Genetic Correlation for Pre-Weaning and Post-Weaning Traits of Mediterranean Buffaloes from Brazil, Estimated By Bayesian Inference

The aim of this study was to estimate genetic, environmental and phenotypic correlation between birth weight (BW) and weight at 205 days age (W205), BW and weight at 365 days age (W365) and W205-W365, using Bayesian inference. The Brazilian Program for Genetic Improvement of Buffaloes provided the data that included 3,883 observations from Mediterranean breed buffaloes. With the purpose to estimate variance and covariance, bivariate analyses were performed using Gibbs sampler that is included in the MTGSAM software. The model for BW, W205 and W365 included additive direct and maternal genetic random effects, maternal environmental random effect and contemporary group as fixed effect. The convergence diagnosis was achieved using Geweke, a method that uses an algorithm implemented in R software through the package Bayesian Output Analysis. The calculated direct genetic correlations were 0.34 (BW-W205), 0.25 (BW-W365) and 0.74 (W205-W365). The environmental correlations were 0.12, 0.11 and 0.72 between BW-W205, BW-W365 and W205-W365, respectively. The phenotypic correlations were low for BW-W205 (0.01) and BW-W365 (0.04), differently than the obtained for W205-W365 with a value of 0.67. The results indicate that BW trait have low genetic, environmental and phenotypic association with the two others traits. The genetic correlation between W205 and W365 was high and suggests that the selection for weight at around 205 days could be beneficial to accelerate the genetic gain.

Genetic Parameters for Growth Traits of Mediterranean Buffaloes from Brazil, Estimated By Bayesian Inference

Quantitative analysis of growth genetic parameters is not available for many breeds of buffaloes making selection and breeding decisions an empirical process that lacks robustness. The objective of this study was to estimate heritability for birth weight (BW), weight at 205 days (W205) and 365 days (W365) of age using Bayesian inference. The Brazilian Program for Genetic Improvement of Buffaloes provided the data. For the traits BW, W205 and W365 of Brazilian Mediterranean buffaloes 5169, 3792 and 3883 observations have been employed for the analysis, respectively. In order to obtain the estimates of variance, univariate analyses were conducted using the Gibbs sampler included in the MTGSAM software. The model for BW, W205 and W365 included additive direct and maternal genetic random effects, random maternal permanent environmental effect and contemporary group that was treated as a fixed effect. The convergence diagnosis was performed employing Geweke, a method that uses an algorithm from the Bayesian Output Analysis package that was implemented using R software environment. The average values for weight traits were 37.6 +/- 4.7 kg for BW, 192.7 +/- 40.3 kg for W205 and 298.6 +/- 67.4 kg for W365. The heritability posterior distributions for direct and maternal effects were symmetric and close to those expected in a normal distribution. Direct heritability estimates obtained using the modes were 0.30 (BW), 0.52 (W205) and 0.54 (W365). The maternal heritability coefficient estimates were 0.31, 0.19 and 0.21 for BW, W205 and W365, respectively. Our data suggests that all growth traits and mainly W205 and W365, have clear potential for yield improvement through direct genetic selection.

Associação genética entre o perfil de ácidos graxos e outras características da carcaça e carne de bovinos da raça Nelore

Pós-graduação em Genética e Melhoramento Animal - FCAV

Determinação da melhor dose de virginiamicina em suplementos para bovinos Nelore em pastejo

Pós-graduação em Zootecnia - FCAV

Produção de leite, duração da lactação e intervalo de partos em búfalas mestiças Murrah

This study aimed to evaluate the potential for milk production (MP), lactation length (LL) and calving interval (CI), analyze the environmental component affecting these traits, and to estimate the heritability and repeatability for milk production in crossbreds of Murrah buffalo cows in the state of Alagoas, Brazil. Data was composed of 487 observations of MP from 136 lactations recorded between the years of 2000 and 2010. In the analysis of variance for PL, the fixed effects were season (1- October to March, 2 -April to September) and year of the beginning of lactation, calving order and the LL (covariate). For the analysis of LL only the fixed effect of year of the beginning of lactation was included, and finally for the CI analysis, year of the beginning of lactation and calving order. The estimates of covariance were obtained using unicharacteristic analysis by Bayesian inference method, applyingan animal model, through Gibbs sampling. The additive genetic, permanent environment and residual effects were included as random effects in the model. The averages (sd) of MP, LL and CI were 2,218.03 kg (408.18), 282.59 days (39.48) e 422.49 days (91.05), respectively. All the effects included in the models were important (P<0.01). The estimates of heritability and repeatability for PL were 0.29 and 0.69, respectively. The results suggest that there is a moderate genetic variability among individuals for PL, indicating the possibility to obtain gain using selection.

Parâmetros genéticos para o perfil de ácidos graxos do longissimus thoracis de bovinos da raça Nelore terminados em confinamento

Pós-graduação em Genética e Melhoramento Animal - FCAV

Effect of IGF1, GH, and PIT1 markers on the genetic parameters of growth and reproduction traits in Canchim cattle

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

Genetic and phenotypic parameters of carcass and organ traits of broiler chickens

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Association between ACTA1 candidate gene and performance, organs and carcass traits in broilers

This study investigates the genetic association of the SNP present in the ACTA1 gene with performance traits, organs and carcass of broilers to help marker-assisted selection of a paternal broiler line (TT) from EMBRAPA Swine and Poultry, Brazil. Genetic and phenotypic data of 1,400 broilers for 68 traits related to body performance, organ weights, weight of carcass parts, and yields as a percentage of organs and carcass parts were used. The maximum likelihood method, considering 4 analytical models, was used to analyze the genetic association between the SNP and these important economic traits. The association analysis was performed using a mixed animal model including the random effect of the animal (polygenic), and the fixed effects of sex (2 levels), hatch (5 levels) and SNP (3 levels), besides the random error. The traits significantly associated (P < 0.05) with the SNP were analyzed, along with body weight at 42 days of age (BW42), by the restricted maximum likelihood method using the multi-trait animal model to estimate genetic parameters. The analysis included the residual and additive genetic random effects and the sex-hatch fixed effect. The additive effects of the SNP were associated with breast meat (BMY), liver yield (LIVY), body weight at 35 days of age (BW35); drumstick skin (DSW), drumstick (DW) and breast (BW) weights. The heritability estimates for these traits, in addition to BW42, ranged from 0.24 ± 0.06 to 0.45 ± 0.08 for LIVY and BW35, respectively. The genetic correlation ranged from 0.02 ± 0.18 for LIVY and BMY to 0.97 ± 0.01 for BW35 and BW42. Based on the results of this study, it can be concluded that ACTA1 gene is associated with performance traits BW35, LIV and BMY, DW, BW and DW adjusted for body weight at 42 days of age. Therefore, the ACTA1 gene is an important molecular marker that could be used together with others already described to increase the economically important traits in broilers.

Degree of multicollinearity and variables involved in linear dependence in additive-dominant models

The objective of this work was to assess the degree of multicollinearity and to identify the variables involved in linear dependence relations in additive-dominant models. Data of birth weight (n=141,567), yearling weight (n=58,124), and scrotal circumference (n=20,371) of Montana Tropical composite cattle were used. Diagnosis of multicollinearity was based on the variance inflation factor (VIF) and on the evaluation of the condition indexes and eigenvalues from the correlation matrix among explanatory variables. The first model studied (RM) included the fixed effect of dam age class at calving and the covariates associated to the direct and maternal additive and non-additive effects. The second model (R) included all the effects of the RM model except the maternal additive effects. Multicollinearity was detected in both models for all traits considered, with VIF values of 1.03 - 70.20 for RM and 1.03 - 60.70 for R. Collinearity increased with the increase of variables in the model and the decrease in the number of observations, and it was classified as weak, with condition index values between 10.00 and 26.77. In general, the variables associated with additive and non-additive effects were involved in multicollinearity, partially due to the natural connection between these covariables as fractions of the biological types in breed composition.

Efficacy of experimental treatments compared with standard treatments in non-inferiority trials: a meta-analysis of randomized controlled trials

Background There is concern that non-inferiority trials might be deliberately designed to conceal that a new treatment is less effective than a standard treatment. In order to test this hypothesis we performed a meta-analysis of non-inferiority trials to assess the average effect of experimental treatments compared with standard treatments. Methods One hundred and seventy non-inferiority treatment trials published in 121 core clinical journals were included. The trials were identified through a search of PubMed (1991 to 20 February 2009). Combined relative risk (RR) from meta-analysis comparing experimental with standard treatments was the main outcome measure. Results The 170 trials contributed a total of 175 independent comparisons of experimental with standard treatments. The combined RR for all 175 comparisons was 0.994 [95% confidence interval (CI) 0.978–1.010] using a random-effects model and 1.002 (95% CI 0.996–1.008) using a fixed-effects model. Of the 175 comparisons, experimental treatment was considered to be non-inferior in 130 (74%). The combined RR for these 130 comparisons was 0.995 (95% CI 0.983–1.006) and the point estimate favoured the experimental treatment in 58% (n = 76) and standard treatment in 42% (n = 54). The median non-inferiority margin (RR) pre-specified by trialists was 1.31 [inter-quartile range (IQR) 1.18–1.59]. Conclusion In this meta-analysis of non-inferiority trials the average RR comparing experimental with standard treatments was close to 1. The experimental treatments that gain a verdict of non-inferiority in published trials do not appear to be systematically less effective than the standard treatments. Importantly, publication bias and bias in the design and reporting of the studies cannot be ruled out and may have skewed the study results in favour of the experimental treatments. Further studies are required to examine the importance of such bias.

Does land-based exercise reduce pain and disability associated with hip osteoarthritis? A meta-analysis of randomized controlled trials

Objective To determine if clinical guidelines recommending therapeutic exercise for people with hip osteoarthritis (OA) are supported by rigorous scientific evidence. Methods A meta-analysis of randomized controlled trials (RCTs) recruiting people with hip OA and comparing some form of land-based exercise program (as opposed to exercises conducted in the water) with a non-exercise group in terms of hip pain and/or self-reported physical function. Results Thirty-two RCTs were identified, but only five met the inclusion criteria. Only one of the five included RCTs restricted recruitment to people with hip OA, the other four RCTs also recruiting participants with knee OA. The five included studies provided data on 204 and 187 hip OA participants for pain and physical function, respectively. Combining the results of the five included RCTs using a fixed-effects model demonstrated a small treatment effect for pain (standardized mean difference (SMD) −0.38; 95% confidence interval (CI) −0.67 to −0.09). No significant benefit in terms of improved self-reported physical function was detected (SMD −0.02; 95% CI −0.31 to 0.28). Conclusion Currently there is only silver level evidence (one small RCT) supporting the benefit of land-based therapeutic exercise for people with symptomatic hip OA in terms of reduced pain and improved physical function. The limited number and small sample size of the included RCTs restricts the confidence that can be attributed to these results.

FUNCTIONAL PRINCIPAL COMPONENTS MODEL FOR HIGH-DIMENSIONAL BRAIN IMAGING

We establish a fundamental equivalence between singular value decomposition (SVD) and functional principal components analysis (FPCA) models. The constructive relationship allows to deploy the numerical efficiency of SVD to fully estimate the components of FPCA, even for extremely high-dimensional functional objects, such as brain images. As an example, a functional mixed effect model is fitted to high-resolution morphometric (RAVENS) images. The main directions of morphometric variation in brain volumes are identified and discussed.

The sleeper effect: Artifact or phenomenon—A brief comment on Bell et al. (2013)

OBJECTIVE: Bell, Marcus, and Goodlad (2013) recently conducted a meta-analysis of randomized controlled additive trials and found that adding an additional component to an existing treatment vis-à-vis the existing treatment produced larger effect sizes on targeted outcomes at 6-months follow-up than at termination, an effect they labeled as a sleeper effect. One of the limitations with Bell et al.'s detection of the sleeper effect was that they did not conduct a statistical test of the size of the effect at follow-up versus termination. METHOD: To statistically test if the differences of effect sizes between the additive conditions and the control conditions at follow-up differed from those at termination, we used a restricted maximum-likelihood random-effect model with known variances to conduct a multilevel longitudinal meta-analysis (k = 30). RESULTS: Although the small effects at termination detected by Bell et al. were replicated (ds = 0.17-0.23), none of the analyses of growth from termination to follow-up produced statistically significant effects (ds < 0.08; p > .20), and when asymmetry was considered using trim-and-fill procedure or the studies after 2000 were analyzed, magnitude of the sleeper effect was negligible (d = 0.00). CONCLUSION: There is no empirical evidence to support the sleeper effect.

Análisis y optimización de la resistencia de interferencia en multicascos

Esta tesis presenta un estudio de la resistencia de interferencia en multicascos, término que engloba las variaciones en la resistencia al avance debidas a la interacción entre cascos. Su característica más notable es que puede ser tanto positiva como negativa, contribuyendo favorablemente en este último caso a la reducción de la resistencia total. Su análisis permanece como un área activa dentro de la comunidad hidrodinámica, si bien se ha detectado una significativa falta de información experimental sobre el flujo entre cascos. En primer lugar se incluye una caracterización de los fenómenos de interferencia, evaluando su impacto en las diferentes componentes de la resistencia al avance. Al igual que la resistencia total, su predicción requiere el uso de técnicas experimentales o numéricas al ser inviable su solución analítica. Ambos procedimientos han sido considerados en esta tesis. El análisis experimental de la resistencia de interferencia supone el núcleo central del trabajo realizado. Se han ensayado dos geometrías diferentes, un catamarán de servicio comercial PESBO junto con un catamarán compuesto por dos Serie 60 (S60) en paralelo. Los ensayos se han llevado a cabo en dos canales de experiencias, CEHINAV y CEHIPAR, midiéndose resistencia al avance, asiento y trimados dinámicos, y cortes de olas en la zona entre cascos. Mención especial a estos últimos, dado que a pesar de ser en la zona central donde ocurren los principales efectos de interferencia, no se encontró información previa publicada en la literatura. Su medición requirió la fabricación de un sistema de soporte especifico para las probetas de medición. Por otro lado, aunque el Serie 60 es una geometría bien conocida en la comunidad hidrodinámica, a conocimiento del autor su comportamiento como multicasco no había sido aun caracterizado experimentalmente. Los bastidores de unión se fabricaron de forma que permitieran variar la separación entre cascos. Además, los multicascos son en general embarcaciones de alta velocidad mostrando asientos y trimados dinámicos significativos. Para cuantificar su efecto en la resistencia total y de interferencia se construyo un sistema de fijación del modelo al carro que los restringiera, posibilitando comparar los resultados en esta condición con los del modelo libre. Como resultado, se han obtenido resultados experimentales de las dos geometrías estudiadas con múltiples separaciones, incluyendo un solo casco, y con modelo fijo y libre. Una de las principales utilidades de los resultados experimentales es servir como referencia para validar modelos de predicción. Como primera aplicación, los datos experimentales obtenidos con el catamarán S60 se han contrastado con las predicciones numéricas de Yeung et al. (2004). El análisis numérico de la resistencia de interferencia se completa con la realización de simulaciones numéricas utilizando dos códigos substancialmente diferentes: Tdynlin y CD--‐Adapco Star--‐CCM+. Los cortes de olas obtenidos en las simulaciones se comparan con los valores experimentales, mostrándose además los campos de presiones y velocidades calculados sobre el casco. La principal aportación de esta tesis es una extensa caracterización experimental de los fenómenos de interferencia, con la intención de servir de referencia para futuros estudios con multicascos. El análisis de los resultados permite comprender mejor el impacto que la interacción entre cascos, así como las variaciones dinámicas de las condiciones de navegación, tienen en las diferentes componentes de la resistencia. Por otro lado, permite apreciar la dependencia de la resistencia de interferencia con la velocidad y separación entre cascos, de cara a su utilización como parámetro de diseño. ABSTRACT This thesis presents a study of the interference resistance in multihulls, which comprises all the variations in the ship resistance due to the interaction between hulls. Its most remarkable characteristic is that it can be positive or negative, contributing in the second case to the reduction of the total ship resistance. Its study remains an active area in the hydrodynamic community, although there is a significant lack of published experimental data regarding the flow between hulls. First of all, the interference phenomena are characterized, evaluating the impact in the different components of the ship resistance. Similar to the total resistance, their prediction requires experimental or numerical techniques, as no analytic solutions are known. Both procedures have been considered in this thesis. The experimental analysis of the interference resistance is the core of the work done. Two different geometries have been tested, a commercial catamaran PESBO and a catamaran composed by two parallel Series 60 (S60). The tests have been carried out in two towing tanks, CEHINAV and CEHIPAR, measuring ship resistance, dynamic sinkage and trim, and wave cuts in--‐between the hulls. Special mention to the wave cuts, as no previous published information was found regarding this zone, even if it is where the main interference effects happen. Their measurement required building a support tripod for the probes, specifically designed for this experimental campaign. In addition, although the Series 60 is a well known hull for experimental and computational analyses, to the author’s knowledge its behavior as a multihull had not yet been experimentally described. The connection frames between the hulls were built so they allowed adjusting the hull spacing. Furthermore, multihulls are usually high--‐speed vessels, acquiring significant dynamic sinkage and trim. To quantify the effect of these dynamic variations of the interference resistance, a clamping system was developed to fixed the model and compare the results with the free model condition. Thus, experimental results have been obtained for various hull separations with the two geometries analyzed, including a single hull, and with free and fixed model. One of the main applications of experimental results is to serve as a reference to validate prediction models. As a first step, the obtained experimental data with the catamaran S60 have been compared with the numerical predictions of Yeung et al. (2004). The numerical analysis of the interference resistance is completed with the inclusion of numerical simulations using two codes substantially different: Tdynlin and CD--‐Adapco Star--‐CCM+. The wave cuts obtained from the simulations are compared with the experimental ones, showing also the pressure and velocity fields over the hulls. The main contribution of this thesis is an extensive experimental characterization of the interference phenomena, aiming to serve as reference for future studies about multihulls. The analysis of the results provides insights into the impact that the interaction between hulls, as well as the dynamic variations of the sailing conditions, have in the different components of the ship resistance. Moreover, it allows us to observe the dependence of the interference resistance on the velocity and hull spacing, useful towards its use as a design parameter.