An empirical evaluation of imputation accuracy for association statistics reveals increased type-I error rates in genome-wide associations

Background: Genome wide association studies (GWAS) are becoming the approach of choice to identify genetic determinants of complex phenotypes and common diseases. The astonishing amount of generated data and the use of distinct genotyping platforms with variable genomic coverage are still analytical challenges. Imputation algorithms combine directly genotyped markers information with haplotypic structure for the population of interest for the inference of a badly genotyped or missing marker and are considered a near zero cost approach to allow the comparison and combination of data generated in different studies. Several reports stated that imputed markers have an overall acceptable accuracy but no published report has performed a pair wise comparison of imputed and empiric association statistics of a complete set of GWAS markers. Results: In this report we identified a total of 73 imputed markers that yielded a nominally statistically significant association at P < 10(-5) for type 2 Diabetes Mellitus and compared them with results obtained based on empirical allelic frequencies. Interestingly, despite their overall high correlation, association statistics based on imputed frequencies were discordant in 35 of the 73 (47%) associated markers, considerably inflating the type I error rate of imputed markers. We comprehensively tested several quality thresholds, the haplotypic structure underlying imputed markers and the use of flanking markers as predictors of inaccurate association statistics derived from imputed markers. Conclusions: Our results suggest that association statistics from imputed markers showing specific MAF (Minor Allele Frequencies) range, located in weak linkage disequilibrium blocks or strongly deviating from local patterns of association are prone to have inflated false positive association signals. The present study highlights the potential of imputation procedures and proposes simple procedures for selecting the best imputed markers for follow-up genotyping studies.

Assessment of factors that confound MRI and neuropathological correlation of human postmortem brain tissue

In spite of considerable technical advance in MRI techniques, the optical resolution of these methods are still limited. Consequently, the delineation of cytoarchitectonic fields based on probabilistic maps and brain volume changes, as well as small-scale changes seen in MRI scans need to be verified by neuronanatomical/neuropathological diagnostic tools. To attend the current interdisciplinary needs of the scientific community, brain banks have to broaden their scope in order to provide high quality tissue suitable for neuroimaging- neuropathology/anatomy correlation studies. The Brain Bank of the Brazilian Aging Brain Research Group (BBBABSG) of the University of Sao Paulo Medical School (USPMS) collaborates with researchers interested in neuroimaging-neuropathological correlation studies providing brains submitted to postmortem MRI in-situ. In this paper we describe and discuss the parameters established by the BBBABSG to select and to handle brains for fine-scale neuroimaging-neuropathological correlation studies, and to exclude inappropriate/unsuitable autopsy brains. We tried to assess the impact of the postmortem time and storage of the corpse on the quality of the MRI scans and to establish fixation protocols that are the most appropriate to these correlation studies. After investigation of a total of 36 brains, postmortem interval and low body temperature proved to be the main factors determining the quality of routine MRI protocols. Perfusion fixation of the brains after autopsy by mannitol 20% followed by formalin 20% was the best method for preserving the original brain shape and volume, and for allowing further routine and immunohistochemical staining. Taken to together, these parameters offer a methodological progress in screening and processing of human postmortem tissue in order to guarantee high quality material for unbiased correlation studies and to avoid expenditures by post-imaging analyses and histological processing of brain tissue.

Correlation between margin fit and microleakage in complete crowns cemented with three luting agents

Microleakage can be related to margin misfit. Also, traditional microleakage techniques are time-consuming. This study evaluated the existence of correlation between in vitro margin fit and a new microleakage technique for complete crowns cemented with 3 different luting agents. Thirty human premolars were prepared for full-coverage crowns with a convergence angle of 6 degrees, chamfer margin of 1.2 mm circumferentially, and occlusal reduction of 1.5 mm. Ni-Cr cast crowns were cemented with either zinc phosphate (ZP) (S.S. White), resin-modified glass-ionomer (RMGI) (Rely X Luting Cement) or a resin-based luting agent (RC) (Enforce). Margin fit (seating discrepancy and margin gap) was evaluated according to criteria in the literature under microscope with 0.001 mm accuracy. After thermal cycling, crowns were longitudinally sectioned and microleakage scores at tooth-cement interface were obtained and recorded at ×100 magnification. Margin fit parameters were compared with the one-way ANOVA test and microleakage scores with Kruskal-Wallis and Dunn's tests (alpha=0.05). Correlation between margin fit and microleakage was analyzed with the Spearman's test (alpha=0.05). Seating discrepancy and marginal gap values ranged from 81.82 µm to 137.22 µm (p=0.117), and from 75.42 µm to 78.49 µm (p=0.940), respectively. Marginal microleakage scores were ZP=3.02, RMGI=0.35 and RC=0.12 (p<0.001), with no differences between RMGI and RC scores. The correlation coefficient values ranged from -0.27 to 0.30 (p>0.05). Conclusion: Margin fit parameters and microleakage showed no strong correlations; cast crowns cemented with RMGI and RC had lower microleakage scores than ZP cement.

Correlation between metal-ceramic bond strength and coefficient of linear thermal expansion difference

The purpose of this study was to evaluate the metal-ceramic bond strength (MCBS) of 6 metal-ceramic pairs (2 Ni-Cr alloys and 1 Pd-Ag alloy with 2 dental ceramics) and correlate the MCBS values with the differences between the coefficients of linear thermal expansion (CTEs) of the metals and ceramics. Verabond (VB) Ni-Cr-Be alloy, Verabond II (VB2), Ni-Cr alloy, Pors-on 4 (P), Pd-Ag alloy, and IPS (I) and Duceram (D) ceramics were used for the MCBS test and dilatometric test. Forty-eight ceramic rings were built around metallic rods (3.0 mm in diameter and 70.0 mm in length) made from the evaluated alloys. The rods were subsequently embedded in gypsum cast in order to perform a tensile load test, which enabled calculating the CMBS. Five specimens (2.0 mm in diameter and 12.0 mm in length) of each material were made for the dilatometric test. The chromel-alumel thermocouple required for the test was welded into the metal test specimens and inserted into the ceramics. ANOVA and Tukey's test revealed significant differences (p=0.01) for the MCBS test results (MPa), with PI showing higher MCBS (67.72) than the other pairs, which did not present any significant differences. The CTE (10-6 oC-1) differences were: VBI (0.54), VBD (1.33), VB2I (-0.14), VB2D (0.63), PI (1.84) and PD (2.62). Pearson's correlation test (r=0.17) was performed to evaluate of correlation between MCBS and CTE differences. Within the limitations of this study and based on the obtained results, there was no correlation between MCBS and CTE differences for the evaluated metal-ceramic pairs.

Previsões climáticas sazonais sobre o Brasil: avaliação do RegCM3 aninhado no modelo global CPTEC/COLA

Este trabalho avalia o desempenho de previsões sazonais do modelo climático regional RegCM3, aninhado ao modelo global CPTEC/COLA. As previsões com o RegCM3 utilizaram 60 km de resolução horizontal num domínio que inclui grande parte da América do Sul. As previsões do RegCM3 e CPTEC/COLA foram avaliadas utilizando as análises de chuva e temperatura do ar do Climate Prediction Center (CPC) e National Centers for Enviromental Prediction (NCEP), respectivamente. Entre maio de 2005 e julho de 2007, 27 previsões sazonais de chuva e temperatura do ar (exceto a temperatura do CPTEC/COLA, que possui 26 previsões) foram avaliadas em três regiões do Brasil: Nordeste (NDE), Sudeste (SDE) e Sul (SUL). As previsões do RegCM3 também foram comparadas com as climatologias das análises. De acordo com os índices estatísticos (bias, coeficiente de correlação, raiz quadrada do erro médio quadrático e coeficiente de eficiência), nas três regiões (NDE, SDE e SUL) a chuva sazonal prevista pelo RegCM3 é mais próxima da observada do que a prevista pelo CPTEC/COLA. Além disto, o RegCM3 também é melhor previsor da chuva sazonal do que da média das observações nas três regiões. Para temperatura, as previsões do RegCM3 são superiores às do CPTEC/COLA nas áreas NDE e SUL, enquanto o CPTEC/COLA é superior no SDE. Finalmente, as previsões de chuva e temperatura do RegCM3 são mais próximas das observações do que a climatologia observada. Estes resultados indicam o potencial de utilização do RegCM3 para previsão sazonal, que futuramente deverá ser explorado através de previsão por conjunto.

Allometric models for estimating the phytomass of a secondary Atlantic Forest area of southeastern Brazil

The purpose of this study was to develop and validate equations to estimate the aboveground phytomass of a 30 years old plot of Atlantic Forest. In two plots of 100 m², a total of 82 trees were cut down at ground level. For each tree, height and diameter were measured. Leaves and woody material were separated in order to determine their fresh weights in field conditions. Samples of each fraction were oven dried at 80 °C to constant weight to determine their dry weight. Tree data were divided into two random samples. One sample was used for the development of the regression equations, and the other for validation. The models were developed using single linear regression analysis, where the dependent variable was the dry mass, and the independent variables were height (h), diameter (d) and d²h. The validation was carried out using Pearson correlation coefficient, paired t-Student test and standard error of estimation. The best equations to estimate aboveground phytomass were: lnDW = -3.068+2.522lnd (r² = 0.91; s y/x = 0.67) and lnDW = -3.676+0.951ln d²h (r² = 0.94; s y/x = 0.56).

Correlation of meta 1 expression with culture stage, cell morphology and infectivity in Leishmania (Leishmania) amazonensis promastigotes

The parasitic protozoan Leishmania (Leishmania) amazonensis alternates between mammalian and insect hosts. In the insect host, the parasites proliferate as procyclic promastigotes andthen differentiate into metacyclic infective forms. The meta 1 gene is preferentially expressed during metacyclogenesis. Meta 1 expression profile determination along parasite growth curves revealed that the meta 1 mRNA level peaked at the early stationary phase then decreased to an intermediate level. No correlation was observed between meta 1 expression and infectivity. Conversely, infectivity correlated with the increase of apoptotic cells in the late stationary phase.

Genotype-phenotype correlation in Brazillian Rett syndrome patients

BACKGROUND: Rett syndrome (RS) is a severe neurodevelopmental X-linked dominant disorder caused by mutations in the MECP2 gene. PURPOSE: To search for point mutations on the MECP2 gene and to establish a correlation between the main point mutations found and the phenotype. METHOD: Clinical evaluation of 105 patients, following a standard protocol. Detection of point mutations on the MECP2 gene was performed on peripheral blood DNA by sequencing the coding region of the gene. RESULTS: Classical RS was seen in 68% of the patients. Pathogenic point mutations were found in 64.1% of all patients and in 70.42% of those with the classical phenotype. Four new sequence variations were found, and their nature suggests patogenicity. Genotype-phenotype correlations were performed. CONCLUSION: Detailed clinical descriptions and identification of the underlying genetic alterations of this Brazilian RS population add to our knowledge of genotype/phenotype correlations, guiding the implementation of mutation searching programs.

Calibration of the dietary data obtained from the Brazilian center of the Natural History of HPV Infection in Men study: the HIM Study

The objective of this study was to estimate the regressions calibration for the dietary data that were measured using the quantitative food frequency questionnaire (QFFQ) in the Natural History of HPV Infection in Men: the HIM Study in Brazil. A sample of 98 individuals from the HIM study answered one QFFQ and three 24-hour recalls (24HR) at interviews. The calibration was performed using linear regression analysis in which the 24HR was the dependent variable and the QFFQ was the independent variable. Age, body mass index, physical activity, income and schooling were used as adjustment variables in the models. The geometric means between the 24HR and the calibration-corrected QFFQ were statistically equal. The dispersion graphs between the instruments demonstrate increased correlation after making the correction, although there is greater dispersion of the points with worse explanatory power of the models. Identification of the regressions calibration for the dietary data of the HIM study will make it possible to estimate the effect of the diet on HPV infection, corrected for the measurement error of the QFFQ.

EMJH medium with 5-fluorouracil and nalidixic acid associated with serial dilution technique used to recover Leptospira spp from experimentally contaminated bovine semen

Bovine semen experimentally contaminated with Leptospira santarosai serovar Guaricura was submitted to the modified EMJH medium with 5-fluorouracil (300mg/L) and nalidixic acid (20mg/L), named as "selective medium" and using the serial dilution technique, in order to evaluate the percentage of recovery of the added microorganism. The selective EMJH medium was found with higher percentage of recovery of leptospiras and minor losses of samples due to contamination with opportunistic microorganisms than the non-selective EMJH medium: 151/376 (40.0%) of positive growth; and 38/376 (10.0%) contamination and 58/376 (15%) and 129/376 (34.0%), respectively. These results were statistically significant (p<0. 0001; Fisher). Differences were found when the frequencies of positive leptospires recovery have been compared in the serial dilution technique (10-1 to 10-4) between the selective and non-selective media at different dilution factors. At 1/10th dilution the percentages found were (0%, 0/80) and (38%, 30/80), at 1/100th dilution, (3%, 2/80) and (49%, 39/80) and at 1/1,000th dilution, (25%, 20/80) and (50%, 40/80), respectively. The percentage of recovery of leptospires was found to be directly proportional to the dilution used. The methodology of the serial dilution technique (setting at least three dilutions) and the use of selective EMJH medium have been found to be efficient for the isolation of leptospires from the bovine semen samples.

Calibração dos dados dietéticos obtidos no centro brasileiro do estudo Natural History of HPV Infection in Men: o Estudo HIM

O objetivo foi estimar as regressões de calibração dos dados dietéticos mensurados pelo questionário quantitativo de freqüência alimentar (QQFA) utilizado no Natural History of HPV Infection in Men: o Estudo HIM. Uma amostra de 98 indivíduos do estudo HIM respondeu, por meio de entrevista, a um QQFA e três recordatórios de 24 horas (R24h). A calibração foi feita por meio de análise de regressão linear, tendo os R24h como variável dependente e o QQFA como variável independente. Idade, índice de massa corporal, atividade física, renda e escolaridade foram utilizadas como variáveis de ajuste nos modelos. As médias geométricas dos R24h e do QQFA corrigido pela calibração são estatisticamente iguais. Os gráficos de dispersão entre os instrumentos demonstraram aumento da correlação após a correção dos dados, porém observa-se maior dispersão dos pontos de acordo com a piora do poder explicativo dos modelos. A identificação das regressões de calibração dos dados dietéticos do estudo HIM permitirá a estimativa do efeito da dieta sobre a infecção por HPV, corrigida pelo erro de medida do QQFA

Anti-oxLDL autoantibodies and their correlation with lipid profile and nutritional status in adolescents

OBJETIVO: Avaliar se o conteúdo de auto-anticorpos anti-LDL oxidada (anti-LDLox) no plasma de adolescentes correlaciona-se com suas medidas antropométricas e com o perfil lipídico. MÉTODOS: O estudo incluiu 150 adolescentes com idade entre 10 e 15 anos, recrutados do ambulatório de obesidade da Universidade Federal de São Paulo (SP) e de escolas públicas de Piracicaba (SP). Foram avaliadas medidas antropométricas, como índice de massa corporal, circunferência de cintura e do braço, classificando os adolescentes em eutrófico, sobrepeso e obeso. Para as análises bioquímicas, foi realizado o perfil lipídico através de métodos enzimáticos colorimétricos, e para detecção do conteúdo de auto-anticorpos anti-LDLox, utilizou-se o método de ELISA. RESULTADOS: Segundo análises das variáveis antropométricas, o grupo obeso apresentou perfil alterado em relação aos grupos eutrófico e sobrepeso (p < 0,01), indicando risco cardiovascular. Quando o perfil lipídico foi avaliado, observaram-se diferenças estatisticamente significativas para as concentrações de colesterol total (p = 0,011), HDL-colesterol (p = 0,001) e LDL-colesterol (p < 0,042) nos grupos eutrófico e obeso. Para as análises de auto-anticorpos anti-LDLox plasmática, os grupos sobrepeso (p = 0,012) e obeso (p < 0,001) apresentaram valores superiores ao grupo eutrófico. Também houve correlações entre os auto-anticorpos anti-LDLox e variáveis antropométricas. CONCLUSÃO: A presença de auto-anticorpos anti-LDLox em adolescentes e as alterações metabólicas no perfil lipídico variaram de modo proporcional com parâmetros antropométricos, o que torna o conteúdo de anti-LDLox um potencial indicador bioquímico de risco para síndrome metabólica

Ventilation behavior in trained and untrained men during incremental test: evidence of one metabolic transition point

This study aimed to describe and compare the ventilation behavior during an incremental test utilizing three mathematical models and to compare the feature of ventilation curve fitted by the best mathematical model between aerobically trained (TR) and untrained ( UT) men. Thirty five subjects underwent a treadmill test with 1 km.h(-1) increases every minute until exhaustion. Ventilation averages of 20 seconds were plotted against time and fitted by: bi-segmental regression model (2SRM); three-segmental regression model (3SRM); and growth exponential model (GEM). Residual sum of squares (RSS) and mean square error (MSE) were calculated for each model. The correlations between peak VO2 (VO2PEAK), peak speed (Speed(PEAK)), ventilatory threshold identified by the best model (VT2SRM) and the first derivative calculated for workloads below (moderate intensity) and above (heavy intensity) VT2SRM were calculated. The RSS and MSE for GEM were significantly higher (p < 0.01) than for 2SRM and 3SRM in pooled data and in UT, but no significant difference was observed among the mathematical models in TR. In the pooled data, the first derivative of moderate intensities showed significant negative correlations with VT2SRM (r = -0.58; p < 0.01) and Speed(PEAK) (r = -0.46; p < 0.05) while the first derivative of heavy intensities showed significant negative correlation with VT2SRM (r = -0.43; p < 0.05). In UT group the first derivative of moderate intensities showed significant negative correlations with VT2SRM (r = -0.65; p < 0.05) and Speed(PEAK) (r = -0.61; p < 0.05), while the first derivative of heavy intensities showed significant negative correlation with VT2SRM (r= -0.73; p < 0.01), Speed(PEAK) (r = -0.73; p < 0.01) and VO2PEAK (r = -0.61; p < 0.05) in TR group. The ventilation behavior during incremental treadmill test tends to show only one threshold. UT subjects showed a slower ventilation increase during moderate intensities while TR subjects showed a slower ventilation increase during heavy intensities.

Topochemical distribution of lignin and hydroxycinnamic acids in sugar-cane cell walls and its correlation with the enzymatic hydrolysis of polysaccharides

Background: Lignin and hemicelluloses are the major components limiting enzyme infiltration into cell walls. Determination of the topochemical distribution of lignin and aromatics in sugar cane might provide important data on the recalcitrance of specific cells. We used cellular ultraviolet (UV) microspectrophotometry (UMSP) to topochemically detect lignin and hydroxycinnamic acids in individual fiber, vessel and parenchyma cell walls of untreated and chlorite-treated sugar cane. Internodes, presenting typical vascular bundles and sucrose-storing parenchyma cells, were divided into rind and pith fractions. Results: Vascular bundles were more abundant in the rind, whereas parenchyma cells predominated in the pith region. UV measurements of untreated fiber cell walls gave absorbance spectra typical of grass lignin, with a band at 278 nm and a pronounced shoulder at 315 nm, assigned to the presence of hydroxycinnamic acids linked to lignin and/or to arabino-methylglucurono-xylans. The cell walls of vessels had the highest level of lignification, followed by those of fibers and parenchyma. Pith parenchyma cell walls were characterized by very low absorbance values at 278 nm; however, a distinct peak at 315 nm indicated that pith parenchyma cells are not extensively lignified, but contain significant amounts of hydroxycinnamic acids. Cellular UV image profiles scanned with an absorbance intensity maximum of 278 nm identified the pattern of lignin distribution in the individual cell walls, with the highest concentration occurring in the middle lamella and cell corners. Chlorite treatment caused a rapid removal of hydroxycinnamic acids from parenchyma cell walls, whereas the thicker fiber cell walls were delignified only after a long treatment duration (4 hours). Untreated pith samples were promptly hydrolyzed by cellulases, reaching 63% of cellulose conversion after 72 hours of hydrolysis, whereas untreated rind samples achieved only 20% hydrolyzation. Conclusion: The low recalcitrance of pith cells correlated with the low UV-absorbance values seen in parenchyma cells. Chlorite treatment of pith cells did not enhance cellulose conversion. By contrast, application of the same treatment to rind cells led to significant removal of hydroxycinnamic acids and lignin, resulting in marked enhancement of cellulose conversion by cellulases.

Disequilibrium Coefficient: A Bayesian Perspective

Hardy-Weinberg Equilibrium (HWE) is an important genetic property that populations should have whenever they are not observing adverse situations as complete lack of panmixia, excess of mutations, excess of selection pressure, etc. HWE for decades has been evaluated; both frequentist and Bayesian methods are in use today. While historically the HWE formula was developed to examine the transmission of alleles in a population from one generation to the next, use of HWE concepts has expanded in human diseases studies to detect genotyping error and disease susceptibility (association); Ryckman and Williams (2008). Most analyses focus on trying to answer the question of whether a population is in HWE. They do not try to quantify how far from the equilibrium the population is. In this paper, we propose the use of a simple disequilibrium coefficient to a locus with two alleles. Based on the posterior density of this disequilibrium coefficient, we show how one can conduct a Bayesian analysis to verify how far from HWE a population is. There are other coefficients introduced in the literature and the advantage of the one introduced in this paper is the fact that, just like the standard correlation coefficients, its range is bounded and it is symmetric around zero (equilibrium) when comparing the positive and the negative values. To test the hypothesis of equilibrium, we use a simple Bayesian significance test, the Full Bayesian Significance Test (FBST); see Pereira, Stern andWechsler (2008) for a complete review. The disequilibrium coefficient proposed provides an easy and efficient way to make the analyses, especially if one uses Bayesian statistics. A routine in R programs (R Development Core Team, 2009) that implements the calculations is provided for the readers.