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Sample records for dominance genetic variances

  1. Dominance Genetic Variance for Traits Under Directional Selection in Drosophila serrata

    Science.gov (United States)

    Sztepanacz, Jacqueline L.; Blows, Mark W.

    2015-01-01

    In contrast to our growing understanding of patterns of additive genetic variance in single- and multi-trait combinations, the relative contribution of nonadditive genetic variance, particularly dominance variance, to multivariate phenotypes is largely unknown. While mechanisms for the evolution of dominance genetic variance have been, and to some degree remain, subject to debate, the pervasiveness of dominance is widely recognized and may play a key role in several evolutionary processes. Theoretical and empirical evidence suggests that the contribution of dominance variance to phenotypic variance may increase with the correlation between a trait and fitness; however, direct tests of this hypothesis are few. Using a multigenerational breeding design in an unmanipulated population of Drosophila serrata, we estimated additive and dominance genetic covariance matrices for multivariate wing-shape phenotypes, together with a comprehensive measure of fitness, to determine whether there is an association between directional selection and dominance variance. Fitness, a trait unequivocally under directional selection, had no detectable additive genetic variance, but significant dominance genetic variance contributing 32% of the phenotypic variance. For single and multivariate morphological traits, however, no relationship was observed between trait–fitness correlations and dominance variance. A similar proportion of additive and dominance variance was found to contribute to phenotypic variance for single traits, and double the amount of additive compared to dominance variance was found for the multivariate trait combination under directional selection. These data suggest that for many fitness components a positive association between directional selection and dominance genetic variance may not be expected. PMID:25783700

  2. Using SNP markers to estimate additive, dominance and imprinting genetic variance

    DEFF Research Database (Denmark)

    Lopes, M S; Bastiaansen, J W M; Janss, Luc

    The contributions of additive, dominance and imprinting effects to the variance of number of teats (NT) were evaluated in two purebred pig populations using SNP markers. Three different random regression models were evaluated, accounting for the mean and: 1) additive effects (MA), 2) additive...... and dominance effects (MAD) and 3) additive, dominance and imprinting effects (MADI). Additive heritability estimates were 0.30, 0.28 and 0.27-0.28 in both lines using MA, MAD and MADI, respectively. Dominance heritability ranged from 0.06 to 0.08 using MAD and MADI. Imprinting heritability ranged from 0.......01 to 0.02. Dominance effects make an important contribution to the genetic variation of NT in the two lines evaluated. Imprinting effects appeared less important for NT than additive and dominance effects. The SNP random regression model presented and evaluated in this study is a feasible approach...

  3. On the additive and dominant variance and covariance of individuals within the genomic selection scope.

    Science.gov (United States)

    Vitezica, Zulma G; Varona, Luis; Legarra, Andres

    2013-12-01

    Genomic evaluation models can fit additive and dominant SNP effects. Under quantitative genetics theory, additive or "breeding" values of individuals are generated by substitution effects, which involve both "biological" additive and dominant effects of the markers. Dominance deviations include only a portion of the biological dominant effects of the markers. Additive variance includes variation due to the additive and dominant effects of the markers. We describe a matrix of dominant genomic relationships across individuals, D, which is similar to the G matrix used in genomic best linear unbiased prediction. This matrix can be used in a mixed-model context for genomic evaluations or to estimate dominant and additive variances in the population. From the "genotypic" value of individuals, an alternative parameterization defines additive and dominance as the parts attributable to the additive and dominant effect of the markers. This approach underestimates the additive genetic variance and overestimates the dominance variance. Transforming the variances from one model into the other is trivial if the distribution of allelic frequencies is known. We illustrate these results with mouse data (four traits, 1884 mice, and 10,946 markers) and simulated data (2100 individuals and 10,000 markers). Variance components were estimated correctly in the model, considering breeding values and dominance deviations. For the model considering genotypic values, the inclusion of dominant effects biased the estimate of additive variance. Genomic models were more accurate for the estimation of variance components than their pedigree-based counterparts.

  4. Estimation of dominance variance in purebred Yorkshire swine.

    Science.gov (United States)

    Culbertson, M S; Mabry, J W; Misztal, I; Gengler, N; Bertrand, J K; Varona, L

    1998-02-01

    We used 179,485 Yorkshire reproductive and 239,354 Yorkshire growth records to estimate additive and dominance variances by Method Fraktur R. Estimates were obtained for number born alive (NBA), 21-d litter weight (LWT), days to 104.5 kg (DAYS), and backfat at 104.5 kg (BF). The single-trait models for NBA and LWT included the fixed effects of contemporary group and regression on inbreeding percentage and the random effects mate within contemporary group, animal permanent environment, animal additive, and parental dominance. The single-trait models for DAYS and BF included the fixed effects of contemporary group, sex, and regression on inbreeding percentage and the random effects litter of birth, dam permanent environment, animal additive, and parental dominance. Final estimates were obtained from six samples for each trait. Regression coefficients for 10% inbreeding were found to be -.23 for NBA, -.52 kg for LWT, 2.1 d for DAYS, and 0 mm for BF. Estimates of additive and dominance variances expressed as a percentage of phenotypic variances were, respectively, 8.8 +/- .5 and 2.2 +/- .7 for NBA, 8.1 +/- 1.1 and 6.3 +/- .9 for LWT, 33.2 +/- .4 and 10.3 +/- 1.5 for DAYS, and 43.6 +/- .9 and 4.8 +/- .7 for BF. The ratio of dominance to additive variances ranged from .78 to .11.

  5. Characterizing the evolution of genetic variance using genetic covariance tensors.

    Science.gov (United States)

    Hine, Emma; Chenoweth, Stephen F; Rundle, Howard D; Blows, Mark W

    2009-06-12

    Determining how genetic variance changes under selection in natural populations has proved to be a very resilient problem in evolutionary genetics. In the same way that understanding the availability of genetic variance within populations requires the simultaneous consideration of genetic variance in sets of functionally related traits, determining how genetic variance changes under selection in natural populations will require ascertaining how genetic variance-covariance (G) matrices evolve. Here, we develop a geometric framework using higher-order tensors, which enables the empirical characterization of how G matrices have diverged among populations. We then show how divergence among populations in genetic covariance structure can then be associated with divergence in selection acting on those traits using key equations from evolutionary theory. Using estimates of G matrices of eight male sexually selected traits from nine geographical populations of Drosophila serrata, we show that much of the divergence in genetic variance occurred in a single trait combination, a conclusion that could not have been reached by examining variation among the individual elements of the nine G matrices. Divergence in G was primarily in the direction of the major axes of genetic variance within populations, suggesting that genetic drift may be a major cause of divergence in genetic variance among these populations.

  6. Estimation of the additive and dominance variances in South African Landrace pigs

    OpenAIRE

    Norris, D.; Varona Aguado, Luís; Visser, D. P.; Theron, H. E.; Voordewind, S. F.; Nesambuni, E. A.

    2006-01-01

    The objective of this study was to estimate dominance variance for number born alive (NBA), 21- day litter weight (LWT21) and interval between parities (FI) in South African Landrace pigs. A total of 26223 NBA, 21335 LWT21 and 16370 FI records were analysed. Bayesian analysis via Gibbs sampling was used to estimate variance components and genetic parameters were calculated from posterior distributions. Estimates of additive genetic variance were 0.669, 43.46 d2 and 9.02 kg2 for NBA, FI and LW...

  7. Bias-variance decomposition in Genetic Programming

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    Kowaliw Taras

    2016-01-01

    Full Text Available We study properties of Linear Genetic Programming (LGP through several regression and classification benchmarks. In each problem, we decompose the results into bias and variance components, and explore the effect of varying certain key parameters on the overall error and its decomposed contributions. These parameters are the maximum program size, the initial population, and the function set used. We confirm and quantify several insights into the practical usage of GP, most notably that (a the variance between runs is primarily due to initialization rather than the selection of training samples, (b parameters can be reasonably optimized to obtain gains in efficacy, and (c functions detrimental to evolvability are easily eliminated, while functions well-suited to the problem can greatly improve performance—therefore, larger and more diverse function sets are always preferable.

  8. Estimation of additive and dominance variance for reproductive traits from different models in Duroc purebred

    OpenAIRE

    Talerngsak Angkuraseranee

    2010-01-01

    The additive and dominance genetic variances of 5,801 Duroc reproductive and growth records were estimated usingBULPF90 PC-PACK. Estimates were obtained for number born alive (NBA), birth weight (BW), number weaned (NW), andweaning weight (WW). Data were analyzed using two mixed model equations. The first model included fixed effects andrandom effects identifying inbreeding depression, additive gene effect and permanent environments effects. The secondmodel was similar to the first model, but...

  9. Estimation of additive and dominance variance for reproductive traits from different models in Duroc purebred

    Directory of Open Access Journals (Sweden)

    Talerngsak Angkuraseranee

    2010-05-01

    Full Text Available The additive and dominance genetic variances of 5,801 Duroc reproductive and growth records were estimated usingBULPF90 PC-PACK. Estimates were obtained for number born alive (NBA, birth weight (BW, number weaned (NW, andweaning weight (WW. Data were analyzed using two mixed model equations. The first model included fixed effects andrandom effects identifying inbreeding depression, additive gene effect and permanent environments effects. The secondmodel was similar to the first model, but included the dominance genotypic effect. Heritability estimates of NBA, BW, NWand WW from the two models were 0.1558/0.1716, 0.1616/0.1737, 0.0372/0.0874 and 0.1584/0.1516 respectively. Proportionsof dominance effect to total phenotypic variance from the dominance model were 0.1024, 0.1625, 0.0470, and 0.1536 for NBA,BW, NW and WW respectively. Dominance effects were found to have sizable influence on the litter size traits analyzed.Therefore, genetic evaluation with the dominance model (Model 2 is found more appropriate than the animal model (Model 1.

  10. Variance in Dominant Grain Size Across the Mississippi River Delta

    Science.gov (United States)

    Miller, K. L.; Chamberlain, E. L.; Esposito, C. R.; Wagner, R. W.; Mohrig, D. C.

    2016-02-01

    Proposals to restore coastal Louisiana often center on Mississippi River diversion projects wherein water and sediment are routed into wetlands and shallow waters in an effort to build land. Successful design and implementation of diversions will include consideration of behavior and characteristics of sediment, both in the river and in the receiving basin. The Mississippi River sediment load is primarily mud (roughly 75%), with the remainder being very-fine to medium sand or organic detritus. The dominance of muds leads many to suggest that diversions should focus on capturing the mud fraction despite the smaller size and longer settling times required for these particles compared to sand; others believe that sand should be the focus. We present a systemic analysis of the texture of land-building sediment in the Mississippi Delta using borehole data from various depositional environments representing a range of spatial scales, system ages, and fluvial and basin characteristics. We include subdelta-scale data from the incipient Wax Lake Delta and from the distal plain of the abandoned Lafourche subdelta, as well as crevasse-scale data from modern Cubit's Gap and the Attakapas splay, an inland Lafourche crevasse. Comparison of these sites demonstrates a large variance in the volumetric mud to sand ratios across the system. We consider the differences to be emblematic of the various forcings on each lobe as it formed and suggest that the most efficient building block for a diversion is a function of the receiving basin and is not uniform across the entire delta.

  11. Genetics of the dominant ataxias

    NARCIS (Netherlands)

    Verbeek, Dineke S.; van de Warrenburg, Bart P. C.

    2011-01-01

    The relevant clinical, genetic, and cell biologic aspects of the dominantly inherited spinocerebellar ataxias (SCAs) are reviewed in this article. SCAs are diseases of the entire nervous system; in addition to cerebellar ataxia, the central (but not obligate) disease feature, many noncerebellar comp

  12. The phenome-wide distribution of genetic variance.

    Science.gov (United States)

    Blows, Mark W; Allen, Scott L; Collet, Julie M; Chenoweth, Stephen F; McGuigan, Katrina

    2015-07-01

    A general observation emerging from estimates of additive genetic variance in sets of functionally or developmentally related traits is that much of the genetic variance is restricted to few trait combinations as a consequence of genetic covariance among traits. While this biased distribution of genetic variance among functionally related traits is now well documented, how it translates to the broader phenome and therefore any trait combination under selection in a given environment is unknown. We show that 8,750 gene expression traits measured in adult male Drosophila serrata exhibit widespread genetic covariance among random sets of five traits, implying that pleiotropy is common. Ultimately, to understand the phenome-wide distribution of genetic variance, very large additive genetic variance-covariance matrices (G) are required to be estimated. We draw upon recent advances in matrix theory for completing high-dimensional matrices to estimate the 8,750-trait G and show that large numbers of gene expression traits genetically covary as a consequence of a single genetic factor. Using gene ontology term enrichment analysis, we show that the major axis of genetic variance among expression traits successfully identified genetic covariance among genes involved in multiple modes of transcriptional regulation. Our approach provides a practical empirical framework for the genetic analysis of high-dimensional phenome-wide trait sets and for the investigation of the extent of high-dimensional genetic constraint.

  13. Analysis of Variance Components for Genetic Markers with Unphased Genotypes.

    Science.gov (United States)

    Wang, Tao

    2016-01-01

    An ANOVA type general multi-allele (GMA) model was proposed in Wang (2014) on analysis of variance components for quantitative trait loci or genetic markers with phased or unphased genotypes. In this study, by applying the GMA model, we further examine estimation of the genetic variance components for genetic markers with unphased genotypes based on a random sample from a study population. In one locus and two loci cases, we first derive the least square estimates (LSE) of model parameters in fitting the GMA model. Then we construct estimators of the genetic variance components for one marker locus in a Hardy-Weinberg disequilibrium population and two marker loci in an equilibrium population. Meanwhile, we explore the difference between the classical general linear model (GLM) and GMA based approaches in association analysis of genetic markers with quantitative traits. We show that the GMA model can retain the same partition on the genetic variance components as the traditional Fisher's ANOVA model, while the GLM cannot. We clarify that the standard F-statistics based on the partial reductions in sums of squares from GLM for testing the fixed allelic effects could be inadequate for testing the existence of the variance component when allelic interactions are present. We point out that the GMA model can reduce the confounding between the allelic effects and allelic interactions at least for independent alleles. As a result, the GMA model could be more beneficial than GLM for detecting allelic interactions.

  14. Genetic heterogeneity of residual variance in broiler chickens

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    Hill William G

    2006-11-01

    Full Text Available Abstract Aims were to estimate the extent of genetic heterogeneity in environmental variance. Data comprised 99 535 records of 35-day body weights from broiler chickens reared in a controlled environment. Residual variance within dam families was estimated using ASREML, after fitting fixed effects such as genetic groups and hatches, for each of 377 genetically contemporary sires with a large number of progeny (> 100 males or females each. Residual variance was computed separately for male and female offspring, and after correction for sampling, strong evidence for heterogeneity was found, the standard deviation between sires in within variance amounting to 15–18% of its mean. Reanalysis using log-transformed data gave similar results, and elimination of 2–3% of outlier data reduced the heterogeneity but it was still over 10%. The correlation between estimates for males and females was low, however. The correlation between sire effects on progeny mean and residual variance for body weight was small and negative (-0.1. Using a data set bigger than any yet presented and on a trait measurable in both sexes, this study has shown evidence for heterogeneity in the residual variance, which could not be explained by segregation of major genes unless very few determined the trait.

  15. Population Bottlenecks Increase Additive Genetic Variance But Do Not Break a Selection Limit in Rainforest Drosophila

    DEFF Research Database (Denmark)

    van Heerwaarden, Belinda; Willi, Yvonne; Kristensen, Torsten N

    2008-01-01

    actually increase additive genetic variance. This has been an important issue in conservation genetics where it has been suggested that small population size might actually experience an increase rather than a decrease in the rate of adaptation. Here we test if bottlenecks can break a selection limit...... for desiccation resistance in the rain forest-restricted fly Drosophila bunnanda. After one generation of single-pair mating, additive genetic variance for desiccation resistance increased to a significant level, on average higher than for the control lines. Line crosses revealed that both dominance and epistatic...... effects were responsible for the divergence in desiccation resistance between the original control and a bottlenecked line exhibiting increased additive genetic variance for desiccation resistance. However, when bottlenecked lines were selected for increased desiccation resistance, there was only a small...

  16. Genetic variance of tolerance and the toxicant threshold model.

    Science.gov (United States)

    Tanaka, Yoshinari; Mano, Hiroyuki; Tatsuta, Haruki

    2012-04-01

    A statistical genetics method is presented for estimating the genetic variance (heritability) of tolerance to pollutants on the basis of a standard acute toxicity test conducted on several isofemale lines of cladoceran species. To analyze the genetic variance of tolerance in the case when the response is measured as a few discrete states (quantal endpoints), the authors attempted to apply the threshold character model in quantitative genetics to the threshold model separately developed in ecotoxicology. The integrated threshold model (toxicant threshold model) assumes that the response of a particular individual occurs at a threshold toxicant concentration and that the individual tolerance characterized by the individual's threshold value is determined by genetic and environmental factors. As a case study, the heritability of tolerance to p-nonylphenol in the cladoceran species Daphnia galeata was estimated by using the maximum likelihood method and nested analysis of variance (ANOVA). Broad-sense heritability was estimated to be 0.199 ± 0.112 by the maximum likelihood method and 0.184 ± 0.089 by ANOVA; both results implied that the species examined had the potential to acquire tolerance to this substance by evolutionary change.

  17. International Diversification Versus Domestic Diversification: Mean-Variance Portfolio Optimization and Stochastic Dominance Approaches

    OpenAIRE

    Fathi Abid; Pui Lam Leung; Mourad Mroua; Wing Keung Wong

    2014-01-01

    This paper applies the mean-variance portfolio optimization (PO) approach and the stochastic dominance (SD) test to examine preferences for international diversification versus domestic diversification from American investors’ viewpoints. Our PO results imply that the domestic diversification strategy dominates the international diversification strategy at a lower risk level and the reverse is true at a higher risk level. Our SD analysis shows that there is no arbitrage opportunity between in...

  18. Non-genetic variance in pigs: genetic analysis of reproduction and production traits

    NARCIS (Netherlands)

    Sell-Kubiak, E.B.

    2015-01-01

    Abstract Sell-Kubiak, E. (2015). Non-genetic variance in pigs: genetic analysis of reproduction and production traits. PhD thesis, Wageningen University, The Netherlands The main objective of this thesis was to study the origin of random variance in reproduction and production trait

  19. International Diversification Versus Domestic Diversification: Mean-Variance Portfolio Optimization and Stochastic Dominance Approaches

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    Fathi Abid

    2014-05-01

    Full Text Available This paper applies the mean-variance portfolio optimization (PO approach and the stochastic dominance (SD test to examine preferences for international diversification versus domestic diversification from American investors’ viewpoints. Our PO results imply that the domestic diversification strategy dominates the international diversification strategy at a lower risk level and the reverse is true at a higher risk level. Our SD analysis shows that there is no arbitrage opportunity between international and domestic stock markets; domestically diversified portfolios with smaller risk dominate internationally diversified portfolios with larger risk and vice versa; and at the same risk level, there is no difference between the domestically and internationally diversified portfolios. Nonetheless, we cannot find any domestically diversified portfolios that stochastically dominate all internationally diversified portfolios, but we find some internationally diversified portfolios with small risk that dominate all the domestically diversified portfolios.

  20. Estimates of genetic variance and variance of predicted genetic merits using pedigree or genomic relationship matrices in six Brown Swiss cattle populations for different traits.

    Science.gov (United States)

    Loberg, A; Dürr, J W; Fikse, W F; Jorjani, H; Crooks, L

    2015-10-01

    The amount of variance captured in genetic estimations may depend on whether a pedigree-based or genomic relationship matrix is used. The purpose of this study was to investigate the genetic variance as well as the variance of predicted genetic merits (PGM) using pedigree-based or genomic relationship matrices in Brown Swiss cattle. We examined a range of traits in six populations amounting to 173 population-trait combinations. A main aim was to determine how using different relationship matrices affect variance estimation. We calculated ratios between different types of estimates and analysed the impact of trait heritability and population size. The genetic variances estimated by REML using a genomic relationship matrix were always smaller than the variances that were similarly estimated using a pedigree-based relationship matrix. The variances from the genomic relationship matrix became closer to estimates from a pedigree relationship matrix as heritability and population size increased. In contrast, variances of predicted genetic merits obtained using a genomic relationship matrix were mostly larger than variances of genetic merit predicted using pedigree-based relationship matrix. The ratio of the genomic to pedigree-based PGM variances decreased as heritability and population size rose. The increased variance among predicted genetic merits is important for animal breeding because this is one of the factors influencing genetic progress. © 2015 Blackwell Verlag GmbH.

  1. Detecting parent of origin and dominant QTL in a two-generation commercial poultry pedigree using variance component methodology

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    Haley Christopher S

    2009-01-01

    Full Text Available Abstract Introduction Variance component QTL methodology was used to analyse three candidate regions on chicken chromosomes 1, 4 and 5 for dominant and parent-of-origin QTL effects. Data were available for bodyweight and conformation score measured at 40 days from a two-generation commercial broiler dam line. One hundred dams were nested in 46 sires with phenotypes and genotypes on 2708 offspring. Linear models were constructed to simultaneously estimate fixed, polygenic and QTL effects. Different genetic models were compared using likelihood ratio test statistics derived from the comparison of full with reduced or null models. Empirical thresholds were derived by permutation analysis. Results Dominant QTL were found for bodyweight on chicken chromosome 4 and for bodyweight and conformation score on chicken chromosome 5. Suggestive evidence for a maternally expressed QTL for bodyweight and conformation score was found on chromosome 1 in a region corresponding to orthologous imprinted regions in the human and mouse. Conclusion Initial results suggest that variance component analysis can be applied within commercial populations for the direct detection of segregating dominant and parent of origin effects.

  2. Intra-population genetic variance for grain iron and zinc contents and agronomic traits in pearl millet

    Institute of Scientific and Technical Information of China (English)

    Mahalingam Govindaraj; Kedar N.Rai; Ponnusamy Shanmugasundaram

    2016-01-01

    Crop biofortification is a sustainable approach for fighting micronutrient malnutrition in the world. The estimation of variance components in genetically broad-based populations provides information about their genetic architecture, allowing the design of an appropriate biofortification breeding method for cross-pollinated crops such as pearl millet. The objective of this study was to estimate intra-population genetic variance using self(S1) and half-sib(HS) progenies in two populations, AIMP92901 and ICMR312. Field trials were evaluated in two contrasting seasons(2009 rainy and 2010 summer; otherwise called environments) in Alfisols at ICRISAT, Patancheru. Analyses of variance showed highly significant variation for S1 s and HS progenies, reflecting high within-population genetic variation for both micronutrients and other key traits. However, the HS showed narrow ranges and lower genetic variances than the S1 for all of the traits. The micronutrients were highly positively correlated in S1(r = 0.77 to 0.86; P < 0.01) and HS(r = 0.74 to 0.77; P < 0.01)progenies of both populations, implying concurrent genetic improvement for both micronutrients. The genetic variance component was different among populations for Fe and Zn contents across environments, with AIMP92901 showing a greater proportion of dominance and ICMR312 greater additive variance for these micronutrients. The estimates of variance(additive and dominance) were specific for each population, given their dependence on the additive and dominance effects of the segregating loci, which also differ among populations. The possible causes for such differences were discussed. The results showed that the expression of these micronutrients in pearl millet shows largely additive variance, so that breeding high-iron hybrids will require incorporation of these micronutrient traits into both parental lines.

  3. Intra-population genetic variance for grain iron and zinc contents and agronomic traits in pearl millet

    Institute of Scientific and Technical Information of China (English)

    Mahalingam Govindaraj; Kedar N. Rai; Ponnusamy Shanmugasundaram

    2016-01-01

    Crop biofortification is a sustainable approach for fighting micronutrient malnutrition in the world. The estimation of variance components in genetically broad-based populations provides information about their genetic architecture, allowing the design of an appropriate biofortification breeding method for cross-pollinated crops such as pearl millet. The objective of this study was to estimate intra-population genetic variance using self (S1) and half-sib (HS) progenies in two populations, AIMP92901 and ICMR312. Field trials were evaluated in two contrasting seasons (2009 rainy and 2010 summer; otherwise called environments) in Alfisols at ICRISAT, Patancheru. Analyses of variance showed highly significant variation for S1s and HS progenies, reflecting high within-population genetic variation for both micronutrients and other key traits. However, the HS showed narrow ranges and lower genetic variances than the S1 for all of the traits. The micronutrients were highly positively correlated in S1 (r=0.77 to 0.86;P<0.01) and HS (r=0.74 to 0.77;P<0.01) progenies of both populations, implying concurrent genetic improvement for both micronutrients. The genetic variance component was different among populations for Fe and Zn contents across environments, with AIMP92901 showing a greater proportion of dominance and ICMR312 greater additive variance for these micronutrients. The estimates of variance (additive and dominance) were specific for each population, given their dependence on the additive and dominance effects of the segregating loci, which also differ among populations. The possible causes for such differences were discussed. The results showed that the expression of these micronutrients in pearl millet shows largely additive variance, so that breeding high-iron hybrids will require incorporation of these micronu-trient traits into both parental lines.

  4. Argentine Population Genetic Structure: Large Variance in Amerindian Contribution

    Science.gov (United States)

    Seldin, Michael F.; Tian, Chao; Shigeta, Russell; Scherbarth, Hugo R.; Silva, Gabriel; Belmont, John W.; Kittles, Rick; Gamron, Susana; Allevi, Alberto; Palatnik, Simon A.; Alvarellos, Alejandro; Paira, Sergio; Caprarulo, Cesar; Guillerón, Carolina; Catoggio, Luis J.; Prigione, Cristina; Berbotto, Guillermo A.; García, Mercedes A.; Perandones, Carlos E.; Pons-Estel, Bernardo A.; Alarcon-Riquelme, Marta E.

    2011-01-01

    Argentine population genetic structure was examined using a set of 78 ancestry informative markers (AIMs) to assess the contributions of European, Amerindian, and African ancestry in 94 individuals members of this population. Using the Bayesian clustering algorithm STRUCTURE, the mean European contribution was 78%, the Amerindian contribution was 19.4%, and the African contribution was 2.5%. Similar results were found using weighted least mean square method: European, 80.2%; Amerindian, 18.1%; and African, 1.7%. Consistent with previous studies the current results showed very few individuals (four of 94) with greater than 10% African admixture. Notably, when individual admixture was examined, the Amerindian and European admixture showed a very large variance and individual Amerindian contribution ranged from 1.5 to 84.5% in the 94 individual Argentine subjects. These results indicate that admixture must be considered when clinical epidemiology or case control genetic analyses are studied in this population. Moreover, the current study provides a set of informative SNPs that can be used to ascertain or control for this potentially hidden stratification. In addition, the large variance in admixture proportions in individual Argentine subjects shown by this study suggests that this population is appropriate for future admixture mapping studies. PMID:17177183

  5. Estimation of genetic variation in residual variance in female and male broiler chickens

    NARCIS (Netherlands)

    Mulder, H.A.; Hill, W.G.; Vereijken, A.; Veerkamp, R.F.

    2009-01-01

    In breeding programs, robustness of animals and uniformity of end product can be improved by exploiting genetic variation in residual variance. Residual variance can be defined as environmental variance after accounting for all identifiable effects. The aims of this study were to estimate genetic va

  6. Genetic variance of sunflower yield components - Heliantus annuus L.

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    Hladni Nada

    2003-01-01

    Full Text Available The main goals of sunflower breeding in Yugoslavia and abroad are increased seed yield and oil content per unit area and increased resistance to diseases, insects and stress conditions via an optimization of plant architecture. In order to determine the mode of inheritance, gene effects and correlations of total leaf number per plant, total leaf area and plant height, six genetically divergent inbred lines of sunflower were subjected to half diallel crosses. Significant differences in mean values of all the traits were found in the F1 and F2 generations. Additive gene effects were more important in the inheritance of total leaf number per plant and plant height, while in the case of total leaf area per plant the nonadditive ones were more important looking at all the combinations in the F1 and F2 generations. The average degree of dominance (Hi/D1/2 was lower than one for total leaf number per plant and plant height, so the mode of inheritance was partial dominance, while with total leaf area the value was higher than one, indicating super dominance as the mode of inheritance. Significant positive correlation was found: between total leaf area per plant and total leaf number per plant (0.285* and plant height (0.278*. The results of the study are of importance for further sunflower breeding work.

  7. Genetic control of residual variance of yearling weight in Nellore beef cattle.

    Science.gov (United States)

    Iung, L H S; Neves, H H R; Mulder, H A; Carvalheiro, R

    2017-04-01

    There is evidence for genetic variability in residual variance of livestock traits, which offers the potential for selection for increased uniformity of production. Different statistical approaches have been employed to study this topic; however, little is known about the concordance between them. The aim of our study was to investigate the genetic heterogeneity of residual variance on yearling weight (YW; 291.15 ± 46.67) in a Nellore beef cattle population; to compare the results of the statistical approaches, the two-step approach and the double hierarchical generalized linear model (DHGLM); and to evaluate the effectiveness of power transformation to accommodate scale differences. The comparison was based on genetic parameters, accuracy of EBV for residual variance, and cross-validation to assess predictive performance of both approaches. A total of 194,628 yearling weight records from 625 sires were used in the analysis. The results supported the hypothesis of genetic heterogeneity of residual variance on YW in Nellore beef cattle and the opportunity of selection, measured through the genetic coefficient of variation of residual variance (0.10 to 0.12 for the two-step approach and 0.17 for DHGLM, using an untransformed data set). However, low estimates of genetic variance associated with positive genetic correlations between mean and residual variance (about 0.20 for two-step and 0.76 for DHGLM for an untransformed data set) limit the genetic response to selection for uniformity of production while simultaneously increasing YW itself. Moreover, large sire families are needed to obtain accurate estimates of genetic merit for residual variance, as indicated by the low heritability estimates (variance on the mean and decreased the estimates of genetic parameters for residual variance. The transformation reduced but did not eliminate all the genetic heterogeneity of residual variance, highlighting its presence beyond the scale effect. The DHGLM showed higher

  8. The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentration in Leaves Acts as a Source of Unexplained Additive Genetic Variance.

    Directory of Open Access Journals (Sweden)

    Simon K G Forsberg

    2015-11-01

    Full Text Available Genome-wide association (GWA analyses have generally been used to detect individual loci contributing to the phenotypic diversity in a population by the effects of these loci on the trait mean. More rarely, loci have also been detected based on variance differences between genotypes. Several hypotheses have been proposed to explain the possible genetic mechanisms leading to such variance signals. However, little is known about what causes these signals, or whether this genetic variance-heterogeneity reflects mechanisms of importance in natural populations. Previously, we identified a variance-heterogeneity GWA (vGWA signal for leaf molybdenum concentrations in Arabidopsis thaliana. Here, fine-mapping of this association reveals that the vGWA emerges from the effects of three independent genetic polymorphisms that all are in strong LD with the markers displaying the genetic variance-heterogeneity. By revealing the genetic architecture underlying this vGWA signal, we uncovered the molecular source of a significant amount of hidden additive genetic variation or "missing heritability". Two of the three polymorphisms underlying the genetic variance-heterogeneity are promoter variants for Molybdate transporter 1 (MOT1, and the third a variant located ~25 kb downstream of this gene. A fourth independent association was also detected ~600 kb upstream of MOT1. Use of a T-DNA knockout allele highlights Copper Transporter 6; COPT6 (AT2G26975 as a strong candidate gene for this association. Our results show that an extended LD across a complex locus including multiple functional alleles can lead to a variance-heterogeneity between genotypes in natural populations. Further, they provide novel insights into the genetic regulation of ion homeostasis in A. thaliana, and empirically confirm that variance-heterogeneity based GWA methods are a valuable tool to detect novel associations of biological importance in natural populations.

  9. Comparison of multiplicative heterogeneous variance adjustment models for genetic evaluations.

    Science.gov (United States)

    Márkus, Sz; Mäntysaari, E A; Strandén, I; Eriksson, J-Å; Lidauer, M H

    2014-06-01

    Two heterogeneous variance adjustment methods and two variance models were compared in a simulation study. The method used for heterogeneous variance adjustment in the Nordic test-day model, which is a multiplicative method based on Meuwissen (J. Dairy Sci., 79, 1996, 310), was compared with a restricted multiplicative method where the fixed effects were not scaled. Both methods were tested with two different variance models, one with a herd-year and the other with a herd-year-month random effect. The simulation study was built on two field data sets from Swedish Red dairy cattle herds. For both data sets, 200 herds with test-day observations over a 12-year period were sampled. For one data set, herds were sampled randomly, while for the other, each herd was required to have at least 10 first-calving cows per year. The simulations supported the applicability of both methods and models, but the multiplicative mixed model was more sensitive in the case of small strata sizes. Estimation of variance components for the variance models resulted in different parameter estimates, depending on the applied heterogeneous variance adjustment method and variance model combination. Our analyses showed that the assumption of a first-order autoregressive correlation structure between random-effect levels is reasonable when within-herd heterogeneity is modelled by year classes, but less appropriate for within-herd heterogeneity by month classes. Of the studied alternatives, the multiplicative method and a variance model with a random herd-year effect were found most suitable for the Nordic test-day model for dairy cattle evaluation.

  10. Prediction of breeding values and selection responses with genetic heterogeneity of environmental variance

    NARCIS (Netherlands)

    Mulder, H.A.; Bijma, P.; Hill, W.G.

    2007-01-01

    There is empirical evidence that genotypes differ not only in mean, but also in environmental variance of the traits they affect. Genetic heterogeneity of environmental variance may indicate genetic differences in environmental sensitivity. The aim of this study was to develop a general framework fo

  11. Genetically controlled environmental variance for sternopleural bristles in Drosophila melanogaster - an experimental test of a heterogeneous variance model

    DEFF Research Database (Denmark)

    Sørensen, Anders Christian; Kristensen, Torsten Nygård; Loeschcke, Volker

    2007-01-01

    quantitative genetics model based on the infinitesimal model, and an extension of this model. In the extended model it is assumed that each individual has its own environmental variance and that this heterogeneity of variance has a genetic component. The heterogeneous variance model was favoured by the data......, indicating that the environmental variance is partly under genetic control. If this heterogeneous variance model also applies to livestock, it would be possible to select for animals with a higher uniformity of products across environmental regimes. Also for evolutionary biology the results are of interest...

  12. Genetic factors explain half of all variance in serum eosinophil cationic protein

    DEFF Research Database (Denmark)

    Elmose, Camilla; Sverrild, Asger; van der Sluis, Sophie

    2014-01-01

    , exhaled nitric oxide, and skin test reactivity, measured. Linear regression analysis and variance component models were used to study factors associated with variation in ECP and the relative genetic influence on ECP levels. RESULTS: Sex (regression coefficient = -0.107, P ... to the most parsimonious variance component model, genetic factors accounted for 57% (CI: 42-72%, P variance in ECP levels, whereas the remainder (43%) was ascribable to non-shared environmental factors. The genetic correlation between ECP and airway responsiveness to methacholine...... was statistically non-significant (r = -0.11, P = 0.50). CONCLUSION: Around half of all variance in serum ECP is explained by genetic factors. Serum ECP is influenced by sex, BMI, and airway responsiveness. Serum ECP and airway responsiveness seem not to share genetic variance....

  13. The Genetic Architecture of Quantitative Traits Cannot Be Inferred from Variance Component Analysis

    Science.gov (United States)

    Huang, Wen; Mackay, Trudy F. C.

    2016-01-01

    Classical quantitative genetic analyses estimate additive and non-additive genetic and environmental components of variance from phenotypes of related individuals without knowing the identities of quantitative trait loci (QTLs). Many studies have found a large proportion of quantitative trait variation can be attributed to the additive genetic variance (VA), providing the basis for claims that non-additive gene actions are unimportant. In this study, we show that arbitrarily defined parameterizations of genetic effects seemingly consistent with non-additive gene actions can also capture the majority of genetic variation. This reveals a logical flaw in using the relative magnitudes of variance components to indicate the relative importance of additive and non-additive gene actions. We discuss the implications and propose that variance component analyses should not be used to infer the genetic architecture of quantitative traits. PMID:27812106

  14. The Genetic Architecture of Quantitative Traits Cannot Be Inferred from Variance Component Analysis.

    Directory of Open Access Journals (Sweden)

    Wen Huang

    2016-11-01

    Full Text Available Classical quantitative genetic analyses estimate additive and non-additive genetic and environmental components of variance from phenotypes of related individuals without knowing the identities of quantitative trait loci (QTLs. Many studies have found a large proportion of quantitative trait variation can be attributed to the additive genetic variance (VA, providing the basis for claims that non-additive gene actions are unimportant. In this study, we show that arbitrarily defined parameterizations of genetic effects seemingly consistent with non-additive gene actions can also capture the majority of genetic variation. This reveals a logical flaw in using the relative magnitudes of variance components to indicate the relative importance of additive and non-additive gene actions. We discuss the implications and propose that variance component analyses should not be used to infer the genetic architecture of quantitative traits.

  15. Sex Modifies Genetic Effects on Residual Variance in Urinary Calcium Excretion in Rat (Rattus norvegicus)

    OpenAIRE

    Perry, Guy M. L.; Nehrke, Keith W.; Bushinsky, David A; Reid, Robert; Lewandowski, Krista L.; Hueber, Paul; Scheinman, Steven J.

    2012-01-01

    Conventional genetics assumes common variance among alleles or genetic groups. However, evidence from vertebrate and invertebrate models suggests that residual genotypic variance may itself be under partial genetic control. Such a phenomenon would have great significance: high-variability alleles might confound the detection of “classically” acting genes or scatter predicted evolutionary outcomes among unpredicted trajectories. Of the few works on this phenomenon, many implicate sex in some a...

  16. Genetics Home Reference: autosomal dominant partial epilepsy with auditory features

    Science.gov (United States)

    ... Facebook Share on Twitter Your Guide to Understanding Genetic Conditions Search MENU Toggle navigation Home Page Search ... Conditions Genes Chromosomes & mtDNA Resources Help Me Understand Genetics Home Health Conditions ADPEAF autosomal dominant partial epilepsy ...

  17. Rapid Divergence of Genetic Variance-Covariance Matrix within a Natural Population

    NARCIS (Netherlands)

    Doroszuk, A.; Wojewodzic, M.W.; Gort, G.; Kammenga, J.E.

    2008-01-01

    The matrix of genetic variances and covariances (G matrix) represents the genetic architecture of multiple traits sharing developmental and genetic processes and is central for predicting phenotypic evolution. These predictions require that the G matrix be stable. Yet the timescale and conditions pr

  18. Genetic variance in micro-environmental sensitivity for milk and milk quality in Walloon Holstein cattle

    NARCIS (Netherlands)

    Vandenplas, J.; Bastin, C.; Gengler, N.; Mulder, H.A.

    2013-01-01

    Animals that are robust to environmental changes are desirable in the current dairy industry. Genetic differences in micro-environmental sensitivity can be studied through heterogeneity of residual variance between animals. However, residual variance between animals is usually assumed to be homogene

  19. Genetic variance in micro-environmental sensitivity for milk and milk quality in Walloon Holstein cattle.

    Science.gov (United States)

    Vandenplas, J; Bastin, C; Gengler, N; Mulder, H A

    2013-09-01

    Animals that are robust to environmental changes are desirable in the current dairy industry. Genetic differences in micro-environmental sensitivity can be studied through heterogeneity of residual variance between animals. However, residual variance between animals is usually assumed to be homogeneous in traditional genetic evaluations. The aim of this study was to investigate genetic heterogeneity of residual variance by estimating variance components in residual variance for milk yield, somatic cell score, contents in milk (g/dL) of 2 groups of milk fatty acids (i.e., saturated and unsaturated fatty acids), and the content in milk of one individual fatty acid (i.e., oleic acid, C18:1 cis-9), for first-parity Holstein cows in the Walloon Region of Belgium. A total of 146,027 test-day records from 26,887 cows in 747 herds were available. All cows had at least 3 records and a known sire. These sires had at least 10 cows with records and each herd × test-day had at least 5 cows. The 5 traits were analyzed separately based on fixed lactation curve and random regression test-day models for the mean. Estimation of variance components was performed by running iteratively expectation maximization-REML algorithm by the implementation of double hierarchical generalized linear models. Based on fixed lactation curve test-day mean models, heritability for residual variances ranged between 1.01×10(-3) and 4.17×10(-3) for all traits. The genetic standard deviation in residual variance (i.e., approximately the genetic coefficient of variation of residual variance) ranged between 0.12 and 0.17. Therefore, some genetic variance in micro-environmental sensitivity existed in the Walloon Holstein dairy cattle for the 5 studied traits. The standard deviations due to herd × test-day and permanent environment in residual variance ranged between 0.36 and 0.45 for herd × test-day effect and between 0.55 and 0.97 for permanent environmental effect. Therefore, nongenetic effects also

  20. Estimates for Genetic Variance Components in Reciprocal Recurrent Selection in Populations Derived from Maize Single-Cross Hybrids

    Directory of Open Access Journals (Sweden)

    Matheus Costa dos Reis

    2014-01-01

    Full Text Available This study was carried out to obtain the estimates of genetic variance and covariance components related to intra- and interpopulation in the original populations (C0 and in the third cycle (C3 of reciprocal recurrent selection (RRS which allows breeders to define the best breeding strategy. For that purpose, the half-sib progenies of intrapopulation (P11 and P22 and interpopulation (P12 and P21 from populations 1 and 2 derived from single-cross hybrids in the 0 and 3 cycles of the reciprocal recurrent selection program were used. The intra- and interpopulation progenies were evaluated in a 10×10 triple lattice design in two separate locations. The data for unhusked ear weight (ear weight without husk and plant height were collected. All genetic variance and covariance components were estimated from the expected mean squares. The breakdown of additive variance into intrapopulation and interpopulation additive deviations (στ2 and the covariance between these and their intrapopulation additive effects (CovAτ found predominance of the dominance effect for unhusked ear weight. Plant height for these components shows that the intrapopulation additive effect explains most of the variation. Estimates for intrapopulation and interpopulation additive genetic variances confirm that populations derived from single-cross hybrids have potential for recurrent selection programs.

  1. Genetic variance of sunflower yield components - Heliantus annuus L.

    OpenAIRE

    Hladni Nada; Škorić Dragan; Kraljević-Balalić Marija

    2003-01-01

    The main goals of sunflower breeding in Yugoslavia and abroad are increased seed yield and oil content per unit area and increased resistance to diseases, insects and stress conditions via an optimization of plant architecture. In order to determine the mode of inheritance, gene effects and correlations of total leaf number per plant, total leaf area and plant height, six genetically divergent inbred lines of sunflower were subjected to half diallel crosses. Significant differences in mean va...

  2. Genetic factors explain half of all variance in serum eosinophil cationic protein.

    Science.gov (United States)

    Elmose, C; Sverrild, A; van der Sluis, S; Kyvik, K O; Backer, V; Thomsen, S F

    2014-12-01

    Eosinophil cationic protein (ECP) is one of four basic proteins of the secretory granules of eosinophils. It has a variety of functions associated with inflammatory responses. Little is known about the causes for variation in serum ECP levels. To identify factors associated with variation in serum ECP and to determine the relative proportion of the variation in ECP due to genetic and non-genetic factors, in an adult twin sample. A sample of 575 twins, selected through a proband with self-reported asthma, had serum ECP, lung function, airway responsiveness to methacholine, exhaled nitric oxide, and skin test reactivity, measured. Linear regression analysis and variance component models were used to study factors associated with variation in ECP and the relative genetic influence on ECP levels. Sex (regression coefficient = -0.107, P variance component model, genetic factors accounted for 57% (CI: 42-72%, P variance in ECP levels, whereas the remainder (43%) was ascribable to non-shared environmental factors. The genetic correlation between ECP and airway responsiveness to methacholine was statistically non-significant (r = -0.11, P = 0.50). Around half of all variance in serum ECP is explained by genetic factors. Serum ECP is influenced by sex, BMI, and airway responsiveness. Serum ECP and airway responsiveness seem not to share genetic variance. © 2014 John Wiley & Sons Ltd.

  3. Analysis of a genetically structured variance heterogeneity model using the Box-Cox transformation

    DEFF Research Database (Denmark)

    Yang, Ye; Christensen, Ole Fredslund; Sorensen, Daniel

    2011-01-01

    of the marginal distribution of the data. To investigate how the scale of measurement affects inferences, the genetically structured heterogeneous variance model is extended to accommodate the family of Box–Cox transformations. Litter size data in rabbits and pigs that had previously been analysed...... in the untransformed scale were reanalysed in a scale equal to the mode of the marginal posterior distribution of the Box–Cox parameter. In the rabbit data, the statistical evidence for a genetic component at the level of the environmental variance is considerably weaker than that resulting from an analysis...... in the original metric. In the pig data, the statistical evidence is stronger, but the coefficient of correlation between additive genetic effects affecting mean and variance changes sign, compared to the results in the untransformed scale. The study confirms that inferences on variances can be strongly affected...

  4. Genetic variance in the adiponutrin gene family and childhood obesity.

    Directory of Open Access Journals (Sweden)

    Lovisa E Johansson

    Full Text Available AIM: The adiponutrin gene family consists of five genes (PNPLA1-5 coding for proteins with both lipolytic and lipogenic properties. PNPLA3 has previously been associated with adult obesity. Here we investigated the possible association between genetic variants in these genes and childhood and adolescent obesity. METHODS/RESULTS: Polymorphisms in the five genes of the adiponutrin gene family were selected and genotyped using the Sequenom platform in a childhood and adolescent obesity case-control study. Six variants in PNPLA1 showed association with obesity (rs9380559, rs12212459, rs1467912, rs4713951, rs10947600, and rs12199580, p0.05. When analyzing these SNPs in relation to phenotypes, two SNPs in the PNPLA3 gene showed association with insulin sensitivity (rs12483959: beta = -0.053, p = 0.016, and rs2072907: beta = -0.049, p = 0.024. No associations were seen for PNPLA2, PNPLA4, and PNPLA5. CONCLUSIONS: Genetic variation in the adiponutrin gene family does not seem to contribute strongly to obesity in children and adolescents. PNPLA1 exhibited a modest effect on obesity and PNPLA3 on insulin sensitivity. These data, however, require confirmation in other cohorts and ethnic groups.

  5. The contribution of dominance and inbreeding depression in estimating variance components for litter size in Pannon White rabbits.

    Science.gov (United States)

    Nagy, I; Gorjanc, G; Curik, I; Farkas, J; Kiszlinger, H; Szendrő, Zs

    2013-08-01

    In a synthetic closed population of Pannon White rabbits, additive (VA ), dominance (VD ) and permanent environmental (VPe ) variance components as well as doe (bF d ) and litter (bF l ) inbreeding depression were estimated for the number of kits born alive (NBA), number of kits born dead (NBD) and total number of kits born (TNB). The data set consisted of 18,398 kindling records of 3883 does collected from 1992 to 2009. Six models were used to estimate dominance and inbreeding effects. The most complete model estimated VA and VD to contribute 5.5 ± 1.1% and 4.8 ± 2.4%, respectively, to total phenotypic variance (VP ) for NBA; the corresponding values for NBD were 1.9 ± 0.6% and 5.3 ± 2.4%, for TNB, 6.2 ± 1.0% and 8.1 ± 3.2% respectively. These results indicate the presence of considerable VD . Including dominance in the model generally reduced VA and VPe estimates, and had only a very small effect on inbreeding depression estimates. Including inbreeding covariates did not affect estimates of any variance component. A 10% increase in doe inbreeding significantly increased NBD (bF d  = 0.18 ± 0.07), while a 10% increase in litter inbreeding significantly reduced NBA (bF l  = -0.41 ± 0.11) and TNB (bF l  = -0.34 ± 0.10). These findings argue for including dominance effects in models of litter size traits in populations that exhibit significant dominance relationships. © 2012 Blackwell Verlag GmbH.

  6. The Evolution of Human Intelligence and the Coefficient of Additive Genetic Variance in Human Brain Size

    Science.gov (United States)

    Miller, Geoffrey F.; Penke, Lars

    2007-01-01

    Most theories of human mental evolution assume that selection favored higher intelligence and larger brains, which should have reduced genetic variance in both. However, adult human intelligence remains highly heritable, and is genetically correlated with brain size. This conflict might be resolved by estimating the coefficient of additive genetic…

  7. Genetic variances, trends and mode of inheritance for hip and elbow dysplasia in Finnish dog populations

    NARCIS (Netherlands)

    Mäki, K.; Groen, A.F.; Liinamo, A.E.; Ojala, M.

    2002-01-01

    The aims of this study were to assess genetic variances, trends and mode of inheritance for hip and elbow dysplasia in Finnish dog populations. The influence of time-dependent fixed effects in the model when estimating the genetic trends was also studied. Official hip and elbow dysplasia screening

  8. Selection for uniformity in livestock by exploiting genetic heterogeneity of environmental variance

    NARCIS (Netherlands)

    Mulder, H.A.; Bijma, P.; Hill, W.G.

    2008-01-01

    In some situations, it is worthwhile to change not only the mean, but also the variability of traits by selection. Genetic variation in residual variance may be utilised to improve uniformity in livestock populations by selection. The objective was to investigate the effects of genetic parameters, b

  9. The Evolution of Human Intelligence and the Coefficient of Additive Genetic Variance in Human Brain Size

    Science.gov (United States)

    Miller, Geoffrey F.; Penke, Lars

    2007-01-01

    Most theories of human mental evolution assume that selection favored higher intelligence and larger brains, which should have reduced genetic variance in both. However, adult human intelligence remains highly heritable, and is genetically correlated with brain size. This conflict might be resolved by estimating the coefficient of additive genetic…

  10. Increasing genetic variance of body mass index during the Swedish obesity epidemic

    DEFF Research Database (Denmark)

    Rokholm, Benjamin; Silventoinen, Karri; Tynelius, Per

    2011-01-01

    There is no doubt that the dramatic worldwide increase in obesity prevalence is due to changes in environmental factors. However, twin and family studies suggest that genetic differences are responsible for the major part of the variation in adiposity within populations. Recent studies show...... that the genetic effects on body mass index (BMI) may be stronger when combined with presumed risk factors for obesity. We tested the hypothesis that the genetic variance of BMI has increased during the obesity epidemic....

  11. Genetic basis of between-individual and within-individual variance of docility.

    Science.gov (United States)

    Martin, J G A; Pirotta, E; Petelle, M B; Blumstein, D T

    2017-04-01

    Between-individual variation in phenotypes within a population is the basis of evolution. However, evolutionary and behavioural ecologists have mainly focused on estimating between-individual variance in mean trait and neglected variation in within-individual variance, or predictability of a trait. In fact, an important assumption of mixed-effects models used to estimate between-individual variance in mean traits is that within-individual residual variance (predictability) is identical across individuals. Individual heterogeneity in the predictability of behaviours is a potentially important effect but rarely estimated and accounted for. We used 11 389 measures of docility behaviour from 1576 yellow-bellied marmots (Marmota flaviventris) to estimate between-individual variation in both mean docility and its predictability. We then implemented a double hierarchical animal model to decompose the variances of both mean trait and predictability into their environmental and genetic components. We found that individuals differed both in their docility and in their predictability of docility with a negative phenotypic covariance. We also found significant genetic variance for both mean docility and its predictability but no genetic covariance between the two. This analysis is one of the first to estimate the genetic basis of both mean trait and within-individual variance in a wild population. Our results indicate that equal within-individual variance should not be assumed. We demonstrate the evolutionary importance of the variation in the predictability of docility and illustrate potential bias in models ignoring variation in predictability. We conclude that the variability in the predictability of a trait should not be ignored, and present a coherent approach for its quantification. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  12. Estimating Modifying Effect of Age on Genetic and Environmental Variance Components in Twin Models.

    Science.gov (United States)

    He, Liang; Sillanpää, Mikko J; Silventoinen, Karri; Kaprio, Jaakko; Pitkäniemi, Janne

    2016-04-01

    Twin studies have been adopted for decades to disentangle the relative genetic and environmental contributions for a wide range of traits. However, heritability estimation based on the classical twin models does not take into account dynamic behavior of the variance components over age. Varying variance of the genetic component over age can imply the existence of gene-environment (G×E) interactions that general genome-wide association studies (GWAS) fail to capture, which may lead to the inconsistency of heritability estimates between twin design and GWAS. Existing parametricG×Einteraction models for twin studies are limited by assuming a linear or quadratic form of the variance curves with respect to a moderator that can, however, be overly restricted in reality. Here we propose spline-based approaches to explore the variance curves of the genetic and environmental components. We choose the additive genetic, common, and unique environmental variance components (ACE) model as the starting point. We treat the component variances as variance functions with respect to age modeled by B-splines or P-splines. We develop an empirical Bayes method to estimate the variance curves together with their confidence bands and provide an R package for public use. Our simulations demonstrate that the proposed methods accurately capture dynamic behavior of the component variances in terms of mean square errors with a data set of >10,000 twin pairs. Using the proposed methods as an alternative and major extension to the classical twin models, our analyses with a large-scale Finnish twin data set (19,510 MZ twins and 27,312 DZ same-sex twins) discover that the variances of the A, C, and E components for body mass index (BMI) change substantially across life span in different patterns and the heritability of BMI drops to ∼50% after middle age. The results further indicate that the decline of heritability is due to increasing unique environmental variance, which provides more

  13. Estimation of the proportion of genetic variance explained by molecular markers

    OpenAIRE

    Bearzoti,Eduardo; Vencovsky, Roland

    1998-01-01

    Estimation of the proportion of genetic variance explained by molecular markers (p) plays an important role in basic studies of quantitative traits, as well as in marker-assisted selection (MAS), if the selection index proposed by Lande and Thompson (Genetics 124: 743-756, 1990) is used. Frequently, the coefficient of determination (R2) is used to account for this proportion. In the present study, a simple estimator of p is presented, which is applicable when a multiple regression approach is...

  14. Genetic control of residual variance of yearling weight in nellore beef cattle

    NARCIS (Netherlands)

    Iung, L.H.S.; Neves, H.H.R.; Mulder, H.A.; Carvalheiro, R.

    2017-01-01

    There is evidence for genetic variability in residual variance of livestock traits, which offers the potential for selection for increased uniformity of production. Different statistical approaches have been employed to study this topic; however, little is known about the concordance between them

  15. GSEVM v.2: MCMC software to analyse genetically structured environmental variance models

    DEFF Research Database (Denmark)

    Ibáñez-Escriche, N; Garcia, M; Sorensen, D

    2010-01-01

    This note provides a description of software that allows to fit Bayesian genetically structured variance models using Markov chain Monte Carlo (MCMC). The gsevm v.2 program was written in Fortran 90. The DOS and Unix executable programs, the user's guide, and some example files are freely availab...

  16. Shared genetic variance between obesity and white matter integrity in Mexican Americans

    Science.gov (United States)

    Spieker, Elena A.; Kochunov, Peter; Rowland, Laura M.; Sprooten, Emma; Winkler, Anderson M.; Olvera, Rene L.; Almasy, Laura; Duggirala, Ravi; Fox, Peter T.; Blangero, John; Glahn, David C.; Curran, Joanne E.

    2015-01-01

    Obesity is a chronic metabolic disorder that may also lead to reduced white matter integrity, potentially due to shared genetic risk factors. Genetic correlation analyses were conducted in a large cohort of Mexican American families in San Antonio (N = 761, 58% females, ages 18–81 years; 41.3 ± 14.5) from the Genetics of Brain Structure and Function Study. Shared genetic variance was calculated between measures of adiposity [(body mass index (BMI; kg/m2) and waist circumference (WC; in)] and whole-brain and regional measurements of cerebral white matter integrity (fractional anisotropy). Whole-brain average and regional fractional anisotropy values for 10 major white matter tracts were calculated from high angular resolution diffusion tensor imaging data (DTI; 1.7 × 1.7 × 3 mm; 55 directions). Additive genetic factors explained intersubject variance in BMI (heritability, h2 = 0.58), WC (h2 = 0.57), and FA (h2 = 0.49). FA shared significant portions of genetic variance with BMI in the genu (ρG = −0.25), body (ρG = −0.30), and splenium (ρG = −0.26) of the corpus callosum, internal capsule (ρG = −0.29), and thalamic radiation (ρG = −0.31) (all p's = 0.043). The strongest evidence of shared variance was between BMI/WC and FA in the superior fronto-occipital fasciculus (ρG = −0.39, p = 0.020; ρG = −0.39, p = 0.030), which highlights region-specific variation in neural correlates of obesity. This may suggest that increase in obesity and reduced white matter integrity share common genetic risk factors. PMID:25763009

  17. Shared genetic variance between obesity and white matter integrity in Mexican-americans

    Directory of Open Access Journals (Sweden)

    Elena A Spieker

    2015-02-01

    Full Text Available Obesity is a chronic metabolic disorder that may also lead to reduced white matter integrity, potentially due to shared genetic risk factors. Genetic correlation analyses were conducted in a large cohort of Mexican American families in San Antonio (N=761, 58% females, ages 18-81y; 41.3±14.5 from the Genetics of Brain Structure and Function Study. Shared genetic variance was calculated between measures of adiposity ((body mass index (BMI; kg/m2 and waist circumference (WC; in and whole-brain and regional measurements of cerebral white matter integrity (fractional anisotropy. Whole-brain average and regional fractional anisotropy values for ten major white matter tracts were calculated from high angular resolution diffusion tensor imaging data (DTI; 1.7×1.7×3 mm; 55 directions. Additive genetic factors explained intersubject variance in BMI (heritability, h2=0.58, WC (h2=0.57, and FA (h2=0.49. FA shared significant portions of genetic variance with BMI in the genu (ρG = -0.25, body (ρG = -0.30, and splenium (ρG = -0.26 of the corpus callosum, internal capsule (ρG = -0.29, and thalamic radiation (ρG = -0.31 (all p’s = .043. The strongest evidence of shared variance was between BMI/WC and FA in the superior fronto-occipital fasciculus (ρG = -0.39, p = .020; ρG = -0.39, p = .030, which highlights region-specific variation in neural correlates of obesity. This may suggest that increase in obesity and reduced white matter integrity share common genetic risk factors.

  18. Fertilization success and the estimation of genetic variance in sperm competitiveness.

    Science.gov (United States)

    Garcia-Gonzalez, Francisco; Evans, Jonathan P

    2011-03-01

    A key question in sexual selection is whether the ability of males to fertilize eggs under sperm competition exhibits heritable genetic variation. Addressing this question poses a significant problem, however, because a male's ability to win fertilizations ultimately depends on the competitive ability of rival males. Attempts to partition genetic variance in sperm competitiveness, as estimated from measures of fertilization success, must therefore account for stochastic effects due to the random sampling of rival sperm competitors. In this contribution, we suggest a practical solution to this problem. We advocate the use of simple cross-classified breeding designs for partitioning sources of genetic variance in sperm competitiveness and fertilization success and show how these designs can be used to avoid stochastic effects due to the random sampling of rival sperm competitors. We illustrate the utility of these approaches by simulating various scenarios for estimating genetic parameters in sperm competitiveness, and show that the probability of detecting additive genetic variance in this trait is restored when stochastic effects due to the random sampling of rival sperm competitors are controlled. Our findings have important implications for the study of the evolutionary maintenance of polyandry.

  19. On the Informativeness of Dominant and Co-Dominant Genetic Markers for Bayesian Supervised Clustering

    DEFF Research Database (Denmark)

    Guillot, Gilles; Carpentier-Skandalis, Alexandra

    2011-01-01

    We study the accuracy of a Bayesian supervised method used to cluster individuals into genetically homogeneous groups on the basis of dominant or codominant molecular markers. We provide a formula relating an error criterion to the number of loci used and the number of clusters. This formula...

  20. Use of genomic models to study genetic control of environmental variance

    DEFF Research Database (Denmark)

    Yang, Ye; Christensen, Ole Fredslund; Sorensen, Daniel

    2011-01-01

    of detecting genetic variation at the level of mean and variance. Implementation is via Markov chain Monte Carlo (McMC) algorithms. The models are compared in terms of a measure of global fit, in their ability to detect QTL effects and in terms of their predictive power. The models are subsequently fitted....... The genomic model commonly found in the literature, with marker effects affecting mean only, is extended to investigate putative effects at the level of the environmental variance. Two classes of models are proposed and their behaviour, studied using simulated data, indicates that they are capable...

  1. Studies on the value of incorporating the effect of dominance in genetic evaluations of dairy cattle, beef cattle and swine

    Directory of Open Access Journals (Sweden)

    Van Tassel CP.

    1998-01-01

    Full Text Available Nonadditive genetic effects are currently ignored in national genetic evaluations of farm animals because of ignorance of thelevel of dominance variance for traits of interest and the difficult computational problems involved. Potential gains fromincluding the effects of dominance in genetic evaluations include “purification” of additive values and availability ofpredictions of specific combining abilities for each pair of prospective parents. This study focused on making evaluation withdominance effects feasible computationally and on ascertaining benefits of such an evaluation for dairy cattle, beef cattle,and swine. Using iteration on data, computing costs for evaluation with dominance effects included costs could be less thantwice expensive as with only an additive model. With Method Â, variance components could be estimated for problemsinvolving up to 10 millions equations. Dominance effects accounted for up to 10% of phenotypic variance; estimates werelarger for growth traits. As a percentage of additive variance, the estimate of dominance variance reached 78% for 21-d litterweight of swine and 47% for post weaning weight of beef cattle. When dominance effects are ignored, additive evaluationsare “contaminated”; effects are greatest for evaluations of dams in a single large family. These changes in ranking wereimportant for dairy cattle, especially for dams of full-sibs, but were less important for swine. Specific combining abilitiescannot be included in sire evaluations and need to be computed separately for each set of parents. The predictions of specificcombining abilities could be used in computerized mating programs via the Internet. Gains from including the dominanceeffect in genetic evaluations would be moderate but would outweigh expenditures to produce those evaluations.

  2. Variance decomposition of MRI-based covariance maps using genetically informative samples and structural equation modeling.

    Science.gov (United States)

    Schmitt, J Eric; Lenroot, Rhoshel K; Ordaz, Sarah E; Wallace, Gregory L; Lerch, Jason P; Evans, Alan C; Prom, Elizabeth C; Kendler, Kenneth S; Neale, Michael C; Giedd, Jay N

    2009-08-01

    The role of genetics in driving intracortical relationships is an important question that has rarely been studied in humans. In particular, there are no extant high-resolution imaging studies on genetic covariance. In this article, we describe a novel method that combines classical quantitative genetic methodologies for variance decomposition with recently developed semi-multivariate algorithms for high-resolution measurement of phenotypic covariance. Using these tools, we produced correlational maps of genetic and environmental (i.e. nongenetic) relationships between several regions of interest and the cortical surface in a large pediatric sample of 600 twins, siblings, and singletons. These analyses demonstrated high, fairly uniform, statistically significant genetic correlations between the entire cortex and global mean cortical thickness. In agreement with prior reports on phenotypic covariance using similar methods, we found that mean cortical thickness was most strongly correlated with association cortices. However, the present study suggests that genetics plays a large role in global brain patterning of cortical thickness in this manner. Further, using specific gyri with known high heritabilities as seed regions, we found a consistent pattern of high bilateral genetic correlations between structural homologues, with environmental correlations more restricted to the same hemisphere as the seed region, suggesting that interhemispheric covariance is largely genetically mediated. These findings are consistent with the limited existing knowledge on the genetics of cortical variability as well as our prior multivariate studies on cortical gyri.

  3. Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174.

    Science.gov (United States)

    Baker, Christopher W; Miller, Craig R; Thaweethai, Tanayott; Yuan, Jeffrey; Baker, Meghan Hollibaugh; Joyce, Paul; Weinreich, Daniel M

    2016-04-07

    Researchers in evolutionary genetics recently have recognized an exciting opportunity in decomposing beneficial mutations into their proximal, mechanistic determinants. The application of methods and concepts from molecular biology and life history theory to studies of lytic bacteriophages (phages) has allowed them to understand how natural selection sees mutations influencing life history. This work motivated the research presented here, in which we explored whether, under consistent experimental conditions, small differences in the genome of bacteriophage φX174 could lead to altered life history phenotypes among a panel of eight genetically distinct clones. We assessed the clones' phenotypes by applying a novel statistical framework to the results of a serially sampled parallel infection assay, in which we simultaneously inoculated each of a large number of replicate host volumes with ∼1 phage particle. We sequentially plated the volumes over the course of infection and counted the plaques that formed after incubation. These counts served as a proxy for the number of phage particles in a single volume as a function of time. From repeated assays, we inferred significant, genetically determined heterogeneity in lysis time and burst size, including lysis time variance. These findings are interesting in light of the genetic and phenotypic constraints on the single-protein lysis mechanism of φX174. We speculate briefly on the mechanisms underlying our results, and we discuss the potential importance of lysis time variance in viral evolution.

  4. Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174

    Directory of Open Access Journals (Sweden)

    Christopher W. Baker

    2016-04-01

    Full Text Available Researchers in evolutionary genetics recently have recognized an exciting opportunity in decomposing beneficial mutations into their proximal, mechanistic determinants. The application of methods and concepts from molecular biology and life history theory to studies of lytic bacteriophages (phages has allowed them to understand how natural selection sees mutations influencing life history. This work motivated the research presented here, in which we explored whether, under consistent experimental conditions, small differences in the genome of bacteriophage φX174 could lead to altered life history phenotypes among a panel of eight genetically distinct clones. We assessed the clones’ phenotypes by applying a novel statistical framework to the results of a serially sampled parallel infection assay, in which we simultaneously inoculated each of a large number of replicate host volumes with ∼1 phage particle. We sequentially plated the volumes over the course of infection and counted the plaques that formed after incubation. These counts served as a proxy for the number of phage particles in a single volume as a function of time. From repeated assays, we inferred significant, genetically determined heterogeneity in lysis time and burst size, including lysis time variance. These findings are interesting in light of the genetic and phenotypic constraints on the single-protein lysis mechanism of φX174. We speculate briefly on the mechanisms underlying our results, and we discuss the potential importance of lysis time variance in viral evolution.

  5. A simple algorithm to estimate genetic variance in an animal threshold model using Bayesian inference

    Directory of Open Access Journals (Sweden)

    Heringstad Bjørg

    2010-07-01

    Full Text Available Abstract Background In the genetic analysis of binary traits with one observation per animal, animal threshold models frequently give biased heritability estimates. In some cases, this problem can be circumvented by fitting sire- or sire-dam models. However, these models are not appropriate in cases where individual records exist on parents. Therefore, the aim of our study was to develop a new Gibbs sampling algorithm for a proper estimation of genetic (covariance components within an animal threshold model framework. Methods In the proposed algorithm, individuals are classified as either "informative" or "non-informative" with respect to genetic (covariance components. The "non-informative" individuals are characterized by their Mendelian sampling deviations (deviance from the mid-parent mean being completely confounded with a single residual on the underlying liability scale. For threshold models, residual variance on the underlying scale is not identifiable. Hence, variance of fully confounded Mendelian sampling deviations cannot be identified either, but can be inferred from the between-family variation. In the new algorithm, breeding values are sampled as in a standard animal model using the full relationship matrix, but genetic (covariance components are inferred from the sampled breeding values and relationships between "informative" individuals (usually parents only. The latter is analogous to a sire-dam model (in cases with no individual records on the parents. Results When applied to simulated data sets, the standard animal threshold model failed to produce useful results since samples of genetic variance always drifted towards infinity, while the new algorithm produced proper parameter estimates essentially identical to the results from a sire-dam model (given the fact that no individual records exist for the parents. Furthermore, the new algorithm showed much faster Markov chain mixing properties for genetic parameters (similar to

  6. Additive genetic variance in polyandry enables its evolution, but polyandry is unlikely to evolve through sexy or good sperm processes.

    Science.gov (United States)

    Travers, L M; Simmons, L W; Garcia-Gonzalez, F

    2016-05-01

    Polyandry is widespread despite its costs. The sexually selected sperm hypotheses ('sexy' and 'good' sperm) posit that sperm competition plays a role in the evolution of polyandry. Two poorly studied assumptions of these hypotheses are the presence of additive genetic variance in polyandry and sperm competitiveness. Using a quantitative genetic breeding design in a natural population of Drosophila melanogaster, we first established the potential for polyandry to respond to selection. We then investigated whether polyandry can evolve through sexually selected sperm processes. We measured lifetime polyandry and offensive sperm competitiveness (P2 ) while controlling for sampling variance due to male × male × female interactions. We also measured additive genetic variance in egg-to-adult viability and controlled for its effect on P2 estimates. Female lifetime polyandry showed significant and substantial additive genetic variance and evolvability. In contrast, we found little genetic variance or evolvability in P2 or egg-to-adult viability. Additive genetic variance in polyandry highlights its potential to respond to selection. However, the low levels of genetic variance in sperm competitiveness suggest that the evolution of polyandry may not be driven by sexy sperm or good sperm processes. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

  7. Estimation of (co)variance components and genetic parameters of greasy fleece weights in Muzaffarnagari sheep.

    Science.gov (United States)

    Mandal, A; Neser, F W C; Roy, R; Rout, P K; Notter, D R

    2009-02-01

    Variance components and genetic parameters for greasy fleece weights of Muzaffarnagari sheep maintained at the Central Institute for Research on Goats, Makhdoom, Mathura, India, over a period of 29 years (1976 to 2004) were estimated by restricted maximum likelihood (REML), fitting six animal models including various combinations of maternal effects. Data on body weights at 6 (W6) and 12 months (W12) of age were also included in the study. Records of 2807 lambs descended from 160 rams and 1202 ewes were used for the study. Direct heritability estimates for fleece weight at 6 (FW6) and 12 months of age (FW12), and total fleece weights up to 1 year of age (TFW) were 0.14, 0.16 and 0.25, respectively. Maternal genetic and permanent environmental effects did not significantly influence any of the traits under study. Genetic correlations among fleece weights and body weights were obtained from multivariate analyses. Direct genetic correlations of FW6 with W6 and W12 were relatively large, ranging from 0.61 to 0.67, but only moderate genetic correlations existed between FW12 and W6 (0.39) and between FW12 and W12 (0.49). The genetic correlation between FW6 and FW12 was very high (0.95), but the corresponding phenotypic correlation was much lower (0.28). Heritability estimates for all traits were at least 0.15, indicating that there is potential for their improvement by selection. The moderate to high positive genetic correlations between fleece weights and body weights at 6 and 12 months of age suggest that some of the genetic factors that influence animal growth also influence wool growth. Thus selection to improve the body weights or fleece weights at 6 months of age will also result in genetic improvement of fleece weights at subsequent stages of growth.

  8. Effect of captivity on genetic variance for five traits in the large milkweed bug (Oncopeltus fasciatus).

    Science.gov (United States)

    Rodríguez-Clark, K M

    2004-07-01

    Understanding the changes in genetic variance which may occur as populations move from nature into captivity has been considered important when populations in captivity are used as models of wild ones. However, the inherent significance of these changes has not previously been appreciated in a conservation context: are the methods aimed at founding captive populations with gene diversity representative of natural populations likely also to capture representative quantitative genetic variation? Here, I investigate changes in heritability and a less traditional measure, evolvability, between nature and captivity for the large milkweed bug, Oncopeltus fasciatus, to address this question. Founders were collected from a 100-km transect across the north-eastern US, and five traits (wing colour, pronotum colour, wing length, early fecundity and later fecundity) were recorded for founders and for their offspring during two generations in captivity. Analyses reveal significant heritable variation for some life history and morphological traits in both environments, with comparable absolute levels of evolvability across all traits (0-30%). Randomization tests show that while changes in heritability and total phenotypic variance were highly variable, additive genetic variance and evolvability remained stable across the environmental transition in the three morphological traits (changing 1-2% or less), while they declined significantly in the two life-history traits (5-8%). Although it is unclear whether the declines were due to selection or gene-by-environment interactions (or both), such declines do not appear inevitable: captive populations with small numbers of founders may contain substantial amounts of the evolvability found in nature, at least for some traits.

  9. Very low levels of direct additive genetic variance in fitness and fitness components in a red squirrel population.

    Science.gov (United States)

    McFarlane, S Eryn; Gorrell, Jamieson C; Coltman, David W; Humphries, Murray M; Boutin, Stan; McAdam, Andrew G

    2014-05-01

    A trait must genetically correlate with fitness in order to evolve in response to natural selection, but theory suggests that strong directional selection should erode additive genetic variance in fitness and limit future evolutionary potential. Balancing selection has been proposed as a mechanism that could maintain genetic variance if fitness components trade off with one another and has been invoked to account for empirical observations of higher levels of additive genetic variance in fitness components than would be expected from mutation-selection balance. Here, we used a long-term study of an individually marked population of North American red squirrels (Tamiasciurus hudsonicus) to look for evidence of (1) additive genetic variance in lifetime reproductive success and (2) fitness trade-offs between fitness components, such as male and female fitness or fitness in high- and low-resource environments. "Animal model" analyses of a multigenerational pedigree revealed modest maternal effects on fitness, but very low levels of additive genetic variance in lifetime reproductive success overall as well as fitness measures within each sex and environment. It therefore appears that there are very low levels of direct genetic variance in fitness and fitness components in red squirrels to facilitate contemporary adaptation in this population.

  10. The Dominance Concept Inventory: A Tool for Assessing Undergraduate Student Alternative Conceptions about Dominance in Mendelian and Population Genetics

    Science.gov (United States)

    Abraham, Joel K.; Perez, Kathryn E.; Price, Rebecca M.

    2014-01-01

    Despite the impact of genetics on daily life, biology undergraduates understand some key genetics concepts poorly. One concept requiring attention is dominance, which many students understand as a fixed property of an allele or trait and regularly conflate with frequency in a population or selective advantage. We present the Dominance Concept…

  11. The effect of a population bottleneck on the evolution of genetic variance/covariance structure.

    Science.gov (United States)

    Jarvis, J P; Cropp, S N; Vaughn, T T; Pletscher, L S; King-Ellison, K; Adams-Hunt, E; Erickson, C; Cheverud, J M

    2011-10-01

    It is well known that standard population genetic theory predicts decreased additive genetic variance (V(a) ) following a population bottleneck and that theoretical models including interallelic and intergenic interactions indicate such loss may be avoided. However, few empirical data from multicellular model systems are available, especially regarding variance/covariance (V/CV) relationships. Here, we compare the V/CV structure of seventeen traits related to body size and composition between control (60 mating pairs/generation) and bottlenecked (2 mating pairs/generation; average F = 0.39) strains of mice. Although results for individual traits vary considerably, multivariate analysis indicates that V(a) in the bottlenecked populations is greater than expected. Traits with patterns and amounts of epistasis predictive of enhanced V(a) also show the largest deviations from additive expectations. Finally, the correlation structure of weekly weights is not significantly different between control and experimental lines but correlations between necropsy traits do differ, especially those involving the heart, kidney and tail length. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

  12. Estimation of the proportion of genetic variance explained by molecular markers

    Directory of Open Access Journals (Sweden)

    Bearzoti Eduardo

    1998-01-01

    Full Text Available Estimation of the proportion of genetic variance explained by molecular markers (p plays an important role in basic studies of quantitative traits, as well as in marker-assisted selection (MAS, if the selection index proposed by Lande and Thompson (Genetics 124: 743-756, 1990 is used. Frequently, the coefficient of determination (R2 is used to account for this proportion. In the present study, a simple estimator of p is presented, which is applicable when a multiple regression approach is used, and progenies are evaluated in replicated trials. The associated sampling distribution was obtained and compared with that of R2. Simulations indicated that, when the number of evaluated progenies is small, the statistics are not satisfactory, in general, due to bias and/or low precision. Coefficient R2 was found adequate in situations where p is high. If a large number of progenies is evaluated (say, a few hundreds, then the proposed estimator appears to be better, with acceptable precision and considerably lower bias than R2. A normal approximation to the sampling distribution of is given, using Taylor's expansion of the expectation and variance of this statistic. Approximate confidence intervals for p, based on normal distribution, are reasonable, if the number of progenies is large. The use of in MAS is illustrated for estimation of the weight given to the molecular score, when a selection index is used.

  13. Estimation of genetic parameters and their sampling variances for quantitative traits in the type 2 modified augmented design

    Institute of Scientific and Technical Information of China (English)

    Frank M. You; Qijian Song; Gaofeng Jia; Yanzhao Cheng; Scott Duguid; Helen Booker; Sylvie Cloutier

    2016-01-01

    The type 2 modified augmented design (MAD2) is an efficient unreplicated experimental design used for evaluating large numbers of lines in plant breeding and for assessing genetic variation in a population. Statistical methods and data adjustment for soil heterogeneity have been previously described for this design. In the absence of replicated test genotypes in MAD2, their total variance cannot be partitioned into genetic and error components as required to estimate heritability and genetic correlation of quantitative traits, the two conventional genetic parameters used for breeding selection. We propose a method of estimating the error variance of unreplicated genotypes that uses replicated controls, and then of estimating the genetic parameters. Using the Delta method, we also derived formulas for estimating the sampling variances of the genetic parameters. Computer simulations indicated that the proposed method for estimating genetic parameters and their sampling variances was feasible and the reliability of the estimates was positively associated with the level of heritability of the trait. A case study of estimating the genetic parameters of three quantitative traits, iodine value, oil content, and linolenic acid content, in a biparental recombinant inbred line population of flax with 243 individuals, was conducted using our statistical models. A joint analysis of data over multiple years and sites was suggested for genetic parameter estimation. A pipeline module using SAS and Perl was developed to facilitate data analysis and appended to the previously developed MAD data analysis pipeline (http://probes.pw.usda.gov/bioinformatics_ tools/MADPipeline/index.html).

  14. Estimation of genetic parameters and their sampling variances for quantitative traits in the type 2 modified augmented design

    Institute of Scientific and Technical Information of China (English)

    Frank M.You; Qijian Song; Gaofeng Jia; Yanzhao Cheng; Scott Duguid; Helen Booker; Sylvie Cloutier

    2016-01-01

    The type 2 modified augmented design(MAD2) is an efficient unreplicated experimental design used for evaluating large numbers of lines in plant breeding and for assessing genetic variation in a population. Statistical methods and data adjustment for soil heterogeneity have been previously described for this design. In the absence of replicated test genotypes in MAD2, their total variance cannot be partitioned into genetic and error components as required to estimate heritability and genetic correlation of quantitative traits, the two conventional genetic parameters used for breeding selection. We propose a method of estimating the error variance of unreplicated genotypes that uses replicated controls, and then of estimating the genetic parameters. Using the Delta method, we also derived formulas for estimating the sampling variances of the genetic parameters.Computer simulations indicated that the proposed method for estimating genetic parameters and their sampling variances was feasible and the reliability of the estimates was positively associated with the level of heritability of the trait. A case study of estimating the genetic parameters of three quantitative traits, iodine value, oil content, and linolenic acid content, in a biparental recombinant inbred line population of flax with 243 individuals, was conducted using our statistical models. A joint analysis of data over multiple years and sites was suggested for genetic parameter estimation. A pipeline module using SAS and Perl was developed to facilitate data analysis and appended to the previously developed MAD data analysis pipeline(http://probes.pw.usda.gov/bioinformatics_ tools/MADPipeline/index.html).

  15. Estimation of genetic parameters and their sampling variances for quantitative traits in the type 2 modified augmented design

    Directory of Open Access Journals (Sweden)

    Frank M. You

    2016-04-01

    Full Text Available The type 2 modified augmented design (MAD2 is an efficient unreplicated experimental design used for evaluating large numbers of lines in plant breeding and for assessing genetic variation in a population. Statistical methods and data adjustment for soil heterogeneity have been previously described for this design. In the absence of replicated test genotypes in MAD2, their total variance cannot be partitioned into genetic and error components as required to estimate heritability and genetic correlation of quantitative traits, the two conventional genetic parameters used for breeding selection. We propose a method of estimating the error variance of unreplicated genotypes that uses replicated controls, and then of estimating the genetic parameters. Using the Delta method, we also derived formulas for estimating the sampling variances of the genetic parameters. Computer simulations indicated that the proposed method for estimating genetic parameters and their sampling variances was feasible and the reliability of the estimates was positively associated with the level of heritability of the trait. A case study of estimating the genetic parameters of three quantitative traits, iodine value, oil content, and linolenic acid content, in a biparental recombinant inbred line population of flax with 243 individuals, was conducted using our statistical models. A joint analysis of data over multiple years and sites was suggested for genetic parameter estimation. A pipeline module using SAS and Perl was developed to facilitate data analysis and appended to the previously developed MAD data analysis pipeline (http://probes.pw.usda.gov/bioinformatics_ tools/MADPipeline/index.html.

  16. Estimation of genetic connectedness diagnostics based on prediction errors without the prediction error variance-covariance matrix.

    Science.gov (United States)

    Holmes, John B; Dodds, Ken G; Lee, Michael A

    2017-03-02

    An important issue in genetic evaluation is the comparability of random effects (breeding values), particularly between pairs of animals in different contemporary groups. This is usually referred to as genetic connectedness. While various measures of connectedness have been proposed in the literature, there is general agreement that the most appropriate measure is some function of the prediction error variance-covariance matrix. However, obtaining the prediction error variance-covariance matrix is computationally demanding for large-scale genetic evaluations. Many alternative statistics have been proposed that avoid the computational cost of obtaining the prediction error variance-covariance matrix, such as counts of genetic links between contemporary groups, gene flow matrices, and functions of the variance-covariance matrix of estimated contemporary group fixed effects. In this paper, we show that a correction to the variance-covariance matrix of estimated contemporary group fixed effects will produce the exact prediction error variance-covariance matrix averaged by contemporary group for univariate models in the presence of single or multiple fixed effects and one random effect. We demonstrate the correction for a series of models and show that approximations to the prediction error matrix based solely on the variance-covariance matrix of estimated contemporary group fixed effects are inappropriate in certain circumstances. Our method allows for the calculation of a connectedness measure based on the prediction error variance-covariance matrix by calculating only the variance-covariance matrix of estimated fixed effects. Since the number of fixed effects in genetic evaluation is usually orders of magnitudes smaller than the number of random effect levels, the computational requirements for our method should be reduced.

  17. The genetic variance for multiple linked quantitative trait loci conditional on marker information in a crossed population.

    Science.gov (United States)

    Matsuda, H; Iwaisaki, H

    2002-01-01

    In the prediction of genetic values and quantitative trait loci (QTLs) mapping via the mixed model method incorporating marker information in animal populations, it is important to model the genetic variance for individuals with an arbitrary pedigree structure. In this study, for a crossed population originated from different genetic groups such as breeds or outbred strains, the variance of additive genetic values for multiple linked QTLs that are contained in a chromosome segment, especially the segregation variance, is investigated assuming the use of marker data. The variance for a finite number of QTLs in one chromosomal segment is first examined for the crossed population with the general pedigree. Then, applying the concept of the expectation of identity-by-descent proportion, an approximation to the mean of the conditional probabilities for the linked QTLs over all loci is obtained, and using it an expression for the variance in the case of an infinite number of linked QTLs marked by flanking markers is derived. It appears that the approach presented can be useful in the segment mapping using, and in the genetic evaluation of, crosses with general pedigrees in the population of concern. The calculation of the segregation variance through the current approach is illustrated numerically, using a small data-set.

  18. Estimates of (co)variance components and genetic parameters for growth traits of Avikalin sheep.

    Science.gov (United States)

    Prince, Leslie Leo L; Gowane, Gopal R; Chopra, Ashish; Arora, Amrit L

    2010-08-01

    (Co)variance components and genetic parameters for various growth traits of Avikalin sheep maintained at Central Sheep and Wool Research Institute, Avikanagar, Rajasthan, India, were estimated by Restricted Maximum Likelihood, fitting six animal models with various combinations of direct and maternal effects. Records of 3,840 animals descended from 257 sires and 1,194 dams were taken for this study over a period of 32 years (1977-2008). Direct heritability estimates (from best model as per likelihood ratio test) for weight at birth, weaning, 6 and 12 months of age, and average daily gain from birth to weaning, weaning to 6 months, and 6 to 12 months were 0.28 +/- 0.03, 0.20 +/- 0.03, 0.28 +/- 0.07, 0.15 +/- 0.04, 0.21 +/- 0.03, 0.16 and 0.03 +/- 0.03, respectively. Maternal heritability for traits declined as animal grows older and it was not at all evident at adult age and for post-weaning daily gain. Maternal permanent environmental effect (c(2)) declined significantly with advancement of age of animal. A small effect of c(2) on post-weaning weights was probably a carryover effect of pre-weaning maternal influence. A significant large negative genetic correlation was observed between direct and maternal genetic effects for all the traits, indicating antagonistic pleiotropy, which needs special care while formulating breeding plans. A fair rate of genetic progress seems possible in the flock by selection for all traits, but direct and maternal genetic correlation needs to be taken in to consideration.

  19. Population divergence along lines of genetic variance and covariance in the invasive plant Lythrum salicaria in eastern North America.

    Science.gov (United States)

    Colautti, Robert I; Barrett, Spencer C H

    2011-09-01

    Evolution during biological invasion may occur over contemporary timescales, but the rate of evolutionary change may be inhibited by a lack of standing genetic variation for ecologically relevant traits and by fitness trade-offs among them. The extent to which these genetic constraints limit the evolution of local adaptation during biological invasion has rarely been examined. To investigate genetic constraints on life-history traits, we measured standing genetic variance and covariance in 20 populations of the invasive plant purple loosestrife (Lythrum salicaria) sampled along a latitudinal climatic gradient in eastern North America and grown under uniform conditions in a glasshouse. Genetic variances within and among populations were significant for all traits; however, strong intercorrelations among measurements of seedling growth rate, time to reproductive maturity and adult size suggested that fitness trade-offs have constrained population divergence. Evidence to support this hypothesis was obtained from the genetic variance-covariance matrix (G) and the matrix of (co)variance among population means (D), which were 79.8% (95% C.I. 77.7-82.9%) similar. These results suggest that population divergence during invasive spread of L. salicaria in eastern North America has been constrained by strong genetic correlations among life-history traits, despite large amounts of standing genetic variation for individual traits. © 2011 The Author(s).

  20. The ARMC5 gene shows extensive genetic variance in primary macronodular adrenocortical hyperplasia

    Science.gov (United States)

    Correa, Ricardo; Zilbermint, Mihail; Berthon, Annabel; Espiard, Stephanie; Batsis, Maria; Papadakis, Georgios Z.; Xekouki, Paraskevi; Lodish, Maya B.; Bertherat, Jerome; Faucz, Fabio R.; Stratakis, Constantine A.

    2015-01-01

    Objective Primary macronodular adrenal hyperplasia (PMAH) is a rare type of Cushing’s syndrome (CS) that results in increased cortisol production and bilateral enlargement of the adrenal glands. Recent work showed that the disease may be caused by germline and somatic mutations in the ARMC5 gene, a likely tumor-suppressor gene (TSG). We investigated 20 different adrenal nodules from one patient with PMAH for ARMC5 somatic sequence changes. Design All of the nodules where obtained from a single patient who underwent bilateral adrenalectomy. DNA was extracted by standard protocols and the ARMC5 sequence was determined by the Sanger method. Results Sixteen of 20 adrenocortical nodules harbored, in addition to what appeared to be the germline mutation, a second somatic variant. The p.Trp476* sequence change was present in all 20 nodules, as well as in normal tissue from the adrenal capsule, identifying it as the germline defect; each of the 16 other variants were found in different nodules: 6 were frame shift, 4 were missense, 3 were nonsense, and 1 was a splice site variation. Allelic losses were confirmed in 2 of the nodules. Conclusion This is the most genetic variance of the ARMC5 gene ever described in a single patient with PMAH: each of 16 adrenocortical nodules had a second new, “private”, and -in most cases- completely inactivating ARMC5 defect, in addition to the germline mutation. The data support the notion that ARMC5 is a TSG that needs a second, somatic hit, to mediate tumorigenesis leading to polyclonal nodularity; however, the driver of this extensive genetic variance of the second ARMC5 allele in adrenocortical tissue in the context of a germline defect and PMAH remains a mystery. PMID:26162405

  1. Autosomal dominant cyclic hematopoiesis: Genetics, phenotype, and natural history

    Energy Technology Data Exchange (ETDEWEB)

    Palmer, S.E.; Stephens, K.; Dale, D.C. [Univ. of Washington, Seattle, WA (United States)

    1994-09-01

    Autosomal dominant cyclic hematopoiesis (ADCH; cyclic neutropenia) is a rare disorder manifested by transient neutropenia that recurs every three weeks. To facilitate mapping the ADCH gene by genetic linkage analysis, we studied 9 ADCH families with 42 affected individuals. Pedigrees revealed AD inheritance with no evidence for decreased penetrance. Similar intra- and interfamilial variable expression was observed, with no evidence to support heterogeneity. At least 3 families displayed apparent new mutations. Many adults developed chronic neutropenia, while offspring always cycled during childhood. Children displayed recurrent oral ulcers, gingivitis, lymphadenopathy, fever, and skin and other infections with additional symptoms. Interestingly, there were no cases of neonatal infection. Some children required multiple hospitalizations for treatment. Four males under age 18 died of Clostridium sepsis following necrotizing enterocolitis; all had affected mothers. No other deaths due to ADCH were found; most had improvement of symptoms and infections as adults. Adults experienced increased tooth loss prior to age 30 (16 out of 27 adults, with 9 edentulous). No increase in myelodysplasia, malignancy, or congenital anomalies was observed. Recombinant G-CSF treatment resulted in dramatic improvement of symptoms and infections. The results suggest that ADCH is not a benign disorder, especially in childhood, and abdominal pain requires immediate evaluation. Diagnosis of ADCH requires serial blood counts in the proband and at least one CBC in relatives to exclude similar disorders. Genetic counseling requires specific histories as well as CBCs of each family member at risk to determine status regardless of symptom history, especially to assess apparent new mutations.

  2. Dominant Genetic Variation and Missing Heritability for Human Complex Traits: Insights from Twin versus Genome-wide Common SNP Models.

    Science.gov (United States)

    Chen, Xu; Kuja-Halkola, Ralf; Rahman, Iffat; Arpegård, Johannes; Viktorin, Alexander; Karlsson, Robert; Hägg, Sara; Svensson, Per; Pedersen, Nancy L; Magnusson, Patrik K E

    2015-11-05

    In order to further illuminate the potential role of dominant genetic variation in the "missing heritability" debate, we investigated the additive (narrow-sense heritability, h(2)) and dominant (δ(2)) genetic variance for 18 human complex traits. Within the same study base (10,682 Swedish twins), we calculated and compared the estimates from classic twin-based structural equation model with SNP-based genomic-relatedness-matrix restricted maximum likelihood [GREML(d)] method. Contributions of δ(2) were evident for 14 traits in twin models (average δ(2)twin = 0.25, range 0.14-0.49), two of which also displayed significant δ(2) in the GREMLd analyses (triglycerides δ(2)SNP = 0.28 and waist circumference δ(2)SNP = 0.19). On average, the proportion of h(2)SNP/h(2)twin was 70% for ADE-fitted traits (for which the best-fitting model included additive and dominant genetic and unique environmental components) and 31% for AE-fitted traits (for which the best-fitting model included additive genetic and unique environmental components). Independent evidence for contribution from shared environment, also in ADE-fitted traits, was obtained from self-reported within-pair contact frequency and age at separation. We conclude that despite the fact that additive genetics appear to constitute the bulk of genetic influences for most complex traits, dominant genetic variation might often be masked by shared environment in twin and family studies and might therefore have a more prominent role than what family-based estimates often suggest. The risk of erroneously attributing all inherited genetic influences (additive and dominant) to the h(2) in too-small twin studies might also lead to exaggerated "missing heritability" (the proportion of h(2) that remains unexplained by SNPs). Copyright © 2015 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  3. fullfact: an R package for the analysis of genetic and maternal variance components from full factorial mating designs.

    Science.gov (United States)

    Houde, Aimee Lee S; Pitcher, Trevor E

    2016-03-01

    Full factorial breeding designs are useful for quantifying the amount of additive genetic, nonadditive genetic, and maternal variance that explain phenotypic traits. Such variance estimates are important for examining evolutionary potential. Traditionally, full factorial mating designs have been analyzed using a two-way analysis of variance, which may produce negative variance values and is not suited for unbalanced designs. Mixed-effects models do not produce negative variance values and are suited for unbalanced designs. However, extracting the variance components, calculating significance values, and estimating confidence intervals and/or power values for the components are not straightforward using traditional analytic methods. We introduce fullfact - an R package that addresses these issues and facilitates the analysis of full factorial mating designs with mixed-effects models. Here, we summarize the functions of the fullfact package. The observed data functions extract the variance explained by random and fixed effects and provide their significance. We then calculate the additive genetic, nonadditive genetic, and maternal variance components explaining the phenotype. In particular, we integrate nonnormal error structures for estimating these components for nonnormal data types. The resampled data functions are used to produce bootstrap-t confidence intervals, which can then be plotted using a simple function. We explore the fullfact package through a worked example. This package will facilitate the analyses of full factorial mating designs in R, especially for the analysis of binary, proportion, and/or count data types and for the ability to incorporate additional random and fixed effects and power analyses.

  4. Genetic and phenotypic variance and covariance components for methane emission and postweaning traits in Angus cattle.

    Science.gov (United States)

    Donoghue, K A; Bird-Gardiner, T; Arthur, P F; Herd, R M; Hegarty, R F

    2016-04-01

    Ruminants contribute 80% of the global livestock greenhouse gas (GHG) emissions mainly through the production of methane, a byproduct of enteric microbial fermentation primarily in the rumen. Hence, reducing enteric methane production is essential in any GHG emissions reduction strategy in livestock. Data on 1,046 young bulls and heifers from 2 performance-recording research herds of Angus cattle were analyzed to provide genetic and phenotypic variance and covariance estimates for methane emissions and production traits and to examine the interrelationships among these traits. The cattle were fed a roughage diet at 1.2 times their estimated maintenance energy requirements and measured for methane production rate (MPR) in open circuit respiration chambers for 48 h. Traits studied included DMI during the methane measurement period, MPR, and methane yield (MY; MPR/DMI), with means of 6.1 kg/d (SD 1.3), 132 g/d (SD 25), and 22.0 g/kg (SD 2.3) DMI, respectively. Four forms of residual methane production (RMP), which is a measure of actual minus predicted MPR, were evaluated. For the first 3 forms, predicted MPR was calculated using published equations. For the fourth (RMP), predicted MPR was obtained by regression of MPR on DMI. Growth and body composition traits evaluated were birth weight (BWT), weaning weight (WWT), yearling weight (YWT), final weight (FWT), and ultrasound measures of eye muscle area, rump fat depth, rib fat depth, and intramuscular fat. Heritability estimates were moderate for MPR (0.27 [SE 0.07]), MY (0.22 [SE 0.06]), and the RMP traits (0.19 [SE 0.06] for each), indicating that genetic improvement to reduce methane emissions is possible. The RMP traits and MY were strongly genetically correlated with each other (0.99 ± 0.01). The genetic correlation of MPR with MY as well as with the RMP traits was moderate (0.32 to 0.63). The genetic correlation between MPR and the growth traits (except BWT) was strong (0.79 to 0.86). These results indicate that

  5. The effect of genetic drift on the variance/covariance components generated by multilocus additive x additive epistatic systems.

    Science.gov (United States)

    López-Fanjul, Carlos; Fernández, Almudena; Toro, Miguel A

    2006-03-21

    The effect of population bottlenecks on the components of the genetic variance/covariance generated by n neutral independent additive x additive loci has been studied theoretically. In its simplest version, this situation can be modelled by specifying the allele frequencies and homozygous effects at each locus, and an additional factor measuring the strength of the n-th order epistatic interaction. The variance/covariance components in an infinitely large panmictic population (ancestral components) were compared with their expected values at equilibrium over replicates randomly derived from the base population, after t bottlenecks of size N (derived components). Formulae were obtained giving the derived components (and the between-line variance) as functions of the ancestral ones (alternatively, in terms of allele frequencies and effects) and the corresponding inbreeding coefficient F(t). The n-th order derived component of the genetic variance/covariance is continuously eroded by inbreeding, but the remaining components may increase initially until a critical F(t) value is attained, which is inversely related to the order of the pertinent component, and subsequently decline to zero. These changes can be assigned to the between-line variances/covariances of gene substitution and epistatic effects induced by drift. Numerical examples indicate that: (1) the derived additive variance/covariance component will generally exceed its ancestral value unless epistasis is weak; (2) the derived epistatic variance/covariance components will generally exceed their ancestral values unless allele frequencies are extreme; (3) for systems showing equal ancestral additive and total non-additive variance/covariance components, those including a smaller number of epistatic loci may generate a larger excess in additive variance/covariance after bottlenecks than others involving a larger number of loci, provided that F(t) is low. Our results indicate that it is unlikely that the rate of

  6. Genetic and Environmental Variance Among F2 Families in a Commercial Breeding Program for Perennial Ryegrass (Lolium perenne L.)

    DEFF Research Database (Denmark)

    Fé, Dario; Greve-Pedersen, Morten; Jensen, Christian Sig

    2013-01-01

    In the joint project “FORAGESELECT”, we aim to implement Genome Wide Selection (GWS) in breeding of perennial ryegrass (Lolium perenne L.), in order to increase genetic response in important agronomic traits such as yield, seed production, stress tolerance and disease resistance, while decreasing...... of this study was to estimate the genetic and environmental variance in the training set composed of F2 families selected from a ten year breeding period. Variance components were estimated on 1193 of those families, sown in 2001, 2003 and 2005 in five locations around Europe. Families were tested together...

  7. Genetic sorting of subordinate species in grassland modulated by intraspecific variation in dominant species.

    Directory of Open Access Journals (Sweden)

    Danny J Gustafson

    Full Text Available Genetic variation in a single species can have predictable and heritable effects on associated communities and ecosystem processes, however little is known about how genetic variation of a dominant species affects plant community assembly. We characterized the genetic structure of a dominant grass (Sorghastrum nutans and two subordinate species (Chamaecrista fasciculata, Silphium integrifolium, during the third growing season in grassland communities established with genetically distinct (cultivated varieties or local ecotypes seed sources of the dominant grasses. There were genetic differences between subordinate species growing in the cultivar versus local ecotype communities, indicating that intraspecific genetic variation in the dominant grasses affected the genetic composition of subordinate species during community assembly. A positive association between genetic diversity of S. nutans, C. fasciculata, and S. integrifolium and species diversity established the role of an intraspecific biotic filter during community assembly. Our results show that intraspecific variation in dominant species can significantly modulate the genetic composition of subordinate species.

  8. Knowledge extraction algorithm for variances handling of CP using integrated hybrid genetic double multi-group cooperative PSO and DPSO.

    Science.gov (United States)

    Du, Gang; Jiang, Zhibin; Diao, Xiaodi; Yao, Yang

    2012-04-01

    Although the clinical pathway (CP) predefines predictable standardized care process for a particular diagnosis or procedure, many variances may still unavoidably occur. Some key index parameters have strong relationship with variances handling measures of CP. In real world, these problems are highly nonlinear in nature so that it's hard to develop a comprehensive mathematic model. In this paper, a rule extraction approach based on combing hybrid genetic double multi-group cooperative particle swarm optimization algorithm (PSO) and discrete PSO algorithm (named HGDMCPSO/DPSO) is developed to discovery the previously unknown and potentially complicated nonlinear relationship between key parameters and variances handling measures of CP. Then these extracted rules can provide abnormal variances handling warning for medical professionals. Three numerical experiments on Iris of UCI data sets, Wisconsin breast cancer data sets and CP variances data sets of osteosarcoma preoperative chemotherapy are used to validate the proposed method. When compared with the previous researches, the proposed rule extraction algorithm can obtain the high prediction accuracy, less computing time, more stability and easily comprehended by users, thus it is an effective knowledge extraction tool for CP variances handling.

  9. Genetics Home Reference: autosomal dominant leukodystrophy with autonomic disease

    Science.gov (United States)

    ... MalaCards: autosomal dominant leukodystrophy with autonomic disease Merck Manual Consumer Version: Overview of ... Organization for Rare Disorders (NORD): Leukodystrophy The Brain Foundation ( ...

  10. Estimates of (co)variance components and genetic parameters for growth traits in Sirohi goat.

    Science.gov (United States)

    Gowane, Gopal R; Chopra, Ashish; Prakash, Ved; Arora, A L

    2011-01-01

    Data were collected over a period of 21 years (1988-2008) to estimate (co)variance components for birth weight (BWT), weaning weight (WWT), 6-month weight (6WT), 9-month weight (9WT), 12-month weight (12WT), average daily gain from birth to weaning (ADG1), weaning to 6WT (ADG2), and from 6WT to 12WT (ADG3) in Sirohi goats maintained at the Central Sheep and Wool Research Institute, Avikanagar, Rajasthan, India. Analyses were carried out by restricted maximum likelihood, fitting six animal models with various combinations of direct and maternal effects. The best model was chosen after testing the improvement of the log-likelihood values. Heritability estimates for BWT, WWT, 6WT, 9WT, 12WT, ADG1, ADG2, and ADG3 were 0.39 ± 0.05, 0.09 ± 0.03, 0.06 ± 0.02, 0.09 ± 0.03, 0.11 ± 0.03, 0.10 ± 0.3, 0.04 ± 0.02, and 0.01 ± 0.01, respectively. For BWT and ADG1, only direct effects were significant. Estimate of maternal permanent environmental effect were important for body weights from weaning to 12WT and also for ADG2 and ADG3. However, direct maternal effects were not significant throughout. Estimate of c (2) were 0.06 ± 0.02, 0.03 ± 0.02, 0.06 ± 0.02, 0.05 ± 0.02, 0.02 ± 0.02, and 0.02 ± 0.02 for 3WT, 6WT, 9WT, 12WT, ADG2, and ADG3, respectively. The estimated repeatabilities across years of ewe effects on kid body weights were 0.10, 0.08, 0.05, 0.08, and 0.08 at birth, weaning, 6, 9, and 12 months of age, respectively. Results suggest possibility of modest rate of genetic progress for body weight traits and ADG1 through selection, whereas only slow progress will be possible for post-weaning gain. Genetic and phenotypic correlations between body weight traits were high and positive. High genetic correlation between 6WT and 9WT suggests that selection of animals at 6 months can be carried out instead of present practice of selection at 9 months.

  11. Genetic (co)variance of rainbow trout (Oncorhynchus mykiss) body weight and its uniformity across production environments.

    Science.gov (United States)

    Sae-Lim, Panya; Kause, Antti; Janhunen, Matti; Vehviläinen, Harri; Koskinen, Heikki; Gjerde, Bjarne; Lillehammer, Marie; Mulder, Han A

    2015-05-19

    When rainbow trout from a single breeding program are introduced into various production environments, genotype-by-environment (GxE) interaction may occur. Although growth and its uniformity are two of the most important traits for trout producers worldwide, GxE interaction on uniformity of growth has not been studied. Our objectives were to quantify the genetic variance in body weight (BW) and its uniformity and the genetic correlation (rg) between these traits, and to investigate the degree of GxE interaction on uniformity of BW in breeding (BE) and production (PE) environments using double hierarchical generalized linear models. Log-transformed data were also used to investigate whether the genetic variance in uniformity of BW, GxE interaction on uniformity of BW, and rg between BW and its uniformity were influenced by a scale effect. Although heritability estimates for uniformity of BW were low and of similar magnitude in BE (0.014) and PE (0.012), the corresponding coefficients of genetic variation reached 19 and 21%, which indicated a high potential for response to selection. The genetic re-ranking for uniformity of BW (rg = 0.56) between BE and PE was moderate but greater after log-transformation, as expressed by the low rg (-0.08) between uniformity in BE and PE, which indicated independent genetic rankings for uniformity in the two environments when the scale effect was accounted for. The rg between BW and its uniformity were 0.30 for BE and 0.79 for PE but with log-transformed BW, these values switched to -0.83 and -0.62, respectively. Genetic variance exists for uniformity of BW in both environments but its low heritability implies that a large number of relatives are needed to reach even moderate accuracy of selection. GxE interaction on uniformity is present for both environments and sib-testing in PE is recommended when the aim is to improve uniformity across environments. Positive and negative rg between BW and its uniformity estimated with original

  12. Speeding Up Microevolution: The Effects of Increasing Temperature on Selection and Genetic Variance in a Wild Bird Population

    Science.gov (United States)

    Husby, Arild; Visser, Marcel E.; Kruuk, Loeske E. B.

    2011-01-01

    The amount of genetic variance underlying a phenotypic trait and the strength of selection acting on that trait are two key parameters that determine any evolutionary response to selection. Despite substantial evidence that, in natural populations, both parameters may vary across environmental conditions, very little is known about the extent to which they may covary in response to environmental heterogeneity. Here we show that, in a wild population of great tits (Parus major), the strength of the directional selection gradients on timing of breeding increased with increasing spring temperatures, and that genotype-by-environment interactions also predicted an increase in additive genetic variance, and heritability, of timing of breeding with increasing spring temperature. Consequently, we therefore tested for an association between the annual selection gradients and levels of additive genetic variance expressed each year; this association was positive, but non-significant. However, there was a significant positive association between the annual selection differentials and the corresponding heritability. Such associations could potentially speed up the rate of micro-evolution and offer a largely ignored mechanism by which natural populations may adapt to environmental changes. PMID:21408101

  13. Shared genetic variance between the features of the metabolic syndrome: Heritability studies

    NARCIS (Netherlands)

    Povel, C.M.; Boer, J.M.A.; Feskens, E.J.M.

    2011-01-01

    Heritability estimates of MetS range from approximately 10%–30%. The genetic variation that is shared among MetS features can be calculated by genetic correlation coefficients. The objective of this paper is to identify MetS feature as well as MetS related features which have much genetic variation

  14. Normal linear models with genetically structured residual variance heterogeneity: a case study

    DEFF Research Database (Denmark)

    Sorensen, Daniel; Waagepetersen, Rasmus Plenge

    2003-01-01

    Normal mixed models with different levels of heterogeneity in the residual variance are fitted to pig litter size data. Exploratory analysis and model assessment is based on examination of various posterior predictive distributions. Comparisons based on Bayes factors and related criteria favour...

  15. Estimating Additive and Non-Additive Genetic Variances and Predicting Genetic Merits Using Genome-Wide Dense Single Nucleotide Polymorphism Markers

    DEFF Research Database (Denmark)

    Su, Guosheng; Christensen, Ole Fredslund; Ostersen, Tage;

    2012-01-01

    Non-additive genetic variation is usually ignored when genome-wide markers are used to study the genetic architecture and genomic prediction of complex traits in human, wild life, model organisms or farm animals. However, non-additive genetic effects may have an important contribution to total...... genetic variation of complex traits. This study presented a genomic BLUP model including additive and non-additive genetic effects, in which additive and non-additive genetic relation matrices were constructed from information of genome-wide dense single nucleotide polymorphism (SNP) markers. In addition...... of genomic predictions for daily gain in pigs. In the analysis of daily gain, four linear models were used: 1) a simple additive genetic model (MA), 2) a model including both additive and additive by additive epistatic genetic effects (MAE), 3) a model including both additive and dominance genetic effects...

  16. A simple algorithm to estimate genetic variance in an animal threshold model using Bayesian inference Genetics Selection Evolution 2010, 42:29

    DEFF Research Database (Denmark)

    Ødegård, Jørgen; Meuwissen, Theo HE; Heringstad, Bjørg

    2010-01-01

    Background In the genetic analysis of binary traits with one observation per animal, animal threshold models frequently give biased heritability estimates. In some cases, this problem can be circumvented by fitting sire- or sire-dam models. However, these models are not appropriate in cases where...... individual records exist on parents. Therefore, the aim of our study was to develop a new Gibbs sampling algorithm for a proper estimation of genetic (co)variance components within an animal threshold model framework. Methods In the proposed algorithm, individuals are classified as either "informative......" or "non-informative" with respect to genetic (co)variance components. The "non-informative" individuals are characterized by their Mendelian sampling deviations (deviance from the mid-parent mean) being completely confounded with a single residual on the underlying liability scale. For threshold models...

  17. Power graph compression reveals dominant relationships in genetic transcription networks.

    Science.gov (United States)

    Ahnert, Sebastian E

    2013-11-01

    We introduce a framework for the discovery of dominant relationship patterns in transcription networks, by compressing the network into a power graph with overlapping power nodes. Our application of this approach to the transcription networks of S. cerevisiae and E. coli, paired with GO term enrichment analysis, provides a highly informative overview of the most prominent relationships in the gene regulatory networks of these two organisms.

  18. Stability of genetic variance and covariance for reproductive characters in the face of climate change in a wild bird population.

    Science.gov (United States)

    Garant, Dany; Hadfield, Jarrod D; Kruuk, Loeske E B; Sheldon, Ben C

    2008-01-01

    Global warming has had numerous effects on populations of animals and plants, with many species in temperate regions experiencing environmental change at unprecedented rates. Populations with low potential for adaptive evolutionary change and plasticity will have little chance of persistence in the face of environmental change. Assessment of the potential for adaptive evolution requires the estimation of quantitative genetic parameters, but it is as yet unclear what impact, if any, global warming will have on the expression of genetic variances and covariances. Here we assess the impact of a changing climate on the genetic architecture underlying three reproductive traits in a wild bird population. We use a large, long-term, data set collected on great tits (Parus major) in Wytham Woods, Oxford, and an 'animal model' approach to quantify the heritability of, and genetic correlations among, laying date, clutch size and egg mass during two periods with contrasting temperature conditions over a 40-year period (1965-1988 [cooler] vs. 1989-2004 [warmer]). We found significant additive genetic variance and heritability for all traits under both temperature regimes. We also found significant negative genetic covariances and correlations between clutch size and egg weight during both periods, and among laying date and clutch size in the colder years only. The overall G matrix comparison among periods, however, showed only a minor difference among periods, thus suggesting that genotype by environment interactions are negligible in this context. Our results therefore suggest that despite substantial changes in temperature and in mean laying date phenotype over the last decades, and despite the large sample sizes available, we are unable to detect any significant change in the genetic architecture of the reproductive traits studied.

  19. Genetic variance and covariance components related to intra- and interpopulation recurrent selection in maize (Zea mays L.

    Directory of Open Access Journals (Sweden)

    Arias Carlos Alberto Arrabal

    1998-01-01

    Full Text Available New genetic variance and covariance components related to intra- and interpopulational recurrent selection methods have been theoretically developed by Souza Jr. (Rev. Bras. Genet. 16: 91-105, 1993 to explain the failure of these methods to concomitantly develop hybrid and per se populations. Intra- and interpopulation half-sib progenies of 100 genotypes were sampled from maize (Zea mays L. populations BR-106 and BR-105 to estimate variance and covariance components and to compare the expected responses to reciprocal (RRS, intrapopulational (HSS, and modified (MRS recurrent selection in interpopulation hybrid, populations per se, and to determine heterosis. Four sets of 100 progenies, two intra- and two interpopulational, were evaluated in partially balanced 10 x 10 lattices arranged in split-blocks with two replications in two years (1991/92 and 1992/93 and two locations in Piracicaba, SP. Data for ear weight, plant and ear height, and ear by plant height ratio were recorded. Populations and interpopulation crosses were high yielding and showed high breeding potential for production of hybrids from inbred lines. Mid parent and the highest parent heterosis were relatively high, but lower than values reported for these populations under other environmental conditions. Additive variance estimates of populations per se and interpopulation crosses confirmed the high potential of these materials. The magnitude of the variance estimates for the deviations from intra- and interpopulation additive effects ( for BR-106 and for BR-105 and covariance between additive effects with these deviations ( for BR-106 and for BR-105 indicated that these new components can significantly influence the effectiveness of breeding methods. Genetic component estimates for BR-105 had relatively small errors, with negative for all traits. Estimates of and had relatively larger errors for BR-106. The MRS method was more effective than the RRS and HSS methods in producing

  20. Pedigree-based estimation of covariance between dominance deviations and additive genetic effects in closed rabbit lines considering inbreeding and using a computationally simpler equivalent model.

    Science.gov (United States)

    Fernández, E N; Legarra, A; Martínez, R; Sánchez, J P; Baselga, M

    2017-06-01

    Inbreeding generates covariances between additive and dominance effects (breeding values and dominance deviations). In this work, we developed and applied models for estimation of dominance and additive genetic variances and their covariance, a model that we call "full dominance," from pedigree and phenotypic data. Estimates with this model such as presented here are very scarce both in livestock and in wild genetics. First, we estimated pedigree-based condensed probabilities of identity using recursion. Second, we developed an equivalent linear model in which variance components can be estimated using closed-form algorithms such as REML or Gibbs sampling and existing software. Third, we present a new method to refer the estimated variance components to meaningful parameters in a particular population, i.e., final partially inbred generations as opposed to outbred base populations. We applied these developments to three closed rabbit lines (A, V and H) selected for number of weaned at the Polytechnic University of Valencia. Pedigree and phenotypes are complete and span 43, 39 and 14 generations, respectively. Estimates of broad-sense heritability are 0.07, 0.07 and 0.05 at the base versus 0.07, 0.07 and 0.09 in the final generations. Narrow-sense heritability estimates are 0.06, 0.06 and 0.02 at the base versus 0.04, 0.04 and 0.01 at the final generations. There is also a reduction in the genotypic variance due to the negative additive-dominance correlation. Thus, the contribution of dominance variation is fairly large and increases with inbreeding and (over)compensates for the loss in additive variation. In addition, estimates of the additive-dominance correlation are -0.37, -0.31 and 0.00, in agreement with the few published estimates and theoretical considerations. © 2017 Blackwell Verlag GmbH.

  1. Who is afraid of math? Two sources of genetic variance for mathematical anxiety.

    Science.gov (United States)

    Wang, Zhe; Hart, Sara Ann; Kovas, Yulia; Lukowski, Sarah; Soden, Brooke; Thompson, Lee A; Plomin, Robert; McLoughlin, Grainne; Bartlett, Christopher W; Lyons, Ian M; Petrill, Stephen A

    2014-09-01

    Emerging work suggests that academic achievement may be influenced by the management of affect as well as through efficient information processing of task demands. In particular, mathematical anxiety has attracted recent attention because of its damaging psychological effects and potential associations with mathematical problem solving and achievement. This study investigated the genetic and environmental factors contributing to the observed differences in the anxiety people feel when confronted with mathematical tasks. In addition, the genetic and environmental mechanisms that link mathematical anxiety with math cognition and general anxiety were also explored. Univariate and multivariate quantitative genetic models were conducted in a sample of 514 12-year-old twin siblings. Genetic factors accounted for roughly 40% of the variation in mathematical anxiety, with the remaining being accounted for by child-specific environmental factors. Multivariate genetic analyses suggested that mathematical anxiety was influenced by the genetic and nonfamilial environmental risk factors associated with general anxiety and additional independent genetic influences associated with math-based problem solving. The development of mathematical anxiety may involve not only exposure to negative experiences with mathematics, but also likely involves genetic risks related to both anxiety and math cognition. These results suggest that integrating cognitive and affective domains may be particularly important for mathematics and may extend to other areas of academic achievement. © 2014 The Authors. Journal of Child Psychology and Psychiatry. © 2014 Association for Child and Adolescent Mental Health.

  2. Who’s Afraid of Math? Two Sources of Genetic Variance for Mathematical Anxiety

    Science.gov (United States)

    Wang, Zhe; Hart, Sara Ann; Kovas, Yulia; Lukowski, Sarah; Soden, Brooke; Thompson, Lee A.; Plomin, Robert; McLoughlin, Grainne; Bartlett, Christopher W.; Lyons, Ian M.; Petrill, Stephen A.

    2015-01-01

    Background Emerging work suggests that academic achievement may be influenced by the management of affect as well as through efficient information processing of task demands. In particular, mathematical anxiety has attracted recent attention because of its damaging psychological effects and potential associations with mathematical problem-solving and achievement. The present study investigated the genetic and environmental factors contributing to the observed differences in the anxiety people feel when confronted with mathematical tasks. In addition, the genetic and environmental mechanisms that link mathematical anxiety with math cognition and general anxiety were also explored. Methods Univariate and multivariate quantitative genetic models were conducted in a sample of 514 12-year-old twin siblings. Results Genetic factors accounted for roughly 40% of the variation in mathematical anxiety, with the remaining being accounted for by child-specific environmental factors. Multivariate genetic analyses suggested that mathematical anxiety was influenced by the genetic and non-familial environmental risk factors associated with general anxiety and additional independent genetic influences associated with math-based problem solving. Conclusions The development of mathematical anxiety may involve not only exposure to negative experiences with mathematics, but also likely involves genetic risks related to both anxiety and math cognition. These results suggest that integrating cognitive and affective domains may be particularly important for mathematics, and may extend to other areas of academic achievement. PMID:24611799

  3. Accuracy of whole-genome prediction using a genetic architecture-enhanced variance-covariance matrix.

    Science.gov (United States)

    Zhang, Zhe; Erbe, Malena; He, Jinlong; Ober, Ulrike; Gao, Ning; Zhang, Hao; Simianer, Henner; Li, Jiaqi

    2015-02-09

    Obtaining accurate predictions of unobserved genetic or phenotypic values for complex traits in animal, plant, and human populations is possible through whole-genome prediction (WGP), a combined analysis of genotypic and phenotypic data. Because the underlying genetic architecture of the trait of interest is an important factor affecting model selection, we propose a new strategy, termed BLUP|GA (BLUP-given genetic architecture), which can use genetic architecture information within the dataset at hand rather than from public sources. This is achieved by using a trait-specific covariance matrix ( T: ), which is a weighted sum of a genetic architecture part ( S: matrix) and the realized relationship matrix ( G: ). The algorithm of BLUP|GA (BLUP-given genetic architecture) is provided and illustrated with real and simulated datasets. Predictive ability of BLUP|GA was validated with three model traits in a dairy cattle dataset and 11 traits in three public datasets with a variety of genetic architectures and compared with GBLUP and other approaches. Results show that BLUP|GA outperformed GBLUP in 20 of 21 scenarios in the dairy cattle dataset and outperformed GBLUP, BayesA, and BayesB in 12 of 13 traits in the analyzed public datasets. Further analyses showed that the difference of accuracies for BLUP|GA and GBLUP significantly correlate with the distance between the T: and G: matrices. The new strategy applied in BLUP|GA is a favorable and flexible alternative to the standard GBLUP model, allowing to account for the genetic architecture of the quantitative trait under consideration when necessary. This feature is mainly due to the increased similarity between the trait-specific relationship matrix ( T: matrix) and the genetic relationship matrix at unobserved causal loci. Applying BLUP|GA in WGP would ease the burden of model selection. Copyright © 2015 Zhang et al.

  4. Increased genetic variance of BMI with a higher prevalence of obesity

    DEFF Research Database (Denmark)

    Rokholm, Benjamin; Silventoinen, Karri; Ängquist, Lars

    2011-01-01

    There is no doubt that the dramatic worldwide increase in obesity prevalence is due to changes in environmental factors. However, twin studies suggest that genetic differences are responsible for the major part of the variation in body mass index (BMI) and other measures of body fatness within...... populations. Several recent studies suggest that the genetic effects on adiposity may be stronger when combined with presumed risk factors for obesity. We tested the hypothesis that a higher prevalence of obesity and overweight and a higher BMI mean is associated with a larger genetic variation in BMI....

  5. Additive-dominance genetic model analyses for late-maturity alpha-amylase activity in a bread wheat factorial crossing population.

    Science.gov (United States)

    Rasul, Golam; Glover, Karl D; Krishnan, Padmanaban G; Wu, Jixiang; Berzonsky, William A; Ibrahim, Amir M H

    2015-12-01

    Elevated level of late maturity α-amylase activity (LMAA) can result in low falling number scores, reduced grain quality, and downgrade of wheat (Triticum aestivum L.) class. A mating population was developed by crossing parents with different levels of LMAA. The F2 and F3 hybrids and their parents were evaluated for LMAA, and data were analyzed using the R software package 'qgtools' integrated with an additive-dominance genetic model and a mixed linear model approach. Simulated results showed high testing powers for additive and additive × environment variances, and comparatively low powers for dominance and dominance × environment variances. All variance components and their proportions to the phenotypic variance for the parents and hybrids were significant except for the dominance × environment variance. The estimated narrow-sense heritability and broad-sense heritability for LMAA were 14 and 54%, respectively. High significant negative additive effects for parents suggest that spring wheat cultivars 'Lancer' and 'Chester' can serve as good general combiners, and that 'Kinsman' and 'Seri-82' had negative specific combining ability in some hybrids despite of their own significant positive additive effects, suggesting they can be used as parents to reduce LMAA levels. Seri-82 showed very good general combining ability effect when used as a male parent, indicating the importance of reciprocal effects. High significant negative dominance effects and high-parent heterosis for hybrids demonstrated that the specific hybrid combinations; Chester × Kinsman, 'Lerma52' × Lancer, Lerma52 × 'LoSprout' and 'Janz' × Seri-82 could be generated to produce cultivars with significantly reduced LMAA level.

  6. BDNF contributes to the genetic variance of milk fat yield in German Holstein cattle

    Directory of Open Access Journals (Sweden)

    Lea G. Zielke

    2011-04-01

    Full Text Available AbstractThe gene encoding the brain derived neurotrophic factor (BDNF has been repeatedly associated with human obesity. As such, it could also contribute to the regulation of energy partitioning and the amount of secreted milk fat during lactation, which plays an important role in milk production in dairy cattle. Therefore, we performed an association study using estimated breeding values of bulls and yield deviations of German Holstein dairy cattle to test the effect of BDNF on milk fat yield. A highly significant effect (corrected p-value =3.362 x10-4 was identified for an SNP 168 kb up-stream of the BDNF transcription start. The association tests provided evidence for an additive allele effect of 5.13 kg of fat per lactation on the estimated breeding value for milk fat yield in bulls and 6.80 kg of fat of the own production performance in cows explaining 1.72% and 0.60% of the phenotypic variance in the analysed populations, respectively. The analyses of bulls and cows consistently showed three haplotype groups that differed significantly from each other, suggesting at least two different mutations in the BDNF-region affecting the milk fat yield. The fat yield increasing alleles also had low but significant positive effects on protein and total milk yield which suggests a general role of the BDNF-region in energy partitioning, rather than a specific regulation of fat synthesis. The results obtained in dairy cattle suggest similar effects of BDNF on milk composition in other species, including man.

  7. [Genetic variance of duck preproinsulin gene and its correlations to the traits of carcasses].

    Science.gov (United States)

    Kong, Xiang-Jie; Liu, Xiao-Lin; Wu, Yan; Wang, Jie

    2008-06-01

    Genetic polymorphisms of exon 2 and partial intron of preproinsulin gene were studied in Peking duck and Cherry Valley duck by PCR-SSCP and DNA sequencing technologies. Two single nucleotide mutations, T179C and C195T, were found, respectively. chi2 test reflects that the tested population of Peking duck and Cherry Valley duck were in the Hardy-Weinberg equilibrium state (P>0.05). The relationships between SNPs and the traits of carcasses were analyzed by the least square analysis, which showed that the genotype BB in three lines of Peking duck was significantly higher in carcass weight, carcass net weight and breast muscle weight than AA and BB (P<0.01) and significantly higher in leg muscle weight and sebum weight than AB (P<0.01). In addition, the genotype AA was significantly greater than AB in sebum rate (P<0.01) and carcass net weight (P<0.05), respectively. However, for Cherry Valley duck, only the genotype AB was significantly higher than AA in sebum weight and abdomen fat weight (P<0.05). The results indicated that there was significant correlation between the genetic polymorphisms of preproinsulin gene and the traits of duck carcasses and the allele B was valuable for increasing the carcass weight and breast muscle weight.

  8. Heritability of blood pressure traits and the genetic contribution to blood pressure variance explained by four blood-pressure-related genes.

    NARCIS (Netherlands)

    Rijn, M.J. van; Schut, A.F.; Aulchenko, Y.S.; Deinum, J.; Sayed-Tabatabaei, F.A.; Yazdanpanah, M.; Isaacs, A.; Axenovich, T.I.; Zorkoltseva, I.V.; Zillikens, M.C.; Pols, H.A.; Witteman, J.C.; Oostra, B.A.; Duijn, C.M. van

    2007-01-01

    OBJECTIVE: To study the heritability of four blood pressure traits and the proportion of variance explained by four blood-pressure-related genes. METHODS: All participants are members of an extended pedigree from a Dutch genetically isolated population. Heritability and genetic correlations of systo

  9. Heritability of blood pressure traits and the genetic contribution to blood pressure variance explained by four blood-pressure-related genes.

    NARCIS (Netherlands)

    Rijn, M.J. van; Schut, A.F.; Aulchenko, Y.S.; Deinum, J.; Sayed-Tabatabaei, F.A.; Yazdanpanah, M.; Isaacs, A.; Axenovich, T.I.; Zorkoltseva, I.V.; Zillikens, M.C.; Pols, H.A.; Witteman, J.C.; Oostra, B.A.; Duijn, C.M. van

    2007-01-01

    OBJECTIVE: To study the heritability of four blood pressure traits and the proportion of variance explained by four blood-pressure-related genes. METHODS: All participants are members of an extended pedigree from a Dutch genetically isolated population. Heritability and genetic correlations of

  10. Temporal Genetic Variance and Propagule-Driven Genetic Structure Characterize Naturalized Rainbow Trout (Oncorhynchus mykiss) from a Patagonian Lake Impacted by Trout Farming

    Science.gov (United States)

    Seeb, Lisa W.; Seeb, James E.; Arismendi, Ivan; Hernández, Cristián E.; Gajardo, Gonzalo; Galleguillos, Ricardo; Cádiz, Maria I.; Musleh, Selim S.

    2015-01-01

    Knowledge about the genetic underpinnings of invasions—a theme addressed by invasion genetics as a discipline—is still scarce amid well documented ecological impacts of non-native species on ecosystems of Patagonia in South America. One of the most invasive species in Patagonia’s freshwater systems and elsewhere is rainbow trout (Oncorhynchus mykiss). This species was introduced to Chile during the early twentieth century for stocking and promoting recreational fishing; during the late twentieth century was reintroduced for farming purposes and is now naturalized. We used population- and individual-based inference from single nucleotide polymorphisms (SNPs) to illuminate three objectives related to the establishment and naturalization of Rainbow Trout in Lake Llanquihue. This lake has been intensively used for trout farming during the last three decades. Our results emanate from samples collected from five inlet streams over two seasons, winter and spring. First, we found that significant intra- population (temporal) genetic variance was greater than inter-population (spatial) genetic variance, downplaying the importance of spatial divergence during the process of naturalization. Allele frequency differences between cohorts, consistent with variation in fish length between spring and winter collections, might explain temporal genetic differences. Second, individual-based Bayesian clustering suggested that genetic structure within Lake Llanquihue was largely driven by putative farm propagules found at one single stream during spring, but not in winter. This suggests that farm broodstock might migrate upstream to breed during spring at that particular stream. It is unclear whether interbreeding has occurred between “pure” naturalized and farm trout in this and other streams. Third, estimates of the annual number of breeders (Nb) were below 73 in half of the collections, suggestive of genetically small and recently founded populations that might experience

  11. Evolution of the additive genetic variance-covariance matrix under continuous directional selection on a complex behavioural phenotype.

    Science.gov (United States)

    Careau, Vincent; Wolak, Matthew E; Carter, Patrick A; Garland, Theodore

    2015-11-22

    Given the pace at which human-induced environmental changes occur, a pressing challenge is to determine the speed with which selection can drive evolutionary change. A key determinant of adaptive response to multivariate phenotypic selection is the additive genetic variance-covariance matrix ( G: ). Yet knowledge of G: in a population experiencing new or altered selection is not sufficient to predict selection response because G: itself evolves in ways that are poorly understood. We experimentally evaluated changes in G: when closely related behavioural traits experience continuous directional selection. We applied the genetic covariance tensor approach to a large dataset (n = 17 328 individuals) from a replicated, 31-generation artificial selection experiment that bred mice for voluntary wheel running on days 5 and 6 of a 6-day test. Selection on this subset of G: induced proportional changes across the matrix for all 6 days of running behaviour within the first four generations. The changes in G: induced by selection resulted in a fourfold slower-than-predicted rate of response to selection. Thus, selection exacerbated constraints within G: and limited future adaptive response, a phenomenon that could have profound consequences for populations facing rapid environmental change. © 2015 The Author(s).

  12. Development of new source diagnostic methods and variance reduction techniques for Monte Carlo eigenvalue problems with a focus on high dominance ratio problems

    Science.gov (United States)

    Wenner, Michael T.

    Obtaining the solution to the linear Boltzmann equation is often is often a daunting task. The time-independent form is an equation of six independent variables which cannot be solved analytically in all but some special problems. Instead, numerical approaches have been devised. This work focuses on improving Monte Carlo methods for its solution in eigenvalue form. First, a statistical method of stationarity detection called the KPSS test adapted as a Monte Carlo eigenvalue source convergence test. The KPSS test analyzes the source center of mass series which was chosen since it should be indicative of overall source behavior, and is physically easy to understand. A source center of mass plot alone serves as a good visual source convergence diagnostic. The KPSS test and three different information theoretic diagnostics were implemented into the well known KENOV.a code inside of the SCALE (version 5) code package from Oak Ridge National Laboratory and compared through analysis of a simple problem and several difficult source convergence benchmarks. Results showed that the KPSS test can add to the overall confidence by identifying more problematic simulations than without its usage. Not only this, the source center of mass information on hand visually aids in the understanding of the problem physics. The second major focus of this dissertation concerned variance reduction methodologies for Monte Carlo eigenvalue problems. The CADIS methodology, based on importance sampling, was adapted to the eigenvalue problems. It was shown that the straight adaption of importance sampling can provide a significant variance reduction in determination of keff (in cases studied up to 30%?). A modified version of this methodology was developed which utilizes independent deterministic importance simulations. In this new methodology, each particle is simulated multiple times, once to every other discretized source region utilizing the importance for that region only. Since each particle

  13. Genetic Analysis and Mapping of Dominant Minute Grain Gene Mi3(t) in Rice

    Institute of Scientific and Technical Information of China (English)

    LIU Ming-wei; LIU Yong; WANG Shi-quan; DENG Qi-ming; LI Ping

    2005-01-01

    Grain size, determined chiefly by grain Iength, is one of the main factors affecting the grain yield in rice production. To study the trait of rice grain size, F1 and F2 populations were developed from crosses Shuhui 881/Y34 and Shuhui 527/Y34, and genetic analysis for minute grain was performed. The F1 populations showed minute grains, and grain size segregations in the two F2 populations were both in accordance with the ratio of 3:1, indicating that minute grain in Y34 was controlled by a completely dominant gene. By using the F2 population from Shuhui 881/Y34, this dominant gene, tentatively designated as Mi3(t), was mapped based on SSR markers in the interval between RM282 (genetic distance of 5.1 cM) and RM6283 (genetic distance of 0.9 cM) on the short arm of chromosome 3.

  14. Genetic Load in Sexual and Asexual Diploids: Segregation, Dominance and Genetic Drift

    OpenAIRE

    Haag, Christoph R.; Roze, Denis

    2007-01-01

    In diploid organisms, sexual reproduction rearranges allelic combinations between loci (recombination) as well as within loci (segregation). Several studies have analyzed the effect of segregation on the genetic load due to recurrent deleterious mutations, but considered infinite populations, thus neglecting the effects of genetic drift. Here, we use single-locus models to explore the combined effects of segregation, selection, and drift. We find that, for partly recessive deleterious alleles...

  15. Genetic and environmental variance and covariance parameters for some reproductive traits of Holstein and Jersey cattle in Antioquia (Colombia

    Directory of Open Access Journals (Sweden)

    Juan Carlos Zambrano

    2014-03-01

    Full Text Available The objective of this study was to estimate the genetic, phenotypic and environmental parameters for calving interval (CI, days open (DO, number of services per conception (NSC and conception rate (CR in Holstein and Jersey cattle in Antioquia (Colombia. Variance and covariance component estimates were obtained by an animal model that was solved using the derivative-free restricted maximum likelihood method. The means and standard deviations for CI, DO, NSC and CR were: 430.32±77.93 days, 127.15±76.96 days, 1.58±1.03 services per conception and 79.88±28.66% in Holstein cattle, and 409.33±86.48 days, 125.62±86.09 days, 1.48±0.98 services per conception and 84.08±27.23% in Jersey cattle, respectively. The heritability estimates (standard errors were: 0.088(0.037, 0.082(0.037, 0.040(0.025 and 0.030(0.026 in Holstein cattle and 0.072(0.098, 0.090(0.104, 0.093(0.097 and 0.147(0.117 in Jersey cattle, respectively. The results show that the genetic, phenotypic and permanent environmental correlations in the two evaluated breeds were favorable for CI × DO, CI × NSC and DO × NSC, but not for CI × CR, DO × CR and NSC × CR. Genetic and permanent environmental correlations were high in most cases in Holstein cattle, whereas in Jersey cattle they were moderate. In contrast, phenotypic correlations were very low in both breeds, except for CI × DO and NSC × CR, which were high. Overall, the genetic component found was very low (<8% in both evaluated breeds and this implies that their selection would take long time and that a good practical management of the herd will be essential in order to improve the reproductive performance.

  16. Genetic (co)variances and breeding value estimation of Gompertz growth curve parameters in Finnish Yorkshire boars, gilts and barrows.

    Science.gov (United States)

    Koivula, M; Sevón-Aimonen, M-L; Strandén, I; Matilainen, K; Serenius, T; Stalder, K J; Mäntysaari, E A

    2008-06-01

    This paper's objectives were to estimate the genetic (co)variance components of the Gompertz growth curve parameters and to evaluate the relationship of estimated breeding values (EBV) based on average daily gain (ADG) and Gompertz growth curves. Finnish Yorkshire central test station performance data was obtained from the Faba Breeding (Vantaa, Finland). The final data set included 121,488 weight records from 10,111 pigs. Heritability estimates for the Gompertz growth parameters mature weight (alpha), logarithm of mature weight to birth weight ratio (beta) and maturation rate (kappa) were 0.44, 0.55 and 0.31, respectively. Genotypic and phenotypic correlations between the growth curve parameters were high and mainly negative. The only positive relationship was found between alpha and beta. Pearson and Spearman rank correlation coefficients between EBV for ADG and daily gain calculated from Gompertz growth curves were 0.79. The Spearman rank correlation between the sire EBV for ADG and Gompertz growth curve parameter-based ADG for all sires with at least 15 progeny was 0.86. Growth curves differ significantly between individuals and this information could be utilized for selection purposes when improving growth rate in pigs.

  17. 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.

  18. Non-dominated Sorting Genetic Algorithms for Heterogeneous Embedded System Design

    Directory of Open Access Journals (Sweden)

    A. K. Rath

    2006-01-01

    Full Text Available The design of complex embedded systems involves the simultaneous optimization of several conflicting and competing objectives. Instead of a single global optimal solution, there exist a set of Pareto optimal solutions. In this study we have used a multi-objective evolutionary optimization algorithms called non-dominated sorting genetic algorithm (NSGA, which will suit to the requirements of designing a complex heterogeneous embedded system. Further, the algorithm is rigorously tested using Video Codec as a case study

  19. Solving multi-objective job shop scheduling problems using a non-dominated sorting genetic algorithm

    Science.gov (United States)

    Piroozfard, Hamed; Wong, Kuan Yew

    2015-05-01

    The efforts of finding optimal schedules for the job shop scheduling problems are highly important for many real-world industrial applications. In this paper, a multi-objective based job shop scheduling problem by simultaneously minimizing makespan and tardiness is taken into account. The problem is considered to be more complex due to the multiple business criteria that must be satisfied. To solve the problem more efficiently and to obtain a set of non-dominated solutions, a meta-heuristic based non-dominated sorting genetic algorithm is presented. In addition, task based representation is used for solution encoding, and tournament selection that is based on rank and crowding distance is applied for offspring selection. Swapping and insertion mutations are employed to increase diversity of population and to perform intensive search. To evaluate the modified non-dominated sorting genetic algorithm, a set of modified benchmarking job shop problems obtained from the OR-Library is used, and the results are considered based on the number of non-dominated solutions and quality of schedules obtained by the algorithm.

  20. A comparison of identity-by-descent and identity-by-state matrices that are used for genetic evaluation and estimation of variance components.

    Science.gov (United States)

    Fernando, R L; Cheng, H; Sun, X; Garrick, D J

    2017-06-01

    The genetic covariance matrix conditional on pedigree is proportional to the pedigree-based additive relationship matrix (PARM), which is twice the matrix of identity-by-descent (IBD) probabilities. In genomic prediction, IBD probabilities in the PARM, which are expected genetic similarities between relatives that are derived from the pedigree, are substituted by realized similarities that are derived from genotypes to obtain a genomic additive relationship matrix (GARM). Different definitions of similarity lead to different GARMs, and two commonly used GARMS are the matrix G, which is based on an allele substitution effect model, and the matrix T, which is based on an allele effect model. We show that although the two matrices T and G are not proportional, they give identical predictions of differences between breeding values. When genomic information is used for variance component estimation, the GARM Gx is computed from genotype covariates that have been standardized to have unit variance. That approach is equivalent to fitting a random regression model using the same standardized covariates. We show that under Hardy-Weinberg and linkage equilibria (LE) that the genetic variance is kσγ2, where σγ2 is the variance of a randomly sampled element from the vector of k substitution effects. However, if linkage disequilibrium (LD) has been generated through selection, covariances between genotypes at different loci will be negative, and therefore, the additive genetic variance will be lower than kσγ2. When the GARM Gx is assumed to be proportional to the genetic covariance matrix, the parameter being estimated is kσγ2. We have demonstrated by simulation that kσγ2 overestimates the additive genetic variance when LD is generated by selection. We argue that unlike the PARM, GARMs are not proportional to a genetic covariance matrix conditional on the observed causal genotypes. The objective here is to recognize the difference between these covariance matrices and

  1. Negative-dominance phenomenon with genetic variants of the cardiac sodium channel Nav1.5.

    Science.gov (United States)

    Sottas, Valentin; Abriel, Hugues

    2016-07-01

    During the past two decades, many pathological genetic variants in SCN5A, the gene encoding the pore-forming subunit of the cardiac (monomeric) sodium channel Na(v)1.5, have been described. Negative dominance is a classical genetic concept involving a "poison" mutant peptide that negatively interferes with the co-expressed wild-type protein, thus reducing its cellular function. This phenomenon has been described for genetic variants of multimeric K(+) channels, which mechanisms are well understood. Unexpectedly, several pathologic SCN5A variants that are linked to Brugada syndrome also demonstrate such a dominant-negative (DN) effect. The molecular determinants of these observations, however, are not yet elucidated. This review article summarizes recent findings that describe the mechanisms underlying the DN phenomenon of genetic variants of K(+), Ca(2+), Cl(-) and Na(+) channels, and in particular Brugada syndrome variants of Na(v)1.5. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Integration of Developmental and Environmental Cues in the Heart edited by Marcus Schaub and Hughes Abriel.

  2. Behavior of genetic (covariance components in populations simulated from non-additive genetic models of dominance and overdominance Comportamento dos componentes de (covariância genética em populações simuladas a partir de modelos genéticos não-aditivos de dominância e sobredominância

    Directory of Open Access Journals (Sweden)

    Elizângela Emídio Cunha

    2010-09-01

    Full Text Available The aim of this work was to investigate the short-term behavior of the genetic variability of quantitative traits simulated from models with additive and non-additive gene action in control and phenotypic selection populations. Both traits, one with low (h² = 0.10 and the other with high (h² = 0.60 heritability, were controlled by 600 biallelic loci. From a standard genome, it was obtained six genetic models which included the following: only the additive gene effects; complete and positive dominance for 25, 50, 75 and 100% of the loci; and positive overdominance for 50% of the loci. In the models with dominance deviation, the additive allelic effects were also included for 100% of the loci. Genetic variability was quantified from generation to generation using the genetic variance components. In the absence of selection, genotypic and additive genetic variances were higher. In the models with non-additive gene action, a small magnitude covariance component raised between the additive and dominance genetic effects whose correlation tended to be positive on the control population and negative under selection. Dominance variance increased as the number of loci with dominance deviation or the value of the deviation increased, implying on the increase in genotypic and additive genetic variances among the successive models.Objetivou-se estudar a variabilidade genética a curto prazo de características quantitativas simuladas a partir de modelos com ação gênica aditiva e não-aditiva em populações controle e de seleção fenotípica. As duas características, uma de baixa (h² = 0,10 e outra de alta (h² = 0,60 herdabilidade, foram controladas por 600 locos bialélicos. A partir de um genoma-padrão, foram obtidos seis modelos genéticos que incluíram: apenas efeitos aditivos dos genes; dominância completa e positiva para 25, 50, 75 e 100% dos locos; e sobredominância positiva para 50% dos locos. Nos modelos com desvio da dominância tamb

  3. Estimation of genetic connectedness diagnostics based on prediction errors without the prediction error variance-covariance matrix

    National Research Council Canada - National Science Library

    John B Holmes; Ken G Dodds; Michael A Lee

    2017-01-01

    .... While various measures of connectedness have been proposed in the literature, there is general agreement that the most appropriate measure is some function of the prediction error variance-covariance matrix...

  4. Importance of over-dominance as the genetic basis of het-erosis in rice

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    n populations derived from commercial hybrid rice combination Shanyou 10, F1 heterosis and F2 inbreeding depression were observed on grain yield (GYD) and number of panicles (NP). Using marker loci evenly distributed on the linkage map as fixing factors, the F2 population was divided into sub-populations. In a large number of sub-populations, significant correlations were observed between heterozygosity and GYD, and between heterozygosity and NP. This was especially true in type III sub-populations in which the genotype of a fixing factor was heterozygotes. In type III sub-populations, 15 QTL for GYD and 13 QTL for NP were detected, of which the majority exhibited over-dominance effects for increasing the trait values. This study showed that over-dominance played an important role in the genetic control of heterosis in rice.

  5. Machado-Joseph disease is genetically different from Holguin dominant ataxia (SCA2)

    Energy Technology Data Exchange (ETDEWEB)

    Silveria, I.; Manaia, A. (Univ. Porto (Portugal) Hopital Necker-Enfants Malades, Paris (France)); Melki, J.; Burlet, P.; Rozet, J.M.; Munnich, A. (Hopital Necker-Enfants Malades, Paris (France)); Magarino, C.; Gispert, S. (Univ. Porto (Portugal) Centro Nacional Genetica Medica, Havana (Cuba)); Lunkes, A.; Auburger, G. (Univ. Hospital, Duesseldorf (Germany))

    1993-09-01

    Machado-Joseph disease (MJD) and Holguin ataxia (SCA2) are autosomal dominant multisystem degenerations with spinocerebellar involvement that are predominant among people of Portuguese-Azorean and of Cuban descent, respectively. Their clinical distinction may at times be difficult to make in individual patients, due to significant phenotypic overlapping (similar overall age-of-onset and duration of cerebellar ataxia, eye movement, and, often, other common problems). The recent mapping of SCA2 to chromosome 12q provided another candidate region for linkage studies of MJD. Original data on 10 families with Holguin ataxia show that the locus of phenylalanine hydroxylase (PAH) on chromosome 12q is linked to SCA2 at 4 cM and is thus far its closest marker. The exclusion of linkage 15 cM on each side of PAH in 16 families with MJD shows that these two forms of dominant ataxia are genetically distinct and at different chromosomal locations (nonallelic). 20 refs., 2 tabs.

  6. Genetic linkage studies in autosomal dominant ataxia families with an MJD phenotype

    Energy Technology Data Exchange (ETDEWEB)

    Silveira, I.; Lopes-Cendes, I.; Paciel, P. [McGill Univ., Montreal (Canada)] [and others

    1994-09-01

    Machado-Joseph disease (MJD) is an autosomal dominant spinocerebellar degeneration which was originally described in patients originating from the Portuguese islands of the Azores. The first non-Portuguese kindred was described in 1979 and was an American black family originating from North Carolina. Since then the number of pedigrees of non-Azorean, non-Portuguese origin has increased with families being reported from other European countries, as well as Brazil, Japan, India, The United States and Australia. The autosomal dominant ataxias are a clinically and genetically heterogeneous group of disorders. To date, genetic analysis of families with autosomal dominant ataxias has permitted the identification of four loci, the SCA1 (spinocerebellar ataxia type 1) locus on chromosome 6p, the SCA2 locus on chromosome 12q, a third locus on chromosome 14q, the MJD/SCA3 and, more recently, the DRPLA (Dentatorubral-pallidoluysian atrophy) locus on chromosome 12p. We ascertained a total of 181 individuals with 60 affected from eight Indian, two Brazilian and one Sicilian-American family; all of them have received the clinical diagnosis of MJD. Recently, we have begun molecular genetic studies in these families in order to test these four candidate regions. The SCA1 mutation and the DRPLA mutation has been found to be an expansion of a CAG repeat. Direct analysis of the SCA1 and DRPLA expansion has been performed in all families and no expansion was found in the affected individuals. We are now running flanking markers for the SCA2 and MJD/SCA3 loci. These results will also be presented.

  7. A Genetic Algorithm Based Approach for Solving the Minimum Dominating Set of Queens Problem

    Directory of Open Access Journals (Sweden)

    Saad Alharbi

    2017-01-01

    Full Text Available In the field of computing, combinatorics, and related areas, researchers have formulated several techniques for the Minimum Dominating Set of Queens Problem (MDSQP pertaining to the typical chessboard based puzzles. However, literature shows that limited research has been carried out to solve the MDSQP using bioinspired algorithms. To fill this gap, this paper proposes a simple and effective solution based on genetic algorithms to solve this classical problem. We report results which demonstrate that near optimal solutions have been determined by the GA for different board sizes ranging from 8 × 8 to 11 × 11.

  8. Importance of over-dominance as the genetic basis of het-erosis in rice

    Institute of Scientific and Technical Information of China (English)

    ZHUANG; Jieyun

    2001-01-01

    [1]Stuber, C. W., Lincoln, S. E., Wolff, D. W. et al., Identification of genetic factors contributing to heterosis in a hybrid from two elite maize inbred lines using molecular markers, Genetics, 1992, 132: 823-839.[2]Xiao, J., Li, J., Yuan, L. et al., Dominance is the major genetic basis of heterosis in rice as revealed by QTL analysis using molecular markers, Genetics, 1995, 140:745-754.[3]Yu, S. B., Li, J. X., Xu, C. G. et al., Importance of epistasis as the genetic basis of rice heterosis, Science in China (in Chi-nese), Ser. C, 1998, 28(4): 333-342.[4]Mackill, D. J., Genome analysis and breeding, in Molecular Biology of Rice (ed. Shimamoto, K.), Tokyo: Springer-Verlag, 1999, 17-41.[5]Lu, Y. J., Zheng, K. L., A simple method for isolation of rice DNA, Chinese J. Rice Sci. (in Chinese), 1992, 6(1): 47-48.[6]McCouch, S. R., Kochert, G., Yu, Z. H. et al., Molecular mapping of rice chromosomes, Theor. Appl. Genet., 1988, 76: 815-829.[7]Lincoln, S., Daley, M., Lander, E., Constructing genetic maps with MAPMAKER/EXP 3.0, Whitehead Institute Technical Report, 3rd ed., 1992.+[8]Causse, M. A., Fulton, T. M., Cho, Y. G. et al., Saturated molecular map of the rice genome based on an interspecific backcross population, Genetics, 1994, 138: 1251-1274.[9]Lincoln, S., Daley, M., Lander, E., Maping genes controlling quantitative traits with MAPMAKER/QTL1.1, Whitehead Institute Technical Report, 3rd ed., 1992.[10]McCouch, S. R., Cho, Y. G., Yano, M. et al., Report on QTL nomenclature, Rice Genet. Newsl., 1997, 14: 11-13.[11]SAS Institute Inc., SAS/STATa user's guide, Version 6, 4th ed., 1994.[12]Li, Z., Pinson, S. R. M., Park, W. D. et al., Epistasis for three grain yield components in rice (Oryza sativa L.), Genetics, 1997, 145: 453-465.[13]Saghai Maroof, M. A., Yang, G. P., Zhang, Q. F. et al., Correlation between molecular marker distance and hybrid perfor-mance in US Southern long grain rice, Crop Sci., 1997, 37:145-150.

  9. Impactos de se ignorarem os efeitos genéticos não-aditivos de dominância na avaliação genética animal Impacts of ignoring the non-additive genetic effects of dominance on animal genetic evaluation

    Directory of Open Access Journals (Sweden)

    Elizângela Emídio Cunha

    2009-12-01

    simulated for the same genomic architecture: one model that included only additive effects of the genes and the other with additive effects and positive and complete dominance into 100% of the loci. Under each genetic model, three base populations were generated corresponding to the characteristics with heritabilities of 0.15 (low, 0.30 (average and 0.60 (high. Starting from the base populations the initial populations were generated which by selection and mating at random, for six consecutive and discrete generations, each one produced 18,000 animals with record. The estimates of the components of variance and heritability obtained in the model with additive gene action were similar to the actual values for all traits, while under dominance gene action, every component was overestimated, especially the additive genetic variance. The non-estimated dominance variance by the animal model adopted was redistributed between the additive genetic and residual components estimated. Accuracy was lost in the genetic evaluation, under the genetic model with dominance, that resulted in smaller correlations between the actual and predicted breeding values of the animals. Additional studies are needed since the simulated genome might not correspond to the true biological systems.

  10. Clinical and genetic analysis of a four-generation family with a distinct autosomal dominant cerebellar ataxia

    NARCIS (Netherlands)

    Schelhaas, H J; Ippel, P F; Hageman, G; Sinke, R J; van der Laan, E N; Beemer, F A

    2001-01-01

    The autosomal dominant cerebellar ataxias (ADCAs) are a heterogeneous group of neurodegenerative disorders characterised by progressive cerebellar dysfunction in combination with a variety of other associative features. Since 1993 ADCAs have been increasingly characterised in terms of their genetic

  11. Clinical and genetic analysis of a four-generation family with a distinct autosomal dominant cerebellar ataxia

    NARCIS (Netherlands)

    Schelhaas, H J; Ippel, P F; Hageman, G; Sinke, R J; van der Laan, E N; Beemer, F A

    2001-01-01

    The autosomal dominant cerebellar ataxias (ADCAs) are a heterogeneous group of neurodegenerative disorders characterised by progressive cerebellar dysfunction in combination with a variety of other associative features. Since 1993 ADCAs have been increasingly characterised in terms of their genetic

  12. Estimation of genetic variance for macro- and micro-environmental sensitivity using double hierarchical generalized linear models

    NARCIS (Netherlands)

    Mulder, H.A.; Ronnegard, L.; Veerkamp, R.F.; Strandberg, E.

    2013-01-01

    Background Genetic variation for environmental sensitivity indicates that animals are genetically different in their response to environmental factors. Environmental factors are either identifiable (e.g. temperature) and called macro-environmental or unknown and called micro-environmental. The

  13. Fuzzy ranking based non-dominated sorting genetic algorithm-II for network overload alleviation

    Directory of Open Access Journals (Sweden)

    Pandiarajan K.

    2014-09-01

    Full Text Available This paper presents an effective method of network overload management in power systems. The three competing objectives 1 generation cost 2 transmission line overload and 3 real power loss are optimized to provide pareto-optimal solutions. A fuzzy ranking based non-dominated sorting genetic algorithm-II (NSGA-II is used to solve this complex nonlinear optimization problem. The minimization of competing objectives is done by generation rescheduling. Fuzzy ranking method is employed to extract the best compromise solution out of the available non-dominated solutions depending upon its highest rank. N-1 contingency analysis is carried out to identify the most severe lines and those lines are selected for outage. The effectiveness of the proposed approach is demonstrated for different contingency cases in IEEE 30 and IEEE 118 bus systems with smooth cost functions and their results are compared with other single objective evolutionary algorithms like Particle swarm optimization (PSO and Differential evolution (DE. Simulation results show the effectiveness of the proposed approach to generate well distributed pareto-optimal non-dominated solutions of multi-objective problem

  14. GREEDY NON-DOMINATED SORTING IN GENETIC ALGORITHM-II FOR VEHICLE ROUTING PROBLEM IN DISTRIBUTION

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Vehicle routing problem in distribution (VRPD) is a widely used type of vehicle routing problem (VRP), which has been proved as NP-Hard, and it is usually modeled as single objective optimization problem when modeling. For multi-objective optimization model, most researches consider two objectives. A multi-objective mathematical model for VRP is proposed, which considers the number of vehicles used, the length of route and the time arrived at each client. Genetic algorithm is one of the most widely used algorithms to solve VRP. As a type of genetic algorithm (GA), non-dominated sorting in genetic algorithm-Ⅱ(NSGA-Ⅱ) also suffers from premature convergence and enclosure competition. In order to avoid these kinds of shortage, a greedy NSGA-Ⅱ (GNSGA-Ⅱ) is proposed for VRP problem. Greedy algorithm is implemented in generating the initial population, cross-over and mutation. All these procedures ensure that NSGA-Ⅱ is prevented from premature convergence and refine the performance of NSGA-Ⅱ at each step. In the distribution problem of a distribution center in Michigan, US, the GNSGA-Ⅱ is compared with NSGA-Ⅱ. As a result, the GNSGA-II is the most efficient one and can get the most optimized solution to VRP problem. Also, in GNSGA-II, premature convergence is better avoided and search efficiency has been improved sharply.

  15. Variance estimation between different body measurements at the females population from Romanian Mioritic Shepherd Dog breed, to develop a genetic improvement program

    Directory of Open Access Journals (Sweden)

    Dorel Dronca

    2016-05-01

    Full Text Available Romanian Mioritic Shepherd Dog, was selected from a natural population breed in Carpathian Mountains. The aim of this paper was to estimate variance at 12 body measurements using 23 females from Romanian Mioritic Shepherd Dog breed. The animals were registered with the Romanian Mioritic Association Club from Romania. In order to develop a genetic improvement program at this effective of 23 females from Romanian Sheperd Dog breed, found in evidence of Romanian Mioritic Association Club from Romania, should be considered the following conclusions on variance those 12 characters studied in this paper, respectively, there is a large variance for the height at the middle back, the height at the croup, the height at the base of the tail, the width of the croup, the length of the tail, the depth of the thorax, the thorax perimeter, the height of the elbow and  for the height at the withers, the body length and the height at the hocks, the variance is middle.

  16. Replication of a gene-environment interaction Via Multimodel inference: additive-genetic variance in adolescents' general cognitive ability increases with family-of-origin socioeconomic status.

    Science.gov (United States)

    Kirkpatrick, Robert M; McGue, Matt; Iacono, William G

    2015-03-01

    The present study of general cognitive ability attempts to replicate and extend previous investigations of a biometric moderator, family-of-origin socioeconomic status (SES), in a sample of 2,494 pairs of adolescent twins, non-twin biological siblings, and adoptive siblings assessed with individually administered IQ tests. We hypothesized that SES would covary positively with additive-genetic variance and negatively with shared-environmental variance. Important potential confounds unaddressed in some past studies, such as twin-specific effects, assortative mating, and differential heritability by trait level, were found to be negligible. In our main analysis, we compared models by their sample-size corrected AIC, and base our statistical inference on model-averaged point estimates and standard errors. Additive-genetic variance increased with SES-an effect that was statistically significant and robust to model specification. We found no evidence that SES moderated shared-environmental influence. We attempt to explain the inconsistent replication record of these effects, and provide suggestions for future research.

  17. Non-dominated sorting genetic algorithm in optimizing ninth order multiple feedback Chebyshev low pass filter

    Science.gov (United States)

    Lim, Wei Jer; Neoh, Siew Chin; Norizan, Mohd Natashah; Mohamad, Ili Salwani

    2015-05-01

    Optimization for complex circuit design often requires large amount of manpower and computational resources. In order to optimize circuit performance, it is critical not only for circuit designers to adjust the component value but also to fulfill objectives such as gain, cutoff frequency, ripple and etc. This paper proposes Non-dominated Sorting Genetic Algorithm II (NSGA-II) to optimize a ninth order multiple feedback Chebyshev low pass filter. Multi-objective Pareto-Based optimization is involved whereby the research aims to obtain the best trade-off for minimizing the pass-band ripple, maximizing the output gain and achieving the targeted cut-off frequency. The developed NSGA-II algorithm is executed on the NGSPICE circuit simulator to assess the filter performance. Overall results show satisfactory in the achievements of the required design specifications.

  18. Service restoration in distribution system using non-dominated sorting genetic algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Yogendra; Das, Biswarup; Sharma, Jaydev [Department of Electrical Engineering, Indian Institute of Technology, Roorkee 247667 (India)

    2006-06-15

    In this paper, a non-dominated sorting genetic algorithm-II (NSGA-II) based approach is presented for service restoration in power distribution systems. In contrast to the conventional GA based methods, the proposed approach does not require weighting factors required for conversion of multi-objective function into an equivalent single objective function. Based on the simulation studies carried out in four different systems, the performance of the proposed scheme has been found to be better than the performance of conventional GA technique based approaches. Moreover, by including the string representing the pre-fault configuration of the distribution system in the initial population, the speed of convergence is enhanced significantly. (author)

  19. Primary shunt hyperbilirubinaemia in a large four-generation family confirming autosomal dominant genetic disorder

    Institute of Scientific and Technical Information of China (English)

    Chun-Lian Wang; Xiao-Wei Liu; Fang-Gen Lu; Xiao-Ping Wu; Chun-Hui Ouyang; Dong-Ye Yang

    2006-01-01

    AIM: To describe the pattern of inheritance and confirm the diagnosdc criteria of primary shunt hyperbilirubinaemia (PSH).METHODS: Forty members of a family pedigree across four generations were included in this study. All family members were interviewed and investigated by physical examination, hematology and liver function test and the pattern of inheritance was analyzed.RESULTS: Nine of the forty family members suffered primary shunt hyperbilirubinaemia. The mature erythrocytes of the propositus were irregular in shape and size.The pedigree showed transmission of the trait through four generations with equal distribution in male and female. No individual with a primary shunt hyperbilirubinaemia was born to unaffected parents. The penetrance was complete in adult.CONCLUSION: The pattern of inheritance is autosomal dominant. The abnormality of erythrocytes and decrease in white blood cell could be supplemented in the diagnosis of PSH. The PSH is a genetic disorder and could by renamed as hereditary shunt hyperbilirubinaemia.

  20. Development of a multi-objective scheduling system for offshore projects based on hybrid non-dominated sorting genetic algorithm

    Directory of Open Access Journals (Sweden)

    Jinghua Li

    2015-03-01

    Full Text Available In order to enhance the efficiency of offshore companies, a multi-objective scheduling system based on hybrid non-dominated sorting genetic algorithm was proposed. An optimized model for multi-objective and multi-execution mode was constructed under the condition of taking time, cost, and resource into account, and then the mathematical model for the same was established. Moreover, the key techniques of the proposed system were elaborated, and the flowchart was designed. Aiming at the weaknesses of non-dominated sorting genetic algorithm which is short for non-dominated sorting genetic algorithm-II in the facet of local search and computational efficiency, Pareto-dominated simulated annealing algorithm was applied in search global solution. Finally, by simulation examples and industrial application, the robustness and outperformance of the improved algorithm were verified.

  1. Fitness of transgenic mosquito Aedes aegypti males carrying a dominant lethal genetic system.

    Science.gov (United States)

    Massonnet-Bruneel, Blandine; Corre-Catelin, Nicole; Lacroix, Renaud; Lees, Rosemary S; Hoang, Kim Phuc; Nimmo, Derric; Alphey, Luke; Reiter, Paul

    2013-01-01

    OX513A is a transgenic strain of Aedes aegypti engineered to carry a dominant, non-sex-specific, late-acting lethal genetic system that is repressed in the presence of tetracycline. It was designed for use in a sterile-insect (SIT) pest control system called RIDL® (Release of Insects carrying a Dominant Lethal gene) by which transgenic males are released in the field to mate with wild females; in the absence of tetracycline, the progeny from such matings will not survive. We investigated the mating fitness of OX513A in the laboratory. Male OX513A were as effective as Rockefeller (ROCK) males at inducing refractoriness to further mating in wild type females and there was no reduction in their ability to inseminate multiple females. They had a lower mating success but yielded more progeny than the wild-type comparator strain (ROCK) when one male of each strain was caged with a ROCK female. Mating success and fertility of groups of 10 males-with different ratios of RIDL to ROCK-competing for five ROCK females was similar, but the median longevity of RIDL males was somewhat (18%) lower. We conclude that the fitness under laboratory conditions of OX513A males carrying a tetracycline repressible lethal gene is comparable to that of males of the wild-type comparator strain.

  2. Fitness of transgenic mosquito Aedes aegypti males carrying a dominant lethal genetic system.

    Directory of Open Access Journals (Sweden)

    Blandine Massonnet-Bruneel

    Full Text Available OX513A is a transgenic strain of Aedes aegypti engineered to carry a dominant, non-sex-specific, late-acting lethal genetic system that is repressed in the presence of tetracycline. It was designed for use in a sterile-insect (SIT pest control system called RIDL® (Release of Insects carrying a Dominant Lethal gene by which transgenic males are released in the field to mate with wild females; in the absence of tetracycline, the progeny from such matings will not survive. We investigated the mating fitness of OX513A in the laboratory. Male OX513A were as effective as Rockefeller (ROCK males at inducing refractoriness to further mating in wild type females and there was no reduction in their ability to inseminate multiple females. They had a lower mating success but yielded more progeny than the wild-type comparator strain (ROCK when one male of each strain was caged with a ROCK female. Mating success and fertility of groups of 10 males-with different ratios of RIDL to ROCK-competing for five ROCK females was similar, but the median longevity of RIDL males was somewhat (18% lower. We conclude that the fitness under laboratory conditions of OX513A males carrying a tetracycline repressible lethal gene is comparable to that of males of the wild-type comparator strain.

  3. Genetic Analysis and Mapping of the Dominant Dwarfing Gene D-53 in Rice

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The dwarfing gene D-53 is one of a few dominant genes for dwarfing in rice (Oryza sativa L.). In the present study, our genetic analysis confirmed that mutant characteristics including dwarfing, profuse tillering, thin stems and small panicles are all controlled by the dominant D-53 gene. We measured the length of each internode of KL908, a D-53-carrying line, and classified the dwarfism of KL908 into the dn-type. In addition, we measured elongation of the second sheath and α-amylase activity in the endosperm, and we characterized KL908 as a dwarf mutant that was neither gibberellic acid-deficient nor gibberellic acid-insensitive. Using a large F2 population obtained by crossing KL908 with a wild-type variety, NJ6, the D-53 gene was mapped to the terminal region of the short arm of chromosome 11, with one simple sequence repeat marker, Ds3, co-segregating, and the other, K81114, located 0.6 cM away.

  4. Genetic transformation of Nannochloropsis oculata with a bacterial phleomycin resistance gene as dominant selective marker

    Science.gov (United States)

    Ma, Xiaolei; Pan, Kehou; Zhang, Lin; Zhu, Baohua; Yang, Guanpin; Zhang, Xiangyang

    2016-04-01

    The gene ble from Streptoalloteichus hindustanus is widely used as a selective antibiotic marker. It can control the phleomycin resistance, and significantly increase the tolerance of hosts to zeocin. The unicellular marine microalga Nannochloropsis oculata is extremely sensitive to zeocin. We selected ble as the selective marker for the genetic transformation of N. oculata. After the algal cells at a density of 2×107 cells mL-1 was digested with 4% hemicellulase and 2% driselase for 1 h, the protoplasts accounted for 90% of the total. The ble was placed at the downstream of promoter HSP70A-RUBS2 isolated from Chlamydomonas reinhardtii, yielding a recombinant expression construct pMS188. The construct was transferred into the protoplasts through electroporation (1 kV, 15 μS). The transformed protoplasts were cultured in fresh f/2 liquid medium, and selected on solid f/2 medium supplemented with 500 ng mL-1 zeocin. The PCR result proved that ble existed in the transformants. Three transformants had been cultured for at least 5 generations without losing ble. Southern blotting analysis showed that the ble has been integrated into the genome of N. oculata. The ble will serve as a new dominant selective marker in genetic engineering N. oculata.

  5. The effects of the genetic background on herbicide resistance fitness cost and its associated dominance in Arabidopsis thaliana.

    Science.gov (United States)

    Paris, M; Roux, F; Bérard, A; Reboud, X

    2008-12-01

    The advantage of the resistance conferred by a mutation can sometimes be offset by a high fitness-cost penalty. This balance will affect possible fate of the resistance allele. Few studies have explored the impact of the genetic background on the expression of the resistance fitness cost and none has attempted to measure the variation in fitness-cost dominance. However, both the fitness penalty and its dominance may modify evolutionary trajectory and outcome. Here the impact of Arabidopsis thaliana intraspecific genetic diversity on fitness cost and its associated dominance was investigated by analysing 12 quantitative traits in crosses between a mutant conferring resistance to the herbicide 2,4-D and nine different natural genetic backgrounds. Fitness cost values were found to be more affected by intraspecific genetic diversity than fitness cost dominance, even though this effect depends on the quantitative trait measured. This observation has implications for the choice of the best strategy for preventing herbicide resistance development. In addition, our results pinpoint a potential compensatory improvement of the resistance fitness cost and its associated dominance by the genetic diversity locally present within a species.

  6. Heritable Micro-environmental Variance Covaries with Fitness in an Outbred Population of Drosophila serrata.

    Science.gov (United States)

    Sztepanacz, Jacqueline L; McGuigan, Katrina; Blows, Mark W

    2017-08-01

    The genetic basis of stochastic variation within a defined environment, and the consequences of such micro-environmental variance for fitness are poorly understood . Using a multigenerational breeding design in Drosophila serrata, we demonstrated that the micro-environmental variance in a set of morphological wing traits in a randomly mating population had significant additive genetic variance in most single wing traits. Although heritability was generally low (micro-environmental variance is an evolvable trait. Multivariate analyses demonstrated that the micro-environmental variance in wings was genetically correlated among single traits, indicating that common mechanisms of environmental buffering exist for this functionally related set of traits. In addition, through the dominance genetic covariance between the major axes of micro-environmental variance and fitness, we demonstrated that micro-environmental variance shares a genetic basis with fitness, and that the pattern of selection is suggestive of variance-reducing selection acting on micro-environmental variance. Copyright © 2017 by the Genetics Society of America.

  7. FADS2 Genetic Variance in Combination with Fatty Acid Intake Might Alter Composition of the Fatty Acids in Brain.

    Directory of Open Access Journals (Sweden)

    Thais S Rizzi

    Full Text Available Multiple lines of evidence suggest that fatty acids (FA play an important role in cognitive function. However, little is known about the functional genetic pathways involved in cognition. The main goals of this study were to replicate previously reported interaction effects between breast feeding (BF and FA desaturase (FADS genetic variation on IQ and to investigate the possible mechanisms by which these variants might moderate BF effect, focusing on brain expression. Using a sample of 534 twins, we observed a trend in the moderation of BF effects on IQ by FADS2 variation. In addition, we made use of publicly available gene expression databases from both humans (193 and mice (93 and showed that FADS2 variants also correlate with FADS1 brain expression (P-value<1.1E-03. Our results provide novel clues for the understanding of the genetic mechanisms regulating FA brain expression and improve the current knowledge of the FADS moderation effect on cognition.

  8. Variance Components and Genetic Parameters Estimated for Fat and Protein Content in Individual Months of Lactation: The Case of Tsigai Sheep.

    Science.gov (United States)

    Oravcová, Marta

    2016-02-01

    The objective of this study was to assess variance components and genetic parameters for fat and protein content in Tsigai sheep using multivariate animal models in which fat and protein content in individual months of lactation were treated as different traits, and univariate models in which fat and protein content were treated as repeated measures of the same traits. Test day measurements were taken between the second and the seventh month of lactation. The fixed effects were lactation number, litter size and days in milk. The random effects were animal genetic effect and permanent environmental effect of ewe. The effect of flock-year-month of test day measurement was fitted either as a fixed (FYM) or random (fym) effect. Heritabilities for fat content were estimated between 0.06 and 0.17 (FYM fitted) and between 0.06 and 0.11 (fym fitted). Heritabilities for protein content were estimated between 0.15 and 0.23 (FYM fitted) and between 0.10 and 0.18 (fym fitted). For fat content, variance ratios of permanent environmental effect of ewe were estimated between 0.04 and 0.11 (FYM fitted) and between 0.02 and 0.06 (fym fitted). For protein content, variance ratios of permanent environmental effect of ewe were estimated between 0.13 and 0.20 (FYM fitted) and between 0.08 and 0.12 (fym fitted). The proportion of phenotypic variance explained by fym effect ranged from 0.39 to 0.43 for fat content and from 0.25 to 0.36 for protein content. Genetic correlations between individual months of lactation ranged from 0.74 to 0.99 (fat content) and from 0.64 to 0.99 (protein content). Fat content heritabilities estimated with univariate animal models roughly corresponded with heritability estimates from multivariate models: 0.13 (FYM fitted) and 0.07 (fym fitted). Protein content heritabilities estimated with univariate animal models also corresponded with heritability estimates from multivariate models: 0.18 (FYM fitted) and 0.13 (fym fitted).

  9. FADS2 Genetic Variance in Combination with Fatty Acid Intake Might Alter Composition of the Fatty Acids in Brain

    NARCIS (Netherlands)

    T.S. Rizzi (Thais); S. van der Sluis (Sophie); C. Derom (Catherine); E. Thiery (Evert); R.E. Kesteren (Ronald); N. Jacobs (Nele); S. van Gestel (Sofie); R. Vlietinck (Robert); M. Verhage (Matthijs); P. Heutink (Peter); D. Posthuma (Danielle)

    2013-01-01

    textabstractMultiple lines of evidence suggest that fatty acids (FA) play an important role in cognitive function. However, little is known about the functional genetic pathways involved in cognition. The main goals of this study were to replicate previously reported interaction effects between brea

  10. Genetic diversity of b-glucuronidase activity among 14 strains of the dominant human gut anaerobe Ruminococcus gnavus

    Directory of Open Access Journals (Sweden)

    Diane Beaud

    2006-01-01

    Full Text Available Bacterial beta-glucuronidase activity in the gut increases the enterohepatic circulation of toxic compounds and plays a major role in the etiology of colon cancer. Previously, we had found that the gus gene, which codes for beta-glucuronidase in a dominant anaerobic species of the gut microbiota, Ruminococcus gnavus strain E1, is transcribed as part of an operon that includes three ORFs that code for beta-glucoside permeases of the phosphotransferase systems. This genetic organization had never been described. We have now compared beta-glucuronidase activity and the genetic environment of the gus gene in 14 strains of Ruminococcus gnavus.We found that five out of the seven glucuronidase-positive R. gnavus strains possessed another glucuronidase gene different from the gusA operon of R. gnavus E1. This dominant commensal intestinal species appears to have a high degree of genetic diversity in the genes that control beta-glucuronidase activity.

  11. Multi-period fuzzy mean-semi variance portfolio selection problem with transaction cost and minimum transaction lots using genetic algorithm

    Directory of Open Access Journals (Sweden)

    Mohammad Ali Barati

    2016-04-01

    Full Text Available Multi-period models of portfolio selection have been developed in the literature with respect to certain assumptions. In this study, for the first time, the portfolio selection problem has been modeled based on mean-semi variance with transaction cost and minimum transaction lots considering functional constraints and fuzzy parameters. Functional constraints such as transaction cost and minimum transaction lots were included. In addition, the returns on assets parameters were considered as trapezoidal fuzzy numbers. An efficient genetic algorithm (GA was designed, results were analyzed using numerical instances and sensitivity analysis were executed. In the numerical study, the problem was solved based on the presence or absence of each mode of constraints including transaction costs and minimum transaction lots. In addition, with the use of sensitivity analysis, the results of the model were presented with the variations of minimum expected rate of programming periods.

  12. Crossing the threshold: gene flow, dominance and the critical level of standing genetic variation required for adaptation to novel environments.

    Science.gov (United States)

    Nuismer, S L; MacPherson, A; Rosenblum, E B

    2012-12-01

    Genetic architecture plays an important role in the process of adaptation to novel environments. One example is the role of allelic dominance, where advantageous recessive mutations have a lower probability of fixation than advantageous dominant mutations. This classic observation, termed 'Haldane's sieve', has been well explored theoretically for single isolated populations adapting to new selective regimes. However, the role of dominance is less well understood for peripheral populations adapting to novel environments in the face of recurrent and maladaptive gene flow. Here, we use a combination of analytical approximations and individual-based simulations to explore how dominance influences the likelihood of adaptation to novel peripheral environments. We demonstrate that in the face of recurrent maladaptive gene flow, recessive alleles can fuel adaptation only when their frequency exceeds a critical threshold within the ancestral range.

  13. Estimates of (co)variance components and genetic parameters for body weights and first greasy fleece weight in Bharat Merino sheep.

    Science.gov (United States)

    Gowane, G R; Chopra, A; Prince, L L L; Paswan, C; Arora, A L

    2010-03-01

    (Co)variance components and genetic parameters of weight at birth (BWT), weaning (3WT), 6, 9 and 12 months of age (6WT, 9WT and 12WT, respectively) and first greasy fleece weight (GFW) of Bharat Merino sheep, maintained at Central Sheep and Wool Research Institute, Avikanagar, Rajasthan, India, were estimated by restricted maximum likelihood, fitting six animal models with various combinations of direct and maternal effects. Data were collected over a period of 10 years (1998 to 2007). A log-likelihood ratio test was used to select the most appropriate univariate model for each trait, which was subsequently used in bivariate analysis. Heritability estimates for BWT, 3WT, 6WT, 9WT and 12WT and first GFW were 0.05 ± 0.03, 0.04 ± 0.02, 0.00, 0.03 ± 0.03, 0.09 ± 0.05 and 0.05 ± 0.03, respectively. There was no evidence for the maternal genetic effect on the traits under study. Maternal permanent environmental effect contributed 19% for BWT and 6% to 11% from 3WT to 9WT and 11% for first GFW. Maternal permanent environmental effect on the post-3WT was a carryover effect of maternal influences during pre-weaning age. A low rate of genetic progress seems possible in the flock through selection. Direct genetic correlations between body weight traits were positive and ranged from 0.36 between BWT and 6WT to 0.94 between 3WT and 6WT and between 6WT and 12WT. Genetic correlations of 3WT with 6WT, 9WT and 12WT were high and positive (0.94, 0.93 and 0.93, respectively), suggesting that genetic gain in post-3WT will be maintained if selection age is reduced to 3 months. The genetic correlations of GFW with live weights were 0.01, 0.16, 0.18, 0.40 and 0.32 for BWT, 3WT, 6WT, 9WT and 12WT, respectively. Correlations of permanent environmental effects of the dam across different traits were high and positive for all the traits (0.45 to 0.98).

  14. A multiobjective non-dominated sorting genetic algorithm (NSGA-II for the Multiple Traveling Salesman Problem

    Directory of Open Access Journals (Sweden)

    Rubén Iván Bolaños

    2015-06-01

    Full Text Available This paper considers a multi-objective version of the Multiple Traveling Salesman Problem (MOmTSP. In particular, two objectives are considered: the minimization of the total traveled distance and the balance of the working times of the traveling salesmen. The problem is formulated as an integer multi-objective optimization model. A non-dominated sorting genetic algorithm (NSGA-II is proposed to solve the MOmTSP. The solution scheme allows one to find a set of ordered solutions in Pareto fronts by considering the concept of dominance. Tests on real world instances and instances adapted from the literature show the effectiveness of the proposed algorithm.

  15. One group of genetically similar Listeria monocytogenes strains frequently dominates and persists in several fish slaughter- and smokehouses

    DEFF Research Database (Denmark)

    Wulff, Gitte; Gram, Lone; Ahrens, Peter;

    2006-01-01

    Contamination of foods with the human pathogen Listeria monocytogenes may occur during processing, and the purpose of this study was to determine whether genetically similar strains colonize different processing plants or whether specific persistent strains are unique to each processing plant. We...... smokehouses and two slaughterhouses and was predominant in three of these plants. A subset of 35 strains was also analyzed by amplified fragment length polymorphism typing, which confirmed the genetic similarity of the groups. Moreover, strains of the dominant RAPD type were indistinguishable from strains...... related may be especially adapted to colonizing the processing equipment or especially resistant to cleaning and disinfection....

  16. Genetic correlations and little genetic variance for reaction norms may limit potential for adaptation to pollution by ionic and nanoparticulate silver in a whitefish (Salmonidae).

    Science.gov (United States)

    Clark, Emily S; Pompini, Manuel; Uppal, Anshu; Wedekind, Claus

    2016-05-01

    For natural populations to adapt to anthropogenic threats, heritable variation must persist in tolerance traits. Silver nanoparticles, the most widely used engineered nanoparticles, are expected to increase in concentrations in freshwaters. Little is known about how these particles affect wild populations, and whether genetic variation persists in tolerance to permit rapid evolutionary responses. We sampled wild adult whitefish and crossed them in vitro full factorially. In total, 2896 singly raised embryos of 48 families were exposed to two concentrations (0.5 μg/L; 100 μg/L) of differently sized silver nanoparticles or ions (silver nitrate). These doses were not lethal; yet higher concentrations prompted embryos to hatch earlier and at a smaller size. The induced hatching did not vary with nanoparticle size and was stronger in the silver nitrate group. Additive genetic variation for hatching time was significant across all treatments, with no apparent environmental dependencies. No genetic variation was found for hatching plasticity. We found some treatment-dependent heritable variation for larval length and yolk volume, and one instance of additive genetic variation for the reaction norm on length at hatching. Our assessment suggests that the effects of silver exposure on additive genetic variation vary according to trait and silver source. While the long-term fitness consequences of low-level silver exposure on whitefish embryos must be further investigated to determine whether it is, in fact, detrimental, our results suggest that the evolutionary potential for adaptation to these types of pollutants may be low.

  17. Extending GelJ for interoperability: Filling the gap in the bioinformatics resources for population genetics analysis with dominant markers.

    Science.gov (United States)

    Domínguez, César; Heras, Jónathan; Mata, Eloy; Pascual, Vico; Vázquez-Garcidueñas, Maria Soledad; Vázquez-Marrufo, Gerardo

    2017-03-01

    The manual transformation of DNA fingerprints of dominant markers into the input of tools for population genetics analysis is a time-consuming and error-prone task; especially when the researcher deals with a large number of samples. In addition, when the researcher needs to use several tools for population genetics analysis, the situation worsens due to the incompatibility of data-formats across tools. The goal of this work consists in automating, from banding patterns of gel images, the input-generation for the great diversity of tools devoted to population genetics analysis. After a thorough analysis of tools for population genetics analysis with dominant markers, and tools for working with phylogenetic trees; we have detected the input requirements of those systems. In the case of programs devoted to phylogenetic trees, the Newick and Nexus formats are widely employed; whereas, each population genetics analysis tool uses its own specific format. In order to handle such a diversity of formats in the latter case, we have developed a new XML format, called PopXML, that takes into account the variety of information required by each population genetics analysis tool. Moreover, the acquired knowledge has been incorporated into the pipeline of the GelJ system - a tool for analysing DNA fingerprint gel images - to reach our automatisation goal. We have implemented, in the GelJ system, a pipeline that automatically generates, from gel banding patterns, the input of tools for population genetics analysis and phylogenetic trees. Such a pipeline has been employed to successfully generate, from thousands of banding patterns, the input of 29 population genetics analysis tools and 32 tools for managing phylogenetic trees. GelJ has become the first tool that fills the gap between gel image processing software and population genetics analysis with dominant markers, phylogenetic reconstruction, and tree editing software. This has been achieved by automating the process of

  18. Geographic Variation in Genetic Dominance of the Color Morphs of the Red-Backed Salamander, PLETHODON CINEREUS.

    Science.gov (United States)

    Highton, R

    1975-06-01

    Female parent-offspring phenotypic data on color morph frequencies in the red-backed salamander, Plethodon cinereus, were obtained from two Virginia localities (164 broods from Greene County and 97 broods from Giles County). The color morph data indicate that the striped morph is genetically dominant in Giles County and recessive in Greene County. It is suggested that epistatic interaction of two or more loci is responsible for the difference between the localities.

  19. Locus BoLA-DRB3 is just an ordinary site of the polygene when explaining genetic variance of somatic cell count and milk yield.

    Science.gov (United States)

    Oprzadek, Jolanta; Sender, Grazyna; Pawlik, Adrianna; Lukaszewicz, Marek

    2015-11-01

    The study aimed at clarifying the problem of the hitherto contradictory results regarding usefulness of BoLA-DRB3 locus as a marker in selection against mastitis and for milk yield. Treating the BoLA-DRB3 locus effect as random was proposed in place of considering it fixed. Somatic cell counts and milk yields recorded monthly on a test day (22,424) of 619 Polish Holstein cows genotyped for BoLA-DRB3 were analysed with an animal model including a random effect for genotype at this locus. The BoLA-DRB3 alleles were defined as restriction patterns obtained with three endonucleases. Two alternative BoLA-DRB3 additive genotype (co)variance structures were constructed for 161 genotypes recorded. One was based on the allelic similarity of the genotypes resulting in element values of 0 (no common allele), 0.5 (one allele in common), and 1 (diagonal). The other considered restriction site similarity (up to 3 in 1 allele) giving element values of 0 (no common restriction sites) and then increasingly in steps of 1/6 up to 6/6 (diagonal), where the numerator represents the number of common sites between genotypes. The DRB3 variance component for the natural logarithm of somatic cell count did not exceed 0.006 of the polygenic additive component or 0.003 for milk yield. Hence, unless we fail to detect the causative site or to properly define traits being the projection of a site, the effect of the genotype at the BoLA-DRB3 locus does not explain variation in somatic cell count and milk yield at a degree expected of a genetic marker.

  20. Genetics Home Reference: cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy

    Science.gov (United States)

    ... Multi-Infarct Dementia Health Topic: Dementia Health Topic: Stroke Genetic and Rare Diseases Information Center (1 link) CADASIL Additional NIH Resources (2 links) National Institute of Neurological Disorders and Stroke: CADASIL Information Page National Institute of Neurological Disorders ...

  1. Sex-linked dominant

    Science.gov (United States)

    Inheritance - sex-linked dominant; Genetics - sex-linked dominant; X-linked dominant; Y-linked dominant ... can be either an autosomal chromosome or a sex chromosome. It also depends on whether the trait ...

  2. Razões entre componentes da variabilidade de características quantitativas simuladas com efeitos genéticos de dominância e sobredominância Ratios between variability components of simulated quantitative traits with genetic effects of dominance and overdominance

    Directory of Open Access Journals (Sweden)

    Elizângela Emídio Cunha

    2009-10-01

    Full Text Available Foram avaliadas as razões entre componentes da variabilidade de características quantitativas simuladas a partir de genoma incorporando efeitos genéticos não-aditivos em populações de acasalamento ao acaso e de seleção fenotípica a curto prazo. Estudaram-se uma característica de baixa (h² = 0,10 e outra de alta herdabilidade (h² = 0,60 influenciadas por 600 locos bialélicos. Cinco modelos de ação gênica foram simulados, dos quais quatro incluíram dominância completa e positiva para 25, 50, 75 e 100% dos locos (D25, D50, D75 e D100, respectivamente; e um modelo incluiu sobredominância positiva para 50% dos locos. Todos os modelos incluíram efeitos aditivos dos alelos para 100% dos locos. As principais razões quantificadas foram d² (variância de dominância/variância fenotípica e d²a (variância de dominância/variância aditiva. Para as duas características, d² e d²a aumentaram de acordo com o acréscimo na variância de dominância, decorrente da inclusão crescente de locos com desvio da dominância e sob sobredominância. No mesmo modelo, ambas as razões, sobretudo d², são mais elevadas sob alta herdabilidade, o que indica que os efeitos da dominância explicam a maior parte da variabilidade total dessa característica sob seleção.Ratios were assessed between variability components of quantitative traits simulated from the genome incorporating non-additive genetic effects in random mating populations and short-term phenotypic selection. A trait of low (h² = 0.10 heritability and another of high (h² = 0.60 heritability were studied, both influenced by 600 bi-allelic loci. Five gene action models were simulated, of which four included complete and positive dominance for 25, 50, 75 and 100% of the loci (D25, D50, D75 and D100, respectively; and one model included positive overdominance for 50% of the loci. Every model included additive effects of the alleles for 100% of the loci. The main quantified ratios were

  3. Partial Dominance, Overdominance and Epistasis as the Genetic Basis of Heterosis in Upland Cotton (Gossypium hirsutum L.)

    Science.gov (United States)

    Wang, Yumei; Hua, Jinping

    2015-01-01

    Determination of genetic basis of heterosis may promote hybrid production in Upland cotton (Gossypium hirsutum L.). This study was designed to explore the genetic mechanism of heterosis for yield and yield components in F2: 3 and F2: 4 populations derived from a hybrid ‘Xinza No. 1’. Replicated yield field trials of the progenies were conducted in 2008 and 2009. Phenotypic data analyses indicated overdominance in F1 for yield and yield components. Additive and dominance effects at single-locus level and digenic epistatic interactions at two-locus level were analyzed by 421 marker loci spanning 3814 cM of the genome. A total of 38 and 49 QTLs controlling yield and yield components were identified in F2: 3 and F2: 4 populations, respectively. Analyses of these QTLs indicated that the effects of partial dominance and overdominance contributed to heterosis in Upland cotton simultaneously. Most of the QTLs showed partial dominance whereas 13 QTLs showing overdominance in F2:3 population, and 19 QTLs showed overdominance in F2:4. Among them, 21 QTLs were common in both F2: 3 and F2: 4 populations. A large number of two-locus interactions for yield and yield components were detected in both generations. AA (additive × additive) epistasis accounted for majority portion of epistatic effects. Thirty three complementary two-locus homozygotes (11/22 and 22/11) were the best genotypes for AA interactions in terms of bolls per plant. Genotypes of double homozygotes, 11/22, 22/11 and 22/22, performed best for AD/DA interactions, while genotype of 11/12 performed best for DD interactions. These results indicated that (1) partial dominance and overdominance effects at single-locus level and (2) epistasis at two-locus level elucidated the genetic basis of heterosis in Upland cotton. PMID:26618635

  4. Variance, genetic control and spatial phenotypic plasticity of morphological and phenological traits in Prunus spinosa and its large fruited forms (P. x fruticans

    Directory of Open Access Journals (Sweden)

    Kristine Vander Mijnsbrugge

    2016-11-01

    diminished at the growth site with the shortest growing season while interestingly, the leaf width was enlarged. Leaf size traits appeared more plastic on the long shoots compared to the short shoots, although partitioning of variance did not display a lesser genetic

  5. Previous estimates of mitochondrial DNA mutation level variance did not account for sampling error: comparing the mtDNA genetic bottleneck in mice and humans.

    Science.gov (United States)

    Wonnapinij, Passorn; Chinnery, Patrick F; Samuels, David C

    2010-04-09

    In cases of inherited pathogenic mitochondrial DNA (mtDNA) mutations, a mother and her offspring generally have large and seemingly random differences in the amount of mutated mtDNA that they carry. Comparisons of measured mtDNA mutation level variance values have become an important issue in determining the mechanisms that cause these large random shifts in mutation level. These variance measurements have been made with samples of quite modest size, which should be a source of concern because higher-order statistics, such as variance, are poorly estimated from small sample sizes. We have developed an analysis of the standard error of variance from a sample of size n, and we have defined error bars for variance measurements based on this standard error. We calculate variance error bars for several published sets of measurements of mtDNA mutation level variance and show how the addition of the error bars alters the interpretation of these experimental results. We compare variance measurements from human clinical data and from mouse models and show that the mutation level variance is clearly higher in the human data than it is in the mouse models at both the primary oocyte and offspring stages of inheritance. We discuss how the standard error of variance can be used in the design of experiments measuring mtDNA mutation level variance. Our results show that variance measurements based on fewer than 20 measurements are generally unreliable and ideally more than 50 measurements are required to reliably compare variances with less than a 2-fold difference.

  6. Within Host Evolution Selects for a Dominant Genotype of Mycobacterium tuberculosis while T Cells Increase Pathogen Genetic Diversity

    Science.gov (United States)

    Copin, Richard; Louie, Eddie; Escuyer, Vincent; Gagneux, Sebastien; Palmer, Guy H.

    2016-01-01

    Molecular epidemiological assessments, drug treatment optimization, and development of immunological interventions all depend on understanding pathogen adaptation and genetic variation, which differ for specific pathogens. Mycobacterium tuberculosis is an exceptionally successful human pathogen, yet beyond knowledge that this bacterium has low overall genomic variation but acquires drug resistance mutations, little is known of the factors that drive its population genomic characteristics. Here, we compared the genetic diversity of the bacteria that established infection to the bacterial populations obtained from infected tissues during murine M. tuberculosis pulmonary infection and human disseminated M. bovis BCG infection. We found that new mutations accumulate during in vitro culture, but that in vivo, purifying selection against new mutations dominates, indicating that M. tuberculosis follows a dominant lineage model of evolution. Comparing bacterial populations passaged in T cell-deficient and immunocompetent mice, we found that the presence of T cells is associated with an increase in the diversity of the M. tuberculosis genome. Together, our findings put M. tuberculosis genetic evolution in a new perspective and clarify the impact of T cells on sequence diversity of M. tuberculosis. PMID:27973588

  7. A New Non-dominated Sorting Genetic Algorithm for Multi-Objective Optimization

    OpenAIRE

    2010-01-01

    This study imitates the gene-therapy process at the forefront of medicine and proposes an innovative evaluative crossover operator. The evaluative crossover integrates a geneevaluation method with a gene-therapy approach in the traditional NSGA-II for finding uniformly distributed Pareto-optimal front of multi-objective optimization problems. To further enhance the advantages of fast non-dominate sorting and diversity preservation in NSGA-II, the proposed gene-evaluation method partially eval...

  8. Multi-objective optimization of water supply network rehabilitation with non-dominated sorting Genetic Algorithm-Ⅱ

    Institute of Scientific and Technical Information of China (English)

    Xi JIN; Jie ZHANG; Jin-liang GAO; Wen-yan WU

    2008-01-01

    Through the transformation of hydraulic constraints into the objective functions associated with a water supply network rehabilitation problem, a non-dominated sorting Genetic Aigorithm-Ⅱ (NSGA-Ⅱ) can be used to solve the altered multi-objective optimization model. The introduction of NSGA-Ⅱ into water supply network optimal rehabilitation problem solves the conflict between one fitness value of standard genetic algorithm (SGA) and multi-objectives of rehabilitation problem. And the uncertainties brought by using weight coefficients or punish functions in conventional methods are controlled. And also by introduction of artificial inducement mutation (AIM) operation, the convergence speed of population is accelerated; this operation not only improves the convergence speed, but also improves the rationality and feasibility of solutions.

  9. Genetic Characteristic of Dominant Ultra Short Stem and Wax Coating Absence for Winter Rye (Secale cereale L.

    Directory of Open Access Journals (Sweden)

    В. В. Скорик

    2010-10-01

    Full Text Available By means of directed hybridization and selection, a new donor of Winter Rye with combination of ultra short stem and absence of wax coating has been synthesized. Markings was offered for the first time for dominant genes of ultra short stem characteristic – HI-3HI-3, and for recessive genes of absence of wax coating characteristic – wcwc. Determination is made of genetic variability, coefficients of inheritance, phenotype and genotype correlation coefficients, on the basis of which a selection strategy by ten quantitative characteristics is proposed. Polypheny and cohesion effects were established. Under certain conception, strategy and tactic of improvement by breeding of Winter Rye characteristics, determination of genetic and statistic parameters between traits of parents and the offspring is required.

  10. Peptide-dominated membranes preceding the genetic takeover by RNA: latest thinking on a classic controversy

    DEFF Research Database (Denmark)

    Egel, Richard

    2009-01-01

    -maintaining protometabolism, assisted by an unfolding set of ribotide-related cofactors. Pairwise complementary ribotide cofactors may have formed docking guides for stochastic peptide formation, before replicating RNA emerged from this subset. Tidally recurring wet-drying cycles and an early onset of photosynthetic...... activities are considered most likely to meet the thermodynamic requirements. Conceivably, the earliest peptide-dominated vesicles were engaged in light harvesting, together with isoprenoid-tethered pigments, rather than providing an external boundary. Early on, the bulk of prebiotic organic matter can have...

  11. Genetic differentiation and genetic diversity of Castanopsis (Fagaceae), the dominant tree species in Japanese broadleaved evergreen forests, revealed by analysis of EST-associated microsatellites.

    Science.gov (United States)

    Aoki, Kyoko; Ueno, Saneyoshi; Kamijo, Takashi; Setoguchi, Hiroaki; Murakami, Noriaki; Kato, Makoto; Tsumura, Yoshihiko

    2014-01-01

    The broadleaved evergreen forests of the East Asian warm temperate zone are characterised by their high biodiversity and endemism, and there is therefore a need to extend our understanding of its genetic diversity and phylogeographic patterns. Castanopsis (Fagaceae) is one of the dominant tree species in the broadleaved evergreen forests of Japan. In this study we investigate the genetic diversity, genetic structure and leaf epidermal morphology of 63 natural populations of C. sieboldii and C. cuspidata, using 32 Expressed Sequence Tag associated microsatellites. The overall genetic differentiation between populations was low (GST = 0.069 in C. sieboldii and GST = 0.057 in C. cuspidata). Neighbor-joining tree and Bayesian clustering analyses revealed that the populations of C. sieboldii and C. cuspidata were genetically clearly differentiated, a result which is consistent with the morphology of their epidermal cell layers. This suggests that C. sieboldii and C. cuspidata should be treated as independent species, although intermediate morphologies are often observed, especially at sites where the two species coexist. The higher level of genetic diversity observed in the Kyushu region (for both species) and the Ryukyu Islands (for C. sieboldii) is consistent with the available fossil pollen data for Castanopsis-type broadleaved evergreen trees during the Last Glacial Maximum and suggests the existence of refugia for Castanopsis forests in southern Japan. Within the C. sieboldii populations, Bayesian clustering analyses detected three clusters, in the western and eastern parts of the main islands and in the Ryukyu Islands. The west-east genetic differentiation observed for this species in the main islands, a pattern which is also found in several plant and animal species inhabiting Castanopsis forests in Japan, suggests that they have been isolated from each other in the western and eastern populations for an extended period of time, and may imply the

  12. Structure and stability of genetic variance-covariance matrices: A Bayesian sparse factor analysis of transcriptional variation in the three-spined stickleback.

    Science.gov (United States)

    Siren, J; Ovaskainen, O; Merilä, J

    2017-07-26

    The genetic variance-covariance matrix (G) is a quantity of central importance in evolutionary biology due to its influence on the rate and direction of multivariate evolution. However, the predictive power of empirically estimated G-matrices is limited for two reasons. First, phenotypes are high-dimensional, whereas traditional statistical methods are tuned to estimate and analyse low-dimensional matrices. Second, the stability of G to environmental effects and over time remains poorly understood. Using Bayesian sparse factor analysis (BSFG) designed to estimate high-dimensional G-matrices, we analysed levels variation and covariation in 10,527 expressed genes in a large (n = 563) half-sib breeding design of three-spined sticklebacks subject to two temperature treatments. We found significant differences in the structure of G between the treatments: heritabilities and evolvabilities were higher in the warm than in the low-temperature treatment, suggesting more and faster opportunity to evolve in warm (stressful) conditions. Furthermore, comparison of G and its phenotypic equivalent P revealed the latter is a poor substitute of the former. Most strikingly, the results suggest that the expected impact of G on evolvability-as well as the similarity among G-matrices-may depend strongly on the number of traits included into analyses. In our results, the inclusion of only few traits in the analyses leads to underestimation in the differences between the G-matrices and their predicted impacts on evolution. While the results highlight the challenges involved in estimating G, they also illustrate that by enabling the estimation of large G-matrices, the BSFG method can improve predicted evolutionary responses to selection. © 2017 John Wiley & Sons Ltd.

  13. Multi-Objective Feature Subset Selection using Non-dominated Sorting Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    A. Khan

    2015-02-01

    Full Text Available This paper presents an evolutionary algorithm based technique to solve multi-objective feature subset selection problem. The data used for classification contains large number of features called attributes. Some of these attributes are not relevant and needs to be eliminated. In classification procedure, each feature has an effect on the accuracy, cost and learning time of the classifier. So, there is a strong requirement to select a subset of the features before building the classifier. This proposed technique treats feature subset selection as multi-objective optimization problem. This research uses one of the latest multi-objective genetic algorithms (NSGA - II. The fitness value of a particular feature subset is measured by using ID3. The testing accuracy acquired is then assigned to the fitness value. This technique is tested on several datasets taken from the UCI machine repository. The experiments demonstrate the feasibility of using NSGA-II for feature subset selection.

  14. Genetic heterogeneity in adult dominant polycystic kidney disease in Cypriot families.

    Science.gov (United States)

    Constantinou-Deltas, C D; Papageorgiou, E; Boteva, K; Christodoulou, K; Breuning, M H; Peter, D J; Pierides, A

    1995-04-01

    Polycystic kidney disease is an inherited heterogeneous disorder that affects approximately 1:1000 Europeans. It is characterized mainly by the formation of cysts in the kidney that lead to end-stage renal failure with late age of onset. Three loci have been identified, PKD1 on the short arm of chromosome 16, which has recently been isolated and characterized, PKD2 on the long arm of chromosome 4, and a third locus of unknown location, that is apparently much rarer. In families that transmit the PKD2 gene there is a significantly later age of onset of symptoms, compared with families that transmit the PKD1 gene, and in general they present with milder progression of symptomatology. For the first time we attempted molecular genetic analysis in seven Cypriot families using highly polymorphic markers around the PKD1 and PKD2 genes. Our data showed that there is genetic and phenotypic heterogeneity among these families. For four of the families we obtained strong evidence for linkage to the PKD1 locus. In two of these families linkage to PKD1 was strengthened by excluding linkage to PKD2 with the use of marker D4S423. In three other families we showed linkage to the PKD2 locus. In the largest of these families one recombinant placed marker D4S1534 distal to D4S231, thereby rendering it the closest proximal marker known to us to date. The application of molecular methods allowed us to make presymptomatic diagnosis for a number of at-risk individuals.

  15. Additive and Over-dominant Effects Resulting from Epistatic Loci Are the Primary Genetic Basis of Heterosis in Rice

    Institute of Scientific and Technical Information of China (English)

    Xiaojin Luo; Yongcai Fu; Peijiang Zhang; Shuang Wu; Feng Tian; Jiayong Liu; Zuofeng Zhu; Jinshui Yang; Chuanqing Sun

    2009-01-01

    A set of 148 F9 recombinant inbred lines (RILs) was developed from the cross of an indica cultivar 93-11 and japonica cultivar DTT13,showing strong F1 heterosis.Subsequently,two backcross F1 (BCF1) populations were constructed by backcrossing these 148 RILs to two parents,93-11 and DT713.These three related populations (281BCF1 lines,148 RILs) were phenotyped for six yield-related traits in two locations.Significant inbreeding depression was detected in the population of RILS and a high level of heterosis was observed in the two BCF1 populations.A total of 42 main-effect quantitative trait loci (M-QTLs) and 109 epistatic effect QTL pairs (E-QTLs) were detected in the three related populations using the mixed model approach.By comparing the genetic effects of these QTLs detected in the RILs,BCF1 performance and mid-parental heterosis (HMp),we found that,in both BCF1 populations,the QTLs detected could be classified into two predominant types:additive and over-domlnant loci,which indicated that the additive and over-dominant effect were more important than complete or partially dominance for M-QTLs and E-QTLs.Further,we found that the E-QTLs detected collectively explained a larger portion of the total phenotypic variation than the M-QTLs in both RILs and BCF1 populations.All of these results suggest that additive and over-dominance resulting from epistatic loci might be the primary genetic basis of heterosis in rice.

  16. Threshold-dominated regulation hides genetic variation in gene expression networks

    Directory of Open Access Journals (Sweden)

    Plahte Erik

    2007-12-01

    Full Text Available Abstract Background In dynamical models with feedback and sigmoidal response functions, some or all variables have thresholds around which they regulate themselves or other variables. A mathematical analysis has shown that when the dose-response functions approach binary or on/off responses, any variable with an equilibrium value close to one of its thresholds is very robust to parameter perturbations of a homeostatic state. We denote this threshold robustness. To check the empirical relevance of this phenomenon with response function steepnesses ranging from a near on/off response down to Michaelis-Menten conditions, we have performed a simulation study to investigate the degree of threshold robustness in models for a three-gene system with one downstream gene, using several logical input gates, but excluding models with positive feedback to avoid multistationarity. Varying parameter values representing functional genetic variation, we have analysed the coefficient of variation (CV of the gene product concentrations in the stable state for the regulating genes in absolute terms and compared to the CV for the unregulating downstream gene. The sigmoidal or binary dose-response functions in these models can be considered as phenomenological models of the aggregated effects on protein or mRNA expression rates of all cellular reactions involved in gene expression. Results For all the models, threshold robustness increases with increasing response steepness. The CVs of the regulating genes are significantly smaller than for the unregulating gene, in particular for steep responses. The effect becomes less prominent as steepnesses approach Michaelis-Menten conditions. If the parameter perturbation shifts the equilibrium value too far away from threshold, the gene product is no longer an effective regulator and robustness is lost. Threshold robustness arises when a variable is an active regulator around its threshold, and this function is maintained by

  17. Statistics of Scientific Procedures on Living Animals 2012: another increase in experimentation - genetically-altered animals dominate again.

    Science.gov (United States)

    Hudson-Shore, Michelle

    2013-09-01

    The Annual Statistics of Scientific Procedures on Living Animals Great Britain 2012 reveal that the level of animal experimentation in Great Britain continues to rise, with just over 4.1 million procedures being started in that year. Despite the previous year's indication that the dominance of the production and use of genetically-altered (GA, i.e. genetically-modified animals plus animals with harmful genetic defects) animal might be abating, it returned with a vengeance in 2012. Breeding increased from 43% to 48% of all procedures, and GA animals were involved in 59% of all the procedures. Indeed, if the breeding of these animals were removed from the statistics, the total number of procedures would actually decline by 2%. In order to honour their pledge to reduce animal use in science, the Coalition Government will have to address this issue. The general trends in the species used, and the numbers and types of procedures, are also reviewed. Finally, forthcoming changes to the statistics are discussed.

  18. Downside Variance Risk Premium

    OpenAIRE

    Feunou, Bruno; Jahan-Parvar, Mohammad R.; Okou, Cédric

    2015-01-01

    We propose a new decomposition of the variance risk premium in terms of upside and downside variance risk premia. The difference between upside and downside variance risk premia is a measure of skewness risk premium. We establish that the downside variance risk premium is the main component of the variance risk premium, and that the skewness risk premium is a priced factor with significant prediction power for aggregate excess returns. Our empirical investigation highlights the positive and s...

  19. A Mean-Variance Hybrid-Entropy Model for Portfolio Selection with Fuzzy Returns

    Directory of Open Access Journals (Sweden)

    Rongxi Zhou

    2015-05-01

    Full Text Available In this paper, we define the portfolio return as fuzzy average yield and risk as hybrid-entropy and variance to deal with the portfolio selection problem with both random uncertainty and fuzzy uncertainty, and propose a mean-variance hybrid-entropy model (MVHEM. A multi-objective genetic algorithm named Non-dominated Sorting Genetic Algorithm II (NSGA-II is introduced to solve the model. We make empirical comparisons by using the data from the Shanghai and Shenzhen stock exchanges in China. The results show that the MVHEM generally performs better than the traditional portfolio selection models.

  20. Multi-objective optimization of an industrial penicillin V bioreactor train using non-dominated sorting genetic algorithm.

    Science.gov (United States)

    Lee, Fook Choon; Rangaiah, Gade Pandu; Ray, Ajay Kumar

    2007-10-15

    Bulk of the penicillin produced is used as raw material for semi-synthetic penicillin (such as amoxicillin and ampicillin) and semi-synthetic cephalosporins (such as cephalexin and cefadroxil). In the present paper, an industrial penicillin V bioreactor train is optimized for multiple objectives simultaneously. An industrial train, comprising a bank of identical bioreactors, is run semi-continuously in a synchronous fashion. The fermentation taking place in a bioreactor is modeled using a morphologically structured mechanism. For multi-objective optimization for two and three objectives, the elitist non-dominated sorting genetic algorithm (NSGA-II) is chosen. Instead of a single optimum as in the traditional optimization, a wide range of optimal design and operating conditions depicting trade-offs of key performance indicators such as batch cycle time, yield, profit and penicillin concentration, is successfully obtained. The effects of design and operating variables on the optimal solutions are discussed in detail.

  1. Multi-objective optimal design of magnetorheological engine mount based on an improved non-dominated sorting genetic algorithm

    Science.gov (United States)

    Zheng, Ling; Duan, Xuwei; Deng, Zhaoxue; Li, Yinong

    2014-03-01

    A novel flow-mode magneto-rheological (MR) engine mount integrated a diaphragm de-coupler and the spoiler plate is designed and developed to isolate engine and the transmission from the chassis in a wide frequency range and overcome the stiffness in high frequency. A lumped parameter model of the MR engine mount in single degree of freedom system is further developed based on bond graph method to predict the performance of the MR engine mount accurately. The optimization mathematical model is established to minimize the total of force transmissibility over several frequency ranges addressed. In this mathematical model, the lumped parameters are considered as design variables. The maximum of force transmissibility and the corresponding frequency in low frequency range as well as individual lumped parameter are limited as constraints. The multiple interval sensitivity analysis method is developed to select the optimized variables and improve the efficiency of optimization process. An improved non-dominated sorting genetic algorithm (NSGA-II) is used to solve the multi-objective optimization problem. The synthesized distance between the individual in Pareto set and the individual in possible set in engineering is defined and calculated. A set of real design parameters is thus obtained by the internal relationship between the optimal lumped parameters and practical design parameters for the MR engine mount. The program flowchart for the improved non-dominated sorting genetic algorithm (NSGA-II) is given. The obtained results demonstrate the effectiveness of the proposed optimization approach in minimizing the total of force transmissibility over several frequency ranges addressed.

  2. Estimation of Epistatic Variance Components and Heritability in Founder Populations and Crosses

    Science.gov (United States)

    Young, Alexander I.; Durbin, Richard

    2014-01-01

    Genetic association studies have explained only a small proportion of the estimated heritability of complex traits, leaving the remaining heritability “missing.” Genetic interactions have been proposed as an explanation for this, because they lead to overestimates of the heritability and are hard to detect. Whether this explanation is true depends on the proportion of variance attributable to genetic interactions, which is difficult to measure in outbred populations. Founder populations exhibit a greater range of kinship than outbred populations, which helps in fitting the epistatic variance. We extend classic theory to founder populations, giving the covariance between individuals due to epistasis of any order. We recover the classic theory as a limit, and we derive a recently proposed estimator of the narrow sense heritability as a corollary. We extend the variance decomposition to include dominance. We show in simulations that it would be possible to estimate the variance from pairwise interactions with samples of a few thousand from strongly bottlenecked human founder populations, and we provide an analytical approximation of the standard error. Applying these methods to 46 traits measured in a yeast (Saccharomyces cerevisiae) cross, we estimate that pairwise interactions explain 10% of the phenotypic variance on average and that third- and higher-order interactions explain 14% of the phenotypic variance on average. We search for third-order interactions, discovering an interaction that is shared between two traits. Our methods will be relevant to future studies of epistatic variance in founder populations and crosses. PMID:25326236

  3. Development and amplification of multiple co-dominant genetic markers from single spores of arbuscular mycorrhizal fungi by nested multiplex PCR

    DEFF Research Database (Denmark)

    Holtgrewe-Stukenbrock, Eva; Rosendahl, Søren

    2005-01-01

    Multiple co-dominant genetic markers from single spores of the arbuscular mycorrhizal (AM) fungi Glomus mosseae, Glomus caledonium, and Glomus geosporum were amplified by nested multiplex PCR using a combination of primers for simultaneous amplification of five loci in one PCR. Subsequently, each...... are homokaryotic. All isolates of G. mosseae had unique genotypes. The amplification of multiple co-dominant genetic markers from single spores by the nested multiplex PCR approach provides an important tool for future studies of AM fungi population genetics and evolution.......Multiple co-dominant genetic markers from single spores of the arbuscular mycorrhizal (AM) fungi Glomus mosseae, Glomus caledonium, and Glomus geosporum were amplified by nested multiplex PCR using a combination of primers for simultaneous amplification of five loci in one PCR. Subsequently, each...

  4. A METHOD FOR PRIORITIZING QUALITATIVE SCENARIOS IN EVALUATING ENTERPRISE ARCHITECTURE USING NON-DOMINATED SORTING GENETIC ALGORITHM II

    Directory of Open Access Journals (Sweden)

    Marzieh Eskandari

    2016-12-01

    Full Text Available In the field of enterprise architecture (EA, qualitative scenarios are used to understand the qualitative characteristics better. In order to reduce the implementation cost, scenarios are prioritized to be able to focus on the higher priority and more important scenarios. There are different methods to evaluate enterprise architecture including architecture Trade-off Analysis Method (ATAM.Prioritizing qualitative scenarios is one of the main phases of this method. Since none of the recent studies meet the prioritizing qualitative scenarios requirements, considering proper prioritizing criteria and reaching an appropriate speed priority, non-dominated sorting genetic algorithms is used in this study (NSGA-II. In addition to previous research standards more criteria were considered in the proposed algorithm, these sets of structures together as gene and in the form of cell array constitute chromosome. The proposed algorithm is evaluated in two case studies in the field of enterprise architecture and architecture software. The results showed the accuracy and the more appropriate speed comparing to the previous works including genetic algorithms.

  5. Influence of Family Structure on Variance Decomposition

    DEFF Research Database (Denmark)

    Edwards, Stefan McKinnon; Sarup, Pernille Merete; Sørensen, Peter

    Partitioning genetic variance by sets of randomly sampled genes for complex traits in D. melanogaster and B. taurus, has revealed that population structure can affect variance decomposition. In fruit flies, we found that a high likelihood ratio is correlated with a high proportion of explained ge...

  6. Influence of Family Structure on Variance Decomposition

    DEFF Research Database (Denmark)

    Edwards, Stefan McKinnon; Sarup, Pernille Merete; Sørensen, Peter

    Partitioning genetic variance by sets of randomly sampled genes for complex traits in D. melanogaster and B. taurus, has revealed that population structure can affect variance decomposition. In fruit flies, we found that a high likelihood ratio is correlated with a high proportion of explained ge...

  7. Nonlinear Epigenetic Variance: Review and Simulations

    Science.gov (United States)

    Kan, Kees-Jan; Ploeger, Annemie; Raijmakers, Maartje E. J.; Dolan, Conor V.; van Der Maas, Han L. J.

    2010-01-01

    We present a review of empirical evidence that suggests that a substantial portion of phenotypic variance is due to nonlinear (epigenetic) processes during ontogenesis. The role of such processes as a source of phenotypic variance in human behaviour genetic studies is not fully appreciated. In addition to our review, we present simulation studies…

  8. Improvement of prediction ability for genomic selection of dairy cattle by including dominance effects.

    Directory of Open Access Journals (Sweden)

    Chuanyu Sun

    Full Text Available Dominance may be an important source of non-additive genetic variance for many traits of dairy cattle. However, nearly all prediction models for dairy cattle have included only additive effects because of the limited number of cows with both genotypes and phenotypes. The role of dominance in the Holstein and Jersey breeds was investigated for eight traits: milk, fat, and protein yields; productive life; daughter pregnancy rate; somatic cell score; fat percent and protein percent. Additive and dominance variance components were estimated and then used to estimate additive and dominance effects of single nucleotide polymorphisms (SNPs. The predictive abilities of three models with both additive and dominance effects and a model with additive effects only were assessed using ten-fold cross-validation. One procedure estimated dominance values, and another estimated dominance deviations; calculation of the dominance relationship matrix was different for the two methods. The third approach enlarged the dataset by including cows with genotype probabilities derived using genotyped ancestors. For yield traits, dominance variance accounted for 5 and 7% of total variance for Holsteins and Jerseys, respectively; using dominance deviations resulted in smaller dominance and larger additive variance estimates. For non-yield traits, dominance variances were very small for both breeds. For yield traits, including additive and dominance effects fit the data better than including only additive effects; average correlations between estimated genetic effects and phenotypes showed that prediction accuracy increased when both effects rather than just additive effects were included. No corresponding gains in prediction ability were found for non-yield traits. Including cows with derived genotype probabilities from genotyped ancestors did not improve prediction accuracy. The largest additive effects were located on chromosome 14 near DGAT1 for yield traits for both

  9. Expected Stock Returns and Variance Risk Premia

    DEFF Research Database (Denmark)

    Bollerslev, Tim; Zhou, Hao

    predicting high (low) future returns. The magnitude of the return predictability of the variance risk premium easily dominates that afforded by standard predictor variables like the P/E ratio, the dividend yield, the default spread, and the consumption-wealth ratio (CAY). Moreover, combining the variance...... risk premium with the P/E ratio results in an R2 for the quarterly returns of more than twenty-five percent. The results depend crucially on the use of "model-free", as opposed to standard Black-Scholes, implied variances, and realized variances constructed from high-frequency intraday, as opposed...

  10. 基于聚类的NSGA-II算法%Non-dominated Sorting Genetic Algorithm II Based on Clustering

    Institute of Scientific and Technical Information of China (English)

    李志强; 蔺想红

    2013-01-01

    According to the uneven distribution of population convergence and poor performance in global search of Non-dominated Sorting Genetic Algorithm II(NSGA-II), a multi-objective evolutionary algorithm, called K-means clustering non-dominated sorting genetic algorithm II(KMCNSGAII) is proposed with combining the theory and the existing algorithm. The KMCNSGAII uses K-means clustering technology and at the same time clusters both all the objective functions and individuals respectively. Then the learning and improvement method is used with respect to individuals after clustering. The KMCNSGAII algorithm is applied to several classical unconstrained and constrained test functions. Experimental results demonstrate that the KMCNSGAII achieves good results with performance evaluation about convergence indicator and diversity indicator, in convergence and diversity of population both are improved significantly compared with NSGA-II.%采用精英策略的非支配排序遗传算法(NSGA-II)种群收敛分布不均匀,全局搜索能力较弱。针对该问题,基于现有的算法,提出一种基于聚类学习机制的多目标进化算法KMCNSGA-II。利用K均值聚类对目标函数和个体分别进行聚类,对聚类后的个体进行局部学习,以提高适应度。将该算法应用于经典的多目标约束和非约束测试函数中,通过收敛性指标世代距离和多样性指标∆进行性能评价。实验结果表明,与NSGA-II算法相比,该算法在算法收敛性和种群多样性保持方面均有明显提高。

  11. Increased wheel-running activity in the genetically skeletal muscle fast-twitch fiber-dominant rats.

    Science.gov (United States)

    Suwa, Masataka; Nakano, Hiroshi; Higaki, Yasuki; Nakamura, Tomohiro; Katsuta, Shigeru; Kumagai, Shuzo

    2003-01-01

    The purpose of the present study was to investigate whether genetic differences in muscle histochemical characteristics were related to the voluntary wheel-running activity level by using genetically fast-twitch fiber-dominant rats (FFDR) and control rats (CR). The rats were divided into four groups; sedentary CR (Sed-CR), wheel-running CR (WR-CR), sedentary FFDR (Sed-FFDR), and wheel-running FFDR (WR-FFDR). Wheel access was started at age 9 wk and lasted for 7 days. The FFDR showed a lower percentage of type I fibers of the deep portion of gastrocnemius and soleus muscles and a higher percentage of both type IIX fibers of the gastrocnemius muscle and type IIA fibers of the soleus muscle compared with CR. A higher capillary density and smaller fiber cross-sectional area were also observed in FFDR. The daily running distance in WR-FFDR was higher than in WR-CR for each 7 days. The total running distance for 7 days in WR-FFDR was 3.2-fold higher than in WR-CR. On day 7 of the 7-day test, the total number of active 1-min intervals for 24 h, the average rpm when they were active, and the maximum rpm for any single 1-min period in the WR-FFDR were significantly higher than in the WR-CR (1.5-, 2.9-, and 2.0-fold, respectively). These results suggest that mechanical or physiological muscle characteristics may thus affect the wheel-running activity level.

  12. Simulation study on heterogeneous variance adjustment for observations with different measurement error variance

    DEFF Research Database (Denmark)

    Pitkänen, Timo; Mäntysaari, Esa A; Nielsen, Ulrik Sander

    2013-01-01

    of variance correction is developed for the same observations. As automated milking systems are becoming more popular the current evaluation model needs to be enhanced to account for the different measurement error variances of observations from automated milking systems. In this simulation study different...... models and different approaches to account for heterogeneous variance when observations have different measurement error variances were investigated. Based on the results we propose to upgrade the currently applied models and to calibrate the heterogeneous variance adjustment method to yield same genetic...

  13. Evidence that BMI and type 2 diabetes share only a minor fraction of genetic variance: a follow-up study of 23,585 monozygotic and dizygotic twins from the Finnish Twin Cohort Study.

    Science.gov (United States)

    Lehtovirta, M; Pietiläinen, K H; Levälahti, E; Heikkilä, K; Groop, L; Silventoinen, K; Koskenvuo, M; Kaprio, J

    2010-07-01

    We investigated whether BMI predicts type 2 diabetes in twins and to what extent that is explained by common genetic factors. This was a population-based twin cohort study. Monozygotic (n = 4,076) and dizygotic (n = 9,109) non-diabetic twin pairs born before 1958 answered a questionnaire in 1975, from which BMI was obtained. Information on incident cases of diabetes was obtained by linkage to nationwide registers until 2005. Altogether, 1,332 twins (6.3% of men, 5.1% of women) developed type 2 diabetes. The HR for type 2 diabetes increased monotonically with a mean of 1.22 (95% CI 1.20-1.24) per BMI unit and of 1.97 (95% CI 1.87-2.08) per SD of BMI. The HRs for lean, overweight, obese and morbidly obese participants were 0.59, 2.96, 6.80 and 13.64 as compared with normal weight participants. Model heritability estimates for bivariate variance due to an additive genetic component and non-shared environmental component were 75% (men) and 71% (women) for BMI, and 73% and 64%, respectively for type 2 diabetes. The correlations between genetic variance components (r (g)) indicated that one fifth of the covariance of BMI and type 2 diabetes was due to shared genetic influences. Although the mean monozygotic concordance for type 2 diabetes was approximately twice the dizygotic one, age of onset of diabetes within twin pair members varied greatly, irrespective of zygosity. A 28-year follow-up of adult Finnish twins showed that despite high trait heritability estimates, only a fraction of covariation in BMI and incident type 2 diabetes was of genetic origin.

  14. Resonance Assignment of the NMR Spectra of Disordered Proteins Using a Multi-Objective Non-Dominated Sorting Genetic Algorithm

    Science.gov (United States)

    Yang, Yu; Fritzsching, Keith J.

    2014-01-01

    A multi-objective genetic algorithm is introduced to predict the assignment of protein solid-state NMR spectra with partial resonance overlap and missing peaks due to broad linewidths, molecular motion, and low sensitivity. This non-dominated sorting genetic algorithm II (NSGA-II) aims to identify all possible assignments that are consistent with the spectra and to compare the relative merit of these assignments. Our approach is modeled after the recently introduced Monte Carlo simulated annealing (MC/SA) protocol, with the key difference that NSGA-II simultaneously optimizes multiple assignment objectives instead of searching for possible assignments based on a single composite score. The multiple objectives include maximizing the number of consistently assigned peaks between multiple spectra (“good connections”), maximizing the number of used peaks, minimizing the number of inconsistently assigned peaks between spectra (“bad connections”), and minimizing the number of assigned peaks that have no matching peaks in the other spectra (“edges”). Using six solid-state NMR protein chemical shift datasets with varying levels of imperfection that was introduced by peak deletion, random chemical shift changes, and manual peak picking of spectra with moderately broad linewidths, we show that the NSGA-II algorithm produces a large number of valid and good assignments rapidly. For high-quality chemical shift peak lists, NSGA-II and MC/SA perform similarly well. However, when the peak lists contain many missing peaks that are uncorrelated between different spectra and have chemical shift deviations between spectra, the modified NSGA-II produces a larger number of valid solutions than MC/SA, and is more effective at distinguishing good from mediocre assignments by avoiding the hazard of suboptimal weighting factors for the various objectives. These two advantages, namely diversity and better evaluation, lead to a higher probability of predicting the correct

  15. Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Yu; Fritzsching, Keith J.; Hong, Mei, E-mail: mhong@iastate.edu [Iowa State University, Department of Chemistry (United States)

    2013-10-17

    A multi-objective genetic algorithm is introduced to predict the assignment of protein solid-state NMR (SSNMR) spectra with partial resonance overlap and missing peaks due to broad linewidths, molecular motion, and low sensitivity. This non-dominated sorting genetic algorithm II (NSGA-II) aims to identify all possible assignments that are consistent with the spectra and to compare the relative merit of these assignments. Our approach is modeled after the recently introduced Monte-Carlo simulated-annealing (MC/SA) protocol, with the key difference that NSGA-II simultaneously optimizes multiple assignment objectives instead of searching for possible assignments based on a single composite score. The multiple objectives include maximizing the number of consistently assigned peaks between multiple spectra (“good connections”), maximizing the number of used peaks, minimizing the number of inconsistently assigned peaks between spectra (“bad connections”), and minimizing the number of assigned peaks that have no matching peaks in the other spectra (“edges”). Using six SSNMR protein chemical shift datasets with varying levels of imperfection that was introduced by peak deletion, random chemical shift changes, and manual peak picking of spectra with moderately broad linewidths, we show that the NSGA-II algorithm produces a large number of valid and good assignments rapidly. For high-quality chemical shift peak lists, NSGA-II and MC/SA perform similarly well. However, when the peak lists contain many missing peaks that are uncorrelated between different spectra and have chemical shift deviations between spectra, the modified NSGA-II produces a larger number of valid solutions than MC/SA, and is more effective at distinguishing good from mediocre assignments by avoiding the hazard of suboptimal weighting factors for the various objectives. These two advantages, namely diversity and better evaluation, lead to a higher probability of predicting the correct

  16. Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm.

    Science.gov (United States)

    Yang, Yu; Fritzsching, Keith J; Hong, Mei

    2013-11-01

    A multi-objective genetic algorithm is introduced to predict the assignment of protein solid-state NMR (SSNMR) spectra with partial resonance overlap and missing peaks due to broad linewidths, molecular motion, and low sensitivity. This non-dominated sorting genetic algorithm II (NSGA-II) aims to identify all possible assignments that are consistent with the spectra and to compare the relative merit of these assignments. Our approach is modeled after the recently introduced Monte-Carlo simulated-annealing (MC/SA) protocol, with the key difference that NSGA-II simultaneously optimizes multiple assignment objectives instead of searching for possible assignments based on a single composite score. The multiple objectives include maximizing the number of consistently assigned peaks between multiple spectra ("good connections"), maximizing the number of used peaks, minimizing the number of inconsistently assigned peaks between spectra ("bad connections"), and minimizing the number of assigned peaks that have no matching peaks in the other spectra ("edges"). Using six SSNMR protein chemical shift datasets with varying levels of imperfection that was introduced by peak deletion, random chemical shift changes, and manual peak picking of spectra with moderately broad linewidths, we show that the NSGA-II algorithm produces a large number of valid and good assignments rapidly. For high-quality chemical shift peak lists, NSGA-II and MC/SA perform similarly well. However, when the peak lists contain many missing peaks that are uncorrelated between different spectra and have chemical shift deviations between spectra, the modified NSGA-II produces a larger number of valid solutions than MC/SA, and is more effective at distinguishing good from mediocre assignments by avoiding the hazard of suboptimal weighting factors for the various objectives. These two advantages, namely diversity and better evaluation, lead to a higher probability of predicting the correct assignment for a

  17. Extreme patterns of variance in small populations: placing limits on human Y-chromosome diversity through time in the Vanuatu Archipelago.

    Science.gov (United States)

    Cox, M

    2007-05-01

    Small populations are dominated by unique patterns of variance, largely characterized by rapid drift of allele frequencies. Although the variance components of genetic datasets have long been recognized, most population genetic studies still treat all sampling locations equally despite differences in sampling and effective population sizes. Because excluding the effects of variance can lead to significant biases in historical reconstruction, variance components should be incorporated explicitly into population genetic analyses. The possible magnitude of variance effects in small populations is illustrated here via a case study of Y-chromosome haplogroup diversity in the Vanuatu Archipelago. Deme-based modelling is used to simulate allele frequencies through time, and conservative confidence bounds are placed on the accumulation of stochastic variance effects, including diachronic genetic drift and contemporary sampling error. When the information content of the dataset has been ascertained, demographic models with parameters falling outside the confidence bounds of the variance components can then be accepted with some statistical confidence. Here I emphasize how aspects of the demographic history of a population can be disentangled from stochastic variance effects, and I illustrate the extreme roles of genetic drift and sampling error for many small human population datasets.

  18. Genetic diagnosis of autosomal dominant polycystic kidney disease by targeted capture and next-generation sequencing: utility and limitations.

    Science.gov (United States)

    Qi, Xiao-Ping; Du, Zhen-Fang; Ma, Ju-Ming; Chen, Xiao-Ling; Zhang, Qing; Fei, Jun; Wei, Xiao-Ming; Chen, Dong; Ke, Hai-Ping; Liu, Xuan-Zhu; Li, Feng; Chen, Zhen-Guang; Su, Zheng; Jin, Hang-Yang; Liu, Wen-Ting; Zhao, Yan; Jiang, Hu-Ling; Lan, Zhang-Zhang; Li, Peng-Fei; Fang, Ming-Yan; Dong, Wei; Zhang, Xian-Ning

    2013-03-01

    Mutation-based molecular diagnostics of autosomal dominant polycystic kidney disease (ADPKD) is complicated by genetic and allelic heterogeneity, large multi-exon genes, and duplication sequences of PKD1. Recently, targeted resequencing by pooling long-range polymerase chain reaction (LR-PCR) amplicons has been used in the identification of mutations in ADPKD. Despite its high sensitivity, specificity and accuracy, LR-PCR is still complicated. We performed whole-exome sequencing on two unrelated typical Chinese ADPKD probands and evaluated the effectiveness of this approach compared with Sanger sequencing. Meanwhile, we performed targeted gene and next-generation sequencing (targeted DNA-HiSeq) on 8 individuals (1 patient from one family, 5 patients and 2 normal individuals from another family). Both whole-exome sequencing and targeted DNA-HiSeq confirmed c.11364delC (p.H3788QfsX37) within the unduplicated region of PKD1 in one proband; in the other family, targeted DNA-HiSeq identified a small insertion, c.401_402insG (p.V134VfsX79), in PKD2. These methods do not overcome the screening complexity of homology. However, the true positives of variants confirmed by targeted gene and next-generation sequencing were 69.4%, 50% and 100% without a false positive in the whole coding region and the duplicated and unduplicated regions, which indicated that the screening accuracy of PKD1 and PKD2 can be largely improved by using a greater sequencing depth and elaborate design of the capture probe.

  19. Generalized analysis of molecular variance.

    Directory of Open Access Journals (Sweden)

    Caroline M Nievergelt

    2007-04-01

    Full Text Available Many studies in the fields of genetic epidemiology and applied population genetics are predicated on, or require, an assessment of the genetic background diversity of the individuals chosen for study. A number of strategies have been developed for assessing genetic background diversity. These strategies typically focus on genotype data collected on the individuals in the study, based on a panel of DNA markers. However, many of these strategies are either rooted in cluster analysis techniques, and hence suffer from problems inherent to the assignment of the biological and statistical meaning to resulting clusters, or have formulations that do not permit easy and intuitive extensions. We describe a very general approach to the problem of assessing genetic background diversity that extends the analysis of molecular variance (AMOVA strategy introduced by Excoffier and colleagues some time ago. As in the original AMOVA strategy, the proposed approach, termed generalized AMOVA (GAMOVA, requires a genetic similarity matrix constructed from the allelic profiles of individuals under study and/or allele frequency summaries of the populations from which the individuals have been sampled. The proposed strategy can be used to either estimate the fraction of genetic variation explained by grouping factors such as country of origin, race, or ethnicity, or to quantify the strength of the relationship of the observed genetic background variation to quantitative measures collected on the subjects, such as blood pressure levels or anthropometric measures. Since the formulation of our test statistic is rooted in multivariate linear models, sets of variables can be related to genetic background in multiple regression-like contexts. GAMOVA can also be used to complement graphical representations of genetic diversity such as tree diagrams (dendrograms or heatmaps. We examine features, advantages, and power of the proposed procedure and showcase its flexibility by

  20. Temporal change in the genetic structure between and within cohorts of a marine fish, Diplodus sargus, induced by a large variance in individual reproductive success.

    Science.gov (United States)

    Planes, S; Lenfant, P

    2002-08-01

    Temporal changes at 16 allozyme loci in the Diplodus sargus population of Banyuls-sur-Mer (Mediterranean Sea, France) were monitored. Temporal genetic variation within a single population was examined over two temporal scales: (i) among three year-classes sampled at the same age, and (ii) within a single year-class sampled three times over a two-year period. We observed a significant change in the genotypic structure within the same cohort during the first two years following settlement and before recruitment into the adult population. In addition, comparison of year-classes showed that cohorts differed significantly one year after settlement, whereas they became similar later on before recruitment into the adult population. The observed changes in the genetic structure within and between year-classes may be the result of complex selective processes or genetic drift. Linkage disequilibrium and genetic relatedness data suggest that these changes are due to large variation in reproductive success, followed by homogenization through adult movement. Overall, these results demonstrated a rapid genetic change within a population.

  1. Variance of genetic parameters for gas accumulations in the Rotliegende of the Western Altmark; Varianz lagerstaettengenetischer Parameter im Rotliegenden der westlichen Altmark

    Energy Technology Data Exchange (ETDEWEB)

    Schumacher, K.H. [Erdoel-Erdgas Gommern GmbH, Gommern (Germany); May, F. [Erdoel-Erdgas Gommern GmbH, Gommern (Germany)

    1993-12-31

    The gas fields of the western Altmark show a distinct zonal variance of gas- and isotope-geochemical and lithological parameters. The diapir-like distribution of methane contents and isotopes ratios gives information not only on the role played by the N-S faults associated with the Rotliegende rifting in providing gas-migration paths, but also on special aspects of the migration process. (orig.) [Deutsch] In den Lagerstaetten der westlichen Altmark tritt eine ausgepraegte zonale Varianz erdgas- und isotopengeochemischer sowie lithologischer Parameter auf. An Hand diapirartiger Erscheinungsbilder der Methangehalts- und Isotopenverteilungen werden neben der Rolle der N-S-gerichteten Bruchstoerungen des Rotliegend-Riftings fuer die Erdgaszufuhr zugleich Besonderheiten des Migrationsablaufes deutlich. (orig.)

  2. Expected Stock Returns and Variance Risk Premia

    DEFF Research Database (Denmark)

    Bollerslev, Tim; Zhou, Hao

    We find that the difference between implied and realized variation, or the variance risk premium, is able to explain more than fifteen percent of the ex-post time series variation in quarterly excess returns on the market portfolio over the 1990 to 2005 sample period, with high (low) premia...... predicting high (low) future returns. The magnitude of the return predictability of the variance risk premium easily dominates that afforded by standard predictor variables like the P/E ratio, the dividend yield, the default spread, and the consumption-wealth ratio (CAY). Moreover, combining the variance...... risk premium with the P/E ratio results in an R2 for the quarterly returns of more than twenty-five percent. The results depend crucially on the use of "model-free", as opposed to standard Black-Scholes, implied variances, and realized variances constructed from high-frequency intraday, as opposed...

  3. A novel homologous dominant selection marker for genetic transformation of Penicillium chrysogenum: overexpression of squalene epoxidase-encoding ergA.

    Science.gov (United States)

    Sigl, Claudia; Handler, Monika; Sprenger, Georg; Kürnsteiner, Hubert; Zadra, Ivo

    2010-11-01

    Genetic engineering requires genetic selection markers. For generation of biosafe strains in industrial applications, homologous dominant selection markers allowing "self-cloning" are best suited but scarce. Here we describe a novel homologous dominant genetic selection system for the filamentous fungus Penicillium chrysogenum based on overexpression of the P. chrysogenum squalene epoxidase-encoding ergA gene, which confers resistance against terbinafine. Terbinafine (TRB) is a potent antifungal drug used in therapy of fungal infections. Overexpression of ergA was driven by the P. chrysogenum endoxylanase xylP promoter that is highly inducible by xylose. The suitability of the novel selection marker cassette for genetic manipulation was proven by its use for targeted deletion of the transcription factor nosA in P. chrysogenum. NosA-deficiency did not affect growth rates on solid or in liquid media, conidiation in light or darkness, and resistance to hydrogen peroxide. However, NosA-deficiency significantly decreased penicillin productivity. As TRB inhibits the growth of a variety of fungal species, this novel selection marker is expected to be suitable for genetic engineering of diverse fungal species.

  4. Variational bayesian method of estimating variance components.

    Science.gov (United States)

    Arakawa, Aisaku; Taniguchi, Masaaki; Hayashi, Takeshi; Mikawa, Satoshi

    2016-07-01

    We developed a Bayesian analysis approach by using a variational inference method, a so-called variational Bayesian method, to determine the posterior distributions of variance components. This variational Bayesian method and an alternative Bayesian method using Gibbs sampling were compared in estimating genetic and residual variance components from both simulated data and publically available real pig data. In the simulated data set, we observed strong bias toward overestimation of genetic variance for the variational Bayesian method in the case of low heritability and low population size, and less bias was detected with larger population sizes in both methods examined. The differences in the estimates of variance components between the variational Bayesian and the Gibbs sampling were not found in the real pig data. However, the posterior distributions of the variance components obtained with the variational Bayesian method had shorter tails than those obtained with the Gibbs sampling. Consequently, the posterior standard deviations of the genetic and residual variances of the variational Bayesian method were lower than those of the method using Gibbs sampling. The computing time required was much shorter with the variational Bayesian method than with the method using Gibbs sampling.

  5. Genetic variance and covariance and breed differences for feed intake and average daily gain to improve feed efficiency in growing cattle.

    Science.gov (United States)

    Retallick, K J; Bormann, J M; Weaber, R L; MacNeil, M D; Bradford, H L; Freetly, H C; Hales, K E; Moser, D W; Snelling, W M; Thallman, R M; Kuehn, L A

    2017-04-01

    Feed costs are a major economic expense in finishing and developing cattle; however, collection of feed intake data is costly. Examining relationships among measures of growth and intake, including breed differences, could facilitate selection for efficient cattle. Objectives of this study were to estimate genetic parameters for growth and intake traits and compare indices for feed efficiency to accelerate selection response. On-test ADFI and on-test ADG (TESTADG) and postweaning ADG (PWADG) records for 5,606 finishing steers and growing heifers were collected at the U.S. Meat Animal Research Center in Clay Center, NE. On-test ADFI and ADG data were recorded over testing periods that ranged from 62 to 148 d. Individual quadratic regressions were fitted for BW on time, and TESTADG was predicted from the resulting equations. We included PWADG in the model to improve estimates of growth and intake parameters; PWADG was derived by dividing gain from weaning weight to yearling weight by the number of days between the weights. Genetic parameters were estimated using multiple-trait REML animal models with TESTADG, ADFI, and PWADG for both sexes as dependent variables. Fixed contemporary groups were cohorts of calves simultaneously tested, and covariates included age on test, age of dam, direct and maternal heterosis, and breed composition. Genetic correlations (SE) between steer TESTADG and ADFI, PWADG and ADFI, and TESTADG and PWADG were 0.33 (0.10), 0.59 (0.06), and 0.50 (0.09), respectively, and corresponding estimates for heifers were 0.66 (0.073), 0.77 (0.05), and 0.88 (0.05), respectively. Indices combining EBV for ADFI with EBV for ADG were developed and evaluated. Greater improvement in feed efficiency can be expected using an unrestricted index versus a restricted index. Heterosis significantly affected each trait contributing to greater ADFI and TESTADG. Breed additive effects were estimated for ADFI, TESTADG, and the efficiency indices.

  6. 立枯丝核菌遗传多样性的研究方法%Methodology in Researching of Genetic Variance of Rhizoctonia solani

    Institute of Scientific and Technical Information of China (English)

    王利红; 姜华; 王艳丽; 孙国昌

    2013-01-01

    Rhizoctonia solani Ktihn is a plant pathogenic fungus with a wide host range and abundant genetic diversity. The study on the genetic diversity of R. solani is a kind of research hotspot. In this paper, we reviewed several techniques widely used in the studies on the genetic diversity of R. solani. We interpreted and described the advantages and disadvantages of each method. Hyphal fusion is a traditional method, which requires the use of a microscope and is time-consuming and labor-intensive. The method for identifying the pattern of isoenzyme is simple, efficient and inexpensive, and has to be associated with other techniques. The fatty acids analysis is easy to be manipulated, and the cost is relatively low, but the method is limited by the strain growth conditions and the way of fatty acid esterified. Many molecular marker methods were used in the research on the genetic diversity of R. solani, each with the pros and cons, by comparison we suggest that the rDNA-ITS is the more appropriate method. The applications of these methods were also discussed in the paper.%立枯丝核菌(Rhizoctonia solani Kühn)是一个集合种,遗传多样性丰富.关于遗传多样性的研究一直是R.solani研究的热点.本文就用于R.solani遗传多样性研究的方法进行了综述.分别解释并阐述了各种方法的优缺点,其中菌丝融合法是研究R.solani遗传多样性的传统方法,该法需借助显微镜且耗时耗力;同工酶法简便、高效、低廉,但常需要与其它方法联用;脂肪酸法操作难度小,价格相对较低,但该法受菌株生长状况和脂肪酸脂化方法的限制;分子标记法方法众多,各有利弊,通过比较发现rDNA-ITS是研究R.solani遗传多样性比较合适的方法.本文还介绍了不同方法在R.solani遗传多样性研究中的具体应用.

  7. The genetic architecture of fitness in a seed beetle: assessing the potential for indirect genetic benefits of female choice

    DEFF Research Database (Denmark)

    Bilde, T.; Friberg, U.; Maklakov, A.A.

    2008-01-01

    Background Quantifying the amount of standing genetic variation in fitness represents an empirical challenge. Unfortunately, the shortage of detailed studies of the genetic architecture of fitness has hampered progress in several domains of evolutionary biology. One such area is the study of sexual...... variance in F1 productivity, but lower genetic variance in egg-to-adult survival, which was strongly influenced by maternal and paternal effects. Conclusion Our results show that, in order to gain a relevant understanding of the genetic architecture of fitness, measures of offspring fitness should...... is the genetic interaction between parental genomes, as indicated by large amounts of non-additive genetic variance (dominance and/or epistasis) for F1 productivity. We discuss the processes that may maintain additive and non-additive genetic variance for fitness and how these relate to indirect selection...

  8. Population genetics of Phytophthora infestans in Denmark reveals dominantly clonal populations and specific alleles linked to metalaxyl-M resistance

    DEFF Research Database (Denmark)

    Montes, Melanie Sarah; Nielsen, B.J.; Schmidt, S.G.;

    2016-01-01

    population of P. infestans was characterized over the course of the 2013 growing season, as was the population genetic structure, using simple sequence repeat (SSR) genotypes and single nucleotide polymorphism (SNP)-based mitochondrial haplotyping of over 80 isolates. Both mating types A1 and A2 were present......Control of the potato late blight pathogen Phytophthora infestans relies heavily on chemicals. The fungicide metalaxyl-M (Mefenoxam) has played an important role in controlling the disease, but insensitivity to the fungicide in certain isolates is now of major concern. A genetic basis...... for resistance to metalaxyl suggests the possibility for linking resistance phenotypes to specific population genetic markers, but in order to do this, the population genetic structure and mode of reproduction in a population must first be well described. The dynamics of metalaxyl-M resistance in the Danish...

  9. Determination of some dominant genetic characteristics and morpho-meristic features for selection of rainbow trout (Oncorhynchus mykiss) broodstocks

    OpenAIRE

    Mahmoudi, Roghaye

    2014-01-01

    In this study, Iranian and French male and female Oncorhynchus mykiss broodstocks were divided into two groups 50 and 24 respectively in Research center of genetic and breeding of coldwater fishes, Yasouj, Iran and the genetic structure of them was investigated using 6 microsatellite markers. Then 19 morphometric and 5 meristic of broodstock were measured and compared in two populations. Along with broodstock maturation, fertilization 1:1(female:male) were randomly assigned and...

  10. Genetics of dementias, Part 4: A spectrum of mutations responsible for the familial autosomal dominant form of Alzheimer’s disease

    Directory of Open Access Journals (Sweden)

    Anna Kowalska

    2009-12-01

    Full Text Available Fifty years ago it was demonstrated that some patients with Alzheimer’s disease (AD had an autosomal dominant Mendelian pattern of disease inheritance. Familial and early-onset cases (familial Alzheimer’s disease, FAD are rather rare and account for only a few percent of the total population of patients. Mutations of the genes for amyloid precursor protein (APP, presenilin 1 (PSEN1, and presenilin 2 (PSEN2 are responsible for development of the disease in 50 percent of patients with FAD. The identification of mutations in FAD genes leads to a better understand of the molecular basis of the cellular pathways leading to neurodegeneration. With the detection of genetic defects responsible for FAD, there is considerable interest in the application of this genetic information in medical practice through genetic testing and counseling for families with Alzheimer’s disease.

  11. Conversations across Meaning Variance

    Science.gov (United States)

    Cordero, Alberto

    2013-01-01

    Progressive interpretations of scientific theories have long been denounced as naive, because of the inescapability of meaning variance. The charge reportedly applies to recent realist moves that focus on theory-parts rather than whole theories. This paper considers the question of what "theory-parts" of epistemic significance (if any) relevantly…

  12. Factors affecting the reproductive success of dominant male meerkats.

    Science.gov (United States)

    Spong, Göran F; Hodge, Sarah J; Young, Andrew J; Clutton-Brock, Tim H

    2008-05-01

    Identifying traits that affect the reproductive success of individuals is fundamental for our understanding of evolutionary processes. In cooperative breeders, a dominant male typically restricts mating access to the dominant female for extended periods, resulting in pronounced variation in reproductive success among males. This may result in strong selection for traits that increase the likelihood of dominance acquisition, dominance retention and reproductive rates while dominant. However, despite considerable research on reproductive skew, few studies have explored the factors that influence these three processes among males in cooperative species. Here we use genetic, behavioural and demographic data to investigate the factors affecting reproductive success in dominant male meerkats (Suricata suricatta). Our data show that dominant males sire the majority of all offspring surviving to 1 year. A male's likelihood of becoming dominant is strongly influenced by age, but not by weight. Tenure length and reproductive rate, both important components of dominant male reproductive success, are largely affected by group size and composition, rather than individual traits. Dominant males in large groups have longer tenures, but after this effect is controlled, male tenure length also correlates negatively to the number of adult females in the group. Male reproductive rate also declines as the number of intra- and extra-group competitors increases. As the time spent in the dominant position and reproductive rate while dominant explain > 80% of the total variance in reproductive success, group composition thus has major implications for male reproductive success.

  13. Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy, genetic homogeneity, and mapping of the locus within a 2-cM interval

    Energy Technology Data Exchange (ETDEWEB)

    Ducros, A.; Alamowitch, S.; Nagy, T. [INSERM U25, Paris (France)] [and others

    1996-01-01

    Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a recently identified autosomal dominant cerebral arteriopathy characterized by the recurrence of subcortical infarcts leading to dementia. A genetic linkage analysis conducted in two large families recently allowed us to map the affected gene on chromosome 19 in a 12-cM interval bracketed by D19S221 and D19S215. In the present study, these first 2 families and 13 additional ones, including a total of 199 potentially informative meiosis, have been genotyped with eight polymorphic markers located between D19S221 and D19S215. All families were linked to chromosome 19. The highest combined lod score (Z{sub max} = 37.24 at {theta} = .01) was obtained with marker D19S841, a new CA{sub n} microsatellite marker that we isolated from chromosome 19 cosmids. The recombinant events observed within these families were used to refine the genetic mapping of CADASIL within a 2-cM interval that is now bracketed by D19S226 and D19S199 on 19p13.1. These data strongly suggest the genetic homogeneity of this recently identified condition and establish the value of its clinical and neuroimaging diagnostic criteria. Besides their importance for the ongoing positional cloning of the CADASIL gene, these data help to refine the genetic mapping of CADASIL relative to familial hemiplegic migraine and hereditary paroxysmal cerebellar ataxia, conditions that we both mapped within the same chromosome 19 region. 35 refs., 5 figs., 2 tabs.

  14. Nominal analysis of "variance".

    Science.gov (United States)

    Weiss, David J

    2009-08-01

    Nominal responses are the natural way for people to report actions or opinions. Because nominal responses do not generate numerical data, they have been underutilized in behavioral research. On those occasions in which nominal responses are elicited, the responses are customarily aggregated over people or trials so that large-sample statistics can be employed. A new analysis is proposed that directly associates differences among responses with particular sources in factorial designs. A pair of nominal responses either matches or does not; when responses do not match, they vary. That analogue to variance is incorporated in the nominal analysis of "variance" (NANOVA) procedure, wherein the proportions of matches associated with sources play the same role as do sums of squares in an ANOVA. The NANOVA table is structured like an ANOVA table. The significance levels of the N ratios formed by comparing proportions are determined by resampling. Fictitious behavioral examples featuring independent groups and repeated measures designs are presented. A Windows program for the analysis is available.

  15. Transcriptomic evidence for the evolution of shoot meristem function in sporophyte-dominant land plants through concerted selection of ancestral gametophytic and sporophytic genetic programs.

    Science.gov (United States)

    Frank, Margaret H; Scanlon, Michael J

    2015-02-01

    Alternation of generations, in which the haploid and diploid stages of the life cycle are each represented by multicellular forms that differ in their morphology, is a defining feature of the land plants (embryophytes). Anciently derived lineages of embryophytes grow predominately in the haploid gametophytic generation from apical cells that give rise to the photosynthetic body of the plant. More recently evolved plant lineages have multicellular shoot apical meristems (SAMs), and photosynthetic shoot development is restricted to the sporophyte generation. The molecular genetic basis for this evolutionary shift from gametophyte-dominant to sporophyte-dominant life cycles remains a major question in the study of land plant evolution. We used laser microdissection and next generation RNA sequencing to address whether angiosperm meristem patterning genes expressed in the sporophytic SAM of Zea mays are expressed in the gametophytic apical cells, or in the determinate sporophytes, of the model bryophytes Marchantia polymorpha and Physcomitrella patens. A wealth of upregulated genes involved in stem cell maintenance and organogenesis are identified in the maize SAM and in both the gametophytic apical cell and sporophyte of moss, but not in Marchantia. Significantly, meiosis-specific genetic programs are expressed in bryophyte sporophytes, long before the onset of sporogenesis. Our data suggest that this upregulated accumulation of meiotic gene transcripts suppresses indeterminate cell fate in the Physcomitrella sporophyte, and overrides the observed accumulation of meristem patterning genes. A model for the evolution of indeterminate growth in the sporophytic generation through the concerted selection of ancestral meristem gene programs from gametophyte-dominant lineages is proposed. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  16. Introduction to variance estimation

    CERN Document Server

    Wolter, Kirk M

    2007-01-01

    We live in the information age. Statistical surveys are used every day to determine or evaluate public policy and to make important business decisions. Correct methods for computing the precision of the survey data and for making inferences to the target population are absolutely essential to sound decision making. Now in its second edition, Introduction to Variance Estimation has for more than twenty years provided the definitive account of the theory and methods for correct precision calculations and inference, including examples of modern, complex surveys in which the methods have been used successfully. The book provides instruction on the methods that are vital to data-driven decision making in business, government, and academe. It will appeal to survey statisticians and other scientists engaged in the planning and conduct of survey research, and to those analyzing survey data and charged with extracting compelling information from such data. It will appeal to graduate students and university faculty who...

  17. Autosomal dominant polycystic kidney disease in University Clinic of Nephrology and Haemodialysis of Cotonou: clinical and genetical findings.

    Science.gov (United States)

    Laleye, A; Awede, B; Agboton, B; Azonbakin, S; Biaou, O; Sagbo, G; Adjagba, M; Audrezet, M P; Ferec, C; Darboux, R

    2012-01-01

    Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary kidney disease, but poorly studied in Africa. Its frequency in the University Clinic of Nephrology and Hemodialysis of Cotonou during the ten last years was 7 cases per year with a hospital prevalence estimated at 18 per 1000. The mean age of patients was 47.2 years extending from 29 to 70 years. Males were predominant with a sex ratio of 1.13. Family history was found in 47% of patients. The most common manifestations were lumbar pain (62%), high blood pressure (59%) urinary tract infections (53%), hematuria (46%), and abdominal masses (43%). Hepatic cysts were the most extra renal manifestations, found in 34% of cases. Renal failure was observed in 72% of patients of our series, six of them were under dialysis. Direct sequencing of polycystin 1 gene enabled us to identify some new mutations: 4 nonsense mutations (p.Q2824X exon 23, p.Q1651X exon 15, p.W1666X exon 15, p.R966W exon 12), a duplication (c_1761.1745 dup exon 9), a deletion (c.9397 + 1_9397 + 8del intron 26) and a deletion-insertion (c.7290_7291delins CTGCA exon 18).

  18. Genetic forms of nephrogenic diabetes insipidus (NDI): Vasopressin receptor defect (X-linked) and aquaporin defect (autosomal recessive and dominant).

    Science.gov (United States)

    Bichet, Daniel G; Bockenhauer, Detlef

    2016-03-01

    Nephrogenic diabetes insipidus (NDI), which can be inherited or acquired, is characterized by an inability to concentrate urine despite normal or elevated plasma concentrations of the antidiuretic hormone, arginine vasopressin (AVP). Polyuria with hyposthenuria and polydipsia are the cardinal clinical manifestations of the disease. About 90% of patients with congenital NDI are males with X-linked NDI who have mutations in the vasopressin V2 receptor (AVPR2) gene encoding the vasopressin V2 receptor. In less than 10% of the families studied, congenital NDI has an autosomal recessive or autosomal dominant mode of inheritance with mutations in the aquaporin-2 (AQP2) gene. When studied in vitro, most AVPR2 and AQP2 mutations lead to proteins trapped in the endoplasmic reticulum and are unable to reach the plasma membrane. Prior knowledge of AVPR2 or AQP2 mutations in NDI families and perinatal mutation testing is of direct clinical value and can avert the physical and mental retardation associated with repeated episodes of dehydration.

  19. A healthy delivery of twins by assisted reproduction followed by preimplantation genetic screening in a woman with X-linked dominant incontinentia pigmenti.

    Science.gov (United States)

    Kim, Myung Joo; Lyu, Sang Woo; Seok, Hyun Ha; Park, Ji Eun; Shim, Sung Han; Yoon, Tae Ki

    2014-12-01

    The purpose of this study is to report a successful twin pregnancy and delivery in a female patient with X-linked dominant incontinentia pigmenti (IP) who underwent assisted reproductive technology followed by preimplantation genetic screening (PGS). A 29-year-old female with IP had a previous history of recurrent spontaneous abortion. A molecular analysis revealed the patient had a de novo mutation, 1308_1309insCCCCTTG(p.Ala438ProfsTer26), in the inhibitor of the kappa B kinase gamma gene located in the Xq28 region. IVF/ICSI and PGS was performed, in which male embryos were sexed using array-based comparative genomic hybridization (aCGH). After IVF/ICSI and PGS using aCGH on seven embryos, two euploid male blastocysts were transferred with a 50% probability of a viable male pregnancy. The dizygotic twin pregnancy was confirmed and the amniocentesis results of each twin were normal with regard to the mutation found in the mother. The patient delivered healthy twin babies during the 37th week of gestation. This case shows the beneficial role of PGS in achieving a successful pregnancy through euploid male embryo gender selection in a woman with X-linked dominant IP with a history of multiple male miscarriages.

  20. Variance decomposition of apolipoproteins and lipids in Danish twins

    DEFF Research Database (Denmark)

    Fenger, Mogens; Schousboe, Karoline; Sørensen, Thorkild I A

    2007-01-01

    OBJECTIVE: Twin studies are used extensively to decompose the variance of a trait, mainly to estimate the heritability of the trait. A second purpose of such studies is to estimate to what extent the non-genetic variance is shared or specific to individuals. To a lesser extent the twin studies have...... been used in bivariate or multivariate analysis to elucidate common genetic factors to two or more traits. METHODS AND RESULTS: In the present study the variances of traits related to lipid metabolism is decomposed in a relatively large Danish twin population, including bivariate analysis to detect...

  1. Fixed effects analysis of variance

    CERN Document Server

    Fisher, Lloyd; Birnbaum, Z W; Lukacs, E

    1978-01-01

    Fixed Effects Analysis of Variance covers the mathematical theory of the fixed effects analysis of variance. The book discusses the theoretical ideas and some applications of the analysis of variance. The text then describes topics such as the t-test; two-sample t-test; the k-sample comparison of means (one-way analysis of variance); the balanced two-way factorial design without interaction; estimation and factorial designs; and the Latin square. Confidence sets, simultaneous confidence intervals, and multiple comparisons; orthogonal and nonorthologonal designs; and multiple regression analysi

  2. Multi-objective parametric optimization of powder mixed electro-discharge machining using response surface methodology and non-dominated sorting genetic algorithm

    Indian Academy of Sciences (India)

    Soumyakant Padhee; Niharranjan Nayak; S K Panda; P R Dhal; S S Mahapatra

    2012-04-01

    Powder mixed electro-discharge machining (EDM) is being widely used in modern metal working industry for producing complex cavities in dies and moulds which are otherwise difficult to create by conventional machining route. It has been experimentally demonstrated that the presence of suspended particle in dielectric fluid significantly increases the surface finish and machining efficiency of EDM process. Concentration of powder (silicon) in the dielectric fluid, pulse on time, duty cycle, and peak current are taken as independent variables on which the machining performance was analysed in terms of material removal rate (MRR) and surface roughness (SR). Experiments have been conducted on an EZNC fuzzy logic Die Sinking EDM machine manufactured by Electronica Machine Tools Ltd. India. A copper electrode having diameter of 25 mm is used to cut EN 31 steel for one hour in each trial. Response surface methodology (RSM) is adopted to study the effect of independent variables on responses and develop predictive models. It is desired to obtain optimal parameter setting that aims at decreasing surface roughness along with larger material removal rate. Since the responses are conflicting in nature, it is difficult to obtain a single combination of cutting parameters satisfying both the objectives in any one solution. Therefore, it is essential to explore the optimization landscape to generate the set of dominant solutions. Non-sorted genetic algorithm (NSGA) has been adopted to optimize the responses such that a set of mutually dominant solutions are found over a wide range of machining parameters.

  3. Realized Variance and Market Microstructure Noise

    DEFF Research Database (Denmark)

    Hansen, Peter R.; Lunde, Asger

    2006-01-01

    We study market microstructure noise in high-frequency data and analyze its implications for the realized variance (RV) under a general specification for the noise. We show that kernel-based estimators can unearth important characteristics of market microstructure noise and that a simple kernel......-based estimator dominates the RV for the estimation of integrated variance (IV). An empirical analysis of the Dow Jones Industrial Average stocks reveals that market microstructure noise its time-dependent and correlated with increments in the efficient price. This has important implications for volatility...... estimation based on high-frequency data. Finally, we apply cointegration techniques to decompose transaction prices and bid-ask quotes into an estimate of the efficient price and noise. This framework enables us to study the dynamic effects on transaction prices and quotes caused by changes in the efficient...

  4. Realized Variance and Market Microstructure Noise

    DEFF Research Database (Denmark)

    Hansen, Peter R.; Lunde, Asger

    2006-01-01

    We study market microstructure noise in high-frequency data and analyze its implications for the realized variance (RV) under a general specification for the noise. We show that kernel-based estimators can unearth important characteristics of market microstructure noise and that a simple kernel......-based estimator dominates the RV for the estimation of integrated variance (IV). An empirical analysis of the Dow Jones Industrial Average stocks reveals that market microstructure noise its time-dependent and correlated with increments in the efficient price. This has important implications for volatility...... estimation based on high-frequency data. Finally, we apply cointegration techniques to decompose transaction prices and bid-ask quotes into an estimate of the efficient price and noise. This framework enables us to study the dynamic effects on transaction prices and quotes caused by changes in the efficient...

  5. Statistical inference on variance components

    NARCIS (Netherlands)

    Verdooren, L.R.

    1988-01-01

    In several sciences but especially in animal and plant breeding, the general mixed model with fixed and random effects plays a great role. Statistical inference on variance components means tests of hypotheses about variance components, constructing confidence intervals for them, estimating them,

  6. A study of heterogeneity of environmental variance for slaughter weight in pigs

    DEFF Research Database (Denmark)

    Ibánez-Escriche, N; Varona, L; Sorensen, D

    2008-01-01

    variance. The study reveals the presence of genetic variation at the level of the mean and the variance, but an absence of correlation, or a small negative correlation, between both types of additive genetic effects. In addition, we show that both, the additive genetic effects on the mean and those...

  7. Localization of a gene (CMT2A) for autosomal dominant Charcot-Marie-Tooth disease type 2 to chromosome 1p and evidence of genetic heterogeneity

    Energy Technology Data Exchange (ETDEWEB)

    Othmane, K.B.; Loprest, L.J.; Wilkinson, K.M. (Duke Univ. Medical Center, Durham, NC (United States)); Middleton, L.T. (Cyprus Institute of Neurology and Genetics, Nicosia (Cyprus)) (and others)

    1993-08-01

    Charcot-Marie-Tooth (CMT) disease type 2 (CMT2) is an inherited peripheral neuropathy characterized by variable age of onset and normal or slightly diminished nerve conduction velocity. CMT2 is pathologically and genetically distinct from CMT type 1 (CMT1). While CMT1 has been shown to be genetically heterogeneous, no chromosomal localization has been established for CMT2. The authors have performed pedigree linkage analysis in six large autosomal dominant CMT2 families and have demonstrated linkage and heterogeneity to a series of microsatellites (D1S160, D1S170, D1S244, D1S228 and D1S199) in the distal region of the short arm of chromosome 1. Significant evidence for heterogeneity was found using admixture analyses and the two-point lod scores. Admixture analyses using the multipoint results for the markers D1S244, D1S228, and D1S199 supported the two-point findings. Three families, DUK662, DUK1241, and 1523 gave posterior probabilities of 1.0, 0.98, and 0.88 of being of the linked type. Multipoint analysis examining the [open quotes]linked[close quotes] families showed that the most favored location for the CMT2A gene is within the interval flanked by D1S244 and D1S228 (odds approximately 70:1 of lying within versus outside that interval). These findings suggest that the CMT2 phenotype is secondary to at least two different genes and demonstrate further heterogeneity in the CMT phenotype.

  8. Identifying source populations and genetic structure for savannah elephants in human-dominated landscapes and protected areas in the Kenya-Tanzania borderlands.

    Directory of Open Access Journals (Sweden)

    Marissa A Ahlering

    Full Text Available We investigated the genetic metapopulation structure of elephants across the trans Rift Valley region of Kenya and Tanzania, one of the remaining strongholds for savannah elephants (Loxodonata africana in East Africa, using microsatellite and mitochondrial DNA (mtDNA markers. We then examined this population structure to determine the source population for a recent colonization event of savannah elephants on community-owned land within the trans rift valley region. Four of the five sampled populations showed significant genetic differentiation (p<0.05 as measured with both mtDNA haplotypes and microsatellites. Only the samples from the adjacent Maasai Mara and Serengeti ecosystems showed no significant differentiation. A phylogenetic neighbour-joining tree constructed from mtDNA haplotypes detected four clades. Clade four corresponds to the F clade of previous mtDNA studies that reported to have originated in forest elephants (Loxodonta cyclotis but to also be present in some savannah elephant populations. The split between clade four and the other three clades corresponded strongly to the geographic distribution of mtDNA haplotypes across the rift valley in the study area. Clade four was the dominant clade detected on the west side of the rift valley with rare occurrences on the east side. Finally, the strong patterns of population differentiation clearly indicated that the recent colonists to the community-owned land in Kenya came from the west side of the rift valley. Our results indicate strong female philopatry within the isolated populations of the trans rift valley region, with gene flow primarily mediated via male movements. The recent colonization event from Maasai Mara or Serengeti suggests there is hope for maintaining connectivity and population viability outside formal protected areas in the region.

  9. Efeitos da Heterogeneidade de Variância Residual entre Grupos de Contemporâneos na Avaliação Genética de Bovinos de Corte Effects of Heterogeneity of Residual Variance among Contemporary Groups on Genetic Evaluation of Beef Cattle

    Directory of Open Access Journals (Sweden)

    Roberto Carvalheiro

    2002-07-01

    Full Text Available O objetivo deste estudo foi investigar, por meio de dados simulados, o efeito da heterogeneidade de variância residual entre grupos de contemporâneos (GC sobre as avaliações genéticas de bovinos de corte, e comparar o uso de uma avaliação genética ponderada (R¹Isigmae² em relação à avaliação que pressupõe homogeneidade de variância (R=Isigmae². A característica estudada foi ganho de peso pós-desmame corrigido para 345 dias, sendo esta simulada com variância fenotípica de 300 kg² e herdabilidade igual a 0,4. A estrutura de um conjunto real de dados foi utilizada para fornecer os GC e os pais referentes às observações de cada animal. Cinco níveis de heterogeneidade de variância residual foram considerados de forma que os componentes de variância fossem, na média, iguais aos da situação de homogeneidade de variância. Na medida em que níveis mais acentuados de heterogeneidade de variância residual foram considerados, os animais foram selecionados dos GC com maior variabilidade, especialmente com pressão de seleção intensa. Em relação à consistência de predição, os produtos e as vacas tiveram seus valores genéticos preditos mais afetados pela heterogeneidade de variância residual do que os touros. O fator de ponderação utilizado reduziu, mas não eliminou o efeito da heterogeneidade de variância. As avaliações genéticas ponderadas apresentaram resultados iguais ou superiores àqueles obtidos pelas avaliações que assumiram homogeneidade de variância. Mesmo quando não necessário, o uso de avaliações ponderadas produziu resultados não inferiores às avaliações que assumiram homogeneidade de variância.The objective of this study was to investigate, via simulated data, the effect of heterogeneity of residual variance among contemporary groups (CG on genetic evaluation of beef cattle, and to compare a weighted genetic evaluation procedure (R¹Isigmae² with one that assumes homogeneity of

  10. Utility functions predict variance and skewness risk preferences in monkeys.

    Science.gov (United States)

    Genest, Wilfried; Stauffer, William R; Schultz, Wolfram

    2016-07-26

    Utility is the fundamental variable thought to underlie economic choices. In particular, utility functions are believed to reflect preferences toward risk, a key decision variable in many real-life situations. To assess the validity of utility representations, it is therefore important to examine risk preferences. In turn, this approach requires formal definitions of risk. A standard approach is to focus on the variance of reward distributions (variance-risk). In this study, we also examined a form of risk related to the skewness of reward distributions (skewness-risk). Thus, we tested the extent to which empirically derived utility functions predicted preferences for variance-risk and skewness-risk in macaques. The expected utilities calculated for various symmetrical and skewed gambles served to define formally the direction of stochastic dominance between gambles. In direct choices, the animals' preferences followed both second-order (variance) and third-order (skewness) stochastic dominance. Specifically, for gambles with different variance but identical expected values (EVs), the monkeys preferred high-variance gambles at low EVs and low-variance gambles at high EVs; in gambles with different skewness but identical EVs and variances, the animals preferred positively over symmetrical and negatively skewed gambles in a strongly transitive fashion. Thus, the utility functions predicted the animals' preferences for variance-risk and skewness-risk. Using these well-defined forms of risk, this study shows that monkeys' choices conform to the internal reward valuations suggested by their utility functions. This result implies a representation of utility in monkeys that accounts for both variance-risk and skewness-risk preferences.

  11. Markov bridges, bisection and variance reduction

    DEFF Research Database (Denmark)

    Asmussen, Søren; Hobolth, Asger

    Time-continuous Markov jump processes is a popular modelling tool in disciplines ranging from computational finance and operations research to human genetics and genomics. The data is often sampled at discrete points in time, and it can be useful to simulate sample paths between the datapoints....... In this paper we firstly consider the problem of generating sample paths from a continuous-time Markov chain conditioned on the endpoints using a new algorithm based on the idea of bisection. Secondly we study the potential of the bisection algorithm for variance reduction. In particular, examples are presented...... where the methods of stratification, importance sampling and quasi Monte Carlo are investigated....

  12. The dominant Australian community-acquired methicillin-resistant Staphylococcus aureus clone ST93-IV [2B] is highly virulent and genetically distinct.

    Directory of Open Access Journals (Sweden)

    Kyra Y L Chua

    Full Text Available Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA USA300 has spread rapidly across North America, and CA-MRSA is also increasing in Australia. However, the dominant Australian CA-MRSA strain, ST93-IV [2B] appears distantly related to USA300 despite strikingly similar clinical and epidemiological profiles. Here, we compared the virulence of a recent Australian ST93 isolate (JKD6159 to other MRSA, including USA300, and found that JKD6159 was the most virulent in a mouse skin infection model. We fully sequenced the genome of JKD6159 and confirmed that JKD6159 is a distinct clone with 7616 single nucleotide polymorphisms (SNPs distinguishing this strain from all other S. aureus genomes. Despite its high virulence there were surprisingly few virulence determinants. However, genes encoding α-hemolysin, Panton-Valentine leukocidin (PVL and α-type phenol soluble modulins were present. Genome comparisons revealed 32 additional CDS in JKD6159 but none appeared to encode new virulence factors, suggesting that this clone's enhanced pathogenicity could lie within subtler genome changes, such as SNPs within regulatory genes. To investigate the role of accessory genome elements in CA-MRSA epidemiology, we next sequenced three additional Australian non-ST93 CA-MRSA strains and compared them with JKD6159, 19 completed S. aureus genomes and 59 additional S. aureus genomes for which unassembled genome sequence data was publicly available (82 genomes in total. These comparisons showed that despite its distinctive genotype, JKD6159 and other CA-MRSA clones (including USA300 share a conserved repertoire of three notable accessory elements (SSCmecIV, PVL prophage, and pMW2. This study demonstrates that the genetically distinct ST93 CA-MRSA from Australia is highly virulent. Our comparisons of geographically and genetically diverse CA-MRSA genomes suggest that apparent convergent evolution in CA-MRSA may be better explained by the rapid

  13. Comprehensive genetic screening of KCNQ4 in a large autosomal dominant nonsyndromic hearing loss cohort: genotype-phenotype correlations and a founder mutation.

    Directory of Open Access Journals (Sweden)

    Takehiko Naito

    Full Text Available The present study of KCNQ4 mutations was carried out to 1 determine the prevalence by unbiased population-based genetic screening, 2 clarify the mutation spectrum and genotype/phenotype correlations, and 3 summarize clinical characteristics. In addition, a review of the reported mutations was performed for better understanding of this deafness gene. The screening using 287 probands from unbiased Japanese autosomal dominant nonsyndromic hearing loss (ADNSHL families identified 19 families with 7 different disease causing mutations, indicating that the frequency is 6.62% (19/287. While the majority were private mutations, one particular recurrent mutation, c.211delC, was observed in 13 unrelated families. Haplotype analysis in the vicinity of c.211delC suggests existence of a common ancestor. The majority of the patients showed all frequency, but high-frequency predominant, sensorineural hearing loss. The present study adds a new typical audiogram configuration characterized by mid-frequency predominant hearing loss caused by the p.V230E mutation. A variant at the N-terminal site (c. 211delC showed typical ski-slope type audiogram configuration. Concerning clinical features, onset age was from 3 to 40 years old, and mostly in the teens, and hearing loss was gradually progressive. Progressive nature is a common feature of patients with KCNQ4 mutations regardless of the mutation type. In conclusion, KCNQ4 mutations are frequent among ADNSHL patients, and therefore screening of the gene and molecular confirmation of these mutations have become important in the diagnosis of these conditions.

  14. Genetics

    Science.gov (United States)

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  15. Modelling volatility by variance decomposition

    DEFF Research Database (Denmark)

    Amado, Cristina; Teräsvirta, Timo

    on the multiplicative decomposition of the variance is developed. It is heavily dependent on Lagrange multiplier type misspecification tests. Finite-sample properties of the strategy and tests are examined by simulation. An empirical application to daily stock returns and another one to daily exchange rate returns...... illustrate the functioning and properties of our modelling strategy in practice. The results show that the long memory type behaviour of the sample autocorrelation functions of the absolute returns can also be explained by deterministic changes in the unconditional variance....

  16. Revision: Variance Inflation in Regression

    Directory of Open Access Journals (Sweden)

    D. R. Jensen

    2013-01-01

    the intercept; and (iv variance deflation may occur, where ill-conditioned data yield smaller variances than their orthogonal surrogates. Conventional VIFs have all regressors linked, or none, often untenable in practice. Beyond these, our models enable the unlinking of regressors that can be unlinked, while preserving dependence among those intrinsically linked. Moreover, known collinearity indices are extended to encompass angles between subspaces of regressors. To reaccess ill-conditioned data, we consider case studies ranging from elementary examples to data from the literature.

  17. Genetic variance and breeding values for resistance to a wind-borne disease [Sphaerotheca macularis (Wallr. ex Fr.)] in strawberry (Fragaria x ananassa Duch.) estimated by exploring mixed and spatial models and pedigree information.

    Science.gov (United States)

    Davik, Jahn; Honne, Bjørn Ivar

    2005-07-01

    A mixed model approach was used to estimate variance components and heritabilities for resistance to powdery mildew, a wind-borne disease in strawberry. In order to improve precision in the statistical computations, spatial error control effects were included to account for systematic environmental variations in the large field trials. Pedigree information was included where feasible. Seedling families obtained from an incomplete 63-by-63 diallel cross were grown at six locations and scored subjectively for mildew attack three times during the growing season. The 63 parents included both European and American cultivars as well as advanced selections from various breeding programmes. A total of 298 full-sib families were realized, including 26 reciprocal families. No reciprocal differences were found. On a plot-mean basis, the broad-sense heritability was found to be intermediate, H(2) = 0.44-0.50, depending on whether the pedigree information was included in the model or not. The increase was mainly due to a substantial increase in the additive variance component. Likewise, the narrow-sense heritability increased from h(2) = 0.39 to h(2) = 0.45 when the pedigree information was included, while the ratio of the specific combining ability variance to the general combining ability variance fell from 13% to 10%. The predicted breeding values of the 63 parents demonstrate that important cultivars such as Elsanta and Korona are unlikely to produce progenies with a high degree of resistance. On the other hand, the Norwegian cultivar Solprins, the Canadian cultivar Kent and the Italian cultivar Patty appeared to give highly resistant progeny. At the full-sib level, the estimated disease scores ranged from 1.15 (Kent x Induka) to 4.19 (Cavendish x Avanta), revealing a huge range of variation for powdery mildew resistance available for selection.

  18. Heterogeneidade genética em atrofia óptica autossômica dominante Genetic heterogeneity in autosomal dominant optic atrophy

    Directory of Open Access Journals (Sweden)

    Juliana Maria Ferraz Sallum

    2002-08-01

    locus para esta doença.Purpose: Autosomal dominant optic atrophy is a hereditary optic neuropathy characterized by progressive visual loss in childhood, color vision anomalies, visual field defects and temporal pallor of the optic disc. This disease has been mapped to a 1.4 cM interval in chromosome 3q28-29 between markers D3S3669 and D3S3562. One family was mapped to chromosome 18q12.2-12.3. Linkage analysis in three families with autosomal dominant optic atrophy with polymorphic DNA markers for chromosome 3q28-29 and 18q12.2-12.3. Methods: 57 individuals from three families underwent ophthalmological examination. Genomic DNA was extracted from blood samples. Linkage analysis was performed between the disease and 11 polymorphic markers around 3q28-qter and 18q12.2-12.3. Polymerase chain reaction (PCR fragments sizes were identified in a scanner gel using a 373 DNA sequencer. These numbers were used as alleles for pedigree analysis. The lod scores were calculated using the MLINK program. Results: All three families presented optic atrophy with autosomal dominant pattern of inheritance, variable expression and high penetrance. Two families were linked to 3q28-29 markers. A maximal lod score of 3.56, at a recombination fraction of zero, was obtained using the marker D3S3669 in one family. The linkage area was defined in a 2 cM interval by haplotype analysis between markers D3S2418 and D3S1305, because patients III.4 and III.14 showed crossing-overs. The third family was not linked to 3q28-29 neither to 18q12.2-12.3. Conclusions: There is genetic heterogeneity in autosomal dominant optic atrophy, because the third family did not map to any known locus. And a third locus for this disease may exist.

  19. Evolution of Robustness and Plasticity under Environmental Fluctuation: Formulation in terms of Phenotypic Variances

    OpenAIRE

    Kaneko, Kunihiko

    2013-01-01

    The characterization of plasticity, robustness, and evolvability, an important issue in biology, is studied in terms of phenotypic fluctuations. By numerically evolving gene regulatory networks, the proportionality between the phenotypic variances of epigenetic and genetic origins is confirmed. The former is given by the variance of the phenotypic fluctuation due to noise in the developmental process; and the latter, by the variance of the phenotypic fluctuation due to genetic mutation. The r...

  20. Analysis of variance: Comfortless questions

    OpenAIRE

    L.V. Nedorezov

    2017-01-01

    In this paper the simplest variant of analysis of variance is under consideration. Three examples from textbooks by Lakin (1990) and Rokitsky (1973) were re-considered. It was obtained that traditional one-way ANOVA and Kruskal - Wallis criterion can lead to unreal results about factor's influence on value of characteristics. Alternative way to solution of the same problem is under consideration too.

  1. Analysis of Variance: Variably Complex

    Science.gov (United States)

    Drummond, Gordon B.; Vowler, Sarah L.

    2012-01-01

    These authors have previously described how to use the "t" test to compare two groups. In this article, they describe the use of a different test, analysis of variance (ANOVA) to compare more than two groups. ANOVA is a test of group differences: do at least two of the means differ from each other? ANOVA assumes (1) normal distribution of…

  2. Male dominance linked to size and age, but not to 'good genes' in brown trout (Salmo trutta

    Directory of Open Access Journals (Sweden)

    Evanno Guillaume

    2007-11-01

    Full Text Available Abstract Background Males that are successful in intra-sexual competition are often assumed to be of superior quality. In the mating system of most salmonid species, intensive dominance fights are common and the winners monopolise most mates and sire most offspring. We drew a random sample of mature male brown trout (Salmo trutta from two wild populations and determined their dominance hierarchy or traits linked to dominance. The fish were then stripped and their sperm was used for in vitro fertilisations in two full-factorial breeding designs. We recorded embryo viability until hatching in both experiments, and juvenile survival during 20 months after release into a natural streamlet in the second experiment. Since offspring of brown trout get only genes from their fathers, we used offspring survival as a quality measure to test (i whether males differ in their genetic quality, and if so, (ii whether dominance or traits linked to dominance reveal 'good genes'. Results We found significant additive genetic variance on embryo survival, i.e. males differed in their genetic quality. Older, heavier and larger males were more successful in intra-sexual selection. However, neither dominance nor dominance indicators like body length, weight or age were significantly linked to genetic quality measured as embryo or juvenile survival. Conclusion We found no evidence that females can improve their offspring's genetic viability by mating with large and dominant males. If there still were advantages of mating with dominant males, they may be linked to non-genetic benefits or to genetic advantages that are context dependent and therefore possibly not revealed under our experimental conditions – even if we found significant additive genetic variation for embryo viability under such conditions.

  3. Additivity dominance

    Directory of Open Access Journals (Sweden)

    Paul Rozin

    2009-10-01

    Full Text Available Judgments of naturalness of foods tend to be more influenced by the process history of a food, rather than its actual constituents. Two types of processing of a ``natural'' food are to add something or to remove something. We report in this study, based on a large random sample of individuals from six countries (France, Germany, Italy, Switzerland, UK and USA that additives are considered defining features of what makes a food not natural, whereas ``subtractives'' are almost never mentioned. In support of this, skim milk (with major subtraction of fat is rated as more natural than whole milk with a small amount of natural vitamin D added. It is also noted that ``additives'' is a common word, with a synonym reported by a native speaker in 17 of 18 languages, whereas ``subtractive'' is lexicalized in only 1 of the 18 languages. We consider reasons for additivity dominance, relating it to omission bias, feature positive bias, and notions of purity.

  4. Expected Stock Returns and Variance Risk Premia

    DEFF Research Database (Denmark)

    Bollerslev, Tim; Tauchen, George; Zhou, Hao

    Motivated by the implications from a stylized self-contained general equilibrium model incorporating the effects of time-varying economic uncertainty, we show that the difference between implied and realized variation, or the variance risk premium, is able to explain a non-trivial fraction...... of the time series variation in post 1990 aggregate stock market returns, with high (low) premia predicting high (low) future returns. Our empirical results depend crucially on the use of "model-free," as opposed to Black- Scholes, options implied volatilities, along with accurate realized variation measures...... constructed from high-frequency intraday, as opposed to daily, data. The magnitude of the predictability is particularly strong at the intermediate quarterly return horizon, where it dominates that afforded by other popular predictor variables, like the P/E ratio, the default spread, and the consumption...

  5. Functional analysis of variance for association studies.

    Directory of Open Access Journals (Sweden)

    Olga A Vsevolozhskaya

    Full Text Available While progress has been made in identifying common genetic variants associated with human diseases, for most of common complex diseases, the identified genetic variants only account for a small proportion of heritability. Challenges remain in finding additional unknown genetic variants predisposing to complex diseases. With the advance in next-generation sequencing technologies, sequencing studies have become commonplace in genetic research. The ongoing exome-sequencing and whole-genome-sequencing studies generate a massive amount of sequencing variants and allow researchers to comprehensively investigate their role in human diseases. The discovery of new disease-associated variants can be enhanced by utilizing powerful and computationally efficient statistical methods. In this paper, we propose a functional analysis of variance (FANOVA method for testing an association of sequence variants in a genomic region with a qualitative trait. The FANOVA has a number of advantages: (1 it tests for a joint effect of gene variants, including both common and rare; (2 it fully utilizes linkage disequilibrium and genetic position information; and (3 allows for either protective or risk-increasing causal variants. Through simulations, we show that FANOVA outperform two popularly used methods - SKAT and a previously proposed method based on functional linear models (FLM, - especially if a sample size of a study is small and/or sequence variants have low to moderate effects. We conduct an empirical study by applying three methods (FANOVA, SKAT and FLM to sequencing data from Dallas Heart Study. While SKAT and FLM respectively detected ANGPTL 4 and ANGPTL 3 associated with obesity, FANOVA was able to identify both genes associated with obesity.

  6. Variance based OFDM frame synchronization

    Directory of Open Access Journals (Sweden)

    Z. Fedra

    2012-04-01

    Full Text Available The paper deals with a new frame synchronization scheme for OFDM systems and calculates the complexity of this scheme. The scheme is based on the computing of the detection window variance. The variance is computed in two delayed times, so a modified Early-Late loop is used for the frame position detection. The proposed algorithm deals with different variants of OFDM parameters including guard interval, cyclic prefix, and has good properties regarding the choice of the algorithm's parameters since the parameters may be chosen within a wide range without having a high influence on system performance. The verification of the proposed algorithm functionality has been performed on a development environment using universal software radio peripheral (USRP hardware.

  7. Variance decomposition in stochastic simulators

    KAUST Repository

    Le Maître, O. P.

    2015-06-28

    This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models.

  8. Variance decomposition in stochastic simulators.

    Science.gov (United States)

    Le Maître, O P; Knio, O M; Moraes, A

    2015-06-28

    This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models.

  9. Variance decomposition in stochastic simulators

    Science.gov (United States)

    Le Maître, O. P.; Knio, O. M.; Moraes, A.

    2015-06-01

    This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models.

  10. Estimativas de variância genética aditiva em populações selecionadas e não-selecionadas via simulação Monte Carlo utilizando o software R Additive genetic variance estimates in selected and unselected populations via Monte Carlo simulation using the R software

    Directory of Open Access Journals (Sweden)

    Ricardo Luis dos Reis

    2009-02-01

    Full Text Available Para disponibilizar um sistema de fornecimento de dados que objetivando-se subsidiar pesquisas de Melhoramento Genético Animal direcionadas à comparação de metodologias de avaliação genética, foi avaliado o comportamento da variância genética aditiva de populações selecionadas e não selecionadas, por seis gerações sucessivas, via simulação Monte Carlo. Por meio de um modelo genético aditivo, foram simuladas populações de 40 animais (20 machos e 20 fêmeas, sob seleção e acasalamento aleatório. Da geração zero até a quinta geração notou-se na população selecionada uma redução de 44,4% na variância genética aditiva, devido a um aumento de 11,58% no coeficiente de endogamia. Na população não selecionada a redução da variância genética aditiva foi menor (27,46% em relação à população selecionada, também devido a aumento de 10,26% no coeficiente de endogamia.The additive genetic variance in selected and unselected populations was evaluated in six successive generations via Monte Carlo simulation. The aim was to build a data system to help researches compare genetic evaluation methodologies in Animal Breeding. By means of an additive genetic model, populations of 40 individuals (20 males and 20 females were simulated, under selected and random mating system. From the generation zero until the fifth generation, the selected population showed reduction of 44.4% in additive genetic variance due to an increase of 11.58% in inbreeding coefficient. In the unselected population the reduction in additive genetic variance was lower (27.46% in relation to the selected population, due to the increasing of 10.26% in inbreeding coefficient.

  11. Understanding the influence of watershed storage caused by human interferences on ET variance

    Science.gov (United States)

    Zeng, R.; Cai, X.

    2014-12-01

    Understanding the temporal variance of evapotranspiration (ET) at the watershed scale remains a challenging task, because it is affected by complex climate conditions, soil properties, vegetation, groundwater and human activities. In a changing environment with extensive and intensive human interferences, understanding ET variance and its factors is important for sustainable water resources management. This study presents an analysis of the effect of storage change caused by human activities on ET variance Irrigation usually filters ET variance through the use of surface and groundwater; however, over-amount irrigation may cause the depletion of watershed storage, which changes the coincidence of water availability and energy supply for ET. This study develops a framework by incorporating the water balance and the Budyko Hypothesis. It decomposes the ET variance to the variances of precipitation, potential ET, catchment storage change, and their covariances. The contributions of ET variance from the various components are scaled by some weighting functions, expressed as long-term climate conditions and catchment properties. ET variance is assessed by records from 32 major river basins across the world. It is found that ET variance is dominated by precipitation variance under hot-dry condition and by evaporative demand variance under cool-wet condition; while the coincidence of water and energy supply controls ET variance under moderate climate condition. Watershed storage change plays an increasing important role in determining ET variance with relatively shorter time scale. By incorporating storage change caused by human interferences, this framework corrects the over-estimation of ET variance in hot-dry climate and under-estimation of ET variance in cool-wet climate. Furthermore, classification of dominant factors on ET variance shows similar patterns as geographic zonation.

  12. µ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype ... frequencies

    Science.gov (United States)

    Genetic marker effects and interactions are estimated with poor precision when minor marker allele frequencies are low. An Angus population was subjected to marker assisted selection for multiple years to increase divergent haplotype and minor marker allele frequencies to 1) estimate effect size an...

  13. Familial resemblance of borderline personality disorder features: genetic or cultural transmission?

    Directory of Open Access Journals (Sweden)

    Marijn A Distel

    Full Text Available Borderline personality disorder is a severe personality disorder for which genetic research has been limited to family studies and classical twin studies. These studies indicate that genetic effects explain 35 to 45% of the variance in borderline personality disorder and borderline personality features. However, effects of non-additive (dominance genetic factors, non-random mating and cultural transmission have generally not been explored. In the present study an extended twin-family design was applied to self-report data of twins (N = 5,017 and their siblings (N = 1,266, parents (N = 3,064 and spouses (N = 939 from 4,015 families, to estimate the effects of additive and non-additive genetic and environmental factors, cultural transmission and non-random mating on individual differences in borderline personality features. Results showed that resemblance among biological relatives could completely be attributed to genetic effects. Variation in borderline personality features was explained by additive genetic (21%; 95% CI 17-26% and dominant genetic (24%; 95% CI 17-31% factors. Environmental influences (55%; 95% CI 51-60% explained the remaining variance. Significant resemblance between spouses was observed, which was best explained by phenotypic assortative mating, but it had only a small effect on the genetic variance (1% of the total variance. There was no effect of cultural transmission from parents to offspring.

  14. Variance-based uncertainty relations

    CERN Document Server

    Huang, Yichen

    2010-01-01

    It is hard to overestimate the fundamental importance of uncertainty relations in quantum mechanics. In this work, I propose state-independent variance-based uncertainty relations for arbitrary observables in both finite and infinite dimensional spaces. We recover the Heisenberg uncertainty principle as a special case. By studying examples, we find that the lower bounds provided by our new uncertainty relations are optimal or near-optimal. I illustrate the uses of our new uncertainty relations by showing that they eliminate one common obstacle in a sequence of well-known works in entanglement detection, and thus make these works much easier to access in applications.

  15. A genetic suppressor of two dominant temperature-sensitive lethal proteasome mutants of Drosophila melanogaster is itself a mutated proteasome subunit gene.

    Science.gov (United States)

    Neuburger, Peter J; Saville, Kenneth J; Zeng, Jue; Smyth, Kerrie-Ann; Belote, John M

    2006-07-01

    Two dominant temperature-sensitive (DTS) lethal mutants of Drosophila melanogaster are Pros26(1) and Prosbeta2(1), previously known as DTS5 and DTS7. Heterozygotes for either mutant die as pupae when raised at 29 degrees , but are normally viable and fertile at 25 degrees . Previous studies have identified these as missense mutations in the genes encoding the beta6 and beta2 subunits of the 20S proteasome, respectively. In an effort to isolate additional proteasome-related mutants a screen for dominant suppressors of Pros26(1) was carried out, resulting in the identification of Pros25(SuDTS) [originally called Su(DTS)], a missense mutation in the gene encoding the 20S proteasome alpha2 subunit. Pros25(SuDTS) acts in a dominant manner to rescue both Pros26(1) and Prosbeta2(1) from their DTS lethal phenotypes. Using an in vivo protein degradation assay it was shown that this suppression occurs by counteracting the dominant-negative effect of the DTS mutant on proteasome activity. Pros25(SuDTS) is a recessive polyphasic lethal at ambient temperatures. The effects of these mutants on larval neuroblast mitosis were also examined. While Prosbeta2(1) shows a modest increase in the number of defective mitotic figures, there were no defects seen with the other two mutants, other than slightly reduced mitotic indexes.

  16. The evolution and consequences of sex-specific reproductive variance.

    Science.gov (United States)

    Mullon, Charles; Reuter, Max; Lehmann, Laurent

    2014-01-01

    Natural selection favors alleles that increase the number of offspring produced by their carriers. But in a world that is inherently uncertain within generations, selection also favors alleles that reduce the variance in the number of offspring produced. If previous studies have established this principle, they have largely ignored fundamental aspects of sexual reproduction and therefore how selection on sex-specific reproductive variance operates. To study the evolution and consequences of sex-specific reproductive variance, we present a population-genetic model of phenotypic evolution in a dioecious population that incorporates previously neglected components of reproductive variance. First, we derive the probability of fixation for mutations that affect male and/or female reproductive phenotypes under sex-specific selection. We find that even in the simplest scenarios, the direction of selection is altered when reproductive variance is taken into account. In particular, previously unaccounted for covariances between the reproductive outputs of different individuals are expected to play a significant role in determining the direction of selection. Then, the probability of fixation is used to develop a stochastic model of joint male and female phenotypic evolution. We find that sex-specific reproductive variance can be responsible for changes in the course of long-term evolution. Finally, the model is applied to an example of parental-care evolution. Overall, our model allows for the evolutionary analysis of social traits in finite and dioecious populations, where interactions can occur within and between sexes under a realistic scenario of reproduction.

  17. Neutrino mass without cosmic variance

    CERN Document Server

    LoVerde, Marilena

    2016-01-01

    Measuring the absolute scale of the neutrino masses is one of the most exciting opportunities available with near-term cosmological datasets. Two quantities that are sensitive to neutrino mass, scale-dependent halo bias $b(k)$ and the linear growth parameter $f(k)$ inferred from redshift-space distortions, can be measured without cosmic variance. Unlike the amplitude of the matter power spectrum, which always has a finite error, the error on $b(k)$ and $f(k)$ continues to decrease as the number density of tracers increases. This paper presents forecasts for statistics of galaxy and lensing fields that are sensitive to neutrino mass via $b(k)$ and $f(k)$. The constraints on neutrino mass from the auto- and cross-power spectra of spectroscopic and photometric galaxy samples are weakened by scale-dependent bias unless a very high density of tracers is available. In the high density limit, using multiple tracers allows cosmic-variance to be beaten and the forecasted errors on neutrino mass shrink dramatically. In...

  18. The ethics of contacting family members of a subject in a genetic research study to return results for an autosomal dominant syndrome.

    Science.gov (United States)

    Taylor, Holly A; Wilfond, Benjamin S

    2013-01-01

    This case explores the ethical landscape around recontacting a subject's relatives to return genetic research results when the informed consent form signed by the original cohort of subjects is silent on whether investigators may share new information with the research subject's family. As a result of rapid advances in genetic technology, methods to identify genetic markers can mature during the life course of a study. In this case, the investigators identified the genetic mutation responsible for the disorder after a number of their original subjects had died. The researchers now have the ability to inform relatives of the subject about their risk of developing the same disease. Mark Rothstein, JD, from the University of Louisville School of Medicine, provides an overview of the medical/scientific, legal, and ethical issues underlying this case. Lauren Milner, PhD, and colleagues at Stanford University explore how the relationship between researcher and subject affect this debate. Seema Shah, JD, and colleagues at the National Institutes of Health and University of California, Los Angeles (UCLA) discuss whether and how requirements of the duty to warn are applicable in this case.

  19. Heritable environmental variance causes nonlinear relationships between traits: application to birth weight and stillbirth of pigs.

    Science.gov (United States)

    Mulder, Herman A; Hill, William G; Knol, Egbert F

    2015-04-01

    There is recent evidence from laboratory experiments and analysis of livestock populations that not only the phenotype itself, but also its environmental variance, is under genetic control. Little is known about the relationships between the environmental variance of one trait and mean levels of other traits, however. A genetic covariance between these is expected to lead to nonlinearity between them, for example between birth weight and survival of piglets, where animals of extreme weights have lower survival. The objectives were to derive this nonlinear relationship analytically using multiple regression and apply it to data on piglet birth weight and survival. This study provides a framework to study such nonlinear relationships caused by genetic covariance of environmental variance of one trait and the mean of the other. It is shown that positions of phenotypic and genetic optima may differ and that genetic relationships are likely to be more curvilinear than phenotypic relationships, dependent mainly on the environmental correlation between these traits. Genetic correlations may change if the population means change relative to the optimal phenotypes. Data of piglet birth weight and survival show that the presence of nonlinearity can be partly explained by the genetic covariance between environmental variance of birth weight and survival. The framework developed can be used to assess effects of artificial and natural selection on means and variances of traits and the statistical method presented can be used to estimate trade-offs between environmental variance of one trait and mean levels of others. Copyright © 2015 by the Genetics Society of America.

  20. The genetics of hybrid male sterility between the allopatric species pair Drosophila persimilis and D. pseudoobscura bogotana: dominant sterility alleles in collinear autosomal regions.

    Science.gov (United States)

    Chang, Audrey S; Noor, Mohamed A F

    2007-05-01

    F(1) hybrid male sterility is thought to result from interactions between loci on the X chromosome and dominant-acting loci on the autosomes. While X-linked loci that contribute to hybrid male sterility have been precisely localized in many animal taxa, their dominant autosomal interactors have been more difficult to localize precisely and/or have been shown to be of relatively smaller effect. Here, we identified and mapped at least four dominant autosomal factors contributing to hybrid male sterility in the allopatric species pair Drosophila persimilis and D. pseudoobscura bogotana. Using these results, we tested predictions of reduced recombination models of speciation. Consistent with these models, three of the four QTL associated with hybrid male sterility occur in collinear (uninverted) regions of these genomes. Furthermore, these QTL do not contribute significantly to hybrid male sterility in crosses between the sympatric species D. persimilis and D. pseudoobscura pseudoobscura. The autosomal loci identified in this study provide the basis for introgression mapping and, ultimately, for molecular cloning of interacting genes that contribute to F(1) hybrid sterility.

  1. Domination, Eternal Domination, and Clique Covering

    Directory of Open Access Journals (Sweden)

    Klostermeyer William F.

    2015-05-01

    Full Text Available Eternal and m-eternal domination are concerned with using mobile guards to protect a graph against infinite sequences of attacks at vertices. Eternal domination allows one guard to move per attack, whereas more than one guard may move per attack in the m-eternal domination model. Inequality chains consisting of the domination, eternal domination, m-eternal domination, independence, and clique covering numbers of graph are explored in this paper.

  2. Warped functional analysis of variance.

    Science.gov (United States)

    Gervini, Daniel; Carter, Patrick A

    2014-09-01

    This article presents an Analysis of Variance model for functional data that explicitly incorporates phase variability through a time-warping component, allowing for a unified approach to estimation and inference in presence of amplitude and time variability. The focus is on single-random-factor models but the approach can be easily generalized to more complex ANOVA models. The behavior of the estimators is studied by simulation, and an application to the analysis of growth curves of flour beetles is presented. Although the model assumes a smooth latent process behind the observed trajectories, smootheness of the observed data is not required; the method can be applied to irregular time grids, which are common in longitudinal studies.

  3. Population Genetic Structure, Abundance, and Health Status of Two Dominant Benthic Species in the Saba Bank National Park, Caribbean Netherlands: Montastraea cavernosa and Xestospongia muta.

    Directory of Open Access Journals (Sweden)

    Didier M de Bakker

    Full Text Available Saba Bank, a submerged atoll in the Caribbean Sea with an area of 2,200 km2, has attained international conservation status due to the rich diversity of species that reside on the bank. In order to assess the role of Saba Bank as a potential reservoir of diversity for the surrounding reefs, we examined the population genetic structure, abundance and health status of two prominent benthic species, the coral Montastraea cavernosa and the sponge Xestospongia muta. Sequence data were collected from 34 colonies of M. cavernosa (nDNA ITS1-5.8S-ITS2; 892 bp and 68 X. muta sponges (mtDNA I3-M11 partition of COI; 544 bp on Saba Bank and around Saba Island, and compared with published data across the wider Caribbean. Our data indicate that there is genetic connectivity between populations on Saba Bank and the nearby Saba Island as well as multiple locations in the wider Caribbean, ranging in distance from 100s-1000s km. The genetic diversity of Saba Bank populations of M. cavernosa (π = 0.055 and X. muta (π = 0.0010 was comparable to those in other regions in the western Atlantic. Densities and health status were determined along 11 transects of 50 m2 along the south-eastern rim of Saba Bank. The densities of M. cavernosa (0.27 ind. m-2, 95% CI: 0.12-0.52 were average, while the densities of X. muta (0.09 ind. m-2, 95% CI: 0.02-0.32 were generally higher with respect to other Caribbean locations. No disease or bleaching was present in any of the specimens of the coral M. cavernosa, however, we did observe partial tissue loss (77.9% of samples as well as overgrowth (48.1%, predominantly by cyanobacteria. In contrast, the majority of observed X. muta (83.5% showed signs of presumed bleaching. The combined results of apparent gene flow among populations on Saba Bank and surrounding reefs, the high abundance and unique genetic diversity, indicate that Saba Bank could function as an important buffer for the region. Either as a natural source of larvae to

  4. Variance components for body weight in Japanese quails (Coturnix japonica

    Directory of Open Access Journals (Sweden)

    RO Resende

    2005-03-01

    Full Text Available The objective of this study was to estimate the variance components for body weight in Japanese quails by Bayesian procedures. The body weight at hatch (BWH and at 7 (BW07, 14 (BW14, 21 (BW21 and 28 days of age (BW28 of 3,520 quails was recorded from August 2001 to June 2002. A multiple-trait animal model with additive genetic, maternal environment and residual effects was implemented by Gibbs sampling methodology. A single Gibbs sampling with 80,000 rounds was generated by the program MTGSAM (Multiple Trait Gibbs Sampling in Animal Model. Normal and inverted Wishart distributions were used as prior distributions for the random effects and the variance components, respectively. Variance components were estimated based on the 500 samples that were left after elimination of 30,000 rounds in the burn-in period and 100 rounds of each thinning interval. The posterior means of additive genetic variance components were 0.15; 4.18; 14.62; 27.18 and 32.68; the posterior means of maternal environment variance components were 0.23; 1.29; 2.76; 4.12 and 5.16; and the posterior means of residual variance components were 0.084; 6.43; 22.66; 31.21 and 30.85, at hatch, 7, 14, 21 and 28 days old, respectively. The posterior means of heritability were 0.33; 0.35; 0.36; 0.43 and 0.47 at hatch, 7, 14, 21 and 28 days old, respectively. These results indicate that heritability increased with age. On the other hand, after hatch there was a marked reduction in the maternal environment variance proportion of the phenotypic variance, whose estimates were 0.50; 0.11; 0.07; 0.07 and 0.08 for BWH, BW07, BW14, BW21 and BW28, respectively. The genetic correlation between weights at different ages was high, except for those estimates between BWH and weight at other ages. Changes in body weight of quails can be efficiently achieved by selection.

  5. Speed Variance and Its Influence on Accidents.

    Science.gov (United States)

    Garber, Nicholas J.; Gadirau, Ravi

    A study was conducted to investigate the traffic engineering factors that influence speed variance and to determine to what extent speed variance affects accident rates. Detailed analyses were carried out to relate speed variance with posted speed limit, design speeds, and other traffic variables. The major factor identified was the difference…

  6. Variance optimal stopping for geometric Levy processes

    DEFF Research Database (Denmark)

    Gad, Kamille Sofie Tågholt; Pedersen, Jesper Lund

    2015-01-01

    The main result of this paper is the solution to the optimal stopping problem of maximizing the variance of a geometric Lévy process. We call this problem the variance problem. We show that, for some geometric Lévy processes, we achieve higher variances by allowing randomized stopping. Furthermore...

  7. Morphological and Genetic Variation along a North-to-South Transect in Stipa purpurea, a Dominant Grass on the Qinghai-Tibetan Plateau: Implications for Response to Climate Change.

    Science.gov (United States)

    Liu, Wensheng; Zhao, Yao; You, Jianling; Qi, Danhui; Zhou, Yin; Chen, Jiakuan; Song, Zhiping

    2016-01-01

    Estimating the potential of species to cope with rapid environmental climatic modifications is of vital importance for determining their future viability and conservation. The variation between existing populations along a climatic gradient may predict how a species will respond to future climate change. Stipa purpurea is a dominant grass species in the alpine steppe and meadow of the Qinghai-Tibetan Plateau (QTP). Ecological niche modelling was applied to S. purpurea, and its distribution was found to be most strongly correlated with the annual precipitation and the mean temperature of the warmest quarter. We established a north-to-south transect over 2000 km long on the QTP reflecting the gradients of temperature and precipitation, and then we estimated the morphological by sampling fruited tussocks and genetic divergence by using 11 microsatellite markers between 20 populations along the transect. Reproductive traits (the number of seeds and reproductive shoots), the reproductive-vegetative growth ratio and the length of roots in the S. purpurea populations varied significantly with climate variables. S. purpurea has high genetic diversity (He = 0.585), a large effective population size (Ne >1,000), and a considerable level of gene flow between populations. The S. purpurea populations have a mosaic genetic structure: some distant populations (over 1000 km apart) clustered genetically, whereas closer populations (transect and might be mediated by seed dispersal via migratory herbivores, such as the chiru (Pantholops hodgsonii). These findings suggest that population performance variation and gene flow both facilitate the response of S. purpurea to climate change.

  8. Heterogeneity of variances for carcass traits by percentage Brahman inheritance.

    Science.gov (United States)

    Crews, D H; Franke, D E

    1998-07-01

    Heterogeneity of carcass trait variances due to level of Brahman inheritance was investigated using records from straightbred and crossbred steers produced from 1970 to 1988 (n = 1,530). Angus, Brahman, Charolais, and Hereford sires were mated to straightbred and crossbred cows to produce straightbred, F1, back-cross, three-breed cross, and two-, three-, and four-breed rotational crossbred steers in four non-overlapping generations. At weaning (mean age = 220 d), steers were randomly assigned within breed group directly to the feedlot for 200 d, or to a backgrounding and stocker phase before feeding. Stocker steers were fed from 70 to 100 d in generations 1 and 2 and from 60 to 120 d in generations 3 and 4. Carcass traits included hot carcass weight, subcutaneous fat thickness and longissimus muscle area at the 12-13th rib interface, carcass weight-adjusted longissimus muscle area, USDA yield grade, estimated total lean yield, marbling score, and Warner-Bratzler shear force. Steers were classified as either high Brahman (50 to 100% Brahman), moderate Brahman (25 to 49% Brahman), or low Brahman (0 to 24% Brahman) inheritance. Two types of animal models were fit with regard to level of Brahman inheritance. One model assumed similar variances between pairs of Brahman inheritance groups, and the second model assumed different variances between pairs of Brahman inheritance groups. Fixed sources of variation in both models included direct and maternal additive and nonadditive breed effects, year of birth, and slaughter age. Variances were estimated using derivative free REML procedures. Likelihood ratio tests were used to compare models. The model accounting for heterogeneous variances had a greater likelihood (P carcass weight, longissimus muscle area, weight-adjusted longissimus muscle area, total lean yield, and Warner-Bratzler shear force, indicating improved fit with percentage Brahman inheritance considered as a source of heterogeneity of variance. Genetic

  9. Genetic architecture of nonadditive inheritance in Arabidopsis thaliana hybrids.

    Science.gov (United States)

    Seymour, Danelle K; Chae, Eunyoung; Grimm, Dominik G; Martín Pizarro, Carmen; Habring-Müller, Anette; Vasseur, François; Rakitsch, Barbara; Borgwardt, Karsten M; Koenig, Daniel; Weigel, Detlef

    2016-11-15

    The ubiquity of nonparental hybrid phenotypes, such as hybrid vigor and hybrid inferiority, has interested biologists for over a century and is of considerable agricultural importance. Although examples of both phenomena have been subject to intense investigation, no general model for the molecular basis of nonadditive genetic variance has emerged, and prediction of hybrid phenotypes from parental information continues to be a challenge. Here we explore the genetics of hybrid phenotype in 435 Arabidopsis thaliana individuals derived from intercrosses of 30 parents in a half diallel mating scheme. We find that nonadditive genetic effects are a major component of genetic variation in this population and that the genetic basis of hybrid phenotype can be mapped using genome-wide association (GWA) techniques. Significant loci together can explain as much as 20% of phenotypic variation in the surveyed population and include examples that have both classical dominant and overdominant effects. One candidate region inherited dominantly in the half diallel contains the gene for the MADS-box transcription factor AGAMOUS-LIKE 50 (AGL50), which we show directly to alter flowering time in the predicted manner. Our study not only illustrates the promise of GWA approaches to dissect the genetic architecture underpinning hybrid performance but also demonstrates the contribution of classical dominance to genetic variance.

  10. Heritable Environmental Variance Causes Nonlinear Relationships Between Traits: Application to Birth Weight and Stillbirth of Pigs

    NARCIS (Netherlands)

    Mulder, H.A.; Hill, W.G.; Knol, E.F.

    2015-01-01

    There is recent evidence from laboratory experiments and analysis of livestock populations that not only the phenotype itself, but also its environmental variance, is under genetic control. Little is known about the relationships between the environmental variance of one trait and mean levels of oth

  11. Heritable Environmental Variance Causes Nonlinear Relationships Between Traits: Application to Birth Weight and Stillbirth of Pigs

    NARCIS (Netherlands)

    Mulder, H.A.; Hill, W.G.; Knol, E.F.

    2015-01-01

    There is recent evidence from laboratory experiments and analysis of livestock populations that not only the phenotype itself, but also its environmental variance, is under genetic control. Little is known about the relationships between the environmental variance of one trait and mean levels of

  12. Pathogenic potential, genetic diversity, and population structure of Escherichia coli strains isolated from a forest-dominated watershed (Comox Lake) in British Columbia, Canada.

    Science.gov (United States)

    Chandran, Abhirosh; Mazumder, Asit

    2015-03-01

    Escherichia coli isolates (n = 658) obtained from drinking water intakes of Comox Lake (2011 to 2013) were screened for the following virulence genes (VGs): stx1 and stx2 (Shiga toxin-producing E. coli [STEC]), eae and the adherence factor (EAF) gene (enteropathogenic E. coli [EPEC]), heat-stable (ST) enterotoxin (variants STh and STp) and heat-labile enterotoxin (LT) genes (enterotoxigenic E. coli [ETEC]), and ipaH (enteroinvasive E. coli [EIEC]). The only genes detected were eae and stx2, which were carried by 37.69% (n = 248) of the isolates. Only eae was harbored by 26.74% (n = 176) of the isolates, representing potential atypical EPEC strains, while only stx2 was detected in 10.33% (n = 68) of the isolates, indicating potential STEC strains. Moreover, four isolates were positive for both the stx2 and eae genes, representing potential EHEC strains. The prevalence of VGs (eae or stx2) was significantly (P < 0.0001) higher in the fall season, and multiple genes (eae plus stx2) were detected only in fall. Repetitive element palindromic PCR (rep-PCR) fingerprint analysis of 658 E. coli isolates identified 335 unique fingerprints, with an overall Shannon diversity (H') index of 3.653. Diversity varied among seasons over the years, with relatively higher diversity during fall. Multivariate analysis of variance (MANOVA) revealed that the majority of the fingerprints showed a tendency to cluster according to year, season, and month. Taken together, the results indicated that the diversity and population structure of E. coli fluctuate on a temporal scale, reflecting the presence of diverse host sources and their behavior over time in the watershed. Furthermore, the occurrence of potentially pathogenic E. coli strains in the drinking water intakes highlights the risk to human health associated with direct and indirect consumption of untreated surface water.

  13. The genetic architecture of fitness in a seed beetle: assessing the potential for indirect genetic benefits of female choice

    Directory of Open Access Journals (Sweden)

    Maklakov AA

    2008-10-01

    Full Text Available Abstract Background Quantifying the amount of standing genetic variation in fitness represents an empirical challenge. Unfortunately, the shortage of detailed studies of the genetic architecture of fitness has hampered progress in several domains of evolutionary biology. One such area is the study of sexual selection. In particular, the evolution of adaptive female choice by indirect genetic benefits relies on the presence of genetic variation for fitness. Female choice by genetic benefits fall broadly into good genes (additive models and compatibility (non-additive models where the strength of selection is dictated by the genetic architecture of fitness. To characterize the genetic architecture of fitness, we employed a quantitative genetic design (the diallel cross in a population of the seed beetle Callosobruchus maculatus, which is known to exhibit post-copulatory female choice. From reciprocal crosses of inbred lines, we assayed egg production, egg-to-adult survival, and lifetime offspring production of the outbred F1 daughters (F1 productivity. Results We used the bio model to estimate six components of genetic and environmental variance in fitness. We found sizeable additive and non-additive genetic variance in F1 productivity, but lower genetic variance in egg-to-adult survival, which was strongly influenced by maternal and paternal effects. Conclusion Our results show that, in order to gain a relevant understanding of the genetic architecture of fitness, measures of offspring fitness should be inclusive and should include quantifications of offspring reproductive success. We note that our estimate of additive genetic variance in F1 productivity (CVA = 14% is sufficient to generate indirect selection on female choice. However, our results also show that the major determinant of offspring fitness is the genetic interaction between parental genomes, as indicated by large amounts of non-additive genetic variance (dominance and/or epistasis

  14. Linear Minimum variance estimation fusion

    Institute of Scientific and Technical Information of China (English)

    ZHU Yunmin; LI Xianrong; ZHAO Juan

    2004-01-01

    This paper shows that a general mulitisensor unbiased linearly weighted estimation fusion essentially is the linear minimum variance (LMV) estimation with linear equality constraint, and the general estimation fusion formula is developed by extending the Gauss-Markov estimation to the random paramem of distributed estimation fusion in the LMV setting.In this setting ,the fused estimator is a weighted sum of local estimatess with a matrix quadratic optimization problem subject to a convex linear equality constraint. Second, we present a unique solution to the above optimization problem, which depends only on the covariance matrixCK. Third, if a priori information, the expectation and covariance, of the estimated quantity is unknown, a necessary and sufficient condition for the above LMV fusion becoming the best unbiased LMV estimation with dnown prior information as the above is presented. We also discuss the generality and usefulness of the LMV fusion formulas developed. Finally, we provied and off-line recursion of Ck for a class of multisensor linear systems with coupled measurement noises.

  15. Autosomal dominant familial Mediterranean fever in Northern European Caucasians associated with deletion of p.M694 residue-a case series and genetic exploration.

    Science.gov (United States)

    Rowczenio, Dorota M; Iancu, Daniela S; Trojer, Hadija; Gilbertson, Janet A; Gillmore, Julian D; Wechalekar, Ashutosh D; Tekman, Mehmet; Stanescu, Horia C; Kleta, Robert; Lane, Thirusha; Hawkins, Philip N; Lachmann, Helen J

    2017-02-01

    This study was undertaken to characterize the phenotype and response to treatment in patients with autosomal dominant FMF caused by MEFV p.M694del mutation and to use haplotype reconstruction to investigate the possibility of common ancestry. MEFV gene was analysed in 3500 subjects with suspected FMF referred to a single UK centre between 2002 and 2014. Patients with p.M694del underwent additional screening of the SAA1 gene as well as haplotype reconstruction of the MEFV locus. The p.M694del variant was identified in 21 patients, sharing an identical disease haplotype that appears to have arisen about 550 years ago. The SAA1.1 allele was found in four patients, including two with AA amyloidosis. The clinical features comprised typical FMF symptoms with median age at onset of 18 years; three patients presented with AA amyloidosis, of whom two had had symptoms of FMF in retrospect. Fifteen patients had received colchicine treatment, all with excellent responses. The p.M694del variant is associated with autosomal dominantly inherited FMF in Northern European Caucasians. Symptoms may develop later in life than in classical recessive FMF but are otherwise similar, as is the response to colchicine treatment. The 14% incidence of AA amyloidosis may reflect delay in diagnosis associated with extreme rarity of FMF in this population. The common haplotype suggests a single founder living in about 1460. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  16. Genetic Variance in Uncoupling Protein 2 in Relation to Obesity, Type 2 Diabetes, and Related Metabolic Traits: Focus on the Functional −866G>A Promoter Variant (rs659366

    Directory of Open Access Journals (Sweden)

    Louise T. Dalgaard

    2011-01-01

    Full Text Available Uncoupling proteins (UCPs are mitochondrial proteins able to dissipate the proton gradient of the inner mitochondrial membrane when activated. This decreases ATP-generation through oxidation of fuels and may theoretically decrease energy expenditure leading to obesity. Evidence from Ucp(−/− mice revealed a role of UCP2 in the pancreatic β-cell, because β-cells without UCP2 had increased glucose-stimulated insulin secretion. Thus, from being a candidate gene for obesity UCP2 became a valid candidate gene for type 2 diabetes mellitus. This prompted a series of studies of the human UCP2 and UCP3 genes with respect to obesity and diabetes. Of special interest was a promoter variant of UCP2 situated 866bp upstream of transcription initiation (−866G>A, rs659366. This variant changes promoter activity and has been associated with obesity and/or type 2 diabetes in several, although not all, studies. The aim of the current paper is to summarize current evidence of association of UCP2 genetic variation with obesity and type 2 diabetes, with focus on the −866G>A polymorphism.

  17. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  18. Clinical and molecular genetic spectrum of autosomal dominant Emery-Dreifuss muscular dystrophy due to mutations of the lamin A/C gene.

    Science.gov (United States)

    Bonne, G; Mercuri, E; Muchir, A; Urtizberea, A; Bécane, H M; Recan, D; Merlini, L; Wehnert, M; Boor, R; Reuner, U; Vorgerd, M; Wicklein, E M; Eymard, B; Duboc, D; Penisson-Besnier, I; Cuisset, J M; Ferrer, X; Desguerre, I; Lacombe, D; Bushby, K; Pollitt, C; Toniolo, D; Fardeau, M; Schwartz, K; Muntoni, F

    2000-08-01

    Emery-Dreifuss muscular dystrophy (EDMD) is characterized by early contractures of the elbows and Achilles tendons, slowly progressive muscle wasting and weakness, and life-threatening cardiomyopathy with conduction blocks. We recently identified LMNA encoding two nuclear envelope proteins, lamins A and C, to be implicated in the autosomal dominant form of EDMD. Here, we report on the variability of the phenotype and spectrum of LMNA mutations in 53 autosomal dominant EDMD patients (36 members of 6 families and 17 sporadic cases). Twelve of the 53 patients showed cardiac involvement exclusively, although the remaining 41 all showed muscle weakness and contractures. We were able to identify a common phenotype among the patients with skeletal muscle involvement, consisting of humeroperoneal wasting and weakness, scapular winging, rigidity of the spine, and elbow and Achilles tendon contractures. The disease course was generally slow, but we observed either a milder phenotype characterized by late onset and a mild degree of weakness and contractures or a more severe phenotype with early presentation and a rapidly progressive course in a few cases. Mutation analysis identified 18 mutations in LMNA (i.e., 1 nonsense mutation, 2 deletions of a codon, and 15 missense mutations). All the mutations were distributed between exons 1 and 9 in the region of LMNA that is common to lamins A and C. LMNA mutations arose de novo in 76% of the cases; 2 of these de novo mutations were typical hot spots, and 2 others were identified in 2 unrelated cases. There was no clear correlation between the phenotype and type or localization of the mutations within the gene. Moreover, a marked inter- and intra-familial variability in the clinical expression of LMNA mutations exists, ranging from patients expressing the full clinical picture of EDMD to those characterized only by cardiac involvement, which points toward a significant role of possible modifier genes in the course of this disease

  19. Multi-objective optimization of discrete time-cost tradeoff problem in project networks using non-dominated sorting genetic algorithm

    Science.gov (United States)

    Shahriari, Mohammadreza

    2016-03-01

    The time-cost tradeoff problem is one of the most important and applicable problems in project scheduling area. There are many factors that force the mangers to crash the time. This factor could be early utilization, early commissioning and operation, improving the project cash flow, avoiding unfavorable weather conditions, compensating the delays, and so on. Since there is a need to allocate extra resources to short the finishing time of project and the project managers are intended to spend the lowest possible amount of money and achieve the maximum crashing time, as a result, both direct and indirect costs will be influenced in the project, and here, we are facing into the time value of money. It means that when we crash the starting activities in a project, the extra investment will be tied in until the end date of the project; however, when we crash the final activities, the extra investment will be tied in for a much shorter period. This study is presenting a two-objective mathematical model for balancing compressing the project time with activities delay to prepare a suitable tool for decision makers caught in available facilities and due to the time of projects. Also drawing the scheduling problem to real world conditions by considering nonlinear objective function and the time value of money are considered. The presented problem was solved using NSGA-II, and the effect of time compressing reports on the non-dominant set.

  20. Genetic influences on political ideologies

    DEFF Research Database (Denmark)

    Hatemi, Peter K; Medland, Sarah E; Klemmensen, Robert

    2014-01-01

    Almost 40 years ago, evidence from large studies of adult twins and their relatives suggested that between 30 and 60 % of the variance in social and political attitudes could be explained by genetic influences. However, these findings have not been widely accepted or incorporated into the dominant...... paradigms that explain the etiology of political ideology. This has been attributed in part to measurement and sample limitations, as well the relative absence of molecular genetic studies. Here we present results from original analyses of a combined sample of over 12,000 twins pairs, ascertained from nine...... different studies conducted in five democracies, sampled over the course of four decades. We provide evidence that genetic factors play a role in the formation of political ideology, regardless of how ideology is measured, the era, or the population sampled. The only exception is a question that explicitly...

  1. Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacteriome in subsurface biofilms that are dominated by the same archaeal species.

    Directory of Open Access Journals (Sweden)

    Alexander J Probst

    Full Text Available Earth harbors an enormous portion of subsurface microbial life, whose microbiome flux across geographical locations remains mainly unexplored due to difficult access to samples. Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current. Due to their unique hydrogeological setting these springs provide accessible windows to subsurface biofilms dominated by the same uncultivated archaeal species, called SM1 Euryarchaeon. Comparative analysis of infrared imaging spectra demonstrated great variations in archaeal membrane composition between biofilms of the two springs, suggesting different SM1 euryarchaeal strains of the same species at both aquifer outlets. This strain variation was supported by ultrastructural and metagenomic analyses of the archaeal biofilms, which included intergenic spacer region sequencing of the rRNA gene operon. At 16S rRNA gene level, PhyloChip G3 DNA microarray detected similar biofilm communities for archaea, but site-specific communities for bacteria. Both biofilms showed an enrichment of different deltaproteobacterial operational taxonomic units, whose families were, however, congruent as were their lipid spectra. Consequently, the function of the major proportion of the bacteriome appeared to be conserved across the geographic locations studied, which was confirmed by dsrB-directed quantitative PCR. Consequently, microbiome differences of these subsurface biofilms exist at subtle nuances for archaea (strain level variation and at higher taxonomic levels for predominant bacteria without a substantial perturbation in bacteriome function. The results of this communication provide deep insight into the dynamics of subsurface microbial life and warrant its future investigation with regard to metabolic and genomic analyses.

  2. Componentes de (covariância e parâmetros genéticos de características de crescimento da raça Simental no Brasil Variance components and genetic parameters estimates for growth traits of Simmental cattle in Brazil

    Directory of Open Access Journals (Sweden)

    L.F.A. Marques

    1999-08-01

    Full Text Available Informações de genealogia e produção, cedidas pela Associação Brasileira de Criadores da Raça Simental (ABCRS, relativas aos pesos desde o nascimento até um ano de idade, foram utilizadas para estimar, sob modelos alternativos, os componentes de variância e os parâmetros genéticos em animais da raça Simental no Brasil. A matriz de parentesco incluiu 25.812 animais dos quais 7587 com dados de produção. O modelo 1 contém, além do erro, o efeito genético direto. Os modelos seguintes contêm os componentes do modelo 1, mais o efeito permanente de ambiente materno (modelo 2, ou o componente genético materno (modelo 3, ambos os componentes (modelo 5, os componentes do modelo 3 mais a covariância entre os efeitos genéticos direto e materno (modelo 4 e todos os componentes citados (modelo 6. Os modelos foram comparados pelo teste de razão de verossimilhança pelo chi² (PBirth, 100-day, weaning and yearling weights of 7587 Simmental cattle, and 25,812 pedigree data were used to estimate genetic parameters using different animal models. The simplest model (model l included additive genetic and residual random effects. Models 2 and 3 were the same as model 1, but included, respectively, maternal permanent and maternal genetic effects. Model 4 did not include permanent effect. The most complete model (model 6 also included maternal additive and permanent effects, assuming covariance between them. Model 5 was the same as model 6, but did not included direct maternal covariance. Contemporary groups considered animals born in the same herd, year and season, from the same sex and raised under the same nutritional system. The models were compared using likelihood ratio tests. The (covariance components and the genetic parameters decreased from the most simple (model 1 to the most complete model (model 6. One-hundred-day weight showed no (.00±.00 maternal genetic variance but moderate maternal environmental permanent effect (.17±.07. The

  3. Genetic and Environmental Stability of Neuroticism From Adolescence to Adulthood.

    Science.gov (United States)

    Nivard, Michel G; Middeldorp, Christel M; Dolan, Conor V; Boomsma, Dorret I

    2015-12-01

    Longitudinal studies of neuroticism have shown that, on average, neuroticism scores decrease from adolescence to adulthood. The heritability of neuroticism is estimated between 0.30 and 0.60 and does not seem to vary greatly as a function of age. Shared environmental effects are rarely reported. Less is known about the role of genetic and environmental influences on the rank order stability of neuroticism in the period from adolescence to adulthood. We studied the stability of neuroticism in a cohort sequential (classical) twin design, from adolescence (age 14 years) to young adulthood (age 32 years). A genetic simplex model that was fitted to the longitudinal neuroticism data showed that the genetic stability of neuroticism was relatively high (genetic correlations between adjacent age bins >0.9), and increased from adolescence to adulthood. Environmental stability was appreciably lower (environmental correlations between adjacent age bins were between 0.3 and 0.6). This low stability was largely due to age-specific environmental variance, which was dominated by measurement error. This attenuated the age-to-age environmental correlations. We constructed an environmental covariance matrix corrected for this error, under the strong assumption that all age-specific environmental variance is error variance. The environmental (co)variance matrix corrected for attenuation revealed highly stable environmental influences on neuroticism (correlations between adjacent age bins were between 0.7 and 0.9). Our results indicate that both genetic and environmental influences have enduring effects on individual differences in neuroticism.

  4. The phenotypic variance gradient - a novel concept.

    Science.gov (United States)

    Pertoldi, Cino; Bundgaard, Jørgen; Loeschcke, Volker; Barker, James Stuart Flinton

    2014-11-01

    Evolutionary ecologists commonly use reaction norms, which show the range of phenotypes produced by a set of genotypes exposed to different environments, to quantify the degree of phenotypic variance and the magnitude of plasticity of morphometric and life-history traits. Significant differences among the values of the slopes of the reaction norms are interpreted as significant differences in phenotypic plasticity, whereas significant differences among phenotypic variances (variance or coefficient of variation) are interpreted as differences in the degree of developmental instability or canalization. We highlight some potential problems with this approach to quantifying phenotypic variance and suggest a novel and more informative way to plot reaction norms: namely "a plot of log (variance) on the y-axis versus log (mean) on the x-axis, with a reference line added". This approach gives an immediate impression of how the degree of phenotypic variance varies across an environmental gradient, taking into account the consequences of the scaling effect of the variance with the mean. The evolutionary implications of the variation in the degree of phenotypic variance, which we call a "phenotypic variance gradient", are discussed together with its potential interactions with variation in the degree of phenotypic plasticity and canalization.

  5. Genetic Analysis on Bent Characters of Cucumber Fruit

    Institute of Scientific and Technical Information of China (English)

    ZHANG Peng; QIN Zhiwei; WANG Lili; ZHOU Xiuyan

    2011-01-01

    Bent varieties and straight varieties were made as parents for the genetic analysis to investigate cucumber bending genetic mechanism. The results showed that the bent characters of the cucumber fruit (BCCF) were quantitative inheritance controlled by multiple genes and major genes. The additive effect played the main role and the dominance effect played the lesser role. Compared with the additive environmental variance, the dominant-environmental variance was more important and the cucumber fruit was more easily affected by the additive effect. The broad heritability and the narrow heritability of BCCF were both higher. The varieties of D0455 and D07299 could be used as parents which were benefit for improving the straight characters of the cucumber fruit

  6. Within-generation mutation variance for litter size in inbred mice.

    Science.gov (United States)

    Casellas, Joaquim; Medrano, Juan F

    2008-08-01

    The mutational input of genetic variance per generation (sigma(m)(2)) is the lower limit of the genetic variability in inbred strains of mice, although greater values could be expected due to the accumulation of new mutations in successive generations. A mixed-model analysis using Bayesian methods was applied to estimate sigma(m)(2) and the across-generation accumulated genetic variability on litter size in 46 generations of a C57BL/6J inbred strain. This allowed for a separate inference on sigma(m)(2) and on the additive genetic variance in the base population (sigma(a)(2)). The additive genetic variance in the base generation was 0.151 and quickly decreased to almost null estimates in generation 10. On the other hand, sigma(m)(2) was moderate (0.035) and the within-generation mutational variance increased up to generation 14, then oscillating between 0.102 and 0.234 in remaining generations. This pattern suggested the existence of a continuous uploading of genetic variability for litter size (h(2)=0.045). Relevant genetic drift was not detected in this population. In conclusion, our approach allowed for separate estimation of sigma(a)(2) and sigma(m)(2) within the mixed-model framework, and the heritability obtained highlighted the significant and continuous influence of new genetic variability affecting the genetic stability of inbred strains.

  7. 多工序车削的自适应搜索非支配排序遗传算法%Adaptive Search Non-Dominated Sorting Genetic Algorithm of Multi-Pass Turning Operations

    Institute of Scientific and Technical Information of China (English)

    陈青艳; 胡成龙; 焦红卫

    2013-01-01

    The optimization of cutting parameters is significant for machining quality,production efftciency and machining economics in practical NC machining process.In order to calculate the optimum goal for minimum unit production cost,an adaptive search non-dominated sorting genetic algorithm (ASNSGA) is applied to multi-pass turning operations nonlinear cutting optimization model subject to various practical cutting constraints,which is based on non-dominated sorting genetic algorithm-Ⅱ.By comparing with those of genetic algorithms (GA),simulated annealing algorithm (SA/PA),scatter search (SS),float encoded genetic algorithm (FEGA),the cutting optimization model experimental results obtained by the proposed multi-pass turning operations nonlinear cutting optimization algorithms,named ASNSGA-Ⅱ,are effective for solving complex nonlinear cutting optimization problem,reducing the unit production cost,and helping for the cutting parameters optimum selection such as feed rate and cutting rate in rough NC machining,feed rate and cutting rate in finish NC machining.%在实际数控生产加工过程中,切削参数的优化对于保证加工质量、提高生产效率和降低加工成本具有非常重要的意义.为计算以单位生产成本最小为优化目标的多工序车削非线性优化模型,在NSGA-Ⅱ算法基础上提出了一种新的自适应搜索非支配排序遗传算法(ASNSGA).多工序车削加工实例结果表明,与模拟退火算法(SA/PA)、分散搜索算法(SS)及浮点编码遗传算法(FEGA)优化算法比较,自适应搜索非支配排序遗传算法得到最低的单位生产成本,有助于数控加工中粗车进给量、粗车切削速度及精车进给量、精车切削速度等切削参数的优化选择.

  8. Implementation of the Realized Genomic Relationship Matrix to Open-Pollinated White Spruce Family Testing for Disentangling Additive from Nonadditive Genetic Effects

    Directory of Open Access Journals (Sweden)

    Omnia Gamal El-Dien

    2016-03-01

    Full Text Available The open-pollinated (OP family testing combines the simplest known progeny evaluation and quantitative genetics analyses as candidates’ offspring are assumed to represent independent half-sib families. The accuracy of genetic parameter estimates is often questioned as the assumption of “half-sibling” in OP families may often be violated. We compared the pedigree- vs. marker-based genetic models by analysing 22-yr height and 30-yr wood density for 214 white spruce [Picea glauca (Moench Voss] OP families represented by 1694 individuals growing on one site in Quebec, Canada. Assuming half-sibling, the pedigree-based model was limited to estimating the additive genetic variances which, in turn, were grossly overestimated as they were confounded by very minor dominance and major additive-by-additive epistatic genetic variances. In contrast, the implemented genomic pairwise realized relationship models allowed the disentanglement of additive from all nonadditive factors through genetic variance decomposition. The marker-based models produced more realistic narrow-sense heritability estimates and, for the first time, allowed estimating the dominance and epistatic genetic variances from OP testing. In addition, the genomic models showed better prediction accuracies compared to pedigree models and were able to predict individual breeding values for new individuals from untested families, which was not possible using the pedigree-based model. Clearly, the use of marker-based relationship approach is effective in estimating the quantitative genetic parameters of complex traits even under simple and shallow pedigree structure.

  9. Implementation of the Realized Genomic Relationship Matrix to Open-Pollinated White Spruce Family Testing for Disentangling Additive from Nonadditive Genetic Effects.

    Science.gov (United States)

    Gamal El-Dien, Omnia; Ratcliffe, Blaise; Klápště, Jaroslav; Porth, Ilga; Chen, Charles; El-Kassaby, Yousry A

    2016-01-22

    The open-pollinated (OP) family testing combines the simplest known progeny evaluation and quantitative genetics analyses as candidates' offspring are assumed to represent independent half-sib families. The accuracy of genetic parameter estimates is often questioned as the assumption of "half-sibling" in OP families may often be violated. We compared the pedigree- vs. marker-based genetic models by analysing 22-yr height and 30-yr wood density for 214 white spruce [Picea glauca (Moench) Voss] OP families represented by 1694 individuals growing on one site in Quebec, Canada. Assuming half-sibling, the pedigree-based model was limited to estimating the additive genetic variances which, in turn, were grossly overestimated as they were confounded by very minor dominance and major additive-by-additive epistatic genetic variances. In contrast, the implemented genomic pairwise realized relationship models allowed the disentanglement of additive from all nonadditive factors through genetic variance decomposition. The marker-based models produced more realistic narrow-sense heritability estimates and, for the first time, allowed estimating the dominance and epistatic genetic variances from OP testing. In addition, the genomic models showed better prediction accuracies compared to pedigree models and were able to predict individual breeding values for new individuals from untested families, which was not possible using the pedigree-based model. Clearly, the use of marker-based relationship approach is effective in estimating the quantitative genetic parameters of complex traits even under simple and shallow pedigree structure.

  10. 21 CFR 1010.4 - Variances.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Variances. 1010.4 Section 1010.4 Food and Drugs... PERFORMANCE STANDARDS FOR ELECTRONIC PRODUCTS: GENERAL General Provisions § 1010.4 Variances. (a) Criteria for... shall modify the tag, label, or other certification required by § 1010.2 to state: (1) That the...

  11. Analysis of variance for model output

    NARCIS (Netherlands)

    Jansen, M.J.W.

    1999-01-01

    A scalar model output Y is assumed to depend deterministically on a set of stochastically independent input vectors of different dimensions. The composition of the variance of Y is considered; variance components of particular relevance for uncertainty analysis are identified. Several analysis of va

  12. The Correct Kriging Variance Estimated by Bootstrapping

    NARCIS (Netherlands)

    den Hertog, D.; Kleijnen, J.P.C.; Siem, A.Y.D.

    2004-01-01

    The classic Kriging variance formula is widely used in geostatistics and in the design and analysis of computer experiments.This paper proves that this formula is wrong.Furthermore, it shows that the formula underestimates the Kriging variance in expectation.The paper develops parametric bootstrappi

  13. Variance Risk Premia on Stocks and Bonds

    DEFF Research Database (Denmark)

    Mueller, Philippe; Sabtchevsky, Petar; Vedolin, Andrea

    is different from the equity variance risk premium. Third, the conditional correlation between stock and bond market variance risk premium switches sign often and ranges between -60% and +90%. We then show that these stylized facts pose a challenge to standard consumption-based asset pricing models....

  14. Influência da heterogeneidade de variâncias na avaliação genética de bovinos de corte da raça Tabapuã Influence of heterogeneity of variances on genetic evaluation of Tabapuã beef cattle

    Directory of Open Access Journals (Sweden)

    J.E.G. Campelo

    2003-12-01

    Full Text Available Verificou-se a influência da heterogeneidade de variâncias na avaliação genética de bovinos de corte da raça Tabapuã. Dados de pesos corrigidos aos 120, 240 e 420 dias de idade foram estratificados com base no desvio-padrão fenotípico do peso aos 120 dias dos grupos de contemporâneos em três classes: baixo (18,9kg desvio-padrão. Nas análises de múltiplas características, em que o peso foi considerado característica distinta em cada classe de desvio-padrão, constatou-se que as variâncias genéticas e residuais foram maiores com o aumento do desvio-padrão da classe. As herdabilidades foram 0,26, 0,32 e 0,37 (peso aos 120 dias, 0,28, 0,35 e 0,35 (peso aos 240 dias e 0,14, 0,18 e 0,18 (peso aos 420 dias nas classes de baixo, médio e alto desvio-padrão, respectivamente. As correlações genéticas entre o mesmo peso, nas classes de baixo e alto desvio-padrão foram inferiores a 0,80. As correlações entre os valores genéticos, obtidos de análises múltiplas e de análise geral (sem as classes, foram superiores a 0,93. Observou-se que os reprodutores seriam classificados de forma similar se for considerada ou não a presença de variâncias heterogêneas nas análises.Data from Tabapuã beef cattle were used to study the influence of variance heterogeneity on genetic evaluation. Adjusted weights at 120, 240 and 420 days of age were classified in three classes of standard deviation: low (18.9kg, based on phenotypic standard deviation of the weight at 120 days of age of the contemporary groups. Multiple trait analyses, considering each class of phenotypic standard deviation as a distinct trait, were performed. The genetic and residual variances increased as the phenotypic standard deviation of the class increased. Heritabilities for low, medium and high phenotypic standard deviation classes were 0.26, 0.32 and 0.37 (weight at 120 days, 0.28, 0.35 and 0.35 (weight at 240 days and 0.14, 0.18 and 0.18 (weight at 420 days

  15. Genetic parameters and heterogeneity of variance to milk yield in Murrah breed for Bayesian inference Heterogeneidade de variâncias e parâmetros genéticos para produção de leite em bubalinos da raça Murrah, mediante inferência Bayesiana

    Directory of Open Access Journals (Sweden)

    Simone Inoe Araújo

    2008-09-01

    Full Text Available Data from 2061 lactations of 532 females of the Murrah breed, daughters of 44 sires, calving from 1975 to 2001 were used to evaluate the effects of heterogeneity at variance on sires genetic evaluation. The standard deviation of the milk yield was used to classify the herds among high and low variability levels. An animal model, used to estimate variance component, included the fixed effect of herds-year, season of calving, animal random effect, permanent and temporary environments. Variance components were estimated to milk yield in both levels, considering the milk yield in each production level as different trait. Estimatives of heritability were 0.39, in general analysis, and equal to 0.33 and 0.41 for milk yield in high and low levels, respectively. Genetic correlations between high and low production levels were 58. The sires were selected according to the environment most changeable where daughters are raised, and not properly for its genetic breeding.Informações de 2061 registros de lactações de 532 fêmeas da raça Murrah, filhas de 44 reprodutores, com parições entre 1975 a 2001, foram utilizadas para se verificar a existência da heterogeneidade de variância para a produção de leite entre rebanhos e o seu impacto na classificação de reprodutores. O desvio padrão da produção de leite entre rebanhos foi utilizado para classificação dos rebanhos em níveis de alta e baixa variabilidade. Utilizou-se um modelo animal que incluiu os efeitos fixos de rebanho-ano, estação de parição, efeitos aleatórios de animal, ambiente permanente e ambiente temporário. Foram estimados os componentes de variância, considerando os rebanhos como uma única amostra e assumindo a produção de leite em cada nível de produção como característica diferente. Médias e componentes de variância foram maiores para o nível de alta produção e as estimativas de herdabilidade foram de 0,39 em ambos os níveis para a produção de leite e 0

  16. Portfolio optimization with mean-variance model

    Science.gov (United States)

    Hoe, Lam Weng; Siew, Lam Weng

    2016-06-01

    Investors wish to achieve the target rate of return at the minimum level of risk in their investment. Portfolio optimization is an investment strategy that can be used to minimize the portfolio risk and can achieve the target rate of return. The mean-variance model has been proposed in portfolio optimization. The mean-variance model is an optimization model that aims to minimize the portfolio risk which is the portfolio variance. The objective of this study is to construct the optimal portfolio using the mean-variance model. The data of this study consists of weekly returns of 20 component stocks of FTSE Bursa Malaysia Kuala Lumpur Composite Index (FBMKLCI). The results of this study show that the portfolio composition of the stocks is different. Moreover, investors can get the return at minimum level of risk with the constructed optimal mean-variance portfolio.

  17. Components of the metabolic syndrome: clustering and genetic variance

    NARCIS (Netherlands)

    Povel, C.M.

    2012-01-01

    Background Abdominal obesity, hyperglycemia, hypertriglyceridemia, low HDL cholesterol levels and hypertension frequently co-occur within individuals. The cluster of these features is referred to as the metabolic syndrome (MetS). The aim

  18. Portfolio optimization using median-variance approach

    Science.gov (United States)

    Wan Mohd, Wan Rosanisah; Mohamad, Daud; Mohamed, Zulkifli

    2013-04-01

    Optimization models have been applied in many decision-making problems particularly in portfolio selection. Since the introduction of Markowitz's theory of portfolio selection, various approaches based on mathematical programming have been introduced such as mean-variance, mean-absolute deviation, mean-variance-skewness and conditional value-at-risk (CVaR) mainly to maximize return and minimize risk. However most of the approaches assume that the distribution of data is normal and this is not generally true. As an alternative, in this paper, we employ the median-variance approach to improve the portfolio optimization. This approach has successfully catered both types of normal and non-normal distribution of data. With this actual representation, we analyze and compare the rate of return and risk between the mean-variance and the median-variance based portfolio which consist of 30 stocks from Bursa Malaysia. The results in this study show that the median-variance approach is capable to produce a lower risk for each return earning as compared to the mean-variance approach.

  19. Modelling dominance in a flexible intercross analysis

    Directory of Open Access Journals (Sweden)

    Besnier Francois

    2009-06-01

    Full Text Available Abstract Background The aim of this paper is to develop a flexible model for analysis of quantitative trait loci (QTL in outbred line crosses, which includes both additive and dominance effects. Our flexible intercross analysis (FIA model accounts for QTL that are not fixed within founder lines and is based on the variance component framework. Genome scans with FIA are performed using a score statistic, which does not require variance component estimation. Results Simulations of a pedigree with 800 F2 individuals showed that the power of FIA including both additive and dominance effects was almost 50% for a QTL with equal allele frequencies in both lines with complete dominance and a moderate effect, whereas the power of a traditional regression model was equal to the chosen significance value of 5%. The power of FIA without dominance effects included in the model was close to those obtained for FIA with dominance for all simulated cases except for QTL with overdominant effects. A genome-wide linkage analysis of experimental data from an F2 intercross between Red Jungle Fowl and White Leghorn was performed with both additive and dominance effects included in FIA. The score values for chicken body weight at 200 days of age were similar to those obtained in FIA analysis without dominance. Conclusion We have extended FIA to include QTL dominance effects. The power of FIA was superior, or similar, to standard regression methods for QTL effects with dominance. The difference in power for FIA with or without dominance is expected to be small as long as the QTL effects are not overdominant. We suggest that FIA with only additive effects should be the standard model to be used, especially since it is more computationally efficient.

  20. Reducing variance in batch partitioning measurements

    Energy Technology Data Exchange (ETDEWEB)

    Mariner, Paul E.

    2010-08-11

    The partitioning experiment is commonly performed with little or no attention to reducing measurement variance. Batch test procedures such as those used to measure K{sub d} values (e.g., ASTM D 4646 and EPA402 -R-99-004A) do not explain how to evaluate measurement uncertainty nor how to minimize measurement variance. In fact, ASTM D 4646 prescribes a sorbent:water ratio that prevents variance minimization. Consequently, the variance of a set of partitioning measurements can be extreme and even absurd. Such data sets, which are commonplace, hamper probabilistic modeling efforts. An error-savvy design requires adjustment of the solution:sorbent ratio so that approximately half of the sorbate partitions to the sorbent. Results of Monte Carlo simulations indicate that this simple step can markedly improve the precision and statistical characterization of partitioning uncertainty.

  1. Grammatical and lexical variance in English

    CERN Document Server

    Quirk, Randolph

    2014-01-01

    Written by one of Britain's most distinguished linguists, this book is concerned with the phenomenon of variance in English grammar and vocabulary across regional, social, stylistic and temporal space.

  2. 78 FR 14122 - Revocation of Permanent Variances

    Science.gov (United States)

    2013-03-04

    ... Occupational Safety and Health Administration Revocation of Permanent Variances AGENCY: Occupational Safety and Health Administration (OSHA), Labor. ACTION: Notice of revocation. SUMMARY: With this notice, OSHA is... into consideration these newly corrected cross references. DATES: The effective date of the...

  3. Importance Sampling Variance Reduction in GRESS ATMOSIM

    Energy Technology Data Exchange (ETDEWEB)

    Wakeford, Daniel Tyler [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-04-26

    This document is intended to introduce the importance sampling method of variance reduction to a Geant4 user for application to neutral particle Monte Carlo transport through the atmosphere, as implemented in GRESS ATMOSIM.

  4. 13 CFR 307.22 - Variances.

    Science.gov (United States)

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Variances. 307.22 Section 307.22 Business Credit and Assistance ECONOMIC DEVELOPMENT ADMINISTRATION, DEPARTMENT OF COMMERCE ECONOMIC... Federal, State and local law....

  5. Genetics Home Reference: autosomal dominant hypocalcemia

    Science.gov (United States)

    ... in the hands and feet (carpopedal spasms) and muscle cramping, prickling or tingling sensations (paresthesias), or twitching of ... plays an important role in the control of muscle movement, and a shortage of this molecule can lead to cramping or twitching of the muscles. Impairment of the ...

  6. Genetics Home Reference: autosomal dominant vitreoretinochoroidopathy

    Science.gov (United States)

    ... normal function of specialized cells called photoreceptors that detect light and color. In the retinal pigment epithelium, bestrophin-1 functions as a channel that transports charged chlorine atoms (chloride ions) across the cell membrane. Mutations in ...

  7. Variance components in discrete force production tasks.

    Science.gov (United States)

    Varadhan, S K M; Zatsiorsky, Vladimir M; Latash, Mark L

    2010-09-01

    The study addresses the relationships between task parameters and two components of variance, "good" and "bad", during multi-finger accurate force production. The variance components are defined in the space of commands to the fingers (finger modes) and refer to variance that does ("bad") and does not ("good") affect total force. Based on an earlier study of cyclic force production, we hypothesized that speeding-up an accurate force production task would be accompanied by a drop in the regression coefficient linking the "bad" variance and force rate such that variance of the total force remains largely unaffected. We also explored changes in parameters of anticipatory synergy adjustments with speeding-up the task. The subjects produced accurate ramps of total force over different times and in different directions (force-up and force-down) while pressing with the four fingers of the right hand on individual force sensors. The two variance components were quantified, and their normalized difference was used as an index of a total force stabilizing synergy. "Good" variance scaled linearly with force magnitude and did not depend on force rate. "Bad" variance scaled linearly with force rate within each task, and the scaling coefficient did not change across tasks with different ramp times. As a result, a drop in force ramp time was associated with an increase in total force variance, unlike the results of the study of cyclic tasks. The synergy index dropped 100-200 ms prior to the first visible signs of force change. The timing and magnitude of these anticipatory synergy adjustments did not depend on the ramp time. Analysis of the data within an earlier model has shown adjustments in the variance of a timing parameter, although these adjustments were not as pronounced as in the earlier study of cyclic force production. Overall, we observed qualitative differences between the discrete and cyclic force production tasks: Speeding-up the cyclic tasks was associated with

  8. Discrimination of frequency variance for tonal sequencesa)

    OpenAIRE

    Byrne, Andrew J.; Viemeister, Neal F.; Stellmack, Mark A.

    2014-01-01

    Real-world auditory stimuli are highly variable across occurrences and sources. The present study examined the sensitivity of human listeners to differences in global stimulus variability. In a two-interval, forced-choice task, variance discrimination was measured using sequences of five 100-ms tone pulses. The frequency of each pulse was sampled randomly from a distribution that was Gaussian in logarithmic frequency. In the non-signal interval, the sampled distribution had a variance of σSTA...

  9. The Variance Composition of Firm Growth Rates

    Directory of Open Access Journals (Sweden)

    Luiz Artur Ledur Brito

    2009-04-01

    Full Text Available Firms exhibit a wide variability in growth rates. This can be seen as another manifestation of the fact that firms are different from one another in several respects. This study investigated this variability using the variance components technique previously used to decompose the variance of financial performance. The main source of variation in growth rates, responsible for more than 40% of total variance, corresponds to individual, idiosyncratic firm aspects and not to industry, country, or macroeconomic conditions prevailing in specific years. Firm growth, similar to financial performance, is mostly unique to specific firms and not an industry or country related phenomenon. This finding also justifies using growth as an alternative outcome of superior firm resources and as a complementary dimension of competitive advantage. This also links this research with the resource-based view of strategy. Country was the second source of variation with around 10% of total variance. The analysis was done using the Compustat Global database with 80,320 observations, comprising 13,221 companies in 47 countries, covering the years of 1994 to 2002. It also compared the variance structure of growth to the variance structure of financial performance in the same sample.

  10. Modelos animais alternativos para estimação de componentes de (covariância e de parâmetros genéticos e fenotípicos do peso ao nascer na raça Nelore Alternative animal models to estimate (co variance components and genetic and phenotypic parameters for birth weight in Nellore cattle

    Directory of Open Access Journals (Sweden)

    Márcia Tereza Vieira Scarpati

    1999-01-01

    artificial insemination were considered. The (co variance components were estimated under four different animal models where direct and maternal genetic and permanent environmental were taken into account by including the appropriate random effects, as well as contemporary groups and age of cow at calving effects, in the statistical model. This procedure allowed the quantification of the contribution of different random effects, especially maternal effects. The number of records was 6511; the overall means 31 kg, and the standard deviation 4,1 kg. The direct, maternal and total estimated heritability ranged from 0.20 to 0.37, 0.11 to 0.13 and 0.22 to 0.37, respectively. The correlation's between genetic direct and maternal effects were negative (-0,14 to ¾0,16. The BW is a trait greatly determined by direct additive genic action, insignificantly affected by maternal phenotype, and with antagonism between the genetic effects. Response to selection for BW would be maximized if based on the parameters obtained by the analysis fitting animal models with direct and maternal effects.

  11. Variance Analysis and Adaptive Sampling for Indirect Light Path Reuse

    Institute of Scientific and Technical Information of China (English)

    Hao Qin; Xin Sun; Jun Yan; Qi-Ming Hou; Zhong Ren; Kun Zhou

    2016-01-01

    In this paper, we study the estimation variance of a set of global illumination algorithms based on indirect light path reuse. These algorithms usually contain two passes — in the first pass, a small number of indirect light samples are generated and evaluated, and they are then reused by a large number of reconstruction samples in the second pass. Our analysis shows that the covariance of the reconstruction samples dominates the estimation variance under high reconstruction rates and increasing the reconstruction rate cannot effectively reduce the covariance. We also find that the covariance represents to what degree the indirect light samples are reused during reconstruction. This analysis motivates us to design a heuristic approximating the covariance as well as an adaptive sampling scheme based on this heuristic to reduce the rendering variance. We validate our analysis and adaptive sampling scheme in the indirect light field reconstruction algorithm and the axis-aligned filtering algorithm for indirect lighting. Experiments are in accordance with our analysis and show that rendering artifacts can be greatly reduced at a similar computational cost.

  12. Variance component estimates for alternative litter size traits in swine.

    Science.gov (United States)

    Putz, A M; Tiezzi, F; Maltecca, C; Gray, K A; Knauer, M T

    2015-11-01

    Litter size at d 5 (LS5) has been shown to be an effective trait to increase total number born (TNB) while simultaneously decreasing preweaning mortality. The objective of this study was to determine the optimal litter size day for selection (i.e., other than d 5). Traits included TNB, number born alive (NBA), litter size at d 2, 5, 10, 30 (LS2, LS5, LS10, LS30, respectively), litter size at weaning (LSW), number weaned (NW), piglet mortality at d 30 (MortD30), and average piglet birth weight (BirthWt). Litter size traits were assigned to biological litters and treated as a trait of the sow. In contrast, NW was the number of piglets weaned by the nurse dam. Bivariate animal models included farm, year-season, and parity as fixed effects. Number born alive was fit as a covariate for BirthWt. Random effects included additive genetics and the permanent environment of the sow. Variance components were plotted for TNB, NBA, and LS2 to LS30 using univariate animal models to determine how variances changed over time. Additive genetic variance was minimized at d 7 in Large White and at d 14 in Landrace pigs. Total phenotypic variance for litter size traits decreased over the first 10 d and then stabilized. Heritability estimates increased between TNB and LS30. Genetic correlations between TNB, NBA, and LS2 to LS29 with LS30 plateaued within the first 10 d. A genetic correlation with LS30 of 0.95 was reached at d 4 for Large White and at d 8 for Landrace pigs. Heritability estimates ranged from 0.07 to 0.13 for litter size traits and MortD30. Birth weight had an h of 0.24 and 0.26 for Large White and Landrace pigs, respectively. Genetic correlations among LS30, LSW, and NW ranged from 0.97 to 1.00. In the Large White breed, genetic correlations between MortD30 with TNB and LS30 were 0.23 and -0.64, respectively. These correlations were 0.10 and -0.61 in the Landrace breed. A high genetic correlation of 0.98 and 0.97 was observed between LS10 and NW for Large White and

  13. Genetic diagnosis of X-linked dominant hypophosphatemic rickets in a cohort study: Tubular reabsorption of phosphate and 1,25(OH2D serum levels are associated with PHEX mutation type

    Directory of Open Access Journals (Sweden)

    García-Miñaur Sixto

    2011-09-01

    Full Text Available Abstract Background Genetic Hypophosphatemic Rickets (HR is a group of diseases characterized by renal phosphate wasting with inappropriately low or normal 1,25-dihydroxyvitamin D3 (1,25(OH2D serum levels. The most common form of HR is X-linked dominant HR (XLHR which is caused by inactivating mutations in the PHEX gene. The purpose of this study was to perform genetic diagnosis in a cohort of patients with clinical diagnosis of HR, to perform genotype-phenotype correlations of those patients and to compare our data with other HR cohort studies. Methods Forty three affected individuals from 36 non related families were analyzed. For the genetic analysis, the PHEX gene was sequenced in all of the patients and in 13 cases the study was complemented by mRNA sequencing and Multiple Ligation Probe Assay. For the genotype-phenotype correlation study, the clinical and biochemical phenotype of the patients was compared with the type of mutation, which was grouped into clearly deleterious or likely causative, using the Mann-Whitney and Fisher's exact test. Results Mutations in the PHEX gene were identified in all the patients thus confirming an XLHR. Thirty four different mutations were found distributed throughout the gene with higher density at the 3' end. The majority of the mutations were novel (69.4%, most of them resulted in a truncated PHEX protein (83.3% and were family specific (88.9%. Tubular reabsorption of phosphate (TRP and 1,25(OH2D serum levels were significantly lower in patients carrying clearly deleterious mutations than in patients carrying likely causative ones (61.39 ± 19.76 vs. 80.14 ± 8.80%, p = 0.028 and 40.93 ± 30.73 vs. 78.46 ± 36.27 pg/ml, p = 0.013. Conclusions PHEX gene mutations were found in all the HR cases analyzed, which was in contrast with other cohort studies. Patients with clearly deleterious PHEX mutations had lower TRP and 1,25(OH2D levels suggesting that the PHEX type of mutation might predict the XLHR

  14. Genetic and environmental contributions to individual differences: the three major dimensions of personality.

    Science.gov (United States)

    Eysenck, H J

    1990-03-01

    This article deals with the contribution of genetic and environmental factors to individual differences in the three major dimensions of personality (Psychoticism, Extraversion, and Neuroticism). Twin studies indicate, and family studies confirm within limits, the strong genetic determination of these and many other personality factors, additive genetic variance accounting for roughly half the total phenotypic variance. On the environmental side, shared family environment plays little or no part, all environmental effects being within-family. Assortative mating, important in the formation of social attitudes, has little impact on personality. Dominance may be important for Extraversion. Epistasis (emergenesis) may account for the comparative low values of dizygotic (DZ) twins' correlations. Evidence for differential heritability of traits is present, but not very strong. It is concluded that behavioral genetics forms a vital part of the psychological understanding of the causes of individual differences in personality.

  15. Genetic analysis of some agronomic traits in groundnut (Arachis hypogaea L.

    Directory of Open Access Journals (Sweden)

    M.K. Alam

    2013-12-01

    Full Text Available A 10×10 half diallel experiment was conducted on groundnut (Arachis hypogaea L. to ascertain the gene action and genetic parameters of ten traits including 50% flowering, no. of pods per plant, plant height, harvest index, pod index, 100 pod weight, 100 kernel weight, pod size, diseases infection and yield per plot. The experiments were carried out in the Department of Genetics and Plant Breeding, Bangladesh Agricultural University (BAU, Mymensingh during the cropping season of 2010-2011. The estimates of gene effects indicated that significance of both additive and non-additive variance for pod size, 100 pod weight and diseases infection among the traits and presence of over dominance satisfying assumptions of diallel except dormancy. However, both the additive and non-additive gene affects together importance to control of most quantitative traits in the groundnut. The average degree of dominance (H1/D 1/2 (H1 = dominance variance, D = additive variance was higher than one, indicating over dominance for all the traits. The narrow-sense heritability was high for 50% flowering (38%, harvest index (35%, pod size (52%, 100 pod weight (35% and yield per plot (41% indicating that great genetic gain could be achieved for them.

  16. Behavior Genetics and the Within-Person Variability of Daily Interpersonal Styles: The Heritability of Flux, Spin and Pulse.

    Science.gov (United States)

    Markey, Patrick M; Racine, Sarah E; Markey, Charlotte N; Hopwood, Christopher J; Keel, Pamela K; Burt, S Alexandra; Neale, Michael C; Sisk, Cheryl L; Boker, Steven M; Klump, Kelly L

    2014-04-01

    A classical twin study was used to estimate the magnitude of genetic and environmental influences on four measurements of within-person variability: dominance flux, warmth flux, spin and pulse. Flux refers to the variability of an individual's interpersonal dominance and warmth. Spin measures changes in the tone of interpersonal styles and pulse measures changes in the intensity of interpersonal styles. Daily reports of interpersonal styles were collected from 494 same-sex female twins (142 monozygotic pairs and 105 dizygotic pairs) over 45 days. For dominance flux, warmth flux, and spin, genetic effects accounted for a larger proportion of variance (37%, 24%, and 30%, respectively) than shared environmental effects (14%, 13%, 0%, respectively), with the remaining variance due to the non-shared environment (62%, 50%, 70% respectively). Pulse appeared to be primarily influenced by the non-shared environment, although conclusions about the contribution of familial influences were difficult to draw from this study.

  17. Discrimination of frequency variance for tonal sequences.

    Science.gov (United States)

    Byrne, Andrew J; Viemeister, Neal F; Stellmack, Mark A

    2014-12-01

    Real-world auditory stimuli are highly variable across occurrences and sources. The present study examined the sensitivity of human listeners to differences in global stimulus variability. In a two-interval, forced-choice task, variance discrimination was measured using sequences of five 100-ms tone pulses. The frequency of each pulse was sampled randomly from a distribution that was Gaussian in logarithmic frequency. In the non-signal interval, the sampled distribution had a variance of σSTAN (2), while in the signal interval, the variance of the sequence was σSIG (2) (with σSIG (2) >  σSTAN (2)). The listener's task was to choose the interval with the larger variance. To constrain possible decision strategies, the mean frequency of the sampling distribution of each interval was randomly chosen for each presentation. Psychometric functions were measured for various values of σSTAN (2). Although the performance was remarkably similar across listeners, overall performance was poorer than that of an ideal observer (IO) which perfectly compares interval variances. However, like the IO, Weber's Law behavior was observed, with a constant ratio of ( σSIG (2)- σSTAN (2)) to σSTAN (2) yielding similar performance. A model which degraded the IO with a frequency-resolution noise and a computational noise provided a reasonable fit to the real data.

  18. Topics on domination

    CERN Document Server

    Hedetniemi, ST

    1991-01-01

    The contributions in this volume are divided into three sections: theoretical, new models and algorithmic. The first section focuses on properties of the standard domination number &ggr;(G), the second section is concerned with new variations on the domination theme, and the third is primarily concerned with finding classes of graphs for which the domination number (and several other domination-related parameters) can be computed in polynomial time.

  19. Dominance in domestic dogs

    NARCIS (Netherlands)

    Borg, Van Der J.A.M.; Schilder, M.B.H.; Vinke, C.M.; Vries, De Han; Petit, Odile

    2015-01-01

    A dominance hierarchy is an important feature of the social organisation of group living animals. Although formal and/or agonistic dominance has been found in captive wolves and free-ranging dogs, applicability of the dominance concept in domestic dogs is highly debated, and quantitative data are

  20. Total well dominated trees

    DEFF Research Database (Denmark)

    Finbow, Arthur; Frendrup, Allan; Vestergaard, Preben D.

    cardinality then G is a total well dominated graph. In this paper we study composition and decomposition of total well dominated trees. By a reversible process we prove that any total well dominated tree can both be reduced to and constructed from a family of three small trees....

  1. Dominance in domestic dogs

    NARCIS (Netherlands)

    Borg, Van Der J.A.M.; Schilder, M.B.H.; Vinke, C.M.; Vries, De Han; Petit, Odile

    2015-01-01

    A dominance hierarchy is an important feature of the social organisation of group living animals. Although formal and/or agonistic dominance has been found in captive wolves and free-ranging dogs, applicability of the dominance concept in domestic dogs is highly debated, and quantitative data are

  2. Dominating Sets and Domination Polynomials of Paths

    Directory of Open Access Journals (Sweden)

    Saeid Alikhani

    2009-01-01

    Full Text Available Let G=(V,E be a simple graph. A set S⊆V is a dominating set of G, if every vertex in V\\S is adjacent to at least one vertex in S. Let 𝒫ni be the family of all dominating sets of a path Pn with cardinality i, and let d(Pn,j=|𝒫nj|. In this paper, we construct 𝒫ni, and obtain a recursive formula for d(Pn,i. Using this recursive formula, we consider the polynomial D(Pn,x=∑i=⌈n/3⌉nd(Pn,ixi, which we call domination polynomial of paths and obtain some properties of this polynomial.

  3. Maximum Variance Hashing via Column Generation

    Directory of Open Access Journals (Sweden)

    Lei Luo

    2013-01-01

    item search. Recently, a number of data-dependent methods have been developed, reflecting the great potential of learning for hashing. Inspired by the classic nonlinear dimensionality reduction algorithm—maximum variance unfolding, we propose a novel unsupervised hashing method, named maximum variance hashing, in this work. The idea is to maximize the total variance of the hash codes while preserving the local structure of the training data. To solve the derived optimization problem, we propose a column generation algorithm, which directly learns the binary-valued hash functions. We then extend it using anchor graphs to reduce the computational cost. Experiments on large-scale image datasets demonstrate that the proposed method outperforms state-of-the-art hashing methods in many cases.

  4. Estimating quadratic variation using realized variance

    DEFF Research Database (Denmark)

    Barndorff-Nielsen, Ole Eiler; Shephard, N.

    2002-01-01

    This paper looks at some recent work on estimating quadratic variation using realized variance (RV) - that is, sums of M squared returns. This econometrics has been motivated by the advent of the common availability of high-frequency financial return data. When the underlying process is a semimar......This paper looks at some recent work on estimating quadratic variation using realized variance (RV) - that is, sums of M squared returns. This econometrics has been motivated by the advent of the common availability of high-frequency financial return data. When the underlying process...... have to impose some weak regularity assumptions. We illustrate the use of the limit theory on some exchange rate data and some stock data. We show that even with large values of M the RV is sometimes a quite noisy estimator of integrated variance. Copyright © 2002 John Wiley & Sons, Ltd....

  5. Milk metabolites and their genetic variability.

    Science.gov (United States)

    Wittenburg, D; Melzer, N; Willmitzer, L; Lisec, J; Kesting, U; Reinsch, N; Repsilber, D

    2013-04-01

    The composition of milk is crucial to evaluate milk performance and quality measures. Milk components partly contribute to breeding scores, and they can be assessed to judge metabolic and energy status of the cow as well as to serve as predictive markers for diseases. In addition to the milk composition measures (e.g., fat, protein, lactose) traditionally recorded during milk performance test via infrared spectroscopy, novel techniques, such as gas chromatography-mass spectrometry, allow for a further analysis of milk into its metabolic components. Gas chromatography-mass spectrometry is suitable for measuring several hundred metabolites with high throughput, and thus it is applicable to study sources of genetic and nongenetic variation of milk metabolites in dairy cows. Heritability and mode of inheritance of metabolite measurements were studied in a linear mixed model approach including expected (pedigree) and realized (genomic) relationship between animals. The genetic variability of 190 milk metabolite intensities was analyzed from 1,295 cows held on 18 farms in Mecklenburg-Western Pomerania, Germany. Besides extensive pedigree information, genotypic data comprising 37,180 single nucleotide polymorphism markers were available. Goodness of fit and significance of genetic variance components based on likelihood ratio tests were investigated with a full model, including marker- and pedigree-based genetic effects. Broad-sense heritability varied from zero to 0.699, with a median of 0.125. Significant additive genetic variance was observed for highly heritable metabolites, but dominance variance was not significantly present. As some metabolites are particularly favorable for human nutrition, for instance, future research should address the identification of locus-specific genetic effects and investigate metabolites as the molecular basis of traditional milk performance test traits.

  6. Quantitative genetics theory for non-inbred populations in linkage disequilibrium

    Directory of Open Access Journals (Sweden)

    José Marcelo Soriano Viana

    2004-01-01

    Full Text Available Although linkage disequilibrium, epistasis and inbreeding are common phenomena in genetic systems that control quantitative traits, theory development and analysis are very complex, especially when they are considered together. The objective of this study is to offer additional quantitative genetics theory to define and analyze, in relation to non-inbred cross pollinating populations, components of genotypic variance, heritabilities and predicted gains, assuming linkage disequilibrium and absence of epistasis. The genotypic variance and its components, additive and due to dominance genetic variances, are invariant over the generations only in regard to completely linked genes and to those in equilibrium. When the population is structured in half-sib families, the additive variance in the parents' generation and the genotypic variance in the population can be estimated. When the population is structured in full-sib families, none of the components of genotypic variance can be estimated. The narrow sense heritability level at plant level can be estimated from the parent-offspring or mid parent-offspring regression. When there is dominance, the narrow sense heritability estimate in the in F2 is biased due to linkage disequilibrium when estimated by the Warner method, but not when estimated by means of the plant F2-family F3 regression. The bias is proportional to the number of pairs of linked genes, without independent assortment, and to the degree of dominance, and tends to be positive when genes in the coupling phase predominate or negative and of higher value when genes in the repulsion phase predominate. Linkage disequilibrium is also cause of bias in estimates of the narrow sense heritabilities at full-sib family mean and at plant within half-sib and full-sib families levels. Generally, the magnitude of the bias is proportional to the number of pairs of genes in disequilibrium and to the frequency of recombining gametes.

  7. Integrating Variances into an Analytical Database

    Science.gov (United States)

    Sanchez, Carlos

    2010-01-01

    For this project, I enrolled in numerous SATERN courses that taught the basics of database programming. These include: Basic Access 2007 Forms, Introduction to Database Systems, Overview of Database Design, and others. My main job was to create an analytical database that can handle many stored forms and make it easy to interpret and organize. Additionally, I helped improve an existing database and populate it with information. These databases were designed to be used with data from Safety Variances and DCR forms. The research consisted of analyzing the database and comparing the data to find out which entries were repeated the most. If an entry happened to be repeated several times in the database, that would mean that the rule or requirement targeted by that variance has been bypassed many times already and so the requirement may not really be needed, but rather should be changed to allow the variance's conditions permanently. This project did not only restrict itself to the design and development of the database system, but also worked on exporting the data from the database to a different format (e.g. Excel or Word) so it could be analyzed in a simpler fashion. Thanks to the change in format, the data was organized in a spreadsheet that made it possible to sort the data by categories or types and helped speed up searches. Once my work with the database was done, the records of variances could be arranged so that they were displayed in numerical order, or one could search for a specific document targeted by the variances and restrict the search to only include variances that modified a specific requirement. A great part that contributed to my learning was SATERN, NASA's resource for education. Thanks to the SATERN online courses I took over the summer, I was able to learn many new things about computers and databases and also go more in depth into topics I already knew about.

  8. Sources of variance in ocular microtremor.

    Science.gov (United States)

    Sheahan, N F; Coakley, D; Bolger, C; O'Neill, D; Fry, G; Phillips, J; Malone, J F

    1994-02-01

    This study presents a preliminary investigation of the sources of variance in the measurement of ocular microtremor frequency in a normal population. When the results from both experienced and relatively inexperienced operators are pooled, factors that contribute significantly to the total variance include the measurement procedure (p < 0.001), day-to-day variations within subjects (p < 0.001), and inter-subject differences (p < 0.01). Operator experience plays a role in determining the measurement precision: the intra-subject coefficient of variation is about 5% for a very experienced operator, and about 14% for a relatively inexperienced operator.

  9. Properties of spontaneous mutational variance and covariance for wing size and shape in Drosophila melanogaster.

    Science.gov (United States)

    Houle, David; Fierst, Janna

    2013-04-01

    We estimated mutational variance-covariance matrices, M, for wing shape and size in two genotypes of Drosophila melanogaster after 192 generations of mutation accumulation. We characterized 21 potentially independent aspects of wing shape and size using geometric morphometrics, and analyzed the data using a likelihood-based factor-analytic approach. We implement a previously unused analysis that describes those directions with the greatest difference in evolvability between pairs of matrices. There are significant mutational effects on 19 of 21 possible aspects of wing form, consistent with the high dimensionality of standing genetic variation for wing shape previously identified in D. melanogaster. Mutations have partially recessive effects, consistent with average dominance around 0.25. Sex-specific matrices are relatively similar, although male-specific matrices are slightly larger, as expected due to dosage compensation on the X chromosome. Genotype-specific matrices are quite different. Matrices may differ both because of sampling error based on small samples of mutations with large phenotypic effects, and because of the mutational properties of the genotypes. Genotypic differences are likely to be involved, as the two genotypes have different molecular mutation rates and properties. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

  10. Managing product inherent variance during treatment

    NARCIS (Netherlands)

    Verdenius, F.

    1996-01-01

    The natural variance of agricultural product parameters complicates recipe planning for product treatment, i.e. the process of transforming a product batch from its initial state to a prespecified final state. For a specific product P, recipes are currently composed by human experts on the basis of

  11. The Variance of Language in Different Contexts

    Institute of Scientific and Technical Information of China (English)

    申一宁

    2012-01-01

    language can be quite different (here referring to the meaning) in different contexts. And there are 3 categories of context: the culture, the situation and the cotext. In this article, we will analysis the variance of language in each of the 3 aspects. This article is written for the purpose of making people understand the meaning of a language under specific better.

  12. Regression calibration with heteroscedastic error variance.

    Science.gov (United States)

    Spiegelman, Donna; Logan, Roger; Grove, Douglas

    2011-01-01

    The problem of covariate measurement error with heteroscedastic measurement error variance is considered. Standard regression calibration assumes that the measurement error has a homoscedastic measurement error variance. An estimator is proposed to correct regression coefficients for covariate measurement error with heteroscedastic variance. Point and interval estimates are derived. Validation data containing the gold standard must be available. This estimator is a closed-form correction of the uncorrected primary regression coefficients, which may be of logistic or Cox proportional hazards model form, and is closely related to the version of regression calibration developed by Rosner et al. (1990). The primary regression model can include multiple covariates measured without error. The use of these estimators is illustrated in two data sets, one taken from occupational epidemiology (the ACE study) and one taken from nutritional epidemiology (the Nurses' Health Study). In both cases, although there was evidence of moderate heteroscedasticity, there was little difference in estimation or inference using this new procedure compared to standard regression calibration. It is shown theoretically that unless the relative risk is large or measurement error severe, standard regression calibration approximations will typically be adequate, even with moderate heteroscedasticity in the measurement error model variance. In a detailed simulation study, standard regression calibration performed either as well as or better than the new estimator. When the disease is rare and the errors normally distributed, or when measurement error is moderate, standard regression calibration remains the method of choice.

  13. Variance Reduction Techniques in Monte Carlo Methods

    NARCIS (Netherlands)

    Kleijnen, Jack P.C.; Ridder, A.A.N.; Rubinstein, R.Y.

    2010-01-01

    Monte Carlo methods are simulation algorithms to estimate a numerical quantity in a statistical model of a real system. These algorithms are executed by computer programs. Variance reduction techniques (VRT) are needed, even though computer speed has been increasing dramatically, ever since the intr

  14. Formative Use of Intuitive Analysis of Variance

    Science.gov (United States)

    Trumpower, David L.

    2013-01-01

    Students' informal inferential reasoning (IIR) is often inconsistent with the normative logic underlying formal statistical methods such as Analysis of Variance (ANOVA), even after instruction. In two experiments reported here, student's IIR was assessed using an intuitive ANOVA task at the beginning and end of a statistics course. In…

  15. Linear transformations of variance/covariance matrices

    NARCIS (Netherlands)

    Parois, P.J.A.; Lutz, M.

    2011-01-01

    Many applications in crystallography require the use of linear transformations on parameters and their standard uncertainties. While the transformation of the parameters is textbook knowledge, the transformation of the standard uncertainties is more complicated and needs the full variance/covariance

  16. Variance Reduction Techniques in Monte Carlo Methods

    NARCIS (Netherlands)

    Kleijnen, Jack P.C.; Ridder, A.A.N.; Rubinstein, R.Y.

    2010-01-01

    Monte Carlo methods are simulation algorithms to estimate a numerical quantity in a statistical model of a real system. These algorithms are executed by computer programs. Variance reduction techniques (VRT) are needed, even though computer speed has been increasing dramatically, ever since the intr

  17. Decomposition of variance for spatial Cox processes

    DEFF Research Database (Denmark)

    Jalilian, Abdollah; Guan, Yongtao; Waagepetersen, Rasmus

    2013-01-01

    Spatial Cox point processes is a natural framework for quantifying the various sources of variation governing the spatial distribution of rain forest trees. We introduce a general criterion for variance decomposition for spatial Cox processes and apply it to specific Cox process models...

  18. Decomposition of variance for spatial Cox processes

    DEFF Research Database (Denmark)

    Jalilian, Abdollah; Guan, Yongtao; Waagepetersen, Rasmus

    Spatial Cox point processes is a natural framework for quantifying the various sources of variation governing the spatial distribution of rain forest trees. We introducea general criterion for variance decomposition for spatial Cox processes and apply it to specific Cox process models with additive...

  19. Decomposition of variance for spatial Cox processes

    DEFF Research Database (Denmark)

    Jalilian, Abdollah; Guan, Yongtao; Waagepetersen, Rasmus

    Spatial Cox point processes is a natural framework for quantifying the various sources of variation governing the spatial distribution of rain forest trees. We introduce a general criterion for variance decomposition for spatial Cox processes and apply it to specific Cox process models...

  20. Improved non-dominated sorting genetic algorithm applied in multi-objective optimization of coal-fired boiler combustion%改进NSGA-Ⅱ算法在锅炉燃烧多目标优化中的应用

    Institute of Scientific and Technical Information of China (English)

    余廷芳; 王林; 彭春华

    2013-01-01

    提出改进非劣分类遗传算法(NSGA-Ⅱ)在燃煤锅炉多目标燃烧优化中的应用,优化的目标是锅炉热损失及NOx排放最小化.首先,采用BP神经网络模型分别建立了300MW燃煤锅炉的NOx排放特性模型和锅炉热损失模型,同时利用锅炉热态实验数据对模型进行了训练和验证,结果表明,BP神经网络模型可以很好地预测锅炉的排放特性和锅炉的热损失特性.在建立的锅炉排放特性和热损失BP神经网络模型基础上,采用非劣分类遗传算法对锅炉进行多目标优化,针对NSGA-Ⅱ在燃煤锅炉燃烧多目标优化问题应用中Pareto解集分布不理想、易早熟收敛的问题,在拥挤算子及交叉算子上进行了相应改进.优化结果表明,改进NSGA-Ⅱ方法与BP神经网络模型结合可以对锅炉燃烧实现有效的多目标寻优、得到理想的Pareto解,是对锅炉燃烧进行多目标优化的有效工具,同改进前的NSGA-Ⅱ优化结果比较,其Pareto优化结果集分布更好、解的质量更优.%This paper discussed the application of improved non-dominated sorting genetic algorithm-Ⅱ (NSGA-Ⅱ) to multi-objective optimization of a coal-fired combustion, the two objectives considered are minimization of overall heat loss and NOx emissions from coal-fired boiler. In the first step,this paper proposed the back propagation(BP) neural network to establish a mathematical model predicting the functional relationship between outputs (NOx emissions & overall heat loss of the boiler) and inputs (operational parameters of the boiler) of a coal-fired boiler. It used a number of field test data from a full-scale operating 300MW boiler to train and verify the BP model. The NOx emissions & heat loss predicted by the BP neural network model shows good agreement with the measured. Then, combined BP model and the non-dominated sorting genetic algorithm Ⅱ (NSGA- Ⅱ) to gain the optimal operating parameters which led to lower NOx emissions

  1. 40 CFR 142.43 - Disposition of a variance request.

    Science.gov (United States)

    2010-07-01

    ... during the period of variance shall specify interim treatment techniques, methods and equipment, and... the specified treatment technique for which the variance was granted is necessary to protect...

  2. Variance estimation between different body measurements at the males population from Romanian Mioritic Shepherd Dog breed

    Directory of Open Access Journals (Sweden)

    Dorel Dronca

    2015-05-01

    Full Text Available Romanian Mioritic Shepherd Dog, was selected from a natural population breed in Carpathian Mountains. The aim of this paper was to estimate variance at 12 body measurements using 26 males from Romanian Mioritic Shepherd Dog breed. The animals were registered with the Romanian Mioritic Association Club from Romania. The statistical data showed that there is a large variance for body length and tail length, a middle variance for the croup width and thorax width and a small variance for height at withers, height at middle of back, height at croup, height at the base of the tail, depth of thorax, thoracic perimeter, elbow height and height of the hock. We recommend of breeders dogs from this breed to take account in genetic improvement programs, of values presented in this paper.

  3. Estimation models of variance components for farrowing interval in swine

    Directory of Open Access Journals (Sweden)

    Aderbal Cavalcante Neto

    2009-02-01

    Full Text Available The main objective of this study was to evaluate the importance of including maternal genetic, common litter environmental and permanent environmental effects in estimation models of variance components for the farrowing interval trait in swine. Data consisting of 1,013 farrowing intervals of Dalland (C-40 sows recorded in two herds were analyzed. Variance components were obtained by the derivative-free restricted maximum likelihood method. Eight models were tested which contained the fixed effects(contemporary group and covariables and the direct genetic additive and residual effects, and varied regarding the inclusion of the maternal genetic, common litter environmental, and/or permanent environmental random effects. The likelihood-ratio test indicated that the inclusion of these effects in the model was unnecessary, but the inclusion of the permanent environmental effect caused changes in the estimates of heritability, which varied from 0.00 to 0.03. In conclusion, the heritability values obtained indicated that this trait appears to present no genetic gain as response to selection. The common litter environmental and the maternal genetic effects did not present any influence on this trait. The permanent environmental effect, however, should be considered in the genetic models for this trait in swine, because its presence caused changes in the additive genetic variance estimates.Este trabalho teve como objetivo principal avaliar a importância da inclusão dos efeitos genético materno, comum de leitegada e de ambiente permanente no modelo de estimação de componentes de variância para a característica intervalo de parto em fêmeas suínas. Foram utilizados dados que consistiam de 1.013 observações de fêmeas Dalland (C-40, registradas em dois rebanhos. As estimativas dos componentes de variância foram realizadas pelo método da máxima verossimilhança restrita livre de derivadas. Foram testados oito modelos, que continham os efeitos

  4. Partitioning of genomic variance using biological pathways

    DEFF Research Database (Denmark)

    Edwards, Stefan McKinnon; Janss, Luc; Madsen, Per;

    for complex diseases reveals patterns that provide insight into the genetic architecture of complex traits. Although many genetic variants with small or moderate effects contribute to the overall genetic variation, it appears that multiple independently associated variants are located in the same genes...... diseases. However, the variants identified as being statistically significant have generally explained only a small fraction of the heritable component of the trait. Insufficient modelling of the underlying genetic architecture may in part explain this missing heritability. Evidence collected across GWAS...

  5. Cosmic variance in the nanohertz gravitational wave background

    CERN Document Server

    Roebber, Elinore; Holz, Daniel; Warren, Michael

    2015-01-01

    We use large N-body simulations and empirical scaling relations between dark matter halos, galaxies, and supermassive black holes to estimate the formation rates of supermassive black hole binaries and the resulting low-frequency stochastic gravitational wave background (GWB). We find this GWB to be relatively insensitive ($\\lesssim10\\%$) to cosmological parameters, with only slight variation between WMAP5 and Planck cosmologies. We find that uncertainty in the astrophysical scaling relations changes the amplitude of the GWB by a factor of $\\sim 2$. Current observational limits are already constraining this predicted range of models. We investigate the Poisson variance in the amplitude of the GWB for randomly-generated populations of supermassive black holes, finding a scatter of order unity per frequency bin below 10 nHz, and increasing to a factor of $\\sim 10$ near 100 nHz. This variance is a result of the rarity of the most massive binaries, which dominate the signal, and acts as a fundamental uncertainty ...

  6. INTERPRETING MAGNETIC VARIANCE ANISOTROPY MEASUREMENTS IN THE SOLAR WIND

    Energy Technology Data Exchange (ETDEWEB)

    TenBarge, J. M.; Klein, K. G.; Howes, G. G. [Department of Physics and Astronomy, University of Iowa, Iowa City, IA (United States); Podesta, J. J., E-mail: jason-tenbarge@uiowa.edu [Space Science Institute, Boulder, CO (United States)

    2012-07-10

    The magnetic variance anisotropy (A{sub m}) of the solar wind has been used widely as a method to identify the nature of solar wind turbulent fluctuations; however, a thorough discussion of the meaning and interpretation of the A{sub m} has not appeared in the literature. This paper explores the implications and limitations of using the A{sub m} as a method for constraining the solar wind fluctuation mode composition and presents a more informative method for interpreting spacecraft data. The paper also compares predictions of the A{sub m} from linear theory to nonlinear turbulence simulations and solar wind measurements. In both cases, linear theory compares well and suggests that the solar wind for the interval studied is dominantly Alfvenic in the inertial and dissipation ranges to scales of k{rho}{sub i} {approx_equal} 5.

  7. Autosomal dominant lamellar ichthyosis.

    Science.gov (United States)

    Toribio, J; Fernández Redondo, V; Peteiro, C; Zulaica, A; Fabeiro, J M

    1986-08-01

    Five members of two generations of one family were affected with lamellar ichthyosis, suggesting autosomal dominant transmission. The clinical and histopathological characteristics of the cases described here are similar to those reported by Traupe et al. (1984) as autosomal dominant lamellar ichthyosis and thus confirm the existence of this new form of ichthyosis.

  8. Linear transformations of variance/covariance matrices.

    Science.gov (United States)

    Parois, Pascal; Lutz, Martin

    2011-07-01

    Many applications in crystallography require the use of linear transformations on parameters and their standard uncertainties. While the transformation of the parameters is textbook knowledge, the transformation of the standard uncertainties is more complicated and needs the full variance/covariance matrix. For the transformation of second-rank tensors it is suggested that the 3 × 3 matrix is re-written into a 9 × 1 vector. The transformation of the corresponding variance/covariance matrix is then straightforward and easily implemented into computer software. This method is applied in the transformation of anisotropic displacement parameters, the calculation of equivalent isotropic displacement parameters, the comparison of refinements in different space-group settings and the calculation of standard uncertainties of eigenvalues.

  9. Variance and covariance of accumulated displacement estimates.

    Science.gov (United States)

    Bayer, Matthew; Hall, Timothy J

    2013-04-01

    Tracking large deformations in tissue using ultrasound can enable the reconstruction of nonlinear elastic parameters, but poses a challenge to displacement estimation algorithms. Such large deformations have to be broken up into steps, each of which contributes an estimation error to the final accumulated displacement map. The work reported here measured the error variance for single-step and accumulated displacement estimates using one-dimensional numerical simulations of ultrasound echo signals, subjected to tissue strain and electronic noise. The covariance between accumulation steps was also computed. These simulations show that errors due to electronic noise are negatively correlated between steps, and therefore accumulate slowly, whereas errors due to tissue deformation are positively correlated and accumulate quickly. For reasonably low electronic noise levels, the error variance in the accumulated displacement estimates is remarkably constant as a function of step size, but increases with the length of the tracking kernel.

  10. The Theory of Variances in Equilibrium Reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Zakharov, Leonid E.; Lewandowski, Jerome; Foley, Elizabeth L.; Levinton, Fred M.; Yuh, Howard Y.; Drozdov, Vladimir; McDonald, Darren

    2008-01-14

    The theory of variances of equilibrium reconstruction is presented. It complements existing practices with information regarding what kind of plasma profiles can be reconstructed, how accurately, and what remains beyond the abilities of diagnostic systems. The σ-curves, introduced by the present theory, give a quantitative assessment of quality of effectiveness of diagnostic systems in constraining equilibrium reconstructions. The theory also suggests a method for aligning the accuracy of measurements of different physical nature.

  11. Eigenvalue variance bounds for covariance matrices

    OpenAIRE

    Dallaporta, Sandrine

    2013-01-01

    This work is concerned with finite range bounds on the variance of individual eigenvalues of random covariance matrices, both in the bulk and at the edge of the spectrum. In a preceding paper, the author established analogous results for Wigner matrices and stated the results for covariance matrices. They are proved in the present paper. Relying on the LUE example, which needs to be investigated first, the main bounds are extended to complex covariance matrices by means of the Tao, Vu and Wan...

  12. High-dimensional regression with unknown variance

    CERN Document Server

    Giraud, Christophe; Verzelen, Nicolas

    2011-01-01

    We review recent results for high-dimensional sparse linear regression in the practical case of unknown variance. Different sparsity settings are covered, including coordinate-sparsity, group-sparsity and variation-sparsity. The emphasize is put on non-asymptotic analyses and feasible procedures. In addition, a small numerical study compares the practical performance of three schemes for tuning the Lasso esti- mator and some references are collected for some more general models, including multivariate regression and nonparametric regression.

  13. Fractional constant elasticity of variance model

    OpenAIRE

    Ngai Hang Chan; Chi Tim Ng

    2007-01-01

    This paper develops a European option pricing formula for fractional market models. Although there exist option pricing results for a fractional Black-Scholes model, they are established without accounting for stochastic volatility. In this paper, a fractional version of the Constant Elasticity of Variance (CEV) model is developed. European option pricing formula similar to that of the classical CEV model is obtained and a volatility skew pattern is revealed.

  14. Fundamentals of exploratory analysis of variance

    CERN Document Server

    Hoaglin, David C; Tukey, John W

    2009-01-01

    The analysis of variance is presented as an exploratory component of data analysis, while retaining the customary least squares fitting methods. Balanced data layouts are used to reveal key ideas and techniques for exploration. The approach emphasizes both the individual observations and the separate parts that the analysis produces. Most chapters include exercises and the appendices give selected percentage points of the Gaussian, t, F chi-squared and studentized range distributions.

  15. Variance and covariance components for liability of piglet survival during different periods

    DEFF Research Database (Denmark)

    Su, G; Sorensen, D; Lund, M S

    2008-01-01

    Variance and covariance components for piglet survival in different periods were estimated from individual records of 133 004 Danish Landrace piglets and 89 928 Danish Yorkshire piglets, using a liability threshold model including both direct and maternal additive genetic effects. At the individual...

  16. Discussion on variance reduction technique for shielding

    Energy Technology Data Exchange (ETDEWEB)

    Maekawa, Fujio [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1998-03-01

    As the task of the engineering design activity of the international thermonuclear fusion experimental reactor (ITER), on 316 type stainless steel (SS316) and the compound system of SS316 and water, the shielding experiment using the D-T neutron source of FNS in Japan Atomic Energy Research Institute has been carried out. However, in these analyses, enormous working time and computing time were required for determining the Weight Window parameter. Limitation or complication was felt when the variance reduction by Weight Window method of MCNP code was carried out. For the purpose of avoiding this difficulty, investigation was performed on the effectiveness of the variance reduction by cell importance method. The conditions of calculation in all cases are shown. As the results, the distribution of fractional standard deviation (FSD) related to neutrons and gamma-ray flux in the direction of shield depth is reported. There is the optimal importance change, and when importance was increased at the same rate as that of the attenuation of neutron or gamma-ray flux, the optimal variance reduction can be done. (K.I.)

  17. Quantitative genetic analysis of injury liability in infants and toddlers

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, K.; Matheny, A.P. Jr. [Univ. of Louisville Medical School, KY (United States)

    1995-02-27

    A threshold model of latent liability was applied to infant and toddler twin data on total count of injuries sustained during the interval from birth to 36 months of age. A quantitative genetic analysis of estimated twin correlations in injury liability indicated strong genetic dominance effects, but no additive genetic variance was detected. Because interpretations involving overdominance have little research support, the results may be due to low order epistasis or other interaction effects. Boys had more injuries than girls, but this effect was found only for groups whose parents were prompted and questioned in detail about their children`s injuries. Activity and impulsivity are two behavioral predictors of childhood injury, and the results are discussed in relation to animal research on infant and adult activity levels, and impulsivity in adult humans. Genetic epidemiological approaches to childhood injury should aid in targeting higher risk children for preventive intervention. 30 refs., 4 figs., 3 tabs.

  18. Applications of non-parametric statistics and analysis of variance on sample variances

    Science.gov (United States)

    Myers, R. H.

    1981-01-01

    Nonparametric methods that are available for NASA-type applications are discussed. An attempt will be made here to survey what can be used, to attempt recommendations as to when each would be applicable, and to compare the methods, when possible, with the usual normal-theory procedures that are avavilable for the Gaussion analog. It is important here to point out the hypotheses that are being tested, the assumptions that are being made, and limitations of the nonparametric procedures. The appropriateness of doing analysis of variance on sample variances are also discussed and studied. This procedure is followed in several NASA simulation projects. On the surface this would appear to be reasonably sound procedure. However, difficulties involved center around the normality problem and the basic homogeneous variance assumption that is mase in usual analysis of variance problems. These difficulties discussed and guidelines given for using the methods.

  19. The Parabolic variance (PVAR), a wavelet variance based on least-square fit

    CERN Document Server

    Vernotte, F; Bourgeois, P -Y; Rubiola, E

    2015-01-01

    The Allan variance (AVAR) is one option among the wavelet variances. However a milestone in the analysis of frequency fluctuations and in the long-term stability of clocks, and certainly the most widely used one, AVAR is not suitable when fast noise processes show up, chiefly because of the poor rejection of white phase noise. The modified Allan variance (MVAR) features high resolution in the presence of white PM noise, but it is poorer for slow phenomena because the wavelet spans over 50% longer time. This article introduces the Parabolic Variance (PVAR), a wavelet variance similar to the Allan variance, based on the Linear Regression (LR) of phase data. The PVAR relates to the Omega frequency counter, which is the topics of a companion article [the reference to the article, or to the ArXiv manuscript, will be provided later]. The PVAR wavelet spans over 2 tau, the same of the AVAR wavelet. After setting the theoretical framework, we analyze the degrees of freedom and the detection of weak noise processes in...

  20. Downhill Domination in Graphs

    OpenAIRE

    Haynes Teresa W.; Hedetniemi Stephen T.; Jamieson Jessie D.; Jamieson William B.

    2014-01-01

    A path π = (v1, v2, . . . , vk+1) in a graph G = (V,E) is a downhill path if for every i, 1 ≤ i ≤ k, deg(vi) ≥ deg(vi+1), where deg(vi) denotes the degree of vertex vi ∈ V. The downhill domination number equals the minimum cardinality of a set S ⊆ V having the property that every vertex v ∈ V lies on a downhill path originating from some vertex in S. We investigate downhill domination numbers of graphs and give upper bounds. In particular, we show that the downhill domination number of a grap...

  1. Downhill Domination in Graphs

    Directory of Open Access Journals (Sweden)

    Haynes Teresa W.

    2014-08-01

    Full Text Available A path π = (v1, v2, . . . , vk+1 in a graph G = (V,E is a downhill path if for every i, 1 ≤ i ≤ k, deg(vi ≥ deg(vi+1, where deg(vi denotes the degree of vertex vi ∈ V. The downhill domination number equals the minimum cardinality of a set S ⊆ V having the property that every vertex v ∈ V lies on a downhill path originating from some vertex in S. We investigate downhill domination numbers of graphs and give upper bounds. In particular, we show that the downhill domination number of a graph is at most half its order, and that the downhill domination number of a tree is at most one third its order. We characterize the graphs obtaining each of these bounds

  2. Dominantly Inherited Nemaline Myopathy

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2003-08-01

    Full Text Available A locus on chromosome 15q21-23 for a dominantly inherited nemaline myopathy with core-like lesions is reported in two unrelated families evaluated at University Medical Center, Nijmegen, The Netherlands.

  3. Double decomposition: decomposing the variance in subcomponents of male extra-pair reproductive success.

    Science.gov (United States)

    Losdat, Sylvain; Arcese, Peter; Reid, Jane M

    2015-09-01

    1. Extra-pair reproductive success (EPRS) is a key component of male fitness in socially monogamous systems and could cause selection on female extra-pair reproduction if extra-pair offspring (EPO) inherit high value for EPRS from their successful extra-pair fathers. However, EPRS is itself a composite trait that can be fully decomposed into subcomponents of variation, each of which can be further decomposed into genetic and environmental variances. However, such decompositions have not been implemented in wild populations, impeding evolutionary inference. 2. We first show that EPRS can be decomposed into the product of three life-history subcomponents: the number of broods available to a focal male to sire EPO, the male's probability of siring an EPO in an available brood and the number of offspring in available broods. This decomposition of EPRS facilitates estimation from field data because all subcomponents can be quantified from paternity data without need to quantify extra-pair matings. Our decomposition also highlights that the number of available broods, and hence population structure and demography, might contribute substantially to variance in male EPRS and fitness. 3. We then used 20 years of complete genetic paternity and pedigree data from wild song sparrows (Melospiza melodia) to partition variance in each of the three subcomponents of EPRS, and thereby estimate their additive genetic variance and heritability conditioned on effects of male coefficient of inbreeding, age and social status. 4. All three subcomponents of EPRS showed some degree of within-male repeatability, reflecting combined permanent environmental and genetic effects. Number of available broods and offspring per brood showed low additive genetic variances. The estimated additive genetic variance in extra-pair siring probability was larger, although the 95% credible interval still converged towards zero. Siring probability also showed inbreeding depression and increased with male age

  4. Bayesian adaptive Markov chain Monte Carlo estimation of genetic parameters.

    Science.gov (United States)

    Mathew, B; Bauer, A M; Koistinen, P; Reetz, T C; Léon, J; Sillanpää, M J

    2012-10-01

    Accurate and fast estimation of genetic parameters that underlie quantitative traits using mixed linear models with additive and dominance effects is of great importance in both natural and breeding populations. Here, we propose a new fast adaptive Markov chain Monte Carlo (MCMC) sampling algorithm for the estimation of genetic parameters in the linear mixed model with several random effects. In the learning phase of our algorithm, we use the hybrid Gibbs sampler to learn the covariance structure of the variance components. In the second phase of the algorithm, we use this covariance structure to formulate an effective proposal distribution for a Metropolis-Hastings algorithm, which uses a likelihood function in which the random effects have been integrated out. Compared with the hybrid Gibbs sampler, the new algorithm had better mixing properties and was approximately twice as fast to run. Our new algorithm was able to detect different modes in the posterior distribution. In addition, the posterior mode estimates from the adaptive MCMC method were close to the REML (residual maximum likelihood) estimates. Moreover, our exponential prior for inverse variance components was vague and enabled the estimated mode of the posterior variance to be practically zero, which was in agreement with the support from the likelihood (in the case of no dominance). The method performance is illustrated using simulated data sets with replicates and field data in barley.

  5. Dominant optic atrophy

    Directory of Open Access Journals (Sweden)

    Lenaers Guy

    2012-07-01

    Full Text Available Abstract Definition of the disease Dominant Optic Atrophy (DOA is a neuro-ophthalmic condition characterized by a bilateral degeneration of the optic nerves, causing insidious visual loss, typically starting during the first decade of life. The disease affects primary the retinal ganglion cells (RGC and their axons forming the optic nerve, which transfer the visual information from the photoreceptors to the lateral geniculus in the brain. Epidemiology The prevalence of the disease varies from 1/10000 in Denmark due to a founder effect, to 1/30000 in the rest of the world. Clinical description DOA patients usually suffer of moderate visual loss, associated with central or paracentral visual field deficits and color vision defects. The severity of the disease is highly variable, the visual acuity ranging from normal to legal blindness. The ophthalmic examination discloses on fundoscopy isolated optic disc pallor or atrophy, related to the RGC death. About 20% of DOA patients harbour extraocular multi-systemic features, including neurosensory hearing loss, or less commonly chronic progressive external ophthalmoplegia, myopathy, peripheral neuropathy, multiple sclerosis-like illness, spastic paraplegia or cataracts. Aetiology Two genes (OPA1, OPA3 encoding inner mitochondrial membrane proteins and three loci (OPA4, OPA5, OPA8 are currently known for DOA. Additional loci and genes (OPA2, OPA6 and OPA7 are responsible for X-linked or recessive optic atrophy. All OPA genes yet identified encode mitochondrial proteins embedded in the inner membrane and ubiquitously expressed, as are the proteins mutated in the Leber Hereditary Optic Neuropathy. OPA1 mutations affect mitochondrial fusion, energy metabolism, control of apoptosis, calcium clearance and maintenance of mitochondrial genome integrity. OPA3 mutations only affect the energy metabolism and the control of apoptosis. Diagnosis Patients are usually diagnosed during their early childhood, because of

  6. Visual SLAM Using Variance Grid Maps

    Science.gov (United States)

    Howard, Andrew B.; Marks, Tim K.

    2011-01-01

    An algorithm denoted Gamma-SLAM performs further processing, in real time, of preprocessed digitized images acquired by a stereoscopic pair of electronic cameras aboard an off-road robotic ground vehicle to build accurate maps of the terrain and determine the location of the vehicle with respect to the maps. Part of the name of the algorithm reflects the fact that the process of building the maps and determining the location with respect to them is denoted simultaneous localization and mapping (SLAM). Most prior real-time SLAM algorithms have been limited in applicability to (1) systems equipped with scanning laser range finders as the primary sensors in (2) indoor environments (or relatively simply structured outdoor environments). The few prior vision-based SLAM algorithms have been feature-based and not suitable for real-time applications and, hence, not suitable for autonomous navigation on irregularly structured terrain. The Gamma-SLAM algorithm incorporates two key innovations: Visual odometry (in contradistinction to wheel odometry) is used to estimate the motion of the vehicle. An elevation variance map (in contradistinction to an occupancy or an elevation map) is used to represent the terrain. The Gamma-SLAM algorithm makes use of a Rao-Blackwellized particle filter (RBPF) from Bayesian estimation theory for maintaining a distribution over poses and maps. The core idea of the RBPF approach is that the SLAM problem can be factored into two parts: (1) finding the distribution over robot trajectories, and (2) finding the map conditioned on any given trajectory. The factorization involves the use of a particle filter in which each particle encodes both a possible trajectory and a map conditioned on that trajectory. The base estimate of the trajectory is derived from visual odometry, and the map conditioned on that trajectory is a Cartesian grid of elevation variances. In comparison with traditional occupancy or elevation grid maps, the grid elevation variance

  7. A relation between information entropy and variance

    CERN Document Server

    Pandey, Biswajit

    2016-01-01

    We obtain an analytic relation between the information entropy and the variance of a distribution in the regime of small fluctuations. We use a set of Monte Carlo simulations of different homogeneous and inhomogeneous distributions to verify the relation and also test it in a set of cosmological N-body simulations. We find that the relation is in excellent agreement with the simulations and is independent of number density and the nature of the distributions. The relation would help us to relate entropy to other conventional measures and widen its scope.

  8. The value of travel time variance

    OpenAIRE

    Fosgerau, Mogens; Engelson, Leonid

    2010-01-01

    This paper considers the value of travel time variability under scheduling preferences that are de�fined in terms of linearly time-varying utility rates associated with being at the origin and at the destination. The main result is a simple expression for the value of travel time variability that does not depend on the shape of the travel time distribution. The related measure of travel time variability is the variance of travel time. These conclusions apply equally to travellers who can free...

  9. Study on Analysis of Variance on the indigenous wild and cultivated rice species of Manipur Valley

    Science.gov (United States)

    Medhabati, K.; Rohinikumar, M.; Rajiv Das, K.; Henary, Ch.; Dikash, Th.

    2012-10-01

    The analysis of variance revealed considerable variation among the cultivars and the wild species for yield and other quantitative characters in both the years of investigation. The highly significant differences among the cultivars in year wise and pooled analysis of variance for all the 12 characters reveal that there are enough genetic variabilities for all the characters studied. The existence of genetic variability is of paramount importance for starting a judicious plant breeding programme. Since introduced high yielding rice cultivars usually do not perform well. Improvement of indigenous cultivars is a clear choice for increase of rice production. The genetic variability of 37 rice germplasms in 12 agronomic characters estimated in the present study can be used in breeding programme

  10. EXPLANATORY VARIANCE IN MAXIMAL OXYGEN UPTAKE

    Directory of Open Access Journals (Sweden)

    Jacalyn J. Robert McComb

    2006-06-01

    Full Text Available The purpose of this study was to develop a prediction equation that could be used to estimate maximal oxygen uptake (VO2max from a submaximal water running protocol. Thirty-two volunteers (n =19 males, n = 13 females, ages 18 - 24 years, underwent the following testing procedures: (a a 7-site skin fold assessment; (b a land VO2max running treadmill test; and (c a 6 min water running test. For the water running submaximal protocol, the participants were fitted with an Aqua Jogger Classic Uni-Sex Belt and a Polar Heart Rate Monitor; the participants' head, shoulders, hips and feet were vertically aligned, using a modified running/bicycle motion. A regression model was used to predict VO2max. The criterion variable, VO2max, was measured using open-circuit calorimetry utilizing the Bruce Treadmill Protocol. Predictor variables included in the model were percent body fat (% BF, height, weight, gender, and heart rate following a 6 min water running protocol. Percent body fat accounted for 76% (r = -0.87, SEE = 3.27 of the variance in VO2max. No other variables significantly contributed to the explained variance in VO2max. The equation for the estimation of VO2max is as follows: VO2max ml.kg-1·min-1 = 56.14 - 0.92 (% BF.

  11. Dimension reduction based on weighted variance estimate

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In this paper, we propose a new estimate for dimension reduction, called the weighted variance estimate (WVE), which includes Sliced Average Variance Estimate (SAVE) as a special case. Bootstrap method is used to select the best estimate from the WVE and to estimate the structure dimension. And this selected best estimate usually performs better than the existing methods such as Sliced Inverse Regression (SIR), SAVE, etc. Many methods such as SIR, SAVE, etc. usually put the same weight on each observation to estimate central subspace (CS). By introducing a weight function, WVE puts different weights on different observations according to distance of observations from CS. The weight function makes WVE have very good performance in general and complicated situations, for example, the distribution of regressor deviating severely from elliptical distribution which is the base of many methods, such as SIR, etc. And compared with many existing methods, WVE is insensitive to the distribution of the regressor. The consistency of the WVE is established. Simulations to compare the performances of WVE with other existing methods confirm the advantage of WVE.

  12. Dimension reduction based on weighted variance estimate

    Institute of Scientific and Technical Information of China (English)

    ZHAO JunLong; XU XingZhong

    2009-01-01

    In this paper,we propose a new estimate for dimension reduction,called the weighted variance estimate (WVE),which includes Sliced Average Variance Estimate (SAVE) as a special case.Bootstrap method is used to select the best estimate from the WVE and to estimate the structure dimension.And this selected best estimate usually performs better than the existing methods such as Sliced Inverse Regression (SIR),SAVE,etc.Many methods such as SIR,SAVE,etc.usually put the same weight on each observation to estimate central subspace (CS).By introducing a weight function,WVE puts different weights on different observations according to distance of observations from CS.The weight function makes WVE have very good performance in general and complicated situations,for example,the distribution of regressor deviating severely from elliptical distribution which is the base of many methods,such as SIR,etc.And compared with many existing methods,WVE is insensitive to the distribution of the regressor.The consistency of the WVE is established.Simulations to compare the performances of WVE with other existing methods confirm the advantage of WVE.

  13. Evolution of Robustness and Plasticity under Environmental Fluctuation: Formulation in Terms of Phenotypic Variances

    Science.gov (United States)

    Kaneko, Kunihiko

    2012-09-01

    The characterization of plasticity, robustness, and evolvability, an important issue in biology, is studied in terms of phenotypic fluctuations. By numerically evolving gene regulatory networks, the proportionality between the phenotypic variances of epigenetic and genetic origins is confirmed. The former is given by the variance of the phenotypic fluctuation due to noise in the developmental process; and the latter, by the variance of the phenotypic fluctuation due to genetic mutation. The relationship suggests a link between robustness to noise and to mutation, since robustness can be defined by the sharpness of the distribution of the phenotype. Next, the proportionality between the variances is demonstrated to also hold over expressions of different genes (phenotypic traits) when the system acquires robustness through the evolution. Then, evolution under environmental variation is numerically investigated and it is found that both the adaptability to a novel environment and the robustness are made compatible when a certain degree of phenotypic fluctuations exists due to noise. The highest adaptability is achieved at a certain noise level at which the gene expression dynamics are near the critical state to lose the robustness. Based on our results, we revisit Waddington's canalization and genetic assimilation with regard to the two types of phenotypic fluctuations.

  14. Quantitative genetics model as the unifying model for defining genomic relationship and inbreeding coefficient.

    Science.gov (United States)

    Wang, Chunkao; Da, Yang

    2014-01-01

    The traditional quantitative genetics model was used as the unifying approach to derive six existing and new definitions of genomic additive and dominance relationships. The theoretical differences of these definitions were in the assumptions of equal SNP effects (equivalent to across-SNP standardization), equal SNP variances (equivalent to within-SNP standardization), and expected or sample SNP additive and dominance variances. The six definitions of genomic additive and dominance relationships on average were consistent with the pedigree relationships, but had individual genomic specificity and large variations not observed from pedigree relationships. These large variations may allow finding least related genomes even within the same family for minimizing genomic relatedness among breeding individuals. The six definitions of genomic relationships generally had similar numerical results in genomic best linear unbiased predictions of additive effects (GBLUP) and similar genomic REML (GREML) estimates of additive heritability. Predicted SNP dominance effects and GREML estimates of dominance heritability were similar within definitions assuming equal SNP effects or within definitions assuming equal SNP variance, but had differences between these two groups of definitions. We proposed a new measure of genomic inbreeding coefficient based on parental genomic co-ancestry coefficient and genomic additive correlation as a genomic approach for predicting offspring inbreeding level. This genomic inbreeding coefficient had the highest correlation with pedigree inbreeding coefficient among the four methods evaluated for calculating genomic inbreeding coefficient in a Holstein sample and a swine sample.

  15. Fuzzy cross-entropy, mean, variance, skewness models for portfolio selection

    Directory of Open Access Journals (Sweden)

    Rupak Bhattacharyya

    2014-01-01

    Full Text Available In this paper, fuzzy stock portfolio selection models that maximize mean and skewness as well as minimize portfolio variance and cross-entropy are proposed. Because returns are typically asymmetric, in addition to typical mean and variance considerations, third order moment skewness is also considered in generating a larger payoff. Cross-entropy is used to quantify the level of discrimination in a return for a given satisfactory return value. As returns are uncertain, stock returns are considered triangular fuzzy numbers. Stock price data from the Bombay Stock Exchange are used to illustrate the effectiveness of the proposed model. The solutions are done by genetic algorithms.

  16. Estimation of (co)variances for genomic regions of flexible sizes

    DEFF Research Database (Denmark)

    Sørensen, Lars P; Janss, Luc; Madsen, Per;

    2012-01-01

    traits such as mammary disease traits in dairy cattle. METHODS: Data on progeny means of six traits related to mastitis resistance in dairy cattle (general mastitis resistance and five pathogen-specific mastitis resistance traits) were analyzed using a bivariate Bayesian SNP-based genomic model......)variances of mastitis resistance traits in dairy cattle using multivariate genomic models......., per chromosome, and in regions of 100 SNP on a chromosome. RESULTS: Genomic proportions of the total variance differed between traits. Genomic correlations were lower than pedigree-based genetic correlations and they were highest between general mastitis and pathogen-specific traits because...

  17. A Mean-variance Problem in the Constant Elasticity of Variance (CEV) Mo del

    Institute of Scientific and Technical Information of China (English)

    Hou Ying-li; Liu Guo-xin; Jiang Chun-lan

    2015-01-01

    In this paper, we focus on a constant elasticity of variance (CEV) model and want to find its optimal strategies for a mean-variance problem under two con-strained controls: reinsurance/new business and investment (no-shorting). First, a Lagrange multiplier is introduced to simplify the mean-variance problem and the corresponding Hamilton-Jacobi-Bellman (HJB) equation is established. Via a power transformation technique and variable change method, the optimal strategies with the Lagrange multiplier are obtained. Final, based on the Lagrange duality theorem, the optimal strategies and optimal value for the original problem (i.e., the efficient strategies and efficient frontier) are derived explicitly.

  18. Stochastic dominance theory for location-scale family

    Directory of Open Access Journals (Sweden)

    Wing-Keung Wong

    2006-01-01

    Full Text Available Meyer (1987 extended the theory of mean-variance criterion to include the comparison among distributions that differ only by location and scale parameters and to include general utility functions with only convexity or concavity restrictions. In this paper, we make some comments on Meyer's paper and extend the results from Tobin (1958 that the indifference curve is convex upwards for risk averters, concave downwards for risk lovers, and horizontal for risk neutral investors to include the general conditions stated by Meyer (1987. We also provide an alternative proof for the theorem. Levy (1989 extended Meyer's results by introducing some inequality relationships between the stochastic-dominance and the mean-variance efficient sets. In this paper, we comment on Levy's findings and show that these relationships do not hold in certain situations. We further develop some properties among the first- and second-degree stochastic dominance efficient sets and the mean-variance efficient set.

  19. Dynamics of Variance Risk Premia, Investors' Sentiment and Return Predictability

    DEFF Research Database (Denmark)

    Rombouts, Jerome V.K.; Stentoft, Lars; Violante, Francesco

    We develop a joint framework linking the physical variance and its risk neutral expectation implying variance risk premia that are persistent, appropriately reacting to changes in level and variability of the variance and naturally satisfying the sign constraint. Using option market data...... and realized variances, our model allows to infer the occurrence and size of extreme variance events, and construct indicators signalling agents sentiment towards future market conditions. Our results show that excess returns are to a large extent explained by fear or optimism towards future extreme variance...

  20. Dominant Voice in Hamlet

    Institute of Scientific and Technical Information of China (English)

    李丹

    2015-01-01

    <正>The Tragedy of Hamlet dramatizes the revenge Prince Hamlet exacts on his uncle Claudius for murdering King Hamlet,Claudius’s brother and Prince Hamlet’s father,and then succeeding to the throne and taking as his wife Gertrude,the old king’s widow and Prince Hamlet’s mother.This paper will discuss something about dominant voice in the play.Dominant voice is the major voice in the country,the society,or the whole world.Those people who have the power or

  1. Stochastic Dominance in Portfolio Analysis and Asset Pricing

    NARCIS (Netherlands)

    A.M. Lizyayev (Andrey)

    2010-01-01

    textabstractStochastic Dominance relation is a probabilistic concept which allows random outcomes such as portfolio returns to be ranked, by utilizing the full information about the distribution of the returns, in contrast to the mean-variance rule or other mean-risk models which only use a single s

  2. Stochastic Dominance in Portfolio Analysis and Asset Pricing

    NARCIS (Netherlands)

    A.M. Lizyayev (Andrey)

    2010-01-01

    textabstractStochastic Dominance relation is a probabilistic concept which allows random outcomes such as portfolio returns to be ranked, by utilizing the full information about the distribution of the returns, in contrast to the mean-variance rule or other mean-risk models which only use a single

  3. The effect of genetic parameters on inheritance of the first pod hight in snap bean - Phaseolus vulgaris L.

    Directory of Open Access Journals (Sweden)

    Zdravković Milan

    2003-01-01

    Full Text Available In order to research the inheritance, gene effect, combination abilities and genetic variance components, we investigated six divergent snap bean genotypes (Supernor, Darija, Grinkrop, Palanačka rana, Šumadinka and Zora and their F1 progeny created by diallel crossing without reciprocals. For the trait of height of forming the first pod, variance of average value of parents and hybrids was highly significant. The value of dominant components (H1 and H2 was higher than additive component (D, meaning that dominant genes control the inheritance of number of pods per plant. The average level of domination √Hl/D is higher than 1, pointing to superdomination. Heritability in broader sence amounts 90% pointing to high contribution in inheriting the number of pods per plant.

  4. Expected Stock Returns and Variance Risk Premia

    DEFF Research Database (Denmark)

    Bollerslev, Tim; Tauchen, George; Zhou, Hao

    constructed from high-frequency intraday, as opposed to daily, data. The magnitude of the predictability is particularly strong at the intermediate quarterly return horizon, where it dominates that afforded by other popular predictor variables, like the P/E ratio, the default spread, and the consumption......-wealth ratio (CAY)....

  5. Dominant cystoid macular dystrophy

    NARCIS (Netherlands)

    Saksens, N.T.M.; Huet, R.A.C. van; Lith-Verhoeven, J.J. van; Hollander, A.I. den; Hoyng, C.B.; Boon, C.J.

    2015-01-01

    OBJECTIVE: To describe the clinical characteristics and long-term follow-up in patients with autosomal dominant cystoid macular dystrophy (DCMD). DESIGN: Retrospective case series. PARTICIPANTS: Ninety-seven patients with DCMD. METHODS: Extensive ophthalmic examination, including visual acuity (VA),

  6. Iron dominated magnets

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, G.E.

    1985-07-01

    These two lectures on iron dominated magnets are meant for the student of accelerator science and contain general treatments of the subjects design and construction. The material is arranged in the categories: General Concepts and Cost Considerations, Profile Configuration and Harmonics, Magnetic Measurements, a few examples of ''special magnets'' and Materials and Practices. Extensive literature is provided.

  7. discourse of domination

    African Journals Online (AJOL)

    suffering justifies the position and work of The Bank and other social forces with similar ... include accounts of the growing and increasingly interwoven resistance in .... tural domination or as parasites able to feed off a social body weakened by the ... through objective analysis of poor people's descriptions of their realities'.

  8. Searching for world domination

    CERN Multimedia

    Quillen, E

    2004-01-01

    "Optimists might believe Microsoft suffered a setback last week that will impede its progress toward world domination, but I suspect the company has already found a way to prevail. At issue before the European Union was Microsoft's bundling of its Windows Media Player with its operating system" (1 page)

  9. Autosomal dominant osteopetrosis revisited

    DEFF Research Database (Denmark)

    Bollerslev, Jens; Henriksen, Kim; Nielsen, Morten Frost Munk

    2013-01-01

    Systematic studies of autosomal dominant osteopetrosis (ADO) were followed by the identification of underlying mutations giving unique possibilities to perform translational studies. What was previously designated ADO1 turned out to be a high bone mass phenotype caused by a missense mutation...

  10. Dominant optic atrophy

    DEFF Research Database (Denmark)

    Lenaers, Guy; Hamel, Christian; Delettre, Cécile

    2012-01-01

    DEFINITION OF THE DISEASE: Dominant Optic Atrophy (DOA) is a neuro-ophthalmic condition characterized by a bilateral degeneration of the optic nerves, causing insidious visual loss, typically starting during the first decade of life. The disease affects primary the retinal ganglion cells (RGC...

  11. The value of travel time variance

    DEFF Research Database (Denmark)

    Fosgerau, Mogens; Engelson, Leonid

    2011-01-01

    This paper considers the value of travel time variability under scheduling preferences that are defined in terms of linearly time varying utility rates associated with being at the origin and at the destination. The main result is a simple expression for the value of travel time variability...... that does not depend on the shape of the travel time distribution. The related measure of travel time variability is the variance of travel time. These conclusions apply equally to travellers who can freely choose departure time and to travellers who use a scheduled service with fixed headway. Depending...... on parameters, travellers may be risk averse or risk seeking and the value of travel time may increase or decrease in the mean travel time....

  12. Power Estimation in Multivariate Analysis of Variance

    Directory of Open Access Journals (Sweden)

    Jean François Allaire

    2007-09-01

    Full Text Available Power is often overlooked in designing multivariate studies for the simple reason that it is believed to be too complicated. In this paper, it is shown that power estimation in multivariate analysis of variance (MANOVA can be approximated using a F distribution for the three popular statistics (Hotelling-Lawley trace, Pillai-Bartlett trace, Wilk`s likelihood ratio. Consequently, the same procedure, as in any statistical test, can be used: computation of the critical F value, computation of the noncentral parameter (as a function of the effect size and finally estimation of power using a noncentral F distribution. Various numerical examples are provided which help to understand and to apply the method. Problems related to post hoc power estimation are discussed.

  13. The influence of mean climate trends and climate variance on beaver survival and recruitment dynamics.

    Science.gov (United States)

    Campbell, Ruairidh D; Nouvellet, Pierre; Newman, Chris; Macdonald, David W; Rosell, Frank

    2012-09-01

    Ecologists are increasingly aware of the importance of environmental variability in natural systems. Climate change is affecting both the mean and the variability in weather and, in particular, the effect of changes in variability is poorly understood. Organisms are subject to selection imposed by both the mean and the range of environmental variation experienced by their ancestors. Changes in the variability in a critical environmental factor may therefore have consequences for vital rates and population dynamics. Here, we examine ≥90-year trends in different components of climate (precipitation mean and coefficient of variation (CV); temperature mean, seasonal amplitude and residual variance) and consider the effects of these components on survival and recruitment in a population of Eurasian beavers (n = 242) over 13 recent years. Within climatic data, no trends in precipitation were detected, but trends in all components of temperature were observed, with mean and residual variance increasing and seasonal amplitude decreasing over time. A higher survival rate was linked (in order of influence based on Akaike weights) to lower precipitation CV (kits, juveniles and dominant adults), lower residual variance of temperature (dominant adults) and lower mean precipitation (kits and juveniles). No significant effects were found on the survival of nondominant adults, although the sample size for this category was low. Greater recruitment was linked (in order of influence) to higher seasonal amplitude of temperature, lower mean precipitation, lower residual variance in temperature and higher precipitation CV. Both climate means and variance, thus proved significant to population dynamics; although, overall, components describing variance were more influential than those describing mean values. That environmental variation proves significant to a generalist, wide-ranging species, at the slow end of the slow-fast continuum of life histories, has broad implications for

  14. Components of variance and heritability of resistance to important fungal diseases agents in grapevine

    Directory of Open Access Journals (Sweden)

    Nikolić Dragan

    2006-01-01

    Full Text Available In four interspecies crossing combinations of grapevine (Seedling 108 x Muscat Hamburg, Muscat Hamburg x Seedling 108, S.V.I8315 x Muscat Hamburg and Muscat Hamburg x S.V.I2375 during three years period, resistance to important fungal diseases agents (Plasmopara viticola and Botrytis cinerea were examined. Based on results of analysis of variance, for investigated characteristics, components of variance, coefficients of genetic and phenotypic variation and coefficient of heritability in a broader sense were calculated. It was established that for both characteristics and in all crossing combinations, genetic variance took the biggest part in total variability. The lowest coefficients of genetic and phenotypic variation were established for both properties in crossing combination Seedling 108 x Muscat Hamburg. The highest coefficients of genetic and phenotypic variation were determined for leaf resistance to Plasmopara viticola in crossing combination Muscat Hamburg x S.V.I2375, and for bunch resistance to Botrytis cinerea in crossing combination Muscat Hamburg x Seedling 108. Considering all investigated crossing combinations, coefficient of heritability for leaf resistance to Plasmopara viticola was from 87.23% to 94.88%, and for bunch resistance to Botrytis cinerea from 88.04% to 93.32%. .

  15. The Parabolic Variance (PVAR): A Wavelet Variance Based on the Least-Square Fit.

    Science.gov (United States)

    Vernotte, Francois; Lenczner, Michel; Bourgeois, Pierre-Yves; Rubiola, Enrico

    2016-04-01

    This paper introduces the parabolic variance (PVAR), a wavelet variance similar to the Allan variance (AVAR), based on the linear regression (LR) of phase data. The companion article arXiv:1506.05009 [physics.ins-det] details the Ω frequency counter, which implements the LR estimate. The PVAR combines the advantages of AVAR and modified AVAR (MVAR). PVAR is good for long-term analysis because the wavelet spans over 2τ, the same as the AVAR wavelet, and good for short-term analysis because the response to white and flicker PM is 1/τ(3) and 1/τ(2), the same as the MVAR. After setting the theoretical framework, we study the degrees of freedom and the confidence interval for the most common noise types. Then, we focus on the detection of a weak noise process at the transition-or corner-where a faster process rolls off. This new perspective raises the question of which variance detects the weak process with the shortest data record. Our simulations show that PVAR is a fortunate tradeoff. PVAR is superior to MVAR in all cases, exhibits the best ability to divide between fast noise phenomena (up to flicker FM), and is almost as good as AVAR for the detection of random walk and drift.

  16. Variation and Genetic Structure in Platanus mexicana (Platanaceae along Riparian Altitudinal Gradient

    Directory of Open Access Journals (Sweden)

    Dulce M. Galván-Hernández

    2015-01-01

    Full Text Available Platanus mexicana is a dominant arboreal species of riparian ecosystems. These ecosystems are associated with altitudinal gradients that can generate genetic differences in the species, especially in the extremes of the distribution. However, studies on the altitudinal effect on genetic variation to riparian species are scarce. In Mexico, the population of P. mexicana along the Colipa River (Veracruz State grows below its reported minimum altitude range, possibly the lowest where this tree grows. This suggests that altitude might be an important factor in population genetics differentiation. We examined the genetic variation and population structuring at four sites with different altitudes (70, 200, 600 and 1700 m a.s.l. using ten inter-simple sequence repeats (ISSR markers. The highest value for Shannon index and Nei’s gene diversity was obtained at 1700 m a.s.l. (He = 0.27, Ne = 1.47, I = 0.42 and polymorphism reached the top value at the middle altitude (% p = 88.57. Analysis of molecular variance (AMOVA and STRUCTURE analysis indicated intrapopulation genetic differentiation. The arithmetic average (UPGMA dendrogram identified 70 m a.s.l. as the most genetically distant site. The genetic structuring resulted from limited gene flow and genetic drift. This is the first report of genetic variation in populations of P. mexicana in Mexico. This research highlights its importance as a dominant species, and its ecological and evolutionary implications in altitudinal gradients of riparian ecosystems.

  17. Developmental quantitative genetic analysis of body weights and morphological traits in the turbot, Scophthalmusmaximus

    Institute of Scientific and Technical Information of China (English)

    WANG Xinan; MA Aijun; MA Deyou

    2015-01-01

    In order to elucidate the genetic mechanism of growth traits in turbot during ontogeny, developmental genetic analysis of the body weights, total lengths, standard lengths and body heights of turbots was conducted by mixed genetic models with additive-dominance effects, based on complete diallel crosses with four different strains of Scophthalmus maximus from Denmark, Norway, Britain, and France. Unconditional genetic analysis revealed that the unconditional additive effects for the four traits were more significant than unconditional dominance effects, meanwhile, the alternative expressions were also observed between the additive and dominant effects for body weights, total lengths and standard lengths. Conditional analysis showed that the developmental periods with active gene expression for body weights, total lengths, standard lengths and body heights were 15–18, 15 and 21–24, 15 and 24, and 21 and 27 months of age, respectively. The proportions of unconditional/conditional variances indicated that the narrow-sense heritabilities of body weights, total lengths and standard lengths were all increased systematically. The accumulative effects of genes controlling the four quantitative traits were mainly additive effects, suggesting that the selection is more efficient for the genetic improvement of turbots. The conditional genetic procedure is a useful tool to understand the expression of genes controlling developmental quantitative traits at a specific developmental period (t-1→t) during ontogeny. It is also important to determine the appropriate developmental period (t-1→t) for trait measurement in developmental quantitative genetic analysis in fish.

  18. A general unified framework to assess the sampling variance of heritability estimates using pedigree or marker-based relationships.

    Science.gov (United States)

    Visscher, Peter M; Goddard, Michael E

    2015-01-01

    Heritability is a population parameter of importance in evolution, plant and animal breeding, and human medical genetics. It can be estimated using pedigree designs and, more recently, using relationships estimated from markers. We derive the sampling variance of the estimate of heritability for a wide range of experimental designs, assuming that estimation is by maximum likelihood and that the resemblance between relatives is solely due to additive genetic variation. We show that well-known results for balanced designs are special cases of a more general unified framework. For pedigree designs, the sampling variance is inversely proportional to the variance of relationship in the pedigree and it is proportional to 1/N, whereas for population samples it is approximately proportional to 1/N(2), where N is the sample size. Variation in relatedness is a key parameter in the quantification of the sampling variance of heritability. Consequently, the sampling variance is high for populations with large recent effective population size (e.g., humans) because this causes low variation in relationship. However, even using human population samples, low sampling variance is possible with high N. Copyright © 2015 by the Genetics Society of America.

  19. Biochemical Genetics of Short-Season Cotton Cultivars that Express Early Maturity Without Senescence

    Institute of Scientific and Technical Information of China (English)

    Shu-Xun YU; Mei-Zhen SONG; Shu-Li FAN; Wu WANG; Ri-Hong YUAN

    2005-01-01

    The present study is aimed to investigate the mechanism of the biochemical genetic in shortseasoned cotton (Gossypium hirsutum L.) (SSC). Ten cultivars from two types of SSC were selected, five SSC with no prematuresenescence crossed with five SSC with premature senescence. The parents, F1, and F2 from the reciprocal crosses were field tested in replication in 2001 and 2002. The results indicated that the activities of protective enzymes of the antioxidant system, such as catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD), were higher in the early maturing SSC with premature senescence compared with activities in the SSC parental cultivars that showed premature senescence, whereas the malondialdehyde (MDA) content in former group was lower than that in latter group. Various genetic variances and heritabilities for these biochemical traits and auxin (IAA), abscisic acid (ABA), and chlorophyll (Chl a+b) contents were also estimated. Significant additive variance for CAT, POD, ABA, and IAA existed, whereas CAT specific activity and SOD activity were largely controlled by dominant effects. Both maternal and dominant variances played equally predominant roles in the specific activity of POD and SOD, MDA, and soluble portents. The relative contribution of the various genetic components to the phenotypic variation varied in the boll-setting period.

  20. Clinical neurogenetics: autosomal dominant spinocerebellar ataxia.

    Science.gov (United States)

    Shakkottai, Vikram G; Fogel, Brent L

    2013-11-01

    The autosomal dominant spinocerebellar ataxias are a diverse and clinically heterogeneous group of disorders characterized by degeneration and dysfunction of the cerebellum and its associated pathways. Clinical and diagnostic evaluation can be challenging because of phenotypic overlap among causes, and a stratified and systematic approach is essential. Recent advances include the identification of additional genes causing dominant genetic ataxia, a better understanding of cellular pathogenesis in several disorders, the generation of new disease models that may stimulate development of new therapies, and the use of new DNA sequencing technologies, including whole-exome sequencing, to improve diagnosis.

  1. Restricted maximum likelihood estimation of variance components from field data for number of pigs born alive.

    Science.gov (United States)

    See, M T; Mabry, J W; Bertrand, J K

    1993-11-01

    Variance components for number of pigs born alive (NBA) were estimated from sow productivity field records collected by purebred breed associations. Data sets analyzed were as follows: Hampshire (n = 13,537), Landrace (n = 10,822), and Spotted (n = 3,949). Variance components for service sire, sire of sow, dam of sow, and residual effects on NBA (adjusted for parity) were estimated. The single-trait model included relationships between service sires, sires of sows, and dams of sows. The model was implemented using an expectation maximization (EM) REML algorithm. A sparse-matrix solver was also used. Heritability estimates for NBA were .13, .13, and .12 for Hampshire, Spotted, and Landrace, respectively. Estimates of maternal genetic (co)variances (m2) expressed as a proportion of the phenotypic variance were .05, .01, and .03 for Hampshire, Spotted, and Landrace, respectively. Results indicated that service sires account for 1 to 2% of the total variation for NBA. Genetic effects influencing NBA seem to be small in these data sets, but selection for increased NBA should be effective.

  2. Bivariate genetic modeling of cardiovascular stress reactivity : Does stress uncover genetic variance?

    NARCIS (Netherlands)

    De Geus, Eco J. C.; Kupper, Nina; Boomsma, Dorret I.; Snieder, Harold

    2007-01-01

    Objective: To test the existence of gene-by-stress interaction by assessing cardiovascular stress reactivity in monozygotic and dizygotic twins. Methods: We studied 160 adolescent (mean age 16.7 +/- 2.0 years; range 13-22 years) and 212 middle-aged twin pairs (mean age 44.2 +/- 6.7 years; range 34-6

  3. Genomic variance estimates: With or without disequilibrium covariances?

    Science.gov (United States)

    Lehermeier, C; de Los Campos, G; Wimmer, V; Schön, C-C

    2017-06-01

    Whole-genome regression methods are often used for estimating genomic heritability: the proportion of phenotypic variance that can be explained by regression on marker genotypes. Recently, there has been an intensive debate on whether and how to account for the contribution of linkage disequilibrium (LD) to genomic variance. Here, we investigate two different methods for genomic variance estimation that differ in their ability to account for LD. By analysing flowering time in a data set on 1,057 fully sequenced Arabidopsis lines with strong evidence for diversifying selection, we observed a large contribution of covariances between quantitative trait loci (QTL) to the genomic variance. The classical estimate of genomic variance that ignores covariances underestimated the genomic variance in the data. The second method accounts for LD explicitly and leads to genomic variance estimates that when added to error variance estimates match the sample variance of phenotypes. This method also allows estimating the covariance between sets of markers when partitioning the genome into subunits. Large covariance estimates between the five Arabidopsis chromosomes indicated that the population structure in the data led to strong LD also between physically unlinked QTL. By consecutively removing population structure from the phenotypic variance using principal component analysis, we show how population structure affects the magnitude of LD contribution and the genomic variance estimates obtained with the two methods. © 2017 Blackwell Verlag GmbH.

  4. Characterizing nonconstant instrumental variance in emerging miniaturized analytical techniques.

    Science.gov (United States)

    Noblitt, Scott D; Berg, Kathleen E; Cate, David M; Henry, Charles S

    2016-04-01

    Measurement variance is a crucial aspect of quantitative chemical analysis. Variance directly affects important analytical figures of merit, including detection limit, quantitation limit, and confidence intervals. Most reported analyses for emerging analytical techniques implicitly assume constant variance (homoskedasticity) by using unweighted regression calibrations. Despite the assumption of constant variance, it is known that most instruments exhibit heteroskedasticity, where variance changes with signal intensity. Ignoring nonconstant variance results in suboptimal calibrations, invalid uncertainty estimates, and incorrect detection limits. Three techniques where homoskedasticity is often assumed were covered in this work to evaluate if heteroskedasticity had a significant quantitative impact-naked-eye, distance-based detection using paper-based analytical devices (PADs), cathodic stripping voltammetry (CSV) with disposable carbon-ink electrode devices, and microchip electrophoresis (MCE) with conductivity detection. Despite these techniques representing a wide range of chemistries and precision, heteroskedastic behavior was confirmed for each. The general variance forms were analyzed, and recommendations for accounting for nonconstant variance discussed. Monte Carlo simulations of instrument responses were performed to quantify the benefits of weighted regression, and the sensitivity to uncertainty in the variance function was tested. Results show that heteroskedasticity should be considered during development of new techniques; even moderate uncertainty (30%) in the variance function still results in weighted regression outperforming unweighted regressions. We recommend utilizing the power model of variance because it is easy to apply, requires little additional experimentation, and produces higher-precision results and more reliable uncertainty estimates than assuming homoskedasticity.

  5. R. A. Fisher. The relevance of the genetical theory of natural selection

    Directory of Open Access Journals (Sweden)

    Paola Monari

    2013-05-01

    Full Text Available Starting from the main statement that “. . . natural selection is not evolution. . . ”, R.A. Fisher built the foundation of the genetic theory of population in his famous work Genetical Theory of Natural Selection (1930. He rewrote the scientific paradigm proposed by Darwin in statistical terms using the calculus of probability and, most importantly, statistics. The key to his formal transposition is in the analysis of variance inwhich Fisher interpreted as phenomenical variability by means of random variability: this completely original result would become a fundamental chapter of statisticalmethod. It is not by chance that at the same time he published his statistical method for research workers in which the analysis of variance dominated his primary elements of the design of experiments.

  6. Variance components estimation for farrowing traits of three purebred pigs in Korea

    Directory of Open Access Journals (Sweden)

    Bryan Irvine Lopez

    2017-09-01

    Full Text Available Objective This study was conducted to estimate breed-specific variance components for total number born (TNB, number born alive (NBA and mortality rate from birth through weaning including stillbirths (MORT of three main swine breeds in Korea. In addition, the importance of including maternal genetic and service sire effects in estimation models was evaluated. Methods Records of farrowing traits from 6,412 Duroc, 18,020 Landrace, and 54,254 Yorkshire sows collected from January 2001 to September 2016 from different farms in Korea were used in the analysis. Animal models and the restricted maximum likelihood method were used to estimate variances in animal genetic, permanent environmental, maternal genetic, service sire and residuals. Results The heritability estimates ranged from 0.072 to 0.102, 0.090 to 0.099, and 0.109 to 0.121 for TNB; 0.087 to 0.110, 0.088 to 0.100, and 0.099 to 0.107 for NBA; and 0.027 to 0.031, 0.050 to 0.053, and 0.073 to 0.081 for MORT in the Duroc, Landrace and Yorkshire breeds, respectively. The proportion of the total variation due to permanent environmental effects, maternal genetic effects, and service sire effects ranged from 0.042 to 0.088, 0.001 to 0.031, and 0.001 to 0.021, respectively. Spearman rank correlations among models ranged from 0.98 to 0.99, demonstrating that the maternal genetic and service sire effects have small effects on the precision of the breeding value. Conclusion Models that include additive genetic and permanent environmental effects are suitable for farrowing traits in Duroc, Landrace, and Yorkshire populations in Korea. This breed-specific variance components estimates for litter traits can be utilized for pig improvement programs in Korea.

  7. Variance components estimation for farrowing traits of three purebred pigs in Korea.

    Science.gov (United States)

    Lopez, Bryan Irvine; Kim, Tae Hun; Makumbe, Milton Tinashe; Song, Chol Won; Seo, Kang Seok

    2017-09-01

    This study was conducted to estimate breed-specific variance components for total number born (TNB), number born alive (NBA) and mortality rate from birth through weaning including stillbirths (MORT) of three main swine breeds in Korea. In addition, the importance of including maternal genetic and service sire effects in estimation models was evaluated. Records of farrowing traits from 6,412 Duroc, 18,020 Landrace, and 54,254 Yorkshire sows collected from January 2001 to September 2016 from different farms in Korea were used in the analysis. Animal models and the restricted maximum likelihood method were used to estimate variances in animal genetic, permanent environmental, maternal genetic, service sire and residuals. The heritability estimates ranged from 0.072 to 0.102, 0.090 to 0.099, and 0.109 to 0.121 for TNB; 0.087 to 0.110, 0.088 to 0.100, and 0.099 to 0.107 for NBA; and 0.027 to 0.031, 0.050 to 0.053, and 0.073 to 0.081 for MORT in the Duroc, Landrace and Yorkshire breeds, respectively. The proportion of the total variation due to permanent environmental effects, maternal genetic effects, and service sire effects ranged from 0.042 to 0.088, 0.001 to 0.031, and 0.001 to 0.021, respectively. Spearman rank correlations among models ranged from 0.98 to 0.99, demonstrating that the maternal genetic and service sire effects have small effects on the precision of the breeding value. Models that include additive genetic and permanent environmental effects are suitable for farrowing traits in Duroc, Landrace, and Yorkshire populations in Korea. This breed-specific variance components estimates for litter traits can be utilized for pig improvement programs in Korea.

  8. Dominating biological networks.

    Directory of Open Access Journals (Sweden)

    Tijana Milenković

    Full Text Available Proteins are essential macromolecules of life that carry out most cellular processes. Since proteins aggregate to perform function, and since protein-protein interaction (PPI networks model these aggregations, one would expect to uncover new biology from PPI network topology. Hence, using PPI networks to predict protein function and role of protein pathways in disease has received attention. A debate remains open about whether network properties of "biologically central (BC" genes (i.e., their protein products, such as those involved in aging, cancer, infectious diseases, or signaling and drug-targeted pathways, exhibit some topological centrality compared to the rest of the proteins in the human PPI network.To help resolve this debate, we design new network-based approaches and apply them to get new insight into biological function and disease. We hypothesize that BC genes have a topologically central (TC role in the human PPI network. We propose two different concepts of topological centrality. We design a new centrality measure to capture complex wirings of proteins in the network that identifies as TC those proteins that reside in dense extended network neighborhoods. Also, we use the notion of domination and find dominating sets (DSs in the PPI network, i.e., sets of proteins such that every protein is either in the DS or is a neighbor of the DS. Clearly, a DS has a TC role, as it enables efficient communication between different network parts. We find statistically significant enrichment in BC genes of TC nodes and outperform the existing methods indicating that genes involved in key biological processes occupy topologically complex and dense regions of the network and correspond to its "spine" that connects all other network parts and can thus pass cellular signals efficiently throughout the network. To our knowledge, this is the first study that explores domination in the context of PPI networks.

  9. Proportionality between variances in gene expression induced by noise and mutation: consequence of evolutionary robustness

    Directory of Open Access Journals (Sweden)

    Kaneko Kunihiko

    2011-01-01

    Full Text Available Abstract Background Characterization of robustness and plasticity of phenotypes is a basic issue in evolutionary and developmental biology. The robustness and plasticity are concerned with changeability of a biological system against external perturbations. The perturbations are either genetic, i.e., due to mutations in genes in the population, or epigenetic, i.e., due to noise during development or environmental variations. Thus, the variances of phenotypes due to genetic and epigenetic perturbations provide quantitative measures for such changeability during evolution and development, respectively. Results Using numerical models simulating the evolutionary changes in the gene regulation network required to achieve a particular expression pattern, we first confirmed that gene expression dynamics robust to mutation evolved in the presence of a sufficient level of transcriptional noise. Under such conditions, the two types of variances in the gene expression levels, i.e. those due to mutations to the gene regulation network and those due to noise in gene expression dynamics were found to be proportional over a number of genes. The fraction of such genes with a common proportionality coefficient increased with an increase in the robustness of the evolved network. This proportionality was generally confirmed, also under the presence of environmental fluctuations and sexual recombination in diploids, and was explained from an evolutionary robustness hypothesis, in which an evolved robust system suppresses the so-called error catastrophe - the destabilization of the single-peaked distribution in gene expression levels. Experimental evidences for the proportionality of the variances over genes are also discussed. Conclusions The proportionality between the genetic and epigenetic variances of phenotypes implies the correlation between the robustness (or plasticity against genetic changes and against noise in development, and also suggests that

  10. Male size composition affects male reproductive variance in Atlantic cod Gadus morhua L. spawning aggregations

    DEFF Research Database (Denmark)

    Bekkevold, Dorte

    2006-01-01

    Estimates of Atlantic cod Gadus morhua reproductive success, determined using experimental spawning groups and genetic paternity assignment of offspring, showed that within-group variance in male size correlated positively with the degree of male mating skew, predicting a decrease in male...... reproductive skew with decreasing size variation among males under natural conditions. (c) 2006 The Author Journal compilation (c) 2006 The Fisheries Society of the British Isles...

  11. Challenging Credit Dominance

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    @@ Europe's widening sovereign debt crisis has brought independent credit ratings to the forefront of the EU's agenda.To directly address the mat ter,the EU announced plans to set up a European creditrating authority for sovereign debt ratings on April 30.This marked a milestone in the international credit history,and the beginning of changes to U.S.-dominated international credit ratings and the pattern of international politics and economics,said Sun Zhe,Director of the Center for U.S.

  12. Gene set analysis using variance component tests

    Science.gov (United States)

    2013-01-01

    Background Gene set analyses have become increasingly important in genomic research, as many complex diseases are contributed jointly by alterations of numerous genes. Genes often coordinate together as a functional repertoire, e.g., a biological pathway/network and are highly correlated. However, most of the existing gene set analysis methods do not fully account for the correlation among the genes. Here we propose to tackle this important feature of a gene set to improve statistical power in gene set analyses. Results We propose to model the effects of an independent variable, e.g., exposure/biological status (yes/no), on multiple gene expression values in a gene set using a multivariate linear regression model, where the correlation among the genes is explicitly modeled using a working covariance matrix. We develop TEGS (Test for the Effect of a Gene Set), a variance component test for the gene set effects by assuming a common distribution for regression coefficients in multivariate linear regression models, and calculate the p-values using permutation and a scaled chi-square approximation. We show using simulations that type I error is protected under different choices of working covariance matrices and power is improved as the working covariance approaches the true covariance. The global test is a special case of TEGS when correlation among genes in a gene set is ignored. Using both simulation data and a published diabetes dataset, we show that our test outperforms the commonly used approaches, the global test and gene set enrichment analysis (GSEA). Conclusion We develop a gene set analyses method (TEGS) under the multivariate regression framework, which directly models the interdependence of the expression values in a gene set using a working covariance. TEGS outperforms two widely used methods, GSEA and global test in both simulation and a diabetes microarray data. PMID:23806107

  13. Accounting for Variance in Hyperspectral Data Coming from Limitations of the Imaging System

    Science.gov (United States)

    Shurygin, B.; Shestakova, M.; Nikolenko, A.; Badasen, E.; Strakhov, P.

    2016-06-01

    Over the course of the past few years, a number of methods was developed to incorporate hyperspectral imaging specifics into generic data mining techniques, traditionally used for hyperspectral data processing. Projection pursuit methods embody the largest class of methods empoyed for hyperspectral image data reduction, however, they all have certain drawbacks making them either hard to use or inefficient. It has been shown that hyperspectral image (HSI) statistics tend to display "heavy tails" (Manolakis2003)(Theiler2005), rendering most of the projection pursuit methods hard to use. Taking into consideration the magnitude of described deviations of observed data PDFs from normal distribution, it is apparent that a priori knowledge of variance in data caused by the imaging system is to be employed in order to efficiently classify objects on HSIs (Kerr, 2015), especially in cases of wildly varying SNR. A number of attempts to describe this variance and compensating techniques has been made (Aiazzi2006), however, new data quality standards are not yet set and accounting for the detector response is made under large set of assumptions. Current paper addresses the issue of hyperspectral image classification in the context of different variance sources based on the knowledge of calibration curves (both spectral and radiometric) obtained for each pixel of imaging camera. A camera produced by ZAO NPO Lepton (Russia) was calibrated and used to obtain a test image. A priori known values of SNR and spectral channel cross-correlation were incorporated into calculating test statistics used in dimensionality reduction and feature extraction. Expectation-Maximization classification algorithm modification for non-Gaussian model as described by (Veracini2010) was further employed. The impact of calibration data coarsening by ignoring non-uniformities on false alarm rate was studied. Case study shows both regions of scene-dominated variance and sensor-dominated variance, leading

  14. Rings dominate western Gulf

    Science.gov (United States)

    Vidal L., Francisco V.; Vidal L., Victor M. V.; Molero, José María Pérez

    Surface and deep circulation of the central and western Gulf of Mexico is controlled by interactions of rings of water pinched from the gulf's Loop Current. The discovery was made by Mexican oceanographers who are preparing a full-color, 8-volume oceanographic atlas of the gulf.Anticyclonic warm-core rings pinch off the Loop Current at a rate of about one to two per year, the scientists of the Grupo de Estudios Oceanográficos of the Instituto de Investigaciones Eléctricas (GEO-IIE) found. The rings migrate west until they collide with the continental shelf break of the western gulf, almost always between 22° and 23°N latitude. On their westward travel they transfer angular momentum and vorticity to the surrounding water, generating cyclonic circulations and vortex pairs that completely dominate the entire surface and deep circulation of the central and western gulf.

  15. Dominant modal decomposition method

    Science.gov (United States)

    Dombovari, Zoltan

    2017-03-01

    The paper deals with the automatic decomposition of experimental frequency response functions (FRF's) of mechanical structures. The decomposition of FRF's is based on the Green function representation of free vibratory systems. After the determination of the impulse dynamic subspace, the system matrix is formulated and the poles are calculated directly. By means of the corresponding eigenvectors, the contribution of each element of the impulse dynamic subspace is determined and the sufficient decomposition of the corresponding FRF is carried out. With the presented dominant modal decomposition (DMD) method, the mode shapes, the modal participation vectors and the modal scaling factors are identified using the decomposed FRF's. Analytical example is presented along with experimental case studies taken from machine tool industry.

  16. Anatomic variance of the iliopsoas tendon.

    Science.gov (United States)

    Philippon, Marc J; Devitt, Brian M; Campbell, Kevin J; Michalski, Max P; Espinoza, Chris; Wijdicks, Coen A; Laprade, Robert F

    2014-04-01

    The iliopsoas tendon has been implicated as a generator of hip pain and a cause of labral injury due to impingement. Arthroscopic release of the iliopsoas tendon has become a preferred treatment for internal snapping hips. Traditionally, the iliopsoas tendon has been considered the conjoint tendon of the psoas major and iliacus muscles, although anatomic variance has been reported. The iliopsoas tendon consists of 2 discrete tendons in the majority of cases, arising from both the psoas major and iliacus muscles. Descriptive laboratory study. Fifty-three nonmatched, fresh-frozen, cadaveric hemipelvis specimens (average age, 62 years; range, 47-70 years; 29 male and 24 female) were used in this study. The iliopsoas muscle was exposed via a Smith-Petersen approach. A transverse incision across the entire iliopsoas musculotendinous unit was made at the level of the hip joint. Each distinctly identifiable tendon was recorded, and the distance from the lesser trochanter was recorded. The prevalence of a single-, double-, and triple-banded iliopsoas tendon was 28.3%, 64.2%, and 7.5%, respectively. The psoas major tendon was consistently the most medial tendinous structure, and the primary iliacus tendon was found immediately lateral to the psoas major tendon within the belly of the iliacus muscle. When present, an accessory iliacus tendon was located adjacent to the primary iliacus tendon, lateral to the primary iliacus tendon. Once considered a rare anatomic variant, the finding of ≥2 distinct tendinous components to the iliacus and psoas major muscle groups is an important discovery. It is essential to be cognizant of the possibility that more than 1 tendon may exist to ensure complete release during endoscopy. Arthroscopic release of the iliopsoas tendon is a well-accepted surgical treatment for iliopsoas impingement. The most widely used site for tendon release is at the level of the anterior hip joint. The findings of this novel cadaveric anatomy study suggest that

  17. A New Look at Genetic and Environmental Architecture on Lipids Using Non-Normal Structural Equation Modeling in Male Twins: The NHLBI Twin Study.

    Science.gov (United States)

    Wu, Sheng-Hui; Ozaki, Koken; Reed, Terry; Krasnow, Ruth E; Dai, Jun

    2017-07-01

    This study examined genetic and environmental influences on the lipid concentrations of 1028 male twins using the novel univariate non-normal structural equation modeling (nnSEM) ADCE and ACE models. In the best fitting nnSEM ADCE model that was also better than the nnSEM ACE model, additive genetic factors (A) explained 4%, dominant genetic factors (D) explained 17%, and common (C) and unique (E) environmental factors explained 47% and 33% of the total variance of high-density lipoprotein cholesterol (HDL-C). The percentage of variation explained for other lipids was 0% (A), 30% (D), 34% (C) and 37% (E) for low-density lipoprotein cholesterol (LDL-C); 30, 0, 31 and 39% for total cholesterol; and 0, 31, 12 and 57% for triglycerides. It was concluded that additive and dominant genetic factors simultaneously affected HDL-C concentrations but not other lipids. Common and unique environmental factors influenced concentrations of all lipids.

  18. Refined genetic mapping of autosomal dominant retinitis pigmentosa locus RP18 reduces the critical region to 2 cM between D1S442 and D1S2858 on chromosome 1q.

    Science.gov (United States)

    Xu, S Y; Rosenberg, T; Gal, A

    1998-04-01

    Linkage analysis was performed on a large Danish family to refine the position of RP18, the locus for autosomal dominant retinitis pigmentosa, mapped previously between D1S534 and D1S305 in chromosome 1p13-q21. We genotyped the family members for five microsatellite-type DNA polymorphisms and mapped RP18 between D1S422 and D1S2858 to a region of less than 2 cM. No obvious candidate gene has yet been assigned to the chromosomal interval defined here.

  19. 40 CFR 190.11 - Variances for unusual operations.

    Science.gov (United States)

    2010-07-01

    ... PROTECTION PROGRAMS ENVIRONMENTAL RADIATION PROTECTION STANDARDS FOR NUCLEAR POWER OPERATIONS Environmental Standards for the Uranium Fuel Cycle § 190.11 Variances for unusual operations. The standards specified...

  20. Simulations of the Hadamard Variance: Probability Distributions and Confidence Intervals.

    Science.gov (United States)

    Ashby, Neil; Patla, Bijunath

    2016-04-01

    Power-law noise in clocks and oscillators can be simulated by Fourier transforming a modified spectrum of white phase noise. This approach has been applied successfully to simulation of the Allan variance and the modified Allan variance in both overlapping and nonoverlapping forms. When significant frequency drift is present in an oscillator, at large sampling times the Allan variance overestimates the intrinsic noise, while the Hadamard variance is insensitive to frequency drift. The simulation method is extended in this paper to predict the Hadamard variance for the common types of power-law noise. Symmetric real matrices are introduced whose traces-the sums of their eigenvalues-are equal to the Hadamard variances, in overlapping or nonoverlapping forms, as well as for the corresponding forms of the modified Hadamard variance. We show that the standard relations between spectral densities and Hadamard variance are obtained with this method. The matrix eigenvalues determine probability distributions for observing a variance at an arbitrary value of the sampling interval τ, and hence for estimating confidence in the measurements.

  1. Network Structure and Biased Variance Estimation in Respondent Driven Sampling.

    Directory of Open Access Journals (Sweden)

    Ashton M Verdery

    Full Text Available This paper explores bias in the estimation of sampling variance in Respondent Driven Sampling (RDS. Prior methodological work on RDS has focused on its problematic assumptions and the biases and inefficiencies of its estimators of the population mean. Nonetheless, researchers have given only slight attention to the topic of estimating sampling variance in RDS, despite the importance of variance estimation for the construction of confidence intervals and hypothesis tests. In this paper, we show that the estimators of RDS sampling variance rely on a critical assumption that the network is First Order Markov (FOM with respect to the dependent variable of interest. We demonstrate, through intuitive examples, mathematical generalizations, and computational experiments that current RDS variance estimators will always underestimate the population sampling variance of RDS in empirical networks that do not conform to the FOM assumption. Analysis of 215 observed university and school networks from Facebook and Add Health indicates that the FOM assumption is violated in every empirical network we analyze, and that these violations lead to substantially biased RDS estimators of sampling variance. We propose and test two alternative variance estimators that show some promise for reducing biases, but which also illustrate the limits of estimating sampling variance with only partial information on the underlying population social network.

  2. Multiperiod Mean-Variance Portfolio Optimization via Market Cloning

    Energy Technology Data Exchange (ETDEWEB)

    Ankirchner, Stefan, E-mail: ankirchner@hcm.uni-bonn.de [Rheinische Friedrich-Wilhelms-Universitaet Bonn, Institut fuer Angewandte Mathematik, Hausdorff Center for Mathematics (Germany); Dermoune, Azzouz, E-mail: Azzouz.Dermoune@math.univ-lille1.fr [Universite des Sciences et Technologies de Lille, Laboratoire Paul Painleve UMR CNRS 8524 (France)

    2011-08-15

    The problem of finding the mean variance optimal portfolio in a multiperiod model can not be solved directly by means of dynamic programming. In order to find a solution we therefore first introduce independent market clones having the same distributional properties as the original market, and we replace the portfolio mean and variance by their empirical counterparts. We then use dynamic programming to derive portfolios maximizing a weighted sum of the empirical mean and variance. By letting the number of market clones converge to infinity we are able to solve the original mean variance problem.

  3. RR-Interval variance of electrocardiogram for atrial fibrillation detection

    Science.gov (United States)

    Nuryani, N.; Solikhah, M.; Nugoho, A. S.; Afdala, A.; Anzihory, E.

    2016-11-01

    Atrial fibrillation is a serious heart problem originated from the upper chamber of the heart. The common indication of atrial fibrillation is irregularity of R peak-to-R-peak time interval, which is shortly called RR interval. The irregularity could be represented using variance or spread of RR interval. This article presents a system to detect atrial fibrillation using variances. Using clinical data of patients with atrial fibrillation attack, it is shown that the variance of electrocardiographic RR interval are higher during atrial fibrillation, compared to the normal one. Utilizing a simple detection technique and variances of RR intervals, we find a good performance of atrial fibrillation detection.

  4. Estimation of Variance Components for Litter Size in the First and Later Parities in Improved Jezersko-Solcava Sheep

    Directory of Open Access Journals (Sweden)

    Dubravko Škorput

    2011-12-01

    Full Text Available Aim of this study was to estimate variance components for litter size in Improved Jezersko-Solcava sheep. Analysis involved 66,082 records from 12,969 animals, for the number of lambs born in all parities (BA, the first parity (B1, and later parities (B2+. Fixed part of model contained the effects of season and age at lambing within parity. Random part of model contained the effects of herd, permanent effect (for repeatability models, and additive genetic effect. Variance components were estimated using the restricted maximum likelihood method. The average number of lambs born was 1.36 in the first parity, while the average in later parities was 1.59 leading also to about 20% higher variance. Several models were tested in order to accommodate markedly different variability in litter size between the first and later parities: single trait model (for BA, B1, and B2+, two-trait model (for B1 and B2+, and single trait model with heterogeneous residual variance (for BA. Comparison of variance components between models showed largest differences for the residual variance, resulting in parsimonious fit for a single trait model for BA with heterogeneous residual variance. Correlations among breeding values from different models were high and showed remarkable performance of the standard single trait repeatability model for BA.

  5. The effect of using approximate gametic variance covariance matrices on marker assisted selection by BLUP.

    Science.gov (United States)

    Totir, Liviu R; Fernando, Rohan L; Dekkers, Jack C M; Fernández, Soledad A; Guldbrandtsen, Bernt

    2004-01-01

    Under additive inheritance, the Henderson mixed model equations (HMME) provide an efficient approach to obtaining genetic evaluations by marker assisted best linear unbiased prediction (MABLUP) given pedigree relationships, trait and marker data. For large pedigrees with many missing markers, however, it is not feasible to calculate the exact gametic variance covariance matrix required to construct HMME. The objective of this study was to investigate the consequences of using approximate gametic variance covariance matrices on response to selection by MABLUP. Two methods were used to generate approximate variance covariance matrices. The first method (Method A) completely discards the marker information for individuals with an unknown linkage phase between two flanking markers. The second method (Method B) makes use of the marker information at only the most polymorphic marker locus for individuals with an unknown linkage phase. Data sets were simulated with and without missing marker data for flanking markers with 2, 4, 6, 8 or 12 alleles. Several missing marker data patterns were considered. The genetic variability explained by marked quantitative trait loci (MQTL) was modeled with one or two MQTL of equal effect. Response to selection by MABLUP using Method A or Method B were compared with that obtained by MABLUP using the exact genetic variance covariance matrix, which was estimated using 15,000 samples from the conditional distribution of genotypic values given the observed marker data. For the simulated conditions, the superiority of MABLUP over BLUP based only on pedigree relationships and trait data varied between 0.1% and 13.5% for Method A, between 1.7% and 23.8% for Method B, and between 7.6% and 28.9% for the exact method. The relative performance of the methods under investigation was not affected by the number of MQTL in the model.

  6. Camera Calibration with Radial Variance Component Estimation

    Science.gov (United States)

    Mélykuti, B.; Kruck, E. J.

    2014-11-01

    Camera calibration plays a more and more important role in recent times. Beside real digital aerial survey cameras the photogrammetric market is dominated by a big number of non-metric digital cameras mounted on UAVs or other low-weight flying platforms. The in-flight calibration of those systems has a significant role to enhance the geometric accuracy of survey photos considerably. It is expected to have a better precision of photo measurements in the center of images then along the edges or in the corners. With statistical methods the accuracy of photo measurements in dependency of the distance of points from image center has been analyzed. This test provides a curve for the measurement precision as function of the photo radius. A high number of camera types have been tested with well penetrated point measurements in image space. The result of the tests led to a general consequence to show a functional connection between accuracy and radial distance and to give a method how to check and enhance the geometrical capability of the cameras in respect to these results.

  7. Analysis of variance of designed chromatographic data sets: The analysis of variance-target projection approach.

    Science.gov (United States)

    Marini, Federico; de Beer, Dalene; Joubert, Elizabeth; Walczak, Beata

    2015-07-31

    Direct application of popular approaches, e.g., Principal Component Analysis (PCA) or Partial Least Squares (PLS) to chromatographic data originating from a well-designed experimental study including more than one factor is not recommended. In the case of a well-designed experiment involving two or more factors (crossed or nested), data are usually decomposed into the contributions associated with the studied factors (and with their interactions), and the individual effect matrices are then analyzed using, e.g., PCA, as in the case of ASCA (analysis of variance combined with simultaneous component analysis). As an alternative to the ASCA method, we propose the application of PLS followed by target projection (TP), which allows a one-factor representation of the model for each column in the design dummy matrix. PLS application follows after proper deflation of the experimental matrix, i.e., to what are called the residuals under the reduced ANOVA model. The proposed approach (ANOVA-TP) is well suited for the study of designed chromatographic data of complex samples. It allows testing of statistical significance of the studied effects, 'biomarker' identification, and enables straightforward visualization and accurate estimation of between- and within-class variance. The proposed approach has been successfully applied to a case study aimed at evaluating the effect of pasteurization on the concentrations of various phenolic constituents of rooibos tea of different quality grades and its outcomes have been compared to those of ASCA.

  8. Onset dominance in lateralization.

    Science.gov (United States)

    Freyman, R L; Zurek, P M; Balakrishnan, U; Chiang, Y C

    1997-03-01

    Saberi and Perrott [Acustica 81, 272-275 (1995)] found that the in-head lateralization of a relatively long-duration pulse train could be controlled by the interaural delay of the single pulse pair that occurs at onset. The present study examined this further, using an acoustic pointer measure of lateralization, with stimulus manipulations designed to determine conditions under which lateralization was consistent with the interaural onset delay. The present stimuli were wideband pulse trains, noise-burst trains, and inharmonic complexes, 250 ms in duration, chosen for the ease with which interaural delays and correlations of select temporal segments of the stimulus could be manipulated. The stimulus factors studied were the periodicity of the ongoing part of the signal as well as the multiplicity and ambiguity of interaural delays. The results, in general, showed that the interaural onset delay controlled lateralization when the steady state binaural cues were relatively weak, either because the spectral components were only sparsely distributed across frequency or because the interaural time delays were ambiguous. Onset dominance can be disrupted by sudden stimulus changes within the train, and several examples of such changes are described. Individual subjects showed strong left-right asymmetries in onset effectiveness. The results have implications for understanding how onset and ongoing interaural delay cues contribute to the location estimates formed by the binaural auditory system.

  9. The dominance of norm

    Directory of Open Access Journals (Sweden)

    Edward L. Rubin

    2017-06-01

    Full Text Available Objective to revisit the debate about rational choice theory from the legal cultural and historical perspectives. Methods dialectic approach to the cognition of social phenomena allowing to analyze them in their historical development and functioning in the context of the integrity of subjective and objective factors this determines the choice of the research methods systemicstructural formallegal and comparative. Results The first part of this chapter will explain the way in which people in societies different from our own were subject to other motivations in situations where selfinterest would tend to dominate in our society. The reasoning is based on three examples one drawn from the history of Ancient Rome one from the High Middle Ages of the European society and one from a contemporary nonWestern culture. The second part of the chapter analyzes the reason why material selfinterest maximizing became a dominant motivation in the modern Western society. The works on historical sociology attribute this development to Calvinism but this hypothesis suffers from some serious defects. In the article we prove that the modern sensibility resulted from much longeracting trends specifically secularization urbanization and commercialization. The final section of the chapter explores the relationship between the Westrsquos prevailing norm of selfinterest maximization and the particular norms that have been discussed in microeconomic theory. It argues that some of these norms are internal to the prevailing one and are thus explicable in terms of material selfinterest but that others reflect additional norms in the general society that exist alongside and sometimes in competition with the prevailing norm of selfinterest maximization. The historicallybased view that selfinterest maximizing is a prevailing norm rather than a human universal allows these other norms to be acknowledged in a plausible and realistic manner rather than being explained away by a

  10. Genetics Home Reference: isolated growth hormone deficiency

    Science.gov (United States)

    ... Genetic Testing (4 links) Genetic Testing Registry: Ateleiotic dwarfism Genetic Testing Registry: Autosomal dominant isolated somatotropin deficiency ... in my area? Other Names for This Condition dwarfism, growth hormone deficiency dwarfism, pituitary growth hormone deficiency ...

  11. An Analysis of Variance Framework for Matrix Sampling.

    Science.gov (United States)

    Sirotnik, Kenneth

    Significant cost savings can be achieved with the use of matrix sampling in estimating population parameters from psychometric data. The statistical design is intuitively simple, using the framework of the two-way classification analysis of variance technique. For example, the mean and variance are derived from the performance of a certain grade…

  12. Gender Variance and Educational Psychology: Implications for Practice

    Science.gov (United States)

    Yavuz, Carrie

    2016-01-01

    The area of gender variance appears to be more visible in both the media and everyday life. Within educational psychology literature gender variance remains underrepresented. The positioning of educational psychologists working across the three levels of child and family, school or establishment and education authority/council, means that they are…

  13. Gender Variance and Educational Psychology: Implications for Practice

    Science.gov (United States)

    Yavuz, Carrie

    2016-01-01

    The area of gender variance appears to be more visible in both the media and everyday life. Within educational psychology literature gender variance remains underrepresented. The positioning of educational psychologists working across the three levels of child and family, school or establishment and education authority/council, means that they are…

  14. Error Variance of Rasch Measurement with Logistic Ability Distributions.

    Science.gov (United States)

    Dimitrov, Dimiter M.

    Exact formulas for classical error variance are provided for Rasch measurement with logistic distributions. An approximation formula with the normal ability distribution is also provided. With the proposed formulas, the additive contribution of individual items to the population error variance can be determined without knowledge of the other test…

  15. A Broadband Beamformer Using Controllable Constraints and Minimum Variance

    DEFF Research Database (Denmark)

    Karimian-Azari, Sam; Benesty, Jacob; Jensen, Jesper Rindom

    2014-01-01

    The minimum variance distortionless response (MVDR) and the linearly constrained minimum variance (LCMV) beamformers are two optimal approaches in the sense of noise reduction. The LCMV beamformer can also reject interferers using linear constraints at the expense of reducing the degree of freedom...

  16. On the Endogeneity of the Mean-Variance Efficient Frontier.

    Science.gov (United States)

    Somerville, R. A.; O'Connell, Paul G. J.

    2002-01-01

    Explains that the endogeneity of the efficient frontier in the mean-variance model of portfolio selection is commonly obscured in portfolio selection literature and in widely used textbooks. Demonstrates endogeneity and discusses the impact of parameter changes on the mean-variance efficient frontier and on the beta coefficients of individual…

  17. Delivery Time Variance Reduction in the Military Supply Chain

    Science.gov (United States)

    2010-03-01

    DELIVERY TIME VARIANCE REDUCTION IN THE MILITARY SUPPLY CHAIN THESIS...IN THE MILITARY SUPPLY CHAIN THESIS Presented to the Faculty Department of Operational Sciences Graduate School of Engineering...March 2010 APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED. AFIT-OR-MS-ENS-10-02 DELIVERY TIME VARIANCE IN THE MILITARY SUPPLY CHAIN Preston

  18. The asymptotic variance of departures in critically loaded queues

    NARCIS (Netherlands)

    A. Al Hanbali; M.R.H. Mandjes (Michel); Y. Nazarathy (Yoni); W. Whitt

    2010-01-01

    htmlabstractWe consider the asymptotic variance of the departure counting process D(t) of the GI/G/1 queue; D(t) denotes the number of departures up to time t. We focus on the case that the system load rho equals 1, and prove that the asymptotic variance rate satisfies lim_t Var D(t)/t = lambda

  19. 76 FR 78698 - Proposed Revocation of Permanent Variances

    Science.gov (United States)

    2011-12-19

    ... Occupational Safety and Health Administration Proposed Revocation of Permanent Variances AGENCY: Occupational... short and plain statement detailing (1) how the proposed revocation would affect the requesting party..., subpart L. The following table provides information about the variances proposed for revocation by...

  20. Adjustment for heterogeneous variances due to days in milk and ...

    African Journals Online (AJOL)

    ARC-IRENE

    Adjustment of heterogeneous variances and a calving year effect in test-day ... Regression Test-Day Model (FRTDM), which assumes equal variances of the response variable at different .... random residual error .... records were included in the selection, while in the unadjusted data set, lactations consisting of six and more.

  1. Productive Failure in Learning the Concept of Variance

    Science.gov (United States)

    Kapur, Manu

    2012-01-01

    In a study with ninth-grade mathematics students on learning the concept of variance, students experienced either direct instruction (DI) or productive failure (PF), wherein they were first asked to generate a quantitative index for variance without any guidance before receiving DI on the concept. Whereas DI students relied only on the canonical…

  2. Time variance effects and measurement error indications for MLS measurements

    DEFF Research Database (Denmark)

    Liu, Jiyuan

    1999-01-01

    Mathematical characteristics of Maximum-Length-Sequences are discussed, and effects of measuring on slightly time-varying systems with the MLS method are examined with computer simulations with MATLAB. A new coherence measure is suggested for the indication of time-variance effects. The results...... of the simulations show that the proposed MLS coherence can give an indication of time-variance effects....

  3. Confidence Intervals of Variance Functions in Generalized Linear Model

    Institute of Scientific and Technical Information of China (English)

    Yong Zhou; Dao-ji Li

    2006-01-01

    In this paper we introduce an appealing nonparametric method for estimating variance and conditional variance functions in generalized linear models (GLMs), when designs are fixed points and random variables respectively. Bias-corrected confidence bands are proposed for the (conditional) variance by local linear smoothers. Nonparametric techniques are developed in deriving the bias-corrected confidence intervals of the (conditional) variance. The asymptotic distribution of the proposed estimator is established and show that the bias-corrected confidence bands asymptotically have the correct coverage properties. A small simulation is performed when unknown regression parameter is estimated by nonparametric quasi-likelihood. The results are also applicable to nonparametric autoregressive times series model with heteroscedastic conditional variance.

  4. Research on variance of subnets in network sampling

    Institute of Scientific and Technical Information of China (English)

    Qi Gao; Xiaoting Li; Feng Pan

    2014-01-01

    In the recent research of network sampling, some sam-pling concepts are misunderstood, and the variance of subnets is not taken into account. We propose the correct definition of the sample and sampling rate in network sampling, as wel as the formula for calculating the variance of subnets. Then, three commonly used sampling strategies are applied to databases of the connecting nearest-neighbor (CNN) model, random network and smal-world network to explore the variance in network sam-pling. As proved by the results, snowbal sampling obtains the most variance of subnets, but does wel in capturing the network struc-ture. The variance of networks sampled by the hub and random strategy are much smal er. The hub strategy performs wel in re-flecting the property of the whole network, while random sampling obtains more accurate results in evaluating clustering coefficient.

  5. Minimum Variance Portfolios in the Brazilian Equity Market

    Directory of Open Access Journals (Sweden)

    Alexandre Rubesam

    2013-03-01

    Full Text Available We investigate minimum variance portfolios in the Brazilian equity market using different methods to estimate the covariance matrix, from the simple model of using the sample covariance to multivariate GARCH models. We compare the performance of the minimum variance portfolios to those of the following benchmarks: (i the IBOVESPA equity index, (ii an equally-weighted portfolio, (iii the maximum Sharpe ratio portfolio and (iv the maximum growth portfolio. Our results show that the minimum variance portfolio has higher returns with lower risk compared to the benchmarks. We also consider long-short 130/30 minimum variance portfolios and obtain similar results. The minimum variance portfolio invests in relatively few stocks with low βs measured with respect to the IBOVESPA index, being easily replicable by individual and institutional investors alike.

  6. The genetics of obesity.

    Science.gov (United States)

    All definitions of the metabolic syndrome include some form of obesity as one of the possible features. Body mass index (BMI) has a known genetic component, currently estimated to account for about 70% of the population variance in weight status for non-syndromal obesity. Much research effort has be...

  7. Genetic variation in variability

    NARCIS (Netherlands)

    Mulder, Herman; Gienapp, Phillip; Visser, Marcel E.

    2016-01-01

    Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations, we know that families can differ in their level of within-family variance, which leads to the intriguing situation th

  8. The genetics of maternal care: direct and indirect genetic effects on phenotype in the dung beetle Onthophagus taurus.

    Science.gov (United States)

    Hunt, John; Simmons, Leigh W

    2002-05-14

    While theoretical models of the evolution of parental care are based on the assumption of underlying genetic variance, surprisingly few quantitative genetic studies of this life-history trait exist. Estimation of the degree of genetic variance in parental care is important because it can be a significant source of maternal effects, which, if genetically based, represent indirect genetic effects. A major prediction of indirect genetic effect theory is that traits without heritable variation can evolve because of the heritable environmental variation that indirect genetic effects provide. In the dung beetle, Onthophagus taurus, females provide care to offspring by provisioning a brood mass. The size of the brood mass has pronounced effects on offspring phenotype. Using a half-sib breeding design we show that the weight of the brood mass females produce exhibits significant levels of additive genetic variance due to sires. However, variance caused by dams is considerably larger, demonstrating that maternal effects are also important. Body size exhibited low additive genetic variance. However, body size exerts a strong maternal influence on the weight of brood masses produced, accounting for 22% of the nongenetic variance in offspring body size. Maternal body size also influenced the number of offspring produced but there was no genetic variance for this trait. Offspring body size and brood mass weight exhibited positive genetic and phenotypic correlations. We conclude that both indirect genetic effects, via maternal care, and nongenetic maternal effects, via female size, play important roles in the evolution of phenotype in this species.

  9. The patterns of genomic variances and covariances across genome for milk production traits between Chinese and Nordic Holstein populations.

    Science.gov (United States)

    Li, Xiujin; Lund, Mogens Sandø; Janss, Luc; Wang, Chonglong; Ding, Xiangdong; Zhang, Qin; Su, Guosheng

    2017-03-15

    With the development of SNP chips, SNP information provides an efficient approach to further disentangle different patterns of genomic variances and covariances across the genome for traits of interest. Due to the interaction between genotype and environment as well as possible differences in genetic background, it is reasonable to treat the performances of a biological trait in different populations as different but genetic correlated traits. In the present study, we performed an investigation on the patterns of region-specific genomic variances, covariances and correlations between Chinese and Nordic Holstein populations for three milk production traits. Variances and covariances between Chinese and Nordic Holstein populations were estimated for genomic regions at three different levels of genome region (all SNP as one region, each chromosome as one region and every 100 SNP as one region) using a novel multi-trait random regression model which uses latent variables to model heterogeneous variance and covariance. In the scenario of the whole genome as one region, the genomic variances, covariances and correlations obtained from the new multi-trait Bayesian method were comparable to those obtained from a multi-trait GBLUP for all the three milk production traits. In the scenario of each chromosome as one region, BTA 14 and BTA 5 accounted for very large genomic variance, covariance and correlation for milk yield and fat yield, whereas no specific chromosome showed very large genomic variance, covariance and correlation for protein yield. In the scenario of every 100 SNP as one region, most regions explained variance and covariance for milk yield and fat yield, and explained variance and covariance. Although overall correlations between two populations for the three traits were positive and high, a few regions still showed weakly positive or highly negative genomic correlations for milk yield and fat yield. The new multi-trait Bayesian method using latent variables

  10. On Dominator Colorings in Graphs

    Indian Academy of Sciences (India)

    S Arumugam; Jay Bagga; K Raja Chandrasekar

    2012-11-01

    A dominator coloring of a graph is a proper coloring of in which every vertex dominates every vertex of at least one color class. The minimum number of colors required for a dominator coloring of is called the dominator chromatic number of and is denoted by $ d(G)$. In this paper we present several results on graphs with $ d(G)=(G)$ and $ d(G)=(G)$ where $(G)$ and $(G)$ denote respectively the chromatic number and the domination number of a graph . We also prove that if $(G)$ is the Mycielskian of , then $ d(G)+1≤ d((G))≤ d(G)+2$.

  11. Estimation of prediction error variances via Monte Carlo sampling methods using different formulations of the prediction error variance

    NARCIS (Netherlands)

    Hickey, J.M.; Veerkamp, R.F.; Calus, M.P.L.; Mulder, H.A.; Thompson, R.

    2009-01-01

    Calculation of the exact prediction error variance covariance matrix is often computationally too demanding, which limits its application in REML algorithms, the calculation of accuracies of estimated breeding values and the control of variance of response to selection. Alternatively Monte Carlo

  12. Estimation of prediction error variances via Monte Carlo sampling methods using different formulations of the prediction error variance

    NARCIS (Netherlands)

    Hickey, J.M.; Veerkamp, R.F.; Calus, M.P.L.; Mulder, H.A.; Thompson, R.

    2009-01-01

    Calculation of the exact prediction error variance covariance matrix is often computationally too demanding, which limits its application in REML algorithms, the calculation of accuracies of estimated breeding values and the control of variance of response to selection. Alternatively Monte Carlo sam

  13. Variance and covariance of actual relationships between relatives at one locus.

    Science.gov (United States)

    Garcia-Cortes, Luis Alberto; Legarra, Andres; Chevalet, Claude; Toro, Miguel Angel

    2013-01-01

    The relationship between pairs of individuals is an important topic in many areas of population and quantitative genetics. It is usually measured as the proportion of the genome identical by descent shared by the pair and it can be inferred from pedigree information. But there is a variance in actual relationships as a consequence of mendelian sampling, whose general formula has not been developed. The goal of this work is to develop this general formula for the one-locus situation,. We provide simple expressions for the variances and covariances of all actual relationships in an arbitrary complex pedigree. The proposed method relies on the use of the nine identity coefficients and the generalized relationship coefficients; formulas have been checked by computer simulation. Finally two examples for a short pedigree of dogs and a long pedigree of sheep are given.

  14. Spinocerebellar ataxias in the Netherlands - Prevalence and age at onset variance analysis

    NARCIS (Netherlands)

    van de Warrenburg, BPC; Sinke, RJ; Verschuuren-Bemelmans, CC; Scheffer, H; Brunt, ER; Ippel, PF; Maat-Kievit, JA; Dooijes, D; Notermans, NC; Lindhout, D; Knoers, NVAM; Kremer, HPH

    2002-01-01

    Background. International prevalence estimates of autosomal dominant cerebellar ataxias (ADCA) vary from 0.3 to 2.0 per 100,000. The prevalence of ADCA in the Netherlands is unknown. Fifteen genetic loci have been identified (SCA-1-8, SCA-10-14, SCA-16, and SCA-17) and nine of the corresponding gene

  15. Spinocerebellar ataxias in the Netherlands: prevalence and age at onset variance analysis.

    NARCIS (Netherlands)

    Warrenburg, B.P.C. van de; Sinke, R.J.; Verschuuren-Bemelmans, C.C.; Scheffer, H.; Brunt, E.R.; Ippel, P.F.; Maat-Kievit, J.A.; Dooijes, D.; Notermans, S.L.H.; Lindhout, D.; Knoers, N.V.A.M.; Kremer, H.P.H.

    2002-01-01

    BACKGROUND: International prevalence estimates of autosomal dominant cerebellar ataxias (ADCA) vary from 0.3 to 2.0 per 100,000. The prevalence of ADCA in the Netherlands is unknown. Fifteen genetic loci have been identified (SCA-1-8, SCA-10-14, SCA-16, and SCA-17) and nine of the corresponding gene

  16. Capturing Option Anomalies with a Variance-Dependent Pricing Kernel

    DEFF Research Database (Denmark)

    Christoffersen, Peter; Heston, Steven; Jacobs, Kris

    2013-01-01

    We develop a GARCH option model with a new pricing kernel allowing for a variance premium. While the pricing kernel is monotonic in the stock return and in variance, its projection onto the stock return is nonmonotonic. A negative variance premium makes it U shaped. We present new semiparametric ...... for the implied volatility puzzle, the overreaction of long-term options to changes in short-term variance, and the fat tails of the risk-neutral return distribution relative to the physical distribution....... evidence to confirm this U-shaped relationship between the risk-neutral and physical probability densities. The new pricing kernel substantially improves our ability to reconcile the time-series properties of stock returns with the cross-section of option prices. It provides a unified explanation......We develop a GARCH option model with a new pricing kernel allowing for a variance premium. While the pricing kernel is monotonic in the stock return and in variance, its projection onto the stock return is nonmonotonic. A negative variance premium makes it U shaped. We present new semiparametric...

  17. Filtered kriging for spatial data with heterogeneous measurement error variances.

    Science.gov (United States)

    Christensen, William F

    2011-09-01

    When predicting values for the measurement-error-free component of an observed spatial process, it is generally assumed that the process has a common measurement error variance. However, it is often the case that each measurement in a spatial data set has a known, site-specific measurement error variance, rendering the observed process nonstationary. We present a simple approach for estimating the semivariogram of the unobservable measurement-error-free process using a bias adjustment of the classical semivariogram formula. We then develop a new kriging predictor that filters the measurement errors. For scenarios where each site's measurement error variance is a function of the process of interest, we recommend an approach that also uses a variance-stabilizing transformation. The properties of the heterogeneous variance measurement-error-filtered kriging (HFK) predictor and variance-stabilized HFK predictor, and the improvement of these approaches over standard measurement-error-filtered kriging are demonstrated using simulation. The approach is illustrated with climate model output from the Hudson Strait area in northern Canada. In the illustration, locations with high or low measurement error variances are appropriately down- or upweighted in the prediction of the underlying process, yielding a realistically smooth picture of the phenomenon of interest.

  18. Meta-analysis of ratios of sample variances.

    Science.gov (United States)

    Prendergast, Luke A; Staudte, Robert G

    2016-05-20

    When conducting a meta-analysis of standardized mean differences (SMDs), it is common to use Cohen's d, or its variants, that require equal variances in the two arms of each study. While interpretation of these SMDs is simple, this alone should not be used as a justification for assuming equal variances. Until now, researchers have either used an F-test for each individual study or perhaps even conveniently ignored such tools altogether. In this paper, we propose a meta-analysis of ratios of sample variances to assess whether the equality of variances assumptions is justified prior to a meta-analysis of SMDs. Quantile-quantile plots, an omnibus test for equal variances or an overall meta-estimate of the ratio of variances can all be used to formally justify the use of less common methods when evidence of unequal variances is found. The methods in this paper are simple to implement and the validity of the approaches are reinforced by simulation studies and an application to a real data set.

  19. Genetics Home Reference: osteopetrosis

    Science.gov (United States)

    ... Autosomal dominant osteopetrosis (ADO), which is also called Albers-Schönberg disease, is typically the mildest type of ... Genetics, pathogenesis and complications of osteopetrosis. Bone. 2008 Jan;42(1):19-29. Epub 2007 Aug 30. ...

  20. Genetic analysis of drought tolerance with respect to fiber traits in upland cotton.

    Science.gov (United States)

    Nasimi, R A; Khan, I A; Iqbal, M A; Khan, A A

    2016-10-05

    Cotton germplasm was analyzed to investigate its potential for developing water stress tolerance in varieties in the future. Four tolerant (NIAB-78, CIM-482, BH-121, and VH-142) and four susceptible (CIM-446, FH-1000, FH-900, and FH-901) lines were identified of 50 accessions based on their seedling root length. A complete set of diallel crosses among eight selected genotypes was subjected to genetic analysis for fiber property traits. Additive and non-additive genetic variance was involved in the inheritance of fiber strength, fineness, and length under normal and drought conditions. A large proportion of genetic variance was additive, which was further supported by moderately high narrow-sense heritability estimates for the characters. Graphic representation of variance versus covariance also depicted additive gene activity with partial dominance and the absence of non-allelic interactions in trait inheritance. The results of this study suggest that drought tolerance of cotton genotypes can be improved through crosses among tolerant genotypes using conventional selection procedures in segregating generations.

  1. Global Gravity Wave Variances from Aura MLS: Characteristics and Interpretation

    Science.gov (United States)

    Wu, Dong L.; Eckermann, Stephen D.

    2008-01-01

    The gravity wave (GW)-resolving capabilities of 118-GHz saturated thermal radiances acquired throughout the stratosphere by the Microwave Limb Sounder (MLS) on the Aura satellite are investigated and initial results presented. Because the saturated (optically thick) radiances resolve GW perturbations from a given altitude at different horizontal locations, variances are evaluated at 12 pressure altitudes between 21 and 51 km using the 40 saturated radiances found at the bottom of each limb scan. Forward modeling simulations show that these variances are controlled mostly by GWs with vertical wavelengths z 5 km and horizontal along-track wavelengths of y 100-200 km. The tilted cigar-shaped three-dimensional weighting functions yield highly selective responses to GWs of high intrinsic frequency that propagate toward the instrument. The latter property is used to infer the net meridional component of GW propagation by differencing the variances acquired from ascending (A) and descending (D) orbits. Because of improved vertical resolution and sensitivity, Aura MLS GW variances are 5?8 times larger than those from the Upper Atmosphere Research Satellite (UARS) MLS. Like UARS MLS variances, monthly-mean Aura MLS variances in January and July 2005 are enhanced when local background wind speeds are large, due largely to GW visibility effects. Zonal asymmetries in variance maps reveal enhanced GW activity at high latitudes due to forcing by flow over major mountain ranges and at tropical and subtropical latitudes due to enhanced deep convective generation as inferred from contemporaneous MLS cloud-ice data. At 21-28-km altitude (heights not measured by the UARS MLS), GW variance in the tropics is systematically enhanced and shows clear variations with the phase of the quasi-biennial oscillation, in general agreement with GW temperature variances derived from radiosonde, rocketsonde, and limb-scan vertical profiles.

  2. Variance components and heritabilities for sow productivity traits estimated from purebred versus crossbred sows.

    Science.gov (United States)

    Ehlers, M J; Mabry, J W; Bertrand, J K; Stalder, K J

    2005-10-01

    Genetic parameters were estimated for number of pigs born alive (NBA), adjusted litter weaning weight (ALWT), and the interval from weaning to first service (W2E) using 2002 purebred litter records and 14 583 crossbred litter records from a swine production unit with a defined great-grandparent, grandparent, and parent stock genetic system structure. Estimation of (co)variance components was carried out by REML methods. Heritability estimates from this study for NBA were 0.155, 0.146, 0.145 for the purebred, crossbred, and pooled data, respectively. Heritability estimates for ALWT were 0.162, 0.195, and 0.183 for the purebred, crossbred and pooled data, respectively. Heritability estimates for W2E were 0.205, 0.239 and 0.202 for the purebred, crossbred and pooled data, respectively. Genetic correlations between NBA and ALWT were weak and positive for the three groups. The genetic correlation between W2E and ALWT were -0.158 for the purebred Yorkshires, 0.031 for the crossbreds and 0.051 for the pooled data. The genetic correlation between W2E and NBA was -0.027 for the purebred Yorkshires, 0.310 for the crossbreds and 0.236 for the pooled data. These similarities suggest that pooling of purebred and crossbred data may be considered, which may potentially increase the accuracy of breeding value estimates, which would result in increased genetic progress.

  3. Variance and covariance components for liability of piglet survival during different periods.

    Science.gov (United States)

    Su, G; Sorensen, D; Lund, M S

    2008-02-01

    Variance and covariance components for piglet survival in different periods were estimated from individual records of 133 004 Danish Landrace piglets and 89 928 Danish Yorkshire piglets, using a liability threshold model including both direct and maternal additive genetic effects. At the individual piglet level, the estimates of direct heritability in Landrace were 0.035, 0.057 and 0.027, and in Yorkshire the estimates were 0.012, 0.030 and 0.025 for liability of survival at farrowing (SVB), from birth to day 5 (SV5) and from day 6 to weaning (SVW), respectively. The estimates of maternal heritability for SVB, SV5 and SVW were, respectively, 0.057, 0.040 and 0.030 in Landrace, and 0.050, 0.038 and 0.019 in Yorkshire. Both direct and maternal genetic correlations between the three survival traits were low and not significantly different from zero, except for a moderate direct genetic correlation between SVB and SV5 and between SV5 and SVW in Landrace. Direct and maternal genetic correlations between piglet birth weight (BW) and SV5 were moderately high, but the correlations between BW and SVB and between BW and SVW were low and most of them were not significantly different from zero. These results suggest that effective genetic improvement in piglet survival before weaning by selection should be based on both direct and maternal additive genetic effects and treat survival in different periods as different traits.

  4. Can Big Five Facets Distinguish between Hedonic and Eudaimonic Well-Being? A Dominance Analysis.

    Science.gov (United States)

    Marrero, Rosario J; Rey, Mar; Hernández-Cabrera, Juan Andrés

    2016-11-22

    In this study, the aim was to analyze the relative importance of Five-Factor Model (FFM) personality facets for eudaimonic or psychological well-being (PWB) and hedonic or subjective well-being (SWB) through dominance analyses. The participants were 1,403 adult residents of Spain (mean age 37.2 years, SD = 13.9). As expected, facets captured a substantial proportion of the variance in PWB and SWB, with PWB being better predicted than SWB (explaining around 36-55% of the variance of PWB vs. 25% of the variance of SWB). Some facets were common to both types of well-being such as depression (explaining between 5-33% of the variance), vulnerability (explaining between 4-21% of the variance), positive emotions (explaining between 2-9% of the variance) and achievement striving (explaining between 2-10% of the variance), whereas others made a unique contribution according to type of well-being. Certain facets had a greater relative importance for women's well-being -e.g., positive emotions explained 9% of the variance of self-acceptance for women vs. 3% for men- and others for men's well-being -e.g., achievement striving explained 9% of the variance of personal growth for men vs. 2% for women-. The present results contribute to the literature by identifying which Big Five facets showed greater relative importance in explaining and distinguishing between PWB and SWB for women and men.

  5. Multiple mating but not recombination causes quantitative increase in offspring genetic diversity for varying genetic architectures.

    Directory of Open Access Journals (Sweden)

    Olav Rueppell

    Full Text Available Explaining the evolution of sex and recombination is particularly intriguing for some species of eusocial insects because they display exceptionally high mating frequencies and genomic recombination rates. Explanations for both phenomena are based on the notion that both increase colony genetic diversity, with demonstrated benefits for colony disease resistance and division of labor. However, the relative contributions of mating number and recombination rate to colony genetic diversity have never been simultaneously assessed. Our study simulates colonies, assuming different mating numbers, recombination rates, and genetic architectures, to assess their worker genotypic diversity. The number of loci has a strong negative effect on genotypic diversity when the allelic effects are inversely scaled to locus number. In contrast, dominance, epistasis, lethal effects, or limiting the allelic diversity at each locus does not significantly affect the model outcomes. Mating number increases colony genotypic variance and lowers variation among colonies with quickly diminishing returns. Genomic recombination rate does not affect intra- and inter-colonial genotypic variance, regardless of mating frequency and genetic architecture. Recombination slightly increases the genotypic range of colonies and more strongly the number of workers with unique allele combinations across all loci. Overall, our study contradicts the argument that the exceptionally high recombination rates cause a quantitative increase in offspring genotypic diversity across one generation. Alternative explanations for the evolution of high recombination rates in social insects are therefore needed. Short-term benefits are central to most explanations of the evolution of multiple mating and high recombination rates in social insects but our results also apply to other species.

  6. Variance computations for functional of absolute risk estimates.

    Science.gov (United States)

    Pfeiffer, R M; Petracci, E

    2011-07-01

    We present a simple influence function based approach to compute the variances of estimates of absolute risk and functions of absolute risk. We apply this approach to criteria that assess the impact of changes in the risk factor distribution on absolute risk for an individual and at the population level. As an illustration we use an absolute risk prediction model for breast cancer that includes modifiable risk factors in addition to standard breast cancer risk factors. Influence function based variance estimates for absolute risk and the criteria are compared to bootstrap variance estimates.

  7. Capturing Option Anomalies with a Variance-Dependent Pricing Kernel

    DEFF Research Database (Denmark)

    Christoffersen, Peter; Heston, Steven; Jacobs, Kris

    2013-01-01

    We develop a GARCH option model with a new pricing kernel allowing for a variance premium. While the pricing kernel is monotonic in the stock return and in variance, its projection onto the stock return is nonmonotonic. A negative variance premium makes it U shaped. We present new semiparametric...... evidence to confirm this U-shaped relationship between the risk-neutral and physical probability densities. The new pricing kernel substantially improves our ability to reconcile the time-series properties of stock returns with the cross-section of option prices. It provides a unified explanation...

  8. Genetic Diversity of Mycobacterium tuberculosis Isolates from Assam, India: Dominance of Beijing Family and Discovery of Two New Clades Related to CAS1_Delhi and EAI Family Based on Spoligotyping and MIRU-VNTR Typing.

    Science.gov (United States)

    Devi, Kangjam Rekha; Bhutia, Rinchenla; Bhowmick, Shovonlal; Mukherjee, Kaustab; Mahanta, Jagadish; Narain, Kanwar

    2015-01-01

    Tuberculosis (TB) is one of the major public health concerns in Assam, a remote state located in the northeastern (NE) region of India. The present study was undertaken to explore the circulating genotypes of Mycobacterium tuberculosis complex (MTBC) in this region. A total of 189 MTBC strains were collected from smear positive pulmonary tuberculosis cases from different designated microscopy centres (DMC) from various localities of Assam. All MTBC isolates were cultured on Lowenstein-Jensen (LJ) media and subsequently genotyped using spoligotyping and 24-loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) typing. Spoligotyping of MTBC isolates revealed 89 distinct spoligo patterns. The most dominant MTBC strain belonged to Beijing lineage and was represented by 35.45% (n = 67) of total isolates, followed by MTBC strains belonging to Central Asian-Delhi (CAS/Delhi) lineage and East African Indian (EAI5) lineage. In addition, in the present study 43 unknown spoligo patterns were detected. The discriminatory power of spoligotyping was found to be 0.8637 based on Hunter Gaston Discriminatory Index (HGDI). On the other hand, 24-loci MIRU-VNTR typing revealed that out of total 189 MTBC isolates from Assam 185 (97.9%) isolates had unique MIRU-VNTR profiles and 4 isolates grouped into 2 clusters. Phylogenetic analysis of 67 Beijing isolates based on 24-loci MIRU-VNTR typing revealed that Beijing isolates from Assam represent two major groups, each comprising of several subgroups. Neighbour-Joining (NJ) phylogenetic tree analysis based on combined spoligotyping and 24-loci MIRU-VNTR data of 78 Non-Beijing isolates was carried out for strain lineage identification as implemented by MIRU-VNTRplus database. The important lineages of MTBC identified were CAS/CAS1_Delhi (41.02%, n = 78) and East-African-Indian (EAI, 33.33%). Interestingly, phylogenetic analysis of orphan (23.28%) MTBC spoligotypes revealed that majority of these orphan

  9. Pricing Volatility Derivatives Under the Modified Constant Elasticity of Variance Model

    OpenAIRE

    Leunglung Chan; Eckhard Platen

    2015-01-01

    This paper studies volatility derivatives such as variance and volatility swaps, options on variance in the modified constant elasticity of variance model using the benchmark approach. The analytical expressions of pricing formulas for variance swaps are presented. In addition, the numerical solutions for variance swaps, volatility swaps and options on variance are demonstrated.

  10. A comparison of strategies for Markov chain Monte Carlo computation in quantitative genetics

    DEFF Research Database (Denmark)

    Waagepetersen, Rasmus; Ibánez-Escriche, Noelia; Sorensen, Daniel

    2008-01-01

    In quantitative genetics, Markov chain Monte Carlo (MCMC) methods are indispensable for statistical inference in non-standard models like generalized linear models with genetic random effects or models with genetically structured variance heterogeneity. A particular challenge for MCMC applications...

  11. Key questions in the genetics and genomics of eco-evolutionary dynamics.

    Science.gov (United States)

    Hendry, A P

    2013-12-01

    Increasing acceptance that evolution can be 'rapid' (or 'contemporary') has generated growing interest in the consequences for ecology. The genetics and genomics of these 'eco-evolutionary dynamics' will be--to a large extent--the genetics and genomics of organismal phenotypes. In the hope of stimulating research in this area, I review empirical data from natural populations and draw the following conclusions. (1) Considerable additive genetic variance is present for most traits in most populations. (2) Trait correlations do not consistently oppose selection. (3) Adaptive differences between populations often involve dominance and epistasis. (4) Most adaptation is the result of genes of small-to-modest effect, although (5) some genes certainly have larger effects than the others. (6) Adaptation by independent lineages to similar environments is mostly driven by different alleles/genes. (7) Adaptation to new environments is mostly driven by standing genetic variation, although new mutations can be important in some instances. (8) Adaptation is driven by both structural and regulatory genetic variation, with recent studies emphasizing the latter. (9) The ecological effects of organisms, considered as extended phenotypes, are often heritable. Overall, the study of eco-evolutionary dynamics will benefit from perspectives and approaches that emphasize standing genetic variation in many genes of small-to-modest effect acting across multiple traits and that analyze overall adaptation or 'fitness'. In addition, increasing attention should be paid to dominance, epistasis and regulatory variation.

  12. Estimation of prediction error variances via Monte Carlo sampling methods using different formulations of the prediction error variance.

    Science.gov (United States)

    Hickey, John M; Veerkamp, Roel F; Calus, Mario P L; Mulder, Han A; Thompson, Robin

    2009-02-09

    Calculation of the exact prediction error variance covariance matrix is often computationally too demanding, which limits its application in REML algorithms, the calculation of accuracies of estimated breeding values and the control of variance of response to selection. Alternatively Monte Carlo sampling can be used to calculate approximations of the prediction error variance, which converge to the true values if enough samples are used. However, in practical situations the number of samples, which are computationally feasible, is limited. The objective of this study was to compare the convergence rate of different formulations of the prediction error variance calculated using Monte Carlo sampling. Four of these formulations were published, four were corresponding alternative versions, and two were derived as part of this study. The different formulations had different convergence rates and these were shown to depend on the number of samples and on the level of prediction error variance. Four formulations were competitive and these made use of information on either the variance of the estimated breeding value and on the variance of the true breeding value minus the estimated breeding value or on the covariance between the true and estimated breeding values.

  13. Dominantly-inherited lop ears.

    Science.gov (United States)

    Leung, Alexander K C; Kong, Albert Y F; Robson, W Lane M; McLeod, D Ross

    2007-10-01

    We describe a four-generation Chinese family that included five members who had an isolated bilateral lop ear anomaly. The presentation suggested a dominant mode of inheritance. The absence of male-to-male transmission does not exclude an X-linked dominant mode of inheritance. Since the phenotypic anomaly of the male proband was no more severe than the affected female members, an autosomal dominant mode of inheritance is most likely. 2007 Wiley-Liss, Inc

  14. minimum variance estimation of yield parameters of rubber tree with ...

    African Journals Online (AJOL)

    2013-03-01

    Mar 1, 2013 ... STAMP, an OxMetric modular software system for time series analysis, was used to estimate the yield ... derlying regression techniques. .... Kalman Filter Minimum Variance Estimation of Rubber Tree Yield Parameters. 83.

  15. Detecting Pulsars with Interstellar Scintillation in Variance Images

    CERN Document Server

    Dai, S; Bell, M E; Coles, W A; Hobbs, G; Ekers, R D; Lenc, E

    2016-01-01

    Pulsars are the only cosmic radio sources known to be sufficiently compact to show diffractive interstellar scintillations. Images of the variance of radio signals in both time and frequency can be used to detect pulsars in large-scale continuum surveys using the next generation of synthesis radio telescopes. This technique allows a search over the full field of view while avoiding the need for expensive pixel-by-pixel high time resolution searches. We investigate the sensitivity of detecting pulsars in variance images. We show that variance images are most sensitive to pulsars whose scintillation time-scales and bandwidths are close to the subintegration time and channel bandwidth. Therefore, in order to maximise the detection of pulsars for a given radio continuum survey, it is essential to retain a high time and frequency resolution, allowing us to make variance images sensitive to pulsars with different scintillation properties. We demonstrate the technique with Murchision Widefield Array data and show th...

  16. Some variance reduction methods for numerical stochastic homogenization.

    Science.gov (United States)

    Blanc, X; Le Bris, C; Legoll, F

    2016-04-28

    We give an overview of a series of recent studies devoted to variance reduction techniques for numerical stochastic homogenization. Numerical homogenization requires that a set of problems is solved at the microscale, the so-called corrector problems. In a random environment, these problems are stochastic and therefore need to be repeatedly solved, for several configurations of the medium considered. An empirical average over all configurations is then performed using the Monte Carlo approach, so as to approximate the effective coefficients necessary to determine the macroscopic behaviour. Variance severely affects the accuracy and the cost of such computations. Variance reduction approaches, borrowed from other contexts in the engineering sciences, can be useful. Some of these variance reduction techniques are presented, studied and tested here.

  17. 40 CFR 141.4 - Variances and exemptions.

    Science.gov (United States)

    2010-07-01

    ... Section 141.4 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS General § 141.4 Variances and exemptions. (a... maintenance of the distribution system. ...

  18. Fundamental Indexes As Proxies For Mean-Variance Efficient Portfolios

    National Research Council Canada - National Science Library

    Kathleen Hodnett; Gearé Botes; Khumbudzo Daswa; Kimberly Davids; Emmanuel Che Fongwa; Candice Fortuin

    2014-01-01

      Mean-variance efficiency was first explained by Markowitz (1952) who derived an efficient frontier comprised of portfolios with the highest expected returns for a given level of risk borne by the investor...

  19. TESTS FOR VARIANCE COMPONENTS IN VARYING COEFFICIENT MIXED MODELS

    National Research Council Canada - National Science Library

    Zaixing Li; Yuedong Wang; Ping Wu; Wangli Xu; Lixing Zhu

    2012-01-01

    .... To address the question of whether a varying coefficient mixed model can be reduced to a simpler varying coefficient model, we develop one-sided tests for the null hypothesis that all the variance components are zero...

  20. Estimating the generalized concordance correlation coefficient through variance components.

    Science.gov (United States)

    Carrasco, Josep L; Jover, Lluís

    2003-12-01

    The intraclass correlation coefficient (ICC) and the concordance correlation coefficient (CCC) are two of the most popular measures of agreement for variables measured on a continuous scale. Here, we demonstrate that ICC and CCC are the same measure of agreement estimated in two ways: by the variance components procedure and by the moment method. We propose estimating the CCC using variance components of a mixed effects model, instead of the common method of moments. With the variance components approach, the CCC can easily be extended to more than two observers, and adjusted using confounding covariates, by incorporating them in the mixed model. A simulation study is carried out to compare the variance components approach with the moment method. The importance of adjusting by confounding covariates is illustrated with a case example.

  1. Variance estimation in neutron coincidence counting using the bootstrap method

    Energy Technology Data Exchange (ETDEWEB)

    Dubi, C., E-mail: chendb331@gmail.com [Physics Department, Nuclear Research Center of the Negev, P.O.B. 9001 Beer Sheva (Israel); Ocherashvilli, A.; Ettegui, H. [Physics Department, Nuclear Research Center of the Negev, P.O.B. 9001 Beer Sheva (Israel); Pedersen, B. [Nuclear Security Unit, Institute for Transuranium Elements, Via E. Fermi, 2749 JRC, Ispra (Italy)

    2015-09-11

    In the study, we demonstrate the implementation of the “bootstrap” method for a reliable estimation of the statistical error in Neutron Multiplicity Counting (NMC) on plutonium samples. The “bootstrap” method estimates the variance of a measurement through a re-sampling process, in which a large number of pseudo-samples are generated, from which the so-called bootstrap distribution is generated. The outline of the present study is to give a full description of the bootstrapping procedure, and to validate, through experimental results, the reliability of the estimated variance. Results indicate both a very good agreement between the measured variance and the variance obtained through the bootstrap method, and a robustness of the method with respect to the duration of the measurement and the bootstrap parameters.

  2. Dimension free and infinite variance tail estimates on Poisson space

    OpenAIRE

    Breton, J. C.; Houdré, C.; Privault, N.

    2004-01-01

    Concentration inequalities are obtained on Poisson space, for random functionals with finite or infinite variance. In particular, dimension free tail estimates and exponential integrability results are given for the Euclidean norm of vectors of independent functionals. In the finite variance case these results are applied to infinitely divisible random variables such as quadratic Wiener functionals, including L\\'evy's stochastic area and the square norm of Brownian paths. In the infinite vari...

  3. The asymptotic variance of departures in critically loaded queues

    NARCIS (Netherlands)

    Al Hanbali, Ahmad; Mandjes, M.R.H.; Nazarathy, Y.; Whitt, W.

    2011-01-01

    We consider the asymptotic variance of the departure counting process D(t) of the GI/G/1 queue; D(t) denotes the number of departures up to time t. We focus on the case where the system load ϱ equals 1, and prove that the asymptotic variance rate satisfies limt→∞varD(t) / t = λ(1 - 2 / π)(ca2 +

  4. Wavelet Variance Analysis of EEG Based on Window Function

    Institute of Scientific and Technical Information of China (English)

    ZHENG Yuan-zhuang; YOU Rong-yi

    2014-01-01

    A new wavelet variance analysis method based on window function is proposed to investigate the dynamical features of electroencephalogram (EEG).The ex-prienmental results show that the wavelet energy of epileptic EEGs are more discrete than normal EEGs, and the variation of wavelet variance is different between epileptic and normal EEGs with the increase of time-window width. Furthermore, it is found that the wavelet subband entropy (WSE) of the epileptic EEGs are lower than the normal EEGs.

  5. Global Variance Risk Premium and Forex Return Predictability

    OpenAIRE

    Aloosh, Arash

    2014-01-01

    In a long-run risk model with stochastic volatility and frictionless markets, I express expected forex returns as a function of consumption growth variances and stock variance risk premiums (VRPs)—the difference between the risk-neutral and statistical expectations of market return variation. This provides a motivation for using the forward-looking information available in stock market volatility indices to predict forex returns. Empirically, I find that stock VRPs predict forex returns at a ...

  6. Multiperiod mean-variance efficient portfolios with endogenous liabilities

    OpenAIRE

    Markus LEIPPOLD; Trojani, Fabio; Vanini, Paolo

    2011-01-01

    We study the optimal policies and mean-variance frontiers (MVF) of a multiperiod mean-variance optimization of assets and liabilities (AL). This makes the analysis more challenging than for a setting based on purely exogenous liabilities, in which the optimization is only performed on the assets while keeping liabilities fixed. We show that, under general conditions for the joint AL dynamics, the optimal policies and the MVF can be decomposed into an orthogonal set of basis returns using exte...

  7. Global Variance Risk Premium and Forex Return Predictability

    OpenAIRE

    Aloosh, Arash

    2014-01-01

    In a long-run risk model with stochastic volatility and frictionless markets, I express expected forex returns as a function of consumption growth variances and stock variance risk premiums (VRPs)—the difference between the risk-neutral and statistical expectations of market return variation. This provides a motivation for using the forward-looking information available in stock market volatility indices to predict forex returns. Empirically, I find that stock VRPs predict forex returns at a ...

  8. Estimating Income Variances by Probability Sampling: A Case Study

    Directory of Open Access Journals (Sweden)

    Akbar Ali Shah

    2010-08-01

    Full Text Available The main focus of the study is to estimate variability in income distribution of households by conducting a survey. The variances in income distribution have been calculated by probability sampling techniques. The variances are compared and relative gains are also obtained. It is concluded that the income distribution has been better as compared to first Household Income and Expenditure Survey (HIES conducted in Pakistan 1993-94.

  9. Testing for Causality in Variance Usinf Multivariate GARCH Models

    OpenAIRE

    Christian M. Hafner; Herwartz, Helmut

    2008-01-01

    Tests of causality in variance in multiple time series have been proposed recently, based on residuals of estimated univariate models. Although such tests are applied frequently, little is known about their power properties. In this paper we show that a convenient alternative to residual based testing is to specify a multivariate volatility model, such as multivariate GARCH (or BEKK), and construct a Wald test on noncausality in variance. We compare both approaches to testing causality in var...

  10. Testing for causality in variance using multivariate GARCH models

    OpenAIRE

    Hafner, Christian; Herwartz, H.

    2004-01-01

    textabstractTests of causality in variance in multiple time series have been proposed recently, based on residuals of estimated univariate models. Although such tests are applied frequently little is known about their power properties. In this paper we show that a convenient alternative to residual based testing is to specify a multivariate volatility model, such as multivariate GARCH (or BEKK), and construct a Wald test on noncausality in variance. We compare both approaches to testing causa...

  11. Population dynamics of a natural red deer population over 200 years detected via substantial changes of genetic variation.

    Science.gov (United States)

    Hoffmann, Gunther Sebastian; Johannesen, Jes; Griebeler, Eva Maria

    2016-05-01

    Most large mammals have constantly been exposed to anthropogenic influence over decades or even centuries. Because of their long generation times and lack of sampling material, inferences of past population genetic dynamics, including anthropogenic impacts, have only relied on the analysis of the structure of extant populations. Here, we investigate for the first time the change in the genetic constitution of a natural red deer population over two centuries, using up to 200-year-old antlers (30 generations) stored in trophy collections. To the best of our knowledge, this is the oldest DNA source ever used for microsatellite population genetic analyses. We demonstrate that government policy and hunting laws may have strong impacts on populations that can lead to unexpectedly rapid changes in the genetic constitution of a large mammal population. A high ancestral individual polymorphism seen in an outbreeding population (1813-1861) was strongly reduced in descendants (1923-1940) during the mid-19th and early 20th century by genetic bottlenecks. Today (2011), individual polymorphism and variance among individuals is increasing in a constant-sized (managed) population. Differentiation was high among periods (F ST > ***); consequently, assignment tests assigned individuals to their own period with >85% probability. In contrast to the high variance observed at nuclear microsatellite loci, mtDNA (D-loop) was monomorphic through time, suggesting that male immigration dominates the genetic evolution in this population.

  12. Genetics of acute inflammation: inflammatory reactions in inbred lines of mice and in their interline crosses.

    Science.gov (United States)

    Stiffel, C; Ibanez, O M; Ribeiro, O G; Decreusefond, C; Mouton, D; Siqueira, M; Biozzi, G

    1990-01-01

    Acute inflammation is induced by the subcutaneous injection of swollen polyacrylamide microbeads, its intensity measured by the cell and protein concentration of the local exudates. A large and continuous range of responses is obtained in different inbred strains of mice, which suggests a polygenic control of the inflammatory response. The variable levels of the global dominance observed in F1 hybrids issued from several parental combinations indicated that the pattern of alleles controlling high or low response was different in each parental strain. Balanced intercrossing of the 8 inbred strains studied has provided a genetically heterogeneous F3 population, presenting a high variability of responses. The value of the genetic part of F3 phenotypic variance, the spread of the interstrain differences, as well as the polygenic nature of the regulation of inflammatory responses pointed out the possibility to perform a bidirectional genetic selection by using the F3 mice as the foundation population, and response to microbeads as the selective phenotypic character.

  13. Variance estimation in the analysis of microarray data

    KAUST Repository

    Wang, Yuedong

    2009-04-01

    Microarrays are one of the most widely used high throughput technologies. One of the main problems in the area is that conventional estimates of the variances that are required in the t-statistic and other statistics are unreliable owing to the small number of replications. Various methods have been proposed in the literature to overcome this lack of degrees of freedom problem. In this context, it is commonly observed that the variance increases proportionally with the intensity level, which has led many researchers to assume that the variance is a function of the mean. Here we concentrate on estimation of the variance as a function of an unknown mean in two models: the constant coefficient of variation model and the quadratic variance-mean model. Because the means are unknown and estimated with few degrees of freedom, naive methods that use the sample mean in place of the true mean are generally biased because of the errors-in-variables phenomenon. We propose three methods for overcoming this bias. The first two are variations on the theme of the so-called heteroscedastic simulation-extrapolation estimator, modified to estimate the variance function consistently. The third class of estimators is entirely different, being based on semiparametric information calculations. Simulations show the power of our methods and their lack of bias compared with the naive method that ignores the measurement error. The methodology is illustrated by using microarray data from leukaemia patients.

  14. Variance estimation for systematic designs in spatial surveys.

    Science.gov (United States)

    Fewster, R M

    2011-12-01

    In spatial surveys for estimating the density of objects in a survey region, systematic designs will generally yield lower variance than random designs. However, estimating the systematic variance is well known to be a difficult problem. Existing methods tend to overestimate the variance, so although the variance is genuinely reduced, it is over-reported, and the gain from the more efficient design is lost. The current approaches to estimating a systematic variance for spatial surveys are to approximate the systematic design by a random design, or approximate it by a stratified design. Previous work has shown that approximation by a random design can perform very poorly, while approximation by a stratified design is an improvement but can still be severely biased in some situations. We develop a new estimator based on modeling the encounter process over space. The new "striplet" estimator has negligible bias and excellent precision in a wide range of simulation scenarios, including strip-sampling, distance-sampling, and quadrat-sampling surveys, and including populations that are highly trended or have strong aggregation of objects. We apply the new estimator to survey data for the spotted hyena (Crocuta crocuta) in the Serengeti National Park, Tanzania, and find that the reported coefficient of variation for estimated density is 20% using approximation by a random design, 17% using approximation by a stratified design, and 11% using the new striplet estimator. This large reduction in reported variance is verified by simulation. © 2011, The International Biometric Society.

  15. Analytic variance estimates of Swank and Fano factors.

    Science.gov (United States)

    Gutierrez, Benjamin; Badano, Aldo; Samuelson, Frank

    2014-07-01

    Variance estimates for detector energy resolution metrics can be used as stopping criteria in Monte Carlo simulations for the purpose of ensuring a small uncertainty of those metrics and for the design of variance reduction techniques. The authors derive an estimate for the variance of two energy resolution metrics, the Swank factor and the Fano factor, in terms of statistical moments that can be accumulated without significant computational overhead. The authors examine the accuracy of these two estimators and demonstrate how the estimates of the coefficient of variation of the Swank and Fano factors behave with data from a Monte Carlo simulation of an indirect x-ray imaging detector. The authors' analyses suggest that the accuracy of their variance estimators is appropriate for estimating the actual variances of the Swank and Fano factors for a variety of distributions of detector outputs. The variance estimators derived in this work provide a computationally convenient way to estimate the error or coefficient of variation of the Swank and Fano factors during Monte Carlo simulations of radiation imaging systems.

  16. Why risk is not variance: an expository note.

    Science.gov (United States)

    Cox, Louis Anthony Tony

    2008-08-01

    Variance (or standard deviation) of return is widely used as a measure of risk in financial investment risk analysis applications, where mean-variance analysis is applied to calculate efficient frontiers and undominated portfolios. Why, then, do health, safety, and environmental (HS&E) and reliability engineering risk analysts insist on defining risk more flexibly, as being determined by probabilities and consequences, rather than simply by variances? This note suggests an answer by providing a simple proof that mean-variance decision making violates the principle that a rational decisionmaker should prefer higher to lower probabilities of receiving a fixed gain, all else being equal. Indeed, simply hypothesizing a continuous increasing indifference curve for mean-variance combinations at the origin is enough to imply that a decisionmaker must find unacceptable some prospects that offer a positive probability of gain and zero probability of loss. Unlike some previous analyses of limitations of variance as a risk metric, this expository note uses only simple mathematics and does not require the additional framework of von Neumann Morgenstern utility theory.

  17. Analytic variance estimates of Swank and Fano factors

    Energy Technology Data Exchange (ETDEWEB)

    Gutierrez, Benjamin; Badano, Aldo; Samuelson, Frank, E-mail: frank.samuelson@fda.hhs.gov [US Food and Drug Administration, Silver Spring, Maryland 20993 (United States)

    2014-07-15

    Purpose: Variance estimates for detector energy resolution metrics can be used as stopping criteria in Monte Carlo simulations for the purpose of ensuring a small uncertainty of those metrics and for the design of variance reduction techniques. Methods: The authors derive an estimate for the variance of two energy resolution metrics, the Swank factor and the Fano factor, in terms of statistical moments that can be accumulated without significant computational overhead. The authors examine the accuracy of these two estimators and demonstrate how the estimates of the coefficient of variation of the Swank and Fano factors behave with data from a Monte Carlo simulation of an indirect x-ray imaging detector. Results: The authors' analyses suggest that the accuracy of their variance estimators is appropriate for estimating the actual variances of the Swank and Fano factors for a variety of distributions of detector outputs. Conclusions: The variance estimators derived in this work provide a computationally convenient way to estimate the error or coefficient of variation of the Swank and Fano factors during Monte Carlo simulations of radiation imaging systems.

  18. Image embedded coding with edge preservation based on local variance analysis for mobile applications

    Science.gov (United States)

    Luo, Gaoyong; Osypiw, David

    2006-02-01

    Transmitting digital images via mobile device is often subject to bandwidth which are incompatible with high data rates. Embedded coding for progressive image transmission has recently gained popularity in image compression community. However, current progressive wavelet-based image coders tend to send information on the lowest-frequency wavelet coefficients first. At very low bit rates, images compressed are therefore dominated by low frequency information, where high frequency components belonging to edges are lost leading to blurring the signal features. This paper presents a new image coder employing edge preservation based on local variance analysis to improve the visual appearance and recognizability of compressed images. The analysis and compression is performed by dividing an image into blocks. Fast lifting wavelet transform is developed with the advantages of being computationally efficient and boundary effects minimized by changing wavelet shape for handling filtering near the boundaries. A modified SPIHT algorithm with more bits used to encode the wavelet coefficients and transmitting fewer bits in the sorting pass for performance improvement, is implemented to reduce the correlation of the coefficients at scalable bit rates. Local variance estimation and edge strength measurement can effectively determine the best bit allocation for each block to preserve the local features by assigning more bits for blocks containing more edges with higher variance and edge strength. Experimental results demonstrate that the method performs well both visually and in terms of MSE and PSNR. The proposed image coder provides a potential solution with parallel computation and less memory requirements for mobile applications.

  19. APLICAÇÃO DA METODOLOGIA DE MODELOS MISTOS (REML/BLUP NA ESTIMAÇÃO DE COMPONENTES DE VARIÂNCIA E PREDIÇÃO DE VALORES GENÉTICOS EM PUPUNHEIRA (Bactris gasipaes APLICATION OF THE MIXED MODEL METHODOLOGY (REML/BLUP IN VARIANCE COMPONENTS ESTIMATION AND PREDICTION OF GENETIC VALUES IN PEACH PALM (Bactris gasipaes

    Directory of Open Access Journals (Sweden)

    JOÃO TOMÉ DE FARIAS NETO

    2001-08-01

    ,70%, PRB (6,15%. Os ganhos genéticos preditos em relação à média da população para PP foram de 7,18% na situação de LP e 8,40% para CP, com tamanho efetivo de 30,38 e 19,00, respectivamente.The peach palm is a very useful plant for feeding Brazilians as fruit or palm heart producer. The interest for the peach palm besides being a perennial culture is: growth in full sun, precocity, rusticity, capacity to shoot, flavor and non-darkening of the palm heart after the cut. Estimates of genetic parameters in peach palm are scarce and constitute the most important tool to guide the improvement programs. The objective of this work was to study the genetic variability and estimate the individual genetic value as selection criterion, using the BLUP/REML procedure (Best linear unbiased prediction/restricted maximum likelihood. Two selection strategies for the palm heart production trait were adopted: a short term (CP - selection of the 9 families with 31 individuals of bigger genetic value and a long term (LP - selection of the 15 families with 53 individuals. The progenies were evaluated in randomized block design with three replications, the plots were composed by rows of five plants, spaced in 2.0 m x 1.0 m and with a row around the experiment in the Experimental Field of Matapi, Porto Grande municipality, Amapa State, Brazil. The evaluation was accomplished to the 26 months after planting (2nd evaluation being collected data of plant height (AP, diameter of the plant to the lap height (DPC, palm heart size (TP, palm heart diameter (DP, residual apical weight (PRA, basal weight (PRB and of the liquid palm heart (PP (exportation type. The data of AP, DPC, TP and DP corresponded to the clump of roots averages that presented more than a stem. However for the characters PA, PRB and PP corresponded the sum of the stems in the clump of roots. In general, the population presented low genetic variability. The narrow sense heritability at the individuals level was: AP (18.44%, DPC

  20. Brain Dominance & Self-Actualization.

    Science.gov (United States)

    Bernhoft, Franklin O.

    Numerous areas associated with brain dominance have been researched since Bogen and Sperry's work with split-brain patients in the 1960s, but only slight attention has been given to the connection between brain dominance and personality. No study appears in the literature seeking to understand optimal mental health as defined by Maslow's…