Differentially expressed genes are typically identified by analyzing the variation between replicate measurements. These procedures implicitly assume that there are no systematic errors in the data even though several sources of systematic error are known. Results-OpWise estimates the amount of systematic error in bacterial microarray data by assuming that genes in the same operon have matching expression patterns. OpWise then performs a Bayesian analysis of a linear model to estimate significance. In simulations, OpWise corrects for systematic error and is robust to deviations from its assumptions. In several bacterial data sets, significant amounts of systematic error are present, and replicate-based approaches overstate the confidence of the changers dramatically, while OpWise does not. Finally, OpWise can identify additional changers by assigning genes higher confidence if they are consistent with other genes in the same operon. Although microarray data can contain large amounts of systematic error, operons provide an external standard and allow for reasonable estimates of significance. OpWise is available at http://microbesonline.org/OpWise.

Plutonium, because of its radioactive nature, ages from the 'inside out' by means of self-irradiation damage and thus produces nanoscale internal defects. The self-irradiation induced defects come in the form of Frenkel-type defects (vacancies and self-interstitial atoms), helium in-growth, and defect clusters. At present there are neither experimental nor theoretical models describing the changes in the electronic structure caused by the aging in Pu. This fact appears to be associated primarily with the absence of reasonably convincing spectroscopic evidence of the changes. This paper demonstrates that Resonant Photoemission, a variant of Photoelectron Spectroscopy, has strong sensitivity to aging of Pu samples. The spectroscopic results are correlated with an extra-atomic screening model [1], and are shown to be the fingerprint of mesoscopic or nanoscale internal damage in the Pu physical structure. This means that a spectroscopic signature of internal damage due to aging in Pu has been established.

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This article discusses the linear response to perturbation of nonexponential renewal processes.