Context dependent substitution biases vary within the human genome

Background: Models of sequence evolution typically assume that different nucleotide positions evolve independently. This assumption is widely appreciated to be an over-simplification. The best known violations involve biases due to adjacent nucleotides. There have also been suggestions that biases exist at larger scales, however this possibility has not been systematically explored. Results: To address this we have developed a method which identifies over- and under-represented substitution patterns and assesses their overall impact on the evolution of genome composition. Our method is designed to account for biases at smaller pattern sizes, removing their effects. We used this method to investigate context bias in the human lineage after the divergence from chimpanzee. We examined bias effects in substitution patterns between 2 and 5 bp long and found significant effects at all sizes. This included some individual three and four base pair patterns with relatively large biases. We also found that bias effects vary across the genome, differing between transposons and non-transposons, between different classes of transposons, and also near and far from genes. Conclusions: We found that nucleotides beyond the immediately adjacent one are responsible for substantial context effects, and that these biases vary across the genome

Quantifying the Importance of Ram Pressure Stripping in a Galaxy Group at 100 Mpc

We examine two members of the NGC 4065 group of galaxies: a bent-double (a.k.a. wide angle tail) radio source and an HI deficient spiral galaxy. Models of the X-ray emitting intragroup gas and the bent-double radio source, NGC 4061, are used to probe the density of intergalactic gas in this group. HI observations reveal an asymmetric, truncated distribution of neutral gas in spiral galaxy, UGC 07049, and the accompanying radio continuum emission reveals strong star formation. We examine the effectiveness of ram pressure stripping as a gas removal mechanism and find that it alone cannot account for the HI deficiency that is observed in UGC 07049 unless this galaxy has passed through the core of the group with a velocity of ~800 km/s. A combination of tidal and ram pressure stripping are necessary to produce the HI deficiency and asymmetry in this galaxy.Comment: 8 pages, 6 figures, MNRAS accepte

Tuning Fermilab Heavy Quarks in 2+1 Flavor Lattice QCD with Application to Hyperfine Splittings

We report the non-perturbative tuning of parameters--- kappa_c, kappa_b, and kappa_crit ---that determine the heavy-quark mass in the Fermilab action. This requires the computation of the masses of Ds^(*) and Bs^(*) mesons comprised of a Fermilab heavy quark and a staggered light quark. Additionally, we report the hyperfine splittings for Ds and Bs mesons as a cross-check of our simulation and analysis methods. We find a splitting of 145 +/- 15 MeV for the Ds system and 40 +/- 9 MeV for the Bs system. These are in good agreement with the Particle Data Group average values of 143.9 +/- 0.4 MeV and 46.1 +/- 1.5 MeV, respectively. The calculations are carried out with the MILC 2+1 flavor gauge configurations at three lattice spacings $a$ approximately 0.15, 0.12, and 0.09 fm.Comment: 34 pages, 8 figures, 26 tables; some sections rearranged for clarity; conclusions unchanged; version accepted by Phys. Rev.

B Mixing in the Standard Model and Beyond: Lattice QCD

We give a brief overview and progress report on our lattice QCD calculation of neutral B mixing hadronic matrix elements needed for Standard Model and Beyond the Standard Model physics. Reference [1] contains more details and results.Comment: 3 pages, 0 figures, Proceedings of the 19th Particles and Nuclei International Conference (PANIC11), Cambridge, MA, U.S.A., July 201

Heliophysics Event Knowledgebase for the Solar Dynamics Observatory and Beyond

The immense volume of data generated by the suite of instruments on SDO requires new tools for efficient identifying and accessing data that is most relevant to research investigations. We have developed the Heliophysics Events Knowledgebase (HEK) to fill this need. The HEK system combines automated data mining using feature-detection methods and high-performance visualization systems for data markup. In addition, web services and clients are provided for searching the resulting metadata, reviewing results, and efficiently accessing the data. We review these components and present examples of their use with SDO data.Comment: 17 pages, 4 figure