Profound effect of profiling platform and normalization strategy on detection of differentially expressed microRNAs

Adequate normalization minimizes the effects of systematic technical variations and is a prerequisite for getting meaningful biological changes. However, there is inconsistency about miRNA normalization performances and recommendations. Thus, we investigated the impact of seven different normalization methods (reference gene index, global geometric mean, quantile, invariant selection, loess, loessM, and generalized procrustes analysis) on intra- and inter-platform performance of two distinct and commonly used miRNA profiling platforms. We included data from miRNA profiling analyses derived from a hybridization-based platform (Agilent Technologies) and an RT-qPCR platform (Applied Biosystems). Furthermore, we validated a subset of miRNAs by individual RT-qPCR assays. Our analyses incorporated data from the effect of differentiation and tumor necrosis factor alpha treatment on primary human skeletal muscle cells and a murine skeletal muscle cell line. Distinct normalization methods differed in their impact on (i) standard deviations, (ii) the area under the receiver operating characteristic (ROC) curve, (iii) the similarity of differential expression. Loess, loessM, and quantile analysis were most effective in minimizing standard deviations on the Agilent and TLDA platform. Moreover, loess, loessM, invariant selection and generalized procrustes analysis increased the area under the ROC curve, a measure for the statistical performance of a test. The Jaccard index revealed that inter-platform concordance of differential expression tended to be increased by loess, loessM, quantile, and GPA normalization of AGL and TLDA data as well as RGI normalization of TLDA data. We recommend the application of loess, or loessM, and GPA normalization for miRNA Agilent arrays and qPCR cards as these normalization approaches showed to (i) effectively reduce standard deviations, (ii) increase sensitivity and accuracy of differential miRNA expression detection as well as (iii) increase inter-platform concordance. Results showed the successful adoption of loessM and generalized procrustes analysis to one-color miRNA profiling experiments

Detecting Photon-Photon Interactions in a Superconducting Circuit

A local interaction between photons can be engineered by coupling a nonlinear system to a transmission line. The required high impedance transmission line can be conveniently formed from a chain of Josephson junctions. The nonlinearity is generated by side-coupling this chain to a Cooper pair box. We propose to probe the resulting photon-photon interactions via their effect on the current-voltage characteristic of a voltage-biased Josephson junction connected to the transmission line. Considering the Cooper pair box to be in the weakly anharmonic regime, we find that the dc current through the probe junction yields features around the voltages $2eV=n\hbar\omega_s$, where $\omega_s$ is the plasma frequency of the superconducting circuit. The features at $n\ge 2$ are a direct signature of the photon-photon interaction in the system.Comment: 10 pages, 7 figure

Functional Characterisation of Alpha-Galactosidase A Mutations as a Basis for a New Classification System in Fabry Disease

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.The study has been supported partially by an unrestricted scientific grant from Shire Human Genetic Therapies (Germany

Infinite qubit rings with maximal nearest neighbor entanglement: the Bethe ansatz solution

We search for translationally invariant states of qubits on a ring that maximize the nearest neighbor entanglement. This problem was initially studied by O'Connor and Wootters [Phys. Rev. A {\bf 63}, 052302 (2001)]. We first map the problem to the search for the ground state of a spin 1/2 Heisenberg XXZ model. Using the exact Bethe ansatz solution in the limit of an infinite ring, we prove the correctness of the assumption of O'Connor and Wootters that the state of maximal entanglement does not have any pair of neighboring spins ``down'' (or, alternatively spins ``up''). For sufficiently small fixed magnetization, however, the assumption does not hold: we identify the region of magnetizations for which the states that maximize the nearest neighbor entanglement necessarily contain pairs of neighboring spins ``down''.Comment: 10 pages, 4 figures; Eq. (45) and Fig. 3 corrected, no qualitative change in conclusion

Discovery of a Magnetic White Dwarf in the Symbiotic Binary Z Andromedae

We report the first result from our survey of rapid variability in symbiotic binaries: the discovery of a persistent oscillation at P=1682.6 +- 0.6 s in the optical emission from the prototype symbiotic, Z Andromedae. The oscillation was detected on all 8 occasions on which the source was observed over a timespan of nearly a year, making it the first such persistent periodic pulse found in a symbiotic binary. The amplitude was typically 2 - 5 mmag, and it was correlated with the optical brightness during a relatively small outburst of the system. The most natural explanation is that the oscillation arises from the rotation of an accreting, magnetic (B_S > 10^5 G) white dwarf. This discovery constrains the outburst mechanisms, since the oscillation emission region near the surface of the white dwarf was visible during the outburst.Comment: Accepted for publication in the Astrophysical Journal (6 pages, including 4 figures), LaTe

Extended Classical Over-Barrier Model for Collisions of Highly Charged Ions with Conducting and Insulating Surfaces

We have extended the classical over-barrier model to simulate the neutralization dynamics of highly charged ions interacting under grazing incidence with conducting and insulating surfaces. Our calculations are based on simple model rates for resonant and Auger transitions. We include effects caused by the dielectric response of the target and, for insulators, localized surface charges. Characteristic deviations regarding the charge transfer processes from conducting and insulating targets to the ion are discussed. We find good agreement with previously published experimental data for the image energy gain of a variety of highly charged ions impinging on Au, Al, LiF and KI crystals.Comment: 32 pages http://pikp28.uni-muenster.de/~ducree

Cross section and analyzing power of pol{p}p -> pn pi+ near threshold

The cross section and analyzing power of the pol{p}p -> pn pi+ reaction near threshold are estimated in terms of data obtained from the pol{p}p -> d pi+ and pp -> pp pi0 reactions. A simple final state interaction theory is developed which depends weakly upon the form of the pion-production operator and includes some Coulomb corrections. Within the uncertainties of the model and the input data, the approach reproduces well the measured energy dependence of the total cross section and the proton analyzing power at a fixed pion c.m. angle of 90deg, from threshold to T_p = 330 MeV. The variation of the differential cross section with pion angle is also very encouraging.Comment: 20 pages, Latex including 4 eps figure

Rubber friction on wet and dry road surfaces: the sealing effect

Rubber friction on wet rough substrates at low velocities is typically 20-30% smaller than for the corresponding dry surfaces. We show that this cannot be due to hydrodynamics and propose a novel explanation based on a sealing effect exerted by rubber on substrate "pools" filled with water. Water effectively smoothens the substrate, reducing the major friction contribution due to induced viscoelastic deformations of the rubber by surface asperities. The theory is illustrated with applications related to tire-road friction.Comment: Format Revtex 4; 8 pages, 11 figures (no color); Published on Phys. Rev. B (http://link.aps.org/abstract/PRB/v71/e035428); previous work on the same topic: cond-mat/041204