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Sample records for dominance genetic variance

  1. Estimation of Additive, Dominance, and Imprinting Genetic Variance Using Genomic Data

    PubMed Central

    Lopes, Marcos S.; Bastiaansen, John W. M.; Janss, Luc; Knol, Egbert F.; Bovenhuis, Henk

    2015-01-01

    Traditionally, exploration of genetic variance in humans, plants, and livestock species has been limited mostly to the use of additive effects estimated using pedigree data. However, with the development of dense panels of single-nucleotide polymorphisms (SNPs), the exploration of genetic variation of complex traits is moving from quantifying the resemblance between family members to the dissection of genetic variation at individual loci. With SNPs, we were able to quantify the contribution of additive, dominance, and imprinting variance to the total genetic variance by using a SNP regression method. The method was validated in simulated data and applied to three traits (number of teats, backfat, and lifetime daily gain) in three purebred pig populations. In simulated data, the estimates of additive, dominance, and imprinting variance were very close to the simulated values. In real data, dominance effects account for a substantial proportion of the total genetic variance (up to 44%) for these traits in these populations. The contribution of imprinting to the total phenotypic variance of the evaluated traits was relatively small (1–3%). Our results indicate a strong relationship between additive variance explained per chromosome and chromosome length, which has been described previously for other traits in other species. We also show that a similar linear relationship exists for dominance and imprinting variance. These novel results improve our understanding of the genetic architecture of the evaluated traits and shows promise to apply the SNP regression method to other traits and species, including human diseases. PMID:26438289

  2. On the Additive and Dominant Variance and Covariance of Individuals Within the Genomic Selection Scope

    PubMed Central

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

    2013-01-01

    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. PMID:24121775

  3. Genetic Dominance & Cellular Processes

    ERIC Educational Resources Information Center

    Seager, Robert D.

    2014-01-01

    In learning genetics, many students misunderstand and misinterpret what "dominance" means. Understanding is easier if students realize that dominance is not a mechanism, but rather a consequence of underlying cellular processes. For example, metabolic pathways are often little affected by changes in enzyme concentration. This means that…

  4. Dominance, Information, and Hierarchical Scaling of Variance Space.

    ERIC Educational Resources Information Center

    Ceurvorst, Robert W.; Krus, David J.

    1979-01-01

    A method for computation of dominance relations and for construction of their corresponding hierarchical structures is presented. The link between dominance and variance allows integration of the mathematical theory of information with least squares statistical procedures without recourse to logarithmic transformations of the data. (Author/CTM)

  5. Variance in the reproductive success of dominant male mountain gorillas.

    PubMed

    Robbins, Andrew M; Gray, Maryke; Uwingeli, Prosper; Mburanumwe, Innocent; Kagoda, Edwin; Robbins, Martha M

    2014-10-01

    Using 30 years of demographic data from 15 groups, this study estimates how harem size, female fertility, and offspring survival may contribute to variance in the siring rates of dominant male mountain gorillas throughout the Virunga Volcano Region. As predicted for polygynous species, differences in harem size were the greatest source of variance in the siring rate, whereas differences in female fertility and offspring survival were relatively minor. Harem size was positively correlated with offspring survival, even after removing all known and suspected cases of infanticide, so the correlation does not seem to reflect differences in the ability of males to protect their offspring. Harem size was not significantly correlated with female fertility, which is consistent with the hypothesis that mountain gorillas have minimal feeding competition. Harem size, offspring survival, and siring rates were not significantly correlated with the proportion of dominant tenures that occurred in multimale groups versus one-male groups; even though infanticide is less likely when those tenures end in multimale groups than one-male groups. In contrast with the relatively small contribution of offspring survival to variance in the siring rates of this study, offspring survival is a major source of variance in the male reproductive success of western gorillas, which have greater predation risks and significantly higher rates of infanticide. If differences in offspring protection are less important among male mountain gorillas than western gorillas, then the relative importance of other factors may be greater for mountain gorillas. Thus, our study illustrates how variance in male reproductive success and its components can differ between closely related species.

  6. Bottleneck Effects on Genetic Variance for Courtship Repertoire

    PubMed Central

    Meffert, L. M.

    1995-01-01

    Bottleneck effects on evolutionary potential in mating behavior were addressed through assays of additive genetic variances and resulting phenotypic responses to drift in the courtship repertoires of six two-pair founder-flush lines and two control populations of the housefly. A simulation addressed the complication that an estimate of the genetic variance for a courtship trait (e.g., male performance vigor or the female requirement for copulation) must involve assays against the background behavior of the mating partners. The additive ``environmental'' effect of the mating partner's phenotype simply dilutes the net parent-offspring covariance for a trait. However, if there is an interaction with this ``environmental'' component, negative parent-offspring covariances can result under conditions of high incompatibility between the population's distributions for male performance and female choice requirements, despite high levels of genetic variance. All six bottlenecked lines exhibited significant differentiation from the controls in at least one measure of the parent-offspring covariance for male performance or female choice (estimated by 50 parent-son and 50 parent-daughter covariances for 10 courtship traits per line) which translated to significant phenotypic drift. However, the average effect across traits or across lines did not yield a significant net increase in genetic variance due to bottlenecks. Concerted phenotypic differentiation due to the founder-flush event provided indirect evidence of directional dominance in a subset of traits. Furthermore, indirect evidence of genotype-environment interactions (potentially producing genotype-genotype effects) was found in the negative parent-offspring covariances predicted by the male-female interaction simulation and by the association of the magnitude of phenotypic drift with the absolute value of the parent-offspring covariance. Hence, nonadditive genetic effects on mating behavior may be important in

  7. Comparing estimates of genetic variance across different relationship models.

    PubMed

    Legarra, Andres

    2016-02-01

    Use of relationships between individuals to estimate genetic variances and heritabilities via mixed models is standard practice in human, plant and livestock genetics. Different models or information for relationships may give different estimates of genetic variances. However, comparing these estimates across different relationship models is not straightforward as the implied base populations differ between relationship models. In this work, I present a method to compare estimates of variance components across different relationship models. I suggest referring genetic variances obtained using different relationship models to the same reference population, usually a set of individuals in the population. Expected genetic variance of this population is the estimated variance component from the mixed model times a statistic, Dk, which is the average self-relationship minus the average (self- and across-) relationship. For most typical models of relationships, Dk is close to 1. However, this is not true for very deep pedigrees, for identity-by-state relationships, or for non-parametric kernels, which tend to overestimate the genetic variance and the heritability. Using mice data, I show that heritabilities from identity-by-state and kernel-based relationships are overestimated. Weighting these estimates by Dk scales them to a base comparable to genomic or pedigree relationships, avoiding wrong comparisons, for instance, "missing heritabilities".

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

    PubMed

    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.

  9. Genetic Variance in the SES-IQ Correlation.

    ERIC Educational Resources Information Center

    Eckland, Bruce K.

    1979-01-01

    Discusses questions dealing with genetic aspects of the correlation between IQ and socioeconomic status (SES). Questions include: How does assortative mating affect the genetic variance of IQ? Is the relationship between an individual's IQ and adult SES a causal one? And how can IQ research improve schools and schooling? (Author/DB)

  10. Selection and genetic (co)variance in bighorn sheep.

    PubMed

    Coltman, David W; O'Donoghue, Paul; Hogg, John T; Festa-Bianchet, Marco

    2005-06-01

    Genetic theory predicts that directional selection should deplete additive genetic variance for traits closely related to fitness, and may favor the maintenance of alleles with antagonistically pleiotropic effects on fitness-related traits. Trait heritability is therefore expected to decline with the degree of association with fitness, and some genetic correlations between selected traits are expected to be negative. Here we demonstrate a negative relationship between trait heritability and association with lifetime reproductive success in a wild population of bighorn sheep (Ovis canadensis) at Ram Mountain, Alberta, Canada. Lower heritability for fitness-related traits, however, was not wholly a consequence of declining genetic variance, because those traits showed high levels of residual variance. Genetic correlations estimated between pairs of traits with significant heritability were positive. Principal component analyses suggest that positive relationships between morphometric traits constitute the main axis of genetic variation. Trade-offs in the form of negative genetic or phenotypic correlations among the traits we have measured do not appear to constrain the potential for evolution in this population.

  11. Quantitative genetics in soybean: Is dominance important?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In soybeans, dominance is generally considered to be non-existent or of little importance. Because genetic variation due to dominance dissipates rapidly with inbreeding, dominance would presumably not be useful in breeding soybean cultivars which are highly inbred. Yet, there is evidence for hetero...

  12. 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.

    PubMed

    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.

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

    PubMed Central

    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

  14. Quantitative genetic divergence and standing genetic (co)variance in thermal reaction norms along latitude.

    PubMed

    Berger, David; Postma, Erik; Blanckenhorn, Wolf U; Walters, Richard J

    2013-08-01

    Although the potential to adapt to warmer climate is constrained by genetic trade-offs, our understanding of how selection and mutation shape genetic (co)variances in thermal reaction norms is poor. Using 71 isofemale lines of the fly Sepsis punctum, originating from northern, central, and southern European climates, we tested for divergence in juvenile development rate across latitude at five experimental temperatures. To investigate effects of evolutionary history in different climates on standing genetic variation in reaction norms, we further compared genetic (co)variances between regions. Flies were reared on either high or low food resources to explore the role of energy acquisition in determining genetic trade-offs between different temperatures. Although the latter had only weak effects on the strength and sign of genetic correlations, genetic architecture differed significantly between climatic regions, implying that evolution of reaction norms proceeds via different trajectories at high latitude versus low latitude in this system. Accordingly, regional genetic architecture was correlated to region-specific differentiation. Moreover, hot development temperatures were associated with low genetic variance and stronger genetic correlations compared to cooler temperatures. We discuss the evolutionary potential of thermal reaction norms in light of their underlying genetic architectures, evolutionary histories, and the materialization of trade-offs in natural environments.

  15. The molecular basis of genetic dominance.

    PubMed Central

    Wilkie, A O

    1994-01-01

    Studies of mutagenesis in many organisms indicate that the majority (over 90%) of mutations are recessive to wild type. If recessiveness represents the 'default' state, what are the distinguishing features that make a minority of mutations give rise to dominant or semidominant characters? This review draws on the rapid expansion in knowledge of molecular and cellular biology to classify the molecular mechanisms of dominant mutation. The categories discussed include (1) reduced gene dosage, expression, or protein activity (haploinsufficiency); (2) increased gene dosage; (3) ectopic or temporally altered mRNA expression; (4) increased or constitutive protein activity; (5) dominant negative effects; (6) altered structural proteins; (7) toxic protein alterations; and (8) new protein functions. This provides a framework for understanding the basis of dominant genetic phenomena in humans and other organisms. Images PMID:8182727

  16. Dominant takeover regimes for genetic algorithms

    NASA Technical Reports Server (NTRS)

    Noever, David; Baskaran, Subbiah

    1995-01-01

    The genetic algorithm (GA) is a machine-based optimization routine which connects evolutionary learning to natural genetic laws. The present work addresses the problem of obtaining the dominant takeover regimes in the GA dynamics. Estimated GA run times are computed for slow and fast convergence in the limits of high and low fitness ratios. Using Euler's device for obtaining partial sums in closed forms, the result relaxes the previously held requirements for long time limits. Analytical solution reveal that appropriately accelerated regimes can mark the ascendancy of the most fit solution. In virtually all cases, the weak (logarithmic) dependence of convergence time on problem size demonstrates the potential for the GA to solve large N-P complete problems.

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

    PubMed Central

    Forsberg, Simon K. G.; Andreatta, Matthew E.; Huang, Xin-Yuan; Danku, John; Salt, David E.; Carlborg, Örjan

    2015-01-01

    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. PMID:26599497

  18. Assessment of the genetic variance of late-onset Alzheimer's disease.

    PubMed

    Ridge, Perry G; Hoyt, Kaitlyn B; Boehme, Kevin; Mukherjee, Shubhabrata; Crane, Paul K; Haines, Jonathan L; Mayeux, Richard; Farrer, Lindsay A; Pericak-Vance, Margaret A; Schellenberg, Gerard D; Kauwe, John S K

    2016-05-01

    Alzheimer's disease (AD) is a complex genetic disorder with no effective treatments. More than 20 common markers have been identified, which are associated with AD. Recently, several rare variants have been identified in Amyloid Precursor Protein (APP), Triggering Receptor Expressed On Myeloid Cells 2 (TREM2) and Unc-5 Netrin Receptor C (UNC5C) that affect risk for AD. Despite the many successes, the genetic architecture of AD remains unsolved. We used Genome-wide Complex Trait Analysis to (1) estimate phenotypic variance explained by genetics; (2) calculate genetic variance explained by known AD single nucleotide polymorphisms (SNPs); and (3) identify the genomic locations of variation that explain the remaining unexplained genetic variance. In total, 53.24% of phenotypic variance is explained by genetics, but known AD SNPs only explain 30.62% of the genetic variance. Of the unexplained genetic variance, approximately 41% is explained by unknown SNPs in regions adjacent to known AD SNPs, and the remaining unexplained genetic variance outside these regions.

  19. Genetic Variance for Body Size in a Natural Population of Drosophila Buzzatii

    PubMed Central

    Ruiz, A.; Santos, M.; Barbadilla, A.; Quezada-Diaz, J. E.; Hasson, E.; Fontdevila, A.

    1991-01-01

    Previous work has shown thorax length to be under directional selection in the Drosophila buzzatii population of Carboneras. In order to predict the genetic consequences of natural selection, genetic variation for this trait was investigated in two ways. First, narrow sense heritability was estimated in the laboratory F(2) generation of a sample of wild flies by means of the offspring-parent regression. A relatively high value, 0.59, was obtained. Because the phenotypic variance of wild flies was 7-9 times that of the flies raised in the laboratory, ``natural'' heritability may be estimated as one-seventh to one-ninth that value. Second, the contribution of the second and fourth chromosomes, which are polymorphic for paracentric inversions, to the genetic variance of thorax length was estimated in the field and in the laboratory. This was done with the assistance of a simple genetic model which shows that the variance among chromosome arrangements and the variance among karyotypes provide minimum estimates of the chromosome's contribution to the additive and genetic variances of the triat, respectively. In males raised under optimal conditions in the laboratory, the variance among second-chromosome karyotypes accounted for 11.43% of the total phenotypic variance and most of this variance was additive; by contrast, the contribution of the fourth chromosome was nonsignificant. The variance among second-chromosome karyotypes accounted for 1.56-1.78% of the total phenotypic variance in wild males and was nonsignificant in wild females. The variance among fourth chromosome karyotypes accounted for 0.14-3.48% of the total phenotypic variance in wild flies. At both chromosomes, the proportion of additive variance was higher in mating flies than in nonmating flies. PMID:1916242

  20. Age at menarche as a fitness trait: nonadditive genetic variance detected in a large twin sample.

    PubMed Central

    Treloar, S A; Martin, N G

    1990-01-01

    The etiological role of genotype and environment in recalled age at menarche was examined using an unselected sample of 1,177 MZ and 711 DZ twin pairs aged 18 years and older. The correlation for onset of menarche between MZ twins was .65 +/- .03, and that for DZ pairs was .18 +/- .04, although these differed somewhat between four birth cohorts. Environmental factors were more important in the older cohorts (perhaps because of less reliable recall). Total genotypic variance (additive plus nonadditive) ranged from 61% in the oldest cohort to 68% in the youngest cohort. In the oldest birth cohort (born before 1939), there was evidence of greater influence of environmental factors on age at menarche in the second-born twin, although there was no other evidence in the data that birth trauma affected timing. The greater part of the genetic variance was nonadditive (dominance or epistasis), and this is typical of a fitness trait. It appears that genetic nonadditivity is in the decreasing direction, and this is consistent with selection for early menarche during human evolution. Breakdown of inbreeding depression as a possible explanation for the secular decline in age at menarche is discussed. PMID:2349942

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

    PubMed Central

    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

  2. Genetic and environmental heterogeneity of residual variance of weight traits in Nellore beef cattle

    PubMed Central

    2012-01-01

    Background Many studies have provided evidence of the existence of genetic heterogeneity of environmental variance, suggesting that it could be exploited to improve robustness and uniformity of livestock by selection. However, little is known about the perspectives of such a selection strategy in beef cattle. Methods A two-step approach was applied to study the genetic heterogeneity of residual variance of weight gain from birth to weaning and long-yearling weight in a Nellore beef cattle population. First, an animal model was fitted to the data and second, the influence of additive and environmental effects on the residual variance of these traits was investigated with different models, in which the log squared estimated residuals for each phenotypic record were analyzed using the restricted maximum likelihood method. Monte Carlo simulation was performed to assess the reliability of variance component estimates from the second step and the accuracy of estimated breeding values for residual variation. Results The results suggest that both genetic and environmental factors have an effect on the residual variance of weight gain from birth to weaning and long-yearling in Nellore beef cattle and that uniformity of these traits could be improved by selecting for lower residual variance, when considering a large amount of information to predict genetic merit for this criterion. Simulations suggested that using the two-step approach would lead to biased estimates of variance components, such that more adequate methods are needed to study the genetic heterogeneity of residual variance in beef cattle. PMID:22672564

  3. Age-dependent genetic variance in a life-history trait in the mute swan.

    PubMed

    Charmantier, Anne; Perrins, Christopher; McCleery, Robin H; Sheldon, Ben C

    2006-01-22

    Genetic variance in characters under natural selection in natural populations determines the way those populations respond to that selection. Whether populations show temporal and/or spatial constancy in patterns of genetic variance and covariance is regularly considered, as this will determine whether selection responses are constant over space and time. Much less often considered is whether characters show differing amounts of genetic variance over the life-history of individuals. Such age-specific variation, if present, has important potential consequences for the force of natural selection and for understanding the causes of variation in quantitative characters. Using data from a long-term study of the mute swan Cygnus olor, we report the partitioning of phenotypic variance in timing of breeding (subject to strong natural selection) into component parts over 12 different age classes. We show that the additive genetic variance and heritability of this trait are strongly age-dependent, with higher additive genetic variance present in young and, particularly, old birds, but little evidence of any genetic variance for birds of intermediate ages. These results demonstrate that age can have a very important influence on the components of variation of characters in natural populations, and consequently that separate age classes cannot be assumed to be equivalent, either with respect to their evolutionary potential or response.

  4. Genetics Home Reference: autosomal dominant hyper-IgE syndrome

    MedlinePlus

    ... 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 autosomal dominant hyper-IgE syndrome ...

  5. Genome-Enabled Estimates of Additive and Nonadditive Genetic Variances and Prediction of Apple Phenotypes Across Environments

    PubMed Central

    Kumar, Satish; Molloy, Claire; Muñoz, Patricio; Daetwyler, Hans; Chagné, David; Volz, Richard

    2015-01-01

    The nonadditive genetic effects may have an important contribution to total genetic variation of phenotypes, so estimates of both the additive and nonadditive effects are desirable for breeding and selection purposes. Our main objectives were to: estimate additive, dominance and epistatic variances of apple (Malus × domestica Borkh.) phenotypes using relationship matrices constructed from genome-wide dense single nucleotide polymorphism (SNP) markers; and compare the accuracy of genomic predictions using genomic best linear unbiased prediction models with or without including nonadditive genetic effects. A set of 247 clonally replicated individuals was assessed for six fruit quality traits at two sites, and also genotyped using an Illumina 8K SNP array. Across several fruit quality traits, the additive, dominance, and epistatic effects contributed about 30%, 16%, and 19%, respectively, to the total phenotypic variance. Models ignoring nonadditive components yielded upwardly biased estimates of additive variance (heritability) for all traits in this study. The accuracy of genomic predicted genetic values (GEGV) varied from about 0.15 to 0.35 for various traits, and these were almost identical for models with or without including nonadditive effects. However, models including nonadditive genetic effects further reduced the bias of GEGV. Between-site genotypic correlations were high (>0.85) for all traits, and genotype-site interaction accounted for <10% of the phenotypic variability. The accuracy of prediction, when the validation set was present only at one site, was generally similar for both sites, and varied from about 0.50 to 0.85. The prediction accuracies were strongly influenced by trait heritability, and genetic relatedness between the training and validation families. PMID:26497141

  6. A new explained-variance based genetic risk score for predictive modeling of disease risk.

    PubMed

    Che, Ronglin; Motsinger-Reif, Alison A

    2012-09-25

    The goal of association mapping is to identify genetic variants that predict disease, and as the field of human genetics matures, the number of successful association studies is increasing. Many such studies have shown that for many diseases, risk is explained by a reasonably large number of variants that each explains a very small amount of disease risk. This is prompting the use of genetic risk scores in building predictive models, where information across several variants is combined for predictive modeling. In the current study, we compare the performance of four previously proposed genetic risk score methods and present a new method for constructing genetic risk score that incorporates explained variance information. The methods compared include: a simple count Genetic Risk Score, an odds ratio weighted Genetic Risk Score, a direct logistic regression Genetic Risk Score, a polygenic Genetic Risk Score, and the new explained variance weighted Genetic Risk Score. We compare the methods using a wide range of simulations in two steps, with a range of the number of deleterious single nucleotide polymorphisms (SNPs) explaining disease risk, genetic modes, baseline penetrances, sample sizes, relative risks (RR) and minor allele frequencies (MAF). Several measures of model performance were compared including overall power, C-statistic and Akaike's Information Criterion. Our results show the relative performance of methods differs significantly, with the new explained variance weighted GRS (EV-GRS) generally performing favorably to the other methods.

  7. Maintenance of Quantitative Genetic Variance Under Partial Self-Fertilization, with Implications for Evolution of Selfing

    PubMed Central

    Lande, Russell; Porcher, Emmanuelle

    2015-01-01

    We analyze two models of the maintenance of quantitative genetic variance in a mixed-mating system of self-fertilization and outcrossing. In both models purely additive genetic variance is maintained by mutation and recombination under stabilizing selection on the phenotype of one or more quantitative characters. The Gaussian allele model (GAM) involves a finite number of unlinked loci in an infinitely large population, with a normal distribution of allelic effects at each locus within lineages selfed for τ consecutive generations since their last outcross. The infinitesimal model for partial selfing (IMS) involves an infinite number of loci in a large but finite population, with a normal distribution of breeding values in lineages of selfing age τ. In both models a stable equilibrium genetic variance exists, the outcrossed equilibrium, nearly equal to that under random mating, for all selfing rates, r, up to critical value, r^, the purging threshold, which approximately equals the mean fitness under random mating relative to that under complete selfing. In the GAM a second stable equilibrium, the purged equilibrium, exists for any positive selfing rate, with genetic variance less than or equal to that under pure selfing; as r increases above r^ the outcrossed equilibrium collapses sharply to the purged equilibrium genetic variance. In the IMS a single stable equilibrium genetic variance exists at each selfing rate; as r increases above r^ the equilibrium genetic variance drops sharply and then declines gradually to that maintained under complete selfing. The implications for evolution of selfing rates, and for adaptive evolution and persistence of predominantly selfing species, provide a theoretical basis for the classical view of Stebbins that predominant selfing constitutes an “evolutionary dead end.” PMID:25969460

  8. Maintenance of Quantitative Genetic Variance Under Partial Self-Fertilization, with Implications for Evolution of Selfing.

    PubMed

    Lande, Russell; Porcher, Emmanuelle

    2015-07-01

    We analyze two models of the maintenance of quantitative genetic variance in a mixed-mating system of self-fertilization and outcrossing. In both models purely additive genetic variance is maintained by mutation and recombination under stabilizing selection on the phenotype of one or more quantitative characters. The Gaussian allele model (GAM) involves a finite number of unlinked loci in an infinitely large population, with a normal distribution of allelic effects at each locus within lineages selfed for τ consecutive generations since their last outcross. The infinitesimal model for partial selfing (IMS) involves an infinite number of loci in a large but finite population, with a normal distribution of breeding values in lineages of selfing age τ. In both models a stable equilibrium genetic variance exists, the outcrossed equilibrium, nearly equal to that under random mating, for all selfing rates, r, up to critical value, [Formula: see text], the purging threshold, which approximately equals the mean fitness under random mating relative to that under complete selfing. In the GAM a second stable equilibrium, the purged equilibrium, exists for any positive selfing rate, with genetic variance less than or equal to that under pure selfing; as r increases above [Formula: see text] the outcrossed equilibrium collapses sharply to the purged equilibrium genetic variance. In the IMS a single stable equilibrium genetic variance exists at each selfing rate; as r increases above [Formula: see text] the equilibrium genetic variance drops sharply and then declines gradually to that maintained under complete selfing. The implications for evolution of selfing rates, and for adaptive evolution and persistence of predominantly selfing species, provide a theoretical basis for the classical view of Stebbins that predominant selfing constitutes an "evolutionary dead end."

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

    ERIC Educational Resources Information Center

    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. Analysis of Quantitative Traits in Two Long-Term Randomly Mated Soybean Populations I. Genetic Variances

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic effects of long term random mating and natural selection aided by genetic male sterility were evaluated in two soybean [Glycine max (L.) Merr.] populations: RSII and RSIII. Population means, variances, and heritabilities were estimated to determine the effects of 26 generations of random...

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

    PubMed

    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.

  12. Simultaneous Estimation of Additive and Mutational Genetic Variance in an Outbred Population of Drosophila serrata

    PubMed Central

    McGuigan, Katrina; Aguirre, J. David; Blows, Mark W.

    2015-01-01

    How new mutations contribute to genetic variation is a key question in biology. Although the evolutionary fate of an allele is largely determined by its heterozygous effect, most estimates of mutational variance and mutational effects derive from highly inbred lines, where new mutations are present in homozygous form. In an attempt to overcome this limitation, middle-class neighborhood (MCN) experiments have been used to assess the fitness effect of new mutations in heterozygous form. However, because MCN populations harbor substantial standing genetic variance, estimates of mutational variance have not typically been available from such experiments. Here we employ a modification of the animal model to analyze data from 22 generations of Drosophila serrata bred in an MCN design. Mutational heritability, measured for eight cuticular hydrocarbons, 10 wing-shape traits, and wing size in this outbred genetic background, ranged from 0.0006 to 0.006 (with one exception), a similar range to that reported from studies employing inbred lines. Simultaneously partitioning the additive and mutational variance in the same outbred population allowed us to quantitatively test the ability of mutation-selection balance models to explain the observed levels of additive and mutational genetic variance. The Gaussian allelic approximation and house-of-cards models, which assume real stabilizing selection on single traits, both overestimated the genetic variance maintained at equilibrium, but the house-of-cards model was a closer fit to the data. This analytical approach has the potential to be broadly applied, expanding our understanding of the dynamics of genetic variance in natural populations. PMID:26384357

  13. Ontogenetic changes in genetic variances of age-dependent plasticity along a latitudinal gradient

    PubMed Central

    Nilsson-Örtman, V; Rogell, B; Stoks, R; Johansson, F

    2015-01-01

    The expression of phenotypic plasticity may differ among life stages of the same organism. Age-dependent plasticity can be important for adaptation to heterogeneous environments, but this has only recently been recognized. Whether age-dependent plasticity is a common outcome of local adaptation and whether populations harbor genetic variation in this respect remains largely unknown. To answer these questions, we estimated levels of additive genetic variation in age-dependent plasticity in six species of damselflies sampled from 18 populations along a latitudinal gradient spanning 3600 km. We reared full sib larvae at three temperatures and estimated genetic variances in the height and slope of thermal reaction norms of body size at three points in time during ontogeny using random regression. Our data show that most populations harbor genetic variation in growth rate (reaction norm height) in all ontogenetic stages, but only some populations and ontogenetic stages were found to harbor genetic variation in thermal plasticity (reaction norm slope). Genetic variances in reaction norm height differed among species, while genetic variances in reaction norm slope differed among populations. The slope of the ontogenetic trend in genetic variances of both reaction norm height and slope increased with latitude. We propose that differences in genetic variances reflect temporal and spatial variation in the strength and direction of natural selection on growth trajectories and age-dependent plasticity. Selection on age-dependent plasticity may depend on the interaction between temperature seasonality and time constraints associated with variation in life history traits such as generation length. PMID:25649500

  14. Complex sources of variance in female dominance rank in a nepotistic society

    PubMed Central

    Lea, Amanda J.; Learn, Niki H.; Theus, Marcus J.; Altmann, Jeanne; Alberts, Susan C.

    2016-01-01

    Many mammalian societies are structured by dominance hierarchies, and an individual’s position within this hierarchy can influence reproduction, behaviour, physiology and health. In nepotistic hierarchies, which are common in cercopithecine primates and also seen in spotted hyaenas, Crocuta crocuta, adult daughters are expected to rank immediately below their mother, and in reverse age order (a phenomenon known as ‘youngest ascendancy’). This pattern is well described, but few studies have systematically examined the frequency or causes of departures from the expected pattern. Using a longitudinal data set from a natural population of yellow baboons, Papio cynocephalus, we measured the influence of maternal kin, paternal kin and group size on female rank positions at two life history milestones, menarche and first live birth. At menarche, most females (73%) ranked adjacent to their family members (i.e. the female held an ordinal rank in consecutive order with other members of her maternal family); however, only 33% of females showed youngest ascendancy within their matriline at menarche. By the time they experienced their first live birth, many females had improved their dominance rank: 78% ranked adjacent to their family members and 49% showed youngest ascendancy within their matriline. The presence of mothers and maternal sisters exerted a powerful influence on rank outcomes. However, the presence of fathers, brothers and paternal siblings did not produce a clear effect on female dominance rank in our analyses, perhaps because females in our data set co-resided with variable numbers and types of paternal and male relatives. Our results also raise the possibility that female body size or competitive ability may influence dominance rank, even in this classically nepotistic species. In total, our analyses reveal that the predictors of dominance rank in nepotistic rank systems are much more complex than previously thought. PMID:26997663

  15. Quantitative genetic variance and multivariate clines in the Ivyleaf morning glory, Ipomoea hederacea

    PubMed Central

    Stock, Amanda J.; Campitelli, Brandon E.; Stinchcombe, John R.

    2014-01-01

    Clinal variation is commonly interpreted as evidence of adaptive differentiation, although clines can also be produced by stochastic forces. Understanding whether clines are adaptive therefore requires comparing clinal variation to background patterns of genetic differentiation at presumably neutral markers. Although this approach has frequently been applied to single traits at a time, we have comparatively fewer examples of how multiple correlated traits vary clinally. Here, we characterize multivariate clines in the Ivyleaf morning glory, examining how suites of traits vary with latitude, with the goal of testing for divergence in trait means that would indicate past evolutionary responses. We couple this with analysis of genetic variance in clinally varying traits in 20 populations to test whether past evolutionary responses have depleted genetic variance, or whether genetic variance declines approaching the range margin. We find evidence of clinal differentiation in five quantitative traits, with little evidence of isolation by distance at neutral loci that would suggest non-adaptive or stochastic mechanisms. Within and across populations, the traits that contribute most to population differentiation and clinal trends in the multivariate phenotype are genetically variable as well, suggesting that a lack of genetic variance will not cause absolute evolutionary constraints. Our data are broadly consistent theoretical predictions of polygenic clines in response to shallow environmental gradients. Ecologically, our results are consistent with past findings of natural selection on flowering phenology, presumably due to season-length variation across the range. PMID:25002704

  16. Quantitative genetic variance and multivariate clines in the Ivyleaf morning glory, Ipomoea hederacea.

    PubMed

    Stock, Amanda J; Campitelli, Brandon E; Stinchcombe, John R

    2014-08-19

    Clinal variation is commonly interpreted as evidence of adaptive differentiation, although clines can also be produced by stochastic forces. Understanding whether clines are adaptive therefore requires comparing clinal variation to background patterns of genetic differentiation at presumably neutral markers. Although this approach has frequently been applied to single traits at a time, we have comparatively fewer examples of how multiple correlated traits vary clinally. Here, we characterize multivariate clines in the Ivyleaf morning glory, examining how suites of traits vary with latitude, with the goal of testing for divergence in trait means that would indicate past evolutionary responses. We couple this with analysis of genetic variance in clinally varying traits in 20 populations to test whether past evolutionary responses have depleted genetic variance, or whether genetic variance declines approaching the range margin. We find evidence of clinal differentiation in five quantitative traits, with little evidence of isolation by distance at neutral loci that would suggest non-adaptive or stochastic mechanisms. Within and across populations, the traits that contribute most to population differentiation and clinal trends in the multivariate phenotype are genetically variable as well, suggesting that a lack of genetic variance will not cause absolute evolutionary constraints. Our data are broadly consistent theoretical predictions of polygenic clines in response to shallow environmental gradients. Ecologically, our results are consistent with past findings of natural selection on flowering phenology, presumably due to season-length variation across the range.

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

    PubMed Central

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

    2016-01-01

    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 parametric G × E interaction 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

  18. Genetic interactions affecting human gene expression identified by variance association mapping

    PubMed Central

    Brown, Andrew Anand; Buil, Alfonso; Viñuela, Ana; Lappalainen, Tuuli; Zheng, Hou-Feng; Richards, J Brent; Small, Kerrin S; Spector, Timothy D; Dermitzakis, Emmanouil T; Durbin, Richard

    2014-01-01

    Non-additive interaction between genetic variants, or epistasis, is a possible explanation for the gap between heritability of complex traits and the variation explained by identified genetic loci. Interactions give rise to genotype dependent variance, and therefore the identification of variance quantitative trait loci can be an intermediate step to discover both epistasis and gene by environment effects (GxE). Using RNA-sequence data from lymphoblastoid cell lines (LCLs) from the TwinsUK cohort, we identify a candidate set of 508 variance associated SNPs. Exploiting the twin design we show that GxE plays a role in ∼70% of these associations. Further investigation of these loci reveals 57 epistatic interactions that replicated in a smaller dataset, explaining on average 4.3% of phenotypic variance. In 24 cases, more variance is explained by the interaction than their additive contributions. Using molecular phenotypes in this way may provide a route to uncovering genetic interactions underlying more complex traits. DOI: http://dx.doi.org/10.7554/eLife.01381.001 PMID:24771767

  19. Quantitative Genetic Analysis of Temperature Regulation in MUS MUSCULUS. I. Partitioning of Variance

    PubMed Central

    Lacy, Robert C.; Lynch, Carol Becker

    1979-01-01

    Heritabilities (from parent-offspring regression) and intraclass correlations of full sibs for a variety of traits were estimated from 225 litters of a heterogeneous stock (HS/Ibg) of laboratory mice. Initial variance partitioning suggested different adaptive functions for physiological, morphological and behavioral adjustments with respect to their thermoregulatory significance. Metabolic heat-production mechanisms appear to have reached their genetic limits, with little additive genetic variance remaining. This study provided no genetic evidence that body size has a close directional association with fitness in cold environments, since heritability estimates for weight gain and adult weight were similar and high, whether or not the animals were exposed to cold. Behavioral heat conservation mechanisms also displayed considerable amounts of genetic variability. However, due to strong evidence from numerous other studies that behavior serves an important adaptive role for temperature regulation in small mammals, we suggest that fluctuating selection pressures may have acted to maintain heritable variation in these traits. PMID:17248909

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We proposed a method to estimate the error variance among non-replicated genotypes, thus to estimate the genetic parameters by using replicated controls. We derived formulas to estimate sampling variances of the genetic parameters. Computer simulation indicated that the proposed methods of estimatin...

  1. Indirect genetics effects and evolutionary constraint: an analysis of social dominance in red deer, Cervus elaphus.

    PubMed

    Wilson, A J; Morrissey, M B; Adams, M J; Walling, C A; Guinness, F E; Pemberton, J M; Clutton-Brock, T H; Kruuk, L E B

    2011-04-01

    By determining access to limited resources, social dominance is often an important determinant of fitness. Thus, if heritable, standard theory predicts mean dominance should evolve. However, dominance is usually inferred from the tendency to win contests, and given one winner and one loser in any dyadic contest, the mean proportion won will always equal 0.5. Here, we argue that the apparent conflict between quantitative genetic theory and common sense is resolved by recognition of indirect genetic effects (IGEs). We estimate selection on, and genetic (co)variance structures for, social dominance, in a wild population of red deer Cervus elaphus, on the Scottish island of Rum. While dominance is heritable and positively correlated with lifetime fitness, contest outcomes depend as much on the genes carried by an opponent as on the genotype of a focal individual. We show how this dependency imposes an absolute evolutionary constraint on the phenotypic mean, thus reconciling theoretical predictions with common sense. More generally, we argue that IGEs likely provide a widespread but poorly recognized source of evolutionary constraint for traits influenced by competition.

  2. Age-specific patterns of genetic variance in Drosophila melanogaster. I. Mortality

    SciTech Connect

    Promislow, D.E.L.; Tatar, M.; Curtsinger, J.W.

    1996-06-01

    Peter Medawar proposed that senescence arises from an age-related decline in the force of selection, which allows late-acting deleterious mutations to accumulate. Subsequent workers have suggested that mutation accumulation could produce an age-related increase in additive genetic variance (V{sub A}) for fitness traits, as recently found in Drosophila melanogaster. Here we report results from a genetic analysis of mortality in 65,134 D. melanogaster. Additive genetic variance for female mortality rates increases from 0.007 in the first week of life to 0.325 by the third week, and then declines to 0.002 by the seventh week. Males show a similar pattern, though total variance is lower than in females. In contrast to a predicted divergence in mortality curves, mortality curves of different genotypes are roughly parallel. Using a three-parameter model, we find significant V{sub A} for the slope and constant term of the curve describing age-specific mortality rates, and also for the rate at which mortality decelerates late in life. These results fail to support a prediction derived from Medawar`s {open_quotes}mutation accumulation{close_quotes} theory for the evolution of senescence. However, our results could be consistent with alternative interpretations of evolutionary models of aging. 65 refs., 2 figs., 2 tabs.

  3. Editing genomic DNA in cancer cells with high genetic variance: benefit or risk?

    PubMed

    Wang, Lin; Wang, Yixiang; Guo, Chuanbin

    2014-05-01

    The generation of stably-transfected cell lines is a common and very important technology in cancer science. Considerable knowledge in the field of life sciences has been gained through the modification of the genetic code. However, there is a risk in evaluating exogenous gene function through editing genomic DNA in a cancer cell with high genetic variance. In the present study, we showed that genomic DNA status should be considered when evaluating the exogenous gene function in a cancer cell line with high variant genome through stable transfection technology, immunostaining, wound healing assay, transwell invasion assay, real-time PCR, western blot and karyotyping analysis. Our results showed that the S100P expression level was not related to the migration and invasion abilities in these stably transfected cell lines derived from a human salivary adenoid cystic carcinoma cell line SACC-83. The MMP expression pattern was detected by western blot analysis which matched the biological behaviors in these cells. The genomic analysis showed that SACC-83 presented hypotetraploid karyotyping with high variance. Our data indicated that establishment of stable transgenic cancer cell lines should consider the status of genetic variance in a cancer cell to avoid any biased conclusion.

  4. Colour ornamentation in the blue tit: quantitative genetic (co)variances across sexes.

    PubMed

    Charmantier, A; Wolak, M E; Grégoire, A; Fargevieille, A; Doutrelant, C

    2017-02-01

    Although secondary sexual traits are commonly more developed in males than females, in many animal species females also display elaborate ornaments or weaponry. Indirect selection on correlated traits in males and/or direct sexual or social selection in females are hypothesized to drive the evolution and maintenance of female ornaments. Yet, the relative roles of these evolutionary processes remain unidentified, because little is known about the genetic correlation that might exist between the ornaments of both sexes, and few estimates of sex-specific autosomal or sex-linked genetic variances are available. In this study, we used two wild blue tit populations with 9 years of measurements on two colour ornaments: one structurally based (blue crown) and one carotenoid based (yellow chest). We found significant autosomal heritability for the chromatic part of the structurally based colouration in both sexes, whereas carotenoid chroma was heritable only in males, and the achromatic part of both colour patches was mostly non heritable. Power limitations, which are probably common among most data sets collected so far in wild populations, prevented estimation of sex-linked genetic variance. Bivariate analyses revealed very strong cross-sex genetic correlations in all heritable traits, although the strength of these correlations was not related to the level of sexual dimorphism. In total, our results suggest that males and females share a majority of their genetic variation underlying colour ornamentation, and hence the evolution of these sex-specific traits may depend greatly on correlated responses to selection in the opposite sex.

  5. Pattern of inbreeding depression, condition dependence, and additive genetic variance in Trinidadian guppy ejaculate traits

    PubMed Central

    Gasparini, Clelia; Devigili, Alessandro; Dosselli, Ryan; Pilastro, Andrea

    2013-01-01

    In polyandrous species, a male's reproductive success depends on his fertilization capability and traits enhancing competitive fertilization success will be under strong, directional selection. This leads to the prediction that these traits should show stronger condition dependence and larger genetic variance than other traits subject to weaker or stabilizing selection. While empirical evidence of condition dependence in postcopulatory traits is increasing, the comparison between sexually selected and ‘control’ traits is often based on untested assumption concerning the different strength of selection acting on these traits. Furthermore, information on selection in the past is essential, as both condition dependence and genetic variance of a trait are likely to be influenced by the pattern of selection acting historically on it. Using the guppy (Poecilia reticulata), a livebearing fish with high levels of multiple paternity, we performed three independent experiments on three ejaculate quality traits, sperm number, velocity, and size, which have been previously shown to be subject to strong, intermediate, and weak directional postcopulatory selection, respectively. First, we conducted an inbreeding experiment to determine the pattern of selection in the past. Second, we used a diet restriction experiment to estimate their level of condition dependence. Third, we used a half-sib/full-sib mating design to estimate the coefficients of additive genetic variance (CVA) underlying these traits. Additionally, using a simulated predator evasion test, we showed that both inbreeding and diet restriction significantly reduced condition. According to predictions, sperm number showed higher inbreeding depression, stronger condition dependence, and larger CVA than sperm velocity and sperm size. The lack of significant genetic correlation between sperm number and velocity suggests that the former may respond to selection independently one from other ejaculate quality traits

  6. Sex-specific genetic variance and the evolution of sexual dimorphism: a systematic review of cross-sex genetic correlations.

    PubMed

    Poissant, Jocelyn; Wilson, Alastair J; Coltman, David W

    2010-01-01

    The independent evolution of the sexes may often be constrained if male and female homologous traits share a similar genetic architecture. Thus, cross-sex genetic covariance is assumed to play a key role in the evolution of sexual dimorphism (SD) with consequent impacts on sexual selection, population dynamics, and speciation processes. We compiled cross-sex genetic correlations (r(MF)) estimates from 114 sources to assess the extent to which the evolution of SD is typically constrained and test several specific hypotheses. First, we tested if r(MF) differed among trait types and especially between fitness components and other traits. We also tested the theoretical prediction of a negative relationship between r(MF) and SD based on the expectation that increases in SD should be facilitated by sex-specific genetic variance. We show that r(MF) is usually large and positive but that it is typically smaller for fitness components. This demonstrates that the evolution of SD is typically genetically constrained and that sex-specific selection coefficients may often be opposite in sign due to sub-optimal levels of SD. Most importantly, we confirm that sex-specific genetic variance is an important contributor to the evolution of SD by validating the prediction of a negative correlation between r(MF) and SD.

  7. The apportionment of total genetic variation by categorical analysis of variance.

    PubMed

    Khang, Tsung Fei; Yap, Von Bing

    2010-01-01

    We wish to suggest the categorical analysis of variance as a means of quantifying the proportion of total genetic variation attributed to different sources of variation. This method potentially challenges researchers to rethink conclusions derived from a well-known method known as the analysis of molecular variance (AMOVA). The CATANOVA framework allows explicit definition, and estimation, of two measures of genetic differentiation. These parameters form the subject of interest in many research programmes, but are often confused with the correlation measures defined in AMOVA, which cannot be interpreted as relative contributions of particular sources of variation. Through a simulation approach, we show that under certain conditions, researchers who use AMOVA to estimate these measures of genetic differentiation may attribute more than justified amounts of total variation to population labels. Moreover, the two measures can also lead to incongruent conclusions regarding the genetic structure of the populations of interest. Fortunately, one of the two measures seems robust to variations in relative sample sizes used. Its merits are illustrated in this paper using mitochondrial haplotype and amplified fragment length polymorphism (AFLP) data.

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

    PubMed Central

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

    2016-01-01

    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. PMID:26921293

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

    PubMed

    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.

  10. Estimation of genetic (co)variances of Gompertz growth function parameters in pigs.

    PubMed

    Coyne, J M; Matilainen, K; Berry, D P; Sevon-Aimonen, M-L; Mäntysaari, E A; Juga, J; Serenius, T; McHugh, N

    2017-04-01

    The objective of this study was to estimate genetic (co)variances for the Gompertz growth function parameters, asymptotic mature weight (A), the ratio of mature weight to birthweight (B) and rate of maturation (k), using alternative modelling approaches. The data set consisted of 51 893 live weight records from 10 201 growing pigs. The growth of each pig was modelled using the Gompertz model employing either a two-step fixed effect or mixed model approach or a one-step mixed model approach using restricted maximum likelihood for the estimation of genetic (co)variance. Heritability estimates for the Gompertz growth function parameters, A (0.40), B (0.69) and k (0.45), were greatest for the one-step approach, compared with the two-step fixed effects approach, A (0.10), B (0.33) and k (0.13), and the two-step mixed model approach, A (0.17), B (0.32) and k (0.18). Inferred genetic correlations (i.e. correlations of estimated breeding values) between growth function parameters within models ranged from -0.78 to 0.76, and across models ranged from 0.28 to 0.73 for parameter A, 0.75 to 0.88 for parameter B and 0.09 to 0.37 for parameter k. Correlations between predicted daily sire live weights based on the Gompertz growth curve parameters' estimated breeding values from 60 to 200 days of age between all three modelled approaches were moderately to strongly correlated (0.75 to 0.95). Results from this study provide heritability estimates for biologically interpretable parameters of pig growth through the quantification of genetic (co)variances, thereby facilitating the estimation of breeding values for inclusion in breeding objectives to aid in breeding and selection decisions.

  11. Genetic selection for increased mean and reduced variance of twinning rate in Belclare ewes.

    PubMed

    Cottle, D J; Gilmour, A R; Pabiou, T; Amer, P R; Fahey, A G

    2016-04-01

    It is sometimes possible to breed for more uniform individuals by selecting animals with a greater tendency to be less variable, that is, those with a smaller environmental variance. This approach has been applied to reproduction traits in various animal species. We have evaluated fecundity in the Irish Belclare sheep breed by analyses of flocks with differing average litter size (number of lambs per ewe per year, NLB) and have estimated the genetic variance in environmental variance of lambing traits using double hierarchical generalized linear models (DHGLM). The data set comprised of 9470 litter size records from 4407 ewes collected in 56 flocks. The percentage of pedigreed lambing ewes with singles, twins and triplets was 30, 54 and 14%, respectively, in 2013 and has been relatively constant for the last 15 years. The variance of NLB increases with the mean in this data; the correlation of mean and standard deviation across sires is 0.50. The breeding goal is to increase the mean NLB without unduly increasing the incidence of triplets and higher litter sizes. The heritability estimates for lambing traits were NLB, 0.09; triplet occurrence (TRI) 0.07; and twin occurrence (TWN), 0.02. The highest and lowest twinning flocks differed by 23% (75% versus 52%) in the proportion of ewes lambing twins. Fitting bivariate sire models to NLB and the residual from the NLB model using a double hierarchical generalized linear model (DHGLM) model found a strong genetic correlation (0.88 ± 0.07) between the sire effect for the magnitude of the residual (VE ) and sire effects for NLB, confirming the general observation that increased average litter size is associated with increased variability in litter size. We propose a threshold model that may help breeders with low litter size increase the percentage of twin bearers without unduly increasing the percentage of ewes bearing triplets in Belclare sheep.

  12. Sex chromosome linked genetic variance and the evolution of sexual dimorphism of quantitative traits.

    PubMed

    Husby, Arild; Schielzeth, Holger; Forstmeier, Wolfgang; Gustafsson, Lars; Qvarnström, Anna

    2013-03-01

    Theory predicts that sex chromsome linkage should reduce intersexual genetic correlations thereby allowing the evolution of sexual dimorphism. Empirical evidence for sex linkage has come largely from crosses and few studies have examined how sexual dimorphism and sex linkage are related within outbred populations. Here, we use data on an array of different traits measured on over 10,000 individuals from two pedigreed populations of birds (collared flycatcher and zebra finch) to estimate the amount of sex-linked genetic variance (h(2)z ). Of 17 traits examined, eight showed a nonzero h(2)Z estimate but only four were significantly different from zero (wing patch size and tarsus length in collared flycatchers, wing length and beak color in zebra finches). We further tested how sexual dimorphism and the mode of selection operating on the trait relate to the proportion of sex-linked genetic variance. Sexually selected traits did not show higher h(2)Z than morphological traits and there was only a weak positive relationship between h(2)Z and sexual dimorphism. However, given the relative scarcity of empirical studies, it is premature to make conclusions about the role of sex chromosome linkage in the evolution of sexual dimorphism.

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

    PubMed

    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.

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

    PubMed

    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.

  15. Colour ornamentation in the blue tit: quantitative genetic (co)variances across sexes

    PubMed Central

    Charmantier, A; Wolak, M E; Grégoire, A; Fargevieille, A; Doutrelant, C

    2017-01-01

    Although secondary sexual traits are commonly more developed in males than females, in many animal species females also display elaborate ornaments or weaponry. Indirect selection on correlated traits in males and/or direct sexual or social selection in females are hypothesized to drive the evolution and maintenance of female ornaments. Yet, the relative roles of these evolutionary processes remain unidentified, because little is known about the genetic correlation that might exist between the ornaments of both sexes, and few estimates of sex-specific autosomal or sex-linked genetic variances are available. In this study, we used two wild blue tit populations with 9 years of measurements on two colour ornaments: one structurally based (blue crown) and one carotenoid based (yellow chest). We found significant autosomal heritability for the chromatic part of the structurally based colouration in both sexes, whereas carotenoid chroma was heritable only in males, and the achromatic part of both colour patches was mostly non heritable. Power limitations, which are probably common among most data sets collected so far in wild populations, prevented estimation of sex-linked genetic variance. Bivariate analyses revealed very strong cross-sex genetic correlations in all heritable traits, although the strength of these correlations was not related to the level of sexual dimorphism. In total, our results suggest that males and females share a majority of their genetic variation underlying colour ornamentation, and hence the evolution of these sex-specific traits may depend greatly on correlated responses to selection in the opposite sex. PMID:27577691

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

    PubMed Central

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

    2014-01-01

    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. PMID:24963372

  17. Rapid divergence of genetic variance-covariance matrix within a natural population.

    PubMed

    Doroszuk, Agnieszka; Wojewodzic, Marcin W; Gort, Gerrit; Kammenga, Jan E

    2008-03-01

    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 promoting G matrix stability in natural populations remain unclear. We studied stability of the G matrix in a 20-year evolution field experiment, where a population of the cosmopolitan parthenogenetic soil nematode Acrobeloides nanus was subjected to drift and divergent selection (benign and stress environments). Selection regime did not influence the level of absolute genetic constraints: under both regimes, two genetic dimensions for three life-history traits were identified. A substantial response to selection in principal components structure and in general matrix pattern was indicated by three statistical methods. G structure was also influenced by drift, with higher divergence under benign conditions. These results show that the G matrix might evolve rapidly in natural populations. The observed high dynamics of G structure probably represents the general feature of asexual species and limits the predictive power of G in phenotypic evolution analyses.

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

    ERIC Educational Resources Information Center

    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…

  19. Additive genetic variance and developmental plasticity in growth trajectories in a wild cooperative mammal.

    PubMed

    Huchard, E; Charmantier, A; English, S; Bateman, A; Nielsen, J F; Clutton-Brock, T

    2014-09-01

    Individual variation in growth is high in cooperative breeders and may reflect plastic divergence in developmental trajectories leading to breeding vs. helping phenotypes. However, the relative importance of additive genetic variance and developmental plasticity in shaping growth trajectories is largely unknown in cooperative vertebrates. This study exploits weekly sequences of body mass from birth to adulthood to investigate sources of variance in, and covariance between, early and later growth in wild meerkats (Suricata suricatta), a cooperative mongoose. Our results indicate that (i) the correlation between early growth (prior to nutritional independence) and adult mass is positive but weak, and there are frequent changes (compensatory growth) in post-independence growth trajectories; (ii) among parameters describing growth trajectories, those describing growth rate (prior to and at nutritional independence) show undetectable heritability while associated size parameters (mass at nutritional independence and asymptotic mass) are moderately heritable (0.09 ≤ h(2) < 0.3); and (iii) additive genetic effects, rather than early environmental effects, mediate the covariance between early growth and adult mass. These results reveal that meerkat growth trajectories remain plastic throughout development, rather than showing early and irreversible divergence, and that the weak effects of early growth on adult mass, an important determinant of breeding success, are partly genetic. In contrast to most cooperative invertebrates, the acquisition of breeding status is often determined after sexual maturity and strongly impacted by chance in many cooperative vertebrates, who may therefore retain the ability to adjust their morphology to environmental changes and social opportunities arising throughout their development, rather than specializing early.

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

    PubMed

    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.

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

    PubMed

    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.

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

    PubMed Central

    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

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

    PubMed

    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 heterogeneity of autosomal dominant polycystic kidney disease in Argentina.

    PubMed Central

    Iglesias, D M; Martín, R S; Fraga, A; Virginillo, M; Kornblihtt, A R; Arrizurieta, E; Viribay, M; San Millán, J L; Herrera, M; Bernath, V

    1997-01-01

    Autosomal dominant polycystic kidney disease (ADPKD) is an inherited disorder with genetic heterogeneity. Up to three loci are involved in this disease, PKD1 on chromosome 16p13.3, PKD2 on 4q21, and a third locus of unknown location. Here we report the existence of locus heterogeneity for this disease in the Argentinian population by performing linkage analysis on 12 families of Caucasian origin. Eleven families showed linkage to PKD 1 and one family showed linkage to PKD2. Two recombinants in the latter family placed the locus PKD2 proximal to D4S1563, in agreement with data recently published on the cloning of this gene. Analysis of clinical data suggests a milder ADPKD phenotype for the PKD2 family. PMID:9350815

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

    SciTech Connect

    Palmer, S.E.; Stephens, K.; Dale, D.C.

    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.

  6. Estimation of variance components and genetic trends for twinning rate in Holstein dairy cattle of Iran.

    PubMed

    Ghavi Hossein-Zadeh, N; Nejati-Javaremi, A; Miraei-Ashtiani, S R; Kohram, H

    2009-07-01

    Calving records from the Animal Breeding Center of Iran, collected from January 1991 to December 2007 and comprising 1,163,594 Holstein calving events from 2,552 herds, were analyzed using a linear animal model, linear sire model, threshold animal model, and threshold sire model to estimate variance components, heritabilities, genetic correlations, and genetic trends for twinning rate in the first, second, and third parities. The overall twinning rate was 3.01%. Mean incidence of twins increased from first to fourth and later parities: 1.10, 3.20, 4.22, and 4.50%, respectively. For first-parity cows, a maximum frequency of twinning was observed from January through April (1.36%), and second- and third-parity cows showed peaks from July to September (at 3.35 and 4.55%, respectively). The phenotypic rate of twinning decreased from 1991 to 2007 for the first, second, and third parities. Sire predicted transmitting abilities were estimated using linear sire model and threshold sire model analyses. Sire transmitting abilities for twinning rate in the first, second, and third parities ranged from -0.30 to 0.42, -0.32 to 0.31, and -0.27 to 0.30, respectively. Heritability estimates of twinning rate for parities 1, 2, and 3 ranged from 1.66 to 10.6%, 1.35 to 9.0%, and 1.10 to 7.3%, respectively, using different models for analysis. Heritability estimates for twinning rate, obtained from the analysis of threshold models, were greater than the estimates of linear models. Solutions for age at calving for the first, second, and third parities demonstrated that cows older at calving were more likely to have twins. Genetic correlations for twinning rate between parities 2 and 3 were greater than correlations between parities 1 and 2 and between parities 1 and 3. There was a slightly increasing trend for twinning rate in parities 1, 2, and 3 over time with the analysis of linear animal and linear sire models, but the trend for twinning rate in parities 1, 2, and 3 with threshold

  7. Genetics, phenotype, and natural history of autosomal dominant cyclic hematopoiesis

    SciTech Connect

    Palmer, S.E. |; Dale, D.C.

    1996-12-30

    Cyclic hematopoiesis (CH, or cyclic neutropenia) is a rare disease manifested by transient severe neutropenia that recurs approximately every 21 days. The hematologic profile of families with the autosomal dominant form (ADCH) has not been well characterized, and it is unknown if the phenotype is distinct from the more common sporadic congenital or acquired forms of CH. We studied nine ADCH families whose children displayed typical CH blood patterns. Pedigrees confirmed dominant inheritance without evidence of heterogeneity or decreased penetrance; three pedigrees suggested new mutations. Families were Caucasian with exception of one with a Cherokee Native American founder. A wide spectrum of symptom severity, ranging from asymptomatic to life-threatening illness, was observed within families. The phenotype changed with age. Children displayed typical neutrophil cycles with symptoms of mucosal ulceration, lymphadenopathy, and infections. Adults often had fewer and milder symptoms, sometimes accompanied by mild chronic neutropenia without distinct cycles. While CH is commonly described as {open_quotes}benign{close_quotes}, four children in three of the nine families died of Clostridium or E. coli colitis, documenting the need for urgent evaluation of abdominal pain. Misdiagnosis with other neutropenias was common but can be avoided by serial blood counts in index cases. Genetic counseling requires specific histories and complete blood counts in relatives at risk to assess status regardless of symptoms, especially to determine individuals with new mutations. We propose diagnostic criteria for ADCH in affected children and adults. Recombinant human granulocyte colony-stimulating factor treatment resulted in dramatic improvement of neutropenia and morbidity. The differential diagnosis from other forms of familial neutropenia is reviewed. 45 refs., 4 figs., 1 tab.

  8. Small Variance in Growth Rate in Annual Plants has Large Effects on Genetic Drift

    Technology Transfer Automated Retrieval System (TEKTRAN)

    When plant size is strongly correlated with plant reproduction, variance in growth rates results in a lognormal distribution of seed production within a population. Fecundity variance affects effective population size (Ne), which reflects the ability of a population to maintain beneficial mutations ...

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

    PubMed

    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.

  10. Genetics Home Reference: autosomal dominant congenital stationary night blindness

    MedlinePlus

    ... stationary night blindness autosomal dominant congenital stationary night blindness Enable Javascript to view the expand/collapse boxes. ... Close All Description Autosomal dominant congenital stationary night blindness is a disorder of the retina , which is ...

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

    MedlinePlus

    ... 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 CADASIL cerebral autosomal dominant arteriopathy ...

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

    PubMed

    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.

  13. Age-specific patterns of genetic variance in Drosophila melanogaster. II. Fecundity and its genetic covariance with age-specific mortality

    SciTech Connect

    Tatar, M.; Promislow, D.E.L.; Khazaeli, A.A.; Curtsinger, J.W.

    1996-06-01

    Under the mutation accumulation model of senescence, it was predicted that the additive genetic variance (V{sub A}) for fitness traits will increase with age. We measured age-specific mortality and fecundity from 65,134 Drosophila melanogaster and estimated genetic variance components, based on reciprocal crosses of extracted second chromosome lines. Elsewhere we report the results for mortality. Here, for fecundity, we report a biomodal pattern for V{sub A} with peaks at 3 days and at 17-31 days. Under the antagonistic pleiotropy model of senescence, it was predicted that negative correlations will exist between early and late life history traits. For fecundity itself we find positive genetic correlations among age classes >3 days but negative nonsignificant correlations between fecundity at 3 days and at older age classes. For fecundity vs. age-specific mortality, we find positive fitness correlations (negative genetic correlations) among the traits at all ages >3 days but a negative fitness correlation between fecundity at 3 days and mortality at the oldest ages (positive genetic correlations). For age-specific mortality itself we find overwhelmingly positive genetic correlations among all age classes. The data suggest that mutation accumulation may be a major source of standing genetic variance for senescence. 75 refs., 4 figs., 1 tab.

  14. Female and male genetic effects on offspring paternity: additive genetic (co)variances in female extra-pair reproduction and male paternity success in song sparrows (Melospiza melodia).

    PubMed

    Reid, Jane M; Arcese, Peter; Keller, Lukas F; Losdat, Sylvain

    2014-08-01

    Ongoing evolution of polyandry, and consequent extra-pair reproduction in socially monogamous systems, is hypothesized to be facilitated by indirect selection stemming from cross-sex genetic covariances with components of male fitness. Specifically, polyandry is hypothesized to create positive genetic covariance with male paternity success due to inevitable assortative reproduction, driving ongoing coevolution. However, it remains unclear whether such covariances could or do emerge within complex polyandrous systems. First, we illustrate that genetic covariances between female extra-pair reproduction and male within-pair paternity success might be constrained in socially monogamous systems where female and male additive genetic effects can have opposing impacts on the paternity of jointly reared offspring. Second, we demonstrate nonzero additive genetic variance in female liability for extra-pair reproduction and male liability for within-pair paternity success, modeled as direct and associative genetic effects on offspring paternity, respectively, in free-living song sparrows (Melospiza melodia). The posterior mean additive genetic covariance between these liabilities was slightly positive, but the credible interval was wide and overlapped zero. Therefore, although substantial total additive genetic variance exists, the hypothesis that ongoing evolution of female extra-pair reproduction is facilitated by genetic covariance with male within-pair paternity success cannot yet be definitively supported or rejected either conceptually or empirically.

  15. Good Genes and Sexual Selection in Dung Beetles (Onthophagus taurus): Genetic Variance in Egg-to-Adult and Adult Viability

    PubMed Central

    Garcia-Gonzalez, Francisco; Simmons, Leigh W.

    2011-01-01

    Whether species exhibit significant heritable variation in fitness is central for sexual selection. According to good genes models there must be genetic variation in males leading to variation in offspring fitness if females are to obtain genetic benefits from exercising mate preferences, or by mating multiply. However, sexual selection based on genetic benefits is controversial, and there is limited unambiguous support for the notion that choosy or polyandrous females can increase the chances of producing offspring with high viability. Here we examine the levels of additive genetic variance in two fitness components in the dung beetle Onthophagus taurus. We found significant sire effects on egg-to-adult viability and on son, but not daughter, survival to sexual maturity, as well as moderate coefficients of additive variance in these traits. Moreover, we do not find evidence for sexual antagonism influencing genetic variation for fitness. Our results are consistent with good genes sexual selection, and suggest that both pre- and postcopulatory mate choice, and male competition could provide indirect benefits to females. PMID:21267411

  16. Sex-specific genetic variances in life-history and morphological traits of the seed beetle Callosobruchus maculatus.

    PubMed

    Hallsson, Lára R; Björklund, Mats

    2012-01-01

    Knowledge of heritability and genetic correlations are of central importance in the study of adaptive trait evolution and genetic constraints. We use a paternal half-sib-full-sib breeding design to investigate the genetic architecture of three life-history and morphological traits in the seed beetle, Callosobruchus maculatus. Heritability was significant for all traits under observation and genetic correlations between traits (r(A)) were low. Interestingly, we found substantial sex-specific genetic effects and low genetic correlations between sexes (r(MF)) in traits that are only moderately (weight at emergence) to slightly (longevity) sexually dimorphic. Furthermore, we found an increased sire ([Formula: see text]) compared to dam ([Formula: see text]) variance component within trait and sex. Our results highlight that the genetic architecture even of the same trait should not be assumed to be the same for males and females. Furthermore, it raises the issue of the presence of unnoticed environmental effects that may inflate estimates of heritability. Overall, our study stresses the fact that estimates of quantitative genetic parameters are not only population, time, environment, but also sex specific. Thus, extrapolation between sexes and studies should be treated with caution.

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

    PubMed Central

    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 Inventory (DCI), an instrument to gather data on selected alternative conceptions about dominance. During development of the 16-item test, we used expert surveys (n = 12), student interviews (n = 42), and field tests (n = 1763) from introductory and advanced biology undergraduates at public and private, majority- and minority-serving, 2- and 4-yr institutions in the United States. In the final field test across all subject populations (n = 709), item difficulty ranged from 0.08 to 0.84 (0.51 ± 0.049 SEM), while item discrimination ranged from 0.11 to 0.82 (0.50 ± 0.048 SEM). Internal reliability (Cronbach's alpha) was 0.77, while test–retest reliability values were 0.74 (product moment correlation) and 0.77 (intraclass correlation). The prevalence of alternative conceptions in the field tests shows that introductory and advanced students retain confusion about dominance after instruction. All measures support the DCI as a useful instrument for measuring undergraduate biology student understanding and alternative conceptions about dominance. PMID:26086665

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

    PubMed

    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 Inventory (DCI), an instrument to gather data on selected alternative conceptions about dominance. During development of the 16-item test, we used expert surveys (n = 12), student interviews (n = 42), and field tests (n = 1763) from introductory and advanced biology undergraduates at public and private, majority- and minority-serving, 2- and 4-yr institutions in the United States. In the final field test across all subject populations (n = 709), item difficulty ranged from 0.08 to 0.84 (0.51 ± 0.049 SEM), while item discrimination ranged from 0.11 to 0.82 (0.50 ± 0.048 SEM). Internal reliability (Cronbach's alpha) was 0.77, while test-retest reliability values were 0.74 (product moment correlation) and 0.77 (intraclass correlation). The prevalence of alternative conceptions in the field tests shows that introductory and advanced students retain confusion about dominance after instruction. All measures support the DCI as a useful instrument for measuring undergraduate biology student understanding and alternative conceptions about dominance.

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

    PubMed

    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.

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

    PubMed

    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.

  1. Genetic Model Fitting in IQ, Assortative Mating & Components of IQ Variance.

    ERIC Educational Resources Information Center

    Capron, Christiane; Vetta, Adrian R.; Vetta, Atam

    1998-01-01

    The biometrical school of scientists who fit models to IQ data traces their intellectual ancestry to R. Fisher (1918), but their genetic models have no predictive value. Fisher himself was critical of the concept of heritability, because assortative mating, such as for IQ, introduces complexities into the study of a genetic trait. (SLD)

  2. Genetic Variance in Processing Speed Drives Variation in Aging of Spatial and Memory Abilities

    ERIC Educational Resources Information Center

    Finkel, Deborah; Reynolds, Chandra A.; McArdle, John J.; Hamagami, Fumiaki; Pedersen, Nancy L.

    2009-01-01

    Previous analyses have identified a genetic contribution to the correlation between declines with age in processing speed and higher cognitive abilities. The goal of the current analysis was to apply the biometric dual change score model to consider the possibility of temporal dynamics underlying the genetic covariance between aging trajectories…

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

    PubMed Central

    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

  4. Genetic diversity and variance of Stentor coeruleus (Ciliophora: Heterotrichea) inferred from inter-simple sequence repeat (ISSR) fingerprinting.

    PubMed

    Zhang, Wen-Jing; Lin, Yuan-Shao; Cao, Wen-Qing; Yang, Jun

    2012-01-01

    We used inter-simple sequence repeat fingerprinting to analyze the genetic structure of 16 populations of Stentor coeruleus from three lakes and three ponds in China. Using 14 polymorphic primers, a total of 99 discernible DNA fragments were detected, among which 76 (76.77%) were polymorphic, indicating median genetic diversity in these populations. Further, both Nei's gene diversity (h) and Shannon's information index (I) between the different populations revealed a median genetic diversity. At the same time, gene flow was interpreted to be low. The main factors responsible for the median level of diversity and low gene flow within populations are probably due to a low frequency of sexual recombinations. Analysis of molecular variance showed that there was high genetic differentiation among the five water bodies. Both cluster analysis and a nonmetric multidimensional scaling analysis suggested that genotypes isolated from the same locations displayed a higher genetic similarity than those from different ones, separating populations into subgroups according to their geographical locations. However, there is a weak positive correlation between the genetic distance and geographical distance.

  5. Direct and maternal (co)variance components, genetic parameters, and annual trends for growth traits of Makooei sheep in Iran.

    PubMed

    Mohammadi, Hossein; Shahrebabak, Mohammad Moradi; Vatankhah, Mahmood; Shahrebabak, Hossein Moradi

    2013-01-01

    Genetic parameters and genetic trends for birth weight (BW), weaning weight (WW), 6-month weight (6MW), and yearling weight (YW) traits were estimated by using records of 5,634 Makooei lambs, descendants of 289 sires and 1,726 dams, born between 1996 and 2009 at the Makooei sheep breeding station, West Azerbaijan, Iran. The (co)variance components were estimated with different animal models using a restricted maximum likelihood procedure and the most appropriate model for each trait was determined by Akaike's Information Criterion. Breeding values of animals were predicted with best linear unbiased prediction methodology under multi-trait animal models and genetic trends were estimated by regression mean breeding values on birth year. The most appropriate model for BW was a model including direct and maternal genetic effects, regardless of their covariance. The model for WW and 6MW included direct additive genetic effects. The model for YW included direct genetic effects only. Direct heritabilities based on the best model were estimated 0.15 ± 0.04, 0.16 ± 0.03, 0.21 ± 0.04, and 0.22 ± 0.06 for BW, WW, 6MW, and YW, respectively, and maternal heritability obtained 0.08 ± 0.02 for BW. Genetic correlations among the traits were positive and varied from 0.28 for BW-YW to 0.66 for BW-WW and phenotypic correlations were generally lower than the genetic correlations. Genetic trends were 8.1 ± 2, 67.4 ± 5, 38.7 ± 4, and 47.6 ± 6 g per year for BW, WW, 6MW, and YW, respectively.

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

    PubMed

    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.

  7. (Co)variance components, genetic parameters and annual trends for calf weights in a Brahman herd kept on floodable savanna.

    PubMed

    Plasse, Dieter; Verde, Omar; Arango, Jesús; Camaripano, Luis; Fossi, Hugo; Romero, Rafael; Rodriguez, Carlos M; Rumbos, José L

    2002-12-31

    (Co)variance components and genetic parameters were estimated for body weights of an elite Brahman herd under a designed, supervised management and genetic program, including strategic artificial insemination (AI). Restricted maximum likelihood methods were used with a univariate animal model for birth weight (BW) and a bivariate model for weaning weight (205-day weight, 205W) and 18-month weight (548-day weight, 548W). Models included random animal direct and maternal genetic effects, maternal permanent environmental effect (c2), and sex-year-month of birth-age of dam and genetic group (identified and unidentified paternity), as fixed effects. Analysis A1 included all calves and analysis A2 included only those with identified sires. Of the 8,066 calves born, 36% were progeny of AI, 11% from single sire and 53% from multi-sire herds. They were born from 1985 to 1998, from 2559 dams and 146 sires (78 identified). Estimates of direct, maternal and total heritabilities from A1 for BW, 205W and 548W were: 0.23, 0.07 and 0.30; 0.08, 0.14 and 0.16; 0.16, 0.04 and 0.28, respectively. Corresponding estimates of direct maternal genetic correlations were 0.22, 0.07 and 0.86, and c2 estimates were 0.04, 0.14 and 0.04, respectively. Estimates of direct and maternal genetic, and permanent environmental correlations between 205W and 548W were: 0.66, 0.70 and 1.00. Variances and genetic parameters from A1 and A2 were, in general, very similar. Estimates of phenotypic, and direct and maternal genetic trends per year from A1 were: 0.393, 0.004 and 0.003 kg (BW), 3.367, 0.142 and 0.115 kg (205W), 1.813, 0.263 and 0.095 kg (548W). Estimates of direct and maternal genetic trends from A2 were: 0.033 and -0.002 kg (BW); 0.186 and 0.276 kg (205W); 0.471 and 0.136 kg (548W). The modern selection methods that have been used recently should be continued, with emphasis on the improvement of cow efficiency for sustainable beef production on floodable savanna combined with improved pasture.

  8. Rare genetic causes of autosomal dominant or recessive hypercholesterolaemia.

    PubMed

    Soutar, Anne K

    2010-02-01

    Familial hypercholesterolaemia (FH) is a human inherited disorder of metabolism characterised by increased serum low-density lipoprotein (LDL) cholesterol. It is caused by defects in the LDL-receptor pathway that impair normal uptake and clearance of LDL by the liver. The commonest cause of FH is mutations in LDLR, the gene for the LDL receptor, but defects also occur in APOB that encodes its major protein ligand. More recently, defects in two other genes, LDLRAP1 and PCSK9, have been found in patients with FH and investigation of these has shed new light on the functioning and complexity of the LDL receptor pathway. Cells from patients with autosomal recessive hypercholesterolaemia (ARH) fail to internalise the LDL receptor because they carry two defective alleles of LDLRAP1, a gene that encodes a specific clathrin adaptor protein. PCSK9 encodes proprotein convertase subtilisin kexin type 9, a secreted protein that binds to the LDL receptor and promotes its degradation. Gain-of function mutations in PCSK9 are autosomal dominant and cause hypercholesterolaemia because they increase the affinity of PCSK9 protein for the LDL receptor, whereas loss-of-function mutations reduce serum cholesterol because LDL-receptor protein is exposed to reduced PCSK9-mediated degradation. Thus, PCSK9 has become a new target for cholesterol-lowering drug therapy.

  9. Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases.

    PubMed

    Naz, Mufassra; Kodamullil, Alpha Tom; Hofmann-Apitius, Martin

    2016-05-01

    The work we present here is based on the recent extension of the syntax of the Biological Expression Language (BEL), which now allows for the representation of genetic variation information in cause-and-effect models. In our article, we describe, how genetic variation information can be used to identify candidate disease mechanisms in diseases with complex aetiology such as Alzheimer's disease and Parkinson's disease. In those diseases, we have to assume that many genetic variants contribute moderately to the overall dysregulation that in the case of neurodegenerative diseases has such a long incubation time until the first clinical symptoms are detectable. Owing to the multilevel nature of dysregulation events, systems biomedicine modelling approaches need to combine mechanistic information from various levels, including gene expression, microRNA (miRNA) expression, protein-protein interaction, genetic variation and pathway. OpenBEL, the open source version of BEL, has recently been extended to match this requirement, and we demonstrate in our article, how candidate mechanisms for early dysregulation events in Alzheimer's disease can be identified based on an integrative mining approach that identifies 'chains of causation' that include single nucleotide polymorphism information in BEL models.

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

    PubMed

    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.

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

    PubMed Central

    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

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

    PubMed

    Benavente, Javiera N; Seeb, Lisa W; Seeb, James E; Arismendi, Ivan; Hernández, Cristián E; Gajardo, Gonzalo; Galleguillos, Ricardo; Cádiz, Maria I; Musleh, Selim S; Gomez-Uchida, Daniel

    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 substantial

  13. Genetic diversity within a dominant plant outweighs plant species diversity in structuring an arthropod community.

    PubMed

    Crawford, Kerri M; Rudgers, Jennifer A

    2013-05-01

    Plant biodiversity is being lost at a rapid rate. This has spurred much interest in elucidating the consequences of this loss for higher trophic levels. Experimental tests have shown that both plant species diversity and genetic diversity within a plant species can influence arthropod community structure. However, the majority of these studies have been conducted in separate systems, so their relative importance is currently unresolved. Furthermore, potential interactions between the two levels of diversity, which likely occur in natural systems, have not been investigated. To clarify these issues, we conducted three experiments in a freshwater sand dune ecosystem. We (1) independently manipulated plant species diversity, (2) independently manipulated genetic diversity within the dominant plant species, Ammophila breviligulata, and (3) jointly manipulated genetic diversity within the dominant plant and species diversity. We found that genetic diversity within the dominant plant species, Ammophila breviligulata, more strongly influenced arthropod communities than plant species diversity, but this effect was dependent on the presence of other species. In species mixtures, A. breviligulata genetic diversity altered overall arthropod community composition, and arthropod richness and abundance peaked at the highest level of genetic diversity. Positive nonadditive effects of diversity were detected, suggesting that arthropods respond to emergent properties of diverse plant communities. However, in the independent manipulations where A. breviligulata was alone, effects of genetic diversity were weaker, with only arthropod richness responding. In contrast, plant species diversity only influenced arthropods when A. breviligulata was absent, and then only influenced herbivore abundance. In addition to showing that genetic diversity within a dominant plant species can have large effects on arthropod community composition, these results suggest that understanding how species

  14. The evolution of interacting phenotypes: genetics and evolution of social dominance.

    PubMed

    Moore, Allen J; Haynes, Kenneth F; Preziosi, Richard F; Moore, Patricia J

    2002-12-01

    Although the argument over genetic influences on social dominance is contentious, genetic models of interacting phenotypes provide a theoretical framework for heritable effects on, and therefore evolution of, social behavior. Here we adapt the interacting phenotype model to show how social dominance can evolve. Our model makes a number of predictions: rapid evolution of behavior, strong correlated responses in associated traits (such as a badge of status), and, because context is important for social dominance, integrated evolution of both dominant and subordinate behavior reflecting direct and indirect genetic effects and social selection. We also describe the results of empirical work, artificial selection based on social status within a hierarchy in the cockroach Nauphoeta cinerea, that we used to test the predictions of our model. There was little change within selection lines in the expression of agonistic behavior, but by just generation 7 of selection, in comparisons between lines, high-line males consistently dominated low and control males, while low-line males were consistently subordinate to high-line and control males. There was a strong correlated response to selection in the pheromonal badge of status. Some correlated responses to selection differed among replicate lines, with the compound that makes males subordinate changed in one replicate, while the compound that confers dominance was altered in the other. Overall, our results are consistent with predictions from models of interacting phenotypes: social dominance is influenced by additive genetic variation, can evolve as a result of social selection, and evolution of social interactions appears to be rapid. Finally, different responses in the replicates allowed us to test very specific predictions regarding the role of the social pheromone in N. cinerea, highlighting the value of artificial selection experiments as a tool in evolutionary behavioral genetic studies.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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

  17. Genetics advances in autosomal dominant focal epilepsies: focus on DEPDC5.

    PubMed

    Baulac, Stéphanie

    2014-01-01

    Rare multiplex families with autosomal dominant focal epilepsies have been described with specific age-related and electroclinical syndromes: autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE), familial temporal lobe epilepsy (FTLE), and familial focal epilepsy with variable foci (FFEVF). Molecular genetic advances in inherited focal epilepsies have pinpointed their genetic heterogeneity and the fact that they are mediated by different biological pathways: ion channel subunit genes have been linked to ADNFLE (CHRNA4, CHRNA2, CHRNB2, and KCNT1, encoding, respectively, the α4, α2, and β2 subunits of the neuronal nicotinic acetylcholine receptor, and a potassium channel subunit); neuronal secreted protein (LGI1-encoding epitempin) has been linked to autosomal dominant epilepsy with auditory features; and mTORC1-repressor DEPDC5 (DEP domain-containing protein 5) gene has recently been reported in a broad spectrum of inherited focal epilepsies (ADNFLE, FTLE, FFEVF). This chapter focuses on DEPDC5, a newly identified gene.

  18. Variance components and genetic parameters for milk production and lactation pattern in an ethiopian multibreed dairy cattle population.

    PubMed

    Gebreyohannes, Gebregziabher; Koonawootrittriron, Skorn; Elzo, Mauricio A; Suwanasopee, Thanathip

    2013-09-01

    The objective of this study was to estimate variance components and genetic parameters for lactation milk yield (LY), lactation length (LL), average milk yield per day (YD), initial milk yield (IY), peak milk yield (PY), days to peak (DP) and parameters (ln(a) and c) of the modified incomplete gamma function (MIG) in an Ethiopian multibreed dairy cattle population. The dataset was composed of 5,507 lactation records collected from 1,639 cows in three locations (Bako, Debre Zeit and Holetta) in Ethiopia from 1977 to 2010. Parameters for MIG were obtained from regression analysis of monthly test-day milk data on days in milk. The cows were purebred (Bos indicus) Boran (B) and Horro (H) and their crosses with different fractions of Friesian (F), Jersey (J) and Simmental (S). There were 23 breed groups (B, H, and their crossbreds with F, J, and S) in the population. Fixed and mixed models were used to analyse the data. The fixed model considered herd-year-season, parity and breed group as fixed effects, and residual as random. The single and two-traits mixed animal repeatability models, considered the fixed effects of herd-year-season and parity subclasses, breed as a function of cow H, F, J, and S breed fractions and general heterosis as a function of heterozygosity, and the random additive animal, permanent environment, and residual effects. For the analysis of LY, LL was added as a fixed covariate to all models. Variance components and genetic parameters were estimated using average information restricted maximum likelihood procedures. The results indicated that all traits were affected (p<0.001) by the considered fixed effects. High grade B×F cows (3/16B 13/16F) had the highest least squares means (LSM) for LY (2,490±178.9 kg), IY (10.5±0.8 kg), PY (12.7±0.9 kg), YD (7.6±0.55 kg) and LL (361.4±31.2 d), while B cows had the lowest LSM values for these traits. The LSM of LY, IY, YD, and PY tended to increase from the first to the fifth parity. Single

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

    PubMed

    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.

  20. Diversity and population structure of a dominant deciduous tree based on morphological and genetic data

    PubMed Central

    Zhang, Qin-di; Jia, Rui-Zhi; Meng, Chao; Ti, Chao-Wen; Wang, Yi-Ling

    2015-01-01

    Knowledge of the genetic diversity and structure of tree species across their geographic ranges is essential for sustainable use and management of forest ecosystems. Acer grosseri Pax., an economically and ecologically important maple species, is mainly distributed in North China. In this study, the genetic diversity and population differentiation of 24 natural populations of this species were evaluated using sequence-related amplified polymorphism markers and morphological characters. The results show that highly significant differences occurred in 32 morphological traits. The coefficient of variation of 34 characters was 18.19 %. Principal component analysis indicated that 18 of 34 traits explained 60.20 % of the total variance. The phenotypic differentiation coefficient (VST) was 36.06 % for all morphological traits. The Shannon–Wiener index of 34 morphological characters was 6.09, while at the population level, it was 1.77. The percentage of polymorphic bands of all studied A. grosseri populations was 82.14 %. Nei's gene diversity (He) and Shannon's information index (I) were 0.35 and 0.50, respectively. Less genetic differentiation was detected among the natural populations (GST = 0.20, ΦST = 0.10). Twenty-four populations of A. grosseri formed two main clusters, which is consistent with morphological cluster analysis. Principal coordinates analysis and STRUCTURE analysis supported the UPGMA-cluster dendrogram. There was no significant correlation between genetic and geographical distances among populations. Both molecular and morphological data suggested that A. grosseri is rich in genetic diversity. The high level of genetic variation within populations could be affected by the biological characters, mating system and lifespan of A. grosseri, whereas the lower genetic diversity among populations could be caused by effective gene exchange, selective pressure from environmental heterogeneity and the species' geographical range. PMID:26311734

  1. Chemical Variation in a Dominant Tree Species: Population Divergence, Selection and Genetic Stability across Environments

    PubMed Central

    O’Reilly-Wapstra, Julianne M.; Miller, Alison M.; Hamilton, Matthew G.; Williams, Dean; Glancy-Dean, Naomi; Potts, Brad M.

    2013-01-01

    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 h2op = 0.24) to high (e.g., macrocarpal G h2op = 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. PMID:23526981

  2. Chemical variation in a dominant tree species: population divergence, selection and genetic stability across environments.

    PubMed

    O'Reilly-Wapstra, Julianne M; Miller, Alison M; Hamilton, Matthew G; Williams, Dean; Glancy-Dean, Naomi; Potts, Brad M

    2013-01-01

    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(2)op = 0.24) to high (e.g., macrocarpal G h(2)op = 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.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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.

  5. Genetic variation within a dominant shrub species determines plant species colonization in a coastal dune ecosystem.

    PubMed

    Crutsinger, Gregory M; Strauss, Sharon Y; Rudgers, Jennifer A

    2010-04-01

    The diversity and structure of plant communities is often determined by the presence and identity of competitively dominant species. Recent studies suggest that intraspecific variation within dominants may also have important community-level consequences. In a coastal dunes ecosystem of northern California, we use a decade-old common garden experiment to test the effects of a genetically based architectural dimorphism within a dominant native shrub, Baccharis pilularis, on plant colonization success and understory plant diversity. We found that erect Baccharis morphs had higher richness and cover of colonizing plant species (both native and exotic species) compared to prostrate morphs, as well as higher biomass of a dominant exotic dune grass (Ammophila arenaria). Trait differences between architectural morphs influenced the abiotic understory environment (light availability, soil surface temperature, and litter depth) and were associated with species colonization success. Taken together, our results demonstrate that incorporating within-species variation, particularly within dominant species, into community ecological research can increase the ability to predict patterns of species diversity and assembly within communities.

  6. Prediction of testcross means and variances among F3 progenies of F1 crosses from testcross means and genetic distances of their parents in maize.

    PubMed

    Melchinger, A E; Gumber, R K; Leipert, R B; Vuylsteke, M; Kuiper, M

    1998-03-01

    Prediction of the means and genetic variances in segregating generations could help to assess the breeding potential of base populations. In this study, we investigated whether the testcross (TC) means and variances of F3 progenies from F1 crosses in European maize can be predicted from the TC means of their parents and F1 crosses and four measures of parental genetic divergence: genetic distance (GD) determined by 194 RFLP or 691 AFLP(TM) (1) markers, mid-parent heterosis (MPH), and absolute difference between the TC means of parents (∣P1-P2∣). The experimental materials comprised six sets of crosses; each set consisted of four elite inbreds from the flint or dent germplasm and the six possible F1 crosses between them, which were evaluated for mid-parent heterosis. Testcross progenies of these materials and 20 random F3 plants per F1 cross were produced with a single-cross tester from the opposite heterotic group and evaluated in two environments. The characters studied were plant height, dry matter content and grain yield. The genetic distance between parent lines ranged between 0.17 and 0.70 for RFLPs and between 0.14 and 0.57 for AFLPs in the six sets. Testcross-means of parents, F1 crosses, and F3 populations averaged across the six crosses in a particular set generally agreed well for all three traits. Bartlett's test revealed heterogeneous TC variances among the six crosses in all sets for plant height, in four sets for grain yield and in five sets for dry matter content. Correlations among the TC means of the parents, F1 crosses, and F3 populations were highly significant and positive for all traits. Estimates of the TC variance among F3 progenies for the 36 crosses showed only low correlations with the four measures of parental genetic divergence for all traits. The results demonstrated that for our material, the TC means of the parents or the parental F1 cross can be used as predictors for the TC means of F3 populations. However, the prediction of the

  7. Gene Loss Dominates As a Source of Genetic Variation within Clonal Pathogenic Bacterial Species.

    PubMed

    Bolotin, Evgeni; Hershberg, Ruth

    2015-07-10

    Some of the most dangerous pathogens such as Mycobacterium tuberculosis and Yersinia pestis evolve clonally. This means that little or no recombination occurs between strains belonging to these species. Paradoxically, although different members of these species show extreme sequence similarity of orthologous genes, some show considerable intraspecies phenotypic variation, the source of which remains elusive. To examine the possible sources of phenotypic variation within clonal pathogenic bacterial species, we carried out an extensive genomic and pan-genomic analysis of the sources of genetic variation available to a large collection of clonal and nonclonal pathogenic bacterial species. We show that while nonclonal species diversify through a combination of changes to gene sequences, gene loss and gene gain, gene loss completely dominates as a source of genetic variation within clonal species. Indeed, gene loss is so prevalent within clonal species as to lead to levels of gene content variation comparable to those found in some nonclonal species that are much more diverged in their gene sequences and that acquire a substantial number of genes horizontally. Gene loss therefore needs to be taken into account as a potential dominant source of phenotypic variation within clonal bacterial species.

  8. Comprehensive Genetic Analysis of Japanese Autosomal Dominant Sensorineural Hearing Loss Patients

    PubMed Central

    Iwasa, Yoh-ichiro; Nishio, Shin-ya; Usami, Shin-ichi

    2016-01-01

    Background In general, autosomal dominant inherited hearing loss does not have a founder mutation, with the causative mutation different in each family. For this reason, there has been a strong need for efficient diagnosis methods for autosomal dominant sensorineural hearing loss (ADSNHL) patients. This study sought to verify the effectiveness of our analysis algorithm for the screening of ADSNHL patients as well as the usefulness of the massively parallel DNA sequencing (MPS). Subjects and Methods Seventy-five Japanese ADSNHL patients from 53 ENT departments nationwide participated in this study. We conducted genetic analysis of 75 ADSNHL patients using the Invader assay, TaqMan genotyping assay and MPS-based genetic screening. Results A total of 46 (61.3%) ADSNHL patients were found to have at least one candidate gene variant. Conclusion We were able to achieve a high mutation detection rate through the combination of the Invader assay, TaqMan genotyping assay and MPS. MPS could be used to successfully identify mutations in rare deafness genes. PMID:27911912

  9. Therapeutic siRNAs for dominant genetic skin disorders including pachyonychia congenita.

    PubMed

    Leachman, Sancy A; Hickerson, Robyn P; Hull, Peter R; Smith, Frances J D; Milstone, Leonard M; Lane, E Birgitte; Bale, Sherri J; Roop, Dennis R; McLean, W H Irwin; Kaspar, Roger L

    2008-09-01

    The field of science and medicine has experienced a flood of data and technology associated with the human genome project. Over 10,000 human diseases have been genetically defined, but little progress has been made with respect to the clinical application of this knowledge. A notable exception to this exists for pachyonychia congenita (PC), a rare, dominant-negative keratin disorder. The establishment of a non-profit organization, PC Project, has led to an unprecedented coalescence of patients, scientists, and physicians with a unified vision of developing novel therapeutics for PC. Utilizing the technological by-products of the human genome project, such as RNA interference (RNAi) and quantitative RT-PCR (qRT-PCR), physicians and scientists have collaborated to create a candidate siRNA therapeutic that selectively inhibits a mutant allele of KRT6A, the most commonly affected PC keratin. In vitro investigation of this siRNA demonstrates potent inhibition of the mutant allele and reversal of the cellular aggregation phenotype. In parallel, an allele-specific quantitative real-time RT-PCR assay has been developed and validated on patient callus samples in preparation for clinical trials. If clinical efficacy is ultimately demonstrated, this "first-in-skin" siRNA may herald a paradigm shift in the treatment of dominant-negative genetic disorders.

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

    PubMed

    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.

  11. Replication of a Gene-Environment Interaction via Multimodel Inference: Additive-Genetic Variance in Adolescents’ General Cognitive Ability Increases with Family-of-Origin Socioeconomic Status

    PubMed Central

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

    2015-01-01

    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. PMID:25539975

  12. Autosomal dominant ataxia: Genetic evidence for locus heterogeneity from a cuban founder-effect population

    PubMed Central

    Auburger, Georg; Diaz, Guillermo Orozco; Capote, Raul Ferreira; Sanchez, Suzana Gispert; Perez, Marta Paradoa; del Cueto, Marianela Estrada; Meneses, Mirna Garcia; Farrall, Martin; Williamson, Robert; Chamberlain, Susan; Baute, Luis Heredero

    1990-01-01

    The locus for autosomal dominant ataxia with a diagnosis of olivo-ponto-cerebellar atrophy at autopsy has been previously assigned to chromosome 6p. However, evidence for two alternative locations has been reported. We have recently described a large potential founder-effect population of such patients in the Holguin province of Cuba. With an estimated 1,000 patients available for analysis, this extensive cluster of families provides a unique opportunity for the definitive localization of the genetic mutation. Linkage analysis between the disease locus in this population and markers within and flanking the HLA region on chromosome 6 were undertaken in 12 families comprising over 100 affected individuals. Despite similarity in the clinical phenotype between those families where the disease locus has been reported to be linked to the HLA locus and the Cuban patients, no evidence of linkage to this region could be demonstrated in the latter. The disease locus was excluded from a 96-cM genetic interval of the short arm of chromosome 6, encompassing the F13A1–HLA–GLO1–MUT/D6S4 loci. These data strongly support the existence of genetic heterogeneity for the disease. PMID:1971152

  13. Autosomal dominant retinitis pigmentosa with apparent incomplete penetrance: a clinical, electrophysiological, psychophysical, and molecular genetic study.

    PubMed Central

    Moore, A T; Fitzke, F; Jay, M; Arden, G B; Inglehearn, C F; Keen, T J; Bhattacharya, S S; Bird, A C

    1993-01-01

    Twenty five symptomatic individuals and six asymptomatic obligate gene carriers from four families with autosomal dominant retinitis pigmentosa (adRP) showing apparent incomplete penetrance have been studied. Symptomatic individuals from three families showed early onset of night blindness, non-recordable rod electroretinograms, and marked elevation of both rod and cone thresholds in all subjects tested. In the fourth family, there was more variation in the age of onset of night blindness and some symptomatic individuals showed well preserved rod and cone function in some retinal areas. All asymptomatic individuals tested had evidence of mild abnormalities of rod and cone function, indicating that these families show marked variation in expressivity rather than true non-penetrance of the adRP gene. No mutations of the rhodopsin or RDS genes were found in these families and the precise genetic mutation(s) remain to be identified. PMID:8025041

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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).

  17. 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 and allele frequencies.

    PubMed

    Tait, R G; Shackelford, S D; Wheeler, T L; King, D A; Casas, E; Thallman, R M; Smith, T P L; Bennett, G L

    2014-02-01

    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 and mode of inheritance for previously reported SNP on targeted beef carcass quality traits; 2) estimate effects of previously reported SNP on nontarget performance traits; and 3) evaluate tenderness SNP specific residual variance models compared to a single residual variance model for tenderness. Divergent haplotypes within µ-calpain (CAPN1), and SNP within calpastatin (CAST) and growth hormone receptor (GHR) were successfully selected to increase their frequencies. Traits evaluated were birth BW, weaning BW, final BW, fat thickness, LM area, USDA marbling score, yield grade, slice shear force (SSF), and visible and near infrared predicted slice shear force. Both CAPN1 and CAST exhibited additive (P < 0.001) modes of inheritance for SSF and neither exhibited dominance (P ≥ 0.19). Furthermore, the interaction between CAPN1 and CAST for SSF was not significant (P = 0.55). Estimated additive effects of CAPN1 (1.049 kg) and CAST (1.257 kg) on SSF were large in this study. Animals homozygous for tender alleles at both CAPN1 and CAST would have 4.61 kg lower SSF (38.6% of the mean) than animals homozygous tough for both markers. There was also an effect of CAST on yield grade (P < 0.02). The tender CAST allele was associated with more red meat yield and less trimmable fat. There were no significant effects (P ≥ 0.23) for GHR on any of the traits evaluated in this study. Furthermore, CAST specific residual variance models were found to fit significantly better (P < 0.001) than single residual variance models for SSF, with the tougher genotypes having larger residual variance. Thus, the risk of a tough steak from the undesired CAST genotype is increased through both an

  18. Genetic control of the environmental variance for birth weight in seven generations of a divergent selection experiment in mice.

    PubMed

    Formoso-Rafferty, N; Cervantes, I; Ibáñez-Escriche, N; Gutiérrez, J P

    2016-06-01

    Data from seven generations of a divergent selection experiment designed for environmental variability of birth weight were analysed to estimate genetic parameters and to explore signs of selection response. A total of 10 783 birth weight records from 638 females and 1127 litters in combination with 10 007 pedigree records were used. Each record of birth weight was assigned to the mother of the pup in a heteroscedastic model, and after seven generations of selection, evidence of success in the selection process was shown. A Bayesian analysis showed that success of the selection process started from the first generation for birth weight and from the second generation for its environmental variability. Genetic parameters were estimated across generations. However, only from the third generation onwards were the records useful to consider the results to be reliable. The results showed a consistent positive and low genetic correlation between the birth weight trait and its environmental variability, which could allow an independent selection process. This study has demonstrated that the genetic control of the birth weight environmental variability is possible in mice. Nevertheless, before the results are applied directly in farm animals, it would be worth confirming any other implications on other important traits, such as robustness, longevity and welfare.

  19. School Performance and Genetic and Environmental Variance in Antisocial Behavior at the Transition from Adolescence to Adulthood

    PubMed Central

    Johnson, Wendy; McGue, Matthew K.; Iacono, William G.

    2009-01-01

    Antisocial behavior increases in adolescence, particularly among those who perform poorly in school. As adolescents move into adulthood, both educational attainment and the extent to which antisocial behavior continues have implications for their abilities to take on constructive social roles. We used a population-representative longitudinal twin study to explore how links between genetic and environmental influences at ages 17 and 24 may be implicated in the developmental processes involved. At age 17, expression of both genetic and nonshared environmental vulnerabilities unique to antisocial behavior was greater among those with low GPA than among those with higher GPA. This suggested that maintenance of high GPA buffered the impact of both genetic and environmental influences encouraging antisocial behavior. When GPA was high, both genetic and environmental influences involved in both traits encouraged good school performance and restrained antisocial behavior. At age 24, however, correlated family environmental influences drove the association between educational attainment and antisocial behavior. Antisocial characteristics involving school performance and educational attainment that transcend generations may slot individuals into social categories that restrict opportunities and reinforce antisocial characteristics. PMID:19586174

  20. (Co)variance components and genetic parameters for growth traits in Arabi sheep using different animal models.

    PubMed

    Shokrollahi, B; Baneh, H

    2012-02-08

    The objective of the present study was to estimate genetic parameters for body weight at different ages in Arabi sheep using data collected from 1999 to 2009. Investigated traits consisted of birth weight (N = 2776), weaning weight (N = 2002) and weight at six months of age (N = 1885). The data were analyzed using restricted maximum likelihood analysis, by fitting univariate and multivariate animal models. All three weight traits were significantly influenced by birth year, sex and birth type. Age of dam only significantly affected birth weight. Log-likelihood ratio tests were conducted to determine the most suitable model for each growth trait in univariate analyses. Direct and total heritability estimates for birth weight, weaning weight and weight at six months of age (based on the best model) were 0.42 and 0.16 (model 4), 0.38 and 0.13 (model 4) and 0.14 and 0.14 (model 1), respectively. Estimation of maternal heritability for birth weight and weaning weight was 0.22 and 0.18, respectively. Genetic and phenotypic correlations among these traits were positive. Phenotypic correlations among traits were low to moderate. Genetic correlations among traits were positive and higher than the corresponding phenotypic correlations. Weaning weight had a strong and significant correlation with weight at six months of age (0.99). We conclude that selection can be made in animals based on weaning weight instead of the present practice of selection based on weight at six months.

  1. Effective population size of steelhead trout: influence of variance in reproductive success, hatchery programs, and genetic compensation between life-history forms.

    PubMed

    Araki, Hitoshi; Waples, Robin S; Ardren, William R; Cooper, Becky; Blouin, Michael S

    2007-03-01

    The effective population size is influenced by many biological factors in natural populations. To evaluate their relative importance, we estimated the effective number of breeders per year (Nb) and effective population size per generation (Ne) in anadromous steelhead trout (Oncorhynchus mykiss) in the Hood River, Oregon (USA). Using demographic data and genetic parentage analysis on an almost complete sample of all adults that returned to the river over 15 years (>15,000 individuals), we estimated Nb for 13 run years and Ne for three entire generations. The results are as follows: (i) the ratio of Ne to the estimated census population size (N) was 0.17-0.40, with large variance in reproductive success among individuals being the primary cause of the reduction in Ne/N; (ii) fish from a traditional hatchery program (Htrad: nonlocal, multiple generations in a hatchery) had negative effects on Nb, not only by reducing mean reproductive success but also by increasing variance in reproductive success among breeding parents, whereas no sign of such effects was found in fish from supplementation hatchery programs (Hsupp: local, single generation in a hatchery); and (iii) Nb was relatively stable among run years, despite the widely fluctuating annual run sizes of anadromous adults. We found high levels of reproductive contribution of nonanadromous parents to anadromous offspring when anadromous run size is small, suggesting a genetic compensation between life-history forms (anadromous and nonanadromous). This is the first study showing that reproductive interaction between different life-history forms can buffer the genetic impact of fluctuating census size on Ne.

  2. Genetic variation within a dominant shrub structures green and brown community assemblages.

    PubMed

    Crutsinger, Gregory M; Rodriguez-Cabal, Mariano A; Roddy, Adam B; Peay, Kabir G; Bastow, Justin L; Kidder, Allison G; Dawson, Todd E; Fine, Paul V A; Rudgers, Jennifer A

    2014-02-01

    Two rising challenges in ecology are understanding the linkages between above- and belowground components of terrestrial ecosystems and connecting genes to their ecological consequences. Here, we blend these emerging perspectives using a long-term common-garden experiment in a coastal dune ecosystem, whose dominant shrub species, Baccharis pilularis, exists as erect or prostrate architectural morphotypes. We explored variation in green (foliage-based) and brown (detritus-based) community assemblages, local ecosystem processes, and understory microclimate between the two morphs. Prostrate morphs supported more individuals, species, and different compositions of foliage arthropods, litter microarthropods, and soil bacteria than erect morphs. The magnitude of community compositional differences was maintained from crown to litter to soil. Despite showing strikingly similar responses, green and brown assemblages were associated with different underlying mechanisms. Differences in estimated shrub biomass best explained variation in the green assemblage, while understory abiotic conditions accounted for variation in the brown assemblage. Prostrate morphs produced more biomass and litter, which corresponded with their strong lateral growth in a windy environment. Compared to erect morphs, the denser canopy and thicker litter layer of prostrate morphs helped create more humid understory conditions. As a result, decomposition rates were higher under prostrate shrubs, despite prostrate litter being of poorer quality. Together, our results support the hypothesis that intraspecific genetic variation in primary producers is a key mediator of above- and belowground linkages, and that integrating the two perspectives can lead to new insights into how terrestrial communities are linked with ecosystem pools and processes.

  3. The genetic structure of Asian corn borer, Ostrinia furnacalis, populations in China: haplotype variance in northern populations and potential impact on management of resistance to transgenic maize.

    PubMed

    Li, Jing; Coates, Brad S; Kim, Kyung Seok; Bourguet, Denis; Ponsard, Sergine; He, Kanglai; Wang, Zhenying

    2014-01-01

    Asian corn borer, Ostrinia furnacalis (Guenée), is a severe pest that infests cultivated maize in the major production regions of China. Populations show genotype-by-environment variation in voltinism, such that populations with a single generation (univoltine) are fixed in Northern China where growing seasons are short. Low genetic differentiation was found among samples from 33 collection sites across China and one site from North Korea (n=1673) using variation at 6 nuclear microsatellite loci (ENA corrected global FST=0.020; P value<0.05). Analysis of molecular variance indicated that geographic region, number of generations or voltinism accounted for <0.38% of the total genetic variation at nuclear loci and was corroborated by clustering of co-ancestries among genotypes using the program STRUCTURE. In contrast, a mitochondrial haplotype network identified 4 distinct clusters, where 70.5% of samples from univoltine populations were within a single group. Univoltine populations were also placed into a unique cluster using Population Graph and Principal component analyses, which showed significant differentiation with multivoltine populations (φST=0.400; P value<0.01). This study suggests that gene flow among O. furnacalis in China may be high among regions, with the exception of northeastern localities. Haplotype variation may be due to random genetic drift resulting from partial reproductive isolation between univoltine and multivoltine O. furnacalis populations. Such reproductive isolation might impact the potential spread of alleles that confer resistance to transgenic maize in China.

  4. Genetic variance contributes to ingestive processes: a survey of eleven inbred mouse strains for fat (Intralipid) intake.

    PubMed

    Lewis, Sarah R; Dym, Cheryl; Chai, Christina; Singh, Amreeta; Kest, Benjamin; Bodnar, Richard J

    2007-01-30

    Genetic variation across inbred and outbred mouse strains have been observed for intake of sweet solutions, salts, bitter tastants and a high-fat diet. Our laboratory recently reported marked strain differences in the amounts and/or percentages of kilocalories of sucrose consumed among 11 inbred and one outbred mouse strains exposed to a wide range of nine sucrose concentrations (0.0001-5%) in two-bottle 24-h preference tests. To assess whether differences in fat intake were similarly associated with genetic variation, the present study examined intake of chow, water and an emulsified fat source (Intralipid) across nine different concentrations (0.00001-5%) in the same 11 inbred and 1 outbred mouse strains using two-bottle 24-h preference tests, which controlled for Intralipid concentration presentation effects, Intralipid and water bottle positions, and measurement of kilocalorie intake consumed as Intralipid or chow. Strains displayed differential increases in Intralipid intake relative to corresponding water with significant effects observed at the seven (BALB/cJ: 0.001% threshold sensitivity), four (AKR/J, C57BL/6J, DBA/2J, SWR/J: 0.5% threshold sensitivity), three (CD-1, C57BL/10J, SJL/J: 1% threshold sensitivity) and two (A/J, CBA/J, C3H/HeJ, 129P3/J: 2% threshold sensitivity) highest concentrations. In assessing the percentage of kilocalories consumed as Intralipid, SWR/J mice consumed significantly more at the three highest concentrations to a greater degree than BALB/cJ, C57BL/6J, CD-1, C3H/HeJ, DBA/J and 129P3/J strains which in turn consumed more than A/J, AKR/J, CBA/J, C57BL/10J and SJL/J mice. Relatively strong (h2 = 0.73-0.79) heritability estimates were obtained for weight-adjusted Intralipid intake at those concentrations (0.001-1%) that displayed the largest strain-specific effects in sensitivity to Intralipid. The identification of strains with diverging abilities to regulate kilocalorie intake when presented with high Intralipid concentrations

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

    PubMed

    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).

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

    PubMed

    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.

  7. Female mate choice predicts paternity success in the absence of additive genetic variance for other female paternity bias mechanisms in Drosophila serrata.

    PubMed

    Collet, J M; Blows, M W

    2014-11-01

    After choosing a first mate, polyandrous females have access to a range of opportunities to bias paternity, such as repeating matings with the preferred male, facilitating fertilization from the best sperm or differentially investing in offspring according to their sire. Female ability to bias paternity after a first mating has been demonstrated in a few species, but unambiguous evidence remains limited by the access to complex behaviours, sperm storage organs and fertilization processes within females. Even when found at the phenotypic level, the potential evolution of any mechanism allowing females to bias paternity other than mate choice remains little explored. Using a large population of pedigreed females, we developed a simple test to determine whether there is additive genetic variation in female ability to bias paternity after a first, chosen, mating. We applied this method in the highly polyandrous Drosophila serrata, giving females the opportunity to successively mate with two males ad libitum. We found that despite high levels of polyandry (females mated more than once per day), the first mate choice was a significant predictor of male total reproductive success. Importantly, there was no detectable genetic variance in female ability to bias paternity beyond mate choice. Therefore, whether or not females can bias paternity before or after copulation, their role on the evolution of sexual male traits is likely to be limited to their first mate choice in D. serrata.

  8. Effects of single nucleotide polymorphism marker density on degree of genetic variance explained and genomic evaluation for carcass traits in Japanese Black beef cattle

    PubMed Central

    2014-01-01

    Background Japanese Black cattle are a beef breed whose meat is well known to excel in meat quality, especially in marbling, and whose effective population size is relatively low in Japan. Unlike dairy cattle, the accuracy of genomic evaluation (GE) for carcass traits in beef cattle, including this breed, has been poorly studied. For carcass weight and marbling score in the breed, as well as the extent of whole genome linkage disequilibrium (LD), the effects of equally-spaced single nucleotide polymorphisms (SNPs) density on genomic relationship matrix (G matrix), genetic variance explained and GE were investigated using the genotype data of about 40,000 SNPs and two statistical models. Results Using all pairs of two adjacent SNPs in the whole SNP set, the means of LD (r 2 ) at ranges 0–0.1, 0.1–0.2, 0.2–0.5 and 0.5–1 Mb were 0.22, 0.13, 0.10 and 0.08, respectively, and 25.7, 13.9, 10.4 and 6.4% of the r 2 values exceeded 0.3, respectively. While about 90% of the genetic variance for carcass weight estimated using all available SNPs was explained using 4,000–6,000 SNPs, the corresponding percentage for marbling score was consistently lower. With the conventional linear model incorporating the G matrix, correlation between the genomic estimated breeding values (GEBVs) obtained using 4,000 SNPs and all available SNPs was 0.99 for carcass weight and 0.98 for marbling score, with an underestimation of the former GEBVs, especially for marbling score. Conclusions The Japanese Black is likely to be in a breed group with a relatively high extent of whole genome LD. The results indicated that the degree of marbling is controlled by only QTLs with relatively small effects, compared with carcass weight, and that using at least 4,000 equally-spaced SNPs, there is a possibility of ranking animals genetically for these carcass traits in this breed. PMID:24491120

  9. 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).

    PubMed

    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.

  10. Genomic analysis of dominance effects on milk production and conformation traits in Fleckvieh cattle

    PubMed Central

    2014-01-01

    Background Estimates of dominance variance in dairy cattle based on pedigree data vary considerably across traits and amount to up to 50% of the total genetic variance for conformation traits and up to 43% for milk production traits. Using bovine SNP (single nucleotide polymorphism) genotypes, dominance variance can be estimated both at the marker level and at the animal level using genomic dominance effect relationship matrices. Yield deviations of high-density genotyped Fleckvieh cows were used to assess cross-validation accuracy of genomic predictions with additive and dominance models. The potential use of dominance variance in planned matings was also investigated. Results Variance components of nine milk production and conformation traits were estimated with additive and dominance models using yield deviations of 1996 Fleckvieh cows and ranged from 3.3% to 50.5% of the total genetic variance. REML and Gibbs sampling estimates showed good concordance. Although standard errors of estimates of dominance variance were rather large, estimates of dominance variance for milk, fat and protein yields, somatic cell score and milkability were significantly different from 0. Cross-validation accuracy of predicted breeding values was higher with genomic models than with the pedigree model. Inclusion of dominance effects did not increase the accuracy of the predicted breeding and total genetic values. Additive and dominance SNP effects for milk yield and protein yield were estimated with a BLUP (best linear unbiased prediction) model and used to calculate expectations of breeding values and total genetic values for putative offspring. Selection on total genetic value instead of breeding value would result in a larger expected total genetic superiority in progeny, i.e. 14.8% for milk yield and 27.8% for protein yield and reduce the expected additive genetic gain only by 4.5% for milk yield and 2.6% for protein yield. Conclusions Estimated dominance variance was substantial

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

    PubMed

    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.

  12. Mating strategies in dominant meerkats: evidence for extra-pair paternity in relation to genetic relatedness between pair mates.

    PubMed

    Leclaire, S; Nielsen, J F; Sharp, S P; Clutton-Brock, T H

    2013-07-01

    Rates of extra-pair paternity (EPP) have frequently been associated with genetic relatedness between social mates in socially monogamous birds. However, evidence is limited in mammals. Here, we investigate whether dominant females use divorce or extra-pair paternity as a strategy to avoid the negative effects of inbreeding when paired with a related male in meerkats Suricata suricatta, a species where inbreeding depression is evident for several traits. We show that dominant breeding pairs seldom divorce, but that rates of EPP are associated with genetic similarity between mates. Although extra-pair males are no more distantly related to the female than social males, they are more heterozygous. Nevertheless, extra-pair pups are not more heterozygous than within-pair pups. Whether females benefit from EPP in terms of increased fitness of the offspring, such as enhanced survival or growth, requires further investigations.

  13. Variance in age-specific sex composition of Pacific halibut catches, and comparison of statistical and genetic methods for reconstructing sex ratios

    NASA Astrophysics Data System (ADS)

    Loher, Timothy; Woods, Monica A.; Jimenez-Hidalgo, Isadora; Hauser, Lorenz

    2016-01-01

    Declines in size at age of Pacific halibut Hippoglossus stenolepis, in concert with sexually-dimorphic growth and a constant minimum commercial size limit, have led to the expectation that the sex composition of commercial catches should be increasingly female-biased. Sensitivity analyses suggest that variance in sex composition of landings may be the most influential source of uncertainty affecting current understanding of spawning stock biomass. However, there is no reliable way to determine sex at landing because all halibut are eviscerated at sea. In 2014, a statistical method based on survey data was developed to estimate the probability that fish of any given length at age (LAA) would be female, derived from the fundamental observation that large, young fish are likely female whereas small, old fish have a high probability of being male. Here, we examine variability in age-specific sex composition using at-sea commercial and closed-season survey catches, and compare the accuracy of the survey-based LAA technique to genetic markers for reconstructing the sex composition of catches. Sexing by LAA performed best for summer-collected samples, consistent with the hypothesis that the ability to characterize catches can be influenced by seasonal demographic shifts. Additionally, differences between survey and commercial selectivity that allow fishers to harvest larger fish within cohorts may generate important mismatch between survey and commercial datasets. Length-at-age-based estimates ranged from 4.7% underestimation of female proportion to 12.0% overestimation, with mean error of 5.8 ± 1.5%. Ratios determined by genetics were closer to true sample proportions and displayed less variability; estimation to within < 1% of true ratios was limited to genetics. Genetic estimation of female proportions ranged from 4.9% underestimation to 2.5% overestimation, with a mean absolute error of 1.2 ± 1.2%. Males were generally more difficult to assign than females: 6.7% of

  14. Variance, Genetic Control, and Spatial Phenotypic Plasticity of Morphological and Phenological Traits in Prunus spinosa and Its Large Fruited Forms (P. x fruticans)

    PubMed Central

    Vander Mijnsbrugge, Kristine; Turcsán, Arion; Depypere, Leander; Steenackers, Marijke

    2016-01-01

    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 control. PMID:27857718

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

    PubMed

    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.

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

    PubMed Central

    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

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

    PubMed

    Liang, Qingzhi; Shang, Lianguang; 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.

  18. Two pedigrees segregating Duane’s retraction syndrome as a dominant trait map to the DURS2 genetic locus

    PubMed Central

    Engle, Elizabeth C.; Andrews, Caroline; Law, Krystal; Demer, Joseph L.

    2010-01-01

    PURPOSE To determine the molecular etiologies of Duane’s retraction syndrome (DRS), we are investigating its genetic bases. We have previously identified the transcription factors SALL4 and HOXA1 as the genes mutated in DRS with radial anomalies, and in DRS with deafness, vascular anomalies, and cognitive deficits, respectively. We know less, however, about the genetic etiology of DRS when it occurs in isolation, and only one genetic locus for isolated DRS, the DURS2 locus on chromosome 2, has been mapped to date. Toward the goal of identifying the DURS2 gene, we have ascertained and studied two pedigrees that segregate DRS as a dominant trait. METHODS We enrolled members of two large dominant DRS pedigrees into our ongoing study of the genetic basis of the congenital cranial dysinnervation disorders, and conducted linkage analysis to determine if their DRS phenotype maps to the DURS2 locus. RESULTS By haplotype analysis, the DRS phenotype in each family co-segregates with markers spanning the DURS2 region, and linkage analysis reveals maximum lod scores of >2, establishing that the DRS phenotype in these two pedigrees maps to the DURS2 locus. CONCLUSIONS These two pedigrees double the published pedigrees known to map to the DURS2 locus, and can thus contribute toward the search for the DURS2 gene. The affected members represent a genetically defined population of DURS2-linked DRS individuals, and hence studies of their clinical and structural features can enhance our understanding of the DURS2 phenotype, as described in the companion paper. PMID:17197532

  19. Confirmation of QTL effects and evidence of genetic dominance of honeybee defensive behavior: results of colony and individual behavioral assays.

    PubMed

    Guzmán-Novoa, Ernesto; Hunt, Greg J; Uribe, José L; Smith, Christine; Arechavaleta-Velasco, Miguel E

    2002-03-01

    The stinging and guarding components of the defensive behavior of European, Africanized, hybrid, and backcross honeybees (Apis mellifera L.) were compared and analyzed at both colony and individual levels. Hybrid and Africanized backcross colonies stung as many times as Africanized ones. European backcross colonies stung more than European bees but not as many times as Africanized or Africanized backcross colonies. The degree of dominance for the number of times that worker bees stung a leather patch was estimated to be 84.3%, 200.8%, and 145.8% for hybrid, backcross European, and backcross Africanized colonies, respectively. Additionally, both guards at the colony entrance and fast-stinging workers of one European backcross colony had a significantly higher frequency of an Africanized DNA marker allele, located near "sting1," a QTL previously implicated in stinging behavior at the colony level. However, guards and fast-stinging bees from a backcross to the Africanized parental colony did not differ from control bees in their frequency for the Africanized and European markers, as would be expected if large genetic dominance effects for sting1 exist. These results support the hypothesis that genetic dominance influences the defensive behavior of honeybees and confirm the effect of sting1 on the defensiveness of individual worker bees.

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

    PubMed Central

    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

  1. The heat-shock response and the molecular basis of genetic dominance.

    PubMed

    Forsdyke, D R

    1994-03-07

    Wild-type alleles are usually dominant over deleterious mutant alleles. For a particular pair of such alleles possible populations include a wild-type homozygote population, a heterozygote population, and a mutant homozygote population. Fisher's theory that dominance would evolve by selection acting on the heterozygote subpopulation has lost ground in favour of the "dose-response" theory under which dominance is an incidental consequence of selection acting on the wild-type homozygote population. This postulates a "margin of safety" in the quantity of wild-type gene product so that heterozygotes with only one copy of a wild-type allele still have sufficient product for normal function. The selective force postulated to lead to the evolution of this margin of safety is some unspecified "extreme environment disturbance". The author has proposed elsewhere that the heat-shock response evolved very early as part of an intracellular system for self/not-self discrimination. This paper proposes that the rapid decrease in quantity of most normal proteins occurring in the heat-shock response would have provided a sufficient selective force for the margin of safety to have evolved.

  2. Genetic Mapping and Dominance of the Amber Suppressor, Su1 (supD), in Escherichia coli K-121

    PubMed Central

    Hoffman, Edwin P.; Wilhelm, Robert C.

    1970-01-01

    In this report Su1 (supD), which is known to suppress “amber” mutations by means of a specific transfer ribonucleic acid, has been mapped relative to his and uvrC and has been found to be located at about 37.5 min on the Taylor and Trotter genetic map of the Escherichia coli K-12 chromosome. In addition, Su1+ has been shown to be dominant over Su1−, which supports the idea that Su1 is the structural gene for the suppressing transfer ribonucleic acid. PMID:4912529

  3. Genetic Differentiation and Genetic Diversity of Castanopsis (Fagaceae), the Dominant Tree Species in Japanese Broadleaved Evergreen Forests, Revealed by Analysis of EST-Associated Microsatellites

    PubMed Central

    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

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

    PubMed

    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

  5. Further evidence for a locus for autosomal dominant juvenile glaucoma on chromosome 1q and evidence for genetic heterogeneity

    SciTech Connect

    Wiggs, J.; Paglinauan, C.; Stawski, S.

    1994-09-01

    Glaucoma is a term used to describe a group of disorders which have in common a characteristic degeneration of the optic nerve associated with typical visual field defects and usually associated with elevated intraocular pressure. Two percent of white Americans and 6-10% of black Americans are affected by the disease. Compelling data indicate that susceptibility to many types of glaucoma is inherited. Hereditary juvenile glaucoma is one form of glaucoma that develops in children and is inherited as an autosomal dominant trait with high penetrance. Using a single large Caucasian pedigree affected with autosomal dominant juvenile glaucoma, Sheffield discovered positive linkage to a group of markers that map to a 30 cM region on the long arm of chromosome 1 (1q21-q31). We have subsequently identified three unrelated Caucasian pedigrees affected with autosomal dominant juvenile glaucoma that also demonstrate linkage to this region on chromosome 1, with the highest combined lod score of 5.12 at theta = .05 for marker D1S218. The identification of critical recombinant individuals in our three pedigrees has allowed us to further localize the disease gene to a 12 cM region between markers D1S242 and D1S431. In addition, we have identified several pedigrees which do not demonstrate linkage to chromosome 1q, including a black family affected with autosomal dominant juvenile glaucoma that is indistinguishable clinically from the disorder affecting the caucasian pedigrees and three pedigrees affected with pigmentary dispersion syndrome, a form of glaucoma that also affects the juvenile population and is also inherited as an autosomal dominant trait. These findings provide evidence for genetic heterogeneity in juvenile glaucoma.

  6. Genetic differentiation in spite of high gene flow in the dominant rainforest tree of southeastern Australia, Nothofagus cunninghamii

    PubMed Central

    Duncan, C J; Worth, J R P; Jordan, G J; Jones, R C; Vaillancourt, R E

    2016-01-01

    Nothofagus cunninghamii is a long-lived, wind-pollinated tree species that dominates the cool temperate rainforests of southeastern Australia. The species' distribution is more or less continuous in western Tasmania but is fragmented elsewhere. However, it is unknown whether this fragmentation has affected the species' genetic architecture. Thus, we examined N. cunninghamii using 12 nuclear microsatellites and 633 individuals from 18 populations spanning the species' natural range. Typical of wind-pollinated trees, there was low range-wide genetic structure (FST=0.04) consistent with significant gene flow across most of the species' range. However, gene flow was not high enough to overcome the effects of drift across some disjunctions. Victorian populations (separated from Tasmania by the 240 km wide Bass Strait) formed a genetic group distinct from Tasmanian populations, had lower diversity (mean allelic richness (Ar)=5.4 in Victoria versus 6.9 in Tasmania) and were significantly more differentiated from one another than those in Tasmania (FST=0.045 in Victoria versus 0.012 in Tasmania). Evidence for bottlenecking was found in small populations that were at least 20 km from other populations. Interestingly, we found little divergence in microsatellite markers between the extremes of genetically based morphological and physiological altitudinal clines suggesting adaptive differentiation is strongly driven by selection because it is likely to be occurring in the presence of gene flow. Even though the cool temperate rainforests of Australia are highly relictual, the species is relatively robust to population fragmentation due to high levels of genetic diversity and gene flow, especially in Tasmania. PMID:26350630

  7. Genetic differentiation in spite of high gene flow in the dominant rainforest tree of southeastern Australia, Nothofagus cunninghamii.

    PubMed

    Duncan, C J; Worth, J R P; Jordan, G J; Jones, R C; Vaillancourt, R E

    2016-01-01

    Nothofagus cunninghamii is a long-lived, wind-pollinated tree species that dominates the cool temperate rainforests of southeastern Australia. The species' distribution is more or less continuous in western Tasmania but is fragmented elsewhere. However, it is unknown whether this fragmentation has affected the species' genetic architecture. Thus, we examined N. cunninghamii using 12 nuclear microsatellites and 633 individuals from 18 populations spanning the species' natural range. Typical of wind-pollinated trees, there was low range-wide genetic structure (FST=0.04) consistent with significant gene flow across most of the species' range. However, gene flow was not high enough to overcome the effects of drift across some disjunctions. Victorian populations (separated from Tasmania by the 240 km wide Bass Strait) formed a genetic group distinct from Tasmanian populations, had lower diversity (mean allelic richness (Ar)=5.4 in Victoria versus 6.9 in Tasmania) and were significantly more differentiated from one another than those in Tasmania (FST=0.045 in Victoria versus 0.012 in Tasmania). Evidence for bottlenecking was found in small populations that were at least 20 km from other populations. Interestingly, we found little divergence in microsatellite markers between the extremes of genetically based morphological and physiological altitudinal clines suggesting adaptive differentiation is strongly driven by selection because it is likely to be occurring in the presence of gene flow. Even though the cool temperate rainforests of Australia are highly relictual, the species is relatively robust to population fragmentation due to high levels of genetic diversity and gene flow, especially in Tasmania.

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

    PubMed Central

    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

  9. The effects of locus number, genetic divergence, and genotyping error on the utility of dominant markers for hybrid identification

    PubMed Central

    Sovic, Michael G; Kubatko, Laura S; Fuerst, Paul A

    2014-01-01

    In surveys of hybrid zones, dominant genetic markers are often used to identify individuals of hybrid origin and assign these individuals to one of several potential hybrid classes. Quantitative analyses that address the statistical power of dominant markers in such inference are scarce. In this study, dominant genotype data were simulated to evaluate the effects of, first, the number of loci analyzed, second, the magnitude of differentiation between the markers scored in the groups that are hybridizing, and third, the level of genotyping error associated with the data when assigning individuals to various parental and hybrid categories. The overall performance of the assignment methods was relatively modest at the lowest level of divergence examined (Fst ˜ 0.4), but improved substantially at higher levels of differentiation (Fst ˜ 0.67 or 0.8). The effect of genotyping error was dependent on the level of divergence between parental taxa, with larger divergences tempering the effects of genotyping error. These results highlight the importance of considering the effects of each of the variables when assigning individuals to various parental and hybrid categories, and can help guide decisions regarding the number of loci employed in future hybridization studies to achieve the power and level of resolution desired. PMID:24634730

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

    PubMed

    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.

  11. Autosomal dominant retinitis pigmentosa: no evidence for nonallelic genetic heterogeneity on 3q.

    PubMed Central

    Kumar-Singh, R; Wang, H; Humphries, P; Farrar, G J

    1993-01-01

    Since the initial report of linkage of autosomal dominant retinitis pigmentosa (adRP) to the long arm of chromosome 3, several mutations in the gene encoding rhodopsin, which also maps to 3q, have been reported in adRP pedigrees. However, there has been some discussion as to the possibility of a second adRP locus on 3q. This suggestion has important diagnostic and research implications and must raise doubts about the usefulness of linked markers for reliable diagnosis of RP patients. In order to address this issue we have performed an admixture test (A-test) on 10 D3S47-linked adRP pedigrees and have found a likelihood ratio of heterogeneity versus homogeneity of 4.90. We performed a second A-test, combining the data from all families with known rhodopsin mutations. In this test we obtained a reduced likelihood ratio of heterogeneity versus homogeneity, of 1.0. On the basis of these statistical analyses we have found no significant support for two adRP loci on chromosome 3q. Furthermore, using 40 CEPH families, we have localized the rhodopsin gene to the D3S47-D3S20 interval, with a maximum lod score (Zm) of 20 and have found that the order qter-D3S47-rhodopsin-D3S20-cen is significantly more likely than any other order. In addition, we have mapped (Zm = 30) the microsatellite marker D3S621 relative to other loci in this region of the genome. PMID:8430695

  12. Evolutionary Dynamics Analysis of Human Metapneumovirus Subtype A2: Genetic Evidence for Its Dominant Epidemic

    PubMed Central

    Li, Jianguo; Ren, Lili; Guo, Li; Xiang, Zichun; Paranhos-Baccalà, Gláucia; Vernet, Guy; Wang, Jianwei

    2012-01-01

    Human metapneumovirus (hMPV) is a respiratory viral pathogen in children worldwide. hMPV is divided into four subtypes: hMPV_A1, hMPV_A2, hMPV_B1, and hMPV_B2. hMPV_A2 can be further divided into hMPV_A2a and A2b based on phylogenetic analysis. The typical prevalence pattern of hMPV involves a shift of the predominant subtype within one or two years. However, hMPV_A2, in particular hMPV_A2b, has circulated worldwide with a several years long term high epidemic. To study this distinct epidemic behavior of hMPV_A2, we analyzed 294 sequences of partial G genes of the virus from different countries. Molecular evolutionary data indicates that hMPV_A2 evolved toward heterogeneity faster than the other subtypes. Specifically, a Bayesian skyline plot analysis revealed that hMPV_A2 has undergone a generally upward fluctuation since 1997, whereas the other subtypes experienced only one upward fluctuation. Although hMPV_A2 showed a lower value of mean dN/dS than the other subtypes, it had the largest number of positive selection sites. Meanwhile, various styles of mutation were observed in the mutation hotspots of hMPV_A2b. Bayesian phylogeography analysis also revealed two fusions of diffusion routes of hMPV_A2b in India (June 2006) and Beijing, China (June 2008). Sequences of hMPV_A2b retrieved from GenBank boosted simultaneously with the two fusions respectively, indicating that fusion of genetic transmission routes from different regions improved survival of hMPV_A2. Epidemic and evolutionary dynamics of hMPV_A2b were similar to those of hMPV_A2. Overall, our findings provide important molecular insights into hMPV epidemics and viral variation, and explain the occurrence of an atypical epidemic of hMPV_A2, particularly hMPV_A2b. PMID:22479641

  13. Nonlinear Epigenetic Variance: Review and Simulations

    ERIC Educational Resources Information Center

    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…

  14. The first Indian-origin family with genetically proven cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL).

    PubMed

    Yadav, Sunaina; Bentley, Paul; Srivastava, Padma; Prasad, Kameshwar; Sharma, Pankaj

    2013-01-01

    We report the first family of Indian origin known to be affected by cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). Seventeen members of the family spanning 3 generations had neurologic syndromes compatible with CADASIL, of whom 5 were genetically confirmed carriers of the Notch3 gene R141C mutation in exon 4 (421(C→T) and 141(Cys→Arg)). Our report highlights that CADASIL not only occurs sporadically in South Asians, but also may account for stroke in South Asians with a strong family history. Furthermore, the similarity of clinical presentations described here to those typical for Caucasian case series suggests that the CADASIL phenotype is preserved across racial groups.

  15. Genetic linkage of autosomal dominant juvenile glaucoma to 1q21-q31 in three affected pedigrees

    SciTech Connect

    Wiggs, J.L.; Paglinauan, C.; Fine, A.; Sporn, C.; Lou, D. ); Haines, J.L. )

    1994-05-15

    Glaucoma is a common disorder that results in irreversible damage to the optic nerve, causing absolute blindness. In most cases, the optic nerve is damaged by an elevation of the intraocular pressure that is the result of an abnormality in the normal drainage function of the trabecular meshwork. A family history of glaucoma is an important risk factor for the disease, suggesting that genetic defects predisposing to this condition are likely. Three pedigrees segregating an autosomal dominant juvenile glaucoma demonstrated significant linkage to a group of closely spaced markers on chromosome 1. These results confirm the initial mapping of this disease and suggest that this region on chromosome 1 contains an important locus for juvenile glaucoma. The authors describe recombination events that improve the localization of the responsible gene, reducing the size of the candidate region from 30 to 12 cM. 27 refs., 2 figs., 1 tab.

  16. A Nonsyndromic Autosomal Dominant Oligodontia with A Novel Mutation of PAX9-A Clinical and Genetic Report

    PubMed Central

    Prasanna, Praveen; Athimuthu, Anantharaj; Bhat, Prasanna Kumar; Puttashamachari, Yogish

    2015-01-01

    Oligodontia is congenital absence of one or more teeth which has familial abnormality and attributable to various mutations or polymorphisms of genes often associated with malformative syndromes. The present case reports a rare case of non syndromic oligodontia in an 8-year-old girl with missing 14 permanent teeth excluding third molars in mixed dentition. It is a rare finding which has not been frequently documented in Indian children. Mutations in MSX1 and PAX9 have been described in families in which inherited oligodontia characteristically involves permanent incisors, lateral incisors, premolars and molars. Our study analysed one large family with dominantly inherited oligodontia clinically and genetically. This phonotype is distinct from oligodontia phenotypes associated with mutations in PAX9. Sequencing of the PAX9 revealed a novel mutation in the paired domain of the molecule. The multiple sequence alignment and SNP analysis of the PAX9 exon 2 revealed two mutations. PMID:26266225

  17. BRAIN ABNORMALITIES IN YOUNG ADULTS AT GENETIC RISK FOR AUTOSOMAL DOMINANT ALZHEIMER’S DISEASE: A CROSS-SECTIONAL STUDY

    PubMed Central

    Reiman, Eric M.; Quiroz, Yakeel T.; Fleisher, Adam S.; Chen, Kewei; Velez-Pardo, Carlos; Jimenez-Del-Rio, Marlene; Fagan, Anne M.; Shah, Aarti R.; Alvarez, Sergio; Arbelaez, Andrés; Giraldo, Margarita; Acosta-Baena, Natalia; Sperling, Reisa A.; Dickerson, Brad; Stern, Chantal E.; Tirado, Victoria; Munoz, Claudia; Reiman, Rebecca A.; Huentelman, Matthew J.; Alexander, Gene E.; Langbaum, Jessica B.S.; Kosik, Kenneth S.; Tariot, Pierre N.; Lopera, Francisco

    2013-01-01

    Summary Background We previously detected functional brain imaging abnormalities in young adults at genetic risk for late-onset Alzheimer’s disease (AD). Here, we sought to characterize structural and functional magnetic resonance imaging (MRI), cerebrospinal fluid (CSF), and plasma biomarker abnormalities in young adults at risk for autosomal dominant early-onset AD. Biomarker measurements were characterized and compared in presenilin 1 (PSEN1) E280A mutation carriers and non-carriers from the world’s largest known autosomal dominant early-onset AD kindred, more than two decades before the carriers’ estimated median age of 44 at the onset of mild cognitive impairment (MCI) and before their estimated age of 28 at the onset of amyloid-β (Aβ) plaque deposition. Methods Biomarker data for this cross-sectional study were acquired in Antioquia, Colombia between July and August, 2010. Forty-four participants from the Colombian Alzheimer’s Prevention Initiative (API) Registry had structural MRIs, functional MRIs during associative memory encoding/novel viewing and control tasks, and cognitive assessments. They included 20 mutation carriers and 24 non-carriers, who were cognitively normal, 18-26 years old and matched for their gender, age, and educational level. Twenty of the participants, including 10 mutation carriers and 10 non-carriers, had lumbar punctures and venipunctures. Primary outcome measures included task-dependent hippocampal/parahippocampal activations and precuneus/posterior cingulate deactivations, regional gray matter reductions, CSF Aβ1-42, total tau and phospho-tau181 levels, and plasma Aβ1-42 levels and Aβ1-42/Aβ1-40 ratios. Structural and functional MRI data were compared using automated brain mapping algorithms and AD-related search regions. Cognitive and fluid biomarkers were compared using Mann-Whitney tests. Findings The mutation carrier and non-carrier groups did not differ significantly in their dementia ratings, neuropsychological

  18. Characterization of macular structure and function in two Swedish families with genetically identified autosomal dominant retinitis pigmentosa

    PubMed Central

    Abdulridha-Aboud, Wissam; Kjellström, Ulrika; Andréasson, Sten

    2016-01-01

    Purpose To study the phenotype in two families with genetically identified autosomal dominant retinitis pigmentosa (adRP) focusing on macular structure and function. Methods Clinical data were collected at the Department of Ophthalmology, Lund University, Sweden, for affected and unaffected family members from two pedigrees with adRP. Examinations included optical coherence tomography (OCT), full-field electroretinography (ffERG), and multifocal electroretinography (mfERG). Molecular genetic screening was performed for known mutations associated with adRP. Results The mode of inheritance was autosomal dominant in both families. The members of the family with a mutation in the PRPF31 (p.IVS6+1G>T) gene had clinical features characteristic of RP, with severely reduced retinal rod and cone function. The degree of deterioration correlated well with increasing age. The mfERG showed only centrally preserved macular function that correlated well with retinal thinning on OCT. The family with a mutation in the RHO (p.R135W) gene had an extreme intrafamilial variability of the phenotype, with more severe disease in the younger generations. OCT showed pathology, but the degree of morphological changes was not correlated with age or with the mfERG results. The mother, with a de novo mutation in the RHO (p.R135W) gene, had a normal ffERG, and her retinal degeneration was detected merely with the reduced mfERG. Conclusions These two families demonstrate the extreme inter- and intrafamilial variability in the clinical phenotype of adRP. This is the first Swedish report of the clinical phenotype associated with a mutation in the PRPF31 (p.IVS6+1G>T) gene. Our results indicate that methods for assessment of the central retinal structure and function may improve the detection and characterization of the RP phenotype. PMID:27212874

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

    NASA Astrophysics Data System (ADS)

    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.

  20. Eco-geographical diversity of cowpea bradyrhizobia in Senegal is marked by dominance of two genetic types.

    PubMed

    Wade, Tatiana Krasova; Le Quéré, Antoine; Laguerre, Gisèle; N'zoué, Angèle; Ndione, Jacques-André; Dorego, Francis; Sadio, Omar; Ndoye, Ibrahima; Neyra, Marc

    2014-03-01

    The genetic diversity of native cowpea rhizobia originating from 60 sites across four eco-geographic zones in Senegal was studied. More than 300 cowpea nodules were analyzed by PCR-RFLP of the 16S-23S rDNA InterGenic Spacer region (IGS). Alignments of IGS sequences indicated that all genotypes were grouping within the Bradyrhizobium genus. The geographical distribution showed that apart from five IGS types, the others were specifically found in only one region. The diversity was significantly higher in the Senegal River valley zone, which presents lower mean annual rainfalls and slightly alkaline soils. Interestingly, two IGS types dominated the Senegalese rhizobial collection, one IGS type (VI) was found on more than half of the nodules collected in the northern Senegal River valley while another IGS type (I) was recovered from the great majority of nodules in the three other regions sampled. Two representative strains from each of these two dominant types were isolated and further analyzed. Multi Locus Sequence Analyses using 6 housekeeping genes indicate that they belong to a new Bradyrhizobium species closely related to B. yuanmingense. Phylogenetic analyses of 2 symbiotic genes nodC and nifH show that they are clustered with B. arachidis. Physiological tests on these strains have shown that under laboratory conditions, the growth of the IGS type VI strains was slightly less affected by a higher osmotic strength in the medium and to alkaline pH, which corroborates the soil physico-chemical parameters.

  1. Immunological loss-of-function due to genetic gain-of-function in humans: autosomal dominance of the third kind

    PubMed Central

    Quartier, Pierre

    2015-01-01

    All the human primary immunodeficiencies (PIDs) recognized as such in the 1950s were Mendelian traits and, whether autosomal or X-linked, displayed recessive inheritance. The first autosomal dominant (AD) PID, hereditary angioedema, was recognized in 1963. However, since the first identification of autosomal recessive (AR), X-linked recessive (XR) and AD PID-causing genes in 1985 (ADA; severe combined immunodeficiency), 1986 (CYBB, chronic granulomatous disease) and 1989 (SERPING1; hereditary angioedema), respectively, the number of genetically defined AD PIDs has increased more rapidly than that of any other type of PID. AD PIDs now account for 61 of the 260 known conditions (23%). All known AR PIDs are caused by alleles with some loss-of-function (LOF). A single XR PID is caused by gain-of-function (GOF) mutations (WASP-related neutropenia, 2001). In contrast, only 44 of 61 AD defects are caused by LOF alleles, which exert dominance by haploinsufficiency or negative dominance. Since 2003, up to 17 AD disorders of the third kind, due to GOF alleles, have been described. Remarkably, six of the 17 genes concerned also harbor monoallelic (STAT3), biallelic (C3, CFB, CARD11, PIK3R1) or both monoallelic and biallelic (STAT1) LOF alleles in patients with other clinical phenotypes. Most heterozygous GOF alleles result in auto-inflammation, auto-immunity, or both, with a wide range of immunological and clinical forms. Some also underlie infections and, fewer, allergies, by impairing or enhancing immunity to non-self. Malignancies are also rare. The enormous diversity of immunological and clinical phenotypes is thought provoking and mirrors the diversity and pleiotropy of the underlying genotypes. These experiments of nature provide a unique insight into the quantitative regulation of human immunity. PMID:25645939

  2. Horka, a dominant mutation of Drosophila, induces nondisjunction and, through paternal effect, chromosome loss and genetic mosaics

    SciTech Connect

    Szabad, J.; Mathe, E.; Puro, J.

    1995-04-01

    Fs(3) Horka (Horka) was described as a dominant female-sterile mutation of Drosophila melanogaster. Genetic and cytological data show that Horka induces mostly equational nondisjunction during spermatogenesis but not chromosome loss and possesses a predominant paternal effect: the X, second, third and the fourth chromosomes, but not the Y, are rendered unstable while undergoing spermatogenesis and may be lost in the descending zygotes. The frequency of Horka-induced chromosome loss is usually 2-4% but varies with the genetic background and can be over 20%. The X chromosome loss occurs during the gonomeric and the initial cleavage divisions. Loss of the X and fourth chromosomes shows no correlation. We propose, based on similarities in the mutant phenotypes with the chromosome destabilizing mutations nonclaret disjunctional and paternal loss, that the normal Horka{sup +} product is required for function of the centromeres and/or nearby regions. Horka is a convenient tool for the generation of gynandromorphs, autosome mosaics and for the study of gene expression in mosaics. 55 refs., 6 figs., 8 tabs.

  3. Does variance in drinking motives explain the genetic overlap between personality and alcohol use disorder symptoms? A twin study of young women

    PubMed Central

    Littlefield, Andrew K.; Agrawal, Arpana; Ellingson, Jarrod M.; Kristjansson, Sean; Madden, Pamela A. F.; Bucholz, Kathleen K.; Slutske, Wendy S.; Heath, Andrew C.; Sher, Kenneth J.

    2011-01-01

    Background Genetic risk for alcohol dependence has been shown to overlap with genetic factors contributing to variation in dimensions of personality. Though drinking motives have been posited as important mediators of the alcohol-personality relation, the extent to which the genetic covariance between alcohol use disorder (AUD) symptoms (i.e. abuse and dependence criteria) and personality is explained by genetic factors contributing to variation in drinking motives remains unclear. Methods Using data from 2,904 young adult female twins, the phenotypic and genetic associations among personality dimensions (constraint [measured by the Multidimensional Personality Questionnaire; Tellegen, 1982], conscientiousness, neuroticism, and agreeableness [measured by the NEO-PI; Costa & McCrae, 1985]), internal drinking motives (enhancement and coping motives [measured by the Drinking Motive Questionnaire; Cooper, 1994]), and AUD symptoms were tested. Results Significant genetic associations were found between all personality measures and AUD symptoms. Coping motives showed significant genetic overlap with AUD symptoms and most personality measures, whereas enhancement motives were not significantly heritable. Adjusting for coping motives, genetic correlations between AUD symptoms and traits of neuroticism and agreeableness were no longer statistically significant. Conclusions Findings suggest that genetic variation in drinking to cope might account for a considerable proportion of the genetic covariance between specific personality dimensions and AUD symptoms. PMID:21790670

  4. Genetic Isolation, Cloning, and Analysis of a Mutator-Induced, Dominant Antimorph of the Maize amylose extender1 Locus.

    PubMed Central

    Stinard, PS; Robertson, DS; Schnable, PS

    1993-01-01

    We report the genetic identification, molecular cloning, and characterization of a dominant mutant at the amylose extender1 locus, Ae1-5180. The identities of our clones are corroborated by their ability to reveal DNA polymorphisms between seven wild-type revertants from Ae1-5180 relative to the Ae1-5180 mutant allele and between four of five independently derived, Mutator (Mu)-induced recessive ae1 alleles relative to their respective wild-type progenitor alleles. The Ae1-5180 mutation is associated with two Mu1 insertions flanked by complex rearrangements of ae1-related sequences. One of the Mu1 elements is flanked by inverted repeats of ae1-related DNA of at least 5.0 kb in length. This Mu1 element and at least some of this flanking inverted repeat DNA are absent or hypermethylated in six of seven wild-type revertants of Ae1-5180 that were analyzed. The second Mu1 element is flanked on one side by the 5.0-kb ae1-specific repeat and on the other side by a sequence that does not hybridize to the ae1-related repeat sequence. This second Mu1 element is present in revertants to the wild type and does not, therefore, appear to affect ae1 gene function. A 2.7-kb ae1 transcript can be detected in wild-type and homozygous ae1-Ref endosperms 20 days after pollination. This transcript is absent in endosperms containing one, two, or three doses of Ae1-5180. This result is consistent with a suppression model to explain the dominant gene action of Ae1-5180 and establishes Ae1-5180 as an antimorphic allele. Homozygous wild-type seedlings produce no detectable transcript, indicating some degree of tissue specificity for ae1 expression. Sequence analyses establish that ae1 encodes starch branching enzyme II. PMID:12271046

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

    PubMed

    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.

  6. Pervasive effects of a dominant foliar endophytic fungus on host genetic and phenotypic expression in a tropical tree

    PubMed Central

    Mejía, Luis C.; Herre, Edward A.; Sparks, Jed P.; Winter, Klaus; García, Milton N.; Van Bael, Sunshine A.; Stitt, Joseph; Shi, Zi; Zhang, Yufan; Guiltinan, Mark J.; Maximova, Siela N.

    2014-01-01

    It is increasingly recognized that macro-organisms (corals, insects, plants, vertebrates) consist of both host tissues and multiple microbial symbionts that play essential roles in their host's ecological and evolutionary success. Consequently, identifying benefits and costs of symbioses, as well as mechanisms underlying them are research priorities. All plants surveyed under natural conditions harbor foliar endophytic fungi (FEF) in their leaf tissues, often at high densities. Despite producing no visible effects on their hosts, experiments have nonetheless shown that FEF reduce pathogen and herbivore damage. Here, combining results from three genomic, and two physiological experiments, we demonstrate pervasive genetic and phenotypic effects of the apparently asymptomatic endophytes on their hosts. Specifically, inoculation of endophyte-free (E−) Theobroma cacao leaves with Colletotrichum tropicale (E+), the dominant FEF species in healthy T. cacao, induces consistent changes in the expression of hundreds of host genes, including many with known defensive functions. Further, E+ plants exhibited increased lignin and cellulose content, reduced maximum rates of photosynthesis (Amax), and enrichment of nitrogen-15 and carbon-13 isotopes. These phenotypic changes observed in E+ plants correspond to changes in expression of specific functional genes in related pathways. Moreover, a cacao gene (Tc00g04254) highly up-regulated by C. tropicale also confers resistance to pathogen damage in the absence of endophytes or their products in host tissues. Thus, the benefits of increased pathogen resistance in E+ plants are derived in part from up-regulation of intrinsic host defense responses, and appear to be offset by potential costs including reduced photosynthesis, altered host nitrogen metabolism, and endophyte heterotrophy of host tissues. Similar effects are likely in most plant-endophyte interactions, and should be recognized in the design and interpretation of genetic

  7. The majority of genetic variation in orangutan personality and subjective well-being is nonadditive.

    PubMed

    Adams, Mark James; King, James E; Weiss, Alexander

    2012-07-01

    The heritability of human personality is well-established. Recent research indicates that nonadditive genetic effects, such as dominance and epistasis, play a large role in personality variation. One possible explanation for the latter finding is that there has been recent selection on human personality. To test this possibility, we estimated additive and nonadditive genetic variance in personality and subjective well-being of zoo-housed orangutans. More than half of the genetic variance in these traits could be attributed to nonadditive genetic effects, modeled as dominance. Subjective well-being had genetic overlap with personality, though less so than has been found in humans or chimpanzees. Since a large portion of nonadditive genetic variance in personality is not unique to humans, the nonadditivity of human personality is not sufficient evidence for recent selection of personality in humans. Nonadditive genetic variance may be a general feature of the genetic structure of personality in primates and other animals.

  8. Generalized analysis of molecular variance.

    PubMed

    Nievergelt, Caroline M; Libiger, Ondrej; Schork, Nicholas J

    2007-04-06

    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 using it to analyze a

  9. Genetic Analysis of the Rhodopsin Gene Identifies a Mosaic Dominant Retinitis Pigmentosa Mutation in a Healthy Individual

    PubMed Central

    Beryozkin, Avigail; Levy, Gal; Blumenfeld, Anat; Meyer, Segev; Namburi, Prasanthi; Morad, Yair; Gradstein, Libe; Swaroop, Anand; Banin, Eyal; Sharon, Dror

    2016-01-01

    Purpose Retinitis pigmentosa (RP) is a group of clinically and genetically heterogeneous hereditary retinal diseases that result in blindness due to photoreceptor degeneration. Mutations in the rhodopsin (RHO) gene are the most common cause of autosomal dominant RP (adRP) and are responsible for 16% to 35% of adRP cases in the Western population. Our purpose was to investigate the contribution of RHO to adRP in the Israeli and Palestinian populations. Methods Thirty-two adRP families participated in the study. Mutation detection was performed by whole exome sequencing (WES) and Sanger sequencing of RHO exons. Fluorescence PCR reactions of serially diluted samples were used to predict the percentage of mosaic cells in blood samples. Results Eight RHO disease-causing mutations were identified in nine families, with only one novel mutation, c.548-638dup91bp, identified in a family where WES failed to detect any causal variant. Segregation analysis revealed that the origin of the mutation is in a mosaic healthy individual carrying the mutation in approximately 13% of blood cells. Conclusions This is the first report of the mutation spectrum of a known adRP gene in the Israeli and Palestinian populations, leading to the identification of seven previously reported mutations and one novel mutation. Our study shows that RHO mutations are a major cause of adRP in this cohort and are responsible for 28% of adRP families. The novel mutation exhibits a unique phenomenon in which an unaffected individual is mosaic for an adRP-causing mutation. PMID:26962691

  10. Direct and maternal (co)variance components, genetic parameters and annual trends for growth traits of Dorper sheep in semi-arid Kenya.

    PubMed

    Kariuki, C M; Ilatsia, Evans D; Kosgey, Isaac S; Kahi, Alexander K

    2010-03-01

    Genetic and phenotypic parameters were estimated for lamb growth traits for the Dorper sheep in semi-arid Kenya using an animal model. Data on lamb growth performance were extracted from available performance records at the Sheep and Goats Station in Naivasha, Kenya. Growth traits considered were body weights at birth (BW0, kg), at 1 month (BW1, kg), at 2 months (BW2, kg), at weaning (WW, kg), at 6 months (BW6, kg), at 9 months (BW9, kg) and at yearling (YW, kg), average daily gain from birth to 6 months (ADG(0-6), gm) and from 6 months to 1 year (ADG(6-12), gm). Direct heritability estimates were, correspondingly, 0.18, 0.36, 0.32, 0.28, 0.21, 0.14, 0.29, 0.12 and 0.30 for BW0, BW1, BW2, WW, BW6, BW9, YW, ADG(0-6) and ADG(6-12). The corresponding maternal genetic heritability estimates for body weights up to 9 months were 0.16, 0.10, 0.10, 0.19, 0.21 and 0.18. Direct-maternal genetic correlations were negative and high ranging between -0.47 to -0.94. Negative genetic correlations were observed for ADG(0-6)-ADG(6-12), BW2-ADG(6-12), WW-ADG(6-12) and BW6-ADG(6-12). Phenotypic correlations ranged from 0.15 to 0.96. Maternal effects are important in the growth performance of the Dorper sheep though a negative correlation exists between direct and maternal genetic effects. The current study has provided important information on the extent of additive genetic variation in the existing flocks that could now be used in determining the merit of breeding rams and ewes for sale to the commercial flocks. The estimates provided would form the basis of designing breeding schemes for the Dorper sheep in Kenya. Implications of the study to future Dorper sheep breeding programmes are also discussed.

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

    PubMed

    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.

  12. The quantum Allan variance

    NASA Astrophysics Data System (ADS)

    Chabuda, Krzysztof; Leroux, Ian D.; Demkowicz-Dobrzański, Rafał

    2016-08-01

    The instability of an atomic clock is characterized by the Allan variance, a measure widely used to describe the noise of frequency standards. We provide an explicit method to find the ultimate bound on the Allan variance of an atomic clock in the most general scenario where N atoms are prepared in an arbitrarily entangled state and arbitrary measurement and feedback are allowed, including those exploiting coherences between succeeding interrogation steps. While the method is rigorous and general, it becomes numerically challenging for large N and long averaging times.

  13. Significant variance in genetic diversity among populations of Schistosoma haematobium detected using microsatellite DNA loci from a genome-wide database

    PubMed Central

    2013-01-01

    Background Urogenital schistosomiasis caused by Schistosoma haematobium is widely distributed across Africa and is increasingly being targeted for control. Genome sequences and population genetic parameters can give insight into the potential for population- or species-level drug resistance. Microsatellite DNA loci are genetic markers in wide use by Schistosoma researchers, but there are few primers available for S. haematobium. Methods We sequenced 1,058,114 random DNA fragments from clonal cercariae collected from a snail infected with a single Schistosoma haematobium miracidium. We assembled and aligned the S. haematobium sequences to the genomes of S. mansoni and S. japonicum, identifying microsatellite DNA loci across all three species and designing primers to amplify the loci in S. haematobium. To validate our primers, we screened 32 randomly selected primer pairs with population samples of S. haematobium. Results We designed >13,790 primer pairs to amplify unique microsatellite loci in S. haematobium, (available at http://www.cebio.org/projetos/schistosoma-haematobium-genome). The three Schistosoma genomes contained similar overall frequencies of microsatellites, but the frequency and length distributions of specific motifs differed among species. We identified 15 primer pairs that amplified consistently and were easily scored. We genotyped these 15 loci in S. haematobium individuals from six locations: Zanzibar had the highest levels of diversity; Malawi, Mauritius, Nigeria, and Senegal were nearly as diverse; but the sample from South Africa was much less diverse. Conclusions About half of the primers in the database of Schistosoma haematobium microsatellite DNA loci should yield amplifiable and easily scored polymorphic markers, thus providing thousands of potential markers. Sequence conservation among S. haematobium, S. japonicum, and S. mansoni is relatively high, thus it should now be possible to identify markers that are universal among Schistosoma

  14. Conversations across Meaning Variance

    ERIC Educational Resources Information Center

    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…

  15. Genetic variance contributes to dopamine and opioid receptor antagonist-induced inhibition of intralipid (fat) intake in inbred and outbred mouse strains.

    PubMed

    Dym, Cheryl T; Bae, Veronica S; Kraft, Tamar; Yakubov, Yakov; Winn, Amanda; Sclafani, Anthony; Bodnar, Richard J

    2010-02-26

    Preference for and intake of solid and emulsified fat (intralipid) solutions vary across different mouse strains. Fat intake in rodents is inhibited by dopamine and opioid receptor antagonists, but any variation in these responses as a function of genetic background is unknown. Therefore, the present study compared the ability of dopamine D1-like (SCH23390) and general opioid (naltrexone) receptor antagonism to alter intake of fat emulsions (intralipid) in mice. Two-hour intakes of 5% intralipid were measured (5-120 min) in seven inbred (BALB/c, C57BL/6, C57BL/10, DBA/2, SJL, SWR, 129P3) and one outbred (CD-1) mouse strains following treatment with vehicle, SCH23390 (50-1600 nmol/kg, ip) and naltrexone (0.001-5 mg/kg, sc). SCH23390 significantly, dose-dependently and differentially reduced intralipid intake at all five (DBA/2, SWR, CD-1), four (SJL, C57BL/6), three (129P3) and one (C57BL/10) of the doses tested, but failed to affect intralipid intake in BALB/c mice. Naltrexone significantly, dose-dependently and differentially reduced intralipid intake at all four (DBA/2), three (SWR, SJL), two (CD-1, C57BL/10) and one (C57BL/6, 129P3) of the doses tested, and also failed to affect intralipid intake in BALB/cJ mice. SCH23390 and naltrexone were respectively 13.3-fold and 9.3-fold more potent in inhibiting intralipid intake in the most sensitive (DBA/2) relative to the least sensitive (BALB/c) mouse strains. A strong positive relationship (r=0.91) was observed for the abilities of SCH23390 and naltrexone to inhibit intralipid intake across strains. These findings indicate that dopaminergic and opioid signaling mechanisms differentially control intralipid intake across different mouse strains, suggesting important genetic and pharmacological interactions in the short-term control of rewarding and post-ingestive consequences of fat intake.

  16. Genetic variance in the HIV-1 founder virus Vpr affects its ability to induce cell cycle G₂arrest and cell apoptosis.

    PubMed

    Jianyuan, Zhao; Jiwei, Ding; Zeyun, Mi; Jinming, Zhou; Tao, Wei; Shan, Cen

    2015-05-01

    In the event of acute infection, only a few HIV-1 viral variants can establish the initial productive clinical infection, and these viral variants are known as transmitted/founder viruses (T/F viruses). As one of the accessory proteins of HIV-1, viral protein R (Vpr) plays an important role in viral replication. Therefore, the characterization of T/F virus Vpr is beneficial to understand how virus replicates in a new host. In this study, flow cytometry was used to analyze the effect of G₂arrest and cell apoptosis induced by the T/F virus Vpr and the chronic strain MJ4 Vpr. The results showed that the ability of T/F virus ZM246 Vpr and ZM247 Vpr inducing G₂arrest and cell apoptosis are more potent than the MJ4 Vpr. The comparison of protein sequences indicated that the amino acids of 77, 85 and 94 contain high freqency mutations, suggesting that these sites may be involved in inducing G₂arrest and cell apoptosis. Taken together, our work suggests that in acute infections, T/F viruses increase the capacity of G₂arrest and cell apoptosis and promote viral replication and transmission in a new host by Vpr genetic mutation.

  17. Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands' environmental gradient.

    PubMed

    Gray, Miranda M; St Amand, Paul; Bello, Nora M; Galliart, Matthew B; Knapp, Mary; Garrett, Karen A; Morgan, Theodore J; Baer, Sara G; Maricle, Brian R; Akhunov, Eduard D; Johnson, Loretta C

    2014-12-01

    Big bluestem (Andropogon gerardii) is an ecologically dominant grass with wide distribution across the environmental gradient of U.S. Midwest grasslands. This system offers an ideal natural laboratory to study population divergence and adaptation in spatially varying climates. Objectives were to: (i) characterize neutral genetic diversity and structure within and among three regional ecotypes derived from 11 prairies across the U.S. Midwest environmental gradient, (ii) distinguish between the relative roles of isolation by distance (IBD) vs. isolation by environment (IBE) on ecotype divergence, (iii) identify outlier loci under selection and (iv) assess the association between outlier loci and climate. Using two primer sets, we genotyped 378 plants at 384 polymorphic AFLP loci across regional ecotypes from central and eastern Kansas and Illinois. Neighbour-joining tree and PCoA revealed strong genetic differentiation between Kansas and Illinois ecotypes, which was better explained by IBE than IBD. We found high genetic variability within prairies (80%) and even fragmented Illinois prairies, surprisingly, contained high within-prairie genetic diversity (92%). Using Bayenv2, 14 top-ranked outlier loci among ecotypes were associated with temperature and precipitation variables. Six of seven BayeScanFST outliers were in common with Bayenv2 outliers. High genetic diversity may enable big bluestem populations to better withstand changing climates; however, population divergence supports the use of local ecotypes in grassland restoration. Knowledge of genetic variation in this ecological dominant and other grassland species will be critical to understanding grassland response and restoration challenges in the face of a changing climate.

  18. Spectral Ambiguity of Allan Variance

    NASA Technical Reports Server (NTRS)

    Greenhall, C. A.

    1996-01-01

    We study the extent to which knowledge of Allan variance and other finite-difference variances determines the spectrum of a random process. The variance of first differences is known to determine the spectrum. We show that, in general, the Allan variance does not. A complete description of the ambiguity is given.

  19. The Rules of Aggression: How Genetic, Chemical and Spatial Factors Affect Intercolony Fights in a Dominant Species, the Mediterranean Acrobat Ant Crematogaster scutellaris.

    PubMed

    Frizzi, Filippo; Ciofi, Claudio; Dapporto, Leonardo; Natali, Chiara; Chelazzi, Guido; Turillazzi, Stefano; Santini, Giacomo

    2015-01-01

    Nest-mate recognition plays a key role in the biology of ants. Although individuals coming from a foreign nest are, in most cases, promptly rejected, the degree of aggressiveness towards non nest-mates may be highly variable among species and relies on genetic, chemical and environmental factors. We analyzed intraspecific relationships among neighboring colonies of the dominant Mediterranean acrobat ant Crematogaster scutellaris integrating genetic, chemical and behavioral analyses. Colony structure, parental relationships between nests, cuticular hydrocarbons profiles (CHCs) and aggressive behavior against non nest-mates were studied in 34 nests located in olive tree trunks. Bayesian clustering analysis of allelic variation at nine species-specific microsatellite DNA markers pooled nests into 14 distinct clusters, each representing a single colony, confirming a polydomous arrangement of nests in this species. A marked genetic separation among colonies was also detected, probably due to long distance dispersion of queens and males during nuptial flights. CHCs profiles varied significantly among colonies and between nests of the same colony. No relationship between CHCs profiles and genetic distances was detected. The level of aggressiveness between colonies was inversely related to chemical and spatial distance, suggesting a 'nasty neighbor' effect. Our findings also suggest that CHCs profiles in C. scutellaris may be linked to external environmental factors rather than genetic relationships.

  20. The Rules of Aggression: How Genetic, Chemical and Spatial Factors Affect Intercolony Fights in a Dominant Species, the Mediterranean Acrobat Ant Crematogaster scutellaris

    PubMed Central

    Frizzi, Filippo; Ciofi, Claudio; Dapporto, Leonardo; Natali, Chiara; Chelazzi, Guido; Turillazzi, Stefano; Santini, Giacomo

    2015-01-01

    Nest-mate recognition plays a key role in the biology of ants. Although individuals coming from a foreign nest are, in most cases, promptly rejected, the degree of aggressiveness towards non nest-mates may be highly variable among species and relies on genetic, chemical and environmental factors. We analyzed intraspecific relationships among neighboring colonies of the dominant Mediterranean acrobat ant Crematogaster scutellaris integrating genetic, chemical and behavioral analyses. Colony structure, parental relationships between nests, cuticular hydrocarbons profiles (CHCs) and aggressive behavior against non nest-mates were studied in 34 nests located in olive tree trunks. Bayesian clustering analysis of allelic variation at nine species-specific microsatellite DNA markers pooled nests into 14 distinct clusters, each representing a single colony, confirming a polydomous arrangement of nests in this species. A marked genetic separation among colonies was also detected, probably due to long distance dispersion of queens and males during nuptial flights. CHCs profiles varied significantly among colonies and between nests of the same colony. No relationship between CHCs profiles and genetic distances was detected. The level of aggressiveness between colonies was inversely related to chemical and spatial distance, suggesting a ‘nasty neighbor’ effect. Our findings also suggest that CHCs profiles in C. scutellaris may be linked to external environmental factors rather than genetic relationships. PMID:26445245

  1. Variance Decomposition Using an IRT Measurement Model

    PubMed Central

    Glas, Cees A. W.; Boomsma, Dorret I.

    2007-01-01

    Large scale research projects in behaviour genetics and genetic epidemiology are often based on questionnaire or interview data. Typically, a number of items is presented to a number of subjects, the subjects’ sum scores on the items are computed, and the variance of sum scores is decomposed into a number of variance components. This paper discusses several disadvantages of the approach of analysing sum scores, such as the attenuation of correlations amongst sum scores due to their unreliability. It is shown that the framework of Item Response Theory (IRT) offers a solution to most of these problems. We argue that an IRT approach in combination with Markov chain Monte Carlo (MCMC) estimation provides a flexible and efficient framework for modelling behavioural phenotypes. Next, we use data simulation to illustrate the potentially huge bias in estimating variance components on the basis of sum scores. We then apply the IRT approach with an analysis of attention problems in young adult twins where the variance decomposition model is extended with an IRT measurement model. We show that when estimating an IRT measurement model and a variance decomposition model simultaneously, the estimate for the heritability of attention problems increases from 40% (based on sum scores) to 73%. PMID:17534709

  2. Genotypic-specific variance in Caenorhabditis elegans lifetime fecundity

    PubMed Central

    Diaz, S Anaid; Viney, Mark

    2014-01-01

    Organisms live in heterogeneous environments, so strategies that maximze fitness in such environments will evolve. Variation in traits is important because it is the raw material on which natural selection acts during evolution. Phenotypic variation is usually thought to be due to genetic variation and/or environmentally induced effects. Therefore, genetically identical individuals in a constant environment should have invariant traits. Clearly, genetically identical individuals do differ phenotypically, usually thought to be due to stochastic processes. It is now becoming clear, especially from studies of unicellular species, that phenotypic variance among genetically identical individuals in a constant environment can be genetically controlled and that therefore, in principle, this can be subject to selection. However, there has been little investigation of these phenomena in multicellular species. Here, we have studied the mean lifetime fecundity (thus a trait likely to be relevant to reproductive success), and variance in lifetime fecundity, in recently-wild isolates of the model nematode Caenorhabditis elegans. We found that these genotypes differed in their variance in lifetime fecundity: some had high variance in fecundity, others very low variance. We find that this variance in lifetime fecundity was negatively related to the mean lifetime fecundity of the lines, and that the variance of the lines was positively correlated between environments. We suggest that the variance in lifetime fecundity may be a bet-hedging strategy used by this species. PMID:25360248

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

    PubMed

    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.

  4. Multi-objective parametric optimization of Inertance type pulse tube refrigerator using response surface methodology and non-dominated sorting genetic algorithm

    NASA Astrophysics Data System (ADS)

    Rout, Sachindra K.; Choudhury, Balaji K.; Sahoo, Ranjit K.; Sarangi, Sunil K.

    2014-07-01

    The modeling and optimization of a Pulse Tube Refrigerator is a complicated task, due to its complexity of geometry and nature. The aim of the present work is to optimize the dimensions of pulse tube and regenerator for an Inertance-Type Pulse Tube Refrigerator (ITPTR) by using Response Surface Methodology (RSM) and Non-Sorted Genetic Algorithm II (NSGA II). The Box-Behnken design of the response surface methodology is used in an experimental matrix, with four factors and two levels. The diameter and length of the pulse tube and regenerator are chosen as the design variables where the rest of the dimensions and operating conditions of the ITPTR are constant. The required output responses are the cold head temperature (Tcold) and compressor input power (Wcomp). Computational fluid dynamics (CFD) have been used to model and solve the ITPTR. The CFD results agreed well with those of the previously published paper. Also using the results from the 1-D simulation, RSM is conducted to analyse the effect of the independent variables on the responses. To check the accuracy of the model, the analysis of variance (ANOVA) method has been used. Based on the proposed mathematical RSM models a multi-objective optimization study, using the Non-sorted genetic algorithm II (NSGA-II) has been performed to optimize the responses.

  5. Nominal analysis of "variance".

    PubMed

    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.

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

    SciTech Connect

    Ducros, A.; Alamowitch, S.; Nagy, T.

    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.

  7. Demerelate: calculating inter-individual relatedness for kinship analysis based on co-dominant diploid genetic markers using R.

    PubMed

    Kraemer, Philipp; Gerlach, Gabriele

    2017-03-09

    The Demerelate package offers algorithms to calculate different inter-individual relatedness measurements. Three different allele sharing indices, five pairwise weighted estimates of relatedness and four pairwise weighted estimates with sample size correction are implemented to analyze kinship structures within populations. Statistics are based on randomization tests; modeling relatedness coefficients by logistic regression, modeling relatedness with geographic distance by mantel correlation and comparing mean relatedness between populations using pairwise t-tests. Demerelate provides an advance on previous software packages by including some estimators not available in R to date, along with FIS , as well as combining analysis of relatedness and spatial structuring. An UPGMA tree visualizes genetic relatedness among individuals. Additionally, Demerelate summarizes information on datasets (allele vs. genotype frequencies; heterozygosity; FIS -values). Demerelate is - to our knowledge - the first R-package implementing basic allele sharing indices such as Blouin's Mxy relatedness, the estimator of Wang corrected for sample size (wangxy ), estimators based on Morans I adapted to genetic relatedness as well as combining all estimators with geographic information. The R environment enables users to better understand relatedness within populations due to the flexibility of Demerelate of accepting different datasets as empirical data, reference data, geographical data and by providing intermediate results. Each statistic and tool can be used separately, which helps to understand the suitability of the data for relatedness analysis, and can be easily implemented in custom pipelines. This article is protected by copyright. All rights reserved.

  8. Genetic mutation, linkage and heterogeneity analysis in Spanish pedigrees and isolated cases of autosomal dominant spinocerebellar ataxia (SCA)

    SciTech Connect

    Volpini, V.; Matilla, T.; Genis, D.

    1994-09-01

    We report a genetic study of 14 Spanish kindreds and 11 isolated cases with SCA. The diagnosis was ascertained in 60 members, but clinical data were only obtained for 35 of them. One defective gene responsible for the disease was localized to 6p22-p23 (SCA1) and the mutation consists of an expansion of an intragenic (CAG){sub n} repeat (REP). We studied all of our genealogical and isolated affected individuals in order to know their 6p mutational status. Thus we detected a large pedigree which has the pathological expansion with {open_quotes}n{close_quotes} in the range of 41 to 57 repeats. The expansion increases through generations and correlates with anticipation. In the Spanish population, the non-pathological range of {open_quotes}n{close_quotes} is from 6 to 39 repeats. These sequences are {open_quotes}protected{close_quotes} having an interrupted repeat configuration, studied by restriction and sequencing analysis. This mutation was not present in the genealogical or isolated affected individuals studied. We also tested our families with the recently reported CAG expansion in 12p-12ter (DRPLA) and obtained negative results. Linkage analysis in non-SCA1, DRPLA families using markers from others chromosomal regions, 12q23-24.1 (SCA2) and 14q24.3-q32 (SCA3), results in negative lod scores and shows genetic heterogeneity in our population.

  9. Testing the genetic predictions of a biogeographical model in a dominant endemic Eastern Pacific coral (Porites panamensis) using a genetic seascape approach

    PubMed Central

    Saavedra-Sotelo, Nancy C; Calderon-Aguilera, Luis E; Reyes-Bonilla, Héctor; Paz-García, David A; López-Pérez, Ramón A; Cupul-Magaña, Amilcar; Cruz-Barraza, José A; Rocha-Olivares, Axayácatl

    2013-01-01

    The coral fauna of the Eastern Tropical Pacific (ETP) is depauperate and peripheral; hence, it has drawn attention to the factors allowing its survival. Here, we use a genetic seascape approach and ecological niche modeling to unravel the environmental factors correlating with the genetic variation of Porites panamensis, a hermatypic coral endemic to the ETP. Specifically, we test if levels of diversity and connectivity are higher among abundant than among depauperate populations, as expected by a geographically relaxed version of the Abundant Center Hypothesis (rel-ACH). Unlike the original ACH, referring to a geographical center of distribution of maximal abundance, the rel-ACH refers only to a center of maximum abundance, irrespective of its geographic position. The patterns of relative abundance of P. panamensis in the Mexican Pacific revealed that northern populations from Baja California represent its center of abundance; and southern depauperate populations along the continental margin are peripheral relative to it. Genetic patterns of diversity and structure of nuclear DNA sequences (ribosomal DNA and a single copy open reading frame) and five alloenzymatic loci partially agreed with rel-ACH predictions. We found higher diversity levels in peninsular populations and significant differentiation between peninsular and continental colonies. In addition, continental populations showed higher levels of differentiation and lower connectivity than peninsular populations in the absence of isolation by distance in each region. Some discrepancies with model expectations may relate to the influence of significant habitat discontinuities in the face of limited dispersal potential. Environmental data analyses and niche modeling allowed us to identify temperature, water clarity, and substrate availability as the main factors correlating with patterns of abundance, genetic diversity, and structure, which may hold the key to the survival of P. panamensis in the face of

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

    PubMed

    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.

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

    PubMed

    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.

  12. Population genetic patterns among social groups of the endangered Central American spider monkey (Ateles geoffroyi) in a human-dominated landscape.

    PubMed

    Hagell, Suzanne; Whipple, Amy V; Chambers, Carol L

    2013-05-01

    SPIDER MONKEYS (GENUS: Ateles) are a widespread Neotropical primate with a highly plastic socioecological strategy. However, the Central American species, Ateles geoffroyi, was recently re-listed as endangered due to the accelerated loss of forest across the subcontinent. There is inconsistent evidence that spider monkey populations could persist when actively protected, but their long-term viability in unprotected, human-dominated landscapes is not known. We analyzed noninvasive genetic samples from 185 individuals in 14 putative social groups on the Rivas Isthmus in southwestern Nicaragua. We found evidence of weak but significant genetic structure in the mitochondrial control region and in eight nuclear microsatellite loci plus negative spatial autocorrelation in Fst and kinship. The overall pattern suggests strong localized mating and at least historical female-biased dispersal, as is expected for this species. Heterozygosity was significantly lower than expected under random mating and lower than that found in other spider monkey populations, possibly reflecting a recent decline in genetic diversity and a threat from inbreeding. We conclude that despite a long history of human disturbance on this landscape, spider monkeys were until recently successful at maintaining gene flow. We consider the recent decline to be further indication of accelerated anthropogenic disturbance, but also of an opportunity to conserve native biodiversity. Spider monkeys are one of many wildlife species in Central America that is threatened by land cover change, and an apt example of how landscape-scale conservation planning could be used to ensure long-term persistence.

  13. Cosmology without cosmic variance

    SciTech Connect

    Bernstein, Gary M.; Cai, Yan -Chuan

    2011-10-01

    The growth of structures in the Universe is described by a function G that is predicted by the combination of the expansion history of the Universe and the laws of gravity within it. We examine the improvements in constraints on G that are available from the combination of a large-scale galaxy redshift survey with a weak gravitational lensing survey of background sources. We describe a new combination of such observations that in principle this yields a measure of the growth rate that is free of sample variance, i.e. the uncertainty in G can be reduced without bound by increasing the number of redshifts obtained within a finite survey volume. The addition of background weak lensing data to a redshift survey increases information on G by an amount equivalent to a 10-fold increase in the volume of a standard redshift-space distortion measurement - if the lensing signal can be measured to sub-per cent accuracy. This argues that a combined lensing and redshift survey over a common low-redshift volume of the Universe is a more powerful test of general relativity than an isolated redshift survey over larger volume at high redshift, especially as surveys begin to cover most of the available sky.

  14. Cosmology without cosmic variance

    DOE PAGES

    Bernstein, Gary M.; Cai, Yan -Chuan

    2011-10-01

    The growth of structures in the Universe is described by a function G that is predicted by the combination of the expansion history of the Universe and the laws of gravity within it. We examine the improvements in constraints on G that are available from the combination of a large-scale galaxy redshift survey with a weak gravitational lensing survey of background sources. We describe a new combination of such observations that in principle this yields a measure of the growth rate that is free of sample variance, i.e. the uncertainty in G can be reduced without bound by increasing themore » number of redshifts obtained within a finite survey volume. The addition of background weak lensing data to a redshift survey increases information on G by an amount equivalent to a 10-fold increase in the volume of a standard redshift-space distortion measurement - if the lensing signal can be measured to sub-per cent accuracy. This argues that a combined lensing and redshift survey over a common low-redshift volume of the Universe is a more powerful test of general relativity than an isolated redshift survey over larger volume at high redshift, especially as surveys begin to cover most of the available sky.« less

  15. Estimating the encounter rate variance in distance sampling

    USGS Publications Warehouse

    Fewster, R.M.; Buckland, S.T.; Burnham, K.P.; Borchers, D.L.; Jupp, P.E.; Laake, J.L.; Thomas, L.

    2009-01-01

    The dominant source of variance in line transect sampling is usually the encounter rate variance. Systematic survey designs are often used to reduce the true variability among different realizations of the design, but estimating the variance is difficult and estimators typically approximate the variance by treating the design as a simple random sample of lines. We explore the properties of different encounter rate variance estimators under random and systematic designs. We show that a design-based variance estimator improves upon the model-based estimator of Buckland et al. (2001, Introduction to Distance Sampling. Oxford: Oxford University Press, p. 79) when transects are positioned at random. However, if populations exhibit strong spatial trends, both estimators can have substantial positive bias under systematic designs. We show that poststratification is effective in reducing this bias. ?? 2008, The International Biometric Society.

  16. Autosomal dominant

    MedlinePlus

    ... whether the trait is dominant or recessive. A single abnormal gene on one of the first 22 nonsex ( autosomal ) chromosomes from either parent can cause an autosomal disorder. Dominant inheritance means ...

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

    PubMed Central

    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 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) for F1 productivity. We

  18. Optimization of an ammonia-cooled rectangular microchannel heat sink using multi-objective non-dominated sorting genetic algorithm (NSGA2)

    NASA Astrophysics Data System (ADS)

    Adham, Ahmed Mohammed; Mohd-Ghazali, Normah; Ahmad, Robiah

    2012-10-01

    The ever decreasing size of modern electronic packaging has induced researchers to search for an effective and efficient heat removal system to handle the continuously increasing power density. Investigations have involved different geometry, material and coolant to address the thermal management issues. This paper reports the potential improvement in the overall performance of a rectangular microchannel heat sink using a new gaseous coolant namely ammonia gas. Using a multi-objective general optimization scheme with the thermal resistance model as an analysis method in combination with a non-dominated sorting genetic algorithm as an optimization technique, it was found that significant reduction in the total thermal resistance up to 34 % for ammonia-cooled compared to air-cooled microchannel heat sink under the same operating conditions is achievable. In addition, a considerable decrease in the microchannel heat sink's mass up to 30 % was achieved due to the different heat sink's material used.

  19. PABPN1 (GCN)11 as a Dominant Allele in Oculopharyngeal Muscular Dystrophy –Consequences in Clinical Diagnosis and Genetic Counselling

    PubMed Central

    Richard, Pascale; Trollet, Capucine; Gidaro, Teresa; Demay, Laurence; Brochier, Guy; Malfatti, Edoardo; Tom, Fernando MS; Fardeau, Michel; Lafor, Pascal; Romero, Norma; Martin-N, Marie-Laure; Sol, Guilhem; Ferrer-Monasterio, Xavier; Saint-Guily, Jean Lacau; Eymard, Bruno

    2015-01-01

    Abstract Oculopharyngeal muscular dystrophy (OPMD) is mainly characterized by ptosis and dysphagia. The genetic cause is a short expansion of a (GCN)10 repeat encoding for polyalanine in the poly(A) binding protein nuclear 1 (PABPN1) gene to (GCN)12–17 repeats. The (GCN)11/Ala11 allele has so far been described to be either a polymorphism or a recessive allele with no effect on the phenotype in the heterozygous state. Here we report the clinical and histopathological phenotype of a patient carrying a single (GCN)11/Ala11 heterozygous allele and presenting an atypical form of OPMD with dysphagia and late and mild oculomotor symptoms. Intranuclear inclusions were observed in his muscle biopsy. This suggests a dominant mode of expression of the (GCN)11/Ala11 allele associated with a partial penetrance of OPMD. PMID:27858728

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

    PubMed Central

    Kim, Myung Joo; Lyu, Sang Woo; Seok, Hyun Ha; Park, Ji Eun

    2014-01-01

    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. PMID:25599040

  1. Sampling Errors of Variance Components.

    ERIC Educational Resources Information Center

    Sanders, Piet F.

    A study on sampling errors of variance components was conducted within the framework of generalizability theory by P. L. Smith (1978). The study used an intuitive approach for solving the problem of how to allocate the number of conditions to different facets in order to produce the most stable estimate of the universe score variance. Optimization…

  2. Information Dominance

    DTIC Science & Technology

    1997-11-01

    Information dominance may be defined as superiority in the generation, manipulation, and use of information sufficient to afford its possessors... information dominance at the strategic level: knowing oneself and one’s enemy; and, at best, inducing them to see things as one does.

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

    SciTech Connect

    Othmane, K.B.; Loprest, L.J.; Wilkinson, K.M. ); Middleton, L.T. )

    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.

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

    PubMed

    Ahlering, Marissa A; Eggert, Lori S; Western, David; Estes, Anna; Munishi, Linus; Fleischer, Robert; Roberts, Melissa; Maldonado, Jesus E

    2012-01-01

    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.

  5. Identifying Source Populations and Genetic Structure for Savannah Elephants in Human-Dominated Landscapes and Protected Areas in the Kenya-Tanzania Borderlands

    PubMed Central

    Ahlering, Marissa A.; Eggert, Lori S.; Western, David; Estes, Anna; Munishi, Linus; Fleischer, Robert; Roberts, Melissa; Maldonado, Jesus E.

    2012-01-01

    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. PMID:23300634

  6. Compound Heterozygosity of Dominant and Recessive COL7A Alleles in a Severely Affected Patient with a Family History of Dystrophic Epidermolysis Bullosa: Clinical Findings, Genetic Testing, and Treatment Implications.

    PubMed

    Watson, Kendra D; Schoch, Jennifer J; Beek, Geoffrey J; Hand, Jennifer L

    2017-03-01

    An 8-year-old girl born to a family with more than three generations of dominant dystrophic epidermolysis bullosa (DDEB) presented with life-threatening confluent skin erosions, mitten hand deformity, and failure to thrive. Reassessment of her family history and genetic testing showed compound heterozygous COL7A mutations, one inherited from her DDEB-affected mother and one from her unaffected, healthy father. This family illustrates the risk of unexpected, severe, autosomal recessive epidermolysis bullosa (EB) in a family with milder, multigenerational autosomal dominant EB. Clinicians should recognize the clinical spectrum of dystrophic EB and recommend genetic consultation when the phenotype conflicts with family history.

  7. A Pkd1-Fbn1 genetic interaction implicates TGF-β signaling in the pathogenesis of vascular complications in autosomal dominant polycystic kidney disease.

    PubMed

    Liu, Dongyan; Wang, Connie J; Judge, Daniel P; Halushka, Marc K; Ni, Jie; Habashi, Jennifer P; Moslehi, Javid; Bedja, Djahida; Gabrielson, Kathleen L; Xu, Hangxue; Qian, Feng; Huso, David; Dietz, Harry C; Germino, Gregory G; Watnick, Terry

    2014-01-01

    Autosomal dominant polycystic kidney disease (ADPKD) is a common cause of renal failure that is due to mutations in two genes, PKD1 and PKD2. Vascular complications, including aneurysms, are a well recognized feature of ADPKD, and a subgroup of families exhibits traits reminiscent of Marfan syndrome (MFS). MFS is caused by mutations in fibrillin-1 (FBN1), which encodes an extracellular matrix protein with homology to latent TGF-β binding proteins. It was recently demonstrated that fibrillin-1 deficiency is associated with upregulation of TGF-β signaling. We investigated the overlap between ADPKD and MFS by breeding mice with targeted mutations in Pkd1 and Fbn1. Double heterozygotes displayed an exacerbation of the typical Fbn1 heterozygous aortic phenotype. We show that the basis of this genetic interaction results from further upregulation of TGF-β signaling caused by Pkd1 haploinsufficiency. In addition, we demonstrate that loss of PKD1 alone is sufficient to induce a heightened responsiveness to TGF-β. Our data link the interaction of two important diseases to a fundamental signaling pathway.

  8. Analysis of variance components of testcross progenies in an autotetraploid species and consequences for recurrent selection with a tester.

    PubMed

    Gallais, A

    1992-01-01

    For autotetraploid species the development of the concept of test value (value in testcross) leads to a simple description of the variance among testcross progenies. When defining directly genetic effects at the level of the value of the progenies, there is no contribution of triand tetragenic interactions. To estimate additive and dominance variances it is only necessary to have the population of progenies structured in half-sib or full-sib families; it is then possible to determine the presence of epistasis using a two-way mating design. When the theory of recurrent selection is applied dominance variance can be neglected for the prediction of genetic advance in one cycle as well for the development of combined selection when progenies are structured in families. The results are similar to those for diploids with two-locus epistasis. The more efficient scheme consists of the development of pair-crossing in off-season generations (for intercrossing) and simultaneous crossing of each plant to the tester. In comparison to the classical scheme, the relative efficiency of such a scheme is 41%. The use of combined selection will further increase this superiority.

  9. Selection enhanced estimates of µ-calpain, calpastatin, and dacylglycerol O-acyltransferase 1 genetic effects on pre-weaning performance, carcass quality traits, and residual variance of tenderness in composite ... cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Selection of the composite MARC III population for markers allowed better estimates of effects and inheritance of markers for targeted carcass quality traits (n=254) and nontargeted traits and an evaluation of SNP specific residual variance models for tenderness. Genotypic effects of CAPN1 haplotyp...

  10. Variance in male lifetime reproductive success and estimation of the degree of polygyny in a primate.

    PubMed

    Dubuc, Constance; Ruiz-Lambides, Angelina; Widdig, Anja

    2014-07-01

    The degree of polygyny is predicted to influence the strength of direct male-male competition, leading to a high variance in male lifetime reproductive success and to reproduction limited to the prime period of adulthood. Here, we explore the variance in male lifetime reproductive success and reproductive time in an anthropoid primate forming multimale-multifemale groups. Males of this species form dominance hierarchies, which are expected to skew reproduction toward few high-ranking males. At the same time, however, females mate with multiple males (polygynandry), which should limit the degree of polygyny. Using 20 years of genetic and demographic data, we calculated lifetime reproductive success for the free-ranging rhesus macaque (Macaca mulatta) population of Cayo Santiago for subjects that died naturally or reached senescence. Our results show that 1) male lifetime reproductive success was significantly skewed (range: 0-47 offspring; males reproducing below average: 62.8%; nonbreeders: 17.4%), 2) variance in male lifetime reproductive success was 5 times larger than in females, and 3) male lifetime reproductive success was more influenced by variation in fecundity (60%) than longevity (25%), suggesting that some direct male-male competition takes place. However, the opportunity for selection (i.e., standardized variance in male lifetime reproductive success) is low compared with that in other large mammal species characterized by a high degree of polygyny. Moreover, male reproductive life extended much beyond the prime period, showing that physical strength was not required to acquire mates. We conclude that rhesus macaques exhibit a moderate degree of polygyny and, therefore, low levels of direct male-male competition for fertile females, despite the fact that males form linear dominance hierarchies.

  11. Genetics

    MedlinePlus

    ... 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 ...

  12. VPSim: Variance propagation by simulation

    SciTech Connect

    Burr, T.; Coulter, C.A.; Prommel, J.

    1997-12-01

    One of the fundamental concepts in a materials control and accountability system for nuclear safeguards is the materials balance (MB). All transfers into and out of a material balance area are measured, as are the beginning and ending inventories. The resulting MB measures the material loss, MB = T{sub in} + I{sub B} {minus} T{sub out} {minus} I{sub E}. To interpret the MB, the authors must estimate its measurement error standard deviation, {sigma}{sub MB}. When feasible, they use a method usually known as propagation of variance (POV) to estimate {sigma}{sub MB}. The application of POV for estimating the measurement error variance of an MB is straightforward but tedious. By applying POV to individual measurement error standard deviations they can estimate {sigma}{sub MB} (or more generally, they can estimate the variance-covariance matrix, {Sigma}, of a sequence of MBs). This report describes a new computer program (VPSim) that uses simulation to estimate the {Sigma} matrix of a sequence of MBs. Given the proper input data, VPSim calculates the MB and {sigma}{sub MB}, or calculates a sequence of n MBs and the associated n-by-n covariance matrix, {Sigma}. The covariance matrix, {Sigma}, contains the variance of each MB in the diagonal entries and the covariance between pairs of MBs in the off-diagonal entries.

  13. Analysis of Variance: Variably Complex

    ERIC Educational Resources Information Center

    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…

  14. Multicomponent, multi-azimuth pre-stack seismic waveform inversion for azimuthally anisotropic media using a parallel and computationally efficient non-dominated sorting genetic algorithm

    NASA Astrophysics Data System (ADS)

    Li, Tao; Mallick, Subhashis

    2015-02-01

    Consideration of azimuthal anisotropy, at least to an orthorhombic symmetry is important in exploring the naturally fractured and unconventional hydrocarbon reservoirs. Full waveform inversion of multicomponent seismic data can, in principle, provide more robust estimates of subsurface elastic parameters and density than the inversion of single component (P wave) seismic data. In addition, azimuthally dependent anisotropy can only be resolved by carefully studying the multicomponent seismic displacement data acquired and processed along different azimuths. Such an analysis needs an inversion algorithm capable of simultaneously optimizing multiple objectives, one for each data component along each azimuth. These multicomponent and multi-azimuthal seismic inversions are non-linear with non-unique solutions; it is therefore appropriate to treat the objectives as a vector and simultaneously optimize each of its components such that the optimal set of solutions could be obtained. The fast non-dominated sorting genetic algorithm (NSGA II) is a robust stochastic global search method capable of handling multiple objectives, but its computational expense increases with increasing number of objectives and the number of model parameters to be inverted for. In addition, an accurate extraction of subsurface azimuthal anisotropy requires multicomponent seismic data acquired at a fine spatial resolution along many source-to-receiver azimuths. Because routine acquisition of such data is prohibitively expensive, they are typically available along two or at most three azimuthal orientations at a spatial resolution where such an inversion could be applied. This paper proposes a novel multi-objective methodology using a parallelized version of NSGA II for waveform inversion of multicomponent seismic displacement data along two azimuths. By scaling the objectives prior to ranking, redefining the crowding distance as functions of the scaled objective and the model spaces, and varying

  15. Hybrid biasing approaches for global variance reduction.

    PubMed

    Wu, Zeyun; Abdel-Khalik, Hany S

    2013-02-01

    A new variant of Monte Carlo-deterministic (DT) hybrid variance reduction approach based on Gaussian process theory is presented for accelerating convergence of Monte Carlo simulation and compared with Forward-Weighted Consistent Adjoint Driven Importance Sampling (FW-CADIS) approach implemented in the SCALE package from Oak Ridge National Laboratory. The new approach, denoted the Gaussian process approach, treats the responses of interest as normally distributed random processes. The Gaussian process approach improves the selection of the weight windows of simulated particles by identifying a subspace that captures the dominant sources of statistical response variations. Like the FW-CADIS approach, the Gaussian process approach utilizes particle importance maps obtained from deterministic adjoint models to derive weight window biasing. In contrast to the FW-CADIS approach, the Gaussian process approach identifies the response correlations (via a covariance matrix) and employs them to reduce the computational overhead required for global variance reduction (GVR) purpose. The effective rank of the covariance matrix identifies the minimum number of uncorrelated pseudo responses, which are employed to bias simulated particles. Numerical experiments, serving as a proof of principle, are presented to compare the Gaussian process and FW-CADIS approaches in terms of the global reduction in standard deviation of the estimated responses.

  16. Functional analysis of variance for association studies.

    PubMed

    Vsevolozhskaya, Olga A; Zaykin, Dmitri V; Greenwood, Mark C; Wei, Changshuai; Lu, Qing

    2014-01-01

    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.

  17. Variance decomposition in stochastic simulators

    SciTech Connect

    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.

  18. Estimating the Modified Allan Variance

    NASA Technical Reports Server (NTRS)

    Greenhall, Charles

    1995-01-01

    The third-difference approach to modified Allan variance (MVAR) leads to a tractable formula for a measure of MVAR estimator confidence, the equivalent degrees of freedom (edf), in the presence of power-law phase noise. The effect of estimation stride on edf is tabulated. A simple approximation for edf is given, and its errors are tabulated. A theorem allowing conservative estimates of edf in the presence of compound noise processes is given.

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

    PubMed

    Distel, Marijn A; Rebollo-Mesa, Irene; Willemsen, Gonneke; Derom, Catherine A; Trull, Timothy J; Martin, Nicholas G; Boomsma, Dorret I

    2009-01-01

    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.

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

    PubMed

    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.

  1. The Evolution and Consequences of Sex-Specific Reproductive Variance

    PubMed Central

    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. PMID:24172130

  2. Estimating the Modified Allan Variance

    NASA Technical Reports Server (NTRS)

    Greenhall, Charles

    1995-01-01

    A paper at the 1992 FCS showed how to express the modified Allan variance (mvar) in terms of the third difference of the cumulative sum of time residuals. Although this reformulated definition was presented merely as a computational trick for simplifying the calculation of mvar estimates, it has since turned out to be a powerful theoretical tool for deriving the statistical quality of those estimates in terms of their equivalent degrees of freedom (edf), defined for an estimator V by edf V = 2(EV)2/(var V). Confidence intervals for mvar can then be constructed from levels of the appropriate 2 distribution.

  3. Mitral disc-valve variance

    PubMed Central

    Berroya, Renato B.; Escano, Fernando B.

    1972-01-01

    This report deals with a rare complication of disc-valve prosthesis in the mitral area. A significant disc poppet and struts destruction of mitral Beall valve prostheses occurred 20 and 17 months after implantation. The resulting valve incompetence in the first case contributed to the death of the patient. The durability of Teflon prosthetic valves appears to be in question and this type of valve probably will be unacceptable if there is an increasing number of disc-valve variance in the future. Images PMID:5017573

  4. 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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  5. A Wavelet Perspective on the Allan Variance.

    PubMed

    Percival, Donald B

    2016-04-01

    The origins of the Allan variance trace back 50 years ago to two seminal papers, one by Allan (1966) and the other by Barnes (1966). Since then, the Allan variance has played a leading role in the characterization of high-performance time and frequency standards. Wavelets first arose in the early 1980s in the geophysical literature, and the discrete wavelet transform (DWT) became prominent in the late 1980s in the signal processing literature. Flandrin (1992) briefly documented a connection between the Allan variance and a wavelet transform based upon the Haar wavelet. Percival and Guttorp (1994) noted that one popular estimator of the Allan variance-the maximal overlap estimator-can be interpreted in terms of a version of the DWT now widely referred to as the maximal overlap DWT (MODWT). In particular, when the MODWT is based on the Haar wavelet, the variance of the resulting wavelet coefficients-the wavelet variance-is identical to the Allan variance when the latter is multiplied by one-half. The theory behind the wavelet variance can thus deepen our understanding of the Allan variance. In this paper, we review basic wavelet variance theory with an emphasis on the Haar-based wavelet variance and its connection to the Allan variance. We then note that estimation theory for the wavelet variance offers a means of constructing asymptotically correct confidence intervals (CIs) for the Allan variance without reverting to the common practice of specifying a power-law noise type a priori. We also review recent work on specialized estimators of the wavelet variance that are of interest when some observations are missing (gappy data) or in the presence of contamination (rogue observations or outliers). It is a simple matter to adapt these estimators to become estimators of the Allan variance. Finally we note that wavelet variances based upon wavelets other than the Haar offer interesting generalizations of the Allan variance.

  6. Statistical genetics of an annual plant, Impatiens capensis. I. Genetic basis of quantitative variation.

    PubMed

    Mitchell-Olds, T; Bergelson, J

    1990-02-01

    Analysis of quantitative genetics in natural populations has been hindered by computational and methodological problems in statistical analysis. We developed and validated a jackknife procedure to test for existence of broad sense heritabilities and dominance or maternal effects influencing quantitative characters in Impatiens capensis. Early life cycle characters showed evidence of dominance and/or maternal effects, while later characters exhibited predominantly environmental variation. Monte Carlo simulations demonstrate that these jackknife tests of variance components are extremely robust to heterogeneous error variances. Statistical methods from human genetics provide evidence for either a major locus influencing germination date, or genes that affect phenotypic variability per se. We urge explicit consideration of statistical behavior of estimation and testing procedures for proper biological interpretation of statistical results.

  7. The contribution of dominance to phenotype prediction in a pine breeding and simulated population

    PubMed Central

    de Almeida Filho, J E; Guimarães, J F R; e Silva, F F; de Resende, M D V; Muñoz, P; Kirst, M; Resende, M F R

    2016-01-01

    Pedigrees and dense marker panels have been used to predict the genetic merit of individuals in plant and animal breeding, accounting primarily for the contribution of additive effects. However, nonadditive effects may also affect trait variation in many breeding systems, particularly when specific combining ability is explored. Here we used models with different priors, and including additive-only and additive plus dominance effects, to predict polygenic (height) and oligogenic (fusiform rust resistance) traits in a structured breeding population of loblolly pine (Pinus taeda L.). Models were largely similar in predictive ability, and the inclusion of dominance only improved modestly the predictions for tree height. Next, we simulated a genetically similar population to assess the ability of predicting polygenic and oligogenic traits controlled by different levels of dominance. The simulation showed an overall decrease in the accuracy of total genomic predictions as dominance increases, regardless of the method used for prediction. Thus, dominance effects may not be accounted for as effectively in prediction models compared with traits controlled by additive alleles only. When the ratio of dominance to total phenotypic variance reached 0.2, the additive–dominance prediction models were significantly better than the additive-only models. However, in the prediction of the subsequent progeny population, this accuracy increase was only observed for the oligogenic trait. PMID:27118156

  8. Warped functional analysis of variance.

    PubMed

    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.

  9. The Effect of an Experimental Bottleneck upon Quantitative Genetic Variation in the Housefly

    PubMed Central

    Bryant, Edwin H.; McCommas, Steven A.; Combs, Lisa M.

    1986-01-01

    Effects of a population bottleneck (founder-flush cycle) upon quantitative genetic variation of morphometric traits were examined in replicated experimental lines of the housefly founded with one, four or 16 pairs of flies. Heritability and additive genetic variances for eight morphometric traits generally increased as a result of the bottleneck, but the pattern of increase among bottleneck sizes differed among traits. Principal axes of the additive genetic correlation matrix for the control line yielded two suites of traits, one associated with general body size and another set largely independent of body size. In the former set containing five of the traits, additive genetic variance was greatest in the bottleneck size of four pairs, whereas in the latter set of two traits the largest additive genetic variance occurred in the smallest bottleneck size of one pair. One trait exhibited changes in additive genetic variance intermediate between these two major responses. These results were inconsistent with models of additive effects of alleles within loci or of additive effects among loci. An observed decline in viability measures and body size in the bottleneck lines also indicated that there was nonadditivity of allelic effects for these traits. Several possible nonadditive models were explored that increased additive genetic variance as a result of a bottleneck. These included a model with complete dominance, a model with overdominance and a model incorporating multiplicative epistasis. PMID:17246359

  10. Speed Variance and Its Influence on Accidents.

    ERIC Educational Resources Information Center

    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…

  11. Nonlinear selection and the evolution of variances and covariances for continuous characters in an anole.

    PubMed

    Revell, L J; Mahler, D L; Sweeney, J R; Sobotka, M; Fancher, V E; Losos, J B

    2010-02-01

    The pattern of genetic variances and covariances among characters, summarized in the additive genetic variance-covariance matrix, G, determines how a population will respond to linear natural selection. However, G itself also evolves in response to selection. In particular, we expect that, over time, G will evolve correspondence with the pattern of multivariate nonlinear natural selection. In this study, we substitute the phenotypic variance-covariance matrix (P) for G to determine if the pattern of multivariate nonlinear selection in a natural population of Anolis cristatellus, an arboreal lizard from Puerto Rico, has influenced the evolution of genetic variances and covariances in this species. Although results varied among our estimates of P and fitness, and among our analytic techniques, we find significant evidence for congruence between nonlinear selection and P, suggesting that natural selection may have influenced the evolution of genetic constraint in this species.

  12. Genetic architecture of nonadditive inheritance in Arabidopsis thaliana hybrids

    PubMed Central

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

    2016-01-01

    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. PMID:27803326

  13. Increasing selection response by Bayesian modeling of heterogeneous environmental variances

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Heterogeneity of environmental variance among genotypes reduces selection response because genotypes with higher variance are more likely to be selected than low-variance genotypes. Modeling heterogeneous variances to obtain weighted means corrected for heterogeneous variances is difficult in likel...

  14. 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

    PubMed Central

    de Bakker, Didier M.; Meesters, Erik H. W. G.; van Bleijswijk, Judith D. L.; Luttikhuizen, Pieternella C.; Breeuwer, Hans J. A. J.; Becking, Leontine E.

    2016-01-01

    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

  15. 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.

    PubMed

    de Bakker, Didier M; Meesters, Erik H W G; van Bleijswijk, Judith D L; Luttikhuizen, Pieternella C; Breeuwer, Hans J A J; Becking, Leontine E

    2016-01-01

    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 replenish

  16. Restricted sample variance reduces generalizability.

    PubMed

    Lakes, Kimberley D

    2013-06-01

    One factor that affects the reliability of observed scores is restriction of range on the construct measured for a particular group of study participants. This study illustrates how researchers can use generalizability theory to evaluate the impact of restriction of range in particular sample characteristics on the generalizability of test scores and to estimate how changes in measurement design could improve the generalizability of the test scores. An observer-rated measure of child self-regulation (Response to Challenge Scale; Lakes, 2011) is used to examine scores for 198 children (Grades K through 5) within the generalizability theory (GT) framework. The generalizability of ratings within relatively developmentally homogeneous samples is examined and illustrates the effect of reduced variance among ratees on generalizability. Forecasts for g coefficients of various D study designs demonstrate how higher generalizability could be achieved by increasing the number of raters or items. In summary, the research presented illustrates the importance of and procedures for evaluating the generalizability of a set of scores in a particular research context.

  17. Medical genetics

    SciTech Connect

    Jorde, L.B.; Carey, J.C.; White, R.L.

    1995-10-01

    This book on the subject of medical genetics is a textbook aimed at a very broad audience: principally, medical students, nursing students, graduate, and undergraduate students. The book is actually a primer of general genetics as applied to humans and provides a well-balanced introduction to the scientific and clinical basis of human genetics. The twelve chapters include: Introduction, Basic Cell Biology, Genetic Variation, Autosomal Dominant and Recessive Inheritance, Sex-linked and Mitochondrial Inheritance, Clinical Cytogenetics, Gene Mapping, Immunogenetics, Cancer Genetics, Multifactorial Inheritance and Common Disease, Genetic Screening, Genetic Diagnosis and Gene Therapy, and Clinical Genetics and Genetic Counseling.

  18. Next generation sequencing to identify novel genetic variants causative of autosomal dominant familial hypercholesterolemia associated with increased risk of coronary heart disease.

    PubMed

    Al-Allaf, Faisal A; Athar, Mohammad; Abduljaleel, Zainularifeen; Taher, Mohiuddin M; Khan, Wajahatullah; Ba-Hammam, Faisal A; Abalkhail, Hala; Alashwal, Abdullah

    2015-07-01

    Familial hypercholesterolemia (FH) is an autosomal dominant inherited disease characterized by elevated plasma low-density lipoprotein cholesterol (LDL-C). It is an autosomal dominant disease, caused by variants in Ldlr, ApoB or Pcsk9, which results in high levels of LDL-cholesterol (LDL-C) leading to early coronary heart disease. Sequencing whole genome for screening variants for FH are not suitable due to high cost. Hence, in this study we performed targeted customized sequencing of FH 12 genes (Ldlr, ApoB, Pcsk9, Abca1, Apoa2, Apoc3, Apon2, Arh, Ldlrap1, Apoc2, ApoE, and Lpl) that have been implicated in the homozygous phenotype of a proband pedigree to identify candidate variants by NGS Ion torrent PGM. Only three genes (Ldlr, ApoB, and Pcsk9) were found to be highly associated with FH based on the variant rate. The results showed that seven deleterious variants in Ldlr, ApoB, and Pcsk9 genes were pathological and were clinically significant based on predictions identified by SIFT and PolyPhen. Targeted customized sequencing is an efficient technique for screening variants among targeted FH genes. Final validation of seven deleterious variants conducted by capillary resulted to only one novel variant in Ldlr gene that was found in exon 14 (c.2026delG, p. Gly676fs). The variant found in Ldlr gene was a novel heterozygous variant derived from a male in the proband.

  19. Pathogenic Potential, Genetic Diversity, and Population Structure of Escherichia coli Strains Isolated from a Forest-Dominated Watershed (Comox Lake) in British Columbia, Canada

    PubMed Central

    Mazumder, Asit

    2014-01-01

    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. PMID:25548059

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

    PubMed

    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.

  1. Genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Capsicum represents one of several well characterized Solanaceous genera. A wealth of classical and molecular genetics research is available for the genus. Information gleaned from its cultivated relatives, tomato and potato, provide further insight for basic and applied studies. Early ...

  2. Genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Maintaining genetic variation in wild populations of Arctic organisms is fundamental to the long-term persistence of high latitude biodiversity. Variability is important because it provides options for species to respond to changing environmental conditions and novel challenges such as emerging path...

  3. Genetic mapping of the human amphiphysin gene (AMPH) at 7p14-p13 excludes its involvement in retinitis pigmentosa 9 or dominant cystoid macular dystrophy

    SciTech Connect

    Yamamoto, R.; Kilimann, M.W.; Li, X.

    1995-10-01

    Amphiphysin is a protein concentrated in neuronal synapses and peripherally associated with synaptic vesicles. It is expressed in many neurons of the central and peripheral nervous systems and also in the adrenal medulla, the anterior and posterior pituitary, cell lines of the endocrine pancreas, and male germ cells. Its subcellular localization and tissue distribution indicate a potential involvement in mechanisms of regulated exocytosis. A role in the dynamic organization of the membrane-associated cytoskeleton is suggested by sequence similarity to the products of two yeast genes, RVS161 and RVS167. Mutation of either of these results in an abnormal actin distribution, disturbs budding morphology, and impairs cell entry into stationary phase. Amphiphysin is the dominant autoantigen in paraneoplastic Stiff-Man syndrome, a neurological autoimmune disorder characterized by progressive rigidity of the body musculature with superimposed painful spasms. 9 refs., 1 fig., 1 tab.

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

    PubMed

    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.

  5. 40 CFR 59.106 - Variance.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Automobile Refinish Coatings § 59.106 Variance. (a) Any regulated...

  6. 40 CFR 59.106 - Variance.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Automobile Refinish Coatings § 59.106 Variance. (a) Any regulated...

  7. 40 CFR 59.106 - Variance.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Automobile Refinish Coatings § 59.106 Variance. (a) Any regulated...

  8. 40 CFR 59.106 - Variance.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Automobile Refinish Coatings § 59.106 Variance. (a) Any regulated...

  9. 40 CFR 59.106 - Variance.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Automobile Refinish Coatings § 59.106 Variance. (a) Any regulated...

  10. Combining Study Outcome Measures Using Dominance Adjusted Weights

    ERIC Educational Resources Information Center

    Makambi, Kepher H.; Lu, Wenxin

    2013-01-01

    Weighting of studies in meta-analysis is usually implemented by using the estimated inverse variances of treatment effect estimates. However, there is a possibility of one study dominating other studies in the estimation process by taking on a weight that is above some upper limit. We implement an estimator of the heterogeneity variance that takes…

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed Central

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

    2016-01-01

    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. PMID:26801647

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

    PubMed

    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.

  14. Multi-objective optimization of combustion, performance and emission parameters in a jatropha biodiesel engine using Non-dominated sorting genetic algorithm-II

    NASA Astrophysics Data System (ADS)

    Dhingra, Sunil; Bhushan, Gian; Dubey, Kashyap Kumar

    2014-03-01

    The present work studies and identifies the different variables that affect the output parameters involved in a single cylinder direct injection compression ignition (CI) engine using jatropha biodiesel. Response surface methodology based on Central composite design (CCD) is used to design the experiments. Mathematical models are developed for combustion parameters (Brake specific fuel consumption (BSFC) and peak cylinder pressure (Pmax)), performance parameter brake thermal efficiency (BTE) and emission parameters (CO, NO x , unburnt HC and smoke) using regression techniques. These regression equations are further utilized for simultaneous optimization of combustion (BSFC, Pmax), performance (BTE) and emission (CO, NO x , HC, smoke) parameters. As the objective is to maximize BTE and minimize BSFC, Pmax, CO, NO x , HC, smoke, a multiobjective optimization problem is formulated. Nondominated sorting genetic algorithm-II is used in predicting the Pareto optimal sets of solution. Experiments are performed at suitable optimal solutions for predicting the combustion, performance and emission parameters to check the adequacy of the proposed model. The Pareto optimal sets of solution can be used as guidelines for the end users to select optimal combination of engine output and emission parameters depending upon their own requirements.

  15. A model for the initiation and progression of non-chromaffin paragangliomas: An autosomal dominant disorder with genetic heterogeneity and genomic imprinting

    SciTech Connect

    Mariman, E.C.M.; Beersum, S.E.C. van; Ropers, H.H.

    1994-09-01

    Non-chromaffin paragangliomas are autosomal dominantly inherited tumors of the head and neck region (frequency: 1:30,000). Genomic imprinting influences the expression of the disorder. Tumor development is restricted to offspring of male disease gene carriers. By linkage analysis and haplotyping of a single family, in which the pattern of inheritance is consistent with genomic imprinting, we have mapped the gene to a 5 cM region of chromosome 11q13.1 between D11S956 and PYGM. A maximum lod score of 7.62 at {theta}=0.0 was obtained for D11S480. This interval does not overlap with the segment 11q22.3-q23.3, to which a locus for glomus tumors has been assigned in other families. Moreover, the 5cM interval was excluded as the location of the disease gene in a second family showing the imprinting phenomenon, whereas an indication for linkage was obtained (Z=+2.65) with markers from the distal locus. These observations argue for the presence of two distinct imprinted genes for paragangliomas on 11q. Clinical findings suggest that at least one, but probably both genes code for tumor suppressor required for tumor initiation. According to this model, imprinting would account for the silencing of the two maternal copies, whereas a paternal copy would be inactive due to an inherited mutation. Tumors would then result from somatic inactivation of the other paternal gene copy in individual cells. In tumors, relaxation of imprinting seems to be a frequent feature. Here, it would necessitate subsequent inactivation of maternal gene copies to allow tumor progression. Indeed, selective loss of maternal alleles in paragangliomas has been observed with markers from 11 q. Definite proof for this model should come from the isolation and expression studies of the involved genes.

  16. Coupling Genetic and Chemical Microbiome Profiling Reveals Heterogeneity of Archaeome and Bacteriome in Subsurface Biofilms That Are Dominated by the Same Archaeal Species

    PubMed Central

    Holman, Hoi-Ying N.; DeSantis, Todd Z.; Wanner, Gerhard; Andersen, Gary L.; Perras, Alexandra K.; Meck, Sandra; Völkel, Jörg; Bechtel, Hans A.; Wirth, Reinhard; Moissl-Eichinger, Christine

    2014-01-01

    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. PMID:24971452

  17. Variance Design and Air Pollution Control

    ERIC Educational Resources Information Center

    Ferrar, Terry A.; Brownstein, Alan B.

    1975-01-01

    Air pollution control authorities were forced to relax air quality standards during the winter of 1972 by granting variances. This paper examines the institutional characteristics of these variance policies from an economic incentive standpoint, sets up desirable structural criteria for institutional design and arrives at policy guidelines for…

  18. 10 CFR 1022.16 - Variances.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 4 2012-01-01 2012-01-01 false Variances. 1022.16 Section 1022.16 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS) COMPLIANCE WITH FLOODPLAIN AND WETLAND ENVIRONMENTAL REVIEW REQUIREMENTS Procedures for Floodplain and Wetland Reviews § 1022.16 Variances. (a) Emergency actions. DOE may...

  19. 10 CFR 1022.16 - Variances.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 4 2014-01-01 2014-01-01 false Variances. 1022.16 Section 1022.16 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS) COMPLIANCE WITH FLOODPLAIN AND WETLAND ENVIRONMENTAL REVIEW REQUIREMENTS Procedures for Floodplain and Wetland Reviews § 1022.16 Variances. (a) Emergency actions. DOE may...

  20. 10 CFR 1022.16 - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Variances. 1022.16 Section 1022.16 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS) COMPLIANCE WITH FLOODPLAIN AND WETLAND ENVIRONMENTAL REVIEW REQUIREMENTS Procedures for Floodplain and Wetland Reviews § 1022.16 Variances. (a) Emergency actions. DOE may...

  1. 10 CFR 1022.16 - Variances.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 4 2011-01-01 2011-01-01 false Variances. 1022.16 Section 1022.16 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS) COMPLIANCE WITH FLOODPLAIN AND WETLAND ENVIRONMENTAL REVIEW REQUIREMENTS Procedures for Floodplain and Wetland Reviews § 1022.16 Variances. (a) Emergency actions. DOE may...

  2. 10 CFR 1022.16 - Variances.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 4 2013-01-01 2013-01-01 false Variances. 1022.16 Section 1022.16 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS) COMPLIANCE WITH FLOODPLAIN AND WETLAND ENVIRONMENTAL REVIEW REQUIREMENTS Procedures for Floodplain and Wetland Reviews § 1022.16 Variances. (a) Emergency actions. DOE may...

  3. 40 CFR 142.41 - Variance request.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ....41 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS IMPLEMENTATION Variances Issued by the Administrator Under Section 1415(a) of the Act § 142.41 Variance request. A supplier of water may request the granting of...

  4. 40 CFR 142.41 - Variance request.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ....41 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS IMPLEMENTATION Variances Issued by the Administrator Under Section 1415(a) of the Act § 142.41 Variance request. A supplier of water may request the granting of...

  5. 40 CFR 142.41 - Variance request.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ....41 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS IMPLEMENTATION Variances Issued by the Administrator Under Section 1415(a) of the Act § 142.41 Variance request. A supplier of water may request the granting of...

  6. Portfolio optimization with mean-variance model

    NASA Astrophysics Data System (ADS)

    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.

  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

    PubMed Central

    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 (< 100 km apart) had diverged significantly, suggesting local adaptation. Asymmetrical long-distance inter-population gene flow occurs along the sampling 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. PMID:27580056

  8. Variance Assistance Document: Land Disposal Restrictions Treatability Variances and Determinations of Equivalent Treatment

    EPA Pesticide Factsheets

    This document provides assistance to those seeking to submit a variance request for LDR treatability variances and determinations of equivalent treatment regarding the hazardous waste land disposal restrictions program.

  9. Gravity Wave Variances and Propagation Derived from AIRS Radiances

    NASA Technical Reports Server (NTRS)

    Gong, Jie; Wu, Dong L.; Eckermann, S. D.

    2012-01-01

    As the first gravity wave (GW) climatology study using nadir-viewing infrared sounders, 50 Atmospheric Infrared Sounder (AIRS) radiance channels are selected to estimate GW variances at pressure levels between 2-100 hPa. The GW variance for each scan in the cross-track direction is derived from radiance perturbations in the scan, independently of adjacent scans along the orbit. Since the scanning swaths are perpendicular to the satellite orbits, which are inclined meridionally at most latitudes, the zonal component of GW propagation can be inferred by differencing the variances derived between the westmost and the eastmost viewing angles. Consistent with previous GW studies using various satellite instruments, monthly mean AIRS variance shows large enhancements over meridionally oriented mountain ranges as well as some islands at winter hemisphere high latitudes. Enhanced wave activities are also found above tropical deep convective regions. GWs prefer to propagate westward above mountain ranges, and eastward above deep convection. AIRS 90 field-of-views (FOVs), ranging from +48 deg. to -48 deg. off nadir, can detect large-amplitude GWs with a phase velocity propagating preferentially at steep angles (e.g., those from orographic and convective sources). The annual cycle dominates the GW variances and the preferred propagation directions for all latitudes. Indication of a weak two-year variation in the tropics is found, which is presumably related to the Quasi-biennial oscillation (QBO). AIRS geometry makes its out-tracks capable of detecting GWs with vertical wavelengths substantially shorter than the thickness of instrument weighting functions. The novel discovery of AIRS capability of observing shallow inertia GWs will expand the potential of satellite GW remote sensing and provide further constraints on the GW drag parameterization schemes in the general circulation models (GCMs).

  10. Inheritance of dermatoglyphic traits in twins: univariate and bivariate variance decomposition analysis.

    PubMed

    Karmakar, Bibha; Malkin, Ida; Kobyliansky, Eugene

    2012-01-01

    Dermatoglyphic traits in a sample of twins were analyzed to estimate the resemblance between MZ and DZ twins and to evaluate the mode of inheritance by using the maximum likelihood-based Variance decomposition analysis. The additive genetic variance component was significant in both sexes for four traits--PII, AB_RC, RC_HB, and ATD_L. AB RC and RC_HB had significant sex differences in means, whereas PII and ATD_L did not. The results of the Bivariate Variance decomposition analysis revealed that PII and RC_HB have a significant correlation in both genetic and residual components. Significant correlation in the additive genetic variance between AB_RC and ATD_L was observed. The same analysis only for the females sub-sample in the three traits RBL, RBR and AB_DIS shows that the additive genetic RBR component was significant and the AB_DIS sibling component was not significant while others cannot be constrained to zero. The additive variance for AB DIS sibling component was not significant. The three components additive, sibling and residual were significantly correlated between each pair of traits revealed by the Bivariate Variance decomposition analysis.

  11. Portfolio optimization using median-variance approach

    NASA Astrophysics Data System (ADS)

    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.

  12. Neural field theory with variance dynamics.

    PubMed

    Robinson, P A

    2013-06-01

    Previous neural field models have mostly been concerned with prediction of mean neural activity and with second order quantities such as its variance, but without feedback of second order quantities on the dynamics. Here the effects of feedback of the variance on the steady states and adiabatic dynamics of neural systems are calculated using linear neural field theory to estimate the neural voltage variance, then including this quantity in the total variance parameter of the nonlinear firing rate-voltage response function, and thus into determination of the fixed points and the variance itself. The general results further clarify the limits of validity of approaches with and without inclusion of variance dynamics. Specific applications show that stability against a saddle-node bifurcation is reduced in a purely cortical system, but can be either increased or decreased in the corticothalamic case, depending on the initial state. Estimates of critical variance scalings near saddle-node bifurcation are also found, including physiologically based normalizations and new scalings for mean firing rate and the position of the bifurcation.

  13. Variance estimation for stratified propensity score estimators.

    PubMed

    Williamson, E J; Morley, R; Lucas, A; Carpenter, J R

    2012-07-10

    Propensity score methods are increasingly used to estimate the effect of a treatment or exposure on an outcome in non-randomised studies. We focus on one such method, stratification on the propensity score, comparing it with the method of inverse-probability weighting by the propensity score. The propensity score--the conditional probability of receiving the treatment given observed covariates--is usually an unknown probability estimated from the data. Estimators for the variance of treatment effect estimates typically used in practice, however, do not take into account that the propensity score itself has been estimated from the data. By deriving the asymptotic marginal variance of the stratified estimate of treatment effect, correctly taking into account the estimation of the propensity score, we show that routinely used variance estimators are likely to produce confidence intervals that are too conservative when the propensity score model includes variables that predict (cause) the outcome, but only weakly predict the treatment. In contrast, a comparison with the analogous marginal variance for the inverse probability weighted (IPW) estimator shows that routinely used variance estimators for the IPW estimator are likely to produce confidence intervals that are almost always too conservative. Because exact calculation of the asymptotic marginal variance is likely to be complex, particularly for the stratified estimator, we suggest that bootstrap estimates of variance should be used in practice.

  14. Genetic variation of individual alpha frequency (IAF) and alpha power in a large adolescent twin sample.

    PubMed

    Smit, Christine M; Wright, Margaret J; Hansell, Narelle K; Geffen, Gina M; Martin, Nicholas G

    2006-08-01

    To further clarify the mode of genetic transmission on individual alpha frequency (IAF) and alpha power, the extent to which individual differences in these alpha indices are influenced by genetic factors were examined in a large sample of adolescent twins (237 MZ, 282 DZ pairs; aged 16). EEG was measured at rest (eyes closed) from the right occipital site, and a second EEG recording for 50 twin pairs obtained approximately 3 months after the initial collection, enabled an estimation of measurement error. Analyses confirmed a strong genetic influence on both IAF (h(2)=0.81) and alpha power (h(2)=0.82), and there was little support for non-additive genetic (dominance) variance. A small but significant negative correlation (-0.18) was found between IAF and alpha power, but genetic influences on IAF and alpha power were largely independent. All non-genetic variance was due to unreliability, with no significant variance attributed to unique environmental factors. Relationships between the alpha and IQ indices were also explored but were generally either non-significant or very low. The findings confirm the high heritability for both IAF and alpha power, they further suggest that the mode of genetic transmission is due to additive genetic factors, that genetic influences on the underlying neural mechanisms of alpha frequency and power are largely specific, and that individual differences in alpha activity are influenced little by developmental plasticity and individual experiences.

  15. Genetic studies: dominant lethal study, sex linked recessive lethal, ames mutagenicity, and heritable translocation test of thermal processed, frozen, electron irradiated, and gamma irradiated chicken. Final report Jun 76-Aug 83

    SciTech Connect

    Sullivan, D.; Lusskin, R.M.; Thomson, G.M.; Kuzdas, C.D.; Ronning, D.C.

    1983-01-01

    Four samples of chicken meat identified as the frozen control, thermally processed, gamma sterilized (5.9 Mrad), and electron sterilized (5.9 MeV), along with negative and positive controls, were evaluated for genetic activity. The samples were evaluated for ability to induce dominant lethal mutations in spermatid and spermatozoan stages of spermatogenesis in mice fed 35 percent chicken meat. The test meat samples were not observed to have an effect on the incidence of the dominant lethal mutations. However, the positive control failed to give a positive response. The meat samples were investigated for mutagenic activity employing Drosophila melanogaster in the sex linked recessive lethal test. The samples were determined to be nonmutagenic in this test and the positive control gave a significant response. Reduced production of offspring in cultures of Drosophila reared on gamma irradiated chicken which could not be overcome by the addition of vitamins was observed. Pre-incubation tests with and without added mutagens revealed that in no case was a positive result observed in the Ames test from chicken meat without an added mutagen. The manner in which chicken meat was processed had no effect upon the response to the Ames test. A heritable translocation test in mice failed to reveal any cytological evidence of translocation heterozygosity in any of the chicken-containing diets.

  16. [Genetics and genetic counseling].

    PubMed

    Izzi, Claudia; Liut, Francesca; Dallera, Nadia; Mazza, Cinzia; Magistroni, Riccardo; Savoldi, Gianfranco; Scolari, Francesco

    2016-01-01

    Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most frequent genetic disease, characterized by progressive development of bilateral renal cysts. Two causative genes have been identified: PKD1 and PKD2. ADPKD phenotype is highly variable. Typically, ADPKD is an adult onset disease. However, occasionally, ADPKD manifests as very early onset disease. The phenotypic variability of ADPKD can be explained at three genetic levels: genic, allelic and gene modifier effects. Recent advances in molecular screening for PKD gene mutations and the introduction of the new next generation sequencing (NGS)- based genotyping approach have generated considerable improvement regarding the knowledge of genetic basis of ADPKD. The purpose of this article is to provide a comprehensive review of the genetics of ADPKD, focusing on new insights in genotype-phenotype correlation and exploring novel clinical approach to genetic testing. Evaluation of these new genetic information requires a multidisciplinary approach involving a nephrologist and a clinical geneticist.

  17. Reducing variance in batch partitioning measurements

    SciTech Connect

    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.

  18. 78 FR 14122 - Revocation of Permanent Variances

    Federal Register 2010, 2011, 2012, 2013, 2014

    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...

  19. 40 CFR 59.206 - Variances.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Consumer Products § 59.206 Variances. (a) Any regulated entity who...

  20. 40 CFR 59.206 - Variances.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Consumer Products § 59.206 Variances. (a) Any regulated entity who...

  1. 40 CFR 59.206 - Variances.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Consumer Products § 59.206 Variances. (a) Any regulated entity who...

  2. 40 CFR 59.206 - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Consumer Products § 59.206 Variances. (a) Any regulated entity who...

  3. 40 CFR 59.206 - Variances.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Consumer Products § 59.206 Variances. (a) Any regulated entity who...

  4. Using pooled data to estimate variance components and breeding values for traits affected by social interactions

    PubMed Central

    2013-01-01

    Background Through social interactions, individuals affect one another’s phenotype. In such cases, an individual’s phenotype is affected by the direct (genetic) effect of the individual itself and the indirect (genetic) effects of the group mates. Using data on individual phenotypes, direct and indirect genetic (co)variances can be estimated. Together, they compose the total genetic variance that determines a population’s potential to respond to selection. However, it can be difficult or expensive to obtain individual phenotypes. Phenotypes on traits such as egg production and feed intake are, therefore, often collected on group level. In this study, we investigated whether direct, indirect and total genetic variances, and breeding values can be estimated from pooled data (pooled by group). In addition, we determined the optimal group composition, i.e. the optimal number of families represented in a group to minimise the standard error of the estimates. Methods This study was performed in three steps. First, all research questions were answered by theoretical derivations. Second, a simulation study was conducted to investigate the estimation of variance components and optimal group composition. Third, individual and pooled survival records on 12 944 purebred laying hens were analysed to investigate the estimation of breeding values and response to selection. Results Through theoretical derivations and simulations, we showed that the total genetic variance can be estimated from pooled data, but the underlying direct and indirect genetic (co)variances cannot. Moreover, we showed that the most accurate estimates are obtained when group members belong to the same family. Additional theoretical derivations and data analyses on survival records showed that the total genetic variance and breeding values can be estimated from pooled data. Moreover, the correlation between the estimated total breeding values obtained from individual and pooled data was surprisingly

  5. Phonocardiographic diagnosis of aortic ball variance.

    PubMed

    Hylen, J C; Kloster, F E; Herr, R H; Hull, P Q; Ames, A W; Starr, A; Griswold, H E

    1968-07-01

    Fatty infiltration causing changes in the silastic poppet of the Model 1000 series Starr-Edwards aortic valve prostheses (ball variance) has been detected with increasing frequency and can result in sudden death. Phonocardiograms were recorded on 12 patients with ball variance confirmed by operation and of 31 controls. Ten of the 12 patients with ball variance were distinguished from the controls by an aortic opening sound (AO) less than half as intense as the aortic closure sound (AC) at the second right intercostal space (AO/AC ratio less than 0.5). Both AO and AC were decreased in two patients with ball variance, with the loss of the characteristic high frequency and amplitude of these sounds. The only patient having a diminished AO/AC ratio (0.42) without ball variance at reoperation had a clot extending over the aortic valve struts. The phonocardiographic findings have been the most reliable objective evidence of ball variance in patients with Starr-Edwards aortic prosthesis of the Model 1000 series.

  6. Novel Use of Derived Genotype Probabilities to Discover Significant Dominance Effects for Milk Production Traits in Dairy Cattle

    PubMed Central

    Boysen, Teide-Jens; Heuer, Claas; Tetens, Jens; Reinhardt, Fritz; Thaller, Georg

    2013-01-01

    The estimation of dominance effects requires the availability of direct phenotypes, i.e., genotypes and phenotypes in the same individuals. In dairy cattle, classical QTL mapping approaches are, however, relying on genotyped sires and daughter-based phenotypes like breeding values. Thus, dominance effects cannot be estimated. The number of dairy bulls genotyped for dense genome-wide marker panels is steadily increasing in the context of genomic selection schemes. The availability of genotyped cows is, however, limited. Within the current study, the genotypes of male ancestors were applied to the calculation of genotype probabilities in cows. Together with the cows’ phenotypes, these probabilities were used to estimate dominance effects on a genome-wide scale. The impact of sample size, the depth of pedigree used in deriving genotype probabilities, the linkage disequilibrium between QTL and marker, the fraction of variance explained by the QTL, and the degree of dominance on the power to detect dominance were analyzed in simulation studies. The effect of relatedness among animals on the specificity of detection was addressed. Furthermore, the approach was applied to a real data set comprising 470,000 Holstein cows. To account for relatedness between animals a mixed-model two-step approach was used to adjust phenotypes based on an additive genetic relationship matrix. Thereby, considerable dominance effects were identified for important milk production traits. The approach might serve as a powerful tool to dissect the genetic architecture of performance and functional traits in dairy cattle. PMID:23222654

  7. Genetics Home Reference: autosomal dominant vitreoretinochoroidopathy

    MedlinePlus

    ... a channel that transports charged chlorine atoms (chloride ions) across the cell membrane. Mutations in the BEST1 ... clear how these versions of bestrophin affect chloride ion transport or lead to the eye abnormalities characteristic ...

  8. Genetics Home Reference: autosomal dominant hypocalcemia

    MedlinePlus

    ... hormone (hypoparathyroidism). This hormone is involved in the regulation of calcium levels in the blood. Abnormal levels ... that increase calcium can also disrupt the normal regulation of other molecules, such as phosphate and magnesium, ...

  9. Accounting for additive genetic mutations on litter size in Ripollesa sheep.

    PubMed

    Casellas, J; Caja, G; Piedrafita, J

    2010-04-01

    Little is known about mutational variability in livestock, among which only a few mutations with relatively large effects have been reported. In this manuscript, mutational variability was analyzed in 1,765 litter size records from 404 Ripollesa ewes to characterize the magnitude of this genetic source of variation and check the suitability of including mutational effects in genetic evaluations of this breed. Threshold animal models accounting for additive genetic mutations were preferred to models without mutational contributions, with an average difference in the deviance information criterion of more than 5 units. Moreover, the statistical relevance of the additive genetic mutation term was checked through a Bayes factor approach, which showed that the models with mutational variability were 8.5 to 22.7 times more probable than the others. The mutational heritability (percentage of the phenotypic variance accounted for by mutational variance) was 0.6 or 0.9%, depending on whether genetic dominance effects were accounted for by the analytical model. The inclusion of mutational effects in the genetic model for evaluating litter size in Ripollesa ewes called for some minor modifications in the genetic merit order of the individuals evaluated, which suggested that the continuous uploading of new additive mutations could be taken into account to optimize the selection scheme. This study is the first attempt to estimate mutational variances in a livestock species and thereby contribute to better characterization of the genetic background of productive traits of interest.

  10. Discrimination of frequency variance for tonal sequences.

    PubMed

    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.

  11. Variance estimation for nucleotide substitution models.

    PubMed

    Chen, Weishan; Wang, Hsiuying

    2015-09-01

    The current variance estimators for most evolutionary models were derived when a nucleotide substitution number estimator was approximated with a simple first order Taylor expansion. In this study, we derive three variance estimators for the F81, F84, HKY85 and TN93 nucleotide substitution models, respectively. They are obtained using the second order Taylor expansion of the substitution number estimator, the first order Taylor expansion of a squared deviation and the second order Taylor expansion of a squared deviation, respectively. These variance estimators are compared with the existing variance estimator in terms of a simulation study. It shows that the variance estimator, which is derived using the second order Taylor expansion of a squared deviation, is more accurate than the other three estimators. In addition, we also compare these estimators with an estimator derived by the bootstrap method. The simulation shows that the performance of this bootstrap estimator is similar to the estimator derived by the second order Taylor expansion of a squared deviation. Since the latter one has an explicit form, it is more efficient than the bootstrap estimator.

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

    PubMed

    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.

  13. Fitted Hanbury-Brown-Twiss radii versus space-time variances in flow-dominated models

    SciTech Connect

    Frodermann, Evan; Heinz, Ulrich; Lisa, Michael Annan

    2006-04-15

    The inability of otherwise successful dynamical models to reproduce the Hanbury-Brown-Twiss (HBT) radii extracted from two-particle correlations measured at the Relativistic Heavy Ion Collider (RHIC) is known as the RHIC HBT Puzzle. Most comparisons between models and experiment exploit the fact that for Gaussian sources the HBT radii agree with certain combinations of the space-time widths of the source that can be directly computed from the emission function without having to evaluate, at significant expense, the two-particle correlation function. We here study the validity of this approach for realistic emission function models, some of which exhibit significant deviations from simple Gaussian behavior. By Fourier transforming the emission function, we compute the two-particle correlation function, and fit it with a Gaussian to partially mimic the procedure used for measured correlation functions. We describe a novel algorithm to perform this Gaussian fit analytically. We find that for realistic hydrodynamic models the HBT radii extracted from this procedure agree better with the data than the values previously extracted from the space-time widths of the emission function. Although serious discrepancies between the calculated and the measured HBT radii remain, we show that a more apples-to-apples comparison of models with data can play an important role in any eventually successful theoretical description of RHIC HBT data.

  14. Fitted Hanbury-Brown Twiss radii versus space-time variances in flow-dominated models

    NASA Astrophysics Data System (ADS)

    Frodermann, Evan; Heinz, Ulrich; Lisa, Michael Annan

    2006-04-01

    The inability of otherwise successful dynamical models to reproduce the Hanbury-Brown Twiss (HBT) radii extracted from two-particle correlations measured at the Relativistic Heavy Ion Collider (RHIC) is known as the RHIC HBT Puzzle. Most comparisons between models and experiment exploit the fact that for Gaussian sources the HBT radii agree with certain combinations of the space-time widths of the source that can be directly computed from the emission function without having to evaluate, at significant expense, the two-particle correlation function. We here study the validity of this approach for realistic emission function models, some of which exhibit significant deviations from simple Gaussian behavior. By Fourier transforming the emission function, we compute the two-particle correlation function, and fit it with a Gaussian to partially mimic the procedure used for measured correlation functions. We describe a novel algorithm to perform this Gaussian fit analytically. We find that for realistic hydrodynamic models the HBT radii extracted from this procedure agree better with the data than the values previously extracted from the space-time widths of the emission function. Although serious discrepancies between the calculated and the measured HBT radii remain, we show that a more apples-to-apples comparison of models with data can play an important role in any eventually successful theoretical description of RHIC HBT data.

  15. Integrating Variances into an Analytical Database

    NASA Technical Reports Server (NTRS)

    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.

  16. Genetics (image)

    MedlinePlus

    ... chromosomes to their child, 22 autosomal and 1 sex chromosome. The inheritance of genetic diseases, abnormalities, or traits ... chromosome the abnormal gene resides on (autosomal or sex chromosome), and by whether the gene itself is dominant ...

  17. Variance in binary stellar population synthesis

    NASA Astrophysics Data System (ADS)

    Breivik, Katelyn; Larson, Shane L.

    2016-03-01

    In the years preceding LISA, Milky Way compact binary population simulations can be used to inform the science capabilities of the mission. Galactic population simulation efforts generally focus on high fidelity models that require extensive computational power to produce a single simulated population for each model. Each simulated population represents an incomplete sample of the functions governing compact binary evolution, thus introducing variance from one simulation to another. We present a rapid Monte Carlo population simulation technique that can simulate thousands of populations in less than a week, thus allowing a full exploration of the variance associated with a binary stellar evolution model.

  18. Genetic diagnosis of X-linked dominant hypophosphatemic rickets in a cohort study: Tubular reabsorption of phosphate and 1,25(OH)2D serum levels are associated with PHEX mutation type

    PubMed Central

    2011-01-01

    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(OH)2D) 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(OH)2D 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(OH)2D levels suggesting that the PHEX type of mutation might predict the XLHR phenotype severity. PMID

  19. A Simple Algorithm for Approximating Confidence on the Modified Allan Variance and the Time Variance

    NASA Technical Reports Server (NTRS)

    Weiss, Marc A.; Greenhall, Charles A.

    1996-01-01

    An approximating algorithm for computing equvalent degrees of freedom of the Modified Allan Variance and its square root, the Modified Allan Deviation (MVAR and MDEV), and the Time Variance and Time Deviation (TVAR and TDEV) is presented, along with an algorithm for approximating the inverse chi-square distribution.

  20. Testing Interaction Effects without Discarding Variance.

    ERIC Educational Resources Information Center

    Lopez, Kay A.

    Analysis of variance (ANOVA) and multiple regression are two of the most commonly used methods of data analysis in behavioral science research. Although ANOVA was intended for use with experimental designs, educational researchers have used ANOVA extensively in aptitude-treatment interaction (ATI) research. This practice tends to make researchers…

  1. 29 CFR 1920.2 - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 7 2010-07-01 2010-07-01 false Variances. 1920.2 Section 1920.2 Labor Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR (CONTINUED) PROCEDURE FOR VARIATIONS FROM SAFETY AND HEALTH REGULATIONS UNDER THE LONGSHOREMEN'S AND HARBOR...

  2. 21 CFR 1010.4 - Variances.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... Dockets Management, except for information regarded as confidential under section 537(e) of the act. (d... Management (HFA-305), Food and Drug Administration, 5630 Fishers Lane, rm. 1061, Rockville, MD 20852. (1) The application for variance shall include the following information: (i) A description of the product and...

  3. Formative Use of Intuitive Analysis of Variance

    ERIC Educational Resources Information Center

    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 both…

  4. Understanding gender variance in children and adolescents.

    PubMed

    Simons, Lisa K; Leibowitz, Scott F; Hidalgo, Marco A

    2014-06-01

    Gender variance is an umbrella term used to describe gender identity, expression, or behavior that falls outside of culturally defined norms associated with a specific gender. In recent years, growing media coverage has heightened public awareness about gender variance in childhood and adolescence, and an increasing number of referrals to clinics specializing in care for gender-variant youth have been reported in the United States. Gender-variant expression, behavior, and identity may present in childhood and adolescence in a number of ways, and youth with gender variance have unique health needs. For those experiencing gender dysphoria, or distress encountered by the discordance between biological sex and gender identity, puberty is often an exceptionally challenging time. Pediatric primary care providers may be families' first resource for education and support, and they play a critical role in supporting the health of youth with gender variance by screening for psychosocial problems and health risks, referring for gender-specific mental health and medical care, and providing ongoing advocacy and support.

  5. 10 CFR 1021.343 - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Variances. 1021.343 Section 1021.343 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS) NATIONAL ENVIRONMENTAL POLICY ACT IMPLEMENTING PROCEDURES Implementing... arrangements for emergency actions having significant environmental impacts. DOE shall document,...

  6. 21 CFR 1010.4 - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... the study was conducted in compliance with the good laboratory practice regulations set forth in part... application for variance shall include the following information: (i) A description of the product and its... equipment, the proposed location of each unit. (viii) Such other information required by regulation or...

  7. Parameterization of Incident and Infragravity Swash Variance

    NASA Astrophysics Data System (ADS)

    Stockdon, H. F.; Holman, R. A.; Sallenger, A. H.

    2002-12-01

    By clearly defining the forcing and morphologic controls of swash variance in both the incident and infragravity frequency bands, we are able to derive a more complete parameterization for extreme runup that may be applicable to a wide range of beach and wave conditions. It is expected that the dynamics of the incident and infragravity bands will have different dependencies on offshore wave conditions and local beach slopes. For example, previous studies have shown that swash variance in the incident band depends on foreshore beach slope while the infragravity variance depends more on a weighted mean slope across the surf zone. Because the physics of each band is parameterized differently, the amount that each frequency band contributes to the total swash variance will vary from site to site and, often, at a single site as the profile configuration changes over time. Using water level time series (measured at the shoreline) collected during nine dynamically different field experiments, we test the expected behavior of both incident and infragravity swash and the contribution each makes to total variance. At the dissipative sites (Iribarren number, \\xi0, <0.3) located in Oregon and the Netherlands, the incident band swash is saturated with respect to offshore wave height. Conversely, on the intermediate and reflective beaches, the amplitudes of both incident and infragravity swash variance grow with increasing offshore wave height. While infragravity band swash at all sites appears to increase linearly with offshore wave height, the magnitudes of the response are somewhat greater on reflective beaches than on dissipative beaches. This means that for the same offshore wave conditions the swash on a steeper foreshore will be larger than that on a more gently sloping foreshore. The potential control of the surf zone slope on infragravity band swash is examined at Duck, North Carolina, (0.3 < \\xi0 < 4.0), where significant differences in the relationship between swash

  8. 42 CFR 456.525 - Request for renewal of variance.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS UTILIZATION CONTROL Utilization Review Plans: FFP, Waivers, and Variances for Hospitals and Mental Hospitals Ur Plan: Remote Facility Variances from...

  9. 42 CFR 456.525 - Request for renewal of variance.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS UTILIZATION CONTROL Utilization Review Plans: FFP, Waivers, and Variances for Hospitals and Mental Hospitals Ur Plan: Remote Facility Variances from...

  10. 42 CFR 456.521 - Conditions for granting variance requests.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS UTILIZATION CONTROL Utilization Review Plans: FFP, Waivers, and Variances for Hospitals and Mental Hospitals Ur Plan: Remote Facility Variances from...

  11. 42 CFR 456.521 - Conditions for granting variance requests.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS UTILIZATION CONTROL Utilization Review Plans: FFP, Waivers, and Variances for Hospitals and Mental Hospitals Ur Plan: Remote Facility Variances from...

  12. Evolutionary genetics of maternal effects

    PubMed Central

    Wolf, Jason B.; Wade, Michael J.

    2016-01-01

    Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single‐locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype‐phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype‐phenotype relationship frequency dependent, resulting in the appearance of negative frequency‐dependent selection, while additive MGEs contribute a component of parent‐of‐origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be “available” to the evolving population. PMID:26969266

  13. Minimum Variance Approaches to Ultrasound Pixel-Based Beamforming.

    PubMed

    Nguyen, Nghia Q; Prager, Richard W

    2017-02-01

    We analyze the principles underlying minimum variance distortionless response (MVDR) beamforming in order to integrate it into a pixel-based algorithm. There is a challenge posed by the low echo signal-to-noise ratio (eSNR) when calculating beamformer contributions at pixels far away from the beam centreline. Together with the well-known scarcity of samples for covariance matrix estimation, this reduces the beamformer performance and degrades the image quality. To address this challenge, we implement the MVDR algorithm in two different ways. First, we develop the conventional minimum variance pixel-based (MVPB) beamformer that performs the MVDR after the pixel-based superposition step. This involves a combination of methods in the literature, extended over multiple transmits to increase the eSNR. Then we propose the coherent MVPB beamformer, where the MVDR is applied to data within individual transmits. Based on pressure field analysis, we develop new algorithms to improve the data alignment and matrix estimation, and hence overcome the low-eSNR issue. The methods are demonstrated on data acquired with an ultrasound open platform. The results show the coherent MVPB beamformer substantially outperforms the conventional MVPB in a series of experiments, including phantom and in vivo studies. Compared to the unified pixel-based beamformer, the newest delay-and-sum algorithm in [1], the coherent MVPB performs well on regions that conform to the diffuse scattering assumptions on which the minimum variance principles are based. It produces less good results for parts of the image that are dominated by specular reflections.

  14. Testcross additive and dominance effects in best linear unbiased prediction of maize single-cross performance.

    PubMed

    Bernardo, R

    1996-11-01

    Best linear unbiased prediction (BLUP) has been found to be useful in maize (Zea mays L.) breeding. The advantage of including both testcross additive and dominance effects (Intralocus Model) in BLUP, rather than only testcross additive effects (Additive Model), has not been clearly demonstrated. The objective of this study was to compare the usefulness of Intralocus and Additive Models for BLUP of maize single-cross performance. Multilocation data from 1990 to 1995 were obtained from the hybrid testing program of Limagrain Genetics. Grain yield, moisture, stalk lodging, and root lodging of untested single crosses were predicted from (1) the performance of tested single crosses and (2) known genetic relationships among the parental inbreds. Correlations between predicted and observed performance were obtained with a delete-one cross-validation procedure. For the Intralocus Model, the correlations ranged from 0.50 to 0.66 for yield, 0.88 to 0.94 for moisture, 0.47 to 0.69 for stalk lodging, and 0.31 to 0.45 for root lodging. The BLUP procedure was consistently more effective with the Intralocus Model than with the Additive Model. When the Additive Model was used instead of the Intralocus Model, the reductions in the correlation were largest for root lodging (0.06-0.35), smallest for moisture (0.00-0.02), and intermediate for yield (0.02-0.06) and stalk lodging (0.02-0.08). The ratio of dominance variance (v D) to total genetic variance (v G) was highest for root lodging (0.47) and lowest for moisture (0.10). The Additive Model may be used if prior information indicates that VD for a given trait has little contribution to VG. Otherwise, the continued use of the Intralocus Model for BLUP of single-cross performance is recommended.

  15. INTERPRETING MAGNETIC VARIANCE ANISOTROPY MEASUREMENTS IN THE SOLAR WIND

    SciTech Connect

    TenBarge, J. M.; Klein, K. G.; Howes, G. G.; Podesta, J. J.

    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.

  16. Analysis of variance of microarray data.

    PubMed

    Ayroles, Julien F; Gibson, Greg

    2006-01-01

    Analysis of variance (ANOVA) is an approach used to identify differentially expressed genes in complex experimental designs. It is based on testing for the significance of the magnitude of effect of two or more treatments taking into account the variance within and between treatment classes. ANOVA is a highly flexible analytical approach that allows investigators to simultaneously assess the contributions of multiple factors to gene expression variation, including technical (dye, batch) effects and biological (sex, genotype, drug, time) ones, as well as interactions between factors. This chapter provides an overview of the theory of linear mixture modeling and the sequence of steps involved in fitting gene-specific models and discusses essential features of experimental design. Commercial and open-source software for performing ANOVA is widely available.

  17. Analysis of Variance of Multiply Imputed Data.

    PubMed

    van Ginkel, Joost R; Kroonenberg, Pieter M

    2014-01-01

    As a procedure for handling missing data, Multiple imputation consists of estimating the missing data multiple times to create several complete versions of an incomplete data set. All these data sets are analyzed by the same statistical procedure, and the results are pooled for interpretation. So far, no explicit rules for pooling F-tests of (repeated-measures) analysis of variance have been defined. In this paper we outline the appropriate procedure for the results of analysis of variance for multiply imputed data sets. It involves both reformulation of the ANOVA model as a regression model using effect coding of the predictors and applying already existing combination rules for regression models. The proposed procedure is illustrated using three example data sets. The pooled results of these three examples provide plausible F- and p-values.

  18. Systems Engineering Programmatic Estimation Using Technology Variance

    NASA Technical Reports Server (NTRS)

    Mog, Robert A.

    2000-01-01

    Unique and innovative system programmatic estimation is conducted using the variance of the packaged technologies. Covariance analysis is performed on the subsystems and components comprising the system of interest. Technological "return" and "variation" parameters are estimated. These parameters are combined with the model error to arrive at a measure of system development stability. The resulting estimates provide valuable information concerning the potential cost growth of the system under development.

  19. Systems Engineering Programmatic Estimation Using Technology Variance

    NASA Technical Reports Server (NTRS)

    Mog, Robert A.

    2000-01-01

    Unique and innovative system programmatic estimation is conducted using the variance of the packaged technologies. Covariance analysis is performed oil the subsystems and components comprising the system of interest. Technological "returns" and "variation" parameters, are estimated. These parameters are combined with the model error to arrive at a measure of system development stability. The resulting estimates provide valuable information concerning the potential cost growth of the system under development.

  20. Directional variance analysis of annual rings

    NASA Astrophysics Data System (ADS)

    Kumpulainen, P.; Marjanen, K.

    2010-07-01

    The wood quality measurement methods are of increasing importance in the wood industry. The goal is to produce more high quality products with higher marketing value than is produced today. One of the key factors for increasing the market value is to provide better measurements for increased information to support the decisions made later in the product chain. Strength and stiffness are important properties of the wood. They are related to mean annual ring width and its deviation. These indicators can be estimated from images taken from the log ends by two-dimensional power spectrum analysis. The spectrum analysis has been used successfully for images of pine. However, the annual rings in birch, for example are less distinguishable and the basic spectrum analysis method does not give reliable results. A novel method for local log end variance analysis based on Radon-transform is proposed. The directions and the positions of the annual rings can be estimated from local minimum and maximum variance estimates. Applying the spectrum analysis on the maximum local variance estimate instead of the original image produces more reliable estimate of the annual ring width. The proposed method is not limited to log end analysis only. It is usable in other two-dimensional random signal and texture analysis tasks.

  1. Variance and skewness in the FIRST survey

    NASA Astrophysics Data System (ADS)

    Magliocchetti, M.; Maddox, S. J.; Lahav, O.; Wall, J. V.

    1998-10-01

    We investigate the large-scale clustering of radio sources in the FIRST 1.4-GHz survey by analysing the distribution function (counts in cells). We select a reliable sample from the the FIRST catalogue, paying particular attention to the problem of how to define single radio sources from the multiple components listed. We also consider the incompleteness of the catalogue. We estimate the angular two-point correlation function w(theta), the variance Psi_2 and skewness Psi_3 of the distribution for the various subsamples chosen on different criteria. Both w(theta) and Psi_2 show power-law behaviour with an amplitude corresponding to a spatial correlation length of r_0~10h^-1Mpc. We detect significant skewness in the distribution, the first such detection in radio surveys. This skewness is found to be related to the variance through Psi_3=S_3(Psi_2)^alpha, with alpha=1.9+/-0.1, consistent with the non-linear gravitational growth of perturbations from primordial Gaussian initial conditions. We show that the amplitude of variance and the skewness are consistent with realistic models of galaxy clustering.

  2. Hypothesis exploration with visualization of variance

    PubMed Central

    2014-01-01

    Background The Consortium for Neuropsychiatric Phenomics (CNP) at UCLA was an investigation into the biological bases of traits such as memory and response inhibition phenotypes—to explore whether they are linked to syndromes including ADHD, Bipolar disorder, and Schizophrenia. An aim of the consortium was in moving from traditional categorical approaches for psychiatric syndromes towards more quantitative approaches based on large-scale analysis of the space of human variation. It represented an application of phenomics—wide-scale, systematic study of phenotypes—to neuropsychiatry research. Results This paper reports on a system for exploration of hypotheses in data obtained from the LA2K, LA3C, and LA5C studies in CNP. ViVA is a system for exploratory data analysis using novel mathematical models and methods for visualization of variance. An example of these methods is called VISOVA, a combination of visualization and analysis of variance, with the flavor of exploration associated with ANOVA in biomedical hypothesis generation. It permits visual identification of phenotype profiles—patterns of values across phenotypes—that characterize groups. Visualization enables screening and refinement of hypotheses about variance structure of sets of phenotypes. Conclusions The ViVA system was designed for exploration of neuropsychiatric hypotheses by interdisciplinary teams. Automated visualization in ViVA supports ‘natural selection’ on a pool of hypotheses, and permits deeper understanding of the statistical architecture of the data. Large-scale perspective of this kind could lead to better neuropsychiatric diagnostics. PMID:25097666

  3. Variance Reduction Factor of Nuclear Data for Integral Neutronics Parameters

    SciTech Connect

    Chiba, G. Tsuji, M.; Narabayashi, T.

    2015-01-15

    We propose a new quantity, a variance reduction factor, to identify nuclear data for which further improvements are required to reduce uncertainties of target integral neutronics parameters. Important energy ranges can be also identified with this variance reduction factor. Variance reduction factors are calculated for several integral neutronics parameters. The usefulness of the variance reduction factors is demonstrated.

  4. Impact of fitting dominance and additive effects on accuracy of genomic prediction of breeding values in layers.

    PubMed

    Heidaritabar, M; Wolc, A; Arango, J; Zeng, J; Settar, P; Fulton, J E; O'Sullivan, N P; Bastiaansen, J W M; Fernando, R L; Garrick, D J; Dekkers, J C M

    2016-10-01

    Most genomic prediction studies fit only additive effects in models to estimate genomic breeding values (GEBV). However, if dominance genetic effects are an important source of variation for complex traits, accounting for them may improve the accuracy of GEBV. We investigated the effect of fitting dominance and additive effects on the accuracy of GEBV for eight egg production and quality traits in a purebred line of brown layers using pedigree or genomic information (42K single-nucleotide polymorphism (SNP) panel). Phenotypes were corrected for the effect of hatch date. Additive and dominance genetic variances were estimated using genomic-based [genomic best linear unbiased prediction (GBLUP)-REML and BayesC] and pedigree-based (PBLUP-REML) methods. Breeding values were predicted using a model that included both additive and dominance effects and a model that included only additive effects. The reference population consisted of approximately 1800 animals hatched between 2004 and 2009, while approximately 300 young animals hatched in 2010 were used for validation. Accuracy of prediction was computed as the correlation between phenotypes and estimated breeding values of the validation animals divided by the square root of the estimate of heritability in the whole population. The proportion of dominance variance to total phenotypic variance ranged from 0.03 to 0.22 with PBLUP-REML across traits, from 0 to 0.03 with GBLUP-REML and from 0.01 to 0.05 with BayesC. Accuracies of GEBV ranged from 0.28 to 0.60 across traits. Inclusion of dominance effects did not improve the accuracy of GEBV, and differences in their accuracies between genomic-based methods were small (0.01-0.05), with GBLUP-REML yielding higher prediction accuracies than BayesC for egg production, egg colour and yolk weight, while BayesC yielded higher accuracies than GBLUP-REML for the other traits. In conclusion, fitting dominance effects did not impact accuracy of genomic prediction of breeding values in

  5. Gaining Cyber Dominance

    DTIC Science & Technology

    2015-01-01

    2014 Carnegie Mellon University Gaining Cyber Dominance Software Engineering Institute Carnegie Mellon University NETCOM G3/5/7 TREX January 2015...JAN 2015 2. REPORT TYPE N/A 3. DATES COVERED 4. TITLE AND SUBTITLE Gaining Cyber Dominance 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c...2014) 4 GCD Overview January 2015 © 2014 Carnegie Mellon University FY15 Initiatives Gaining Cyber Dominance Program • Army topology development

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

    NASA Technical Reports Server (NTRS)

    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.

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

    SciTech Connect

    Phillips, K.; Matheny, A.P. Jr.

    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.

  8. Minimum variance and variance of outgoing quality limit MDS-1(c1, c2) plans

    NASA Astrophysics Data System (ADS)

    Raju, C.; Vidya, R.

    2016-06-01

    In this article, the outgoing quality (OQ) and total inspection (TI) of multiple deferred state sampling plans MDS-1(c1,c2) are studied. It is assumed that the inspection is rejection rectification. Procedures for designing MDS-1(c1,c2) sampling plans with minimum variance of OQ and TI are developed. A procedure for obtaining a plan for a designated upper limit for the variance of the OQ (VOQL) is outlined.

  9. Gravity Wave Variance in LIMS Temperatures. Part II: Comparison with the Zonal-Mean Momentum Balance.

    NASA Astrophysics Data System (ADS)

    Fetzer, Eric J.; Gille, John C.

    1996-02-01

    Zonal-mean gravity wave variance in the Limb Infrared Monitor of the Stratosphere (LIMS) temperature data is seen to correlate strongly with the residual term in the LIMS zonal-mean momentum budget throughout much of the observed mesosphere. This momentum residual is attributed to gravity wave momentum transport at scales that cannot be directly sampled by the LIMS instrument Correlation is highest in the vicinity of the fall and winter mesospheric jets, where both gravity wave variance and momentum residual reach their largest values. Correlation is also high in the Southern Hemisphere subtropical mesophere, where gravity wave variance and the momentum residual have broad temporal maxima during the easterly acceleration of the stratopause semi-annual oscillation (SAO). This subtropical correlation has important implications for the SAO eastward acceleration, which several studies suggest is forced by gravity wave momentum flux divergence. Correlation between gravity wave variance and inferred gravity wave momentum flux divergence is unexpected because variance is dominated by large scales and long periods (inertio-gravity waves), while both theoretical arguments and ground-based observations indicate that momentum transport is dominated by periods under 1 h. The results of this study suggest a broadband gravity wave field experiencing forcing and loss processes, which are largely independent of frequency.

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

    PubMed

    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

  11. Variance of high contrast textures is sensed using negative half-wave rectification.

    PubMed

    Chubb, C; Nam, J H

    2000-01-01

    A rectifying transformation is required to sense variations in texture contrast. Various theoretical and practical considerations have inclined researchers to suppose that this rectification is full-wave, rather than half-wave. In the studies reported here, observers are asked to judge which of two texture patches has higher texture variance. Textures are composed of small squares, with each square being painted with one of nine different luminances. Different texture variances are achieved by manipulating the histograms of the texture patches to be compared. When the nine luminances range linearly from 0 to 160 cd/m(2), the transformation mediating judgments of texture variance takes the form of a negative half-wave rectifier: texture variance judgments are determined exclusively by the frequencies of luminances below mean luminance in the textures being compared. However, when the nine luminances range linearly from 60 to 100 cd/m(2), two of three observers use a full-wave rectifying transformation in making texture variance judgments; the third observer continued to use a negative half-wave rectifier. The unexpectedly asymmetric roles played by low versus high luminances in texture variance judgments suggest that the off-center system may play a dominant role in human perception of texture contrast.

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

    PubMed

    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.

  13. Decomposing genomic variance using information from GWA, GWE and eQTL analysis.

    PubMed

    Ehsani, A; Janss, L; Pomp, D; Sørensen, P

    2016-04-01

    A commonly used procedure in genome-wide association (GWA), genome-wide expression (GWE) and expression quantitative trait locus (eQTL) analyses is based on a bottom-up experimental approach that attempts to individually associate molecular variants with complex traits. Top-down modeling of the entire set of genomic data and partitioning of the overall variance into subcomponents may provide further insight into the genetic basis of complex traits. To test this approach, we performed a whole-genome variance components analysis and partitioned the genomic variance using information from GWA, GWE and eQTL analyses of growth-related traits in a mouse F2 population. We characterized the mouse trait genetic architecture by ordering single nucleotide polymorphisms (SNPs) based on their P-values and studying the areas under the curve (AUCs). The observed traits were found to have a genomic variance profile that differed significantly from that expected of a trait under an infinitesimal model. This situation was particularly true for both body weight and body fat, for which the AUCs were much higher compared with that of glucose. In addition, SNPs with a high degree of trait-specific regulatory potential (SNPs associated with subset of transcripts that significantly associated with a specific trait) explained a larger proportion of the genomic variance than did SNPs with high overall regulatory potential (SNPs associated with transcripts using traditional eQTL analysis). We introduced AUC measures of genomic variance profiles that can be used to quantify relative importance of SNPs as well as degree of deviation of a trait's inheritance from an infinitesimal model. The shape of the curve aids global understanding of traits: The steeper the left-hand side of the curve, the fewer the number of SNPs controlling most of the phenotypic variance.

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

    NASA Astrophysics Data System (ADS)

    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

  15. Visual SLAM Using Variance Grid Maps

    NASA Technical Reports Server (NTRS)

    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

  16. The defect variance of random spherical harmonics

    NASA Astrophysics Data System (ADS)

    Marinucci, Domenico; Wigman, Igor

    2011-09-01

    The defect of a function f:M\\rightarrow {R} is defined as the difference between the measure of the positive and negative regions. In this paper, we begin the analysis of the distribution of defect of random Gaussian spherical harmonics. By an easy argument, the defect is non-trivial only for even degree and the expected value always vanishes. Our principal result is evaluating the defect variance, asymptotically in the high-frequency limit. As other geometric functionals of random eigenfunctions, the defect may be used as a tool to probe the statistical properties of spherical random fields, a topic of great interest for modern cosmological data analysis.

  17. Changes in variance explained by top SNP windows over generations for three traits in broiler chicken

    PubMed Central

    Fragomeni, Breno de Oliveira; Misztal, Ignacy; Lourenco, Daniela Lino; Aguilar, Ignacio; Okimoto, Ronald; Muir, William M.

    2014-01-01

    The purpose of this study was to determine if the set of genomic regions inferred as accounting for the majority of genetic variation in quantitative traits remain stable over multiple generations of selection. The data set contained phenotypes for five generations of broiler chicken for body weight, breast meat, and leg score. The population consisted of 294,632 animals over five generations and also included genotypes of 41,036 single nucleotide polymorphism (SNP) for 4,866 animals, after quality control. The SNP effects were calculated by a GWAS type analysis using single step genomic BLUP approach for generations 1–3, 2–4, 3–5, and 1–5. Variances were calculated for windows of 20 SNP. The top ten windows for each trait that explained the largest fraction of the genetic variance across generations were examined. Across generations, the top 10 windows explained more than 0.5% but less than 1% of the total variance. Also, the pattern of the windows was not consistent across generations. The windows that explained the greatest variance changed greatly among the combinations of generations, with a few exceptions. In many cases, a window identified as top for one combination, explained less than 0.1% for the other combinations. We conclude that identification of top SNP windows for a population may have little predictive power for genetic selection in the following generations for the traits here evaluated. PMID:25324857

  18. Evolution of Robustness and Plasticity under Environmental Fluctuation: Formulation in Terms of Phenotypic Variances

    NASA Astrophysics Data System (ADS)

    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.

  19. Changes in variance explained by top SNP windows over generations for three traits in broiler chicken.

    PubMed

    Fragomeni, Breno de Oliveira; Misztal, Ignacy; Lourenco, Daniela Lino; Aguilar, Ignacio; Okimoto, Ronald; Muir, William M

    2014-01-01

    The purpose of this study was to determine if the set of genomic regions inferred as accounting for the majority of genetic variation in quantitative traits remain stable over multiple generations of selection. The data set contained phenotypes for five generations of broiler chicken for body weight, breast meat, and leg score. The population consisted of 294,632 animals over five generations and also included genotypes of 41,036 single nucleotide polymorphism (SNP) for 4,866 animals, after quality control. The SNP effects were calculated by a GWAS type analysis using single step genomic BLUP approach for generations 1-3, 2-4, 3-5, and 1-5. Variances were calculated for windows of 20 SNP. The top ten windows for each trait that explained the largest fraction of the genetic variance across generations were examined. Across generations, the top 10 windows explained more than 0.5% but less than 1% of the total variance. Also, the pattern of the windows was not consistent across generations. The windows that explained the greatest variance changed greatly among the combinations of generations, with a few exceptions. In many cases, a window identified as top for one combination, explained less than 0.1% for the other combinations. We conclude that identification of top SNP windows for a population may have little predictive power for genetic selection in the following generations for the traits here evaluated.

  20. River meanders - Theory of minimum variance

    USGS Publications Warehouse

    Langbein, Walter Basil; Leopold, Luna Bergere

    1966-01-01

    Meanders are the result of erosion-deposition processes tending toward the most stable form in which the variability of certain essential properties is minimized. This minimization involves the adjustment of the planimetric geometry and the hydraulic factors of depth, velocity, and local slope.The planimetric geometry of a meander is that of a random walk whose most frequent form minimizes the sum of the squares of the changes in direction in each successive unit length. The direction angles are then sine functions of channel distance. This yields a meander shape typically present in meandering rivers and has the characteristic that the ratio of meander length to average radius of curvature in the bend is 4.7.Depth, velocity, and slope are shown by field observations to be adjusted so as to decrease the variance of shear and the friction factor in a meander curve over that in an otherwise comparable straight reach of the same riverSince theory and observation indicate meanders achieve the minimum variance postulated, it follows that for channels in which alternating pools and riffles occur, meandering is the most probable form of channel geometry and thus is more stable geometry than a straight or nonmeandering alinement.

  1. Variance and Skewness in the FIRST Survey

    NASA Astrophysics Data System (ADS)

    Magliocchetti, M.; Maddox, S. J.; Lahav, O.; Wall, J. V.

    We investigate the large-scale clustering of radio sources by analysing the distribution function of the FIRST 1.4 GHz survey. We select a reliable galaxy sample from the FIRST catalogue, paying particular attention to the definition of single radio sources from the multiple components listed in the FIRST catalogue. We estimate the variance, Ψ2, and skewness, Ψ3, of the distribution function for the best galaxy subsample. Ψ2 shows power-law behaviour as a function of cell size, with an amplitude corresponding a spatial correlation length of r0 ~10 h-1 Mpc. We detect significant skewness in the distribution, and find that it is related to the variance through the relation Ψ3 = S3 (Ψ2)α with α = 1.9 +/- 0.1 consistent with the non-linear growth of perturbations from primordial Gaussian initial conditions. We show that the amplitude of clustering (corresponding to a spatial correlation length of r0 ~10 h-1 Mpc) and skewness are consistent with realistic models of galaxy clustering.

  2. Multivariate Granger causality and generalized variance

    NASA Astrophysics Data System (ADS)

    Barrett, Adam B.; Barnett, Lionel; Seth, Anil K.

    2010-04-01

    Granger causality analysis is a popular method for inference on directed interactions in complex systems of many variables. A shortcoming of the standard framework for Granger causality is that it only allows for examination of interactions between single (univariate) variables within a system, perhaps conditioned on other variables. However, interactions do not necessarily take place between single variables but may occur among groups or “ensembles” of variables. In this study we establish a principled framework for Granger causality in the context of causal interactions among two or more multivariate sets of variables. Building on Geweke’s seminal 1982 work, we offer additional justifications for one particular form of multivariate Granger causality based on the generalized variances of residual errors. Taken together, our results support a comprehensive and theoretically consistent extension of Granger causality to the multivariate case. Treated individually, they highlight several specific advantages of the generalized variance measure, which we illustrate using applications in neuroscience as an example. We further show how the measure can be used to define “partial” Granger causality in the multivariate context and we also motivate reformulations of “causal density” and “Granger autonomy.” Our results are directly applicable to experimental data and promise to reveal new types of functional relations in complex systems, neural and otherwise.

  3. Multivariate Granger causality and generalized variance.

    PubMed

    Barrett, Adam B; Barnett, Lionel; Seth, Anil K

    2010-04-01

    Granger causality analysis is a popular method for inference on directed interactions in complex systems of many variables. A shortcoming of the standard framework for Granger causality is that it only allows for examination of interactions between single (univariate) variables within a system, perhaps conditioned on other variables. However, interactions do not necessarily take place between single variables but may occur among groups or "ensembles" of variables. In this study we establish a principled framework for Granger causality in the context of causal interactions among two or more multivariate sets of variables. Building on Geweke's seminal 1982 work, we offer additional justifications for one particular form of multivariate Granger causality based on the generalized variances of residual errors. Taken together, our results support a comprehensive and theoretically consistent extension of Granger causality to the multivariate case. Treated individually, they highlight several specific advantages of the generalized variance measure, which we illustrate using applications in neuroscience as an example. We further show how the measure can be used to define "partial" Granger causality in the multivariate context and we also motivate reformulations of "causal density" and "Granger autonomy." Our results are directly applicable to experimental data and promise to reveal new types of functional relations in complex systems, neural and otherwise.

  4. Quantitative genetics model as the unifying model for defining genomic relationship and inbreeding coefficient.

    PubMed

    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.

  5. Variance partitioning of stream diatom, fish, and invertebrate indicators of biological condition

    USGS Publications Warehouse

    Zuellig, Robert E.; Carlisle, Daren M.; Meador, Michael R.; Potapova, Marina

    2012-01-01

    Stream indicators used to make assessments of biological condition are influenced by many possible sources of variability. To examine this issue, we used multiple-year and multiple-reach diatom, fish, and invertebrate data collected from 20 least-disturbed and 46 developed stream segments between 1993 and 2004 as part of the US Geological Survey National Water Quality Assessment Program. We used a variance-component model to summarize the relative and absolute magnitude of 4 variance components (among-site, among-year, site × year interaction, and residual) in indicator values (observed/expected ratio [O/E] and regional multimetric indices [MMI]) among assemblages and between basin types (least-disturbed and developed). We used multiple-reach samples to evaluate discordance in site assessments of biological condition caused by sampling variability. Overall, patterns in variance partitioning were similar among assemblages and basin types with one exception. Among-site variance dominated the relative contribution to the total variance (64–80% of total variance), residual variance (sampling variance) accounted for more variability (8–26%) than interaction variance (5–12%), and among-year variance was always negligible (0–0.2%). The exception to this general pattern was for invertebrates at least-disturbed sites where variability in O/E indicators was partitioned between among-site and residual (sampling) variance (among-site  =  36%, residual  =  64%). This pattern was not observed for fish and diatom indicators (O/E and regional MMI). We suspect that unexplained sampling variability is what largely remained after the invertebrate indicators (O/E predictive models) had accounted for environmental differences among least-disturbed sites. The influence of sampling variability on discordance of within-site assessments was assemblage or basin-type specific. Discordance among assessments was nearly 2× greater in developed basins (29–31%) than in least

  6. Dominant optic atrophy

    PubMed Central

    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) 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 bilateral, mild

  7. Variability of indoor and outdoor VOC measurements: An analysis using variance components

    PubMed Central

    Jia, Chunrong; Batterman, Stuart A.; Relyea, George E.

    2014-01-01

    This study examines concentrations of volatile organic compounds (VOCs) measured inside and outside of 162 residences in southeast Michigan, U.S.A. Nested analyses apportioned four sources of variation: city, residence, season, and measurement uncertainty. Indoor measurements were dominated by seasonal and residence effects, accounting for 50 and 31%, respectively, of the total variance. Contributions from measurement uncertainty (<20%) and city effects (<10%) were small. For outdoor measurements, season, city and measurement variation accounted for 43, 29 and 27% of variance, respectively, while residence location had negligible impact (<2%). These results show that, to obtain representative estimates of indoor concentrations, measurements in multiple seasons are required. In contrast, outdoor VOC concentrations can use multi-seasonal measurements at centralized locations. Error models showed that uncertainties at low concentrations might obscure effects of other factors. Variance component analyses can be used to interpret existing measurements, design effective exposure studies, and determine whether the instrumentation and protocols are satisfactory. PMID:21995872

  8. Decomposing variation in male reproductive success: age-specific variances and covariances through extra-pair and within-pair reproduction.

    PubMed

    Lebigre, Christophe; Arcese, Peter; Reid, Jane M

    2013-07-01

    Age-specific variances and covariances in reproductive success shape the total variance in lifetime reproductive success (LRS), age-specific opportunities for selection, and population demographic variance and effective size. Age-specific (co)variances in reproductive success achieved through different reproductive routes must therefore be quantified to predict population, phenotypic and evolutionary dynamics in age-structured populations. While numerous studies have quantified age-specific variation in mean reproductive success, age-specific variances and covariances in reproductive success, and the contributions of different reproductive routes to these (co)variances, have not been comprehensively quantified in natural populations. We applied 'additive' and 'independent' methods of variance decomposition to complete data describing apparent (social) and realised (genetic) age-specific reproductive success across 11 cohorts of socially monogamous but genetically polygynandrous song sparrows (Melospiza melodia). We thereby quantified age-specific (co)variances in male within-pair and extra-pair reproductive success (WPRS and EPRS) and the contributions of these (co)variances to the total variances in age-specific reproductive success and LRS. 'Additive' decomposition showed that within-age and among-age (co)variances in WPRS across males aged 2-4 years contributed most to the total variance in LRS. Age-specific (co)variances in EPRS contributed relatively little. However, extra-pair reproduction altered age-specific variances in reproductive success relative to the social mating system, and hence altered the relative contributions of age-specific reproductive success to the total variance in LRS. 'Independent' decomposition showed that the (co)variances in age-specific WPRS, EPRS and total reproductive success, and the resulting opportunities for selection, varied substantially across males that survived to each age. Furthermore, extra-pair reproduction increased

  9. The contribution of the mitochondrial genome to sex-specific fitness variance.

    PubMed

    Smith, Shane R T; Connallon, Tim

    2017-03-28

    Maternal inheritance of mitochondrial DNA (mtDNA) facilitates the evolutionary accumulation of mutations with sex-biased fitness effects. Whereas maternal inheritance closely aligns mtDNA evolution with natural selection in females, it makes it indifferent to evolutionary changes that exclusively benefit males. The constrained response of mtDNA to selection in males can lead to asymmetries in the relative contributions of mitochondrial genes to female versus male fitness variation. Here, we examine the impact of genetic drift and the distribution of fitness effects (DFE) among mutations-including the correlation of mutant fitness effects between the sexes-on mitochondrial genetic variation for fitness. We show how drift, genetic correlations, and skewness of the DFE determine the relative contributions of mitochondrial genes to male versus female fitness variance. When mutant fitness effects are weakly correlated between the sexes, and the effective population size is large, mitochondrial genes should contribute much more to male than to female fitness variance. In contrast, high fitness correlations and small population sizes tend to equalize the contributions of mitochondrial genes to female versus male variance. We discuss implications of these results for the evolution of mitochondrial genome diversity and the genetic architecture of female and male fitness.

  10. 40 CFR 59.509 - Can I get a variance?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... its application is complete. (d) The Administrator will issue a variance if the criteria specified in... entity will achieve compliance with this subpart. (f) A variance will cease to be effective upon...

  11. 40 CFR 59.509 - Can I get a variance?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... its application is complete. (d) The Administrator will issue a variance if the criteria specified in... entity will achieve compliance with this subpart. (f) A variance will cease to be effective upon...

  12. Applications of Variance Fractal Dimension: a Survey

    NASA Astrophysics Data System (ADS)

    Phinyomark, Angkoon; Phukpattaranont, Pornchai; Limsakul, Chusak

    2012-04-01

    Chaotic dynamical systems are pervasive in nature and can be shown to be deterministic through fractal analysis. There are numerous methods that can be used to estimate the fractal dimension. Among the usual fractal estimation methods, variance fractal dimension (VFD) is one of the most significant fractal analysis methods that can be implemented for real-time systems. The basic concept and theory of VFD are presented. Recent research and the development of several applications based on VFD are reviewed and explained in detail, such as biomedical signal processing and pattern recognition, speech communication, geophysical signal analysis, power systems and communication systems. The important parameters that need to be considered in computing the VFD are discussed, including the window size and the window increment of the feature, and the step size of the VFD. Directions for future research of VFD are also briefly outlined.

  13. Considering Oil Production Variance as an Indicator of Peak Production

    DTIC Science & Technology

    2010-06-07

    Acquisition Cost ( IRAC ) Oil Prices. Source: Data used to construct graph acquired from the EIA (http://tonto.eia.doe.gov/country/timeline/oil_chronology.cfm...Acquisition Cost ( IRAC ). Production vs. Price – Variance Comparison Oil production variance and oil price variance have never been so far

  14. A New Nonparametric Levene Test for Equal Variances

    ERIC Educational Resources Information Center

    Nordstokke, David W.; Zumbo, Bruno D.

    2010-01-01

    Tests of the equality of variances are sometimes used on their own to compare variability across groups of experimental or non-experimental conditions but they are most often used alongside other methods to support assumptions made about variances. A new nonparametric test of equality of variances is described and compared to current "gold…

  15. A New Algorithm Using the Non-dominated Tree to improve Non-dominated Sorting.

    PubMed

    Gustavsson, Patrik; Syberfeldt, Anna

    2017-01-19

    Non-dominated sorting is a technique often used in evolutionary algorithms to determine the quality of solutions in a population. The most common algorithm is the Fast Non-dominated Sort (FNS). This algorithm, however, has the drawback that its performance deteriorates when the population size grows. The same drawback applies also to other non-dominating sorting algorithms such as the Efficient Non-dominated Sort with Binary Strategy (ENS-BS). An algorithm suggested to overcome this drawback is the Divide-and-Conquer Non-dominated Sort (DCNS) which works well on a limited number of objectives but deteriorates when the number of objectives grows. This paper presents a new, more efficient, algorithm called the Efficient Non-dominated Sort with Non-Dominated Tree (ENS-NDT). ENS-NDT is an extension of the ENS-BS algorithm and uses a novel Non-Dominated Tree (NDTree) to speed up the non-dominated sorting. ENS-NDT is able to handle large population sizes and a large number of objectives more efficiently than existing algorithms for non-dominated sorting. In the paper, it is shown that with ENS-NDT the runtime of multi-objective optimization algorithms such as the Non-Dominated Sorting Genetic Algorithm II (NSGA-II) can be substantially reduced.

  16. Variation and Genetic Structure in Platanus mexicana (Platanaceae) along Riparian Altitudinal Gradient

    PubMed Central

    Galván-Hernández, Dulce M.; Lozada-García, J. Armando; Flores-Estévez, Norma; Galindo-González, Jorge; Vázquez-Torres, S. Mario

    2015-01-01

    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. PMID:25607732

  17. Variation and genetic structure in Platanus mexicana (Platanaceae) along riparian altitudinal gradient.

    PubMed

    Galván-Hernández, Dulce M; Lozada-García, J Armando; Flores-Estévez, Norma; Galindo-González, Jorge; Vázquez-Torres, S Mario

    2015-01-19

    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.

  18. Death, dying, and domination.

    PubMed

    Spindelman, Marc

    2008-06-01

    This Article critiques conventional liberal arguments for the right to die on liberal grounds. It contends that these arguments do not go far enough to recognize and address private, and in particular structural, forms of domination. It presents an alternative that does, which is thus more respectful of true freedom in the context of death and dying, and also more consistent with liberalism. After discussing obstacles to the achievement of a right to die that encompasses freedom from both public and private domination, the Article closes with a significant reform project within bioethics that might help bring it about.

  19. Autosomal dominant vitreoretinochoroidopathy (ADVIRC).

    PubMed Central

    Blair, N P; Goldberg, M F; Fishman, G A; Salzano, T

    1984-01-01

    We report the second family recognised to have autosomal dominant vitreoretinochoroidopathy. The clinical features were (1) autosomal dominant inheritance; (2) peripheral, coarse pigmentary degeneration of the fundus for 360 degrees, with a relatively discrete posterior border in the equatorial region (this finding may be pathognomonic); (3) superficial punctate yellowish-white opacities in the retina; (4) various vascular abnormalities; (5) breakdown of the blood-retinal barrier; (6) retinal neovascularisation; (7) vitreous abnormalities; and (8) choroidal atrophy. Visual reduction was mainly due to macular oedema or vitreous haemorrhage. Images PMID:6689931

  20. Genetic effects of individual chromosomes in cotton cultivars detected by using chromosome substitution lines as genetic probes.

    PubMed

    Wu, Jixiang; Jenkins, Johnie N; McCarty, Jack C; Saha, Sukumar

    2010-12-01

    Determination of chromosomes or chromosome arms with desirable genes in different inbred lines and/or crosses should provide useful genetic information for crop improvement. In this study, we applied a modified additive-dominance model to analyze a data set of 13 cotton chromosome substitution lines and their recurrent parent TM-1, five commercial cultivars, and their 70 F(2) hybrids. The chromosome additive and dominance variance components for eight agronomic and fiber traits were determined. On average, each chromosome or chromosome arm was associated with 6.5 traits in terms of additive and/or dominance effects. The chromosomes or chromosome arms, which contributed significant additive variances for the traits investigated, included 2, 16, 18, 25, 5sh (short arm), 14sh, 15sh, 22sh, and 22Lo (long arm). Chromosome additive effects were also predicted in this study. The results showed that CS-B 25 was favorably associated with several fiber traits, while FM966 was favorably associated with both yield and fiber traits with alleles on multiple chromosomes or chromosome arms. Thus, this study should provide valuable genetic information on pure line development for several improved traits such as yield and fiber quality.

  1. Assortative mating by fitness and sexually antagonistic genetic variation.

    PubMed

    Arnqvist, Göran

    2011-07-01

    Recent documentations of sexually antagonistic genetic variation in fitness have spurred an interest in the mechanisms that may act to maintain such variation in natural populations. Using individual-based simulations, I show that positive assortative mating by fitness increases the amount of sexually antagonistic genetic variance in fitness, primarily by elevating the equilibrium frequency of heterozygotes, over most of the range of sex-specific selection and dominance. Further, although the effects of assortative mating by fitness on the protection conditions of polymorphism in sexually antagonistic loci were relatively minor, it widens the protection conditions under most reasonable scenarios (e.g., under heterozygote superiority when fitness is averaged across the sexes) but can also somewhat narrow the protection conditions under other circumstances. The near-ubiquity of assortative mating in nature suggests that it may contribute to upholding standing sexually antagonistic genetic variation in fitness.

  2. Autosomal dominant genes (image)

    MedlinePlus

    ... disease. One of the parents will have the disease (since it is dominant) in this mode of inheritance and that person is called the CARRIER. Only one parent must be a carrier in order for the child to inherit the disease.

  3. Iron dominated magnets

    SciTech Connect

    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.

  4. Sensitivity analysis of simulated SOA loadings using a variance-based statistical approach

    NASA Astrophysics Data System (ADS)

    Shrivastava, Manish; Zhao, Chun; Easter, Richard C.; Qian, Yun; Zelenyuk, Alla; Fast, Jerome D.; Liu, Ying; Zhang, Qi; Guenther, Alex

    2016-06-01

    We investigate the sensitivity of secondary organic aerosol (SOA) loadings simulated by a regional chemical transport model to seven selected model parameters using a modified volatility basis-set (VBS) approach: four involving emissions of anthropogenic and biogenic volatile organic compounds, anthropogenic semivolatile and intermediate volatility organics (SIVOCs), and NOx; two involving dry deposition of SOA precursor gases, and one involving particle-phase transformation of SOA to low volatility. We adopt a quasi-Monte Carlo sampling approach to effectively sample the high-dimensional parameter space, and perform a 250 member ensemble of simulations using a regional model, accounting for some of the latest advances in SOA treatments based on our recent work. We then conduct a variance-based sensitivity analysis using the generalized linear model method to study the responses of simulated SOA loadings to the model parameters. Analysis of SOA variance from all 250 simulations shows that the volatility transformation parameter, which controls whether or not SOA that starts as semivolatile is rapidly transformed to nonvolatile SOA by particle-phase processes such as oligomerization and/or accretion, is the dominant contributor to variance of simulated surface-level daytime SOA (65% domain average contribution). We also split the simulations into two subsets of 125 each, depending on whether the volatility transformation is turned on/off. For each subset, the SOA variances are dominated by the parameters involving biogenic VOC and anthropogenic SIVOC emissions. Furthermore, biogenic VOC emissions have a larger contribution to SOA variance when the SOA transformation to nonvolatile is on, while anthropogenic SIVOC emissions have a larger contribution when the transformation is off. NOx contributes less than 4.3% to SOA variance, and this low contribution is mainly attributed to dominance of intermediate to high NOx conditions throughout the simulated domain. However

  5. Cyclostationary analysis with logarithmic variance stabilisation

    NASA Astrophysics Data System (ADS)

    Borghesani, Pietro; Shahriar, Md Rifat

    2016-03-01

    Second order cyclostationary (CS2) components in vibration or acoustic emission signals are typical symptoms of a wide variety of faults in rotating and alternating mechanical systems. The square envelope spectrum (SES), obtained via Hilbert transform of the original signal, is at the basis of the most common indicators used for detection of CS2 components. It has been shown that the SES is equivalent to an autocorrelation of the signal's discrete Fourier transform, and that CS2 components are a cause of high correlations in the frequency domain of the signal, thus resulting in peaks in the SES. Statistical tests have been proposed to determine if peaks in the SES are likely to belong to a normal variability in the signal or if they are proper symptoms of CS2 components. Despite the need for automated fault recognition and the theoretical soundness of these tests, this approach to machine diagnostics has been mostly neglected in industrial applications. In fact, in a series of experimental applications, even with proper pre-whitening steps, it has been found that healthy machines might produce high spectral correlations and therefore result in a highly biased SES distribution which might cause a series of false positives. In this paper a new envelope spectrum is defined, with the theoretical intent of rendering the hypothesis test variance-free. This newly proposed indicator will prove unbiased in case of multiple CS2 sources of spectral correlation, thus reducing the risk of false alarms.

  6. Correcting an analysis of variance for clustering.

    PubMed

    Hedges, Larry V; Rhoads, Christopher H

    2011-02-01

    A great deal of educational and social data arises from cluster sampling designs where clusters involve schools, classrooms, or communities. A mistake that is sometimes encountered in the analysis of such data is to ignore the effect of clustering and analyse the data as if it were based on a simple random sample. This typically leads to an overstatement of the precision of results and too liberal conclusions about precision and statistical significance of mean differences. This paper gives simple corrections to the test statistics that would be computed in an analysis of variance if clustering were (incorrectly) ignored. The corrections are multiplicative factors depending on the total sample size, the cluster size, and the intraclass correlation structure. For example, the corrected F statistic has Fisher's F distribution with reduced degrees of freedom. The corrected statistic reduces to the F statistic computed by ignoring clustering when the intraclass correlations are zero. It reduces to the F statistic computed using cluster means when the intraclass correlations are unity, and it is in between otherwise. A similar adjustment to the usual statistic for testing a linear contrast among group means is described.

  7. A fast minimum variance beamforming method using principal component analysis.

    PubMed

    Kim, Kyuhong; Park, Suhyun; Kim, Jungho; Park, Sung-Bae; Bae, MooHo

    2014-06-01

    Minimum variance (MV) beamforming has been studied for improving the performance of a diagnostic ultrasound imaging system. However, it is not easy for the MV beamforming to be implemented in a real-time ultrasound imaging system because of the enormous amount of computation time associated with the covariance matrix inversion. In this paper, to address this problem, we propose a new fast MV beamforming method that almost optimally approximates the MV beamforming while reducing the computational complexity greatly through dimensionality reduction using principal component analysis (PCA). The principal components are estimated offline from pre-calculated conventional MV weights. Thus, the proposed method does not directly calculate the MV weights but approximates them by a linear combination of a few selected dominant principal components. The combinational weights are calculated in almost the same way as in MV beamforming, but in the transformed domain of beamformer input signal by the PCA, where the dimension of the transformed covariance matrix is identical to the number of some selected principal component vectors. Both computer simulation and experiment were carried out to verify the effectiveness of the proposed method with echo signals from simulation as well as phantom and in vivo experiments. It is confirmed that our method can reduce the dimension of the covariance matrix down to as low as 2 × 2 while maintaining the good image quality of MV beamforming.

  8. [Dominant Thalamus and Aphasia].

    PubMed

    Nakano, Akiko; Shimomura, Tatsuo

    2015-12-01

    Many studies have shown that lesions of the dominant thalamus precipitate language disorders in a similar manner to transcortical aphasias, in a phenomenon known as "thalamic aphasia." In some cases, however, aphasia may not occur or may appear transiently following thalamic lesions. Furthermore, dominant thalamic lesions can produce changes in character, as observed in patients with amnesic disorder. Previous work has explored the utility of thalamic aphasia as a discriminative feature for classification of aphasia. Although the thalamus may be involved in the function of the brainstem reticular activating system and play a role in attentional network and in memory of Papez circuit or Yakovlev circuit, the mechanism by which thalamic lesion leads to the emergence of aphasic disorders is unclear. In this review, we we survey historical and recent literature on thalamic aphasia in an attempt to understand the neural processes affected by thalamic lesions.

  9. Evolution of dominance mechanisms at a butterfly mimicry supergene

    PubMed Central

    Le Poul, Yann; Whibley, Annabel; Chouteau, Mathieu; Prunier, Florence; Llaurens, Violaine; Joron, Mathieu

    2014-01-01

    Genetic dominance in polymorphic loci may respond to selection; however, the evolution of dominance in complex traits remains a puzzle. We analyse dominance at a wing-patterning supergene controlling local mimicry polymorphism in the butterfly Heliconius numata. Supergene alleles are associated with chromosomal inversion polymorphism, defining ancestral versus derived alleles. Using controlled crosses and the new procedure, Colour Pattern Modelling, allowing whole-wing pattern comparisons, we estimate dominance coefficients between alleles. Here we show strict dominance in sympatry favouring mimicry and inconsistent dominance throughout the wing between alleles from distant populations. Furthermore, dominance among derived alleles is uncoordinated across wing-pattern elements, producing mosaic heterozygous patterns determined by a hierarchy in colour expression. By contrast, heterozygotes with an ancestral allele show complete, coordinated dominance of the derived allele, independently of colours. Therefore, distinct dominance mechanisms have evolved in association with supergene inversions, in response to strong selection on mimicry polymorphism. PMID:25429605

  10. Accounting for Variance in Hyperspectral Data Coming from Limitations of the Imaging System

    NASA Astrophysics Data System (ADS)

    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

  11. Potential variance affecting homeotic Ultrabithorax and Antennapedia phenotypes in Drosophila melanogaster.

    PubMed Central

    Gibson, G; Wemple, M; van Helden, S

    1999-01-01

    Introgression of homeotic mutations into wild-type genetic backgrounds results in a wide variety of phenotypes and implies that major effect modifiers of extreme phenotypes are not uncommon in natural populations of Drosophila. A composite interval mapping procedure was used to demonstrate that one major effect locus accounts for three-quarters of the variance for haltere to wing margin transformation in Ultrabithorax flies, yet has no obvious effect on wild-type development. Several other genetic backgrounds result in enlargement of the haltere significantly beyond the normal range of haploinsufficient phenotypes, suggesting genetic variation in cofactors that mediate homeotic protein function. Introgression of Antennapedia produces lines with heritable phenotypes ranging from almost complete suppression to perfect antennal leg formation, as well as transformations that are restricted to either the distal or proximal portion of the appendage. It is argued that the existence of "potential" variance, which is genetic variation whose effects are not observable in wild-type individuals, is a prerequisite for the uncoupling of genetic from phenotypic divergence. PMID:10049924

  12. A general unified framework to assess the sampling variance of heritability estimates using pedigree or marker-based relationships.

    PubMed

    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.

  13. [Autosomal dominant polycystic kidney].

    PubMed

    Jorge Adad, S; Estevão Barbosa, M; Fácio Luíz, J M; Furlan Rodrigues, M C; Iwamoto, S

    1996-01-01

    A 48-year-old male had autosomic dominant polycystic kidneys with dimensions, to the best of our knowledge, never previously reported; the right kidney weighed 15,100 g and measured 53 x 33 x 9cm and the left one 10.200 g and 46 x 21 x 7cm, with cysts measuring up to 14cm in diameter. Nephrectomy was done to control persistent hematuria and to relief disconfort caused by the large kidneys. The renal function is stable four years after transplantation.

  14. Multiperiod Mean-Variance Portfolio Optimization via Market Cloning

    SciTech Connect

    Ankirchner, Stefan; Dermoune, Azzouz

    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.

  15. Network Structure and Biased Variance Estimation in Respondent Driven Sampling.

    PubMed

    Verdery, Ashton M; Mouw, Ted; Bauldry, Shawn; Mucha, Peter J

    2015-01-01

    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.

  16. Network Structure and Biased Variance Estimation in Respondent Driven Sampling

    PubMed Central

    Verdery, Ashton M.; Mouw, Ted; Bauldry, Shawn; Mucha, Peter J.

    2015-01-01

    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. PMID:26679927

  17. RR-Interval variance of electrocardiogram for atrial fibrillation detection

    NASA Astrophysics Data System (ADS)

    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.

  18. Simulations of the Hadamard Variance: Probability Distributions and Confidence Intervals.

    PubMed

    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.

  19. Estimates of genetic parameters of body weight in descendants of X-irradiated rat spermatogonia.

    PubMed

    Gianola, D; Chapman, A B; Rutledge, J J

    1977-08-01

    Effects of nine generations of 450r per generation of ancestral spermatogonial X irradiation of inbred rats on genetic parameters of body weight at 3, 6, and 10 weeks of age and of weight gains between these periods were studied. Covariances among relatives were estimated by mixed model and regression techniques in randomly selected lines with (R) and without (C) radiation history. Analyses of the data were based on five linear genetic models combining additive direct, additive indirect (maternal), dominance and environmental effects. Parameters in these models were estimated by generalized least-squares. A model including direct and indirect genetic effects fit more closely to the data in both R and C lines. Overdominance of induced mutations did not seem to be present. Ancestral irradiation increased maternal additive genetic variances of body weights and gains but not direct genetic variances. Theoretically, due to a negative direct-maternal genetic correlation, within full-sib family selection would be ineffective in increasing body weight at six weeks in both R and C lines. However, progress from mass selection would be expected to be faster in the R lines.

  20. Genome-wide interaction of genotype by erythrocyte n-3 PUFAs contributes to phenotypic variance of diabetes-related traits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    While genome-wide association studies (GWAS) and candidate gene approach have identified many genetic variants that contribute to disease risk as main effects, the impact of genotype by environment (GxE) interactions remains rather under-surveyed. The present study aimed to examine variance contribu...

  1. Autosomal dominant polycystic kidney disease diagnosed in utero. Review.

    PubMed

    Nowak, Magdalena; Huras, Hubert; Wiecheć, Marcin; Jach, Robert; Radoń-Pokracka, Małgorzata; Górecka, Joanna

    2016-01-01

    Autosomal dominant polycystic kidney disease (ADPKD) is one of most common inherited renal diseases. It is estimated that very early onset ADPKD affects even 2% patients. The purpose of this article is to provide a comprehensive review of genetics, prenatal diagnosis and prognosis in very early onset autosomal dominant polycystic kidney disease.

  2. Counterspace Operations for Information Dominance

    DTIC Science & Technology

    1999-03-01

    INTERNET DOCUMENT INFORMATION FORM A. Report Title: Counterspace perations for Information Dominance B. DATE Report Downloaded From the Internet 3/10...Representative for resolution. Counterspace perations for Information Dominance by James G. Lee INTRODUCTION The Problem The launch of the Soviet...information gap between friendly and enemy forces. This positive information gap has been referred to as information dominance . Information Dominance The

  3. Analysis of variance of designed chromatographic data sets: The analysis of variance-target projection approach.

    PubMed

    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.

  4. Genome-wide evaluation for quantitative trait loci under the variance component model

    PubMed Central

    Han, Lide

    2010-01-01

    The identity-by-descent (IBD) based variance component analysis is an important method for mapping quantitative trait loci (QTL) in outbred populations. The interval-mapping approach and various modified versions of it may have limited use in evaluating the genetic variances of the entire genome because they require evaluation of multiple models and model selection. In this study, we developed a multiple variance component model for genome-wide evaluation using both the maximum likelihood (ML) method and the MCMC implemented Bayesian method. We placed one QTL in every few cM on the entire genome and estimated the QTL variances and positions simultaneously in a single model. Genomic regions that have no QTL usually showed no evidence of QTL while regions with large QTL always showed strong evidence of QTL. While the Bayesian method produced the optimal result, the ML method is computationally more efficient than the Bayesian method. Simulation experiments were conducted to demonstrate the efficacy of the new methods. Electronic supplementary material The online version of this article (doi:10.1007/s10709-010-9497-1) contains supplementary material, which is available to authorized users. PMID:20835884

  5. Camera Calibration with Radial Variance Component Estimation

    NASA Astrophysics Data System (ADS)

    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.

  6. Role of dominant visibles in mutagenicity testing

    SciTech Connect

    Searle, A.G.; Beechey, C.

    1986-01-01

    Our results suggest that inclusion of growth retardation as one of the components of the dominant visible category will make this a useful end-point for mutational studies in which it is important to gauge the extent to which transmissible genetic damage of a particularly relevant kind is induced in mammals. These visibles are easily scored and the use of an automated weighing device would lessen subjectivity. In the present experiment with 5Gy + 5Gy spermatogonial X-irradiation (24h interval) 7309 offspring have been examined at weaning age and 23 heritable dominant visibles identified. These included 12 with growth retardation, one of which was mutant at the steel (S1) locus, as were 3-4 others of normal size. However, only 46 out of 112 offspring recorded as small were actually kept for genetic tests, while only 30 (65%) of these could be fully tested because of death or infertility in the others. Thus this experiment throws some light on the induction of presumptive dominant sub-lethals which survive until weaning age, a little-studied category. Twelve out of the 30 fully tested small mice (40%) proved to carry dominant visible mutations. If this proportion is applied to the total recorded as small then we can derive an overall total of about 45 mutations for growth retardation. It is hoped to determine the actual rate of induction of these by further work.

  7. Rings dominate western Gulf

    NASA Astrophysics Data System (ADS)

    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.

  8. Dominant modal decomposition method

    NASA Astrophysics Data System (ADS)

    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.

  9. Genetic control of inflorescence in common bean.

    PubMed

    Guilherme, S R; Ramalho, M A P; de F B Abreu, A; Pereira, L A

    2014-12-04

    The number of pods per common bean plant is a primary component of grain yield, which depends on the number of flowers produced and on the flower set. Thus, a larger number of flowers per plant would increase yield. Lines with inflorescences that had a large number of flowers compared to common bean plants now under cultivation were identified. We analyzed the genetic control of this trait and its association with grain yield. The cultivar BRSMG Talismã was crossed with 2 lines, L.59583 and L.59692, which have a large number of flowers. The F1, F2, and F3 generations were obtained. These generations were assessed together with the parents in a randomized block experimental design with 2 replications. The traits assessed included length of inflorescence, number of pods per inflorescence, number of pods per plant, number of grains per plant, 100-grain weight, and grain yield per plant. Mean genetic components and variance were estimated. The traits length of inflorescence and number of pods per inflorescence exhibited genetic control with predominance that showed an additive effect. In the 2 crosses, genetic control of grain yield and of its primary components showed that the allelic interaction of dominance was high. The wide variability in the traits assessed may be used to increase yield of the common bean plant by increasing the number of flowers on the plant.

  10. Refined genetic mapping of autosomal dominant retinitis pigmentosa locus RP18 reduces the critical region to 2 cM between D1S442 and D1S2858 on chromosome 1q.

    PubMed

    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.

  11. 29 CFR 1905.5 - Effect of variances.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 5 2010-07-01 2010-07-01 false Effect of variances. 1905.5 Section 1905.5 Labor Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR RULES OF PRACTICE FOR VARIANCES, LIMITATIONS, VARIATIONS, TOLERANCES, AND EXEMPTIONS UNDER THE WILLIAMS-STEIGER OCCUPATIONAL SAFETY AND HEALTH ACT...

  12. 36 CFR 27.4 - Variances and exceptions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 36 Parks, Forests, and Public Property 1 2013-07-01 2013-07-01 false Variances and exceptions. 27.4 Section 27.4 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR CAPE COD NATIONAL SEASHORE; ZONING STANDARDS § 27.4 Variances and exceptions. (a) Zoning bylaws...

  13. 36 CFR 27.4 - Variances and exceptions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Variances and exceptions. 27.4 Section 27.4 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR CAPE COD NATIONAL SEASHORE; ZONING STANDARDS § 27.4 Variances and exceptions. (a) Zoning bylaws...

  14. 36 CFR 27.4 - Variances and exceptions.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 36 Parks, Forests, and Public Property 1 2012-07-01 2012-07-01 false Variances and exceptions. 27.4 Section 27.4 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR CAPE COD NATIONAL SEASHORE; ZONING STANDARDS § 27.4 Variances and exceptions. (a) Zoning bylaws...

  15. 36 CFR 27.4 - Variances and exceptions.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 36 Parks, Forests, and Public Property 1 2014-07-01 2014-07-01 false Variances and exceptions. 27.4 Section 27.4 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR CAPE COD NATIONAL SEASHORE; ZONING STANDARDS § 27.4 Variances and exceptions. (a) Zoning bylaws...

  16. 36 CFR 27.4 - Variances and exceptions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 36 Parks, Forests, and Public Property 1 2011-07-01 2011-07-01 false Variances and exceptions. 27.4 Section 27.4 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR CAPE COD NATIONAL SEASHORE; ZONING STANDARDS § 27.4 Variances and exceptions. (a) Zoning bylaws...

  17. Relating the Hadamard Variance to MCS Kalman Filter Clock Estimation

    NASA Technical Reports Server (NTRS)

    Hutsell, Steven T.

    1996-01-01

    The Global Positioning System (GPS) Master Control Station (MCS) currently makes significant use of the Allan Variance. This two-sample variance equation has proven excellent as a handy, understandable tool, both for time domain analysis of GPS cesium frequency standards, and for fine tuning the MCS's state estimation of these atomic clocks. The Allan Variance does not explicitly converge for the nose types of alpha less than or equal to minus 3 and can be greatly affected by frequency drift. Because GPS rubidium frequency standards exhibit non-trivial aging and aging noise characteristics, the basic Allan Variance analysis must be augmented in order to (a) compensate for a dynamic frequency drift, and (b) characterize two additional noise types, specifically alpha = minus 3, and alpha = minus 4. As the GPS program progresses, we will utilize a larger percentage of rubidium frequency standards than ever before. Hence, GPS rubidium clock characterization will require more attention than ever before. The three sample variance, commonly referred to as a renormalized Hadamard Variance, is unaffected by linear frequency drift, converges for alpha is greater than minus 5, and thus has utility for modeling noise in GPS rubidium frequency standards. This paper demonstrates the potential of Hadamard Variance analysis in GPS operations, and presents an equation that relates the Hadamard Variance to the MCS's Kalman filter process noises.

  18. 40 CFR 141.4 - Variances and exemptions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 24 2013-07-01 2013-07-01 false Variances and exemptions. 141.4 Section 141.4 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS General § 141.4 Variances and exemptions....

  19. 40 CFR 141.4 - Variances and exemptions.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 23 2014-07-01 2014-07-01 false Variances and exemptions. 141.4 Section 141.4 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS General § 141.4 Variances and exemptions....

  20. 40 CFR 141.4 - Variances and exemptions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 23 2011-07-01 2011-07-01 false Variances and exemptions. 141.4 Section 141.4 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS General § 141.4 Variances and exemptions....

  1. 40 CFR 141.4 - Variances and exemptions.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 24 2012-07-01 2012-07-01 false Variances and exemptions. 141.4 Section 141.4 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS General § 141.4 Variances and exemptions....

  2. 40 CFR 141.4 - Variances and exemptions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 22 2010-07-01 2010-07-01 false Variances and exemptions. 141.4 Section 141.4 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS General § 141.4 Variances and exemptions....

  3. Determining Sample Sizes for Precise Contrast Analysis with Heterogeneous Variances

    ERIC Educational Resources Information Center

    Jan, Show-Li; Shieh, Gwowen

    2014-01-01

    The analysis of variance (ANOVA) is one of the most frequently used statistical analyses in practical applications. Accordingly, the single and multiple comparison procedures are frequently applied to assess the differences among mean effects. However, the underlying assumption of homogeneous variances may not always be tenable. This study…

  4. 76 FR 78698 - Proposed Revocation of Permanent Variances

    Federal Register 2010, 2011, 2012, 2013, 2014

    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...

  5. Gender Variance and Educational Psychology: Implications for Practice

    ERIC Educational Resources Information Center

    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…

  6. 42 CFR 456.522 - Content of request for variance.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS UTILIZATION CONTROL Utilization Review Plans: FFP, Waivers, and Variances for Hospitals and Mental Hospitals Ur Plan: Remote Facility Variances from Time..., mental hospital, and ICF located within a 50-mile radius of the facility; (e) The distance and...

  7. A Study of Variance Estimation Methods. Working Paper Series.

    ERIC Educational Resources Information Center

    Zhang, Fan; Weng, Stanley; Salvucci, Sameena; Hu, Ming-xiu

    This working paper contains reports of five studies of variance estimation methods. The first, An Empirical Study of Poststratified Estimator, by Fan Zhang uses data from the National Household Education Survey to illustrate use of poststratified estimation. The second paper, BRR Variance Estimation Using BPLX Hadamard Procedure, by Stanley Weng…

  8. Conceptual Complexity and the Bias/Variance Tradeoff

    ERIC Educational Resources Information Center

    Briscoe, Erica; Feldman, Jacob

    2011-01-01

    In this paper we propose that the conventional dichotomy between exemplar-based and prototype-based models of concept learning is helpfully viewed as an instance of what is known in the statistical learning literature as the "bias/variance tradeoff". The bias/variance tradeoff can be thought of as a sliding scale that modulates how closely any…

  9. Variances and Covariances of Kendall's Tau and Their Estimation.

    ERIC Educational Resources Information Center

    Cliff, Norman; Charlin, Ventura

    1991-01-01

    Variance formulas of H. E. Daniels and M. G. Kendall (1947) are generalized to allow for the presence of ties and variance of the sample tau correlation. Applications of these generalized formulas are discussed and illustrated using data from a 1965 study of contraceptive use in 15 developing countries. (SLD)

  10. Onset dominance in lateralization.

    PubMed

    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.

  11. Variance component model to account for sample structure in genome-wide association studies.

    PubMed

    Kang, Hyun Min; Sul, Jae Hoon; Service, Susan K; Zaitlen, Noah A; Kong, Sit-Yee; Freimer, Nelson B; Sabatti, Chiara; Eskin, Eleazar

    2010-04-01

    Although genome-wide association studies (GWASs) have identified numerous loci associated with complex traits, imprecise modeling of the genetic relatedness within study samples may cause substantial inflation of test statistics and possibly spurious associations. Variance component approaches, such as efficient mixed-model association (EMMA), can correct for a wide range of sample structures by explicitly accounting for pairwise relatedness between individuals, using high-density markers to model the phenotype distribution; but such approaches are computationally impractical. We report here a variance component approach implemented in publicly available software, EMMA eXpedited (EMMAX), that reduces the computational time for analyzing large GWAS data sets from years to hours. We apply this method to two human GWAS data sets, performing association analysis for ten quantitative traits from the Northern Finland Birth Cohort and seven common diseases from the Wellcome Trust Case Control Consortium. We find that EMMAX outperforms both principal component analysis and genomic control in correcting for sample structure.

  12. Estimation of breeding values for mean and dispersion, their variance and correlation using double hierarchical generalized linear models.

    PubMed

    Felleki, M; Lee, D; Lee, Y; Gilmour, A R; Rönnegård, L

    2012-12-01

    The possibility of breeding for uniform individuals by selecting animals expressing a small response to environment has been studied extensively in animal breeding. Bayesian methods for fitting models with genetic components in the residual variance have been developed for this purpose, but have limitations due to the computational demands. We use the hierarchical (h)-likelihood from the theory of double hierarchical generalized linear models (DHGLM) to derive an estimation algorithm that is computationally feasible for large datasets. Random effects for both the mean and residual variance parts of the model are estimated together with their variance/covariance components. An important feature of the algorithm is that it can fit a correlation between the random effects for mean and variance. An h-likelihood estimator is implemented in the R software and an iterative reweighted least square (IRWLS) approximation of the h-likelihood is implemented using ASReml. The difference in variance component estimates between the two implementations is investigated, as well as the potential bias of the methods, using simulations. IRWLS gives the same results as h-likelihood in simple cases with no severe indication of bias. For more complex cases, only IRWLS could be used, and bias did appear. The IRWLS is applied on the pig litter size data previously analysed by Sorensen & Waagepetersen (2003) using Bayesian methodology. The estimates we obtained by using IRWLS are similar to theirs, with the estimated correlation between the random genetic effects being -0·52 for IRWLS and -0·62 in Sorensen & Waagepetersen (2003).

  13. 40 CFR 260.33 - Procedures for variances from classification as a solid waste, for variances to be classified as...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... classification as a solid waste, for variances to be classified as a boiler, or for non-waste determinations. 260... from classification as a solid waste, for variances to be classified as a boiler, or for non-waste... as boilers, or applications for non-waste determinations. (a) The applicant must apply to...

  14. 40 CFR 260.33 - Procedures for variances from classification as a solid waste, for variances to be classified as...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... classification as a solid waste, for variances to be classified as a boiler, or for non-waste determinations. 260... from classification as a solid waste, for variances to be classified as a boiler, or for non-waste... as boilers, or applications for non-waste determinations. (a) The applicant must apply to...

  15. 40 CFR 260.33 - Procedures for variances from classification as a solid waste, for variances to be classified as...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... classification as a solid waste, for variances to be classified as a boiler, or for non-waste determinations. 260... from classification as a solid waste, for variances to be classified as a boiler, or for non-waste... as boilers, or applications for non-waste determinations. (a) The applicant must apply to...

  16. 40 CFR 260.33 - Procedures for variances from classification as a solid waste, for variances to be classified as...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... classification as a solid waste, for variances to be classified as a boiler, or for non-waste determinations. 260... from classification as a solid waste, for variances to be classified as a boiler, or for non-waste... as boilers, or applications for non-waste determinations. (a) The applicant must apply to...

  17. 40 CFR 260.33 - Procedures for variances from classification as a solid waste, for variances to be classified as...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... classification as a solid waste, for variances to be classified as a boiler, or for non-waste determinations. 260... from classification as a solid waste, for variances to be classified as a boiler, or for non-waste... as boilers, or applications for non-waste determinations. (a) The applicant must apply to...

  18. The population genetic theory of hidden variation and genetic robustness.

    PubMed

    Hermisson, Joachim; Wagner, Günter P

    2004-12-01

    One of the most solid generalizations of transmission genetics is that the phenotypic variance of populations carrying a major mutation is increased relative to the wild type. At least some part of this higher variance is genetic and due to release of previously hidden variation. Similarly, stressful environments also lead to the expression of hidden variation. These two observations have been considered as evidence that the wild type has evolved robustness against genetic variation, i.e., genetic canalization. In this article we present a general model for the interaction of a major mutation or a novel environment with the additive genetic basis of a quantitative character under stabilizing selection. We introduce an approximation to the genetic variance in mutation-selection-drift balance that includes the previously used stochastic Gaussian and house-of-cards approximations as limiting cases. We then show that the release of hidden genetic variation is a generic property of models with epistasis or genotype-environment interaction, regardless of whether the wild-type genotype is canalized or not. As a consequence, the additive genetic variance increases upon a change in the environment or the genetic background even if the mutant character state is as robust as the wild-type character. Estimates show that this predicted increase can be considerable, in particular in large populations and if there are conditionally neutral alleles at the loci underlying the trait. A brief review of the relevant literature suggests that the assumptions of this model are likely to be generic for polygenic traits. We conclude that the release of hidden genetic variance due to a major mutation or environmental stress does not demonstrate canalization of the wild-type genotype.

  19. Filtered kriging for spatial data with heterogeneous measurement error variances.

    PubMed

    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.

  20. Global Gravity Wave Variances from Aura MLS: Characteristics and Interpretation

    NASA Technical Reports Server (NTRS)

    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.

  1. Genotype-specific environmental impact on the variance of blood values in inbred and F1 hybrid mice.

    PubMed

    Klempt, Martina; Rathkolb, Birgit; Fuchs, Edith; de Angelis, Martin Hrabé; Wolf, Eckhard; Aigner, Bernhard

    2006-02-01

    Mice are important models for biomedical research because of the possibility of standardizing genetic background and environmental conditions, which both affect phenotypic variability. Inbred mouse strains as well as F1 hybrid mice are routinely used as genetically defined animal models; however, only a few studies investigated the variance of phenotypic parameters in inbred versus F1 hybrid mice and the potential interference of the genetic background with different housing conditions. Thus, we analyzed the ranges of clinical chemical and hematologic parameters in C3H and C57BL/6 inbred mice and their reciprocal F1 hybrids (B6C3F1, C3B6F1) in two different mouse facilities. Two thirds of the blood parameters examined in the same strain differed between the facilities for both the inbred strains and the F1 hybrid lines. The relation of the values between inbred and F1 hybrid mice was also affected by the facility. The variance of blood parameters in F1 hybrid mice compared with their parental inbred strains was inconsistent in one facility but generally smaller in the other facility. A subsequent study of F1 hybrid animals derived from the parental strains C3H and BALB/c, which was done in the latter housing unit, detected no general difference in the variance of blood parameters between F1 hybrid and inbred mice. Our study clearly demonstrates the possibility of major interactions between genotype and environment regarding the variance of clinical chemical and hematologic parameters.

  2. Can Big Five Facets Distinguish between Hedonic and Eudaimonic Well-Being? A Dominance Analysis.

    PubMed

    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.

  3. A survey of dominant mutations in Arabidopsis thaliana.

    PubMed

    Meinke, David W

    2013-02-01

    Following the recent publication of a comprehensive dataset of 2400 genes with a loss-of-function mutant phenotype in Arabidopsis (Arabidopsis thaliana), questions remain concerning the diversity of dominant mutations in Arabidopsis. Most of these dominant phenotypes are expected to result from inappropriate gene expression, novel protein function, or disrupted protein complexes. This review highlights the major classes of dominant mutations observed in model organisms and presents a collection of 200 Arabidopsis genes associated with a dominant or semidominant phenotype. Emphasis is placed on mutants identified through forward genetic screens of mutagenized or activation-tagged populations. These datasets illustrate the variety of genetic changes and protein functions that underlie dominance in Arabidopsis and may ultimately contribute to phenotypic variation in flowering plants.

  4. Multiple mating but not recombination causes quantitative increase in offspring genetic diversity for varying genetic architectures.

    PubMed

    Rueppell, Olav; Meier, Stephen; Deutsch, Roland

    2012-01-01

    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.

  5. Estimation of prediction error variances via Monte Carlo sampling methods using different formulations of the prediction error variance.

    PubMed

    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.

  6. Blinded sample size re-estimation in superiority and noninferiority trials: bias versus variance in variance estimation.

    PubMed

    Friede, Tim; Kieser, Meinhard

    2013-01-01

    The internal pilot study design allows for modifying the sample size during an ongoing study based on a blinded estimate of the variance thus maintaining the trial integrity. Various blinded sample size re-estimation procedures have been proposed in the literature. We compare the blinded sample size re-estimation procedures based on the one-sample variance of the pooled data with a blinded procedure using the randomization block information with respect to bias and variance of the variance estimators, and the distribution of the resulting sample sizes, power, and actual type I error rate. For reference, sample size re-estimation based on the unblinded variance is also included in the comparison. It is shown that using an unbiased variance estimator (such as the one using the randomization block information) for sample size re-estimation does not guarantee that the desired power is achieved. Moreover, in situations that are common in clinical trials, the variance estimator that employs the randomization block length shows a higher variability than the simple one-sample estimator and in turn the sample size resulting from the related re-estimation procedure. This higher variability can lead to a lower power as was demonstrated in the setting of noninferiority trials. In summary, the one-sample estimator obtained from the pooled data is extremely simple to apply, shows good performance, and is therefore recommended for application.

  7. 40 CFR 59.509 - Can I get a variance?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...) NATIONAL VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Aerosol Coatings § 59.509 Can I get a variance? (a)...

  8. 40 CFR 59.509 - Can I get a variance?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...) NATIONAL VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Aerosol Coatings § 59.509 Can I get a variance? (a)...

  9. RISK ANALYSIS, ANALYSIS OF VARIANCE: GETTING MORE FROM OUR DATA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Analysis of variance (ANOVA) and regression are common statistical techniques used to analyze agronomic experimental data and determine significant differences among yields due to treatments or other experimental factors. Risk analysis provides an alternate and complimentary examination of the same...

  10. Some variance reduction methods for numerical stochastic homogenization.

    PubMed

    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.

  11. Genetic and Statistical Analyses of Strong Selection on Polygenic Traits: What, Me Normal?

    PubMed Central

    Turelli, M.; Barton, N. H.

    1994-01-01

    We develop a general population genetic framework for analyzing selection on many loci, and apply it to strong truncation and disruptive selection on an additive polygenic trait. We first present statistical methods for analyzing the infinitesimal model, in which offspring breeding values are normally distributed around the mean of the parents, with fixed variance. These show that the usual assumption of a Gaussian distribution of breeding values in the population gives remarkably accurate predictions for the mean and the variance, even when disruptive selection generates substantial deviations from normality. We then set out a general genetic analysis of selection and recombination. The population is represented by multilocus cumulants describing the distribution of haploid genotypes, and selection is described by the relation between mean fitness and these cumulants. We provide exact recursions in terms of generating functions for the effects of selection on non-central moments. The effects of recombination are simply calculated as a weighted sum over all the permutations produced by meiosis. Finally, the new cumulants that describe the next generation are computed from the non-central moments. Although this scheme is applied here in detail only to selection on an additive trait, it is quite general. For arbitrary epistasis and linkage, we describe a consistent infinitesimal limit in which the short-term selection response is dominated by infinitesimal allele frequency changes and linkage disequilibria. Numerical multilocus results show that the standard Gaussian approximation gives accurate predictions for the dynamics of the mean and genetic variance in this limit. Even with intense truncation selection, linkage disequilibria of order three and higher never cause much deviation from normality. Thus, the empirical deviations frequently found between predicted and observed responses to artificial selection are not caused by linkage

  12. Hidden item variance in multiple mini-interview scores.

    PubMed

    Zaidi, Nikki L Bibler; Swoboda, Christopher M; Kelcey, Benjamin M; Manuel, R Stephen

    2017-05-01

    The extant literature has largely ignored a potentially significant source of variance in multiple mini-interview (MMI) scores by "hiding" the variance attributable to the sample of attributes used on an evaluation form. This potential source of hidden variance can be defined as rating items, which typically comprise an MMI evaluation form. Due to its multi-faceted, repeated measures format, reliability for the MMI has been primarily evaluated using generalizability (G) theory. A key assumption of G theory is that G studies model the most important sources of variance to which a researcher plans to generalize. Because G studies can only attribute variance to the facets that are modeled in a G study, failure to model potentially substantial sources of variation in MMI scores can result in biased estimates of variance components. This study demonstrates the implications of hiding the item facet in MMI studies when true item-level effects exist. An extensive Monte Carlo simulation study was conducted to examine whether a commonly used hidden item, person-by-station (p × s|i) G study design results in biased estimated variance components. Estimates from this hidden item model were compared with estimates from a more complete person-by-station-by-item (p × s × i) model. Results suggest that when true item-level effects exist, the hidden item model (p × s|i) will result in biased variance components which can bias reliability estimates; therefore, researchers should consider using the more complete person-by-station-by-item model (p × s × i) when evaluating generalizability of MMI scores.

  13. Key questions in the genetics and genomics of eco-evolutionary dynamics.

    PubMed

    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.

  14. Allan variance of time series models for measurement data

    NASA Astrophysics Data System (ADS)

    Zhang, Nien Fan

    2008-10-01

    The uncertainty of the mean of autocorrelated measurements from a stationary process has been discussed in the literature. However, when the measurements are from a non-stationary process, how to assess their uncertainty remains unresolved. Allan variance or two-sample variance has been used in time and frequency metrology for more than three decades as a substitute for the classical variance to characterize the stability of clocks or frequency standards when the underlying process is a 1/f noise process. However, its applications are related only to the noise models characterized by the power law of the spectral density. In this paper, from the viewpoint of the time domain, we provide a statistical underpinning of the Allan variance for discrete stationary processes, random walk and long-memory processes such as the fractional difference processes including the noise models usually considered in time and frequency metrology. Results show that the Allan variance is a better measure of the process variation than the classical variance of the random walk and the non-stationary fractional difference processes including the 1/f noise.

  15. Variance estimation in the analysis of microarray data.

    PubMed

    Wang, Yuedong; Ma, Yanyuan; Carroll, Raymond J

    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.

  16. Variance estimation for systematic designs in spatial surveys.

    PubMed

    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.

  17. Sensitivity analyses of turbulence theory-based variance-covariance matrices of tropospheric slant delays

    NASA Astrophysics Data System (ADS)

    Vennebusch, M.; Schön, S.

    2009-04-01

    Atmospheric turbulence induces physical correlations on any space geodetic technique based on electromagnetic waves. Thus, also GNSS phase observations are both temporally and spatially correlated due to refractivity fluctuations along the signal's path from the transmitter to the receiver. Currently, these physical correlations are rarely considered in GNSS data analysis; yielding too optimistic parameter variances and covariances. Based on turbulence theory, Schön and Brunner (2008) developed a formulation of the variances and covariances induced by refractivity fluctuations in the troposphere. This model adequately describes the variance-covariance matrix (VCM) of tropospheric slant delays. The parametrisation is mainly based on the turbulence structure constant, the outer scale length, the integration height, the wind direction and the observation geometry. The VCM can adequately be used to determine synthetic slant delay time series. In this paper, this strategy will be described by using an exemplary GPS configuration. Furthermore, the latest results of simulation studies and sensitivity analyses of this VCM model w.r.t. the model parameters are presented. As a result, the most dominant parameters (that should be either determined with special care or precisely known) will be identified.

  18. Finger enslaving in the dominant and non-dominant hand.

    PubMed

    Wilhelm, Luke A; Martin, Joel R; Latash, Mark L; Zatsiorsky, Vladimir M

    2014-02-01

    During single-finger force production, the non-instructed fingers unintentionally produce force (finger enslaving). In this study, enslaving effects were compared between the dominant and non-dominant hands. The test consisted of a series of maximum voluntary contractions with different finger combinations. Enslaving matrices were calculated by means of training an artificial neural network. The dominant hand was found to be stronger, but there was found to be no difference between the overall enslaving effects in the dominant and non-dominant hands. There was no correlation between the magnitude of finger enslaving and the performance in such tests as the Edinburgh Handedness Inventory, the Grooved Pegboard test, and the Jebsen-Taylor Hand Function test. Each one of those three tests showed a significant difference between the dominant and non-dominant hand performances. Eleven subjects were retested after two months, and it was found that enslaving effects did not fluctuate significantly between the two testing sessions. While the dominant and non-dominant hands are involved differently in everyday tasks, e.g. in writing or eating, this practice does not cause significant differences in enslaving between the hands.

  19. 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.

    PubMed

    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

  20. Effects of functional group mass variance on vibrational properties and thermal transport in graphene

    NASA Astrophysics Data System (ADS)

    Lindsay, L.; Kuang, Y.

    2017-03-01

    Intrinsic thermal resistivity critically depends on features of phonon dispersions dictated by harmonic interatomic forces and masses. Here we present the effects of functional group mass variance on vibrational properties and thermal conductivity (κ ) of functionalized graphene from first-principles calculations. We use graphane, a buckled graphene backbone with covalently bonded hydrogen atoms on both sides, as the base material and vary the mass of the hydrogen atoms to simulate the effect of mass variance from other functional groups. We find nonmonotonic behavior of κ with increasing mass of the functional group and an unusual crossover from acoustic-dominated to optic-dominated thermal transport behavior. We connect this crossover to changes in the phonon dispersion with varying mass which suppress acoustic phonon velocities, but also give unusually high velocity optic modes. Further, we show that out-of-plane acoustic vibrations contribute significantly more to thermal transport than in-plane acoustic modes despite breaking of a reflection-symmetry-based scattering selection rule responsible for their large contributions in graphene. This work demonstrates the potential for manipulation and engineering of thermal transport properties in two-dimensional materials toward targeted applications.

  1. Effects of functional group mass variance on vibrational properties and thermal transport in graphene

    DOE PAGES

    Lindsay, L.; Kuang, Y.

    2017-03-13

    Intrinsic thermal resistivity critically depends on features of phonon dispersions dictated by harmonic interatomic forces and masses. We present the effects of functional group mass variance on vibrational properties and thermal conductivity (κ ) of functionalized graphene from first principles calculations. We also use graphane, a buckled graphene backbone with covalently bonded Hydrogen atoms on both sides, as the base material and vary the mass of the Hydrogen atoms to simulate the effect of mass variance from other functional groups. We find non-monotonic behavior of κ with increasing mass of the functional group and an unusual cross-over from acoustic-dominated tomore » optic-dominated thermal transport behavior. We connect this cross-over to changes in the phonon dispersion with varying mass which suppress acoustic phonon velocities, but also give unusually high velocity optic modes. Further, we show that out-of-plane acoustic vibrations contribute significantly more to thermal transport than in-plane acoustic modes despite breaking of a reflection symmetry based scattering selection rule responsible for their large contributions in graphene. Our work demonstrates the potential for manipulation and engineering of thermal transport properties in two dimensional materials toward targeted applications.« less

  2. Developing and Fielding Information Dominance

    DTIC Science & Technology

    2002-01-01

    Developing and Fielding Information Dominance Space and Naval Warfare Systems Command’s IT-21 Blocks 1 and 2 2002 Command and Control Research and...00-00-2002 4. TITLE AND SUBTITLE Developing and Fielding Information Dominance 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER...force levels were uncertain, the necessary role of information dominance to maintaining strategic superiority was not. Platform Centric Warfare, with its

  3. Variance in prey abundance influences time budgets of breeding seabirds: Evidence from pigeon guillemots Cepphus columba

    USGS Publications Warehouse

    Litzow, Michael A.; Piatt, J.F.

    2003-01-01

    We use data on pigeon guillemots Cepphus columba to test the hypothesis that discretionary time in breeding seabirds is correlated with variance in prey abundance. We measured the amount of time that guillemots spent at the colony before delivering fish to chicks ("resting time") in relation to fish abundance as measured by beach seines and bottom trawls. Radio telemetry showed that resting time was inversely correlated with time spent diving for fish during foraging trips (r = -0.95). Pigeon guillemots fed their chicks either Pacific sand lance Ammodytes hexapterus, a schooling midwater fish, which exhibited high interannual variance in abundance (CV = 181%), or a variety of non-schooling demersal fishes, which were less variable in abundance (average CV = 111%). Average resting times were 46% higher at colonies where schooling prey dominated the diet. Individuals at these colonies reduced resting times 32% during years of low food abundance, but did not reduce meal delivery rates. In contrast, individuals feeding on non-schooling fishes did not reduce resting times during low food years, but did reduce meal delivery rates by 27%. Interannual variance in resting times was greater for the schooling group than for the non-schooling group. We conclude from these differences that time allocation in pigeon guillemots is more flexible when variable schooling prey dominate diets. Resting times were also 27% lower for individuals feeding two-chick rather than one-chick broods. The combined effects of diet and brood size on adult time budgets may help to explain higher rates of brood reduction for pigeon guillemot chicks fed non-schooling fishes.

  4. Accounting for heterogeneous variances in multitrait evaluation of Jersey type traits.

    PubMed

    Gengler, N; Wiggans, G R; Thornton, L L M; Wright, J R; Druet, T

    2006-08-01

    The multitrait genetic evaluation system for type traits was modified to estimate adjustments for heterogeneous variance (HV) simultaneously with estimated breeding values (EBV) for final score and 14 linear traits. Each variance within herd, year, and parity was regressed toward a predicted variance, which was determined by fitting a model with fixed effects of the mean final score for herd, size of the contemporary group, appraisal month, and year-season and a random effect for herd-appraisal date. Herd-appraisal date was included as a random effect to regress the observed heterogeneity for a given herd-appraisal date toward the fixed effects. Method R was used to estimate variances for the heterogeneity model in each EBV iteration. To evaluate the effect of the adjustment, parent averages were calculated from evaluations with recent appraisals removed. The adjustment slightly improved correlations within birth year between those parent averages and EBV from current data on bulls for most traits, but did not improve correlations for final score, strength, dairy form, teat length, or foot angle. Annual trends for EBV were lower with HV adjustment than for unadjusted EBV for all traits except final score and rump angle for cows and rump width for bulls, which were essentially unchanged. Standard deviations of Mendelian sampling (evaluation minus mean of parent evaluations) declined less over time for HV-adjusted than for unadjusted evaluations. The slope at year 2000 of Mendelian-sampling standard deviations from HV-adjusted evaluations ranged from 10.0% for udder depth to 42.7% for teat length compared with the slope for unadjusted evaluations. This HV adjustment, which was implemented for USDA evaluations in May 2001 for Jerseys and in 2002 for other breeds, improves the accuracy of evaluations, particularly comparisons over time, by accounting for the change in variation.

  5. The decline in fitness with inbreeding: evidence for negative dominance-by-dominance epistasis in Drosophila melanogaster.

    PubMed

    Sharp, N P; Agrawal, A F

    2016-04-01

    Genetic interactions can play an important role in the evolution of reproductive strategies. In particular, negative dominance-by-dominance epistasis for fitness can theoretically favour sex and recombination. This form of epistasis can be detected statistically because it generates nonlinearity in the relationship between fitness and inbreeding coefficient. Measures of fitness in progressively inbred lines tend to show limited evidence for epistasis. However, tests of this kind can be biased against detecting an accelerating decline due to line losses at higher inbreeding levels. We tested for dominance-by-dominance epistasis in Drosophila melanogaster by examining viability at five inbreeding levels that were generated simultaneously, avoiding the bias against detecting nonlinearity that has affected previous studies. We find an accelerating rate of fitness decline with inbreeding, indicating that dominance-by-dominance epistasis is negative on average, which should favour sex and recombination.

  6. Estimating Variances of Horizontal Wind Fluctuations in Stable Conditions

    NASA Astrophysics Data System (ADS)

    Luhar, Ashok K.

    2010-05-01

    Information concerning the average wind speed and the variances of lateral and longitudinal wind velocity fluctuations is required by dispersion models to characterise turbulence in the atmospheric boundary layer. When the winds are weak, the scalar average wind speed and the vector average wind speed need to be clearly distinguished and both lateral and longitudinal wind velocity fluctuations assume equal importance in dispersion calculations. We examine commonly-used methods of estimating these variances from wind-speed and wind-direction statistics measured separately, for example, by a cup anemometer and a wind vane, and evaluate the implied relationship between the scalar and vector wind speeds, using measurements taken under low-wind stable conditions. We highlight several inconsistencies inherent in the existing formulations and show that the widely-used assumption that the lateral velocity variance is equal to the longitudinal velocity variance is not necessarily true. We derive improved relations for the two variances, and although data under stable stratification are considered for comparison, our analysis is applicable more generally.

  7. Practice reduces task relevant variance modulation and forms nominal trajectory

    NASA Astrophysics Data System (ADS)

    Osu, Rieko; Morishige, Ken-Ichi; Nakanishi, Jun; Miyamoto, Hiroyuki; Kawato, Mitsuo

    2015-12-01

    Humans are capable of achieving complex tasks with redundant degrees of freedom. Much attention has been paid to task relevant variance modulation as an indication of online feedback control strategies to cope with motor variability. Meanwhile, it has been discussed that the brain learns internal models of environments to realize feedforward control with nominal trajectories. Here we examined trajectory variance in both spatial and temporal domains to elucidate the relative contribution of these control schemas. We asked subjects to learn reaching movements with multiple via-points, and found that hand trajectories converged to stereotyped trajectories with the reduction of task relevant variance modulation as learning proceeded. Furthermore, variance reduction was not always associated with task constraints but was highly correlated with the velocity profile. A model assuming noise both on the nominal trajectory and motor command was able to reproduce the observed variance modulation, supporting an expression of nominal trajectories in the brain. The learning-related decrease in task-relevant modulation revealed a reduction in the influence of optimal feedback around the task constraints. After practice, the major part of computation seems to be taken over by the feedforward controller around the nominal trajectory with feedback added only when it becomes necessary.

  8. Increased spatial variance accompanies reorganization of two continental shelf ecosystems.

    PubMed

    Litzow, Michael A; Urban, J Daniel; Laurel, Benjamin J

    2008-09-01

    Phase transitions between alternate stable states in marine ecosystems lead to disruptive changes in ecosystem services, especially fisheries productivity. We used trawl survey data spanning phase transitions in the North Pacific (Gulf of Alaska) and the North Atlantic (Scotian Shelf) to test for increases in ecosystem variability that might provide early warning of such transitions. In both time series, elevated spatial variability in a measure of community composition (ratio of cod [Gadus sp.] abundance to prey abundance) accompanied transitions between ecosystem states, and variability was negatively correlated with distance from the ecosystem transition point. In the Gulf of Alaska, where the phase transition was apparently the result of a sudden perturbation (climate regime shift), variance increased one year before the transition in mean state occurred. On the Scotian Shelf, where ecosystem reorganization was the result of persistent overfishing, a significant increase in variance occurred three years before the transition in mean state was detected. However, we could not reject the alternate explanation that increased variance may also have simply been inherent to the final stable state in that ecosystem. Increased variance has been previously observed around transition points in models, but rarely in real ecosystems, and our results demonstrate the possible management value in tracking the variance of key parameters in exploited ecosystems.

  9. Direct and maternal (co)variance components and heritability estimates for body weights in Chokla sheep.

    PubMed

    Kushwaha, B P; Mandal, A; Arora, A L; Kumar, R; Kumar, S; Notter, D R

    2009-08-01

    Estimates of (co)variance components were obtained for weights at birth, weaning and 6, 9 and 12 months of age in Chokla sheep maintained at the Central Sheep and Wool Research Institute, Avikanagar, Rajasthan, India, over a period of 21 years (1980-2000). Records of 2030 lambs descended from 150 rams and 616 ewes were used in the study. Analyses were carried out by restricted maximum likelihood (REML) fitting an animal model and ignoring or including maternal genetic or permanent environmental effects. Six different animal models were fitted for all traits. The best model was chosen after testing the improvement of the log-likelihood values. Direct heritability estimates were inflated substantially for all traits when maternal effects were ignored. Heritability estimates for weight at birth, weaning and 6, 9 and 12 months of age were 0.20, 0.18, 0.16, 0.22 and 0.23, respectively in the best models. Additive maternal and maternal permanent environmental effects were both significant at birth, accounting for 9% and 12% of phenotypic variance, respectively, but the source of maternal effects (additive versus permanent environmental) at later ages could not be clearly identified. The estimated repeatabilities across years of ewe effects on lamb body weights were 0.26, 0.14, 0.12, 0.13, and 0.15 at birth, weaning, 6, 9 and 12 months of age, respectively. These results indicate that modest rates of genetic progress are possible for all weights.

  10. Spatial and temporal genetic structure in a hybrid cordgrass invasion.

    PubMed

    Sloop, C M; Ayres, D R; Strong, D R

    2011-04-01

    Invasive hybrids and their spread dynamics pose unique opportunities to study evolutionary processes. Invasive hybrids of native Spartina foliosa and introduced S. alterniflora have expanded throughout San Francisco Bay intertidal habitats within the past 35 years by deliberate plantation and seeds floating on the tide. Our goals were to assess spatial and temporal scales of genetic structure in Spartina hybrid populations within the context of colonization history. We genotyped adult and seedling Spartina using 17 microsatellite loci and mapped their locations in three populations. All sampled seedlings were hybrids. Bayesian ordination analysis distinguished hybrid populations from parent species, clearly separated the population that originated by plantation from populations that originated naturally by seed and aligned most seedlings within each population. Population genetic structure estimated by analysis of molecular variance was substantial (F(ST)=0.21). Temporal genetic structure among age classes varied highly between populations. At one population, the divergence between adults and 2004 seedlings was low (F(ST)=0.02) whereas at another population this divergence was high (F(ST)=0.26). This latter result was consistent with local recruitment of self-fertilized seed produced by only a few parental plants. We found fine-scale spatial genetic structure at distances less than ∼200 m, further supporting local seed and/or pollen dispersal. We posit a few self-fertile plants dominating local recruitment created substantial spatial genetic structure despite initial long-distance, human dispersal of hybrid Spartina through San Francisco Bay. Fine-scale genetic structure may more strongly develop when local recruits are dominated by the offspring of a few self-fertile plants.

  11. Early onset autosomal dominant spinocerebellar ataxia with miosis: four cases.

    PubMed

    Timby, Niklas; Stattin, Eva-Lena; Kristiansen, Ingela; Eriksson, Urban; Erikson, Anders

    2008-01-01

    Previously, at least 29 different forms of autosomal dominant spinocerebellar ataxias (SCAs) have been described. We describe a family with four members through three generations with autosomal dominant ataxia in combination with miosis and hyperreflexia. This family's ataxia does not match any of the previously described SCAs and is probably a novel form of SCA. To continue with the search for the genetic background of this disease, more cases are needed.

  12. Dominance Hierarchies in Young Children

    ERIC Educational Resources Information Center

    Edelman, Murray S.; Omark, Donald R.

    1973-01-01

    This study uses the ethological approach of seeking species characteristics and phylogenetic continuities in an investigation of human behavior. Among primates a striking consistency is the presence of some form of dominance hierarchy in many species. The present study examines peer group dominance hierarchies as they are perceived by children in…

  13. Brain Dominance & Self-Actualization.

    ERIC Educational Resources Information Center

    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…

  14. Dominant Leadership Style in Schools

    ERIC Educational Resources Information Center

    Rajbhandari, Mani Man Singh

    2006-01-01

    The dominant leadership style is defined by the situation and the kind of organizational environment and climate. This, however, does not sufficiently define the leadership qualities in school organizations. There are other factors which also determine the dominant leadership style, which are the traits and style, teachers commitments, pass out…

  15. Sensitivity analysis of simulated SOA loadings using a variance-based statistical approach: SENSITIVITY ANALYSIS OF SOA

    SciTech Connect

    Shrivastava, Manish; Zhao, Chun; Easter, Richard C.; Qian, Yun; Zelenyuk, Alla; Fast, Jerome D.; Liu, Ying; Zhang, Qi; Guenther, Alex

    2016-04-08

    We investigate the sensitivity of secondary organic aerosol (SOA) loadings simulated by a regional chemical transport model to 7 selected tunable model parameters: 4 involving emissions of anthropogenic and biogenic volatile organic compounds, anthropogenic semi-volatile and intermediate volatility organics (SIVOCs), and NOx, 2 involving dry deposition of SOA precursor gases, and one involving particle-phase transformation of SOA to low volatility. We adopt a quasi-Monte Carlo sampling approach to effectively sample the high-dimensional parameter space, and perform a 250 member ensemble of simulations using a regional model, accounting for some of the latest advances in SOA treatments based on our recent work. We then conduct a variance-based sensitivity analysis using the generalized linear model method to study the responses of simulated SOA loadings to the tunable parameters. Analysis of SOA variance from all 250 simulations shows that the volatility transformation parameter, which controls whether particle-phase transformation of SOA from semi-volatile SOA to non-volatile is on or off, is the dominant contributor to variance of simulated surface-level daytime SOA (65% domain average contribution). We also split the simulations into 2 subsets of 125 each, depending on whether the volatility transformation is turned on/off. For each subset, the SOA variances are dominated by the parameters involving biogenic VOC and anthropogenic SIVOC emissions. Furthermore, biogenic VOC emissions have a larger contribution to SOA variance when the SOA transformation to non-volatile is on, while anthropogenic SIVOC emissions have a larger contribution when the transformation is off. NOx contributes less than 4.3% to SOA variance, and this low contribution is mainly attributed to dominance of intermediate to high NOx conditions throughout the simulated domain. The two parameters related to dry deposition of SOA precursor gases also have very low contributions to SOA variance

  16. Saturation of number variance in embedded random-matrix ensembles.

    PubMed

    Prakash, Ravi; Pandey, Akhilesh

    2016-05-01

    We study fluctuation properties of embedded random matrix ensembles of noninteracting particles. For ensemble of two noninteracting particle systems, we find that unlike the spectra of classical random matrices, correlation functions are nonstationary. In the locally stationary region of spectra, we study the number variance and the spacing distributions. The spacing distributions follow the Poisson statistics, which is a key behavior of uncorrelated spectra. The number variance varies linearly as in the Poisson case for short correlation lengths but a kind of regularization occurs for large correlation lengths, and the number variance approaches saturation values. These results are known in the study of integrable systems but are being demonstrated for the first time in random matrix theory. We conjecture that the interacting particle cases, which exhibit the characteristics of classical random matrices for short correlation lengths, will also show saturation effects for large correlation lengths.

  17. Monte Carlo variance reduction approaches for non-Boltzmann tallies

    SciTech Connect

    Booth, T.E.

    1992-12-01

    Quantities that depend on the collective effects of groups of particles cannot be obtained from the standard Boltzmann transport equation. Monte Carlo estimates of these quantities are called non-Boltzmann tallies and have become increasingly important recently. Standard Monte Carlo variance reduction techniques were designed for tallies based on individual particles rather than groups of particles. Experience with non-Boltzmann tallies and analog Monte Carlo has demonstrated the severe limitations of analog Monte Carlo for many non-Boltzmann tallies. In fact, many calculations absolutely require variance reduction methods to achieve practical computation times. Three different approaches to variance reduction for non-Boltzmann tallies are described and shown to be unbiased. The advantages and disadvantages of each of the approaches are discussed.

  18. Impact of Damping Uncertainty on SEA Model Response Variance

    NASA Technical Reports Server (NTRS)

    Schiller, Noah; Cabell, Randolph; Grosveld, Ferdinand

    2010-01-01

    Statistical Energy Analysis (SEA) is commonly used to predict high-frequency vibroacoustic levels. This statistical approach provides the mean response over an ensemble of random subsystems that share the same gross system properties such as density, size, and damping. Recently, techniques have been developed to predict the ensemble variance as well as the mean response. However these techniques do not account for uncertainties in the system properties. In the present paper uncertainty in the damping loss factor is propagated through SEA to obtain more realistic prediction bounds that account for both ensemble and damping variance. The analysis is performed on a floor-equipped cylindrical test article that resembles an aircraft fuselage. Realistic bounds on the damping loss factor are determined from measurements acquired on the sidewall of the test article. The analysis demonstrates that uncertainties in damping have the potential to significantly impact the mean and variance of the predicted response.

  19. Divergent clonal selection dominates medulloblastoma at recurrence

    PubMed Central

    Morrissy, A. Sorana; Garzia, Livia; Shih, David J. H.; Zuyderduyn, Scott; Huang, Xi; Skowron, Patryk; Remke, Marc; Cavalli, Florence M. G.; Ramaswamy, Vijay; Lindsay, Patricia E.; Jelveh, Salomeh; Donovan, Laura K.; Wang, Xin; Luu, Betty; Zayne, Kory; Li, Yisu; Mayoh, Chelsea; Thiessen, Nina; Mercier, Eloi; Mungall, Karen L.; Ma, Yusanne; Tse, Kane; Zeng, Thomas; Shumansky, Karey; Roth, Andrew J. L.; Shah, Sohrab; Farooq, Hamza; Kijima, Noriyuki; Holgado, Borja L.; Lee, John J. Y.; Matan-Lithwick, Stuart; Liu, Jessica; Mack, Stephen C.; Manno, Alex; Michealraj, K. A.; Nor, Carolina; Peacock, John; Qin, Lei; Reimand, Juri; Rolider, Adi; Thompson, Yuan Y.; Wu, Xiaochong; Pugh, Trevor; Ally, Adrian; Bilenky, Mikhail; Butterfield, Yaron S. N.; Carlsen, Rebecca; Cheng, Young; Chuah, Eric; Corbett, Richard D.; Dhalla, Noreen; He, An; Lee, Darlene; Li, Haiyan I.; Long, William; Mayo, Michael; Plettner, Patrick; Qian, Jenny Q.; Schein, Jacqueline E.; Tam, Angela; Wong, Tina; Birol, Inanc; Zhao, Yongjun; Faria, Claudia C.; Pimentel, José; Nunes, Sofia; Shalaby, Tarek; Grotzer, Michael; Pollack, Ian F.; Hamilton, Ronald L.; Li, Xiao-Nan; Bendel, Anne E.; Fults, Daniel W.; Walter, Andrew W.; Kumabe, Toshihiro; Tominaga, Teiji; Collins, V. Peter; Cho, Yoon-Jae; Hoffman, Caitlin; Lyden, David; Wisoff, Jeffrey H.; Garvin, James H.; Stearns, Duncan S.; Massimi, Luca; Schüller, Ulrich; Sterba, Jaroslav; Zitterbart, Karel; Puget, Stephanie; Ayrault, Olivier; Dunn, Sandra E.; Tirapelli, Daniela P. C.; Carlotti, Carlos G.; Wheeler, Helen; Hallahan, Andrew R.; Ingram, Wendy; MacDonald, Tobey J.; Olson, Jeffrey J.; Van Meir, Erwin G.; Lee, Ji-Yeoun; Wang, Kyu-Chang; Kim, Seung-Ki; Cho, Byung-Kyu; Pietsch, Torsten; Fleischhack, Gudrun; Tippelt, Stephan; Ra, Young Shin; Bailey, Simon; Lindsey, Janet C.; Clifford, Steven C.; Eberhart, Charles G.; Cooper, Michael K.; Packer, Roger J.; Massimino, Maura; Garre, Maria Luisa; Bartels, Ute; Tabori, Uri; Hawkins, Cynthia E.; Dirks, Peter; Bouffet, Eric; Rutka, James T.; Wechsler-Reya, Robert J.; Weiss, William A.; Collier, Lara S.; Dupuy, Adam J.; Korshunov, Andrey; Jones, David T. W.; Kool, Marcel; Northcott, Paul A.; Pfister, Stefan M.; Largaespada, David A.; Mungall, Andrew J.; Moore, Richard A.; Jabado, Nada; Bader, Gary D.; Jones, Steven J. M.; Malkin, David; Marra, Marco A.; Taylor, Michael D.

    2016-01-01

    The development of targeted anti-cancer therapies through the study of cancer genomes is intended to increase survival rates and decrease treatment-related toxicity. We treated a transposon–driven, functional genomic mouse model of medulloblastoma with ‘humanized’ in vivo therapy (microneurosurgical tumour resection followed by multi-fractionated, image-guided radiotherapy). Genetic events in recurrent murine medulloblastoma exhibit a very poor overlap with those in matched murine diagnostic samples (<5%). Whole-genome sequencing of 33 pairs of human diagnostic and post-therapy medulloblastomas demonstrated substantial genetic divergence of the dominant clone after therapy (<12% diagnostic events were retained at recurrence). In both mice and humans, the dominant clone at recurrence arose through clonal selection of a pre-existing minor clone present at diagnosis. Targeted therapy is unlikely to be effective in the absence of the target, therefore our results offer a simple, proximal, and remediable explanation for the failure of prior clinical trials of targeted therapy. PMID:26760213

  20. Nature vs nurture: are leaders born or made? A behavior genetic investigation of leadership style.

    PubMed

    Johnson, A M; Vernon, P A; McCarthy, J M; Molson, M; Harris, J A; Jang, K L

    1998-12-01

    With the recent resurgence in popularity of trait theories of leadership, it is timely to consider the genetic determination of the multiple factors comprising the leadership construct. Individual differences in personality traits have been found to be moderately to highly heritable, and so it follows that if there are reliable personality trait differences between leaders and non-leaders, then there may be a heritable component to these individual differences. Despite this connection between leadership and personality traits, however, there are no studies of the genetic basis of leadership using modern behavior genetic methodology. The present study proposes to address the lack of research in this area by examining the heritability of leadership style, as measured by self-report psychometric inventories. The Multifactor Leadership Questionnaire (MLQ), the Leadership Ability Evaluation, and the Adjective Checklist were completed by 247 adult twin pairs (183 monozygotic and 64 same-sex dizygotic). Results indicated that most of the leadership dimensions examined in this study are heritable, as are two higher level factors (resembling transactional and transformational leadership) derived from an obliquely rotated principal components factors analysis of the MLQ. Univariate analyses suggested that 48% of the variance in transactional leadership may be explained by additive heritability, and 59% of the variance in transformational leadership may be explained by non-additive (dominance) heritability. Multivariate analyses indicated that most of the variables studied shared substantial genetic covariance, suggesting a large overlap in the underlying genes responsible for the leadership dimensions.

  1. Genomewide mapping reveals a combination of different genetic effects causing the genetic basis of heterosis in two elite rice hybrids.

    PubMed

    Li, Lanzhi; He, Xiaohong; Zhang, Hongyan; Wang, Zhiming; Sun, Congwei; Mou, Tongmin; Li, Xinqi; Zhang, Yuanming; Hu, Zhongli

    2015-06-01

    North Carolina design III (NCIII) is one of the most powerful and widely used mating designs for understanding the genetic basis of heterosis. However, the quantitative trait mapping (QTL) conducted in previous studies with this design was mainly based on analysis of variance (ANOVA), composite interval or multiple interval mapping methods. These methodologies could not investigate all kinds of genetic effects, especially epistatic effects, simultaneously on the whole genome. In this study, with a statistical method for mapping epistatic QTL associated with heterosis using the recombinant inbred line (RIL)-based NCIII design, we conducted QTL mapping for nine agronomic traits of two elite hybrids to characterize the mode of gene action contributing to heterosis on a whole genomewide scale. In total, 23 main-effect QTL (M-QTL) and 23 digenic interactions in IJ (indica x japonica) hybrids, 11 M-QTL and 82 digenic interactions in II (indica x indica) hybrid QTLs were identified in the present study. The variation explained by individual M-QTL or interactions ranged from 2.3 to 11.0%. The number of digenic interactions and the total variation explained by interactions of each trait were larger than those of M-QTL. The augmented genetic effect ratio of most M-QTL and digenic interactions in (L1 - L2) data of two backcross populations (L1 and L2) showed complete dominance or overdominance, and in (L1 + L2) data showed an additive effect. Our results indicated that the dominance, overdominance and epistatic effect were important in conditioning the genetic basis of heterosis of the two elite hybrids. The relative contributions of the genetic components varied with traits and the genetic basis of the two hybrids was different.

  2. The diminishing dominance of the dominant hemisphere: Language fMRI in focal epilepsy.

    PubMed

    Tailby, Chris; Abbott, David F; Jackson, Graeme D

    2017-01-01

    "Which is the dominant hemisphere?" is a question that arises frequently in patients considered for neurosurgery. The concept of the dominant hemisphere implies uniformity of language lateralisation throughout the brain. It is increasingly recognised that this is not the case in the healthy control brain, and it is especially not so in neurological diseases such as epilepsy. In the present work we adapt our published objective lateralisation method (based on the construction of laterality curves) for use with sub-lobar cortical, subcortical and cerebellar regions of interest (ROIs). We apply this method to investigate regional lateralisation of language activation in 12 healthy controls and 18 focal epilepsy patients, using three different block design language fMRI paradigms, each tapping different aspects of language processing. We compared lateralisation within each ROI across tasks, and investigated how the quantity of data collected affected the ability to robustly estimate laterality across ROIs. In controls, lateralisation was stronger, and the variance across individuals smaller, in cortical ROIs, particularly in the Inferior Frontal (Broca) region. Lateralisation within temporal ROIs was dependent on the nature of the language task employed. One of the healthy controls was left lateralised anteriorly and right lateralised posteriorly. Consistent with previous work, departures from normality occurred in ~ 15-50% of focal epilepsy patients across the different ROIs, with atypicality most common in the Lateral Temporal (Wernicke) region. Across tasks and ROIs the absolute magnitude of the laterality estimate increased and its across participant variance decreased as more cycles of task and rest were included, stabilising at ~ 4 cycles (~ 4 min of data collection). Our data highlight the importance of considering language as a complex task where lateralisation varies at the subhemispheric scale. This is especially important for presurgical planning for

  3. The mean and variance of phylogenetic diversity under rarefaction.

    PubMed

    Nipperess, David A; Matsen, Frederick A

    2013-06-01

    Phylogenetic diversity (PD) depends on sampling depth, which complicates the comparison of PD between samples of different depth. One approach to dealing with differing sample depth for a given diversity statistic is to rarefy, which means to take a random subset of a given size of the original sample. Exact analytical formulae for the mean and variance of species richness under rarefaction have existed for some time but no such solution exists for PD.We have derived exact formulae for the mean and variance of PD under rarefaction. We confirm that these formulae are correct by comparing exact solution mean and variance to that calculated by repeated random (Monte Carlo) subsampling of a dataset of stem counts of woody shrubs of Toohey Forest, Queensland, Australia. We also demonstrate the application of the method using two examples: identifying hotspots of mammalian diversity in Australasian ecoregions, and characterising the human vaginal microbiome.There is a very high degree of correspondence between the analytical and random subsampling methods for calculating mean and variance of PD under rarefaction, although the Monte Carlo method requires a large number of random draws to converge on the exact solution for the variance.Rarefaction of mammalian PD of ecoregions in Australasia to a common standard of 25 species reveals very different rank orderings of ecoregions, indicating quite different hotspots of diversity than those obtained for unrarefied PD. The application of these methods to the vaginal microbiome shows that a classical score used to quantify bacterial vaginosis is correlated with the shape of the rarefaction curve.The analytical formulae for the mean and variance of PD under rarefaction are both exact and more efficient than repeated subsampling. Rarefaction of PD allows for many applications where comparisons of samples of different depth is required.

  4. Enhancing area of review capabilities: Implementing a variance program

    SciTech Connect

    De Leon, F.

    1995-12-01

    The Railroad Commission of Texas (RRC) has regulated oil-field injection well operations since issuing its first injection permit in 1938. The Environmental Protection Agency (EPA) granted the RRC primary enforcement responsibility for the Class H Underground Injection Control (UIC) Program in April 1982. At that time, the added level of groundwater protection afforded by an Area of Review (AOR) on previously permitted Class H wells was not deemed necessary or cost effective. A proposed EPA rule change will require AORs to be performed on all pre-primacy Class II wells unless a variance can be justified. A variance methodology has been developed by researchers at the University of Missouri-Rolla in conjunction with the American Petroleum Institute (API). This paper will outline the RRC approach to implementing the AOR variance methodology. The RRC`s UIC program tracks 49,256 pre-primacy wells. Approximately 25,598 of these wells have active permits and will be subject to the proposed AOR requirements. The potential workload of performing AORs or granting variances for this many wells makes the development of a Geographic Information System (GIS) imperative. The RRC has recently completed a digitized map of the entire state and has spotted 890,000 of an estimated 1.2 million wells. Integrating this digital state map into a GIS will allow the RRC to tie its many data systems together. Once in place, this integrated data system will be used to evaluate AOR variances for pre-primacy wells on a field-wide basis. It will also reduce the regulatory cost of permitting by allowing the RRC staff to perform AORs or grant variances for the approximately 3,000 new and amended permit applications requiring AORs each year.

  5. Familial pulmonary hypertension. Evidence of autosomal dominant inheritance.

    PubMed Central

    Thompson, P; McRae, C

    1970-01-01

    A patient with primary pulmonary hypertension is the fourth member of a family proven to have the disease. The patient's father married twice; the disease appeared in both families, and was transmitted through two generations. Multiple genetic and environmental factors may result in pulmonary hypertension, but the distribution of cases in this family and in others reported is consistent with the autosomal dominant inheritance of a single genetic trait. PMID:5212347

  6. The dynamic Allan Variance IV: characterization of atomic clock anomalies.

    PubMed

    Galleani, Lorenzo; Tavella, Patrizia

    2015-05-01

    The number of applications where precise clocks play a key role is steadily increasing, satellite navigation being the main example. Precise clock anomalies are hence critical events, and their characterization is a fundamental problem. When an anomaly occurs, the clock stability changes with time, and this variation can be characterized with the dynamic Allan variance (DAVAR). We obtain the DAVAR for a series of common clock anomalies, namely, a sinusoidal term, a phase jump, a frequency jump, and a sudden change in the clock noise variance. These anomalies are particularly common in space clocks. Our analytic results clarify how the clock stability changes during these anomalies.

  7. Entropy, Fisher Information and Variance with Frost-Musulin Potenial

    NASA Astrophysics Data System (ADS)

    Idiodi, J. O. A.; Onate, C. A.

    2016-09-01

    This study presents the Shannon and Renyi information entropy for both position and momentum space and the Fisher information for the position-dependent mass Schrödinger equation with the Frost-Musulin potential. The analysis of the quantum mechanical probability has been obtained via the Fisher information. The variance information of this potential is equally computed. This controls both the chemical properties and physical properties of some of the molecular systems. We have observed the behaviour of the Shannon entropy. Renyi entropy, Fisher information and variance with the quantum number n respectively.

  8. Studying Variance in the Galactic Ultra-compact Binary Population

    NASA Astrophysics Data System (ADS)

    Larson, Shane; Breivik, Katelyn

    2017-01-01

    In the years preceding LISA, Milky Way compact binary population simulations can be used to inform the science capabilities of the mission. Galactic population simulation efforts generally focus on high fidelity models that require extensive computational power to produce a single simulated population for each model. Each simulated population represents an incomplete sample of the functions governing compact binary evolution, thus introducing variance from one simulation to another. We present a rapid Monte Carlo population simulation technique that can simulate thousands of populations on week-long timescales, thus allowing a full exploration of the variance associated with a binary stellar evolution model.

  9. The principle of stationary variance in quantum field theory

    NASA Astrophysics Data System (ADS)

    Siringo, Fabio

    2014-02-01

    The principle of stationary variance is advocated as a viable variational approach to quantum field theory (QFT). The method is based on the principle that the variance of energy should be at its minimum when the state of a quantum system reaches its best approximation for an eigenstate. While not too much popular in quantum mechanics (QM), the method is shown to be valuable in QFT and three special examples are given in very different areas ranging from Heisenberg model of antiferromagnetism (AF) to quantum electrodynamics (QED) and gauge theories.

  10. Variance components models for gene-environment interaction in twin analysis.

    PubMed

    Purcell, Shaun

    2002-12-01

    Gene-environment interaction is likely to be a common and important source of variation for complex behavioral traits. Often conceptualized as the genetic control of sensitivity to the environment, it can be incorporated in variance components twin analyses by partitioning genetic effects into a mean part, which is independent of the environment, and a part that is a linear function of the environment. The model allows for one or more environmental moderator variables (that possibly interact with each other) that may i). be continuous or binary ii). differ between twins within a pair iii). interact with residual environmental as well as genetic effects iv) have nonlinear moderating properties v). show scalar (different magnitudes) or qualitative (different genes) interactions vi). be correlated with genetic effects acting upon the trait, to allow for a test of gene-environment interaction in the presence of gene-environment correlation. Aspects and applications of a class of models are explored by simulation, in the context of both individual differences twin analysis and, in a companion paper (Purcell & Sham, 2002) sibpair quantitative trait locus linkage analysis. As well as elucidating environmental pathways, consideration of gene-environment interaction in quantitative and molecular studies will potentially direct and enhance gene-mapping efforts.

  11. Non-syndromic autosomal-dominant deafness.

    PubMed

    Petersen, M B

    2002-07-01

    Non-syndromic deafness is a paradigm of genetic heterogeneity. More than 70 loci have been mapped, and 25 of the nuclear genes responsible for non-syndromic deafness have been identified. Autosomal-dominant genes are responsible for about 20% of the cases of hereditary non-syndromic deafness, with 16 different genes identified to date. In the present article we review these 16 genes, their function and their contribution to deafness in different populations. The complexity is underlined by the fact that several of the genes are involved in both dominant and recessive non-syndromic deafness or in both non-syndromic and syndromic deafness. Mutations in eight of the genes have so far been detected in only single dominant deafness families, and their contribution to deafness on a population base might therefore be limited, or is currently unknown. Identification of all genes involved in hereditary hearing loss will help in the understanding of the basic mechanisms underlying normal hearing, will facilitate early diagnosis and intervention and might offer opportunities for rational therapy.

  12. 10 CFR 52.93 - Exemptions and variances.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Exemptions and variances. 52.93 Section 52.93 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS... referencing a nuclear power reactor manufactured under a manufacturing license issued under subpart F of...

  13. 10 CFR 52.93 - Exemptions and variances.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 2 2011-01-01 2011-01-01 false Exemptions and variances. 52.93 Section 52.93 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS... referencing a nuclear power reactor manufactured under a manufacturing license issued under subpart F of...

  14. 10 CFR 52.93 - Exemptions and variances.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 2 2014-01-01 2014-01-01 false Exemptions and variances. 52.93 Section 52.93 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS... referencing a nuclear power reactor manufactured under a manufacturing license issued under subpart F of...

  15. 10 CFR 52.93 - Exemptions and variances.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 2 2013-01-01 2013-01-01 false Exemptions and variances. 52.93 Section 52.93 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS... referencing a nuclear power reactor manufactured under a manufacturing license issued under subpart F of...

  16. 10 CFR 52.93 - Exemptions and variances.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 2 2012-01-01 2012-01-01 false Exemptions and variances. 52.93 Section 52.93 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS... referencing a nuclear power reactor manufactured under a manufacturing license issued under subpart F of...

  17. Variance Components for NLS: Partitioning the Design Effect.

    ERIC Educational Resources Information Center

    Folsom, Ralph E., Jr.

    This memorandum demonstrates a variance components methodology for partitioning the overall design effect (D) for a ratio mean into stratification (S), unequal weighting (W), and clustering (C) effects, so that D = WSC. In section 2, a sample selection scheme modeled after the National Longitudinal Study of the High School Class of 1972 (NKS)…

  18. Allan Variance Calculation for Nonuniformly Spaced Input Data

    DTIC Science & Technology

    2015-01-01

    Approved for public release; distribution is unlimited. 13. SUPPLEMENTARY NOTES 14. ABSTRACT The Allan Variance ( AV ) characterizes the...temporal randomness in sensor output data streams at various times scales. The conventional formula for calculating the AV assumes that the data...presents a modified approach to AV calculation, which accommodates nonuniformly spaced time samples. The basic concept of the modified approach is

  19. Variance in Math Achievement Attributable to Visual Cognitive Constructs

    ERIC Educational Resources Information Center

    Oehlert, Jeremy J.

    2012-01-01

    Previous research has reported positive correlations between math achievement and the cognitive constructs of spatial visualization, working memory, and general intelligence; however, no single study has assessed variance in math achievement attributable to all three constructs, examined in combination. The current study fills this gap in the…

  20. Temporal Relation Extraction in Outcome Variances of Clinical Pathways.

    PubMed

    Yamashita, Takanori; Wakata, Yoshifumi; Hamai, Satoshi; Nakashima, Yasuharu; Iwamoto, Yukihide; Franagan, Brendan; Nakashima, Naoki; Hirokawa, Sachio

    2015-01-01

    Recently the clinical pathway has progressed with digitalization and the analysis of activity. There are many previous studies on the clinical pathway but not many feed directly into medical practice. We constructed a mind map system that applies the spanning tree. This system can visualize temporal relations in outcome variances, and indicate outcomes that affect long-term hospitalization.

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

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ....43 Section 142.43 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS IMPLEMENTATION Variances Issued by the... issue a denial. Such notice shall include a statement of reasons for the proposed denial, and...

  2. Numbers Of Degrees Of Freedom Of Allan-Variance Estimators

    NASA Technical Reports Server (NTRS)

    Greenhall, Charles A.

    1992-01-01

    Report discusses formulas for estimation of Allan variances. Presents algorithms for closed-form approximations of numbers of degrees of freedom characterizing results obtained when various estimators applied to five power-law components of classical mathematical model of clock noise.

  3. 41 CFR 50-204.1a - Variances.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... PUBLIC CONTRACTS, DEPARTMENT OF LABOR 204-SAFETY AND HEALTH STANDARDS FOR FEDERAL SUPPLY CONTRACTS Scope... Public Contracts Act and the Occupational Safety and Health Act of 1970. ... 41 Public Contracts and Property Management 1 2013-07-01 2013-07-01 false Variances....

  4. 41 CFR 50-204.1a - Variances.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... PUBLIC CONTRACTS, DEPARTMENT OF LABOR 204-SAFETY AND HEALTH STANDARDS FOR FEDERAL SUPPLY CONTRACTS Scope... Public Contracts Act and the Occupational Safety and Health Act of 1970. ... 41 Public Contracts and Property Management 1 2014-07-01 2014-07-01 false Variances....

  5. 41 CFR 50-204.1a - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... PUBLIC CONTRACTS, DEPARTMENT OF LABOR 204-SAFETY AND HEALTH STANDARDS FOR FEDERAL SUPPLY CONTRACTS Scope... Public Contracts Act and the Occupational Safety and Health Act of 1970. ... 41 Public Contracts and Property Management 1 2010-07-01 2010-07-01 true Variances....

  6. 41 CFR 50-204.1a - Variances.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... PUBLIC CONTRACTS, DEPARTMENT OF LABOR 204-SAFETY AND HEALTH STANDARDS FOR FEDERAL SUPPLY CONTRACTS Scope... Public Contracts Act and the Occupational Safety and Health Act of 1970. ... 41 Public Contracts and Property Management 1 2012-07-01 2009-07-01 true Variances....

  7. The Variance of Intraclass Correlations in Three and Four Level

    ERIC Educational Resources Information Center

    Hedges, Larry V.; Hedberg, Eric C.; Kuyper, Arend M.

    2012-01-01

    Intraclass correlations are used to summarize the variance decomposition in popula- tions with multilevel hierarchical structure. There has recently been considerable interest in estimating intraclass correlations from surveys or designed experiments to provide design parameters for planning future large-scale randomized experiments. The large…

  8. 40 CFR 190.11 - Variances for unusual operations.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ....11 Section 190.11 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) RADIATION 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...

  9. 40 CFR 190.11 - Variances for unusual operations.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ....11 Section 190.11 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) RADIATION 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...

  10. 40 CFR 190.11 - Variances for unusual operations.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ....11 Section 190.11 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) RADIATION 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...

  11. 40 CFR 190.11 - Variances for unusual operations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ....11 Section 190.11 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) RADIATION 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...

  12. 40 CFR 190.11 - Variances for unusual operations.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ....11 Section 190.11 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) RADIATION 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...

  13. Infinite variance in fermion quantum Monte Carlo calculations

    NASA Astrophysics Data System (ADS)

    Shi, Hao; Zhang, Shiwei

    2016-03-01

    For important classes of many-fermion problems, quantum Monte Carlo (QMC) methods allow exact calculations of ground-state and finite-temperature properties without the sign problem. The list spans condensed matter, nuclear physics, and high-energy physics, including the half-filled repulsive Hubbard model, the spin-balanced atomic Fermi gas, and lattice quantum chromodynamics calculations at zero density with Wilson Fermions, and is growing rapidly as a number of problems have been discovered recently to be free of the sign problem. In these situations, QMC calculations are relied on to provide definitive answers. Their results are instrumental to our ability to understand and compute properties in fundamental models important to multiple subareas in quantum physics. It is shown, however, that the most commonly employed algorithms in such situations have an infinite variance problem. A diverging variance causes the estimated Monte Carlo statistical error bar to be incorrect, which can render the results of the calculation unreliable or meaningless. We discuss how to identify the infinite variance problem. An approach is then proposed to solve the problem. The solution does not require major modifications to standard algorithms, adding a "bridge link" to the imaginary-time path integral. The general idea is applicable to a variety of situations where the infinite variance problem may be present. Illustrative results are presented for the ground state of the Hubbard model at half-filling.

  14. 21 CFR 821.2 - Exemptions and variances.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES MEDICAL DEVICE TRACKING REQUIREMENTS General Provisions § 821.2 Exemptions and variances. (a) A... following: (1) The name of the device and device class and representative labeling showing the intended...

  15. 21 CFR 821.2 - Exemptions and variances.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES MEDICAL DEVICE TRACKING REQUIREMENTS General Provisions § 821.2 Exemptions and variances. (a) A... following: (1) The name of the device and device class and representative labeling showing the intended...

  16. 21 CFR 821.2 - Exemptions and variances.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES MEDICAL DEVICE TRACKING REQUIREMENTS General Provisions § 821.2 Exemptions and variances. (a) A... following: (1) The name of the device and device class and representative labeling showing the intended...

  17. Perspective projection for variance pose face recognition from camera calibration

    NASA Astrophysics Data System (ADS)

    Fakhir, M. M.; Woo, W. L.; Chambers, J. A.; Dlay, S. S.

    2016-04-01

    Variance pose is an important research topic in face recognition. The alteration of distance parameters across variance pose face features is a challenging. We provide a solution for this problem using perspective projection for variance pose face recognition. Our method infers intrinsic camera parameters of the image which enable the projection of the image plane into 3D. After this, face box tracking and centre of eyes detection can be identified using our novel technique to verify the virtual face feature measurements. The coordinate system of the perspective projection for face tracking allows the holistic dimensions for the face to be fixed in different orientations. The training of frontal images and the rest of the poses on FERET database determine the distance from the centre of eyes to the corner of box face. The recognition system compares the gallery of images against different poses. The system initially utilises information on position of both eyes then focuses principally on closest eye in order to gather data with greater reliability. Differentiation between the distances and position of the right and left eyes is a unique feature of our work with our algorithm outperforming other state of the art algorithms thus enabling stable measurement in variance pose for each individual.

  18. Explaining Common Variance Shared by Early Numeracy and Literacy

    ERIC Educational Resources Information Center

    Davidse, N. J.; De Jong, M. T.; Bus, A. G.

    2014-01-01

    How can it be explained that early literacy and numeracy share variance? We specifically tested whether the correlation between four early literacy skills (rhyming, letter knowledge, emergent writing, and orthographic knowledge) and simple sums (non-symbolic and story condition) reduced after taking into account preschool attention control,…

  19. The Threat of Common Method Variance Bias to Theory Building

    ERIC Educational Resources Information Center

    Reio, Thomas G., Jr.

    2010-01-01

    The need for more theory building scholarship remains one of the pressing issues in the field of HRD. Researchers can employ quantitative, qualitative, and/or mixed methods to support vital theory-building efforts, understanding however that each approach has its limitations. The purpose of this article is to explore common method variance bias as…

  20. Analysis of Variance: What Is Your Statistical Software Actually Doing?

    ERIC Educational Resources Information Center

    Li, Jian; Lomax, Richard G.

    2011-01-01

    Users assume statistical software packages produce accurate results. In this article, the authors systematically examined Statistical Package for the Social Sciences (SPSS) and Statistical Analysis System (SAS) for 3 analysis of variance (ANOVA) designs, mixed-effects ANOVA, fixed-effects analysis of covariance (ANCOVA), and nested ANOVA. For each…