A mixed model QTL analysis for sugarcane multiple-harvest-location trial data

Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane.

Simple heuristics for the assembly line worker assignment and balancing problem

We propose simple heuristics for the assembly line worker assignment and balancing problem. This problem typically occurs in assembly lines in sheltered work centers for the disabled. Different from the well-known simple assembly line balancing problem, the task execution times vary according to the assigned worker. We develop a constructive heuristic framework based on task and worker priority rules defining the order in which the tasks and workers should be assigned to the workstations. We present a number of such rules and compare their performance across three possible uses: as a stand-alone method, as an initial solution generator for meta-heuristics, and as a decoder for a hybrid genetic algorithm. Our results show that the heuristics are fast, they obtain good results as a stand-alone method and are efficient when used as a initial solution generator or as a solution decoder within more elaborate approaches.

A Poisson mixed model with nonnormal random effect distribution

In this paper, we propose a random intercept Poisson model in which the random effect is assumed to follow a generalized log-gamma (GLG) distribution. This random effect accommodates (or captures) the overdispersion in the counts and induces within-cluster correlation. We derive the first two moments for the marginal distribution as well as the intraclass correlation. Even though numerical integration methods are, in general, required for deriving the marginal models, we obtain the multivariate negative binomial model from a particular parameter setting of the hierarchical model. An iterative process is derived for obtaining the maximum likelihood estimates for the parameters in the multivariate negative binomial model. Residual analysis is proposed and two applications with real data are given for illustration. (C) 2011 Elsevier B.V. All rights reserved.

Two extensions for the ALWABP: Parallel stations and collaborative approach

In this article, we introduce two new variants of the Assembly Line Worker Assignment and Balancing Problem (ALWABP) that allow parallelization of and collaboration between heterogeneous workers. These new approaches suppose an additional level of complexity in the Line Design and Assignment process, but also higher flexibility; which may be particularly useful in practical situations where the aim is to progressively integrate slow or limited workers in conventional assembly lines. We present linear models and heuristic procedures for these two new problems. Computational results show the efficiency of the proposed approaches and the efficacy of the studied layouts in different situations. (C) 2012 Elsevier B.V. All rights reserved.

Effects of different cryopreservation methods on post-thaw culture conditions of in vitro produced bovine embryos

The aim of this work was to evaluate the effect of cryopreservation protocols on subsequent development of in vitro produced bovine embryos under different culture conditions. Expanded in vitro produced blastocysts (n = 600) harvested on days 7-9 were submitted to controlled freezing [slow freezing group: 10% ethylene glycol (EG) for 10 min and 1.2 degrees C/min cryopreservation]; quick-freezing [rapid freezing group: 10% EG for 10 min, 20% EG + 20% glycerol (Gly) for 30 s]; or vitrification [vitrification group: 10% EG for 10 min, 25% EG + 25% Gly for 30 s] protocols. Control group embryos were not exposed to cryoprotectant or cryopreservation protocols and the hatching rate was evaluated on day 12 post-insemination. In order to evaluate development, frozen-thawed embryos were subjected to granulosa cell co-culture in TCM199 or SOFaa for 4 days. Data were analyzed by PROC MIXED model using SAS Systems for Windows (R). Values were significant at p < 0.05. The hatching rate of the control group was 46.09%. In embryos cultured in TCM199, slow freezing and vitrification group hatching rates were 44.65 +/- 5.94% and 9.43 +/- 6.77%, respectively. In embryos cultured in SOFaa, slow freezing and vitrification groups showed hatching rates of 11.65 +/- 3.37 and 8.67 +/- 4.47%, respectively. In contrast, the rapid freezing group embryos did not hatch, regardless of culture medium. The slow freezing group showed higher hatching rates than other cryopreservation groups. Under such conditions, controlled freezing (1.2 degrees C/min) can be an alternative to cryopreservation of in vitro produced bovine embryos.

Prediction with measurement errors in finite populations

We address the problem of selecting the best linear unbiased predictor (BLUP) of the latent value (e.g., serum glucose fasting level) of sample subjects with heteroskedastic measurement errors. Using a simple example, we compare the usual mixed model BLUP to a similar predictor based on a mixed model framed in a finite population (FPMM) setup with two sources of variability, the first of which corresponds to simple random sampling and the second, to heteroskedastic measurement errors. Under this last approach, we show that when measurement errors are subject-specific, the BLUP shrinkage constants are based on a pooled measurement error variance as opposed to the individual ones generally considered for the usual mixed model BLUP. In contrast, when the heteroskedastic measurement errors are measurement condition-specific, the FPMM BLUP involves different shrinkage constants. We also show that in this setup, when measurement errors are subject-specific, the usual mixed model predictor is biased but has a smaller mean squared error than the FPMM BLUP which points to some difficulties in the interpretation of such predictors. (C) 2011 Elsevier By. All rights reserved.

Efeitos gênicos de caracteres associados à eficiência no uso de nitrogênio em milho

Os objetivos deste trabalho foram determinar o controle genético da eficiência no uso do nitrogênio (EUN), identificar a importância das eficiências na absorção (EAN) e na utilização (EUtN) na sua composição,  e quantificar relação entre produção de matéria seca da parte aérea (MPS) e do sistema radicular com a EUN e  com seus componentes. Foram avaliadas 41 combinações híbridas em duas disponibilidades de N: baixa (BN)  e alta (AN). Utilizou-se o delineamento de blocos ao acaso com duas repetições, em arranjo fatorial simples  (combinação híbrida x disponibilidade de N). As análises estatísticas foram realizadas por meio das equações  de modelos mistos. Correlações de elevada magnitude foram detectadas entre EAN e EUN, bem como entre  essas eficiências e a MPS, tanto em BN como em AN. Em ambas as disponibilidades de N, efeitos genéticos  aditivos apresentaram maior importância para os caracteres associados à EUN. Dessa forma, a seleção baseada  no desempenho individual de linhagens quanto à MPS pode possibilitar a obtenção de genótipos com alta  EUN. Independentemente da disponibilidade de N, a EAN é o componente mais importante da EUN.

The effect of implant design on insertion torque and immediate micromotion

Objectives: To evaluate the effect of insertion torque on micromotion to a lateral force in three different implant designs. Material and methods: Thirty-six implants with identical thread design, but different cutting groove design were divided in three groups: (1) non-fluted (no cutting groove, solid screw-form); (2) fluted (901 cut at the apex, tap design); and (3) Blossomt (Patent pending) (non-fluted with engineered trimmed thread design). The implants were screwed into polyurethane foam blocks and the insertion torque was recorded after each turn of 901 by a digital torque gauge. Controlled lateral loads of 10N followed by increments of 5 up to 100N were sequentially applied by a digital force gauge on a titanium abutment. Statistical comparison was performed with two-way mixed model ANOVA that evaluated implant design group, linear effects of turns and displacement loads, and their interaction. Results: While insertion torque increased as a function of number of turns for each design, the slope and final values increased (Po0.001) progressively from the Blossomt to the fluted to the non-fluted design (M +/- standard deviation [SD] = 64.1 +/- 26.8, 139.4 +/- 17.2, and 205.23 +/- 24.3 Ncm, respectively). While a linear relationship between horizontal displacement and lateral force was observed for each design, the slope and maximal displacement increased (Po0.001) progressively from the Blossomt to the fluted to the non-fluted design (M +/- SD 530 +/- 57.7, 585.9 +/- 82.4, and 782.33 +/- 269.4 mm, respectively). There was negligible to moderate levels of association between insertion torque and lateral displacement in the Blossomt, fluted and non-fluted design groups, respectively. Conclusion: Insertion torque was reduced in implant macrodesigns that incorporated cutting edges, and lesser insertion torque was generally associated with decreased micromovement. However, insertion torque and micromotion were unrelated within implant designs, particularly for those designs showing the least insertion torque.

Evaluation of a nanometer roughness scale resorbable media-processed surface: a study in dogs

Objectives: This study compared the biomechanical fixation and bone-to-implant contact (BIC) of implants with different surfaces treatment (experimental resorbable blasting media-processed nanometer roughness scale surface, and control dual acid-etched) in a dog model. Material and methods: Surface characterization was made in six implants by means of scanning electron microscopic imaging, atomic force microscopy to evaluate roughness parameters, and X-ray photoelectron spectroscopy (XPS) for chemical assessment. The animal model comprised the bilateral placement of control (n = 24) and experimental surface (n = 24) implants along the proximal tibiae of six mongrel dogs, which remained in place for 2 or 4 weeks. Half of the specimens were biomechanically tested (torque), and the other half was subjected to histomorphologic/ morphometric evaluation. BIC and resistance to failure measures were each evaluated as a function of time and surface treatment in a mixed model ANOVA. Results: Surface texturing was significantly higher for the experimental compared with the control surface. The survey XPS spectra detected O, C, Al, and Ti at the control group, and Ca (similar to 0.2-0.9%) and P (similar to 1.7-4.1%) besides O, C, Al, and Ti at experimental surfaces. While no statistical difference in BIC was found between experimental and control surfaces or between 2 and 4 weeks in vivo, both longer time and use of experimental surface significantly increased resistance to failure. Conclusions: The experimental surface resulted in enhanced biomechanical fixation but comparable BIC relative to control, suggesting higher bone mechanical properties around the experimental implants.

Diminished Mycophenolic Acid Exposure Caused by Omeprazole May Be Clinically Relevant in the First Week Posttransplantation

Background: Some studies have reported a decreased absorption of mycophenolic acid (MPA) from mycophenolate mofetil (MMF) in renal transplanted (RTx) patients under proton-pump inhibitors (PPIs). There is still a lack of information regarding (1) whether this effect occurs when MMF is administered with either tacrolimus or cyclosporine A [calcineurin inhibitors (CNIs)], (2) whether the effect has the same amplitude during the first year after RTx, and finally (3) whether this decrease in exposure is clinically relevant. Methods: We retrospectively analyzed the omeprazole effect in 348 12-hour pharmacokinetic samplings [area under the curve (AUC) 0-12h] performed on days 7, 14, 30, 60, 180, and 360 after RTx in 77 patients who participated in previous trials. Results: For all periods, the groups with and without PPI did not differ in all variables. By mixed-model analysis of variance, PPI reduced the MPA AUC(0-12h) (P < 0.0008) in the patients under both CNIs mainly due to decreased absorption (P = 0.049). In the tacrolimus group, a lower exposure seemed also due to a decreased MPA reabsorption at 10-12 hours. The PPI effect remains throughout the first year but was clinically more important on day 7. By Cox analysis, the use of PPI was associated with a 25% less chance of being adequately exposed to MPA (95% confidence interval 0.58-0.99, P = 0.04). Similarly, the number of patients underexposed to MPA (AUC < 30 ng.h/mL) was higher at most periods in the PPI group but again not statistically significant. Conclusions: These data indicate that PPI decreases the MPA exposure when associated with both CNIs but particularly in the first week after RTx. In this period, the MMF dose should be increased. This effect lasts throughout the first year but does not seem to be clinically relevant after the first week.

A Bayesian nonparametric model for Taguchi's on-line quality monitoring procedure for attributes

A Bayesian nonparametric model for Taguchi's on-line quality monitoring procedure for attributes is introduced. The proposed model may accommodate the original single shift setting to the more realistic situation of gradual quality deterioration and allows the incorporation of an expert's opinion on the production process. Based on the number of inspections to be carried out until a defective item is found, the Bayesian operation for the distribution function that represents the increasing sequence of defective fractions during a cycle considering a mixture of Dirichlet processes as prior distribution is performed. Bayes estimates for relevant quantities are also obtained. (C) 2012 Elsevier B.V. All rights reserved.

A model of road effect using line integrals and a test of the performance of two new road indices using the distribution of small mammals in an Atlantic Forest landscape

Effects of roads on wildlife and its habitat have been measured using metrics, such as the nearest road distance, road density, and effective mesh size. In this work we introduce two new indices: (1) Integral Road Effect (IRE), which measured the sum effects of points in a road at a fixed point in the forest; and (2) Average Value of the Infinitesimal Road Effect (AVIRE), which measured the average of the effects of roads at this point. IRE is formally defined as the line integral of a special function (the infinitesimal road effect) along the curves that model the roads, whereas AVIRE is the quotient of IRE by the length of the roads. Combining tools of ArcGIS software with a numerical algorithm, we calculated these and other road and habitat cover indices in a sample of points in a human-modified landscape in the Brazilian Atlantic Forest, where data on the abundance of two groups of small mammals (forest specialists and habitat generalists) were collected in the field. We then compared through the Akaike Information Criterion (AIC) a set of candidate regression models to explain the variation in small mammal abundance, including models with our two new road indices (AVIRE and IRE) or models with other road effect indices (nearest road distance, mesh size, and road density), and reference models (containing only habitat indices, or only the intercept without the effect of any variable). Compared to other road effect indices, AVIRE showed the best performance to explain abundance of forest specialist species, whereas the nearest road distance obtained the best performance to generalist species. AVIRE and habitat together were included in the best model for both small mammal groups, that is, higher abundance of specialist and generalist small mammals occurred where there is lower average road effect (less AVIRE) and more habitat. Moreover, AVIRE was not significantly correlated with habitat cover of specialists and generalists differing from the other road effect indices, except mesh size, which allows for separating the effect of roads from the effect of habitat on small mammal communities. We suggest that the proposed indices and GIS procedures could also be useful to describe other spatial ecological phenomena, such as edge effect in habitat fragments. (C) 2012 Elsevier B.V. All rights reserved.