TFBSTools: an R/bioconductor package for transcription factor binding site analysis.

Summary: The ability to efficiently investigate transcription factor binding sites (TFBSs) genome-wide is central to computational studies of gene regulation. TFBSTools is an R/Bioconductor package for the analysis and manipulation of TFBSs and their associated transcription factor profile matrices. TFBStools provides a toolkit for handling TFBS profile matrices, scanning sequences and alignments including whole genomes, and querying the JASPAR database. The functionality of the package can be easily extended to include advanced statistical analysis, data visualization and data integration. Availability and implementation: The package is implemented in R and available under GPL-2 license from the Bioconductor website (http://bioconductor.org/packages/TFBSTools/). Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Stochastic L-BFGS: Improved Convergence Rates and Practical Acceleration Strategies

We revisit the stochastic limited-memory BFGS (L-BFGS) algorithm. By proposing a new framework for the convergence analysis, we prove improved convergence rates and computational complexities of the stochastic L-BFGS algorithms compared to previous works. In addition, we propose several practical acceleration strategies to speed up the empirical performance of such algorithms. We also provide theoretical analyses for most of the strategies. Experiments on large-scale logistic and ridge regression problems demonstrate that our proposed strategies yield significant improvements vis-\`a-vis competing state-of-the-art algorithms

X-ray Scattering Halos from the Galactic Center: Implications for Diffuse Emission Around SgrA*

We consider the absorption and scattering of X-rays observed from the Galactic center. One objective is to characterize the intrinsic X-ray emission from the central black hole, SgrA*, in its quiescent and flaring states. We correct the fluxes observed by the Chandra and XMM telescopes for absorption and scattering, using realistic models for the dust grain size distribution, gas and dust abundances and spatial distributions. However, there are still large uncertainties. Since much of the intervening dust is close to SgrA*, the scattered halo of X-ray photons is very concentrated: its intensity can dominate the Chandra PSF inside 1", and so affects estimates of the point source flux. It also broadens the radial intensity profiles of Galactic center sources - observations of this effect can help constrain models of the spatial distribution of the dust. We estimate that the combined scattering halos from observed Galactic center sources within 10" of SgrA* contribute up to ~10% of the observed diffuse emission in this region. Dust-scattered photons suffer a time delay relative to the photons that arrive directly. For dust that is 100 pc towards us from the Galactic center, this delay is about 1000 s at angles of 1", and 100 ks at 10". We illustrate how the evolution of the scattering halo following X-ray flares from SgrA* or other sources can also help to constrain the dust's line of sight distribution. We discuss the implications of X-ray scattering halos for the intensity of diffuse emission that has been reported within a few arcseconds of SgrA*: in the most extreme, yet viable, model we consider, ~1/3 of it is due to dust scattering of an unresolved source. The remainder results from an extended source of emission.Comment: 24 pages, including 10 figures, ApJ accepte

Soliton self-modulation of the turbulence amplitude and plasma rotation

The space-uniform amplitude envelope of the Ion Temperature Gradient driven turbulence is unstable to small perturbations and evolves to nonuniform, soliton-like modulated profiles. The induced poloidal asymmetry of the transport fluxes can generate spontaneous poloidal spin-up of the tokamak plasma.Comment: Latex file, 66 pages, 24 postscript figures included. New section on rotation five new figures, comparison with magnetic pumping dampin