Identification of differentially expressed genes in high-density oligonucleotide arrays accounting for the quantification limits of the technology

In DNA microarray analysis, there is often interest in isolating a few genes that best discriminate between tissue types. This is especially important in cancer, where different clinicopathologic groups are known to vary in their outcomes and response to therapy. The identification of a small subset of gene expression patterns distinctive for tumor subtypes can help design treatment strategies and improve diagnosis. Toward this goal, we propose a methodology for the analysis of high-density oligonucleotide arrays. The gene expression measures are modeled as censored data to account for the quantification limits of the technology, and two gene selection criteria based on contrasts from an analysis of covariance (ANCOVA) model are presented. The model is formulated in a hierarchical Bayesian framework, which in addition to making the fit of the model straightforward and computationally efficient, allows us to borrow strength across genes. The elicitation of hierarchical priors, as well as issues related to parameter identifiability and posterior propriety, are discussed in detail. We examine the performance of our proposed method on simulated data, then present a detailed case study of an endometrial cancer dataset.     

The role of sulphidogenesis in anaerobic treatment phase of tannery wastewater treatment in advanced integrated wastewater pond system

An outdoor experiment was conducted to study the competitionbetween Sulphate Reducing Bacteria (SRB) and Methanogenic Archaea (MA) in anaerobictreatment phase of tannery wastewater treatment in pilot-scale Advanced FacultativePond (AFP). The relative electron flow towards sulphate reduction was higher (59–83%) than towardsmethanogenesis (17–41%), although the COD recovery within thereactor varied between 15 and 90%. The results also demonstrated that the flow of electrons towards SRBincreased with increase of the sulphate concentration and decrease of the COD : SO₄ ⁼ ratio.     

Helicobacter pylori-selective antibacterials based on inhibition of pyrimidine biosynthesis

We report the discovery of a class of pyrazole-based compounds that are potent inhibitors of the dihydroorotate dehydrogenase of Helicobacter pylori but that do not inhibit the cognate enzymes from Gram-positive bacteria or humans. In culture these compounds inhibit the growth of H. pylori selectively, showing no effect on other Gram-negative or Gram-positive bacteria or human cell lines. These compounds represent the first examples of H. pylori-specific antibacterial agents. Cellular activity within this structural class appears to be due to dihydroorotate dehydrogenase inhibition. Minor structural changes that abrogate in vitro inhibition of the enzyme likewise eliminate cellular activity. Furthermore, the minimum inhibitory concentrations of these compounds increase upon addition of orotate to the culture medium in a concentration-dependent manner, consistent with dihydroorotate dehydrogenase inhibition as the mechanism of cellular inhibition. The data presented here suggest that targeted inhibition of de novo pyrimidine biosynthesis may be a valuable mechanism for the development of antimicrobial agents selective for H. pylori.     

Genomic regions associated with chocolate spot (Botrytis fabae Sard.) resistance in faba bean (Vicia faba L.)

Molecular Breeding - Maize (Zea mays L.) is the most important food crop in the world, with significant acreage and production across the globe. However, it is affected by low temperatures...     

Isoniazid Prophylactic Therapy for the Prevention of Tuberculosis in HIV Infected Adults: A Systematic Review and Meta-Analysis of Randomized Trials

Background

Infection with Human Immunodeficiency virus (HIV) is an important risk factor for Tuberculosis (TB). Anti-Retroviral Therapy (ART) has improved the prognosis of HIV and reduced the risk of TB infected patients. Isoniazid Preventive Therapy (IPT) aims to reduce the development of active TB in patients with latent TB.

Objective

Systematically review and synthesize effect estimates of IPT for TB prevention in adult HIV patients. Secondary objectives were to assess the effect of IPT on HIV disease progression, all-cause mortality and adverse drug reaction (ADR).

Search Strategy

Electronic databases were searched to identify relevant articles in English available by September 11^th 2015.

Selection Criteria

Research articles comparing IPT to placebo or no treatment in HIV infected adults using randomized clinical trials.

Data Analysis

A qualitative review included study-level information on randomization and treatment allocation. Effect estimates were pooled using random-effects models to account for between-study heterogeneity.

Main Results

This review assessed ten randomized clinical trials that assigned 7619 HIV patients to IPT or placebo. An overall 35% of TB risk reduction (RR = 0.65, 95% CI (0.51, 0.84)) was found in all participants, however, larger benefit of IPT was observed in Tuberculin Skin Test (TST) positive participants, with pooled relative risk reduction of 52% [RR = 0.48; 95% CI (0.29, 0.82)] and with a prediction interval ranging from 0.13 to 1.81. There was no statistically significant effect of IPT on TB occurrence in TST negative or unknown participants. IPT also reduced the risk of HIV disease progression in all participants (RR = 0.69; 95% CI (0.48, 0.99)) despite no benefits observed in TST strata. All-cause mortality was not affected by IPT although participants who had 12 months of IPT tend to have a reduced risk (RR = 0.65; 95% CI(0.47, 0.90)). IPT had an elevated, yet statistically non-significant, risk of adverse drug reaction [RR = 1.20; 95% CI (1.20, 1.71)]. Only a single study assessed the effect of IPT in combination with ART in preventing TB and occurrence of multi-drug resistant tuberculosis.

Conclusions

IPT use substantially contributes in preventing TB in persons with HIV in general and in TST positive individuals in particular. More evidence is needed to explain discrepancies in the protective effect of IPT in these individuals.     

The Impact of Trachomatous Trichiasis on Quality of Life: A Case Control Study

Background

Trachomatous trichiasis is thought to have a profound effect on quality of life (QoL), however, there is little research in this area. We measured vision and health-related QoL in a case-control study in Amhara Region, Ethiopia.

Methodology/Principal Findings

We recruited 1000 adult trichiasis cases and 200 trichiasis-free controls, matched to every fifth trichiasis case on age (+/- two years), sex and location. Vision-related quality of life (VRQoL) and health-related quality of life (HRQoL) were measured using the WHO/PBD-VF20 and WHOQOL-BREF questionnaires. Comparisons were made using linear regression adjusted for age, sex and socioeconomic status. Trichiasis cases had substantially lower VRQoL than controls on all subscales (overall eyesight, visual symptom, general functioning and psychosocial, p<0.0001), even in the sub-group with normal vision (p<0.0001). Lower VRQoL scores in cases were associated with longer trichiasis duration, central corneal opacity, visual impairment and poor contrast sensitivity. Trichiasis cases had lower HRQoL in all domains (Physical-health, Psychological, Social, Environment, p<0.0001), lower overall QoL (mean, 34.5 v 64.6; p<0.0001) and overall health satisfaction (mean, 38.2 v 71.7; p<0.0001). This association persisted in a sub-group analysis of cases and controls with normal vision. Not having a marriage partner (p<0.0001), visual impairment (p = 0.0068), daily labouring (p<0.0001), presence of other health problems (p = 0.0018) and low self-rated wealth (p<0.0001) were independently associated with lower overall QoL scores in cases. Among cases, trichiasis caused 596 (59%) to feel embarrassed, 913 (91.3%) to worry they may lose their remaining eyesight and 681 (68.1%) to have sleep disturbance.

Conclusions/Significance

Trachomatous trichiasis substantially reduces vision and health related QoL and is disabling, even without visual impairment. Prompt trichiasis intervention is needed both to prevent vision loss and to alleviate physical and psychological suffering, social exclusion and improve overall well-being. Implementation of the full SAFE strategy is needed to prevent the development of trachomatous trichiasis.     

LC‐MS/MS‐based serum proteomics for identification of candidate biomarkers for hepatocellular carcinoma

Associating changes in protein levels with the onset of cancer has been widely investigated to identify clinically relevant diagnostic biomarkers. In the present study, we analyzed sera from 205 patients recruited in the United States and Egypt for biomarker discovery using label‐free proteomic analysis by LC‐MS/MS. We performed untargeted proteomic analysis of sera to identify candidate proteins with statistically significant differences between hepatocellular carcinoma (HCC) and patients with liver cirrhosis. We further evaluated the significance of 101 proteins in sera from the same 205 patients through targeted quantitation by MRM on a triple quadrupole mass spectrometer. This led to the identification of 21 candidate protein biomarkers that were significantly altered in both the United States and Egyptian cohorts. Among the 21 candidates, ten were previously reported as HCC‐associated proteins (eight exhibiting consistent trends with our observation), whereas 11 are new candidates discovered by this study. Pathway analysis based on the significant proteins reveals upregulation of the complement and coagulation cascades pathway and downregulation of the antigen processing and presentation pathway in HCC cases versus patients with liver cirrhosis. The results of this study demonstrate the power of combining untargeted and targeted quantitation methods for a comprehensive serum proteomic analysis, to evaluate changes in protein levels and discover novel diagnostic biomarkers. All MS data have been deposited in the ProteomeXchange with identifier PXD001171 ( http://proteomecentral.proteomexchange.org/dataset/PXD001171 ).     

Power and type I error rate of false discovery rate approaches in genome-wide association studies

In genome-wide genetic studies with a large number of markers, balancing the type I error rate and power is a challenging issue. Recently proposed false discovery rate (FDR) approaches are promising solutions to this problem. Using the 100 simulated datasets of a genome-wide marker map spaced about 3 cM and phenotypes from the Genetic Analysis Workshop 14, we studied the type I error rate and power of Storey's FDR approach, and compared it to the traditional Bonferroni procedure. We confirmed that Storey's FDR approach had a strong control of FDR. We found that Storey's FDR approach only provided weak control of family-wise error rate (FWER). For these simulated datasets, Storey's FDR approach only had slightly higher power than the Bonferroni procedure. In conclusion, Storey's FDR approach is more powerful than the Bonferroni procedure if strong control of FDR or weak control of FWER is desired. Storey's FDR approach has little power advantage over the Bonferroni procedure if there is low linkage disequilibrium among the markers. Further evaluation of the type I error rate and power of the FDR approaches for higher linkage disequilibrium and for haplotype analyses is warranted.     

Wavelet thresholding with bayesian false discovery rate control

The false discovery rate (FDR) procedure has become a popular method for handling multiplicity in high-dimensional data. The definition of FDR has a natural Bayesian interpretation; it is the expected proportion of null hypotheses mistakenly rejected given a measure of evidence for their truth. In this article, we propose controlling the positive FDR using a Bayesian approach where the rejection rule is based on the posterior probabilities of the null hypotheses. Correspondence between Bayesian and frequentist measures of evidence in hypothesis testing has been studied in several contexts. Here we extend the comparison to multiple testing with control of the FDR and illustrate the procedure with an application to wavelet thresholding. The problem consists of recovering signal from noisy measurements. This involves extracting wavelet coefficients that result from true signal and can be formulated as a multiple hypotheses-testing problem. We use simulated examples to compare the performance of our approach to the Benjamini and Hochberg (1995, Journal of the Royal Statistical Society, Series B57, 289-300) procedure. We also illustrate the method with nuclear magnetic resonance spectral data from human brain.     

Attitudes of local people towards the mountain nyala (Tragelaphus buxtoni) in Munessa,Ethiopia

Due to their direct dependence on wildlife products for subsistent use, people living in poverty are often viewed as being in conflict with wildlife conservation. We studied the attitudes of local people towards mountain nyala (Tragelaphus buxtoni) in Munessa, Ethiopia. A household survey (n = 214) was used to examine the socio‐economic characteristics and beliefs of local people from three peasant associations and one village. Generally, the study revealed that local people had positive attitudes towards mountain nyala, its conservation and population increase, which is consistent with our predictions. For example, a greater percentage of the respondents had positive (62.5%) rather than negative (37.5%) attitudes towards mountain nyala and its conservation. Moreover, the larger proportion of the respondents had positive (66.67%) rather than negative (33.3%) attitudes towards an increase in mountain nyala population. However, compared to socio‐economic characteristics, beliefs towards mountain nyala were more powerful and consistent predictor of attitudes and explained much of the variances of the two groups of the dependent variables. Thus, informing local communities about the value of mountain nyala (e.g. recreational and economic) through conservation education, advocating the need for sustainable utilization and introducing an economic benefit sharing may improve positive attitude and increase participation of local people in conservation and management of the mountain nyala population in Munessa.