6,206 research outputs found
Probabilities of spurious connections in gene networks: Application to expression time series
Motivation: The reconstruction of gene networks from gene expression
microarrays is gaining popularity as methods improve and as more data become
available. The reliability of such networks could be judged by the probability
that a connection between genes is spurious, resulting from chance fluctuations
rather than from a true biological relationship. Results: Unlike the false
discovery rate and positive false discovery rate, the decisive false discovery
rate (dFDR) is exactly equal to a conditional probability without assuming
independence or the randomness of hypothesis truth values. This property is
useful not only in the common application to the detection of differential gene
expression, but also in determining the probability of a spurious connection in
a reconstructed gene network. Estimators of the dFDR can estimate each of three
probabilities: 1. The probability that two genes that appear to be associated
with each other lack such association. 2. The probability that a time ordering
observed for two associated genes is misleading. 3. The probability that a time
ordering observed for two genes is misleading, either because they are not
associated or because they are associated without a lag in time. The first
probability applies to both static and dynamic gene networks, and the other two
only apply to dynamic gene networks. Availability: Cross-platform software for
network reconstruction, probability estimation, and plotting is free from
http://www.davidbickel.com as R functions and a Java application.Comment: Like q-bio.GN/0404032, this was rejected in March 2004 because it was
submitted to the math archive. The only modification is a corrected reference
to q-bio.GN/0404032, which was not modified at al
Why NiAl is an itinerant ferromagnet but NiGa is not
NiAl and NiGa are closely related materials on opposite sides of a
ferromagnetic quantum critical point. The Stoner factor of Ni is virtually the
same in both compounds and the density of states is larger in NiGa. So,
according to the Stoner theory, it should be more magnetic, and, in LDA
calculations, it is. However, experimentally, it is a paramagnet, while
NiAl is an itinerant ferromagnet. We show that the critical spin
fluctuations are stronger than in NiGa, due to a weaker q-dependence of the
susceptibility, and this effect is strong enough to reverse the trend. The
approach combines LDA calculations with the Landau theory and the
fluctuation-dissipation theorem using the same momentum cut-off for both
materials. The calculations provide evidence for strong, beyond LDA, spin
fluctuations associated with the critical point in both materials, but stronger
in NiGa than in NiAl.Comment: replaced (incorrect version submitted
Randomized Benchmarking of Quantum Gates
A key requirement for scalable quantum computing is that elementary quantum
gates can be implemented with sufficiently low error. One method for
determining the error behavior of a gate implementation is to perform process
tomography. However, standard process tomography is limited by errors in state
preparation, measurement and one-qubit gates. It suffers from inefficient
scaling with number of qubits and does not detect adverse error-compounding
when gates are composed in long sequences. An additional problem is due to the
fact that desirable error probabilities for scalable quantum computing are of
the order of 0.0001 or lower. Experimentally proving such low errors is
challenging. We describe a randomized benchmarking method that yields estimates
of the computationally relevant errors without relying on accurate state
preparation and measurement. Since it involves long sequences of randomly
chosen gates, it also verifies that error behavior is stable when used in long
computations. We implemented randomized benchmarking on trapped atomic ion
qubits, establishing a one-qubit error probability per randomized pi/2 pulse of
0.00482(17) in a particular experiment. We expect this error probability to be
readily improved with straightforward technical modifications.Comment: 13 page
Slip-velocity of large neutrally-buoyant particles in turbulent flows
We discuss possible definitions for a stochastic slip velocity that describes
the relative motion between large particles and a turbulent flow. This
definition is necessary because the slip velocity used in the standard drag
model fails when particle size falls within the inertial subrange of ambient
turbulence. We propose two definitions, selected in part due to their
simplicity: they do not require filtration of the fluid phase velocity field,
nor do they require the construction of conditional averages on particle
locations. A key benefit of this simplicity is that the stochastic slip
velocity proposed here can be calculated equally well for laboratory, field,
and numerical experiments. The stochastic slip velocity allows the definition
of a Reynolds number that should indicate whether large particles in turbulent
flow behave (a) as passive tracers; (b) as a linear filter of the velocity
field; or (c) as a nonlinear filter to the velocity field. We calculate the
value of stochastic slip for ellipsoidal and spherical particles (the size of
the Taylor microscale) measured in laboratory homogeneous isotropic turbulence.
The resulting Reynolds number is significantly higher than 1 for both particle
shapes, and velocity statistics show that particle motion is a complex
non-linear function of the fluid velocity. We further investigate the nonlinear
relationship by comparing the probability distribution of fluctuating
velocities for particle and fluid phases
Multicanonical Study of Coarse-Grained Off-Lattice Models for Folding Heteropolymers
We have performed multicanonical simulations of hydrophobic-hydrophilic
heteropolymers with two simple effective, coarse-grained off-lattice models to
study the influence of specific interactions in the models on conformational
transitions of selected sequences with 20 monomers. Another aspect of the
investigation was the comparison with the purely hydrophobic homopolymer and
the study of general conformational properties induced by the "disorder" in the
sequence of a heteropolymer. Furthermore, we applied an optimization algorithm
to sequences with up to 55 monomers and compared the global-energy minimum
found with lowest-energy states identified within the multicanonical
simulation. This was used to find out how reliable the multicanonical method
samples the free-energy landscape, in particular for low temperatures.Comment: 11 pages, RevTeX, 10 Postscript figures, Author Information under
http://www.physik.uni-leipzig.de/index.php?id=2
A Nonparametric Method for the Derivation of α/β Ratios from the Effect of Fractionated Irradiations
Multifractionation isoeffect data are commonly analysed under the assumption that cell survival determines the observed tissue or tumour response, and that it follows a linear-quadratic dose dependence. The analysis is employed to derive the α/β ratios of the linear-quadratic dose dependence, and different methods have been developed for this purpose. A common method uses the so-called Fe plot. A more complex but also more rigorous method has been introduced by Lam et al. (1979). Their method, which is based on numerical optimization procedures, is generalized and somewhat simplified in the present study. Tumour-regrowth data are used to explain the nonparametric procedure which provides α/β ratios without the need to postulate analytical expressions for the relationship between cell survival and regrowth delay
Transcriptional adaptation of Mycobacterium tuberculosis within macrophages: Insights into the phagosomal environment
Little is known about the biochemical environment in phagosomes harboring an infectious agent. To assess the state of this organelle we captured the transcriptional responses of Mycobacterium tuberculosis (MTB) in macrophages from wild-type and nitric oxide (NO) synthase 2–deficient mice before and after immunologic activation. The intraphagosomal transcriptome was compared with the transcriptome of MTB in standard broth culture and during growth in diverse conditions designed to simulate features of the phagosomal environment. Genes expressed differentially as a consequence of intraphagosomal residence included an interferon � – and NO-induced response that intensifies an iron-scavenging program, converts the microbe from aerobic to anaerobic respiration, and induces a dormancy regulon. Induction of genes involved in the activation and �-oxidation of fatty acids indicated that fatty acids furnish carbon and energy. Induction of �E-dependent, sodium dodecyl sulfate–regulated genes and genes involved in mycolic acid modification pointed to damage and repair of the cell envelope. Sentinel genes within the intraphagosomal transcriptome were induced similarly by MTB in the lungs of mice. The microbial transcriptome thus served as a bioprobe of the MTB phagosomal environment
The Abelian Manna model on two fractal lattices
We analyze the avalanche size distribution of the Abelian Manna model on two
different fractal lattices with the same dimension d_g=ln(3)/ln(2), with the
aim to probe for scaling behavior and to study the systematic dependence of the
critical exponents on the dimension and structure of the lattices. We show that
the scaling law D(2-tau)=d_w generalizes the corresponding scaling law on
regular lattices, in particular hypercubes, where d_w=2. Furthermore, we
observe that the lattice dimension d_g, the fractal dimension of the random
walk on the lattice d_w, and the critical exponent D, form a plane in 3D
parameter space, i.e. they obey the linear relationship D=0.632(3) d_g +
0.98(1) d_w - 0.49(3).Comment: 4 pages, 3 figures, 3 tables, submitted to PRE as a Brief Repor
Spectral Density on the Lattice
Spectral density in the pseudoscalar and vector channels is extracted from
the SU(2) lattice quenched data. It is shown to consist of three sharp poles
within the energy range accessible on the lattice.Comment: 38 pages, uuencoded tar-compressed ps-fil
- …