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Fixed Effects (fixed + effects)
Terms modified by Fixed Effects Selected AbstractsEstimation of heritability for hip dysplasia in German Shepherd Dogs in FinlandJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 2 2000M. Leppaänen The heritability of hip dysplasia in the German Shepherd Dog was estimated by applying the animal model and the Restricted Maximum Likelihood (REML) method to a data-set which consisted of the hip scores of 10 335 dogs. Fixed effects of the model were the month and the year of birth, screening age, the panelist responsible for screening and the origin of the animal's sire. The litter and the breeder had only minor effects on hip joints. Heritability estimates were moderate (0.31,0.35). The moderate heritability, which was found in this study, enables a much better genetic gain in the breeding programme, if proper evaluation methods, such as BLUP animal model, and effective selection is used instead of phenotypic selection. Zusammenfassung Schätzung der Heritabilität der Hüftgelenksdysplasie beim Deutschen Schäferhund in Finnland. Die Heritabilität der Hüftgelenksdysplasie beim Deutschen Schäferhund wurde mit Hilfe des Tiermodells und der Restricted Maximum Likelihood (REML) Methode anhand von Hüftgelenksgutachten von 10 335 Hunden geschätzt. Als fixe Effekte wurden im Modell ,Geburtsmonat' und ,-jahr', ,Röntgenalter', Einfluß des ,Gutachters' und ,Herkunft des Vaters' berücksichtigt. Die Effekte ,Wurf' und ,Züchter' hatten nur einen geringen Einfluß auf die Hüftgelenke. Die Heritabilitätsschätzungen betrugen 0.31 bis 0.35. Die in dieser Studie geschätzten Heritabilitäten ermöglichen es, zusammen mit geeigneten Methoden, wie beispielsweise dem BLUP-Tiermodell und einer effektiven Selektion, einen schnelleren Zuchtfortschritt zu erreichen, als nur phänotypisch zu selektieren. [source] A Bayesian Hierarchical Model for Classification with Selection of Functional PredictorsBIOMETRICS, Issue 2 2010Hongxiao Zhu Summary In functional data classification, functional observations are often contaminated by various systematic effects, such as random batch effects caused by device artifacts, or fixed effects caused by sample-related factors. These effects may lead to classification bias and thus should not be neglected. Another issue of concern is the selection of functions when predictors consist of multiple functions, some of which may be redundant. The above issues arise in a real data application where we use fluorescence spectroscopy to detect cervical precancer. In this article, we propose a Bayesian hierarchical model that takes into account random batch effects and selects effective functions among multiple functional predictors. Fixed effects or predictors in nonfunctional form are also included in the model. The dimension of the functional data is reduced through orthonormal basis expansion or functional principal components. For posterior sampling, we use a hybrid Metropolis,Hastings/Gibbs sampler, which suffers slow mixing. An evolutionary Monte Carlo algorithm is applied to improve the mixing. Simulation and real data application show that the proposed model provides accurate selection of functional predictors as well as good classification. [source] Contemporary egg size divergence among sympatric grayling demes with common ancestorsECOLOGY OF FRESHWATER FISH, Issue 1 2008F. Gregersen Abstract, This study documents divergence in egg size that has occurred over less than 25 generations among sympatric demes of European grayling (Thymallus thymallus) from Lake Lesjaskogsvatnet in Norway. A cluster analysis identified two clusters of tributaries: one of small, warm tributaries (SW) and the other of large, cold tributaries (LC). Spawning occurs more regularly and up to 4 weeks earlier in SW tributaries compared with that in LC ones. We explored numerous mixed models predicting egg size from year (random effect), basin and tributary (fixed effects), and female length. The most supported model estimated length-adjusted egg size to be larger in SW tributaries compared with that in LC tributaries. Combinations of density-dependent (competition for food/space) and density-independent (temperature) factors along with phenotypic plasticity and maternal effects are discussed as potential differentiation sources. We suggest high temperatures (increased metabolism) to reinforce the selective advantage of large eggs under conditions with highly density-dependent fry interactions. [source] Retention in methadone maintenance drug treatment for prescription-type opioid primary users compared to heroin usersADDICTION, Issue 5 2009Caleb J. Banta-Green ABSTRACT Aims To assess retention in methadone maintenance treatment for prescription-type opioid primary (PTOP) users compared to heroin users. Design and participants A retrospective cohort study was carried out to examine the association between opiate types used on 12-month retention. The study population consisted of adults admitted to one of 11 not-for-profit methadone maintenance clinics in 2004 and 2005 throughout Washington State (n = 2308). Logistic regression analyses with fixed effects for treatment agencies were conducted. Measurements Opiate use type in past 30 days: any heroin use or primary prescription opioid without heroin use. Demographics, other drugs used, self-reported medical and psychiatric concerns, social, familial and legal issues, public assistance type and housing stability were documented at intake using a comprehensive biopsychosocial instrument, the Treatment and Assessment Reports Generation Tool. Findings The odds of being retained in treatment for PTOP compared to heroin users not adjusting for other factors was 1.33 (95% confidence interval [CI], 1.03, 1.71). In the final logistic regression model the odds of retention for PTOP compared to heroin users was 1.25 (95% CI, 0.93, 1.67), indicating that there was no statistically significant difference in treatment retention by opiate type after adjusting for demographics, treatment agencies, other drug use, public assistance type, medical, psychiatric, social, legal and familial factors. Conclusion The findings of this study suggest that PTOP can be treated at methadone maintenance treatment facilities at least as effectively as heroin users in terms of treatment retention. [source] Meta-analysis of standardized incidence and mortality rates of childhood leukaemia in proximity to nuclear facilitiesEUROPEAN JOURNAL OF CANCER CARE, Issue 4 2007P.J. BAKER phd The meta-analysis combined and statistically analysed studies of childhood leukaemia and nuclear facilities. Focus was on studies that calculated standardized rates for individual facilities. Due to variability between study designs, eight separate analyses were performed stratified by age and zone. One hundred and thirty-six sites were used in at least one analysis. Unadjusted, fixed effects and random effects models were used. Meta-rates greater than one were found in all models at all stratification levels often achieving statistical significance. Caution must be used when interpreting these results. The meta-analysis was able to show an increase in childhood leukaemia near nuclear facilities, but does not support a hypothesis to explain the excess. Each type of model utilized has limitations. Fixed effects models give greater weight to larger studies; however, population density may be a risk factor. Random effects models give greater weight to smaller studies that may be more likely to be affected by publication bias. A limitation of the overall study design is that standardized rates must be available for individual sites which led to exclusion of studies that only calculated rates for multiple sites and those that presented other statistical methods. Further, dose-response studies do not support excess rates found near nuclear facilities. However, it cannot be ignored that the majority of studies have found elevated rates, although not usually statistically significant. [source] Sampling and analytical plus subsampling variance components for five soil indicators observed at regional scaleEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 5 2009B. G. Rawlins Summary When comparing soil baseline measurements with resampled values there are four main sources of error. These are: i) location (errors in relocating the sample site), ii) sampling errors (representing the site with a sample of material) iii) subsampling error (selecting material for analysis) and iv) analytical error (error in laboratory measurements). In general we cannot separate the subsampling and analytical sources of error (since we always analyse a different subsample of a specimen), so in this paper we combine these two sources into subsampling plus analytical error. More information is required on the relative magnitudes of location and sampling errors for the design of effective resampling strategies to monitor changes in soil indicators. Recently completed soil surveys of the UK with widely differing soils included a duplicate site and subsampling protocol to quantify ii), and the sum of iii) and iv) above. Sampling variances are estimated from measurements on duplicate samples , two samples collected on a support of side length 20 m separated by a short distance (21 m). Analytical and subsampling variances are estimated from analyses of two subsamples from each duplicate site. After accounting for variation caused by region, parent material class and land use, we undertook a nested analysis of data from 196 duplicate sites across three regions to estimate the relative magnitude of medium-scale (between sites), sampling and subsampling plus analytical variance components, for five topsoil indicators: total metal concentrations of copper (Cu), nickel (Ni) and zinc (Zn), soil pH and soil organic carbon (SOC) content. The variance components for each indicator diminish by about an order of magnitude from medium-scale, to sampling, to analytical plus subsampling. Each of the three fixed effects (parent material, land use and region) were statistically significant for each of the five indicators. The most effective way to minimise the overall uncertainty of our observations at sample sites is to reduce the sampling variance. [source] Modelflow estimates of cardiac output compared with Doppler ultrasound during acute changes in vascular resistance in womenEXPERIMENTAL PHYSIOLOGY, Issue 4 2010Kenneth S. Dyson We compared Modelflow (MF) estimates of cardiac stroke volume (SV) from the finger pressure-pulse waveform (Finometer®) with pulsed Doppler ultrasound (DU) of the ascending aorta during acute changes in total peripheral resistance (TPR) in the supine and head-up-tilt (HUT) postures. Twenty-four women were tested during intravenous infusion of 0.005 or 0.01 ,g kg,1 min,1 isoprenaline, 10 or 50 ng kg,1 min,1 noradrenaline and 0.3 mg sublingual nitroglycerine. Responses to static hand-grip exercise (SHG), graded lower body negative pressure (LBNP, from ,20 to ,45 mmHg) and 45 deg HUT were evaluated on separate days. Bland,Altman analysis indicated that SVMF yielded lower estimates than SVDU during infusion of 0.01 ,g kg,1 min,1 isoprenaline (SVMF 92.7 ± 15.5 versus SVDU 104.3 ± 22.9 ml, P= 0.03) and SHG (SVMF 78.8 ± 12.0 versus SVDU 106.1 ± 28.5 ml, P < 0.01), while larger estimates were recorded with SVMF during ,45 mmHg LBNP (SVMF 52.6 ± 10.7 versus SVDU 46.2 ± 14.5 ml, P= 0.04) and HUT (SVMF 59.3 ± 13.6 versus SVDU 45.2 ± 11.3 ml, P < 0.01). Linear regression analysis revealed a relationship (r2= 0.41, P < 0.01) between the change in TPR from baseline and the between-methods discrepancy in SV measurements. This relationship held up under all of the experimental protocols (regression for fixed effects, P= 0.46). These results revealed a discrepancy in MF estimates of SV, in comparison with those measured by DU, during acute changes in TPR. [source] Robustness of inference on measured covariates to misspecification of genetic random effects in family studiesGENETIC EPIDEMIOLOGY, Issue 1 2003Ruth M.Pfeiffer Abstract Family studies to identify disease-related genes frequently collect only families with multiple cases. It is often desirable to determine if risk factors that are known to influence disease risk in the general population also play a role in the study families. If so, these factors should be incorporated into the genetic analysis to control for confounding. Pfeiffer et al. [2001 Biometrika 88: 933,948] proposed a variance components or random effects model to account for common familial effects and for different genetic correlations among family members. After adjusting for ascertainment, they found maximum likelihood estimates of the measured exposure effects. Although it is appealing that this model accounts for genetic correlations as well as for the ascertainment of families, in order to perform an analysis one needs to specify the distribution of random genetic effects. The current work investigates the robustness of the proposed model with respect to various misspecifications of genetic random effects in simulations. When the true underlying genetic mechanism is polygenic with a small dominant component, or Mendelian with low allele frequency and penetrance, the effects of misspecification on the estimation of fixed effects in the model are negligible. The model is applied to data from a family study on nasopharyngeal carcinoma in Taiwan. Genet Epidemiol 24:14,23, 2003. © 2003 Wiley-Liss, Inc. [source] The pervasive influence of sampling and methodological artefacts on a macroecological pattern: the abundance,occupancy relationshipGLOBAL ECOLOGY, Issue 4 2008Peter D. Wilson ABSTRACT Aim To investigate the influence of sampling and methodological artefacts on the correlation between abundance and occupancy. Location Global scope. Methods A fixed effects weighted regression model was fitted to standardized effect size for 175 examples of correlations between abundance and occupancy. A regression tree model with standard effect size as the dependent variable was also fitted to the data. Results Standard effect size, and therefore the correlation between abundance and occupancy, was found to be strongly influenced by the type of abundance measure used to characterize the abundance,occupancy relationship. Local mean abundance (also referred to as ecological mean abundance) was primarily responsible for negative correlations. Negative correlations also resulted from a mismatch in the sampling extents of abundance and occupancy measures. Main conclusions The combination of abundance and occupancy measures selected to characterize the abundance,occupancy relationship for a given set of data has a profound impact on the sign of the correlation between the selected measures. Previous attempts to understand the processes giving rise to the pattern represented by the abundance,occupancy relationship have confounded sampling artefacts (e.g. spatial extent of abundance and occupancy information) and methodological artefacts (e.g. combining a truncated abundance measure such as local mean abundance with an untruncated occupancy measure such as proportion of occupied samples). Thus, a revision of the approach currently used to define and evaluate competing explanatory models of the abundance,occupancy relationship appears to be necessary. [source] Effect of Prescription Drug Coverage on Health of the ElderlyHEALTH SERVICES RESEARCH, Issue 5p1 2008Nasreen Khan Objective. To estimate the effect of prescription drug insurance on health, as measured by self-reported poor health status, functional disability, and hospitalization among the elderly. Data. Analyses are based on a nationally representative sample of noninstitutionalized elderly (,65 years of age) from the Medicare Current Beneficiary Survey (MCBS) for years 1992,2000. Study Design. Estimates are obtained using multivariable regression models that control for observed characteristics and unmeasured person-specific effects (i.e., fixed effects). Principal Findings. In general, prescription drug insurance was not associated with significant changes in self-reported health, functional disability, and hospitalization. The lone exception was for prescription drug coverage obtained through a Medicare HMO. In this case, prescription drug insurance decreased functional disability slightly. Among those elderly with chronic illness and older (71 years or more) elderly, prescription drug insurance was associated with slightly improved functional disability. Conclusions. Findings suggest that prescription drug coverage had little effect on health or hospitalization for the general population of elderly, but may have some health benefits for chronically ill or older elderly. [source] Do perineal exercises during pregnancy prevent the development of urinary incontinence?INTERNATIONAL JOURNAL OF UROLOGY, Issue 10 2008A systematic review Objectives: The aim of the current article was to conduct a systematic review of the performance of perineal exercises during pregnancy and their utility in the prevention of urinary incontinence. Methods: Randomized controlled studies (RCT) of a low-risk obstetric population (primiparas or nulliparas) who had done perineal exercises only during pregnancy met the inclusion criteria. Articles published between 1966 and 2007 from periodicals indexed in the LILACS, SCIELO, PubMed/MEDLINE, SCIRUS and Cochrane Library databases were selected, using the following keywords: ,urinary incontinence', ,pregnancy', ,pelvic floor' and ,exercise'. The Jadad scale was applied to assess the internal validity of the RCT and two meta-analysis: one of fixed effects and the other of random effects were carried out with data extracted from the RCT, using the Stata 9.2 statistical software and adopting a significance level of 0.05. Results: Four RCTs with high methodological quality, involving a total of 675 women were included. They indicated that perineal muscle exercise significantly reduced the development of urinary incontinence from 6 weeks to 3 months after delivery (odds ratio = 0.45; confidence interval: 0.3 to 0.66). However, when evaluating this effect during the 34th and 35th gestational week, a meta-analysis showed that the results were not significant (odds ratio = 0.13; confidence interval: 0.00 to 3.77). Conclusion: Pelvic floor muscle exercises may be effective at reducing the development of postpartum urinary incontinence, despite clinical heterogeneity among the RCT. [source] Estimates of genetic parameters for conformation measures and scores in Finnhorse and Standardbred foalsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2010E. Schroderus Summary The aim of this study was to estimate genetic parameters for conformation measures and scores in the Finnhorse and the Standardbred foals presented in foal shows. Studied traits included height at withers and at croup, six subjectively evaluated conformation traits and overall grade. Data were from 10-year period (1995,2004) and consisted of 5821 Finnhorse foals (1,3 years old) with 7644 records and 2570 Standardbred foals (1,2 years old) with 2864 records. Variance components were estimated with REML , animal model using VCE4 program. The model included age class, year of judging, sex and region as fixed effects, and additive genetic, permanent environmental and residual as random effects. Estimates of heritability for measured traits were very high in both breeds (0.88,0.90). Estimates of heritability for conformation traits varied from 0.13 to 0.32 in the Finnhorse and from 0.06 to 0.47 in the Standardbred. In both breeds, estimates of heritability were lowest for hooves and movements at walk, and highest for type and body conformation among scored traits. Estimate of heritability for overall grade was in the Finnhorse 0.32 and in the Standardbred 0.34. Genetic correlations between overall grade and different conformation traits were 0.35,0.84 in the Finnhorse and 0.31,0.88 in the Standardbred. Thus, selection based on the overall grade would improve all studied characteristics. [source] Effects of breed, sex and halothane genotype on fatty acid composition of triacylglycerols and phospholipids in pork longissimus muscleJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 4 2009S. Zhang Summary The objective of this study was to estimate the effects of breed, sex, and halothane (HAL-1843TM) genotype on fatty acid composition of triacylglycerols (TAG) and phospholipids (PL) extracted from porcine longissimus muscle (LM). Purebred Yorkshire (n = 131), Duroc (n = 136), Hampshire (n = 49), Spotted (n = 35), Chester White (n = 74), Poland China (n = 51), Berkshire (n = 169) and Landrace (n = 82) pigs (n = 727; 427 barrows and 300 gilts) from the 1994 and 2001 National Barrow Show Sire Progeny Tests were used. For statistical analyses, a mixed model was used that included fixed effects of breed, sex, HAL-1843TM genotype, year, slaughter date within each year, interaction of breed × sex and random effects of sire and dam within breed. Breeds and sex were significantly associated with the percentages of the majority fatty acids in TAG. Duroc pigs had greater total saturated fatty acids (SFA) and lower total monounsaturated fatty acids (MUFA) (p < 0.05) contents than did pigs of all other breeds except Berkshire (p > 0.05). The concentration of total polyunsaturated fatty acids (PUFA) was the greatest in Hampshire pigs (p < 0.05). The content of total SFA was greater (p < 0.01), whereas the concentrations of total MUFA and PUFA were lower (p < 0.01) in barrows than those in gilts. The contents of major SFA in PL did not differ significantly among pigs from different breeds and sex groups. However, breed and sex significantly affected the concentrations of major MUFA and PUFA in PL and strong negative correlation between the total contents of MUFA and PUFA in PL was observed in the current study. Chester White pigs had greater total MUFA and lower total PUFA contents (p < 0.05) in PL than did pigs of all other breeds except Spotted (p > 0.05). In contrast to breed and sex effects, the concentrations of fatty acids in PL were more affected by HAL-1843TM genotype than those in TAG. The content of C16:0, a major SFA in PL, differed significantly in pigs with different HAL-1843TM genotypes. In conclusion, these results suggest that breed and sex are important sources of the variations for fatty acid composition of TAG and PL in LM. [source] Identifiability of parameters and behaviour of MCMC chains: a case study using the reaction norm modelJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 2 2009M.M. Shariati Summary Markov chain Monte Carlo (MCMC) enables fitting complex hierarchical models that may adequately reflect the process of data generation. Some of these models may contain more parameters than can be uniquely inferred from the distribution of the data, causing non-identifiability. The reaction norm model with unknown covariates (RNUC) is a model in which unknown environmental effects can be inferred jointly with the remaining parameters. The problem of identifiability of parameters at the level of the likelihood and the associated behaviour of MCMC chains were discussed using the RNUC as an example. It was shown theoretically that when environmental effects (covariates) are considered as random effects, estimable functions of the fixed effects, (co)variance components and genetic effects are identifiable as well as the environmental effects. When the environmental effects are treated as fixed and there are other fixed factors in the model, the contrasts involving environmental effects, the variance of environmental sensitivities (genetic slopes) and the residual variance are the only identifiable parameters. These different identifiability scenarios were generated by changing the formulation of the model and the structure of the data and the models were then implemented via MCMC. The output of MCMC sampling schemes was interpreted in the light of the theoretical findings. The erratic behaviour of the MCMC chains was shown to be associated with identifiability problems in the likelihood, despite propriety of posterior distributions, achieved by arbitrarily chosen uniform (bounded) priors. In some cases, very long chains were needed before the pattern of behaviour of the chain may signal the existence of problems. The paper serves as a warning concerning the implementation of complex models where identifiability problems can be difficult to detect a priori. We conclude that it would be good practice to experiment with a proposed model and to understand its features before embarking on a full MCMC implementation. [source] Genetic parameters of racing merit of thoroughbred horses in PolandJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2004M. Sobczynska Summary The study aimed at estimating variance components of racing ability traits in thoroughbred horses as a contribution to defining the breeding objective for this breed. Data collected were 12 143 placings at finish (square root) and 8641 earnings (log) won by 1414 horses running in 1693 races over the period of 1998,2001. Age of horses ranged from 2 to 5+ years, and the distances were from 1000 to 3200 m. Horses were from 11 state stables, from private breeders (one collective group), and from foreign breeding (another collective group within the factor ,breeder'). Variance components were estimated by the residual maximal likelihood (REML) method. Statistical analysis accounted for fixed effects of year, age, race, breeder (optional), sex, weight carried and distance, and for the random effects of rider, permanent environment, and animal additive genetics. Pedigrees were at least three generations deep. When breeder effect was excluded from the model, heritability coefficients were 0.12 and 0.18, repeatability 0.23 and 0.34 for earnings and placings at finish, respectively. Zusammenfassung Die vorliegende Studie befasst sich mit der Varianzkomponentenschätzung für Merkmale der Rennleistung von Vollblutpferden als einen Beitrag, um die Zuchtziele näher zu definieren. Die Daten stammen aus 12143 Platzierungen (Quadratwurzel) und 8641 Gewinnsummen (Logarithmus) von 1414 Pferden in 1693 Rennen aus den Jahren 1998 bis 2001. Das Alter der Pferde reichte von zwei bis neun Jahre, die Renndistanzen von 1000 bis 3200 m. Die Pferde stammten aus 11 Ställen, von Privatzüchtern (ein gemeinsamer Zusammenschluß) und aus fremder Zucht (eine weitere zusammengeschlossene Gruppe innerhalb der Gruppe ,,Züchter''). Die Varianzkomponenten wurden mit der REML-Methode geschätzt. Die statistischen Analysen berücksichtigten als fixe Effekte Jahr, Alter, Rasse, Züchter (optional), Geschlecht, zu tragendes Gewicht und Distanz, sowie als zufällige Effekte Reiter, permanente Umwelt und der additiv genetische Tiereffekt. Die Pedigrees umfassten wenigstens drei Generationen. Ohne den Effekt des Züchters im Modell wurden für Gewinnsummen und Platzierungen Heritabilitäten von 0,12 und 0,18 sowie Wiederholbarkeiten von 0,23 und 0,34 geschätzt. [source] Estimation of genetic parameters for canine hip dysplasia in the Swiss Newfoundland populationJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 3 2003E. Dietschi Summary Variance components and genetic parameters for hip dysplasia (HD) in a population of 1372 Newfoundlands were estimated using restricted maximum likelihood method applied to animal models comprising fixed effects of gender, screening expert and HD grading system. All models investigated included a random direct genetic effect, but differed for combinations of random maternal genetic effect, permanent maternal environmental effect and kennel effect. Although kennels had no effect on HD, the permanent maternal environmental effects, however were significant. The results for the maternal genetic effect were ambiguous. These results suggest a confounding of these three random effects. The model that included the fixed effects, the direct genetic effect and the permanent maternal environmental effect was the most parsimonious combined with an optimal fit. The heritability estimated with this model was 0.28 and the proportion of the permanent maternal environmental effect of the phenotypic variance was 0.10. The effects of gender and screening expert were significant but not the one of HD grading system. Zusammenfassung Schätzung genetischer Populationsparameter für die Hüftgelenksdysplasie bei den Neufundländern in der Schweiz In einer Hundepopulation von 1372 Neufundländern wurden für die Hüftgelenksdysplasie mit Hilfe der "restricted maximum likelihood method" Varianzkomponenten und genetische Parameter geschätzt, wobei ein Tiermodell zu Grunde gelegt wurde. Alle verwendeten Modelle enthielten einen zufälligen direkten genetischen Effekt und in unterschiedlichen Kombinationen einen zufälligen maternalen Effekt, einen zufälligen permanent maternalen Umwelteffekt und einen zufälligen Zwinger-Effekt. Als fixe Effekte wurden das Geschlecht, der Auswertungs-Experte und das HD-Einteilungssystem berücksichtigt. Der Zwinger hat keinen Einfluss auf die Hüftgelenksdysplasie, aber der permanent maternale Umwelteffekt ist signifikant. Der maternal genetische Effekt verhält sich je nach Modell unterschiedlich. Diese Resultate legen eine Vermengung dieser drei Effekte nahe. Die beste Anpassung an die Daten zeigt dasjenige Modell, das die fixen Effekte, den direkten genetischen Effekt und den permanent maternalen Umwelteffekt enthält. Die mit diesem Modell geschätzte Heritabilität beträgt 0,28 und der Anteil des permanent maternalen Umwelteffektes an der phänotypischen Varianz 0,10. Das Geschlecht und die Auswertungs-Experten sind signifikant, das HD-Einteilungssystem nicht. [source] Bayesian inference strategies for the prediction of genetic merit using threshold models with an application to calving ease scores in Italian Piemontese cattleJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 4 2002K. Kizilkaya Summary First parity calving difficulty scores from Italian Piemontese cattle were analysed using a threshold mixed effects model. The model included the fixed effects of age of dam and sex of calf and their interaction and the random effects of sire, maternal grandsire, and herd-year-season. Covariances between sire and maternal grandsire effects were modelled using a numerator relationship matrix based on male ancestors. Field data consisted of 23 953 records collected between 1989 and 1998 from 4741 herd-year-seasons. Variance and covariance components were estimated using two alternative approximate marginal maximum likelihood (MML) methods, one based on expectation-maximization (EM) and the other based on Laplacian integration. Inferences were compared to those based on three separate runs or sequences of Markov Chain Monte Carlo (MCMC) sampling in order to assess the validity of approximate MML estimates derived from data with similar size and design structure. Point estimates of direct heritability were 0.24, 0.25 and 0.26 for EM, Laplacian and MCMC (posterior mean), respectively, whereas corresponding maternal heritability estimates were 0.10, 0.11 and 0.12, respectively. The covariance between additive direct and maternal effects was found to be not different from zero based on MCMC-derived confidence sets. The conventional joint modal estimates of sire effects and associated standard errors based on MML estimates of variance and covariance components differed little from the respective posterior means and standard deviations derived from MCMC. Therefore, there may be little need to pursue computation-intensive MCMC methods for inference on genetic parameters and genetic merits using conventional threshold sire and maternal grandsire models for large datasets on calving ease. Zusammenfassung Die Kalbeschwierigkeiten bei italienischen Piemonteser Erstkalbskühen wurden mittels eines gemischten Threshold Modells untersucht. Im Modell wurden die fixen Einflüsse vom Alter der Kuh und dem Geschlecht des Kalbes, der Interaktion zwischen beiden und die zufälligen Effekte des Großvaters der Mutter und der Herden-Jahr-Saisonklasse berücksichtigt. Die Kovarianz zwischen dem Vater der Kuh und dem Großvater der Mutter wurde über die nur auf väterlicher Verwandtschaft basierenden Verwandtschaftsmatrix berücksichtigt. Es wurden insgesamt 23953 Datensätze aus den Jahren 1989 bis 1998 von 4741 Herden-Jahr-Saisonklassen ausgewertet. Die Varianz- und Kovarianzkomponenten wurden mittels zweier verschiedener approximativer marginal Maximum Likelihood (MML) Methoden geschätzt, die erste basierend auf Expectation-Maximierung (EM) und die zweite auf Laplacian Integration. Rückschlüsse wurden verglichen mit solchen, basierend auf drei einzelne Läufe oder Sequenzen von Markov Chain Monte Carlo (MCMC) Stichproben, um die Gültigkeit der approximativen MML Schätzer aus Daten mit ähnlicher Größe und Struktur zu prüfen. Die Punktschätzer der direkten Heritabilität lagen bei 0,24; 0,25 und 0,26 für EM, Laplacian und MCMC (Posterior Mean), während die entsprechenden maternalen Heritabilitäten bei 0,10, 0,11 und 0,12 lagen. Die Kovarianz zwischen dem direkten additiven und dem maternalen Effekt wurden als nicht von Null verschieden geschätzt, basierend auf MCMC abgeleiteten Konfidenzintervallen. Die konventionellen Schätzer der Vatereffekte und deren Standardfehler aus den MML-Schätzungen der Varianz- und Kovarianzkomponenten differieren leicht von denen aus der MCMC Analyse. Daraus folgend besteht wenig Bedarf die rechenintensiven MCMC-Methoden anzuwenden, um genetische Parameter und den genetischen Erfolg zu schätzen, wenn konventionelle Threshold Modelle für große Datensätze mit Vätern und mütterlichen Großvätern mit Kalbeschwierigkeiten genutzt werden. [source] Estimates of environmental effects and genetic parameters for body measurements and weight in Brahman cattle raised in MexicoJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 4 2002C. D. U. Magnabosco Summary A Derivative Free Restricted Maximum Likelihood (DFREML) algorithm was used with single trait and two traits animal models to estimate the variance and covariance components and thus, heritabilities and phenotypic, genetic and environmental correlations among nine different body measurements and weights of Brahman cattle raised in Mexico. The following measurements were considered: hip width, pin width, hip-pin width, anterior height, posterior height, body length, thorax perimeter, scrotal circumference and weight. The analysis was based on a total of 1018 animals, born between 1992 and 1995, from 17 herds in the Mexican States of Chiapas, San Luis Potosi, Tabasco, Tamaulipas and Veracruz. The model included the following fixed effects: herd, year-season of birth, sex, age of the animal and feed management. The only random effect was the direct additive genetic contribution of each animal. All fixed effects in the model were significant for all traits (p < 0.05). Estimated heritabilities for the traits were: hip width 0.57, pin width 0.32, hip-pin width 0.41, anterior height 0.56, posterior height 0.54, body length 0.32, thorax perimeter 0.49, scrotal circumference 0.02 and weight 0.66. The magnitude of the heritabilities was medium to high, with the exception of scrotal circumference. The genetic correlations among all body measurements were consistently positive and high, ranging from 0.64 to 1.00. Although other measures showed higher genetic correlations with weight, thorax perimeter combines a high value (0.70) with ease and repeatability, making it a useful field measurement to estimate body weight when scales are not available. Resumen Estimados de efectos ambientales y parámetros genéticos para medidas corporales y peso vivo en ganado brahman criado en méjico Fue usado un algoritmo de Máxima Verosimilitud Restricta Libre de Derivadas (DFREML) con modelos animales para una y dos características para estimar componentes de (co)varianzas, heredabilidades y correlaciones fenotípicas, genéticas y ambientales entre nueve diferentes medidas corporales y peso vivo de ganado Brahman criado en México. Fueron considerados los siguientes rasgos: ancho anterior de la grupa, ancho posterior de la grupa, largo de la grupa, altura a la cruz, altura a la grupa, largo del cuerpo, perímetro toráxico, perímetro escrotal y peso vivo. Se usaron datos de 1018 animales, nacidos entre 1992 y 1995, procedentes de 17 rebaños de los Estados mejicanos de Chiapas, San Luis Potosí, Tabasco, Tamaulipas y Veracruz. El modelo matemático incluyó los siguientes efectos fijos: rebaño, año-época de nacimiento, sexo, clase de edad del animal y manejo alimentar. Se consideró el efecto aditivo directo de cada animal como el único efecto aleatorio. Todos los efectos fijos del modelo fueron significativos para todas las características (P < 0.05). Las heredabilidades estimadas fueron: ancho anterior de la grupa 0.57, ancho posterior de la grupa 0.32, largo de la grupa 0.41, altura a la cruz 0.56, altura a la grupa 0.54, largo del cuerpo 0.32, perímetro toráxico 0.49, perímetro escrotal 0.02 y peso vivo 0.66. Las magnitudes de las heredabilidades fueron de medias a altas, con excepción del perímetro escrotal. Las correlaciones genéticas entre todas las medidas corporales fueron consistentemente positivas y altas, variando de 0.64 a 1.00. Aunque otras medidas corporales mostraron altas correlaciones genéticas con el peso vivo, el perímetro toráxico combina un alto valor de esa correlación (0.70) con facilidad de medición y alta repetibilidad, haciendo de esta una medida útil, para estimar el peso vivo, en condiciones de campo donde no se dispone de balanza. [source] Simple preconditioners for the conjugate gradient method: experience with test day modelsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 3 2002I. STRANDÉN Preconditioned conjugate gradient method can be used to solve large mixed model equations quickly. Convergence of the method depends on the quality of the preconditioner. Here, the effect of simple preconditioners on the number of iterations until convergence was studied by solving breeding values for several test day models. The test day records were from a field data set, and several simulated data sets with low and high correlations among regression coefficients. The preconditioner matrices had diagonal or block diagonal parts. Transformation of the mixed model equations by diagonalization of the genetic covariance matrix was studied as well. Preconditioner having the whole block of the fixed effects was found to be advantageous. A block diagonal preconditioner for the animal effects reduced the number of iterations the higher the correlations among animal effects, but increased memory usage of the preconditioner. Diagonalization of the animal genetic covariance matrix often reduced the number of iterations considerably without increased memory usage. Einfache Preconditioners für die `Conjugate Gradient Method': Erfahrungen mit Testtagsmodellen Die `Preconditioned Conjugate Gradient Methode' kann benutzt werden um große `Mixed Model' Gleichungssysteme schnell zu lösen. In diesem Beitrag wurde der Einfluss von einfachen Preconditioners auf die Anzahl an Iterationen bis zur Konvergenz bei der Schätzung von Zuchtwerten bei verschiedenen Testtagsmodellen untersucht. Die Testtagsdaten stammen aus einem Felddatensatz und mehreren simulierten Datensätzen mit unterschiedlichen Korrelationen zwischen den Regressionskoeffizienten. Die Preconditioner Matrix bestand aus Diagonalen oder Blockdiagonalen Teilen. Eine Transformation der Mixed Modell Gleichungen durch Diagonalisierung der genetischen Kovarianzmatrix wurde ebenfalls untersucht. Preconditioners mit dem Block der fixen Effekte zeigten sich immer überlegen. Ein Blockdiagonaler Preconditioner für den Tiereffekt reduzierte die Anzahl an Iterationen mit höher werden Korrelationen zwischen den Tiereffekten, aber erhöhte den Speicherbedarf. Eine Diagonalisierung der genetischen Kovarianzmatrix reduzierte sehr oft die Anzahl an Iterationen erheblich ohne den Speicherbedarf zu erhöhen. [source] Estimates of direct and maternal genetic effects for weights from birth to 600 days of age in Nelore cattleJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 2 2001Galvão de Albuquerque Estimates of direct and maternal variance and heritability for weights at each week (up to 280 days of age) and month of age (up to 600 days of age) in Zebu cattle are presented. More than one million records on 200 000 animals, weighed every 90 days from birth to 2 years of age, were available. Data were split according to week (data sets 1) or month (data sets 2) of age at recording, creating 54 and 21 data sets, respectively. The model of analysis included contemporary groups as fixed effects, and age of dam (linear and quadratic) and age of calf (linear) effects as covariables. Random effects fitted were additive direct and maternal genetic effects, and maternal permanent environmental effect. Direct heritability estimates decreased from 0.28 at birth, to 0.12,0.13 at about 150 days of age, stayed more or less constant at 0.14,0.16 until 270 days of age and increased with age after that, up to 0.25,0.26. Maternal heritability estimates increased from birth (0.01) to a peak of 0.14 for data sets 1 and 0.07,0.08 for data sets 2 at about 180,210 days of age, before decreasing slowly to 0.07 and 0.05, respectively, at 300 days, and then rapidly diminished after 300 days of age. Permanent environmental effects were 1.5 to four times higher than genetic maternal effects and showed a similar trend. Schätzung von direkten und maternal genetischen Effekten für Gewichte von der Geburt bis zum 600. Lebenstag beim Nelore-Rind Es werden Schätzwerte für die direkte und maternale Varianz sowie für Heritabilitäten der Gewichte in jeder Woche (bis zum 280. Lebenstag) und für jeden Monat (bis zum 600. Lebenstag) beim Zebu Rind gezeigt. Mehr als eine Million Datensätze vom 200.000 Tieren standen zur Verfügung, die alle 90 Tage bis zum zweiten Lebensjahr gewogen wurden. Die Daten wurden entsprechend dem Alter in Wochen (Datenset 1) oder Monaten (Datenset 2) aufgeteilt, woraus 54 bzw. 21 Datensets entstanden. Die Modelle beinhalteten Tiergruppen, die zur gleichen Zeit gelebt haben, als fixen Effekt, das Alter der Mutter (linear und quadratisch) und das Alter des Kalbes (linear) als Kovariablen. Als zufällige Effekte wurden der additive direkte, maternal genetische Effekt und maternal permanente Umwelteffekt berücksichtigt. Direkte Heritabilitätsschätzungen nahmen von 0,28 von Geburt auf 0,12,0,13 bei ca. 150 Lebenstagen ab, blieben mehr oder weniger konstant bei 0,14,0,16 bis zum 270. Lebenstag und nahmen ab dem 270. Lebenstag auf 0,25,0,26 zu. Maternale Heritabilitätsschätzungen nahmen von Geburt (0,01) zu einem Peak von 0, 14 beim Datenset 1 und 0,07,0,8 beim Datenset 2 bis ca. 180,210 Lebenstagen zu, bevor sie langsam wieder auf 0,07 bzw. 0,05 bei einem Alter von 300 Tagen sanken. Nach 300 Lebenstagen sanken sie rapide ab. Permanente Umwelteffekte waren 1,5 bis vierfach höher als genetisch maternale Effekte und zeigten einen ähnlichen Trend. [source] The use of marker-based relationship information to estimate the heritability of body weight in a natural population: a cautionary taleJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 1 2002S. C. Thomas A number of procedures have been developed that allow the genetic parameters of natural populations to be estimated using relationship information inferred from marker data rather than known pedigrees. Three published approaches are available; the regression, pair-wise likelihood and Markov Chain Monte Carlo (MCMC) sib-ship reconstruction methods. These were applied to body weight and molecular data collected from the Soay sheep population of St. Kilda, which has a previously determined pedigree. The regression and pair-wise likelihood approaches do not specify an exact pedigree and yielded unreliable heritability estimates, that were sensitive to alteration of the fixed effects. The MCMC method, which specifies a pedigree prior to heritability estimation, yielded results closer to those determined using the known pedigree. In populations of low average relationship, such as the Soay sheep population, determination of a reliable pedigree is more useful than indirect approaches that do not specify a pedigree. [source] Does sex education affect adolescent sexual behaviors and health?JOURNAL OF POLICY ANALYSIS AND MANAGEMENT, Issue 4 2006Joseph J. SabiaArticle first published online: 6 SEP 200 This study examines whether offering sex education to young teenagers affects several measures of adolescent sexual behavior and health: virginity status, contraceptive use, frequency of intercourse, likelihood of pregnancy, and probability of contracting a sexually transmitted disease. Using data from the National Longitudinal Study of Adolescent Health, I find that while sex education is associated with adverse health outcomes, there is little evidence of a causal link after controlling for unobserved heterogeneity via fixed effects and instrumental variables. These findings suggest that those on each side of the ideological debate over sex education are, in a sense, both correct and mistaken. Opponents are correct in observing that sex education is associated with adverse health outcomes, but are generally incorrect in interpreting this relationship causally. Proponents are generally correct in claiming that sex education does not encourage risky sexual activity, but are incorrect in asserting that investments in typical schoolbased sex education programs produce measurable health benefits. © 2006 by the Association for Public Policy Analysis and Management [source] On the analysis of long-term experimentsJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES A (STATISTICS IN SOCIETY), Issue 1 2007Thomas M. Loughin Summary., Long-term experiments are commonly used tools in agronomy, soil science and other disciplines for comparing the effects of different treatment regimes over an extended length of time. Periodic measurements, typically annual, are taken on experimental units and are often analysed by using customary tools and models for repeated measures. These models contain nothing that accounts for the random environmental variations that typically affect all experimental units simultaneously and can alter treatment effects. This added variability can dominate that from all other sources and can adversely influence the results of a statistical analysis and interfere with its interpretation. The effect that this has on the standard repeated measures analysis is quantified by using an alternative model that allows for random variations over time. This model, however, is not useful for analysis because the random effects are confounded with fixed effects that are already in the repeated measures model. Possible solutions are reviewed and recommendations are made for improving statistical analysis and interpretation in the presence of these extra random variations. [source] Influence diagnostics and outlier tests for semiparametric mixed modelsJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES B (STATISTICAL METHODOLOGY), Issue 3 2002Wing-Kam Fung Summary. Semiparametric mixed models are useful in biometric and econometric applications, especially for longitudinal data. Maximum penalized likelihood estimators (MPLEs) have been shown to work well by Zhang and co-workers for both linear coefficients and nonparametric functions. This paper considers the role of influence diagnostics in the MPLE by extending the case deletion and subject deletion analysis of linear models to accommodate the inclusion of a nonparametric component. We focus on influence measures for the fixed effects and provide formulae that are analogous to those for simpler models and readily computable with the MPLE algorithm. We also establish an equivalence between the case or subject deletion model and a mean shift outlier model from which we derive tests for outliers. The influence diagnostics proposed are illustrated through a longitudinal hormone study on progesterone and a simulated example. [source] Sources of Phenotypic and Genetic Variation for Seawater Growth in Five North American Atlantic Salmon, Salmo salar, StocksJOURNAL OF THE WORLD AQUACULTURE SOCIETY, Issue 3 2010William R. Wolters In 2003, pedigreed families were obtained from two St. John's River sources, Penobscot River, Gaspè, and landlocked salmon stocks. Eyed eggs were disinfected upon arrival, and incubated in separate hatching jars. Fry were transferred prior to first feeding into individual 0.1-m3 tanks receiving 8 L/min of oxygen-saturated freshwater from a recirculating biological filtration system. At approximately 30 d after the initiation of feeding, fish densities were equalized to 250 fish/tank, fed 5% of the tank's total biomass in 3,4 daily feedings. When the fish were approximately 40 g, approximately 30 fish from each family were pit tagged and stocked communally into three replicated 10-m3 smolt tanks. Approximately 1 mo prior to stocking into sea cages for performance evaluations, evaluations of serum chloride levels and gill Na+, K+ -ATPase activity were measured on subsamples from all stocks in freshwater and following seawater challenge. Smolts were stocked into sea cages in June 2005, harvested in February 2007, and evaluated for carcass weight, sex, and stage of sexual maturity. Data were analyzed by the mixed model ANOVA to determine the random effects of sire and dam (sire), and the fixed effects of sex, salmon stock, ploidy level, and replicate smolt tank on carcass weight with smolt weight as a covariate. Sire and dam variance components were significantly different from zero, and the fixed effects of salmon stock, sex × stock interaction, and smolt weight at stocking were significant (P < 0.05). There were no significant differences among sexes, replicate smolt tank, or ploidy level for carcass weight. Overall, St. John's River fish had the fastest growth with a carcass weight >4.1 kg compared with the slowest growth in landlocked fish at 1.7 kg. Grilsing was also highest in St. John's River fish (ca. 4,6%) and lowest in Penobscot River fish (0%). The sire heritability for carcass weight calculated from the sire variance component using the mixed model ANOVA or MTDFREML was 0.26 ± 0.14. Data were used to calculate breeding values on captive sibling adult brood fish, and a line selected for carcass weight was spawned in the fall of 2007, and eggs from these fish were released to industry. [source] Matching Inefficiencies, Regional Disparities, and UnemploymentLABOUR, Issue 3 2009Sanna-Mari Hynninen Our results suggest that there would be a substantial decline in aggregate unemployment if (i) all local labour offices operated with full efficiency or (ii) they shared the same structure of job seekers and vacant jobs as the most favourable office. In the former case an increase in hirings would lower the average unemployment rate by 2.4 percentage points. In the latter case the decrease would be 1.4 percentage points. Further, we find that fixed effects are positively correlated with both a more favourable structure and higher efficiency. This suggests that the fixed effects may capture some part of time-invariant features in the structure and inefficiency. Thus, the role of structural factors and inefficiency in regional unemployment disparities may be higher than estimated. [source] Comparison of three diagrammatic keys for the quantification of late blight in tomato leavesPLANT PATHOLOGY, Issue 6 2009F. M. Corrêa Three diagrammatic grading keys were designed for the assessment of the severity of late blight (caused by Phytophthora infestans) in tomato leaves. Simplified and broad keys considered, respectively, six (3, 12, 22, 40, 60 and 77%) and eight (3, 6, 12, 22, 40, 60, 77 and 90%) levels of disease severity, whilst a modified key based on a previous proposal for potato late blight considered six levels (1, 5, 10, 16, 32 and 50%). The keys were validated by 24 evaluators who assessed digital images of tomato leaves exhibiting different areas with lesions. Evaluator errors were compared using a mixed model in which evaluators were considered as random effects and the keys and evaluations as fixed effects. The accuracy and precision of the evaluators were compared by simple linear regression between the estimated and actual values of disease severity. The repeatability of evaluators was assessed using Pearson's correlation coefficient. There was significant (P , 0·001) variability amongst the errors made by evaluators, although the precision of each of the three keys was high with a coefficient of determination (R2) of 0·96, 0·93 and 0·83 for the simplified, broad and modified key, respectively. Repeatability of estimations amongst the evaluators was adequate (correlation coefficients of 0·91, 0·91 and 0·90 for the three keys, respectively). The simplified and broad keys resulted in higher precision and accuracy for the estimation of severity than did the modified key. Since the simplified key considers a smaller number of disease severity levels, its use is recommended in the assessment of late blight in tomato leaves. [source] Does Voting History Matter?AMERICAN JOURNAL OF POLITICAL SCIENCE, Issue 1 2009Analysing Persistence in Turnout Individuals who vote in one election are more likely to vote in the next. Yet modelling the causal relationship between past and current voting decisions is intrinsically difficult, as this positive association can exist due to habit formation or unobserved heterogeneity. This article overcomes this problem using longitudinal data from the British National Child Development Study (NCDS) to examine voter turnout across three elections. It distinguishes between unobserved heterogeneity caused by fixed individual characteristics and the initial conditions problem, which occurs when voting behavior in a previous, but unobserved, period influences current voting behavior. It finds that, controlling for fixed effects, unobserved heterogeneity has little impact on the estimated degree of habit in voter turnout; however, failing to control for initial conditions reduces the estimate by a half. The results imply that voting in one election increases the probability of voting in a subsequent election by 13%. [source] Testing for stationarity in heterogeneous panel dataTHE ECONOMETRICS JOURNAL, Issue 2 2000Kaddour Hadri This paper proposes a residual-based Lagrange multiplier (LM) test for a null that the individual observed series are stationary around a deterministic level or around a deterministic trend against the alternative of a unit root in panel data. The tests which are asymptotically similar under the null, belong to the locally best invariant (LBI) test statistics. The asymptotic distributions of the statistics are derived under the null and are shown to be normally distributed. Finite sample sizes and powers are considered in a Monte Carlo experiment. The empirical sizes of the tests are close to the true size even in small samples. The testing procedure is easy to apply, including, to panel data models with fixed effects, individual deterministic trends and heterogeneous errors across cross-sections. It is also shown how to apply the tests to the more general case of serially correlated disturbance terms. [source] Methods of privatization and economic growth in transition economies1THE ECONOMICS OF TRANSITION, Issue 4 2007John Bennett Privatization; transition economies; economic growth; panel data Abstract We examine how different methods of privatization might have affected growth in transition economies. Using several econometric specifications, including fixed effects and GMM, we estimate a cross-country panel growth model for 1990,2003. We find only voucher privatization to have been significantly associated with faster growth. Moreover, neither private sector development per se nor capital market development exercised a significant influence. We speculate that voucher privatization may have been effective because of the speed with which links between firms and the state were severed. [source] | |||||||||||||||||||||||||