Análise Bayesiana de dados composicionais na presença de covariáveis

Pós-graduação em Matematica Aplicada e Computacional - FCT

Genetic Parameters for Productive and Reproductive Traits for Milk Buffalo in Brazil

Knowing the genetic parameters of productive and reproductive traits in milking buffaloes is essential for planning and implementing of a program genetic selection. In Brazil, this information is still scarce. The objective of this study was to verify the existence of genetic variability in milk yield of buffaloes and their constituents, and reproductive traits for the possibility of application of the selection. A total of 9,318 lactations records from 3,061 cows were used to estimate heritabilities for milk yield (MY), fat percentage (%F), protein percentage (%P), length of lactation (LL), age of first calving (AFC) and calving interval (CI) and the genetic correlations among traits MY, %F and %P. The (co) variance components were estimated using multiple-trait analysis by Bayesian inference method, applying an animal model, through Gibbs sampling. The model included the fixed effects of contemporary groups (herd-year and calving season), number of milking (2 levels), and age of cow at calving as (co) variable (quadratic and linear effect). The additive genetic, permanent environmental, and residual effects were included as random effects in the model. Estimated heritability values for MY, % F, % P, LL, AFC and CI were 0.24, 0.34, 0.40, 0.09, 0.16 and 0.05, respectively. The genetic correlation estimates among MY and % F, MY and % P and % F and % P were -0.29, -0.18 and 0.25, respectively. The production of milk and its constituents showed enough genetic variation to respond to a selection program. Negative estimates of genetic correlations between milk production and its components suggest that selection entails a reduction in the other.

Multiple-trait genomic evaluation for milk yield and milk quality traits using genomic and phenotypic data in buffalo in Brazil

The use of markers distributed all long the genome may increase the accuracy of the predicted additive genetic value of young animals that are candidates to be selected as reproducers. In commercial herds, due to the cost of genotyping, only some animals are genotyped and procedures, divided in two or three steps, are done in order to include these genomic data in genetic evaluation. However, genomic evaluation may be calculated using one unified step that combines phenotypic data, pedigree and genomics. The aim of the study was to compare a multiple-trait model using only pedigree information with another using pedigree and genomic data. In this study, 9,318 lactations from 3061 buffaloes were used, 384 buffaloes were genotyped using a Illumina bovine chip (Illumina Infinium (R) bovineHD BeadChip). Seven traits were analyzed milk yield (MY), fat yield (FY), protein yield (PY), lactose yield (LY), fat percentage (F%), protein percentage (P%) and somatic cell score (SCSt). Two analyses were done: one using phenotypic and pedigree information (matrix A) and in the other using a matrix based in pedigree and genomic information (one step, matrix H). The (co) variance components were estimated using multiple-trait analysis by Bayesian inference method, applying an animal model, through Gibbs sampling. The model included the fixed effects of contemporary groups (herd-year-calving season), number of milking (2 levels), and age of buffalo at calving as (co) variable (quadratic and linear effect). The additive genetic, permanent environmental, and residual effects were included as random effects in the model. The heritability estimates using matrix A were 0.25, 0.22, 0.26, 0.17, 0.37, 0.42 and 0.26 and using matrix H were 0.25, 0.24, 0.26, 0.18, 0.38, 0.46 and 0.26 for MY, FY, PY, LY, % F, % P and SCCt, respectively. The estimates of the additive genetic effect for the traits were similar in both analyses, but the accuracy were bigger using matrix H (superior to 15% for traits studied). The heritability estimates were moderated indicating genetic gain under selection. The use of genomic information in the analyses increases the accuracy. It permits a better estimation of the additive genetic value of the animals.

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.

Aplicações clássicas da técnica de espalhamento de raios-x a baixo ângulo em materiais nanoestruturados

The small angle X-ray scattering (SAXS) technique has been used with very much versatility and success in the structural characterization of nanostructured materials. The present work deals with a study of the principles of the SAXS technique and of some classical models employed in the structural characterization of nanostructured materials. Particularly, the study of the models and of the associated methodologies is applied to a set of samples of silica gels, of varied typical structures, prepared in the Laboratório de Novos Materiais of the Departamento de Física of the IGCE. The work discusses in an introductory chapter the principles of the SAXS technique and the foundation of classical models often used in the structural characterization of materials. The classical models and the associated methodologies were applied to a variety of silica gel structures. The studies include: i) the scattering from a system of particles - Guinier's law; ii) the asymptotic scattering from a two-phase system - Porod's law; iii) systematic deviation from Porod's law - Surface Fractal; iv) heterogeneities in solids with random size distribution - DAB Model; and v) the scattering from mass fractal structures. The analyses were carried out from experimental SAXS data obtained in several opportunities at the Laboratório Nacional de Luz Síncrotron (LNLS)

Estimation methods of non-additive effects for characteristics of weight and scrotal circumference in crossbred beef cattle

The objective of this study was to investigate, in a population of crossbred cattle, the obtainment of the non-additive genetic effects for the characteristics weight at 205 and 390 days and scrotal circumference, and to evaluate the consideration of these effects in the prediction of breeding values of sires using different estimation methodologies. In method 1, the data were pre-adjusted for the non-additive effects obtained by least squares means method in a model that considered the direct additive, maternal and non-additive fixed genetic effects, the direct and total maternal heterozygosities, and epistasis. In method 2, the non-additive effects were considered covariates in genetic model. Genetic values for adjusted and non-adjusted data were predicted considering additive direct and maternal effects, and for weight at 205 days, also the permanent environmental effect, as random effects in the model. The breeding values of the categories of sires considered for the weight characteristic at 205 days were organized in files, in order to verify alterations in the magnitude of the predictions and ranking of animals in the two methods of correction data for the non-additives effects. The non-additive effects were not similar in magnitude and direction in the two estimation methods used, nor for the characteristics evaluated. Pearson and Spearman correlations between breeding values were higher than 0.94, and the use of different methods does not imply changes in the selection of animals.

Diet and the risk of head and neck cancer: a pooled analysis in the INHANCE consortium

We investigated the association between diet and head and neck cancer (HNC) risk using data from the International Head and Neck Cancer Epidemiology (INHANCE) consortium. The INHANCE pooled data included 22 case-control studies with 14,520 cases and 22,737 controls. Center-specific quartiles among the controls were used for food groups, and frequencies per week were used for single food items. A dietary pattern score combining high fruit and vegetable intake and low red meat intake was created. Odds ratios (OR) and 95% confidence intervals (CI) for the dietary items on the risk of HNC were estimated with a two-stage random-effects logistic regression model. An inverse association was observed for higher-frequency intake of fruit (4th vs. 1st quartile OR = 0.52, 95% CI = 0.43-0.62, p (trend) < 0.01) and vegetables (OR = 0.66, 95% CI = 0.49-0.90, p (trend) = 0.01). Intake of red meat (OR = 1.40, 95% CI = 1.13-1.74, p (trend) = 0.13) and processed meat (OR = 1.37, 95% CI = 1.14-1.65, p (trend) < 0.01) was positively associated with HNC risk. Higher dietary pattern scores, reflecting high fruit/vegetable and low red meat intake, were associated with reduced HNC risk (per score increment OR = 0.90, 95% CI = 0.84-0.97).

Análise de concorrência no mercado mundial de café verde

A literatura argumenta que o Brasil, embora ainda seja o maior exportador mundial de café verde, tem perdido poder neste mercado, pois a concorrência (rivalidade e probabilidade de entrada) imposta por países como a Colômbia e o Vietnã é forte o suficiente para tornar este mercado bastante competitivo. Assim, este artigo avalia o padrão recente de concorrência do mercado mundial de café verde utilizando uma metodologia econométrica mais usualmente empregada em análise antitruste. Para avaliar o comportamento dos consumidores, foram estimadas as elasticidades-preço da demanda mundial de café verde, por tipo de café, usando o modelo de demanda Logit Multinomial Antitruste. Para avaliar o comportamento de equilíbrio de mercado foram realizados testes de instabilidade de share de quantidade por meio de análise de cointegração em painel. Os resultados apontam para aumento da concorrência à variedade de café brasileiro por parte da demanda e manutenção de sharede quantidades como configuração de equilíbrio de mercado.

Fattori eziologici della Sindrome del Tunnel Carpale: una revisione sistematica con meta-analisi degli studi analitici

OBIETTIVO: sintetizzare le evidenze disponibili sulla relazione tra i fattori di rischio (personali e lavorativi) e l’insorgenza della Sindrome del Tunnel Carpale (STC). METODI: è stata condotta una revisione sistematica della letteratura su database elettronici considerando gli studi caso-controllo e di coorte. Abbiamo valutato la qualità del reporting degli studi con la checklist STROBE. Le stime studio-specifiche sono state espresse come OR (IC95%) e combinate con una meta-analisi condotta con un modello a effetti casuali. La presenza di eventuali bias di pubblicazione è stata valutata osservando l’asimmetria del funnel plot e con il test di Egger. RISULTATI: Sono stati selezionati 29 studi di cui 19 inseriti nella meta-analisi: 13 studi caso-controllo e 6 di coorte. La meta-analisi ha mostrato un aumento significativo di casi di STC tra i soggetti obesi sia negli studi caso-controllo [OR 2,4 (1,9-3,1); I(2)=70,7%] che in quelli di coorte [OR 2,0 (1,6-2,7); I(2)=0%]. L'eterogeneità totale era significativa (I(2)=59,6%). Risultati simili si sono ottenuti per i diabetici e soggetti affetti da malattie della tiroide. L’esposizione al fumo non era associata alla STC sia negli studi caso-controllo [OR 0,7 (0,4-1,1); I(2)=83,2%] che di coorte [OR 0,8 (0,6-1,2); I(2)=45,8%]. A causa delle molteplici modalità di valutazione non è stato possibile calcolare una stima combinata delle esposizioni professionali con tecniche meta-analitiche. Dalla revisione, è risultato che STC è associata con: esposizione a vibrazioni, movimenti ripetitivi e posture incongrue di mano-polso. CONCLUSIONI: I risultati della revisione sistematica confermano le evidenze dell'esistenza di un'associazione tra fattori di rischio personali e STC. Nonostante la diversa qualità dei dati sull'esposizione e le differenze degli effetti dei disegni di studio, i nostri risultati indicano elementi di prova sufficienti di un legame tra fattori di rischio professionali e STC. La misurazione dell'esposizione soprattutto per i fattori di rischio professionali, è un obiettivo necessario per studi futuri.

The local safety net, health insurance, preventable hospitalizations and costs: Harris County (Houston), Texas

The aim of this study was to examine the association between determinants of access to healthcare and preventable hospitalizations, based on Davidson et al.'s framework for evaluating the effects of individual and community determinants on access to healthcare. The study population consisted of the low income, non-elderly, hospitalized adults residing in Harris County, Texas in 2004. The objectives of this study were to examine the proportion of the variance in preventable hospitalizations at the ZIP-code level, to analyze the association between the proximity to the nearest safety net clinic and preventable hospitalizations, to examine how the safety net capacity relates to preventable hospitalizations, to compare the relative strength of the associations of health insurance and the proximity to the nearest safety net clinic with preventable hospitalizations, and to estimate and compare the costs of preventable hospitalizations in Harris County with the average cost in the literature. The data were collected from Texas Health Care Information Collection (2004), Census 2000, and Project Safety Net (2004). A total of 61,841 eligible individuals were included in the final data analysis. A random-intercept multi-level model was constructed with two different levels of data: the individual level and the ZIP-code level. The results of this study suggest that ZIP-code characteristics explain about two percent of the variance in preventable hospitalizations and safety net capacity was marginally significantly associated with preventable hospitalizations (p= 0.062). Proximity to the nearest safety net clinic was not related to preventable hospitalizations; however, health insurance was significantly associated with a decreased risk of preventable hospitalization. The average direct cost was $6,466 per preventable hospitalization, which is significantly different from reports in the literature. ^

Enlarged tracheoesophageal puncture: A systematic review and retrospective analysis

Background. An enlarged tracheoesophageal puncture (TEP) results in aspiration around the voice prosthesis (VP) and may lead to pneumonia. The aims of this research were: (1) to conduct a systematic review and meta-analysis on enlarged TEP; (2) to analyze preoperative, perioperative, and postoperative risk factors for enlarged TEP; and (3) to evaluate control of leakage around the VP using conservative treatments and adverse events in patients with enlarged TEP.^ Methods. A systematic review was conducted (1978-2008). A summary risk estimate was calculated using a random-effects meta-analysis model. A retrospective cohort study was completed. Patients who underwent total laryngectomy and TEP at The University of Texas M. D. Anderson Cancer Center (MDACC) were included. Multiple logistic regression methods were used to assess risk factors for enlargement. Descriptive and bivariate statistics were calculated to evaluate outcomes and adverse events. Results: Twenty-seven manuscripts were included in the systematic review. The summary risk estimate of enlarged TEP/leakage around the VP was 7.2% (95% CI: 4.8%-9.6%). Temporary VP removal and TEP-site injections were the most commonly reported treatments. Neither prosthetic diameter (p=0.076) nor timing of TEP (p=0.297) significantly increased risk of enlargement per stratified analyses of published outcomes. The cumulative incidence of enlarged TEP was 18.6% (36/194, 95% CI: 13.0%-24.1%) in the MDACC cohort. Enlarged TEP occurred exclusively in irradiated patients. Adjusting for length of follow-up and timing of TEP, advanced nodal disease (ORadjusted: 4.3, 95% CI: 1.0-19.1), stricture (ORadjusted : 3.2, 95% CI: 1.2-8.6), and locoregional recurrence/distant metastasis after laryngectomy (ORadjusted: 6.2, 95% CI: 2.3-16.4) increased risk of enlarged TEP. At last follow-up, conservative methods controlled leakage around the VP in 81% (29/36) of patients. Unresolved leakage was associated with recurrent cancer (p=0.081) and TEP-site irregularity (p=0.003). Relative to those without enlargement, enlarged TEP patients had significantly higher risk of pneumonia (RR: 3.4, 95% CI: 1.9-6.2).^ Conclusions. These data establish that enlarged TEP poses serious health risks, and provide insight into medical and oncologic factors that may contribute to development of this complication. In addition, this research supports the use of conservative treatments to address leakage after enlarged TEP in lieu of complete TEP closure.^

Control rod drop surveillance using two friction coefficients

In the case of large burnup, a control rod (CR) guide tube in the pressurized water reactor of a commercial nuclear power plant might bend. As a consequence, a CR drop experiment may indicate an event of a CR partially inserted and whether the CR should be deemed inoperable. Early prevention of such an event can be achieved by measuring two friction coefficients: the hydraulic coefficient and the sliding coefficient. The hydraulic coefficient hardly changes, so that the curvature of the guide tube can only be detected thanks to a variation of the sliding coefficient. A simple model for the CR drop is established and validated with CR drop experiments. If tmx denotes the instant of CR maximum velocity, a linear relationship between (tmx)_2 and the sliding coefficient is found.

Evolution of RNA editing in trypanosome mitochondria

Two different RNA editing systems have been described in the kinetoplast-mitochondrion of trypanosomatid protists. The first involves the precise insertion and deletion of U residues mostly within the coding regions of maxicircle-encoded mRNAs to produce open reading frames. This editing is mediated by short overlapping complementary guide RNAs encoded in both the maxicircle and the minicircle molecules and involves a series of enzymatic cleavage-ligation steps. The second editing system is a C34 to U34 modification in the anticodon of the imported tRNATrp, thereby permitting the decoding of the UGA stop codon as tryptophan. U-insertion editing probably originated in an ancestor of the kinetoplastid lineage and appears to have evolved in some cases by the replacement of the original pan-edited cryptogene with a partially edited cDNA. The driving force for the evolutionary fixation of these retroposition events was postulated to be the stochastic loss of entire minicircle sequence classes and their encoded guide RNAs upon segregation of the single kinetoplast DNA network into daughter cells at cell division. A large plasticity in the relative abundance of minicircle sequence classes has been observed during cell culture in the laboratory. Computer simulations provide theoretical evidence for this plasticity if a random distribution and segregation model of minicircles is assumed. The possible evolutionary relationship of the C to U and U-insertion editing systems is discussed.

Mapeamento associativo para múltiplos ambientes e múltiplos locos, visando tolerância à seca em milho

A seca é um dos estresses abióticos mais importantes na cultura do milho, o qual ocasiona reduções significativas na produção de grãos. A arquitetura genética da tolerância à seca é complexa, fazendo-se necessária a melhor compreensão desse caráter. Estudos envolvendo mapeamento associativo são úteis por explorarem a variação genética de caracteres quantitativos e, adicionalmente, levam em conta informações acerca de genótipos, ambientes e interações genótipo por ambiente (G × E). Ao considerar efeitos de G × E em modelos de mapeamento associativo há possibilidade de identificar regiões no genoma associadas à condições e ambientes específicos. Este trabalho teve como objetivo detectar associações relacionadas à tolerância à seca em milho por meio de um modelo de mapeamento associativo para múltiplos ambientes e múltiplos locos, o qual permitiu distinguir associações com efeitos ambiente-específico daquelas com efeitos principais e de interação associação por ambiente (QEI). O painel associativo foi composto por 190 linhagens, classificadas de acordo com os grupos heteróticos quanto ao tipo de grão. Marcadores SNPs (∼500k) foram utilizados para a genotipagem do painel associativo. Duas linhagens (L228-3 e L3) foram usadas como testadores comuns e os híbridos obtidos foram avaliados em duas localidades (Janaúba-MG e Teresina-PI), dois anos agrícolas (2010 e 2011), sob duas condições de tratamento (irrigado e não irrigado). Ao total, consideraram-se seis caracteres: peso de grãos, intervalo de florescimento, florescimento feminino e masculino, altura de planta e de espiga. Consideraram-se dois grupos de mapeamento, agrupados de acordo com os testadores utilizados. SNPs foram úteis para testar associações ao longo do genoma do milho e investigar o relacionamento genético entre indivíduos. O modelo de mapeamento associativo, com inclusão de informações sobre interação G × E, detectou o total de 179 associações, e o maior número de associações foram relacionadas aos caracteres de florescimento. A maioria das associações (168) apresentaram QEI significativo, sendo que o tamanho e a magnitude desses efeitos distinguiram-se de acordo com o ambiente em avaliação. Apenas o caráter florescimento feminino não apresentou associações com efeitos estáveis ao longo dos ambientes em estudo. A detecção de algumas associações em posições próximas do genoma evidenciam possíveis efeitos de pleiotropia. Algumas associações foram co-localizadas em regiões do genoma do milho relacionadas à tolerância à seca, sendo que algumas dessas associações estavam envolvidas a fatores pertencentes à vias metabólicas de interesse. O presente estudo forneceu informações úteis para a compreensão da base genética da tolerância à seca em milho sob os ambientes específicos em avaliação.

Stochastic choice analysis of tourism destinations

The analysis of tourist destination choice, defined by intra-country administrative units and by product types “coastal/inland and village/city”, permits the characterisation of tourist flow behaviour, which is fundamental for public planning and business management. In this study, we analyse the determinant factors of tourist destination choice, proposing various research hypotheses relative to the impact of destination attributes and the personal characteristics of tourists. The methodology applied estimates Nested and Random Coefficients Multinomial Logit Models, which allow control over possible correlations among different destinations. The empirical application is realised in Spain on a sample of 3,781 individuals and allows us to conclude that prices, distance to the destination and personal motivations are determinants in destination choice.