Bayesian longitudinal data analysis with mixed models and thick-tailed distributions using MCMC

Linear mixed effects models are frequently used to analyse longitudinal data, due to their flexibility in modelling the covariance structure between and within observations. Further, it is easy to deal with unbalanced data, either with respect to the number of observations per subject or per time period, and with varying time intervals between observations. In most applications of mixed models to biological sciences, a normal distribution is assumed both for the random effects and for the residuals. This, however, makes inferences vulnerable to the presence of outliers. Here, linear mixed models employing thick-tailed distributions for robust inferences in longitudinal data analysis are described. Specific distributions discussed include the Student-t, the slash and the contaminated normal. A Bayesian framework is adopted, and the Gibbs sampler and the Metropolis-Hastings algorithms are used to carry out the posterior analyses. An example with data on orthodontic distance growth in children is discussed to illustrate the methodology. Analyses based on either the Student-t distribution or on the usual Gaussian assumption are contrasted. The thick-tailed distributions provide an appealing robust alternative to the Gaussian process for modelling distributions of the random effects and of residuals in linear mixed models, and the MCMC implementation allows the computations to be performed in a flexible manner.

Radiative properties of the skin and haircoat of cattle and other animals

Radiative properties (reflectance rho, transmittance tau, and absorptance alpha) were determined for wavelengths from 300 to 850 nm in the haircoat and the skin of water buffalo, deer (Pantanal deer, Blastocerus dichotomus), and cattle of the Holstein, Simmental, Canchim, Brangus, and Nelore breeds. The results showed that white hairs have higher rho (0.60 to 0.67) than the other coat colors, but the gray coats (mixed white and dark hair) of the Nelore cattle presented higher rho than that of the white coats of the European breeds at wavelengths lower than 600 nm. The light gray colored skin of the Canchim cattle had higher rho (0. 66) than the non-pigmented skin of Holstein (0.53). Red skins presented rho values higher than those of dark gray and black skins. Buffalo skin (dark gray) presented an average rho of 0.23+/-0.02 and alpha of 0.77+/-0.02. The red haircoat of the deer presented rho lower (0.37) than that of cattle of the same color (0.58). However, there was little difference between deer and cattle with respect to reflectance and absorptance of the skin. As for the spectral transmittance of the skin, it was very low and about the same for both species, until 600 nm. In the range 600 to 850 nm, the tau values for cattle rose to 0. 17, while those for deer increased only to 0.12.

Species diversity and seasonality of free-living ticks (Acari : Ixodidae) in the natural habitat of wild Marsh deer (Blastocerus dichotomus) in Southeastern Brazil

This study evaluated the presence and seasonal activity of free-living ticks in remaining marsh areas by the Parana river, in Brazil. Eight field trips (once per season) for collection of ticks were performed during 2 years. Using CO2 traps, dragging, and visual inspection of vegetation, five free-living tick species were collected, in the following order of abundance: Amblyomma cajennense, Amblyom\ma dubitatum, Amblyomma triste, Amblyomma coelebs, and Amblyomma nodosum. The seasonal pattern of A. cajennense was characterized by the highest peaks for adult ticks in the summer/spring months, for nymphs in the winter and for larvae in the autumn and winter. A. dubitatum and A. triste presented similar seasonal patterns characterized by peaks of adult ticks in the autumn. Nymphs of A. dubitatum peaked in the winter of the first year and in the winter/spring of the second year. A. triste was the only species to be collected in significantly higher numbers in the marsh than in surrounding drier areas such as forest patches. Among domestic animals living close the marsh areas, horses were infested by Anocentor nitens, A. cajennense, and Boophilus microplus, bovines were infested solely by B. microplus, and dogs were infested by Rhipicephalus sanguineus. Adults of A. triste showed to be well adapted to the marsh environment. This result, at least partially, explains local previous observations on the association of A. triste with marsh deer, as this vertebrate host inhabits mainly the marsh area. (c) 2006 Published by Elsevier B.V.

CYTOGENETIC ANALYSIS OF THE PAMPAS DEER, OZOTOCEROS-BEZOARTICUS (MAMMALIA, CERVIDAE)

The chromosome constitution of five males and three females of the Pampas deer (Ozotoceros bezoarticus) coming mainly from the region of Corumba-MS, was studied. The diploid number of the species was reconfirmed as 68 chromosomes with Fundamental Number (FN) = 74. The X chromosome was the largest and the Y the smallest in the genome. Constitutive heterochromatin demonstrated by C banding was present in the centromeric region of all chromosomes, except in pair number two, which had none, and in chromosome X which had a stained region in the telomere on the long arm, Chromosomes pairs 3 and 4 bore Ag-NORs. The banding patterns differed from those of previous reports for this species. This may be due to subspecific differences.

Conservation genetics of the endangered Pampas deer (Ozotoceros bezoarticus)

The Pampas deer (Ozotoceros bezoarticus L. 1758) is the most endangered neotropical cervid, and in the past occupied a wide range of open habitats including grassland, pampas, savanna, and cerrado (Brazil) from 5 degrees to 41 degrees S. To better understand the effect of habitat fragmentation on gene flow and genetic variation, and to uncover genetic units for conservation, we examined DNA sequences from the mitochondrial control region of 54 individuals from six localities distributed throughout the present geographical range of the Pampas deer. Our results suggest that the control region of the Pampas deer is one of the most polymorphic of any mammal. This remarkably high variability probably reflects large historic population sizes of millions of individuals in contrast to numbers of fewer than 80 000 today. Gene flow between populations is generally close to one migrant per generation and, with the exception of two populations from Argentina, all populations are significantly differentiated. The degree of gene flow was correlated with geographical distance between populations, a result consistent with limited dispersal being the primary determinant of genetic differentiation between populations. The molecular genetic results provide a mandate for habitat restoration and reintroduction of Pampas deer so that levels of genetic variation can be preserved and historic patterns of abundance can be reconstructed. However, the source of individuals for reintroduction generally should be from populations geographically closest to those now in danger of extinction.

Robust Bayesian analysis of heavy-tailed stochastic volatility models using scale mixtures of normal distributions

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

Multiwavelength visible and white light generation by upconversion emission in Ho/Tm/Yb triply doped fluorogermanate glass-ceramic

Energy transfer excited multiwavelength visible upconversion emission and white light generation is described in a single sample of PbGeO(3)-PbF(2)-CdF(2) glass-ceramic triply doped With Ho/Tm/Yb under single infrared laser excitation. Blue (475 nm), green (540 mn), and red (650 nm), upconversion luminescence signals are generated, and the emissions are assigned, respectively, to thulium ((1)G(4)-(3)H(6)), and holmium ((5)S(2);(5)F(4)) -> (5)I(8), (5)F(5) -> (5)I(8)) ions transitions, both excited via successive energy transfers from ytterbium ions. It is experimentally shown that with a proper combination of the rare earth ions contents, white light may be produced, with the simultaneous generation of fluorescence with controllable intensities at the wavelengths of the three primary colours in a single sample and using a single near-infrared excitation source.

Population genetic structure and dispersal in white-lipped peccaries (Tayassu pecari) from the Brazilian Pantanal

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

Estimates of genetic parameters, and cluster and principal components analyses of breeding values related to egg production traits in a White Leghorn population

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

Prevalence and molecular characterization of Anaplasmataceae agents in free-ranging Brazilian marsh deer (Blastocerus dichotomus)

Anaplasmataceae organisms comprise a group of obligate intracellular gram-negative, tick-borne bacteria that can infect both animals and humans. In the present work we investigate the presence of Ehrlichia, Anaplasrna, and Neorickettsia species in blood samples from Brazilian marsh deer (Blastocerus dichotomus), using both molecular and serologic techniques. Blood was collected from 143 deer captured along floodplains of the Parana River, near the Porto Primavera hydroelectric power plant. Before and after flooding, marsh deer were captured for a wide range research program under the financial support of São Paulo State Energy Company (CESP), between 1998 and 2001. Samples were divided into four groups according to time and location of capture and named MS01 (n = 99), MS02 (n = 18) (Mato Grosso do Sul, before and after flooding, respectively), PX (n = 9; Peixe River, after flooding), and AGUA (n = 17; Aguapei River, after flooding). The seroprevalences for Ehrlichia chaffeensis and Anaplasma phagocytophilum were 76.76% and 20.2% in MS01, 88.88% and 5.55% in MS02, 88.88% and 22.22% in PX, and 94.12% and 5.88% in AGUA, respectively. Sixty-one animals (42.65% of the total population) were PCR-positive for E. chaffeensis PCR (100.0% identity based on 16S rRNA, dsb, and groESL genes). Seventy deer (48.95% of the total population) were PCR-positive for Anaplasma spp. (99.0% of identity with A. platys, and in the same clade as A. phagocytophilum, A. bovis, and A. platys based on 16S rRNA phylogenetic analysis). Our results demonstrate that Brazilian marsh deer are exposed to E. chaffeensis and Anaplasma spp. and may act as reservoirs for these rickettsial agents, playing a role in disease transmission to humans and other animals. (c) 2012 Elsevier Ltd. All rights reserved.

The use of auxiliary courts by the lek-forming White-bearded Manakin Manacus manacus (Aves, Pipridae)

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

Comparison of two methods of synchronization of estrus in brown brocket deer (Mazama gouazoubira)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

STOMACH CONTENTS ANALYSIS of WHITE MARLIN (TETRAPTURUS ALBIDUS) CAUGHT OFF SOUTHERN and SOUTHEASTERN BRAZIL: A BAYESIAN ANALYSIS.

This study proposes to ascertain the importance of each alimentary category in the Tetrapturus albidus diet composition, as well as to propose the use of the Bayesian approach for analysis of these data. The stomachs were collected during fishing cruises carried out by the Santos-SP longliner from July 2007 to June 2008. For Bayesian model formulation, each alimentary item was clustered in four food categories as: teleost, cephalopod, crustaceans, and others. To estimate the proportion of each food category, the multinomial model with Dirichlet conjugate prior distribution was used. After the stomach contents analysis, 133 food items were identified, which belonged to 9 taxa. The most important food category is constituted by cephalopod molluscs, followed by teleost fishes. The food category comprised of crustaceans presents a low contribution and in this case it could be considered to be an accidental food item. The Bayesian approach means a distinct view in relation to traditional methods, as it permits one to incorporate information obtained from the literature. It should be useful to analyse great top predators, which are usually caught in small numbers.