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

On the perceptual aesthetics of interactive objects

In this paper we measured the aesthetics of interactive objects (IOs), which are three-dimensional physical artefacts that exhibit autonomous behaviour when ‎handled. The aim of the research was threefold: firstly, to investigate whether aesthetic preference for distinctive objects' structures emerges in compound stimulation; secondly, to explore whether there exists aesthetic preference for distinctive objects’ behaviours; and lastly, to test whether there exists aesthetic preference for specific combinations of objects' structures and behaviours. The following variables were systematically manipulated: 1) IOs’ contour (rounded vs. angular); 2) IOs’ size (small vs. large); 3) IOs’ surface texture (rough vs. smooth); and 4) IOs’ behaviour (Lighting, Sounding, Vibrating, and Quiescent). Results show that behaviour was the dominant factor: it influenced aesthetics more than any other characteristic; Vibrating IOs were preferred over Lighting and Sounding IOs, supporting the importance of haptic processing in aesthetics. Results did not confirm the size and smoothness effects previously reported in vision and touch respectively, which suggests that for the aesthetics preference that emerges in isolated conditions may be different in compound stimulation. Finally, results corroborate the smooth curvature effect

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

Methane Flux from Drained Northern Peatlands: Effect of a Persistent Water Table Lowering on Flux

Measurements of CH4 flux from drained and undrained sites in three northern Ontario peatlands (a treed fen, a forested bog, and a treed bog) were made from the beginning of May to the end of October 1991. In the drained portions, the water table had been lowered between 0.1 and 0.5 m, compared to the water table of the undrained portion of the peatlands. The mean seasonal CH4 flux from the undrained portions of three peatlands was small, ranging from 0 to 8 mg m-2d-1, but similar to the CH4 flux from other treed and forested northern peatlands. The mean seasonal CH4 flux from the drained portion of the peatlands was either near zero or slightly negative (i.e., uptake): fluxes ranged from 0.1 to -0.4 mg m-2d-1. Profiles of CH4 in the air-filled pores in the unsaturated zone, and the water-filled pores of the saturated zone of the peat at the undrained sites, showed that all the CH4 produced at depth was consumed within 0.2 m of the water table and that atmospheric CH4 was consumed in the upper 0.15 m of the peatland. On the basis of laboratory incubations of peat slurries to determine CH4 production and consumption potentials, the lowering of the water table eliminated the near-surface zone of CH4 production that existed in the undrained peatland. However, drainage did not alter significantly the potential for CH4 oxidation between the water table and peatland surface but increased the thickness of the layer over which CH4 oxidation could take place. These changes occurred with a drop in the mean summer water table of only 0.1 m (from -0.2 to -0.3 m) suggesting that only a small negative change in soil moisture would be required to significantly reduce CH4 flux from northern peatlands

Rediscovery of the anti-pancreatic antibodies and evaluation of their prognostic value in a prospective clinical cohort of Crohn's patients: the importance of specific target antigens (GP2 and CUZD1).

BACKGROUNDS: Glycoprotein 2[GP2] and CUB zona pellucida-like domain 1[CUZD1] belong to protein families involved in gut innate immunity processes and have recently been identified as specific targets of anti-pancreatic autoantibodies [PAbs] in Crohn's disease[CD]. We aimed to determine the prognostic potential of novel target-specific PAbs regarding long-term disease course of an adult CD patient cohort. METHODS: Sera of 458 consecutive well-characterised IBD patients from a single referral IBD centre were tested by enzyme-linked immunosorbent assay [ELISA] with isoform 4 of recombinant GP2 [anti-MZGP2 and anti-GP2 IgA/IgG] and indirect immunofluorescence test [IIFT] system with GP2 and CUZD1 expressing transfected HEK 293 cells [anti-rPAg2 and rPAg1 IgA/IgG]. Clinical data were available on complicated disease or surgical interventions as well as disease activity and medical treatment during the prospective follow-up [median, 108 months]. RESULTS: Totals of 12.4% and 20.8% of CD patients were positive for IgA/IgG type of anti-GP2 and anti-CUZD1, respectively, with a significant difference compared with UC [p < 0.01]. Antibody status was stable over time. Agreement among three different anti-GP2 assays was good. Positivity for PAbs, mainly IgA subtypes, predicted a faster progression towards complicated disease course. In Kaplan-Meier analysis, time to surgery or development of perianal disease was associated with anti-GP2 IgA [pLogRank < 0.01] or anti-CUZD1 IgA [pLogRank < 0.001] positivity, respectively. Anti-CUZD1 IgA remained an independent predictor in the multivariate Cox-regression model (hazard ratio [HR]: 3.43, 95% confidence interval [CI]: 1.68-7.02, p < 0.001). CONCLUSIONS: The present study has shown that specific PAbs [especially IgA subtype] predict complicated disease course including the development of perianal disease in CD

A composite functional equation from algebraic aspect

In this paper we discuss the composite functional equation f(x+2f(y))=f(x)+y+f(y) on an Abelian group. This equation originates from Problem 10854 of the American Mathematical Monthly. We give an algebraic description of the solutions on uniquely 3-divisible Abelian groups, and then we construct all solutions f of this equation on finite Abelian groups without elements of order 3 and on divisible Abelian groups without elements of order 3 including the additive group of real numbers

Detection of Extended He II Reionization in the Temperature Evolution of the Intergalactic Medium

We present new measurements of the temperature of the intergalactic medium (IGM) derived from the Lyman-alpha forest over 2.0 < z < 4.8. The small-scale structure in the forest of 61 high-resolution QSO spectra is quantified using a new statistic, the curvature, and the conversion to temperature calibrated using a suite of hydrodynamic simulations. At each redshift we focus on obtaining the temperature at an optimal overdensity probed by the Lyman-alpha forest, T(Delta), where the temperature is nearly a one-to-one function of the curvature regardless of the slope of the temperature-density relation. The median 2-sigma statistical uncertainty in these measurements is 8 per cent, though there may be comparable systematic errors due to the unknown amount of Jeans smoothing in the IGM. We use our T(Delta) results to infer the temperature at the mean density, T0. Even for a maximally steep temperature-density relation, T0 must increase from ~8000 K at z ~ 4.4 to >~12000 K at z ~ 2.8. This increase is not consistent with the monotonic decline in T0 expected in the absence of He II reionization. We therefore interpret the observed rise in temperature as evidence of He II reionization beginning at z >~ 4.4. The evolution of T0 is consistent with an end to He II reionization at z ~ 3, as suggested by opacity measurements of the He II Lyman-alpha forest, although the redshift at which T0 peaks will depend somewhat on the evolution of the temperature-density relation. These new temperature measurements suggest that the heat input due to the reionization of He II dominates the thermal balance of the IGM over an extended period with Delta_z >~ 1.Comment: 19 pages, 15 figures, accepted to MNRA