Restricted Procedure Research Articles

Genetic components of carcass and meat quality traits in Meishan and Large White pigs and their reciprocal crosses

AbstractThe prospect that genes from the Chinese Meishan pig will be used to improve reproductive performance of European pigs requires that the Meishan is evaluated for traits of economic importance and the genetics of any breed effects investigated. Entire male and female pigs of four genotypes; purebred Meishan (MS) and Large White (LW) pigs and both reciprocal Fl crossbred genotypes (MS ♂ × LW ♀and LW ♂ × MS ♀), were fed ad libitum and slaughtered at about 70 kg. After slaughter, carcass weight, dimensions and conformation were recorded and fat depths at the shoulder, mid back and loin were measured on the carcass, together with fat depths and eye muscle dimensions recorded on a section cut at the last rib position. Drip loss, muscle reflectance and pH were measured and subjective assessments of fat firmness, fat separation, muscle marbling and muscle colour were made. Genotypic means and genetic crossbreeding effects (direct additive and heterosis effects and maternal additive effects) were estimated using restricted maximum likelihood procedures. When compared with the LW, MS carcasses had a similar killing-out proportion but were shorter with a poorer conformation. MS carcasses had substantially greater fat depths and reduced eye muscle dimensions in comparison with the LW. Differences between genotypes for fat depths and muscle dimensions were largely controlled by direct additive gene action, there was little evidence of direct heterosis and hence Fl crosses were intermediate between the purebreds. Significant genotype × sex interaction meant that genotypic differences for these traits were much greater in females than in males. Significant direct additive genetic differences between female genotypes were found for fat firmness, fat separation and drip loss, but these effects may in part have been a consequence of subcutaneous fat depth differences between genotypes. The degree of marbling was greater in MS females than in females of the other three genotypes and these genotypic differences did not seem to be associated with subcutaneous fat depth. Muscle from MS males was darker in colour with a lower reflectance than that from LW males. Genotype × sex interaction was such that genotypic differences for meat and fat quality traits differed between sexes.

Simulation of Moisture Deficits and Areal Interpolation by Universal Cokriging

Simulation models for calculating moisture deficits for areas of land require interpolation procedures to arrive from point observations to area‐covering statements. We use both (1) calculate first, interpolate later (CI) procedures, which interpolate calculated model results for test locations, and (2) procedures which interpolate basic soil data toward test locations, followed by model calculations, interpolate first, calculate later (IC) procedures. In this study several CI and IC procedures which simulate moisture deficits are compared by means of a test set of 100 observations, yielding the mean standard error (MSE). CI procedures consistently produced lower MSE values than IC procedures. Parameters of the pseudocovariance function (PCF), which models the spatial structure of bivariate increments in universal cokriging, were estimated by means of the restricted maximum likelihood procedure. Compared to universal kriging, universal cokriging yielded comparable MSE values, but a lower mean variance of the prediction error. Best results in this study were obtained by pointwise simulation model calculations, followed by statistical interpolations.

Vegetation patterns and structuring processes in coastal shell-beds at Akerøya, Hvaler, SE Norway.

Abstract The vegetation of shell-beds is studied in an island on the coast of Skagerak, SE Norway. Within this restricted area 125 sample plots, 1 m2 each, were distributed by a restricted random procedure. Frequency in subplots and percentage cover were used for estimation of species abundance. A set of 33 environmental variables was obtained from each sample plot. Ecological gradients corresponding to the main vegetational gradients are identified by means of DCA ordination results correlated with environmental data. DCA ordination results are further interpreted by the use of an earlier classification of the vegetation and by application of Grime’s strategy concept. The following complex gradients were recognized: ( 1) the primary successional gradient, influenced by variables dependent on site age, e.g. elevation, distance from the sea, and rate of decomposition of mollusc shells, (2) the secondary successional gradient, from open meadow vegetation via open shrub vegetation to dense shrub vegetation, highly correlated with variables independent of site age, e.g intensity of grazing, (3) the nutrient availability gradient, and (4) the soil moisture gradient. Interpretation of relations between coenoclines and environmental variables was performed by Kendall rank correlation and relationships among ecological variables analysed by PCA ordination. Direct gradient analysis by rh-DCCA is used as a supplement to DCA. The ratio between the rh-DCCA eigenvalue of the first ordination axis and the corresponding eigenvalue of the first residual (unconstrained) axis is used to quantify the importance of each environmental variable. The performed multivariate analyses show that the successional pathways on shell-bed shores are dependent on the grazing pressure. The relative importance of the following structuring processes is discussed: (1) interspecific interaction (competition, coexistence and facilitation), (2) destabilizing factors (disturbance and fluctuations), (3) stress, and (4) chance. Ordination and association analyses shows that Juniperus communis is the most important structuring species in the material. Grazing is necessary to reduce overgrowth by junipers and to maintain a high species diversity. The field data are used for inspection of the performance of different rescaling and detrending options, available with DCA ordination. Non-linear rescaling appears to be less influenced by deviant sample plots as compared to linear rescaling, and the S.D. units of the axes produced by non-linear rescaling are considered better interpretable in terms of a unimodal model of species responses to ecological gradients. Available options for detrending by polynomials are shown to be inferior to the detrending by segments option, as polynomial detrending may impose a polynomial distortion on the point configuration in the ordination space.

Genetic variation and covariation for growth, parasite resistance and heat tolerance in tropical cattle

Genetic parameters for growth, parasite resistance and heat tolerance in zebu-cross cattle in a tropical environment were estimated by restricted maximum likelihood procedures using various forms of an animal model. Heritability estimates for direct additive genetic effects for liveweights at birth, weaning, 12 and 18 months were 0.61, 0.20, 0.25 and 0.26, respectively and corresponding maternal additive genetic effects were 0.11, 0.32, 0.20 and 0.09. Estimates of genetic correlations between direct and maternal additive genetic effects were zero. Weight gains during the dry season were genetically uncorrelated or slightly negatively correlated to birth weight, preweaning weight gain or gains during the wet season. Heritability estimates for rectal temperature, numbers of ticks, buffalo flies and worms were 0.19, 0.34, 0.06 and 0.28, respectively, with corresponding repeatability estimates of 0.23, 0.45, 0.06 and 0.29. Phenotypic correlations between adaptive traits (heat tolerance and parasite resistance) and growth traits were low. Genetic correlations between growth and rectal temperature were negative. Genetic correlations of growth traits with worm and fly burdens were positive and with tick burdens were zero. It was concluded that in reasonably adapted genotypes, selection for growth in the Australian tropics would result in improved heat tolerance and reduced resistance to parasites. The effect of genotype on parameter estimates is discussed.

Estimates of genetic parameters for live animal ultrasound, actual carcass data, and growth traits in beef cattle.

Growth and carcass measurements were made on 2,411 Hereford steers slaughtered at a constant weight from a designed reference sire program involving 137 sires. A second data set consisted of ultrasound measures of backfat (USFAT) and longissimus muscle area (USREA) from 3,482 yearling Hereford cattle representing 441 sires. Restricted maximum likelihood procedures were used to estimate genetic parameters among carcass traits and live animal weight traits from these two separate data sets. Heritability estimates for the slaughter weight constant steer carcass backfat (FAT) and longissimus muscle area (REA) were .49 and .46, respectively. In addition, FAT had a negative genetic correlation with REA (-.37), weaning weight (-.28), and yearling weight (-.13) but positive with marbling (.19) and carcass weight (.36). Marbling was moderately heritable (.35) and highly correlated with total postweaning average daily gain (.54) and feedlot relative growth rate (.62). Heritability estimates for weight constant USFAT and USREA were .26 and .25, respectively. The genetic correlation between weight constant USFAT and USREA was positive (.39), indicating that in these young animals USFAT does not seem to be an indication of maturity. Mean USFAT measures and variability were small (.48 +/- .17 cm, n = 3,482). Results indicate that carcass fat on slaughter steers and ultrasound measures of backfat on young breeding animals may have different relationships with growth and muscling. These relationships need to be explored before wide scale selection based on ultrasound is implemented.

Canonical analysis of contingency tables with linear constraints

A generalized least squares approach is presented for incorporating linear constraints on the standardized row and column scores obtained from a canonical analysis of a contingency table. The method is easy to implement and may simplify considerably the interpretation of a data matrix. The approach is compared to a restricted maximum likelihood procedure.

Estimation of direct and maternal genetic variance for litter size in Canadian Yorkshire and Landrace swine using an animal model.

Estimates of additive direct heritability (h2a) for traits such as litter size may be biased by maternal effects. The size of these effects was estimated using a derivative-free restricted maximum likelihood procedure under an animal model. First-parity records from Yorkshire (Y) and Landrace (L) gilts were obtained from the Quebec Record of Performance sow productivity program for 21,127 litters born between 1977 and 1987. Direct (sigma 2a) and maternal (sigma 2m) additive genetic variances, their covariance (sigma am) and error variance (sigma 2e) were estimated for total numbers born (NOBN), born alive (NOBA) and weaned (NOWN). Analysis of purebred Y and crossbred litters indicated that estimates of sigma 2a were of similar magnitude for all traits, with h2a ranging from .06 to .13. Except for L litters, estimates of sigma 2m were relatively low for NOBN and NOBA, and increased in size for NOWN, with h2m ranging from 0 to .08. Also, estimates of sigma am were negative, except for NOBN and NOBA with crossbred litters, and became increasingly negative for NOWN. Results from purebred L litters indicated there was a stronger negative correlation between direct and maternal genetic effects for NOBN and NOBA than for NOWN.

A strong restriction of the inductive completion procedure

The procedure of Knuth & Bendix (In: Computational Problems in Abstract Algebras ,Pergamon Press, 1970, pp. 263–297) completes a system of equations into a confluent one. It proceeds by adding critical pairs when equations superpose themselves in an ambiguous way. Huet & Hullot (Proc. 21st Symp. Foundations in Computer Science, 1980, pp 96–107) have shown that, for theories with constructors satisfying a so-called principle of definition , the Knuth-Bendix procedure can be used to prove that conjectures are inductive theorems of a given theory (proofs by inductive completion). In this paper, we show that this is the case even when the procedure is restricted in a linear selecting manner: first, critical pairs are generated in a linear manner by superposition of one equation of the initial theory into one equation issued from critical pairs (no superposition between two equations both issued from critical pairs); second, for each critical pair, the occurrence of superposition with theory equations is uniquely determined by a selection function . p Unlike the Knuth-Bendix procedure, our procedure, when terminating with success, does not produce a confluent system in general. However, the generated system is guaranteed to have the ground-confluence property (confluence for terms without variables). This result suffices to guarantee the conjecture validity. Our restricted completion procedure terminates in many cases where the inductive completion procedure loops, generating infinitely many critical pairs. The procedure applies to theories without constructors (Jouannaud & Kounalis, Proc. Symp. on Logic in Computer Science, Cambridge, MA, 1986, pp. 358–366) and extends to conditional theories and conditional conjectures. It can also incorporate various techniques used in classical induction. The procedure then combines the efficiency of classical induction method with the simplicity of inductive completion.

Management of pavement rehabilitation

The development of a decision support system (DSS) for pavement management is described. The system contains forecasting and optimization models. The forecasting model is used to predict the condition of stretches of road. The optimization model has the form of a linear programming problem with additional logical constraints. The solution method proposed for this model is based on the simplex method for linear programming, with a restricted basis entry procedure. Results of a sensitivity analysis on the optimization model are reported, and the implementation of the DSS on a microcomputer is discussed.

Corrections to “Restricted Subset Selection Procedures for Simulation”

Correction to Sullivan, D. W., J. R. Wilson. 1989. Restricted subset selection procedures for simulation. Opns. Res. 37 52–71.

Restricted Subset Selection Procedures for Simulation

This paper develops two procedures for screening a set of normal populations with unknown moments in order that the final subset of selected populations satisfies the following requirements involving the user specified parameters P*, δ, and m: With probability at least P*, the selected subset will contain a population whose mean lies less than the distance δ from the largest mean. Although the size of the selected subset is random, at most m populations will finally be chosen, where m is usually taken small enough to reserve adequate resources for a more intensive follow-up study. The exact procedure VE is a two-stage random sampling scheme that is designed to compare transient or steady-state simulation models based on independent replications of each model. The heuristic procedure VS is a modification of VE that is designed to compare steady-state simulation models based on a single prolonged run of each model. A complete justification is given for VE together with tables of the constants required by both procedures and an algorithm for computing these constants. Experimental results are summarized to gauge the robustness of VE against departures from normality and to evaluate the performance of VS on several types of stationary stochastic processes.

Properties of the urn randomization in clinical trials

In this article we review the important statistical properties of the urn randomization (design) for assigning patients to treatment groups in a clinical trial. The urn design is the most widely studied member of the family of adaptive biased-coin designs. Such designs are a compromise between designs that yield perfect balance in treatment assignments and complete randomization which eliminates experimental bias. The urn design forces a small-sized trial to be balanced but approaches complete randomization as the size of the trial ( n) increases. Thus, the urn design is not as vulnerable to experimental bias as are other restricted randomization procedures. In a clinical trial it may be difficult to postulate that the study subjects constitute a random sample from a well-defined homogeneous population. In this case, a randomization model provides a preferred basis for statistical inference. We describe the large-sample permutational null distributions of linear rank statistics for testing the equality of treatment groups based on the urn design. In general, these permutation tests may be different from those based on the population model, which is equivalent to assuming complete randomization. Poststratified subgroup analyses can also be performed on the basis of the urn design permutational distribution. This provides a basis for analyzing the subset of patients with observed responses when some patients' responses can be assumed to be missing-at-random. For multiple mutually exclusive strata, these tests are correlated. For this case, a combined covariate-adjusted test of treatment effect is described. Finally, we show how to generalize the urn design to a prospectively stratified trial with a fairly large number of strata.

Estimation of genetic parameters for milk production in the first three lactations

Variance and covariance components were estimated for milk-production traits in the first 3 lactations. The data set comprised 95 910 first, 74 088 second and 55 371 third lactation records of cows, sired by 603 black and white AI bulls in Lower Saxony (F.R.G.). Estimation was by two multiple trait restricted maximum likelihood procedures, differing by allowance of non-zero residual covariances (MT-O-REML and MT-REML). Further, correlations between traits within lactations were estimated using Henderson's method III (H-III). The results revealed a clearly antagonistic relationship between milk yield and percentages of fat and protein, with correlations in the range -0.40 to -0.50. In comparison with H-III estimates, genetic variances and especially covariances increased markedly when using REML and all available data. Error (co) variances were of the same magnitude for all methods used. Estimated genetic correlations between corresponding traits in Lactations 1 and 2 were greater than 0.90, while for Lactations 2 and 3 the correlation was unity. Results suggest that dairy performance in the first 3 lactations, at least in Lactation 2 and 3, genetically should be regarded as one trait.

An ecological approach to the investigation of a beech forest in Vestfold, SE Norway

The vegetation in a beech forest, Fritzøehusparken, is analysed using one hundred sample plots, each 25 m2, distributed by a restricted random procedure. Percentage cover and frequency in subplots are used for quantification of species amounts, and their relative performance are evaluated. Advantages of choosing frequency in subplots are discussed. Thirteen environmental variables are measured from each of the sample plots. The vegetation is divided into four topographical/ecological types. This classification served as a reference in the further treatment. Ecological gradients corresponding to the most important vegetational gradients in the beech forest are identified by means of DCA ordination followed by statistical interpretation. Two main complex gradients were recognized; (1) the gradient in nutrient conditions, and (2), the gradient inlitter‐wind conditions. The advantages of using DCA and statistical interpretation with integration of ecological measurements are emphasized.

Spatial autocorrelation of ABO serotypes in mediaeval cemeteries as an indicator of ethnic and familial structure

Hungarian cemeteries in an effort to detect familial structure. Different ethnic groups buried in separate areas dominated the spatial pattern in two cemeteries, leaving insufficient power to test for familial patterns. In a third, ethnically homogeneous cemetery, no evidence of familial structure was found. A simulation showed that familial structure could readily be detected by the methods applied when it exists in an ethnically homogeneous population. The spatial autocorrelation methods employed would have detected the ethnic diversity in the two cemeteries containing graves from different populations, even in the absence of archaeological information to that effect. A restricted randomization procedure was developed to test two alternative hypotheses concerning the ethnic designations of the occupants of the cemetery at Szentendre. As a result of this test, the hypothesis that graves located in a rough circle (putative Lombards) differ serologically from those located at the periphery (putative nonLombards) is strongly preferred over a second hypothesis based on grave goods which would imply spatially random placement of the graves of the two ethnic units.

A theoretical study of the estimation of the correlation scale in spatially variable fields: 1. Stationary fields

The correlation scale of the stochastic component of various soil properties plays an essential role in the interpolation of spatial phenomena using kriging techniques and in the solution of transport problems in heterogeneous media using stochastic modeling. In this study the uncertainty of the estimation of the correlation scales of stationary fields was analyzed by generating realizations of a set of two‐dimensional isotropic second‐order stationary functions with given correlation scales. Results from simulations of 100 independent realizations showed that the variance of the estimate of the correlation scale decreases as the number of the sample points n increases and when the size of the correlation scale of the underlying process relative to the field area decreases, whereas the biasedness decreases as n increases arid the underlying correlation scale increases. Results of variogram model fitting and cross‐validation tests involving single realizations showed that both the accuracy of the estimates of the correlation scales and the fitted variogram model consistency increase as both the sample points and the correlation scale of the underlying process increase. Analysis of the effect of the grid size on the estimates of the correlation scale showed that reasonable estimates can be obtained when the distance between the sampling points is smaller than half the range of the underlying process. Estimates of correlation scales based on data along transects may underestimate the correlation scale of the underlying process by a factor of 2 or greater. A comparison between different estimation procedures showed that in general estimates of both the variance Ĉ (0) and the integral scale Ĵ provided by the restricted maximum likelihood procedure are higher than those provided by the maximum likelihood procedure, which, in turn, are higher than those provided by fitting the nonparametric estimates of the variogram using the minimum mean‐square deviation criterion. Results of the objective model validation tests, however, implied that generally all these estimates are accurate and consistent with the data, suggesting that a given realization of a given stationary process may be adequately described by different sets of Ĵ and Ĉ(0). This may not affect the results of kriging estimation which requires the ratio C(0)/J, but may pose problems in stochastic transport modeling which requires the values of Ĵ and Ĉ(0) individually.

Between Algorithms: A “Short Cut” Restricted Maximum Likelihood Procedure to Estimate Variance Components

A restricted maximum likelihood procedure is described to estimate variance and covariance components in a multivariate mixed model when records are missing for some traits. The algorithm combines features of an expectation-maximization algorithm to estimate the within random effects components with the method of scoring to estimate the between random effects components. The procedure is computationally less demanding per round of iteration than the method of scoring, although the number of iterates required to reach convergence is increased. A computing strategy is described for the example of estimating genetic parameters for first and later lactations of dairy cows.

Heritability estimate for temperament scores in German shepherd dogs and its genetic correlation with hip dysplasia.

Temperament and hip dysplasia scores of 575 German shepherd dogs bred and evaluated by the United States Army's Division of Bio-Sensor Research between 1968 and 1976 were examined. The records represented 4 years, 18 sires, and 71 dams. Restricted maximum-likelihood procedures were used to obtain variance component estimates from which the heritabilities and genetic correlation were estimated. Heritability estimates for the temperament and hip dysplasia scores were 0.51 and 0.26, respectively. The genetic correlation between the two traits was estimated as −0.33. Males showed significantly higher temperament scores than females.

Genetic and Phenotypic Statistics of Lactation Cell Counts in Different Lactations of Holstein Cows

Between February 1977 and February 1982, 680,246 monthly test-day observations of somatic cell count were taken for Holstein cows having completed 79,124 lactations in 941 herds on the Quebec Dairy Herd Analysis Service. Data were transformed to natural log scale, and analyses were separate within five parity groups. Two lactational measures of cell count, geometric mean, and weighted (by test-day milk yield) mean of the log of monthly cell counts were calculated for each lactation. Maximum likelihood, iterative Minimum Norm Quadratic Unbiased Estimation, and multivariate Restricted Maximum Likelihood procedures were used for estimation of genetic and phenotypic parameters.Repeatabilities of log test-day cell counts and log of test-day cell counts corrected for milk yield were the same at each parity, .36, .41, .42, .42, and .42 in first, second, third, fourth, and fifth and later parities. Repeatabilities of lactational measures of cell count were .33 between first and second parities, .40 between second and third parities, .13 between first and third parities, and .27 between first, second, and third parities.Heritabilities of measures of lactational cell count were small from .06 to .14 in the five parities. Genetic correlations between measures of lactational cell count in different parities were close to unity, .90 to .97.

Heritabilities of Relative Percentages of Major Bovine Casein and Serum Proteins in Test-Day Milk Samples

Individual milk samples were obtained from Holstein cows in 62 herds in Quebec from November 1979 to November 1981. Milk samples were analyzed for somatic cell count and relative percentages of αs-, β-, and κ-caseins, β-lactoglobulin, α-lactalbumin bovine serum albumin, and immunoglobulins. The model used to analyze the data included herd, month of test, age of cow, and somatic cell count as fixed effects and sire, cow within sire, and error as random effects. Restricted maximum likelihood procedures were used to fit the model to the data. Heritabilities obtained for relative percentages of αs-, β-, and κ-caseins were .02, .03, and .005. Heritabilities obtained for relative percentages of β-lactoglobulin, α-lactalbumin, bovine serum albumin, and immunoglobulins were .24, .14, .15, and .02.