Inferring cellular regulatory networks with Bayesian model averaging for linear regression (BMALR)

Bayesian network and linear regression methods have been widely applied to reconstruct cellular regulatory networks. In this work, we propose a Bayesian model averaging for linear regression (BMALR) method to infer molecular interactions in biological systems. This method uses a new closed form solution to compute the posterior probabilities of the edges from regulators to the target gene within a hybrid framework of Bayesian model averaging and linear regression methods. We have assessed the performance of BMALR by benchmarking on both in silico DREAM datasets and real experimental datasets. The results show that BMALR achieves both high prediction accuracy and high computational efficiency across different benchmarks. A pre-processing of the datasets with the log transformation can further improve the performance of BMALR, leading to a new top overall performance. In addition, BMALR can achieve robust high performance in community predictions when it is combined with other competing methods. The proposed method BMALR is competitive compared to the existing network inference methods. Therefore, BMALR will be useful to infer regulatory interactions in biological networks. A free open source software tool for the BMALR algorithm is available at https://sites.google.com/site/bmalr4netinfer/

Optical Flashes and Very Early Afterglows in Wind Environments

The interaction of a relativistic fireball with its ambient medium is described through two shocks: a reverse shock that propagates into the fireball, and a forward shock that propagates into the medium. The observed optical flash of GRB 990123 has been considered to be the emission from such a reverse shock. The observational properties of afterglows suggest that the progenitors of some GRBs may be massive stars and their surrounding media may be stellar winds. We here study very early afterglows from the reverse and forward shocks in winds. An optical flash mainly arises from the relativistic reverse shock while a radio flare is produced by the forward shock. The peak flux densities of optical flashes are larger than 1 Jy for typical parameters, if we do not take into account some appropriate dust obscuration along the line of sight. The radio flare always has a long lasting constant flux, which will not be covered up by interstellar scintillation. The non-detections of optical flashes brighter than about 9th magnitude may constrain the GRBs isotropic energies to be no more than a few $10^{52}$ ergs and wind intensities to be relatively weak.Comment: 21 pages, 6 figures, accepted by MNRAS on March 7, 200

Heavy Pentaquarks

We construct the spin-flavor wave functions of the possible heavy pentaquarks containing an anti-charm or anti-bottom quark using various clustered quark models. Then we estimate the masses and magnetic moments of the $J^P={1\over 2}^+$ or ${3\over 2}^+$ heavy pentaquarks. We emphasize the difference in the predictions of these models. Future experimental searches at BESIII, CLEOc, BELLE, and LEP may find these interesting states