Probabilistic estimation of microarray data reliability and underlying gene expression

Background: The availability of high throughput methods for measurement of mRNA concentrations makes the reliability of conclusions drawn from the data and global quality control of samples and hybridization important issues. We address these issues by an information theoretic approach, applied to discretized expression values in replicated gene expression data. Results: Our approach yields a quantitative measure of two important parameter classes: First, the probability $P(\sigma | S)$ that a gene is in the biological state $\sigma$ in a certain variety, given its observed expression $S$ in the samples of that variety. Second, sample specific error probabilities which serve as consistency indicators of the measured samples of each variety. The method and its limitations are tested on gene expression data for developing murine B-cells and a $t$-test is used as reference. On a set of known genes it performs better than the $t$-test despite the crude discretization into only two expression levels. The consistency indicators, i.e. the error probabilities, correlate well with variations in the biological material and thus prove efficient. Conclusions: The proposed method is effective in determining differential gene expression and sample reliability in replicated microarray data. Already at two discrete expression levels in each sample, it gives a good explanation of the data and is comparable to standard techniques.Comment: 11 pages, 4 figure

Music Making Connections

The Covid-19 pandemic has made mental health issues sky rocket. Many people are suffering from anxiety, depression, OCD and many other mental health problems now more than ever. Without the in-person interactions, many people are eager to be able to hug friends and family again. People are also eager to see their favorite music artist live in concert again. In this paper, we discuss how music can help your mental health, how to prevent contracting the coronavirus, and ways you can help speed up the process of getting life back to normal

East Asia and the global/transatlantic/Western crisis

This paper introduces the special collection on East Asia and the Global Crisis. After justifying why a focus on East Asia is appropriate, it draws out the main themes that run through the individual contributions. These are the extent to which the region is decoupling from the global economy (or the West), the increasing legitimacy of statist alternatives to neoliberal development strategies, and the impact of crises on the definition of ―region‖ and the functioning of regional institutions and governance mechanisms

The Corrosion Protection of Copper and Copper Alloys using an Electrodeposited Conducting Polypyrrole Coating

Adherent polypyrrole films were electropolymerized from a near neutral sodium oxalate solution at pure Cu, CuZn and CuNi electrodes. The growth of these films was facilitated by the formation of a pseudo-passive oxalate layer. This layer was sufficiently protective to minimize dissolution of the substrate, but sufficiently conductive to enable the electropolymerization of pyrrole at the interface, and the generation of an adherent polypyrrole film. The rate of electropolymerization at the CuNi layer was reduced significantly by the formation of a nickel-rich oxide phase, however, the presence of Cu2+ increased the rate of polymer growth, enabling the formation of a thin polypyrrole layer during the early stages of polymerization. Likewise, the presence of zinc in the oxalate layer generated at the CuZn electrode reduced somewhat the rate of polymer formation. These films exhibited good corrosion protection properties in an acidified chloride solution

The influence of sodium salts on binary mixtures of bitter-tasting compounds

In order to study potential mixture interactions among bitter compounds, selected sodium salts were added to five compounds presented either alone or as binary bitter- ompound mixtures. Each compound was tested at a concentration that elicited &lsquo;weak&rsquo; perceived bitterness. The bitter compounds were mixed at these concentrations to form a subset of possible binary mixtures. For comparison, the concentration of each solitary compound was doubled to measure bitterness inhibition at the higher intensity level elicited by the mixtures. The following sodium salts were tested for bitterness inhibition: 100 mM sodium chloride (salty), 100 mM sodium gluconate (salty), 100 and 20 mM monosodium glutamate (umami), and 50 mM adenosine monophosphate disodium salt (umami). Sucrose (sweet) was also employed as a bitterness suppressor. The sodium salts differentially suppressed the bitterness of compounds and their binary combinations. Although most bitter compounds were suppressed, the bitterness of tetralone was not suppressed, nor was the bitterness of the binary mixtures that contained it. In general, the percent suppression of binary mixtures of compounds was predicted by the average percent suppression of its two components. Within the constraints of the present study, the bitterness of mixtures was suppressed by sodium salts and sucrose independently, with few bitter interactions. This is consistent with observations that the bitter taste system integrates the bitterness of multi-compound solutions linearly.<br /

Effectiveness of blood pressure-lowering drug treatment by levels of absolute risk: Post hoc analysis of the Australian National Blood Pressure Study

Objectives: In many current guidelines, blood pressure (BP)-lowering drug treatment for primary prevention of cardiovascular disease (CVD) is based on absolute risk. However, in clinical practice, therapeutic decisions are often based on BP levels alone. We sought to investigate which approach was superior by conducting a post hoc analysis of the Australian National Blood Pressure (ANBP) cohort, a seminal study establishing the efficacy of BP lowering in mild hypertensive' persons. Design: A post hoc subgroup analysis of the ANBP trial results by baseline absolute risk tertile. Setting and participants: 3244 participants aged 35-69 years in a community-based randomised placebo controlled trial of blood pressure-lowering medication. Interventions Chlorothiazide500 mg versus placebo. Primary outcome measures All-cause mortality and non-fatal events (non-fatal CVD, congestive cardiac failure, renal failure, hypertensive retinopathy or encephalopathy). Results: Treatment effects were assessed by HR, absolute risk reduction and number needed to treat. Participants had an average 5-year CVD risk in the intermediate range (10.5±6.5) with moderately elevated BP (mean 159/103 mmHg) and were middle aged (52±8 years). In a subgroup analysis, the relative effects (HR) and absolute effects (absolute risk reduction and number needed to treat) did not statistically differ across the three risk groups except for the absolute benefit in all-cause mortality (p for heterogeneity=0.04). With respect to absolute benefit, drug treatment significantly reduced the number of events in the high-risk group regarding any event with a number needed to treat of 18 (10 to 64), death from any cause with 45 (25 to 196) and major CVD events with 23 (12 to 193). Conclusion: Our analysis confirms that the benefit of treatment was substantial only in the high-risk tertile, reaffirming the rationale of treating elevated blood pressure in the setting of all risk factors rather than in isolation

Psychosocial factors related to children’s active school travel : A comparison of two European regions

Peer reviewedPublisher PD