Application of Volcano Plots in Analyses of mRNA Differential Expressions with Microarrays

Volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log10(p-value) from the t test). We review the basic and an interactive use of the volcano plot, and its crucial role in understanding the regularized t-statistic. The joint filtering gene selection criterion based on regularized statistics has a curved discriminant line in the volcano plot, as compared to the two perpendicular lines for the "double filtering" criterion. This review attempts to provide an unifying framework for discussions on alternative measures of differential expression, improved methods for estimating variance, and visual display of a microarray analysis result. We also discuss the possibility to apply volcano plots to other fields beyond microarray.Comment: 8 figure

Evolution of dopant-induced helium nanoplasmas

Two-component nanoplasmas generated by strong-field ionization of doped helium nanodroplets are studied in a pump-probe experiment using few-cycle laser pulses in combination with molecular dynamics simulations. High yields of helium ions and a pronounced, droplet size-dependent resonance structure in the pump-probe transients reveal the evolution of the dopant-induced helium nanoplasma. The pump-probe dynamics is interpreted in terms of strong inner ionization by the pump pulse and resonant heating by the probe pulse which controls the final charge states detected via the frustration of electron-ion recombination

Signal of Quark Deconfinement in the Timing Structure of Pulsar Spin-Down

The conversion of nuclear matter to quark matter in the core of a rotating neutron star alters its moment of inertia. Hence the epoch over which conversion takes place will be signaled in the spin-down "signal_prl.tex" 581 lines, 22203 characters characteristics of pulsars. We find that an observable called the braking index should be easily measurable during the transition epoch and can have a value far removed (by orders of magnitude) from the canonical value of three expected for magnetic dipole radiation, and may have either sign. The duration of the transition epoch is governed by the slow loss of angular momentum to radiation and is further prolonged by the reduction in the moment of inertia caused by the phase change which can even introduce an era of spin-up. We estimate that about one in a hundred pulsars may be passing through this phase. The phenomenon is analogous to ``bachbending'' observed in the moment of inertia of rotating nuclei observed in the 1970's, which also signaled a change in internal structure with changing spin.Comment: 5 pages, 4 figures, Revtex. (May 12, 1997, submitted to PRL

Psychosocial Screening in Disorders/Differences of Sex Development: Psychometric Evaluation of the Psychosocial Assessment Tool

© 2019 S. Karger AG, Basel. Background/Aims: Utilization of a psychosocial screener to identify families affected by a disorder/difference of sex development (DSD) and at risk for adjustment challenges may facilitate efficient use of team resources to optimize care. The Psychosocial Assessment Tool (PAT) has been used in other pediatric conditions. The current study explored the reliability and validity of the PAT (modified for use within the DSD population; PAT-DSD). Methods: Participants were 197 families enrolled in the DSD-Translational Research Network (DSD-TRN) who completed a PAT-DSD during a DSD clinic visit. Psychosocial data were extracted from the DSD-TRN clinical registry. Internal reliability of the PAT-DSD was tested using the Kuder-Richardson-20 coefficient. Validity was examined by exploring the correlation of the PAT-DSD with other measures of caregiver distress and child emotional-behavioral functioning. Results: One-third of families demonstrated psychosocial risk (27.9% Targeted and 6.1% Clinical level of risk). Internal reliability of the PAT-DSD Total score was high (α = 0.86); 4 of 8 subscales met acceptable internal reliability. A priori predicted relationships between the PAT-DSD and other psychosocial measures were supported. The PAT-DSD Total score related to measures of caregiver distress (r = 0.40, p \u3c 0.001) and to both caregiver-reported and patient self-reported behavioral problems (r = 0.61, p \u3c 0.00; r = 0.37, p \u3c 0.05). Conclusions: This study provides evidence for the reliability and validity of the PAT-DSD. Given variability in the internal reliability across subscales, this measure is best used to screen for overall family risk, rather than to assess specific psychosocial concerns

MLP: a MATLAB toolbox for rapid and reliable auditory threshold estimation

In this paper, we present MLP, a MATLAB toolbox enabling auditory thresholds estimation via the adaptive Maximum Likelihood procedure proposed by David Green (1990, 1993). This adaptive procedure is particularly appealing for those psychologists that need to estimate thresholds with a good degree of accuracy and in a short time. Together with a description of the toolbox, the current text provides an introduction to the threshold estimation theory and a theoretical explanation of the maximum likelihood adaptive procedure. MLP comes with a graphical interface and it is provided with several built-in, classic psychoacoustics experiments ready to use at a mouse click

Intrinsic gain modulation and adaptive neural coding

In many cases, the computation of a neural system can be reduced to a receptive field, or a set of linear filters, and a thresholding function, or gain curve, which determines the firing probability; this is known as a linear/nonlinear model. In some forms of sensory adaptation, these linear filters and gain curve adjust very rapidly to changes in the variance of a randomly varying driving input. An apparently similar but previously unrelated issue is the observation of gain control by background noise in cortical neurons: the slope of the firing rate vs current (f-I) curve changes with the variance of background random input. Here, we show a direct correspondence between these two observations by relating variance-dependent changes in the gain of f-I curves to characteristics of the changing empirical linear/nonlinear model obtained by sampling. In the case that the underlying system is fixed, we derive relationships relating the change of the gain with respect to both mean and variance with the receptive fields derived from reverse correlation on a white noise stimulus. Using two conductance-based model neurons that display distinct gain modulation properties through a simple change in parameters, we show that coding properties of both these models quantitatively satisfy the predicted relationships. Our results describe how both variance-dependent gain modulation and adaptive neural computation result from intrinsic nonlinearity.Comment: 24 pages, 4 figures, 1 supporting informatio

Atmospheric neutrino oscillation analysis with sub-leading effects in Super-Kamiokande I, II, and III

We present a search for non-zero theta_{13} and deviations of sin^2 theta_{23} from 0.5 in the oscillations of atmospheric neutrino data from Super-Kamiokande -I, -II, and -III. No distortions of the neutrino flux consistent with non-zero theta_{13} are found and both neutrino mass hierarchy hypotheses are in agreement with the data. The data are best fit at Delta m^2 = 2.1 x 10^-3 eV^2, sin^2 theta_{13} = 0.0, and sin^2 theta_{23} =0.5. In the normal (inverted) hierarchy theta_{13} and Delta m^2 are constrained at the one-dimensional 90% C.L. to sin^2 theta_{13} < 0.04 (0.09) and 1.9 (1.7) x 10^-3 < Delta m^2 < 2.6 (2.7) x 10^-3 eV^2. The atmospheric mixing angle is within 0.407 <= sin^2 theta_{23} <= 0.583 at 90% C.L.Comment: 17 Pages, 14 figures. To be submitted to Phys. Rev. D Minor update to text after referee comments. Figures modified for better grayscale printing

Search for Matter-Dependent Atmospheric Neutrino Oscillations in Super-Kamiokande

We consider muon neutrino to tau neutrino oscillations in the context of the Mass Varying Neutrino (MaVaN) model, where the neutrino mass can vary depending on the electron density along the flight path of the neutrino. Our analysis assumes a mechanism with dependence only upon the electron density, hence ordinary matter density, of the medium through which the neutrino travels. Fully-contained, partially-contained and upward-going muon atmospheric neutrino data from the Super--Kamiokande detector, taken from the entire SK--I period of 1489 live days, are compared to MaVaN model predictions. We find that, for the case of 2-flavor oscillations, and for the specific models tested, oscillation independent of electron density is favored over density dependence. Assuming maximal mixing, the best-fit case and the density-independent case do not differ significantly.Comment: 6 pages, 1 figur

Set-valued orthogonal additivity

We study the set-valued Cauchy equation postulated for orthogonal vectors. We give its general solution as well as we look for selections of functions satisfying the equation