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.

A model-based approach for assessing in vivo combination therapy interactions

We present an approach for evaluating the efficacy of combination antitumor agent schedules that accounts for order and timing of drug administration. Our model-based approach compares in vivo tumor volume data over a time course and offers a quantitative definition for additivity of drug effects, relative to which synergism and antagonism are interpreted. We begin by fitting data from individual mice receiving at most one drug to a differential equation tumor growth/drug effect model and combine individual parameter estimates to obtain population statistics. Using two null hypotheses: (i) combination therapy is consistent with additivity or (ii) combination therapy is equivalent to treating with the more effective single agent alone, we compute predicted tumor growth trajectories and their distribution for combination treated animals. We illustrate this approach by comparing entire observed and expected tumor volume trajectories for a data set in which HER-2/neu-overexpressing MCF-7 human breast cancer xenografts are treated with a humanized, anti-HER-2 monoclonal antibody (rhuMAb HER-2), doxorubicin, or one of five proposed combination therapy schedules.

The correlation of the indentation size effect measured with indenters of various shapes

Experimental results are presented which show that the indentation size effect for pyramidal and spherical indenters can be correlated. For a pyramidal indenter, the hardness measured in crystalline materials usually increases with decreasing depth of penetration, which is known as the indentation size effect. Spherical indentation also shows an indentation size effect. However, for a spherical indenter, hardness is not affected by depth, but increases with decreasing sphere radius. The correlation for pyramidal and spherical indenter shapes is based on geometrically necessary dislocations and work-hardening. The Nix and Gao indentation size effect model (J. Mech. Phys. Solids 46 (1998) 411) for conical indenters is extended to indenters of various shapes and compared to the experimental results. © 2002 Elsevier Science Ltd. All rights reserved.

Parameterized Link Functions in Generalized Linear Random Effect Models: a Case Study on Breast Cancer Treatment

In non-linear random effects some attention has been very recently devoted to the analysis ofsuitable transformation of the response variables separately (Taylor 1996) or not (Oberg and Davidian 2000) from the transformations of the covariates and, as far as we know, no investigation has been carried out on the choice of link function in such models. In our study we consider the use of a random effect model when a parameterized family of links (Aranda-Ordaz 1981, Prentice 1996, Pregibon 1980, Stukel 1988 and Czado 1997) is introduced. We point out the advantages and the drawbacks associated with the choice of this data-driven kind of modeling. Difficulties in the interpretation of regression parameters, and therefore in understanding the influence of covariates, as well as problems related to loss of efficiency of estimates and overfitting, are discussed. A case study on radiotherapy usage in breast cancer treatment is discussed.

Three essays on a longitudinal analysis of business start-ups using the Kauffman Firm Survey

This dissertation focused on the longitudinal analysis of business start-ups using three waves of data from the Kauffman Firm Survey. ^ The first essay used the data from years 2004-2008, and examined the simultaneous relationship between a firm's capital structure, human resource policies, and its impact on the level of innovation. The firm leverage was calculated as, debt divided by total financial resources. Index of employee well-being was determined by a set of nine dichotomous questions asked in the survey. A negative binomial fixed effects model was used to analyze the effect of employee well-being and leverage on the count data of patents and copyrights, which were used as a proxy for innovation. The paper demonstrated that employee well-being positively affects the firm's innovation, while a higher leverage ratio had a negative impact on the innovation. No significant relation was found between leverage and employee well-being.^ The second essay used the data from years 2004-2009, and inquired whether a higher entrepreneurial speed of learning is desirable, and whether there is a linkage between the speed of learning and growth rate of the firm. The change in the speed of learning was measured using a pooled OLS estimator in repeated cross-sections. There was evidence of a declining speed of learning over time, and it was concluded that a higher speed of learning is not necessarily a good thing, because speed of learning is contingent on the entrepreneur's initial knowledge, and the precision of the signals he receives from the market. Also, there was no reason to expect speed of learning to be related to the growth of the firm in one direction over another.^ The third essay used the data from years 2004-2010, and determined the timing of diversification activities by the business start-ups. It captured when a start-up diversified for the first time, and explored the association between an early diversification strategy adopted by a firm, and its survival rate. A semi-parametric Cox proportional hazard model was used to examine the survival pattern. The results demonstrated that firms diversifying at an early stage in their lives show a higher survival rate; however, this effect fades over time.^

The Effect of Slum Redevelopment on Child Health Outcomes: Evidence from Mumbai

As the population of urban poor living in slums increases, governments are trying to relocate people into government-provided free housing. Slum redevelopment affects every part of a household’s livelihood, but most importantly the health and wellbeing of younger generations. This paper investigates the effect of slum redevelopment schemes on child stunting levels. Data was collected in forty-one buildings under the slum-redevelopment program in Mumbai. The study demonstrates through a fixed effect regression analysis that an additional year of living in the building is associated with an increase in the height-for-age Z-score by 0.124 standard deviations. Possible explanations include an improvement in the overall hygienic environment, sanitation conditions, indoor air pollution, and access to health and water facilities. However, anecdotal evidence suggests that water contamination, loss of livelihood and increased expenses could worsen health outcomes for residents. This study prompts more research on the health effects of slum redevelopment projects, which are becoming increasingly common in the rapidly urbanizing developing world.

The effect of alcohol consumption on household income in Ireland

This paper presents a study of the effects of alcohol consumption on household income in Ireland using the Slán National Health and Lifestyle Survey 2007 dataset, accounting for endogeneity and selection bias. Drinkers are categorised into one of four categories based on the recommended weekly drinking levels by the Irish Health Promotion Unit; those who never drank, non-drinkers, moderate and heavy drinkers. A multinomial logit OLS Two Step Estimate is used to explain individual's choice of drinking status and to correct for selection bias which would result in the selection into a particular category of drinking being endogenous. Endogeneity which may arise through the simultaneity of drinking status and income either due to the reverse causation between the two variables, income affecting alcohol consumption or alcohol consumption affecting income, or due to unobserved heterogeneity, is addressed. This paper finds that the household income of drinkers is higher than that of non-drinkers and of those who never drank. There is very little difference between the household income of moderate and heavy drinkers, with heavy drinkers earning slightly more. Weekly household income for those who never drank is €454.20, non-drinkers is €506.26, compared with €683.36 per week for moderate drinkers and €694.18 for heavy drinkers.