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.

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.

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.

Stickiness in a bouncer model: A slowing mechanism for Fermi acceleration

Some phase space transport properties for a conservative bouncer model are studied. The dynamics of the model is described by using a two-dimensional measure preserving mapping for the variables' velocity and time. The system is characterized by a control parameter epsilon and experiences a transition from integrable (epsilon = 0) to nonintegrable (epsilon not equal 0). For small values of epsilon, the phase space shows a mixed structure where periodic islands, chaotic seas, and invariant tori coexist. As the parameter epsilon increases and reaches a critical value epsilon(c), all invariant tori are destroyed and the chaotic sea spreads over the phase space, leading the particle to diffuse in velocity and experience Fermi acceleration (unlimited energy growth). During the dynamics the particle can be temporarily trapped near periodic and stable regions. We use the finite time Lyapunov exponent to visualize this effect. The survival probability was used to obtain some of the transport properties in the phase space. For large epsilon, the survival probability decays exponentially when it turns into a slower decay as the control parameter epsilon is reduced. The slower decay is related to trapping dynamics, slowing the Fermi Acceleration, i.e., unbounded growth of the velocity.

Evaluation of rhamnolipid and surfactin to reduce the adhesion and remove biofilms of individual and mixed cultures of food pathogenic bacteria

Biofilms represent a great concern for food industry, since they can be a source of persistent contamination leading to food spoilage and to the transmission of diseases. To avoid the adhesion of bacteria and the formation of biofilms, an alternative is the pre-conditioning of surfaces using biosurfactants, microbial compounds that can modify the physicochemical properties of surfaces changing bacterial interactions and consequently adhesion. Different concentrations of the biosurfactants, surfactin from Bacillus subtilis and rhamnolipids from Pseudomonas aeruginosa, were evaluated to reduce the adhesion and to disrupt biofilms of food-borne pathogenic bacteria. Individual cultures and mixed cultures of Staphylococcus aureus, Listeria monocytogenes and Salmonella Enteritidis were studied using polystyrene as the model surface. The pre-conditioning with surfactin 0.25% reduced by 42.0% the adhesion of L monocytogenes and S. Enteritidis, whereas the treatment using rhamnolipids 1.0% reduced by 57.8% adhesion of L monocytogenes and by 67.8% adhesion of S. aureus to polystyrene.Biosurfactants were less effective to avoid adhesion of mixed cultures of the bacteria when compared with individual cultures. After 2 h contact with surfactin at 0.1% concentration, the pre-formed biofilms of S. aureus were reduced by 63.7%, L. monocytogenesby 95.9%, S. Enteritidis by 35.5% and the mixed culture biofilm by 58.5%. The rhamnolipids at 0.25% concentration removed 58.5% the biofilm of S. aureus, 26.5% of L monocytogenes, 23.0% of S. Enteritidis and 24.0% the mixed culture after 2 h contact. In general, the increase in concentration of biosurfactants and in the time of contact decreased biofilm removal percentage. These results suggest that surfactin and rhamnolipids can be explored to control the attachment and to disrupt biofilms of individual and mixed cultures of the food-borne pathogens. (C) 2011 Elsevier Ltd. All rights reserved.

Influence Assessment in an Heteroscedastic Errors-in-Variables Model

The main goal of this article is to consider influence assessment in models with error-prone observations and variances of the measurement errors changing across observations. The techniques enable to identify potential influential elements and also to quantify the effects of perturbations in these elements on some results of interest. The approach is illustrated with data from the WHO MONICA Project on cardiovascular disease.

The Cysteine-Rich Protein Thimet Oligopeptidase as a Model of the Structural Requirements for S-glutathiolation and Oxidative Oligomerization

Thimet oligopeptidase (EP24.15) is a cysteine-rich metallopeptidase containing fifteen Cys residues and no intra-protein disulfide bonds. Previous work on this enzyme revealed that the oxidative oligomerization of EP24.15 is triggered by S-glutathiolation at physiological GSSG levels (10-50 mu M) via a mechanism based on thiol-disulfide exchange. In the present work, our aim was to identify EP24.15 Cys residues that are prone to S-glutathiolation and to determine which structural features in the cysteinyl bulk are responsible for the formation of mixed disulfides through the reaction with GSSG and, in this particular case, the Cys residues within EP24.15 that favor either S-glutathiolation or inter-protein thiol-disulfide exchange. These studies were conducted by in silico structural analyses and simulations as well as site-specific mutation. S-glutathiolation was determined by mass spectrometric analyses and western blotting with anti-glutathione antibody. The results indicated that the stabilization of a thiolate sulfhydryl and the solvent accessibility of the cysteines are necessary for S-thiolation. The Solvent Access Surface analysis of the Cys residues prone to glutathione modification showed that the S-glutathiolated Cys residues are located inside pockets where the sulfur atom comes into contact with the solvent and that the positively charged amino acids are directed toward these Cys residues. The simulation of a covalent glutathione docking onto the same Cys residues allowed for perfect glutathione posing. A mutation of the Arg residue 263 that forms a saline bridge to the Cys residue 175 significantly decreased the overall S-glutathiolation and oligomerization of EP24.15. The present results show for the first time the structural requirements for protein S-glutathiolation by GSSG and are consistent with our previous hypothesis that EP24.15 oligomerization is dependent on the electron transfer from specific protonated Cys residues of one molecule to previously S-glutathionylated Cys residues of another one.

Assessment of variance components in nonlinear mixed-effects elliptical models

The issue of assessing variance components is essential in deciding on the inclusion of random effects in the context of mixed models. In this work we discuss this problem by supposing nonlinear elliptical models for correlated data by using the score-type test proposed in Silvapulle and Silvapulle (1995). Being asymptotically equivalent to the likelihood ratio test and only requiring the estimation under the null hypothesis, this test provides a fairly easy computable alternative for assessing one-sided hypotheses in the context of the marginal model. Taking into account the possible non-normal distribution, we assume that the joint distribution of the response variable and the random effects lies in the elliptical class, which includes light-tailed and heavy-tailed distributions such as Student-t, power exponential, logistic, generalized Student-t, generalized logistic, contaminated normal, and the normal itself, among others. We compare the sensitivity of the score-type test under normal, Student-t and power exponential models for the kinetics data set discussed in Vonesh and Carter (1992) and fitted using the model presented in Russo et al. (2009). Also, a simulation study is performed to analyze the consequences of the kurtosis misspecification.

Antimicrobial effect of endodontic solutions used as final irrigants on a dentine biofilm model

Aim To evaluate the residual biovolume of live bacterial cells, the mean biofilm thickness and the substratum coverage found in mixed biofilms treated with different endodontic irrigant solutions. Methodology Twenty-five bovine dentine specimens were infected intraorally using a removable orthodontic device. Five samples were used for each irrigant solution: 2% chlorhexidine, 1% sodium hypochlorite (NaOCl), 10% citric acid, 17% EDTA and distilled water. The solutions were used for 5 min. The samples were stained using the Live/Dead technique and evaluated using a confocal microscope. Differences in the amount of total biovolume (mu m3), number of surviving cells (mu m3), mean biofilm thickness (mu m) and substratum coverage (%) of the treated biofilms were determined using nonparametric statistical tests (P < 0.05). Results Similar values of biovolume total, biovolume of live subpopulations and substratum coverage were found in 2% chlorhexidine, 10% citric acid, 17% EDTA and distilled water-treated biofilms (P > 0.05). The lower values of the studied parameters were found in 1% NaOCl-treated dentine (P < 0.05) with the exception of the mean biofilm height criteria that did not reveal significant differences amongst the irrigant solutions (P > 0.05). Conclusions One per cent sodium hypochlorite was the only irrigant that had a significant effect on biofilm viability and architecture.

Structure and Ionic Conductivity in the Mixed-Network Former Chalcogenide Glass System [Na2S](2/3)[(B2S3)(x)(P2S5)(1-x)](1/3)

Glasses in the system [Na2S](2/3)[(B2S3)(x)(P2S5)(1-x)](1/3) (0.0 <= x <= 1.0) were prepared by the melt quenching technique, and their properties were characterized by thermal analysis and impedance spectroscopy. Their atomic-level structures were comprehensively characterized by Raman spectroscopy and B-11, P-31, and Na-23 high resolution solid state magic-angle spinning (MAS) NMR techniques. P-31 MAS NMR peak assignments were made by the presence or absence of homonuclear indirect P-31-P-31 spin-spin interactions as detected using homonuclear J-resolved and refocused INADEQUATE techniques. The extent of B-S-P connectivity in the glassy network was quantified by P-31{B-11} and B-11{P-31} rotational echo double resonance spectroscopy. The results clearly illustrate that the network modifier alkali sulfide, Na2S, is not proportionally shared between the two network former components, B and P. Rather, the thiophosphate (P) component tends to attract a larger concentration of network modifier species than predicted by the bulk composition, and this results in the conversion of P2S74-, pyrothiophosphate, Na/P = 2:1, units into PS43-, orthothiophosphate, Na/P = 3:1, groups. Charge balance is maintained by increasing the net degree of polymerization of the thioborate (B) units through the formation of covalent bridging sulfur (BS) units, B S B. Detailed inspection of the B-11 MAS NMR spectra reveals that multiple thioborate units are formed, ranging from neutral BS3/2 groups all the way to the fully depolymerized orthothioborate (BS33-) species. On the basis of these results, a comprehensive and quantitative structural model is developed for these glasses, on the basis of which the compositional trends in the glass transition temperatures (T-g) and ionic conductivities can be rationalized. Up to x = 0.4, the dominant process can be described in a simplified way by the net reaction equation P-1 + B-1 reversible arrow P-0 + B-4, where the superscripts denote the number of BS atoms for the respective network former species. Above x = 0.4, all of the thiophosphate units are of the P-0 type and both pyro-(B-1) and orthothioborate (B-0) species make increasing contributions to the network structure with increasing x. In sharp contrast to the situation in sodium borophosphate glasses, four-coordinated thioborate species are generally less abundant and heteroatomic B-S-P linkages appear to not exist. On the basis of this structural information, compositional trends in the ionic conductivities are discussed in relation to the nature of the charge-compensating anionic species and the spatial distribution of the charge carriers.