Comparison of multiplex ligation-dependent probe amplification and real-time PCR accuracy for gene copy number quantification using the beta-defensin locus

The reliable quantification of gene copy number variations is a precondition for future investigations regarding their functional relevance. To date, there is no generally accepted gold standard method for copy number quantification, and methods in current use have given inconsistent results in selected cohorts. In this study, we compare two methods for copy number quantification. beta-defensin gene copy numbers were determined in parallel in 80 genomic DNA samples by real-time PCR and multiplex ligation-dependent probe amplification (MLPA). The pyrosequencing-based paralog ratio test (PPRT) was used as a standard of comparison in 79 out of 80 samples. Realtime PCR and MPLA results confirmed concordant DEFB4, DEFB103A, and DEFB104A copy numbers within samples. These two methods showed identical results in 32 out of 80 samples; 29 of these 32 samples comprised four or fewer copies. The coefficient of variation of MLPA is lower compared with PCR. In addition, the consistency between MLPA and PPRT is higher than either PCR/MLPA or PCR/PPRT consistency. In summary, these results suggest that MLPA is superior to real-time PCR in beta-defensin copy number quantification.

Copy number variation of the Beta-defensin genes in europeans: no supporting evidence for association with lung function, chronic obstructive pulmonary disease or asthma

Lung function measures are heritable, predict mortality and are relevant in diagnosis of chronic obstructive pulmonary disease (COPD). COPD and asthma are diseases of the airways with major public health impacts and each have a heritable component. Genome-wide association studies of SNPs have revealed novel genetic associations with both diseases but only account for a small proportion of the heritability. Complex copy number variation may account for some of the missing heritability. A well-characterised genomic region of complex copy number variation contains beta-defensin genes (DEFB103, DEFB104 and DEFB4), which have a role in the innate immune response. Previous studies have implicated these and related genes as being associated with asthma or COPD. We hypothesised that copy number variation of these genes may play a role in lung function in the general population and in COPD and asthma risk. We undertook copy number typing of this locus in 1149 adult and 689 children using a paralogue ratio test and investigated association with COPD, asthma and lung function. Replication of findings was assessed in a larger independent sample of COPD cases and smoking controls. We found evidence for an association of beta-defensin copy number with COPD in the adult cohort (OR = 1.4, 95%CI:1.02-1.92, P = 0.039) but this finding, and findings from a previous study, were not replicated in a larger follow-up sample(OR = 0.89, 95%CI:0.72-1.07, P = 0.217). No robust evidence of association with asthma in children was observed. We found no evidence for association between beta-defensin copy number and lung function in the general populations. Our findings suggest that previous reports of association of beta-defensin copy number with COPD should be viewed with caution. Suboptimal measurement of copy number can lead to spurious associations. Further beta-defensin copy number measurement in larger sample sizes of COPD cases and children with asthma are needed.

Multicentre validation of the Geneva Risk Score for hospitalised medical patients at risk of venous thromboembolism. Explicit ASsessment of Thromboembolic RIsk and Prophylaxis for Medical PATients in SwitzErland (ESTIMATE).

There is a need to validate risk assessment tools for hospitalised medical patients at risk of venous thromboembolism (VTE). We investigated whether a predefined cut-off of the Geneva Risk Score, as compared to the Padua Prediction Score, accurately distinguishes low-risk from high-risk patients regardless of the use of thromboprophylaxis. In the multicentre, prospective Explicit ASsessment of Thromboembolic RIsk and Prophylaxis for Medical PATients in SwitzErland (ESTIMATE) cohort study, 1,478 hospitalised medical patients were enrolled of whom 637 (43%) did not receive thromboprophylaxis. The primary endpoint was symptomatic VTE or VTE-related death at 90 days. The study is registered at ClinicalTrials.gov, number NCT01277536. According to the Geneva Risk Score, the cumulative rate of the primary endpoint was 3.2% (95% confidence interval [CI] 2.2-4.6%) in 962 high-risk vs 0.6% (95% CI 0.2-1.9%) in 516 low-risk patients (p=0.002); among patients without prophylaxis, this rate was 3.5% vs 0.8% (p=0.029), respectively. In comparison, the Padua Prediction Score yielded a cumulative rate of the primary endpoint of 3.5% (95% CI 2.3-5.3%) in 714 high-risk vs 1.1% (95% CI 0.6-2.3%) in 764 low-risk patients (p=0.002); among patients without prophylaxis, this rate was 3.2% vs 1.5% (p=0.130), respectively. Negative likelihood ratio was 0.28 (95% CI 0.10-0.83) for the Geneva Risk Score and 0.51 (95% CI 0.28-0.93) for the Padua Prediction Score. In conclusion, among hospitalised medical patients, the Geneva Risk Score predicted VTE and VTE-related mortality and compared favourably with the Padua Prediction Score, particularly for its accuracy to identify low-risk patients who do not require thromboprophylaxis.

Cluster of Bacteria Associated with Peri-Implantitis.

BACKGROUND Information on the microbiota in peri-implantitis is limited. We hypothesized that neither gender nor a history of periodontitis/smoking or the microbiota at implants differ by implant status. MATERIALS AND METHODS Baseline microbiological samples collected at one implant in each of 166 participants with peri-implantitis and from 47 individuals with a healthy implant were collected and analyzed by DNA-DNA checkerboard hybridization (78 species). Clinical and radiographic data defined implant status. RESULTS Nineteen bacterial species were found at higher counts from implants with peri-implantitis including Aggregatibacter actinomycetemcomitans, Campylobacter gracilis, Campylobacter rectus, Campylobacter showae, Helicobacter pylori, Haemophilus influenzae, Porphyromonas gingivalis, Staphylococcus aureus, Staphylococcus anaerobius, Streptococcus intermedius, Streptococcus mitis, Tannerella forsythia, Treponema denticola, and Treponema socranskii (p < .001). Receiver operating characteristic curve analysis identified T. forsythia, P. gingivalis, T. socranskii, Staph. aureus, Staph. anaerobius, Strep. intermedius, and Strep. mitis in peri-implantitis comprising 30% of the total microbiota. When adjusted for gender (not significant [NS]), smoking status (NS), older age (p = .003), periodontitis history (p < .01), and T. forsythia (likelihood ratio 3.6, 95% confidence interval 1.4, 9.1, p = .007) were associated with peri-implantitis. CONCLUSION A cluster of bacteria including T. forsythia and Staph. aureus are associated with peri-implantitis.

Using Bayes' rule to define the value of evidence from syndromic surveillance

In this work we propose the adoption of a statistical framework used in the evaluation of forensic evidence as a tool for evaluating and presenting circumstantial "evidence" of a disease outbreak from syndromic surveillance. The basic idea is to exploit the predicted distributions of reported cases to calculate the ratio of the likelihood of observing n cases given an ongoing outbreak over the likelihood of observing n cases given no outbreak. The likelihood ratio defines the Value of Evidence (V). Using Bayes' rule, the prior odds for an ongoing outbreak are multiplied by V to obtain the posterior odds. This approach was applied to time series on the number of horses showing clinical respiratory symptoms or neurological symptoms. The separation between prior beliefs about the probability of an outbreak and the strength of evidence from syndromic surveillance offers a transparent reasoning process suitable for supporting decision makers. The value of evidence can be translated into a verbal statement, as often done in forensics or used for the production of risk maps. Furthermore, a Bayesian approach offers seamless integration of data from syndromic surveillance with results from predictive modeling and with information from other sources such as disease introduction risk assessments.

Tracking of plasma lipids and lipoproteins, within-person and year-to-year variability in plasma cholesterol levels among participants from age 8 to 18 in Project HeartBeat!

Coronary heart disease remains the leading cause of death in the United States and increased blood cholesterol level has been found to be a major risk factor with roots in childhood. Tracking of cholesterol, i.e., the tendency to maintain a particular cholesterol level relative to the rest of the population, and variability in blood lipid levels with increase in age have implications for cholesterol screening and assessment of lipid levels in children for possible prevention of further rise to prevent adulthood heart disease. In this study the pattern of change in plasma lipids, over time, and their tracking were investigated. Also, within-person variance and retest reliability defined as the square root of within-person variance for plasma total cholesterol, HDL-cholesterol, LDL-cholesterol, and triglycerides and their relation to age, sex and body mass index among participants from age 8 to 18 years were investigated. ^ In Project HeartBeat!, 678 healthy children aged 8, 11 and 14 years at baseline were enrolled and examined at 4-monthly intervals for up to 4 years. We examined the relationship between repeated observations by Pearson's correlations. Age- and sex-specific quintiles were calculated and the probability of participants to remain in the uppermost quintile of their respective distribution was evaluated with life table methods. Plasma total cholesterol, HDL-C and LDL-C at baseline were strongly and significantly correlated with measurements at subsequent visits across the sex and age groups. Plasma triglyceride at baseline was also significantly correlated with subsequent measurements but less strongly than was the case for other plasma lipids. The probability to remain in the upper quintile was also high (60 to 70%) for plasma total cholesterol, HDL-C and LDL-C. ^ We used a mixed longitudinal, or synthetic cohort design with continuous observations from age 8 to 18 years to estimate within person variance of plasma total cholesterol, HDL-C, LDL-C and triglycerides. A total of 5809 measurements were available for both cholesterol and triglycerides. A multilevel linear model was used. Within-person variance among repeated measures over up to four years of follow-up was estimated for total cholesterol, HDL-C, LDL-C and triglycerides separately. The relationship of within-person and inter-individual variance with age, sex, and body mass index was evaluated. Likelihood ratio tests were conducted by calculating the deviation of −2log (likelihood) within the basic model and alternative models. The square root of within-person variance provided the retest reliability (within person standard deviation) for plasma total cholesterol, HDL-C, LDL-C and triglycerides. We found 13.6 percent retest reliability for plasma cholesterol, 6.1 percent for HDL-cholesterol, 11.9 percent for LDL-cholesterol and 32.4 percent for triglycerides. Retest reliability of plasma lipids was significantly related with age and body mass index. It increased with increase in body mass index and age. These findings have implications for screening guidelines, as participants in the uppermost quintile tended to maintain their status in each of the age groups during a four-year follow-up. The magnitude of within-person variability of plasma lipids influences the ability to classify children into risk categories recommended by the National Cholesterol Education Program. ^

Diabetes genes and risk of prostate cancer in the Atherosclerosis Risk in Communities study

Prostate cancer (PrCa) is a leading cause of morbidity and mortality, yet the etiology remains uncertain. Meta-analyses show that PrCa risk is reduced by 16% in men with type 2 diabetes (T2D), but the mechanism is unknown. Recent genome-wide association studies and meta-analyses have found single nucleotide polymorphisms (SNPs) that consistently predict T2D risk. We evaluated associations of incident PrCa with 14 T2D SNPs in the Atherosclerosis Risk in Communities (ARIC) study. From 1987-2000, there were 397 incident PrCa cases ascertained from state or local cancer registries among 6,642 men (1,560 blacks and 5,082 whites) aged 45-64 years at baseline. Genotypes were determined by TaqMan assay. Cox proportional hazards models were used to assess the association between PrCa and increasing number of T2D risk-raising alleles for individual SNPs and for genetic risk scores (GRS) comprised of the number of T2D risk-raising alleles across SNPs. Two-way gene-gene interactions were evaluated with likelihood ratio tests. Using additive genetic models, the T2D risk-raising allele was associated with significantly reduced risk of PrCa for IGF2BP2 rs4402960 (hazard ratio [HR]=0.79; P=0.07 among blacks only), SLC2A2 rs5400 (race-adjusted HR=0.85; P=0.05) and UCP2 rs660339 (race-adjusted HR=0.84; P=0.02), but significantly increased risk of PrCa for CAPN10 rs3792267 (race-adjusted HR=1.20; P=0.05). No other SNPs were associated with PrCa using an additive genetic model. However, at least one copy of the T2D risk-raising allele for TCF7L2 rs7903146 was associated with reduced PrCa risk using a dominant genetic model (race-adjusted HR=0.79; P=0.03). These results imply that the T2D-PrCa association may be partly due to shared genetic variation, but these results should be verified since multiple tests were performed. When the combined, additive effects of these SNPs were tested using a GRS, there was nearly a 10% reduction in risk of PrCa per T2D risk-raising allele (race-adjusted HR=0.92; P=0.02). SNPs in IGF2BP2, KCNJ11 and SLC2A2 were also involved in multiple synergistic gene-gene interactions on a multiplicative scale. In conclusion, it appears that the T2D-PrCa association may be due, in part, to common genetic variation. Further knowledge of T2D gene-PrCa mechanisms may improve understanding of PrCa etiology and may inform PrCa prevention and treatment.^

BEST SUBSET SELECTION FOR CATEGORICAL DATA

When choosing among models to describe categorical data, the necessity to consider interactions makes selection more difficult. With just four variables, considering all interactions, there are 166 different hierarchical models and many more non-hierarchical models. Two procedures have been developed for categorical data which will produce the "best" subset or subsets of each model size where size refers to the number of effects in the model. Both procedures are patterned after the Leaps and Bounds approach used by Furnival and Wilson for continuous data and do not generally require fitting all models. For hierarchical models, likelihood ratio statistics (G('2)) are computed using iterative proportional fitting and "best" is determined by comparing, among models with the same number of effects, the Pr((chi)(,k)('2) (GREATERTHEQ) G(,ij)('2)) where k is the degrees of freedom for ith model of size j. To fit non-hierarchical as well as hierarchical models, a weighted least squares procedure has been developed.^ The procedures are applied to published occupational data relating to the occurrence of byssinosis. These results are compared to previously published analyses of the same data. Also, the procedures are applied to published data on symptoms in psychiatric patients and again compared to previously published analyses.^ These procedures will make categorical data analysis more accessible to researchers who are not statisticians. The procedures should also encourage more complex exploratory analyses of epidemiologic data and contribute to the development of new hypotheses for study. ^

Homogenization of Portuguese long-term temperature data series: Lisbon, Coimbra and Porto

Three long-term temperature data series measured in Portugal were studied to detect and correct non-climatic homogeneity breaks and are now available for future studies of climate variability. Series of monthly minimum (Tmin) and maximum (Tmax) temperatures measured in the three Portuguese meteorological stations of Lisbon (from 1856 to 2008), Coimbra (from 1865 to 2005) and Porto (from 1888 to 2001) were studied to detect and correct non-climatic homogeneity breaks. These series together with monthly series of average temperature (Taver) and temperature range (DTR) derived from them were tested in order to detect homogeneity breaks, using, firstly, metadata, secondly, a visual analysis and, thirdly, four widely used homogeneity tests: von Neumann ratio test, Buishand test, standard normal homogeneity test and Pettitt test. The homogeneity tests were used in absolute (using temperature series themselves) and relative (using sea-surface temperature anomalies series obtained from HadISST2 close to the Portuguese coast or already corrected temperature series as reference series) modes. We considered the Tmin, Tmax and DTR series as most informative for the detection of homogeneity breaks due to the fact that Tmin and Tmax could respond differently to changes in position of a thermometer or other changes in the instrument's environment; Taver series have been used, mainly, as control. The homogeneity tests show strong inhomogeneity of the original data series, which could have both internal climatic and non-climatic origins. Homogeneity breaks which have been identified by the last three mentioned homogeneity tests were compared with available metadata containing data, such as instrument changes, changes in station location and environment, observing procedures, etc. Significant homogeneity breaks (significance 95% or more) that coincide with known dates of instrumental changes have been corrected using standard procedures. It was also noted that some significant homogeneity breaks, which could not be connected to the known dates of any changes in the park of instruments or stations location and environment, could be caused by large volcanic eruptions. The corrected series were again tested for homogeneity: the corrected series were considered free of non-climatic breaks when the tests of most of monthly series showed no significant (significance 95% or more) homogeneity breaks that coincide with dates of known instrument changes. Corrected series are now available in the frame of ERA-CLIM FP7 project for future studies of climate variability.

Analysis of symptoms of rural workers exposed to pesticides

This cross-sectional study was conducted in southern Minas Gerais, in two counties: São Gonçalo do Sapucaí and Silvianópolis. Presented as objective to verify the important variables associated with the occurrence of symptoms of subacute intoxication related to pesticides exposure. A questionnaire was dedicated to a sample of 412 workers. An analysis of non-conditional logistic regression was applied gradually. The likelihood ratio method was used to define the significant variables in the final model. Of the analysed population, 59.2% reported symptoms typical of subacute intoxication. Of the respondents, 91.5% reported knowing the deleterious effects associated with exposure to pesticides. The adjusted model was found with the significant variables: being male that presented Prevalence Odds Ratio (POR) adjusted . PORof 0.54 (95% CI 0.36 to 0.81), already hospitalized for poisoning with pesticides, POR of 3.26 (95% CI 1.08 to 9.82), living in the rural area of residence., POR of 2.17 (95% CI 1.20 to 3.93) and type of employment relationship or temporary employment, POR of 2.32 (95% CI 1.08 to 4.95).

An empirical analysis on the efficiency of the microfinance investment market

This paper empirically analyzes the market efficiency of microfinance investment funds. For the empirical analysis, we use an index of the microfinance investment funds and apply two kinds of variance ratio tests to examine whether or not this index follows a random walk. We use the entire sample period from December 2003 to June 2010 as well as two sub-samples which divide the entire period before and after January 2007. The empirical evidence demonstrates that the index does not follow a random walk, suggesting that the market of the microfinance investment funds is not efficient. This result is not affected by changes in either empirical techniques or sample periods.

Language recognition using phonotactic-based shifted delta coefficients and multiple phone recognizers

A new language recognition technique based on the application of the philosophy of the Shifted Delta Coefficients (SDC) to phone log-likelihood ratio features (PLLR) is described. The new methodology allows the incorporation of long-span phonetic information at a frame-by-frame level while dealing with the temporal length of each phone unit. The proposed features are used to train an i-vector based system and tested on the Albayzin LRE 2012 dataset. The results show a relative improvement of 33.3% in Cavg in comparison with different state-of-the-art acoustic i-vector based systems. On the other hand, the integration of parallel phone ASR systems where each one is used to generate multiple PLLR coefficients which are stacked together and then projected into a reduced dimension are also presented. Finally, the paper shows how the incorporation of state information from the phone ASR contributes to provide additional improvements and how the fusion with the other acoustic and phonotactic systems provides an important improvement of 25.8% over the system presented during the competition.

Accelerated evolution as a consequence of transitions to mutualism

Differential rates of nucleotide substitutions among taxa are a common observation in molecular phylogenetic studies, yet links between rates of DNA evolution and traits or behaviors of organisms have proved elusive. Likelihood ratio testing is used here for the first time to evaluate specific hypotheses that account for the induction of shifts in rates of DNA evolution. A molecular phylogenetic investigation of mutualist (lichen-forming fungi and fungi associated with liverworts) and nonmutualist fungi revealed four independent transitions to mutualism. We demonstrate a highly significant association between mutualism and increased rates of nucleotide substitutions in nuclear ribosomal DNA, and we demonstrate that a transition to mutualism preceded the rate acceleration of nuclear ribosomal DNA in these lineages. Our results suggest that the increased rate of evolution after the adoption of a mutualist lifestyle is generalized across the genome of these mutualist fungi.

Use of umbilical artery Doppler velocimetry in the monitoring of pregnancy in women with pre-existing diabetes

Background: The usefulness of umbilical artery Doppler velocimetry for the monitoring of diabetic pregnancies is controversial. The aim of the present study was to assess whether umbilical artery Doppler velocity waveform analysis can predict adverse perinatal outcomes for pregnancies complicated by pre-existing diabetes mellitus. Methods: All diabetic pregnancies (type 1 and 2) delivered at Mater Mothers' Hospital, Queensland, between 1 January 1995 and 31 December 1999 were included. All pregnant diabetic women were monitored with umbilical artery Doppler velocimetry at 28, 32, 36, and 38 weeks' gestation. Adverse perinatal outcome was defined as pregnancies with one or more of the following: small-for-gestational age, Caesarean section for non-reassuring cardiotocography, fetal acidaemia at delivery, 1-min Apgar of 3 or less, 5-min Apgar of less than 7, hypoxic ischaemic encephalopathy or perinatal death. Abnormal umbilical artery Doppler velocimetry was defined as a pulsatility index of 95th centile or higher for gestation. Results: One hundred and four pregnancies in women with pre-existing diabetes had umbilical arterial Doppler studies carried out during the study period. Twenty-three pregnancies (22.1%) had an elevated pulsatility index. If the scans were carried out within 2 weeks of delivery, 71% of pregnancies with abnormal umbilical Doppler had adverse outcomes (P < 0.01; likelihood ratio, 4.2). However, the sensitivity was 35%; specificity was 94%; positive predictive value was 80%; and negative predictive value was 68%. Only 30% of women with adverse perinatal outcomes had abnormal umbilical arterial Doppler flow. Conclusion: Umbilical artery Doppler velocimetry is not a good predictor of adverse perinatal outcomes in diabetic pregnancies.

Genomewide Linkage Scan of 409 European-ancestry and African American Families with Schizophrenia: Suggestive Evidence of Linkage at 8p23.3-p21.2 and 11p13.1-q14.1 in the Combined Sample

We report the clinical characteristics of a schizophrenia sample of 409 pedigrees-263 of European ancestry ( EA) and 146 of African American ancestry ( AA)-together with the results of a genome scan ( with a simple tandem repeat polymorphism interval of 9 cM) and follow-up fine mapping. A family was required to have a proband with schizophrenia ( SZ) and one or more siblings of the proband with SZ or schizoaffective disorder. Linkage analyses included 403 independent full-sibling affected sibling pairs ( ASPs) ( 279 EA and 124 AA) and 100 all-possible half-sibling ASPs ( 15 EA and 85 AA). Nonparametric multipoint linkage analysis of all families detected two regions with suggestive evidence of linkage at 8p23.3-q12 and 11p11.2-q22.3 ( empirical Z likelihood-ratio score [ Z(lr)] threshold >= 2.65) and, in exploratory analyses, two other regions at 4p16.1-p15.32 in AA families and at 5p14.3-q11.2 in EA families. The most significant linkage peak was in chromosome 8p; its signal was mainly driven by the EA families. Z(lr) scores >= 2.0 in 8p were observed from 30.7 cM to 61.7 cM ( Center for Inherited Disease Research map locations). The maximum evidence in the full sample was a multipoint Z(lr) of 3.25 ( equivalent Kong-Cox LOD of 2.30) near D8S1771 ( at 52 cM); there appeared to be two peaks, both telomeric to neuregulin 1 ( NRG1). There is a paracentric inversion common in EA individuals within this region, the effect of which on the linkage evidence remains unknown in this and in other previously analyzed samples. Fine mapping of 8p did not significantly alter the significance or length of the peak. We also performed fine mapping of 4p16.3-p15.2, 5p15.2-q13.3, 10p15.3-p14, 10q25.3-q26.3, and 11p13-q23.3. The highest increase in Z(lr) scores was observed for 5p14.1-q12.1, where the maximum Z(lr) increased from 2.77 initially to 3.80 after fine mapping in the EA families.