NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference.

MOTIVATION: Reconstruction of gene regulatory networks (GRNs) is of utmost interest to biologists and is vital for understanding the complex regulatory mechanisms within the cell. Despite various methods developed for reconstruction of GRNs from gene expression profiles, they are notorious for high false positive rate owing to the noise inherited in the data, especially for the dataset with a large number of genes but a small number of samples. RESULTS: In this work, we present a novel method, namely NARROMI, to improve the accuracy of GRN inference by combining ordinary differential equation-based recursive optimization (RO) and information theory-based mutual information (MI). In the proposed algorithm, the noisy regulations with low pairwise correlations are first removed by using MI, and the redundant regulations from indirect regulators are further excluded by RO to improve the accuracy of inferred GRNs. In particular, the RO step can help to determine regulatory directions without prior knowledge of regulators. The results on benchmark datasets from Dialogue for Reverse Engineering Assessments and Methods challenge and experimentally determined GRN of Escherichia coli show that NARROMI significantly outperforms other popular methods in terms of false positive rates and accuracy. AVAILABILITY: All the source data and code are available at: http://csb.shu.edu.cn/narromi.htm

Magnetization-induced optical nonlinearity in ferromagnetic GaMnAs

International audienceWe report the observation of a coherent nonlinear signal in pump-probe experiments on a ferromagnetic GaMnAs. The coherent signal, which is originating due to coherent interaction between pump and probe beams, depends on the polarization configuration of each beam and follows the sample magnetization as it changes with the applied magnetic field and/or the sample temperature. Cop. 2007 American Institute of Physics

The Causes of Quasi-homologous CMEs

In this paper, we identified the magnetic source locations of 142 quasi-homologous (QH) coronal mass ejections (CMEs), of which 121 are from solar cycle (SC) 23 and 21 from SC 24. Among those CMEs, 63% originated from the same source location as their predecessor (defined as S-type), while 37% originated from a different location within the same active region as their predecessor (defined as D-type). Their distinctly different waiting time distributions, peaking around 7.5 and 1.5 hr for S- and D-type CMEs, suggest that they might involve different physical mechanisms with different characteristic timescales. Through detailed analysis based on nonlinear force-free coronal magnetic field modeling of two exemplary cases, we propose that the S-type QH CMES might involve a recurring energy release process from the same source location (by magnetic free energy replenishment), whereas the D-type QH CMEs can happen when a flux tube system is disturbed by a nearby CME

Quantum phase transition of condensed bosons in optical lattices

In this paper we study the superfluid-Mott-insulator phase transition of ultracold dilute gas of bosonic atoms in an optical lattice by means of Green function method and Bogliubov transformation as well. The superfluid- Mott-insulator phase transition condition is determined by the energy-band structure with an obvious interpretation of the transition mechanism. Moreover the superfluid phase is explained explicitly from the energy spectrum derived in terms of Bogliubov approach.Comment: 13 pages, 1 figure

Generalized liquid crystals: giant fluctuations and the vestigial chiral order of I , O and T matter

Theoretical Physic

Do maternal health problems influence child's worrying status? Evidence from the British Cohort Study

Conventional methods apply symmetric prior distributions such as a normal distribution or a Laplace distribution for regression coefficients, which may be suitable for median regression and exhibit no robustness to outliers. This work develops a quantile regression on linear panel data model without heterogeneity from a Bayesian point of view, i.e. upon a location-scale mixture representation of the asymmetric Laplace error distribution, and provides how the posterior distribution is summarized using Markov chain Monte Carlo methods. Applying this approach to the 1970 British Cohort Study (BCS) data, it finds that a different maternal health problem has different influence on child's worrying status at different quantiles. In addition, applying stochastic search variable selection for maternal health problems to the 1970 BCS data, it finds that maternal nervous breakdown, among the 25 maternal health problems, contributes most to influence the child's worrying status

Poisson-Nernst-Planck Systems for Narrow Tubular-like Membrane Channels

We study global dynamics of the Poisson-Nernst-Planck (PNP) system for flows of two types of ions through a narrow tubular-like membrane channel. As the radius of the cross-section of the three-dimensional tubular-like membrane channel approaches zero, a one-dimensional limiting PNP system is derived. This one-dimensional limiting system differs from previous studied one-dimensional PNP systems in that it encodes the defining geometry of the three-dimensional membrane channel. To justify this limiting process, we show that the global attractors of the three-dimensional PNP systems are upper semi-continuous to that of the limiting PNP system. We then examine the dynamics of the one-dimensional limiting PNP system. For large Debye number, the steady-state of the one-dimensional limiting PNP system is completed analyzed using the geometric singular perturbation theory. For a special case, an entropy-type Lyapunov functional is constructed to show the global, asymptotic stability of the steady-state

Effective R-parity violation from supersymmetry breaking

We present a scenario in which Yukawa-like R-parity violating (RPV) couplings are naturally suppressed. In our framework, RPV is assumed to originate from the SUSY breaking mechanism and then transmitted into the SUSY Lagrangian only through soft SUSY breaking operators in the scalar potential. The RPV Yukawa-like operators of the superpotential, conventionally parametrized by the couplings \lambda, \lambda' and \lambda'', are then generated through loops containing the SUSY scalars, the gauginos and the soft RPV interactions and are, therefore, manifest as effective operators with a typical strength of order 10^{-3}.Comment: 4 pages, 2 figures, Revtex4. Main changes with respect to Version 1 are: improved discussions on RGE effects, discussion added on neutrino masses, a toy model added for the proposed scenario. Conclusions remain unchanged. As will appear in Phys. Rev.

Strong-coupling perturbation theory for the two-dimensional Bose-Hubbard model in a magnetic field

The Bose-Hubbard model in an external magnetic field is investigated with strong-coupling perturbation theory. The lowest-order secular equation leads to the problem of a charged particle moving on a lattice in the presence of a magnetic field, which was first treated by Hofstadter. We present phase diagrams for the two-dimensional square and triangular lattices, showing a change in shape of the phase lobes away from the well-known power-law behavior in zero magnetic field. Some qualitative agreement with experimental work on Josephson-junction arrays is found for the insulating phase behavior at small fields.Comment: 7 pages, 5 figures include

Attitudes to a male contraceptive pill in a group of contraceptive users in the UK

BACKGROUND. Small scale trials of male hormonal contraception have produced encouraging results. Attitudes to and beliefs about a proposed male pill may affect uptake. METHODS. This paper examines attitudes towards a proposed ‘male contraceptive pill’ among a self selected sample of 54 men and 134 women, living in a non-metropolitan centre in the East of England, United Kingdom who were already users of contraception. Thirty four respondents were also interviewed and their views on the male pill were qualitatively analysed. RESULTS. The acceptability of a male pill was high with just under half (49.5%) of respondents indicating that they would use it. Gender, length of relationship, age and educational achievement did not affect the reported acceptability. 42% of respondents expressed concerns that men would forget to take a male pill. Women were significantly more likely to express this concern than men. 26% of respondents expressed health concerns. Willingness to take a male pill was associated with expressing the view that increased protection against pregnancy would be an advantage of such a method. Those unwilling or undecided were more likely to express concerns about the effect of a pill on future fertility. CONCLUSIONS. A male pill was accepted as a potential aid to increased fertility control by a large proportion of a convenience sample of contraceptive users in the East of England. If a male pill were to be marketed in the UK this study suggests that concerns about effects on future fertility and health risks may need to be addressed