Using the ratio of means as the effect size measure in combining results of microarray experiments

<p>Abstract</p> <p>Background</p> <p>Development of efficient analytic methodologies for combining microarray results is a major challenge in gene expression analysis. The widely used effect size models are thought to provide an efficient modeling framework for this purpose, where the measures of association for each study and each gene are combined, weighted by the standard errors. A significant disadvantage of this strategy is that the quality of different data sets may be highly variable, but this information is usually neglected during the integration. Moreover, it is widely known that the estimated standard deviations are probably unstable in the commonly used effect size measures (such as standardized mean difference) when sample sizes in each group are small.</p> <p>Results</p> <p>We propose a re-parameterization of the traditional mean difference based effect measure by using the log ratio of means as an effect size measure for each gene in each study. The estimated effect sizes for all studies were then combined under two modeling frameworks: the quality-unweighted random effects models and the quality-weighted random effects models. We defined the quality measure as a function of the detection p-value, which indicates whether a transcript is reliably detected or not on the Affymetrix gene chip. The new effect size measure is evaluated and compared under the quality-weighted and quality-unweighted data integration frameworks using simulated data sets, and also in several data sets of prostate cancer patients and controls. We focus on identifying differentially expressed biomarkers for prediction of cancer outcomes.</p> <p>Conclusion</p> <p>Our results show that the proposed effect size measure (log ratio of means) has better power to identify differentially expressed genes, and that the detected genes have better performance in predicting cancer outcomes than the commonly used effect size measure, the standardized mean difference (SMD), under both quality-weighted and quality-unweighted data integration frameworks. The new effect size measure and the quality-weighted microarray data integration framework provide efficient ways to combine microarray results.</p

Oral gram-negative rods and yeasts in hospitalized patients

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Exploration of the material property space for chemical looping air separation applied to carbon capture and storage

Oxy-fuel combustion is one route to large scale carbon capture and storage. Fuel is combusted in oxygen rather than air, allowing pure CO2 to be captured and sequestered. Currently, the required oxygen is produced via cryogenic air separation, which imposes a significant energy penalty. Chemical looping air separation (CLAS) is an alternative process for the production of oxygen, and relies on the repeated oxidation and reduction of solid oxygen carriers (typically metal oxides). The energy efficiency is governed by the thermodynamic properties of the oxygen carrier material, and how well the CLAS process can be heat-integrated with the process consuming oxygen. In this study, key thermodynamic properties have been identified and assessed using a steady state model of a CLAS-oxy-fuel power plant. It is demonstrated that energy penalties as low as 1.5 percentage points can be obtained for a narrow range of material properties. Based on density functional theory calculations, 14 oxygen carrier systems, which are novel or have received little attention, have been identified that could potentially achieve this minimal energy penalt

Identifying cis- and trans-acting single-nucleotide polymorphisms controlling lymphocyte gene expression in humans

Assuming multiple loci play a role in regulating the expression level of a single phenotype, we propose a new approach to identify cis- and trans-acting loci that regulate gene expression. Using the Problem 1 data set made available for Genetic Analysis Workshop 15 (GAW15), we identified many expression phenotypes that have significant evidence of association and linkage to one or more chromosomal regions. In particular, six of ten phenotypes that we found to be regulated by cis- and trans-acting loci were also mapped by a previous analysis of these data in which a total of 27 phenotypes were identified with expression levels regulated by cis-acting determinants. However, in general, the p-values associated with these regulators identified in our study were larger than in their studies, since we had also identified other factors regulating expression. In fact, we found that most of the gene expression phenotypes are influenced by at least one trans-acting locus. Our study also shows that much of the observable heritability in the phenotypes could be explained by simple single-nucleotide polymorphism associations; residual heritability was reduced and the remaining heritability may represent complex regulation systems with interactions or noise

Comparison of hyperpronation and supination‑flexion techniques in children presented to emergency department with painful pronation

Context: Radial head subluxation, also known as ‘pulled elbow’, ‘dislocated elbow’ or ‘nursemaid’s elbow’, is one of the most common upper extremity injuries in young children and a common reason to visit Emergency Department (ED).Aim: To compare supination of the wrist followed by flexion of the elbow (the traditional reduction technique) to hyperpronation of the wrist in the reduction of radial head subluxations (nursemaid’s elbow) maneuvers in children presented to ED with painful pronation and to determine which method is less painful by children.Settings and Design: This prospective randomize study involved a consecutive sampling of children between 1‑5 year old who were presented to the ED with painful pronation.Materials and Methods: The initial procedure was repeated if baseline functioning did not return 20 minutes after the initial reduction attempt. Failure of that technique 30 minutes after the initial reduction attempt resulted in a cross‑over to the alternate method of reduction.Statistical analysis used: Datas were analyzed using SPSS for Windows 16.0. Mean, standard deviation, independent samples t test, Chi‑square test, and paired t test were used in the assessment of pain scores before and after reduction.Results: When pain scores before and after reduction were compared between groups to determine which technique is less painful by children, no significant difference was found between groups.Conclusions: It was found that in the reduction of radial head subluxations, the hyperpronation technique is more effective in children who were presented to ED with painful pronation compared with supination‑flexion. However, there was no significant difference between these techniques in terms of pain.Key words: Child, emergency department, nursemaid’s elbow, pain, pulled elbo

Use of magnetic powder to effectively improve the performance of sequencing batch reactors (SBRs) in municipal wastewater treatment

© 2017 Elsevier Ltd This study aims to investigate the effect of adding magnetic powder in the sequencing batch reactor (SBR) on the reactor performance and microbial community. Results indicated that, the magnetic activated sludge sequencing batch reactor (MAS-SBR) had 7.76% and 4.76% higher ammonia nitrogen (NH4+-N) and chemical oxygen demand (COD) removal efficiencies than that of the conventional SBR (C-SBR). The MAS-SBR also achieved 6.86% sludge reduction compared with the C-SBR. High-throughput sequencing demonstrated that the dominant phyla of both SBRs (present as ≥1% of the sequence reads) were Protebacteria, Bacteroidetes, Chloroflexi, Saccharibacteria, Chlorobi, Firmicutes, Actinobactoria, Acidobacteria, Planctomycetes and unclassified_Bacteria. The relative abundance of Protebacteria and Bacteroidetes simultaneously declined whereas the other 8 phyla increased following the addition of magnetic powder. Adding magnetic powder in the SBR significantly affected the microbial diversity and richness of activated sludge, consequently affecting the reactor performance

Statins are underused in recent-onset Parkinson's disease with increased vascular risk : findings from the UK Tracking Parkinson's and Oxford Parkinson's Disease Centre (OPDC) discovery cohorts

Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.Peer reviewedPublisher PD

Effect of magnetic powder on membrane fouling mitigation and microbial community/composition in membrane bioreactors (MBRs) for municipal wastewater treatment

© 2017 Elsevier Ltd This study aims to investigate the usefulness of magnetic powder addition in membrane bioreactors (MBRs) for membrane fouling mitigation and its effect on microbial community and composition. The comparison between the two MBRs (one with magnetic powder (MAS-MBR) and one without magnetic powder (C-MBR)) was carried out to treat synthetic municipal wastewater. Results showed that bioflocculation and adsorption of magnetic powder contributed only minimally to membrane fouling mitigation while the slower fouling rate might be ascribed to magnetic bio-effect. The macromolecules (larger than 500 kDa and 300–500 kDa) of soluble microbial product from the MAS-MBR were reduced by 24.06% and 11.11%, respectively. High-throughput sequencing demonstrated the most abundant genera of biofilm sludge indicated lower abundance in bulk sludge from the MAS-MBR compared to the C-MBR. It is possible that less membrane fouling is connected to reductions in large molecules and pioneer bacteria from bulk sludge

Regularity of the Solutions to SPDEs in Metric Measure Spaces

In this paper we study the regularity of non-linear parabolic PDEs and stochastic PDEs on metric measure spaces admitting heat kernel estimates. In particular we consider mild function solutions to abstract Cauchy problems and show that the unique solution is Hölder continuous in time with values in a suitable fractional Sobolev space. As this analysis is done via a-priori estimates, we can apply this result to stochastic PDEs on metric measure spaces and solve the equation in a pathwise sense for almost all paths. The main example of noise term is of fractional Brownian type and the metric measure spaces can be classical as well as given by various fractal structures. The whole approach is low dimensional and works for spectral dimensions less than 4