within (p <0.05. Mahalanobis’ distance was used as a measure of genetic dissimilarity. Significant differences for the assessed traits were detected between fisális populations. The ratio error among by within indicated no need for sampling within the experimental unit. Dissimilarity was greatest between Lages and Vacaria. The most discriminating traits were capsule weight, fruit weight and fruit diameter. The multivariate contrasts indicated differences between the populations of Vacaria and from Caçador, Lages and Peru, selected for hybridizations.

  5. Minimization over randomly selected lines

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    Ismet Sahin

    2013-07-01

    Full Text Available This paper presents a population-based evolutionary optimization method for minimizing a given cost function. The mutation operator of this method selects randomly oriented lines in the cost function domain, constructs quadratic functions interpolating the cost function at three different points over each line, and uses extrema of the quadratics as mutated points. The crossover operator modifies each mutated point based on components of two points in population, instead of one point as is usually performed in other evolutionary algorithms. The stopping criterion of this method depends on the number of almost degenerate quadratics. We demonstrate that the proposed method with these mutation and crossover operations achieves faster and more robust convergence than the well-known Differential Evolution and Particle Swarm algorithms.

  6. Selectivity and sparseness in randomly connected balanced networks.

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    Cengiz Pehlevan

    Full Text Available Neurons in sensory cortex show stimulus selectivity and sparse population response, even in cases where no strong functionally specific structure in connectivity can be detected. This raises the question whether selectivity and sparseness can be generated and maintained in randomly connected networks. We consider a recurrent network of excitatory and inhibitory spiking neurons with random connectivity, driven by random projections from an input layer of stimulus selective neurons. In this architecture, the stimulus-to-stimulus and neuron-to-neuron modulation of total synaptic input is weak compared to the mean input. Surprisingly, we show that in the balanced state the network can still support high stimulus selectivity and sparse population response. In the balanced state, strong synapses amplify the variation in synaptic input and recurrent inhibition cancels the mean. Functional specificity in connectivity emerges due to the inhomogeneity caused by the generative statistical rule used to build the network. We further elucidate the mechanism behind and evaluate the effects of model parameters on population sparseness and stimulus selectivity. Network response to mixtures of stimuli is investigated. It is shown that a balanced state with unselective inhibition can be achieved with densely connected input to inhibitory population. Balanced networks exhibit the "paradoxical" effect: an increase in excitatory drive to inhibition leads to decreased inhibitory population firing rate. We compare and contrast selectivity and sparseness generated by the balanced network to randomly connected unbalanced networks. Finally, we discuss our results in light of experiments.

  7. Impact of selective genotyping in the training population on accuracy and bias of genomic selection.

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    Zhao, Yusheng; Gowda, Manje; Longin, Friedrich H; Würschum, Tobias; Ranc, Nicolas; Reif, Jochen C

    2012-08-01

    Estimating marker effects based on routinely generated phenotypic data of breeding programs is a cost-effective strategy to implement genomic selection. Truncation selection in breeding populations, however, could have a strong impact on the accuracy to predict genomic breeding values. The main objective of our study was to investigate the influence of phenotypic selection on the accuracy and bias of genomic selection. We used experimental data of 788 testcross progenies from an elite maize breeding program. The testcross progenies were evaluated in unreplicated field trials in ten environments and fingerprinted with 857 SNP markers. Random regression best linear unbiased prediction method was used in combination with fivefold cross-validation based on genotypic sampling. We observed a substantial loss in the accuracy to predict genomic breeding values in unidirectional selected populations. In contrast, estimating marker effects based on bidirectional selected populations led to only a marginal decrease in the prediction accuracy of genomic breeding values. We concluded that bidirectional selection is a valuable approach to efficiently implement genomic selection in applied plant breeding programs.

  8. Random and non-random mating populations: Evolutionary dynamics in meiotic drive.

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    Sarkar, Bijan

    2016-01-01

    Game theoretic tools are utilized to analyze a one-locus continuous selection model of sex-specific meiotic drive by considering nonequivalence of the viabilities of reciprocal heterozygotes that might be noticed at an imprinted locus. The model draws attention to the role of viability selections of different types to examine the stable nature of polymorphic equilibrium. A bridge between population genetics and evolutionary game theory has been built up by applying the concept of the Fundamental Theorem of Natural Selection. In addition to pointing out the influences of male and female segregation ratios on selection, configuration structure reveals some noted results, e.g., Hardy-Weinberg frequencies hold in replicator dynamics, occurrence of faster evolution at the maximized variance fitness, existence of mixed Evolutionarily Stable Strategy (ESS) in asymmetric games, the tending evolution to follow not only a 1:1 sex ratio but also a 1:1 different alleles ratio at particular gene locus. Through construction of replicator dynamics in the group selection framework, our selection model introduces a redefining bases of game theory to incorporate non-random mating where a mating parameter associated with population structure is dependent on the social structure. Also, the model exposes the fact that the number of polymorphic equilibria will depend on the algebraic expression of population structure. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Non-Selective Evolution of Growing Populations.

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    Karl Wienand

    Full Text Available Non-selective effects, like genetic drift, are an important factor in modern conceptions of evolution, and have been extensively studied for constant population sizes (Kimura, 1955; Otto and Whitlock, 1997. Here, we consider non-selective evolution in the case of growing populations that are of small size and have varying trait compositions (e.g. after a population bottleneck. We find that, in these conditions, populations never fixate to a trait, but tend to a random limit composition, and that the distribution of compositions "freezes" to a steady state. This final state is crucially influenced by the initial conditions. We obtain these findings from a combined theoretical and experimental approach, using multiple mixed subpopulations of two Pseudomonas putida strains in non-selective growth conditions (Matthijs et al, 2009 as model system. The experimental results for the population dynamics match the theoretical predictions based on the Pólya urn model (Eggenberger and Pólya, 1923 for all analyzed parameter regimes. In summary, we show that exponential growth stops genetic drift. This result contrasts with previous theoretical analyses of non-selective evolution (e.g. genetic drift, which investigated how traits spread and eventually take over populations (fixate (Kimura, 1955; Otto and Whitlock, 1997. Moreover, our work highlights how deeply growth influences non-selective evolution, and how it plays a key role in maintaining genetic variability. Consequently, it is of particular importance in life-cycles models (Melbinger et al, 2010; Cremer et al, 2011; Cremer et al, 2012 of periodically shrinking and expanding populations.

  10. Influence of Maximum Inbreeding Avoidance under BLUP EBV Selection on Pinzgau Population Diversity

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    Radovan Kasarda

    2011-05-01

    Full Text Available Evaluated was effect of mating (random vs. maximum avoidance of inbreeding under BLUP EBV selection strategy. Existing population structure was under Monte Carlo stochastic simulation analyzed from the point to minimize increase of inbreeding. Maximum avoidance of inbreeding under BLUP selection resulted into comparable increase of inbreeding then random mating in average of 10 generation development. After 10 generations of simulation of mating strategy was observed ΔF= 6,51 % (2 sires, 5,20 % (3 sires, 3,22 % (4 sires resp. 2,94 % (5 sires. With increased number of sires selected, decrease of inbreeding was observed. With use of 4, resp. 5 sires increase of inbreeding was comparable to random mating with phenotypic selection. For saving of genetic diversity and prevention of population loss is important to minimize increase of inbreeding in small populations. Classical approach was based on balancing ratio of sires and dams in mating program. Contrariwise in the most of commercial populations small number of sires was used with high mating ratio.

  11. Field-based random sampling without a sampling frame: control selection for a case-control study in rural Africa.

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    Crampin, A C; Mwinuka, V; Malema, S S; Glynn, J R; Fine, P E

    2001-01-01

    Selection bias, particularly of controls, is common in case-control studies and may materially affect the results. Methods of control selection should be tailored both for the risk factors and disease under investigation and for the population being studied. We present here a control selection method devised for a case-control study of tuberculosis in rural Africa (Karonga, northern Malawi) that selects an age/sex frequency-matched random sample of the population, with a geographical distribution in proportion to the population density. We also present an audit of the selection process, and discuss the potential of this method in other settings.

  12. Familial versus mass selection in small populations

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    Couvet Denis

    2003-07-01

    Full Text Available Abstract We used diffusion approximations and a Markov-chain approach to investigate the consequences of familial selection on the viability of small populations both in the short and in the long term. The outcome of familial selection was compared to the case of a random mating population under mass selection. In small populations, the higher effective size, associated with familial selection, resulted in higher fitness for slightly deleterious and/or highly recessive alleles. Conversely, because familial selection leads to a lower rate of directional selection, a lower fitness was observed for more detrimental genes that are not highly recessive, and with high population sizes. However, in the long term, genetic load was almost identical for both mass and familial selection for populations of up to 200 individuals. In terms of mean time to extinction, familial selection did not have any negative effect at least for small populations (N ≤ 50. Overall, familial selection could be proposed for use in management programs of small populations since it increases genetic variability and short-term viability without impairing the overall persistence times.

  13. Strategies for implementing genomic selection in family-based aquaculture breeding schemes: double haploid sib test populations

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    Nirea Kahsay G

    2012-10-01

    Full Text Available Abstract Background Simulation studies have shown that accuracy and genetic gain are increased in genomic selection schemes compared to traditional aquaculture sib-based schemes. In genomic selection, accuracy of selection can be maximized by increasing the precision of the estimation of SNP effects and by maximizing the relationships between test sibs and candidate sibs. Another means of increasing the accuracy of the estimation of SNP effects is to create individuals in the test population with extreme genotypes. The latter approach was studied here with creation of double haploids and use of non-random mating designs. Methods Six alternative breeding schemes were simulated in which the design of the test population was varied: test sibs inherited maternal (Mat, paternal (Pat or a mixture of maternal and paternal (MatPat double haploid genomes or test sibs were obtained by maximum coancestry mating (MaxC, minimum coancestry mating (MinC, or random (RAND mating. Three thousand test sibs and 3000 candidate sibs were genotyped. The test sibs were recorded for a trait that could not be measured on the candidates and were used to estimate SNP effects. Selection was done by truncation on genome-wide estimated breeding values and 100 individuals were selected as parents each generation, equally divided between both sexes. Results Results showed a 7 to 19% increase in selection accuracy and a 6 to 22% increase in genetic gain in the MatPat scheme compared to the RAND scheme. These increases were greater with lower heritabilities. Among all other scenarios, i.e. Mat, Pat, MaxC, and MinC, no substantial differences in selection accuracy and genetic gain were observed. Conclusions In conclusion, a test population designed with a mixture of paternal and maternal double haploids, i.e. the MatPat scheme, increases substantially the accuracy of selection and genetic gain. This will be particularly interesting for traits that cannot be recorded on the

  14. Assessment of fracture risk: value of random population-based samples--the Geelong Osteoporosis Study.

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    Henry, M J; Pasco, J A; Seeman, E; Nicholson, G C; Sanders, K M; Kotowicz, M A

    2001-01-01

    Fracture risk is determined by bone mineral density (BMD). The T-score, a measure of fracture risk, is the position of an individual's BMD in relation to a reference range. The aim of this study was to determine the magnitude of change in the T-score when different sampling techniques were used to produce the reference range. Reference ranges were derived from three samples, drawn from the same region: (1) an age-stratified population-based random sample, (2) unselected volunteers, and (3) a selected healthy subset of the population-based sample with no diseases or drugs known to affect bone. T-scores were calculated using the three reference ranges for a cohort of women who had sustained a fracture and as a group had a low mean BMD (ages 35-72 yr; n = 484). For most comparisons, the T-scores for the fracture cohort were more negative using the population reference range. The difference in T-scores reached 1.0 SD. The proportion of the fracture cohort classified as having osteoporosis at the spine was 26, 14, and 23% when the population, volunteer, and healthy reference ranges were applied, respectively. The use of inappropriate reference ranges results in substantial changes to T-scores and may lead to inappropriate management.

  15. Accuracy of genomic selection for alfalfa biomass yield in different reference populations.

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    Annicchiarico, Paolo; Nazzicari, Nelson; Li, Xuehui; Wei, Yanling; Pecetti, Luciano; Brummer, E Charles

    2015-12-01

    Genomic selection based on genotyping-by-sequencing (GBS) data could accelerate alfalfa yield gains, if it displayed moderate ability to predict parent breeding values. Its interest would be enhanced by predicting ability also for germplasm/reference populations other than those for which it was defined. Predicting accuracy may be influenced by statistical models, SNP calling procedures and missing data imputation strategies. Landrace and variety material from two genetically-contrasting reference populations, i.e., 124 elite genotypes adapted to the Po Valley (sub-continental climate; PV population) and 154 genotypes adapted to Mediterranean-climate environments (Me population), were genotyped by GBS and phenotyped in separate environments for dry matter yield of their dense-planted half-sib progenies. Both populations showed no sub-population genetic structure. Predictive accuracy was higher by joint rather than separate SNP calling for the two data sets, and using random forest imputation of missing data. Highest accuracy was obtained using Support Vector Regression (SVR) for PV, and Ridge Regression BLUP and SVR for Me germplasm. Bayesian methods (Bayes A, Bayes B and Bayesian Lasso) tended to be less accurate. Random Forest Regression was the least accurate model. Accuracy attained about 0.35 for Me in the range of 0.30-0.50 missing data, and 0.32 for PV at 0.50 missing data, using at least 10,000 SNP markers. Cross-population predictions based on a smaller subset of common SNPs implied a relative loss of accuracy of about 25% for Me and 30% for PV. Genome-wide association analyses based on large subsets of M. truncatula-aligned markers revealed many SNPs with modest association with yield, and some genome areas hosting putative QTLs. A comparison of genomic vs. conventional selection for parent breeding value assuming 1-year vs. 5-year selection cycles, respectively, indicated over three-fold greater predicted yield gain per unit time for genomic selection

  16. Application of random effects to the study of resource selection by animals.

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    Gillies, Cameron S; Hebblewhite, Mark; Nielsen, Scott E; Krawchuk, Meg A; Aldridge, Cameron L; Frair, Jacqueline L; Saher, D Joanne; Stevens, Cameron E; Jerde, Christopher L

    2006-07-01

    1. Resource selection estimated by logistic regression is used increasingly in studies to identify critical resources for animal populations and to predict species occurrence. 2. Most frequently, individual animals are monitored and pooled to estimate population-level effects without regard to group or individual-level variation. Pooling assumes that both observations and their errors are independent, and resource selection is constant given individual variation in resource availability. 3. Although researchers have identified ways to minimize autocorrelation, variation between individuals caused by differences in selection or available resources, including functional responses in resource selection, have not been well addressed. 4. Here we review random-effects models and their application to resource selection modelling to overcome these common limitations. We present a simple case study of an analysis of resource selection by grizzly bears in the foothills of the Canadian Rocky Mountains with and without random effects. 5. Both categorical and continuous variables in the grizzly bear model differed in interpretation, both in statistical significance and coefficient sign, depending on how a random effect was included. We used a simulation approach to clarify the application of random effects under three common situations for telemetry studies: (a) discrepancies in sample sizes among individuals; (b) differences among individuals in selection where availability is constant; and (c) differences in availability with and without a functional response in resource selection. 6. We found that random intercepts accounted for unbalanced sample designs, and models with random intercepts and coefficients improved model fit given the variation in selection among individuals and functional responses in selection. Our empirical example and simulations demonstrate how including random effects in resource selection models can aid interpretation and address difficult assumptions

  17. Training set optimization under population structure in genomic selection.

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    Isidro, Julio; Jannink, Jean-Luc; Akdemir, Deniz; Poland, Jesse; Heslot, Nicolas; Sorrells, Mark E

    2015-01-01

    Population structure must be evaluated before optimization of the training set population. Maximizing the phenotypic variance captured by the training set is important for optimal performance. The optimization of the training set (TRS) in genomic selection has received much interest in both animal and plant breeding, because it is critical to the accuracy of the prediction models. In this study, five different TRS sampling algorithms, stratified sampling, mean of the coefficient of determination (CDmean), mean of predictor error variance (PEVmean), stratified CDmean (StratCDmean) and random sampling, were evaluated for prediction accuracy in the presence of different levels of population structure. In the presence of population structure, the most phenotypic variation captured by a sampling method in the TRS is desirable. The wheat dataset showed mild population structure, and CDmean and stratified CDmean methods showed the highest accuracies for all the traits except for test weight and heading date. The rice dataset had strong population structure and the approach based on stratified sampling showed the highest accuracies for all traits. In general, CDmean minimized the relationship between genotypes in the TRS, maximizing the relationship between TRS and the test set. This makes it suitable as an optimization criterion for long-term selection. Our results indicated that the best selection criterion used to optimize the TRS seems to depend on the interaction of trait architecture and population structure.

  18. Generalizing Evidence From Randomized Clinical Trials to Target Populations

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    Cole, Stephen R.; Stuart, Elizabeth A.

    2010-01-01

    Properly planned and conducted randomized clinical trials remain susceptible to a lack of external validity. The authors illustrate a model-based method to standardize observed trial results to a specified target population using a seminal human immunodeficiency virus (HIV) treatment trial, and they provide Monte Carlo simulation evidence supporting the method. The example trial enrolled 1,156 HIV-infected adult men and women in the United States in 1996, randomly assigned 577 to a highly active antiretroviral therapy and 579 to a largely ineffective combination therapy, and followed participants for 52 weeks. The target population was US people infected with HIV in 2006, as estimated by the Centers for Disease Control and Prevention. Results from the trial apply, albeit muted by 12%, to the target population, under the assumption that the authors have measured and correctly modeled the determinants of selection that reflect heterogeneity in the treatment effect. In simulations with a heterogeneous treatment effect, a conventional intent-to-treat estimate was biased with poor confidence limit coverage, but the proposed estimate was largely unbiased with appropriate confidence limit coverage. The proposed method standardizes observed trial results to a specified target population and thereby provides information regarding the generalizability of trial results. PMID:20547574

  19. Accuracy of genomic selection in European maize elite breeding populations.

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    Zhao, Yusheng; Gowda, Manje; Liu, Wenxin; Würschum, Tobias; Maurer, Hans P; Longin, Friedrich H; Ranc, Nicolas; Reif, Jochen C

    2012-03-01

    Genomic selection is a promising breeding strategy for rapid improvement of complex traits. The objective of our study was to investigate the prediction accuracy of genomic breeding values through cross validation. The study was based on experimental data of six segregating populations from a half-diallel mating design with 788 testcross progenies from an elite maize breeding program. The plants were intensively phenotyped in multi-location field trials and fingerprinted with 960 SNP markers. We used random regression best linear unbiased prediction in combination with fivefold cross validation. The prediction accuracy across populations was higher for grain moisture (0.90) than for grain yield (0.58). The accuracy of genomic selection realized for grain yield corresponds to the precision of phenotyping at unreplicated field trials in 3-4 locations. As for maize up to three generations are feasible per year, selection gain per unit time is high and, consequently, genomic selection holds great promise for maize breeding programs.

  20. Reliability of pedigree-based and genomic evaluations in selected populations

    NARCIS (Netherlands)

    Gorjanc, G.; Bijma, P.; Hickey, J.M.

    2015-01-01

    Background: Reliability is an important parameter in breeding. It measures the precision of estimated breeding values (EBV) and, thus, potential response to selection on those EBV. The precision of EBV is commonly measured by relating the prediction error variance (PEV) of EBV to the base population

  1. Differential privacy-based evaporative cooling feature selection and classification with relief-F and random forests.

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    Le, Trang T; Simmons, W Kyle; Misaki, Masaya; Bodurka, Jerzy; White, Bill C; Savitz, Jonathan; McKinney, Brett A

    2017-09-15

    Classification of individuals into disease or clinical categories from high-dimensional biological data with low prediction error is an important challenge of statistical learning in bioinformatics. Feature selection can improve classification accuracy but must be incorporated carefully into cross-validation to avoid overfitting. Recently, feature selection methods based on differential privacy, such as differentially private random forests and reusable holdout sets, have been proposed. However, for domains such as bioinformatics, where the number of features is much larger than the number of observations p≫n , these differential privacy methods are susceptible to overfitting. We introduce private Evaporative Cooling, a stochastic privacy-preserving machine learning algorithm that uses Relief-F for feature selection and random forest for privacy preserving classification that also prevents overfitting. We relate the privacy-preserving threshold mechanism to a thermodynamic Maxwell-Boltzmann distribution, where the temperature represents the privacy threshold. We use the thermal statistical physics concept of Evaporative Cooling of atomic gases to perform backward stepwise privacy-preserving feature selection. On simulated data with main effects and statistical interactions, we compare accuracies on holdout and validation sets for three privacy-preserving methods: the reusable holdout, reusable holdout with random forest, and private Evaporative Cooling, which uses Relief-F feature selection and random forest classification. In simulations where interactions exist between attributes, private Evaporative Cooling provides higher classification accuracy without overfitting based on an independent validation set. In simulations without interactions, thresholdout with random forest and private Evaporative Cooling give comparable accuracies. We also apply these privacy methods to human brain resting-state fMRI data from a study of major depressive disorder. Code

  2. Kin groups and trait groups: population structure and epidemic disease selection.

    Science.gov (United States)

    Fix, A G

    1984-10-01

    A Monte Carlo simulation based on the population structure of a small-scale human population, the Semai Senoi of Malaysia, has been developed to study the combined effects of group, kin, and individual selection. The population structure resembles D.S. Wilson's structured deme model in that local breeding populations (Semai settlements) are subdivided into trait groups (hamlets) that may be kin-structured and are not themselves demes. Additionally, settlement breeding populations are connected by two-dimensional stepping-stone migration approaching 30% per generation. Group and kin-structured group selection occur among hamlets the survivors of which then disperse to breed within the settlement population. Genetic drift is modeled by the process of hamlet formation; individual selection as a deterministic process, and stepping-stone migration as either random or kin-structured migrant groups. The mechanism for group selection is epidemics of infectious disease that can wipe out small hamlets particularly if most adults become sick and social life collapses. Genetic resistance to a disease is an individual attribute; however, hamlet groups with several resistant adults are less likely to disintegrate and experience high social mortality. A specific human gene, hemoglobin E, which confers resistance to malaria, is studied as an example of the process. The results of the simulations show that high genetic variance among hamlet groups may be generated by moderate degrees of kin-structuring. This strong microdifferentiation provides the potential for group selection. The effect of group selection in this case is rapid increase in gene frequencies among the total set of populations. In fact, group selection in concert with individual selection produced a faster rate of gene frequency increase among a set of 25 populations than the rate within a single unstructured population subject to deterministic individual selection. Such rapid evolution with plausible rates of

  3. Genetic diversity of Kenyan Prosopis populations based on random ...

    African Journals Online (AJOL)

    To determine whether naturally established stands consist of a single or mixture of species, six populations from Bamburi, Bura, Isiolo, Marigat, Taveta and Turkwel were compared for relatedness with reference to Prosopis chilensis, Prosopis juliflora and Prosopis pallida using random amplified polymorphic DNA markers.

  4. Blocked Randomization with Randomly Selected Block Sizes

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    Jimmy Efird

    2010-12-01

    Full Text Available When planning a randomized clinical trial, careful consideration must be given to how participants are selected for various arms of a study. Selection and accidental bias may occur when participants are not assigned to study groups with equal probability. A simple random allocation scheme is a process by which each participant has equal likelihood of being assigned to treatment versus referent groups. However, by chance an unequal number of individuals may be assigned to each arm of the study and thus decrease the power to detect statistically significant differences between groups. Block randomization is a commonly used technique in clinical trial design to reduce bias and achieve balance in the allocation of participants to treatment arms, especially when the sample size is small. This method increases the probability that each arm will contain an equal number of individuals by sequencing participant assignments by block. Yet still, the allocation process may be predictable, for example, when the investigator is not blind and the block size is fixed. This paper provides an overview of blocked randomization and illustrates how to avoid selection bias by using random block sizes.

  5. Test Population Selection from Weibull-Based, Monte Carlo Simulations of Fatigue Life

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    Vlcek, Brian L.; Zaretsky, Erwin V.; Hendricks, Robert C.

    2012-01-01

    Fatigue life is probabilistic and not deterministic. Experimentally establishing the fatigue life of materials, components, and systems is both time consuming and costly. As a result, conclusions regarding fatigue life are often inferred from a statistically insufficient number of physical tests. A proposed methodology for comparing life results as a function of variability due to Weibull parameters, variability between successive trials, and variability due to size of the experimental population is presented. Using Monte Carlo simulation of randomly selected lives from a large Weibull distribution, the variation in the L10 fatigue life of aluminum alloy AL6061 rotating rod fatigue tests was determined as a function of population size. These results were compared to the L10 fatigue lives of small (10 each) populations from AL2024, AL7075 and AL6061. For aluminum alloy AL6061, a simple algebraic relationship was established for the upper and lower L10 fatigue life limits as a function of the number of specimens failed. For most engineering applications where less than 30 percent variability can be tolerated in the maximum and minimum values, at least 30 to 35 test samples are necessary. The variability of test results based on small sample sizes can be greater than actual differences, if any, that exists between materials and can result in erroneous conclusions. The fatigue life of AL2024 is statistically longer than AL6061 and AL7075. However, there is no statistical difference between the fatigue lives of AL6061 and AL7075 even though AL7075 had a fatigue life 30 percent greater than AL6061.

  6. The signature of positive selection at randomly chosen loci.

    OpenAIRE

    Przeworski, Molly

    2002-01-01

    In Drosophila and humans, there are accumulating examples of loci with a significant excess of high-frequency-derived alleles or high levels of linkage disequilibrium, relative to a neutral model of a random-mating population of constant size. These are features expected after a recent selective sweep. Their prevalence suggests that positive directional selection may be widespread in both species. However, as I show here, these features do not persist long after the sweep ends: The high-frequ...

  7. Local randomization in neighbor selection improves PRM roadmap quality

    KAUST Repository

    McMahon, Troy; Jacobs, Sam; Boyd, Bryan; Tapia, Lydia; Amato, Nancy M.

    2012-01-01

    Probabilistic Roadmap Methods (PRMs) are one of the most used classes of motion planning methods. These sampling-based methods generate robot configurations (nodes) and then connect them to form a graph (roadmap) containing representative feasible pathways. A key step in PRM roadmap construction involves identifying a set of candidate neighbors for each node. Traditionally, these candidates are chosen to be the k-closest nodes based on a given distance metric. In this paper, we propose a new neighbor selection policy called LocalRand(k,K'), that first computes the K' closest nodes to a specified node and then selects k of those nodes at random. Intuitively, LocalRand attempts to benefit from random sampling while maintaining the higher levels of local planner success inherent to selecting more local neighbors. We provide a methodology for selecting the parameters k and K'. We perform an experimental comparison which shows that for both rigid and articulated robots, LocalRand results in roadmaps that are better connected than the traditional k-closest policy or a purely random neighbor selection policy. The cost required to achieve these results is shown to be comparable to k-closest. © 2012 IEEE.

  8. Local randomization in neighbor selection improves PRM roadmap quality

    KAUST Repository

    McMahon, Troy

    2012-10-01

    Probabilistic Roadmap Methods (PRMs) are one of the most used classes of motion planning methods. These sampling-based methods generate robot configurations (nodes) and then connect them to form a graph (roadmap) containing representative feasible pathways. A key step in PRM roadmap construction involves identifying a set of candidate neighbors for each node. Traditionally, these candidates are chosen to be the k-closest nodes based on a given distance metric. In this paper, we propose a new neighbor selection policy called LocalRand(k,K\\'), that first computes the K\\' closest nodes to a specified node and then selects k of those nodes at random. Intuitively, LocalRand attempts to benefit from random sampling while maintaining the higher levels of local planner success inherent to selecting more local neighbors. We provide a methodology for selecting the parameters k and K\\'. We perform an experimental comparison which shows that for both rigid and articulated robots, LocalRand results in roadmaps that are better connected than the traditional k-closest policy or a purely random neighbor selection policy. The cost required to achieve these results is shown to be comparable to k-closest. © 2012 IEEE.

  9. Selection bias in population-based cancer case-control studies due to incomplete sampling frame coverage.

    Science.gov (United States)

    Walsh, Matthew C; Trentham-Dietz, Amy; Gangnon, Ronald E; Nieto, F Javier; Newcomb, Polly A; Palta, Mari

    2012-06-01

    Increasing numbers of individuals are choosing to opt out of population-based sampling frames due to privacy concerns. This is especially a problem in the selection of controls for case-control studies, as the cases often arise from relatively complete population-based registries, whereas control selection requires a sampling frame. If opt out is also related to risk factors, bias can arise. We linked breast cancer cases who reported having a valid driver's license from the 2004-2008 Wisconsin women's health study (N = 2,988) with a master list of licensed drivers from the Wisconsin Department of Transportation (WDOT). This master list excludes Wisconsin drivers that requested their information not be sold by the state. Multivariate-adjusted selection probability ratios (SPR) were calculated to estimate potential bias when using this driver's license sampling frame to select controls. A total of 962 cases (32%) had opted out of the WDOT sampling frame. Cases age <40 (SPR = 0.90), income either unreported (SPR = 0.89) or greater than $50,000 (SPR = 0.94), lower parity (SPR = 0.96 per one-child decrease), and hormone use (SPR = 0.93) were significantly less likely to be covered by the WDOT sampling frame (α = 0.05 level). Our results indicate the potential for selection bias due to differential opt out between various demographic and behavioral subgroups of controls. As selection bias may differ by exposure and study base, the assessment of potential bias needs to be ongoing. SPRs can be used to predict the direction of bias when cases and controls stem from different sampling frames in population-based case-control studies.

  10. TEHRAN AIR POLLUTANTS PREDICTION BASED ON RANDOM FOREST FEATURE SELECTION METHOD

    Directory of Open Access Journals (Sweden)

    A. Shamsoddini

    2017-09-01

    Full Text Available Air pollution as one of the most serious forms of environmental pollutions poses huge threat to human life. Air pollution leads to environmental instability, and has harmful and undesirable effects on the environment. Modern prediction methods of the pollutant concentration are able to improve decision making and provide appropriate solutions. This study examines the performance of the Random Forest feature selection in combination with multiple-linear regression and Multilayer Perceptron Artificial Neural Networks methods, in order to achieve an efficient model to estimate carbon monoxide and nitrogen dioxide, sulfur dioxide and PM2.5 contents in the air. The results indicated that Artificial Neural Networks fed by the attributes selected by Random Forest feature selection method performed more accurate than other models for the modeling of all pollutants. The estimation accuracy of sulfur dioxide emissions was lower than the other air contaminants whereas the nitrogen dioxide was predicted more accurate than the other pollutants.

  11. Tehran Air Pollutants Prediction Based on Random Forest Feature Selection Method

    Science.gov (United States)

    Shamsoddini, A.; Aboodi, M. R.; Karami, J.

    2017-09-01

    Air pollution as one of the most serious forms of environmental pollutions poses huge threat to human life. Air pollution leads to environmental instability, and has harmful and undesirable effects on the environment. Modern prediction methods of the pollutant concentration are able to improve decision making and provide appropriate solutions. This study examines the performance of the Random Forest feature selection in combination with multiple-linear regression and Multilayer Perceptron Artificial Neural Networks methods, in order to achieve an efficient model to estimate carbon monoxide and nitrogen dioxide, sulfur dioxide and PM2.5 contents in the air. The results indicated that Artificial Neural Networks fed by the attributes selected by Random Forest feature selection method performed more accurate than other models for the modeling of all pollutants. The estimation accuracy of sulfur dioxide emissions was lower than the other air contaminants whereas the nitrogen dioxide was predicted more accurate than the other pollutants.

  12. The genetic consequences of selection in natural populations.

    Science.gov (United States)

    Thurman, Timothy J; Barrett, Rowan D H

    2016-04-01

    The selection coefficient, s, quantifies the strength of selection acting on a genetic variant. Despite this parameter's central importance to population genetic models, until recently we have known relatively little about the value of s in natural populations. With the development of molecular genetic techniques in the late 20th century and the sequencing technologies that followed, biologists are now able to identify genetic variants and directly relate them to organismal fitness. We reviewed the literature for published estimates of natural selection acting at the genetic level and found over 3000 estimates of selection coefficients from 79 studies. Selection coefficients were roughly exponentially distributed, suggesting that the impact of selection at the genetic level is generally weak but can occasionally be quite strong. We used both nonparametric statistics and formal random-effects meta-analysis to determine how selection varies across biological and methodological categories. Selection was stronger when measured over shorter timescales, with the mean magnitude of s greatest for studies that measured selection within a single generation. Our analyses found conflicting trends when considering how selection varies with the genetic scale (e.g., SNPs or haplotypes) at which it is measured, suggesting a need for further research. Besides these quantitative conclusions, we highlight key issues in the calculation, interpretation, and reporting of selection coefficients and provide recommendations for future research. © 2016 John Wiley & Sons Ltd.

  13. The signature of positive selection at randomly chosen loci.

    Science.gov (United States)

    Przeworski, Molly

    2002-03-01

    In Drosophila and humans, there are accumulating examples of loci with a significant excess of high-frequency-derived alleles or high levels of linkage disequilibrium, relative to a neutral model of a random-mating population of constant size. These are features expected after a recent selective sweep. Their prevalence suggests that positive directional selection may be widespread in both species. However, as I show here, these features do not persist long after the sweep ends: The high-frequency alleles drift to fixation and no longer contribute to polymorphism, while linkage disequilibrium is broken down by recombination. As a result, loci chosen without independent evidence of recent selection are not expected to exhibit either of these features, even if they have been affected by numerous sweeps in their genealogical history. How then can we explain the patterns in the data? One possibility is population structure, with unequal sampling from different subpopulations. Alternatively, positive selection may not operate as is commonly modeled. In particular, the rate of fixation of advantageous mutations may have increased in the recent past.

  14. An Improved Real-Coded Population-Based Extremal Optimization Method for Continuous Unconstrained Optimization Problems

    Directory of Open Access Journals (Sweden)

    Guo-Qiang Zeng

    2014-01-01

    Full Text Available As a novel evolutionary optimization method, extremal optimization (EO has been successfully applied to a variety of combinatorial optimization problems. However, the applications of EO in continuous optimization problems are relatively rare. This paper proposes an improved real-coded population-based EO method (IRPEO for continuous unconstrained optimization problems. The key operations of IRPEO include generation of real-coded random initial population, evaluation of individual and population fitness, selection of bad elements according to power-law probability distribution, generation of new population based on uniform random mutation, and updating the population by accepting the new population unconditionally. The experimental results on 10 benchmark test functions with the dimension N=30 have shown that IRPEO is competitive or even better than the recently reported various genetic algorithm (GA versions with different mutation operations in terms of simplicity, effectiveness, and efficiency. Furthermore, the superiority of IRPEO to other evolutionary algorithms such as original population-based EO, particle swarm optimization (PSO, and the hybrid PSO-EO is also demonstrated by the experimental results on some benchmark functions.

  15. 47 CFR 1.1602 - Designation for random selection.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Designation for random selection. 1.1602 Section 1.1602 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL PRACTICE AND PROCEDURE Random Selection Procedures for Mass Media Services General Procedures § 1.1602 Designation for random selection...

  16. Opportunity for natural selection among some selected population groups of Northeast India.

    Science.gov (United States)

    Das, Farida Ahmed; Mithun, Sikdar

    2010-05-01

    Selection potential based on differential fertility and mortality has been computed for seven population groups inhabiting different geographical locations of Northeast India. Crow's as well as Johnston and Kensinger's index have been used for the present purpose. Irrespective of the methodology, the total index of selection was found to be highest among the Deoris followed by the Kaibartas. The lowest selection index was found among the Oraon population. If the relative contribution of fertility and mortality components to the total index is considered to be multiplicative, it is observed that in all these communities the fertility component exceeds that of mortality component, which may indicate initiation of demographic transitional phase in the selected populations with the betterment of healthcare and socioeconomic condition within the last few decades.

  17. 47 CFR 1.1603 - Conduct of random selection.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Conduct of random selection. 1.1603 Section 1.1603 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL PRACTICE AND PROCEDURE Random Selection Procedures for Mass Media Services General Procedures § 1.1603 Conduct of random selection. The...

  18. Testing for a genetic response to sexual selection in a wild Drosophila population.

    Science.gov (United States)

    Gosden, T P; Thomson, J R; Blows, M W; Schaul, A; Chenoweth, S F

    2016-06-01

    In accordance with the consensus that sexual selection is responsible for the rapid evolution of display traits on macroevolutionary scales, microevolutionary studies suggest sexual selection is a widespread and often strong form of directional selection in nature. However, empirical evidence for the contemporary evolution of sexually selected traits via sexual rather than natural selection remains weak. In this study, we used a novel application of quantitative genetic breeding designs to test for a genetic response to sexual selection on eight chemical display traits from a field population of the fly, Drosophila serrata. Using our quantitative genetic approach, we were able to detect a genetically based difference in means between groups of males descended from fathers who had either successfully sired offspring or were randomly collected from the same wild population for one of these display traits, the diene (Z,Z)-5,9-C27 : 2 . Our experimental results, in combination with previous laboratory studies on this system, suggest that both natural and sexual selection may be influencing the evolutionary trajectories of these traits in nature, limiting the capacity for a contemporary evolutionary response. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

  19. Population-based versus practice-based recall for childhood immunizations: a randomized controlled comparative effectiveness trial.

    Science.gov (United States)

    Kempe, Allison; Saville, Alison; Dickinson, L Miriam; Eisert, Sheri; Reynolds, Joni; Herrero, Diana; Beaty, Brenda; Albright, Karen; Dibert, Eva; Koehler, Vicky; Lockhart, Steven; Calonge, Ned

    2013-06-01

    We compared the effectiveness and cost-effectiveness of population-based recall (Pop-recall) versus practice-based recall (PCP-recall) at increasing immunizations among preschool children. This cluster-randomized trial involved children aged 19 to 35 months needing immunizations in 8 rural and 6 urban Colorado counties. In Pop-recall counties, recall was conducted centrally using the Colorado Immunization Information System (CIIS). In PCP-recall counties, practices were invited to attend webinar training using CIIS and offered financial support for mailings. The percentage of up-to-date (UTD) and vaccine documentation were compared 6 months after recall. A mixed-effects model assessed the association between intervention and whether a child became UTD. Ten of 195 practices (5%) implemented recall in PCP-recall counties. Among children needing immunizations, 18.7% became UTD in Pop-recall versus 12.8% in PCP-recall counties (P immunization rates in preschool children.

  20. Opportunity for natural selection among some selected population groups of Northeast India

    Science.gov (United States)

    Das, Farida Ahmed; Mithun, Sikdar

    2010-01-01

    BACKGROUND: Selection potential based on differential fertility and mortality has been computed for seven population groups inhabiting different geographical locations of Northeast India. MATERIALS AND METHODS: Crow’s as well as Johnston and Kensinger’s index have been used for the present purpose. RESULTS AND CONCLUSION: Irrespective of the methodology, the total index of selection was found to be highest among the Deoris followed by the Kaibartas. The lowest selection index was found among the Oraon population. If the relative contribution of fertility and mortality components to the total index is considered to be multiplicative, it is observed that in all these communities the fertility component exceeds that of mortality component, which may indicate initiation of demographic transitional phase in the selected populations with the betterment of healthcare and socioeconomic condition within the last few decades. PMID:21031053

  1. Development of a "Myeloma Risk Score" using a population-based registry on paraproteinemia and myeloma

    NARCIS (Netherlands)

    Ong, F; Hermans, J; Noordijk, E M; De Kieviet, W; Seelen, P J; Wijermans, P W; Kluin-Nelemans, J C

    1997-01-01

    Diagnostic systems for monoclonal gammopathies use bone marrow and X-ray examinations to exclude multiple myeloma (MM). Data from a population-based registry of unselected patients with paraproteinemia indicate that these tests are often done only when MM is suspected. We used 441 randomly selected

  2. Breeding common bean populations for traits using selection index

    Directory of Open Access Journals (Sweden)

    Dayane Cristina Lima

    2015-02-01

    Full Text Available A common bean (Phaseolus vulgarisL. cultivar must combine desirable genotypes for several traits in order to be accepted by producers and consumers. This study aimed to evaluate selection efficiency when segregating bean populations for traits, by means of a selection index, in order to obtain superior progenies for traits considered. A total of 16 populations from the F4 and F5generations were evaluated in 2011 and 2012, respectively. The traits evaluated were plant architecture, plant disease, grain type and yield. Using standard scores (Z, the sum of the four traits (∑Z was obtained and, based on this information, the best populations were identified. The evaluation of selection effectiveness was performed on 31 progenies from each population. The 496 progenies plus eight controls were evaluated in the F5:6and F5:7 generations for the same traits in July and November 2012, respectively. The selection, using the index based on the sum of standardized variables (∑Z, was efficient for identifying populations with superior progenies for all the traits considered.

  3. Population-Based Study of Trachoma in Guatemala.

    Science.gov (United States)

    Silva, Juan Carlos; Diaz, Marco Antonio; Maul, Eugenio; Munoz, Beatriz E; West, Sheila K

    2015-01-01

    A prevalence survey for active trachoma in children aged under 10 years and trichiasis in women aged 40 years and older was carried out in four districts in the Sololá region in Guatemala, which is suspected of still having a trachoma problem. Population-based surveys were undertaken in three districts, within 15 randomly selected communities in each district. In addition, in a fourth district that borders the third district chosen, we surveyed the small northern sub-district, by randomly selecting three communities in each community, 100 children aged under 10 years were randomly selected, and all females over 40 years. Five survey teams were trained and standardized. Trachoma was graded using the World Health Organization simplified grading scheme and ocular swabs were taken in cases of clinical follicular or inflammatory trachoma. Prevalence estimates were calculated at district and sub-district level. Trachoma rates at district level varied from 0-5.1%. There were only two sub-districts where active trachoma approached 10% (Nahualá Costa, 8.1%, and Santa Catarina Costa, 7.3%). Trichiasis rates in females aged 40 years and older varied from 0-3%. Trachoma was likely a problem in the past. Trachoma is disappearing in the Sololá region in Guatemala. Health leadership may consider further mapping of villages around the areas with an especially high rate of trachoma and infection, and instituting trichiasis surgery and active trachoma intervention where needed.

  4. Background Selection in Partially Selfing Populations

    Science.gov (United States)

    Roze, Denis

    2016-01-01

    Self-fertilizing species often present lower levels of neutral polymorphism than their outcrossing relatives. Indeed, selfing automatically increases the rate of coalescence per generation, but also enhances the effects of background selection and genetic hitchhiking by reducing the efficiency of recombination. Approximations for the effect of background selection in partially selfing populations have been derived previously, assuming tight linkage between deleterious alleles and neutral loci. However, loosely linked deleterious mutations may have important effects on neutral diversity in highly selfing populations. In this article, I use a general method based on multilocus population genetics theory to express the effect of a deleterious allele on diversity at a linked neutral locus in terms of moments of genetic associations between loci. Expressions for these genetic moments at equilibrium are then computed for arbitrary rates of selfing and recombination. An extrapolation of the results to the case where deleterious alleles segregate at multiple loci is checked using individual-based simulations. At high selfing rates, the tight linkage approximation underestimates the effect of background selection in genomes with moderate to high map length; however, another simple approximation can be obtained for this situation and provides accurate predictions as long as the deleterious mutation rate is not too high. PMID:27075726

  5. Non-random mating for selection with restricted rates of inbreeding and overlapping generations

    NARCIS (Netherlands)

    Sonesson, A.K.; Meuwissen, T.H.E.

    2002-01-01

    Minimum coancestry mating with a maximum of one offspring per mating pair (MC1) is compared with random mating schemes for populations with overlapping generations. Optimum contribution selection is used, whereby $\\\\\\\\Delta F$ is restricted. For schemes with $\\\\\\\\Delta F$ restricted to 0.25% per

  6. Endogamia e limite de seleção em populações selecionadas obtidas por simulação Inbreeding and selection limit in selected population obtained by simulation

    Directory of Open Access Journals (Sweden)

    Fernanda Cristina Breda

    2004-12-01

    Full Text Available Objetivou-se, com este trabalho, avaliar o comportamento do coeficiente de endogamia e do limite de seleção considerando população-base selecionada. Utilizou-se o programa GENESYS para a simulação do genoma constituído de uma única característica quantitativa com valor de herdabilidade igual a 0,40, população-base, população inicial e populações sob seleção. Foram consideradas três gerações distintas como gerações bases, gerações zero (G0PB, três (G3PB e sete (G7PB. As populações foram selecionadas a partir dos valores genéticos obtidos pelo melhor preditor linear não-viesado (BLUP e com base no desempenho individual, sendo considerados: a dois tamanhos efetivos de população (Ne1 = 38,09 e Ne2 = 88,88 e b dois sistemas de acasalamentos dos reprodutores selecionados (reprodutores acasalados aleatoriamente - RAA e exclusão de irmãos completos - EIC. Os parâmetros avaliados foram: coeficiente médio de endogamia, percentagem de locos fixados favoravelmente e limite de seleção. A não-utilização da população-base verdadeira (G0PB subestimou os coeficientes de endogamia. As populações que utilizaram as gerações três e sete como base apresentaram as mesmas taxas de fixação de alelos favoráveis e os mesmos valores do limite de seleção das populações que consideraram a G0PB.Objective was to evaluate the behavior average inbreeding coefficient associated to the selection limit considering selected population as base population. GENESYS program was used for simulation of the genome (one trait of h² = 0.40, base population, initial population and populations under selection. Three different generations were considered as base generations, zero (G0PB, three (G3PB and seven (G7PB. Populations were selected based on best linear unbiased predictor (BLUP and on individual phenotype in which were considered: a two effective population sizes (Ne1 = 38.09 and Ne2 = 88.88 and b two mating systems (random mating

  7. Fine mapping quantitative trait loci under selective phenotyping strategies based on linkage and linkage disequilibrium criteria

    DEFF Research Database (Denmark)

    Ansari-Mahyari, S; Berg, P; Lund, M S

    2009-01-01

    disequilibrium-based sampling criteria (LDC) for selecting individuals to phenotype are compared to random phenotyping in a quantitative trait loci (QTL) verification experiment using stochastic simulation. Several strategies based on LAC and LDC for selecting the most informative 30%, 40% or 50% of individuals...... for phenotyping to extract maximum power and precision in a QTL fine mapping experiment were developed and assessed. Linkage analyses for the mapping was performed for individuals sampled on LAC within families and combined linkage disequilibrium and linkage analyses was performed for individuals sampled across...... the whole population based on LDC. The results showed that selecting individuals with similar haplotypes to the paternal haplotypes (minimum recombination criterion) using LAC compared to random phenotyping gave at least the same power to detect a QTL but decreased the accuracy of the QTL position. However...

  8. Risk-based audit selection of dairy farms.

    Science.gov (United States)

    van Asseldonk, M A P M; Velthuis, A G J

    2014-02-01

    Dairy farms are audited in the Netherlands on numerous process standards. Each farm is audited once every 2 years. Increasing demands for cost-effectiveness in farm audits can be met by introducing risk-based principles. This implies targeting subpopulations with a higher risk of poor process standards. To select farms for an audit that present higher risks, a statistical analysis was conducted to test the relationship between the outcome of farm audits and bulk milk laboratory results before the audit. The analysis comprised 28,358 farm audits and all conducted laboratory tests of bulk milk samples 12 mo before the audit. The overall outcome of each farm audit was classified as approved or rejected. Laboratory results included somatic cell count (SCC), total bacterial count (TBC), antimicrobial drug residues (ADR), level of butyric acid spores (BAB), freezing point depression (FPD), level of free fatty acids (FFA), and cleanliness of the milk (CLN). The bulk milk laboratory results were significantly related to audit outcomes. Rejected audits are likely to occur on dairy farms with higher mean levels of SCC, TBC, ADR, and BAB. Moreover, in a multivariable model, maxima for TBC, SCC, and FPD as well as standard deviations for TBC and FPD are risk factors for negative audit outcomes. The efficiency curve of a risk-based selection approach, on the basis of the derived regression results, dominated the current random selection approach. To capture 25, 50, or 75% of the population with poor process standards (i.e., audit outcome of rejected), respectively, only 8, 20, or 47% of the population had to be sampled based on a risk-based selection approach. Milk quality information can thus be used to preselect high-risk farms to be audited more frequently. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  9. A Permutation Importance-Based Feature Selection Method for Short-Term Electricity Load Forecasting Using Random Forest

    Directory of Open Access Journals (Sweden)

    Nantian Huang

    2016-09-01

    Full Text Available The prediction accuracy of short-term load forecast (STLF depends on prediction model choice and feature selection result. In this paper, a novel random forest (RF-based feature selection method for STLF is proposed. First, 243 related features were extracted from historical load data and the time information of prediction points to form the original feature set. Subsequently, the original feature set was used to train an RF as the original model. After the training process, the prediction error of the original model on the test set was recorded and the permutation importance (PI value of each feature was obtained. Then, an improved sequential backward search method was used to select the optimal forecasting feature subset based on the PI value of each feature. Finally, the optimal forecasting feature subset was used to train a new RF model as the final prediction model. Experiments showed that the prediction accuracy of RF trained by the optimal forecasting feature subset was higher than that of the original model and comparative models based on support vector regression and artificial neural network.

  10. Recurrent Selection and Participatory Plant Breeding for Improvement of Two Organic Open-Pollinated Sweet Corn (Zea mays L. Populations

    Directory of Open Access Journals (Sweden)

    Adrienne C. Shelton

    2015-04-01

    Full Text Available Organic growers face unique challenges when raising sweet corn, and benefit from varieties that maintain high eating quality, germinate consistently, deter insect pests, and resist diseases. Genotype by environment rank changes can occur in the performance of cultivars grown on conventional and organic farms, yet few varieties have been bred specifically for organic systems. The objective of this experiment was to evaluate the changes made to open-pollinated sweet corn populations using recurrent selection and a participatory plant breeding (PPB methodology. From 2008 to 2011, four cycles of two open-pollinated (OP sweet corn populations were selected on a certified organic farm in Minnesota using a modified ear-to-row recurrent selection scheme. Selections were made in collaboration with an organic farmer, with selection criteria based on traits identified by the farmer. In 2012 and 2013, the population cycles were evaluated in a randomized complete block design in two certified organic locations in Wisconsin, with multiple replications in each environment. Significant linear trends were found among cycles of selection for quantitative and qualitative traits, suggesting the changes were due to recurrent selection and PPB methodology for these populations. However, further improvement is necessary to satisfy the requirements for a useful cultivar for organic growers.

  11. The mathematics of random mutation and natural selection for multiple simultaneous selection pressures and the evolution of antimicrobial drug resistance.

    Science.gov (United States)

    Kleinman, Alan

    2016-12-20

    The random mutation and natural selection phenomenon act in a mathematically predictable behavior, which when understood leads to approaches to reduce and prevent the failure of the use of these selection pressures when treating infections and cancers. The underlying principle to impair the random mutation and natural selection phenomenon is to use combination therapy, which forces the population to evolve to multiple selection pressures simultaneously that invoke the multiplication rule of probabilities simultaneously as well. Recently, it has been seen that combination therapy for the treatment of malaria has failed to prevent the emergence of drug-resistant variants. Using this empirical example and the principles of probability theory, the derivation of the equations describing this treatment failure is carried out. These equations give guidance as to how to use combination therapy for the treatment of cancers and infectious diseases and prevent the emergence of drug resistance. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  12. Genetic parameters for residual feed intake in a random population of Pekin duck

    Directory of Open Access Journals (Sweden)

    Yunsheng Zhang

    2017-02-01

    Full Text Available Objective The feed intake (FI and feed efficiency are economically important traits in ducks. To obtain insight into this economically important trait, we designed an experiment based on the residual feed intake (RFI and feed conversion ratio (FCR of a random population Pekin duck. Methods Two thousand and twenty pedigreed random population Pekin ducks were established from 90 males mated to 450 females in two hatches. Traits analyzed in the study were body weight at the 42th day (BW42, 15 to 42 days average daily gain (ADG, 15 to 42 days FI, 15 to 42 days FCR, and 15 to 42 days RFI to assess their genetic inter-relationships. The genetic parameters for feed efficiency traits were estimated using restricted maximum likelihood (REML methodology applied to a sire-dam model for all traits using the ASREML software. Results Estimates heritability of BW42, ADG, FI, FCR, and RFI were 0.39, 0.38, 0.33, 0.38, and 0.41, respectively. The genetic correlation was high between RFI and FI (0.77 and moderate between RFI and FCR (0.54. The genetic correlation was high and moderate between FCR and ADG (−0.80, and between FCR and BW42 (−0.64, and between FCR and FI (0.49, respectively. Conclusion Thus, selection on RFI was expected to improve feed efficiency, and reduce FI. Selection on RFI thus improves the feed efficiency of animals without impairing their FI and increase growth rate.

  13. Randomized Trial of a Family-based, Automated, Conversational Obesity Treatment Program for Underserved Populations

    Science.gov (United States)

    Wright, J. A.; Phillips, B.D.; Watson, B.L.; Newby, P.K.; Norman, G. J.; Adams, W.G.

    2013-01-01

    Objective To evaluate the acceptability and feasibility of a scalable obesity treatment program integrated with pediatric primary care and delivered using interactive voice technology (IVR) to families from underserved populations. Design and Methods Fifty parent-child dyads (child 9–12 yrs, BMI >95th percentile) were recruited from a pediatric primary care clinic and randomized to either an IVR or a wait-list control (WLC) group. The majority were lower-income, African-American (72%) families. Dyads received IVR calls for 12 weeks. Call content was informed by two evidenced-based interventions. Anthropometric and behavioral variables were assessed at baseline and 3 mo follow-up. Results Forty-three dyads completed the study. IVR parents ate 1 cup more fruit than WLC (p 75% agreed that the calls were useful, made for people like them, credible, and helped them eat healthy foods. Conclusion An obesity treatment program delivered via IVR may be an acceptable and feasible resource for families from underserved populations. PMID:23512915

  14. Long-term response to genomic selection: effects of estimation method and reference population structure for different genetic architectures.

    Science.gov (United States)

    Bastiaansen, John W M; Coster, Albart; Calus, Mario P L; van Arendonk, Johan A M; Bovenhuis, Henk

    2012-01-24

    Genomic selection has become an important tool in the genetic improvement of animals and plants. The objective of this study was to investigate the impacts of breeding value estimation method, reference population structure, and trait genetic architecture, on long-term response to genomic selection without updating marker effects. Three methods were used to estimate genomic breeding values: a BLUP method with relationships estimated from genome-wide markers (GBLUP), a Bayesian method, and a partial least squares regression method (PLSR). A shallow (individuals from one generation) or deep reference population (individuals from five generations) was used with each method. The effects of the different selection approaches were compared under four different genetic architectures for the trait under selection. Selection was based on one of the three genomic breeding values, on pedigree BLUP breeding values, or performed at random. Selection continued for ten generations. Differences in long-term selection response were small. For a genetic architecture with a very small number of three to four quantitative trait loci (QTL), the Bayesian method achieved a response that was 0.05 to 0.1 genetic standard deviation higher than other methods in generation 10. For genetic architectures with approximately 30 to 300 QTL, PLSR (shallow reference) or GBLUP (deep reference) had an average advantage of 0.2 genetic standard deviation over the Bayesian method in generation 10. GBLUP resulted in 0.6% and 0.9% less inbreeding than PLSR and BM and on average a one third smaller reduction of genetic variance. Responses in early generations were greater with the shallow reference population while long-term response was not affected by reference population structure. The ranking of estimation methods was different with than without selection. Under selection, applying GBLUP led to lower inbreeding and a smaller reduction of genetic variance while a similar response to selection was

  15. Generation and monitoring of discrete stable random processes using multiple immigration population models

    Energy Technology Data Exchange (ETDEWEB)

    Matthews, J O; Hopcraft, K I; Jakeman, E [Applied Mathematics Division, School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD (United Kingdom)

    2003-11-21

    Some properties of classical population processes that comprise births, deaths and multiple immigrations are investigated. The rates at which the immigrants arrive can be tailored to produce a population whose steady state fluctuations are described by a pre-selected distribution. Attention is focused on the class of distributions with a discrete stable law, which have power-law tails and whose moments and autocorrelation function do not exist. The separate problem of monitoring and characterizing the fluctuations is studied, analysing the statistics of individuals that leave the population. The fluctuations in the size of the population are transferred to the times between emigrants that form an intermittent time series of events. The emigrants are counted with a detector of finite dynamic range and response time. This is modelled through clipping the time series or saturating it at an arbitrary but finite level, whereupon its moments and correlation properties become finite. Distributions for the time to the first counted event and for the time between events exhibit power-law regimes that are characteristic of the fluctuations in population size. The processes provide analytical models with which properties of complex discrete random phenomena can be explored, and in addition provide generic means by which random time series encompassing a wide range of intermittent and other discrete random behaviour may be generated.

  16. Generation and monitoring of discrete stable random processes using multiple immigration population models

    International Nuclear Information System (INIS)

    Matthews, J O; Hopcraft, K I; Jakeman, E

    2003-01-01

    Some properties of classical population processes that comprise births, deaths and multiple immigrations are investigated. The rates at which the immigrants arrive can be tailored to produce a population whose steady state fluctuations are described by a pre-selected distribution. Attention is focused on the class of distributions with a discrete stable law, which have power-law tails and whose moments and autocorrelation function do not exist. The separate problem of monitoring and characterizing the fluctuations is studied, analysing the statistics of individuals that leave the population. The fluctuations in the size of the population are transferred to the times between emigrants that form an intermittent time series of events. The emigrants are counted with a detector of finite dynamic range and response time. This is modelled through clipping the time series or saturating it at an arbitrary but finite level, whereupon its moments and correlation properties become finite. Distributions for the time to the first counted event and for the time between events exhibit power-law regimes that are characteristic of the fluctuations in population size. The processes provide analytical models with which properties of complex discrete random phenomena can be explored, and in addition provide generic means by which random time series encompassing a wide range of intermittent and other discrete random behaviour may be generated

  17. Discriminative Projection Selection Based Face Image Hashing

    Science.gov (United States)

    Karabat, Cagatay; Erdogan, Hakan

    Face image hashing is an emerging method used in biometric verification systems. In this paper, we propose a novel face image hashing method based on a new technique called discriminative projection selection. We apply the Fisher criterion for selecting the rows of a random projection matrix in a user-dependent fashion. Moreover, another contribution of this paper is to employ a bimodal Gaussian mixture model at the quantization step. Our simulation results on three different databases demonstrate that the proposed method has superior performance in comparison to previously proposed random projection based methods.

  18. Altruism Can Proliferate through Population Viscosity despite High Random Gene Flow

    Science.gov (United States)

    Schonmann, Roberto H.; Vicente, Renato; Caticha, Nestor

    2013-01-01

    The ways in which natural selection can allow the proliferation of cooperative behavior have long been seen as a central problem in evolutionary biology. Most of the literature has focused on interactions between pairs of individuals and on linear public goods games. This emphasis has led to the conclusion that even modest levels of migration would pose a serious problem to the spread of altruism through population viscosity in group structured populations. Here we challenge this conclusion, by analyzing evolution in a framework which allows for complex group interactions and random migration among groups. We conclude that contingent forms of strong altruism that benefits equally all group members, regardless of kinship and without greenbeard effects, can spread when rare under realistic group sizes and levels of migration, due to the assortment of genes resulting only from population viscosity. Our analysis combines group-centric and gene-centric perspectives, allows for arbitrary strength of selection, and leads to extensions of Hamilton’s rule for the spread of altruistic alleles, applicable under broad conditions. PMID:23991035

  19. Altruism can proliferate through population viscosity despite high random gene flow.

    Directory of Open Access Journals (Sweden)

    Roberto H Schonmann

    Full Text Available The ways in which natural selection can allow the proliferation of cooperative behavior have long been seen as a central problem in evolutionary biology. Most of the literature has focused on interactions between pairs of individuals and on linear public goods games. This emphasis has led to the conclusion that even modest levels of migration would pose a serious problem to the spread of altruism through population viscosity in group structured populations. Here we challenge this conclusion, by analyzing evolution in a framework which allows for complex group interactions and random migration among groups. We conclude that contingent forms of strong altruism that benefits equally all group members, regardless of kinship and without greenbeard effects, can spread when rare under realistic group sizes and levels of migration, due to the assortment of genes resulting only from population viscosity. Our analysis combines group-centric and gene-centric perspectives, allows for arbitrary strength of selection, and leads to extensions of Hamilton's rule for the spread of altruistic alleles, applicable under broad conditions.

  20. Natural Selection in Large Populations

    Science.gov (United States)

    Desai, Michael

    2011-03-01

    I will discuss theoretical and experimental approaches to the evolutionary dynamics and population genetics of natural selection in large populations. In these populations, many mutations are often present simultaneously, and because recombination is limited, selection cannot act on them all independently. Rather, it can only affect whole combinations of mutations linked together on the same chromosome. Methods common in theoretical population genetics have been of limited utility in analyzing this coupling between the fates of different mutations. In the past few years it has become increasingly clear that this is a crucial gap in our understanding, as sequence data has begun to show that selection appears to act pervasively on many linked sites in a wide range of populations, including viruses, microbes, Drosophila, and humans. I will describe approaches that combine analytical tools drawn from statistical physics and dynamical systems with traditional methods in theoretical population genetics to address this problem, and describe how experiments in budding yeast can help us directly observe these evolutionary dynamics.

  1. Materials selection for oxide-based resistive random access memories

    International Nuclear Information System (INIS)

    Guo, Yuzheng; Robertson, John

    2014-01-01

    The energies of atomic processes in resistive random access memories (RRAMs) are calculated for four typical oxides, HfO 2 , TiO 2 , Ta 2 O 5 , and Al 2 O 3 , to define a materials selection process. O vacancies have the lowest defect formation energy in the O-poor limit and dominate the processes. A band diagram defines the operating Fermi energy and O chemical potential range. It is shown how the scavenger metal can be used to vary the O vacancy formation energy, via controlling the O chemical potential, and the mean Fermi energy. The high endurance of Ta 2 O 5 RRAM is related to its more stable amorphous phase and the adaptive lattice rearrangements of its O vacancy

  2. The Oslo Health Study: The impact of self-selection in a large, population-based survey

    Science.gov (United States)

    Søgaard, Anne Johanne; Selmer, Randi; Bjertness, Espen; Thelle, Dag

    2004-01-01

    Background Research on health equity which mainly utilises population-based surveys, may be hampered by serious selection bias due to a considerable number of invitees declining to participate. Sufficient information from all the non-responders is rarely available to quantify this bias. Predictors of attendance, magnitude and direction of non-response bias in prevalence estimates and association measures, are investigated based on information from all 40 888 invitees to the Oslo Health Study. Methods The analyses were based on linkage between public registers in Statistics Norway and the Oslo Health Study, a population-based survey conducted in 2000/2001 inviting all citizens aged 30, 40, 45, 59–60 and 75–76 years. Attendance was 46%. Weighted analyses, logistic regression and sensitivity analyses are performed to evaluate possible selection bias. Results The response rate was positively associated with age, educational attendance, total income, female gender, married, born in a Western county, living in the outer city residential regions and not receiving disability benefit. However, self-rated health, smoking, BMI and mental health (HCSL) in the attendees differed only slightly from estimated prevalence values in the target population when weighted by the inverse of the probability of attendance. Observed values differed only moderately provided that the non-attending individuals differed from those attending by no more than 50%. Even though persons receiving disability benefit had lower attendance, the associations between disability and education, residential region and marital status were found to be unbiased. The association between country of birth and disability benefit was somewhat more evident among attendees. Conclusions Self-selection according to sociodemographic variables had little impact on prevalence estimates. As indicated by disability benefit, unhealthy persons attended to a lesser degree than healthy individuals, but social inequality in

  3. The Oslo Health Study: The impact of self-selection in a large, population-based survey

    Directory of Open Access Journals (Sweden)

    Bjertness Espen

    2004-05-01

    Full Text Available Abstract Background Research on health equity which mainly utilises population-based surveys, may be hampered by serious selection bias due to a considerable number of invitees declining to participate. Sufficient information from all the non-responders is rarely available to quantify this bias. Predictors of attendance, magnitude and direction of non-response bias in prevalence estimates and association measures, are investigated based on information from all 40 888 invitees to the Oslo Health Study. Methods The analyses were based on linkage between public registers in Statistics Norway and the Oslo Health Study, a population-based survey conducted in 2000/2001 inviting all citizens aged 30, 40, 45, 59–60 and 75–76 years. Attendance was 46%. Weighted analyses, logistic regression and sensitivity analyses are performed to evaluate possible selection bias. Results The response rate was positively associated with age, educational attendance, total income, female gender, married, born in a Western county, living in the outer city residential regions and not receiving disability benefit. However, self-rated health, smoking, BMI and mental health (HCSL in the attendees differed only slightly from estimated prevalence values in the target population when weighted by the inverse of the probability of attendance. Observed values differed only moderately provided that the non-attending individuals differed from those attending by no more than 50%. Even though persons receiving disability benefit had lower attendance, the associations between disability and education, residential region and marital status were found to be unbiased. The association between country of birth and disability benefit was somewhat more evident among attendees. Conclusions Self-selection according to sociodemographic variables had little impact on prevalence estimates. As indicated by disability benefit, unhealthy persons attended to a lesser degree than healthy individuals

  4. Oncogenic human papillomavirus genital infection in southern Iranian women: population-based study versus clinic-based data

    Directory of Open Access Journals (Sweden)

    Eghbali Seyed

    2012-09-01

    Full Text Available Abstract Background Epidemiological studies on genital human papilloma viruses infection (HPVs in general population are crucial for the implementation of health policy guidelines for developing the strategies to prevent the primary and secondary cervical cancer. In different parts of Iran, there is a lack of population-based studies to determine the prevalence of HPV in the general population. The aim of this population-based study is to compare the prevalence rate of genital HPV infection among reproductive women with our previous clinic-based data, which showed a prevalence rate of 5% in women in southern Iran. Results Using general primers for all genotypes of HPV, of 799 randomly selected women, five (0.63%, 95% CI 0.23-1.55% tested positive for HPV DNA. Overall, seven different HPV genotypes were detected: six types (16, 18, 31, 33, 51 and 56 were carcinogenic, or “high risk genotypes” and one genotype (HPV-66 was “probably carcinogenic.” Conclusions In a population-based study, the prevalence of HPV infection among southern Iranian women was lower than that observed worldwide. However, our gynaecological clinic-based study on the prevalence of HPV infection showed results comparable with other studies in the Middle East and Persian Gulf countries. Since gynaecological clinic-based data may generally overestimate HPV prevalence, estimates of prevalence according to clinic-based data should be adjusted downward by the population-based survey estimates.

  5. Materials selection for oxide-based resistive random access memories

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Yuzheng; Robertson, John [Engineering Department, Cambridge University, Cambridge CB2 1PZ (United Kingdom)

    2014-12-01

    The energies of atomic processes in resistive random access memories (RRAMs) are calculated for four typical oxides, HfO{sub 2}, TiO{sub 2}, Ta{sub 2}O{sub 5}, and Al{sub 2}O{sub 3}, to define a materials selection process. O vacancies have the lowest defect formation energy in the O-poor limit and dominate the processes. A band diagram defines the operating Fermi energy and O chemical potential range. It is shown how the scavenger metal can be used to vary the O vacancy formation energy, via controlling the O chemical potential, and the mean Fermi energy. The high endurance of Ta{sub 2}O{sub 5} RRAM is related to its more stable amorphous phase and the adaptive lattice rearrangements of its O vacancy.

  6. Recurrent pain is associated with decreased selective attention in a population-based sample.

    Science.gov (United States)

    Gijsen, C P; Dijkstra, J B; van Boxtel, M P J

    2011-01-01

    Studies which have examined the impact of pain on cognitive functioning in the general population are scarce. In the present study we assessed the predictive value of recurrent pain on cognitive functioning in a population-based study (N=1400). Furthermore, we investigated the effect of pain on cognitive functioning in individuals with specific pain complaints (i.e. back pain, gastric pain, muscle pain and headache). Cognitive functioning was assessed using the Stroop Color-Word Interference test (Stroop interference), the Letter-Digit-Substitution test (LDST) and the Visual Verbal learning Task (VVLT). Pain was measured with the COOP/WONCA pain scale (Dartmouth Primary Care Cooperative Information Project/World Organization of National Colleges, Academies, and Academic Associations of General Practice /Family Physicians). We controlled for the effects of age, sex, level of education and depressive symptoms. It was demonstrated that pain had a negative impact on the performance on the Stroop interference but not on the VVLT and the LDST. This indicates that subjects who reported extreme pain had more problems with selective attention and were more easily distracted. Effects were in general larger in the specific pain groups when compared to the associations found in the total group. Implications of these findings are discussed. The experience of recurrent pain has a negative influence on selective attention in a healthy population. Copyright © 2010 International Association for the Study of Pain. Published by Elsevier B.V. All rights reserved.

  7. Pediatric selective mutism therapy: a randomized controlled trial.

    Science.gov (United States)

    Esposito, Maria; Gimigliano, Francesca; Barillari, Maria R; Precenzano, Francesco; Ruberto, Maria; Sepe, Joseph; Barillari, Umberto; Gimigliano, Raffaele; Militerni, Roberto; Messina, Giovanni; Carotenuto, Marco

    2017-10-01

    Selective mutism (SM) is a rare disease in children coded by DSM-5 as an anxiety disorder. Despite the disabling nature of the disease, there is still no specific treatment. The aims of this study were to verify the efficacy of six-month standard psychomotor treatment and the positive changes in lifestyle, in a population of children affected by SM. Randomized controlled trial registered in the European Clinical Trials Registry (EuDract 2015-001161-36). University third level Centre (Child and Adolescent Neuropsychiatry Clinic). Study population was composed by 67 children in group A (psychomotricity treatment) (35 M, mean age 7.84±1.15) and 71 children in group B (behavioral and educational counseling) (37 M, mean age 7.75±1.36). Psychomotor treatment was administered by trained child therapists in residential settings three times per week. Each child was treated for the whole period by the same therapist and all the therapists shared the same protocol. The standard psychomotor session length is of 45 minutes. At T0 and after 6 months (T1) of treatments, patients underwent a behavioral and SM severity assessment. To verify the effects of the psychomotor management, the Child Behavior Checklist questionnaire (CBCL) and Selective Mutism Questionnaire (SMQ) were administered to the parents. After 6 months of psychomotor treatment SM children showed a significant reduction among CBCL scores such as in social relations, anxious/depressed, social problems and total problems (Pselective mutism, even if further studies are needed. The present study identifies in psychomotricity a safe and efficacy therapy for pediatric selective mutism.

  8. Comparing methods of targeting obesity interventions in populations: An agent-based simulation.

    Science.gov (United States)

    Beheshti, Rahmatollah; Jalalpour, Mehdi; Glass, Thomas A

    2017-12-01

    Social networks as well as neighborhood environments have been shown to effect obesity-related behaviors including energy intake and physical activity. Accordingly, harnessing social networks to improve targeting of obesity interventions may be promising to the extent this leads to social multiplier effects and wider diffusion of intervention impact on populations. However, the literature evaluating network-based interventions has been inconsistent. Computational methods like agent-based models (ABM) provide researchers with tools to experiment in a simulated environment. We develop an ABM to compare conventional targeting methods (random selection, based on individual obesity risk, and vulnerable areas) with network-based targeting methods. We adapt a previously published and validated model of network diffusion of obesity-related behavior. We then build social networks among agents using a more realistic approach. We calibrate our model first against national-level data. Our results show that network-based targeting may lead to greater population impact. We also present a new targeting method that outperforms other methods in terms of intervention effectiveness at the population level.

  9. Population stochasticity, random determination of handedness, and the genetic basis of antisymmetry.

    Science.gov (United States)

    Kamimura, Yoshitaka

    2011-12-07

    Conspicuous lateral asymmetries of organisms are classified into two major categories: antisymmetry (AS), characterized by almost equal frequencies of dextral and sinistral morphs, and directional asymmetry (DA), in which one morph dominates. I compared and characterized two types of genes, both with existing examples, in their roles in the evolutionary transitions between AS and DA for the first time. Handedness genes (HGs) determine the chirality in a strict sense, while randomization genes (RGs) randomize the chirality. A theory predicts that, in an AS population maintained by HGs under negative frequency-dependent selection, RGs harness fluctuation of the morph frequencies as their driving force and thus increase their frequency until half of the population flips the phenotype. These predictions were confirmed by simulations. Consequently, RGs mask the genetic effects of HGs, which provides a possible explanation for the apparent lack of a genetic basis for AS in empirical AS studies. Copyright © 2011 Elsevier Ltd. All rights reserved.

  10. The genealogy of sequences containing multiple sites subject to strong selection in a subdivided population.

    Science.gov (United States)

    Nordborg, Magnus; Innan, Hideki

    2003-03-01

    A stochastic model for the genealogy of a sample of recombining sequences containing one or more sites subject to selection in a subdivided population is described. Selection is incorporated by dividing the population into allelic classes and then conditioning on the past sizes of these classes. The past allele frequencies at the selected sites are thus treated as parameters rather than as random variables. The purpose of the model is not to investigate the dynamics of selection, but to investigate effects of linkage to the selected sites on the genealogy of the surrounding chromosomal region. This approach is useful for modeling strong selection, when it is natural to parameterize the past allele frequencies at the selected sites. Several models of strong balancing selection are used as examples, and the effects on the pattern of neutral polymorphism in the chromosomal region are discussed. We focus in particular on the statistical power to detect balancing selection when it is present.

  11. Simulating a base population in honey bee for molecular genetic studies.

    Science.gov (United States)

    Gupta, Pooja; Conrad, Tim; Spötter, Andreas; Reinsch, Norbert; Bienefeld, Kaspar

    2012-06-27

    Over the past years, reports have indicated that honey bee populations are declining and that infestation by an ecto-parasitic mite (Varroa destructor) is one of the main causes. Selective breeding of resistant bees can help to prevent losses due to the parasite, but it requires that a robust breeding program and genetic evaluation are implemented. Genomic selection has emerged as an important tool in animal breeding programs and simulation studies have shown that it yields more accurate breeding value estimates, higher genetic gain and low rates of inbreeding. Since genomic selection relies on marker data, simulations conducted on a genomic dataset are a pre-requisite before selection can be implemented. Although genomic datasets have been simulated in other species undergoing genetic evaluation, simulation of a genomic dataset specific to the honey bee is required since this species has a distinct genetic and reproductive biology. Our software program was aimed at constructing a base population by simulating a random mating honey bee population. A forward-time population simulation approach was applied since it allows modeling of genetic characteristics and reproductive behavior specific to the honey bee. Our software program yielded a genomic dataset for a base population in linkage disequilibrium. In addition, information was obtained on (1) the position of markers on each chromosome, (2) allele frequency, (3) χ(2) statistics for Hardy-Weinberg equilibrium, (4) a sorted list of markers with a minor allele frequency less than or equal to the input value, (5) average r(2) values of linkage disequilibrium between all simulated marker loci pair for all generations and (6) average r2 value of linkage disequilibrium in the last generation for selected markers with the highest minor allele frequency. We developed a software program that takes into account the genetic and reproductive biology specific to the honey bee and that can be used to constitute a genomic

  12. Emerging prion disease drives host selection in a wildlife population

    Science.gov (United States)

    Robinson, Stacie J.; Samuel, Michael D.; Johnson, Chad J.; Adams, Marie; McKenzie, Debbie I.

    2012-01-01

    Infectious diseases are increasingly recognized as an important force driving population dynamics, conservation biology, and natural selection in wildlife populations. Infectious agents have been implicated in the decline of small or endangered populations and may act to constrain population size, distribution, growth rates, or migration patterns. Further, diseases may provide selective pressures that shape the genetic diversity of populations or species. Thus, understanding disease dynamics and selective pressures from pathogens is crucial to understanding population processes, managing wildlife diseases, and conserving biological diversity. There is ample evidence that variation in the prion protein gene (PRNP) impacts host susceptibility to prion diseases. Still, little is known about how genetic differences might influence natural selection within wildlife populations. Here we link genetic variation with differential susceptibility of white-tailed deer to chronic wasting disease (CWD), with implications for fitness and disease-driven genetic selection. We developed a single nucleotide polymorphism (SNP) assay to efficiently genotype deer at the locus of interest (in the 96th codon of the PRNP gene). Then, using a Bayesian modeling approach, we found that the more susceptible genotype had over four times greater risk of CWD infection; and, once infected, deer with the resistant genotype survived 49% longer (8.25 more months). We used these epidemiological parameters in a multi-stage population matrix model to evaluate relative fitness based on genotype-specific population growth rates. The differences in disease infection and mortality rates allowed genetically resistant deer to achieve higher population growth and obtain a long-term fitness advantage, which translated into a selection coefficient of over 1% favoring the CWD-resistant genotype. This selective pressure suggests that the resistant allele could become dominant in the population within an

  13. Activation of professional and personal network relations when experiencing a symptom: a population-based cross-sectional study

    DEFF Research Database (Denmark)

    Elnegaard, Sandra; Andersen, Rikke Sand; Pedersen, Anette Fischer

    2017-01-01

    Objective To describe patterns of disclosure of symptoms experienced among people in the general population to persons in their personal and/or professional network. Design A population-based cross-sectional study. Data were collected from a web-based survey. Setting The general population...... in Denmark. Participants 100 000 individuals randomly selected, representative of the adult Danish population aged ≥20 years were invited. Approximately 5% were not eligible for inclusion. 49 706 (men=23 240; women=26 466) of 95 253 eligible individuals completed the questionnaire; yielding a response rate...... of 52.2%. Individuals completing all questions regarding social network relations form the study base (n=44 313). Primary and secondary outcome measures Activation of personal and/or professional relations when experiencing a symptom. Results The 44 313 individuals reported in total 260 079 symptom...

  14. Continuous-Time Mean-Variance Portfolio Selection with Random Horizon

    International Nuclear Information System (INIS)

    Yu, Zhiyong

    2013-01-01

    This paper examines the continuous-time mean-variance optimal portfolio selection problem with random market parameters and random time horizon. Treating this problem as a linearly constrained stochastic linear-quadratic optimal control problem, I explicitly derive the efficient portfolios and efficient frontier in closed forms based on the solutions of two backward stochastic differential equations. Some related issues such as a minimum variance portfolio and a mutual fund theorem are also addressed. All the results are markedly different from those in the problem with deterministic exit time. A key part of my analysis involves proving the global solvability of a stochastic Riccati equation, which is interesting in its own right

  15. Continuous-Time Mean-Variance Portfolio Selection with Random Horizon

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Zhiyong, E-mail: yuzhiyong@sdu.edu.cn [Shandong University, School of Mathematics (China)

    2013-12-15

    This paper examines the continuous-time mean-variance optimal portfolio selection problem with random market parameters and random time horizon. Treating this problem as a linearly constrained stochastic linear-quadratic optimal control problem, I explicitly derive the efficient portfolios and efficient frontier in closed forms based on the solutions of two backward stochastic differential equations. Some related issues such as a minimum variance portfolio and a mutual fund theorem are also addressed. All the results are markedly different from those in the problem with deterministic exit time. A key part of my analysis involves proving the global solvability of a stochastic Riccati equation, which is interesting in its own right.

  16. Testing, Selection, and Implementation of Random Number Generators

    National Research Council Canada - National Science Library

    Collins, Joseph C

    2008-01-01

    An exhaustive evaluation of state-of-the-art random number generators with several well-known suites of tests provides the basis for selection of suitable random number generators for use in stochastic simulations...

  17. DNA-based random number generation in security circuitry.

    Science.gov (United States)

    Gearheart, Christy M; Arazi, Benjamin; Rouchka, Eric C

    2010-06-01

    DNA-based circuit design is an area of research in which traditional silicon-based technologies are replaced by naturally occurring phenomena taken from biochemistry and molecular biology. This research focuses on further developing DNA-based methodologies to mimic digital data manipulation. While exhibiting fundamental principles, this work was done in conjunction with the vision that DNA-based circuitry, when the technology matures, will form the basis for a tamper-proof security module, revolutionizing the meaning and concept of tamper-proofing and possibly preventing it altogether based on accurate scientific observations. A paramount part of such a solution would be self-generation of random numbers. A novel prototype schema employs solid phase synthesis of oligonucleotides for random construction of DNA sequences; temporary storage and retrieval is achieved through plasmid vectors. A discussion of how to evaluate sequence randomness is included, as well as how these techniques are applied to a simulation of the random number generation circuitry. Simulation results show generated sequences successfully pass three selected NIST random number generation tests specified for security applications.

  18. Population based reference intervals for common blood haematological and biochemical parameters in the akuapem north district.

    Science.gov (United States)

    Koram, Ka; Addae, Mm; Ocran, Jc; Adu-Amankwah, S; Rogers, Wo; Nkrumah, Fk

    2007-12-01

    To estimate the reference intervals for commonly used blood haematology and biochemical parameters in an adult (18-55yrs) population of residents of Mampong Akuapem. This was a population based cross sectional study of a randomly selected sample of the adult population of Mampong. The sample was selected from an updated census list of the Mampong area. Median values (95% range) for measured parameters were established as follows: Haemoglobin, (males) 14.2 g/dl (females) 12.0 g/dl Alanine aminotransferase (ALT), (female) 19.6 U/L (males) 26.1 U/L and Creatinine, (males) 108 mmol/L (females) 93 mmol/L. In comparison to reference values that are commonly used in Ghana, the haemoglobulin levels from this study were lower, and liver function parameters higher. This could be a result of genetic or environmental differences and calls for the need to establish site specific reference values applicable to our population.

  19. Bounce Back Now! Protocol of a population-based randomized controlled trial to examine the efficacy of a Web-based intervention with disaster-affected families.

    Science.gov (United States)

    Ruggiero, Kenneth J; Davidson, Tatiana M; McCauley, Jenna; Gros, Kirstin Stauffacher; Welsh, Kyleen; Price, Matthew; Resnick, Heidi S; Danielson, Carla Kmett; Soltis, Kathryn; Galea, Sandro; Kilpatrick, Dean G; Saunders, Benjamin E; Nissenboim, Josh; Muzzy, Wendy; Fleeman, Anna; Amstadter, Ananda B

    2015-01-01

    Disasters have far-reaching and potentially long-lasting effects on youth and families. Research has consistently shown a clear increase in the prevalence of several mental health disorders after disasters, including depression and posttraumatic stress disorder. Widely accessible evidence-based interventions are needed to address this unmet need for youth and families, who are underrepresented in disaster research. Rapid growth in Internet and Smartphone access, as well as several Web based evaluation studies with various adult populations has shown that Web-based interventions are likely to be feasible in this context and can improve clinical outcomes. Such interventions also are generally cost-effective, can be targeted or personalized, and can easily be integrated in a stepped care approach to screening and intervention delivery. This is a protocol paper that describes an innovative study design in which we evaluate a self-help Web-based resource, Bounce Back Now, with a population-based sample of disaster affected adolescents and families. The paper includes description and justification for sampling selection and procedures, selection of assessment measures and methods, design of the intervention, and statistical evaluation of critical outcomes. Unique features of this study design include the use of address-based sampling to recruit a population-based sample of disaster-affected adolescents and parents, telephone and Web-based assessments, and development and evaluation of a highly individualized Web intervention for adolescents. Challenges related to large-scale evaluation of technology-delivered interventions with high-risk samples in time-sensitive research are discussed, as well as implications for future research and practice. Published by Elsevier Inc.

  20. High-level 13C-enrichment of random and synchronous populations of Chlamydomonas reinhardii

    International Nuclear Information System (INIS)

    Price, R.L.; Crissman, H.A.; Martin, J.C.; Kollman, V.H.

    1975-01-01

    The alga Chlamydomonas reinhardii was grown in suspension culture at high levels of 13 C-enrichment (98 mol percent) both in synchronous and random populations for the purpose of investigating possible macro- and ultrastructural changes in the cell as induced by essentially total carbon replacement. The algae, grown in spinner flasks, were analyzed using a newly developed multiparameter flow-system technique applied to characterizing various algal genera. The versatility of this technique provides for measuring and processing several cell characteristics simultaneously and separating cells according to selected combinations of parameters. In these studies, cell volume (by Coulter aperture) and DNA and chlorophyll content were determined simultaneously. Cell ultrastructure was examined at various levels of isotope enrichment and time periods by electron microscopy. The data presented for synchronous growth of this organism demonstrate the absence of biological effects (considering the parameters measured) due to the almost total replacement of cellular 12 C with 13 C. Interpretational problems encountered when looking for biological effects on random populations are discussed

  1. Selection signatures in worldwide sheep populations.

    Science.gov (United States)

    Fariello, Maria-Ines; Servin, Bertrand; Tosser-Klopp, Gwenola; Rupp, Rachel; Moreno, Carole; San Cristobal, Magali; Boitard, Simon

    2014-01-01

    The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinpointing several new selection signatures in the sheep genome and distinguishing those related to modern breeding objectives and to earlier post-domestication constraints. The newly identified regions, together with the ones previously identified, reveal the extensive genome response to selection on morphology, color and adaptation to new environments.

  2. Computer-aided system of evaluation for population-based all-in-one service screening (CASE-PASS): from study design to outcome analysis with bias adjustment.

    Science.gov (United States)

    Chen, Li-Sheng; Yen, Amy Ming-Fang; Duffy, Stephen W; Tabar, Laszlo; Lin, Wen-Chou; Chen, Hsiu-Hsi

    2010-10-01

    Population-based routine service screening has gained popularity following an era of randomized controlled trials. The evaluation of these service screening programs is subject to study design, data availability, and the precise data analysis for adjusting bias. We developed a computer-aided system that allows the evaluation of population-based service screening to unify these aspects and facilitate and guide the program assessor to efficiently perform an evaluation. This system underpins two experimental designs: the posttest-only non-equivalent design and the one-group pretest-posttest design and demonstrates the type of data required at both the population and individual levels. Three major analyses were developed that included a cumulative mortality analysis, survival analysis with lead-time adjustment, and self-selection bias adjustment. We used SAS AF software to develop a graphic interface system with a pull-down menu style. We demonstrate the application of this system with data obtained from a Swedish population-based service screen and a population-based randomized controlled trial for the screening of breast, colorectal, and prostate cancer, and one service screening program for cervical cancer with Pap smears. The system provided automated descriptive results based on the various sources of available data and cumulative mortality curves corresponding to the study designs. The comparison of cumulative survival between clinically and screen-detected cases without a lead-time adjustment are also demonstrated. The intention-to-treat and noncompliance analysis with self-selection bias adjustments are also shown to assess the effectiveness of the population-based service screening program. Model validation was composed of a comparison between our adjusted self-selection bias estimates and the empirical results on effectiveness reported in the literature. We demonstrate a computer-aided system allowing the evaluation of population-based service screening

  3. Clonality, genetic diversity and support for the diversifying selection hypothesis in natural populations of a flower-living yeast.

    Science.gov (United States)

    Herrera, C M; Pozo, M I; Bazaga, P

    2011-11-01

    Vast amounts of effort have been devoted to investigate patterns of genetic diversity and structuring in plants and animals, but similar information is scarce for organisms of other kingdoms. The study of the genetic structure of natural populations of wild yeasts can provide insights into the ecological and genetic correlates of clonality, and into the generality of recent hypotheses postulating that microbial populations lack the potential for genetic divergence and allopatric speciation. Ninety-one isolates of the flower-living yeast Metschnikowia gruessii from southeastern Spain were DNA fingerprinted using amplified fragment length polymorphism (AFLP) markers. Genetic diversity and structuring was investigated with band-based methods and model- and nonmodel-based clustering. Linkage disequilibrium tests were used to assess reproduction mode. Microsite-dependent, diversifying selection was tested by comparing genetic characteristics of isolates from bumble bee vectors and different floral microsites. AFLP polymorphism (91%) and genotypic diversity were very high. Genetic diversity was spatially structured, as shown by amova (Φ(st)  = 0.155) and clustering. The null hypothesis of random mating was rejected, clonality seeming the prevailing reproductive mode in the populations studied. Genetic diversity of isolates declined from bumble bee mouthparts to floral microsites, and frequency of five AFLP markers varied significantly across floral microsites, thus supporting the hypothesis of diversifying selection on clonal lineages. Wild populations of clonal fungal microbes can exhibit levels of genetic diversity and spatial structuring that are not singularly different from those shown by sexually reproducing plants or animals. Microsite-dependent, divergent selection can maintain high local and regional genetic diversity in microbial populations despite extensive clonality. © 2011 Blackwell Publishing Ltd.

  4. Large-scale Reconstructions and Independent, Unbiased Clustering Based on Morphological Metrics to Classify Neurons in Selective Populations.

    Science.gov (United States)

    Bragg, Elise M; Briggs, Farran

    2017-02-15

    This protocol outlines large-scale reconstructions of neurons combined with the use of independent and unbiased clustering analyses to create a comprehensive survey of the morphological characteristics observed among a selective neuronal population. Combination of these techniques constitutes a novel approach for the collection and analysis of neuroanatomical data. Together, these techniques enable large-scale, and therefore more comprehensive, sampling of selective neuronal populations and establish unbiased quantitative methods for describing morphologically unique neuronal classes within a population. The protocol outlines the use of modified rabies virus to selectively label neurons. G-deleted rabies virus acts like a retrograde tracer following stereotaxic injection into a target brain structure of interest and serves as a vehicle for the delivery and expression of EGFP in neurons. Large numbers of neurons are infected using this technique and express GFP throughout their dendrites, producing "Golgi-like" complete fills of individual neurons. Accordingly, the virus-mediated retrograde tracing method improves upon traditional dye-based retrograde tracing techniques by producing complete intracellular fills. Individual well-isolated neurons spanning all regions of the brain area under study are selected for reconstruction in order to obtain a representative sample of neurons. The protocol outlines procedures to reconstruct cell bodies and complete dendritic arborization patterns of labeled neurons spanning multiple tissue sections. Morphological data, including positions of each neuron within the brain structure, are extracted for further analysis. Standard programming functions were utilized to perform independent cluster analyses and cluster evaluations based on morphological metrics. To verify the utility of these analyses, statistical evaluation of a cluster analysis performed on 160 neurons reconstructed in the thalamic reticular nucleus of the thalamus

  5. Effect of calcium and vitamin D supplementation on bone mineral density in women aged 65-71 years: a 3-year randomized population-based trial (OSTPRE-FPS).

    Science.gov (United States)

    Kärkkäinen, M; Tuppurainen, M; Salovaara, K; Sandini, L; Rikkonen, T; Sirola, J; Honkanen, R; Jurvelin, J; Alhava, E; Kröger, H

    2010-12-01

    The Osteoporosis Risk Factor and Prevention-Fracture Prevention Study (OSTPRE-FPS) was a randomized population-based open trial (n = 593). The supplementation group (n = 287) received daily cholecalciferol 800 IU + calcium 1,000 mg for 3 years while the control group (n = 306) received neither supplementation nor placebo. Daily vitamin D and calcium supplementation have a positive effect on the skeleton in ambulatory postmenopausal women. vitamin D deficiency is common in the elderly, and vitamin D levels are associated with low bone mineral density (BMD). The working hypothesis was that vitamin D and calcium supplementation could prevent bone loss in ambulatory postmenopausal women. the OSTPRE-FPS was a randomized population-based open trial with a 3-year follow-up in 3,432 women (aged 66 to 71 years). A randomly selected subsample of 593 subjects underwent BMD measurements. The supplementation group (n = 287) received daily cholecalciferol 800 IU + calcium 1,000 mg for 3 years while the control group (n = 306) received neither supplementation nor placebo. in the intention-to-treat analysis, total body BMD (n = 362) increased significantly more in the intervention group than in the control group (0.84% vs. 0.19%, p = 0.011). The BMD change differences at the lumbar spine (p = 0.372), femoral neck (p = 0.188), trochanter (p = 0.085), and total proximal femur (p = 0.070) were statistically nonsignificant. Analyses in compliant women (≥ 80% of use) resulted in stronger and statistically significant effects at the total body and femoral regions. daily vitamin D and calcium supplementation have a positive effect on the skeleton in ambulatory postmenopausal women with adequate nutritional calcium intake.

  6. Genome-wide association data classification and SNPs selection using two-stage quality-based Random Forests.

    Science.gov (United States)

    Nguyen, Thanh-Tung; Huang, Joshua; Wu, Qingyao; Nguyen, Thuy; Li, Mark

    2015-01-01

    Single-nucleotide polymorphisms (SNPs) selection and identification are the most important tasks in Genome-wide association data analysis. The problem is difficult because genome-wide association data is very high dimensional and a large portion of SNPs in the data is irrelevant to the disease. Advanced machine learning methods have been successfully used in Genome-wide association studies (GWAS) for identification of genetic variants that have relatively big effects in some common, complex diseases. Among them, the most successful one is Random Forests (RF). Despite of performing well in terms of prediction accuracy in some data sets with moderate size, RF still suffers from working in GWAS for selecting informative SNPs and building accurate prediction models. In this paper, we propose to use a new two-stage quality-based sampling method in random forests, named ts-RF, for SNP subspace selection for GWAS. The method first applies p-value assessment to find a cut-off point that separates informative and irrelevant SNPs in two groups. The informative SNPs group is further divided into two sub-groups: highly informative and weak informative SNPs. When sampling the SNP subspace for building trees for the forest, only those SNPs from the two sub-groups are taken into account. The feature subspaces always contain highly informative SNPs when used to split a node at a tree. This approach enables one to generate more accurate trees with a lower prediction error, meanwhile possibly avoiding overfitting. It allows one to detect interactions of multiple SNPs with the diseases, and to reduce the dimensionality and the amount of Genome-wide association data needed for learning the RF model. Extensive experiments on two genome-wide SNP data sets (Parkinson case-control data comprised of 408,803 SNPs and Alzheimer case-control data comprised of 380,157 SNPs) and 10 gene data sets have demonstrated that the proposed model significantly reduced prediction errors and outperformed

  7. Opportunity for natural selection among five population groups of Manipur, North East India.

    Science.gov (United States)

    Asghar, M; Meitei, S Y; Luxmi, Y; Achoubi, N; Meitei, K S; Murry, B; Sachdeva, M P; Saraswathy, K N

    2014-01-01

    Opportunity for natural selection among five population groups of Manipur in comparison with other North East Indian population has been studied. Crow's index as well as Johnston and Kensinger's index for natural selection were calculated based on differential fertility and mortality. The mortality component was found to be lower compared to fertility component in all the populations which may attribute to comparatively improved and easily accessible health care facilities. However, different selection pressures, artificial and natural, seem to be influencing the selection intensity through induced abortion and spontaneous abortion among the two non-tribal migrant groups: Bamon and Muslims, respectively. This study highlights the probable interaction of artificial and natural selection in determining the evolutionary fate of any population group.

  8. Random genetic drift, natural selection, and noise in human cranial evolution.

    Science.gov (United States)

    Roseman, Charles C

    2016-08-01

    This study assesses the extent to which relationships among groups complicate comparative studies of adaptation in recent human cranial variation and the extent to which departures from neutral additive models of evolution hinder the reconstruction of population relationships among groups using cranial morphology. Using a maximum likelihood evolutionary model fitting approach and a mixed population genomic and cranial data set, I evaluate the relative fits of several widely used models of human cranial evolution. Moreover, I compare the goodness of fit of models of cranial evolution constrained by genomic variation to test hypotheses about population specific departures from neutrality. Models from population genomics are much better fits to cranial variation than are traditional models from comparative human biology. There is not enough evolutionary information in the cranium to reconstruct much of recent human evolution but the influence of population history on cranial variation is strong enough to cause comparative studies of adaptation serious difficulties. Deviations from a model of random genetic drift along a tree-like population history show the importance of environmental effects, gene flow, and/or natural selection on human cranial variation. Moreover, there is a strong signal of the effect of natural selection or an environmental factor on a group of humans from Siberia. The evolution of the human cranium is complex and no one evolutionary process has prevailed at the expense of all others. A holistic unification of phenome, genome, and environmental context, gives us a strong point of purchase on these problems, which is unavailable to any one traditional approach alone. Am J Phys Anthropol 160:582-592, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  9. Assessing Genomic Selection Prediction Accuracy in a Dynamic Barley Breeding Population

    Directory of Open Access Journals (Sweden)

    A. H. Sallam

    2015-03-01

    Full Text Available Prediction accuracy of genomic selection (GS has been previously evaluated through simulation and cross-validation; however, validation based on progeny performance in a plant breeding program has not been investigated thoroughly. We evaluated several prediction models in a dynamic barley breeding population comprised of 647 six-row lines using four traits differing in genetic architecture and 1536 single nucleotide polymorphism (SNP markers. The breeding lines were divided into six sets designated as one parent set and five consecutive progeny sets comprised of representative samples of breeding lines over a 5-yr period. We used these data sets to investigate the effect of model and training population composition on prediction accuracy over time. We found little difference in prediction accuracy among the models confirming prior studies that found the simplest model, random regression best linear unbiased prediction (RR-BLUP, to be accurate across a range of situations. In general, we found that using the parent set was sufficient to predict progeny sets with little to no gain in accuracy from generating larger training populations by combining the parent set with subsequent progeny sets. The prediction accuracy ranged from 0.03 to 0.99 across the four traits and five progeny sets. We explored characteristics of the training and validation populations (marker allele frequency, population structure, and linkage disequilibrium, LD as well as characteristics of the trait (genetic architecture and heritability, . Fixation of markers associated with a trait over time was most clearly associated with reduced prediction accuracy for the mycotoxin trait DON. Higher trait in the training population and simpler trait architecture were associated with greater prediction accuracy.

  10. Performance Evaluation of User Selection Protocols in Random Networks with Energy Harvesting and Hardware Impairments

    Directory of Open Access Journals (Sweden)

    Tan Nhat Nguyen

    2016-01-01

    Full Text Available In this paper, we evaluate performances of various user selection protocols under impact of hardware impairments. In the considered protocols, a Base Station (BS selects one of available Users (US to serve, while the remaining USs harvest the energy from the Radio Frequency (RF transmitted by the BS. We assume that all of the US randomly appear around the BS. In the Random Selection Protocol (RAN, the BS randomly selects a US to transmit the data. In the second proposed protocol, named Minimum Distance Protocol (MIND, the US that is nearest to the BS will be chosen. In the Optimal Selection Protocol (OPT, the US providing the highest channel gain between itself and the BS will be served. For performance evaluation, we derive exact and asymptotic closed-form expressions of average Outage Probability (OP over Rayleigh fading channels. We also consider average harvested energy per a US. Finally, Monte-Carlo simulations are then performed to verify the theoretical results.

  11. Elevated incidence rates of diabetes in Peru: report from PERUDIAB, a national urban population-based longitudinal study

    OpenAIRE

    Seclen, Segundo Nicolas; Rosas, Moises Ernesto; Arias, Arturo Jaime; Medina, Cecilia Alexandra

    2017-01-01

    Objective A recent report from a non-nationally representative, geographically diverse sample in four separate communities in Peru suggests an unusually high diabetes incidence. We aimed to estimate the national diabetes incidence rate using PERUDIAB, a probabilistic, national urban population-based longitudinal study. Research design and methods 662 subjects without diabetes, selected by multistage, cluster, random sampling of households, representing the 24 administrative and the 3 (coast, ...

  12. Effectiveness of a two-step population-based osteoporosis screening program using FRAX

    DEFF Research Database (Denmark)

    Rubin, K H; Rothmann, M J; Holmberg, T

    2018-01-01

    The Risk-stratified Osteoporosis Strategy Evaluation (ROSE) study investigated the effectiveness of a two-step screening program for osteoporosis in women. We found no overall reduction in fractures from systematic screening compared to the current case-finding strategy. The group of moderate......- to high-risk women, who accepted the invitation to DXA, seemed to benefit from the program. INTRODUCTION: The purpose of the ROSE study was to investigate the effectiveness of a two-step population-based osteoporosis screening program using the Fracture Risk Assessment Tool (FRAX) derived from a self......-administered questionnaire to select women for DXA scan. After the scanning, standard osteoporosis management according to Danish national guidelines was followed. METHODS: Participants were randomized to either screening or control group, and randomization was stratified according to age and area of residence. Inclusion...

  13. Simulating a base population in honey bee for molecular genetic studies

    Directory of Open Access Journals (Sweden)

    Gupta Pooja

    2012-06-01

    Full Text Available Abstract Background Over the past years, reports have indicated that honey bee populations are declining and that infestation by an ecto-parasitic mite (Varroa destructor is one of the main causes. Selective breeding of resistant bees can help to prevent losses due to the parasite, but it requires that a robust breeding program and genetic evaluation are implemented. Genomic selection has emerged as an important tool in animal breeding programs and simulation studies have shown that it yields more accurate breeding value estimates, higher genetic gain and low rates of inbreeding. Since genomic selection relies on marker data, simulations conducted on a genomic dataset are a pre-requisite before selection can be implemented. Although genomic datasets have been simulated in other species undergoing genetic evaluation, simulation of a genomic dataset specific to the honey bee is required since this species has a distinct genetic and reproductive biology. Our software program was aimed at constructing a base population by simulating a random mating honey bee population. A forward-time population simulation approach was applied since it allows modeling of genetic characteristics and reproductive behavior specific to the honey bee. Results Our software program yielded a genomic dataset for a base population in linkage disequilibrium. In addition, information was obtained on (1 the position of markers on each chromosome, (2 allele frequency, (3 χ2 statistics for Hardy-Weinberg equilibrium, (4 a sorted list of markers with a minor allele frequency less than or equal to the input value, (5 average r2 values of linkage disequilibrium between all simulated marker loci pair for all generations and (6 average r2 value of linkage disequilibrium in the last generation for selected markers with the highest minor allele frequency. Conclusion We developed a software program that takes into account the genetic and reproductive biology specific to the honey bee

  14. Algorithms for selecting informative marker panels for population assignment.

    Science.gov (United States)

    Rosenberg, Noah A

    2005-11-01

    Given a set of potential source populations, genotypes of an individual of unknown origin at a collection of markers can be used to predict the correct source population of the individual. For improved efficiency, informative markers can be chosen from a larger set of markers to maximize the accuracy of this prediction. However, selecting the loci that are individually most informative does not necessarily produce the optimal panel. Here, using genotypes from eight species--carp, cat, chicken, dog, fly, grayling, human, and maize--this univariate accumulation procedure is compared to new multivariate "greedy" and "maximin" algorithms for choosing marker panels. The procedures generally suggest similar panels, although the greedy method often recommends inclusion of loci that are not chosen by the other algorithms. In seven of the eight species, when applied to five or more markers, all methods achieve at least 94% assignment accuracy on simulated individuals, with one species--dog--producing this level of accuracy with only three markers, and the eighth species--human--requiring approximately 13-16 markers. The new algorithms produce substantial improvements over use of randomly selected markers; where differences among the methods are noticeable, the greedy algorithm leads to slightly higher probabilities of correct assignment. Although none of the approaches necessarily chooses the panel with optimal performance, the algorithms all likely select panels with performance near enough to the maximum that they all are suitable for practical use.

  15. Identifying Copy Number Variants under Selection in Geographically Structured Populations Based on -statistics

    Directory of Open Access Journals (Sweden)

    Hae-Hiang Song

    2012-06-01

    Full Text Available Large-scale copy number variants (CNVs in the human provide the raw material for delineating population differences, as natural selection may have affected at least some of the CNVs thus far discovered. Although the examination of relatively large numbers of specific ethnic groups has recently started in regard to inter-ethnic group differences in CNVs, identifying and understanding particular instances of natural selection have not been performed. The traditional FST measure, obtained from differences in allele frequencies between populations, has been used to identify CNVs loci subject to geographically varying selection. Here, we review advances and the application of multinomial-Dirichlet likelihood methods of inference for identifying genome regions that have been subject to natural selection with the FST estimates. The contents of presentation are not new; however, this review clarifies how the application of the methods to CNV data, which remains largely unexplored, is possible. A hierarchical Bayesian method, which is implemented via Markov Chain Monte Carlo, estimates locus-specific FST and can identify outlying CNVs loci with large values of FST. By applying this Bayesian method to the publicly available CNV data, we identified the CNV loci that show signals of natural selection, which may elucidate the genetic basis of human disease and diversity.

  16. Randomized trial of a population-based, home-delivered intervention for preschool language delay.

    Science.gov (United States)

    Wake, Melissa; Tobin, Sherryn; Levickis, Penny; Gold, Lisa; Ukoumunne, Obioha C; Zens, Naomi; Goldfeld, Sharon; Le, Ha; Law, James; Reilly, Sheena

    2013-10-01

    Population approaches to lessen the adverse impacts of preschool language delay remain elusive. We aimed to determine whether systematic ascertainment of language delay at age 4 years, followed by a 10-month, 1-on-1 intervention, improves language and related outcomes at age 5 years. A randomized trial nested within a cross-sectional ascertainment of language delay. Children with expressive and/or receptive language scores more than 1.25 SD below the mean at age 4 years entered the trial. Children randomly allocated to the intervention received 18 1-hour home-based therapy sessions. The primary outcomes were receptive and expressive language (Clinical Evaluation of Language Fundamentals - Preschool, 2(nd) Edition) and secondary outcomes were child phonological skills, letter awareness, pragmatic skills, behavior, and quality of life. A total of 1464 children were assessed for language delay at age 4 years. Of 266 eligible children, 200 (13.6%) entered the trial, with 91 intervention (92% of 99) and 88 control (87% of 101) children retained at age 5 years. At age 5 years, there was weak evidence of benefit to expressive (adjusted mean difference, intervention - control, 2.0; 95% confidence interval [CI] -0.5 to 4.4; P = .12) but not receptive (0.6; 95% CI -2.5 to 3.8; P = .69) language. The intervention improved phonological awareness skills (5.0; 95% CI 2.2 to 7.8; P language intervention was successfully delivered by non-specialist staff, found to be acceptable and feasible, and has the potential to improve long-term consequences of early language delay within a public health framework.

  17. Lineage dynamics and mutation-selection balance in non-adapting asexual populations

    Science.gov (United States)

    Pénisson, Sophie; Sniegowski, Paul D.; Colato, Alexandre; Gerrish, Philip J.

    2013-02-01

    In classical population genetics, mutation-selection balance refers to the equilibrium frequency of a deleterious allele established and maintained under two opposing forces: recurrent mutation, which tends to increase the frequency of the allele; and selection, which tends to decrease its frequency. In a haploid population, if μ denotes the per capita rate of production of the deleterious allele by mutation and s denotes the selective disadvantage of carrying the allele, then the classical mutation-selection balance frequency of the allele is approximated by μ/s. This calculation assumes that lineages carrying the mutant allele in question—the ‘focal allele’—do not accumulate deleterious mutations linked to the focal allele. In principle, indirect selection against the focal allele caused by such additional mutations can decrease the frequency of the focal allele below the classical mutation-selection balance. This effect of indirect selection will be strongest in an asexual population, in which the entire genome is in linkage. Here, we use an approach based on a multitype branching process to investigate this effect, analyzing lineage dynamics under mutation, direct selection, and indirect selection in a non-adapting asexual population. We find that the equilibrium balance between recurrent mutation to the focal allele and the forces of direct and indirect selection against the focal allele is closely approximated by γμ/(s + U) (s = 0 if the focal allele is neutral), where γ ≈ eθθ-(ω+θ)(ω + θ)(Γ(ω + θ) - Γ(ω + θ,θ)), \\theta =U/\\tilde {s}, and \\omega =s/\\tilde {s}; U denotes the genomic deleterious mutation rate and \\tilde {s} denotes the geometric mean selective disadvantage of deleterious mutations elsewhere on the genome. This mutation-selection balance for asexual populations can remain surprisingly invariant over wide ranges of the mutation rate.

  18. Random walk on a population of random walkers

    International Nuclear Information System (INIS)

    Agliari, E; Burioni, R; Cassi, D; Neri, F M

    2008-01-01

    We consider a population of N labelled random walkers moving on a substrate, and an excitation jumping among the walkers upon contact. The label X(t) of the walker carrying the excitation at time t can be viewed as a stochastic process, where the transition probabilities are a stochastic process themselves. Upon mapping onto two simpler processes, the quantities characterizing X(t) can be calculated in the limit of long times and low walkers density. The results are compared with numerical simulations. Several different topologies for the substrate underlying diffusion are considered

  19. Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools.

    Science.gov (United States)

    Fuller, Zachary L; Niño, Elina L; Patch, Harland M; Bedoya-Reina, Oscar C; Baumgarten, Tracey; Muli, Elliud; Mumoki, Fiona; Ratan, Aakrosh; McGraw, John; Frazier, Maryann; Masiga, Daniel; Schuster, Stephen; Grozinger, Christina M; Miller, Webb

    2015-07-10

    With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population dynamics and signatures of selection across the genome using several well-established tests, including F ST, pN/pS, and McDonald-Kreitman. We applied these techniques to study populations of honey bees (Apis mellifera) in East Africa. In Kenya, there are several described A. mellifera subspecies, which are thought to be localized to distinct ecological regions. We performed whole genome sequencing of 11 worker honey bees from apiaries distributed throughout Kenya and identified 3.6 million putative single-nucleotide polymorphisms. The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome. While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region. We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea. These results lay the groundwork for future studies of adaptive ecological evolution in honey bees, and demonstrate the use of new, freely available web-based tools and workflows ( http://usegalaxy.org/r/kenyanbee ) that can be applied to any model system with genomic information.

  20. Anxiety disorders in young people: a population-based study

    Directory of Open Access Journals (Sweden)

    Thaíse Campos Mondin

    2013-12-01

    Full Text Available Objective: To assess the prevalence of anxiety disorders and associated factors in young adults. Methods: Cross-sectional population-based study of individuals between the ages of 18 and 24 years randomly selected from 89 census-based sectors to ensure an adequate sample size. Household selection within the sectors was performed according to a systematic sampling process. Anxiety disorders were assessed using the Mini International Neuropsychiatric Interview (MINI. The final sample comprised 1,560 young adults. Results: Of the participants who were diagnosed with anxiety disorders, 12.3% had agoraphobia, 9.7% had generalised anxiety disorder, 4.0% had social phobia, 3.3% had obsessive-compulsive disorder, 2.5% had panic disorder, and 2.1% had post-traumatic stress disorder; only 23.8% had received any previous treatment. Anxiety disorders were associated with sex, socioeconomic status, psychiatric problems in parents, alcohol abuse, and tobacco use. Conclusions: The identification of factors associated with anxiety disorders in young people enables us to develop intervention strategies. Anxiety disorders are not only highly prevalent but are also associated with significant functional impairment, significant reductions in quality of life, lower productivity, and higher rates of comorbidities.

  1. Transgender Population Size in the United States: a Meta-Regression of Population-Based Probability Samples

    Science.gov (United States)

    Sevelius, Jae M.

    2017-01-01

    Background. Transgender individuals have a gender identity that differs from the sex they were assigned at birth. The population size of transgender individuals in the United States is not well-known, in part because official records, including the US Census, do not include data on gender identity. Population surveys today more often collect transgender-inclusive gender-identity data, and secular trends in culture and the media have created a somewhat more favorable environment for transgender people. Objectives. To estimate the current population size of transgender individuals in the United States and evaluate any trend over time. Search methods. In June and July 2016, we searched PubMed, Cumulative Index to Nursing and Allied Health Literature, and Web of Science for national surveys, as well as “gray” literature, through an Internet search. We limited the search to 2006 through 2016. Selection criteria. We selected population-based surveys that used probability sampling and included self-reported transgender-identity data. Data collection and analysis. We used random-effects meta-analysis to pool eligible surveys and used meta-regression to address our hypothesis that the transgender population size estimate would increase over time. We used subsample and leave-one-out analysis to assess for bias. Main results. Our meta-regression model, based on 12 surveys covering 2007 to 2015, explained 62.5% of model heterogeneity, with a significant effect for each unit increase in survey year (F = 17.122; df = 1,10; b = 0.026%; P = .002). Extrapolating these results to 2016 suggested a current US population size of 390 adults per 100 000, or almost 1 million adults nationally. This estimate may be more indicative for younger adults, who represented more than 50% of the respondents in our analysis. Authors’ conclusions. Future national surveys are likely to observe higher numbers of transgender people. The large variety in questions used to ask

  2. Parallel selection on TRPV6 in human populations.

    Science.gov (United States)

    Hughes, David A; Tang, Kun; Strotmann, Rainer; Schöneberg, Torsten; Prenen, Jean; Nilius, Bernd; Stoneking, Mark

    2008-02-27

    We identified and examined a candidate gene for local directional selection in Europeans, TRPV6, and conclude that selection has acted on standing genetic variation at this locus, creating parallel soft sweep events in humans. A novel modification of the extended haplotype homozygosity (EHH) test was utilized, which compares EHH for a single allele across populations, to investigate the signature of selection at TRPV6 and neighboring linked loci in published data sets for Europeans, Asians and African-Americans, as well as in newly-obtained sequence data for additional populations. We find that all non-African populations carry a signature of selection on the same haplotype at the TRPV6 locus. The selective footprints, however, are significantly differentiated between non-African populations and estimated to be younger than an ancestral population of non-Africans. The possibility of a single selection event occurring in an ancestral population of non-Africans was tested by simulations and rejected. The putatively-selected TRPV6 haplotype contains three candidate sites for functional differences, namely derived non-synonymous substitutions C157R, M378V and M681T. Potential functional differences between the ancestral and derived TRPV6 proteins were investigated by cloning the ancestral and derived forms, transfecting cell lines, and carrying out electrophysiology experiments via patch clamp analysis. No statistically-significant differences in biophysical channel function were found, although one property of the protein, namely Ca(2+) dependent inactivation, may show functionally relevant differences between the ancestral and derived forms. Although the reason for selection on this locus remains elusive, this is the first demonstration of a widespread parallel selection event acting on standing genetic variation in humans, and highlights the utility of between population EHH statistics.

  3. Parallel selection on TRPV6 in human populations.

    Directory of Open Access Journals (Sweden)

    David A Hughes

    Full Text Available We identified and examined a candidate gene for local directional selection in Europeans, TRPV6, and conclude that selection has acted on standing genetic variation at this locus, creating parallel soft sweep events in humans. A novel modification of the extended haplotype homozygosity (EHH test was utilized, which compares EHH for a single allele across populations, to investigate the signature of selection at TRPV6 and neighboring linked loci in published data sets for Europeans, Asians and African-Americans, as well as in newly-obtained sequence data for additional populations. We find that all non-African populations carry a signature of selection on the same haplotype at the TRPV6 locus. The selective footprints, however, are significantly differentiated between non-African populations and estimated to be younger than an ancestral population of non-Africans. The possibility of a single selection event occurring in an ancestral population of non-Africans was tested by simulations and rejected. The putatively-selected TRPV6 haplotype contains three candidate sites for functional differences, namely derived non-synonymous substitutions C157R, M378V and M681T. Potential functional differences between the ancestral and derived TRPV6 proteins were investigated by cloning the ancestral and derived forms, transfecting cell lines, and carrying out electrophysiology experiments via patch clamp analysis. No statistically-significant differences in biophysical channel function were found, although one property of the protein, namely Ca(2+ dependent inactivation, may show functionally relevant differences between the ancestral and derived forms. Although the reason for selection on this locus remains elusive, this is the first demonstration of a widespread parallel selection event acting on standing genetic variation in humans, and highlights the utility of between population EHH statistics.

  4. Study on Quality Improvement Effect and Separate Character of Soybean Male Sterile (MS1) Recurrent Selection Population

    Institute of Scientific and Technical Information of China (English)

    ZHAO Shuang-jin; ZHANG Meng-chen; JIANG Chun-zhi; YANG Chun-yan; LIU Bing-qiang; CUI Jue

    2007-01-01

    To solve the problem that soybean has narrow genetic base, we constructed a series of male sterile recurrent selection populations, and studied the effects of quality improvement and practical value. An LD-base population, which fits to our ecology type was constructed by 6 years' gene enrichment through the introduction of new genes from 23 local varieties and recurrent selection. The LD-base populations were then improved by making crosses with high protein and high oil genotypes. As a result we obtained a high protein sub-population (db) and a high oil sub-population (gy). For the db sub-population, the protein content is 1.18% higher than the base population, 22.38% of the individuals contain 45% or more of protein, which is 10.99% higher than the base population. For the gy sub-population, oil content is 0.24% higher than the base population. Individuals with oil content of 20% or more are 11.05% higher than the base population. The quantitative characters such as flowering date, mature date, pod habit, and hilum color, etc., all showed wide range of separation, and the segregation ratio approached balance. The c.v. of branch number of ms1 recurrent population (72.8%) is higher than general cross-population (57.3%), and the c.v. of 100 seed weight of ms1 (18.1%) is higher than general cross population (16.5%), the coefficient of variation of plant height, pods per plant, and seeds per pod were not significantly different. It was demonstrated in this paper that the quality character of ms1 male sterile recurrent selection population was improved by adding new genes. And the segregation of other characters widened, making the populations suitable for the objective of soybean breeding. In this paper, we also discussed the breeding method, key technology, and selection effect of soybean ms1 population.

  5. [Population-based breast cancer screening: certainties, controversies, and future perspectives].

    Science.gov (United States)

    Apesteguía Ciriza, Luis; Pina Insausti, Luis Javier

    2014-01-01

    Population-based breast cancer screening programs based on mammography must maintain a high level of quality, so the results must be constantly monitored. Although most authors consider that these programs have decreased the mortality due to breast cancer by about 30%, others claim that the mortality has decreased by only about 12% due to errors in the randomization of patients, because the rate of advanced tumors has hardly decreased and because adjuvant treatment also improves survival. Other criticisms focus on overdiagnosis and overtreatment. We believe that despite the unquestionable value of mammographic screening, we should be open to certain changes such as the stratification of patients by their level of risk and the introduction of complementary techniques like tomosynthesis, ultrasonography, and magnetic resonance imaging in selected cases. Copyright © 2012 SERAM. Published by Elsevier Espana. All rights reserved.

  6. Selection signatures in worldwide sheep populations.

    OpenAIRE

    Fariello, Maria-Ines; Servin, Bertrand; Tosser-Klopp, Gwenola; Rupp, Rachel; Moreno, Carole; San Cristobal, Magali; Boitard, Simon; Drögemüller, Cord; The International Sheep Genomics Consortium, ISGC

    2014-01-01

    The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep popula...

  7. Selection Signatures in Worldwide Sheep Populations

    OpenAIRE

    Fariello, Maria-Ines; Servin, Bertrand; Tosser-Klopp, Gwenola; Rupp, Rachel; Moreno, Carole; Cristobal, Magali San; Boitard, Simon

    2014-01-01

    The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep popula...

  8. Ancestral informative marker selection and population structure visualization using sparse Laplacian eigenfunctions.

    Directory of Open Access Journals (Sweden)

    Jun Zhang

    Full Text Available Identification of a small panel of population structure informative markers can reduce genotyping cost and is useful in various applications, such as ancestry inference in association mapping, forensics and evolutionary theory in population genetics. Traditional methods to ascertain ancestral informative markers usually require the prior knowledge of individual ancestry and have difficulty for admixed populations. Recently Principal Components Analysis (PCA has been employed with success to select SNPs which are highly correlated with top significant principal components (PCs without use of individual ancestral information. The approach is also applicable to admixed populations. Here we propose a novel approach based on our recent result on summarizing population structure by graph laplacian eigenfunctions, which differs from PCA in that it is geometric and robust to outliers. Our approach also takes advantage of the priori sparseness of informative markers in the genome. Through simulation of a ring population and the real global population sample HGDP of 650K SNPs genotyped in 940 unrelated individuals, we validate the proposed algorithm at selecting most informative markers, a small fraction of which can recover the similar underlying population structure efficiently. Employing a standard Support Vector Machine (SVM to predict individuals' continental memberships on HGDP dataset of seven continents, we demonstrate that the selected SNPs by our method are more informative but less redundant than those selected by PCA. Our algorithm is a promising tool in genome-wide association studies and population genetics, facilitating the selection of structure informative markers, efficient detection of population substructure and ancestral inference.

  9. Gamified physical activation of young men--a Multidisciplinary Population-Based Randomized Controlled Trial (MOPO study).

    Science.gov (United States)

    Ahola, Riikka; Pyky, Riitta; Jämsä, Timo; Mäntysaari, Matti; Koskimäki, Heli; Ikäheimo, Tiina M; Huotari, Maija-Leena; Röning, Juha; Heikkinen, Hannu I; Korpelainen, Raija

    2013-01-14

    Inactive and unhealthy lifestyles are common among adolescent men. The planned intervention examines the effectiveness of an interactive, gamified activation method, based on tailored health information, peer networks and participation, on physical activity, health and wellbeing in young men. We hypothesize that following the intervention the physical activation group will have an improved physical activity, as well as self-determined and measured health compared with the controls. Conscription-aged men (18 years) attending compulsory annual call-ups for military service in the city of Oulu in Finland (n = 1500) will be randomized to a 6-months intervention (n = 640) or a control group (n = 640) during the fall 2013. A questionnaire on health, health behaviour, diet and wellbeing is administered in the beginning and end of the intervention. In addition, anthropometric measures (height, weight and waist circumference), body composition, grip strength, heart rate variability and aerobic fitness will be measured. The activation group utilizes an online gamified activation method in combination with communal youth services, objective physical activity measurement, social networking, tailored health information and exercise programs according to baseline activity level and the readiness of changes of each individual. Daily physical activity of the participants is monitored in both the activation and control groups. The activation service rewards improvements in physical activity or reductions in sedentary behaviour. The performance and completion of the military service of the participants will also be followed. The study will provide new information of physical activity, health and health behaviour of young men. Furthermore, a novel model including methods for increasing physical activity among young people is developed and its effects tested through an intervention. This unique gamified service for activating young men can provide a translational model for community

  10. On subset selection from Logistic populations

    NARCIS (Netherlands)

    Laan, van der P.

    1990-01-01

    Some distributional results are derived for subset selection from Logistic populations, differing only in their location parameter. The probability of correct selection is determined. Exact and numerical results concerning the expected subset size are presented.

  11. Genome-wide detection and characterization of positive selection in human populations.

    Science.gov (United States)

    Sabeti, Pardis C; Varilly, Patrick; Fry, Ben; Lohmueller, Jason; Hostetter, Elizabeth; Cotsapas, Chris; Xie, Xiaohui; Byrne, Elizabeth H; McCarroll, Steven A; Gaudet, Rachelle; Schaffner, Stephen F; Lander, Eric S; Frazer, Kelly A; Ballinger, Dennis G; Cox, David R; Hinds, David A; Stuve, Laura L; Gibbs, Richard A; Belmont, John W; Boudreau, Andrew; Hardenbol, Paul; Leal, Suzanne M; Pasternak, Shiran; Wheeler, David A; Willis, Thomas D; Yu, Fuli; Yang, Huanming; Zeng, Changqing; Gao, Yang; Hu, Haoran; Hu, Weitao; Li, Chaohua; Lin, Wei; Liu, Siqi; Pan, Hao; Tang, Xiaoli; Wang, Jian; Wang, Wei; Yu, Jun; Zhang, Bo; Zhang, Qingrun; Zhao, Hongbin; Zhao, Hui; Zhou, Jun; Gabriel, Stacey B; Barry, Rachel; Blumenstiel, Brendan; Camargo, Amy; Defelice, Matthew; Faggart, Maura; Goyette, Mary; Gupta, Supriya; Moore, Jamie; Nguyen, Huy; Onofrio, Robert C; Parkin, Melissa; Roy, Jessica; Stahl, Erich; Winchester, Ellen; Ziaugra, Liuda; Altshuler, David; Shen, Yan; Yao, Zhijian; Huang, Wei; Chu, Xun; He, Yungang; Jin, Li; Liu, Yangfan; Shen, Yayun; Sun, Weiwei; Wang, Haifeng; Wang, Yi; Wang, Ying; Xiong, Xiaoyan; Xu, Liang; Waye, Mary M Y; Tsui, Stephen K W; Xue, Hong; Wong, J Tze-Fei; Galver, Luana M; Fan, Jian-Bing; Gunderson, Kevin; Murray, Sarah S; Oliphant, Arnold R; Chee, Mark S; Montpetit, Alexandre; Chagnon, Fanny; Ferretti, Vincent; Leboeuf, Martin; Olivier, Jean-François; Phillips, Michael S; Roumy, Stéphanie; Sallée, Clémentine; Verner, Andrei; Hudson, Thomas J; Kwok, Pui-Yan; Cai, Dongmei; Koboldt, Daniel C; Miller, Raymond D; Pawlikowska, Ludmila; Taillon-Miller, Patricia; Xiao, Ming; Tsui, Lap-Chee; Mak, William; Song, You Qiang; Tam, Paul K H; Nakamura, Yusuke; Kawaguchi, Takahisa; Kitamoto, Takuya; Morizono, Takashi; Nagashima, Atsushi; Ohnishi, Yozo; Sekine, Akihiro; Tanaka, Toshihiro; Tsunoda, Tatsuhiko; Deloukas, Panos; Bird, Christine P; Delgado, Marcos; Dermitzakis, Emmanouil T; Gwilliam, Rhian; Hunt, Sarah; Morrison, Jonathan; Powell, Don; Stranger, Barbara E; Whittaker, Pamela; Bentley, David R; Daly, Mark J; de Bakker, Paul I W; Barrett, Jeff; Chretien, Yves R; Maller, Julian; McCarroll, Steve; Patterson, Nick; Pe'er, Itsik; Price, Alkes; Purcell, Shaun; Richter, Daniel J; Sabeti, Pardis; Saxena, Richa; Schaffner, Stephen F; Sham, Pak C; Varilly, Patrick; Altshuler, David; Stein, Lincoln D; Krishnan, Lalitha; Smith, Albert Vernon; Tello-Ruiz, Marcela K; Thorisson, Gudmundur A; Chakravarti, Aravinda; Chen, Peter E; Cutler, David J; Kashuk, Carl S; Lin, Shin; Abecasis, Gonçalo R; Guan, Weihua; Li, Yun; Munro, Heather M; Qin, Zhaohui Steve; Thomas, Daryl J; McVean, Gilean; Auton, Adam; Bottolo, Leonardo; Cardin, Niall; Eyheramendy, Susana; Freeman, Colin; Marchini, Jonathan; Myers, Simon; Spencer, Chris; Stephens, Matthew; Donnelly, Peter; Cardon, Lon R; Clarke, Geraldine; Evans, David M; Morris, Andrew P; Weir, Bruce S; Tsunoda, Tatsuhiko; Johnson, Todd A; Mullikin, James C; Sherry, Stephen T; Feolo, Michael; Skol, Andrew; Zhang, Houcan; Zeng, Changqing; Zhao, Hui; Matsuda, Ichiro; Fukushima, Yoshimitsu; Macer, Darryl R; Suda, Eiko; Rotimi, Charles N; Adebamowo, Clement A; Ajayi, Ike; Aniagwu, Toyin; Marshall, Patricia A; Nkwodimmah, Chibuzor; Royal, Charmaine D M; Leppert, Mark F; Dixon, Missy; Peiffer, Andy; Qiu, Renzong; Kent, Alastair; Kato, Kazuto; Niikawa, Norio; Adewole, Isaac F; Knoppers, Bartha M; Foster, Morris W; Clayton, Ellen Wright; Watkin, Jessica; Gibbs, Richard A; Belmont, John W; Muzny, Donna; Nazareth, Lynne; Sodergren, Erica; Weinstock, George M; Wheeler, David A; Yakub, Imtaz; Gabriel, Stacey B; Onofrio, Robert C; Richter, Daniel J; Ziaugra, Liuda; Birren, Bruce W; Daly, Mark J; Altshuler, David; Wilson, Richard K; Fulton, Lucinda L; Rogers, Jane; Burton, John; Carter, Nigel P; Clee, Christopher M; Griffiths, Mark; Jones, Matthew C; McLay, Kirsten; Plumb, Robert W; Ross, Mark T; Sims, Sarah K; Willey, David L; Chen, Zhu; Han, Hua; Kang, Le; Godbout, Martin; Wallenburg, John C; L'Archevêque, Paul; Bellemare, Guy; Saeki, Koji; Wang, Hongguang; An, Daochang; Fu, Hongbo; Li, Qing; Wang, Zhen; Wang, Renwu; Holden, Arthur L; Brooks, Lisa D; McEwen, Jean E; Guyer, Mark S; Wang, Vivian Ota; Peterson, Jane L; Shi, Michael; Spiegel, Jack; Sung, Lawrence M; Zacharia, Lynn F; Collins, Francis S; Kennedy, Karen; Jamieson, Ruth; Stewart, John

    2007-10-18

    With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.

  12. [Intel random number generator-based true random number generator].

    Science.gov (United States)

    Huang, Feng; Shen, Hong

    2004-09-01

    To establish a true random number generator on the basis of certain Intel chips. The random numbers were acquired by programming using Microsoft Visual C++ 6.0 via register reading from the random number generator (RNG) unit of an Intel 815 chipset-based computer with Intel Security Driver (ISD). We tested the generator with 500 random numbers in NIST FIPS 140-1 and X(2) R-Squared test, and the result showed that the random number it generated satisfied the demand of independence and uniform distribution. We also compared the random numbers generated by Intel RNG-based true random number generator and those from the random number table statistically, by using the same amount of 7500 random numbers in the same value domain, which showed that the SD, SE and CV of Intel RNG-based random number generator were less than those of the random number table. The result of u test of two CVs revealed no significant difference between the two methods. Intel RNG-based random number generator can produce high-quality random numbers with good independence and uniform distribution, and solves some problems with random number table in acquisition of the random numbers.

  13. Screening for type 2 diabetes in a high-risk population: study design and feasibility of a population-based randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Klijs Bart

    2012-08-01

    Full Text Available Abstract Background We describe the design and present the results of the first year of a population-based study of screening for type 2 diabetes in individuals at high risk of developing the disease. High risk is defined as having abdominal obesity. Methods Between 2006 and 2007, 79,142 inhabitants of two Dutch municipalities aged 40–74 years were approached to participate in screening. Eligible participants had a self-reported waist circumference of ≥80 cm for women and ≥94 cm for men, and no known pre-existing diabetes. Of the respondents (n = 20,578; response rate 26%, 16,135 were abdominally obese. In total, 10,609 individuals gave written informed consent for participation and were randomized into either the screening (n = 5305 or the control arm (n = 5304. Participants in the screening arm were invited to have their fasting plasma glucose (FPG measured and were referred to their general practitioner (GP if it was ≥6.1 mmol/L. In addition, blood lipids were determined in the screening arm, because abdominal obesity is often associated with cardiovascular risk factors. Participants in both arms received written healthy lifestyle information. Between-group differences were analyzed with Chi-square tests and logistic regression (categorical variables and unpaired t-tests (continuous variables. Results The screening attendance rate was 84.1%. Attending screening was associated with age at randomization (OR = 1.03, 95% CI 1.02-1.04, being married (OR = 1.57, 95% CI 1.33-1.83 and not-smoking currently (OR = 0.52, 95% CI 0.44-0.62. Of the individuals screened, 5.6% had hyperglycemia, and a further 11.6% had an estimated absolute cardiovascular disease risk of 5% or higher, according to the Systematic Coronary Risk Evaluation risk model. These participants were referred to their GP. Conclusions Self-reported home-assessed waist circumference could feasibly detect persons at high risk of hyperglycemia or

  14. Prevalence of Latent Mycobacterium Tuberculosis Infection (LTBI) in Saudi Arabia; Population based survey.

    Science.gov (United States)

    Balkhy, Hanan H; El Beltagy, Kamel; El-Saed, Aiman; Aljasir, Badr; Althaqafi, Abdulhakeem; Alothman, Adel F; Alshalaan, Mohammad; Al-Jahdali, Hamdan

    2017-07-01

    The annual risk of tuberculosis infection (ARTI) data in Saudi Arabia has not been updated since 1993. To estimate the prevalence of latent TB infection (LTBI) and ARTI in a population-based sample in Saudi Arabia using Tuberculin skin test (TST) and QuantiFERON TB Gold in tube (QFT-GIT) test. A population-based cross sectional study was conducted between July 2010 and March 2013. Participants were randomly selected from the population served by the primary healthcare centers of the Ministry of National Guard Health Affairs in Riyadh, Jeddah, Alhassa and Dammam, Saudi Arabia. A total of 1369 participants were included. The overall prevalence of LTBI was similar using TST and QFT-GIT (9.3% and 9.1% respectively, p=0.872) but stratified prevalence rates were variable in all sociodemographic groups except marital status. Additionally, the prevalence rates of LTBI using either test alone showed significant differences by several sociodemographic and behavioral characteristics. The overall ARTI was 0.36% using TST and 0.35% using QFT-GIT. We are reporting much lower estimates for the prevalence of LTBI and the ARTI in a population-based sample in Saudi Arabia relative to the data that have been used for more than two decades. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  15. Comparison of confirmed inactive and randomly selected compounds as negative training examples in support vector machine-based virtual screening.

    Science.gov (United States)

    Heikamp, Kathrin; Bajorath, Jürgen

    2013-07-22

    The choice of negative training data for machine learning is a little explored issue in chemoinformatics. In this study, the influence of alternative sets of negative training data and different background databases on support vector machine (SVM) modeling and virtual screening has been investigated. Target-directed SVM models have been derived on the basis of differently composed training sets containing confirmed inactive molecules or randomly selected database compounds as negative training instances. These models were then applied to search background databases consisting of biological screening data or randomly assembled compounds for available hits. Negative training data were found to systematically influence compound recall in virtual screening. In addition, different background databases had a strong influence on the search results. Our findings also indicated that typical benchmark settings lead to an overestimation of SVM-based virtual screening performance compared to search conditions that are more relevant for practical applications.

  16. Accuracy of genomic selection in biparental populations of flax (Linum usitatissimum L.

    Directory of Open Access Journals (Sweden)

    Frank M. You

    2016-08-01

    Full Text Available Flax is an important economic crop for seed oil and stem fiber. Phenotyping of traits such as seed yield, seed quality, stem fiber yield, and quality characteristics is expensive and time consuming. Genomic selection (GS refers to a breeding approach aimed at selecting preferred individuals based on genomic estimated breeding values predicted by a statistical model based on the relationship between phenotypes and genome-wide genetic markers. We evaluated the prediction accuracy of GS (rMP and the efficiency of GS relative to phenotypic selection (RE for three GS models: ridge regression best linear unbiased prediction (RR-BLUP, Bayesian LASSO (BL, and Bayesian ridge regression (BRR, for seed yield, oil content, iodine value, linoleic, and linolenic acid content with a full and a common set of genome-wide simple sequence repeat markers in each of three biparental populations. The three GS models generated similar rMP and RE, while BRR displayed a higher coefficient of determination (R2 of the fitted models than did RR-BLUP or BL. The mean rMP and RE varied for traits with different heritabilities and was affected by the genetic variation of the traits in the populations. GS for seed yield generated a mean RE of 1.52 across populations and marker sets, a value significantly superior to that for direct phenotypic selection. Our empirical results provide the first validation of GS in flax and demonstrate that GS could increase genetic gain per unit time for linseed breeding. Further studies for selection of training populations and markers are warranted.

  17. Adding cows to the reference population makes a small dairy population competitive

    DEFF Research Database (Denmark)

    Thomasen, Jørn Rind; Sørensen, Anders Christian; Lund, Mogens Sandø

    2014-01-01

    of progeny-tested bulls per year was tested at 6 levels: 15, 40, 60, 100, 250, and 500; and (2) each year, 2,000 firstlactation cows were randomly selected from the cow population for genotyping or, alternatively, an additional 2,000 first-lactation cows were randomly selected and typed in the first 2 yr...

  18. Phenotypic selection in natural populations: what limits directional selection?

    Science.gov (United States)

    Kingsolver, Joel G; Diamond, Sarah E

    2011-03-01

    Studies of phenotypic selection document directional selection in many natural populations. What factors reduce total directional selection and the cumulative evolutionary responses to selection? We combine two data sets for phenotypic selection, representing more than 4,600 distinct estimates of selection from 143 studies, to evaluate the potential roles of fitness trade-offs, indirect (correlated) selection, temporally varying selection, and stabilizing selection for reducing net directional selection and cumulative responses to selection. We detected little evidence that trade-offs among different fitness components reduced total directional selection in most study systems. Comparisons of selection gradients and selection differentials suggest that correlated selection frequently reduced total selection on size but not on other types of traits. The direction of selection on a trait often changes over time in many temporally replicated studies, but these fluctuations have limited impact in reducing cumulative directional selection in most study systems. Analyses of quadratic selection gradients indicated stabilizing selection on body size in at least some studies but provided little evidence that stabilizing selection is more common than disruptive selection for most traits or study systems. Our analyses provide little evidence that fitness trade-offs, correlated selection, or stabilizing selection strongly constrains the directional selection reported for most quantitative traits.

  19. Evolution of a Fluctuating Population in a Randomly Switching Environment.

    Science.gov (United States)

    Wienand, Karl; Frey, Erwin; Mobilia, Mauro

    2017-10-13

    Environment plays a fundamental role in the competition for resources, and hence in the evolution of populations. Here, we study a well-mixed, finite population consisting of two strains competing for the limited resources provided by an environment that randomly switches between states of abundance and scarcity. Assuming that one strain grows slightly faster than the other, we consider two scenarios-one of pure resource competition, and one in which one strain provides a public good-and investigate how environmental randomness (external noise) coupled to demographic (internal) noise determines the population's fixation properties and size distribution. By analytical means and simulations, we show that these coupled sources of noise can significantly enhance the fixation probability of the slower-growing species. We also show that the population size distribution can be unimodal, bimodal, or multimodal and undergoes noise-induced transitions between these regimes when the rate of switching matches the population's growth rate.

  20. Population Genetics and Natural Selection in Rheumatic Disease.

    Science.gov (United States)

    Ramos, Paula S

    2017-08-01

    Human genetic diversity is the result of population genetic forces. This genetic variation influences disease risk and contributes to health disparities. Natural selection is an important influence on human genetic variation. Because immune and inflammatory function genes are enriched for signals of positive selection, the prevalence of rheumatic disease-risk alleles seen in different populations is partially the result of differing selective pressures (eg, due to pathogens). This review summarizes the genetic regions associated with susceptibility to different rheumatic diseases and concomitant evidence for natural selection, including known agents of selection exerting selective pressure in these regions. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Population-centered Risk- and Evidence-based Dental Interprofessional Care Team (PREDICT): study protocol for a randomized controlled trial.

    Science.gov (United States)

    Cunha-Cruz, Joana; Milgrom, Peter; Shirtcliff, R Michael; Bailit, Howard L; Huebner, Colleen E; Conrad, Douglas; Ludwig, Sharity; Mitchell, Melissa; Dysert, Jeanne; Allen, Gary; Scott, JoAnna; Mancl, Lloyd

    2015-06-20

    To improve the oral health of low-income children, innovations in dental delivery systems are needed, including community-based care, the use of expanded duty auxiliary dental personnel, capitation payments, and global budgets. This paper describes the protocol for PREDICT (Population-centered Risk- and Evidence-based Dental Interprofessional Care Team), an evaluation project to test the effectiveness of new delivery and payment systems for improving dental care and oral health. This is a parallel-group cluster randomized controlled trial. Fourteen rural Oregon counties with a publicly insured (Medicaid) population of 82,000 children (0 to 21 years old) and pregnant women served by a managed dental care organization are randomized into test and control counties. In the test intervention (PREDICT), allied dental personnel provide screening and preventive services in community settings and case managers serve as patient navigators to arrange referrals of children who need dentist services. The delivery system intervention is paired with a compensation system for high performance (pay-for-performance) with efficient performance monitoring. PREDICT focuses on the following: 1) identifying eligible children and gaining caregiver consent for services in community settings (for example, schools); 2) providing risk-based preventive and caries stabilization services efficiently at these settings; 3) providing curative care in dental clinics; and 4) incentivizing local delivery teams to meet performance benchmarks. In the control intervention, care is delivered in dental offices without performance incentives. The primary outcome is the prevalence of untreated dental caries. Other outcomes are related to process, structure and cost. Data are collected through patient and staff surveys, clinical examinations, and the review of health and administrative records. If effective, PREDICT is expected to substantially reduce disparities in dental care and oral health. PREDICT can be

  2. Brain Tumor Segmentation Based on Random Forest

    Directory of Open Access Journals (Sweden)

    László Lefkovits

    2016-09-01

    Full Text Available In this article we present a discriminative model for tumor detection from multimodal MR images. The main part of the model is built around the random forest (RF classifier. We created an optimization algorithm able to select the important features for reducing the dimensionality of data. This method is also used to find out the training parameters used in the learning phase. The algorithm is based on random feature properties for evaluating the importance of the variable, the evolution of learning errors and the proximities between instances. The detection performances obtained have been compared with the most recent systems, offering similar results.

  3. Phenology of Scramble Polygyny in a Wild Population of Chrysolemid Beetles: The Opportunity for and the Strength of Sexual Selection

    Science.gov (United States)

    Baena, Martha Lucía; Macías-Ordóñez, Rogelio

    2012-01-01

    Recent debate has highlighted the importance of estimating both the strength of sexual selection on phenotypic traits, and the opportunity for sexual selection. We describe seasonal fluctuations in mating dynamics of Leptinotarsa undecimlineata (Coleoptera: Chrysomelidae). We compared several estimates of the opportunity for, and the strength of, sexual selection and male precopulatory competition over the reproductive season. First, using a null model, we suggest that the ratio between observed values of the opportunity for sexual selections and their expected value under random mating results in unbiased estimates of the actual nonrandom mating behavior of the population. Second, we found that estimates for the whole reproductive season often misrepresent the actual value at any given time period. Third, mating differentials on male size and mobility, frequency of male fighting and three estimates of the opportunity for sexual selection provide contrasting but complementary information. More intense sexual selection associated to male mobility, but not to male size, was observed in periods with high opportunity for sexual selection and high frequency of male fights. Fourth, based on parameters of spatial and temporal aggregation of female receptivity, we describe the mating system of L. undecimlineata as a scramble mating polygyny in which the opportunity for sexual selection varies widely throughout the season, but the strength of sexual selection on male size remains fairly weak, while male mobility inversely covaries with mating success. We suggest that different estimates for the opportunity for, and intensity of, sexual selection should be applied in order to discriminate how different behavioral and demographic factors shape the reproductive dynamic of populations. PMID:22761675

  4. Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences.

    Science.gov (United States)

    Warris, Sven; Boymans, Sander; Muiser, Iwe; Noback, Michiel; Krijnen, Wim; Nap, Jan-Peter

    2014-01-13

    Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge. Statistical analyses of pre-miRNA sequences indicated that their 2D structure tends to have a minimal free energy (MFE) significantly lower than MFE values of equivalently randomized sequences with the same nucleotide composition, in contrast to other classes of non-coding RNA. The computation of many MFEs is, however, too intensive to allow for genome-wide screenings. Using a local grid infrastructure, MFE distributions of random sequences were pre-calculated on a large scale. These distributions follow a normal distribution and can be used to determine the MFE distribution for any given sequence composition by interpolation. It allows on-the-fly calculation of the normal distribution for any candidate sequence composition. The speedup achieved makes genome-wide screening with this characteristic of a pre-miRNA sequence practical. Although this particular property alone will not be able to distinguish miRNAs from other sequences sufficiently discriminative, the MFE-based P-value should be added to the parameters of choice to be included in the selection of potential miRNA candidates for experimental verification.

  5. Subset selection for an epsilon-best population : efficiency results

    NARCIS (Netherlands)

    Laan, van der P.

    1991-01-01

    An almost best or an \\epsilon-best population is defined as a population with location parameter on a distance not larger than \\epsilon (\\geq 0) from the best population (with largest value of the location parameter). For the subset selection tables with the relative efficiency of selecting an

  6. Web based health surveys: Using a Two Step Heckman model to examine their potential for population health analysis.

    Science.gov (United States)

    Morrissey, Karyn; Kinderman, Peter; Pontin, Eleanor; Tai, Sara; Schwannauer, Mathias

    2016-08-01

    In June 2011 the BBC Lab UK carried out a web-based survey on the causes of mental distress. The 'Stress Test' was launched on 'All in the Mind' a BBC Radio 4 programme and the test's URL was publicised on radio and TV broadcasts, and made available via BBC web pages and social media. Given the large amount of data created, over 32,800 participants, with corresponding diagnosis, demographic and socioeconomic characteristics; the dataset are potentially an important source of data for population based research on depression and anxiety. However, as respondents self-selected to participate in the online survey, the survey may comprise a non-random sample. It may be only individuals that listen to BBC Radio 4 and/or use their website that participated in the survey. In this instance using the Stress Test data for wider population based research may create sample selection bias. Focusing on the depression component of the Stress Test, this paper presents an easy-to-use method, the Two Step Probit Selection Model, to detect and statistically correct selection bias in the Stress Test. Using a Two Step Probit Selection Model; this paper did not find a statistically significant selection on unobserved factors for participants of the Stress Test. That is, survey participants who accessed and completed an online survey are not systematically different from non-participants on the variables of substantive interest. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Selection processes in a citrus hybrid population using RAPD markers

    Directory of Open Access Journals (Sweden)

    Oliveira Roberto Pedroso de

    2003-01-01

    Full Text Available The objective of this work was to evaluate the processes of selection in a citrus hybrid population using segregation analysis of RAPD markers. The segregation of 123 RAPD markers between 'Cravo' mandarin (Citrus reticulata Blanco and 'Pêra' sweet orange (C. sinensis (L. Osbeck was analysed in a F1 progeny of 94 hybrids. Genetic composition, diversity, heterozygosity, differences in chromosomal structure and the presence of deleterious recessive genes are discussed based on the segregation ratios obtained. A high percentage of markers had a skeweness of the 1:1 expected segregation ratio in the F1 population. Many markers showed a 3:1 segregation ratio in both varieties and 1:3 in 'Pêra' sweet orange, probably due to directional selection processes. The distribution analysis of the frequencies of the segregant markers in a hybrid population is a simple method which allows a better understanding of the genetics of citrus group.

  8. Selective population rate coding: a possible computational role of gamma oscillations in selective attention.

    Science.gov (United States)

    Masuda, Naoki

    2009-12-01

    Selective attention is often accompanied by gamma oscillations in local field potentials and spike field coherence in brain areas related to visual, motor, and cognitive information processing. Gamma oscillations are implicated to play an important role in, for example, visual tasks including object search, shape perception, and speed detection. However, the mechanism by which gamma oscillations enhance cognitive and behavioral performance of attentive subjects is still elusive. Using feedforward fan-in networks composed of spiking neurons, we examine a possible role for gamma oscillations in selective attention and population rate coding of external stimuli. We implement the concept proposed by Fries ( 2005 ) that under dynamic stimuli, neural populations effectively communicate with each other only when there is a good phase relationship among associated gamma oscillations. We show that the downstream neural population selects a specific dynamic stimulus received by an upstream population and represents it by population rate coding. The encoded stimulus is the one for which gamma rhythm in the corresponding upstream population is resonant with the downstream gamma rhythm. The proposed role for gamma oscillations in stimulus selection is to enable top-down control, a neural version of time division multiple access used in communication engineering.

  9. Comorbidity profile of poliomyelitis survivors in a Chinese population: a population-based study.

    Science.gov (United States)

    Kang, Jiunn-Horng; Lin, Herng-Ching

    2011-06-01

    Previous reports of comorbid conditions in poliomyelitis survivors mainly focused on some disease categories, such as respiratory diseases, gastrointestinal diseases, psychiatric diseases, neurological diseases and cancer. Data regarding a wide spectrum of medical comorbidities in patients with poliomyelitis is still sparse. This study aimed to investigate and profile the wide range of comorbidities among the survivors of paralytic poliomyelitis in a Chinese population. In total, 2,032 paralytic poliomyelitis patients were selected as the study group and the comparison group consisted of 10,160 randomly selected enrollees. The comorbidities for analysis were based on a modified version of the Elixhauser Comorbidity Index. Conditional logistic regression analyses were computed to investigate the risk of comorbidities for these two groups. As compared to controls, patients with paralytic poliomyelitis had significantly higher prevalence of hypertension, ischemic heart disease, hyperlipidemia, congestive heart failure, cardiac arrhythmias, peripheral vascular disorder, stroke, paralysis, migraines, Parkinson's disease, rheumatoid arthritis, ankylosing spondylitis, pulmonary circulation disorders, chronic pulmonary disease, liver disease, peptic ulcers, hepatitis B or C, deficiency anemias, depression, and lymphoma. Most of the differences are of clinical interest, ORs often being between 2 and 3. No significant difference between poliomyelitis patients and controls was observed in the prevalence of SLE, tuberculosis, alcohol abuse and drug abuse. Our findings demonstrate that survivors of paralytic poliomyelitis in Taiwan are at higher risk of having multiple medical comorbidities although some potential confounding factors including educational level, marital status, obesity and physical activity are not available in our database. The pattern is generally consistent with previous observations from Western populations. Nevertheless, we found several novel associations

  10. Informing resource-poor populations and the delivery of entitled health and social services in rural India: a cluster randomized controlled trial.

    Science.gov (United States)

    Pandey, Priyanka; Sehgal, Ashwini R; Riboud, Michelle; Levine, David; Goyal, Madhav

    2007-10-24

    A lack of awareness about entitled health and social services may contribute to poor delivery of such services in developing countries, especially among individuals of low socioeconomic status. To determine the impact of informing resource-poor rural populations about entitled services. Community-based, cluster randomized controlled trial conducted from May 2004 to May 2005 in 105 randomly selected village clusters in Uttar Pradesh state in India. Households (548 intervention and 497 control) were selected by a systematic sampling design, including both low-caste and mid- to high-caste households. Four to 6 public meetings were held in each intervention village cluster to disseminate information on entitled health services, entitled education services, and village governance requirements. No intervention took place in control village clusters. Visits by nurse midwife; prenatal examinations, tetanus vaccinations, and prenatal supplements received by pregnant women; vaccinations received by infants; excess school fees charged; occurrence of village council meetings; and development work in villages. At baseline, there were no significant differences in self-reported delivery of health and social services. After 1 year, intervention villagers reported better delivery of several services compared with control villagers: in a multivariate analysis, 30% more prenatal examinations (95% confidence interval [CI], 17%-43%; P India about entitled services enhanced the delivery of health and social services among both low- and mid- to high-caste households. Interventions that emphasize educating resource-poor populations about entitled services may improve the delivery of such services. clinicaltrials.gov Identifier: NCT00421291.

  11. A random forest classifier for detecting rare variants in NGS data from viral populations

    Directory of Open Access Journals (Sweden)

    Raunaq Malhotra

    Full Text Available We propose a random forest classifier for detecting rare variants from sequencing errors in Next Generation Sequencing (NGS data from viral populations. The method utilizes counts of varying length of k-mers from the reads of a viral population to train a Random forest classifier, called MultiRes, that classifies k-mers as erroneous or rare variants. Our algorithm is rooted in concepts from signal processing and uses a frame-based representation of k-mers. Frames are sets of non-orthogonal basis functions that were traditionally used in signal processing for noise removal. We define discrete spatial signals for genomes and sequenced reads, and show that k-mers of a given size constitute a frame.We evaluate MultiRes on simulated and real viral population datasets, which consist of many low frequency variants, and compare it to the error detection methods used in correction tools known in the literature. MultiRes has 4 to 500 times less false positives k-mer predictions compared to other methods, essential for accurate estimation of viral population diversity and their de-novo assembly. It has high recall of the true k-mers, comparable to other error correction methods. MultiRes also has greater than 95% recall for detecting single nucleotide polymorphisms (SNPs and fewer false positive SNPs, while detecting higher number of rare variants compared to other variant calling methods for viral populations. The software is available freely from the GitHub link https://github.com/raunaq-m/MultiRes. Keywords: Sequencing error detection, Reference free methods, Next-generation sequencing, Viral populations, Multi-resolution frames, Random forest classifier

  12. Prevalence of at-risk genotypes for genotoxic effects decreases with age in a randomly selected population in Flanders: a cross sectional study

    Directory of Open Access Journals (Sweden)

    van Delft Joost HM

    2011-10-01

    Full Text Available Abstract Background We hypothesized that in Flanders (Belgium, the prevalence of at-risk genotypes for genotoxic effects decreases with age due to morbidity and mortality resulting from chronic diseases. Rather than polymorphisms in single genes, the interaction of multiple genetic polymorphisms in low penetrance genes involved in genotoxic effects might be of relevance. Methods Genotyping was performed on 399 randomly selected adults (aged 50-65 and on 442 randomly selected adolescents. Based on their involvement in processes relevant to genotoxicity, 28 low penetrance polymorphisms affecting the phenotype in 19 genes were selected (xenobiotic metabolism, oxidative stress defense and DNA repair, respectively 13, 6 and 9 polymorphisms. Polymorphisms which, based on available literature, could not clearly be categorized a priori as leading to an 'increased risk' or a 'protective effect' were excluded. Results The mean number of risk alleles for all investigated polymorphisms was found to be lower in the 'elderly' (17.0 ± 2.9 than the 'adolescent' (17.6 ± 3.1 subpopulation (P = 0.002. These results were not affected by gender nor smoking. The prevalence of a high (> 17 = median number of risk alleles was less frequent in the 'elderly' (40.6% than the 'adolescent' (51.4% subpopulation (P = 0.002. In particular for phase II enzymes, the mean number of risk alleles was lower in the 'elderly' (4.3 ± 1.6 than the 'adolescent' age group (4.8 ± 1.9 P 4 = median number of risk alleles was less frequent in the 'elderly' (41.3% than the adolescent subpopulation (56.3%, P 8 = median number of risk alleles for DNA repair enzyme-coding genes was lower in the 'elderly' (37,3% than the 'adolescent' subpopulation (45.6%, P = 0.017. Conclusions These observations are consistent with the hypothesis that, in Flanders, the prevalence of at-risk alleles in genes involved in genotoxic effects decreases with age, suggesting that persons carrying a higher number of

  13. Effectiveness of a two-step population-based osteoporosis screening program using FRAX: the randomized Risk-stratified Osteoporosis Strategy Evaluation (ROSE) study.

    Science.gov (United States)

    Rubin, K H; Rothmann, M J; Holmberg, T; Høiberg, M; Möller, S; Barkmann, R; Glüer, C C; Hermann, A P; Bech, M; Gram, J; Brixen, K

    2018-03-01

    The Risk-stratified Osteoporosis Strategy Evaluation (ROSE) study investigated the effectiveness of a two-step screening program for osteoporosis in women. We found no overall reduction in fractures from systematic screening compared to the current case-finding strategy. The group of moderate- to high-risk women, who accepted the invitation to DXA, seemed to benefit from the program. The purpose of the ROSE study was to investigate the effectiveness of a two-step population-based osteoporosis screening program using the Fracture Risk Assessment Tool (FRAX) derived from a self-administered questionnaire to select women for DXA scan. After the scanning, standard osteoporosis management according to Danish national guidelines was followed. Participants were randomized to either screening or control group, and randomization was stratified according to age and area of residence. Inclusion took place from February 2010 to November 2011. Participants received a self-administered questionnaire, and women in the screening group with a FRAX score ≥ 15% (major osteoporotic fractures) were invited to a DXA scan. Primary outcome was incident clinical fractures. Intention-to-treat analysis and two per-protocol analyses were performed. A total of 3416 fractures were observed during a median follow-up of 5 years. No significant differences were found in the intention-to-treat analyses with 34,229 women included aged 65-80 years. The per-protocol analyses showed a risk reduction in the group that underwent DXA scanning compared to women in the control group with a FRAX ≥ 15%, in regard to major osteoporotic fractures, hip fractures, and all fractures. The risk reduction was most pronounced for hip fractures (adjusted SHR 0.741, p = 0.007). Compared to an office-based case-finding strategy, the two-step systematic screening strategy had no overall effect on fracture incidence. The two-step strategy seemed, however, to be beneficial in the group of women who were

  14. Organic Ferroelectric-Based 1T1T Random Access Memory Cell Employing a Common Dielectric Layer Overcoming the Half-Selection Problem.

    Science.gov (United States)

    Zhao, Qiang; Wang, Hanlin; Ni, Zhenjie; Liu, Jie; Zhen, Yonggang; Zhang, Xiaotao; Jiang, Lang; Li, Rongjin; Dong, Huanli; Hu, Wenping

    2017-09-01

    Organic electronics based on poly(vinylidenefluoride/trifluoroethylene) (P(VDF-TrFE)) dielectric is facing great challenges in flexible circuits. As one indispensable part of integrated circuits, there is an urgent demand for low-cost and easy-fabrication nonvolatile memory devices. A breakthrough is made on a novel ferroelectric random access memory cell (1T1T FeRAM cell) consisting of one selection transistor and one ferroelectric memory transistor in order to overcome the half-selection problem. Unlike complicated manufacturing using multiple dielectrics, this system simplifies 1T1T FeRAM cell fabrication using one common dielectric. To achieve this goal, a strategy for semiconductor/insulator (S/I) interface modulation is put forward and applied to nonhysteretic selection transistors with high performances for driving or addressing purposes. As a result, high hole mobility of 3.81 cm 2 V -1 s -1 (average) for 2,6-diphenylanthracene (DPA) and electron mobility of 0.124 cm 2 V -1 s -1 (average) for N,N'-1H,1H-perfluorobutyl dicyanoperylenecarboxydiimide (PDI-FCN 2 ) are obtained in selection transistors. In this work, we demonstrate this technology's potential for organic ferroelectric-based pixelated memory module fabrication. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. High-Tg Polynorbornene-Based Block and Random Copolymers for Butanol Pervaporation Membranes

    Science.gov (United States)

    Register, Richard A.; Kim, Dong-Gyun; Takigawa, Tamami; Kashino, Tomomasa; Burtovyy, Oleksandr; Bell, Andrew

    Vinyl addition polymers of substituted norbornene (NB) monomers possess desirably high glass transition temperatures (Tg); however, until very recently, the lack of an applicable living polymerization chemistry has precluded the synthesis of such polymers with controlled architecture, or copolymers with controlled sequence distribution. We have recently synthesized block and random copolymers of NB monomers bearing hydroxyhexafluoroisopropyl and n-butyl substituents (HFANB and BuNB) via living vinyl addition polymerization with Pd-based catalysts. Both series of polymers were cast into the selective skin layers of thin film composite (TFC) membranes, and these organophilic membranes investigated for the isolation of n-butanol from dilute aqueous solution (model fermentation broth) via pervaporation. The block copolymers show well-defined microphase-separated morphologies, both in bulk and as the selective skin layers on TFC membranes, while the random copolymers are homogeneous. Both block and random vinyl addition copolymers are effective as n-butanol pervaporation membranes, with the block copolymers showing a better flux-selectivity balance. While polyHFANB has much higher permeability and n-butanol selectivity than polyBuNB, incorporating BuNB units into the polymer (in either a block or random sequence) limits the swelling of the polyHFANB and thereby improves the n-butanol pervaporation selectivity.

  16. A probabilistic method for testing and estimating selection differences between populations.

    Science.gov (United States)

    He, Yungang; Wang, Minxian; Huang, Xin; Li, Ran; Xu, Hongyang; Xu, Shuhua; Jin, Li

    2015-12-01

    Human populations around the world encounter various environmental challenges and, consequently, develop genetic adaptations to different selection forces. Identifying the differences in natural selection between populations is critical for understanding the roles of specific genetic variants in evolutionary adaptation. Although numerous methods have been developed to detect genetic loci under recent directional selection, a probabilistic solution for testing and quantifying selection differences between populations is lacking. Here we report the development of a probabilistic method for testing and estimating selection differences between populations. By use of a probabilistic model of genetic drift and selection, we showed that logarithm odds ratios of allele frequencies provide estimates of the differences in selection coefficients between populations. The estimates approximate a normal distribution, and variance can be estimated using genome-wide variants. This allows us to quantify differences in selection coefficients and to determine the confidence intervals of the estimate. Our work also revealed the link between genetic association testing and hypothesis testing of selection differences. It therefore supplies a solution for hypothesis testing of selection differences. This method was applied to a genome-wide data analysis of Han and Tibetan populations. The results confirmed that both the EPAS1 and EGLN1 genes are under statistically different selection in Han and Tibetan populations. We further estimated differences in the selection coefficients for genetic variants involved in melanin formation and determined their confidence intervals between continental population groups. Application of the method to empirical data demonstrated the outstanding capability of this novel approach for testing and quantifying differences in natural selection. © 2015 He et al.; Published by Cold Spring Harbor Laboratory Press.

  17. An alternative procedure for estimating the population mean in simple random sampling

    Directory of Open Access Journals (Sweden)

    Housila P. Singh

    2012-03-01

    Full Text Available This paper deals with the problem of estimating the finite population mean using auxiliary information in simple random sampling. Firstly we have suggested a correction to the mean squared error of the estimator proposed by Gupta and Shabbir [On improvement in estimating the population mean in simple random sampling. Jour. Appl. Statist. 35(5 (2008, pp. 559-566]. Later we have proposed a ratio type estimator and its properties are studied in simple random sampling. Numerically we have shown that the proposed class of estimators is more efficient than different known estimators including Gupta and Shabbir (2008 estimator.

  18. Distributional and efficiency results for subset selection

    NARCIS (Netherlands)

    Laan, van der P.

    1996-01-01

    Assume k (??k \\geq 2) populations are given. The associated independent random variables have continuous distribution functions with an unknown location parameter. The statistical selec??tion goal is to select a non??empty subset which contains the best population,?? that is the pop??ulation with

  19. Does daily vitamin D 800 IU and calcium 1000 mg supplementation decrease the risk of falling in ambulatory women aged 65-71 years? A 3-year randomized population-based trial (OSTPRE-FPS).

    Science.gov (United States)

    Kärkkäinen, Matti K; Tuppurainen, Marjo; Salovaara, Kari; Sandini, Lorenzo; Rikkonen, Toni; Sirola, Joonas; Honkanen, Risto; Arokoski, Jari; Alhava, Esko; Kröger, Heikki

    2010-04-01

    The hypothesis was that the calcium and vitamin D supplementation prevents falls at the population level. The OSTPRE-FPS was a randomized population-based open-trial with 3-year follow-up. The supplementation group (n=1566) received daily cholecalciferol 800IU+calcium carbonate 1000mg, while the control group (n=1573) received no supplementation or placebo. A randomly selected subsample of 593 subjects underwent a detailed measurement program including serum 25(OH)D measurements. The occurrence of falls was the primary outcome of the study. The participants in the subsample were telephoned at 4 months intervals and the rest of the trial population was interviewed by phone once a year. In the entire trial population (ETP), there were 812 women with 1832 falls in the intervention group and 833 women with 1944 falls in the control group (risk ratio was 0.98, 95% CI 0.92-1.05, P=0.160). The supplementation was not associated with single or multiple falls in the ETP. However, in the subsample, multiple fall incidence decreased by 30% (odds ratio (OR) 0.70, 95% CI 0.50-0.97, P=0.034) in the supplementation group. Further, the supplementation decreased the incidence of multiple falls requiring medical attention (OR 0.72, 95% CI 0.53-0.97, P=0.031) in the ETP. The mean compliance in the entire trial population was 78% and in the subsample 79%. Overall, the primary analysis showed no association between calcium and vitamin D supplementation and risk of falls. However, the results of a post hoc analysis suggested that there was a decreased risk of multiple falls requiring medical attention: this finding requires confirmation. Copyright 2009 Elsevier Ireland Ltd. All rights reserved.

  20. Long-term effective population sizes, temporal stability of genetic composition and potential for local adaptation in anadromous brown trout ( Salmo trutta ) populations

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Ruzzante, D.E.; Eg Nielsen, Einar

    2002-01-01

    temporal samples from the same populations than among samples from different populations. Estimates of N-e, using a likelihood-based implementation of the temporal method, revealed N-e greater than or equal to 500 in two of three populations for which we have historical data. A third population in a small...... (3 km) river showed Ne greater than or equal to 300. Assuming a stepping-stone model of gene flow we considered the relative roles of gene flow, random genetic drift and selection to assess the possibilities for local adaptation. The requirements for local adaptation were fulfilled, but only...... adaptations resulting from strong selection were expected to occur at the level of individual populations. Adaptations resulting from weak selection were more likely to occur on a regional basis, i.e. encompassing several populations. N-e appears to have declined recently in at least one of the studied...

  1. Population based estimates of non-fatal injuries in the capital of Iran.

    Science.gov (United States)

    Saadat, Soheil; Mafi, Mostafa; Sharif-Alhoseini, Mahdi

    2011-07-31

    Fatal injuries are at the top of the injury pyramid; however, non-fatal injuries are quite common and impose huge medical expenses on the population. Relying on hospital data will underestimate the incidence of non-fatal injuries. The aim of this study was to estimate the annual incidence and out of pocket medical expenses of all injuries in urban population of Tehran (the capital city of Iran). Using the cluster random sampling approach, a household survey of residents of greater Tehran was performed on April 2008. At randomly selected residential locations, interviewers asked one adult person to report all injuries which have occurred during the past year for all household members, as well as the type of injury, place of occurrence, the activity, cause of accidents resulting in injuries, the amount of out of pocket medical expenses for injury, and whether they referred to hospital. This study included 2,450 households residing in Tehran during 2007-8. The annual incidence of all injuries was 188.7 (180.7-196.9), significant injuries needing any medical care was 68.8 (63.7-74.2), fractures was 19.3 (16.6 - 22.4), and injuries resulted in hospitalization was 16.7 (14.2 - 19.6) per 1000 population. The annual incidence of fatal injuries was 33 (7-96) per 100,000 Population. In children aged 15 or less, the annual incidence of all injuries was 137.2 (120.0 - 155.9), significant injuries needing any medical care was 64.2 (52.2 - 78.0), fractures was 21.8 (15.0 - 30.7), and injuries resulted in hospitalization was 6.8 (3.3 - 12.5) per 1000 population. The mean out of pocket medical expense for injuries was 19.9 USD. This population based study showed that the real incidence of non-fatal injuries in the capital of Iran is more than the formal hospital-based estimates. These injuries impose non trivial medical and indirect cost on the community. The out of pocket medical expense of non-fatal injuries to Tehran population is estimated as 27 million USD per year. Effective

  2. Phenotypic selection varies with pollination intensity across populations of Sabatia angularis.

    Science.gov (United States)

    Emel, Sarah L; Franks, Steven J; Spigler, Rachel B

    2017-07-01

    Pollinators are considered primary selective agents acting on plant traits, and thus variation in the strength of the plant-pollinator interaction might drive variation in the opportunity for selection and selection intensity across plant populations. Here, we examine whether these critical evolutionary parameters covary with pollination intensity across wild populations of the biennial Sabatia angularis. We quantified pollination intensity in each of nine S. angularis populations as mean stigmatic pollen load per population. For female fitness and three components, fruit number, fruit set (proportion of flowers setting fruit) and number of seeds per fruit, we evaluated whether the opportunity for selection varied with pollination intensity. We used phenotypic selection analyses to test for interactions between pollination intensity and selection gradients for five floral traits, including flowering phenology. The opportunity for selection via fruit set and seeds per fruit declined significantly with increasing pollen receipt, as expected. We demonstrated significant directional selection on multiple traits across populations. We also found that selection intensity for all traits depended on pollination intensity. Consistent with general theory about the relationship between biotic interaction strength and the intensity of selection, our study suggests that variation in pollination intensity drives variation in selection across S. angularis populations. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  3. Happy@Work: protocol for a web-based randomized controlled trial to improve mental well-being among an Asian working population.

    Science.gov (United States)

    Yuan, Qi; Liu, Su; Tang, Szehang; Zhang, Dexing

    2014-07-04

    Mental health issues pose a serious concern in the workplace for the huge productivity loss and financial burden associated with it. Unlike the traditional 'fixing-what-is-wrong' approach, positive psychology offers a less-stigmatized way to promote mental health. Psychological capital, a concept originated from positive psychology, has been proven effective in improving mental well-being and work performance. However, little evidence exists for its implementation among Asian working population or its cost-benefit for organizations adopting such promotion strategy. The current study is designed to assess the protective effects of a web-based psychology capital intervention among Hong Kong working population on individuals' mental health and work performance, as well as organizations' return-on-investment. A two-arm randomized controlled trial design will be adopted. Eligible working adults will be randomly allocated to either the intervention group or the waiting-list control group, with 177 participants in each arm. The intervention, which consists of four web-based training sessions, each targeting one of the psychological capital components (hope, efficacy, optimism and resilience), will be implemented over a 4-week period. On-line surveys will assess the participants in each group at baseline, intervention completion, 1 and 3 months after the completion. The primary outcome is individuals' psychological capital level; secondary outcomes include individuals' well-being, depressive symptoms, work engagement and productivity. Return-on-investment will be calculated from the employers' perspective based on productivity gain, savings in medical expenditure, as well as operation and time costs. Analysis will follow the intention-to-treat principle. This is the first experimental study that explores the applicability of psychological capital development among Asian population. Through investigating changes in individuals' work productivity from absenteeism and

  4. Influence of population selection on the 99th percentile reference value for cardiac troponin assays.

    Science.gov (United States)

    Collinson, Paul O; Heung, Yen Ming; Gaze, David; Boa, Frances; Senior, Roxy; Christenson, Robert; Apple, Fred S

    2012-01-01

    We sought to determine the effect of patient selection on the 99th reference percentile of 2 sensitive and 1 high-sensitivity (hs) cardiac troponin assays in a well-defined reference population. Individuals>45 years old were randomly selected from 7 representative local community practices. Detailed information regarding the participants was collected via questionnaires. The healthy reference population was defined as individuals who had no history of vascular disease, hypertension, or heavy alcohol intake; were not receiving cardiac medication; and had blood pressure60 mL·min(-1)·(1.73 m2)(-1), and normal cardiac function according to results of echocardiography. Samples were stored at -70 °C until analysis for cardiac troponin I (cTnI) and cardiac troponin T (cTnT) and N-terminal pro-B-type natriuretic peptide. Application of progressively more stringent population selection strategies to the initial baseline population of 545 participants until the only individuals who remained were completely healthy according to the study criteria reduced the number of outliers seen and led to a progressive decrease in the 99th-percentile value obtained for the Roche hs-cTnT assay and the sensitive Beckman cTnI assay but not for the sensitive Siemens Ultra cTnI assay. Furthermore, a sex difference found in the baseline population for the hs-cTnT (P=0.0018) and Beckman cTnI assays (Pstrategy significantly influenced the 99th percentile reference values determined for troponin assays and the observed sex differences in troponin concentrations.

  5. Code-specific learning rules improve action selection by populations of spiking neurons.

    Science.gov (United States)

    Friedrich, Johannes; Urbanczik, Robert; Senn, Walter

    2014-08-01

    Population coding is widely regarded as a key mechanism for achieving reliable behavioral decisions. We previously introduced reinforcement learning for population-based decision making by spiking neurons. Here we generalize population reinforcement learning to spike-based plasticity rules that take account of the postsynaptic neural code. We consider spike/no-spike, spike count and spike latency codes. The multi-valued and continuous-valued features in the postsynaptic code allow for a generalization of binary decision making to multi-valued decision making and continuous-valued action selection. We show that code-specific learning rules speed up learning both for the discrete classification and the continuous regression tasks. The suggested learning rules also speed up with increasing population size as opposed to standard reinforcement learning rules. Continuous action selection is further shown to explain realistic learning speeds in the Morris water maze. Finally, we introduce the concept of action perturbation as opposed to the classical weight- or node-perturbation as an exploration mechanism underlying reinforcement learning. Exploration in the action space greatly increases the speed of learning as compared to exploration in the neuron or weight space.

  6. Population structure, migration, and diversifying selection in the Netherlands

    Science.gov (United States)

    Abdellaoui, Abdel; Hottenga, Jouke-Jan; Knijff, Peter de; Nivard, Michel G; Xiao, Xiangjun; Scheet, Paul; Brooks, Andrew; Ehli, Erik A; Hu, Yueshan; Davies, Gareth E; Hudziak, James J; Sullivan, Patrick F; van Beijsterveldt, Toos; Willemsen, Gonneke; de Geus, Eco J; Penninx, Brenda W J H; Boomsma, Dorret I

    2013-01-01

    Genetic variation in a population can be summarized through principal component analysis (PCA) on genome-wide data. PCs derived from such analyses are valuable for genetic association studies, where they can correct for population stratification. We investigated how to capture the genetic population structure in a well-characterized sample from the Netherlands and in a worldwide data set and examined whether (1) removing long-range linkage disequilibrium (LD) regions and LD-based SNP pruning significantly improves correlations between PCs and geography and (2) whether genetic differentiation may have been influenced by migration and/or selection. In the Netherlands, three PCs showed significant correlations with geography, distinguishing between: (1) North and South; (2) East and West; and (3) the middle-band and the rest of the country. The third PC only emerged with minimized LD, which also significantly increased correlations with geography for the other two PCs. In addition to geography, the Dutch North–South PC showed correlations with genome-wide homozygosity (r=0.245), which may reflect a serial-founder effect due to northwards migration, and also with height (♂: r=0.142, ♀: r=0.153). The divergence between subpopulations identified by PCs is partly driven by selection pressures. The first three PCs showed significant signals for diversifying selection (545 SNPs - the majority within 184 genes). The strongest signal was observed between North and South for the functional SNP in HERC2 that determines human blue/brown eye color. Thus, this study demonstrates how to increase ancestry signals in a relatively homogeneous population and how those signals can reveal evolutionary history. PMID:23531865

  7. Selection of examples in case-based computer-aided decision systems

    International Nuclear Information System (INIS)

    Mazurowski, Maciej A; Zurada, Jacek M; Tourassi, Georgia D

    2008-01-01

    Case-based computer-aided decision (CB-CAD) systems rely on a database of previously stored, known examples when classifying new, incoming queries. Such systems can be particularly useful since they do not need retraining every time a new example is deposited in the case base. The adaptive nature of case-based systems is well suited to the current trend of continuously expanding digital databases in the medical domain. To maintain efficiency, however, such systems need sophisticated strategies to effectively manage the available evidence database. In this paper, we discuss the general problem of building an evidence database by selecting the most useful examples to store while satisfying existing storage requirements. We evaluate three intelligent techniques for this purpose: genetic algorithm-based selection, greedy selection and random mutation hill climbing. These techniques are compared to a random selection strategy used as the baseline. The study is performed with a previously presented CB-CAD system applied for false positive reduction in screening mammograms. The experimental evaluation shows that when the development goal is to maximize the system's diagnostic performance, the intelligent techniques are able to reduce the size of the evidence database to 37% of the original database by eliminating superfluous and/or detrimental examples while at the same time significantly improving the CAD system's performance. Furthermore, if the case-base size is a main concern, the total number of examples stored in the system can be reduced to only 2-4% of the original database without a decrease in the diagnostic performance. Comparison of the techniques shows that random mutation hill climbing provides the best balance between the diagnostic performance and computational efficiency when building the evidence database of the CB-CAD system.

  8. Asymmetric hearing loss in a random population of patients with mild to moderate sensorineural hearing loss.

    Science.gov (United States)

    Segal, Nili; Shkolnik, Mark; Kochba, Anat; Segal, Avichai; Kraus, Mordechai

    2007-01-01

    We evaluated the correlation of asymmetric hearing loss, in a random population of patients with mild to moderate sensorineural hearing loss, to several clinical factors such as age, sex, handedness, and noise exposure. We randomly selected, from 8 hearing institutes in Israel, 429 patients with sensorineural hearing loss of at least 30 dB at one frequency and a speech reception threshold not exceeding 30 dB. Patients with middle ear disease or retrocochlear disorders were excluded. The results of audiometric examinations were compared binaurally and in relation to the selected factors. The left ear's hearing threshold level was significantly higher than that of the right ear at all frequencies except 1.0 kHz (p < .05). One hundred fifty patients (35%) had asymmetric hearing loss (more than 10 dB difference between ears). In most of the patients (85%) the binaural difference in hearing threshold level, at any frequency, was less than 20 dB. Age, handedness, and sex were not found to be correlated to asymmetric hearing loss. Noise exposure was found to be correlated to asymmetric hearing loss.

  9. Primitive polynomials selection method for pseudo-random number generator

    Science.gov (United States)

    Anikin, I. V.; Alnajjar, Kh

    2018-01-01

    In this paper we suggested the method for primitive polynomials selection of special type. This kind of polynomials can be efficiently used as a characteristic polynomials for linear feedback shift registers in pseudo-random number generators. The proposed method consists of two basic steps: finding minimum-cost irreducible polynomials of the desired degree and applying primitivity tests to get the primitive ones. Finally two primitive polynomials, which was found by the proposed method, used in pseudorandom number generator based on fuzzy logic (FRNG) which had been suggested before by the authors. The sequences generated by new version of FRNG have low correlation magnitude, high linear complexity, less power consumption, is more balanced and have better statistical properties.

  10. Comparison of address-based sampling and random-digit dialing methods for recruiting young men as controls in a case-control study of testicular cancer susceptibility.

    Science.gov (United States)

    Clagett, Bartholt; Nathanson, Katherine L; Ciosek, Stephanie L; McDermoth, Monique; Vaughn, David J; Mitra, Nandita; Weiss, Andrew; Martonik, Rachel; Kanetsky, Peter A

    2013-12-01

    Random-digit dialing (RDD) using landline telephone numbers is the historical gold standard for control recruitment in population-based epidemiologic research. However, increasing cell-phone usage and diminishing response rates suggest that the effectiveness of RDD in recruiting a random sample of the general population, particularly for younger target populations, is decreasing. In this study, we compared landline RDD with alternative methods of control recruitment, including RDD using cell-phone numbers and address-based sampling (ABS), to recruit primarily white men aged 18-55 years into a study of testicular cancer susceptibility conducted in the Philadelphia, Pennsylvania, metropolitan area between 2009 and 2012. With few exceptions, eligible and enrolled controls recruited by means of RDD and ABS were similar with regard to characteristics for which data were collected on the screening survey. While we find ABS to be a comparably effective method of recruiting young males compared with landline RDD, we acknowledge the potential impact that selection bias may have had on our results because of poor overall response rates, which ranged from 11.4% for landline RDD to 1.7% for ABS.

  11. LOD score exclusion analyses for candidate genes using random population samples.

    Science.gov (United States)

    Deng, H W; Li, J; Recker, R R

    2001-05-01

    While extensive analyses have been conducted to test for, no formal analyses have been conducted to test against, the importance of candidate genes with random population samples. We develop a LOD score approach for exclusion analyses of candidate genes with random population samples. Under this approach, specific genetic effects and inheritance models at candidate genes can be analysed and if a LOD score is < or = - 2.0, the locus can be excluded from having an effect larger than that specified. Computer simulations show that, with sample sizes often employed in association studies, this approach has high power to exclude a gene from having moderate genetic effects. In contrast to regular association analyses, population admixture will not affect the robustness of our analyses; in fact, it renders our analyses more conservative and thus any significant exclusion result is robust. Our exclusion analysis complements association analysis for candidate genes in random population samples and is parallel to the exclusion mapping analyses that may be conducted in linkage analyses with pedigrees or relative pairs. The usefulness of the approach is demonstrated by an application to test the importance of vitamin D receptor and estrogen receptor genes underlying the differential risk to osteoporotic fractures.

  12. Insights into population ecology and sexual selection in snakes through the application of DNA-based genetic markers.

    Science.gov (United States)

    Gibbs, H L; Weatherhead, P J

    2001-01-01

    Hypervariable genetic markers have revolutionized studies of kinship, behavioral ecology, and population biology in vertebrate groups such as birds, but their use in snakes remains limited. To illustrate the value of such markers in snakes, we review studies that have used microsatellite DNA loci to analyze local population differentiation and parentage in snakes. Four ecologically distinct species of snakes all show evidence for differentiation at small spatial scales (2-15 km), but with substantial differences among species. This result highlights how genetic analysis can reveal hidden aspects of the natural history of difficult-to-observe taxa, and it raises important questions about the ecological factors that may contribute to restricted gene flow. A 3-year study of genetic parentage in marked populations of the northern water snake showed that (1) participation in mating aggregations was a poor predictor of genetic-based measures of reproductive success; (2) multiple paternity was high, yet there was no detectable fitness advantage to multiple mating by females; and (3) the opportunity for selection was far higher in males than in females due to a larger variance in male reproductive success, and yet this resulted in no detectable selection on morphological variation in males. Thus genetic markers have provided accurate measures of individual reproductive success in this species, an important step toward resolving the adaptive significance of key features including multiple paternity and reversed sexual size dimorphism. Overall these studies illustrate how genetic analyses of snakes provide previously unobtainable information of long-standing interest to behavioral ecologists.

  13. Awareness of association between periodontitis and PLBW among selected population of practising gynecologists in Andhra Pradesh

    Directory of Open Access Journals (Sweden)

    Rajasekhar Nutalapati

    2011-01-01

    Settings and Design: Random, cross-sectional study in a population of practicing gynecologists from Andhra Pradesh. Materials and Methods: A random study population was selected from the practicing gynecologists in Khammam and Hyderabad. Sixty practicing gynecologists, 30 each in Khammam and Hyderabad, were approached and they consented to join the study. Data were collected in questionnaire format from the subject population. Collected data were statistically analyzed. Chi-square test with Yates correction was used to analyze the data. A " P" value of <0.05 was taken as a significant difference. Results: 73.3% of the gynecologists said that their patients complain of bleeding gums, swellings and mobility. 58.3% of the gynecologists were aware that gum diseases occur at a higher rate in pregnant females. 38.3% of the gynecologists were aware that periodontal diseases can affect the outcome of delivery. No significant difference was found between the awareness levels of gynecologists in Khammam and in Hyderabad. Conclusions: There is a need for interdisciplinary approach for the prevention of PLBW cases by the integration of periodontal care into obstetric management. Effort should be made to increase awareness among the gynecologists.

  14. Prediction of plant promoters based on hexamers and random triplet pair analysis

    Directory of Open Access Journals (Sweden)

    Noman Nasimul

    2011-06-01

    Full Text Available Abstract Background With an increasing number of plant genome sequences, it has become important to develop a robust computational method for detecting plant promoters. Although a wide variety of programs are currently available, prediction accuracy of these still requires further improvement. The limitations of these methods can be addressed by selecting appropriate features for distinguishing promoters and non-promoters. Methods In this study, we proposed two feature selection approaches based on hexamer sequences: the Frequency Distribution Analyzed Feature Selection Algorithm (FDAFSA and the Random Triplet Pair Feature Selecting Genetic Algorithm (RTPFSGA. In FDAFSA, adjacent triplet-pairs (hexamer sequences were selected based on the difference in the frequency of hexamers between promoters and non-promoters. In RTPFSGA, random triplet-pairs (RTPs were selected by exploiting a genetic algorithm that distinguishes frequencies of non-adjacent triplet pairs between promoters and non-promoters. Then, a support vector machine (SVM, a nonlinear machine-learning algorithm, was used to classify promoters and non-promoters by combining these two feature selection approaches. We referred to this novel algorithm as PromoBot. Results Promoter sequences were collected from the PlantProm database. Non-promoter sequences were collected from plant mRNA, rRNA, and tRNA of PlantGDB and plant miRNA of miRBase. Then, in order to validate the proposed algorithm, we applied a 5-fold cross validation test. Training data sets were used to select features based on FDAFSA and RTPFSGA, and these features were used to train the SVM. We achieved 89% sensitivity and 86% specificity. Conclusions We compared our PromoBot algorithm to five other algorithms. It was found that the sensitivity and specificity of PromoBot performed well (or even better with the algorithms tested. These results show that the two proposed feature selection methods based on hexamer frequencies

  15. Dietary Patterns Associated with Alzheimer’s Disease: Population Based Study

    Directory of Open Access Journals (Sweden)

    Katarzyna Gustaw-Rothenberg

    2009-04-01

    Full Text Available Recently dietary pattern analysis has emerged as a way for examining diet-disease relations in Alzheimer’s disease. In contrast with the conventional approach, which focuses on a single nutrient or a few nutrients or foods, this method considers overall eating patterns. We examined the dietary patterns defined by factor analysis using data collected with a food-frequency questionnaire in people with Alzheimer’s disease (AD as compared to healthy controls. The diet data were obtained during population based study of the prevalence of Alzheimer’s disease in a population in Poland. Stratified sampling and random selection strategies were combined to obtain a representative population for screening (age group > 55. From the population screened three times, 71 people were diagnosed with Alzheimer’s according to DSM-IV, and were recruited for further diet risk factors assessment. A group of people with Alzheimer disease (n = 71; F/M 42/29 and the same number of healthy, age and gender matched control were recruited for the study. Patients and their caregivers as well as controls were presented with a food frequency questionnaire based on the 12 food groups. Factor analysis (principal component was used to derive food patterns. The analysis was conducted using the factor procedure. The factors were rotated by an orthogonal transformation (Varimax rotation to achieve simpler structure with greater interpretability. Using factor analysis, we identified major eating patterns, one for Alzheimer’s patients and a different one for control group. The AD dietary pattern, FACTOR AD was characterized by a high intake of meat, butter, high-fat dairy products, eggs, and refined sugar, whereas the other pattern, (FACTOR C was characterized by a high intake of grains and vegetables. These data indicate the existence of dietary patterns defined by factor analysis with data from a food frequency questionnaire, characteristic for Alzheimer’s disease in a

  16. Phenology of scramble polygyny in a wild population of chrysomelid beetles: the opportunity for and the strength of sexual selection [corrected].

    Directory of Open Access Journals (Sweden)

    Martha Lucía Baena

    Full Text Available Recent debate has highlighted the importance of estimating both the strength of sexual selection on phenotypic traits, and the opportunity for sexual selection. We describe seasonal fluctuations in mating dynamics of Leptinotarsa undecimlineata (Coleoptera: Chrysomelidae. We compared several estimates of the opportunity for, and the strength of, sexual selection and male precopulatory competition over the reproductive season. First, using a null model, we suggest that the ratio between observed values of the opportunity for sexual selections and their expected value under random mating results in unbiased estimates of the actual nonrandom mating behavior of the population. Second, we found that estimates for the whole reproductive season often misrepresent the actual value at any given time period. Third, mating differentials on male size and mobility, frequency of male fighting and three estimates of the opportunity for sexual selection provide contrasting but complementary information. More intense sexual selection associated to male mobility, but not to male size, was observed in periods with high opportunity for sexual selection and high frequency of male fights. Fourth, based on parameters of spatial and temporal aggregation of female receptivity, we describe the mating system of L. undecimlineata as a scramble mating polygyny in which the opportunity for sexual selection varies widely throughout the season, but the strength of sexual selection on male size remains fairly weak, while male mobility inversely covaries with mating success. We suggest that different estimates for the opportunity for, and intensity of, sexual selection should be applied in order to discriminate how different behavioral and demographic factors shape the reproductive dynamic of populations.

  17. Ethnicity, social disadvantage and psychotic-like experiences in a healthy population based sample.

    Science.gov (United States)

    Morgan, C; Fisher, H; Hutchinson, G; Kirkbride, J; Craig, T K; Morgan, K; Dazzan, P; Boydell, J; Doody, G A; Jones, P B; Murray, R M; Leff, J; Fearon, P

    2009-03-01

    We sought to investigate the prevalence and social correlates of psychotic-like experiences in a general population sample of Black and White British subjects. Data were collected from randomly selected community control subjects, recruited as part of the AESOP study, a three-centre population based study of first-episode psychosis. The proportion of subjects reporting one or more psychotic-like experience was 19% (n = 72/372). These were more common in Black Caribbean (OR 2.08) and Black African subjects (OR 4.59), compared with White British. In addition, a number of indicators of childhood and adult disadvantage were associated with psychotic-like experiences. When these variables were simultaneously entered into a regression model, Black African ethnicity, concentrated adult disadvantage, and separation from parents retained a significant effect. The higher prevalence of psychotic-like experiences in the Black Caribbean, but not Black African, group was explained by high levels of social disadvantage over the life course.

  18. 40 CFR 761.308 - Sample selection by random number generation on any two-dimensional square grid.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Sample selection by random number... § 761.79(b)(3) § 761.308 Sample selection by random number generation on any two-dimensional square... area created in accordance with paragraph (a) of this section, select two random numbers: one each for...

  19. Lithium and renal and upper urinary tract tumors - results from a nationwide population-based study

    DEFF Research Database (Denmark)

    Kessing, Lars Vedel; Gerds, Thomas Alexander; Feldt-Rasmussen, Bo

    2015-01-01

    OBJECTIVES: A recent alarming finding suggested an increased risk of renal tumors among long-term lithium users. The objectives of the present study were to estimate rates of renal and upper urinary tract tumors (RUT), malignant and benign, among individuals exposed to successive prescriptions...... for lithium, anticonvulsants, and other psychotropic agents used for bipolar disorder, and among unexposed individuals. METHODS: This was a nationwide, population-based longitudinal study including time-specific data from all individuals exposed to lithium (n = 24,272) or anticonvulsants (n = 386,255), all...... individuals with a diagnosis of bipolar disorder (n = 9,651), and a randomly selected sample of 1,500,000 from the Danish population. The study period was from 1995 to 2012, inclusive. Outcomes were hazard rate ratios (HR) for RUT in three groups: (i) combined malignant and benign, (ii) malignant, and (iii...

  20. Optimization of the Dutch Matrix Test by Random Selection of Sentences From a Preselected Subset

    Directory of Open Access Journals (Sweden)

    Rolph Houben

    2015-04-01

    Full Text Available Matrix tests are available for speech recognition testing in many languages. For an accurate measurement, a steep psychometric function of the speech materials is required. For existing tests, it would be beneficial if it were possible to further optimize the available materials by increasing the function’s steepness. The objective is to show if the steepness of the psychometric function of an existing matrix test can be increased by selecting a homogeneous subset of recordings with the steepest sentence-based psychometric functions. We took data from a previous multicenter evaluation of the Dutch matrix test (45 normal-hearing listeners. Based on half of the data set, first the sentences (140 out of 311 with a similar speech reception threshold and with the steepest psychometric function (≥9.7%/dB were selected. Subsequently, the steepness of the psychometric function for this selection was calculated from the remaining (unused second half of the data set. The calculation showed that the slope increased from 10.2%/dB to 13.7%/dB. The resulting subset did not allow the construction of enough balanced test lists. Therefore, the measurement procedure was changed to randomly select the sentences during testing. Random selection may interfere with a representative occurrence of phonemes. However, in our material, the median phonemic occurrence remained close to that of the original test. This finding indicates that phonemic occurrence is not a critical factor. The work highlights the possibility that existing speech tests might be improved by selecting sentences with a steep psychometric function.

  1. Gamified physical activation of young men – a Multidisciplinary Population-Based Randomized Controlled Trial (MOPO study

    Directory of Open Access Journals (Sweden)

    Ahola Riikka

    2013-01-01

    Full Text Available Abstract Background Inactive and unhealthy lifestyles are common among adolescent men. The planned intervention examines the effectiveness of an interactive, gamified activation method, based on tailored health information, peer networks and participation, on physical activity, health and wellbeing in young men. We hypothesize that following the intervention the physical activation group will have an improved physical activity, as well as self-determined and measured health compared with the controls. Methods/design Conscription-aged men (18 years attending compulsory annual call-ups for military service in the city of Oulu in Finland (n = 1500 will be randomized to a 6-months intervention (n = 640 or a control group (n = 640 during the fall 2013. A questionnaire on health, health behaviour, diet and wellbeing is administered in the beginning and end of the intervention. In addition, anthropometric measures (height, weight and waist circumference, body composition, grip strength, heart rate variability and aerobic fitness will be measured. The activation group utilizes an online gamified activation method in combination with communal youth services, objective physical activity measurement, social networking, tailored health information and exercise programs according to baseline activity level and the readiness of changes of each individual. Daily physical activity of the participants is monitored in both the activation and control groups. The activation service rewards improvements in physical activity or reductions in sedentary behaviour. The performance and completion of the military service of the participants will also be followed. Discussion The study will provide new information of physical activity, health and health behaviour of young men. Furthermore, a novel model including methods for increasing physical activity among young people is developed and its effects tested through an intervention. This unique gamified service

  2. An investigation of the statistical power of neutrality tests based on comparative and population genetic data

    DEFF Research Database (Denmark)

    Zhai, Weiwei; Nielsen, Rasmus; Slatkin, Montgomery

    2009-01-01

    In this report, we investigate the statistical power of several tests of selective neutrality based on patterns of genetic diversity within and between species. The goal is to compare tests based solely on population genetic data with tests using comparative data or a combination of comparative...... and population genetic data. We show that in the presence of repeated selective sweeps on relatively neutral background, tests based on the d(N)/d(S) ratios in comparative data almost always have more power to detect selection than tests based on population genetic data, even if the overall level of divergence...... selection. The Hudson-Kreitman-Aguadé test is the most powerful test for detecting positive selection among the population genetic tests investigated, whereas McDonald-Kreitman test typically has more power to detect negative selection. We discuss our findings in the light of the discordant results obtained...

  3. Treatment selection in a randomized clinical trial via covariate-specific treatment effect curves.

    Science.gov (United States)

    Ma, Yunbei; Zhou, Xiao-Hua

    2017-02-01

    For time-to-event data in a randomized clinical trial, we proposed two new methods for selecting an optimal treatment for a patient based on the covariate-specific treatment effect curve, which is used to represent the clinical utility of a predictive biomarker. To select an optimal treatment for a patient with a specific biomarker value, we proposed pointwise confidence intervals for each covariate-specific treatment effect curve and the difference between covariate-specific treatment effect curves of two treatments. Furthermore, to select an optimal treatment for a future biomarker-defined subpopulation of patients, we proposed confidence bands for each covariate-specific treatment effect curve and the difference between each pair of covariate-specific treatment effect curve over a fixed interval of biomarker values. We constructed the confidence bands based on a resampling technique. We also conducted simulation studies to evaluate finite-sample properties of the proposed estimation methods. Finally, we illustrated the application of the proposed method in a real-world data set.

  4. An individual-based probabilistic model for simulating fisheries population dynamics

    Directory of Open Access Journals (Sweden)

    Jie Cao

    2016-12-01

    Full Text Available The purpose of stock assessment is to support managers to provide intelligent decisions regarding removal from fish populations. Errors in assessment models may have devastating impacts on the population fitness and negative impacts on the economy of the resource users. Thus, accuracte estimations of population size, growth rates are critical for success. Evaluating and testing the behavior and performance of stock assessment models and assessing the consequences of model mis-specification and the impact of management strategies requires an operating model that accurately describe the dynamics of the target species, and can resolve spatial and seasonal changes. In addition, the most thorough evaluations of assessment models use an operating model that takes a different form than the assessment model. This paper presents an individual-based probabilistic model used to simulate the complex dynamics of populations and their associated fisheries. Various components of population dynamics are expressed as random Bernoulli trials in the model and detailed life and fishery histories of each individual are tracked over their life span. The simulation model is designed to be flexible so it can be used for different species and fisheries. It can simulate mixing among multiple stocks and link stock-recruit relationships to environmental factors. Furthermore, the model allows for flexibility in sub-models (e.g., growth and recruitment and model assumptions (e.g., age- or size-dependent selectivity. This model enables the user to conduct various simulation studies, including testing the performance of assessment models under different assumptions, assessing the impacts of model mis-specification and evaluating management strategies.

  5. Lines of Descent Under Selection

    Science.gov (United States)

    Baake, Ellen; Wakolbinger, Anton

    2017-11-01

    We review recent progress on ancestral processes related to mutation-selection models, both in the deterministic and the stochastic setting. We mainly rely on two concepts, namely, the killed ancestral selection graph and the pruned lookdown ancestral selection graph. The killed ancestral selection graph gives a representation of the type of a random individual from a stationary population, based upon the individual's potential ancestry back until the mutations that define the individual's type. The pruned lookdown ancestral selection graph allows one to trace the ancestry of individuals from a stationary distribution back into the distant past, thus leading to the stationary distribution of ancestral types. We illustrate the results by applying them to a prototype model for the error threshold phenomenon.

  6. Evolution of premating reproductive isolation among conspecific populations of the sea rock-pool beetle Ochthebius urbanelliae driven by reinforcing natural selection.

    Science.gov (United States)

    Porretta, Daniele; Urbanelli, Sandra

    2012-04-01

    How natural selection might be involved in speciation remains a fundamental question in evolutionary biology. When two or more species co-occur in the same areas, natural selection may favor divergence in mating traits. By acting in sympatric but not allopatric populations, natural selection can also affect mate choice within species and ultimately initiate speciation among conspecific populations. Here, we address this potential effect in the sea rock-pool beetles Ochthebius quadricollis and O. urbanelliae. The two species, which inhabit the Mediterranean coasts, co-occurr syntopically in an area along the Italian Tyrrhenian coast and completed reproductive isolation by reinforcement. In this article, through mating trials under laboratory conditions between conspecific populations, we found in O. quadricollis no deviations from random mating. Conversely, in O. urbanelliae, we found a clear pattern of premating isolation between the reinforced populations sympatric with O. quadricollis and those nonreinforced allopatric. This pattern is consistent with the view that natural selection, which completed the reproductive isolation between the two species in sympatry, led incidentally also to partial premating reproductive isolation (I(PSI) estimator from 0.683 to 0.792) between conspecific populations of O. urbanelliae. This case study supports an until recently underappreciated role of natural selection resulting from species interactions in initiating speciation. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

  7. Interference-aware random beam selection for spectrum sharing systems

    KAUST Repository

    Abdallah, Mohamed M.

    2012-09-01

    Spectrum sharing systems have been introduced to alleviate the problem of spectrum scarcity by allowing secondary unlicensed networks to share the spectrum with primary licensed networks under acceptable interference levels to the primary users. In this paper, we develop interference-aware random beam selection schemes that provide enhanced throughput for the secondary link under the condition that the interference observed at the primary link is within a predetermined acceptable value. For a secondary transmitter equipped with multiple antennas, our schemes select a random beam, among a set of power- optimized orthogonal random beams, that maximizes the capacity of the secondary link while satisfying the interference constraint at the primary receiver for different levels of feedback information describing the interference level at the primary receiver. For the proposed schemes, we develop a statistical analysis for the signal-to-noise and interference ratio (SINR) statistics as well as the capacity of the secondary link. Finally, we present numerical results that study the effect of system parameters including number of beams and the maximum transmission power on the capacity of the secondary link attained using the proposed schemes. © 2012 IEEE.

  8. Interference-aware random beam selection for spectrum sharing systems

    KAUST Repository

    Abdallah, Mohamed M.; Sayed, Mostafa M.; Alouini, Mohamed-Slim; Qaraqe, Khalid A.

    2012-01-01

    . In this paper, we develop interference-aware random beam selection schemes that provide enhanced throughput for the secondary link under the condition that the interference observed at the primary link is within a predetermined acceptable value. For a secondary

  9. Association between selective serotonin reuptake inhibitors and upper gastrointestinal bleeding: population based case-control study

    Science.gov (United States)

    de Abajo, Francisco José; Rodríguez, Luis Alberto García; Montero, Dolores

    1999-01-01

    Objective To examine the association between selective serotonin reuptake inhibitors and risk of upper gastrointestinal bleeding. Design Population based case-control study. Setting General practices included in the UK general practice research database. Subjects 1651 incident cases of upper gastrointestinal bleeding and 248 cases of ulcer perforation among patients aged 40 to 79 years between April 1993 and September 1997, and 10 000 controls matched for age, sex, and year that the case was identified. Interventions Review of computer profiles for all potential cases, and an internal validation study to confirm the accuracy of the diagnosis on the basis of the computerised information. Main outcome measures Current use of selective serotonin reuptake inhibitors or other antidepressants within 30 days before the index date. Results Current exposure to selective serotonin reuptake inhibitors was identified in 3.1% (52 of 1651) of patients with upper gastrointestinal bleeding but only 1.0% (95 of 10 000) of controls, giving an adjusted rate ratio of 3.0 (95% confidence interval 2.1 to 4.4). This effect measure was not modified by sex, age, dose, or treatment duration. A crude incidence of 1 case per 8000 prescriptions was estimated. A small association was found with non-selective serotonin reuptake inhibitors (relative risk 1.4, 1.1 to 1.9) but not with antidepressants lacking this inhibitory effect. None of the groups of antidepressants was associated with ulcer perforation. The concurrent use of selective serotonin reuptake inhibitors with non-steroidal anti-inflammatory drugs increased the risk of upper gastrointestinal bleeding beyond the sum of their independent effects (15.6, 6.6 to 36.6). A smaller interaction was also found between selective serotonin reuptake inhibitors and low dose aspirin (7.2, 3.1 to 17.1). Conclusions Selective serotonin reuptake inhibitors increase the risk of upper gastrointestinal bleeding. The absolute effect is, however

  10. Population SAMC vs SAMC: Convergence and Applications to Gene Selection Problems

    KAUST Repository

    Faming Liang, Mingqi Wu

    2013-01-01

    The Bayesian model selection approach has been adopted by more and more people when analyzing a large data. However, it is known that the reversible jump MCMC (RJMCMC) algorithm, which is perhaps the most popular MCMC algorithm for Bayesian model selection, is prone to get trapped into local modes when the model space is complex. The stochastic approximation Monte Carlo (SAMC) algorithm essentially overcomes the local trap problem suffered by conventional MCMC algorithms by introducing a self-adjusting mechanism based on the past samples. In this paper, we propose a population SAMC (Pop-SAMC) algorithm, which works on a population of SAMC chains and can make use of crossover operators from genetic algorithms to further improve its efficiency. Under mild conditions, we show the convergence of this algorithm. Comparing to the single chain SAMC algorithm, Pop-SAMC provides a more efficient self-adjusting mechanism and thus can converge faster. The effectiveness of Pop-SAMC for Bayesian model selection problems is examined through a change-point identification problem and a gene selection problem. The numerical results indicate that Pop-SAMC significantly outperforms both the single chain SAMC and RJMCMC.

  11. On random age and remaining lifetime for populations of items

    DEFF Research Database (Denmark)

    Finkelstein, M.; Vaupel, J.

    2015-01-01

    We consider items that are incepted into operation having already a random (initial) age and define the corresponding remaining lifetime. We show that these lifetimes are identically distributed when the age distribution is equal to the equilibrium distribution of the renewal theory. Then we...... develop the population studies approach to the problem and generalize the setting in terms of stationary and stable populations of items. We obtain new stochastic comparisons for the corresponding population ages and remaining lifetimes that can be useful in applications. Copyright (c) 2014 John Wiley...

  12. The long-term effect of a population-based life-style intervention on smoking and alcohol consumption

    DEFF Research Database (Denmark)

    Baumann, Sophie; Toft, Ulla Marie Nørgaard; Aadahl, Mette

    2015-01-01

    AIMS: To examine whether improvements in smoking and alcohol consumption throughout the 5-year course of a population-based multi-factorial life-style intervention were sustained 5 years after its discontinuation. DESIGN: Population-based randomized controlled trial. SETTING: Suburbs of Copenhage...

  13. Predicting rates of inbreeding in populations undergoing selection

    NARCIS (Netherlands)

    Woolliams, J.A.; Bijma, P.

    2000-01-01

    Tractable forms of predicting rates of inbreeding (F) in selected populations with general indices, nonrandom mating, and overlapping generations were developed, with the principal results assuming a period of equilibrium in the selection process. An existing theorem concerning the relationship

  14. Simulated Performance Evaluation of a Selective Tracker Through Random Scenario Generation

    DEFF Research Database (Denmark)

    Hussain, Dil Muhammad Akbar

    2006-01-01

    performance assessment. Therefore, a random target motion scenario is adopted. Its implementation in particular for testing the proposed selective track splitting algorithm using Kalman filters is investigated through a number of performance parameters which gives the activity profile of the tracking scenario......  The paper presents a simulation study on the performance of a target tracker using selective track splitting filter algorithm through a random scenario implemented on a digital signal processor.  In a typical track splitting filter all the observation which fall inside a likelihood ellipse...... are used for update, however, in our proposed selective track splitting filter less number of observations are used for track update.  Much of the previous performance work [1] has been done on specific (deterministic) scenarios. One of the reasons for considering the specific scenarios, which were...

  15. Random Decrement Based FRF Estimation

    DEFF Research Database (Denmark)

    Brincker, Rune; Asmussen, J. C.

    to speed and quality. The basis of the new method is the Fourier transformation of the Random Decrement functions which can be used to estimate the frequency response functions. The investigations are based on load and response measurements of a laboratory model of a 3 span bridge. By applying both methods...... that the Random Decrement technique is based on a simple controlled averaging of time segments of the load and response processes. Furthermore, the Random Decrement technique is expected to produce reliable results. The Random Decrement technique will reduce leakage, since the Fourier transformation...

  16. Random Decrement Based FRF Estimation

    DEFF Research Database (Denmark)

    Brincker, Rune; Asmussen, J. C.

    1997-01-01

    to speed and quality. The basis of the new method is the Fourier transformation of the Random Decrement functions which can be used to estimate the frequency response functions. The investigations are based on load and response measurements of a laboratory model of a 3 span bridge. By applying both methods...... that the Random Decrement technique is based on a simple controlled averaging of time segments of the load and response processes. Furthermore, the Random Decrement technique is expected to produce reliable results. The Random Decrement technique will reduce leakage, since the Fourier transformation...

  17. Which Individuals To Choose To Update the Reference Population? Minimizing the Loss of Genetic Diversity in Animal Genomic Selection Programs

    Directory of Open Access Journals (Sweden)

    Sonia E. Eynard

    2018-01-01

    Full Text Available Genomic selection (GS is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, GS allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study, we propose a modification of the reference population composition to mitigate diversity loss. Since the high cost of phenotyping is the limiting factor for GS, our findings are of major economic interest. This study aims to answer the following questions: how would decisions on the reference population affect the breeding population, and how to best select individuals to update the reference population and balance maximizing genetic gain and minimizing loss of genetic diversity? We investigated three updating strategies for the reference population: random, truncation, and optimal contribution (OC strategies. OC maximizes genetic merit for a fixed loss of genetic diversity. A French Montbéliarde dairy cattle population with 50K SNP chip genotypes and simulations over 10 generations were used to compare these different strategies using milk production as the trait of interest. Candidates were selected to update the reference population. Prediction bias and both genetic merit and diversity were measured. Changes in the reference population composition slightly affected the breeding population. Optimal contribution strategy appeared to be an acceptable compromise to maintain both genetic gain and diversity in the reference and the breeding populations.

  18. Which Individuals To Choose To Update the Reference Population? Minimizing the Loss of Genetic Diversity in Animal Genomic Selection Programs.

    Science.gov (United States)

    Eynard, Sonia E; Croiseau, Pascal; Laloë, Denis; Fritz, Sebastien; Calus, Mario P L; Restoux, Gwendal

    2018-01-04

    Genomic selection (GS) is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, GS allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study, we propose a modification of the reference population composition to mitigate diversity loss. Since the high cost of phenotyping is the limiting factor for GS, our findings are of major economic interest. This study aims to answer the following questions: how would decisions on the reference population affect the breeding population, and how to best select individuals to update the reference population and balance maximizing genetic gain and minimizing loss of genetic diversity? We investigated three updating strategies for the reference population: random, truncation, and optimal contribution (OC) strategies. OC maximizes genetic merit for a fixed loss of genetic diversity. A French Montbéliarde dairy cattle population with 50K SNP chip genotypes and simulations over 10 generations were used to compare these different strategies using milk production as the trait of interest. Candidates were selected to update the reference population. Prediction bias and both genetic merit and diversity were measured. Changes in the reference population composition slightly affected the breeding population. Optimal contribution strategy appeared to be an acceptable compromise to maintain both genetic gain and diversity in the reference and the breeding populations. Copyright © 2018 Eynard et al.

  19. An explicit semantic relatedness measure based on random walk

    Directory of Open Access Journals (Sweden)

    HU Sihui

    2016-10-01

    Full Text Available The semantic relatedness calculation of open domain knowledge network is a significant issue.In this paper,pheromone strategy is drawn from the thought of ant colony algorithm and is integrated into the random walk which is taken as the basic framework of calculating the semantic relatedness degree.The pheromone distribution is taken as a criterion of determining the tightness degree of semantic relatedness.A method of calculating semantic relatedness degree based on random walk is proposed and the exploration process of calculating the semantic relatedness degree is presented in a dominant way.The method mainly contains Path Select Model(PSM and Semantic Relatedness Computing Model(SRCM.PSM is used to simulate the path selection of ants and pheromone release.SRCM is used to calculate the semantic relatedness by utilizing the information returned by ants.The result indicates that the method could complete semantic relatedness calculation in linear complexity and extend the feasible strategy of semantic relatedness calculation.

  20. Selection in a subdivided population with local extinction and recolonization.

    Science.gov (United States)

    Cherry, Joshua L

    2003-01-01

    In a subdivided population, local extinction and subsequent recolonization affect the fate of alleles. Of particular interest is the interaction of this force with natural selection. The effect of selection can be weakened by this additional source of stochastic change in allele frequency. The behavior of a selected allele in such a population is shown to be equivalent to that of an allele with a different selection coefficient in an unstructured population with a different size. This equivalence allows use of established results for panmictic populations to predict such quantities as fixation probabilities and mean times to fixation. The magnitude of the quantity N(e)s(e), which determines fixation probability, is decreased by extinction and recolonization. Thus deleterious alleles are more likely to fix, and advantageous alleles less likely to do so, in the presence of extinction and recolonization. Computer simulations confirm that the theoretical predictions of both fixation probabilities and mean times to fixation are good approximations. PMID:12807797

  1. Lack of Correlation Between Depression and Coronary Artery Calcification in a Non-Selected Danish Population

    DEFF Research Database (Denmark)

    Devantier, Torben Albert; Nørgaard, Bjarne Linde; Sand, Niels Peter

    2013-01-01

    BACKGROUND: Depression is associated with coronary artery disease, and atherosclerosis seems to play a central role in this relation. In several studies, multislice computed tomography (CT) has been applied for detection and quantification of coronary artery calcification (CAC) in relation...... to depression. To our knowledge, only one previous study has investigated the relation between CAC and depression in an unselected population. METHODS: A total of 617 persons were randomly selected from the background population. The participants underwent CT of the heart and were screened for depression by use...... of the Major Depression Inventory questionnaire. Quantification of CAC was performed using the Agatston method. The Mann-Whitney U test, Spearman's correlational analysis, and logistic regression were used to assess the association between depression and CAC. RESULTS: The median Agatston score...

  2. Selection bias and subject refusal in a cluster-randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Rochelle Yang

    2017-07-01

    Full Text Available Abstract Background Selection bias and non-participation bias are major methodological concerns which impact external validity. Cluster-randomized controlled trials are especially prone to selection bias as it is impractical to blind clusters to their allocation into intervention or control. This study assessed the impact of selection bias in a large cluster-randomized controlled trial. Methods The Improved Cardiovascular Risk Reduction to Enhance Rural Primary Care (ICARE study examined the impact of a remote pharmacist-led intervention in twelve medical offices. To assess eligibility, a standardized form containing patient demographics and medical information was completed for each screened patient. Eligible patients were approached by the study coordinator for recruitment. Both the study coordinator and the patient were aware of the site’s allocation prior to consent. Patients who consented or declined to participate were compared across control and intervention arms for differing characteristics. Statistical significance was determined using a two-tailed, equal variance t-test and a chi-square test with adjusted Bonferroni p-values. Results were adjusted for random cluster variation. Results There were 2749 completed screening forms returned to research staff with 461 subjects who had either consented or declined participation. Patients with poorly controlled diabetes were found to be significantly more likely to decline participation in intervention sites compared to those in control sites. A higher mean diastolic blood pressure was seen in patients with uncontrolled hypertension who declined in the control sites compared to those who declined in the intervention sites. However, these findings were no longer significant after adjustment for random variation among the sites. After this adjustment, females were now found to be significantly more likely to consent than males (odds ratio = 1.41; 95% confidence interval = 1.03, 1

  3. Sleep apnea and risk of vertigo: A nationwide population-based cohort study.

    Science.gov (United States)

    Tsai, Ming-Shao; Lee, Li-Ang; Tsai, Yao-Te; Yang, Yao-Hsu; Liu, Chia-Yen; Lin, Meng-Hung; Hsu, Cheng-Ming; Chen, Chin-Kuo; Li, Hsueh-Yu

    2018-03-01

    To investigate the risk of vertigo in patients with sleep apnea. Retrospective cohort study. This study used data from the National Health Insurance Research Database of Taiwan, a population-based database. A total of 5,025 patients who were newly diagnosed with sleep apnea between January 1, 1997, and December 31, 2012, were identified from the Longitudinal Health Insurance Database 2000, a nationally representative database of 1 million randomly selected patients. Moreover, 20,100 patients without sleep apnea were matched at a 1:4 ratio by age, sex, socioeconomic status, and urbanization level. Patients were followed up until death or the end of the study period (December 31, 2013). The primary outcome was the occurrence of vertigo. Patients with sleep apnea had a significantly higher cumulative incidence of vertigo than those without sleep apnea (P vertigo (hazard ratio, 1.71; 95% confidence interval [CI], 1.48-1.97; P diabetes mellitus, hypertension, stroke, and obesity. Sleep apnea was demonstrated to be an independent risk factor for vertigo. This is the first nationwide population-based cohort study to investigate the association between sleep apnea and vertigo. The findings strongly support that sleep apnea is an independent risk factor for vertigo. Based on the study results, physicians should be aware of potential vertigo occurrence following sleep apnea. 4. Laryngoscope, 128:763-768, 2017. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  4. Extinction transition in stochastic population dynamics in a random, convective environment

    International Nuclear Information System (INIS)

    Juhász, Róbert

    2013-01-01

    Motivated by modeling the dynamics of a population living in a flowing medium where the environmental factors are random in space, we have studied an asymmetric variant of the one-dimensional contact process, where the quenched random reproduction rates are systematically greater in one direction than in the opposite one. The spatial disorder turns out to be a relevant perturbation but, according to results of Monte Carlo simulations, the behavior of the model at the extinction transition is different from the (infinite-randomness) critical behavior of the disordered symmetric contact process. Depending on the strength a of the asymmetry, the critical population drifts either with a finite velocity or with an asymptotically vanishing velocity as x(t) ∼ t μ(a) , where μ(a) < 1. Dynamical quantities are non-self-averaging at the extinction transition; the survival probability, for instance, shows multiscaling, i.e. it is characterized by a broad spectrum of effective exponents. For a sufficiently weak asymmetry, a Griffiths phase appears below the extinction transition, where the survival probability decays as a non-universal power of the time while, above the transition, another extended phase emerges, where the front of the population advances anomalously with a diffusion exponent continuously varying with the control parameter. (paper)

  5. From Protocols to Publications: A Study in Selective Reporting of Outcomes in Randomized Trials in Oncology

    Science.gov (United States)

    Raghav, Kanwal Pratap Singh; Mahajan, Sminil; Yao, James C.; Hobbs, Brian P.; Berry, Donald A.; Pentz, Rebecca D.; Tam, Alda; Hong, Waun K.; Ellis, Lee M.; Abbruzzese, James; Overman, Michael J.

    2015-01-01

    Purpose The decision by journals to append protocols to published reports of randomized trials was a landmark event in clinical trial reporting. However, limited information is available on how this initiative effected transparency and selective reporting of clinical trial data. Methods We analyzed 74 oncology-based randomized trials published in Journal of Clinical Oncology, the New England Journal of Medicine, and The Lancet in 2012. To ascertain integrity of reporting, we compared published reports with their respective appended protocols with regard to primary end points, nonprimary end points, unplanned end points, and unplanned analyses. Results A total of 86 primary end points were reported in 74 randomized trials; nine trials had greater than one primary end point. Nine trials (12.2%) had some discrepancy between their planned and published primary end points. A total of 579 nonprimary end points (median, seven per trial) were planned, of which 373 (64.4%; median, five per trial) were reported. A significant positive correlation was found between the number of planned and nonreported nonprimary end points (Spearman r = 0.66; P < .001). Twenty-eight studies (37.8%) reported a total of 65 unplanned end points; 52 (80.0%) of which were not identified as unplanned. Thirty-one (41.9%) and 19 (25.7%) of 74 trials reported a total of 52 unplanned analyses involving primary end points and 33 unplanned analyses involving nonprimary end points, respectively. Studies reported positive unplanned end points and unplanned analyses more frequently than negative outcomes in abstracts (unplanned end points odds ratio, 6.8; P = .002; unplanned analyses odd ratio, 8.4; P = .007). Conclusion Despite public and reviewer access to protocols, selective outcome reporting persists and is a major concern in the reporting of randomized clinical trials. To foster credible evidence-based medicine, additional initiatives are needed to minimize selective reporting. PMID:26304898

  6. Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding.

    Science.gov (United States)

    Grenier, Cécile; Cao, Tuong-Vi; Ospina, Yolima; Quintero, Constanza; Châtel, Marc Henri; Tohme, Joe; Courtois, Brigitte; Ahmadi, Nourollah

    2015-01-01

    Genomic selection (GS) is a promising strategy for enhancing genetic gain. We investigated the accuracy of genomic estimated breeding values (GEBV) in four inter-related synthetic populations that underwent several cycles of recurrent selection in an upland rice-breeding program. A total of 343 S2:4 lines extracted from those populations were phenotyped for flowering time, plant height, grain yield and panicle weight, and genotyped with an average density of one marker per 44.8 kb. The relative effect of the linkage disequilibrium (LD) and minor allele frequency (MAF) thresholds for selecting markers, the relative size of the training population (TP) and of the validation population (VP), the selected trait and the genomic prediction models (frequentist and Bayesian) on the accuracy of GEBVs was investigated in 540 cross validation experiments with 100 replicates. The effect of kinship between the training and validation populations was tested in an additional set of 840 cross validation experiments with a single genomic prediction model. LD was high (average r2 = 0.59 at 25 kb) and decreased slowly, distribution of allele frequencies at individual loci was markedly skewed toward unbalanced frequencies (MAF average value 15.2% and median 9.6%), and differentiation between the four synthetic populations was low (FST ≤0.06). The accuracy of GEBV across all cross validation experiments ranged from 0.12 to 0.54 with an average of 0.30. Significant differences in accuracy were observed among the different levels of each factor investigated. Phenotypic traits had the biggest effect, and the size of the incidence matrix had the smallest. Significant first degree interaction was observed for GEBV accuracy between traits and all the other factors studied, and between prediction models and LD, MAF and composition of the TP. The potential of GS to accelerate genetic gain and breeding options to increase the accuracy of predictions are discussed.

  7. Selection dramatically reduces effective population size in HIV-1 infection

    Directory of Open Access Journals (Sweden)

    Mittler John E

    2008-05-01

    Full Text Available Abstract Background In HIV-1 evolution, a 100–100,000 fold discrepancy between census size and effective population size (Ne has been noted. Although it is well known that selection can reduce Ne, high in vivo mutation and recombination rates complicate attempts to quantify the effects of selection on HIV-1 effective size. Results We use the inbreeding coefficient and the variance in allele frequency at a linked neutral locus to estimate the reduction in Ne due to selection in the presence of mutation and recombination. With biologically realistic mutation rates, the reduction in Ne due to selection is determined by the strength of selection, i.e., the stronger the selection, the greater the reduction. However, the dependence of Ne on selection can break down if recombination rates are very high (e.g., r ≥ 0.1. With biologically likely recombination rates, our model suggests that recurrent selective sweeps similar to those observed in vivo can reduce within-host HIV-1 effective population sizes by a factor of 300 or more. Conclusion Although other factors, such as unequal viral reproduction rates and limited migration between tissue compartments contribute to reductions in Ne, our model suggests that recurrent selection plays a significant role in reducing HIV-1 effective population sizes in vivo.

  8. Identifying selected regions from heterozygosity and divergence using a light-coverage genomic dataset from two human populations.

    Directory of Open Access Journals (Sweden)

    Taras K Oleksyk

    2008-03-01

    Full Text Available When a selective sweep occurs in the chromosomal region around a target gene in two populations that have recently separated, it produces three dramatic genomic consequences: 1 decreased multi-locus heterozygosity in the region; 2 elevated or diminished genetic divergence (F(ST of multiple polymorphic variants adjacent to the selected locus between the divergent populations, due to the alternative fixation of alleles; and 3 a consequent regional increase in the variance of F(ST (S(2F(ST for the same clustered variants, due to the increased alternative fixation of alleles in the loci surrounding the selection target. In the first part of our study, to search for potential targets of directional selection, we developed and validated a resampling-based computational approach; we then scanned an array of 31 different-sized moving windows of SNP variants (5-65 SNPs across the human genome in a set of European and African American population samples with 183,997 SNP loci after correcting for the recombination rate variation. The analysis revealed 180 regions of recent selection with very strong evidence in either population or both. In the second part of our study, we compared the newly discovered putative regions to those sites previously postulated in the literature, using methods based on inspecting patterns of linkage disequilibrium, population divergence and other methodologies. The newly found regions were cross-validated with those found in nine other studies that have searched for selection signals. Our study was replicated especially well in those regions confirmed by three or more studies. These validated regions were independently verified, using a combination of different methods and different databases in other studies, and should include fewer false positives. The main strength of our analysis method compared to others is that it does not require dense genotyping and therefore can be used with data from population-based genome SNP scans

  9. Chronic kidney disease and obesity in Ireland: comparison of self-reported coronary artery disease in population study with clinic attendees.

    LENUS (Irish Health Repository)

    Lannin, U

    2015-02-01

    Obesity is a growing issue in Ireland. The link between obesity, CKD and CAD has not previously been described in the Irish population. The prevalence of obesity and CKD was compared across 3 groups: population based estimates with self-reported CAD, population based estimates without self-reported CAD (SLAN-07) and a random selection of cardiology outpatients with CAD. The SLAN-07 is a representative survey of 1207 randomly selected participants ≥ 45 years. Validated methods measured parameters including waist circumference, blood pressure and markers of renal function specifically glomerular filtration rate (eGFR) and albumin: creatinine ratio. The Cardiology clinic surveyed a random selection of 126 participants ≥ 45 years with CAD. Similar parameters were measured using the validated methods utilised in SLAN-07 study. Prevalence of obesity and renal disease was significantly higher in both CAD groups. At population level, risk factors were modelled using logistic regression to compare odds of participants with self-reported CAD with those without. Age, hypertension, obesity, elevated waist circumference, renal disease and diabetes are significantly associated with existing CAD. Obesity and CKD are more frequent in patients with CAD. Routine evaluation is essential to facilitate more intensive management of these risk factors.

  10. Automatic learning-based beam angle selection for thoracic IMRT

    International Nuclear Information System (INIS)

    Amit, Guy; Marshall, Andrea; Purdie, Thomas G.; Jaffray, David A.; Levinshtein, Alex; Hope, Andrew J.; Lindsay, Patricia; Pekar, Vladimir

    2015-01-01

    Purpose: The treatment of thoracic cancer using external beam radiation requires an optimal selection of the radiation beam directions to ensure effective coverage of the target volume and to avoid unnecessary treatment of normal healthy tissues. Intensity modulated radiation therapy (IMRT) planning is a lengthy process, which requires the planner to iterate between choosing beam angles, specifying dose–volume objectives and executing IMRT optimization. In thorax treatment planning, where there are no class solutions for beam placement, beam angle selection is performed manually, based on the planner’s clinical experience. The purpose of this work is to propose and study a computationally efficient framework that utilizes machine learning to automatically select treatment beam angles. Such a framework may be helpful for reducing the overall planning workload. Methods: The authors introduce an automated beam selection method, based on learning the relationships between beam angles and anatomical features. Using a large set of clinically approved IMRT plans, a random forest regression algorithm is trained to map a multitude of anatomical features into an individual beam score. An optimization scheme is then built to select and adjust the beam angles, considering the learned interbeam dependencies. The validity and quality of the automatically selected beams evaluated using the manually selected beams from the corresponding clinical plans as the ground truth. Results: The analysis included 149 clinically approved thoracic IMRT plans. For a randomly selected test subset of 27 plans, IMRT plans were generated using automatically selected beams and compared to the clinical plans. The comparison of the predicted and the clinical beam angles demonstrated a good average correspondence between the two (angular distance 16.8° ± 10°, correlation 0.75 ± 0.2). The dose distributions of the semiautomatic and clinical plans were equivalent in terms of primary target volume

  11. Evaluation of peptide selection approaches for epitope‐based vaccine design

    DEFF Research Database (Denmark)

    Schubert, B.; Lund, Ole; Nielsen, Morten

    2013-01-01

    A major challenge in epitope-based vaccine (EV) design stems from the vast genomic variation of pathogens and the diversity of the host cellular immune system. Several computational approaches have been published to assist the selection of potential T cell epitopes for EV design. So far, no thoro......A major challenge in epitope-based vaccine (EV) design stems from the vast genomic variation of pathogens and the diversity of the host cellular immune system. Several computational approaches have been published to assist the selection of potential T cell epitopes for EV design. So far...... in terms of in silico measurements simulating important vaccine properties like the ability of inducing protection against a multivariant pathogen in a population; the predicted immunogenicity; pathogen, allele, and population coverage; as well as the conservation of selected epitopes. Additionally, we...... evaluate the use of human leukocyte antigen (HLA) supertypes with regards to their applicability for population-spanning vaccine design. The results showed that in terms of induced protection methods that simultaneously aim to optimize pathogen and HLA coverage significantly outperform methods focusing...

  12. The effect of morphometric atlas selection on multi-atlas-based automatic brachial plexus segmentation

    International Nuclear Information System (INIS)

    Van de Velde, Joris; Wouters, Johan; Vercauteren, Tom; De Gersem, Werner; Achten, Eric; De Neve, Wilfried; Van Hoof, Tom

    2015-01-01

    The present study aimed to measure the effect of a morphometric atlas selection strategy on the accuracy of multi-atlas-based BP autosegmentation using the commercially available software package ADMIRE® and to determine the optimal number of selected atlases to use. Autosegmentation accuracy was measured by comparing all generated automatic BP segmentations with anatomically validated gold standard segmentations that were developed using cadavers. Twelve cadaver computed tomography (CT) atlases were included in the study. One atlas was selected as a patient in ADMIRE®, and multi-atlas-based BP autosegmentation was first performed with a group of morphometrically preselected atlases. In this group, the atlases were selected on the basis of similarity in the shoulder protraction position with the patient. The number of selected atlases used started at two and increased up to eight. Subsequently, a group of randomly chosen, non-selected atlases were taken. In this second group, every possible combination of 2 to 8 random atlases was used for multi-atlas-based BP autosegmentation. For both groups, the average Dice similarity coefficient (DSC), Jaccard index (JI) and Inclusion index (INI) were calculated, measuring the similarity of the generated automatic BP segmentations and the gold standard segmentation. Similarity indices of both groups were compared using an independent sample t-test, and the optimal number of selected atlases was investigated using an equivalence trial. For each number of atlases, average similarity indices of the morphometrically selected atlas group were significantly higher than the random group (p < 0,05). In this study, the highest similarity indices were achieved using multi-atlas autosegmentation with 6 selected atlases (average DSC = 0,598; average JI = 0,434; average INI = 0,733). Morphometric atlas selection on the basis of the protraction position of the patient significantly improves multi-atlas-based BP autosegmentation accuracy

  13. Using ArcMap, Google Earth, and Global Positioning Systems to select and locate random households in rural Haiti.

    Science.gov (United States)

    Wampler, Peter J; Rediske, Richard R; Molla, Azizur R

    2013-01-18

    A remote sensing technique was developed which combines a Geographic Information System (GIS); Google Earth, and Microsoft Excel to identify home locations for a random sample of households in rural Haiti. The method was used to select homes for ethnographic and water quality research in a region of rural Haiti located within 9 km of a local hospital and source of health education in Deschapelles, Haiti. The technique does not require access to governmental records or ground based surveys to collect household location data and can be performed in a rapid, cost-effective manner. The random selection of households and the location of these households during field surveys were accomplished using GIS, Google Earth, Microsoft Excel, and handheld Garmin GPSmap 76CSx GPS units. Homes were identified and mapped in Google Earth, exported to ArcMap 10.0, and a random list of homes was generated using Microsoft Excel which was then loaded onto handheld GPS units for field location. The development and use of a remote sensing method was essential to the selection and location of random households. A total of 537 homes initially were mapped and a randomized subset of 96 was identified as potential survey locations. Over 96% of the homes mapped using Google Earth imagery were correctly identified as occupied dwellings. Only 3.6% of the occupants of mapped homes visited declined to be interviewed. 16.4% of the homes visited were not occupied at the time of the visit due to work away from the home or market days. A total of 55 households were located using this method during the 10 days of fieldwork in May and June of 2012. The method used to generate and field locate random homes for surveys and water sampling was an effective means of selecting random households in a rural environment lacking geolocation infrastructure. The success rate for locating households using a handheld GPS was excellent and only rarely was local knowledge required to identify and locate households. This

  14. Using ArcMap, Google Earth, and Global Positioning Systems to select and locate random households in rural Haiti

    Directory of Open Access Journals (Sweden)

    Wampler Peter J

    2013-01-01

    Full Text Available Abstract Background A remote sensing technique was developed which combines a Geographic Information System (GIS; Google Earth, and Microsoft Excel to identify home locations for a random sample of households in rural Haiti. The method was used to select homes for ethnographic and water quality research in a region of rural Haiti located within 9 km of a local hospital and source of health education in Deschapelles, Haiti. The technique does not require access to governmental records or ground based surveys to collect household location data and can be performed in a rapid, cost-effective manner. Methods The random selection of households and the location of these households during field surveys were accomplished using GIS, Google Earth, Microsoft Excel, and handheld Garmin GPSmap 76CSx GPS units. Homes were identified and mapped in Google Earth, exported to ArcMap 10.0, and a random list of homes was generated using Microsoft Excel which was then loaded onto handheld GPS units for field location. The development and use of a remote sensing method was essential to the selection and location of random households. Results A total of 537 homes initially were mapped and a randomized subset of 96 was identified as potential survey locations. Over 96% of the homes mapped using Google Earth imagery were correctly identified as occupied dwellings. Only 3.6% of the occupants of mapped homes visited declined to be interviewed. 16.4% of the homes visited were not occupied at the time of the visit due to work away from the home or market days. A total of 55 households were located using this method during the 10 days of fieldwork in May and June of 2012. Conclusions The method used to generate and field locate random homes for surveys and water sampling was an effective means of selecting random households in a rural environment lacking geolocation infrastructure. The success rate for locating households using a handheld GPS was excellent and only

  15. The Prevalence of Amblyopia and Its Determinants in a Population-based Study.

    Science.gov (United States)

    Faghihi, Mohammad; Hashemi, Hassan; Nabovati, Payam; Saatchi, Mohammad; Yekta, Abbasali; Rafati, Shokoofeh; Ostadimoghaddam, Hadi; Khabazkhoob, Mehdi

    2017-12-01

    To determine the prevalence of amblyopia and its determinants in a population-based study in Mashhad County, Iran. This cross-sectional, population-based study was conducted on the population of Mashhad County aged >1 year using randomized stratified cluster sampling. Examinations were performed after selection of the participants and their free transportation to the sampling site. The examinations included the measurement of uncorrected and corrected visual acuity, cycloplegic and non-cycloplegic refraction, cover testing, slit-lamp biomicroscopy, and ophthalmoscopy. In this study, amblyopia was defined as best corrected visual acuity (BCVA) of 20/30 or less or 2-line interocular optotype acuity differences with no pathology. After considering the exclusion criteria, the data of 2739 individuals, 65.6% of whom were women, were analyzed. The mean age of the participants was 29.5±17.5 years. The prevalence of amblyopia was 4.6% (95% CI: 3.77%-5.43%) in the total population. The lowest prevalence was 2.24% in the age group 5-15 years (95% CI: 0.99%-3.48%) and the highest prevalence was 7.14% in the age group 55-65 years (95% CI: 2.64%-11.56%). Anisometropic amblyopia was observed in 45.24% of the amblyopic participants. Isometropic, mixed (strabismic/anisometropic), and strabismic amblyopia were other common causes of amblyopia, with a prevalence of 24.6%, 16.67%, and 13.49% in amblyopic patients, respectively. The odds ratio (OR) of having amblyopia for each 1-year increase in age was 1.02 (95% CI: 1.01-1.03). Amblyopia was less common in people with better socioeconomic status. This study showed the prevalence of amblyopia in all age groups in a population-based study for the first time. The findings of this study regarding the relatively high prevalence of amblyopia in the older population and its lower prevalence in young people indicate attention to amblyopia in recent years.

  16. Epidemiology of Haemophilus influenzae bacteremia: A multi-national population-based assessment

    DEFF Research Database (Denmark)

    Laupland, Kevin B; Schønheyder, Henrik C; Østergaard, Christian

    2011-01-01

    OBJECTIVES: Haemophilus influenzae is an important cause of invasive infection but contemporary data in non-selected populations is limited. METHODS: Population-based surveillance for Haemophilus influenzae bacteremia was conducted in seven regions in Australia, Canada, and Denmark during 2000-20...

  17. Isoenzymatic variability in tropical maize populations under reciprocal recurrent selection

    Directory of Open Access Journals (Sweden)

    Pinto Luciana Rossini

    2003-01-01

    Full Text Available Maize (Zea mays L. is one of the crops in which the genetic variability has been extensively studied at isoenzymatic loci. The genetic variability of the maize populations BR-105 and BR-106, and the synthetics IG-3 and IG-4, obtained after one cycle of a high-intensity reciprocal recurrent selection (RRS, was investigated at seven isoenzymatic loci. A total of twenty alleles were identified, and most of the private alleles were found in the BR-106 population. One cycle of reciprocal recurrent selection (RRS caused reductions of 12% in the number of alleles in both populations. Changes in allele frequencies were also observed between populations and synthetics, mainly for the Est 2 locus. Populations presented similar values for the number of alleles per locus, percentage of polymorphic loci, and observed and expected heterozygosities. A decrease of the genetic variation values was observed for the synthetics as a consequence of genetic drift effects and reduction of the effective population sizes. The distribution of the genetic diversity within and between populations revealed that most of the diversity was maintained within them, i.e. BR-105 x BR-106 (G ST = 3.5% and IG-3 x IG-4 (G ST = 4.0%. The genetic distances between populations and synthetics increased approximately 21%. An increase in the genetic divergence between the populations occurred without limiting new selection procedures.

  18. Automatic Recognition of Chinese Personal Name Using Conditional Random Fields and Knowledge Base

    Directory of Open Access Journals (Sweden)

    Chuan Gu

    2015-01-01

    Full Text Available According to the features of Chinese personal name, we present an approach for Chinese personal name recognition based on conditional random fields (CRF and knowledge base in this paper. The method builds multiple features of CRF model by adopting Chinese character as processing unit, selects useful features based on selection algorithm of knowledge base and incremental feature template, and finally implements the automatic recognition of Chinese personal name from Chinese document. The experimental results on open real corpus demonstrated the effectiveness of our method and obtained high accuracy rate and high recall rate of recognition.

  19. Interference-aware random beam selection schemes for spectrum sharing systems

    KAUST Repository

    Abdallah, Mohamed; Qaraqe, Khalid; Alouini, Mohamed-Slim

    2012-01-01

    users. In this work, we develop interference-aware random beam selection schemes that provide enhanced performance for the secondary network under the condition that the interference observed by the receivers of the primary network is below a

  20. Comparison of mental distress in patients with low back pain and a population-based control group measured by Symptoms Check List

    DEFF Research Database (Denmark)

    Christensen, Jan; Fisker, Annette; Mortensen, Erik Lykke

    2015-01-01

    . The objective of this study was to compare mental symptoms and distress as measured by the Symptoms Check List-90 in sick-listed or at risk of being sick-listed patients with low back pain with a population-based control group. METHODS: Mental distress was compared in a group of patients with low back pain (n......=770) and a randomly selected population-based reference group (n=909). Established Danish cut-off values for mental distress were used to evaluate the mental distress status in the low back pain and control group and logistic regression was used to calculate odds ratios for the Global Severity Index......PURPOSE: Mental distress is common in persons experiencing low back pain and who are sick-listed or at risk of being sick-listed. It is, however, not known how mental distress measured by the Symptoms Check List-90 differs between patients with low back pain and the general population...

  1. Asthma exacerbation and proximity of residence to major roads: a population-based matched case-control study among the pediatric Medicaid population in Detroit, Michigan

    Directory of Open Access Journals (Sweden)

    Wahl Robert

    2011-04-01

    Full Text Available Abstract Background The relationship between asthma and traffic-related pollutants has received considerable attention. The use of individual-level exposure measures, such as residence location or proximity to emission sources, may avoid ecological biases. Method This study focused on the pediatric Medicaid population in Detroit, MI, a high-risk population for asthma-related events. A population-based matched case-control analysis was used to investigate associations between acute asthma outcomes and proximity of residence to major roads, including freeways. Asthma cases were identified as all children who made at least one asthma claim, including inpatient and emergency department visits, during the three-year study period, 2004-06. Individually matched controls were randomly selected from the rest of the Medicaid population on the basis of non-respiratory related illness. We used conditional logistic regression with distance as both categorical and continuous variables, and examined non-linear relationships with distance using polynomial splines. The conditional logistic regression models were then extended by considering multiple asthma states (based on the frequency of acute asthma outcomes using polychotomous conditional logistic regression. Results Asthma events were associated with proximity to primary roads with an odds ratio of 0.97 (95% CI: 0.94, 0.99 for a 1 km increase in distance using conditional logistic regression, implying that asthma events are less likely as the distance between the residence and a primary road increases. Similar relationships and effect sizes were found using polychotomous conditional logistic regression. Another plausible exposure metric, a reduced form response surface model that represents atmospheric dispersion of pollutants from roads, was not associated under that exposure model. Conclusions There is moderately strong evidence of elevated risk of asthma close to major roads based on the results obtained

  2. Asthma exacerbation and proximity of residence to major roads: a population-based matched case-control study among the pediatric Medicaid population in Detroit, Michigan

    Science.gov (United States)

    2011-01-01

    Background The relationship between asthma and traffic-related pollutants has received considerable attention. The use of individual-level exposure measures, such as residence location or proximity to emission sources, may avoid ecological biases. Method This study focused on the pediatric Medicaid population in Detroit, MI, a high-risk population for asthma-related events. A population-based matched case-control analysis was used to investigate associations between acute asthma outcomes and proximity of residence to major roads, including freeways. Asthma cases were identified as all children who made at least one asthma claim, including inpatient and emergency department visits, during the three-year study period, 2004-06. Individually matched controls were randomly selected from the rest of the Medicaid population on the basis of non-respiratory related illness. We used conditional logistic regression with distance as both categorical and continuous variables, and examined non-linear relationships with distance using polynomial splines. The conditional logistic regression models were then extended by considering multiple asthma states (based on the frequency of acute asthma outcomes) using polychotomous conditional logistic regression. Results Asthma events were associated with proximity to primary roads with an odds ratio of 0.97 (95% CI: 0.94, 0.99) for a 1 km increase in distance using conditional logistic regression, implying that asthma events are less likely as the distance between the residence and a primary road increases. Similar relationships and effect sizes were found using polychotomous conditional logistic regression. Another plausible exposure metric, a reduced form response surface model that represents atmospheric dispersion of pollutants from roads, was not associated under that exposure model. Conclusions There is moderately strong evidence of elevated risk of asthma close to major roads based on the results obtained in this population-based

  3. GALEX-SELECTED LYMAN BREAK GALAXIES AT z {approx} 2: COMPARISON WITH OTHER POPULATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Haberzettl, L.; Williger, G. [Department of Physics and Astronomy, University of Louisville, Louisville KY 20492 (United States); Lehnert, M. D. [GEPI, Observatoire de Paris, UMR 8111 du CNRS, 5 Place Jules Janssen, 92195 Meudon (France); Nesvadba, N. [Institut d' Astrophysique Spatiale, CNRS, Universite Paris-Sud, Bat. 120-121, 91405 Orsay (France); Davies, L. [Department of Physics, H H Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL (United Kingdom)

    2012-01-20

    We present results of a search for bright Lyman break galaxies (LBGs) at 1.5 {<=} z {<=} 2.5 in the GOODS-S field using an NUV-dropout technique in combination with color selection. We derived a sample of 73 LBG candidates. We compare our selection efficiencies to BM/BX and BzK methods (techniques solely based on ground-based data sets), and find the NUV data to provide greater efficiency for selecting star-forming galaxies. We estimate LBG candidate ages, masses, star formation rates, and extinction from fitting PEGASE synthesis evolution models. We find that about 20% of our LBG candidates are comparable to infrared-luminous LBGs or submillimeter galaxies which are thought to be precursors of massive elliptical galaxies today. Overall, we can show that although BM/BX and BzK methods do identify star-forming galaxies at z {approx} 2, the sample they provide biases against those star-forming galaxies which are more massive and contain sizeable red stellar populations. A true Lyman break criterion at z {approx} 2 is therefore more directly comparable to the populations found at z {approx} 3, which does contain a red fraction.

  4. GALEX-SELECTED LYMAN BREAK GALAXIES AT z ∼ 2: COMPARISON WITH OTHER POPULATIONS

    International Nuclear Information System (INIS)

    Haberzettl, L.; Williger, G.; Lehnert, M. D.; Nesvadba, N.; Davies, L.

    2012-01-01

    We present results of a search for bright Lyman break galaxies (LBGs) at 1.5 ≤ z ≤ 2.5 in the GOODS-S field using an NUV-dropout technique in combination with color selection. We derived a sample of 73 LBG candidates. We compare our selection efficiencies to BM/BX and BzK methods (techniques solely based on ground-based data sets), and find the NUV data to provide greater efficiency for selecting star-forming galaxies. We estimate LBG candidate ages, masses, star formation rates, and extinction from fitting PEGASE synthesis evolution models. We find that about 20% of our LBG candidates are comparable to infrared-luminous LBGs or submillimeter galaxies which are thought to be precursors of massive elliptical galaxies today. Overall, we can show that although BM/BX and BzK methods do identify star-forming galaxies at z ∼ 2, the sample they provide biases against those star-forming galaxies which are more massive and contain sizeable red stellar populations. A true Lyman break criterion at z ∼ 2 is therefore more directly comparable to the populations found at z ∼ 3, which does contain a red fraction.

  5. Precision of systematic and random sampling in clustered populations: habitat patches and aggregating organisms.

    Science.gov (United States)

    McGarvey, Richard; Burch, Paul; Matthews, Janet M

    2016-01-01

    Natural populations of plants and animals spatially cluster because (1) suitable habitat is patchy, and (2) within suitable habitat, individuals aggregate further into clusters of higher density. We compare the precision of random and systematic field sampling survey designs under these two processes of species clustering. Second, we evaluate the performance of 13 estimators for the variance of the sample mean from a systematic survey. Replicated simulated surveys, as counts from 100 transects, allocated either randomly or systematically within the study region, were used to estimate population density in six spatial point populations including habitat patches and Matérn circular clustered aggregations of organisms, together and in combination. The standard one-start aligned systematic survey design, a uniform 10 x 10 grid of transects, was much more precise. Variances of the 10 000 replicated systematic survey mean densities were one-third to one-fifth of those from randomly allocated transects, implying transect sample sizes giving equivalent precision by random survey would need to be three to five times larger. Organisms being restricted to patches of habitat was alone sufficient to yield this precision advantage for the systematic design. But this improved precision for systematic sampling in clustered populations is underestimated by standard variance estimators used to compute confidence intervals. True variance for the survey sample mean was computed from the variance of 10 000 simulated survey mean estimates. Testing 10 published and three newly proposed variance estimators, the two variance estimators (v) that corrected for inter-transect correlation (ν₈ and ν(W)) were the most accurate and also the most precise in clustered populations. These greatly outperformed the two "post-stratification" variance estimators (ν₂ and ν₃) that are now more commonly applied in systematic surveys. Similar variance estimator performance rankings were found with

  6. Population and antenatal-based HIV prevalence estimates in a high contracepting female population in rural South Africa

    Directory of Open Access Journals (Sweden)

    Barnighausen Till

    2007-07-01

    Full Text Available Abstract Background To present and compare population-based and antenatal-care (ANC sentinel surveillance HIV prevalence estimates among women in a rural South African population where both provision of ANC services and family planning is prevalent and fertility is declining. With a need, in such settings, to understand how to appropriately adjust ANC sentinel surveillance estimates to represent HIV prevalence in general populations, and with evidence of possible biases inherent to both surveillance systems, we explore differences between the two systems. There is particular emphasis on unrepresentative selection of ANC clinics and unrepresentative testing in the population. Methods HIV sero-prevalence amongst blood samples collected from women consenting to test during the 2005 annual longitudinal population-based serological survey was compared to anonymous unlinked HIV sero-prevalence amongst women attending antenatal care (ANC first visits in six clinics (January to May 2005. Both surveillance systems were conducted as part of the Africa Centre Demographic Information System. Results Population-based HIV prevalence estimates for all women (25.2% and pregnant women (23.7% were significantly lower than that for ANC attendees (37.7%. A large proportion of women attending urban or peri-urban clinics would be predicted to be resident within rural areas. Although overall estimates remained significantly different, presenting and standardising estimates by age and location (clinic for ANC-based estimates and individual-residence for population-based estimates made some group-specific estimates from the two surveillance systems more predictive of one another. Conclusion It is likely that where ANC coverage and contraceptive use is widespread and fertility is low, population-based surveillance under-estimates HIV prevalence due to unrepresentative testing by age, residence and also probably by HIV status, and that ANC sentinel surveillance over

  7. Quantifying selection in evolving populations using time-resolved genetic data

    Science.gov (United States)

    Illingworth, Christopher J. R.; Mustonen, Ville

    2013-01-01

    Methods which uncover the molecular basis of the adaptive evolution of a population address some important biological questions. For example, the problem of identifying genetic variants which underlie drug resistance, a question of importance for the treatment of pathogens, and of cancer, can be understood as a matter of inferring selection. One difficulty in the inference of variants under positive selection is the potential complexity of the underlying evolutionary dynamics, which may involve an interplay between several contributing processes, including mutation, recombination and genetic drift. A source of progress may be found in modern sequencing technologies, which confer an increasing ability to gather information about evolving populations, granting a window into these complex processes. One particularly interesting development is the ability to follow evolution as it happens, by whole-genome sequencing of an evolving population at multiple time points. We here discuss how to use time-resolved sequence data to draw inferences about the evolutionary dynamics of a population under study. We begin by reviewing our earlier analysis of a yeast selection experiment, in which we used a deterministic evolutionary framework to identify alleles under selection for heat tolerance, and to quantify the selection acting upon them. Considering further the use of advanced intercross lines to measure selection, we here extend this framework to cover scenarios of simultaneous recombination and selection, and of two driver alleles with multiple linked neutral, or passenger, alleles, where the driver pair evolves under an epistatic fitness landscape. We conclude by discussing the limitations of the approach presented and outlining future challenges for such methodologies.

  8. Simultaneous inference of selection and population growth from patterns of variation in the human genome

    DEFF Research Database (Denmark)

    Williamson, Scott H.; Hernandez, Ryan; Fledel-Alon, Adi

    2005-01-01

    Natural selection and demographic forces can have similar effects on patterns of DNA polymorphism. Therefore, to infer selection from samples of DNA sequences, one must simultaneously account for demographic effects. Here we take a model-based approach to this problem by developing predictions fo......-specific methods, and (iii) strong evidence for very recent population growth....... for patterns of polymorphism in the presence of both population size change and natural selection. If data are available from different functional classes of variation, and a priori information suggests that mutations in one of those classes are selectively neutral, then the putatively neutral class can...... this method to a large polymorphism data set from 301 human genes and find (i) widespread negative selection acting on standing nonsynonymous variation, (ii) that the fitness effects of nonsynonymous mutations are well predicted by several measures of amino acid exchangeability, especially site...

  9. Post-stratification based on a choice of a randomization device

    Directory of Open Access Journals (Sweden)

    Sarjinder Singh

    2014-06-01

    Full Text Available In this paper, we use the idea of post-stratification based on the respondents’ choice of a particular randomization device in order to estimate the population proportion of a sensitive characteristic. The proposed idea gives full freedom to the respondents and is expected to result in greater cooperation from them as well as to provide some increase in the relative efficiency of the newly proposed estimator.

  10. Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding.

    Directory of Open Access Journals (Sweden)

    Cécile Grenier

    Full Text Available Genomic selection (GS is a promising strategy for enhancing genetic gain. We investigated the accuracy of genomic estimated breeding values (GEBV in four inter-related synthetic populations that underwent several cycles of recurrent selection in an upland rice-breeding program. A total of 343 S2:4 lines extracted from those populations were phenotyped for flowering time, plant height, grain yield and panicle weight, and genotyped with an average density of one marker per 44.8 kb. The relative effect of the linkage disequilibrium (LD and minor allele frequency (MAF thresholds for selecting markers, the relative size of the training population (TP and of the validation population (VP, the selected trait and the genomic prediction models (frequentist and Bayesian on the accuracy of GEBVs was investigated in 540 cross validation experiments with 100 replicates. The effect of kinship between the training and validation populations was tested in an additional set of 840 cross validation experiments with a single genomic prediction model. LD was high (average r2 = 0.59 at 25 kb and decreased slowly, distribution of allele frequencies at individual loci was markedly skewed toward unbalanced frequencies (MAF average value 15.2% and median 9.6%, and differentiation between the four synthetic populations was low (FST ≤0.06. The accuracy of GEBV across all cross validation experiments ranged from 0.12 to 0.54 with an average of 0.30. Significant differences in accuracy were observed among the different levels of each factor investigated. Phenotypic traits had the biggest effect, and the size of the incidence matrix had the smallest. Significant first degree interaction was observed for GEBV accuracy between traits and all the other factors studied, and between prediction models and LD, MAF and composition of the TP. The potential of GS to accelerate genetic gain and breeding options to increase the accuracy of predictions are discussed.

  11. An opinion formation based binary optimization approach for feature selection

    Science.gov (United States)

    Hamedmoghadam, Homayoun; Jalili, Mahdi; Yu, Xinghuo

    2018-02-01

    This paper proposed a novel optimization method based on opinion formation in complex network systems. The proposed optimization technique mimics human-human interaction mechanism based on a mathematical model derived from social sciences. Our method encodes a subset of selected features to the opinion of an artificial agent and simulates the opinion formation process among a population of agents to solve the feature selection problem. The agents interact using an underlying interaction network structure and get into consensus in their opinions, while finding better solutions to the problem. A number of mechanisms are employed to avoid getting trapped in local minima. We compare the performance of the proposed method with a number of classical population-based optimization methods and a state-of-the-art opinion formation based method. Our experiments on a number of high dimensional datasets reveal outperformance of the proposed algorithm over others.

  12. Selective Pressures Explain Differences in Flower Color among Gentiana lutea Populations.

    Science.gov (United States)

    Sobral, Mar; Veiga, Tania; Domínguez, Paula; Guitián, Javier A; Guitián, Pablo; Guitián, José M

    2015-01-01

    Flower color variation among plant populations might reflect adaptation to local conditions such as the interacting animal community. In the northwest Iberian Peninsula, flower color of Gentiana lutea varies longitudinally among populations, ranging from orange to yellow. We explored whether flower color is locally adapted and the role of pollinators and seed predators as agents of selection by analyzing the influence of flower color on (i) pollinator visitation rate and (ii) escape from seed predation and (iii) by testing whether differences in pollinator communities correlate with flower color variation across populations. Finally, (iv) we investigated whether variation in selective pressures explains flower color variation among 12 G. lutea populations. Flower color influenced pollinator visits and differences in flower color among populations were related to variation in pollinator communities. Selective pressures on flower color vary among populations and explain part of flower color differences among populations of G. lutea. We conclude that flower color in G. lutea is locally adapted and that pollinators play a role in this adaptation.

  13. Selective Pressures Explain Differences in Flower Color among Gentiana lutea Populations.

    Directory of Open Access Journals (Sweden)

    Mar Sobral

    Full Text Available Flower color variation among plant populations might reflect adaptation to local conditions such as the interacting animal community. In the northwest Iberian Peninsula, flower color of Gentiana lutea varies longitudinally among populations, ranging from orange to yellow. We explored whether flower color is locally adapted and the role of pollinators and seed predators as agents of selection by analyzing the influence of flower color on (i pollinator visitation rate and (ii escape from seed predation and (iii by testing whether differences in pollinator communities correlate with flower color variation across populations. Finally, (iv we investigated whether variation in selective pressures explains flower color variation among 12 G. lutea populations. Flower color influenced pollinator visits and differences in flower color among populations were related to variation in pollinator communities. Selective pressures on flower color vary among populations and explain part of flower color differences among populations of G. lutea. We conclude that flower color in G. lutea is locally adapted and that pollinators play a role in this adaptation.

  14. Parallel selection on TRPV6 in human populations

    OpenAIRE

    Hughes, David A; Tang, Kun; Strotmann, Rainer; Schöneberg, Torsten; Prenen, Jean; Nilius, Bernd; Stoneking, Mark

    2008-01-01

    We identified and examined a candidate gene for local directional selection in Europeans, TRPV6, and conclude that selection has acted on standing genetic variation at this locus, creating parallel soft sweep events in humans. A novel modification of the extended haplotype homozygosity (EHH) test was utilized, which compares EHH for a single allele across populations, to investigate the signature of selection at TRPV6 and neighboring linked loci in published data sets for Europeans, Asians an...

  15. Population-based intervention for cardiovascular diseases related knowledge and behaviours in Asian Indian women.

    Science.gov (United States)

    Pandey, Ravindra Mohan; Agrawal, Aachu; Misra, Anoop; Vikram, Naval Kishore; Misra, Puneet; Dey, Sanjit; Rao, Shobha; Vasantha Devi, K P; Usha Menon, V; Revathi, R; Sharma, Vinita; Gupta, Rajeev

    2013-01-01

    There is poor knowledge and behaviors regarding chronic diseases related nutritional and lifestyle factors among women in low income countries. To evaluate efficacy of a multilevel population-based intervention in improving knowledge and practices for related factors we performed a study in India. Population based study among women 35-70 years was performed in four urban and five rural locations. Stratified sampling was performed and we enrolled 4624 (rural 2616, urban 2008) of eligible 8000 women (58%). Demographic details, medical history, diet, physical activity and anthropometry were recorded and blood hemoglobin, glucose and total cholesterol determined. Knowledge and behaviors regarding diet in chronic diseases were inquired in a randomly selected 100 women at each site (n = 900). A systematic multilevel population based intervention (using posters, handouts, street plays, public lectures, group lectures and focused group discussions) was administered over 6 months at each site. The questionnaire was re-administered at the end in random 100 women (n = 900) and differences determined. Descriptive statistics are reported. Comparison of parameters before and after intervention was assessed using Mann Whitney test. Prevalence (%) of chronic disease related lifestyles and risk factors in rural/urban women, respectively, was illiteracy in 63.6/29.4, smoking/tobacco use 39.3/18.9, high fat intake 93.6/93.4, high salt intake 18.2/12.6, low physical activity 59.5/70.2, overweight/obesity 22.5/45.6, truncal obesity 13.0/44.3, hypertension 31.6/48.2, hypercholesterolemia 13.5/27.7, and diabetes in 4.3/15.1 percent. Composite chronic diseases knowledge at baseline vs after intervention increased significantly in overall (32.0 vs 62.0), rural (29.0 vs 63.5) and urban (39.5 vs 60.5) groups (p women in rural and urban locations in India increased chronic disease knowledge but failed to influence practices. Copyright © 2013. Published by Elsevier B.V.

  16. Unilateral Vocal Fold Paralysis and Risk of Pneumonia: A Nationwide Population-Based Cohort Study.

    Science.gov (United States)

    Tsai, Ming-Shao; Yang, Yao-Hsu; Liu, Chia-Yen; Lin, Meng-Hung; Chang, Geng-He; Tsai, Yao-Te; Li, Hsueh-Yu; Tsai, Ying-Huang; Hsu, Cheng-Ming

    2018-05-01

    Objective To investigate pneumonia risk among patients with unilateral vocal fold paralysis (UVFP). Study Design Retrospective population-based cohort study. Setting This study used data from the National Health Insurance Research Database of Taiwan, a nationwide population-based database. Subjects and Methods A total of 419 patients newly diagnosed with UVFP between January 1, 1997, and December 31, 2013, were identified from the Longitudinal Health Insurance Database 2000, a nationally representative database of 1 million randomly selected patients. Moreover, 1676 patients without UVFP were matched to patients with UVFP at a 1:4 ratio based on age, sex, socioeconomic status, urbanization level, and site-specific cancers. Patients were followed up until death or the end of the study period (December 31, 2013). The primary outcome was the occurrence of pneumonia. Results The cumulative incidence of pneumonia was significantly higher for patients with UVFP than those without UFVP ( P < .001). The adjusted Cox proportional hazard model showed that UVFP was significantly associated with a higher incidence of pneumonia (hazard ratio, 1.97; 95% CI, 1.35-2.86; P < .001). Subgroup analyses demonstrated that UVFP was an independent risk factor of pneumonia for 4 subgroups: young (18-50 years), older (≥51 years), male, and cancer. Conclusion This is the first nationwide population-based cohort study to investigate the association between UVFP and pneumonia. The findings indicate that UVFP is an independent risk factor of pneumonia. Given the study results, physicians should be aware of the potential for pneumonia occurrence following UVFP.

  17. LOD score exclusion analyses for candidate QTLs using random population samples.

    Science.gov (United States)

    Deng, Hong-Wen

    2003-11-01

    While extensive analyses have been conducted to test for, no formal analyses have been conducted to test against, the importance of candidate genes as putative QTLs using random population samples. Previously, we developed an LOD score exclusion mapping approach for candidate genes for complex diseases. Here, we extend this LOD score approach for exclusion analyses of candidate genes for quantitative traits. Under this approach, specific genetic effects (as reflected by heritability) and inheritance models at candidate QTLs can be analyzed and if an LOD score is < or = -2.0, the locus can be excluded from having a heritability larger than that specified. Simulations show that this approach has high power to exclude a candidate gene from having moderate genetic effects if it is not a QTL and is robust to population admixture. Our exclusion analysis complements association analysis for candidate genes as putative QTLs in random population samples. The approach is applied to test the importance of Vitamin D receptor (VDR) gene as a potential QTL underlying the variation of bone mass, an important determinant of osteoporosis.

  18. Analysis and applications of a frequency selective surface via a random distribution method

    International Nuclear Information System (INIS)

    Xie Shao-Yi; Huang Jing-Jian; Yuan Nai-Chang; Liu Li-Guo

    2014-01-01

    A novel frequency selective surface (FSS) for reducing radar cross section (RCS) is proposed in this paper. This FSS is based on the random distribution method, so it can be called random surface. In this paper, the stacked patches serving as periodic elements are employed for RCS reduction. Previous work has demonstrated the efficiency by utilizing the microstrip patches, especially for the reflectarray. First, the relevant theory of the method is described. Then a sample of a three-layer variable-sized stacked patch random surface with a dimension of 260 mm×260 mm is simulated, fabricated, and measured in order to demonstrate the validity of the proposed design. For the normal incidence, the 8-dB RCS reduction can be achieved both by the simulation and the measurement in 8 GHz–13 GHz. The oblique incidence of 30° is also investigated, in which the 7-dB RCS reduction can be obtained in a frequency range of 8 GHz–14 GHz. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  19. Directional selection effects on patterns of phenotypic (co)variation in wild populations.

    Science.gov (United States)

    Assis, A P A; Patton, J L; Hubbe, A; Marroig, G

    2016-11-30

    Phenotypic (co)variation is a prerequisite for evolutionary change, and understanding how (co)variation evolves is of crucial importance to the biological sciences. Theoretical models predict that under directional selection, phenotypic (co)variation should evolve in step with the underlying adaptive landscape, increasing the degree of correlation among co-selected traits as well as the amount of genetic variance in the direction of selection. Whether either of these outcomes occurs in natural populations is an open question and thus an important gap in evolutionary theory. Here, we documented changes in the phenotypic (co)variation structure in two separate natural populations in each of two chipmunk species (Tamias alpinus and T. speciosus) undergoing directional selection. In populations where selection was strongest (those of T. alpinus), we observed changes, at least for one population, in phenotypic (co)variation that matched theoretical expectations, namely an increase of both phenotypic integration and (co)variance in the direction of selection and a re-alignment of the major axis of variation with the selection gradient. © 2016 The Author(s).

  20. POPULATION BASED COLORECTAL CANCER SCREENING: COMPARISON OF TWO FAECAL OCCULT BLOOD TESTS

    Directory of Open Access Journals (Sweden)

    Miren Begoña eZubero

    2014-01-01

    Full Text Available Background: The aim of screening for colorectal cancer is to improve prognosis by the detection of cancer at its early stages. In order to inform the decision on the specific test to be used in the population-based programme in the Basque Autonomous Region (Spain, we compared two immunochemical faecal occult blood quantitative tests (I-FOBT. Methods: Residents of selected study areas, aged 50-69 years, were invited to participate in the screening. Two tests based on latex agglutination (OC-Sensor and FOB Gold were randomly assigned to different study areas. A colonoscopy was offered to patients with a positive test result. The cut-off point used to classify a result as positive, according to manufacturer’s recommendations, was 100 ng/ml for both tests. Results: The invited population included 37,999 individuals. Participation rates were 61.8% (n=11,162 for OC-Sensor and 59.1% (n=11,786 for FOB Gold, (p=0.008. Positive rate for OC-Sensor was 6.6% (n=737 and 8.5% (n=1,002 for FOB Gold, (pConclusions: OC-Sensor test appears to be superior for I-FOBT based CRC screening, given its acceptance, ease of use, associated small number of errors and its screening accuracy. FOB-Gold on the other hand, has higher rate of positive values, with more colonoscopies performed, it shows higher detection incidence rates, but involves more false positives.

  1. A school-based randomized controlled trial to improve physical activity among Iranian high school girls

    Directory of Open Access Journals (Sweden)

    Ghofranipour Fazloalha

    2008-04-01

    Full Text Available Abstract Background Physical activity (PA rates decline precipitously during the high school years and are consistently lower among adolescent girls than adolescent boys. Due to cultural barriers, this problem might be exacerbated in female Iranian adolescents. However, little intervention research has been conducted to try to increase PA participation rates with this population. Because PA interventions in schools have the potential to reach many children and adolescents, this study reports on PA intervention research conducted in all-female Iranian high schools. Methods A randomized controlled trial was conducted to examine the effects of two six-month tailored interventions on potential determinants of PA and PA behavior. Students (N = 161 were randomly allocated to one of three conditions: an intervention based on Pender's Health Promotion model (HP, an intervention based on an integration of the health promotion model and selected constructs from the Transtheoretical model (THP, and a control group (CON. Measures were administered prior to the intervention, at post-intervention and at a six-month follow-up. Results Repeated measure ANOVAs showed a significant interaction between group and time for perceived benefits, self efficacy, interpersonal norms, social support, behavioral processes, and PA behavior, indicating that both intervention groups significantly improved across the 24-week intervention, whereas the control group did not. Participants in the THP group showed greater use of counter conditioning and stimulus control at post-intervention and at follow-up. While there were no significant differences in PA between the HP and CON groups at follow-up, a significant difference was still found between the THP and the CON group. Conclusion This study provides the first evidence of the effectiveness of a PA intervention based on Pender's HP model combined with selected aspects of the TTM on potential determinants to increase PA among

  2. Environmental change disrupts communication and sexual selection in a stickleback population.

    Science.gov (United States)

    Candolin, Ulrika; Tukiainen, Iina; Bertell, Elina

    2016-04-01

    Environmental change that disrupts communication during mate choice and alters sexual selection could influence population dynamics. Yet little is known about such long-term effects. We investigated experimentally the consequences that disrupted visual communication during mate choice has for the quantity and viability of offspring produced in a threespine stickleback population (Gasterosteus aculeatus). We further related the results to long-term monitoring of population dynamics in the field to determine if changes are apparent under natural conditions. The results show that impaired visual communication because of algal blooms reduces reliability of male visual signals as indicators of offspring survival during their first weeks of life. This relaxes sexual selection but has no effect on the number of offspring hatching, as most males have a high hatching success in turbid water. Despite eutrophication and high turbidity levels that interfere with communication during mate choice, the population has grown during recent decades. Large numbers of offspring hatching, combined with high variation in juvenile fitness, has probably shifted selection to later life history stages and maintained a viable population. Together with reduced cost of sexual selection and ongoing ecosystem changes caused by human activities, this could have promoted population growth. These results point to the complexity of ecosystems and the necessity to consider all influencing factors when attempting to understand impacts of human activities on populations.

  3. Natural selection and infectious disease in human populations

    Science.gov (United States)

    Karlsson, Elinor K.; Kwiatkowski, Dominic P.; Sabeti, Pardis C.

    2015-01-01

    The ancient biological 'arms race' between microbial pathogens and humans has shaped genetic variation in modern populations, and this has important implications for the growing field of medical genomics. As humans migrated throughout the world, populations encountered distinct pathogens, and natural selection increased the prevalence of alleles that are advantageous in the new ecosystems in both host and pathogens. This ancient history now influences human infectious disease susceptibility and microbiome homeostasis, and contributes to common diseases that show geographical disparities, such as autoimmune and metabolic disorders. Using new high-throughput technologies, analytical methods and expanding public data resources, the investigation of natural selection is leading to new insights into the function and dysfunction of human biology. PMID:24776769

  4. Hebbian Learning in a Random Network Captures Selectivity Properties of the Prefrontal Cortex

    Science.gov (United States)

    Lindsay, Grace W.

    2017-01-01

    Complex cognitive behaviors, such as context-switching and rule-following, are thought to be supported by the prefrontal cortex (PFC). Neural activity in the PFC must thus be specialized to specific tasks while retaining flexibility. Nonlinear “mixed” selectivity is an important neurophysiological trait for enabling complex and context-dependent behaviors. Here we investigate (1) the extent to which the PFC exhibits computationally relevant properties, such as mixed selectivity, and (2) how such properties could arise via circuit mechanisms. We show that PFC cells recorded from male and female rhesus macaques during a complex task show a moderate level of specialization and structure that is not replicated by a model wherein cells receive random feedforward inputs. While random connectivity can be effective at generating mixed selectivity, the data show significantly more mixed selectivity than predicted by a model with otherwise matched parameters. A simple Hebbian learning rule applied to the random connectivity, however, increases mixed selectivity and enables the model to match the data more accurately. To explain how learning achieves this, we provide analysis along with a clear geometric interpretation of the impact of learning on selectivity. After learning, the model also matches the data on measures of noise, response density, clustering, and the distribution of selectivities. Of two styles of Hebbian learning tested, the simpler and more biologically plausible option better matches the data. These modeling results provide clues about how neural properties important for cognition can arise in a circuit and make clear experimental predictions regarding how various measures of selectivity would evolve during animal training. SIGNIFICANCE STATEMENT The prefrontal cortex is a brain region believed to support the ability of animals to engage in complex behavior. How neurons in this area respond to stimuli—and in particular, to combinations of stimuli (

  5. 24 CFR 960.407 - Selection preference for mixed population developments.

    Science.gov (United States)

    2010-04-01

    ... population developments. 960.407 Section 960.407 Housing and Urban Development Regulations Relating to... Elderly Families and Disabled Families in Mixed Population Projects § 960.407 Selection preference for mixed population developments. (a) The PHA must give preference to elderly families and disabled...

  6. Genetic Gains in Grain Yield of a Maize Population Improved through Marker Assisted Recurrent Selection under Stress and Non-stress Conditions in West Africa

    Directory of Open Access Journals (Sweden)

    Rekiya O. Abdulmalik

    2017-05-01

    Full Text Available Marker-assisted recurrent selection (MARS is a breeding method used to accumulate favorable alleles that for example confer tolerance to drought in inbred lines from several genomic regions within a single population. A bi-parental cross formed from two parents that combine resistance to Striga hermonthica with drought tolerance, which was improved through MARS, was used to assess changes in the frequency of favorable alleles and its impact on inbred line improvement. A total of 200 testcrosses of randomly selected S1 lines derived from the original (C0 and advanced selection cycles of this bi-parental population, were evaluated under drought stress (DS and well-watered (WW conditions at Ikenne and under artificial Striga infestation at Abuja and Mokwa in Nigeria in 2014 and 2015. Also, 60 randomly selected S1 lines each derived from the four cycles (C0, C1, C2, C3 were genotyped with 233 SNP markers using KASP assay. The results showed that the frequency of favorable alleles increased with MARS in the bi-parental population with none of the markers showing fixation. The gain in grain yield was not significant under DS condition due to the combined effect of DS and armyworm infestation in 2015. Because the parents used for developing the bi-parental cross combined tolerance to drought with resistance to Striga, improvement in grain yield under DS did not result in undesirable changes in resistance to the parasite in the bi-parental maize population improved through MARS. MARS increased the mean number of combinations of favorable alleles in S1 lines from 114 in C0 to 124 in C3. The level of heterozygosity decreased by 15%, while homozygosity increased by 13% due to the loss of some genotypes in the population. This study demonstrated the effectiveness of MARS in increasing the frequency of favorable alleles for tolerance to drought without disrupting the level of resistance to Striga in a bi-parental population targeted as a source of improved

  7. Genetic Gains in Grain Yield of a Maize Population Improved through Marker Assisted Recurrent Selection under Stress and Non-stress Conditions in West Africa.

    Science.gov (United States)

    Abdulmalik, Rekiya O; Menkir, Abebe; Meseka, Silvestro K; Unachukwu, Nnanna; Ado, Shehu G; Olarewaju, Joseph D; Aba, Daniel A; Hearne, Sarah; Crossa, Jose; Gedil, Melaku

    2017-01-01

    Marker-assisted recurrent selection (MARS) is a breeding method used to accumulate favorable alleles that for example confer tolerance to drought in inbred lines from several genomic regions within a single population. A bi-parental cross formed from two parents that combine resistance to Striga hermonthica with drought tolerance, which was improved through MARS, was used to assess changes in the frequency of favorable alleles and its impact on inbred line improvement. A total of 200 testcrosses of randomly selected S 1 lines derived from the original (C 0 ) and advanced selection cycles of this bi-parental population, were evaluated under drought stress (DS) and well-watered (WW) conditions at Ikenne and under artificial Striga infestation at Abuja and Mokwa in Nigeria in 2014 and 2015. Also, 60 randomly selected S 1 lines each derived from the four cycles (C 0 , C 1 , C 2 , C 3 ) were genotyped with 233 SNP markers using KASP assay. The results showed that the frequency of favorable alleles increased with MARS in the bi-parental population with none of the markers showing fixation. The gain in grain yield was not significant under DS condition due to the combined effect of DS and armyworm infestation in 2015. Because the parents used for developing the bi-parental cross combined tolerance to drought with resistance to Striga , improvement in grain yield under DS did not result in undesirable changes in resistance to the parasite in the bi-parental maize population improved through MARS. MARS increased the mean number of combinations of favorable alleles in S 1 lines from 114 in C 0 to 124 in C 3 . The level of heterozygosity decreased by 15%, while homozygosity increased by 13% due to the loss of some genotypes in the population. This study demonstrated the effectiveness of MARS in increasing the frequency of favorable alleles for tolerance to drought without disrupting the level of resistance to Striga in a bi-parental population targeted as a source of improved

  8. Rapid Cycling Genomic Selection in a Multiparental Tropical Maize Population.

    Science.gov (United States)

    Zhang, Xuecai; Pérez-Rodríguez, Paulino; Burgueño, Juan; Olsen, Michael; Buckler, Edward; Atlin, Gary; Prasanna, Boddupalli M; Vargas, Mateo; San Vicente, Félix; Crossa, José

    2017-07-05

    Genomic selection (GS) increases genetic gain by reducing the length of the selection cycle, as has been exemplified in maize using rapid cycling recombination of biparental populations. However, no results of GS applied to maize multi-parental populations have been reported so far. This study is the first to show realized genetic gains of rapid cycling genomic selection (RCGS) for four recombination cycles in a multi-parental tropical maize population. Eighteen elite tropical maize lines were intercrossed twice, and self-pollinated once, to form the cycle 0 (C 0 ) training population. A total of 1000 ear-to-row C 0 families was genotyped with 955,690 genotyping-by-sequencing SNP markers; their testcrosses were phenotyped at four optimal locations in Mexico to form the training population. Individuals from families with the best plant types, maturity, and grain yield were selected and intermated to form RCGS cycle 1 (C 1 ). Predictions of the genotyped individuals forming cycle C 1 were made, and the best predicted grain yielders were selected as parents of C 2 ; this was repeated for more cycles (C 2 , C 3 , and C 4 ), thereby achieving two cycles per year. Multi-environment trials of individuals from populations C 0, C 1 , C 2 , C 3 , and C 4 , together with four benchmark checks were evaluated at two locations in Mexico. Results indicated that realized grain yield from C 1 to C 4 reached 0.225 ton ha -1 per cycle, which is equivalent to 0.100 ton ha -1  yr -1 over a 4.5-yr breeding period from the initial cross to the last cycle. Compared with the original 18 parents used to form cycle 0 (C 0 ), genetic diversity narrowed only slightly during the last GS cycles (C 3 and C 4 ). Results indicate that, in tropical maize multi-parental breeding populations, RCGS can be an effective breeding strategy for simultaneously conserving genetic diversity and achieving high genetic gains in a short period of time. Copyright © 2017 Zhang et al.

  9. DNABP: Identification of DNA-Binding Proteins Based on Feature Selection Using a Random Forest and Predicting Binding Residues.

    Science.gov (United States)

    Ma, Xin; Guo, Jing; Sun, Xiao

    2016-01-01

    DNA-binding proteins are fundamentally important in cellular processes. Several computational-based methods have been developed to improve the prediction of DNA-binding proteins in previous years. However, insufficient work has been done on the prediction of DNA-binding proteins from protein sequence information. In this paper, a novel predictor, DNABP (DNA-binding proteins), was designed to predict DNA-binding proteins using the random forest (RF) classifier with a hybrid feature. The hybrid feature contains two types of novel sequence features, which reflect information about the conservation of physicochemical properties of the amino acids, and the binding propensity of DNA-binding residues and non-binding propensities of non-binding residues. The comparisons with each feature demonstrated that these two novel features contributed most to the improvement in predictive ability. Furthermore, to improve the prediction performance of the DNABP model, feature selection using the minimum redundancy maximum relevance (mRMR) method combined with incremental feature selection (IFS) was carried out during the model construction. The results showed that the DNABP model could achieve 86.90% accuracy, 83.76% sensitivity, 90.03% specificity and a Matthews correlation coefficient of 0.727. High prediction accuracy and performance comparisons with previous research suggested that DNABP could be a useful approach to identify DNA-binding proteins from sequence information. The DNABP web server system is freely available at http://www.cbi.seu.edu.cn/DNABP/.

  10. Selfing for the design of genomic selection experiments in biparental plant populations.

    Science.gov (United States)

    McClosky, Benjamin; LaCombe, Jason; Tanksley, Steven D

    2013-11-01

    Self-fertilization (selfing) is commonly used for population development in plant breeding, and it is well established that selfing increases genetic variance between lines, thus increasing response to phenotypic selection. Furthermore, numerous studies have explored how selfing can be deployed to maximal benefit in the context of traditional plant breeding programs (Cornish in Heredity 65:201-211,1990a, Heredity 65:213-220,1990b; Liu et al. in Theor Appl Genet 109:370-376, 2004; Pooni and Jinks in Heredity 54:255-260, 1985). However, the impact of selfing on response to genomic selection has not been explored. In the current study we examined how selfing impacts the two key aspects of genomic selection-GEBV prediction (training) and selection response. We reach the following conclusions: (1) On average, selfing increases genomic selection gains by more than 70 %. (2) The gains in genomic selection response attributable to selfing hold over a wide range population sizes (100-500), heritabilities (0.2-0.8), and selection intensities (0.01-0.1). However, the benefits of selfing are dramatically reduced as the number of QTLs drops below 20. (3) The major cause of the improved response to genomic selection with selfing is through an increase in the occurrence of superior genotypes and not through improved GEBV predictions. While performance of the training population improves with selfing (especially with low heritability and small population sizes), the magnitude of these improvements is relatively small compared with improvements observed in the selection population. To illustrate the value of these insights, we propose a practical genomic selection scheme that substantially shortens the number of generations required to fully capture the benefits of selfing. Specifically, we provide simulation evidence that indicates the proposed scheme matches or exceeds the selection gains observed in advanced populations (i.e. F 8 and doubled haploid) across a broad range of

  11. Association of bladder pain syndrome/interstitial cystitis with urinary calculus: a nationwide population-based study.

    Science.gov (United States)

    Keller, Joseph; Chen, Yi-Kuang; Lin, Herng-Ching

    2013-04-01

    Although one prior study reported an association between bladder pain syndrome/interstitial cystitis (BPS/IC) and urinary calculi (UC), no population-based study to date has been conducted to explore this relationship. Therefore, using a population-based data set in Taiwan, this study set out to investigate the association between BPS/IC and a prior diagnosis of UC. This study included 9,269 cases who had received their first-time diagnosis of BPS/IC between 2006 and 2007 and 46,345 randomly selected controls. We used conditional logistic regression analysis to compute the odds ratio (OR) and its corresponding 95 % confidence interval (CI) for having been previously diagnosed with UC between cases and controls. There was a significant difference in the prevalence of prior UC between cases and controls (8.1 vs 4.3 %, p calculus, ureter calculus, bladder calculus, and unspecified calculus when compared to controls were 1.58 (95 % CI = 1.38-1.81), 1.73 (95 % CI = 1.45-2.05), 3.80 (95 % CI = 2.18-6.62), and 1.83 (95 % CI = 1.59-2.11), respectively. This work generates the hypothesis that UC may be associated with BPS/IC.

  12. Statistical aspects of evolution under natural selection, with implications for the advantage of sexual reproduction.

    Science.gov (United States)

    Crouch, Daniel J M

    2017-10-27

    The prevalence of sexual reproduction remains mysterious, as it poses clear evolutionary drawbacks compared to reproducing asexually. Several possible explanations exist, with one of the most likely being that finite population size causes linkage disequilibria to randomly generate and impede the progress of natural selection, and that these are eroded by recombination via sexual reproduction. Previous investigations have either analysed this phenomenon in detail for small numbers of loci, or performed population simulations for many loci. Here we present a quantitative genetic model for fitness, based on the Price Equation, in order to examine the theoretical consequences of randomly generated linkage disequilibria when there are many loci. In addition, most previous work has been concerned with the long-term consequences of deleterious linkage disequilibria for population fitness. The expected change in mean fitness between consecutive generations, a measure of short-term evolutionary success, is shown under random environmental influences to be related to the autocovariance in mean fitness between the generations, capturing the effects of stochastic forces such as genetic drift. Interaction between genetic drift and natural selection, due to randomly generated linkage disequilibria, is demonstrated to be one possible source of mean fitness autocovariance. This suggests a possible role for sexual reproduction in reducing the negative effects of genetic drift, thereby improving the short-term efficacy of natural selection. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Population genetic data of the NGM SElect STR loci in Chinese Han population from Zhejiang region, China.

    Science.gov (United States)

    Zhou, Anju; Wu, Weiwei; Liu, Qiuling; Wu, Yeda; Lu, Dejian

    2013-03-01

    Genetic variations of the 17 NGM SElect STR loci in Chinese Han samples from the Zhejiang region were analyzed. The results show that the NGM SElect is a highly genetic informative system in Zhejiang Han, and this population shows quite different genetic data from other major populations in the world with the exception of the Fujian Han.

  14. The National Women's Health Study: assembly and description of a population-based reproductive cohort

    Directory of Open Access Journals (Sweden)

    Prior Susan

    2004-08-01

    Full Text Available Abstract Background Miscarriage is a common event but is remarkably difficult to measure in epidemiological studies. Few large-scale population-based studies have been conducted in the UK. Methods This was a population-based two-stage postal survey of reproductive histories of adult women living in the United Kingdom in 2001, sampled from the electronic electoral roll. In Stage 1 a short "screening" questionnaire was sent to over 60,000 randomly selected women in order to identify those aged 55 and under who had ever been pregnant or ever attempted to achieve a pregnancy, from whom a brief reproductive history was requested. Stage 2 involved a more lengthy questionnaire requesting detailed information on every pregnancy (and fertility problems, and questions relating to socio-demographic, behavioural and other factors for the most recent pregnancy in order to examine risk factors for miscarriage. Data on stillbirth, multiple birth and maternal age are compared to national data in order to assess response bias. Results The response rate was 49% for Stage 1 and 73% for the more targeted Stage 2. A total of 26,050 questionnaires were returned in Stage 1. Of the 17,748 women who were eligible on the grounds of age, 27% reported that they had never been pregnant and had never attempted to conceive a child. The remaining 13,035 women reported a total of 30,661 pregnancies. Comparison of key reproductive indicators (stillbirth and multiple birth rates and maternal age at first birth with national statistics showed that the data look remarkably similar to the general population. Conclusions This study has enabled the assembly of a large population-based dataset of women's reproductive histories which appears unbiased compared to the general UK population and which will enable investigation of hard-to-measure outcomes such as miscarriage and infertility.

  15. Survivor bias in Mendelian randomization analysis

    DEFF Research Database (Denmark)

    Vansteelandt, Stijn; Dukes, Oliver; Martinussen, Torben

    2017-01-01

    Mendelian randomization studies employ genotypes as experimental handles to infer the effect of genetically modified exposures (e.g. vitamin D exposure) on disease outcomes (e.g. mortality). The statistical analysis of these studies makes use of the standard instrumental variables framework. Many...... of these studies focus on elderly populations, thereby ignoring the problem of left truncation, which arises due to the selection of study participants being conditional upon surviving up to the time of study onset. Such selection, in general, invalidates the assumptions on which the instrumental variables...... analysis rests. We show that Mendelian randomization studies of adult or elderly populations will therefore, in general, return biased estimates of the exposure effect when the considered genotype affects mortality; in contrast, standard tests of the causal null hypothesis that the exposure does not affect...

  16. Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection.

    Science.gov (United States)

    Ojosnegros, Samuel; Agudo, Rubén; Sierra, Macarena; Briones, Carlos; Sierra, Saleta; González-López, Claudia; Domingo, Esteban; Cristina, Juan

    2008-07-17

    The molecular events and evolutionary forces underlying lethal mutagenesis of virus (or virus extinction through an excess of mutations) are not well understood. Here we apply for the first time phylogenetic methods and Partition Analysis of Quasispecies (PAQ) to monitor genetic distances and intra-population structures of mutant spectra of foot-and-mouth disease virus (FMDV) quasispecies subjected to mutagenesis by base and nucleoside analogues. Phylogenetic and PAQ analyses have revealed a highly dynamic variation of intrapopulation diversity of FMDV quasispecies. The population diversity first suffers striking expansions in the presence of mutagens and then compressions either when the presence of the mutagenic analogue was discontinued or when a mutation that decreased sensitivity to a mutagen was selected. The pattern of mutations found in the populations was in agreement with the behavior of the corresponding nucleotide analogues with FMDV in vitro. Mutations accumulated at preferred genomic sites, and dn/ds ratios indicate the operation of negative (or purifying) selection in populations subjected to mutagenesis. No evidence of unusually elevated genetic distances has been obtained for FMDV populations approaching extinction. Phylogenetic and PAQ analysis provide adequate procedures to describe the evolution of viral sequences subjected to lethal mutagenesis. These methods define the changes of intra-population structure more precisely than mutation frequencies and Shannon entropies. PAQ is very sensitive to variations of intrapopulation genetic distances. Strong negative (or purifying) selection operates in FMDV populations subjected to enhanced mutagenesis. The quantifications provide evidence that extinction does not imply unusual increases of intrapopulation complexity, in support of the lethal defection model of virus extinction.

  17. From Protocols to Publications: A Study in Selective Reporting of Outcomes in Randomized Trials in Oncology.

    Science.gov (United States)

    Raghav, Kanwal Pratap Singh; Mahajan, Sminil; Yao, James C; Hobbs, Brian P; Berry, Donald A; Pentz, Rebecca D; Tam, Alda; Hong, Waun K; Ellis, Lee M; Abbruzzese, James; Overman, Michael J

    2015-11-01

    The decision by journals to append protocols to published reports of randomized trials was a landmark event in clinical trial reporting. However, limited information is available on how this initiative effected transparency and selective reporting of clinical trial data. We analyzed 74 oncology-based randomized trials published in Journal of Clinical Oncology, the New England Journal of Medicine, and The Lancet in 2012. To ascertain integrity of reporting, we compared published reports with their respective appended protocols with regard to primary end points, nonprimary end points, unplanned end points, and unplanned analyses. A total of 86 primary end points were reported in 74 randomized trials; nine trials had greater than one primary end point. Nine trials (12.2%) had some discrepancy between their planned and published primary end points. A total of 579 nonprimary end points (median, seven per trial) were planned, of which 373 (64.4%; median, five per trial) were reported. A significant positive correlation was found between the number of planned and nonreported nonprimary end points (Spearman r = 0.66; P medicine, additional initiatives are needed to minimize selective reporting. © 2015 by American Society of Clinical Oncology.

  18. Gaussian process-based Bayesian nonparametric inference of population size trajectories from gene genealogies.

    Science.gov (United States)

    Palacios, Julia A; Minin, Vladimir N

    2013-03-01

    Changes in population size influence genetic diversity of the population and, as a result, leave a signature of these changes in individual genomes in the population. We are interested in the inverse problem of reconstructing past population dynamics from genomic data. We start with a standard framework based on the coalescent, a stochastic process that generates genealogies connecting randomly sampled individuals from the population of interest. These genealogies serve as a glue between the population demographic history and genomic sequences. It turns out that only the times of genealogical lineage coalescences contain information about population size dynamics. Viewing these coalescent times as a point process, estimating population size trajectories is equivalent to estimating a conditional intensity of this point process. Therefore, our inverse problem is similar to estimating an inhomogeneous Poisson process intensity function. We demonstrate how recent advances in Gaussian process-based nonparametric inference for Poisson processes can be extended to Bayesian nonparametric estimation of population size dynamics under the coalescent. We compare our Gaussian process (GP) approach to one of the state-of-the-art Gaussian Markov random field (GMRF) methods for estimating population trajectories. Using simulated data, we demonstrate that our method has better accuracy and precision. Next, we analyze two genealogies reconstructed from real sequences of hepatitis C and human Influenza A viruses. In both cases, we recover more believed aspects of the viral demographic histories than the GMRF approach. We also find that our GP method produces more reasonable uncertainty estimates than the GMRF method. Copyright © 2013, The International Biometric Society.

  19. Reducing under-reporting of stigmatized health events using the List Experiment: results from a randomized, population-based study of abortion in Liberia.

    Science.gov (United States)

    Moseson, Heidi; Massaquoi, Moses; Dehlendorf, Christine; Bawo, Luke; Dahn, Bernice; Zolia, Yah; Vittinghoff, Eric; Hiatt, Robert A; Gerdts, Caitlin

    2015-12-01

    Direct measurement of sensitive health events is often limited by high levels of under-reporting due to stigma and concerns about privacy. Abortion in particular is notoriously difficult to measure. This study implements a novel method to estimate the cumulative lifetime incidence of induced abortion in Liberia. In a randomly selected sample of 3219 women ages 15–49 years in June 2013 in Liberia, we implemented the ‘Double List Experiment’. To measure abortion incidence, each woman was read two lists: (A) a list of non-sensitive items and (B) a list of correlated non-sensitive items with abortion added. The sensitive item, abortion, was randomly added to either List A or List B for each respondent. The respondent reported a simple count of the options on each list that she had experienced, without indicating which options. Difference in means calculations between the average counts for each list were then averaged to provide an estimate of the population proportion that has had an abortion. The list experiment estimates that 32% [95% confidence interval (CI): 0.29-0.34) of respondents surveyed had ever had an abortion (26% of women in urban areas, and 36% of women in rural areas, P-value for difference Liberia, indicating the potential utility of this method to reduce under-reporting in the measurement of abortion. The method could be widely applied to measure other stigmatized health topics, including sexual behaviours, sexual assault or domestic violence.

  20. Using Random Forests to Select Optimal Input Variables for Short-Term Wind Speed Forecasting Models

    Directory of Open Access Journals (Sweden)

    Hui Wang

    2017-10-01

    Full Text Available Achieving relatively high-accuracy short-term wind speed forecasting estimates is a precondition for the construction and grid-connected operation of wind power forecasting systems for wind farms. Currently, most research is focused on the structure of forecasting models and does not consider the selection of input variables, which can have significant impacts on forecasting performance. This paper presents an input variable selection method for wind speed forecasting models. The candidate input variables for various leading periods are selected and random forests (RF is employed to evaluate the importance of all variable as features. The feature subset with the best evaluation performance is selected as the optimal feature set. Then, kernel-based extreme learning machine is constructed to evaluate the performance of input variables selection based on RF. The results of the case study show that by removing the uncorrelated and redundant features, RF effectively extracts the most strongly correlated set of features from the candidate input variables. By finding the optimal feature combination to represent the original information, RF simplifies the structure of the wind speed forecasting model, shortens the training time required, and substantially improves the model’s accuracy and generalization ability, demonstrating that the input variables selected by RF are effective.

  1. Pseudo-random number generator based on asymptotic deterministic randomness

    Science.gov (United States)

    Wang, Kai; Pei, Wenjiang; Xia, Haishan; Cheung, Yiu-ming

    2008-06-01

    A novel approach to generate the pseudorandom-bit sequence from the asymptotic deterministic randomness system is proposed in this Letter. We study the characteristic of multi-value correspondence of the asymptotic deterministic randomness constructed by the piecewise linear map and the noninvertible nonlinearity transform, and then give the discretized systems in the finite digitized state space. The statistic characteristics of the asymptotic deterministic randomness are investigated numerically, such as stationary probability density function and random-like behavior. Furthermore, we analyze the dynamics of the symbolic sequence. Both theoretical and experimental results show that the symbolic sequence of the asymptotic deterministic randomness possesses very good cryptographic properties, which improve the security of chaos based PRBGs and increase the resistance against entropy attacks and symbolic dynamics attacks.

  2. Pseudo-random number generator based on asymptotic deterministic randomness

    International Nuclear Information System (INIS)

    Wang Kai; Pei Wenjiang; Xia Haishan; Cheung Yiuming

    2008-01-01

    A novel approach to generate the pseudorandom-bit sequence from the asymptotic deterministic randomness system is proposed in this Letter. We study the characteristic of multi-value correspondence of the asymptotic deterministic randomness constructed by the piecewise linear map and the noninvertible nonlinearity transform, and then give the discretized systems in the finite digitized state space. The statistic characteristics of the asymptotic deterministic randomness are investigated numerically, such as stationary probability density function and random-like behavior. Furthermore, we analyze the dynamics of the symbolic sequence. Both theoretical and experimental results show that the symbolic sequence of the asymptotic deterministic randomness possesses very good cryptographic properties, which improve the security of chaos based PRBGs and increase the resistance against entropy attacks and symbolic dynamics attacks

  3. The reliability of randomly selected final year pharmacy students in ...

    African Journals Online (AJOL)

    Employing ANOVA, factorial experimental analysis, and the theory of error, reliability studies were conducted on the assessment of the drug product chloroquine phosphate tablets. The G–Study employed equal numbers of the factors for uniform control, and involved three analysts (randomly selected final year Pharmacy ...

  4. A comparison of two methods for prediction of response and rates of inbreeding in selected populations with the results obtained in two selection experiments

    Directory of Open Access Journals (Sweden)

    Verrier Etienne

    2005-05-01

    Full Text Available Abstract Selection programmes are mainly concerned with increasing genetic gain. However, short-term progress should not be obtained at the expense of the within-population genetic variability. Different prediction models for the evolution within a small population of the genetic mean of a selected trait, its genetic variance and its inbreeding have been developed but have mainly been validated through Monte Carlo simulation studies. The purpose of this study was to compare theoretical predictions to experimental results. Two deterministic methods were considered, both grounded on a polygenic additive model. Differences between theoretical predictions and experimental results arise from differences between the true and the assumed genetic model, and from mathematical simplifications applied in the prediction methods. Two sets of experimental lines of chickens were used in this study: the Dutch lines undergoing true truncation mass selection, the other lines (French undergoing mass selection with a restriction on the representation of the different families. This study confirmed, on an experimental basis, that modelling is an efficient approach to make useful predictions of the evolution of selected populations although the basic assumptions considered in the models (polygenic additive model, normality of the distribution, base population at the equilibrium, etc. are not met in reality. The two deterministic methods compared yielded results that were close to those observed in real data, especially when the selection scheme followed the rules of strict mass selection: for instance, both predictions overestimated the genetic gain in the French experiment, whereas both predictions were close to the observed values in the Dutch experiment.

  5. Rule-based versus probabilistic selection for active surveillance using three definitions of insignificant prostate cancer

    NARCIS (Netherlands)

    L.D.F. Venderbos (Lionne); M.J. Roobol-Bouts (Monique); C.H. Bangma (Chris); R.C.N. van den Bergh (Roderick); L.P. Bokhorst (Leonard); D. Nieboer (Daan); Godtman, R; J. Hugosson (Jonas); van der Kwast, T; E.W. Steyerberg (Ewout)

    2016-01-01

    textabstractTo study whether probabilistic selection by the use of a nomogram could improve patient selection for active surveillance (AS) compared to the various sets of rule-based AS inclusion criteria currently used. We studied Dutch and Swedish patients participating in the European Randomized

  6. Comparative analysis of instance selection algorithms for instance-based classifiers in the context of medical decision support

    International Nuclear Information System (INIS)

    Mazurowski, Maciej A; Tourassi, Georgia D; Malof, Jordan M

    2011-01-01

    When constructing a pattern classifier, it is important to make best use of the instances (a.k.a. cases, examples, patterns or prototypes) available for its development. In this paper we present an extensive comparative analysis of algorithms that, given a pool of previously acquired instances, attempt to select those that will be the most effective to construct an instance-based classifier in terms of classification performance, time efficiency and storage requirements. We evaluate seven previously proposed instance selection algorithms and compare their performance to simple random selection of instances. We perform the evaluation using k-nearest neighbor classifier and three classification problems: one with simulated Gaussian data and two based on clinical databases for breast cancer detection and diagnosis, respectively. Finally, we evaluate the impact of the number of instances available for selection on the performance of the selection algorithms and conduct initial analysis of the selected instances. The experiments show that for all investigated classification problems, it was possible to reduce the size of the original development dataset to less than 3% of its initial size while maintaining or improving the classification performance. Random mutation hill climbing emerges as the superior selection algorithm. Furthermore, we show that some previously proposed algorithms perform worse than random selection. Regarding the impact of the number of instances available for the classifier development on the performance of the selection algorithms, we confirm that the selection algorithms are generally more effective as the pool of available instances increases. In conclusion, instance selection is generally beneficial for instance-based classifiers as it can improve their performance, reduce their storage requirements and improve their response time. However, choosing the right selection algorithm is crucial.

  7. Fault diagnosis in spur gears based on genetic algorithm and random forest

    Science.gov (United States)

    Cerrada, Mariela; Zurita, Grover; Cabrera, Diego; Sánchez, René-Vinicio; Artés, Mariano; Li, Chuan

    2016-03-01

    There are growing demands for condition-based monitoring of gearboxes, and therefore new methods to improve the reliability, effectiveness, accuracy of the gear fault detection ought to be evaluated. Feature selection is still an important aspect in machine learning-based diagnosis in order to reach good performance of the diagnostic models. On the other hand, random forest classifiers are suitable models in industrial environments where large data-samples are not usually available for training such diagnostic models. The main aim of this research is to build up a robust system for the multi-class fault diagnosis in spur gears, by selecting the best set of condition parameters on time, frequency and time-frequency domains, which are extracted from vibration signals. The diagnostic system is performed by using genetic algorithms and a classifier based on random forest, in a supervised environment. The original set of condition parameters is reduced around 66% regarding the initial size by using genetic algorithms, and still get an acceptable classification precision over 97%. The approach is tested on real vibration signals by considering several fault classes, one of them being an incipient fault, under different running conditions of load and velocity.

  8. Neighborhood deprivation is strongly associated with participation in a population-based health check

    DEFF Research Database (Denmark)

    Bender, Anne Mette; Kawachi, Ichiro; Jørgensen, Torben

    2015-01-01

    BACKGROUND: We sought to examine whether neighborhood deprivation is associated with participation in a large population-based health check. Such analyses will help answer the question whether health checks, which are designed to meet the needs of residents in deprived neighborhoods, may increase...... participation and prove to be more effective in preventing disease. In Europe, no study has previously looked at the association between neighborhood deprivation and participation in a population-based health check. METHODS: The study population comprised 12,768 persons invited for a health check including...... screening for ischemic heart disease and lifestyle counseling. The study population was randomly drawn from a population of 179,097 persons living in 73 neighborhoods in Denmark. Data on neighborhood deprivation (percentage with basic education, with low income and not in work) and individual socioeconomic...

  9. Random selection of items. Selection of n1 samples among N items composing a stratum

    International Nuclear Information System (INIS)

    Jaech, J.L.; Lemaire, R.J.

    1987-02-01

    STR-224 provides generalized procedures to determine required sample sizes, for instance in the course of a Physical Inventory Verification at Bulk Handling Facilities. The present report describes procedures to generate random numbers and select groups of items to be verified in a given stratum through each of the measurement methods involved in the verification. (author). 3 refs

  10. Population structure, genetic variation and linkage disequilibrium in perennial ryegrass populations divergently selected for freezing tolerance

    Directory of Open Access Journals (Sweden)

    Mallikarjuna Rao eKovi

    2015-11-01

    Full Text Available Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF] and 27 of Unselected [US] from the second generation of the two divergently selected populations and an unselected control population were genotyped using 278 genome-wide SNPs derived from Lolium perenne L. transcriptome sequence. Our studies showed that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two Fst outlier methods; finite island model (fdist by LOSITAN and hierarchical structure model using ARLEQUIN detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation and abiotic stress and might be the potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.

  11. Low genetic diversity and local adaptive divergence of Dracaena cambodiana (Liliaceae) populations associated with historical population bottlenecks and natural selection: an endangered long-lived tree endemic to Hainan Island, China.

    Science.gov (United States)

    Zheng, D-J; Xie, L-S; Zhu, J-H; Zhang, Z-L

    2012-09-01

    Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long-lived trees. Dracaena cambodiana is an endangered, long-lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D. cambodiana were detected using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D. cambodiana populations, which was further supported by habitat-private fragments. We suggest that the current genetic diversity and population differentiation of D. cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D. cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  12. Population genetics inference for longitudinally-sampled mutants under strong selection.

    Science.gov (United States)

    Lacerda, Miguel; Seoighe, Cathal

    2014-11-01

    Longitudinal allele frequency data are becoming increasingly prevalent. Such samples permit statistical inference of the population genetics parameters that influence the fate of mutant variants. To infer these parameters by maximum likelihood, the mutant frequency is often assumed to evolve according to the Wright-Fisher model. For computational reasons, this discrete model is commonly approximated by a diffusion process that requires the assumption that the forces of natural selection and mutation are weak. This assumption is not always appropriate. For example, mutations that impart drug resistance in pathogens may evolve under strong selective pressure. Here, we present an alternative approximation to the mutant-frequency distribution that does not make any assumptions about the magnitude of selection or mutation and is much more computationally efficient than the standard diffusion approximation. Simulation studies are used to compare the performance of our method to that of the Wright-Fisher and Gaussian diffusion approximations. For large populations, our method is found to provide a much better approximation to the mutant-frequency distribution when selection is strong, while all three methods perform comparably when selection is weak. Importantly, maximum-likelihood estimates of the selection coefficient are severely attenuated when selection is strong under the two diffusion models, but not when our method is used. This is further demonstrated with an application to mutant-frequency data from an experimental study of bacteriophage evolution. We therefore recommend our method for estimating the selection coefficient when the effective population size is too large to utilize the discrete Wright-Fisher model. Copyright © 2014 by the Genetics Society of America.

  13. Methodology of a study on the French population exposure to 50 Hz magnetic fields

    International Nuclear Information System (INIS)

    Bedja, M.; Magne, I.; Souques, M.; Lambrozo, J.; Le Brusquet, L.; Fleury, G.; Azoulay, A.; Deschamps, F.; Carlsberg, A.

    2010-01-01

    The characterisation of population exposure to a 50-Hz magnetic field (MF) is important for assessing health effects of electromagnetic fields. With the aim of estimating and characterising the exposure of the French population to 50-Hz MFs, two representative samples of the population were made. A random selection method based on the distribution of households in different regions of France was used. The samples were carried out starting from a random polling of telephone numbers of households (listed, unlisted fixed phones and cell phones only). A total of 95 362 telephone numbers were dialed to have 2148 volunteers (1060 children and 1088 adults). They all agreed to carrying an EMDEX II meter, measuring and recording MFs, and to filling out a timetable for a 24-hour period. In this article, the methodology of the sample selection and the collection of all necessary information for the realisation of this study are presented. (authors)

  14. Selective Predation of a Stalking Predator on Ungulate Prey.

    Directory of Open Access Journals (Sweden)

    Marco Heurich

    Full Text Available Prey selection is a key factor shaping animal populations and evolutionary dynamics. An optimal forager should target prey that offers the highest benefits in terms of energy content at the lowest costs. Predators are therefore expected to select for prey of optimal size. Stalking predators do not pursue their prey long, which may lead to a more random choice of prey individuals. Due to difficulties in assessing the composition of available prey populations, data on prey selection of stalking carnivores are still scarce. We show how the stalking predator Eurasian lynx (Lynx lynx selects prey individuals based on species identity, age, sex and individual behaviour. To address the difficulties in assessing prey population structure, we confirm inferred selection patterns by using two independent data sets: (1 data of 387 documented kills of radio-collared lynx were compared to the prey population structure retrieved from systematic camera trapping using Manly's standardized selection ratio alpha and (2 data on 120 radio-collared roe deer were analysed using a Cox proportional hazards model. Among the larger red deer prey, lynx selected against adult males-the largest and potentially most dangerous prey individuals. In roe deer lynx preyed selectively on males and did not select for a specific age class. Activity during high risk periods reduced the risk of falling victim to a lynx attack. Our results suggest that the stalking predator lynx actively selects for size, while prey behaviour induces selection by encounter and stalking success rates.

  15. Lifestyle factors and experience of respiratory alarm symptoms in the general population

    DEFF Research Database (Denmark)

    Sele, Lisa Maria Falk; Balasubramaniam, Kirubakaran; Elnegaard, Sandra

    2015-01-01

    BACKGROUND: The first step in the diagnosis of lung cancer is for individuals in the general population to recognise respiratory alarm symptoms (RAS). Knowledge is sparse about RAS and factors associated with experiencing RAS in the general population. This study aimed to estimate the prevalence...... of RAS in the general population, and to analyse possible associations between lifestyle factors and experiencing RAS. METHODS: A web-based survey comprising 100 000 individuals randomly selected from the Danish Civil Registration System. Items regarding experience of RAS (prolonged coughing, shortness...

  16. Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection

    Directory of Open Access Journals (Sweden)

    Sierra Saleta

    2008-07-01

    Full Text Available Abstract Background The molecular events and evolutionary forces underlying lethal mutagenesis of virus (or virus extinction through an excess of mutations are not well understood. Here we apply for the first time phylogenetic methods and Partition Analysis of Quasispecies (PAQ to monitor genetic distances and intra-population structures of mutant spectra of foot-and-mouth disease virus (FMDV quasispecies subjected to mutagenesis by base and nucleoside analogues. Results Phylogenetic and PAQ analyses have revealed a highly dynamic variation of intrapopulation diversity of FMDV quasispecies. The population diversity first suffers striking expansions in the presence of mutagens and then compressions either when the presence of the mutagenic analogue was discontinued or when a mutation that decreased sensitivity to a mutagen was selected. The pattern of mutations found in the populations was in agreement with the behavior of the corresponding nucleotide analogues with FMDV in vitro. Mutations accumulated at preferred genomic sites, and dn/ds ratios indicate the operation of negative (or purifying selection in populations subjected to mutagenesis. No evidence of unusually elevated genetic distances has been obtained for FMDV populations approaching extinction. Conclusion Phylogenetic and PAQ analysis provide adequate procedures to describe the evolution of viral sequences subjected to lethal mutagenesis. These methods define the changes of intra-population structure more precisely than mutation frequencies and Shannon entropies. PAQ is very sensitive to variations of intrapopulation genetic distances. Strong negative (or purifying selection operates in FMDV populations subjected to enhanced mutagenesis. The quantifications provide evidence that extinction does not imply unusual increases of intrapopulation complexity, in support of the lethal defection model of virus extinction.

  17. Population structure and strong divergent selection shape phenotypic diversification in maize landraces.

    Science.gov (United States)

    Pressoir, G; Berthaud, J

    2004-02-01

    To conserve the long-term selection potential of maize, it is necessary to investigate past and present evolutionary processes that have shaped quantitative trait variation. Understanding the dynamics of quantitative trait evolution is crucial to future crop breeding. We characterized population differentiation of maize landraces from the State of Oaxaca, Mexico for quantitative traits and molecular markers. Qst values were much higher than Fst values obtained for molecular markers. While low values of Fst (0.011 within-village and 0.003 among-villages) suggest that considerable gene flow occurred among the studied populations, high levels of population differentiation for quantitative traits were observed (ie an among-village Qst value of 0.535 for kernel weight). Our results suggest that although quantitative traits appear to be under strong divergent selection, a considerable amount of gene flow occurs among populations. Furthermore, we characterized nonproportional changes in the G matrix structure both within and among villages that are consequences of farmer selection. As a consequence of these differences in the G matrix structure, the response to multivariate selection will be different from one population to another. Large changes in the G matrix structure could indicate that farmers select for genes of major and pleiotropic effect. Farmers' decision and selection strategies have a great impact on phenotypic diversification in maize landraces.

  18. Genetic diversity and natural selection footprints of the glycine amidinotransferase gene in various human populations.

    Science.gov (United States)

    Khan, Asifullah; Tian, Lei; Zhang, Chao; Yuan, Kai; Xu, Shuhua

    2016-01-05

    The glycine amidinotransferase gene (GATM) plays a vital role in energy metabolism in muscle tissues and is associated with multiple clinically important phenotypes. However, the genetic diversity of the GATM gene remains poorly understood within and between human populations. Here we analyzed the 1,000 Genomes Project data through population genetics approaches and observed significant genetic diversity across the GATM gene among various continental human populations. We observed considerable variations in GATM allele frequencies and haplotype composition among different populations. Substantial genetic differences were observed between East Asian and European populations (FST = 0.56). In addition, the frequency of a distinct major GATM haplotype in these groups was congruent with population-wide diversity at this locus. Furthermore, we identified GATM as the top differentiated gene compared to the other statin drug response-associated genes. Composite multiple analyses identified signatures of positive selection at the GATM locus, which was estimated to have occurred around 850 generations ago in European populations. As GATM catalyzes the key step of creatine biosynthesis involved in energy metabolism, we speculate that the European prehistorical demographic transition from hunter-gatherer to farming cultures was the driving force of selection that fulfilled creatine-based metabolic requirement of the populations.

  19. The accuracy of prediction of genomic selection in elite hybrid rye populations surpasses the accuracy of marker-assisted selection and is equally augmented by multiple field evaluation locations and test years.

    Science.gov (United States)

    Wang, Yu; Mette, Michael Florian; Miedaner, Thomas; Gottwald, Marlen; Wilde, Peer; Reif, Jochen C; Zhao, Yusheng

    2014-07-04

    Marker-assisted selection (MAS) and genomic selection (GS) based on genome-wide marker data provide powerful tools to predict the genotypic value of selection material in plant breeding. However, case-to-case optimization of these approaches is required to achieve maximum accuracy of prediction with reasonable input. Based on extended field evaluation data for grain yield, plant height, starch content and total pentosan content of elite hybrid rye derived from testcrosses involving two bi-parental populations that were genotyped with 1048 molecular markers, we compared the accuracy of prediction of MAS and GS in a cross-validation approach. MAS delivered generally lower and in addition potentially over-estimated accuracies of prediction than GS by ridge regression best linear unbiased prediction (RR-BLUP). The grade of relatedness of the plant material included in the estimation and test sets clearly affected the accuracy of prediction of GS. Within each of the two bi-parental populations, accuracies differed depending on the relatedness of the respective parental lines. Across populations, accuracy increased when both populations contributed to estimation and test set. In contrast, accuracy of prediction based on an estimation set from one population to a test set from the other population was low despite that the two bi-parental segregating populations under scrutiny shared one parental line. Limiting the number of locations or years in field testing reduced the accuracy of prediction of GS equally, supporting the view that to establish robust GS calibration models a sufficient number of test locations is of similar importance as extended testing for more than one year. In hybrid rye, genomic selection is superior to marker-assisted selection. However, it achieves high accuracies of prediction only for selection candidates closely related to the plant material evaluated in field trials, resulting in a rather pessimistic prognosis for distantly related material

  20. Response to family selection and genetic parameters in Japanese quail selected for four week breast weight

    DEFF Research Database (Denmark)

    Khaldari, Majid; Yeganeh, Hassan Mehrabani; Pakdel, Abbas

    2011-01-01

    An experiment was conducted to investigate the effect of short-term selection for 4 week breast weight (4wk BRW), and to estimate genetic parameters of body weight, and carcass traits. A selection (S) line and control (C) line was randomly selected from a base population. Data were collected over...... was 0.35±0.06. There were a significant difference for BW, and carcass weights but not for carcass percent components between lines (Pcarcass and leg weights were 0.46, 0.41 and 0.47, and 13.2, 16.2, 4.4 %, respectively....... The genetic correlations of BRW with BW, carcass, leg, and back weights were 0.85, 0.88 and 0.72, respectively. Selection for 4 wk BRW improved feed conversion ratio (FCR) about 0.19 units over the selection period. Inbreeding caused an insignificant decline of the mean of some traits. Results from...

  1. A microsatellite-based analysis for the detection of selection on BTA1 and BTA20 in northern Eurasian cattle (Bos taurus populations

    Directory of Open Access Journals (Sweden)

    Li Meng-Hua

    2010-08-01

    Full Text Available Abstract Background Microsatellites surrounding functionally important candidate genes or quantitative trait loci have received attention as proxy measures of polymorphism level at the candidate loci themselves. In cattle, selection for economically important traits is a long-term strategy and it has been reported that microsatellites are linked to these important loci. Methods We have investigated the variation of seven microsatellites on BTA1 (Bos taurus autosome 1 and 16 on BTA20, using bovine populations of typical production types and horn status in northern Eurasia. Genetic variability of these loci and linkage disequilibrium among these loci were compared with those of 28 microsatellites on other bovine chromosomes. Four different tests were applied to detect molecular signatures of selection. Results No marked difference in locus variability was found between microsatellites on BTA1, BTA20 and the other chromosomes in terms of different diversity indices. Average D' values of pairwise syntenic markers (0.32 and 0.28 across BTA 1 and BTA20 respectively were significantly (P FST-test indicated elevated or decreased genetic differentiation, at SOD1 and AGLA17 markers respectively, deviating significantly (P SOD1 and AGLA17. Our data also indicate significant intergenic linkage disequilibrium around the candidate loci and suggest that hitchhiking selection has played a role in shaping the pattern of observed linkage disequilibrium. Conclusion Hitchhiking due to tight linkage with alleles at candidate genes, e.g. the POLL gene, is a possible explanation for this pattern. The potential impact of selective breeding by man on cattle populations is discussed in the context of selection effects. Our results also suggest that a practical approach to detect loci under selection is to simultaneously apply multiple neutrality tests based on different assumptions and estimations.

  2. The Link of Self-Reported Insomnia Symptoms and Sleep Duration with Metabolic Syndrome: A Chinese Population-Based Study.

    Science.gov (United States)

    Lin, Shih-Chieh; Sun, Chien-An; You, San-Lin; Hwang, Lee-Ching; Liang, Chun-Yu; Yang, Tsan; Bai, Chyi-Huey; Chen, Chien-Hua; Wei, Cheng-Yu; Chou, Yu-Ching

    2016-06-01

    The aims of this study are to investigate the relationships of metabolic syndrome (MetS) with insomnia symptoms and sleep duration in a Chinese adult population. Data from a nationwide epidemiological survey conducted on residents from randomly selected districts in Taiwan in 2007 were used for this cross-sectional population-based study. A total of 4,197 participants were included in this study. Insomnia symptoms, including difficulty initiating sleep (DIS), difficulty maintaining sleep (DMS), early morning awakening (EMA), were assessed using the Insomnia Self-Assessment Inventory questionnaire. Subjects were divided into 3 groups based upon their reported sleep duration (insomnia symptoms (OR [95% CI] was 1.54 [1.05-2.47]). However, there was no significant combined effect of insomnia symptoms and sleep duration on the prevalence of MetS. The current investigation shows that short sleep duration and insomnia symptoms, specifically DIS and DMS, were significant correlates of MetS. These findings should be replicated in prospective studies using both sleep duration and sleep quality measures. © 2016 Associated Professional Sleep Societies, LLC.

  3. Selection and adaptation in irradiated plant and animal populations: a review

    International Nuclear Information System (INIS)

    Hart, D.R.

    1981-03-01

    Available literature on the effects of ionizing radiation on mutation rates, variability and adaptive responses to selection in exposed plant and animal populations is reviewed. Accumulated variability, and hence potential selection differentials, may be increased by many times due to induced mutation. The radiation dose that maximizes induced mutation varies greatly among species, strains and genetic systems. Induced variability tends to enhance the respose to selection, but this effect may be delayed or prevented by an initial reduction in the heritability of induced variation. Significantly, the detrimental effects of harmful mutations in irradiated populations may exceed the beneficial effects of selection for adaptive characteristics. Selection for radioresistance may occur at lethal or sub-lethal radiation doses but dose relationships are highly variable. (author)

  4. Prevalence of spondylolysis and its relationship with low back pain in selected population.

    Science.gov (United States)

    Ko, Sang-Bong; Lee, Sang-Wook

    2011-03-01

    To determine the prevalence of spondylolysis in a selected population and evaluate the association of spondylolysis with low back pain (LBP). Spondylolysis is widespread in the general population but the prevalence of spondylolysis and its relationship with LBP in the Korean population is controversial. A sample of 855 participants (age, 20 to 86 years) from our medical center who underwent multidetector computed tomography (CT) imaging to assess abdominal and urological lesions were enrolled in this study. The occurrence of LBP requiring medication in the preceding 12 months was evaluated using a self-report questionnaire (a modified Nordic Low Back Pain Questionnaire). The presence of spondylolysis was characterized by CT imaging. Multiple logistic regression models were used to examine the association between spondylolysis and LBP, while adjusting for gender and age. Seventy-eight study subjects (9%) demonstrated spondylolysis on CT imaging. There was no significant difference between the age groups (p = 0.177). The p-value of gender was 0.033 but this was not significant due to the selected population bias. Three hundred eleven study subjects (36%) had back pain. There was a significant difference between gender (p = 0.001). No significant association was identified between spondylolysis and the occurrence of LBP. The prevalence of LBP was 36.37% and the prevalence of lumbar spondylolysis in a selected population, who visited hospital for abdominal or urological lesions except LBP, was 9.12% based on CT imaging. Males demonstrated a similar presence of LBP to females but a significantly higher incidence of spondylolysis (p = 0.033). The prevalence of spondylolysis was not associated with the presence of LBP and age in adulthood.

  5. Association Between Zolpidem Use and Glaucoma Risk: A Taiwanese Population-Based Case-Control Study

    OpenAIRE

    Ho, Yi-Hao; Chang, Yue-Cune; Huang, Wei-Cheng; Chen, Hsin-Yi; Lin, Che-Chen; Sung, Fung-Chang

    2015-01-01

    Background To date, the relationship between zolpidem use and subsequent risk of glaucoma in a Taiwanese population has not been assessed. Methods We used data from the National Health Insurance system to investigate whether zolpidem use was related to glaucoma risk. A 1:4 matched case-control study was conducted. The cases were patients newly diagnosed with glaucoma from 2001 to 2010. The controls were randomly selected non-glaucoma subjects matched by sex and age (?5 years). Zolpidem exposu...

  6. Acceptance sampling using judgmental and randomly selected samples

    Energy Technology Data Exchange (ETDEWEB)

    Sego, Landon H.; Shulman, Stanley A.; Anderson, Kevin K.; Wilson, John E.; Pulsipher, Brent A.; Sieber, W. Karl

    2010-09-01

    We present a Bayesian model for acceptance sampling where the population consists of two groups, each with different levels of risk of containing unacceptable items. Expert opinion, or judgment, may be required to distinguish between the high and low-risk groups. Hence, high-risk items are likely to be identifed (and sampled) using expert judgment, while the remaining low-risk items are sampled randomly. We focus on the situation where all observed samples must be acceptable. Consequently, the objective of the statistical inference is to quantify the probability that a large percentage of the unsampled items in the population are also acceptable. We demonstrate that traditional (frequentist) acceptance sampling and simpler Bayesian formulations of the problem are essentially special cases of the proposed model. We explore the properties of the model in detail, and discuss the conditions necessary to ensure that required samples sizes are non-decreasing function of the population size. The method is applicable to a variety of acceptance sampling problems, and, in particular, to environmental sampling where the objective is to demonstrate the safety of reoccupying a remediated facility that has been contaminated with a lethal agent.

  7. Designing a smoking cessation intervention for the unique needs of homeless persons: a community-based randomized clinical trial.

    Science.gov (United States)

    Goldade, Kate; Whembolua, Guy-Lucien; Thomas, Janet; Eischen, Sara; Guo, Hongfei; Connett, John; Des Jarlais, Don; Resnicow, Ken; Gelberg, Lillian; Owen, Greg; Grant, Jon; Ahluwalia, Jasjit S; Okuyemi, Kolawole S

    2011-12-01

    Although smoking prevalence remains strikingly high in homeless populations (~70% and three times the US national average), smoking cessation studies usually exclude homeless persons. Novel evidence-based interventions are needed for this high-risk subpopulation of smokers. To describe the aims and design of a first-ever smoking cessation clinical trial in the homeless population. The study was a two-group randomized community-based trial that enrolled participants (n = 430) residing across eight homeless shelters and transitional housing units in Minnesota. The study objective was to test the efficacy of motivational interviewing (MI) for enhancing adherence to nicotine replacement therapy (NRT; nicotine patch) and smoking cessation outcomes. Participants were randomized to one of the two groups: active (8 weeks of NRT + 6 sessions of MI) or control (NRT + standard care). Participants attended six in-person assessment sessions and eight retention visits at a location of their choice over 6 months. Nicotine patch in 2-week doses was administered at four visits over the first 8 weeks of the 26-week trial. The primary outcome was cotinine-verified 7-day point-prevalence abstinence at 6 months. Secondary outcomes included adherence to nicotine patch assessed through direct observation and patch counts. Other outcomes included the mediating and/or moderating effects of comorbid psychiatric and substance abuse disorders. Lessons learned from the community-based cessation randomized trial for improving recruitment and retention in a mobile and vulnerable population included: (1) the importance of engaging the perspectives of shelter leadership by forming and convening a Community Advisory Board; (2) locating the study at the shelters for more visibility and easier access for participants; (3) minimizing exclusion criteria to allow enrollment of participants with stable psychiatric comorbid conditions; (4) delaying the baseline visit from the eligibility visit by a week

  8. A cluster-based randomized controlled trial promoting community participation in arsenic mitigation efforts in Bangladesh

    OpenAIRE

    George, Christine Marie; van Geen, Alexander; Slavkovich, Vesna; Singha, Ashit; Levy, Diane; Islam, Tariqul; Ahmed, Kazi Matin; Moon-Howard, Joyce; Tarozzi, Alessandro; Liu, Xinhua; Factor-Litvak, Pam; Graziano, Joseph

    2012-01-01

    Abstract Objective To reduce arsenic (As) exposure, we evaluated the effectiveness of training community members to perform water arsenic (WAs) testing and provide As education compared to sending representatives from outside communities to conduct these tasks. Methods We conducted a cluster based randomized controlled trial of 20 villages in Singair, Bangladesh. Fifty eligible respondents were randomly selected in each village. In 10 villages, a community member provided As education and WAs...

  9. A comparison of random forest and its Gini importance with standard chemometric methods for the feature selection and classification of spectral data

    Directory of Open Access Journals (Sweden)

    Himmelreich Uwe

    2009-07-01

    Full Text Available Abstract Background Regularized regression methods such as principal component or partial least squares regression perform well in learning tasks on high dimensional spectral data, but cannot explicitly eliminate irrelevant features. The random forest classifier with its associated Gini feature importance, on the other hand, allows for an explicit feature elimination, but may not be optimally adapted to spectral data due to the topology of its constituent classification trees which are based on orthogonal splits in feature space. Results We propose to combine the best of both approaches, and evaluated the joint use of a feature selection based on a recursive feature elimination using the Gini importance of random forests' together with regularized classification methods on spectral data sets from medical diagnostics, chemotaxonomy, biomedical analytics, food science, and synthetically modified spectral data. Here, a feature selection using the Gini feature importance with a regularized classification by discriminant partial least squares regression performed as well as or better than a filtering according to different univariate statistical tests, or using regression coefficients in a backward feature elimination. It outperformed the direct application of the random forest classifier, or the direct application of the regularized classifiers on the full set of features. Conclusion The Gini importance of the random forest provided superior means for measuring feature relevance on spectral data, but – on an optimal subset of features – the regularized classifiers might be preferable over the random forest classifier, in spite of their limitation to model linear dependencies only. A feature selection based on Gini importance, however, may precede a regularized linear classification to identify this optimal subset of features, and to earn a double benefit of both dimensionality reduction and the elimination of noise from the classification task.

  10. Distribution of orientation selectivity in recurrent networks of spiking neurons with different random topologies.

    Science.gov (United States)

    Sadeh, Sadra; Rotter, Stefan

    2014-01-01

    Neurons in the primary visual cortex are more or less selective for the orientation of a light bar used for stimulation. A broad distribution of individual grades of orientation selectivity has in fact been reported in all species. A possible reason for emergence of broad distributions is the recurrent network within which the stimulus is being processed. Here we compute the distribution of orientation selectivity in randomly connected model networks that are equipped with different spatial patterns of connectivity. We show that, for a wide variety of connectivity patterns, a linear theory based on firing rates accurately approximates the outcome of direct numerical simulations of networks of spiking neurons. Distance dependent connectivity in networks with a more biologically realistic structure does not compromise our linear analysis, as long as the linearized dynamics, and hence the uniform asynchronous irregular activity state, remain stable. We conclude that linear mechanisms of stimulus processing are indeed responsible for the emergence of orientation selectivity and its distribution in recurrent networks with functionally heterogeneous synaptic connectivity.

  11. On theoretical models of gene expression evolution with random genetic drift and natural selection.

    Directory of Open Access Journals (Sweden)

    Osamu Ogasawara

    2009-11-01

    Full Text Available The relative contributions of natural selection and random genetic drift are a major source of debate in the study of gene expression evolution, which is hypothesized to serve as a bridge from molecular to phenotypic evolution. It has been suggested that the conflict between views is caused by the lack of a definite model of the neutral hypothesis, which can describe the long-run behavior of evolutionary change in mRNA abundance. Therefore previous studies have used inadequate analogies with the neutral prediction of other phenomena, such as amino acid or nucleotide sequence evolution, as the null hypothesis of their statistical inference.In this study, we introduced two novel theoretical models, one based on neutral drift and the other assuming natural selection, by focusing on a common property of the distribution of mRNA abundance among a variety of eukaryotic cells, which reflects the result of long-term evolution. Our results demonstrated that (1 our models can reproduce two independently found phenomena simultaneously: the time development of gene expression divergence and Zipf's law of the transcriptome; (2 cytological constraints can be explicitly formulated to describe long-term evolution; (3 the model assuming that natural selection optimized relative mRNA abundance was more consistent with previously published observations than the model of optimized absolute mRNA abundances.The models introduced in this study give a formulation of evolutionary change in the mRNA abundance of each gene as a stochastic process, on the basis of previously published observations. This model provides a foundation for interpreting observed data in studies of gene expression evolution, including identifying an adequate time scale for discriminating the effect of natural selection from that of random genetic drift of selectively neutral variations.

  12. Strong selection during the last millennium for African ancestry in the admixed population of Madagascar.

    Science.gov (United States)

    Pierron, Denis; Heiske, Margit; Razafindrazaka, Harilanto; Pereda-Loth, Veronica; Sanchez, Jazmin; Alva, Omar; Arachiche, Amal; Boland, Anne; Olaso, Robert; Deleuze, Jean-Francois; Ricaut, Francois-Xavier; Rakotoarisoa, Jean-Aimé; Radimilahy, Chantal; Stoneking, Mark; Letellier, Thierry

    2018-03-02

    While admixed populations offer a unique opportunity to detect selection, the admixture in most of the studied populations occurred too recently to produce conclusive signals. By contrast, Malagasy populations originate from admixture between Asian and African populations that occurred ~27 generations ago, providing power to detect selection. We analyze local ancestry across the genomes of 700 Malagasy and identify a strong signal of recent positive selection, with an estimated selection coefficient >0.2. The selection is for African ancestry and affects 25% of chromosome 1, including the Duffy blood group gene. The null allele at this gene provides resistance to Plasmodium vivax malaria, and previous studies have suggested positive selection for this allele in the Malagasy population. This selection event also influences numerous other genes implicated in immunity, cardiovascular diseases, and asthma and decreases the Asian ancestry genome-wide by 10%, illustrating the role played by selection in recent human history.

  13. Individual based population inference using tagging data

    DEFF Research Database (Denmark)

    Pedersen, Martin Wæver; Thygesen, Uffe Høgsbro; Baktoft, Henrik

    A hierarchical framework for simultaneous analysis of multiple related individual datasets is presented. The approach is very similar to mixed effects modelling as known from statistical theory. The model used at the individual level is, in principle, irrelevant as long as a maximum likelihood...... estimate and its uncertainty (Hessian) can be computed. The individual model used in this text is a hidden Markov model. A simulation study concerning a two-dimensional biased random walk is examined to verify the consistency of the hierarchical estimation framework. In addition, a study based on acoustic...... telemetry data from pike illustrates how the framework can identify individuals that deviate from the remaining population....

  14. Hybrid Feature Selection Approach Based on GRASP for Cancer Microarray Data

    Directory of Open Access Journals (Sweden)

    Arpita Nagpal

    2017-01-01

    Full Text Available Microarray data usually contain a large number of genes, but a small number of samples. Feature subset selection for microarray data aims at reducing the number of genes so that useful information can be extracted from the samples. Reducing the dimension of data sets further helps in improving the computational efficiency of the learning model. In this paper, we propose a modified algorithm based on the tabu search as local search procedures to a Greedy Randomized Adaptive Search Procedure (GRASP for high dimensional microarray data sets. The proposed Tabu based Greedy Randomized Adaptive Search Procedure algorithm is named as TGRASP. In TGRASP, a new parameter has been introduced named as Tabu Tenure and the existing parameters, NumIter and size have been modified. We observed that different parameter settings affect the quality of the optimum. The second proposed algorithm known as FFGRASP (Firefly Greedy Randomized Adaptive Search Procedure uses a firefly optimization algorithm in the local search optimzation phase of the greedy randomized adaptive search procedure (GRASP. Firefly algorithm is one of the powerful algorithms for optimization of multimodal applications. Experimental results show that the proposed TGRASP and FFGRASP algorithms are much better than existing algorithm with respect to three performance parameters viz. accuracy, run time, number of a selected subset of features. We have also compared both the approaches with a unified metric (Extended Adjusted Ratio of Ratios which has shown that TGRASP approach outperforms existing approach for six out of nine cancer microarray datasets and FFGRASP performs better on seven out of nine datasets.

  15. Selection of 3013 Containers for Field Surveillance

    International Nuclear Information System (INIS)

    Larry Peppers; Elizabeth Kelly; James McClard; Gary Friday; Theodore Venetz; Jerry Stakebade

    2007-01-01

    This report revises and combines three earlier reports dealing with the binning, statistical sampling, and sample selection of 3013 containers for field surveillance. It includes changes to the binning specification resulting from completion of the Savannah River Site packaging campaign and new information from the shelf-life program and field surveillance activities. The revised bin assignments result in changes to the random sample specification. These changes are necessary to meet the statistical requirements of the surveillance program. This report will be reviewed regularly and revised as needed. Section 1 of this report summarizes the results of an extensive effort to assign all of the current and projected 3013 containers in the Department of Energy (DOE) inventory to one of three bins (Innocuous, Pressure and Corrosion, or Pressure) based on potential failure mechanisms. Grouping containers into bins provides a framework to make a statistical selection of individual containers from the entire population for destructive and nondestructive field surveillance. The binning process consisted of three main steps. First, the packaged containers were binned using information in the Integrated Surveillance Program database and a decision tree. The second task was to assign those containers that could not be binned using the decision tree to a specific bin using container-by-container engineering review. The final task was to evaluate containers not yet packaged and assign them to bins using process knowledge. The technical basis for the decisions made during the binning process is included in Section 1. A composite decision tree and a summary table show all of the containers projected to be in the DOE inventory at the conclusion of packaging at all sites. Decision trees that provide an overview of the binning process and logic are included for each site. Section 2 of this report describes the approach to the statistical selection of containers for surveillance and

  16. The genealogy of samples in models with selection.

    Science.gov (United States)

    Neuhauser, C; Krone, S M

    1997-02-01

    We introduce the genealogy of a random sample of genes taken from a large haploid population that evolves according to random reproduction with selection and mutation. Without selection, the genealogy is described by Kingman's well-known coalescent process. In the selective case, the genealogy of the sample is embedded in a graph with a coalescing and branching structure. We describe this graph, called the ancestral selection graph, and point out differences and similarities with Kingman's coalescent. We present simulations for a two-allele model with symmetric mutation in which one of the alleles has a selective advantage over the other. We find that when the allele frequencies in the population are already in equilibrium, then the genealogy does not differ much from the neutral case. This is supported by rigorous results. Furthermore, we describe the ancestral selection graph for other selective models with finitely many selection classes, such as the K-allele models, infinitely-many-alleles models. DNA sequence models, and infinitely-many-sites models, and briefly discuss the diploid case.

  17. Computational intelligence-based polymerase chain reaction primer selection based on a novel teaching-learning-based optimisation.

    Science.gov (United States)

    Cheng, Yu-Huei

    2014-12-01

    Specific primers play an important role in polymerase chain reaction (PCR) experiments, and therefore it is essential to find specific primers of outstanding quality. Unfortunately, many PCR constraints must be simultaneously inspected which makes specific primer selection difficult and time-consuming. This paper introduces a novel computational intelligence-based method, Teaching-Learning-Based Optimisation, to select the specific and feasible primers. The specified PCR product lengths of 150-300 bp and 500-800 bp with three melting temperature formulae of Wallace's formula, Bolton and McCarthy's formula and SantaLucia's formula were performed. The authors calculate optimal frequency to estimate the quality of primer selection based on a total of 500 runs for 50 random nucleotide sequences of 'Homo species' retrieved from the National Center for Biotechnology Information. The method was then fairly compared with the genetic algorithm (GA) and memetic algorithm (MA) for primer selection in the literature. The results show that the method easily found suitable primers corresponding with the setting primer constraints and had preferable performance than the GA and the MA. Furthermore, the method was also compared with the common method Primer3 according to their method type, primers presentation, parameters setting, speed and memory usage. In conclusion, it is an interesting primer selection method and a valuable tool for automatic high-throughput analysis. In the future, the usage of the primers in the wet lab needs to be validated carefully to increase the reliability of the method.

  18. Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

    Science.gov (United States)

    Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R

    2015-02-01

    Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

  19. Genomic selection and association mapping in rice (Oryza sativa: effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

    Directory of Open Access Journals (Sweden)

    Jennifer Spindel

    2015-02-01

    Full Text Available Genomic Selection (GS is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

  20. Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines

    Science.gov (United States)

    Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R.

    2015-01-01

    Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline. PMID:25689273

  1. Addendum to "Population-Based Prevention of Child Maltreatment: The U.S. Triple P System Population Trial".

    Science.gov (United States)

    Prinz, Ronald J; Sanders, Matthew R; Shapiro, Cheri J; Whitaker, Daniel J; Lutzker, John R

    2016-04-01

    A previous article published several years ago (Prinz et al. Prevention Science, 10, 1-12, 2009) described the main results of a place-randomized-design study focused on the prevention of child-maltreatment-related outcomes at a population level through the implementation of a multilevel system of parenting and family support (the Triple P-Positive Parenting Program). The current report, prepared at the encouragement of the journal, provides additional details about procedures, measures, and design-related decisions, presents an additional analysis of the main outcome variables, and poses questions about the study and its implications. We also offer guidance about how the field can move forward to build on this line of research. From the outset, the three designated primary child maltreatment outcomes were county-wide rates for substantiated child maltreatment cases, out-of-home placements, and hospital-treated child maltreatment injuries, derived from independent data sources available through administrative archival records. Baseline equivalence between the two intervention conditions was reaffirmed. The additional analysis, which made use of a 5-year baseline (replacing a 1-year baseline) and ANCOVA, yielded large effect sizes for all three outcomes that converged with those from the original analyses. Overall, the study underscored the potential for community-wide parenting and family support to produce population-level preventive impact on child maltreatment. Issues addressed included (1) the need for replication of population-oriented maltreatment prevention strategies like the one tested in this randomized experiment, (2) the need to demonstrate that a parenting-based population approach to maltreatment prevention can also impact children's adjustment apart from child abuse, and (3) the role of implementation science for achieving greater population reach and maintenance over time.

  2. Estimation of the ancestral effective population sizes of African great apes under different selection regimes.

    Science.gov (United States)

    Schrago, Carlos G

    2014-08-01

    Reliable estimates of ancestral effective population sizes are necessary to unveil the population-level phenomena that shaped the phylogeny and molecular evolution of the African great apes. Although several methods have previously been applied to infer ancestral effective population sizes, an analysis of the influence of the selective regime on the estimates of ancestral demography has not been thoroughly conducted. In this study, three independent data sets under different selective regimes were used were composed to tackle this issue. The results showed that selection had a significant impact on the estimates of ancestral effective population sizes of the African great apes. The inference of the ancestral demography of African great apes was affected by the selection regime. The effects, however, were not homogeneous along the ancestral populations of great apes. The effective population size of the ancestor of humans and chimpanzees was more impacted by the selection regime when compared to the same parameter in the ancestor of humans, chimpanzees and gorillas. Because the selection regime influenced the estimates of ancestral effective population size, it is reasonable to assume that a portion of the discrepancy found in previous studies that inferred the ancestral effective population size may be attributable to the differential action of selection on the genes sampled.

  3. Footprints of directional selection in wild Atlantic salmon populations: evidence for parasite-driven evolution?

    Science.gov (United States)

    Zueva, Ksenia J; Lumme, Jaakko; Veselov, Alexey E; Kent, Matthew P; Lien, Sigbjørn; Primmer, Craig R

    2014-01-01

    Mechanisms of host-parasite co-adaptation have long been of interest in evolutionary biology; however, determining the genetic basis of parasite resistance has been challenging. Current advances in genome technologies provide new opportunities for obtaining a genome-scale view of the action of parasite-driven natural selection in wild populations and thus facilitate the search for specific genomic regions underlying inter-population differences in pathogen response. European populations of Atlantic salmon (Salmo salar L.) exhibit natural variance in susceptibility levels to the ectoparasite Gyrodactylus salaris Malmberg 1957, ranging from resistance to extreme susceptibility, and are therefore a good model for studying the evolution of virulence and resistance. However, distinguishing the molecular signatures of genetic drift and environment-associated selection in small populations such as land-locked Atlantic salmon populations presents a challenge, specifically in the search for pathogen-driven selection. We used a novel genome-scan analysis approach that enabled us to i) identify signals of selection in salmon populations affected by varying levels of genetic drift and ii) separate potentially selected loci into the categories of pathogen (G. salaris)-driven selection and selection acting upon other environmental characteristics. A total of 4631 single nucleotide polymorphisms (SNPs) were screened in Atlantic salmon from 12 different northern European populations. We identified three genomic regions potentially affected by parasite-driven selection, as well as three regions presumably affected by salinity-driven directional selection. Functional annotation of candidate SNPs is consistent with the role of the detected genomic regions in immune defence and, implicitly, in osmoregulation. These results provide new insights into the genetic basis of pathogen susceptibility in Atlantic salmon and will enable future searches for the specific genes involved.

  4. A population-based survey in Australia of men's and women's perceptions of genetic risk and predictive genetic testing and implications for primary care.

    Science.gov (United States)

    Taylor, S

    2011-01-01

    Community attitudes research regarding genetic issues is important when contemplating the potential value and utilisation of predictive testing for common diseases in mainstream health services. This article aims to report population-based attitudes and discuss their relevance to integrating genetic services in primary health contexts. Men's and women's attitudes were investigated via population-based omnibus telephone survey in Queensland, Australia. Randomly selected adults (n = 1,230) with a mean age of 48.8 years were interviewed regarding perceptions of genetic determinants of health; benefits of genetic testing that predict 'certain' versus 'probable' future illness; and concern, if any, regarding potential misuse of genetic test information. Most (75%) respondents believed genetic factors significantly influenced health status; 85% regarded genetic testing positively although attitudes varied with age. Risk-based information was less valued than certainty-based information, but women valued risk information significantly more highly than men. Respondents reported 'concern' (44%) and 'no concern' (47%) regarding potential misuse of genetic information. This study contributes important population-based data as most research has involved selected individuals closely impacted by genetic disorders. While community attitudes were positive regarding genetic testing, genetic literacy is important to establish. The nature of gender differences regarding risk perception merits further study and has policy and service implications. Community concern about potential genetic discrimination must be addressed if health benefits of testing are to be maximised. Larger questions remain in scientific, policy, service delivery, and professional practice domains before predictive testing for common disorders is efficacious in mainstream health care. Copyright © 2011 S. Karger AG, Basel.

  5. A Community-Based Randomized Trial of Hepatitis B Screening Among High-Risk Vietnamese Americans.

    Science.gov (United States)

    Ma, Grace X; Fang, Carolyn Y; Seals, Brenda; Feng, Ziding; Tan, Yin; Siu, Philip; Yeh, Ming Chin; Golub, Sarit A; Nguyen, Minhhuyen T; Tran, Tam; Wang, Minqi

    2017-03-01

    To evaluate the effectiveness of a community-based liver cancer prevention program on hepatitis B virus (HBV) screening among low-income, underserved Vietnamese Americans at high risk. We conducted a cluster randomized trial involving 36 Vietnamese community-based organizations and 2337 participants in Pennsylvania, New Jersey, and New York City between 2009 and 2014. We randomly assigned 18 community-based organizations to a community-based multilevel HBV screening intervention (n = 1131). We randomly assigned the remaining 18 community-based organizations to a general cancer education program (n = 1206), which included information about HBV-related liver cancer prevention. We assessed HBV screening rates at 6-month follow-up. Intervention participants were significantly more likely to have undergone HBV screening (88.1%) than were control group participants (4.6%). In a Cochran-Mantel-Haenszel analysis, the intervention effect on screening outcomes remained statistically significant after adjustment for demographic and health care access variables, including income, having health insurance, having a regular health provider, and English proficiency. A community-based, culturally appropriate, multilevel HBV screening intervention effectively increases screening rates in a high-risk, hard-to-reach Vietnamese American population.

  6. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations.

    Science.gov (United States)

    Tobler, M; Plath, M; Riesch, R; Schlupp, I; Grasse, A; Munimanda, G K; Setzer, C; Penn, D J; Moodley, Y

    2014-05-01

    The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution). © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  7. Menstrual pad, a cervical cancer screening tool, a population-based study in rural India.

    Science.gov (United States)

    Budukh, Atul; Palayekar, Vrushali; Maheshwari, Amita; Deodhar, Kedar; Purwar, Pallavi; Bagal, Sonali; Vadigoppula, Ashok; Lokhande, Manoj; Panse, Nandkumar; Dikshit, Rajesh; Badwe, Rajendra

    2017-07-12

    In the rural areas of India, women generally use a piece of old cloth as a menstrual device. The aim of this study was to detect human papilloma virus (HPV) from menstrual blood on the menstrual pad and assess whether this could be a useful screening tool for cervical cancer. In Jamkhed area of rural Maharashtra, (population A), we collected menstrual pads from women who provided consent in the 30-50 year age group. The women who had provided menstrual pads underwent HC2 testing. We standardized the method for extracting DNA by PCR from the menstrual pad. The women who tested HPV positive, on the basis of HC2/PCR testing, underwent colposcopy. In the rural population of Pune area of Maharashtra state (population B), menstrual pads were collected. HPV was tested using the PCR method. HPV-positive women and a few HPV-negative women, selected randomly, underwent colposcopy and HC2 testing. In population A, 164 women provided their used menstrual pads and also underwent an HC2 screening test. Of these, six (3.2%) cases were reported as HPV positive. In population B, 365 women provided their used menstrual pads for HPV testing, of which 18 (4.9%) cases were diagnosed as HPV positive. The women who tested HPV positive, on the basis of PCR testing, and 10% randomly selected HPV-negative cases (37) and 18 women who voluntary requested testing underwent colposcopy and HC2 testing. The sensitivity of menstrual pad HPV testing compared with gold standard HC2 testing was 83% [95% confidence interval (CI): 0.47-0.97], 67% (95% CI: 0.30-0.91) and specificity was 99% (95% CI: 0.96-0.99), 88% (95% CI: 0.77-0.94) in population A and population B, respectively. The sensitivity of diagnosing CIN lesion was 83% (95% CI: 0.44-0.97) and specificity was 95% (95% CI: 0.91-0.97). On the basis of the sensitivity and specificity results, and the completely noninvasive, simple and convenient method of detecting HPV, menstrual pad might be considered a cervical cancer screening tool in rural

  8. A Time-Series Water Level Forecasting Model Based on Imputation and Variable Selection Method.

    Science.gov (United States)

    Yang, Jun-He; Cheng, Ching-Hsue; Chan, Chia-Pan

    2017-01-01

    Reservoirs are important for households and impact the national economy. This paper proposed a time-series forecasting model based on estimating a missing value followed by variable selection to forecast the reservoir's water level. This study collected data from the Taiwan Shimen Reservoir as well as daily atmospheric data from 2008 to 2015. The two datasets are concatenated into an integrated dataset based on ordering of the data as a research dataset. The proposed time-series forecasting model summarily has three foci. First, this study uses five imputation methods to directly delete the missing value. Second, we identified the key variable via factor analysis and then deleted the unimportant variables sequentially via the variable selection method. Finally, the proposed model uses a Random Forest to build the forecasting model of the reservoir's water level. This was done to compare with the listing method under the forecasting error. These experimental results indicate that the Random Forest forecasting model when applied to variable selection with full variables has better forecasting performance than the listing model. In addition, this experiment shows that the proposed variable selection can help determine five forecast methods used here to improve the forecasting capability.

  9. A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations

    DEFF Research Database (Denmark)

    Clemente, Florian J.; Cardona, Alexia; Inchley, Charlotte E.

    2014-01-01

    Arctic populations live in an environment characterized by extreme cold and the absence of plant foods for much of the year and are likely to have undergone genetic adaptations to these environmental conditions in the time they have been living there. Genome-wide selection scans based on genotype......, using whole-genome high-coverage sequence data, we identified the most likely causative variant as a nonsynonymous G>A transition (rs80356779; c.1436C>T [p.Pro479Leu] on the reverse strand) in CPT1A, a key regulator of mitochondrial long-chain fatty-acid oxidation. Remarkably, the derived allele...... this variant to high frequency in circum-Arctic populations within the last 6–23 ka despite associated deleterious consequences, possibly as a result of the selective advantage it originally provided to either a high-fat diet or a cold environment....

  10. Greater fruit selection following an appearance-based compared with a health-based health promotion poster

    Science.gov (United States)

    2016-01-01

    Abstract Background This study investigated the impact of an appearance-based compared with a traditional health-based public health message for healthy eating. Methods A total of 166 British University students (41 males; aged 20.6 ± 1.9 years) were randomized to view either an appearance-based (n = 82) or a health-based (n = 84) fruit promotion poster. Intentions to consume fruit and immediate fruit selection (laboratory observation) were assessed immediately after poster viewing, and subsequent self-report fruit consumption was assessed 3 days later. Results Intentions to consume fruit were not predicted by poster type (largest β = 0.03, P = 0.68) but were associated with fruit-based liking, past consumption, attitudes and social norms (smallest β = 0.16, P = 0.04). Immediate fruit selection was greater following the appearance-based compared with the health-based poster (β = −0.24, P poster (β = −0.22, P = 0.03), but this effect became non-significant on consideration of participant characteristics (β = −0.15, P = 0.13), and was instead associated with fruit-based liking and past consumption (smallest β = 0.24, P = 0.03). Conclusions These findings demonstrate the clear value of an appearance-based compared with a health-based health promotion poster for increasing fruit selection. A distinction between outcome measures and the value of a behavioural measure is also demonstrated. PMID:28158693

  11. Visual coding with a population of direction-selective neurons.

    Science.gov (United States)

    Fiscella, Michele; Franke, Felix; Farrow, Karl; Müller, Jan; Roska, Botond; da Silveira, Rava Azeredo; Hierlemann, Andreas

    2015-10-01

    The brain decodes the visual scene from the action potentials of ∼20 retinal ganglion cell types. Among the retinal ganglion cells, direction-selective ganglion cells (DSGCs) encode motion direction. Several studies have focused on the encoding or decoding of motion direction by recording multiunit activity, mainly in the visual cortex. In this study, we simultaneously recorded from all four types of ON-OFF DSGCs of the rabbit retina using a microelectronics-based high-density microelectrode array (HDMEA) and decoded their concerted activity using probabilistic and linear decoders. Furthermore, we investigated how the modification of stimulus parameters (velocity, size, angle of moving object) and the use of different tuning curve fits influenced decoding precision. Finally, we simulated ON-OFF DSGC activity, based on real data, in order to understand how tuning curve widths and the angular distribution of the cells' preferred directions influence decoding performance. We found that probabilistic decoding strategies outperformed, on average, linear methods and that decoding precision was robust to changes in stimulus parameters such as velocity. The removal of noise correlations among cells, by random shuffling trials, caused a drop in decoding precision. Moreover, we found that tuning curves are broad in order to minimize large errors at the expense of a higher average error, and that the retinal direction-selective system would not substantially benefit, on average, from having more than four types of ON-OFF DSGCs or from a perfect alignment of the cells' preferred directions. Copyright © 2015 the American Physiological Society.

  12. Interference-aware random beam selection schemes for spectrum sharing systems

    KAUST Repository

    Abdallah, Mohamed

    2012-10-19

    Spectrum sharing systems have been recently introduced to alleviate the problem of spectrum scarcity by allowing secondary unlicensed networks to share the spectrum with primary licensed networks under acceptable interference levels to the primary users. In this work, we develop interference-aware random beam selection schemes that provide enhanced performance for the secondary network under the condition that the interference observed by the receivers of the primary network is below a predetermined/acceptable value. We consider a secondary link composed of a transmitter equipped with multiple antennas and a single-antenna receiver sharing the same spectrum with a primary link composed of a single-antenna transmitter and a single-antenna receiver. The proposed schemes select a beam, among a set of power-optimized random beams, that maximizes the signal-to-interference-plus-noise ratio (SINR) of the secondary link while satisfying the primary interference constraint for different levels of feedback information describing the interference level at the primary receiver. For the proposed schemes, we develop a statistical analysis for the SINR statistics as well as the capacity and bit error rate (BER) of the secondary link.

  13. Population structure from NOS genes correlates with geographical differences in coronary incidence across Europe.

    Science.gov (United States)

    Carreras-Torres, Robert; Ferran, Albert; Zanetti, Daniela; Esteban, Esther; Varesi, Laurent; Pojskic, Naris; Coia, Valentina; Chaabani, Hassen; Via, Marc; Moral, Pedro

    2016-12-01

    The population analysis of cardiovascular risk and non-risk genetic variation can help to identify adaptive or random demographic processes that shaped coronary incidence variation across geography. In this study, 114 single nucleotide polymorphisms and 17 tandem repeat polymorphisms from Nitric Oxide Synthases (NOS) regions were analyzed in 1686 individuals from 35 populations from Europe, North Africa, and the Middle East. NOS genes encode for key enzymes on nitric oxide availability, which is involved in several cardiovascular processes. These genetic variations were used to test for selection and to infer the population structure of NOS regions. Moreover, we tested whether the variation in the incidence of coronary events and in the levels of classical risk factors in 11 of these European populations could be explained by the population structure estimates. Our results supported, first, the absence of clear signs of selection for NOS genetic variants associated with cardiovascular diseases, and second, the presence of a continuous genetic pattern of variation across European and North African populations without a Mediterranean barrier for gene flow. Finally, population structure estimates from NOS regions are closely correlated with coronary event rates and classical risk parameters (explaining 39-98%) among European populations. Our results reinforce the hypothesis that genetic bases of cardiovascular diseases and associated complex phenotypes could be geographically shaped by random demographic processes. © 2016 Wiley Periodicals, Inc.

  14. [Limitations of Social Participation in General Population - Normative Data of the IMET based on a Population-Based Survey in Northern Germany].

    Science.gov (United States)

    Deck, R; Walther, A L; Staupendahl, A; Katalinic, A

    2015-12-01

    Medical rehabilitation in Germany is characterized by the biopsychosocial model of the ICF. Its complexity makes it less suitable for studies in rehabilitation sciences. For an implementation of the ICF, specific assessment instruments that are able to measure activity and participation efficiently in rehabilitation are needed. Instruments measuring social participation are rarely available in German language and have been employed only in a handful of empirical works. The "Index zur Messung von Einschränkungen der Teilhabe" (IMET) was developed in 2005 and measures participation of people with different chronic diseases as described in the ICF. The IMET has been applied in many studies in rehabilitation science, but as reference values were not available so far, the results could not be classified. In a population survey, 5 004 residents in Luebeck were randomly selected by the registration office and sent a short questionnaire. The questionnaire contained questions on the overall state of health, quality of life, prevalence of chronic diseases and limitations of participation (IMET). The completed questionnaire was returned by 2 755 of 4 692 eligible people (58.7%). 731 residents declined participation. Therefore, the participation quota is 43.1%. The mean age of participants was 53 years (SD: 17.1), 53% were women.Limitations of participation varied according to sex and age. Men tended to be more limited in their participation. As expected, limitations in participation increased with age. Participants with a low level of education showed a significantly higher rate of participation restrictions than people with a higher level of education. The IMET correlated significantly with the health status and quality of life as well as with the prevalence of various chronic diseases. The random sample of Luebeck inhabitants comprised people between 19 and 79 years of age. The age distribution of our sample deviated from the German population with younger people being

  15. A web- and mobile phone-based intervention to prevent obesity in 4-year-olds (MINISTOP): a population-based randomized controlled trial.

    Science.gov (United States)

    Delisle, Christine; Sandin, Sven; Forsum, Elisabet; Henriksson, Hanna; Trolle-Lagerros, Ylva; Larsson, Christel; Maddison, Ralph; Ortega, Francisco B; Ruiz, Jonatan R; Silfvernagel, Kristin; Timpka, Toomas; Löf, Marie

    2015-02-07

    Childhood obesity is an increasing health problem globally. Overweight and obesity may be established as early as 2-5 years of age, highlighting the need for evidence-based effective prevention and treatment programs early in life. In adults, mobile phone based interventions for weight management (mHealth) have demonstrated positive effects on body mass, however, their use in child populations has yet to be examined. The aim of this paper is to report the study design and methodology of the MINSTOP (Mobile-based Intervention Intended to Stop Obesity in Preschoolers) trial. A two-arm, parallel design randomized controlled trial in 300 healthy Swedish 4-year-olds is conducted. After baseline measures, parents are allocated to either an intervention- or control group. The 6- month mHealth intervention consists of a web-based application (the MINSTOP app) to help parents promote healthy eating and physical activity in children. MINISTOP is based on the Social Cognitive Theory and involves the delivery of a comprehensive, personalized program of information and text messages based on existing guidelines for a healthy diet and active lifestyle in pre-school children. Parents also register physical activity and intakes of candy, soft drinks, vegetables as well as fruits of their child and receive feedback through the application. Primary outcomes include body fatness and energy intake, while secondary outcomes are time spent in sedentary, moderate, and vigorous physical activity, physical fitness and intakes of fruits and vegetables, snacks, soft drinks and candy. Food and energy intake (Tool for Energy balance in Children, TECH), body fatness (pediatric option for BodPod), physical activity (Actigraph wGT3x-BT) and physical fitness (the PREFIT battery of five fitness tests) are measured at baseline, after the intervention (six months after baseline) and at follow-up (12 months after baseline). This novel study will evaluate the effectiveness of a mHealth program for

  16. A general population genetic framework for antagonistic selection that accounts for demography and recurrent mutation.

    Science.gov (United States)

    Connallon, Tim; Clark, Andrew G

    2012-04-01

    Antagonistic selection--where alleles at a locus have opposing effects on male and female fitness ("sexual antagonism") or between components of fitness ("antagonistic pleiotropy")--might play an important role in maintaining population genetic variation and in driving phylogenetic and genomic patterns of sexual dimorphism and life-history evolution. While prior theory has thoroughly characterized the conditions necessary for antagonistic balancing selection to operate, we currently know little about the evolutionary interactions between antagonistic selection, recurrent mutation, and genetic drift, which should collectively shape empirical patterns of genetic variation. To fill this void, we developed and analyzed a series of population genetic models that simultaneously incorporate these processes. Our models identify two general properties of antagonistically selected loci. First, antagonistic selection inflates heterozygosity and fitness variance across a broad parameter range--a result that applies to alleles maintained by balancing selection and by recurrent mutation. Second, effective population size and genetic drift profoundly affect the statistical frequency distributions of antagonistically selected alleles. The "efficacy" of antagonistic selection (i.e., its tendency to dominate over genetic drift) is extremely weak relative to classical models, such as directional selection and overdominance. Alleles meeting traditional criteria for strong selection (N(e)s > 1, where N(e) is the effective population size, and s is a selection coefficient for a given sex or fitness component) may nevertheless evolve as if neutral. The effects of mutation and demography may generate population differences in overall levels of antagonistic fitness variation, as well as molecular population genetic signatures of balancing selection.

  17. Group based prenatal care in a low-and high risk population in the Netherlands: a study protocol for a stepped wedge cluster randomized controlled trial.

    Science.gov (United States)

    van Zwicht, Birgit S; Crone, Matty R; van Lith, Jan M M; Rijnders, Marlies E B

    2016-11-15

    CenteringPregnancy (CP) is a multifaceted group based care-model integrated in routine prenatal care, combining health assessment, education, and support. CP has shown some positive results on perinatal outcomes. However, the effects are less obvious when limited to the results of randomized controlled trials: as there are few trials and there is a variation in reported outcomes. Furthermore, former research was mostly conducted in the United States of America and in specific (often high risk) populations. Our study aims to evaluate the effects of CP in the Netherlands in a general population of pregnant women (low and high risk). Furthermore we aim to explore the mechanisms leading to the eventual effects by measuring potential mediating factors. We will perform a stepped wedge cluster randomized controlled trial, in a Western region in the Netherlands. Inclusion criteria are care, women in the intervention period (starting at the randomized time-point) will be offered the choice between individual care or CP. Primary outcomes are maternal and neonatal morbidity, retrieved from a national routine database. Secondary outcomes are health behavior, psychosocial outcomes, satisfaction, health care utilization and process outcomes, collected through self-administered questionnaires, group-evaluations and individual interviews. We will conduct intention-to-treat analyses. Also a per protocol analysis will be performed comparing the three subgroups: control group, CP-participants and non-CP-participants, using multilevel techniques to account for clustering effects. This study contributes to the evidence regarding the effect of CP and gives a first indication of the effect and implementation of CP in both low and high-risk pregnancies in a high-income Western society other than the USA. Also, measuring factors that are hypothesized to mediate the effect of CP will enable to explain the mechanisms that lead to effects on maternal and neonatal outcomes. Dutch Trial

  18. Natural and sexual selection giveth and taketh away reproductive barriers: models of population divergence in guppies.

    Science.gov (United States)

    Labonne, Jacques; Hendry, Andrew P

    2010-07-01

    The standard predictions of ecological speciation might be nuanced by the interaction between natural and sexual selection. We investigated this hypothesis with an individual-based model tailored to the biology of guppies (Poecilia reticulata). We specifically modeled the situation where a high-predation population below a waterfall colonizes a low-predation population above a waterfall. Focusing on the evolution of male color, we confirm that divergent selection causes the appreciable evolution of male color within 20 generations. The rate and magnitude of this divergence were reduced when dispersal rates were high and when female choice did not differ between environments. Adaptive divergence was always coupled to the evolution of two reproductive barriers: viability selection against immigrants and hybrids. Different types of sexual selection, however, led to contrasting results for another potential reproductive barrier: mating success of immigrants. In some cases, the effects of natural and sexual selection offset each other, leading to no overall reproductive isolation despite strong adaptive divergence. Sexual selection acting through female choice can thus strongly modify the effects of divergent natural selection and thereby alter the standard predictions of ecological speciation. We also found that under no circumstances did divergent selection cause appreciable divergence in neutral genetic markers.

  19. Hip Fracture in People with Erectile Dysfunction: A Nationwide Population-Based Cohort Study.

    Directory of Open Access Journals (Sweden)

    Chieh-Hsin Wu

    Full Text Available The aims of this study were to investigate the risk of hip fracture and contributing factors in patients with erectile dysfunction(ED. This population-based study was performed using the Taiwan National Health Insurance Research Database. The analysis included 4636 patients aged ≥ 40 years who had been diagnosed with ED (International Classification of Diseases, Ninth Revision, Clinical Modification codes 302.72, 607.84 during 1996-2010. The control group included 18,544 randomly selected age-matched patients without ED (1:4 ratio. The association between ED and hip fracture risk was estimated using a Cox proportional hazard regression model. During the follow-up period, 59 (1.27% patients in the ED group and 140 (0.75% patients in the non-ED group developed hip fracture. After adjusting for covariates, the overall incidence of hip fracture was 3.74-times higher in the ED group than in the non-ED group (2.03 vs. 0.50 per 1000 person-years, respectively. The difference in the overall incidence of hip fracture was largest during the 3-year follow-up period (hazard ratio = 7.85; 95% confidence interval = 2.94-20.96; P <0.0001. To the best of our knowledge, this nationwide population-based study is the first to investigate the relationship between ED and subsequent hip fracture in an Asian population. The results showed that ED patients had a higher risk of developing hip fracture. Patients with ED, particularly those aged 40-59 years, should undergo bone mineral density examinations as early as possible and should take measures to reduce the risk of falls.

  20. A random spatial sampling method in a rural developing nation

    Science.gov (United States)

    Michelle C. Kondo; Kent D.W. Bream; Frances K. Barg; Charles C. Branas

    2014-01-01

    Nonrandom sampling of populations in developing nations has limitations and can inaccurately estimate health phenomena, especially among hard-to-reach populations such as rural residents. However, random sampling of rural populations in developing nations can be challenged by incomplete enumeration of the base population. We describe a stratified random sampling method...

  1. The reverse effects of random perturbation on discrete systems for single and multiple population models

    International Nuclear Information System (INIS)

    Kang, Li; Tang, Sanyi

    2016-01-01

    Highlights: • The discrete single species and multiple species models with random perturbation are proposed. • The complex dynamics and interesting bifurcation behavior have been investigated. • The reverse effects of random perturbation on discrete systems have been discussed and revealed. • The main results can be applied for pest control and resources management. - Abstract: The natural species are likely to present several interesting and complex phenomena under random perturbations, which have been confirmed by simple mathematical models. The important questions are: how the random perturbations influence the dynamics of the discrete population models with multiple steady states or multiple species interactions? and is there any different effects for single species and multiple species models with random perturbation? To address those interesting questions, we have proposed the discrete single species model with two stable equilibria and the host-parasitoid model with Holling type functional response functions to address how the random perturbation affects the dynamics. The main results indicate that the random perturbation does not change the number of blurred orbits of the single species model with two stable steady states compared with results for the classical Ricker model with same random perturbation, but it can strength the stability. However, extensive numerical investigations depict that the random perturbation does not influence the complexities of the host-parasitoid models compared with the results for the models without perturbation, while it does increase the period of periodic orbits doubly. All those confirm that the random perturbation has a reverse effect on the dynamics of the discrete single and multiple population models, which could be applied in reality including pest control and resources management.

  2. Topology-selective jamming of fully-connected, code-division random-access networks

    Science.gov (United States)

    Polydoros, Andreas; Cheng, Unjeng

    1990-01-01

    The purpose is to introduce certain models of topology selective stochastic jamming and examine its impact on a class of fully-connected, spread-spectrum, slotted ALOHA-type random access networks. The theory covers dedicated as well as half-duplex units. The dominant role of the spatial duty factor is established, and connections with the dual concept of time selective jamming are discussed. The optimal choices of coding rate and link access parameters (from the users' side) and the jamming spatial fraction are numerically established for DS and FH spreading.

  3. The population-based Barcelona-Asymptomatic Intracranial Atherosclerosis Study (ASIA: rationale and design

    Directory of Open Access Journals (Sweden)

    Pera Guillem

    2011-02-01

    Full Text Available Abstract Background Large-artery intracranial atherosclerosis may be the most frequent cause of ischemic stroke worldwide. Traditional approaches have attempted to target the disease when it is already symptomatic. However, early detection of intracranial atherosclerosis may allow therapeutic intervention while the disease is still asymptomatic. The prevalence and natural history of asymptomatic intracranial atherosclerosis in Caucasians remain unclear. The aims of the Barcelona-ASymptomatic Intracranial Atherosclerosis (ASIA study are (1 to determine the prevalence of ASIA in a moderate-high vascular risk population, (2 to study its prognostic impact on the risk of suffering future major ischemic events, and (3 to identify predictors of the development, progression and clinical expression of this condition. Methods/Design Cross-over and cohort, population-based study. A randomly selected representative sample of 1,503 subjects with a mild-moderate-high vascular risk (as defined by a REGICOR score ≥ 5% and with neither a history of cerebrovascular nor ischemic heart disease will be studied. At baseline, all individuals will undergo extracranial and transcranial Color-Coded Duplex (TCCD ultrasound examinations to detect presence and severity of extra and intracranial atherosclerosis. Intracranial stenoses will be assessed by magnetic resonance angiography (MRA. Clinical and demographic variables will be recorded and blood samples will be drawn to investigate clinical, biological and genetic factors associated with the presence of ASIA. A long-term clinical and sonographic follow-up will be conducted thereafter to identify predictors of disease progression and of incident vascular events. Discussion The Barcelona-ASIA is a population-based study aiming to evaluate the prevalence and clinical importance of asymptomatic intracranial large-artery atherosclerosis in Caucasians. The ASIA project may provide a unique scientific resource to better

  4. The population-based Barcelona-Asymptomatic Intracranial Atherosclerosis Study (ASIA): rationale and design.

    Science.gov (United States)

    López-Cancio, Elena; Dorado, Laura; Millán, Mónica; Reverté, Silvia; Suñol, Anna; Massuet, Anna; Mataró, María; Galán, Amparo; Alzamora, Maite; Pera, Guillem; Torán, Pere; Dávalos, Antoni; Arenillas, Juan F

    2011-02-17

    Large-artery intracranial atherosclerosis may be the most frequent cause of ischemic stroke worldwide. Traditional approaches have attempted to target the disease when it is already symptomatic. However, early detection of intracranial atherosclerosis may allow therapeutic intervention while the disease is still asymptomatic. The prevalence and natural history of asymptomatic intracranial atherosclerosis in Caucasians remain unclear. The aims of the Barcelona-ASymptomatic Intracranial Atherosclerosis (ASIA) study are (1) to determine the prevalence of ASIA in a moderate-high vascular risk population, (2) to study its prognostic impact on the risk of suffering future major ischemic events, and (3) to identify predictors of the development, progression and clinical expression of this condition. Cross-over and cohort, population-based study. A randomly selected representative sample of 1,503 subjects with a mild-moderate-high vascular risk (as defined by a REGICOR score ≥ 5%) and with neither a history of cerebrovascular nor ischemic heart disease will be studied. At baseline, all individuals will undergo extracranial and transcranial Color-Coded Duplex (TCCD) ultrasound examinations to detect presence and severity of extra and intracranial atherosclerosis. Intracranial stenoses will be assessed by magnetic resonance angiography (MRA). Clinical and demographic variables will be recorded and blood samples will be drawn to investigate clinical, biological and genetic factors associated with the presence of ASIA. A long-term clinical and sonographic follow-up will be conducted thereafter to identify predictors of disease progression and of incident vascular events. The Barcelona-ASIA is a population-based study aiming to evaluate the prevalence and clinical importance of asymptomatic intracranial large-artery atherosclerosis in Caucasians. The ASIA project may provide a unique scientific resource to better understand the dynamics of intracranial atherosclerosis from

  5. A Rewritable, Random-Access DNA-Based Storage System.

    Science.gov (United States)

    Yazdi, S M Hossein Tabatabaei; Yuan, Yongbo; Ma, Jian; Zhao, Huimin; Milenkovic, Olgica

    2015-09-18

    We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing read-only methods that require decoding the whole file in order to read one data fragment. Our system is based on new constrained coding techniques and accompanying DNA editing methods that ensure data reliability, specificity and sensitivity of access, and at the same time provide exceptionally high data storage capacity. As a proof of concept, we encoded parts of the Wikipedia pages of six universities in the USA, and selected and edited parts of the text written in DNA corresponding to three of these schools. The results suggest that DNA is a versatile media suitable for both ultrahigh density archival and rewritable storage applications.

  6. Risk of Parkinson's disease following zolpidem use: a retrospective, population-based cohort study.

    Science.gov (United States)

    Huang, Hui-Chun; Tsai, Chon-Haw; Muo, Chih-Hsin; Lin, Kang-Hsu; Lu, Ming-Kuei; Sung, Fung-Chang; Kao, Chia-Hung

    2015-01-01

    To evaluate the influence of long-term zolpidem use on the incidence of developing Parkinson's disease. 2,961 subjects who used zolpidem for the first time longer than 3 months between 1998 and 2000 were identified in the National Health Insurance system of Taiwan. Subjects without a history of zolpidem use were randomly selected as a comparison cohort and frequency matched to zolpidem users based on age, sex, and index date. The diagnosis of Parkinson's disease was based on the criteria of the International Classification of Diseases, Ninth Revision, Clinical Modification. Its incidence until the end of 2009 was calculated and its hazard ratios (HRs) and 95% CIs were estimated using Cox proportional hazards regression models and Kaplan-Meier analysis. The overall incidence of Parkinson's disease was greater among zolpidem users than in the comparison cohort (HR = 1.88; 95% CI, 1.45-2.45). However, there was no difference in Parkinson's disease incidence between these 2 cohorts after 5 years of observation. The risk of Parkinson's disease increased with increasing zolpidem dose, with an HR of 0.70 for low-dose users (zolpidem only (HR = 2.35; 95% CI, 1.66-3.33) compared to those using benzodiazepines only (HR = 1.31; 95% CI, 0.91-1.90). By stratified analysis, zolpidem use with concurrent depression (HR = 4.79) increased the risk of Parkinson's disease compared to that of zolpidem users without concurrent depression. Zolpidem use might unmask preclinical Parkinson's disease, especially in patients with depression. However, large population-based, unbiased, randomized trials are warranted to confirm this finding. © Copyright 2015 Physicians Postgraduate Press, Inc.

  7. Population structure of a lodgepole pine (Pinus contorta) and jack pine (P. banksiana) complex as revealed by random amplified polymorphic DNA.

    Science.gov (United States)

    Ye, Terrance Z; Yang, Rong-Cai; Yeh, Francis C

    2002-06-01

    We studied the population structure of a lodgepole (Pinus contorta Dougl.) and jack pine (Pinus banksiana Lamb.) complex in west central Alberta and neighboring areas by assessing random amplified polymorphic DNA (RAPD) variability in 23 lodgepole pine, 9 jack pine, and 8 putative hybrid populations. Of 200 random primers screened, 10 that amplified 39 sharp and reproducible RAPDs were chosen for the study. None of the 39 RAPDs were unique to the parental species. RAPD diversity ranged from 0.085 to 0.190 among populations and averaged 0.143 for lodgepole pine, 0.156 for jack pine, 0.152 for hybrids, and 0.148 for all 40 populations. The estimated population differentiation based on G(ST) was 0.168 for hybrids, 0.162 for lodgepole pine, 0.155 for jack pine, and 0.247 across all 40 populations. Cluster analysis of genetic distances generally separated jack pine from lodgepole pine and hybrids, but no division could be identified that further separated lodgepole pine from hybrids. The observed weak to mild trend of "introgression by distance" in the complex and neighbouring areas was consistent with the view that introgressive hybridization between lodgepole and jack pines within and outside the hybrid zone may have been through secondary contact and primary intergradation, respectively.

  8. Phenotypic selection on flowering phenology and pollination efficiency traits between Primula populations with different pollinator assemblages.

    Science.gov (United States)

    Wu, Yun; Li, Qing-Jun

    2017-10-01

    Floral traits have largely been attributed to phenotypic selection in plant-pollinator interactions. However, the strength of this link has rarely been ascertained with real pollinators. We conducted pollinator observations and estimated selection through female fitness on flowering phenology and floral traits between two Primula secundiflora populations. We quantified pollinator-mediated selection by subtracting estimates of selection gradients of plants receiving supplemental hand pollination from those of plants receiving open pollination. There was net directional selection for an earlier flowering start date at populations where the dominant pollinators were syrphid flies, and flowering phenology was also subjected to stabilized quadratic selection. However, a later flowering start date was significantly selected at populations where the dominant pollinators were legitimate (normal pollination through the corolla tube entrance) and illegitimate bumblebees (abnormal pollination through nectar robbing hole which located at the corolla tube), and flowering phenology was subjected to disruptive quadratic selection. Wider corolla tube entrance diameter was selected at both populations. Furthermore, the strength of net directional selection on flowering start date and corolla tube entrance diameter was stronger at the population where the dominant pollinators were syrphid flies. Pollinator-mediated selection explained most of the between-population variations in the net directional selection on flowering phenology and corolla tube entrance diameter. Our results suggested the important influence of pollinator-mediated selection on floral evolution. Variations in pollinator assemblages not only resulted in variation in the direction of selection but also the strength of selection on floral traits.

  9. Linking resource selection and mortality modeling for population estimation of mountain lions in Montana

    Science.gov (United States)

    Robinson, Hugh S.; Ruth, Toni K.; Gude, Justin A.; Choate, David; DeSimone, Rich; Hebblewhite, Mark; Matchett, Marc R.; Mitchell, Michael S.; Murphy, Kerry; Williams, Jim

    2015-01-01

    To be most effective, the scale of wildlife management practices should match the range of a particular species’ movements. For this reason, combined with our inability to rigorously or regularly census mountain lion populations, several authors have suggested that mountain lions be managed in a source-sink or metapopulation framework. We used a combination of resource selection functions, mortality estimation, and dispersal modeling to estimate cougar population levels in Montana statewide and potential population level effects of planned harvest levels. Between 1980 and 2012, 236 independent mountain lions were collared and monitored for research in Montana. From these data we used 18,695 GPS locations collected during winter from 85 animals to develop a resource selection function (RSF), and 11,726 VHF and GPS locations from 142 animals along with the locations of 6343 mountain lions harvested from 1988–2011 to validate the RSF model. Our RSF model validated well in all portions of the State, although it appeared to perform better in Montana Fish, Wildlife and Parks (MFWP) Regions 1, 2, 4 and 6, than in Regions 3, 5, and 7. Our mean RSF based population estimate for the total population (kittens, juveniles, and adults) of mountain lions in Montana in 2005 was 3926, with almost 25% of the entire population in MFWP Region 1. Estimates based on a high and low reference population estimates produce a possible range of 2784 to 5156 mountain lions statewide. Based on a range of possible survival rates we estimated the mountain lion population in Montana to be stable to slightly increasing between 2005 and 2010 with lambda ranging from 0.999 (SD = 0.05) to 1.02 (SD = 0.03). We believe these population growth rates to be a conservative estimate of true population growth. Our model suggests that proposed changes to female harvest quotas for 2013–2015 will result in an annual statewide population decline of 3% and shows that, due to reduced dispersal, changes to

  10. A comparison of statistical methods for genomic selection in a mice population

    Directory of Open Access Journals (Sweden)

    Neves Haroldo HR

    2012-11-01

    Full Text Available Abstract Background The availability of high-density panels of SNP markers has opened new perspectives for marker-assisted selection strategies, such that genotypes for these markers are used to predict the genetic merit of selection candidates. Because the number of markers is often much larger than the number of phenotypes, marker effect estimation is not a trivial task. The objective of this research was to compare the predictive performance of ten different statistical methods employed in genomic selection, by analyzing data from a heterogeneous stock mice population. Results For the five traits analyzed (W6W: weight at six weeks, WGS: growth slope, BL: body length, %CD8+: percentage of CD8+ cells, CD4+/ CD8+: ratio between CD4+ and CD8+ cells, within-family predictions were more accurate than across-family predictions, although this superiority in accuracy varied markedly across traits. For within-family prediction, two kernel methods, Reproducing Kernel Hilbert Spaces Regression (RKHS and Support Vector Regression (SVR, were the most accurate for W6W, while a polygenic model also had comparable performance. A form of ridge regression assuming that all markers contribute to the additive variance (RR_GBLUP figured among the most accurate for WGS and BL, while two variable selection methods ( LASSO and Random Forest, RF had the greatest predictive abilities for %CD8+ and CD4+/ CD8+. RF, RKHS, SVR and RR_GBLUP outperformed the remainder methods in terms of bias and inflation of predictions. Conclusions Methods with large conceptual differences reached very similar predictive abilities and a clear re-ranking of methods was observed in function of the trait analyzed. Variable selection methods were more accurate than the remainder in the case of %CD8+ and CD4+/CD8+ and these traits are likely to be influenced by a smaller number of QTL than the remainder. Judged by their overall performance across traits and computational requirements, RR

  11. Day-ahead load forecast using random forest and expert input selection

    International Nuclear Information System (INIS)

    Lahouar, A.; Ben Hadj Slama, J.

    2015-01-01

    Highlights: • A model based on random forests for short term load forecast is proposed. • An expert feature selection is added to refine inputs. • Special attention is paid to customers behavior, load profile and special holidays. • The model is flexible and able to handle complex load signal. • A technical comparison is performed to assess the forecast accuracy. - Abstract: The electrical load forecast is getting more and more important in recent years due to the electricity market deregulation and integration of renewable resources. To overcome the incoming challenges and ensure accurate power prediction for different time horizons, sophisticated intelligent methods are elaborated. Utilization of intelligent forecast algorithms is among main characteristics of smart grids, and is an efficient tool to face uncertainty. Several crucial tasks of power operators such as load dispatch rely on the short term forecast, thus it should be as accurate as possible. To this end, this paper proposes a short term load predictor, able to forecast the next 24 h of load. Using random forest, characterized by immunity to parameter variations and internal cross validation, the model is constructed following an online learning process. The inputs are refined by expert feature selection using a set of if–then rules, in order to include the own user specifications about the country weather or market, and to generalize the forecast ability. The proposed approach is tested through a real historical set from the Tunisian Power Company, and the simulation shows accurate and satisfactory results for one day in advance, with an average error exceeding rarely 2.3%. The model is validated for regular working days and weekends, and special attention is paid to moving holidays, following non Gregorian calendar

  12. Comparison of Address-based Sampling and Random-digit Dialing Methods for Recruiting Young Men as Controls in a Case-Control Study of Testicular Cancer Susceptibility

    OpenAIRE

    Clagett, Bartholt; Nathanson, Katherine L.; Ciosek, Stephanie L.; McDermoth, Monique; Vaughn, David J.; Mitra, Nandita; Weiss, Andrew; Martonik, Rachel; Kanetsky, Peter A.

    2013-01-01

    Random-digit dialing (RDD) using landline telephone numbers is the historical gold standard for control recruitment in population-based epidemiologic research. However, increasing cell-phone usage and diminishing response rates suggest that the effectiveness of RDD in recruiting a random sample of the general population, particularly for younger target populations, is decreasing. In this study, we compared landline RDD with alternative methods of control recruitment, including RDD using cell-...

  13. Somatic symptom profiles in the general population: a latent class analysis in a Danish population-based health survey

    Directory of Open Access Journals (Sweden)

    Eliasen M

    2017-08-01

    Full Text Available Marie Eliasen,1 Torben Jørgensen,1–3 Andreas Schröder,4 Thomas Meinertz Dantoft,1 Per Fink,4 Chalotte Heinsvig Poulsen,1,5 Nanna Borup Johansen,1 Lene Falgaard Eplov,5 Sine Skovbjerg,1 Svend Kreiner2 1Research Centre for Prevention and Health, Centre for Health, The Capital Region of Denmark, Glostrup, 2Department of Public Health, University of Copenhagen, Copenhagen, 3Department of Clinical Medicine, Aalborg University, Aalborg, 4Research Clinic for Functional Disorders and Psychosomatics, Aarhus University Hospital, Aarhus C, 5Mental Health Centre Copenhagen, The Capital Region of Denmark, Hellerup, Denmark Purpose: The aim of this study was to identify and describe somatic symptom profiles in the general adult population in order to enable further epidemiological research within multiple somatic symptoms.Methods: Information on 19 self-reported common somatic symptoms was achieved from a population-based questionnaire survey of 36,163 randomly selected adults in the Capital Region of Denmark (55.4% women. The participants stated whether they had been considerably bothered by each symptom within 14 days prior to answering the questionnaire. We used latent class analysis to identify the somatic symptom profiles. The profiles were further described by their association with age, sex, chronic disease, and self-perceived health.Results: We identified 10 different somatic symptom profiles defined by number, type, and site of the symptoms. The majority of the population (74.0% had a profile characterized by no considerable bothering symptoms, while a minor group of 3.9% had profiles defined by a high risk of multiple somatic symptoms. The remaining profiles were more likely to be characterized by a few specific symptoms. The profiles could further be described by their associations with age, sex, chronic disease, and self-perceived health.Conclusion: The identified somatic symptom profiles could be distinguished by number, type, and site of

  14. Highly selective population of two excited states in nonresonant two-photon absorption

    International Nuclear Information System (INIS)

    Zhang Hui; Zhang Shi-An; Sun Zhen-Rong

    2011-01-01

    A nonresonant two-photon absorption process can be manipulated by tailoring the ultra-short laser pulse. In this paper, we theoretically demonstrate a highly selective population of two excited states in the nonresonant two-photon absorption process by rationally designing a spectral phase distribution. Our results show that one excited state is maximally populated while the other state population is widely tunable from zero to the maximum value. We believe that the theoretical results may play an important role in the selective population of a more complex nonlinear process comprising nonresonant two-photon absorption, such as resonance-mediated (2+1)-three-photon absorption and (2+1)-resonant multiphoton ionization. (atomic and molecular physics)

  15. Peculiarities of the statistics of spectrally selected fluorescence radiation in laser-pumped dye-doped random media

    Science.gov (United States)

    Yuvchenko, S. A.; Ushakova, E. V.; Pavlova, M. V.; Alonova, M. V.; Zimnyakov, D. A.

    2018-04-01

    We consider the practical realization of a new optical probe method of the random media which is defined as the reference-free path length interferometry with the intensity moments analysis. A peculiarity in the statistics of the spectrally selected fluorescence radiation in laser-pumped dye-doped random medium is discussed. Previously established correlations between the second- and the third-order moments of the intensity fluctuations in the random interference patterns, the coherence function of the probe radiation, and the path difference probability density for the interfering partial waves in the medium are confirmed. The correlations were verified using the statistical analysis of the spectrally selected fluorescence radiation emitted by a laser-pumped dye-doped random medium. Water solution of Rhodamine 6G was applied as the doping fluorescent agent for the ensembles of the densely packed silica grains, which were pumped by the 532 nm radiation of a solid state laser. The spectrum of the mean path length for a random medium was reconstructed.

  16. A Copula Based Approach for Design of Multivariate Random Forests for Drug Sensitivity Prediction.

    Science.gov (United States)

    Haider, Saad; Rahman, Raziur; Ghosh, Souparno; Pal, Ranadip

    2015-01-01

    Modeling sensitivity to drugs based on genetic characterizations is a significant challenge in the area of systems medicine. Ensemble based approaches such as Random Forests have been shown to perform well in both individual sensitivity prediction studies and team science based prediction challenges. However, Random Forests generate a deterministic predictive model for each drug based on the genetic characterization of the cell lines and ignores the relationship between different drug sensitivities during model generation. This application motivates the need for generation of multivariate ensemble learning techniques that can increase prediction accuracy and improve variable importance ranking by incorporating the relationships between different output responses. In this article, we propose a novel cost criterion that captures the dissimilarity in the output response structure between the training data and node samples as the difference in the two empirical copulas. We illustrate that copulas are suitable for capturing the multivariate structure of output responses independent of the marginal distributions and the copula based multivariate random forest framework can provide higher accuracy prediction and improved variable selection. The proposed framework has been validated on genomics of drug sensitivity for cancer and cancer cell line encyclopedia database.

  17. Identifying footprints of selection in stocked brown trout populations: a spatio-temporal approach

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Meier, Kristian; Mensberg, Karen-Lise Dons

    2010-01-01

    Studies of interactions between farmed and wild salmonid fishes have suggested reduced fitness of farmed strains in the wild, but evidence for selection at the genic level is lacking. We studied three brown trout populations in Denmark which have been significantly admixed with stocked hatchery...... trout (19–64%), along with two hatchery strains used for stocking. The wild populations were represented by contemporary samples (2000–2006) and two of them by historical samples (1943–1956). We analysed 61 microsatellite loci, nine of which showed putative functional relationships [expressed sequence...... trout. In the most strongly admixed population, however, there was no evidence for selection, possibly because of immigration by stocked trout overcoming selection against hatchery-derived alleles or supportive breeding practices allowing hatchery strain trout to escape natural selection. To our...

  18. Who participates in a randomized trial of mindfulness-based stress reduction (MBSR) after breast cancer?

    DEFF Research Database (Denmark)

    Würtzen, Hanne; Oksbjerg Dalton, Susanne; Kaae Andersen, Klaus

    2013-01-01

    Danish population-based registries and clinical databases to determine differences in demographics, breast cancer and co-morbidity among 1208 women eligible for a randomized controlled trial (www.clinicaltrials.gov identifier: NCT00990977) of mindfulness-based stress reduction MBSR. RESULTS: Participants......BACKGROUND: Discussion regarding the necessity to identify patients with both the need and motivation for psychosocial intervention is ongoing. Evidence for an effect of mindfulness-based interventions among cancer patients is based on few studies with no systematic enrollment. METHODS: We used...

  19. Strategic conservation of orchard germplasm based on indigenous knowledge and genetic diversity: a case study of sour orange populations in China.

    Science.gov (United States)

    Ming, Feng; Liu, Qi-Kun; Shi, Jin-Lei; Wang, Wei; Lu, Bao-Rong

    2009-01-01

    To effectively conserve sour orange (Citrus aurantium L.) germplasm on two islands at the estuary of the Yangtze River in China, we estimated genetic variation and relationships of the known parental trees and their proposed descendents (young trees) using the fingerprints of random amplified polymorphic DNA (RAPD). Results based on RAPD analyses showed considerable genetic diversity in the parental populations (H(e)=0.202). The overall populations including the parental and young trees showed slightly higher genetic diversity (H(e)=0.298) than the parents, with about 10% variation between populations. An unweighted pair group method with arithmetic mean analysis dendrogram based on cluster analysis of the Jaccard similarity among individuals demonstrated a more complicated relationship of the parental and young trees from the two islands, although the young trees showed a clear association with parental trees. This indicates a significant contribution of parental trees in establishing the sour orange populations on the two islands. According to farmers' knowledge, conservation of only one or two parental trees would be sufficient because they believed that the whole populations were generated from a single mother tree. However, this study suggests that preserving most parental trees and some selected young trees with distant genetic relationships should be an effective conservation strategy for sour orange germplasm on the two islands.

  20. Using variable combination population analysis for variable selection in multivariate calibration.

    Science.gov (United States)

    Yun, Yong-Huan; Wang, Wei-Ting; Deng, Bai-Chuan; Lai, Guang-Bi; Liu, Xin-bo; Ren, Da-Bing; Liang, Yi-Zeng; Fan, Wei; Xu, Qing-Song

    2015-03-03

    Variable (wavelength or feature) selection techniques have become a critical step for the analysis of datasets with high number of variables and relatively few samples. In this study, a novel variable selection strategy, variable combination population analysis (VCPA), was proposed. This strategy consists of two crucial procedures. First, the exponentially decreasing function (EDF), which is the simple and effective principle of 'survival of the fittest' from Darwin's natural evolution theory, is employed to determine the number of variables to keep and continuously shrink the variable space. Second, in each EDF run, binary matrix sampling (BMS) strategy that gives each variable the same chance to be selected and generates different variable combinations, is used to produce a population of subsets to construct a population of sub-models. Then, model population analysis (MPA) is employed to find the variable subsets with the lower root mean squares error of cross validation (RMSECV). The frequency of each variable appearing in the best 10% sub-models is computed. The higher the frequency is, the more important the variable is. The performance of the proposed procedure was investigated using three real NIR datasets. The results indicate that VCPA is a good variable selection strategy when compared with four high performing variable selection methods: genetic algorithm-partial least squares (GA-PLS), Monte Carlo uninformative variable elimination by PLS (MC-UVE-PLS), competitive adaptive reweighted sampling (CARS) and iteratively retains informative variables (IRIV). The MATLAB source code of VCPA is available for academic research on the website: http://www.mathworks.com/matlabcentral/fileexchange/authors/498750. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Community-based intermittent mass testing and treatment for malaria in an area of high transmission intensity, western Kenya: study design and methodology for a cluster randomized controlled trial.

    Science.gov (United States)

    Samuels, Aaron M; Awino, Nobert; Odongo, Wycliffe; Abong'o, Benard; Gimnig, John; Otieno, Kephas; Shi, Ya Ping; Were, Vincent; Allen, Denise Roth; Were, Florence; Sang, Tony; Obor, David; Williamson, John; Hamel, Mary J; Patrick Kachur, S; Slutsker, Laurence; Lindblade, Kim A; Kariuki, Simon; Desai, Meghna

    2017-06-07

    Most human Plasmodium infections in western Kenya are asymptomatic and are believed to contribute importantly to malaria transmission. Elimination of asymptomatic infections requires active treatment approaches, such as mass testing and treatment (MTaT) or mass drug administration (MDA), as infected persons do not seek care for their infection. Evaluations of community-based approaches that are designed to reduce malaria transmission require careful attention to study design to ensure that important effects can be measured accurately. This manuscript describes the study design and methodology of a cluster-randomized controlled trial to evaluate a MTaT approach for malaria transmission reduction in an area of high malaria transmission. Ten health facilities in western Kenya were purposively selected for inclusion. The communities within 3 km of each health facility were divided into three clusters of approximately equal population size. Two clusters around each health facility were randomly assigned to the control arm, and one to the intervention arm. Three times per year for 2 years, after the long and short rains, and again before the long rains, teams of community health volunteers visited every household within the intervention arm, tested all consenting individuals with malaria rapid diagnostic tests, and treated all positive individuals with an effective anti-malarial. The effect of mass testing and treatment on malaria transmission was measured through population-based longitudinal cohorts, outpatient visits for clinical malaria, periodic population-based cross-sectional surveys, and entomological indices.

  2. The dynamics of diverse segmental amplifications in populations of Saccharomyces cerevisiae adapting to strong selection.

    Science.gov (United States)

    Payen, Celia; Di Rienzi, Sara C; Ong, Giang T; Pogachar, Jamie L; Sanchez, Joseph C; Sunshine, Anna B; Raghuraman, M K; Brewer, Bonita J; Dunham, Maitreya J

    2014-03-20

    Population adaptation to strong selection can occur through the sequential or parallel accumulation of competing beneficial mutations. The dynamics, diversity, and rate of fixation of beneficial mutations within and between populations are still poorly understood. To study how the mutational landscape varies across populations during adaptation, we performed experimental evolution on seven parallel populations of Saccharomyces cerevisiae continuously cultured in limiting sulfate medium. By combining quantitative polymerase chain reaction, array comparative genomic hybridization, restriction digestion and contour-clamped homogeneous electric field gel electrophoresis, and whole-genome sequencing, we followed the trajectory of evolution to determine the identity and fate of beneficial mutations. During a period of 200 generations, the yeast populations displayed parallel evolutionary dynamics that were driven by the coexistence of independent beneficial mutations. Selective amplifications rapidly evolved under this selection pressure, in particular common inverted amplifications containing the sulfate transporter gene SUL1. Compared with single clones, detailed analysis of the populations uncovers a greater complexity whereby multiple subpopulations arise and compete despite a strong selection. The most common evolutionary adaptation to strong selection in these populations grown in sulfate limitation is determined by clonal interference, with adaptive variants both persisting and replacing one another.

  3. Goal selection versus process control while learning to use a brain-computer interface

    Science.gov (United States)

    Royer, Audrey S.; Rose, Minn L.; He, Bin

    2011-06-01

    A brain-computer interface (BCI) can be used to accomplish a task without requiring motor output. Two major control strategies used by BCIs during task completion are process control and goal selection. In process control, the user exerts continuous control and independently executes the given task. In goal selection, the user communicates their goal to the BCI and then receives assistance executing the task. A previous study has shown that goal selection is more accurate and faster in use. An unanswered question is, which control strategy is easier to learn? This study directly compares goal selection and process control while learning to use a sensorimotor rhythm-based BCI. Twenty young healthy human subjects were randomly assigned either to a goal selection or a process control-based paradigm for eight sessions. At the end of the study, the best user from each paradigm completed two additional sessions using all paradigms randomly mixed. The results of this study were that goal selection required a shorter training period for increased speed, accuracy, and information transfer over process control. These results held for the best subjects as well as in the general subject population. The demonstrated characteristics of goal selection make it a promising option to increase the utility of BCIs intended for both disabled and able-bodied users.

  4. An econometric method for estimating population parameters from non-random samples: An application to clinical case finding.

    Science.gov (United States)

    Burger, Rulof P; McLaren, Zoë M

    2017-09-01

    The problem of sample selection complicates the process of drawing inference about populations. Selective sampling arises in many real world situations when agents such as doctors and customs officials search for targets with high values of a characteristic. We propose a new method for estimating population characteristics from these types of selected samples. We develop a model that captures key features of the agent's sampling decision. We use a generalized method of moments with instrumental variables and maximum likelihood to estimate the population prevalence of the characteristic of interest and the agents' accuracy in identifying targets. We apply this method to tuberculosis (TB), which is the leading infectious disease cause of death worldwide. We use a national database of TB test data from South Africa to examine testing for multidrug resistant TB (MDR-TB). Approximately one quarter of MDR-TB cases was undiagnosed between 2004 and 2010. The official estimate of 2.5% is therefore too low, and MDR-TB prevalence is as high as 3.5%. Signal-to-noise ratios are estimated to be between 0.5 and 1. Our approach is widely applicable because of the availability of routinely collected data and abundance of potential instruments. Using routinely collected data to monitor population prevalence can guide evidence-based policy making. Copyright © 2017 John Wiley & Sons, Ltd.

  5. Comparison of Three Plot Selection Methods for Estimating Change in Temporally Variable, Spatially Clustered Populations.

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, William L. [Bonneville Power Administration, Portland, OR (US). Environment, Fish and Wildlife

    2001-07-01

    Monitoring population numbers is important for assessing trends and meeting various legislative mandates. However, sampling across time introduces a temporal aspect to survey design in addition to the spatial one. For instance, a sample that is initially representative may lose this attribute if there is a shift in numbers and/or spatial distribution in the underlying population that is not reflected in later sampled plots. Plot selection methods that account for this temporal variability will produce the best trend estimates. Consequently, I used simulation to compare bias and relative precision of estimates of population change among stratified and unstratified sampling designs based on permanent, temporary, and partial replacement plots under varying levels of spatial clustering, density, and temporal shifting of populations. Permanent plots produced more precise estimates of change than temporary plots across all factors. Further, permanent plots performed better than partial replacement plots except for high density (5 and 10 individuals per plot) and 25% - 50% shifts in the population. Stratified designs always produced less precise estimates of population change for all three plot selection methods, and often produced biased change estimates and greatly inflated variance estimates under sampling with partial replacement. Hence, stratification that remains fixed across time should be avoided when monitoring populations that are likely to exhibit large changes in numbers and/or spatial distribution during the study period. Key words: bias; change estimation; monitoring; permanent plots; relative precision; sampling with partial replacement; temporary plots.

  6. Maximum relevance, minimum redundancy band selection based on neighborhood rough set for hyperspectral data classification

    International Nuclear Information System (INIS)

    Liu, Yao; Chen, Yuehua; Tan, Kezhu; Xie, Hong; Wang, Liguo; Xie, Wu; Yan, Xiaozhen; Xu, Zhen

    2016-01-01

    Band selection is considered to be an important processing step in handling hyperspectral data. In this work, we selected informative bands according to the maximal relevance minimal redundancy (MRMR) criterion based on neighborhood mutual information. Two measures MRMR difference and MRMR quotient were defined and a forward greedy search for band selection was constructed. The performance of the proposed algorithm, along with a comparison with other methods (neighborhood dependency measure based algorithm, genetic algorithm and uninformative variable elimination algorithm), was studied using the classification accuracy of extreme learning machine (ELM) and random forests (RF) classifiers on soybeans’ hyperspectral datasets. The results show that the proposed MRMR algorithm leads to promising improvement in band selection and classification accuracy. (paper)

  7. Detection of selection signatures of population-specific genomic regions selected during domestication process in Jinhua pigs.

    Science.gov (United States)

    Li, Zhengcao; Chen, Jiucheng; Wang, Zhen; Pan, Yuchun; Wang, Qishan; Xu, Ningying; Wang, Zhengguang

    2016-12-01

    Chinese pigs have been undergoing both natural and artificial selection for thousands of years. Jinhua pigs are of great importance, as they can be a valuable model for exploring the genetic mechanisms linked to meat quality and other traits such as disease resistance, reproduction and production. The purpose of this study was to identify distinctive footprints of selection between Jinhua pigs and other breeds utilizing genome-wide SNP data. Genotyping by genome reducing and sequencing was implemented in order to perform cross-population extended haplotype homozygosity to reveal strong signatures of selection for those economically important traits. This work was performed at a 2% genome level, which comprised 152 006 SNPs genotyped in a total of 517 individuals. Population-specific footprints of selective sweeps were searched for in the genome of Jinhua pigs using six native breeds and three European breeds as reference groups. Several candidate genes associated with meat quality, health and reproduction, such as GH1, CRHR2, TRAF4 and CCK, were found to be overlapping with the significantly positive outliers. Additionally, the results revealed that some genomic regions associated with meat quality, immune response and reproduction in Jinhua pigs have evolved directionally under domestication and subsequent selections. The identified genes and biological pathways in Jinhua pigs showed different selection patterns in comparison with the Chinese and European breeds. © 2016 Stichting International Foundation for Animal Genetics.

  8. A Time-Series Water Level Forecasting Model Based on Imputation and Variable Selection Method

    Directory of Open Access Journals (Sweden)

    Jun-He Yang

    2017-01-01

    Full Text Available Reservoirs are important for households and impact the national economy. This paper proposed a time-series forecasting model based on estimating a missing value followed by variable selection to forecast the reservoir’s water level. This study collected data from the Taiwan Shimen Reservoir as well as daily atmospheric data from 2008 to 2015. The two datasets are concatenated into an integrated dataset based on ordering of the data as a research dataset. The proposed time-series forecasting model summarily has three foci. First, this study uses five imputation methods to directly delete the missing value. Second, we identified the key variable via factor analysis and then deleted the unimportant variables sequentially via the variable selection method. Finally, the proposed model uses a Random Forest to build the forecasting model of the reservoir’s water level. This was done to compare with the listing method under the forecasting error. These experimental results indicate that the Random Forest forecasting model when applied to variable selection with full variables has better forecasting performance than the listing model. In addition, this experiment shows that the proposed variable selection can help determine five forecast methods used here to improve the forecasting capability.

  9. Feasible Initial Population with Genetic Diversity for a Population-Based Algorithm Applied to the Vehicle Routing Problem with Time Windows

    Directory of Open Access Journals (Sweden)

    Marco Antonio Cruz-Chávez

    2016-01-01

    Full Text Available A stochastic algorithm for obtaining feasible initial populations to the Vehicle Routing Problem with Time Windows is presented. The theoretical formulation for the Vehicle Routing Problem with Time Windows is explained. The proposed method is primarily divided into a clustering algorithm and a two-phase algorithm. The first step is the application of a modified k-means clustering algorithm which is proposed in this paper. The two-phase algorithm evaluates a partial solution to transform it into a feasible individual. The two-phase algorithm consists of a hybridization of four kinds of insertions which interact randomly to obtain feasible individuals. It has been proven that different kinds of insertions impact the diversity among individuals in initial populations, which is crucial for population-based algorithm behavior. A modification to the Hamming distance method is applied to the populations generated for the Vehicle Routing Problem with Time Windows to evaluate their diversity. Experimental tests were performed based on the Solomon benchmarking. Experimental results show that the proposed method facilitates generation of highly diverse populations, which vary according to the type and distribution of the instances.

  10. Persistency of Prediction Accuracy and Genetic Gain in Synthetic Populations Under Recurrent Genomic Selection

    Directory of Open Access Journals (Sweden)

    Dominik Müller

    2017-03-01

    Full Text Available Recurrent selection (RS has been used in plant breeding to successively improve synthetic and other multiparental populations. Synthetics are generated from a limited number of parents ( Np , but little is known about how Np affects genomic selection (GS in RS, especially the persistency of prediction accuracy (rg , g ^ and genetic gain. Synthetics were simulated by intermating Np= 2–32 parent lines from an ancestral population with short- or long-range linkage disequilibrium (LDA and subjected to multiple cycles of GS. We determined rg , g ^ and genetic gain across 30 cycles for different training set (TS sizes, marker densities, and generations of recombination before model training. Contributions to rg , g ^ and genetic gain from pedigree relationships, as well as from cosegregation and LDA between QTL and markers, were analyzed via four scenarios differing in (i the relatedness between TS and selection candidates and (ii whether selection was based on markers or pedigree records. Persistency of rg , g ^ was high for small Np , where predominantly cosegregation contributed to rg , g ^ , but also for large Np , where LDA replaced cosegregation as the dominant information source. Together with increasing genetic variance, this compensation resulted in relatively constant long- and short-term genetic gain for increasing Np > 4, given long-range LDA in the ancestral population. Although our scenarios suggest that information from pedigree relationships contributed to rg , g ^ for only very few generations in GS, we expect a longer contribution than in pedigree BLUP, because capturing Mendelian sampling by markers reduces selective pressure on pedigree relationships. Larger TS size (NTS and higher marker density improved persistency of rg , g ^ and hence genetic gain, but additional recombinations could not increase genetic gain.

  11. Detecting Positive Selection of Korean Native Goat Populations Using Next-Generation Sequencing

    Science.gov (United States)

    Lee, Wonseok; Ahn, Sojin; Taye, Mengistie; Sung, Samsun; Lee, Hyun-Jeong; Cho, Seoae; Kim, Heebal

    2016-01-01

    Goats (Capra hircus) are one of the oldest species of domesticated animals. Native Korean goats are a particularly interesting group, as they are indigenous to the area and were raised in the Korean peninsula almost 2,000 years ago. Although they have a small body size and produce low volumes of milk and meat, they are quite resistant to lumbar paralysis. Our study aimed to reveal the distinct genetic features and patterns of selection in native Korean goats by comparing the genomes of native Korean goat and crossbred goat populations. We sequenced the whole genome of 15 native Korean goats and 11 crossbred goats using next-generation sequencing (Illumina platform) to compare the genomes of the two populations. We found decreased nucleotide diversity in the native Korean goats compared to the crossbred goats. Genetic structural analysis demonstrated that the native Korean goat and crossbred goat populations shared a common ancestry, but were clearly distinct. Finally, to reveal the native Korean goat’s selective sweep region, selective sweep signals were identified in the native Korean goat genome using cross-population extended haplotype homozygosity (XP-EHH) and a cross-population composite likelihood ratio test (XP-CLR). As a result, we were able to identify candidate genes for recent selection, such as the CCR3 gene, which is related to lumbar paralysis resistance. Combined with future studies and recent goat genome information, this study will contribute to a thorough understanding of the native Korean goat genome. PMID:27989103

  12. Detecting Positive Selection of Korean Native Goat Populations Using Next-Generation Sequencing.

    Science.gov (United States)

    Lee, Wonseok; Ahn, Sojin; Taye, Mengistie; Sung, Samsun; Lee, Hyun-Jeong; Cho, Seoae; Kim, Heebal

    2016-12-01

    Goats ( Capra hircus ) are one of the oldest species of domesticated animals. Native Korean goats are a particularly interesting group, as they are indigenous to the area and were raised in the Korean peninsula almost 2,000 years ago. Although they have a small body size and produce low volumes of milk and meat, they are quite resistant to lumbar paralysis. Our study aimed to reveal the distinct genetic features and patterns of selection in native Korean goats by comparing the genomes of native Korean goat and crossbred goat populations. We sequenced the whole genome of 15 native Korean goats and 11 crossbred goats using next-generation sequencing (Illumina platform) to compare the genomes of the two populations. We found decreased nucleotide diversity in the native Korean goats compared to the crossbred goats. Genetic structural analysis demonstrated that the native Korean goat and crossbred goat populations shared a common ancestry, but were clearly distinct. Finally, to reveal the native Korean goat's selective sweep region, selective sweep signals were identified in the native Korean goat genome using cross-population extended haplotype homozygosity (XP-EHH) and a cross-population composite likelihood ratio test (XP-CLR). As a result, we were able to identify candidate genes for recent selection, such as the CCR3 gene, which is related to lumbar paralysis resistance. Combined with future studies and recent goat genome information, this study will contribute to a thorough understanding of the native Korean goat genome.

  13. Rich: Region-based Intelligent Cluster-Head Selection and Node Deployment Strategy in Concentric-based WSNs

    Directory of Open Access Journals (Sweden)

    FAN, C.-S.

    2013-11-01

    Full Text Available In a random deployment, sensor nodes are scattered randomly in the sensing field. Hence, the coverage can not be guaranteed. In contrast, the coverage of uniformly deployment is in general larger than the random deployment. However, uniformly deployment strategy may cause unbalanced traffic pattern in wireless sensor networks (WSNs. In this situation, larger load may be imposed to CHs (cluster heads around the sink. Therefore, CHs close to the sink use up their energy earlier than those farther away from the sink. To overcome this problem, we propose a novel node deployment strategy in the concentric model, namely, Region-based Intelligent Cluster-Head selection and node deployment strategy (called Rich. The coverage, energy consumption and data routing issues are well investigated and taken into consideration in the proposed Rich scheme. The simulation results show that the proposed Rich alleviates the unbalanced traffic pattern significantly, prolongs network lifetime and achieves satisfactory coverage ratio.

  14. COPD prevalence in a random population survey: a matter of definition.

    Science.gov (United States)

    Shirtcliffe, P; Weatherall, M; Marsh, S; Travers, J; Hansell, A; McNaughton, A; Aldington, S; Muellerova, H; Beasley, R

    2007-08-01

    A recent American Thoracic Society and European Respiratory Society joint Task Force report recommends using a lower limit of normal (LLN) of forced expiratory volume in one second/forced vital capacity as opposed to a fixed ratio of definitions of airflow obstruction based on post-bronchodilator spirometry is not known. Detailed written questionnaires, full pulmonary function tests (including pre- and post-bronchodilator flow-volume loops) and atopy testing were completed in 749 subjects recruited from a random population sample. The GOLD-defined, age-adjusted prevalence (95% confidence interval) for adults aged >or=40 yrs was 14.2 (11.0-17.0)% compared with an LLN-defined, age-adjusted, post-bronchodilator prevalence in the same group of 9.0 (6.7-11.3)%. The prevalence of chronic obstructive pulmonary disease varied markedly depending on the definition used. Further research using longitudinal rather than cross-sectional data will help decide the preferred approach in chronic obstructive pulmonary disease prevalence surveys.

  15. The epidemiology of neck pain: what we have learned from our population-based studies

    Science.gov (United States)

    Côté, Pierre; Cassidy, J. David; Carroll, Linda

    2003-01-01

    Background: There are few population-based studies on the epidemiology of neck pain in the general population. Purpose: To synthesize the findings of two large population-based studies of the epidemiology of neck pain and whiplash-associated disorders from the province of Saskatchewan, Canada. Study Design and Methods: We conducted two population-based cohort studies of neck pain and its related disability in Saskatchewan, Canada. First, the Saskatchewan Health and Back Pain Survey was designed to determine the prevalence and factors associated with neck pain in randomly selected adults. Second, we conducted a cohort study of the incidence and prognosis of whiplash and studied whether a change in the insurance system from tort to no-fault was related to a reduction in the number of whiplash claims and faster recovery. Results: In 1995, the six-month prevalence of neck pain was 54.2% and 4.6% of adults experienced disabling neck pain in the previous six-months. Neck pain was associated with education, comorbidities, smoking, self-reported general health and a history of neck injury in a motor vehicle collision. The incidence of treated and/or compensated whiplash injury was estimated at 834/100,000 adults in 1994, and dropped by 28% to 598/100,000 adults in 1995, after tort reform. Compared to tort, the median time-to-recovery was more than 230 days faster under no-fault. The strongest predictors of recovery were age, gender, education, injury severity, lawyer involvement and type of initial care provider. Conclusion: Neck pain is a public health problem. The incidence and prognosis of whiplash injuries are greatly influenced by compensation for pain and suffering, legal factors, injury severity and sociodemographic characteristics. Overall, neck pain is a multifaceted disabling problem that deserves more attention. When treating patients with neck pain, clinicians need to recognize that it is more than a physical problem and that its prognosis is influenced by

  16. A Heckman Selection- t Model

    KAUST Repository

    Marchenko, Yulia V.

    2012-03-01

    Sample selection arises often in practice as a result of the partial observability of the outcome of interest in a study. In the presence of sample selection, the observed data do not represent a random sample from the population, even after controlling for explanatory variables. That is, data are missing not at random. Thus, standard analysis using only complete cases will lead to biased results. Heckman introduced a sample selection model to analyze such data and proposed a full maximum likelihood estimation method under the assumption of normality. The method was criticized in the literature because of its sensitivity to the normality assumption. In practice, data, such as income or expenditure data, often violate the normality assumption because of heavier tails. We first establish a new link between sample selection models and recently studied families of extended skew-elliptical distributions. Then, this allows us to introduce a selection-t (SLt) model, which models the error distribution using a Student\\'s t distribution. We study its properties and investigate the finite-sample performance of the maximum likelihood estimators for this model. We compare the performance of the SLt model to the conventional Heckman selection-normal (SLN) model and apply it to analyze ambulatory expenditures. Unlike the SLNmodel, our analysis using the SLt model provides statistical evidence for the existence of sample selection bias in these data. We also investigate the performance of the test for sample selection bias based on the SLt model and compare it with the performances of several tests used with the SLN model. Our findings indicate that the latter tests can be misleading in the presence of heavy-tailed data. © 2012 American Statistical Association.

  17. How Random Is Social Behaviour? Disentangling Social Complexity through the Study of a Wild House Mouse Population

    Science.gov (United States)

    Perony, Nicolas; Tessone, Claudio J.; König, Barbara; Schweitzer, Frank

    2012-01-01

    Out of all the complex phenomena displayed in the behaviour of animal groups, many are thought to be emergent properties of rather simple decisions at the individual level. Some of these phenomena may also be explained by random processes only. Here we investigate to what extent the interaction dynamics of a population of wild house mice (Mus domesticus) in their natural environment can be explained by a simple stochastic model. We first introduce the notion of perceptual landscape, a novel tool used here to describe the utilisation of space by the mouse colony based on the sampling of individuals in discrete locations. We then implement the behavioural assumptions of the perceptual landscape in a multi-agent simulation to verify their accuracy in the reproduction of observed social patterns. We find that many high-level features – with the exception of territoriality – of our behavioural dataset can be accounted for at the population level through the use of this simplified representation. Our findings underline the potential importance of random factors in the apparent complexity of the mice's social structure. These results resonate in the general context of adaptive behaviour versus elementary environmental interactions. PMID:23209394

  18. Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies.

    Science.gov (United States)

    Chen, Jun; Källman, Thomas; Ma, Xiao-Fei; Zaina, Giusi; Morgante, Michele; Lascoux, Martin

    2016-07-07

    The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower FST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both FST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI. Copyright © 2016 Chen et al.

  19. Farm Population of the United States: 1974. Current Population Reports, Farm Population.

    Science.gov (United States)

    Banks, Vera J.; And Others

    Based on data derived primarily from the Current Population Survey of the Bureau of the Census, this statistical report presents demographic and labor force characteristics of the U.S. farm population and a comparison of selected characteristics of the farm and nonfarm population. Tabular data are presented as follows: (1) Population of the U.S.,…

  20. Evolution of the metabolome in response to selection for increased immunity in populations of Drosophila melanogaster.

    Science.gov (United States)

    Gogna, Navdeep; Sharma, Rakesh; Gupta, Vanika; Dorai, Kavita; Prasad, N G

    2017-01-01

    We used NMR-based metabolomics to test two hypotheses-(i) there will be evolved differences in the metabolome of selected and control populations even under un-infected conditions and (ii) post infection, the metabolomes of the selected and control populations will respond differently. We selected replicate populations of Drosophila melanogaster for increased survivorship (I) against a gram-negative pathogen. We subjected the selected (I) and their control populations (S) to three different treatments: (1) infected with heat-killed bacteria (i), (2) sham infected (s), and (3) untreated (u). We performed 1D and 2D NMR experiments to identify the metabolic differences. Multivariate analysis of the metabolic profiles of the untreated (Iu and Su) flies yielded higher concentrations of lipids, organic acids, sugars, amino acids, NAD and AMP in the Iu treatment as compared to the Su treatment, showing that even in the absence of infection, the metabolome of the I and S regimes was different. In the S and I regimes, post infection/injury, concentration of metabolites directly or indirectly associated with energy related pathways (lipids, organic acids, sugars) declined while the concentration of metabolites that are probably associated with immune response (amino acids) increased. However, in most cases, the I regime flies had a higher concentration of such metabolites even under un-infected conditions. The change in the metabolite concentration upon infection/injury was not always comparable between I and S regimes (in case of lactate, alanine, leucine, lysine, threonine) indicating that the I and S regimes had evolved to respond differentially to infection and to injury.

  1. Differential evolution enhanced with multiobjective sorting-based mutation operators.

    Science.gov (United States)

    Wang, Jiahai; Liao, Jianjun; Zhou, Ying; Cai, Yiqiao

    2014-12-01

    Differential evolution (DE) is a simple and powerful population-based evolutionary algorithm. The salient feature of DE lies in its mutation mechanism. Generally, the parents in the mutation operator of DE are randomly selected from the population. Hence, all vectors are equally likely to be selected as parents without selective pressure at all. Additionally, the diversity information is always ignored. In order to fully exploit the fitness and diversity information of the population, this paper presents a DE framework with multiobjective sorting-based mutation operator. In the proposed mutation operator, individuals in the current population are firstly sorted according to their fitness and diversity contribution by nondominated sorting. Then parents in the mutation operators are proportionally selected according to their rankings based on fitness and diversity, thus, the promising individuals with better fitness and diversity have more opportunity to be selected as parents. Since fitness and diversity information is simultaneously considered for parent selection, a good balance between exploration and exploitation can be achieved. The proposed operator is applied to original DE algorithms, as well as several advanced DE variants. Experimental results on 48 benchmark functions and 12 real-world application problems show that the proposed operator is an effective approach to enhance the performance of most DE algorithms studied.

  2. Randomized clinical trial of Appendicitis Inflammatory Response score-based management of patients with suspected appendicitis.

    Science.gov (United States)

    Andersson, M; Kolodziej, B; Andersson, R E

    2017-10-01

    The role of imaging in the diagnosis of appendicitis is controversial. This prospective interventional study and nested randomized trial analysed the impact of implementing a risk stratification algorithm based on the Appendicitis Inflammatory Response (AIR) score, and compared routine imaging with selective imaging after clinical reassessment. Patients presenting with suspicion of appendicitis between September 2009 and January 2012 from age 10 years were included at 21 emergency surgical centres and from age 5 years at three university paediatric centres. Registration of clinical characteristics, treatments and outcomes started during the baseline period. The AIR score-based algorithm was implemented during the intervention period. Intermediate-risk patients were randomized to routine imaging or selective imaging after clinical reassessment. The baseline period included 1152 patients, and the intervention period 2639, of whom 1068 intermediate-risk patients were randomized. In low-risk patients, use of the AIR score-based algorithm resulted in less imaging (19·2 versus 34·5 per cent; P appendicitis (6·8 versus 9·7 per cent; P = 0·034). Intermediate-risk patients randomized to the imaging and observation groups had the same proportion of negative appendicectomies (6·4 versus 6·7 per cent respectively; P = 0·884), number of admissions, number of perforations and length of hospital stay, but routine imaging was associated with an increased proportion of patients treated for appendicitis (53·4 versus 46·3 per cent; P = 0·020). AIR score-based risk classification can safely reduce the use of diagnostic imaging and hospital admissions in patients with suspicion of appendicitis. Registration number: NCT00971438 ( http://www.clinicaltrials.gov). © 2017 BJS Society Ltd Published by John Wiley & Sons Ltd.

  3. A selective sweep on a deleterious mutation in CPT1A in Arctic populations

    KAUST Repository

    Clemente, Florian J.

    2014-11-01

    Arctic populations live in an environment characterized by extreme cold and the absence of plant foods for much of the year and are likely to have undergone genetic adaptations to these environmental conditions in the time they have been living there. Genome-wide selection scans based on genotype data from native Siberians have previously highlighted a 3 Mb chromosome 11 region containing 79 protein-coding genes as the strongest candidates for positive selection in Northeast Siberians. However, it was not possible to determine which of the genes might be driving the selection signal. Here, using whole-genome high-coverage sequence data, we identified the most likely causative variant as a nonsynonymous G>A transition (rs80356779; c.1436C>T [p.Pro479Leu] on the reverse strand) in CPT1A, a key regulator of mitochondrial long-chain fatty-acid oxidation. Remarkably, the derived allele is associated with hypoketotic hypoglycemia and high infant mortality yet occurs at high frequency in Canadian and Greenland Inuits and was also found at 68% frequency in our Northeast Siberian sample. We provide evidence of one of the strongest selective sweeps reported in humans; this sweep has driven this variant to high frequency in circum-Arctic populations within the last 6-23 ka despite associated deleterious consequences, possibly as a result of the selective advantage it originally provided to either a high-fat diet or a cold environment.

  4. A selective sweep on a deleterious mutation in CPT1A in Arctic populations

    KAUST Repository

    Clemente, Florian J.; Cardona, Alexia; Inchley, Charlotte E.; Peter, Benjamin M.; Jacobs, Guy; Pagani, Luca; Lawson, Daniel John; Antã o, Tiago; Vicente, Má rio; Mitt, Mario; Degiorgio, Michael; Faltyskova, Zuzana; Xue, Yali; Ayub, Qasim; Szpak, Michal; Mä gi, Reedik; Eriksson, Anders; Manica, Andrea; Raghavan, Maanasa; Rasmussen, Morten Arendt Rendt; Rasmussen, Simon B.; Willerslev, Eske; Vidal-Puig, Antonio J.; Tyler-Smith, Chris; Villems, Richard; Nielsen, Rasmus Wedel; Metspalu, Mait; Malyarchuk, Boris A.; Derenko, Miroslava V.; Kivisild, Toomas

    2014-01-01

    Arctic populations live in an environment characterized by extreme cold and the absence of plant foods for much of the year and are likely to have undergone genetic adaptations to these environmental conditions in the time they have been living there. Genome-wide selection scans based on genotype data from native Siberians have previously highlighted a 3 Mb chromosome 11 region containing 79 protein-coding genes as the strongest candidates for positive selection in Northeast Siberians. However, it was not possible to determine which of the genes might be driving the selection signal. Here, using whole-genome high-coverage sequence data, we identified the most likely causative variant as a nonsynonymous G>A transition (rs80356779; c.1436C>T [p.Pro479Leu] on the reverse strand) in CPT1A, a key regulator of mitochondrial long-chain fatty-acid oxidation. Remarkably, the derived allele is associated with hypoketotic hypoglycemia and high infant mortality yet occurs at high frequency in Canadian and Greenland Inuits and was also found at 68% frequency in our Northeast Siberian sample. We provide evidence of one of the strongest selective sweeps reported in humans; this sweep has driven this variant to high frequency in circum-Arctic populations within the last 6-23 ka despite associated deleterious consequences, possibly as a result of the selective advantage it originally provided to either a high-fat diet or a cold environment.

  5. Genetic changeover in Drosophila populations

    International Nuclear Information System (INIS)

    Wallace, B.

    1986-01-01

    Three populations of Drosophila melanogaster that were daughter populations of two others with histories of high, continuous radiation exposure [population 5 (irradiated, small population size) gave rise to populations 17 (small) and 18 (large); population 6 (irradiated, large population size) gave rise to population 19 (large)] were maintained for 1 year with no radiation exposure. The frequency with which random combinations of second chromosomes taken from population 19 proved to be lethal changed abruptly after about 8 months, thus revealing the origin of a selectively favored element in that population. (This element may or may not have been the cause of the lethality.) A comparison of the loss of lethals in populations 17 and 18 with a loss that occurred concurrently in the still-irradiated population 5 suggests that a second, selectively favored element had arisen in that population just before populations 17 and 18 were split off. This element was on a nonlethal chromosome. The result in population 5 was the elimination of many lethals from that population, followed by a subsequent increase as mutations occurred in the favored nonlethal chromosome. Populations 17 and 18, with no radiation exposure, underwent a loss of lethals with no subsequent increase. The events described here, as well as others to be described elsewhere, suggest that populations may be subject to episodic periods of rapid gene frequency changes that occur under intense selection pressure. In the instances in which the changeover was revealed by the elimination of preexisting lethals, earlier lethal frequencies were reduced by approximately one-half; the selectively favored elements appear, then, to be favored in the heterozygous--not homozygous--condition

  6. Screening for type 2 diabetes in a high-risk population: Study design and feasibility of a population-based randomized controlled trial

    NARCIS (Netherlands)

    B. Klijs (Bart); S.J. Otto (Suzie); R.J. Heine (Robert); Y. van der Graaf (Yolanda); J.J. Lous (Jan); H.J. de Koning (Harry)

    2012-01-01

    textabstractBackground: We describe the design and present the results of the first year of a population-based study of screening for type 2 diabetes in individuals at high risk of developing the disease. High risk is defined as having abdominal obesity. Methods. Between 2006 and 2007, 79,142

  7. Exploration of the association between chronic periodontal disease and erectile dysfunction from a population-based view point.

    Science.gov (United States)

    Tsao, C-W; Liu, C-Y; Cha, T-L; Wu, S-T; Chen, S-C; Hsu, C-Y

    2015-06-01

    Several cross-sectional studies have indicated an association between chronic periodontal disease (CPD) and cardiovascular disease and metabolic syndrome. Erectile dysfunction (ED) also shares pathological mechanisms with these diseases. Using a nationwide population-based data set, we examined the association between ED and CPD and assessed the effect of dental extraction (DE) on ED prevalence in different aged CPD populations in Taiwan. We identified 5105 patients with ED and randomly selected 10 210 patients as controls. Of these patients, 2617 (17.09%) were diagnosed with CPD according to the index data: 1196 (23.43%) in the ED group and 1421 (13.92%) in the control group. After adjusting for comorbid factors, patients with ED were more likely to have been diagnosed with prior CPD than controls (OR = 1.79, 95% CI = 1.64-1.96, P < 0.001). Moreover, the association was much stronger in the populations aged less than 30 years (OR = 2.13, 95% CI = 1.23-3.70, P < 0.001) and more than 59 years (OR = 2.27, 95% CI = 1.99-2.59, P < 0.001). Dental extraction seems to attenuate damage to the penile endothelial beds caused by CPD-related inflammation and overcame the process of ED in the middle-aged and older populations. © 2014 Blackwell Verlag GmbH.

  8. Random inbreeding, isonymy, and population isolates in Argentina.

    Science.gov (United States)

    Dipierri, José; Rodríguez-Larralde, Alvaro; Barrai, Italo; Camelo, Jorge López; Redomero, Esperanza Gutiérrez; Rodríguez, Concepción Alonso; Ramallo, Virginia; Bronberg, Rubén; Alfaro, Emma

    2014-07-01

    Population isolates are an important tool in identifying and mapping genes of Mendelian diseases and complex traits. The geographical identification of isolates represents a priority from a genetic and health care standpoint. The purpose of this study is to analyze the spatial distribution of consanguinity by random isonymy (F ST) in Argentina and its relationship with the isolates previously identified in the country. F ST was estimated from the surname distribution of 22.6 million electors registered for the year 2001 in the 24 provinces, 5 geographical regions, and 510 departments of the country. Statistically significant spatial clustering of F ST was determined using the SaTScan V5.1 software. F ST exhibited a marked regional and departamental variation, showing the highest values towards the North and West of Argentina. The clusters of high consanguinity by random isonymy followed the same distribution. Recognized Argentinean genetic isolates are mainly localized at the north of the country, in clusters of high inbreeding. Given the availability of listings of surnames in high-capacity storage devices for different countries, estimating F ST from them can provide information on inbreeding for all levels of administrative subdivisions, to be used as a demographic variable for the identification of isolates within the country for public health purposes.

  9. Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naïve Bayes.

    Directory of Open Access Journals (Sweden)

    Wangchao Lou

    Full Text Available Developing an efficient method for determination of the DNA-binding proteins, due to their vital roles in gene regulation, is becoming highly desired since it would be invaluable to advance our understanding of protein functions. In this study, we proposed a new method for the prediction of the DNA-binding proteins, by performing the feature rank using random forest and the wrapper-based feature selection using forward best-first search strategy. The features comprise information from primary sequence, predicted secondary structure, predicted relative solvent accessibility, and position specific scoring matrix. The proposed method, called DBPPred, used Gaussian naïve Bayes as the underlying classifier since it outperformed five other classifiers, including decision tree, logistic regression, k-nearest neighbor, support vector machine with polynomial kernel, and support vector machine with radial basis function. As a result, the proposed DBPPred yields the highest average accuracy of 0.791 and average MCC of 0.583 according to the five-fold cross validation with ten runs on the training benchmark dataset PDB594. Subsequently, blind tests on the independent dataset PDB186 by the proposed model trained on the entire PDB594 dataset and by other five existing methods (including iDNA-Prot, DNA-Prot, DNAbinder, DNABIND and DBD-Threader were performed, resulting in that the proposed DBPPred yielded the highest accuracy of 0.769, MCC of 0.538, and AUC of 0.790. The independent tests performed by the proposed DBPPred on completely a large non-DNA binding protein dataset and two RNA binding protein datasets also showed improved or comparable quality when compared with the relevant prediction methods. Moreover, we observed that majority of the selected features by the proposed method are statistically significantly different between the mean feature values of the DNA-binding and the non DNA-binding proteins. All of the experimental results indicate that

  10. Blind Measurement Selection: A Random Matrix Theory Approach

    KAUST Repository

    Elkhalil, Khalil

    2016-12-14

    This paper considers the problem of selecting a set of $k$ measurements from $n$ available sensor observations. The selected measurements should minimize a certain error function assessing the error in estimating a certain $m$ dimensional parameter vector. The exhaustive search inspecting each of the $n\\\\choose k$ possible choices would require a very high computational complexity and as such is not practical for large $n$ and $k$. Alternative methods with low complexity have recently been investigated but their main drawbacks are that 1) they require perfect knowledge of the measurement matrix and 2) they need to be applied at the pace of change of the measurement matrix. To overcome these issues, we consider the asymptotic regime in which $k$, $n$ and $m$ grow large at the same pace. Tools from random matrix theory are then used to approximate in closed-form the most important error measures that are commonly used. The asymptotic approximations are then leveraged to select properly $k$ measurements exhibiting low values for the asymptotic error measures. Two heuristic algorithms are proposed: the first one merely consists in applying the convex optimization artifice to the asymptotic error measure. The second algorithm is a low-complexity greedy algorithm that attempts to look for a sufficiently good solution for the original minimization problem. The greedy algorithm can be applied to both the exact and the asymptotic error measures and can be thus implemented in blind and channel-aware fashions. We present two potential applications where the proposed algorithms can be used, namely antenna selection for uplink transmissions in large scale multi-user systems and sensor selection for wireless sensor networks. Numerical results are also presented and sustain the efficiency of the proposed blind methods in reaching the performances of channel-aware algorithms.

  11. Strategyproof Peer Selection using Randomization, Partitioning, and Apportionment

    OpenAIRE

    Aziz, Haris; Lev, Omer; Mattei, Nicholas; Rosenschein, Jeffrey S.; Walsh, Toby

    2016-01-01

    Peer review, evaluation, and selection is a fundamental aspect of modern science. Funding bodies the world over employ experts to review and select the best proposals of those submitted for funding. The problem of peer selection, however, is much more general: a professional society may want to give a subset of its members awards based on the opinions of all members; an instructor for a MOOC or online course may want to crowdsource grading; or a marketing company may select ideas from group b...

  12. Screening for type 2 diabetes in a high-risk population: study design and feasibility of a population-based randomized controlled trial

    NARCIS (Netherlands)

    Klijs, B.; Otto, S.J.; Heine, R.J.; van der Graaf, Y.; Lous, J.J.; Koning, H.J.

    2012-01-01

    Background: We describe the design and present the results of the first year of a population-based study of screening for type 2 diabetes in individuals at high risk of developing the disease. High risk is defined as having abdominal obesity. Methods. Between 2006 and 2007, 79,142 inhabitants of two

  13. Attitudes towards Electronic Cigarettes Regulation in Indoor Workplaces and Selected Public and Private Places: A Population-Based Cross-Sectional Study

    Science.gov (United States)

    Martínez-Sánchez, Jose M.; Ballbè, Montse; Fu, Marcela; Martín-Sánchez, Juan C.; Gottlieb, Mark; Saltó, Esteve; Vardavas, Constantine I.; Daynard, Richard; Connolly, Gregory N.; Fernández, Esteve

    2014-01-01

    Background Currently, there is an intensive debate about the regulation of the use of electronic cigarettes (e-cigarettes) in indoor places. The aim of this study was to assess the attitudes toward e-cigarette use in indoor workplaces and selected public and private venues among the general population in Barcelona (Spain) in 2013–2014. Methods This is a cross-sectional study of a representative sample of the population of Barcelona (n = 736). The field work was conducted between May 2013 and February 2014. We computed the prevalence and the adjusted odds ratios (OR) derived from multivariable logistic regression models. Results The awareness of e-cigarettes was 82.3%. Forty five percent of respondents did not agree with the use of e-cigarettes in public places and 52.3% in workplaces. The proportion of disapproval of the use of e-cigarettes in indoor places was higher at 71.5% for schools and 65.8% for hospitals and health care centers; while the prevalence of disapproval of e-cigarette use in homes and cars was lower (18.0% and 32.5%, respectively). Respondents who disagreed on the use of e-cigarettes in indoor workplaces were more likely to be older (OR = 1.64 and 1.97 for groups 45–64 and ≧65 years old, respectively), those with a high educational level (OR = 1.60), and never and former smokers (OR = 2.34 and 2.16, respectively). Increased scores in the Fagerström test for cigarette dependence were also related to increased support for their use. Conclusions Based on this population based study, half of the general population of Barcelona does not support the use of e-cigarettes in indoor workplaces and public places, with the percentage reaching 65% for use in schools, hospitals and health care centers. Consequently, there is good societal support in Spain for the politicians and legislators to promote policies restricting e-cigarettes use in workplaces and public places, including hospitality venues. PMID:25469996

  14. Prey selection by a reintroduced lion population in the Greater ...

    African Journals Online (AJOL)

    Prey selection by a reintroduced lion population in the Greater Makalali Conservancy, South Africa. Dave Druce, Heleen Genis, Jonathan Braak, Sophie Greatwood, Audrey Delsink, Ross Kettles, Luke Hunter, Rob Slotow ...

  15. Genome Scan for Selection in Structured Layer Chicken Populations Exploiting Linkage Disequilibrium Information.

    Directory of Open Access Journals (Sweden)

    Mahmood Gholami

    Full Text Available An increasing interest is being placed in the detection of genes, or genomic regions, that have been targeted by selection because identifying signatures of selection can lead to a better understanding of genotype-phenotype relationships. A common strategy for the detection of selection signatures is to compare samples from distinct populations and to search for genomic regions with outstanding genetic differentiation. The aim of this study was to detect selective signatures in layer chicken populations using a recently proposed approach, hapFLK, which exploits linkage disequilibrium information while accounting appropriately for the hierarchical structure of populations. We performed the analysis on 70 individuals from three commercial layer breeds (White Leghorn, White Rock and Rhode Island Red, genotyped for approximately 1 million SNPs. We found a total of 41 and 107 regions with outstanding differentiation or similarity using hapFLK and its single SNP counterpart FLK respectively. Annotation of selection signature regions revealed various genes and QTL corresponding to productions traits, for which layer breeds were selected. A number of the detected genes were associated with growth and carcass traits, including IGF-1R, AGRP and STAT5B. We also annotated an interesting gene associated with the dark brown feather color mutational phenotype in chickens (SOX10. We compared FST, FLK and hapFLK and demonstrated that exploiting linkage disequilibrium information and accounting for hierarchical population structure decreased the false detection rate.

  16. A two-stage cluster sampling method using gridded population data, a GIS, and Google EarthTM imagery in a population-based mortality survey in Iraq

    Directory of Open Access Journals (Sweden)

    Galway LP

    2012-04-01

    Full Text Available Abstract Background Mortality estimates can measure and monitor the impacts of conflict on a population, guide humanitarian efforts, and help to better understand the public health impacts of conflict. Vital statistics registration and surveillance systems are rarely functional in conflict settings, posing a challenge of estimating mortality using retrospective population-based surveys. Results We present a two-stage cluster sampling method for application in population-based mortality surveys. The sampling method utilizes gridded population data and a geographic information system (GIS to select clusters in the first sampling stage and Google Earth TM imagery and sampling grids to select households in the second sampling stage. The sampling method is implemented in a household mortality study in Iraq in 2011. Factors affecting feasibility and methodological quality are described. Conclusion Sampling is a challenge in retrospective population-based mortality studies and alternatives that improve on the conventional approaches are needed. The sampling strategy presented here was designed to generate a representative sample of the Iraqi population while reducing the potential for bias and considering the context specific challenges of the study setting. This sampling strategy, or variations on it, are adaptable and should be considered and tested in other conflict settings.

  17. Bridging Emergent Attributes and Darwinian Principles in Teaching Natural Selection

    Science.gov (United States)

    Xu, Dongchen; Chi, Michelene T. H.

    2016-01-01

    Students often have misconceptions about natural selection as they misuse a direct causal schema to explain the process. Natural selection is in fact an emergent process where random interactions lead to changes in a population. The misconceptions stem from students' lack of emergent schema for natural selection. In order to help students…

  18. TU-AB-202-10: How Effective Are Current Atlas Selection Methods for Atlas-Based Auto-Contouring in Radiotherapy Planning?

    Energy Technology Data Exchange (ETDEWEB)

    Peressutti, D; Schipaanboord, B; Kadir, T; Gooding, M [Mirada Medical Limited, Science and Medical Technology, Oxford (United Kingdom); Soest, J van; Lustberg, T; Elmpt, W van; Dekker, A [Maastricht University Medical Centre, Department of Radiation Oncology MAASTRO - GROW School for Oncology Developmental Biology, Maastricht (Netherlands)

    2016-06-15

    Purpose: To investigate the effectiveness of atlas selection methods for improving atlas-based auto-contouring in radiotherapy planning. Methods: 275 H&N clinically delineated cases were employed as an atlas database from which atlases would be selected. A further 40 previously contoured cases were used as test patients against which atlas selection could be performed and evaluated. 26 variations of selection methods proposed in the literature and used in commercial systems were investigated. Atlas selection methods comprised either global or local image similarity measures, computed after rigid or deformable registration, combined with direct atlas search or with an intermediate template image. Workflow Box (Mirada-Medical, Oxford, UK) was used for all auto-contouring. Results on brain, brainstem, parotids and spinal cord were compared to random selection, a fixed set of 10 “good” atlases, and optimal selection by an “oracle” with knowledge of the ground truth. The Dice score and the average ranking with respect to the “oracle” were employed to assess the performance of the top 10 atlases selected by each method. Results: The fixed set of “good” atlases outperformed all of the atlas-patient image similarity-based selection methods (mean Dice 0.715 c.f. 0.603 to 0.677). In general, methods based on exhaustive comparison of local similarity measures showed better average Dice scores (0.658 to 0.677) compared to the use of either template image (0.655 to 0.672) or global similarity measures (0.603 to 0.666). The performance of image-based selection methods was found to be only slightly better than a random (0.645). Dice scores given relate to the left parotid, but similar results patterns were observed for all organs. Conclusion: Intuitively, atlas selection based on the patient CT is expected to improve auto-contouring performance. However, it was found that published approaches performed marginally better than random and use of a fixed set of

  19. Vernal keratoconjunctivitis in school children in Rwanda and its association with socio-economic status: a population-based survey.

    Science.gov (United States)

    Smedt, Stefan De; Nkurikiye, John; Fonteyne, Yannick; Hogewoning, Arjan; Esbroeck, Marjan Van; Bacquer, Dirk De; Tuft, Stephen; Gilbert, Clare; Delanghe, Joris; Kestelyn, Philippe

    2011-10-01

    Vernal keratoconjunctivitis (VKC) is an allergic eye disease and an important cause of hospital referral among children in Africa and Asia. Hospital-based studies have suggested a role for parasites in its pathogenesis. To determine the prevalence and risk factors for VKC in Central Africa, we conducted a nested population-based case control study in Rwanda, involving randomly selected primary schools from different environments (rural/urban) and climate. A prevalence of VKC of 4.0% (95% confidence interval 3.3-4.7%) was found among 3,041 children studied (participation rate 94.7%). The intestinal parasitic burden was not related to VKC. Besides hot dry climate (odds ratio [OR] = 1.5, P = 0.05) and male gender (OR = 1.7, P = 0.005), multivariate analysis identified higher economic status as a risk for VKC (OR = 1.4, P = 0.005). The effect on VKC of higher economic status appears not to act through differences in parasitic intestinal load.

  20. Metropolitan migration and population growth in selected developing countries.

    Science.gov (United States)

    1983-01-01

    The purpose of this article is to estimate the components of metropolitan population growth in selected developing countries during 1960-1970 period. The study examines population growth in 26 cities: 5 are in Africa, 8 in Asia, and 13 in Latin America, using data from national census publications. These cities in general are the political capitals of their countries, but some additional large cities were selected in Brazil, Mexico, and South Africa. All cities, at the beginning of the 1960-1970 decade had over 500,000 population; Accra, the only exception, reached this population level during the 1960s. Some cities had over 4 million residents in 1970. Net migration contributed about 37% to total metropolitan population growth; the remainder of the growth is attributable to natural increase. Migration has a much stronger impact on metropolitan growth than suggested by the above figure: 1) Several metropolitan areas, for various reasons, are unlikely to receive many migrants; without those cities, the share of metropolitan growth from net migration is 44%. 2) Estimates of the natural increase of migrants after their arrival in the metropolitan areas, when added to migration itself, changes the total contribution of migration to 49% in some metropolitan areas. 3) Even where net migration contributes a smaller proportion to metropolitan growth than natural increase, the rates of net migration are generally high and should be viewed in the context of rapid metropolitan population growth from natural increase alone. Finally, the paper also compares the components of metropolitan growth with the components of growth in the remaining urban areas. The results show that the metropolitan areas, in general, grow faster than the remaining urban areas, and that this more rapid growth is mostly due to a higher rate of net migration. Given the significance of migration for metropolitan growth, further investigations of the effects of these migration streams, particularly with

  1. QUANTITATIVE GENETICS OF MORPHOLOGICAL DIFFERENTIATION IN PEROMYSCUS. II. ANALYSIS OF SELECTION AND DRIFT.

    Science.gov (United States)

    Lofsvold, David

    1988-01-01

    The hypothesis that the morphological divergence of local populations of Peromyscus is due to random genetic drift was evaluated by testing the proportionality of the among-locality covariance matrix, L, and the additive genetic covariance matrix, G. Overall, significant proportionality of L̂ and Ĝ was not observed, indicating the evolutionary divergence of local populations does not result from random genetic drift. The forces of selection needed to differentiate three taxa of Peromyscus were reconstructed to examine the divergence of species and subspecies. The selection gradients obtained illustrate the inadequacy of univariate analyses of selection by finding that some characters evolve in the direction opposite to the force of selection acting directly on them. A retrospective selection index was constructed using the estimated selection gradients, and truncation selection on this index was used to estimate the minimum selective mortality per generation required to produce the observed change. On any of the time scales used, the proportion of the population that would need to be culled was quite low, the greatest being of the same order of magnitude as the selective intensities observed in extant natural populations. Thus, entirely plausible intensities of directional natural selection can produce species-level differences in a period of time too short to be resolved in the fossil record. © 1988 The Society for the Study of Evolution.

  2. Initial characterisation of low and high seed dormancy populations of Lolium rigidum produced by repeated selection.

    Science.gov (United States)

    Goggin, Danica E; Emery, R J Neil; Powles, Stephen B; Steadman, Kathryn J

    2010-10-15

    The physiological and biochemical bases of seed dormancy in Lolium rigidum (annual ryegrass) are largely unknown, and study of this process is complicated by the outcrossing nature of the species and the strong influence of environment on seed dormancy. In order to identify heritable biochemical factors contributing to seed dormancy in L. rigidum, seeds from a field-collected population were used to select sub-populations with consistently low or high seed dormancy over four generations. Low-dormancy seeds showed constitutive alpha-amylase activity prior to imbibition, higher concentrations of polyphenols and cis-zeatin, and lower abscisic acid and cis-zeatin riboside concentrations than high-dormancy seeds. Selection for high dormancy was associated with a reduction in response to dark-stratification for 21d at 20 degrees C (an effective means of releasing dormancy in the original, unselected population) over successive generations, but fluridone remained effective in breaking dormancy. Crossing of low- and high-dormancy populations indicated that dormancy level was not dependent upon the maternal genotype of the seed, and that the constitutive alpha-amylase activity and high seed anthocyanin concentrations characteristic of the low-dormancy populations were not correlated to high basal germination ability. Copyright (c) 2010 Elsevier GmbH. All rights reserved.

  3. Family losses following truncation selection in populations of half-sib families

    Science.gov (United States)

    J. H. Roberds; G. Namkoong; H. Kang

    1980-01-01

    Family losses during truncation selection may be sizable in populations of half-sib families. Substantial losses may occur even in populations containing little or no variation among families. Heavier losses will occur, however, under conditions of high heritability where there is considerable family variation. Standard deviations and therefore variances of family loss...

  4. A mindfulness-based stress prevention training for medical students (MediMind): study protocol for a randomized controlled trial.

    Science.gov (United States)

    Kuhlmann, Sophie Merle; Bürger, Arne; Esser, Günter; Hammerle, Florian

    2015-02-08

    Medical training is very demanding and associated with a high prevalence of psychological distress. Compared to the general population, medical students are at a greater risk of developing a psychological disorder. Various attempts of stress management training in medical school have achieved positive results on minimizing psychological distress; however, there are often limitations. Therefore, the use of a rigorous scientific method is needed. The present study protocol describes a randomized controlled trial to examine the effectiveness of a specifically developed mindfulness-based stress prevention training for medical students that includes selected elements of cognitive behavioral strategies (MediMind). This study protocol presents a prospective randomized controlled trial, involving four assessment time points: baseline, post-intervention, one-year follow-up and five-year follow-up. The aims include evaluating the effect on stress, coping, psychological morbidity and personality traits with validated measures. Participants are allocated randomly to one of three conditions: MediMind, Autogenic Training or control group. Eligible participants are medical or dental students in the second or eighth semester of a German university. They form a population of approximately 420 students in each academic term. A final total sample size of 126 (at five-year follow-up) is targeted. The trainings (MediMind and Autogenic Training) comprise five weekly sessions lasting 90 minutes each. MediMind will be offered to participants of the control group once the five-year follow-up is completed. The allotment is randomized with a stratified allocation ratio by course of studies, semester, and gender. After descriptive statistics have been evaluated, inferential statistical analysis will be carried out with a repeated measures ANOVA-design with interactions between time and group. Effect sizes will be calculated using partial η-square values. Potential limitations of this study

  5. A new logistic dynamic particle swarm optimization algorithm based on random topology.

    Science.gov (United States)

    Ni, Qingjian; Deng, Jianming

    2013-01-01

    Population topology of particle swarm optimization (PSO) will directly affect the dissemination of optimal information during the evolutionary process and will have a significant impact on the performance of PSO. Classic static population topologies are usually used in PSO, such as fully connected topology, ring topology, star topology, and square topology. In this paper, the performance of PSO with the proposed random topologies is analyzed, and the relationship between population topology and the performance of PSO is also explored from the perspective of graph theory characteristics in population topologies. Further, in a relatively new PSO variant which named logistic dynamic particle optimization, an extensive simulation study is presented to discuss the effectiveness of the random topology and the design strategies of population topology. Finally, the experimental data are analyzed and discussed. And about the design and use of population topology on PSO, some useful conclusions are proposed which can provide a basis for further discussion and research.

  6. An optical authentication system based on imaging of excitation-selected lanthanide luminescence.

    Science.gov (United States)

    Carro-Temboury, Miguel R; Arppe, Riikka; Vosch, Tom; Sørensen, Thomas Just

    2018-01-01

    Secure data encryption relies heavily on one-way functions, and copy protection relies on features that are difficult to reproduce. We present an optical authentication system based on lanthanide luminescence from physical one-way functions or physical unclonable functions (PUFs). They cannot be reproduced and thus enable unbreakable encryption. Further, PUFs will prevent counterfeiting if tags with unique PUFs are grafted onto products. We have developed an authentication system that comprises a hardware reader, image analysis, and authentication software and physical keys that we demonstrate as an anticounterfeiting system. The physical keys are PUFs made from random patterns of taggants in polymer films on glass that can be imaged following selected excitation of particular lanthanide(III) ions doped into the individual taggants. This form of excitation-selected imaging ensures that by using at least two lanthanide(III) ion dopants, the random patterns cannot be copied, because the excitation selection will fail when using any other emitter. With the developed reader and software, the random patterns are read and digitized, which allows a digital pattern to be stored. This digital pattern or digital key can be used to authenticate the physical key in anticounterfeiting or to encrypt any message. The PUF key was produced with a staggering nominal encoding capacity of 7 3600 . Although the encoding capacity of the realized authentication system reduces to 6 × 10 104 , it is more than sufficient to completely preclude counterfeiting of products.

  7. A randomized controlled open trial of population-based disease and case management in a Medicare Plus Choice health maintenance organization.

    Science.gov (United States)

    Martin, David C; Berger, Marc L; Anstatt, David T; Wofford, Jonathan; Warfel, DeAnn; Turpin, Robin S; Cannuscio, Carolyn C; Teutsch, Steven M; Mansheim, Bernard J

    2004-10-01

    The object of this study was to examine the effect of population-based disease management and case management on resource use, self-reported health status, and member satisfaction with and retention in a Medicare Plus Choice health maintenance organization (HMO). Study design consisted of a prospective, randomized controlled open trial of 18 months' duration. Participants were 8504 Medicare beneficiaries aged 65 and older who had been continuously enrolled for at least 12 months in a network model Medicare Plus Choice HMO serving a contiguous nine-county metropolitan area. Members were care managed with an expert clinical information system and frequent telephone contact. Main outcomes included self-reported health status measured by the Medical Outcomes Study 36-Item Short-Form Health Survey (SF-36), resource use measured by admission rates and bed-days per thousand per year, member satisfaction, and costs measured by paid claims. More favorable outcomes occurred in the intervention group for satisfaction with the health plan (P management and case management led to improved self-reported satisfaction and social function but not to a global net decrease in resource use or improved member retention.

  8. Selected fishery and population parameters of eight shore-angling ...

    African Journals Online (AJOL)

    Selected fishery and population parameters of eight shore-angling species in the ... Five different estimates of natural mortality (M), and the coefficients of ... for the most abundant species, blacktail Diplodus capensis, with a mean CPUE of 0.252 ... Keywords: catch per unit effort; fisheries management; marine protected area; ...

  9. Allozyme diversity of selected and natural loblolly pine populations

    Science.gov (United States)

    Ronald C. Schmidtling; E. Carroll; T. LaFarge

    1999-01-01

    Loblolly pine (Pinus taeda L.) megagametophytes and embryos were examined electrophoretically to compare the extent and distribution of genetic variability in allozymes of selected and wild populations. Range-wide collections of three different types were investigated in this study. These consisted of seed sampled from (1) a provenance test...

  10. Comparing Effectiveness of Mindfulness-Based Relapse Prevention with Treatment as Usual on Impulsivity and Relapse for Methadone-Treated Patients: A Randomized Clinical Trial.

    Science.gov (United States)

    Yaghubi, Mehdi; Zargar, Fatemeh; Akbari, Hossein

    2017-07-01

    Impulsivity is one of the causes of relapse that can affect treatment outcomes. Studies have shown that addiction treatments can reduce impulsivity in drug-dependent individuals. Studies also have suggested that mindfulness is associated with impulsivity. However, no study has investigated the effectiveness of the mindfulness-based intervention on impulsivity in opioid-dependent individuals. This study aimed to compare the effectiveness of mindfulness-based relapse prevention (MBRP) with treatment as usual (TAU) in terms of impulsivity and relapse for methadone-treated patients. The present randomized controlled clinical trial was performed in Kashan, Iran, in 2015. The study population was opioid-dependent patients referred to Maintenance Treatment Centers. Seventy patients were selected by random sampling and were assigned in two groups (MBRP and TAU) randomly. The participants of two groups filled out Barratt impulsivity scale (BIS-11) as a pre-test and 8 weeks later as post-test and 2 months later as a follow-up. Both groups received methadone-therapy. The MBRP group received 8 sessions of group therapy, while the control group did not receive any group psychotherapy session. Finally, data from 60 patients were analyzed statistically. The MBRP group had decreased impulsivity significantly (P relapse frequency (P relapse probability. These findings suggest that MBRP is useful for opioid-dependent individuals with high-level impulsivity, and relapse prevention.

  11. Parity and 11-Year Serum Thyrotropin and Thyroid Autoantibody Change: A Longitudinal Population-Based Study

    DEFF Research Database (Denmark)

    Bjergved, Lena; Carlé, Allan; Jørgensen, Torben

    2016-01-01

    thyrotropin (TSH), as well as change in thyroid peroxidase autoantibody (TPOAb) status. A random sample of 4649 people aged 18-65 years participated in a population-based study in the period 1997-1998. In the study presented here, 1749 non-pregnant women with no history of thyroid disease were included who...

  12. Use of traditional eye medicine and self-medication in rural India: A population-based study.

    Science.gov (United States)

    Gupta, Noopur; Vashist, Praveen; Tandon, Radhika; Gupta, Sanjeev K; Kalaivani, Mani; Dwivedi, S N

    2017-01-01

    To determine the type and nature of traditional eye medicine (TEM), their sources and use and practices related to self-medication for ophthalmic diseases in a rural Indian population. A population-based, cross-sectional study was conducted in 25 randomly selected clusters of Rural Gurgaon, Haryana, India as part of CORE (Cornea Opacity Rural Epidemiological) study. In addition to comprehensive ophthalmic examination, health-seeking behavior and use of self-medication and TEM was assessed in the adult population using a semi-structured questionnaire. Physical verification of available ophthalmic medications in the enumerated households was conducted by the study team. Descriptive statistics were computed along with multivariable logistic regression analysis to determine associated factors for use of self-medication and TEM. Of the 2160 participants interviewed, 396 (18.2%) reported using ophthalmic medications without consulting an ophthalmologist, mainly for symptoms like watering (37.1%), redness (27.7%), itching (19.2%) and infection (13.6%). On physical verification of available eye drops that were being used without prescription, 26.4% participants were practicing self-medication. Steroid, expired/unlabeled and indigenous eye drops were being used by 151(26.5%), 120(21.1%) and 75 (13.2%) participants respectively. Additionally, 25.7% (529) participants resorted to home remedies like 'kajal'(61.4%), honey (31.4%), ghee (11.7%) and rose water (9.1%). Use of TEM is prevalent in this population. The rampant use of steroid eye drops without prescription along with use of expired or unlabelled eye drops warrants greater emphasis on safe eye care practices in this population. Public awareness and regulatory legislations must be implemented to decrease harmful effects arising due to such practices.

  13. Hyperspectral band selection based on consistency-measure of neighborhood rough set theory

    International Nuclear Information System (INIS)

    Liu, Yao; Xie, Hong; Wang, Liguo; Tan, Kezhu; Chen, Yuehua; Xu, Zhen

    2016-01-01

    Band selection is a well-known approach for reducing dimensionality in hyperspectral imaging. In this paper, a band selection method based on consistency-measure of neighborhood rough set theory (CMNRS) was proposed to select informative bands from hyperspectral images. A decision-making information system was established by the reflection spectrum of soybeans’ hyperspectral data between 400 nm and 1000 nm wavelengths. The neighborhood consistency-measure, which reflects not only the size of the decision positive region, but also the sample distribution in the boundary region, was used as the evaluation function of band significance. The optimal band subset was selected by a forward greedy search algorithm. A post-pruning strategy was employed to overcome the over-fitting problem and find the minimum subset. To assess the effectiveness of the proposed band selection technique, two classification models (extreme learning machine (ELM) and random forests (RF)) were built. The experimental results showed that the proposed algorithm can effectively select key bands and obtain satisfactory classification accuracy. (paper)

  14. Optimizing Event Selection with the Random Grid Search

    Energy Technology Data Exchange (ETDEWEB)

    Bhat, Pushpalatha C. [Fermilab; Prosper, Harrison B. [Florida State U.; Sekmen, Sezen [Kyungpook Natl. U.; Stewart, Chip [Broad Inst., Cambridge

    2017-06-29

    The random grid search (RGS) is a simple, but efficient, stochastic algorithm to find optimal cuts that was developed in the context of the search for the top quark at Fermilab in the mid-1990s. The algorithm, and associated code, have been enhanced recently with the introduction of two new cut types, one of which has been successfully used in searches for supersymmetry at the Large Hadron Collider. The RGS optimization algorithm is described along with the recent developments, which are illustrated with two examples from particle physics. One explores the optimization of the selection of vector boson fusion events in the four-lepton decay mode of the Higgs boson and the other optimizes SUSY searches using boosted objects and the razor variables.

  15. Novel pseudo-random number generator based on quantum random walks

    Science.gov (United States)

    Yang, Yu-Guang; Zhao, Qian-Qian

    2016-02-01

    In this paper, we investigate the potential application of quantum computation for constructing pseudo-random number generators (PRNGs) and further construct a novel PRNG based on quantum random walks (QRWs), a famous quantum computation model. The PRNG merely relies on the equations used in the QRWs, and thus the generation algorithm is simple and the computation speed is fast. The proposed PRNG is subjected to statistical tests such as NIST and successfully passed the test. Compared with the representative PRNG based on quantum chaotic maps (QCM), the present QRWs-based PRNG has some advantages such as better statistical complexity and recurrence. For example, the normalized Shannon entropy and the statistical complexity of the QRWs-based PRNG are 0.999699456771172 and 1.799961178212329e-04 respectively given the number of 8 bits-words, say, 16Mbits. By contrast, the corresponding values of the QCM-based PRNG are 0.999448131481064 and 3.701210794388818e-04 respectively. Thus the statistical complexity and the normalized entropy of the QRWs-based PRNG are closer to 0 and 1 respectively than those of the QCM-based PRNG when the number of words of the analyzed sequence increases. It provides a new clue to construct PRNGs and also extends the applications of quantum computation.

  16. Novel pseudo-random number generator based on quantum random walks.

    Science.gov (United States)

    Yang, Yu-Guang; Zhao, Qian-Qian

    2016-02-04

    In this paper, we investigate the potential application of quantum computation for constructing pseudo-random number generators (PRNGs) and further construct a novel PRNG based on quantum random walks (QRWs), a famous quantum computation model. The PRNG merely relies on the equations used in the QRWs, and thus the generation algorithm is simple and the computation speed is fast. The proposed PRNG is subjected to statistical tests such as NIST and successfully passed the test. Compared with the representative PRNG based on quantum chaotic maps (QCM), the present QRWs-based PRNG has some advantages such as better statistical complexity and recurrence. For example, the normalized Shannon entropy and the statistical complexity of the QRWs-based PRNG are 0.999699456771172 and 1.799961178212329e-04 respectively given the number of 8 bits-words, say, 16Mbits. By contrast, the corresponding values of the QCM-based PRNG are 0.999448131481064 and 3.701210794388818e-04 respectively. Thus the statistical complexity and the normalized entropy of the QRWs-based PRNG are closer to 0 and 1 respectively than those of the QCM-based PRNG when the number of words of the analyzed sequence increases. It provides a new clue to construct PRNGs and also extends the applications of quantum computation.

  17. Increasing prevalence and high incidence of celiac disease in elderly people: a population-based study.

    Science.gov (United States)

    Vilppula, Anitta; Kaukinen, Katri; Luostarinen, Liisa; Krekelä, Ilkka; Patrikainen, Heikki; Valve, Raisa; Mäki, Markku; Collin, Pekka

    2009-06-29

    Celiac disease may emerge at any age, but little is known of its appearance in elderly people. We evaluated the prevalence of the condition in individuals over 55 years of age, and determined the incidence of biopsy-proven celiac disease (CDb) and celiac disease including seropositive subjects for anti-tissue transglutaminase antibodies (CDb+s). The study based on prevalence figures in 2815 randomly selected subjects who had undergone a clinical examination and serologic screening for celiac disease in 2002. A second screening in the same population was carried out in 2005, comprising now 2216 individuals. Positive tissue transglutaminase antibodies were confirmed with small bowel biopsy. Within three years the prevalence of CDb increased from 2.13 to 2.34%, and that of CDb+s from 2.45 to 2.70%. Five new cases were found among patients previously seronegative; two had minor abdominal symptoms and three were asymptomatic. The incidence of celiac disease in 2002-2005 was 0.23%, giving an annual incidence of 0.08% in this population. The prevalence of celiac disease was high in elderly people, but the symptoms were subtle. Repeated screening detected five biopsy-proven cases in three years, indicating that the disorder may develop even in the elderly. Increased alertness to the disorder is therefore warranted.

  18. Selection Component Analysis of Natural Polymorphisms using Population Samples Including Mother-Offspring Combinations, II

    DEFF Research Database (Denmark)

    Jarmer, Hanne Østergaard; Christiansen, Freddy Bugge

    1981-01-01

    Population samples including mother-offspring combinations provide information on the selection components: zygotic selection, sexual selection, gametic seletion and fecundity selection, on the mating pattern, and on the deviation from linkage equilibrium among the loci studied. The theory...

  19. Hand Grip Strength: age and gender stratified normative data in a population-based study

    Directory of Open Access Journals (Sweden)

    Taylor Anne W

    2011-04-01

    Full Text Available Abstract Background The North West Adelaide Health Study is a representative longitudinal cohort study of people originally aged 18 years and over. The aim of this study was to describe normative data for hand grip strength in a community-based Australian population. Secondary aims were to investigate the relationship between body mass index (BMI and hand grip strength, and to compare Australian data with international hand grip strength norms. Methods The sample was randomly selected and recruited by telephone interview. Overall, 3 206 (81% of those recruited participants returned to the clinic during the second stage (2004-2006 which specifically focused on the collection of information relating to musculoskeletal conditions. Results Following the exclusion of 435 participants who had hand pain and/or arthritis, 1366 men and 1312 women participants provided hand grip strength measurement. The study population was relatively young, with 41.5% under 40 years; and their mean BMI was 28.1 kg/m2 (SD 5.5. Higher hand grip strength was weakly related to higher BMI in adults under the age of 30 and over the age of 70, but inversely related to higher BMI between these ages. Australian norms from this sample had amongst the lowest of the hand grip strength of the internationally published norms, except those from underweight populations. Conclusions This population demonstrated higher BMI and lower grip strength in younger participants than much of the international published, population data. A complete exploration of the relationship between BMI and hand grip strength was not fully explored as there were very few participants with BMI in the underweight range. The age and gender grip strength values are lower in younger adults than those reported in international literature.

  20. Exact Markov chains versus diffusion theory for haploid random mating.

    Science.gov (United States)

    Tyvand, Peder A; Thorvaldsen, Steinar

    2010-05-01

    Exact discrete Markov chains are applied to the Wright-Fisher model and the Moran model of haploid random mating. Selection and mutations are neglected. At each discrete value of time t there is a given number n of diploid monoecious organisms. The evolution of the population distribution is given in diffusion variables, to compare the two models of random mating with their common diffusion limit. Only the Moran model converges uniformly to the diffusion limit near the boundary. The Wright-Fisher model allows the population size to change with the generations. Diffusion theory tends to under-predict the loss of genetic information when a population enters a bottleneck. 2010 Elsevier Inc. All rights reserved.

  1. Genetic structure of populations of Mugil cephalus using RAPD ...

    African Journals Online (AJOL)

    Dr.Suresh

    2013-10-30

    , Andhra Pradesh and. Tamil Nadu in India was studied using randomly amplified polymorphic DNA (RAPD) markers. Five selective primers provided distinct and consistent RAPD profiles in all the four populations. The bands.

  2. Mindfulness-Based Cognitive Therapy as a Treatment for Chronic Tinnitus: A Randomized Controlled Trial

    OpenAIRE

    McKenna, L.; Marks, E. M.; Hallsworth, C. A.; Schaette, R.

    2017-01-01

    BACKGROUND: Tinnitus is experienced by up to 15% of the population and can lead to significant disability and distress. There is rarely a medical or surgical target and psychological therapies are recommended. We investigated whether mindfulness-based cognitive therapy (MBCT) could offer an effective new therapy for tinnitus. METHODS: This single-site randomized controlled trial compared MBCT to intensive relaxation training (RT) for chronic, distressing tinnitus in adults. Both treatments in...

  3. Trait variation and genetic diversity in a banana genomic selection training population

    Science.gov (United States)

    Nyine, Moses; Uwimana, Brigitte; Swennen, Rony; Batte, Michael; Brown, Allan; Christelová, Pavla; Hřibová, Eva; Lorenzen, Jim

    2017-01-01

    Banana (Musa spp.) is an important crop in the African Great Lakes region in terms of income and food security, with the highest per capita consumption worldwide. Pests, diseases and climate change hamper sustainable production of bananas. New breeding tools with increased crossbreeding efficiency are being investigated to breed for resistant, high yielding hybrids of East African Highland banana (EAHB). These include genomic selection (GS), which will benefit breeding through increased genetic gain per unit time. Understanding trait variation and the correlation among economically important traits is an essential first step in the development and selection of suitable GS models for banana. In this study, we tested the hypothesis that trait variations in bananas are not affected by cross combination, cycle, field management and their interaction with genotype. A training population created using EAHB breeding material and its progeny was phenotyped in two contrasting conditions. A high level of correlation among vegetative and yield related traits was observed. Therefore, genomic selection models could be developed for traits that are easily measured. It is likely that the predictive ability of traits that are difficult to phenotype will be similar to less difficult traits they are highly correlated with. Genotype response to cycle and field management practices varied greatly with respect to traits. Yield related traits accounted for 31–35% of principal component variation under low and high input field management conditions. Resistance to Black Sigatoka was stable across cycles but varied under different field management depending on the genotype. The best cross combination was 1201K-1xSH3217 based on selection response (R) of hybrids. Genotyping using simple sequence repeat (SSR) markers revealed that the training population was genetically diverse, reflecting a complex pedigree background, which was mostly influenced by the male parents. PMID:28586365

  4. Trait variation and genetic diversity in a banana genomic selection training population.

    Directory of Open Access Journals (Sweden)

    Moses Nyine

    Full Text Available Banana (Musa spp. is an important crop in the African Great Lakes region in terms of income and food security, with the highest per capita consumption worldwide. Pests, diseases and climate change hamper sustainable production of bananas. New breeding tools with increased crossbreeding efficiency are being investigated to breed for resistant, high yielding hybrids of East African Highland banana (EAHB. These include genomic selection (GS, which will benefit breeding through increased genetic gain per unit time. Understanding trait variation and the correlation among economically important traits is an essential first step in the development and selection of suitable GS models for banana. In this study, we tested the hypothesis that trait variations in bananas are not affected by cross combination, cycle, field management and their interaction with genotype. A training population created using EAHB breeding material and its progeny was phenotyped in two contrasting conditions. A high level of correlation among vegetative and yield related traits was observed. Therefore, genomic selection models could be developed for traits that are easily measured. It is likely that the predictive ability of traits that are difficult to phenotype will be similar to less difficult traits they are highly correlated with. Genotype response to cycle and field management practices varied greatly with respect to traits. Yield related traits accounted for 31-35% of principal component variation under low and high input field management conditions. Resistance to Black Sigatoka was stable across cycles but varied under different field management depending on the genotype. The best cross combination was 1201K-1xSH3217 based on selection response (R of hybrids. Genotyping using simple sequence repeat (SSR markers revealed that the training population was genetically diverse, reflecting a complex pedigree background, which was mostly influenced by the male parents.

  5. Trait variation and genetic diversity in a banana genomic selection training population.

    Science.gov (United States)

    Nyine, Moses; Uwimana, Brigitte; Swennen, Rony; Batte, Michael; Brown, Allan; Christelová, Pavla; Hřibová, Eva; Lorenzen, Jim; Doležel, Jaroslav

    2017-01-01

    Banana (Musa spp.) is an important crop in the African Great Lakes region in terms of income and food security, with the highest per capita consumption worldwide. Pests, diseases and climate change hamper sustainable production of bananas. New breeding tools with increased crossbreeding efficiency are being investigated to breed for resistant, high yielding hybrids of East African Highland banana (EAHB). These include genomic selection (GS), which will benefit breeding through increased genetic gain per unit time. Understanding trait variation and the correlation among economically important traits is an essential first step in the development and selection of suitable GS models for banana. In this study, we tested the hypothesis that trait variations in bananas are not affected by cross combination, cycle, field management and their interaction with genotype. A training population created using EAHB breeding material and its progeny was phenotyped in two contrasting conditions. A high level of correlation among vegetative and yield related traits was observed. Therefore, genomic selection models could be developed for traits that are easily measured. It is likely that the predictive ability of traits that are difficult to phenotype will be similar to less difficult traits they are highly correlated with. Genotype response to cycle and field management practices varied greatly with respect to traits. Yield related traits accounted for 31-35% of principal component variation under low and high input field management conditions. Resistance to Black Sigatoka was stable across cycles but varied under different field management depending on the genotype. The best cross combination was 1201K-1xSH3217 based on selection response (R) of hybrids. Genotyping using simple sequence repeat (SSR) markers revealed that the training population was genetically diverse, reflecting a complex pedigree background, which was mostly influenced by the male parents.

  6. Registry-based randomized controlled trials merged the strength of randomized controlled trails and observational studies and give rise to more pragmatic trials.

    Science.gov (United States)

    Mathes, Tim; Buehn, Stefanie; Prengel, Peggy; Pieper, Dawid

    2018-01-01

    The objective of this study was to analyze the features of registry-based randomized trials (rRCTs). We systematically searched PubMed for rRCTs. Study selection was performed independently by two reviewers. We extracted all data in standardized tables and prepared descriptive summary statistics. The search resulted in 1,202 hits. We included 71 rRCTs. Most rRCTs were from Denmark and Sweden. Chronic conditions were considered in 82.2%. A preventive intervention was examined in 45.1%. The median of included patients was 2,000 (range: 69-246,079). Definition of the study population was mostly broad. Study procedures were regularly little standardized. The number of included and analyzed patients was the same in 82.1%. In half of the rRCTs, more than one registry was utilized. Various linkage techniques were used. In median, two outcomes were collected from the registry/ies. The median follow-up of the rRCTs was 5.3 years (range: 6 weeks to 27 years). Information on quality of registry data was reported in 11.3%. rRCTs can provide valid (randomization, low lost-to-follow-up rates, generalizable) patient important long-term comparative-effectiveness data for relative little effort. Researchers planning an RCT should always check whether existing registries can be used for data collection. Reporting on data quality must be improved for use in evidence synthesis. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Mating schemes for optimum contribution selection with constrained rates of inbreeding

    NARCIS (Netherlands)

    Sonesson, A.K.; Meuwissen, T.H.E.

    2000-01-01

    The effect of non-random mating on genetic response was compared for populations with discrete generations. Mating followed a selection step where the average coancestry of selected animals was constrained, while genetic response was maximised. Minimum coancestry (MC), Minimum coancestry with a

  8. U.S. Census Annual Estimates of the Resident Population for Selected Age Groups by Sex for the United States

    Data.gov (United States)

    U.S. Department of Health & Human Services — 2010-2015. U.S. Census Annual Estimates of the Resident Population for Selected Age Groups by Sex for the United States. The estimates are based on the 2010 Census...

  9. Genetic variation of seedling traits in a random mating population of sunflower

    International Nuclear Information System (INIS)

    Habib, S.

    2004-01-01

    Forty S/sub 1/ families obtained from a random mating population of sunflower were evaluated in the laboratory for various seedling traits. The objectives of this study were to investigate the extent and nature of genetic variability and to determine the estimates of genotypic and phenotypic correlations among ten seedling traits prevailing in a random mating population of sunflower. The results indicated that significant differences existed among the 40 S/sub 1/ families for all the traits evaluated. Genotypic and phenotypic coefficients of variation were comparatively high for emergence rate index, root/shoot ratio, dry root weight, fresh root weight and fresh shoot weight. The estimates of broad-sense heritability were high and significant for all the traits. The study of genotypic and phenotypic correlations among these traits revealed that generally, the seedlings which took more time to emerge were vigorous for most of the traits except fresh shoot length. However, rapidly emerging seedlings had higher emergence percentage. The root traits appeared to be better indicators of seedling vigour compared to other traits as these traits exhibited strong and positive genotypic and phenotypic correlations among them. (author)

  10. An automatic optimum number of well-distributed ground control lines selection procedure based on genetic algorithm

    Science.gov (United States)

    Yavari, Somayeh; Valadan Zoej, Mohammad Javad; Salehi, Bahram

    2018-05-01

    The procedure of selecting an optimum number and best distribution of ground control information is important in order to reach accurate and robust registration results. This paper proposes a new general procedure based on Genetic Algorithm (GA) which is applicable for all kinds of features (point, line, and areal features). However, linear features due to their unique characteristics are of interest in this investigation. This method is called Optimum number of Well-Distributed ground control Information Selection (OWDIS) procedure. Using this method, a population of binary chromosomes is randomly initialized. The ones indicate the presence of a pair of conjugate lines as a GCL and zeros specify the absence. The chromosome length is considered equal to the number of all conjugate lines. For each chromosome, the unknown parameters of a proper mathematical model can be calculated using the selected GCLs (ones in each chromosome). Then, a limited number of Check Points (CPs) are used to evaluate the Root Mean Square Error (RMSE) of each chromosome as its fitness value. The procedure continues until reaching a stopping criterion. The number and position of ones in the best chromosome indicate the selected GCLs among all conjugate lines. To evaluate the proposed method, a GeoEye and an Ikonos Images are used over different areas of Iran. Comparing the obtained results by the proposed method in a traditional RFM with conventional methods that use all conjugate lines as GCLs shows five times the accuracy improvement (pixel level accuracy) as well as the strength of the proposed method. To prevent an over-parametrization error in a traditional RFM due to the selection of a high number of improper correlated terms, an optimized line-based RFM is also proposed. The results show the superiority of the combination of the proposed OWDIS method with an optimized line-based RFM in terms of increasing the accuracy to better than 0.7 pixel, reliability, and reducing systematic

  11. Alleles versus genotypes: Genetic interactions and the dynamics of selection in sexual populations

    Science.gov (United States)

    Neher, Richard

    2010-03-01

    Physical interactions between amino-acids are essential for protein structure and activity, while protein-protein interactions and regulatory interactions are central to cellular function. As a consequence of these interactions, the combined effect of two mutations can differ from the sum of the individual effects of the mutations. This phenomenon of genetic interaction is known as epistasis. However, the importance of epistasis and its effects on evolutionary dynamics are poorly understood, especially in sexual populations where recombination breaks up existing combinations of alleles to produce new ones. Here, we present a computational model of selection dynamics involving many epistatic loci in a recombining population. We demonstrate that a large number of polymorphic interacting loci can, despite frequent recombination, exhibit cooperative behavior that locks alleles into favorable genotypes leading to a population consisting of a set of competing clones. As the recombination rate exceeds a certain critical value this ``genotype selection'' phase disappears in an abrupt transition giving way to ``allele selection'' - the phase where different loci are only weakly correlated as expected in sexually reproducing populations. Clustering of interacting sets of genes on a chromosome leads to the emergence of an intermediate regime, where localized blocks of cooperating alleles lock into genetic modules. Large populations attain highest fitness at a recombination rate just below critical, suggesting that natural selection might tune recombination rates to balance the beneficial aspect of exploration of genotype space with the breaking up of synergistic allele combinations.

  12. The temporal distribution of directional gradients under selection for an optimum.

    Science.gov (United States)

    Chevin, Luis-Miguel; Haller, Benjamin C

    2014-12-01

    Temporal variation in phenotypic selection is often attributed to environmental change causing movements of the adaptive surface relating traits to fitness, but this connection is rarely established empirically. Fluctuating phenotypic selection can be measured by the variance and autocorrelation of directional selection gradients through time. However, the dynamics of these gradients depend not only on environmental changes altering the fitness surface, but also on evolution of the phenotypic distribution. Therefore, it is unclear to what extent variability in selection gradients can inform us about the underlying drivers of their fluctuations. To investigate this question, we derive the temporal distribution of directional gradients under selection for a phenotypic optimum that is either constant or fluctuates randomly in various ways in a finite population. Our analytical results, combined with population- and individual-based simulations, show that although some characteristic patterns can be distinguished, very different types of change in the optimum (including a constant optimum) can generate similar temporal distributions of selection gradients, making it difficult to infer the processes underlying apparent fluctuating selection. Analyzing changes in phenotype distributions together with changes in selection gradients should prove more useful for inferring the mechanisms underlying estimated fluctuating selection. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  13. The relationship between blood viscosity and blood pressure in a random sample of the population aged 55 to 74 years.

    Science.gov (United States)

    Fowkes, F G; Lowe, G D; Rumley, A; Lennie, S E; Smith, F B; Donnan, P T

    1993-05-01

    Blood viscosity is elevated in hypertensive subjects, but the association of viscosity with arterial blood pressure in the general population, and the influence of social, lifestyle and disease characteristics on this association, are not established. In the Edinburgh Artery Study, 1592 men and women aged 55-74 years selected randomly from the general population attended a university clinic. A fasting blood sample was taken for the measurement of blood viscosity and its major determinants (haematocrit, plasma viscosity and fibrinogen). Systolic pressure was related univariately to blood viscosity (P viscosity (P index. Diastolic pressure was related univariately to blood viscosity (P viscosity (P viscosity and systolic pressure was confined to males. Blood viscosity was associated equally with systolic and diastolic pressures in males, and remained independently related on multivariate analysis adjusting for age, sex, body mass index, social class, smoking, alcohol intake, exercise, angina, HDL and non-HDL cholesterol, diabetes mellitus, plasma viscosity, fibrinogen, and haematocrit.

  14. Persistency of Prediction Accuracy and Genetic Gain in Synthetic Populations Under Recurrent Genomic Selection.

    Science.gov (United States)

    Müller, Dominik; Schopp, Pascal; Melchinger, Albrecht E

    2017-03-10

    Recurrent selection (RS) has been used in plant breeding to successively improve synthetic and other multiparental populations. Synthetics are generated from a limited number of parents [Formula: see text] but little is known about how [Formula: see text] affects genomic selection (GS) in RS, especially the persistency of prediction accuracy ([Formula: see text]) and genetic gain. Synthetics were simulated by intermating [Formula: see text]= 2-32 parent lines from an ancestral population with short- or long-range linkage disequilibrium ([Formula: see text]) and subjected to multiple cycles of GS. We determined [Formula: see text] and genetic gain across 30 cycles for different training set ( TS ) sizes, marker densities, and generations of recombination before model training. Contributions to [Formula: see text] and genetic gain from pedigree relationships, as well as from cosegregation and [Formula: see text] between QTL and markers, were analyzed via four scenarios differing in (i) the relatedness between TS and selection candidates and (ii) whether selection was based on markers or pedigree records. Persistency of [Formula: see text] was high for small [Formula: see text] where predominantly cosegregation contributed to [Formula: see text], but also for large [Formula: see text] where [Formula: see text] replaced cosegregation as the dominant information source. Together with increasing genetic variance, this compensation resulted in relatively constant long- and short-term genetic gain for increasing [Formula: see text] > 4, given long-range LD A in the ancestral population. Although our scenarios suggest that information from pedigree relationships contributed to [Formula: see text] for only very few generations in GS, we expect a longer contribution than in pedigree BLUP, because capturing Mendelian sampling by markers reduces selective pressure on pedigree relationships. Larger TS size ([Formula: see text]) and higher marker density improved persistency of

  15. Group selection on population size affects life-history patterns in the entomopathogenic nematode Steinernema carpocapsae.

    Science.gov (United States)

    Bashey, Farrah; Lively, Curtis M

    2009-05-01

    Selection is recognized to operate on multiple levels. In disease organisms, selection among hosts is thought to provide an important counterbalance to selection for faster growth within hosts. We performed three experiments, each selecting for a divergence in group size in the entomopathogenic nematode, Steinernema carpocapsae. These nematodes infect and kill insect larvae, reproduce inside the host carcass, and emerge as infective juveniles. We imposed selection on group size by selecting among hosts for either high or low numbers of emerging nematodes. Our goal was to determine whether this trait could respond to selection at the group level, and if so, to examine what other traits would evolve as correlated responses. One of the three experiments showed a significant response to group selection. In that experiment, the high-selected treatment consistently produced more emerging nematodes per host than the low-selected treatment. In addition, nematodes were larger and they emerged later from hosts in the low-selected lines. Despite small effective population sizes, the effects of inbreeding were small in this experiment. Thus, selection among hosts can be effective, leading to both a direct evolutionary response at the population level, as well as to correlated responses in populational and individual traits.

  16. HLA DNA sequence variation among human populations: molecular signatures of demographic and selective events.

    Directory of Open Access Journals (Sweden)

    Stéphane Buhler

    2011-02-01

    Full Text Available Molecular differences between HLA alleles vary up to 57 nucleotides within the peptide binding coding region of human Major Histocompatibility Complex (MHC genes, but it is still unclear whether this variation results from a stochastic process or from selective constraints related to functional differences among HLA molecules. Although HLA alleles are generally treated as equidistant molecular units in population genetic studies, DNA sequence diversity among populations is also crucial to interpret the observed HLA polymorphism. In this study, we used a large dataset of 2,062 DNA sequences defined for the different HLA alleles to analyze nucleotide diversity of seven HLA genes in 23,500 individuals of about 200 populations spread worldwide. We first analyzed the HLA molecular structure and diversity of these populations in relation to geographic variation and we further investigated possible departures from selective neutrality through Tajima's tests and mismatch distributions. All results were compared to those obtained by classical approaches applied to HLA allele frequencies.Our study shows that the global patterns of HLA nucleotide diversity among populations are significantly correlated to geography, although in some specific cases the molecular information reveals unexpected genetic relationships. At all loci except HLA-DPB1, populations have accumulated a high proportion of very divergent alleles, suggesting an advantage of heterozygotes expressing molecularly distant HLA molecules (asymmetric overdominant selection model. However, both different intensities of selection and unequal levels of gene conversion may explain the heterogeneous mismatch distributions observed among the loci. Also, distinctive patterns of sequence divergence observed at the HLA-DPB1 locus suggest current neutrality but old selective pressures on this gene. We conclude that HLA DNA sequences advantageously complement HLA allele frequencies as a source of data used

  17. Could non-grade based selection improve medical student socio-demographic diversity?

    DEFF Research Database (Denmark)

    O'Neill, Lotte Dyhrberg

    2013-01-01

    selected with a non-grade-based or ’non-cognitive’ admission program. The two admission groups were compared on seven social indices (doctor parent, ethnic origin, father’s education, mother’s education, parenthood, parents live together, parent on benefit). Result: Selection strategy made no difference...... to the social diversity of admitted medical students. The non-cognitive admission program studied was not a useful initiative for improving medical student diversity nor did it further disadvantaged educationally vulnerable population groups in these cohorts. Discussion: The social heritage and general...

  18. Selecting Populations for Non-Analogous Climate Conditions Using Universal Response Functions: The Case of Douglas-Fir in Central Europe.

    Science.gov (United States)

    Chakraborty, Debojyoti; Wang, Tongli; Andre, Konrad; Konnert, Monika; Lexer, Manfred J; Matulla, Christoph; Schueler, Silvio

    2015-01-01

    Identifying populations within tree species potentially adapted to future climatic conditions is an important requirement for reforestation and assisted migration programmes. Such populations can be identified either by empirical response functions based on correlations of quantitative traits with climate variables or by climate envelope models that compare the climate of seed sources and potential growing areas. In the present study, we analyzed the intraspecific variation in climate growth response of Douglas-fir planted within the non-analogous climate conditions of Central and continental Europe. With data from 50 common garden trials, we developed Universal Response Functions (URF) for tree height and mean basal area and compared the growth performance of the selected best performing populations with that of populations identified through a climate envelope approach. Climate variables of the trial location were found to be stronger predictors of growth performance than climate variables of the population origin. Although the precipitation regime of the population sources varied strongly none of the precipitation related climate variables of population origin was found to be significant within the models. Overall, the URFs explained more than 88% of variation in growth performance. Populations identified by the URF models originate from western Cascades and coastal areas of Washington and Oregon and show significantly higher growth performance than populations identified by the climate envelope approach under both current and climate change scenarios. The URFs predict decreasing growth performance at low and middle elevations of the case study area, but increasing growth performance on high elevation sites. Our analysis suggests that population recommendations based on empirical approaches should be preferred and population selections by climate envelope models without considering climatic constrains of growth performance should be carefully appraised before

  19. Selecting Populations for Non-Analogous Climate Conditions Using Universal Response Functions: The Case of Douglas-Fir in Central Europe

    Science.gov (United States)

    Chakraborty, Debojyoti; Wang, Tongli; Andre, Konrad; Konnert, Monika; Lexer, Manfred J.; Matulla, Christoph; Schueler, Silvio

    2015-01-01

    Identifying populations within tree species potentially adapted to future climatic conditions is an important requirement for reforestation and assisted migration programmes. Such populations can be identified either by empirical response functions based on correlations of quantitative traits with climate variables or by climate envelope models that compare the climate of seed sources and potential growing areas. In the present study, we analyzed the intraspecific variation in climate growth response of Douglas-fir planted within the non-analogous climate conditions of Central and continental Europe. With data from 50 common garden trials, we developed Universal Response Functions (URF) for tree height and mean basal area and compared the growth performance of the selected best performing populations with that of populations identified through a climate envelope approach. Climate variables of the trial location were found to be stronger predictors of growth performance than climate variables of the population origin. Although the precipitation regime of the population sources varied strongly none of the precipitation related climate variables of population origin was found to be significant within the models. Overall, the URFs explained more than 88% of variation in growth performance. Populations identified by the URF models originate from western Cascades and coastal areas of Washington and Oregon and show significantly higher growth performance than populations identified by the climate envelope approach under both current and climate change scenarios. The URFs predict decreasing growth performance at low and middle elevations of the case study area, but increasing growth performance on high elevation sites. Our analysis suggests that population recommendations based on empirical approaches should be preferred and population selections by climate envelope models without considering climatic constrains of growth performance should be carefully appraised before

  20. Plasma sterols and depressive symptom severity in a population-based cohort.

    Directory of Open Access Journals (Sweden)

    Basar Cenik

    Full Text Available Convergent evidence strongly suggests major depressive disorder is heterogeneous in its etiology and clinical characteristics. Depression biomarkers hold potential for identifying etiological subtypes, improving diagnostic accuracy, predicting treatment response, and personalization of treatment. Human plasma contains numerous sterols that have not been systematically studied. Changes in cholesterol concentrations have been implicated in suicide and depression, suggesting plasma sterols may be depression biomarkers. Here, we investigated associations between plasma levels of 34 sterols (measured by mass spectrometry and scores on the Quick Inventory of Depressive Symptomatology-Self Report (QIDS-SR16 scale in 3117 adult participants in the Dallas Heart Study, an ethnically diverse, population-based cohort. We built a random forest model using feature selection from a pool of 43 variables including demographics, general health indicators, and sterol concentrations. This model comprised 19 variables, 13 of which were sterol concentrations, and explained 15.5% of the variation in depressive symptoms. Desmosterol concentrations below the fifth percentile (1.9 ng/mL, OR 1.9, 95% CI 1.2-2.9 were significantly associated with depressive symptoms of at least moderate severity (QIDS-SR16 score ≥10.5. This is the first study reporting a novel association between plasma concentrations cholesterol precursors and depressive symptom severity.

  1. [On the extinction of populations with several types in a random environment].

    Science.gov (United States)

    Bacaër, Nicolas

    2018-03-01

    This study focuses on the extinction rate of a population that follows a continuous-time multi-type branching process in a random environment. Numerical computations in a particular example inspired by an epidemic model suggest an explicit formula for this extinction rate, but only for certain parameter values. Copyright © 2018 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

  2. Comparative Evaluations of Randomly Selected Four Point-of-Care Glucometer Devices in Addis Ababa, Ethiopia.

    Science.gov (United States)

    Wolde, Mistire; Tarekegn, Getahun; Kebede, Tedla

    2018-05-01

    Point-of-care glucometer (PoCG) devices play a significant role in self-monitoring of the blood sugar level, particularly in the follow-up of high blood sugar therapeutic response. The aim of this study was to evaluate blood glucose test results performed with four randomly selected glucometers on diabetes and control subjects versus standard wet chemistry (hexokinase) methods in Addis Ababa, Ethiopia. A prospective cross-sectional study was conducted on randomly selected 200 study participants (100 participants with diabetes and 100 healthy controls). Four randomly selected PoCG devices (CareSens N, DIAVUE Prudential, On Call Extra, i-QARE DS-W) were evaluated against hexokinase method and ISO 15197:2003 and ISO 15197:2013 standards. The minimum and maximum blood sugar values were recorded by CareSens N (21 mg/dl) and hexokinase method (498.8 mg/dl), respectively. The mean sugar values of all PoCG devices except On Call Extra showed significant differences compared with the reference hexokinase method. Meanwhile, all four PoCG devices had strong positive relationship (>80%) with the reference method (hexokinase). On the other hand, none of the four PoCG devices fulfilled the minimum accuracy measurement set by ISO 15197:2003 and ISO 15197:2013 standards. In addition, the linear regression analysis revealed that all four selected PoCG overestimated the glucose concentrations. The overall evaluation of the selected four PoCG measurements were poorly correlated with standard reference method. Therefore, before introducing PoCG devices to the market, there should be a standardized evaluation platform for validation. Further similar large-scale studies on other PoCG devices also need to be undertaken.

  3. Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphisms

    Directory of Open Access Journals (Sweden)

    Ramoni Marco F

    2007-03-01

    Full Text Available Abstract Background Recent studies have shown that when individuals are grouped on the basis of genetic similarity, group membership corresponds closely to continental origin. There has been considerable debate about the implications of these findings in the context of larger debates about race and the extent of genetic variation between groups. Some have argued that clustering according to continental origin demonstrates the existence of significant genetic differences between groups and that these differences may have important implications for differences in health and disease. Others argue that clustering according to continental origin requires the use of large amounts of genetic data or specifically chosen markers and is indicative only of very subtle genetic differences that are unlikely to have biomedical significance. Results We used small numbers of randomly selected single nucleotide polymorphisms (SNPs from the International HapMap Project to train naïve Bayes classifiers for prediction of ancestral continent of origin. Predictive accuracy was tested on two independent data sets. Genetically similar groups should be difficult to distinguish, especially if only a small number of genetic markers are used. The genetic differences between continentally defined groups are sufficiently large that one can accurately predict ancestral continent of origin using only a minute, randomly selected fraction of the genetic variation present in the human genome. Genotype data from only 50 random SNPs was sufficient to predict ancestral continent of origin in our primary test data set with an average accuracy of 95%. Genetic variations informative about ancestry were common and widely distributed throughout the genome. Conclusion Accurate characterization of ancestry is possible using small numbers of randomly selected SNPs. The results presented here show how investigators conducting genetic association studies can use small numbers of arbitrarily

  4. [Scrotal temperature in 258 healthy men, randomly selected from a population of men aged 18 to 23 years old. Statistical analysis, epidemiologic observations, and measurement of the testicular diameters].

    Science.gov (United States)

    Valeri, A; Mianné, D; Merouze, F; Bujan, L; Altobelli, A; Masson, J

    1993-06-01

    Scrotal hyperthermia can induce certain alterations in spermatogenesis. The basal scrotal temperature used to define hyperthermia is usually 33 degrees C. However, no study, conducted according to a strict methodology has validated this mean measurement. We therefore randomly selected 258 men between the ages of 18 and 23 years from a population of 2,000 young French men seen at the National Service Selection Centre in order to measure the scrotal temperature over each testis and in the median raphe in order to determine the mean and median values for these temperatures. For a mean room temperature of 23 +/- 0.5 degrees C with a range of 18 to 31 degrees C, the mean right and left scrotal temperature was 34.2 +/- 0.1 degree C and the mean medioscrotal temperature was 34.4 +/- 0.1 degree C. Scrotal temperature was very significantly correlated to room temperature and its variations. It was therefore impossible to define a normal value for scrotal temperature. Only measurement of scrotal temperature at neutral room temperature, between 21 and 25 degrees C, is able to provide a reference value for scrotal temperature. In this study, the mean scrotal temperature under these conditions was 34.4 +/- 0.2 degree C, i.e. 2.5 degrees C less than body temperature. In the 12.9% of cases with left varicocele, left scrotal temperature was significantly higher than in the absence of varicocele and was also higher than right Scrotal temperature. The authors also determined the dimensions of the testes.(ABSTRACT TRUNCATED AT 250 WORDS)

  5. Psychiatric morbidity, quality of life, and perceived social support among elderly population: a community-based study

    Directory of Open Access Journals (Sweden)

    Pallavi Kwan

    2016-01-01

    Full Text Available Background: The growth in the elderly population means an inevitable increase in general physical health, psychobiological and mental health-related problems. Aim of the study: The present study aims to examine psychiatric morbidity, quality of life, and perceived social support among elderly population. Research design: A cross-sectional community-based study was conducted. People in age group of 60 years and above, who were permanent members of their respective households of Ranga Pukri Para and Dekargaon village in Tezpur, Sonitpur district of Assam, were the sample for the present study. One thousand four hundred and ninety adult populations had been identified as sample frame from the electorate list. One hundred and four people of age 60 years and above had been identified from the list for the study purpose. Random sampling method was used for selection of the sample. Semi-structured socio-demographic datasheet, General Health Questionnaire-12 (GHQ-12, CAGE questionnaire, Multidimensional Scale of Perceived Social Support, and World Health Organization Quality of Life (WHOQOL-BREF scale were administered to the respondents. Results: Based on the GHQ-12 score, it was found that 24% of the respondents showed an indication of mental health problems and from the CAGE score, it indicated that 13% of the respondents were found to be misusing or was in dependence in alcohol. The result from the present study indicated that elderly population was getting more family social support, followed by friends and from significant others. The result indicated that the mean score was low in the domain of social relationships. Environment domain was high followed by physical health and psychological domains of WHOQOL-BREF. Conclusion: In the elderly population, overall health can be influenced by multiple factors, including a person’s physical, psychological, behavioural, and social factors. The mental health professionals can provide resources, services

  6. A selective sweep in a Varroa destructor resistant honeybee (Apis mellifera) population.

    Science.gov (United States)

    Lattorff, H Michael G; Buchholz, Josephine; Fries, Ingemar; Moritz, Robin F A

    2015-04-01

    The mite Varroa destructor is one of the most dangerous parasites of the Western honeybee (Apis mellifera) causing enormous colony losses worldwide. Various chemical treatments for the control of the Varroa mite are currently in use, which, however, lead to residues in bee products and often to resistance in mites. This facilitated the exploration of alternative treatment methods and breeding for mite resistant honeybees has been in focus for breeders in many parts of the world with variable results. Another approach has been applied to a honeybee population on Gotland (Sweden) that was exposed to natural selection and survived Varroa-infestation for more than 10years without treatment. Eventually this population became resistant to the parasite by suppressing the reproduction of the mite. A previous QTL mapping study had identified a region on chromosome 7 with major loci contributing to the mite resistance. Here, a microsatellite scan of the significant candidate QTL regions was used to investigate potential footprints of selection in the original population by comparing the study population on Gotland before (2000) and after selection (2007). Genetic drift had caused an extreme loss of genetic diversity in the 2007 population for all genetic markers tested. In addition to this overall reduction of heterozygosity, two loci on chromosome 7 showed an even stronger and significant reduction in diversity than expected from genetic drift alone. Within the selective sweep eleven genes are annotated, one of them being a putative candidate to interfere with reduced mite reproduction. A glucose-methanol-choline oxidoreductase (GMCOX18) might be involved in changing volatiles emitted by bee larvae that might be essential to trigger oogenesis in Varroa. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Public goods games in populations with fluctuating size.

    Science.gov (United States)

    McAvoy, Alex; Fraiman, Nicolas; Hauert, Christoph; Wakeley, John; Nowak, Martin A

    2018-05-01

    Many mathematical frameworks of evolutionary game dynamics assume that the total population size is constant and that selection affects only the relative frequency of strategies. Here, we consider evolutionary game dynamics in an extended Wright-Fisher process with variable population size. In such a scenario, it is possible that the entire population becomes extinct. Survival of the population may depend on which strategy prevails in the game dynamics. Studying cooperative dilemmas, it is a natural feature of such a model that cooperators enable survival, while defectors drive extinction. Although defectors are favored for any mixed population, random drift could lead to their elimination and the resulting pure-cooperator population could survive. On the other hand, if the defectors remain, then the population will quickly go extinct because the frequency of cooperators steadily declines and defectors alone cannot survive. In a mutation-selection model, we find that (i) a steady supply of cooperators can enable long-term population survival, provided selection is sufficiently strong, and (ii) selection can increase the abundance of cooperators but reduce their relative frequency. Thus, evolutionary game dynamics in populations with variable size generate a multifaceted notion of what constitutes a trait's long-term success. Copyright © 2018 Elsevier Inc. All rights reserved.

  8. Efeitos da seleção individual e da seleção baseada no BLUP em populações diferentes, quanto ao tipo de acasalamento Individual selection and selection based on BLUP effects in different populations, according to mating design

    Directory of Open Access Journals (Sweden)

    E.E. Cunha

    2004-02-01

    Full Text Available Dados simulados foram utilizados para avaliar o desempenho da seleção individual e da seleção baseada no melhor preditor linear não-viesado (BLUP, em populações que diferiam entre si, quanto ao tipo de acasalamento, no decorrer de 50 gerações. Estudou-se uma característica quantitativa com herdabilidade igual a 0,10, em populações de 600 indivíduos, que apresentaram a seguinte estrutura: valores de razão sexual (d, de 10 e 50, tamanhos efetivos de população (Ne, de 36,36 e 7,84 e intensidade de seleção dos machos (i m, de 2,23 e 2,82. Em cada valor de d, formaram-se populações correspondentes ao tipo de acasalamento, em todas as gerações: acasalamentos preferenciais de meios-irmãos e irmãos completos, acasalamentos preferenciais entre meios-irmãos, acasalamentos ao acaso, exclusão de acasalamentos entre irmãos completos e exclusão de acasalamentos de meios-irmãos e irmãos completos. As características avaliadas ao longo das gerações foram: valores fenotípicos médios, consangüinidade média, perda percentual por fixação de alelos desfavoráveis e limite da seleção. Observou-se que o BLUP, o tipo de acasalamento, excluindo acasalamentos entre irmãos e a menor razão sexual, juntos, proporcionaram os melhores resultados de valores fenotípicos, durante 45 gerações de seleção. Nessa estratégia de seleção, verificou-se também atraso no número de gerações necessárias para se atingir determinado nível de consangüinidade.The performance of individual selection and of selection based on best linear unbiased prediction (BLUP for simulated data of a low heritability trait (h²=.10 selected for fifty generation in a population of 600 animals with different mating structures were evaluated. The mating structures evaluated were: mating ratio (d of 10 and 50, population size (Ne 36.36 and 7.84 and male selection intensity (i m of 2.23 and 2.82. For each d level half and full sib matings, half sib matings

  9. Predictive Validity of an Empirical Approach for Selecting Promising Message Topics: A Randomized-Controlled Study

    Science.gov (United States)

    Lee, Stella Juhyun; Brennan, Emily; Gibson, Laura Anne; Tan, Andy S. L.; Kybert-Momjian, Ani; Liu, Jiaying; Hornik, Robert

    2016-01-01

    Several message topic selection approaches propose that messages based on beliefs pretested and found to be more strongly associated with intentions will be more effective in changing population intentions and behaviors when used in a campaign. This study aimed to validate the underlying causal assumption of these approaches which rely on cross-sectional belief–intention associations. We experimentally tested whether messages addressing promising themes as identified by the above criterion were more persuasive than messages addressing less promising themes. Contrary to expectations, all messages increased intentions. Interestingly, mediation analyses showed that while messages deemed promising affected intentions through changes in targeted promising beliefs, messages deemed less promising also achieved persuasion by influencing nontargeted promising beliefs. Implications for message topic selection are discussed. PMID:27867218

  10. Population genomic analyses based on 1 million SNPs in commercial egg layers.

    Directory of Open Access Journals (Sweden)

    Mahmood Gholami

    Full Text Available Identifying signatures of selection can provide valuable insight about the genes or genomic regions that are or have been under selective pressure, which can lead to a better understanding of genotype-phenotype relationships. A common strategy for selection signature detection is to compare samples from several populations and search for genomic regions with outstanding genetic differentiation. Wright's fixation index, FST, is a useful index for evaluation of genetic differentiation between populations. The aim of this study was to detect selective signatures between different chicken groups based on SNP-wise FST calculation. A total of 96 individuals of three commercial layer breeds and 14 non-commercial fancy breeds were genotyped with three different 600K SNP-chips. After filtering a total of 1 million SNPs were available for FST calculation. Averages of FST values were calculated for overlapping windows. Comparisons of these were then conducted between commercial egg layers and non-commercial fancy breeds, as well as between white egg layers and brown egg layers. Comparing non-commercial and commercial breeds resulted in the detection of 630 selective signatures, while 656 selective signatures were detected in the comparison between the commercial egg-layer breeds. Annotation of selection signature regions revealed various genes corresponding to productions traits, for which layer breeds were selected. Among them were NCOA1, SREBF2 and RALGAPA1 associated with reproductive traits, broodiness and egg production. Furthermore, several of the detected genes were associated with growth and carcass traits, including POMC, PRKAB2, SPP1, IGF2, CAPN1, TGFb2 and IGFBP2. Our approach demonstrates that including different populations with a specific breeding history can provide a unique opportunity for a better understanding of farm animal selection.

  11. Remote population-based intervention for disruptive behavior at age four: study protocol for a randomized trial of Internet-assisted parent training (Strongest Families Finland-Canada)

    Science.gov (United States)

    2013-01-01

    Background Oppositional Defiant Disorder (ODD) is characterized by angry and noncompliant behaviour. It is the most common disruptive behaviour disorder (DBD), with prevalence estimates of 6-9% for preschoolers and is closely linked to several long-term difficulties, including disorders of conduct, mood, anxiety, impulse-control, and substance abuse. ODD in children is related to parental depression, family dysfunction, and impairments in parental work performance. Children displaying early DBDs exhibit more symptoms of greater severity, more frequent offences, and commit more serious crimes later in life. The goal of the Strongest Families™ Finland Canada (SFFC) Smart Website intervention research program is to develop and evaluate an affordable, accessible, effective secondary prevention parent training program for disruptive behaviour in preschoolers to prevent the negative sequelae of ODD. Strongest Families is an 11-session program with two booster sessions that focuses on teaching skills to: strengthen parent–child relationships; reinforce positive behaviour; reduce conflict; manage daily transitions; plan for potentially problematic situations; promote emotional regulation and pro-social behaviour and decrease antisocial behaviour. Methods/design This protocol paper describes an ongoing population-based randomized controlled trial (RCT) of high-risk 4 year-olds attending well-child clinics in Turku, Finland and environs to examine the effectiveness of the Strongest Families Smart Website intervention compared to an Education Control condition. Randomization consists of a 1:1 ratio for intervention versus the education group, stratified by the child’s sex. The participants randomized to the intervention group receive access to the Strongest Families Smart Website and weekly telephone coaching sessions. The participants randomized to the Education Control condition receive access to a static website with parenting tips. Children are followed using

  12. Remote population-based intervention for disruptive behavior at age four: study protocol for a randomized trial of Internet-assisted parent training (Strongest Families Finland-Canada).

    Science.gov (United States)

    McGrath, Patrick J; Sourander, Andre; Lingley-Pottie, Patricia; Ristkari, Terja; Cunningham, Charles; Huttunen, Jukka; Filbert, Katharine; Aromaa, Minna; Corkum, Penny; Hinkka-Yli-Salomäki, Susanna; Kinnunen, Malin; Lampi, Katja; Penttinen, Anne; Sinokki, Atte; Unruh, Anita; Vuorio, Jenni; Watters, Carolyn

    2013-10-21

    Oppositional Defiant Disorder (ODD) is characterized by angry and noncompliant behaviour. It is the most common disruptive behaviour disorder (DBD), with prevalence estimates of 6-9% for preschoolers and is closely linked to several long-term difficulties, including disorders of conduct, mood, anxiety, impulse-control, and substance abuse. ODD in children is related to parental depression, family dysfunction, and impairments in parental work performance. Children displaying early DBDs exhibit more symptoms of greater severity, more frequent offences, and commit more serious crimes later in life. The goal of the Strongest Families Finland Canada (SFFC) Smart Website intervention research program is to develop and evaluate an affordable, accessible, effective secondary prevention parent training program for disruptive behaviour in preschoolers to prevent the negative sequelae of ODD. Strongest Families is an 11-session program with two booster sessions that focuses on teaching skills to: strengthen parent-child relationships; reinforce positive behaviour; reduce conflict; manage daily transitions; plan for potentially problematic situations; promote emotional regulation and pro-social behaviour and decrease antisocial behaviour. This protocol paper describes an ongoing population-based randomized controlled trial (RCT) of high-risk 4 year-olds attending well-child clinics in Turku, Finland and environs to examine the effectiveness of the Strongest Families Smart Website intervention compared to an Education Control condition. Randomization consists of a 1:1 ratio for intervention versus the education group, stratified by the child's sex. The participants randomized to the intervention group receive access to the Strongest Families Smart Website and weekly telephone coaching sessions. The participants randomized to the Education Control condition receive access to a static website with parenting tips. Children are followed using parental and daycare teacher measures

  13. Hitchhiking and Selective Sweeps of Plasmodium falciparum Sulfadoxine and Pyrimethamine Resistance Alleles in a Population from Central Africa▿ †

    Science.gov (United States)

    McCollum, Andrea M.; Basco, Leonardo K.; Tahar, Rachida; Udhayakumar, Venkatachalam; Escalante, Ananias A.

    2008-01-01

    Sulfadoxine-pyrimethamine (SP) resistance in Plasmodium falciparum is encoded by a number of mutations in the dihydrofolate reductase (dhfr) and dihydropteroate synthetase (dhps) genes. Here, we have characterized point mutations in dhfr and dhps and microsatellite loci around dhfr on chromosome 4 and dhps on chromosome 8 as well as neutral markers on chromosomes 2 and 3 in 332 samples from Yaoundé, Cameroon. The triple mutant dhfr haplotype that originated in Southeast Asia is the most predominant in this sample set, but we also find additional independent haplotypes at low frequency and an incipient process of genetic differentiation among alleles of Southeast Asian origin. As reported for other African populations, we find evidence of a selective sweep for resistant dhfr mutants in this Cameroonian population due to drug selection. Although we find evidence for a selective sweep in dhps mutants associated with SP resistance, the dynamics of dhps mutants appear different than those observed for dhfr mutants. Overall, our results yield support for the use of microsatellite markers to track resistant parasites; however, the detection of resistant dhfr alleles in low frequency, the evidence of divergence among dhfr alleles that share a common evolutionary origin, and the distinct dynamics of resistant dhps alleles emphasize the importance of comprehensive, population-based investigations to evaluate the effects of drug selection on parasite populations. PMID:18765692

  14. Population genomics identifies the origin and signatures of selection of Korean weedy rice

    OpenAIRE

    He, Qiang; Kim, Kyu?Won; Park, Yong?Jin

    2016-01-01

    Summary Weedy rice is the same biological species as cultivated rice (Oryza sativa); it is also a noxious weed infesting rice fields worldwide. Its formation and population?selective or ?adaptive signatures are poorly understood. In this study, we investigated the phylogenetics, population structure and signatures of selection of Korean weedy rice by determining the whole genomes of 30 weedy rice, 30 landrace rice and ten wild rice samples. The phylogenetic tree and results of ancestry infere...

  15. Progressive sampling-based Bayesian optimization for efficient and automatic machine learning model selection.

    Science.gov (United States)

    Zeng, Xueqiang; Luo, Gang

    2017-12-01

    Machine learning is broadly used for clinical data analysis. Before training a model, a machine learning algorithm must be selected. Also, the values of one or more model parameters termed hyper-parameters must be set. Selecting algorithms and hyper-parameter values requires advanced machine learning knowledge and many labor-intensive manual iterations. To lower the bar to machine learning, miscellaneous automatic selection methods for algorithms and/or hyper-parameter values have been proposed. Existing automatic selection methods are inefficient on large data sets. This poses a challenge for using machine learning in the clinical big data era. To address the challenge, this paper presents progressive sampling-based Bayesian optimization, an efficient and automatic selection method for both algorithms and hyper-parameter values. We report an implementation of the method. We show that compared to a state of the art automatic selection method, our method can significantly reduce search time, classification error rate, and standard deviation of error rate due to randomization. This is major progress towards enabling fast turnaround in identifying high-quality solutions required by many machine learning-based clinical data analysis tasks.

  16. Fault Diagnosis for Hydraulic Servo System Using Compressed Random Subspace Based ReliefF

    Directory of Open Access Journals (Sweden)

    Yu Ding

    2018-01-01

    Full Text Available Playing an important role in electromechanical systems, hydraulic servo system is crucial to mechanical systems like engineering machinery, metallurgical machinery, ships, and other equipment. Fault diagnosis based on monitoring and sensory signals plays an important role in avoiding catastrophic accidents and enormous economic losses. This study presents a fault diagnosis scheme for hydraulic servo system using compressed random subspace based ReliefF (CRSR method. From the point of view of feature selection, the scheme utilizes CRSR method to determine the most stable feature combination that contains the most adequate information simultaneously. Based on the feature selection structure of ReliefF, CRSR employs feature integration rules in the compressed domain. Meanwhile, CRSR substitutes information entropy and fuzzy membership for traditional distance measurement index. The proposed CRSR method is able to enhance the robustness of the feature information against interference while selecting the feature combination with balanced information expressing ability. To demonstrate the effectiveness of the proposed CRSR method, a hydraulic servo system joint simulation model is constructed by HyPneu and Simulink, and three fault modes are injected to generate the validation data.

  17. Strong evidence for a genetic contribution to late-onset Alzheimer's disease mortality: a population-based study.

    Directory of Open Access Journals (Sweden)

    John S K Kauwe

    Full Text Available Alzheimer's disease (AD is an international health concern that has a devastating effect on patients and families. While several genetic risk factors for AD have been identified much of the genetic variance in AD remains unexplained. There are limited published assessments of the familiality of Alzheimer's disease. Here we present the largest genealogy-based analysis of AD to date.We assessed the familiality of AD in The Utah Population Database (UPDB, a population-based resource linking electronic health data repositories for the state with the computerized genealogy of the Utah settlers and their descendants. We searched UPDB for significant familial clustering of AD to evaluate the genetic contribution to disease. We compared the Genealogical Index of Familiality (GIF between AD individuals and randomly selected controls and estimated the Relative Risk (RR for a range of family relationships. Finally, we identified pedigrees with a significant excess of AD deaths.The GIF analysis showed that pairs of individuals dying from AD were significantly more related than expected. This excess of relatedness was observed for both close and distant relationships. RRs for death from AD among relatives of individuals dying from AD were significantly increased for both close and more distant relatives. Multiple pedigrees had a significant excess of AD deaths.These data strongly support a genetic contribution to the observed clustering of individuals dying from AD. This report is the first large population-based assessment of the familiality of AD mortality and provides the only reported estimates of relative risk of AD mortality in extended relatives to date. The high-risk pedigrees identified show a true excess of AD mortality (not just multiple cases and are greater in depth and width than published AD pedigrees. The presence of these high-risk pedigrees strongly supports the possibility of rare predisposition variants not yet identified.

  18. Warning signal brightness variation: sexual selection may work under the radar of natural selection in populations of a polytypic poison frog.

    Science.gov (United States)

    Crothers, Laura R; Cummings, Molly E

    2013-05-01

    Though theory predicts consistency of warning signals in aposematic species to facilitate predator learning, variation in these signals often occurs in nature. The strawberry poison frog Dendrobates pumilio is an exceptionally polytypic (populations are phenotypically distinct) aposematic frog exhibiting variation in warning color and brightness. In the Solarte population, males and females both respond differentially to male brightness variation. Here, we demonstrate through spectrophotometry and visual modeling that aposematic brightness variation within this population is likely visible to two putative predators (crabs, snakes) and conspecifics but not to the presumed major predator (birds). This study thus suggests that signal brightness within D. pumilio populations can be shaped by sexual selection, with limited opportunity for natural selection to influence this trait due to predator sensory constraints. Because signal brightness changes can ultimately lead to changes in hue, our findings at the within-population level can provide insights into understanding this polytypism at across-population scales.

  19. Prevalence, Co-Occurrence and Associations with Self-Perceived Health and Limitations Due To Physical Health - A Danish Population-Based Study

    DEFF Research Database (Denmark)

    Eliasen, Marie; Kreiner, Svend; Ebstrup, Jeanette F

    2016-01-01

    ) the associations between the symptoms, and 3) the associations between the somatic symptoms, self-perceived health and limitations due to physical health accounting for the co-occurrence of symptoms. Information on 19 somatic symptoms, self-perceived health and limitations due to physical health was achieved from...... a population-based questionnaire survey of 36,163 randomly selected adults in the Capital Region of Denmark in 2006/07. Chain graph models were used to transparently identify and describe the associations between symptoms, self-perceived health and limitations due to physical health. In total, 94...... all strongly directly associated with both of the outcomes (γ>0.30). Chest pain was strongly associated with self-perceived health, and other musculoskeletal symptoms and urinary retention were strongly associated with limitations due to physical health. Other symptoms were either moderate...

  20. Is alexithymia a risk factor for major depression, personality disorder, or alcohol use disorders? A prospective population-based study.

    Science.gov (United States)

    Honkalampi, Kirsi; Koivumaa-Honkanen, Heli; Lehto, Soili M; Hintikka, Jukka; Haatainen, Kaisa; Rissanen, Teemu; Viinamäki, Heimo

    2010-03-01

    Disagreements concerning the stability of alexithymia and its ability to predict subsequent psychiatric disorders prevail. The aim of this 7-year follow-up study was to examine whether alexithymia predicts subsequent major depression, personality disorder, or alcohol use disorders in a population-based sample. The four-phase Kuopio Depression Study (KUDEP) was conducted in the eastern part of Central Finland. The study population (aged 25-64, n=2050) was randomly selected from the National Population Register. Data were collected in 1998, 1999, and 2001. In 2005, a subsample (n=333, 43 were excluded) of the 3-year follow-up population (1998-2001) was gathered and their diagnoses of mental disorders were confirmed by the Structure Clinical Interview for DSM-IV Axis I (SCID-I). Alexithymia was measured using the Toronto Alexithymia Scale (TAS-20) and depressive symptoms using the Beck Depression Inventory (BDI-21). For both of these measures, two groups were formed based on the median of their sum score (summing the 1998, 1999, and 2001 scores). Logistic regression analyses were performed. BDI sum scores, but not those of TAS, were associated with subsequent major depressive disorder, personality disorder, and alcohol use disorders in 2005. The BDI sum scores explained 35.7% of the variation in concurrent TAS sum scores. Alexithymia did not predict diagnoses of major depressive disorder, personality disorder, or alcohol use disorders. Alexithymia was closely linked to concurrent depressive symptoms. Thus, depressive symptoms may act as a mediator between alexithymia and psychiatric morbidity. Copyright 2010 Elsevier Inc. All rights reserved.

  1. Fuzzy Random λ-Mean SAD Portfolio Selection Problem: An Ant Colony Optimization Approach

    Science.gov (United States)

    Thakur, Gour Sundar Mitra; Bhattacharyya, Rupak; Mitra, Swapan Kumar

    2010-10-01

    To reach the investment goal, one has to select a combination of securities among different portfolios containing large number of securities. Only the past records of each security do not guarantee the future return. As there are many uncertain factors which directly or indirectly influence the stock market and there are also some newer stock markets which do not have enough historical data, experts' expectation and experience must be combined with the past records to generate an effective portfolio selection model. In this paper the return of security is assumed to be Fuzzy Random Variable Set (FRVS), where returns are set of random numbers which are in turn fuzzy numbers. A new λ-Mean Semi Absolute Deviation (λ-MSAD) portfolio selection model is developed. The subjective opinions of the investors to the rate of returns of each security are taken into consideration by introducing a pessimistic-optimistic parameter vector λ. λ-Mean Semi Absolute Deviation (λ-MSAD) model is preferred as it follows absolute deviation of the rate of returns of a portfolio instead of the variance as the measure of the risk. As this model can be reduced to Linear Programming Problem (LPP) it can be solved much faster than quadratic programming problems. Ant Colony Optimization (ACO) is used for solving the portfolio selection problem. ACO is a paradigm for designing meta-heuristic algorithms for combinatorial optimization problem. Data from BSE is used for illustration.

  2. Hypothyroidism and Risk of Mild Cognitive Impairment in Elderly Persons - A Population Based Study

    Science.gov (United States)

    Parsaik, Ajay K; Singh, Balwinder; Roberts, Rosebud O; Pankratz, Shane; Edwards, Kelly K.; Geda, Yonas E; Gharib, H; Boeve, Bradley F; Knopman, David S; Petersen, Ronald C

    2014-01-01

    IMPORTANCE Association of clinical and subclinical hypothyroidism with mild cognitive impairment (MCI) is not established. OBJECTIVE To evaluate the association of clinical and subclinical hypothyroidism with MCI in a large population based cohort. DESIGN A cross-sectional, population-based study. SETTING Olmsted County, Minnesota. PARTICIPANTS Randomly selected participants were aged 70 to 89 years on October 1, 2004, and were without documented prevalent dementia. A total of 2,050 participants were evaluated and underwent in-person interview, neurological evaluation and neuropsychological testing to assess performance in memory, attention/executive function, visuospatial, and language domains. Subjects were diagnosed by consensus as cognitively normal, MCI or dementia according to published criteria. Clinical and subclinical hypothyroidism was ascertained from a medical records-linkage system. MAIN OUTCOME MEASURES Association of clinical and subclinical hypothyroidism with MCI. Results Among 1904 eligible participants, the frequency of MCI was 16% in 1450 subjects with normal thyroid function, 17% in 313 subjects with clinical hypothyroidism, and 18% in 141 subjects with subclinical hypothyroidism. After adjusting for covariates (age, gender, education, education years, sex, ApoE ε 4, depression, diabetes, hypertension, stroke, BMI and coronary artery disease) we found no significant association between clinical or subclinial hypothyroidism and MCI [OR 0.99 (95% CI 0.66–1.48) and OR 0.88 (95% CI 0.38–2.03) respectively]. No effect of gender interaction was seen on these effects. In stratified analysis, the odds of MCI with clinical and subclinical hypothyroidisn among males was 1.02 (95%CI, 0.57–1.82) and 1.29 (95%CI 0.68–2.44), among females was 1.04 (95% 0.66–1.66) and 0.86 (95% CI 0.37–2.02) respectively. Conclusion In this population based cohort of eldery, neither clinical nor subclinical hypothyrpodism was associated with MCI. Our findings

  3. Detecting Signatures of Positive Selection along Defined Branches of a Population Tree Using LSD.

    Science.gov (United States)

    Librado, Pablo; Orlando, Ludovic

    2018-06-01

    Identifying the genomic basis underlying local adaptation is paramount to evolutionary biology, and bears many applications in the fields of conservation biology, crop, and animal breeding, as well as personalized medicine. Although many approaches have been developed to detect signatures of positive selection within single populations and population pairs, the increasing wealth of high-throughput sequencing data requires improved methods capable of handling multiple, and ideally large number of, populations in a single analysis. In this study, we introduce LSD (levels of exclusively shared differences), a fast and flexible framework to perform genome-wide selection scans, along the internal and external branches of a given population tree. We use forward simulations to demonstrate that LSD can identify branches targeted by positive selection with remarkable sensitivity and specificity. We illustrate a range of potential applications by analyzing data from the 1000 Genomes Project and uncover a list of adaptive candidates accompanying the expansion of anatomically modern humans out of Africa and their spread to Europe.

  4. Site selection and evaluation for nuclear power plants with respect to population distribution

    International Nuclear Information System (INIS)

    1980-01-01

    This safety guide, relating population distribution to site selection and evaluation, for nuclear power plants, forms part of the IAEA's programme, referred to as the NUSS programme (Nuclear Safety Standards). The guide presents population distribution data, requirements, examples of site screening methods, and an overview of radiological impact assessment with respect to population distribution

  5. Resolving the Conflict Between Associative Overdominance and Background Selection

    Science.gov (United States)

    Zhao, Lei; Charlesworth, Brian

    2016-01-01

    In small populations, genetic linkage between a polymorphic neutral locus and loci subject to selection, either against partially recessive mutations or in favor of heterozygotes, may result in an apparent selective advantage to heterozygotes at the neutral locus (associative overdominance) and a retardation of the rate of loss of variability by genetic drift at this locus. In large populations, selection against deleterious mutations has previously been shown to reduce variability at linked neutral loci (background selection). We describe analytical, numerical, and simulation studies that shed light on the conditions under which retardation vs. acceleration of loss of variability occurs at a neutral locus linked to a locus under selection. We consider a finite, randomly mating population initiated from an infinite population in equilibrium at a locus under selection. With mutation and selection, retardation occurs only when S, the product of twice the effective population size and the selection coefficient, is of order 1. With S >> 1, background selection always causes an acceleration of loss of variability. Apparent heterozygote advantage at the neutral locus is, however, always observed when mutations are partially recessive, even if there is an accelerated rate of loss of variability. With heterozygote advantage at the selected locus, loss of variability is nearly always retarded. The results shed light on experiments on the loss of variability at marker loci in laboratory populations and on the results of computer simulations of the effects of multiple selected loci on neutral variability. PMID:27182952

  6. Population-based contracting (population health): part II.

    Science.gov (United States)

    Jacofsky, D J

    2017-11-01

    Modern healthcare contracting is shifting the responsibility for improving quality, enhancing community health and controlling the total cost of care for patient populations from payers to providers. Population-based contracting involves capitated risk taken across an entire population, such that any included services within the contract are paid for by the risk-bearing entity throughout the term of the agreement. Under such contracts, a risk-bearing entity, which may be a provider group, a hospital or another payer, administers the contract and assumes risk for contractually defined services. These contracts can be structured in various ways, from professional fee capitation to full global per member per month diagnosis-based risk. The entity contracting with the payer must have downstream network contracts to provide the care and facilities that it has agreed to provide. Population health is a very powerful model to reduce waste and costs. It requires a deep understanding of the nuances of such contracting and the appropriate infrastructure to manage both networks and risk. Cite this article: Bone Joint J 2017;99-B:1431-4. ©2017 The British Editorial Society of Bone & Joint Surgery.

  7. A comparison of two methods for prediction of response and rates of inbreeding in selected populations with the results obtained in two selection experiments

    NARCIS (Netherlands)

    Loywyck, V.; Bijma, P.; Pinard-van der Laan, M.H.; Arendonk, van J.A.M.; Verrier, E.

    2005-01-01

    Selection programmes are mainly concerned with increasing genetic gain. However, short-term progress should not be obtained at the expense of the within-population genetic variability. Different prediction models for the evolution within a small population of the genetic mean of a selected trait,

  8. Stochastic noncooperative and cooperative evolutionary game strategies of a population of biological networks under natural selection.

    Science.gov (United States)

    Chen, Bor-Sen; Yeh, Chin-Hsun

    2017-12-01

    We review current static and dynamic evolutionary game strategies of biological networks and discuss the lack of random genetic variations and stochastic environmental disturbances in these models. To include these factors, a population of evolving biological networks is modeled as a nonlinear stochastic biological system with Poisson-driven genetic variations and random environmental fluctuations (stimuli). To gain insight into the evolutionary game theory of stochastic biological networks under natural selection, the phenotypic robustness and network evolvability of noncooperative and cooperative evolutionary game strategies are discussed from a stochastic Nash game perspective. The noncooperative strategy can be transformed into an equivalent multi-objective optimization problem and is shown to display significantly improved network robustness to tolerate genetic variations and buffer environmental disturbances, maintaining phenotypic traits for longer than the cooperative strategy. However, the noncooperative case requires greater effort and more compromises between partly conflicting players. Global linearization is used to simplify the problem of solving nonlinear stochastic evolutionary games. Finally, a simple stochastic evolutionary model of a metabolic pathway is simulated to illustrate the procedure of solving for two evolutionary game strategies and to confirm and compare their respective characteristics in the evolutionary process. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Evolution in an Afternoon: Rapid Natural Selection and Adaptation of Bacterial Populations

    Science.gov (United States)

    Delpech, Roger

    2009-01-01

    This paper describes a simple, rapid and low-cost technique for growing bacteria (or other microbes) in an environmental gradient, in order to determine the tolerance of the microbial population to varying concentrations of sodium chloride ions, and suggests how the evolutionary response of a microbial population to the selection pressure of the…

  10. Using latent selection difference to model persistence in a declining population.

    Directory of Open Access Journals (Sweden)

    Mara E Erickson

    Full Text Available Population persistence is a direct measure of the viability of a population. Monitoring the distribution of declining populations or subpopulations over time can yield estimates of persistence, which we show can be modeled as a latent selection difference (LSD contrasting attributes of sites where populations have persisted versus those that have not. Predicted persistence can be modeled with predictor covariates to identify factors correlated with species persistence. We demonstrate how to model persistence based on changes in occupancy that can include adjustments for detection probability. Using a known historical distribution of the western grebe (Aechmophorus occidentalis, we adapted methods originally developed for occupancy modeling to evaluate how environmental covariates including emergent vegetation and human developments have affected western grebe persistence in Alberta. The relative probability of persistence was correlated with the extent of shoreline bulrush (Scirpus lacustris, which is important vegetation for nesting cover. We also documented that western grebe populations were less likely to persist on lakes in the boreal forest, primarily located on the northern boundary of the species' range. Factors influencing occupancy were different than those determining persistence by western grebes; persistence and occupancy were not correlated. Persistence was more likely on lakes with recreational development, reflecting reliance by grebes on the larger, fish-bearing waterbodies that also are attractive for lakeshore development. Unfortunately, the correlation with recreational development on Alberta's lakes puts grebes at risk for loss of brood-rearing habitats--primary threats to altricial birds--if steps are not taken to prevent disturbance to bulrush stands. Identifying factors related to the persistence of a species--especially one in decline--is a fundamental step in conservation management.

  11. Association of zolpidem use and subsequent increased risk of epilepsy: a population-based, case-control study.

    Science.gov (United States)

    Harnod, Tomor; Wang, Yu-Chiao; Sung, Fung-Chang; Kao, Chia-Hung

    2014-10-01

    To evaluate the impact of long-term zolpidem use on the subsequent risk of epilepsy. We used data from the National Health Insurance system of Taiwan to conduct a population-based case-control study. We identified 4,972 newly diagnosed epilepsy patients (ICD-9-CM code 345) for the period of 2005-2010 as cases. For each epilepsy case, 4 controls without a history of epilepsy were randomly selected from the rest of the population. Zolpidem was used as a predictor of epilepsy. Patients with epilepsy exhibited an adjusted odds ratio (OR) of 1.86 (95% CI, 1.70-2.03) and were, therefore, more strongly associated with zolpidem exposure than control patients were. The adjusted OR of epilepsy increased with the increase of mean zolpidem exposure (g/y). Compared with the OR of nonusers, the adjusted OR was 1.64 (95% CI, 1.44-1.86) for those who had taken zolpidem and 2.38 (95% CI, 2.06-2.74) for those who had taken ≥ 20.0 g/y of zolpidem. An adjusted OR of 3.55 (95% CI, 2.94-4.28) was noted to be associated with epilepsy when users had stopped taking the drug less than 7 days earlier. The estimated risk declined to an OR of 1.62 (95% CI, 1.47-1.78) when users had stopped taking the drug more than 90 days earlier. This population-based, retrospective case-control study revealed a possible increase in epilepsy risk with zolpidem use, at either typical or supratherapeutic doses. These findings might stimulate public interest in safety issues regarding zolpidem use. © Copyright 2014 Physicians Postgraduate Press, Inc.

  12. Association between Kawasaki Disease and Autism: A Population-Based Study in Taiwan

    Directory of Open Access Journals (Sweden)

    Ho-Chang Kuo

    2014-04-01

    Full Text Available Objective: The association between Kawasaki disease and autism has rarely been studied in Asian populations. By using a nationwide Taiwanese population-based claims database, we tested the hypothesis that Kawasaki disease may increase the risk of autism in Taiwan. Materials and Methods: Our study cohort consisted of patients who had received the diagnosis of Kawasaki disease (ICD-9-CM: 446.1 between 1997 and 2005 (N = 563. For a comparison cohort, five age- and gender-matched control patients for every patient in the study cohort were selected using random sampling (N = 2,815. All subjects were tracked for 5 years from the date of cohort entry to identify whether they had developed autism (ICD-9-CM code 299.0 or not. Cox proportional hazard regressions were then performed to evaluate 5-year autism-free survival rates. Results: The main finding of this study was that patients with Kawasaki disease seem to not be at increased risk of developing autism. Of the total patients, four patients developed autism during the 5-year follow-up period, among whom two were Kawasaki disease patients and two were in the comparison cohort. Further, the adjusted hazard ratios (AHR (AHR: 4.81; 95% confidence interval: 0.68–34.35; P = 0.117 did not show any statistical significance between the Kawasaki disease group and the control group during the 5-year follow-up. Conclusion: Our study indicated that patients with Kawasaki disease are not at increased risk of autism.

  13. Thyroid Antibodies, Autoimmunity and Cognitive Decline: Is There a Population-Based Link

    Directory of Open Access Journals (Sweden)

    Kate Napthali

    2014-05-01

    Full Text Available Background: Autoimmunity is considered an uncommon but under-recognised cause of cognitive decline. Methods: Serum samples from 3,253 randomly selected subjects enrolled in the Hunter Community Study, aged 55-85 years, were assayed for thyrotropin stimulatory hormone, anti-thyroid peroxidase antibodies (TPO-Ab, anti-nuclear antibodies (ANA and extractable nuclear antigens (ENA. Cognitive function was assessed using the Audio Recorded Cognitive Screen (ARCS tool. Results: TPO-Ab were found in 8.4% and ANA in 27.9% of the study population, of whom 3% had positive ENA findings. No relationship was found between the ARCS score and either TPO-Ab (coefficient = 0.133; 95% CI -0.20, 0.82, p = 0.616, ANA at a low (coefficient = 1.01; 95% CI -2.58, 0.55, p = 0.203 or a high titre (coefficient = -0.65; 95% CI -2.59, 1.28, p = 0.508, or ENA antibodies (coefficient = 5.12; 95% CI -0.53, 10.77; p = 0.076. Conclusions: Autoantibody findings are common in an aging population and are not associated with cognitive decline.

  14. Towards a pro-health food-selection model for gatekeepers in ...

    African Journals Online (AJOL)

    The purpose of this study was to develop a pro-health food selection model for gatekeepers of Bulawayo high-density suburbs in Zimbabwe. Gatekeepers in five suburbs constituted the study population from which a sample of 250 subjects was randomly selected. Of the total respondents (N= 182), 167 had their own ...

  15. Factors Associated with High Use of a Workplace Web-Based Stress Management Program in a Randomized Controlled Intervention Study

    Science.gov (United States)

    Hasson, H.; Brown, C.; Hasson, D.

    2010-01-01

    In web-based health promotion programs, large variations in participant engagement are common. The aim was to investigate determinants of high use of a worksite self-help web-based program for stress management. Two versions of the program were offered to randomly selected departments in IT and media companies. A static version of the program…

  16. Effects of the Ordering of Natural Selection and Population Regulation Mechanisms on Wright-Fisher Models.

    Science.gov (United States)

    He, Zhangyi; Beaumont, Mark; Yu, Feng

    2017-07-05

    We explore the effect of different mechanisms of natural selection on the evolution of populations for one- and two-locus systems. We compare the effect of viability and fecundity selection in the context of the Wright-Fisher model with selection under the assumption of multiplicative fitness. We show that these two modes of natural selection correspond to different orderings of the processes of population regulation and natural selection in the Wright-Fisher model. We find that under the Wright-Fisher model these two different orderings can affect the distribution of trajectories of haplotype frequencies evolving with genetic recombination. However, the difference in the distribution of trajectories is only appreciable when the population is in significant linkage disequilibrium. We find that as linkage disequilibrium decays the trajectories for the two different models rapidly become indistinguishable. We discuss the significance of these findings in terms of biological examples of viability and fecundity selection, and speculate that the effect may be significant when factors such as gene migration maintain a degree of linkage disequilibrium. Copyright © 2017 He et al.

  17. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    Energy Technology Data Exchange (ETDEWEB)

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMcahon, Katherine D.; Mamlstrom, Rex R.

    2014-05-12

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ecotype model? of diversification, but not previously observed in natural populations.

  18. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    Energy Technology Data Exchange (ETDEWEB)

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMahon, Katherine D.; Malmstrom, Rex R.

    2014-06-18

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ‘ecotype model’ of diversification, but not previously observed in natural populations.

  19. Host population structure and treatment frequency maintain balancing selection on drug resistance

    Science.gov (United States)

    Baskerville, Edward B.; Colijn, Caroline; Hanage, William; Fraser, Christophe; Lipsitch, Marc

    2017-01-01

    It is a truism that antimicrobial drugs select for resistance, but explaining pathogen- and population-specific variation in patterns of resistance remains an open problem. Like other common commensals, Streptococcus pneumoniae has demonstrated persistent coexistence of drug-sensitive and drug-resistant strains. Theoretically, this outcome is unlikely. We modelled the dynamics of competing strains of S. pneumoniae to investigate the impact of transmission dynamics and treatment-induced selective pressures on the probability of stable coexistence. We find that the outcome of competition is extremely sensitive to structure in the host population, although coexistence can arise from age-assortative transmission models with age-varying rates of antibiotic use. Moreover, we find that the selective pressure from antibiotics arises not so much from the rate of antibiotic use per se but from the frequency of treatment: frequent antibiotic therapy disproportionately impacts the fitness of sensitive strains. This same phenomenon explains why serotypes with longer durations of carriage tend to be more resistant. These dynamics may apply to other potentially pathogenic, microbial commensals and highlight how population structure, which is often omitted from models, can have a large impact. PMID:28835542

  20. A genomic portrait of haplotype diversity and signatures of selection in indigenous southern African populations.

    Directory of Open Access Journals (Sweden)

    Emile R Chimusa

    2015-03-01

    Full Text Available We report a study of genome-wide, dense SNP (∼ 900K and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between indigenous San, Niger-Congo-speaking and populations of Eurasian ancestry. This finding illustrates the need to account for stratification in genome-wide association studies, and that admixture mapping would likely be a successful approach in these populations. We developed a strategy to detect the signature of selection prior to and following putative admixture events. Several genomic regions show an unusual excess of Niger-Kordofanian, and unusual deficiency of both San and Eurasian ancestry, which were considered the footprints of selection after population admixture. Several SNPs with strong allele frequency differences were observed predominantly between the admixed indigenous southern African populations, and their ancestral Eurasian populations. Interestingly, many candidate genes, which were identified within the genomic regions showing signals for selection, were associated with southern African-specific high-risk, mostly communicable diseases, such as malaria, influenza, tuberculosis, and human immunodeficiency virus/AIDs. This observation suggests a potentially important role that these genes might have played in adapting to the environment. Additionally, our analyses of haplotype structure, linkage disequilibrium, recombination, copy number variation and genome-wide admixture highlight, and support the unique position of San relative to both African and non-African populations. This study contributes to a better understanding of population ancestry and selection in south-eastern African populations; and the data and results obtained will support research into the genetic contributions to infectious as well as non-communicable diseases in the region.

  1. A genomic portrait of haplotype diversity and signatures of selection in indigenous southern African populations.

    Science.gov (United States)

    Chimusa, Emile R; Meintjies, Ayton; Tchanga, Milaine; Mulder, Nicola; Seoighe, Cathal; Seioghe, Cathal; Soodyall, Himla; Ramesar, Rajkumar

    2015-03-01

    We report a study of genome-wide, dense SNP (∼ 900K) and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between indigenous San, Niger-Congo-speaking and populations of Eurasian ancestry. This finding illustrates the need to account for stratification in genome-wide association studies, and that admixture mapping would likely be a successful approach in these populations. We developed a strategy to detect the signature of selection prior to and following putative admixture events. Several genomic regions show an unusual excess of Niger-Kordofanian, and unusual deficiency of both San and Eurasian ancestry, which were considered the footprints of selection after population admixture. Several SNPs with strong allele frequency differences were observed predominantly between the admixed indigenous southern African populations, and their ancestral Eurasian populations. Interestingly, many candidate genes, which were identified within the genomic regions showing signals for selection, were associated with southern African-specific high-risk, mostly communicable diseases, such as malaria, influenza, tuberculosis, and human immunodeficiency virus/AIDs. This observation suggests a potentially important role that these genes might have played in adapting to the environment. Additionally, our analyses of haplotype structure, linkage disequilibrium, recombination, copy number variation and genome-wide admixture highlight, and support the unique position of San relative to both African and non-African populations. This study contributes to a better understanding of population ancestry and selection in south-eastern African populations; and the data and results obtained will support research into the genetic contributions to infectious as well as non-communicable diseases in the region.

  2. Random forest variable selection in spatial malaria transmission modelling in Mpumalanga Province, South Africa

    Directory of Open Access Journals (Sweden)

    Thandi Kapwata

    2016-11-01

    Full Text Available Malaria is an environmentally driven disease. In order to quantify the spatial variability of malaria transmission, it is imperative to understand the interactions between environmental variables and malaria epidemiology at a micro-geographic level using a novel statistical approach. The random forest (RF statistical learning method, a relatively new variable-importance ranking method, measures the variable importance of potentially influential parameters through the percent increase of the mean squared error. As this value increases, so does the relative importance of the associated variable. The principal aim of this study was to create predictive malaria maps generated using the selected variables based on the RF algorithm in the Ehlanzeni District of Mpumalanga Province, South Africa. From the seven environmental variables used [temperature, lag temperature, rainfall, lag rainfall, humidity, altitude, and the normalized difference vegetation index (NDVI], altitude was identified as the most influential predictor variable due its high selection frequency. It was selected as the top predictor for 4 out of 12 months of the year, followed by NDVI, temperature and lag rainfall, which were each selected twice. The combination of climatic variables that produced the highest prediction accuracy was altitude, NDVI, and temperature. This suggests that these three variables have high predictive capabilities in relation to malaria transmission. Furthermore, it is anticipated that the predictive maps generated from predictions made by the RF algorithm could be used to monitor the progression of malaria and assist in intervention and prevention efforts with respect to malaria.

  3. Neutral Theory: From Complex Population History to Natural Selection and Sociocultural Phenomena in Human Populations.

    Science.gov (United States)

    Austerlitz, Frédéric; Heyer, Evelyne

    2018-06-01

    Here, we present a synthetic view on how Kimura's Neutral theory has helped us gaining insight on the different evolutionary forces that shape human evolution. We put this perspective in the frame of recent emerging challenges: the use of whole genome data for reconstructing population histories, natural selection on complex polygenic traits, and integrating cultural processes in human evolution.

  4. Fairness and Trust in Structured Populations

    Directory of Open Access Journals (Sweden)

    Corina E. Tarnita

    2015-07-01

    Full Text Available Classical economic theory assumes that people are rational and selfish, but behavioral experiments often point to inconsistent behavior, typically attributed to “other regarding preferences.” The Ultimatum Game, used to study fairness, and the Trust Game, used to study trust and trustworthiness, have been two of the most influential and well-studied examples of inconsistent behavior. Recently, evolutionary biologists have attempted to explain the evolution of such preferences using evolutionary game theoretic models. While deterministic evolutionary game theoretic models agree with the classical economics predictions, recent stochastic approaches that include uncertainty and the possibility of mistakes have been successful in accounting for both the evolution of fairness and the evolution of trust. Here I explore the role of population structure by generalizing and expanding these existing results to the case of non-random interactions. This is a natural extension since such interactions do not occur randomly in the daily lives of individuals. I find that, in the limit of weak selection, population structure increases the space of fair strategies that are selected for but it has little-to-no effect on the optimum strategy played in the Ultimatum Game. In the Trust Game, in the limit of weak selection, I find that some amount of trust and trustworthiness can evolve even in a well-mixed population; however, the optimal strategy, although trusting if the return on investment is sufficiently high, is never trustworthy. Population structure biases selection towards strategies that are both trusting and trustworthy trustworthy and reduces the critical return threshold, but, much like in the case of fairness, it does not affect the winning strategy. Further considering the effects of reputation and structure, I find that they act synergistically to promote the evolution of trustworthiness.

  5. Genome-wide scans between two honeybee populations reveal putative signatures of human-mediated selection.

    Science.gov (United States)

    Parejo, M; Wragg, D; Henriques, D; Vignal, A; Neuditschko, M

    2017-12-01

    Human-mediated selection has left signatures in the genomes of many domesticated animals, including the European dark honeybee, Apis mellifera mellifera, which has been selected by apiculturists for centuries. Using whole-genome sequence information, we investigated selection signatures in spatially separated honeybee subpopulations (Switzerland, n = 39 and France, n = 17). Three different test statistics were calculated in windows of 2 kb (fixation index, cross-population extended haplotype homozygosity and cross-population composite likelihood ratio) and combined into a recently developed composite selection score. Applying a stringent false discovery rate of 0.01, we identified six significant selective sweeps distributed across five chromosomes covering eight genes. These genes are associated with multiple molecular and biological functions, including regulation of transcription, receptor binding and signal transduction. Of particular interest is a selection signature on chromosome 1, which corresponds to the WNT4 gene, the family of which is conserved across the animal kingdom with a variety of functions. In Drosophila melanogaster, WNT4 alleles have been associated with differential wing, cross vein and abdominal phenotypes. Defining phenotypic characteristics of different Apis mellifera ssp., which are typically used as selection criteria, include colour and wing venation pattern. This signal is therefore likely to be a good candidate for human mediated-selection arising from different applied breeding practices in the two managed populations. © 2017 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.

  6. Pareto genealogies arising from a Poisson branching evolution model with selection.

    Science.gov (United States)

    Huillet, Thierry E

    2014-02-01

    We study a class of coalescents derived from a sampling procedure out of N i.i.d. Pareto(α) random variables, normalized by their sum, including β-size-biasing on total length effects (β Poisson-Dirichlet (α, -β) Ξ-coalescent (α ε[0, 1)), or to a family of continuous-time Beta (2 - α, α - β)Λ-coalescents (α ε[1, 2)), or to the Kingman coalescent (α ≥ 2). We indicate that this class of coalescent processes (and their scaling limits) may be viewed as the genealogical processes of some forward in time evolving branching population models including selection effects. In such constant-size population models, the reproduction step, which is based on a fitness-dependent Poisson Point Process with scaling power-law(α) intensity, is coupled to a selection step consisting of sorting out the N fittest individuals issued from the reproduction step.

  7. Multistage Selection and the Financing of New Ventures

    OpenAIRE

    Jonathan T. Eckhardt; Scott Shane; Frédéric Delmar

    2006-01-01

    Using a random sample of 221 new Swedish ventures initiated in 1998, we examine why some new ventures are more likely than others to successfully be awarded capital from external sources. We examine venture financing as a staged selection process in which two sequential selection events systematically winnow the population of ventures and influence which ventures receive financing. For a venture to receive external financing its founders must first select it as a candidate for external fundin...

  8. Two-Year Outcomes of a Population-Based Intervention for Preschool Language Delay: An RCT.

    Science.gov (United States)

    Wake, Melissa; Levickis, Penny; Tobin, Sherryn; Gold, Lisa; Ukoumunne, Obioha C; Goldfeld, Sharon; Zens, Naomi; Le, Ha N D; Law, James; Reilly, Sheena

    2015-10-01

    We have previously shown short-term benefits to phonology, letter knowledge, and possibly expressive language from systematically ascertaining language delay at age 4 years followed by the Language for Learning intervention. Here, we report the trial's definitive 6-year outcomes. Randomized trial nested in a population-based ascertainment. Children with language scores >1.25 SD below the mean at age 4 were randomized, with intervention children receiving 18 1-hour home-based therapy sessions. Primary outcome was receptive/expressive language. Secondary outcomes were phonological, receptive vocabulary, literacy, and narrative skills; parent-reported pragmatic language, behavior, and health-related quality of life; costs of intervention; and health service use. For intention-to-treat analyses, trial arms were compared using linear regression models. Of 1464 children assessed at age 4, 266 were eligible and 200 randomized; 90% and 82% of intervention and control children were retained respectively. By age 6, mean language scores had normalized, but there was little evidence of a treatment effect for receptive (adjusted mean difference 2.3; 95% confidence interval [CI] -1.2 to 5.7; P = .20) or expressive (0.8; 95% CI -1.6 to 3.2; P = .49) language. Of the secondary outcomes, only phonological awareness skills (effect size 0.36; 95% CI 0.08-0.65; P = .01) showed benefit. Costs were higher for intervention families (mean difference AU$4276; 95% CI: $3424 to $5128). Population-based intervention targeting 4-year-old language delay was feasible but did not have lasting impacts on language, possibly reflecting resolution in both groups. Long-term literacy benefits remain possible but must be weighed against its cost. Copyright © 2015 by the American Academy of Pediatrics.

  9. Modeling the effects of trophy selection and environmental disturbance on a simulated population of African lions.

    Science.gov (United States)

    Whitman, Karyl L; Starfield, Anthony M; Quadling, Henley; Packer, Craig

    2007-06-01

    Tanzania is a premier destination for trophy hunting of African lions (Panthera leo) and is home to the most extensive long-term study of unhunted lions. Thus, it provides a unique opportunity to apply data from a long-term field study to a conservation dilemma: How can a trophy-hunted species whose reproductive success is closely tied to social stability be harvested sustainably? We used an individually based, spatially explicit, stochastic model, parameterized with nearly 40 years of behavioral and demographic data on lions in the Serengeti, to examine the separate effects of trophy selection and environmental disturbance on the viability of a simulated lion population in response to annual harvesting. Female population size was sensitive to the harvesting of young males (> or = 3 years), whereas hunting represented a relatively trivial threat to population viability when the harvest was restricted to mature males (> or = 6 years). Overall model performance was robust to environmental disturbance and to errors in age assessment based on nose coloration as an index used to age potential trophies. Introducing an environmental disturbance did not eliminate the capacity to maintain a viable breeding population when harvesting only older males, and initially depleted populations recovered within 15-25 years after the disturbance to levels comparable to hunted populations that did not experience a catastrophic event. These results are consistent with empirical observations of lion resilience to environmental stochasticity.

  10. The value of cows in reference populations for genomic selection of new functional traits

    DEFF Research Database (Denmark)

    Buch, Line Hjortø; Kargo, Morten; Berg, Peer

    2012-01-01

    Today, almost all reference populations consist of progeny tested bulls. However, older progeny tested bulls do not have reliable estimated breeding values (EBV) for new traits. Thus, to be able to select for these new traits, it is necessary to build a reference population. We used a deterministic...... of the direct genomic values (DGV) for a new functional trait, regardless of its heritability. For small-scale recording, we compared two scenarios where the reference population consisted of the 2000 cows with phenotypic records or the 30 sires of these cows in the first year with measurements of the new...... to achieve accuracies of the DGV that enable selection for new functional traits recorded on a large scale within 3 years from commencement of recording; and (iv) a higher heritability benefits a reference population of cows more than a reference population of bulls....

  11. Knowledge and attitude towards total knee arthroplasty among the public in Saudi Arabia: a nationwide population-based study.

    Science.gov (United States)

    Al-Mohrej, Omar A; Alshammari, Faris O; Aljuraisi, Abdulrahman M; Bin Amer, Lujain A; Masuadi, Emad M; Al-Kenani, Nader S

    2018-04-01

    Studies on total knee arthroplasty (TKA) in Saudi Arabia are scarce, and none have reported the knowledge and attitude of the procedure in Saudi Arabia. Our study aims to measure the knowledge and attitude of TKA among the adult Saudi population. To encompass a representative sample of this cross-sectional survey, all 13 administrative areas were used as ready-made geographical clusters. For each cluster, stratified random sampling was performed to maximize participation in the study. In each area, random samples of mobile phone numbers were selected with a probability proportional to the administrative area population size. Sample size calculation was based on the assumption that 50% of the participants would have some level of knowledge, with a 2% margin of error and 95% confidence level. To reach our intended sample size of 1540, we contacted 1722 participants with a response rate of 89.4%. The expected percentage of public knowledge was 50%; however, the actual percentage revealed by this study was much lower (29.7%). A stepwise multiple logistic regression was used to assess the factors that positively affected the knowledge score regarding TKA. Age [P = 0.016 with OR of 0.47], higher income [P = 0.001 with OR of 0.52] and participants with a positive history of TKA or that have known someone who underwent the surgery [P Saudi Arabia concerning TKA, its indications and results. We recommend that doctors use the results of our survey to assess their conversations with their patients, and to determine whether the results of the procedure are adequately clarified.

  12. Nasal morphological characteristics of the Serbian population

    OpenAIRE

    Jovanović J.; Jeremić D.; Jovanović B.; Vulović Maja; Sazdanović P.; Sazdanović Maja; Ognjanović Neda; Stojadinović D.; Jeremić Katarina; Marković N.; Živanović-Mačužić Ivana

    2014-01-01

    The aim of this study was to determine the nasal parameters in the population of central Serbia and to compare them with those determined in earlier studies in different populations. The research was conducted on 496 randomly selected persons (262 males and 234 females), aged 18-65 years. The measured parameters were nasal height and nasal breadth and the standard spreading caliper with scale was used for measurements. There were significant differences in ...

  13. [Medication use among community-dwelling older Icelanders. Population-based study in urban and rural areas].

    Science.gov (United States)

    Sigurdardottir, Arun K; Arnadottir, Solveig Asa; Gunnarsdottir, Elín Díanna

    2011-12-01

    To describe medication use among older community-dwelling Icelanders by collecting information on number of medicine, polypharmacy (>5 medications), and medications by ATC categories. Moreover, to explore the relationship between medication use and various influential factors emphasizing residency in urban and rural areas. Population-based, cross-sectional study. Participants were randomly selected from the National registry in one urban (n=118) and two rural (n=68) areas. 1) ≥ 65 years old, 2) community-dwelling, 3) able to communicate verbally. Information on medication use was obtained from each person's medication list and interviews. A questionnaire and five standardized instruments were used to assess the potential influencing factors. On average, participants used 3.9 medications and prevalence of polypharmacy was 41%. Men used 3.5 medications on average and women 4.4 (p=0.018). Compared to rural residents, urban residents had fewer medical diagnoses, better mobility, less pain, and fewer depressive symptoms. By controlling for the effects of these variables, more medications were associated with urban living (pbetter scores on health assessments.

  14. A web- and mobile phone-based intervention to prevent obesity in 4-year-olds (MINISTOP): a population-based randomized controlled trial

    OpenAIRE

    Delisle, Christine; Sandin, Sven; Forsum, Elisabet; Henriksson, Hanna; Trolle-Lagerros, Ylva; Larsson, Christel; Maddison, Ralph; Ortega, Francisco B.; Ruiz, Jonatan R.; Silfvernagel, Kristin; Timpka, Toomas; Löf, Marie

    2015-01-01

    Background: Childhood obesity is an increasing health problem globally. Overweight and obesity may be established as early as 2-5 years of age, highlighting the need for evidence-based effective prevention and treatment programs early in life. In adults, mobile phone based interventions for weight management (mHealth) have demonstrated positive effects on body mass, however, their use in child populations has yet to be examined. The aim of this paper is to report the study design and methodol...

  15. Prevalence and risk factors associated with dry eye symptoms: a population based study in Indonesia

    Science.gov (United States)

    Lee, A J; Lee, J; Saw, S-M; Gazzard, G; Koh, D; Widjaja, D; Tan, D T H

    2002-01-01

    Aim: To determine the prevalence and identify associated risk factors for dry eye syndrome in a population in Sumatra, Indonesia. Methods: A one stage cluster sampling procedure was conducted to randomly select 100 households in each of the five rural villages and one provincial town of the Riau province, Indonesia, from April to June 2001. Interviewers collected demographic, lifestyle, and medical data from 1058 participants aged 21 years or over. Symptoms of dry eye were assessed using a six item validated questionnaire. Presence of one or more of the six dry eye symptoms often or all the time was analysed. Presence of pterygium was documented. Results: Prevalence of one or more of the six dry eye symptoms often or all the time adjusted for age was 27.5% (95% confidence interval (CI) 24.8 to 30.2). After adjusting for all significant variables, independent risk factors for dry eye were pterygium (p<0.001, multivariate odds ratio (OR) 1.8; 95% CI 1.4 to 2.5) and a history of current cigarette smoking (p=0.05, multivariate OR 1.5; 95% CI 1.0 to 2.2). Conclusions: This population based study provides prevalence rates of dry eye symptoms in a tropical developing nation. From our findings, pterygium is a possible independent risk factor for dry eye symptoms. PMID:12446361

  16. Increasing prevalence and high incidence of celiac disease in elderly people: A population-based study

    Directory of Open Access Journals (Sweden)

    Vilppula Anitta

    2009-06-01

    Full Text Available Abstract Background Celiac disease may emerge at any age, but little is known of its appearance in elderly people. We evaluated the prevalence of the condition in individuals over 55 years of age, and determined the incidence of biopsy-proven celiac disease (CDb and celiac disease including seropositive subjects for anti-tissue transglutaminase antibodies (CDb+s. Methods The study based on prevalence figures in 2815 randomly selected subjects who had undergone a clinical examination and serologic screening for celiac disease in 2002. A second screening in the same population was carried out in 2005, comprising now 2216 individuals. Positive tissue transglutaminase antibodies were confirmed with small bowel biopsy. Results Within three years the prevalence of CDb increased from 2.13 to 2.34%, and that of CDb+s from 2.45 to 2.70%. Five new cases were found among patients previously seronegative; two had minor abdominal symptoms and three were asymptomatic. The incidence of celiac disease in 2002–2005 was 0.23%, giving an annual incidence of 0.08% in this population. Conclusion The prevalence of celiac disease was high in elderly people, but the symptoms were subtle. Repeated screening detected five biopsy-proven cases in three years, indicating that the disorder may develop even in the elderly. Increased alertness to the disorder is therefore warranted.

  17. Combined impact of negative lifestyle factors on cardiovascular risk in children: a randomized prospective study

    OpenAIRE

    Meyer, Ursina; Schindler, Christian; Bloesch, Tamara; Schmocker, Eliane; Zahner, Lukas; Puder, Jardena J; Kriemler, Susi

    2014-01-01

    PURPOSE: Negative lifestyle factors are known to be associated with increased cardiovascular risk (CVR) in children, but research on their combined impact on a general population of children is sparse. Therefore, we aimed to quantify the combined impact of easily assessable negative lifestyle factors on the CVR scores of randomly selected children after 4 years. METHODS: Of the 540 randomly selected 6- to 13-year-old children, 502 children participated in a baseline health assessment, and ...

  18. Sequence-Based Prediction of RNA-Binding Proteins Using Random Forest with Minimum Redundancy Maximum Relevance Feature Selection

    Directory of Open Access Journals (Sweden)

    Xin Ma

    2015-01-01

    Full Text Available The prediction of RNA-binding proteins is one of the most challenging problems in computation biology. Although some studies have investigated this problem, the accuracy of prediction is still not sufficient. In this study, a highly accurate method was developed to predict RNA-binding proteins from amino acid sequences using random forests with the minimum redundancy maximum relevance (mRMR method, followed by incremental feature selection (IFS. We incorporated features of conjoint triad features and three novel features: binding propensity (BP, nonbinding propensity (NBP, and evolutionary information combined with physicochemical properties (EIPP. The results showed that these novel features have important roles in improving the performance of the predictor. Using the mRMR-IFS method, our predictor achieved the best performance (86.62% accuracy and 0.737 Matthews correlation coefficient. High prediction accuracy and successful prediction performance suggested that our method can be a useful approach to identify RNA-binding proteins from sequence information.

  19. Randomizing Roaches: Exploring the "Bugs" of Randomization in Experimental Design

    Science.gov (United States)

    Wagler, Amy; Wagler, Ron

    2014-01-01

    Understanding the roles of random selection and random assignment in experimental design is a central learning objective in most introductory statistics courses. This article describes an activity, appropriate for a high school or introductory statistics course, designed to teach the concepts, values and pitfalls of random selection and assignment…

  20. OCCUPATION AND EPICONDYLITIS: A POPULATION-BASED STUDY

    Science.gov (United States)

    Walker-Bone, Karen; Palmer, Keith T; Reading, Isabel C; Coggon, David; Cooper, Cyrus

    2012-01-01

    Objectives To explore the relationship between occupational exposures and lateral and medial epicondylitis and the effect of epicondylitis on sickness absence in a population sample of working aged adults. Methods This was a cross-sectional study of 9696 randomly selected adults aged 25-64 years involving a screening questionnaire and standardised physical examination. Age- and sex-specific prevalence rates of epicondylitis were estimated and associations with occupational risk factors explored. Results Among 6038 respondents, 636 (11%) reported elbow pain in the last week. 0.7% of those surveyed were diagnosed with lateral epicondylitis and 0.6% with medial epicondylitis. Lateral epicondylitis was associated with manual work (OR 4.0, 95% CI 1.9-8.4). In multivariate analyses, repetitive bending/straightening elbow > 1 hour day was independently associated with lateral (OR 2.5, 95% CI 1.2-5.5) and medial epicondylitis (OR 5.1, 95% CI 1.8-14.3). 5% of adults with epicondylitis took sickness absence because of their elbow symptoms in the past 12 months (median 29 days). Conclusions Repetitive exposure to bending/straightening the elbow was a significant risk factor for medial and lateral epicondylitis. Epicondylitis is associated with prolonged sickness absence in 5% of affected working-aged adults. PMID:22019808

  1. Population-based screening versus case detection.

    Directory of Open Access Journals (Sweden)

    Thomas Ravi

    2002-01-01

    Full Text Available India has a large burden of blindness and population-based screening is a strategy commonly employed to detect disease and prevent morbidity. However, not all diseases are amenable to screening. This communication examines the issue of "population-based screening" versus "case detection" in the Indian scenario. Using the example of glaucoma, it demonstrates that given the poor infrastructure, for a "rare" disease, case detection is more effective than population-based screening.

  2. Prediction of residential radon exposure of the whole Swiss population: comparison of model-based predictions with measurement-based predictions.

    Science.gov (United States)

    Hauri, D D; Huss, A; Zimmermann, F; Kuehni, C E; Röösli, M

    2013-10-01

    Radon plays an important role for human exposure to natural sources of ionizing radiation. The aim of this article is to compare two approaches to estimate mean radon exposure in the Swiss population: model-based predictions at individual level and measurement-based predictions based on measurements aggregated at municipality level. A nationwide model was used to predict radon levels in each household and for each individual based on the corresponding tectonic unit, building age, building type, soil texture, degree of urbanization, and floor. Measurement-based predictions were carried out within a health impact assessment on residential radon and lung cancer. Mean measured radon levels were corrected for the average floor distribution and weighted with population size of each municipality. Model-based predictions yielded a mean radon exposure of the Swiss population of 84.1 Bq/m(3) . Measurement-based predictions yielded an average exposure of 78 Bq/m(3) . This study demonstrates that the model- and the measurement-based predictions provided similar results. The advantage of the measurement-based approach is its simplicity, which is sufficient for assessing exposure distribution in a population. The model-based approach allows predicting radon levels at specific sites, which is needed in an epidemiological study, and the results do not depend on how the measurement sites have been selected. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  3. Methicillin-sensitive and methicillin-resistant Staphylococcus aureus nasal carriage in a random sample of non-hospitalized adult population in northern Germany.

    Directory of Open Access Journals (Sweden)

    Jaishri Mehraj

    Full Text Available OBJECTIVE: The findings from truly randomized community-based studies on Staphylococcus aureus nasal colonization are scarce. Therefore we have examined point prevalence and risk factors of S. aureus nasal carriage in a non-hospitalized population of Braunschweig, northern Germany. METHODS: A total of 2026 potential participants were randomly selected through the resident's registration office and invited by mail. They were requested to collect a nasal swab at home and return it by mail. S. aureus was identified by culture and PCR. Logistic regression was used to determine risk factors of S. aureus carriage. RESULTS: Among the invitees, 405 individuals agreed to participate and 389 provided complete data which was included in the analysis. The median age of the participants was 49 years (IQR: 39-61 and 61% were females. S. aureus was isolated in 85 (21.9%; 95% CI: 18.0-26.2% of the samples, five of which were MRSA (1.29%; 95% CI: 0.55-2.98%. In multiple logistic regression, male sex (OR = 3.50; 95% CI: 2.01-6.11 and presence of allergies (OR = 2.43; 95% CI: 1.39-4.24 were found to be associated with S. aureus nasal carriage. Fifty five different spa types were found, that clustered into nine distinct groups. MRSA belonged to the hospital-associated spa types t032 and t025 (corresponds to MLST CC 22, whereas MSSA spa types varied and mostly belonged to spa-CC 012 (corresponds to MLST CC 30, and spa-CC 084 (corresponds to MLST CC 15. CONCLUSION: This first point prevalence study of S. aureus in a non-hospitalized population of Germany revealed prevalence, consistent with other European countries and supports previous findings on male sex and allergies as risk factors of S. aureus carriage. The detection of hospital-associated MRSA spa types in the community indicates possible spread of these strains from hospitals into the community.

  4. Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population.

    Directory of Open Access Journals (Sweden)

    Timothée Bonnet

    2017-01-01

    Full Text Available In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called "stasis paradox" highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative genetic models are able to provide us with an understanding of the causes and consequences of

  5. Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population

    Science.gov (United States)

    Wandeler, Peter; Camenisch, Glauco

    2017-01-01

    In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called “stasis paradox” highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic) positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative) genetic models are able to provide us with an understanding of the causes and consequences of selection that is

  6. Randomized phase II study of paclitaxel/carboplatin intercalated with gefitinib compared to paclitaxel/carboplatin alone for chemotherapy-naïve non-small cell lung cancer in a clinically selected population excluding patients with non-smoking adenocarcinoma or mutated EGFR

    International Nuclear Information System (INIS)

    Choi, Yoon Ji; Lee, Dae Ho; Choi, Chang Min; Lee, Jung Shin; Lee, Seung Jin; Ahn, Jin-Hee; Kim, Sang-We

    2015-01-01

    Considering cell cycle dependent cytotoxicity, intercalation of chemotherapy and epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) may be a treatment option in non-small cell lung cancer (NSCLC). This randomized phase 2 study compared the efficacy of paclitaxel and carboplatin (PC) intercalated with gefitinib (G) versus PC alone in a selected, chemotherapy-naïve population of advanced NSCLC patients with a history of smoking or wild-type EGFR. Eligible patients were chemotherapy-naïve advanced NSCLC patients with Eastern Cooperative Oncology Group performance status of 0—2. Non-smoking patients with adenocarcinoma or patients with activating EGFR mutation were excluded because they could benefit from gefitinib alone. Eligible patients were randomized to one of the following treatment arms: PCG, P 175 mg/m 2 , and C AUC 5 administered intravenously on day 1 intercalated with G 250 mg orally on days 2 through 15 every 3 weeks for four cycles followed by G 250 mg orally until progressive disease; or PC, same dosing schedule for four cycles only. The primary endpoint was the objective response rate (ORR), and the secondary endpoints included progression-free survival (PFS), overall survival (OS), and toxicity profile. A total of 90 patients participated in the study. The ORRs were 41.9 % (95 % confidence interval (CI) 27.0–57.9 %) for the PCG arm and 39.5 % (95 % CI 25.0–55.6 %) for the PC arm (P = 0.826). No differences in PFS (4.1 vs. 4.1 months, P = 0.781) or OS (9.3 vs. 10.5 months, P = 0.827) were observed between the PCG and PC arms. Safety analyses showed a similar incidence of drug-related grade 3/4 toxicity. Rash and pruritus were more frequent in the PCG than in the PC arm. PCG did not improve ORR, PFS, and OS compared to PC chemotherapy alone for NSCLC in a clinically selected population excluding non-smoking adenocarcinoma or mutated EGFR. The study is registered with ClinicalTrials.gov (NCT01196234). Registration date is 08/09/2010

  7. Medical illness, medication use and suicide in seniors: a population-based case-control study.

    Science.gov (United States)

    Voaklander, D C; Rowe, B H; Dryden, D M; Pahal, J; Saar, P; Kelly, K D

    2008-02-01

    Suicide among seniors is a significant health problem in north America, particularly for men in whom the rates rise steadily after 50 years of age. The goal of this study was to examine elder suicides identified from a large population-based database using case-control methods to determine disease and medication factors related to suicide. A population-based 1 : 5 case-control study was conducted comparing seniors aged 66 years and older who had died by suicide with age and sex-matched controls. Case data were obtained through British Columbia (BC) Vital Statistics, whereas controls were randomly selected from the BC Health Insurance Registry. Cases and controls were linked to the provincial PharmaCare database to determine medication use and the provincial Physician Claims and Inpatient Hospitalization databases to determine co-morbidity. Between 1993 and 2002 a total of 602 seniors died by suicide in BC giving an annual rate of 13.2 per 100,000. Firearms were the most common mechanism (28%), followed by hanging/suffocation (25%), self-poisoning (21%), and jumping from height (7%). In the adjusted logistic model, variables related to suicide included: lower socioeconomic status, depression/psychosis, neurosis, stroke, cancer, liver disease, parasuicide, benzodiazepine use, narcotic pain killer use and diuretic use. There was an elevated risk for those prescribed inappropriate benzodiazepines and for those using strong narcotic pain killers. This study is consistent with previous studies that have identified a relationship between medical or psychiatric co-morbidity and suicide in seniors. In addition, new and potentially useful information confirms that certain types and dosages of benzodiazepines are harmful to seniors and their use should be avoided.

  8. Recurrent selection in inbred popcorn families

    Directory of Open Access Journals (Sweden)

    Daros Máskio

    2004-01-01

    Full Text Available Although much appreciated in Brazil, commercial popcorn is currently cropped on a fairly small scale. A number of problems need to be solved to increase production, notably the obtaintion of seeds with good agronomic traits and good culinary characteristics. With the objective of developing superior genotypes in popcorn, a second cycle of intrapopulation recurrent selection based on inbred S1 families was carried out. From the first cycle of selection over the UNB-2U population, 222 S1 families were obtained, which were then divided into six sets and evaluated in a randomized complete block design with two replications within the sets. Experiments were carried out in two Brazilian localities. The analysis of variance revealed environmental effects for all evaluated traits, except popping and stand, showing that, for most traits, these environments affected genotype behavior in different ways. In addition, the set as source of variation was significant for most of the evaluated traits, indicating that dividing the families into sets was an efficient strategy. Genotype-by-environment interaction was detected for most traits, except popping expansion and stand. Differences among genotypes were also detected (1% F-test, making viable the proposition of using the genetic variability in the popcorn population as a basis for future recurrent selection cycles. Superior families were selected using the Smith and Hazel classic index, with predicted genetic gains of 17.8% for popping expansion and 26.95% for yield.

  9. Evidence for natural selection at the melanocortin-3 receptor gene in European and African populations.

    Science.gov (United States)

    Yoshiuchi, Issei

    2016-08-01

    Obesity is increasing steadily in worldwide prevalence and is known to cause serious health problems in association with type 2 diabetes mellitus (T2DM), including hypertension, stroke, and cardiovascular diseases. According to the thrifty gene hypothesis, the natural selection of obesity-related genes is important during feast and famine because they control body weight and fat levels. Past human adaptations to environmental changes in food supply, lifestyle, and geography may have influenced the selection of genes associated with the metabolism of glucose, lipids, and energy. The melanocortin-3 receptor gene (MC3R) is associated with obesity, with MC3R-deficient mice showing increased fat mass. MC3R variations are also linked with childhood obesity and insulin resistance. Here, we aimed to uncover evidence of selection at MC3R. We performed a three-step method to detect selection at MC3R using HapMap population data. We used Wright's F statistics as a measure of population differentiation, the long-range haplotype test to identify extended haplotypes, and the integrated haplotype score (iHS) to detect selection at MC3R. We observed high population differentiation between European and African populations at two MC3R childhood obesity- and insulin resistance-associated single-nucleotide polymorphisms (rs3746619 and rs3827103) using Wright's F statistics. The iHS revealed evidence of natural selection at MC3R. These findings provide evidence for natural selection at MC3R. Further investigation is warranted into adaptive evolution at T2DM- and obesity-associated genes.

  10. The [O III] Profiles of Infrared-selected Active Galactic Nuclei: More Powerful Outflows in the Obscured Population

    Science.gov (United States)

    DiPompeo, M. A.; Hickox, R. C.; Carroll, C. M.; Runnoe, J. C.; Mullaney, J. R.; Fischer, T. C.

    2018-03-01

    We explore the kinematics of ionized gas via the [O III] λ5007 emission lines in active galactic nuclei (AGNs) selected on the basis of their mid-infrared (IR) emission, and split into obscured and unobscured populations based on their optical‑IR colors. After correcting for differences in redshift distributions, we provide composite spectra of spectroscopically and photometrically defined obscured/Type 2 and unobscured/Type 1 AGNs from 3500 to 7000 Å. The IR-selected obscured sources contain a mixture of narrow-lined Type 2 AGNs and intermediate sources that have broad Hα emission and significantly narrower Hβ. Using both [O III] luminosities and AGN luminosities derived from optical‑IR spectral energy distribution fitting, we find evidence for enhanced large-scale obscuration in the obscured sources. In matched bins of luminosity we find that the obscured population typically has broader, more blueshifted [O III] emission than in the unobscured sample, suggestive of more powerful AGN-driven outflows. This trend is not seen in spectroscopically classified samples, and is unlikely to be entirely explained by orientation effects. In addition, outflow velocities increase from small to moderate AGN E(B ‑ V) values, before flattening out (as traced by FWHM) and even decreasing (as traced by blueshift). While difficult to fully interpret in a single physical model, due to both the averaging over populations and the spatially averaged spectra, these results agree with previous findings that simple geometric unification models are insufficient for the IR-selected AGN population, and may fit into an evolutionary model for obscured and unobscured AGNs.

  11. Gastroesophageal reflux disease and atrial fibrillation: a nationwide population-based study.

    Directory of Open Access Journals (Sweden)

    Chin-Chou Huang

    Full Text Available OBJECTIVES: Precise mechanisms of atrial fibrillation (AF are uncertain, but their association with esophageal disorders has been recently proposed. The association between gastroesophageal reflux disease (GERD, the most common gastroesophageal disorder, and AF remains undetermined. We therefore aimed to investigate the association between GERD and later development of AF. METHODS AND RESULTS: Patients with GERD were identified from the 1,000,000-person cohort dataset sampled from the Taiwan National Health Insurance database. The study cohort comprised 29,688 newly diagnosed adult GERD patients; 29,597 randomly selected age-, gender-, comobidity-matched subjects comprised the comparison cohort. Cox proportional hazard regressions were performed as a means of comparing the AF-free survival rate for the two cohorts. During a maximum three years of follow-up, a total of 351 patients experienced AF, including 184 (0.62% patients in the GERD cohort and 167 (0.56% in the control group. The log-rank test showed that patients with GERD had significantly higher incidence of AF than those without GERD (p = 0.024. After Cox proportional hazard regression model analysis, GERD was independently associated with the increased risk of AF (hazard ratio, 1.31; 95% confidence interval, 1.06-1.61, p = 0.013. CONCLUSION: GERD was independently associated with an increased risk of future AF in a nationwide population-based cohort.

  12. Risk Attitudes, Sample Selection and Attrition in a Longitudinal Field Experiment

    DEFF Research Database (Denmark)

    Harrison, Glenn W.; Lau, Morten Igel

    with respect to risk attitudes. Our design builds in explicit randomization on the incentives for participation. We show that there are significant sample selection effects on inferences about the extent of risk aversion, but that the effects of subsequent sample attrition are minimal. Ignoring sample...... selection leads to inferences that subjects in the population are more risk averse than they actually are. Correcting for sample selection and attrition affects utility curvature, but does not affect inferences about probability weighting. Properly accounting for sample selection and attrition effects leads...... to findings of temporal stability in overall risk aversion. However, that stability is around different levels of risk aversion than one might naively infer without the controls for sample selection and attrition we are able to implement. This evidence of “randomization bias” from sample selection...

  13. Analysis of creative mathematic thinking ability in problem based learning model based on self-regulation learning

    Science.gov (United States)

    Munahefi, D. N.; Waluya, S. B.; Rochmad

    2018-03-01

    The purpose of this research identified the effectiveness of Problem Based Learning (PBL) models based on Self Regulation Leaning (SRL) on the ability of mathematical creative thinking and analyzed the ability of mathematical creative thinking of high school students in solving mathematical problems. The population of this study was students of grade X SMA N 3 Klaten. The research method used in this research was sequential explanatory. Quantitative stages with simple random sampling technique, where two classes were selected randomly as experimental class was taught with the PBL model based on SRL and control class was taught with expository model. The selection of samples at the qualitative stage was non-probability sampling technique in which each selected 3 students were high, medium, and low academic levels. PBL model with SRL approach effectived to students’ mathematical creative thinking ability. The ability of mathematical creative thinking of low academic level students with PBL model approach of SRL were achieving the aspect of fluency and flexibility. Students of academic level were achieving fluency and flexibility aspects well. But the originality of students at the academic level was not yet well structured. Students of high academic level could reach the aspect of originality.

  14. Toll-like receptor variation in the bottlenecked population of the Seychelles warbler: computer simulations see the 'ghost of selection past' and quantify the 'drift debt'.

    Science.gov (United States)

    Gilroy, D L; Phillips, K P; Richardson, D S; van Oosterhout, C

    2017-07-01

    Balancing selection can maintain immunogenetic variation within host populations, but detecting its signal in a postbottlenecked population is challenging due to the potentially overriding effects of drift. Toll-like receptor genes (TLRs) play a fundamental role in vertebrate immune defence and are predicted to be under balancing selection. We previously characterized variation at TLR loci in the Seychelles warbler (Acrocephalus sechellensis), an endemic passerine that has undergone a historical bottleneck. Five of seven TLR loci were polymorphic, which is in sharp contrast to the low genomewide variation observed. However, standard population genetic statistical methods failed to detect a contemporary signature of selection at any TLR locus. We examined whether the observed TLR polymorphism could be explained by neutral evolution, simulating the population's demography in the software DIYABC. This showed that the posterior distributions of mutation rates had to be unrealistically high to explain the observed genetic variation. We then conducted simulations with an agent-based model using typical values for the mutation rate, which indicated that weak balancing selection has acted on the three TLR genes. The model was able to detect evidence of past selection elevating TLR polymorphism in the prebottleneck populations, but was unable to discern any effects of balancing selection in the contemporary population. Our results show drift is the overriding evolutionary force that has shaped TLR variation in the contemporary Seychelles warbler population, and the observed TLR polymorphisms might be merely the 'ghost of selection past'. Forecast models predict immunogenetic variation in this species will continue to be eroded in the absence of contemporary balancing selection. Such 'drift debt' occurs when a gene pool has not yet reached its new equilibrium level of polymorphism, and this loss could be an important threat to many recently bottlenecked populations. © 2017

  15. Population-level effects of automated smoking cessation help programs: a randomized controlled trial.

    Science.gov (United States)

    Borland, Ron; Balmford, James; Benda, Peter

    2013-03-01

    To test the population impact of offering automated smoking cessation interventions via the internet and/or by mobile phone. Pragmatic randomized controlled trial with five conditions: offer of (i) minimal intervention control; (ii) QuitCoach personalized tailored internet-delivered advice program; (iii) onQ, an interactive automated text-messaging program; (iv) an integration of both QuitCoach and onQ; and (v) a choice of either alone or the combined program. Australia, via a mix of internet and telephone contacts. A total of 3530 smokers or recent quitters recruited from those interested in quitting, and seeking self-help resources (n = 1335) or cold-contacted from internet panels (n = 2195). The primary outcome was self-report of 6 months sustained abstinence at 7 months post-recruitment. Only 42.5% of those offered one of the interventions took it up to a minimal level. The intervention groups combined had a non-significantly higher 6-month sustained abstinence rate than the control [odds ratio (OR) = 1.48; 95% confidence interval (CI): 0.98-2.24] (missing cases treated as smokers), with no differences between the interventions. Among those who used an intervention, there was a significant overall increase in abstinence (OR = 1.95; CI: 1.04-3.67), but not clearly so when analysing only cases with reported outcomes. Success rates were greater among those recruited after seeking information compared to those cold-contacted. Smokers interested in quitting who were assigned randomly to an offer of either the QuitCoach internet-based support program and/or the interactive automated text-messaging program had non-significantly greater odds of quitting for at least 6 months than those randomized to an offer of a simple information website. © 2012 The Authors, Addiction © 2012 Society for the Study of Addiction.

  16. Comparisons of Growth and Survival Performance Among Selected Families and Wild Populations of Fenneropenaeus chinensis

    Science.gov (United States)

    Luo, Kun; Kong, Jie; Meng, Xianhong; Luan, Sheng; Cao, Baoxiang; Chen, Baolong

    2018-04-01

    In this study, families of selected population for growth (SP_BWT), selected population for white spot syndrome virus (WSSV) resistance (SP_RW), Bohai wild population (WP_BH) and Huanghai wild population (WP_HH) of F. chinensis were constructed through artificial insemination and with the standardized procedure of larvae rearing. Growth and survival performance were studied among four populations after a 70 days common test. The results showed that the maximum least square mean of body weight was 17.50 g in SP_BWT while the minimum was 13.03 g in WP_HH. Compared with WP_BH, body weight of SP_BWT increased by 23.41% ( P 0.05). Body weights of SP_BWT and SP_RW were significantly higher than that of WP_HH, which increased by 34.31% ( P populations was 0.19, 0.18, 0.17 and 0.16 g d-1, respectively. Coefficient of variation of body weight among four populations was high, which ranged from 32.67% to 35.25%. Such a range showed that there was the potentiality for further improvement in selected populations. Coefficient of variation of survival rate among four populations was low, varying between 3.20% and 5.90%. The difference of survival was highly significant ( P populations ( P growth performances were also observed among different families in each population. The body weight of 798F family was the highest. The absolute growth rate (AGR) was 0.25 g d-1, 150% higher than that of the lowest one, 0.1 g d-1 in 807F family. Survival rate of families among four populations was different. The highest was 94.74%, and the lowest was 71.88%.

  17. Sample size estimation and sampling techniques for selecting a representative sample

    Directory of Open Access Journals (Sweden)

    Aamir Omair

    2014-01-01

    Full Text Available Introduction: The purpose of this article is to provide a general understanding of the concepts of sampling as applied to health-related research. Sample Size Estimation: It is important to select a representative sample in quantitative research in order to be able to generalize the results to the target population. The sample should be of the required sample size and must be selected using an appropriate probability sampling technique. There are many hidden biases which can adversely affect the outcome of the study. Important factors to consider for estimating the sample size include the size of the study population, confidence level, expected proportion of the outcome variable (for categorical variables/standard deviation of the outcome variable (for numerical variables, and the required precision (margin of accuracy from the study. The more the precision required, the greater is the required sample size. Sampling Techniques: The probability sampling techniques applied for health related research include simple random sampling, systematic random sampling, stratified random sampling, cluster sampling, and multistage sampling. These are more recommended than the nonprobability sampling techniques, because the results of the study can be generalized to the target population.

  18. Spike-based population coding and working memory.

    Directory of Open Access Journals (Sweden)

    Martin Boerlin

    2011-02-01

    Full Text Available Compelling behavioral evidence suggests that humans can make optimal decisions despite the uncertainty inherent in perceptual or motor tasks. A key question in neuroscience is how populations of spiking neurons can implement such probabilistic computations. In this article, we develop a comprehensive framework for optimal, spike-based sensory integration and working memory in a dynamic environment. We propose that probability distributions are inferred spike-per-spike in recurrently connected networks of integrate-and-fire neurons. As a result, these networks can combine sensory cues optimally, track the state of a time-varying stimulus and memorize accumulated evidence over periods much longer than the time constant of single neurons. Importantly, we propose that population responses and persistent working memory states represent entire probability distributions and not only single stimulus values. These memories are reflected by sustained, asynchronous patterns of activity which make relevant information available to downstream neurons within their short time window of integration. Model neurons act as predictive encoders, only firing spikes which account for new information that has not yet been signaled. Thus, spike times signal deterministically a prediction error, contrary to rate codes in which spike times are considered to be random samples of an underlying firing rate. As a consequence of this coding scheme, a multitude of spike patterns can reliably encode the same information. This results in weakly correlated, Poisson-like spike trains that are sensitive to initial conditions but robust to even high levels of external neural noise. This spike train variability reproduces the one observed in cortical sensory spike trains, but cannot be equated to noise. On the contrary, it is a consequence of optimal spike-based inference. In contrast, we show that rate-based models perform poorly when implemented with stochastically spiking neurons.

  19. Signatures of natural selection at the FTO (fat mass and obesity associated locus in human populations.

    Directory of Open Access Journals (Sweden)

    Xuanshi Liu

    Full Text Available Polymorphisms in the first intron of FTO have been robustly replicated for associations with obesity. In the Sorbs, a Slavic population resident in Germany, the strongest effect on body mass index (BMI was found for a variant in the third intron of FTO (rs17818902. Since this may indicate population specific effects of FTO variants, we initiated studies testing FTO for signatures of selection in vertebrate species and human populations.First, we analyzed the coding region of 35 vertebrate FTO orthologs with Phylogenetic Analysis by Maximum Likelihood (PAML, ω = dN/dS to screen for signatures of selection among species. Second, we investigated human population (Europeans/CEU, Yoruba/YRI, Chinese/CHB, Japanese/JPT, Sorbs SNP data for footprints of selection using DnaSP version 4.5 and the Haplotter/PhaseII. Finally, using ConSite we compared transcription factor (TF binding sites at sequences harbouring FTO SNPs in intron three.PAML analyses revealed strong conservation in coding region of FTO (ω<1. Sliding-window results from population genetic analyses provided highly significant (p<0.001 signatures for balancing selection specifically in the third intron (e.g. Tajima's D in Sorbs = 2.77. We observed several alterations in TF binding sites, e.g. TCF3 binding site introduced by the rs17818902 minor allele.Population genetic analysis revealed signatures of balancing selection at the FTO locus with a prominent signal in intron three, a genomic region with strong association with BMI in the Sorbs. Our data support the hypothesis that genes associated with obesity may have been under evolutionary selective pressure.

  20. Emergence of multilevel selection in the prisoner's dilemma game on coevolving random networks

    International Nuclear Information System (INIS)

    Szolnoki, Attila; Perc, Matjaz

    2009-01-01

    We study the evolution of cooperation in the prisoner's dilemma game, whereby a coevolutionary rule is introduced that molds the random topology of the interaction network in two ways. First, existing links are deleted whenever a player adopts a new strategy or its degree exceeds a threshold value; second, new links are added randomly after a given number of game iterations. These coevolutionary processes correspond to the generic formation of new links and deletion of existing links that, especially in human societies, appear frequently as a consequence of ongoing socialization, change of lifestyle or death. Due to the counteraction of deletions and additions of links the initial heterogeneity of the interaction network is qualitatively preserved, and thus cannot be held responsible for the observed promotion of cooperation. Indeed, the coevolutionary rule evokes the spontaneous emergence of a powerful multilevel selection mechanism, which despite the sustained random topology of the evolving network, maintains cooperation across the whole span of defection temptation values.

  1. Selective adaptation in networks of heterogeneous populations: model, simulation, and experiment.

    Directory of Open Access Journals (Sweden)

    Avner Wallach

    2008-02-01

    Full Text Available Biological systems often change their responsiveness when subject to persistent stimulation, a phenomenon termed adaptation. In neural systems, this process is often selective, allowing the system to adapt to one stimulus while preserving its sensitivity to another. In some studies, it has been shown that adaptation to a frequent stimulus increases the system's sensitivity to rare stimuli. These phenomena were explained in previous work as a result of complex interactions between the various subpopulations of the network. A formal description and analysis of neuronal systems, however, is hindered by the network's heterogeneity and by the multitude of processes taking place at different time-scales. Viewing neural networks as populations of interacting elements, we develop a framework that facilitates a formal analysis of complex, structured, heterogeneous networks. The formulation developed is based on an analysis of the availability of activity dependent resources, and their effects on network responsiveness. This approach offers a simple mechanistic explanation for selective adaptation, and leads to several predictions that were corroborated in both computer simulations and in cultures of cortical neurons developing in vitro. The framework is sufficiently general to apply to different biological systems, and was demonstrated in two different cases.

  2. Improved methods in Agrobacterium-mediated transformation of almond using positive (mannose/pmi) or negative (kanamycin resistance) selection-based protocols.

    Science.gov (United States)

    Ramesh, Sunita A; Kaiser, Brent N; Franks, Tricia; Collins, Graham; Sedgley, Margaret

    2006-08-01

    A protocol for Agrobacterium-mediated transformation with either kanamycin or mannose selection was developed for leaf explants of the cultivar Prunus dulcis cv. Ne Plus Ultra. Regenerating shoots were selected on medium containing 15 muM kanamycin (negative selection), while in the positive selection strategy, shoots were selected on 2.5 g/l mannose supplemented with 15 g/l sucrose. Transformation efficiencies based on PCR analysis of individual putative transformed shoots from independent lines relative to the initial numbers of leaf explants tested were 5.6% for kanamycin/nptII and 6.8% for mannose/pmi selection, respectively. Southern blot analysis on six randomly chosen PCR-positive shoots confirmed the presence of the nptII transgene in each, and five randomly chosen lines identified to contain the pmi transgene by PCR showed positive hybridisation to a pmi DNA probe. The positive (mannose/pmi) and the negative (kanamycin) selection protocols used in this study have greatly improved transformation efficiency in almond, which were confirmed with PCR and Southern blot. This study also demonstrates that in almond the mannose/pmi selection protocol is appropriate and can result in higher transformation efficiencies over that of kanamycin/nptII selection protocols.

  3. Experimental nonlocality-based randomness generation with nonprojective measurements

    Science.gov (United States)

    Gómez, S.; Mattar, A.; Gómez, E. S.; Cavalcanti, D.; Farías, O. Jiménez; Acín, A.; Lima, G.

    2018-04-01

    We report on an optical setup generating more than one bit of randomness from one entangled bit (i.e., a maximally entangled state of two qubits). The amount of randomness is certified through the observation of Bell nonlocal correlations. To attain this result we implemented a high-purity entanglement source and a nonprojective three-outcome measurement. Our implementation achieves a gain of 27% of randomness as compared with the standard methods using projective measurements. Additionally, we estimate the amount of randomness certified in a one-sided device-independent scenario, through the observation of Einstein-Podolsky-Rosen steering. Our results prove that nonprojective quantum measurements allow extending the limits for nonlocality-based certified randomness generation using current technology.

  4. Emergence of clones in sexual populations

    International Nuclear Information System (INIS)

    Neher, Richard A; Vucelja, Marija; Mezard, Mark; Shraiman, Boris I

    2013-01-01

    In sexual population, recombination reshuffles genetic variation and produces novel combinations of existing alleles, while selection amplifies the fittest genotypes in the population. If recombination is more rapid than selection, populations consist of a diverse mixture of many genotypes, as is observed in many populations. In the opposite regime, which is realized for example in the facultatively sexual populations that outcross in only a fraction of reproductive cycles, selection can amplify individual genotypes into large clones. Such clones emerge when the fitness advantage of some of the genotypes is large enough that they grow to a significant fraction of the population despite being broken down by recombination. The occurrence of this ‘clonal condensation’ depends, in addition to the outcrossing rate, on the heritability of fitness. Clonal condensation leads to a strong genetic heterogeneity of the population which is not adequately described by traditional population genetics measures, such as linkage disequilibrium. Here we point out the similarity between clonal condensation and the freezing transition in the random energy model of spin glasses. Guided by this analogy we explicitly calculate the probability, Y, that two individuals are genetically identical as a function of the key parameters of the model. While Y is the analog of the spin-glass order parameter, it is also closely related to rate of coalescence in population genetics: two individuals that are part of the same clone have a recent common ancestor. (paper)

  5. Assessing the accuracy and stability of variable selection methods for random forest modeling in ecology

    Science.gov (United States)

    Random forest (RF) modeling has emerged as an important statistical learning method in ecology due to its exceptional predictive performance. However, for large and complex ecological datasets there is limited guidance on variable selection methods for RF modeling. Typically, e...

  6. Phenotypic selection on leaf water use efficiency and related ecophysiological traits for natural populations of desert sunflowers.

    Science.gov (United States)

    Donovan, Lisa A; Dudley, Susan A; Rosenthal, David M; Ludwig, Fulco

    2007-05-01

    Plant water-use efficiency (WUE) is expected to affect plant fitness and thus be under natural selection in arid habitats. Although many natural population studies have assessed plant WUE, only a few related WUE to fitness. The further determination of whether selection on WUE is direct or indirect through functionally related traits has yielded no consistent results. For natural populations of two desert annual sunflowers, Helianthus anomalus and H. deserticola, we used phenotypic selection analysis with vegetative biomass as the proxy for fitness to test (1) whether there was direct and indirect selection on WUE (carbon isotope ratio) and related traits (leaf N, area, succulence) and (2) whether direct selection was consistent with hypothesized drought/dehydration escape and avoidance strategies. There was direct selection for lower WUE in mesic and dry H. anomalus populations, consistent with dehydration escape, even though it is the longer lived of the two species. For mesic H. anomalus, direct selection favored lower WUE and higher N, suggesting that plants may be "wasting water" to increase N delivery via the transpiration stream. For the shorter lived H. deserticola in the direr habitat, there was indirect selection for lower WUE, inconsistent with drought escape. There was also direct selection for higher leaf N, succulence and leaf size. There was no direct selection for higher WUE consistent with dehydration avoidance in either species. Thus, in these natural populations of two desert dune species higher fitness was associated with some combination direct and indirect selection for lower WUE, higher leaf N and larger leaf size. Our understanding of the adaptive value of plant ecophysiological traits will benefit from further consideration of related traits such as leaf nitrogen and more tests in natural populations.

  7. SDE based regression for random PDEs

    KAUST Repository

    Bayer, Christian

    2016-01-01

    A simulation based method for the numerical solution of PDE with random coefficients is presented. By the Feynman-Kac formula, the solution can be represented as conditional expectation of a functional of a corresponding stochastic differential equation driven by independent noise. A time discretization of the SDE for a set of points in the domain and a subsequent Monte Carlo regression lead to an approximation of the global solution of the random PDE. We provide an initial error and complexity analysis of the proposed method along with numerical examples illustrating its behaviour.

  8. SDE based regression for random PDEs

    KAUST Repository

    Bayer, Christian

    2016-01-06

    A simulation based method for the numerical solution of PDE with random coefficients is presented. By the Feynman-Kac formula, the solution can be represented as conditional expectation of a functional of a corresponding stochastic differential equation driven by independent noise. A time discretization of the SDE for a set of points in the domain and a subsequent Monte Carlo regression lead to an approximation of the global solution of the random PDE. We provide an initial error and complexity analysis of the proposed method along with numerical examples illustrating its behaviour.

  9. Reproductive habitat selection in alien and native populations of the genus Discoglossus

    Science.gov (United States)

    Escoriza, Daniel; Boix, Dani

    2014-08-01

    The existence of suitable breeding habitats is an important factor explaining the regional presence of an anuran species. This study examined patterns of habitat selection in populations of three species of the genus Discoglossus: Discoglossusgalganoi (south-western Iberian Peninsula), Discoglossusscovazzi (Morocco) and Discoglossuspictus (three different areas were included in the study: Sicily, Tunisia and north-eastern Iberian Peninsula). The populations of D. pictus on the Iberian Peninsula are allochthonous, and analysis of these patterns may provide insights into the processes that regulate the invasion phase. The hypotheses tested were: (i) congeneric species show the same patterns of habitat selection, and alien species have been established following these patterns; (ii) there are differences in species associations between assemblages structured deterministically and by chance, i.e. native versus invaded assemblages. The larval habitats of three species of this genus were characterized by measuring physical and chemical parameters of the water bodies. We examined the covariation between the presence of Discoglossus species and the species richness of sympatric anurans, and investigated a possible relationship between morphological similarity (as a proxy of functional group) and overlap in habitat use. The results showed that congeneric species are morphologically conservative and also select very similar types of aquatic habitat. The alien population and other sympatric species showed a high degree of overlap in habitat use, which was greater than that observed in the native assemblage with a similar functional richness. Species associations were not structured on the basis of morphological similarity in any of the assemblages. Among native populations, the presence of Discoglossus was either negatively correlated or not significantly correlated with species richness. Only the alien population showed a positive correlation between its presence and species

  10. Intelligent Fault Diagnosis of HVCB with Feature Space Optimization-Based Random Forest.

    Science.gov (United States)

    Ma, Suliang; Chen, Mingxuan; Wu, Jianwen; Wang, Yuhao; Jia, Bowen; Jiang, Yuan

    2018-04-16

    Mechanical faults of high-voltage circuit breakers (HVCBs) always happen over long-term operation, so extracting the fault features and identifying the fault type have become a key issue for ensuring the security and reliability of power supply. Based on wavelet packet decomposition technology and random forest algorithm, an effective identification system was developed in this paper. First, compared with the incomplete description of Shannon entropy, the wavelet packet time-frequency energy rate (WTFER) was adopted as the input vector for the classifier model in the feature selection procedure. Then, a random forest classifier was used to diagnose the HVCB fault, assess the importance of the feature variable and optimize the feature space. Finally, the approach was verified based on actual HVCB vibration signals by considering six typical fault classes. The comparative experiment results show that the classification accuracy of the proposed method with the origin feature space reached 93.33% and reached up to 95.56% with optimized input feature vector of classifier. This indicates that feature optimization procedure is successful, and the proposed diagnosis algorithm has higher efficiency and robustness than traditional methods.

  11. The use of odd random phase electrochemical impedance spectroscopy to study lithium-based corrosion inhibition by active protective coatings

    NARCIS (Netherlands)

    Meeusen, M.; Visser, P.; Fernández Macía, L.; Hubin, A.; Terryn, H.A.; Mol, J.M.C.

    2018-01-01

    In this work, the study of the time-dependent behaviour of lithium carbonate based inhibitor technology for the active corrosion protection of aluminium alloy 2024-T3 is presented. Odd random phase electrochemical impedance spectroscopy (ORP-EIS) is selected as the electrochemical tool to study

  12. Chemical variation in a dominant tree species: population divergence, selection and genetic stability across environments.

    Directory of Open Access Journals (Sweden)

    Julianne M O'Reilly-Wapstra

    Full Text Available Understanding among and within population genetic variation of ecologically important plant traits provides insight into the potential evolutionary processes affecting those traits. The strength and consistency of selection driving variability in traits would be affected by plasticity in differences among genotypes across environments (G×E. We investigated population divergence, selection and environmental plasticity of foliar plant secondary metabolites (PSMs in a dominant tree species, Eucalyptus globulus. Using two common garden trials we examined variation in PSMs at multiple genetic scales; among 12 populations covering the full geographic range of the species and among up to 60 families within populations. Significant genetic variation in the expression of many PSMs resides both among and within populations of E. globulus with moderate (e.g., sideroxylonal A h(2op = 0.24 to high (e.g., macrocarpal G h(2op = 0.48 narrow sense heritabilities and high coefficients of additive genetic variation estimated for some compounds. A comparison of Qst and Fst estimates suggest that variability in some of these traits may be due to selection. Importantly, there was no genetic by environment interaction in the expression of any of the quantitative chemical traits despite often significant site effects. These results provide evidence that natural selection has contributed to population divergence in PSMs in E. globulus, and identifies the formylated phloroglucinol compounds (particularly sideroxylonal and a dominant oil, 1,8-cineole, as candidates for traits whose genetic architecture has been shaped by divergent selection. Additionally, as the genetic differences in these PSMs that influence community phenotypes is stable across environments, the role of plant genotype in structuring communities is strengthened and these genotypic differences may be relatively stable under global environmental changes.

  13. [Inverse probability weighting (IPW) for evaluating and "correcting" selection bias].

    Science.gov (United States)

    Narduzzi, Silvia; Golini, Martina Nicole; Porta, Daniela; Stafoggia, Massimo; Forastiere, Francesco

    2014-01-01

    the Inverse probability weighting (IPW) is a methodology developed to account for missingness and selection bias caused by non-randomselection of observations, or non-random lack of some information in a subgroup of the population. to provide an overview of IPW methodology and an application in a cohort study of the association between exposure to traffic air pollution (nitrogen dioxide, NO₂) and 7-year children IQ. this methodology allows to correct the analysis by weighting the observations with the probability of being selected. The IPW is based on the assumption that individual information that can predict the probability of inclusion (non-missingness) are available for the entire study population, so that, after taking account of them, we can make inferences about the entire target population starting from the nonmissing observations alone.The procedure for the calculation is the following: firstly, we consider the entire population at study and calculate the probability of non-missing information using a logistic regression model, where the response is the nonmissingness and the covariates are its possible predictors.The weight of each subject is given by the inverse of the predicted probability. Then the analysis is performed only on the non-missing observations using a weighted model. IPW is a technique that allows to embed the selection process in the analysis of the estimates, but its effectiveness in "correcting" the selection bias depends on the availability of enough information, for the entire population, to predict the non-missingness probability. In the example proposed, the IPW application showed that the effect of exposure to NO2 on the area of verbal intelligence quotient of children is stronger than the effect showed from the analysis performed without regard to the selection processes.

  14. Identifying signatures of natural selection in Tibetan and Andean populations using dense genome scan data.

    Directory of Open Access Journals (Sweden)

    Abigail Bigham

    2010-09-01

    Full Text Available High-altitude hypoxia (reduced inspired oxygen tension due to decreased barometric pressure exerts severe physiological stress on the human body. Two high-altitude regions where humans have lived for millennia are the Andean Altiplano and the Tibetan Plateau. Populations living in these regions exhibit unique circulatory, respiratory, and hematological adaptations to life at high altitude. Although these responses have been well characterized physiologically, their underlying genetic basis remains unknown. We performed a genome scan to identify genes showing evidence of adaptation to hypoxia. We looked across each chromosome to identify genomic regions with previously unknown function with respect to altitude phenotypes. In addition, groups of genes functioning in oxygen metabolism and sensing were examined to test the hypothesis that particular pathways have been involved in genetic adaptation to altitude. Applying four population genetic statistics commonly used for detecting signatures of natural selection, we identified selection-nominated candidate genes and gene regions in these two populations (Andeans and Tibetans separately. The Tibetan and Andean patterns of genetic adaptation are largely distinct from one another, with both populations showing evidence of positive natural selection in different genes or gene regions. Interestingly, one gene previously known to be important in cellular oxygen sensing, EGLN1 (also known as PHD2, shows evidence of positive selection in both Tibetans and Andeans. However, the pattern of variation for this gene differs between the two populations. Our results indicate that several key HIF-regulatory and targeted genes are responsible for adaptation to high altitude in Andeans and Tibetans, and several different chromosomal regions are implicated in the putative response to selection. These data suggest a genetic role in high-altitude adaption and provide a basis for future genotype/phenotype association

  15. A population-based survey of prevalence of diabetes and correlates in an urban slum community in Nairobi, Kenya.

    Science.gov (United States)

    Ayah, Richard; Joshi, Mark D; Wanjiru, Rosemary; Njau, Elijah K; Otieno, C Fredrick; Njeru, Erastus K; Mutai, Kenneth K

    2013-04-20

    Urban slum populations in Africa continue to grow faster than national populations. Health strategies that focus on non-communicable diseases (NCD) in this segment of the population are generally lacking. We determined the prevalence of diabetes and associated cardiovascular disease (CVD) risk factors correlates in Kibera, Nairobi's largest slum. We conducted a population-based household survey utilising cluster sampling with probability proportional to size. Households were selected using a random walk method and consenting residents aged 18 years and above were recruited. The WHO STEPS instrument was administered. A random capillary blood sugar (RCBS) was obtained; known persons with diabetes and subjects with a RCBS >11.1 had an 8 hours fasting blood sugar (FBS) drawn. Diabetes was defined as a RCBS of  ≥ 11.1 mmol/l and a FBS of  ≥ 7.0 mmol/l, or a prior diagnosis or receiving diabetes drug treatment. Out of 2061 enrolled; 50.9% were males, mean age was 33.4 years and 87% had a minimum of primary education. Only 10.6% had ever had a blood sugar measurement. Age adjusted prevalence of diabetes was 5.3% (95% CI 4.2-6.4) and prevalence increased with age peaking at 10.5% (95% CI 6.8-14.3%) in the 45-54 year age category. Diabetes mellitus (DM) correlates were: 13.1% smoking, 74.9% alcohol consumption, 75.7% high level of physical activity; 16.3% obese and 29% overweight with higher rates in women.Among persons with diabetes the odds of obesity, elevated waist circumference and hypertension were three, two and three fold respectively compared to those without diabetes. Cardiovascular risk factors among subjects with diabetes were high and mirrored that of the entire sample; however they had a significantly higher use of tobacco. This previously unstudied urban slum has a high prevalence of DM yet low screening rates. Key correlates include cigarette smoking and high alcohol consumption. However high levels of physical activity were also reported. Findings

  16. The Evaluation of Teachers' Job Performance Based on Total Quality Management (TQM)

    Science.gov (United States)

    Shahmohammadi, Nayereh

    2017-01-01

    This study aimed to evaluate teachers' job performance based on total quality management (TQM) model. This was a descriptive survey study. The target population consisted of all primary school teachers in Karaj (N = 2917). Using Cochran formula and simple random sampling, 340 participants were selected as sample. A total quality management…

  17. Population genetic structure analysis in endangered Hordeum ...

    African Journals Online (AJOL)

    Administrator

    2011-09-07

    Sep 7, 2011 ... populations are grown by few local farmers in low-input farming systems. Based on 117 random ... Triticeae of the Poaceae (Graminae) family found throughout the ... populations and phylogeography is made easy by the.

  18. A Random-Dot Kinematogram for Web-Based Vision Research

    Directory of Open Access Journals (Sweden)

    Sivananda Rajananda

    2018-01-01

    Full Text Available Web-based experiments using visual stimuli have become increasingly common in recent years, but many frequently-used stimuli in vision research have yet to be developed for online platforms. Here, we introduce the first open access random-dot kinematogram (RDK for use in web browsers. This fully customizable RDK offers options to implement several different types of noise (random position, random walk, random direction and parameters to control aperture shape, coherence level, the number of dots, and other features. We include links to commented JavaScript code for easy implementation in web-based experiments, as well as an example of how this stimulus can be integrated as a plugin with a JavaScript library for online studies (jsPsych.

  19. Statins and Hip Fracture Prevention – A Population Based Cohort Study in Women

    Science.gov (United States)

    Helin-Salmivaara, Arja; Korhonen, Maarit J.; Lehenkari, Petri; Junnila, Seppo Y. T.; Neuvonen, Pertti J.; Ruokoniemi, Päivi; Huupponen, Risto

    2012-01-01

    Objective To study the association of long-term statin use and the risk of low-energy hip fractures in middle-aged and elderly women. Design A register-based cohort study. Setting Finland. Participants Women aged 45–75 years initiating statin therapy between 1996 and 2001 with adherence to statins ≥80% during the subsequent five years (n = 40 254), a respective cohort initiating hypertension drugs (n = 41 610), and women randomly selected from the population (n = 62 585). Main Outcome Measures Incidence rate of and hazard ratio (HR) for low-energy hip fracture during the follow-up extending up to 7 years after the 5-year exposure period. Results Altogether 199 low-energy hip fractures occurred during the 135 330 person-years (py) of follow-up in the statin cohort, giving an incidence rate of 1.5 hip fractures per 1000 py. In the hypertension and the population cohorts, the rates were 2.0 per 1000 py (312 fractures per 157 090 py) and 1.0 per 1000 py (212 fractures per 216 329 py), respectively. Adjusting for a propensity score and individual variables strongly predicting the outcome, good adherence to statins for five years was associated with a 29% decreased risk (HR 0.71; 95% CI 0.58–0.86) of a low-energy hip fracture in comparison with adherent use of hypertension drugs. The association was of the same magnitude when comparing the statin users with the population cohort, the HR being 0.69 (0.55–0.87). When women with poor (statins were compared to those with good adherence to hypertension drugs (≥80%) or to the population cohort, the protective effect associated with statin use attenuated with the decreasing level of adherence. Conclusions 5-year exposure to statins is associated with a reduced risk of low-energy hip fracture in women aged 50–80 years without prior hospitalizations for fractures. PMID:23144731

  20. Random drift versus selection in academic vocabulary: an evolutionary analysis of published keywords.

    Science.gov (United States)

    Bentley, R Alexander

    2008-08-27

    The evolution of vocabulary in academic publishing is characterized via keyword frequencies recorded in the ISI Web of Science citations database. In four distinct case-studies, evolutionary analysis of keyword frequency change through time is compared to a model of random copying used as the null hypothesis, such that selection may be identified against it. The case studies from the physical sciences indicate greater selection in keyword choice than in the social sciences. Similar evolutionary analyses can be applied to a wide range of phenomena; wherever the popularity of multiple items through time has been recorded, as with web searches, or sales of popular music and books, for example.