Progressive Mauve: Multiple alignment of genomes with gene flux and rearrangement

Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a method to align two or more genomes that have undergone large-scale recombination, particularly genomes that have undergone substantial amounts of gene gain and loss (gene flux). The method utilizes a novel alignment objective score, referred to as a sum-of-pairs breakpoint score. We also apply a probabilistic alignment filtering method to remove erroneous alignments of unrelated sequences, which are commonly observed in other genome alignment methods. We describe new metrics for quantifying genome alignment accuracy which measure the quality of rearrangement breakpoint predictions and indel predictions. The progressive genome alignment algorithm demonstrates markedly improved accuracy over previous approaches in situations where genomes have undergone realistic amounts of genome rearrangement, gene gain, loss, and duplication. We apply the progressive genome alignment algorithm to a set of 23 completely sequenced genomes from the genera Escherichia, Shigella, and Salmonella. The 23 enterobacteria have an estimated 2.46Mbp of genomic content conserved among all taxa and total unique content of 15.2Mbp. We document substantial population-level variability among these organisms driven by homologous recombination, gene gain, and gene loss. Free, open-source software implementing the described genome alignment approach is available from http://gel.ahabs.wisc.edu/mauve .Comment: Revision dated June 19, 200

Patterns of base composition within and between animal mitochondrial genomes

Nucleotide composition of a DNA molecule is a product of base substitution. Variation in nucleotide composition indicates a change in the pattern of substitution at either the level of the underlying mutational spectrum or the constraints imposed by natural selection. This work explores patterns of nucleotide usage within and between animal mitochondrial genomes and the evolutionary mechanisms that have shaped these patterns. Fourfold degenerate sites are expected to reflect the underlying mutational spectrum. Three simple measures of compositional bias, taking into account the strand-specific nature of nucleotide distribution in mtDNA, reveal considerable variation among fourfold degenerate sites of metazoan mitochondrial genomes. Log-linear analysis of intramolecular compositional patterns of mammalian mtDNA demonstrates that fourfold degenerate sites from even a single strand of the genome are not homogeneous. Rather, base composition varies among codon families and around the circular genome. A companion analysis of two additional taxonomic groups, molluscs and insects, also reveals compositional variation among codon families and between strands. The observed intramolecular variation cannot be explained solely by a simple strand-specific mutational pressure, but requires either a contextual bias to the mutational process or translational level natural selection as well. First and second codon position base composition and amino acid frequencies regressed on fourfold degenerate site composition show how mutational biases at the DNA level translate to amino acid biases in mitochondrial proteins

Sex and Race Differences in Faculty Salaries, Tenure, Rank, and Productivity: Why, on Average, Do Women, African Americans, and Hispanics Have Lower Salaries, Tenure, and Rank?

This study examined the status and conditions of salaries, tenure, rank attainment, and productivity of men and women college faculty and faculty of each of five racial groups. It is based on a subset of data on 8,114 faculty members drawn from the 1992-93 National Study of Postsecondary Faculty. The results, based on descriptive and multivariate analyses, indicate that, even after controlling for experience, education, productivity, and institutional characteristics, women received 11.3 percent lower salaries than men, had lower probabilities than men of being tenured, and were less likely than men to be full professors. While Hispanic and Black faculty received salaries comparable to those of Whites, Hispanic and Black faculty were less likely than other faculty to be tenured. The study also found that, after controlling for race, education; experience, instructional and research activities, and institutional type, women faculty had 16.7 percent higher levels of career productivity standardized by teaching field than men. Hispanic faculty were found to be 17.1 percent more productive than faculty of other race groups. The implications of these and other findings for higher education are discussed. Four appendixes provide multivariate analysis data

Neutrino trapping and accretion models for Gamma-Ray Bursts

Many models of Gamma Ray Bursts invoke a central engine consisting of a black hole of a few solar masses accreting matter from a disk at a rate of a fraction to a few solar masses per second. Popham et al. and Narayan et al. have shown that, for Mdot >~ 0.1 Msun/s, accretion proceeds via neutrino cooling and neutrinos can carry away a significant amount of energy from the inner regions of the disks. We improve on these calculations by including a simple prescription for neutrino transfer and neutrino opacities in such regions. We find that the flows become optically thick to neutrinos inside a radius R~6-40R_s for Mdot in the range of 0.1 -10 Msun/s, where R_s is the black hole Schwarzchild radius. Most of the neutrino emission comes from outside this region and, the neutrino luminosity stays roughly constant at a value L_{\nu} ~ 10^{53} erg/s. We show that, for Mdot > 1 Msun/s, neutrinos are sufficiently trapped that energy advection becomes the dominant cooling mechanism in the flow. These results imply that neutrino annihilation in hyperaccreting black holes is an inefficient mechanism for liberating large amounts of energy. Extraction of rotational energy by magnetic processes remains the most viable mechanism

Neutrino Cooled disk in GRB central engine

At the extreme densities and temperatures typical of the central engine of GRBs, the accreting torus is cooled mainly by advection and by neutrino emission. The latter process is dominated by electron and positron capture onto nucleons ($\beta$ reactions). We calculate the reaction rates and the nuclear composition of matter, assuming that the torus consists of helium, eletron-positron pairs, free neutrons and protons. After determining the equation of state and solving for the disk structure for a given initial accretion rate, we subsequently follow its time evolution. We find that, for accretion rates of the order of $10 M_{\odot}$/s, likely typical for the early stages of the accretion event, the disk becomes unstable, giving rise to variable energy output. This instability may play an important role for producing internal shocks.Comment: 4 pages, 3 figures; to appear in Proceedings of the Conference "Astrophysical Sources of High Energy Particles and Radiation", held in Torun, Poland, 20-24 June 200

Infrared and X-ray variability of the transient Anomalous X-ray Pulsar XTE J1810-197

We report on observations aimed at searching for flux variations from the proposed IR counterpart of the Anomalous X-ray Pulsar XTE J1810-197. These data, obtained in March 2004 with the adaptive optics camera NAOS-CONICA at the ESO VLT, show that the candidate proposed by Israel et al. (2004) was fainter by Delta H=0.7+/-0.2 and Delta Ks=0.5+/-0.1 with respect to October 2003, confirming it as the IR counterpart of XTE J1810-197. We also report on an XMM-Newton observation carried out the day before the VLT observations. The 0.5-10 keV absorbed flux of the source was 2.2x10^-11 erg/s/cm^2, which is less by a factor of about two compared to the previous XMM-Newton observation on September 2003. Therefore, we conclude that a similar flux decrease took place in the X-ray and IR bands. We briefly discuss these results in the framework of the proposed mechanism(s) responsible for the IR variable emission of Anomalous X-ray Pulsars.Comment: accepted by A&A Letter

Research Qestions and Data Resource Needs For Examining Student Access to Higher Education

This paper examines some of the important policy issues pertaining to student access to higher education and raises evaluation questions for which evaluation research is needed. For illustrative purposes, the paper presents data that show the progress the nation has made in expanding access persistence and degree completion for various segments of the population at different levels, types and qualities of colleges and universitie

Hyper-Eddington accretion in GRB

Popularmo dels of the GRB origin associate this event with a cosmic explosion, birth of a stellar mass black hole and jet ejection. Due to the shock collisions that happen in the jet, the gamma rays are produced and we detect a burst of duration up to several tens of seconds. This burst duration is determined by the lifetime of the central engine, which may be different in various scenarios. Characteristically, the observed bursts have a bimodal distribution and constitute the two classes: short (t < 2 s) and long bursts. Theoretical models invoke the mergers of two neutron stars or a neutron star with a black hole, or, on the other hand, a massive starexplosion (collapsar). In any of these models we have a phase of disc accretion onto a newly born black hole: the disc is formed from the disrupted neutron star or fed by the material fallback from the ejected collapsar envelope. The disc is extremely hot and dense, and the accretion rate is orders of magnitude higher than the Eddington rate. In such physical conditions the main cooling mechanism is neutrino emission, and one of possible ways of energy extraction from the accretion disc is the neutrino-antineutrino annihilation

Salary, Promotion, and Tenure Status of Minority and Women Faculty in U.S. Colleges and Universities

This report examines differences among postsecondary faculty members by gender and by race/ethnicity. Comparisons were made on several human capital (e.g., education and experience) and structural (e.g., academic discipline and institution type) variables as well as faculty outcomes (salary, tenure, and rank). A multivariate analysis of factors associated with salary was also conducted. Male faculty in this group were compared to female faculty, and comparisons were also made among four racial/ethnic groups: black, non-Hispanic; white, non- Hispanic; Hispanic; and Asian/Pacific Islander. Generated from the 1992-93 National Study of Postsecondary Faculty (NSOPF:93), the analyses presented in this report are based on U.S. citizens with faculty status at 2- and 4-year (and above) institutions who indicated that their primary activity in the fall of 1992 was teaching. Most analyses were also restricted to full-time faculty members. NSOPF:93 is the second in a series of surveys on faculty conducted by the U.S. Department of Education, National Center for Education Statistics

Random strategies are nearly optimal for generalized van der Waerden Games

In a (1 : q) Maker-Breaker game, one of the central questions is to find (or at least estimate) the maximal value of q that allows Maker to win the game. Based on the ideas of Bednarska and Luczak [Bednarska, M., and T. Luczak, Biased positional games for which random strategies are nearly optimal, Combinatorica, 20 (2000), 477–488], who studied biased H-games, we prove general winning criteria for Maker and Breaker and a hypergraph generalization of their result. Furthermore, we study the biased version of a strong generalization of the van der Waerden games introduced by Beck [Beck, J., Van der Waerden and Ramsey type games, Combinatorica, 1 (1981), 103–116] and apply our criteria to determine the threshold bias of these games up to constant factor. As in the result of [Bednarska, M., and T. Luczak, Biased positional games for which random strategies are nearly optimal, Combinatorica, 20 (2000), 477–488], the random strategy for Maker is again the best known strategy.Postprint (updated version