Robust linear mixed models with normal/independent distributions and Bayesian MCMC implementation

Linear mixed effects models have been widely used in analysis of data where responses are clustered around some random effects, so it is not reasonable to assume independence between observations in the same cluster. In most biological applications, it is assumed that the distributions of the random effects and of the residuals are Gaussian. This makes inferences vulnerable to the presence of outliers. Here, linear mixed effects models with normal/independent residual distributions for robust inferences are described. Specific distributions examined include univariate and multivariate versions of the Student-t, the slash and the contaminated normal. A Bayesian framework is adopted and Markov chain Monte Carlo is used to carry out the posterior analysis. The procedures are illustrated using birth weight data on rats in a texicological experiment. Results from the Gaussian and robust models are contrasted, and it is shown how the implementation can be used for outlier detection. The thick-tailed distributions provide an appealing robust alternative to the Gaussian process in linear mixed models, and they are easily implemented using data augmentation and MCMC techniques.

Strategies to model scheduling decisions to plan the soft drink production process

In this paper we present a mixed integer model that integrates lot sizing and lot scheduling decisions for the production planning of a soft drink company. The main contribution of the paper is to present a model that differ from others in the literature for the constraints related to the scheduling decisions. The proposed strategy is compared to other strategies presented in the literature.

Mating system of a population of Myracrodruon urundeuva F.F. & M.F. Allemão using the fAFLP molecular marker

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

Avaliação dos desempenhos produtivo e reprodutivo de um rebanho bubalino no Estado do Ceará

Foram avaliados os desempenhos produtivo e reprodutivo de um rebanho bubalino, localizado no município de Paracuru, litoral oeste do Estado do Ceará. Os animais foram mantidos em sistema intensivo e submetidos a duas ordenhas diárias. Foram analisadas informações de 87 fêmeas da raça Murrah, entre os anos de 1984 e 1998. As análises estatísticas foram efetuadas por meio do procedimento GLM (SAS, 1990), usando um modelo linear misto. As médias observadas para produção total de leite, duração da lactação, produção de leite no pico de lactação, idade ao primeiro parto e intervalo de partos foram: 2130,80+535,60kg, 301,41+49,30dias, 9,78+1,95kg, 1132,69+166,99dias e 430,79+100,44dias, respectivamente. Alta porcentagem de parições das ocorreu no período chuvoso (79,3%) e apenas 20,7%, no período seco. A produção total de leite e a produção no pico de lactação foram influenciadas pelos efeitos do ano e ordem de parto. A duração da lactação foi influenciada pelos efeitos do ano e mês de parto. A idade ao primeiro parto foi influenciada pelo efeito do ano de nascimento da búfala. O intervalo de partos foi influenciado pelo mês do parto anterior, além dos efeitos do mês dentro do ano de parto e mês de nascimento da búfala.

Variação genética em progênies de Myracrodruon urundeuva F.F. & M.F. Allemão em três sistemas de cultivo

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

Saúde do trabalhador na atenção básica: análise a partir de uma experiência municipal

Este texto apresenta um relato da experiência de implantação de ações de saúde do trabalhador nos serviços de atenção básica no município de Amparo, no estado de São Paulo, ocorrida durante a gestão do período 2001 a 2008, visando contribuir na premente necessidade do SUS de implantação das ações de saúde do trabalhador. A análise realizada pelas autoras, protagonistas na gestão do processo, ressalta alguns dos elementos-chave para a efetiva implantação de ações de saúde do trabalhador na rede de atenção básica. Dentre eles, a Estratégia Saúde da Família (ESF), ao lado de outros elementos - como o modelo de matriciamento com ação pedagógica contínua e participação nos colegiados de gestão, a educação permanente e o protagonismo dos trabalhadores da saúde -, mostrou-se um facilitador do processo. Como elementos estruturantes da construção efetivada, apontam-se o modelo de gestão colegiada adotado pela secretaria e a forma de implantação do Centro de Referência de Saúde do Trabalhador no município. Todo esse arranjo promoveu uma interlocução permanente entre as equipes de saúde, da atenção básica e da referência especializada que foi indispensável para a experiência ocorrida.

Use of survival analysis as a tool for the genetic improvement of age at first conception in Nellore cattle

Restricted breeding seasons in beef cattle lead to censoring of reproductive data. In this paper, age at first conception (AFC) of Nellore females exposed to the sires for the first time between 11 and 16 months of age, was studied aiming to verify the possibility of genetically advance sexual precocity using a survival model. The final data set contained 6699 records of AFC in days. Records of females that did not calve in the next year following exposure to the sire were considered censored (77.5% of total). The model used was a Weibull mixed survival model including effects of contemporary groups, period (fixed) and animal (random). The effect of the contemporary groups on AFC was important (p < 0.01). Heritabilities were 0.51 and 0.76 in logarithmic and original scales respectively. Results indicate that it is possible to genetically advance sexual precocity, using the outcome of survival analysis of AFC as selection criterion. They also suggest that improvements of the environment could advance sexual precocity too, thus an adequate pregnancy rate for farmers could quickly be achieved.

The effect of adhesive and flowable composite on postoperative sensitivity: 2-Week results

Objective: To measure 2-week postoperative sensitivity in Class II composite restorations placed with a self-etching adhesive (Clearfil SE Bond) or a total-etch adhesive (Prime&Bond NT) with or without a flowable composite as cervical increment. Method and materials: Upon approval by the University of Guarulhos Committee on Human Subjects, 100 restorations were inserted in 46 patients who required Class II restorations in their molars and premolars. Enamel and dentin walls were conditioned with a self-etching primer (for Clearfil SE Bond) or etched with 34% phosphoric acid (for Prime&Bond NT). A 1- to 2-mm-thick increment of a flowable composite (Filtek Flow) was used in the proximal box in 50% of the restorations of each adhesive. Preparations were restored with a packable composite (Surefil). The restorations were evaluated preoperatively and 2 weeks postoperatively for sensitivity to cold, air, and masticatory forces using a visual analog scale. Marginal integrity of the accessible margins was also evaluated. Statistical analysis used a mixed linear model with subject as a random effect. Results: Ninety-eight teeth from 44 subjects were observed at 2 weeks. The type of adhesive and use of flowable composite had no significant effects or interaction for any of the four outcomes of interest, ie, change from baseline to 2 weeks in sensitivity and response time for the cold or air stimulus. For the air stimulus, the overall average change from baseline was not significant for either sensitivity or response time. For the cold stimulus, the overall average change from baseline was significant for both sensitivity and response time. No case of sensitivity to masticatory forces was observed. Conclusion: No differences in postoperative sensitivity were observed between a self-etch adhesive and a total-etch adhesive at 2 weeks. The use of flowable composite did not decrease postoperative sensitivity.

Análise de ligação e associação no genoma com gagueira desenvolvimental persistente em famílias do Estado de São Paulo-Brasil

Pós-graduação em Ciências Biológicas (Genética) - IBB

Comparação de ajustes do modelo de Gompertz a dados de crescimento

Pós-graduação em Biometria - IBB

Quantitative genetic study of age at subsequent rebreeding in Nellore cattle by using survival analysis

The continuous trait age at subsequent rebreeding (ASR) was evaluated using survival analysis in Nellore breed cows that conceived for the first time at approximately 14 months of age. This methodology was chosen because the restricted breeding season produces censored data. The dataset contained 2885 records of ASR (in days). Records of females that did not produce calves in the following year after being exposed to a sire were considered censored (48.3% of the total). The statistical model used was a Weibull mixed survival model, which included fixed effects of contemporary groups (CG) and period and a random effect of individual animal. The effect of contemporary groups on ASR was significant (P < 0.01). Heritabilities obtained for ASR were 0.03 and 0.04 in logarithmic and original scales, respectively. These results indicate that the genetic selection response for subsequent reproduction of 2-year-old Nellore breed females is not expected to be effective based on survival analysis. Furthermore, these results suggest that environmental improvement is fundamental to this important trait. It should be highlighted that an increase in the average date of birth can produce an adverse effect in the future, since this cannot be compensated by genetic improvement.

Sistema de reprodução em populações naturais de Peltophorum dubium

A Multi-locus mixed mating model and correlated mating model were used to analyze the mating system of four natural populations of Peltophorum dubium (Sprengel) Taubert from Western Sao Paulo State, Brazil. Open pollinated seeds were collected from 19 to 33 seed-trees per population and evaluated by allozyme electrophoresis analysis. Significant differences between pollen and ovule gene frequencies were detected in more than 50% of loci in each population, indicating deviations from random mating, probably due to correlated mating, self-fertilizations and mating among relatives. The comparison the fixation index estimated from seed trees ((F) over cap (m), ranged from 0.009 to 0.285) with their progenies ((F) over cap (p), ranged from 0.127 to 0.364) suggested selection against inbreeding between offspring of adult stages. The estimates of multi-locus outcrossing rate (t(m)) ranged from 0.557 to 0.924, indicating that the species has a mixed-mating system. Differences between multi-locus and single-locus outcrossing rate (t(m)-t(s))was positive and significantly different from zero for all populations, with values ranging from 0.092 to 0.111, suggesting mating among relatives within the populations, probably due to the presence of intra-population spatial genetic structure. The mean coefficient of co-ancestry (Theta) within progenies ranged from 0.147 to 0.251; confirming that the progenies are compounded by mixtures of different kinds of relatedness. The results are discussed from the view of genetic improvement and conservation of the species.

On the mKdV-Liouville hierarchy and its self-similarity reduction

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

Liquid nitrogen for the treatment of actinic keratosis: A longitudinal assessment

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

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.