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 /

Optimal input states and feedback for interferometric phase estimation

We derive optimal N-photon two-mode input states for interferometric phase measurements. Under canonical measurements the phase variance scales as N-2 for these states, as compared to N-1 or N-1/2 for states considered bq previous authors. We prove, that it is not possible to realize the canonical measurement by counting photons in the outputs of the interferometer, even if an adjustable auxiliary phase shift is allowed in the interferometer. However. we introduce a feedback algorithm based on Bayesian inference to control this auxiliary phase shift. This makes the measurement close to a canonical one, with a phase variance scaling slightly above N-2. With no feedback, the best result (given that the phase to be measured is completely unknown) is a scaling of N-1. For optimal input states having up to four photons, our feedback scheme is the best possible one, but for higher photon numbers more complicated schemes perform marginally better

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

Peer reviewedPublisher PD