Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology

Genome-wide association studies (GWAS) have been widely used in genetic dissection of complex traits. However, common methods are all based on a fixed-SNP-effect mixed linear model (MLM) and single marker analysis, such as efficient mixed model analysis (EMMA). These methods require Bonferroni correction for multiple tests, which often is too conservative when the number of markers is extremely large. To address this concern, we proposed a random-SNP-effect MLM (RMLM) and a multi-locus RMLM (MRMLM) for GWAS. The RMLM simply treats the SNP-effect as random, but it allows a modified Bonferroni correction to be used to calculate the threshold p value for significance tests. The MRMLM is a multi-locus model including markers selected from the RMLM method with a less stringent selection criterion. Due to the multi-locus nature, no multiple test correction is needed. Simulation studies show that the MRMLM is more powerful in QTN detection and more accurate in QTN effect estimation than the RMLM, which in turn is more powerful and accurate than the EMMA. To demonstrate the new methods, we analyzed six flowering time related traits in Arabidopsis thaliana and detected more genes than previous reported using the EMMA. Therefore, the MRMLM provides an alternative for multi-locus GWAS.

Edible oil from Tiger nut (Cyperus esculentus L.): mechanical pressing and aqueous enzymatic extraction methods

The tiger nut tuber of the Cyperus esculentus L. plant is an unusual storage system with similar amounts of starch and lipid. The extraction of its oil employing both mechanical pressing and aqueous enzymatic extraction (AEE) methods was investigated and an examination of the resulting products was carried out. The effects of particle size and moisture content of the tuber on the yield of tiger nut oil with pressing were initially studied. Smaller particles were found to enhance oil yields while a range of moisture content was observed to favour higher oil yields. When samples were first subjected to high pressures up to 700 MPa before pressing at 38 MPa there was no increase in the oil yields. Ground samples incubated with a mixture of α- Amylase, Alcalase, and Viscozyme (a mixture of cell wall degrading enzyme) as a pre-treatment, increased oil yield by pressing and 90% of oil was recovered as a result. When aqueous enzymatic extraction was carried out on ground samples, the use of α- Amylase, Alcalase, and Celluclast independently improved extraction oil yields compared to oil extraction without enzymes by 34.5, 23.4 and 14.7% respectively. A mixture of the three enzymes further augmented the oil yield and different operational factors were individually studied for their effects on the process. These include time, total mixed enzyme concentration, linear agitation speed, and solid-liquid ratio. The largest oil yields were obtained with a solid-liquid ratio of 1:6, mixed enzyme concentration of 1% (w/w) and 6 h incubation time although the longer time allowed for the formation of an emulsion. Using stationary samples during incubation surprisingly gave the highest oil yields, and this was observed to be as a result of gravity separation occurring during agitation. Furthermore, the use of high pressure processing up to 300 MPa as a pre-treatment enhanced oil yields but additional pressure increments had a detrimental effect. The quality of oils recovered from both mechanical and aqueous enzymatic extraction based on the percentage free fatty acid (% FFA) and peroxide values (PV) all reflected the good stabilities of the oils with the highest % FFA of 1.8 and PV of 1.7. The fatty acid profiles of all oils also remained unchanged. The level of tocopherols in oils were enhanced with both enzyme aided pressing (EAP) and high pressure processing before AEE. Analysis on the residual meals revealed DP 3 and DP 4 oligosaccharides present in EAP samples but these would require further assessment on their identity and quality.

Robust linear mixed models with skew-normal independent distributions from a Bayesian perspective

Linear mixed models were developed to handle clustered data and have been a topic of increasing interest in statistics for the past 50 years. Generally. the normality (or symmetry) of the random effects is a common assumption in linear mixed models but it may, sometimes, be unrealistic, obscuring important features of among-subjects variation. In this article, we utilize skew-normal/independent distributions as a tool for robust modeling of linear mixed models under a Bayesian paradigm. The skew-normal/independent distributions is an attractive class of asymmetric heavy-tailed distributions that includes the skew-normal distribution, skew-t, skew-slash and the skew-contaminated normal distributions as special cases, providing an appealing robust alternative to the routine use of symmetric distributions in this type of models. The methods developed are illustrated using a real data set from Framingham cholesterol study. (C) 2009 Elsevier B.V. All rights reserved.

Local Influence Analysis for Skew-Normal Linear Mixed Models

In this article, we consider local influence analysis for the skew-normal linear mixed model (SN-LMM). As the observed data log-likelihood associated with the SN-LMM is intractable, Cook`s well-known approach cannot be applied to obtain measures of local influence. Instead, we develop local influence measures following the approach of Zhu and Lee (2001). This approach is based on the use of an EM-type algorithm and is measurement invariant under reparametrizations. Four specific perturbation schemes are discussed. Results obtained for a simulated data set and a real data set are reported, illustrating the usefulness of the proposed methodology.

Electrostatic layer-by-layer and electrophoretic depositions as methods for electrochromic nanoparticle immobilization

The present paper describes the immobilization of nanoparticles onto conducting substrates by using both electrostatic layer-by-layer and electrophoretic deposition (EPD) methods. These two techniques were compared in high-performance electrochromic electrodes based on mixed nickel hydroxide nanoparticles. In addition to easy handling, EPD seems to be the most suitable method for the immobilization of nanoparticles, leading to higher electrochromic efficiencies, lower response times and higher stability upon coloration and bleaching cycling. (C) 2008 Elsevier Ltd. All rights reserved.

Synthesis, characterization and adsorption properties of porous mixed valent diruthenium(II,III)-terephthalate and diruthenium(II,III)-adipate polymers

Two porous mixed valent diruthenium(II,III)-dicarboxylate compounds have been prepared and characterized by spectroscopic methods, X-ray diffraction and thermogravimetry. Crystalline solids of [Ru(2)(tere)(2)Cl] center dot 3.5H(2)O (tere=terephthalate) and [Ru(2)(adip)(2)Cl] center dot 1.5H(2)O (adip=adipate) consist of extended chains in which polymeric layers of multiply metal-metal bonded [Ru(2)](5+) cores are bridged by dicarboxylate ligands in paddlewheel type geometries. Units of [Ru(2)(dicarboxylate)(2)](n)(+) are linked by axial bridging chloride ions generating three-dimensional networks. The polymers loose non-bonded water molecules at low temperatures but do not undergo thermal decomposition below 280-300 degrees C. Both of compounds exhibit high BET surface areas, [Ru(2)(tere)(2)Cl]: 235 m(2) g(-1) and [Ru(2)(adip)(2)Cl]: 281 m(2) g(-1), and occlude similar numbers of mol of N(2) per mol of metal. The terephthalate ligand generated an organized structure with supermicropores (total pore size of 0.24 cm(3) g(-1)) while the adipate ligand led to a mesoporous structure (total pore sizes of 0.47 cm(3) g(-1)) for the corresponding diruthenium(II,III)-dicarboxylate polymers. (c) 2008 Elsevier B.V. All rights reserved.

Mixed-Ligand Complexes of Technetium and Rhenium with Tridentate Benzamidines and Bidentate Benzoylthioureas

Mixed-ligand complexes of technetium(V) or rhenium(V) containing tridentate N-[(dialkylamino)(thiocarbonyl)]benzamidine (H(2)L(1)) and bidentate N,N-dialkyl-N`-benzoylthiourea (HL(2)) ligands were formed in high yields when (NBu(4))[MOCl(4)] (M = Tc or Re) or [ReOCl(3)(PPh(3))(2)] was treated with mixtures of the proligands. Other approaches for the synthesis of the products are reactions of [MOCl(L(1))] complexes with HL(2) or compounds of the-composition [ReOCl(2)(PPh(3))(L(2))] with H(2)L(1). The resulting air-stable [MO(L(1))(L(2))] complexes possess potential for the development of metal-based radiopharmaceuticals. [TcO(L(1))(L(2))] complexes are readily reduced by PPh3 with formation of [Tc(L(1))(L(2))(PPh(3))]. The resulting Tc(III) complexes undergo two almost-reversible oxidation steps corresponding to one-electron transfer processes. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)

Novel Statistical Methods in Quantitative Genetics : Modeling Genetic Variance for Quantitative Trait Loci Mapping and Genomic Evaluation

This thesis develops and evaluates statistical methods for different types of genetic analyses, including quantitative trait loci (QTL) analysis, genome-wide association study (GWAS), and genomic evaluation. The main contribution of the thesis is to provide novel insights in modeling genetic variance, especially via random effects models. In variance component QTL analysis, a full likelihood model accounting for uncertainty in the identity-by-descent (IBD) matrix was developed. It was found to be able to correctly adjust the bias in genetic variance component estimation and gain power in QTL mapping in terms of precision.  Double hierarchical generalized linear models, and a non-iterative simplified version, were implemented and applied to fit data of an entire genome. These whole genome models were shown to have good performance in both QTL mapping and genomic prediction. A re-analysis of a publicly available GWAS data set identified significant loci in Arabidopsis that control phenotypic variance instead of mean, which validated the idea of variance-controlling genes.  The works in the thesis are accompanied by R packages available online, including a general statistical tool for fitting random effects models (hglm), an efficient generalized ridge regression for high-dimensional data (bigRR), a double-layer mixed model for genomic data analysis (iQTL), a stochastic IBD matrix calculator (MCIBD), a computational interface for QTL mapping (qtl.outbred), and a GWAS analysis tool for mapping variance-controlling loci (vGWAS).

Parameter estimation of Poisson generalized linear mixed models based on three different statistical principles : a simulation study

Generalized linear mixed models are flexible tools for modeling non-normal data and are useful for accommodating overdispersion in Poisson regression models with random effects. Their main difficulty resides in the parameter estimation because there is no analytic solution for the maximization of the marginal likelihood. Many methods have been proposed for this purpose and many of them are implemented in software packages. The purpose of this study is to compare the performance of three different statistical principles - marginal likelihood, extended likelihood, Bayesian analysis-via simulation studies. Real data on contact wrestling are used for illustration.

Detection of mixed microbial biofilms on central venous catheters removed from Intensive care Unit Patients

Cateteres venosos centrais inseridos em pacientes internados em unidade de terapia intensiva foram avaliados por métodos microbiológicos (cultura semi-quantitativa) e microscopia eletrônica de varredura a fim de detectar adesão microbiana e correlacionar com a cultura de sangue. Durante o período de estudo, foram avaliados 59 pacientes com cateter venoso central. A idade dos pacientes, sexo, sítio de inserção e tempo de permanência do cateter foram anotados. O cateter era de poliuretano não tunelizado e de único lúmen. O sangue para cultura foi coletado no momento da remoção do cateter. de 63 pontas de cateteres, 30 (47,6%) foram colonizadas e a infecção encontrada em 5 (23,8%) cateteres. A infecção foi mais prevalente em 26 pacientes (41,3%) com cateteres inseridos em veia subclávia do que nos 3 (3,2%) inseridos em veia jugular. A infecção foi observada com mais freqüência em cateteres com tempo de permanência maior do que sete dias. Os microrganismos isolados incluíram 32 estafilococos coagulase-negativa (29,7%), 61 bactérias Gram-negativas (52,9%), 9 estafilcocos coagulase-positiva (8,3%) e 3 leveduras (2,7%). Como agentes causais de infecções em unidade de terapia intensiva foram isolados E. aerogenes, P. aeruginosa, A. baumannii. Os antimicrobianos com maior atividade in vitro contra as bactérias Gram-negativas foram o imipenem e contra as Gram-positivas vancomicina, cefepime, penicilina, rifampicina e tetraciclina. As análises por microscopia eletrônica de varredura revelaram biofilmes sobre a superfície de todos os cateteres examinados.

ZnO-TiO2 composite formed by mixed oxides via polyol

Among the researches on preparation and test of nanostructured materials, titanium dioxide and zinc oxide have been the most frequent studied oxides. In order to extend their properties, composites have been prepared using three different methods: Polyol Method, Sol-gel Process and a combination of the two processes (hybrid process). Recent research showed best properties in composite materials than in pure oxides. In this work is presented the preparation and the structural characterization of ZnO-TiO2 composite nanostructures to be tested for their performance in electrocatalysis and in further trial on photovoltaic cells.

Intravaginal electrical stimulation: a randomized, double-blind study on the treatment of mixed urinary incontinence

Background the aim of this study was to compare effective and sham intravaginal electrical stimulation (IES) in treating mixed urinary incontinence. Methods. Between January 2001 and February 2002, 40 women were randomly distributed, in a double-blind study, into two groups: group G1 (n = 20), effective IES, and group G2 (n = 20), sham IES, with follow up at one month. Different parameters was studied: 1. clinical questionnaire, 2. body mass index; 3. 60-min pad test; 4. urodynamic study. The protocol of IES consisted of three 20-min sessions per week over a seven-week period. The Dualpex Uro 996 used a frequency of 4 Hz. Results. There was no statistically significant difference in the demographic data of both groups. The number of micturitions per 24 h after treatment was reduced significantly in both groups. Urge incontinence was reduced to 15% in G1 and 31.5% in G2; there was no significant difference between the groups. In the analog wetness and discomfort sensation evaluations were reduced significantly in both groups. The pretreatment urodynamic study showed no statistical difference in urodynamic parameters between the groups. Ten percent of the women presented involuntary detrusor contractions. In the 60-min pad test, there was a significant reduction in both groups. In regards to satisfaction level, after treatment, 80% of G1 patients and 65% of G2 patients were satisfied. There was no statistically significant difference between the groups. Conclusion. Significant improvement was provided by effective and sham electrostimulation, questioning the effectiveness of electrostimulation as a monotherapy.

Molecular diagnostic methods for identifying Serrasalmid fish (Pacu, Pirapitinga, and Tambaqui) and their hybrids in the Brazilian aquaculture industry

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

Effects of self-, chase and mixed self/cross-pollinations on pistil longevity and fruit set in Ceiba species (Bombacaceae) with late-acting self-incompatibility

Background and aims Late-acting self-incompatibility (LSI). in which selfed flowers fail to form fruits despite apparently successful growth of the pollen tubes to the ovules, is a contentious and still poorly understood phenomenon. Some studies have indicated pollen tube-pistil interactions, and major gene control. Others favour an early acting inbreeding depression explanation.Methods Experimental pollinations, including selfs (in a subsample of which the style was cut before pollen tubes reached the ovary), chase self/cross-pollinations, crosses, and mixed self/cross-pollinations were used to study floral/pistil longevity and effect on fruit set and seed yield in two Ceiba species known to have LSI.Results Self-pollinations, including those with a cut style, had extended floral longevity compared with unpollinated flowers. Chase pollinations in which cross-pollen was applied up to 3 h after selfing set fruits, but with reduced seed set compared with crosses. Those with cross-pollen applied at 4 and 8 h after self-pollination all failed to set fruits. Flowers subjected to 1 : 1 and 2 : 1 self/cross-pollinations all produced fruits but again with a significantly lower seed set compared with crosses.Conclusions Extended floral longevity initiated with self-pollen tubes growing in the style indicates some kind of pollen tube-pistil interaction. Fruit set only in chase pollinations up to 3 h implies that self-pollen tubes either grow more slowly in the style or penetrate ovules more slowly on arrival at the ovary compared with cross-tubes. This agrees with previous observations indicating that the incidence of penetrated ovules is initially lower in selfed compared with crossed pistils. However, the low seed yield from mixed pollinations indicates that self- and cross-pollen tubes arrive at the ovary and penetrate ovules more or less simultaneously. Possible explanations for these discordant results are discussed. (C) 2004 Annals of Botany Company.

Effect of conditioning methods on the microtensile bond strength of phosphate monomer-based cement on zirconia ceramic in dry and aged conditions

The objective of this study was to evaluate the durability of bond strength between a resin cement and aluminous ceramic submitted to various surface conditioning methods. Twenty-four blocks (5 X 5 X 4 mm 3) of a glass-in filtrated zirconia-alumina ceramic (inCeram Zirconia Classic) were randomly divided into three surface treatment groups: ST1-Air-abrasion with 110-mu m Al2O3 particles + silanization; ST2-Laboratory tribochemical silica coating method (110-mu m Al2O3, ilO-PM Silica) (Rocatec) + silanization; ST3-Chairside tribochemical silica coating method (30-mu m SiOx) (CoJet) + silanization. Each treated ceramic block was placed in its silicone mold with the treated surface exposed. The resin cement (Panavia F) was prepared and injected into the mold over the treated surface. Specimens were sectioned to achieve nontrimmed bar specimens (14 sp/block) that were randomly divided into two conditions: (a) Dry-microtensile test after sectioning; (b) Thermocycling (TC)-(6,000X, 5-55 degrees C) and water storage (150 days). Thus, six experimental groups were obtained (11 = 50): Gr1-ST1 + dry; Gr2-ST1 + TC. Gr3-ST2 + dry; Gr4-ST2 + TC; Gr5-ST3 + dry; Gr6ST3 + TC. After microtensile testing, the failure types were noted. ST2 (25.1 +/- 11) and ST3 (24.1 +/- 7.4) presented statistically higher bond strength (MPa) than that of STI (17.5 +/- 8) regardless of aging conditions (p < 0.0001). While Gr2 revealed the lowest results (13.3 +/- 6.4), the other groups (21.7 +/- 7.4-25. 9 +/- 9.1) showed statistically no significant differences (two-way ANOVA and Tukey's test, a 0.05). The majority of the failures were mixed (82%) followed by adhesive failures (18%). Gr2 presented significantly higher incidence of ADHESIVE failures (54%) than those of other groups (p = 0.0001). Both laboratory and chairside silica coating plus silanization showed durable bond strength. After aging, airabrasion with 110-mu m Al2O3 + silanization showed the largest decrease indicating that aging is fundamental for bond strength testing for acid-resistant Arconia ceramics in order to estimate their long-term performance in the mouth. (c) 2007 Wiley Periodicals, Inc.