24,177 research outputs found
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 , where
is the plasma frequency of the superconducting circuit. The features
at 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
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