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.

Stochastic scheduling - A flow shop no wait application and solutions

Minimizing the makespan of a flow-shop no-wait (FSNW) schedule where the processing times are randomly distributed is an important NP-Complete Combinatorial Optimization Problem. In spite of this, it can be found only in very few papers in the literature. By considering the Start Interval Concept, this problem can be formulated, in a practical way, in function of the probability of the success in preserve FSNW constraints for all tasks execution. With this formulation, for the particular case with 3 machines, this paper presents different heuristics solutions: by integrating local optimization steps with insertion procedures and by using genetic algorithms for search the solution space. Computational results and performance evaluations are commented. Copyright (C) 1998 IFAC.

Fabrication of phytic acid sensor based on mixed phytase-lipid Langmuir-Blodgett films

This paper reports the surface activity of phytase at the air-water interface, its interaction with lipid monolayers, and the construction of a new phytic acid biosensor on the basis of the Langmuir-Blodgett (LB) technique. Phytase was inserted in the subphase solution of dipalmitoylphosphatidylglycerol (DPPG) Langmuir monolayers, and its incorporation to the air-water interface was monitored with surface pressure measurements. Phytase was able to incorporate into DPPG monolayers even at high surface pressures, ca. 30 mN/m, under controlled ionic strength, pH, and temperature. Mixed Langmuir monolayers of phytase and DPPG were characterized by surface pressure-area and surface potential-area isotherms, and the presence of the enzyme provided an expansion in the monolayers ( when compared to the pure lipid at the interface). The enzyme incorporation also led to significant changes in the equilibrium surface compressibility (in-plane elasticity), especially in liquid-expanded and liquid-condensed regions. The dynamic surface elasticity for phytase-containing interfaces was investigated using harmonic oscillation and axisymmetric drop shape analysis. The insertion of the enzyme at DPPG monolayers caused an increase in the dynamic surface elasticity at 30 mN m(-1), indicating a strong interaction between the enzyme and lipid molecules at a high-surface packing. Langmuir-Blodgett (LB) films containing 35 layers of mixed phytase-DPPG were characterized by ultraviolet-visible and fluorescence spectroscopy and crystal quartz microbalance nanogravimetry. The ability in detecting phytic acid was studied with voltammetric measurements.

Detection of catechol using mixed Langmuir-Blodgett films of a phospholipid and phthalocyanines as voltammetric sensors

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

On Duffin-Kemmer-Petiau particles with a mixed minimal-nonminimal vector coupling and the nondegenerate bound-states for the one-dimensional inversely linear background

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Resonant x-ray diffraction as a tool to calculate mixed valence ratios: Application to Prussian Blue materials

An approach is proposed here to calculate mixed valence ratios in molecular compounds. Synchrotron x-ray powder diffraction experiments were conducted to determine the Fe(+3)/Fe(+2) ratio in Prussian Blue compounds, which were elected as an example of the use of this approach. As a result, a resonant x-ray diffraction measurement provided direct evidence that the vacant [Fe(CN)(6)] group was randomly absent from similar to 31% of the structure, which was indicated by structural differences caused by variations in the anomalous dispersion term. These findings are very important for a deeper understanding of the changes occurring in properties during in situ compositional variations. (c) 2008 American Institute of Physics.

Use of Pyrosequencing and Denaturing Gradient Gel Electrophoresis to Examine the Effects of Probiotics and Essential Oil Blends on Digestive Microflora in Broilers Under Mixed Eimeria Infection

A protective digestive microflora helps prevent and reduce broiler infection and colonization by enteropathogens. In the current experiment, broilers fed diets supplemented with probiotics and essential oil (EO) blends were infected with a standard mixed Eimeria spp. to determine effects of performance enhancers on ileal and cecal microbial communities (MCs). Eight treatment groups included four controls (uninfected-unmedicated [UU], unmedicated-infected, the antibiotic BMD plus the ionophore Coban as positive control, and the ionophore as negative control), and four treatments (probiotics BC-30 and Calsporin; and EO, Crina Poultry Plus, and Crina PoultryAF). Day-old broilers were raised to 14 days in floor pens on used litter and then were moved to Petersime batteries and inoculated at 15 days with mixed Eimeria spp. Ileal and cecal samples were collected at 14 days and 7 days postinfection. Digesta DNA was subjected to pyrosequencing for sequencing of individual cecal bacteria and denaturing gradient gel electrophoresis (DGGE) for determination of changes in ileal and cecal MC according to percentage similarity coefficient (%SC). Pyrosequencing is very sensitive detecting shifts in individual bacterial sequences, whereas DGGE is able to detect gross shifts in entire MC. These combined techniques offer versatility toward identifying feed additive and mild Eimeria infection modulation of broiler MC. Pyrosequencing detected 147 bacterial species sequences. Additionally, pyrosequencing revealed the presence of relatively low levels of the potential human enteropathogens Campylobacter sp. and four Shigella spp. as well as the potential poultry pathogen Clostridiun perfringens. Pre- and postinfection changes in ileal (56%SC) and cecal (78.5%SC) DGGE profiles resulted from the coccidia infection and with increased broiler age. Probiotics and EO changed MC from those seen in UU ilea and ceca. Results potentially reflect the performance enhancement above expectations in comparison to broilers not given the probiotics or the specific EO blends as feed supplements.

Selection of alfalfa cultivars adapted for tropical environments with repeated measures using PROC MIXED of SAS (R) System

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

Thermal behaviour and analytical study of the production of TiSnOx from the mixed 8-hydroxyquinolinates

Solubility and pH precipitation studies were carried out to obtain the binuclear complex {[TiO(C9H6NO)2][Sn(C9H6NO) 2]} involving 8-hydroxyquinoline as chelating agent. The compound, the individual mononuclear complexes and their physical mixture were evaluated by means of techniques such as TG, DTA, elemental analysis, X-ray diffraction, IR spectroscopy. The properties of the original compounds and also the thermoanalytical conditions exerted a great influence on the degree of crystallinity and on the crystalline phase of the mixed oxide obtained as final product of the thermal decomposition.

On the regularization of mixed complementarity problems

A variational inequality problem (VIP) satisfying a constraint qualification can be reduced to a mixed complementarity problem (MCP). Monotonicity of the VIP implies that the MCP is also monotone. Introducing regularizing perturbations, a sequence of strictly monotone mixed complementarity problems is generated. It is shown that, if the original problem is solvable, the sequence of computable inexact solutions of the strictly monotone MCP's is bounded and every accumulation point is a solution. Under an additional condition on the precision used for solving each subproblem, the sequence converges to the minimum norm solution of the MCP. Copyright © 2000 by Marcel Dekker, Inc.

On the solution of bounded and unbounded mixed complementarity problems

A reformulation of the bounded mixed complementarity problem is introduced. It is proved that the level sets of the objective function are bounded and, under reasonable assumptions, stationary points coincide with solutions of the original variational inequality problem. Therefore, standard minimization algorithms applied to the new reformulation must succeed. This result is applied to the compactification of unbounded mixed complementarity problems. © 2001 OPA (Overseas Publishers Association) N.V. Published by license under the Gordon and Breach Science Publishers imprint, a member of the Taylor & Francis Group.

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.