Interação genótipo – ambiente no peso ao sobreano na raça Nelore

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The STATFLUX code: a statistical method for calculation of flow and set of parameters, based on the Multiple-Compartment Biokinetical Model

The code STATFLUX, implementing a new and simple statistical procedure for the calculation of transfer coefficients in radionuclide transport to animals and plants, is proposed. The method is based on the general multiple-compartment model, which uses a system of linear equations involving geometrical volume considerations. Flow parameters were estimated by employing two different least-squares procedures: Derivative and Gauss-Marquardt methods, with the available experimental data of radionuclide concentrations as the input functions of time. The solution of the inverse problem, which relates a given set of flow parameter with the time evolution of concentration functions, is achieved via a Monte Carlo Simulation procedure.Program summaryTitle of program: STATFLUXCatalogue identifier: ADYS_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADYS_v1_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions: noneComputer for which the program is designed and others on which it has been tested: Micro-computer with Intel Pentium III, 3.0 GHzInstallation: Laboratory of Linear Accelerator, Department of Experimental Physics, University of São Paulo, BrazilOperating system: Windows 2000 and Windows XPProgramming language used: Fortran-77 as implemented in Microsoft Fortran 4.0. NOTE: Microsoft Fortran includes non-standard features which are used in this program. Standard Fortran compilers such as, g77, f77, ifort and NAG95, are not able to compile the code and therefore it has not been possible for the CPC Program Library to test the program.Memory, required to execute with typical data: 8 Mbytes of RAM memory and 100 MB of Hard disk memoryNo. of bits in a word: 16No. of lines in distributed program, including test data, etc.: 6912No. of bytes in distributed Program, including test data, etc.: 229 541Distribution format: tar.gzNature of the physical problem: the investigation of transport mechanisms for radioactive substances, through environmental pathways, is very important for radiological protection of populations. One such pathway, associated with the food chain, is the grass-animal-man sequence. The distribution of trace elements in humans and laboratory animals has been intensively studied over the past 60 years [R.C. Pendlenton, C.W. Mays, R.D. Lloyd, A.L. Brooks, Differential accumulation of iodine-131 from local fallout in people and milk, Health Phys. 9 (1963) 1253-1262]. In addition, investigations on the incidence of cancer in humans, and a possible causal relationship to radioactive fallout, have been undertaken [E.S. Weiss, M.L. Rallison, W.T. London, W.T. Carlyle Thompson, Thyroid nodularity in southwestern Utah school children exposed to fallout radiation, Amer. J. Public Health 61 (1971) 241-249; M.L. Rallison, B.M. Dobyns, F.R. Keating, J.E. Rall, F.H. Tyler, Thyroid diseases in children, Amer. J. Med. 56 (1974) 457-463; J.L. Lyon, M.R. Klauber, J.W. Gardner, K.S. Udall, Childhood leukemia associated with fallout from nuclear testing, N. Engl. J. Med. 300 (1979) 397-402]. From the pathways of entry of radionuclides in the human (or animal) body, ingestion is the most important because it is closely related to life-long alimentary (or dietary) habits. Those radionuclides which are able to enter the living cells by either metabolic or other processes give rise to localized doses which can be very high. The evaluation of these internally localized doses is of paramount importance for the assessment of radiobiological risks and radiological protection. The time behavior of trace concentration in organs is the principal input for prediction of internal doses after acute or chronic exposure. The General Multiple-Compartment Model (GMCM) is the powerful and more accepted method for biokinetical studies, which allows the calculation of concentration of trace elements in organs as a function of time, when the flow parameters of the model are known. However, few biokinetics data exist in the literature, and the determination of flow and transfer parameters by statistical fitting for each system is an open problem.Restriction on the complexity of the problem: This version of the code works with the constant volume approximation, which is valid for many situations where the biological half-live of a trace is lower than the volume rise time. Another restriction is related to the central flux model. The model considered in the code assumes that exist one central compartment (e.g., blood), that connect the flow with all compartments, and the flow between other compartments is not included.Typical running time: Depends on the choice for calculations. Using the Derivative Method the time is very short (a few minutes) for any number of compartments considered. When the Gauss-Marquardt iterative method is used the calculation time can be approximately 5-6 hours when similar to 15 compartments are considered. (C) 2006 Elsevier B.V. All rights reserved.

Random regression analyses using B-spline functions to model growth of Nellore cattle

The objective of this study was to estimate (co)variance components using random regression on B-spline functions to weight records obtained from birth to adulthood. A total of 82 064 weight records of 8145 females obtained from the data bank of the Nellore Breeding Program (PMGRN/Nellore Brazil) which started in 1987, were used. The models included direct additive and maternal genetic effects and animal and maternal permanent environmental effects as random. Contemporary group and dam age at calving (linear and quadratic effect) were included as fixed effects, and orthogonal Legendre polynomials of age (cubic regression) were considered as random covariate. The random effects were modeled using B-spline functions considering linear, quadratic and cubic polynomials for each individual segment. Residual variances were grouped in five age classes. Direct additive genetic and animal permanent environmental effects were modeled using up to seven knots (six segments). A single segment with two knots at the end points of the curve was used for the estimation of maternal genetic and maternal permanent environmental effects. A total of 15 models were studied, with the number of parameters ranging from 17 to 81. The models that used B-splines were compared with multi-trait analyses with nine weight traits and to a random regression model that used orthogonal Legendre polynomials. A model fitting quadratic B-splines, with four knots or three segments for direct additive genetic effect and animal permanent environmental effect and two knots for maternal additive genetic effect and maternal permanent environmental effect, was the most appropriate and parsimonious model to describe the covariance structure of the data. Selection for higher weight, such as at young ages, should be performed taking into account an increase in mature cow weight. Particularly, this is important in most of Nellore beef cattle production systems, where the cow herd is maintained on range conditions. There is limited modification of the growth curve of Nellore cattle with respect to the aim of selecting them for rapid growth at young ages while maintaining constant adult weight.

Use of the EM algorithm to detect QTL affecting multiple-traits in an across half-sib family analysis

QTL detection experiments in livestock species commonly use the half-sib design. Each male is mated to a number of females, each female producing a limited number of progeny. Analysis consists of attempting to detect associations between phenotype and genotype measured on the progeny. When family sizes are limiting experimenters may wish to incorporate as much information as possible into a single analysis. However, combining information across sires is problematic because of incomplete linkage disequilibrium between the markers and the QTL in the population. This study describes formulae for obtaining MLEs via the expectation maximization (EM) algorithm for use in a multiple-trait, multiple-family analysis. A model specifying a QTL with only two alleles, and a common within sire error variance is assumed. Compared to single-family analyses, power can be improved up to fourfold with multi-family analyses. The accuracy and precision of QTL location estimates are also substantially improved. With small family sizes, the multi-family, multi-trait analyses reduce substantially, but not totally remove, biases in QTL effect estimates. In situations where multiple QTL alleles are segregating the multi-family analysis will average out the effects of the different QTL alleles.

Covariance functions for body weight from birth to maturity in Nellore cows

The objective of this study was to estimate (co)variance functions using random regression models on Legendre polynomials for the analysis of repeated measures of BW from birth to adult age. A total of 82,064 records from 8,145 females were analyzed. Different models were compared. The models included additive direct and maternal effects, and animal and maternal permanent environmental effects as random terms. Contemporary group and dam age at calving (linear and quadratic effect) were included as fixed effects, and orthogonal Legendre polynomials of animal age (cubic regression) were considered as random co-variables. Eight models with polynomials of third to sixth order were used to describe additive direct and maternal effects, and animal and maternal permanent environmental effects. Residual effects were modeled using 1 (i.e., assuming homogeneity of variances across all ages) or 5 age classes. The model with 5 classes was the best to describe the trajectory of residuals along the growth curve. The model including fourth- and sixth-order polynomials for additive direct and animal permanent environmental effects, respectively, and third-order polynomials for maternal genetic and maternal permanent environmental effects were the best. Estimates of (co) variance obtained with the multi-trait and random regression models were similar. Direct heritability estimates obtained with the random regression models followed a trend similar to that obtained with the multi-trait model. The largest estimates of maternal heritability were those of BW taken close to 240 d of age. In general, estimates of correlation between BW from birth to 8 yr of age decreased with increasing distance between ages.

Do mediterranean genera not included in Tachet et al. (2002) have mediterranean trait characteristics?

Do mediterranean genera not included in Tachet et al. 2002 have mediterranean trait characteristics? Multiple-trait databases are increasingly used in community ecology in different regions of the world. In Europe, Tachet et al.(2002) compiled an aquatic macroinvertebrate database for 473 taxa using information on 11 biological traits described by 63 categories. However, less studied regions, at the time of the compilation of the database, such as the mediterranean Basin, can harbour exclusive genera, which were not included in Tachet"s database. In a large-scale study across the mediterranean Basin, we found 44 genera that were not included in Tachet"s database (NEW genera). Our main aim was to compile trait information for these NEW genera and assess whether these genera had specific traits that could explain their exclusivity to the Mediterranean region. We compared the trait characteristics of NEW genera to those of genera only found in Mediterranean or temperate regions that were included in the Tachet"s database (MED and TEM genera, respectively). We found that NEW genera had more mediterranean characteristics than TEM genera and that some trait categories of NEW genera were even more mediterranean-like than the traits of MED genera (e.g., diapause). Therefore, our results suggest that the specific biological traits of these NEW genera allow them to cope successfully and exclusively with the harsh environmental conditions of the mediterranean climate rivers, which could partially explain their absence in Tachet"s database. Other explanations, such as the limited dispersal ability of these NEW genera to reach and colonize temperate Europe or the rarity of these NEW genera, should also be considered. We provide biological traits of the NEW genera to be used in future studies on the mediterranean river ecology.

Thread Scheduling Mechanisms for Multiple-Context Parallel Processors

Scheduling tasks to efficiently use the available processor resources is crucial to minimizing the runtime of applications on shared-memory parallel processors. One factor that contributes to poor processor utilization is the idle time caused by long latency operations, such as remote memory references or processor synchronization operations. One way of tolerating this latency is to use a processor with multiple hardware contexts that can rapidly switch to executing another thread of computation whenever a long latency operation occurs, thus increasing processor utilization by overlapping computation with communication. Although multiple contexts are effective for tolerating latency, this effectiveness can be limited by memory and network bandwidth, by cache interference effects among the multiple contexts, and by critical tasks sharing processor resources with less critical tasks. This thesis presents techniques that increase the effectiveness of multiple contexts by intelligently scheduling threads to make more efficient use of processor pipeline, bandwidth, and cache resources. This thesis proposes thread prioritization as a fundamental mechanism for directing the thread schedule on a multiple-context processor. A priority is assigned to each thread either statically or dynamically and is used by the thread scheduler to decide which threads to load in the contexts, and to decide which context to switch to on a context switch. We develop a multiple-context model that integrates both cache and network effects, and shows how thread prioritization can both maintain high processor utilization, and limit increases in critical path runtime caused by multithreading. The model also shows that in order to be effective in bandwidth limited applications, thread prioritization must be extended to prioritize memory requests. We show how simple hardware can prioritize the running of threads in the multiple contexts, and the issuing of requests to both the local memory and the network. Simulation experiments show how thread prioritization is used in a variety of applications. Thread prioritization can improve the performance of synchronization primitives by minimizing the number of processor cycles wasted in spinning and devoting more cycles to critical threads. Thread prioritization can be used in combination with other techniques to improve cache performance and minimize cache interference between different working sets in the cache. For applications that are critical path limited, thread prioritization can improve performance by allowing processor resources to be devoted preferentially to critical threads. These experimental results show that thread prioritization is a mechanism that can be used to implement a wide range of scheduling policies.

Genetic parameters and environmental effects on temperament score and reproductive traits of Nellore cattle

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estimation of genetic parameters for body weights, scrotal circumference, and testicular volume measured at different ages in Nellore cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Bayesian inference in genetic parameter estimation of visual scores in Nellore beef-cattle

The aim of this study was to estimate the components of variance and genetic parameters for the visual scores which constitute the Morphological Evaluation System (MES), such as body structure (S), precocity (P) and musculature (M) in Nellore beef-cattle at the weaning and yearling stages, by using threshold Bayesian models. The information used for this was gleaned from visual scores of 5,407 animals evaluated at the weaning and 2,649 at the yearling stages. The genetic parameters for visual score traits were estimated through two-trait analysis, using the threshold animal model, with Bayesian statistics methodology and MTGSAM (Multiple Trait Gibbs Sampler for Animal Models) threshold software. Heritability estimates for S, P and M were 0.68, 0.65 and 0.62 (at weaning) and 0.44, 0.38 and 0.32 (at the yearling stage), respectively. Heritability estimates for S, P and M were found to be high, and so it is expected that these traits should respond favorably to direct selection. The visual scores evaluated at the weaning and yearling stages might be used in the composition of new selection indexes, as they presented sufficient genetic variability to promote genetic progress in such morphological traits.

Genetic parameters for buffalo milk yield and milk quality traits using Bayesian inference

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genetic parameters for milk yield analyzed by test-day models in Murrah buffaloes in Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Breeding value accuracy estimates for growth traits using random regression and multi-trait models in Nelore cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genetic parameters of total milk yield and factors describing the shape of lactation curve in dairy buffaloes

The objective of this study was to apply factor analysis to describe lactation curves in dairy buffaloes in order to estimate the phenotypic and genetic association between common latent factors and cumulative milk yield. A total of 31 257 monthly test-day milk yield records from buffaloes belonging to herds located in the state of São Paulo were used to estimate two common latent factors, which were then analysed in a multi-trait animal model for estimating genetic parameters. Estimates of (co)variance components for the two common latent factors and cumulated 270-d milk yield were obtained by Bayesian inference using a multiple trait animal model. Contemporary group, number of milkings per day (two levels) and age of buffalo cow at calving (linear and quadratic) as covariate were included in the model as fixed effects. The additive genetic, permanent environmental and residual effects were included as random effects. The first common latent factor (F1) was associated with persistency of lactation and the second common latent factor (F2) with the level of production in early lactation. Heritability estimates for Fl and F2 were 0.12 and 0.07, respectively. Genetic correlation estimates between El and F2 with cumulative milk yield were positive and moderate (0.63 and 0.52). Multivariate statistics employing factor analysis allowed the extraction of two variables (latent factors) that described the shape of the lactation curve. It is expected that the response to selection to increase lactation persistency is higher than the response obtained from selecting animals to increase lactation peak. Selection for higher total milk yield would result in a favourable correlated response to increase the level of production in early lactation and the lactation persistency.

Population parameters in Brazilian Thoroughbred

The information in this study has been provided by the Brazilian Association of Racehorse Breeders [Associação do Brasileira dos Criadores do Cavalo de Corrida (ABCCC)]. It can be found in the files on the CD-ROM developed by the ABCCC in 1999. A total of 5008 finishing time records related to 2545 winning horses that ran in the classical calendar on Brazilian hippodromes during 25 years (197498) were analysed. There were a total of 9949 horses on the relationship matrix. The variance components were estimated using the multiple-trait derivate-free restricted maximum likelihood (MTDFREML) program, for an animal model. Generation intervals were higher in the maternal side (10.91 years) than in the paternal one (10.41 years). The estimates for genetic permanent environmental and phenotypic variances and heritability were 0.291, 0.161, 3.486 and 0.08, respectively. The phenotypic standard deviation for time in races was 1.86729 s. Genetic time trend on Thoroughbred races in Brazil was small and could be accelerated if selection considered the trait time effectively. With respect to the animal's country of birth, the results show that there has been an intense participation of foreign animals in breeding Brazilian Thoroughbreds.