Local false discovery rate facilitates comparison of different microarray experiments

The local false discovery rate (LFDR) estimates the probability of falsely identifying specific genes with changes in expression. In computer simulations, LFDR <10% successfully identified genes with changes in expression, while LFDR >90% identified genes without changes. We used LFDR to compare different microarray experiments quantitatively: (i) Venn diagrams of genes with and without changes in expression, (ii) scatter plots of the genes, (iii) correlation coefficients in the scatter plots and (iv) distributions of gene function. To illustrate, we compared three methods for pre-processing microarray data. Correlations between methods were high (r = 0.84–0.92). However, responses were often different in magnitude, and sometimes discordant, even though the methods used the same raw data. LFDR complements functional assessments like gene set enrichment analysis. To illustrate, we compared responses to ultraviolet radiation (UV), ionizing radiation (IR) and tobacco smoke. Compared to unresponsive genes, genes responsive to both UV and IR were enriched for cell cycle, mitosis, and DNA repair functions. Genes responsive to UV but not IR were depleted for cell adhesion functions. Genes responsive to tobacco smoke were enriched for detoxification functions. Thus, LFDR reveals differences and similarities among experiments

From collaborative virtual research environment SOA to teaching and learning environment SOA

This paper explores the extension of the CORE VRE SOA to a collaborative virtual teaching and learning environment (CVTLE) SOA. Key points are brought up to date from a number of projects researching and developing a CVTLE and its component services. Issues remain: there are few implementations of the key services needed to demonstrate the CVTLE concept; there are questions about the feasibility of such an enterprise; there are overlapping standards; questions about the source and use of user profile data remain difficult to answer; as does the issue of where and how to coordinate, control, and monitor such a teaching and learning syste

Probing the Reionization History of the Universe using the Cosmic Microwave Background Polarization

The recent discovery of a Gunn--Peterson (GP) trough in the spectrum of the redshift 6.28 SDSS quasar has raised the tantalizing possibility that we have detected the reionization of the universe. However, a neutral fraction (of hydrogen) as small as 0.1% is sufficient to cause the GP trough, hence its detection alone cannot rule out reionization at a much earlier epoch. The Cosmic Microwave Background (CMB) polarization anisotropy offers an alternative way to explore the dark age of the universe. We show that for most models constrained by the current CMB data and by the discovery of a GP trough (showing that reionization occurred at z > 6.3), MAP can detect the reionization signature in the polarization power spectrum. The expected 1-sigma error on the measurement of the electron optical depth is around 0.03 with a weak dependence on the value of that optical depth. Such a constraint on the optical depth will allow MAP to achieve a 1-sigma error on the amplitude of the primordial power spectrum of 6%. MAP with two years (Planck with one year) of observation can distinguish a model with 50% (6%) partial ionization between redshifts of 6.3 and 20 from a model in which hydrogen was completely neutral at redshifts greater than 6.3. Planck will be able to distinguish between different reionization histories even when they imply the same optical depth to electron scattering for the CMB photons.Comment: ApJ version. Added Figure 2 and reference

Capturing Cognitive Fingerprints from Keystroke Dynamics

Conventional authentication systems identify a user only at the entry point. Keystroke dynamics can continuously authenticate users by their typing rhythms without extra devices. This article presents a new feature called cognitive typing rhythm (CTR) to continuously verify the identities of computer users. Two machine techniques, SVM and KRR, have been developed for the system. The best results from experiments conducted with 1,977 users show a false-rejection rate of 0.7 percent and a false-acceptance rate of 5.5 percent. CTR therefore constitutes a cognitive fingerprint for continuous. Its effectiveness has been verified through a large-scale dataset. This article is part of a special issue on security

Effect of specimen preparation method on the stress-strain behavior of sand in plane-strain compression tests

Experimental results are presented in this paper to study the effect of specimen preparation method on the stress-strain behavior of sand in plane-strain compression tests. The data obtained from K0 consolidation, drained, undrained and strain path tests conducted on medium loose specimens prepared by the moist-tamping (MT) and the water sedimentation (WS) methods are compared. The test data show that the plane-strain compression behavior of medium loose sand under K0, drained and strain-path controlled (including undrained) conditions is affected by the speci- men preparation method. Under K0 conditions, the K0 values obtained from the MT specimens are generally lower than those obtained from the WS specimens. Under drained conditions, more contractive behavior was observed for the MT sand. However, the failure stress ratio (or the failure friction angle) was not affected by the specimen preparation method. The data presented in this paper also illustrate that the compression behavior of medium loose sand in strain-path testing can be affected by the specimen preparation method. However, the differences in the stress-strain behavior will also depend on the strain increment ratio (d v/d 1) imposed on the specimens. In general, different behaviors of the moist-tamped and water- deposited specimens reflect the influence of soil fabrics on the stress-strain behavior of sand

Detection of Coherent Vorticity Structures using Time-Scale Resolved Acoustic Spectroscopy

We describe here an experimental technique based on the acoustic scattering phenomenon allowing the direct probing of the vorticity field in a turbulent flow. Using time-frequency distributions, recently introduced in signal analysis theory, for the analysis of the scattered acoustic signals, we show how the legibility of these signals is significantly improved (time resolved spectroscopy). The method is illustrated on data extracted from a highly turbulent jet flow : discrete vorticity events are clearly evidenced. We claim that the recourse to time-frequency distributions lead to an operational definition of coherent structures associated with phase stationarity in the time-frequency plane.Comment: 26 pages, 6 figures. Latex2e format Revised version : Added references, figures and Changed conten

Experimental determination of the 6s^2 ^1S_0 -> 5d6s ^3 D_1 magnetic-dipole transition amplitude in atomic ytterbium

We report on a measurement of the highly forbidden 6s^2 ^1S_0 \to 5d6s ^3 D_1 magnetic-dipole transition in atomic ytterbium using the Stark-interference technique. This amplitude is important in interpreting a future parity nonconservation experiment that exploits the same transition. We find $| | ~ = ~ 1.33(6)_{Stat}(20)_{\beta} \times 10^{-4} \mu_0$, where the larger uncertainty comes from the previously measured vector transition polarizability $\beta$. The $M1$ amplitude is small and should not limit the precision of the parity nonconservation experiment.Comment: 4 pages, 5 figures Paper resubmitted with minor corrections and additions based on comments from referee

Complete and Prolonged Response to Immune Checkpoint Blockade in POLE-Mutated Colorectal Cancer

Enid Robertson Logan Faculty Fellowship Fund6 month embargo; published online: 21 June 2019This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]