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

Afterglow Observations Shed New Light on the Nature of X-ray Flashes

X-ray flashes (XRFs) and X-ray rich gamma-ray bursts (XRGRBs) share many observational characteristics with long duration GRBs, but the reason for which their prompt emission peaks at lower photon energies, $E_p$, is still under debate. Although many different models have been invoked in order to explain the lower $E_p$ values, their implications for the afterglow emission were not considered in most cases, mainly because observations of XRF afterglows have become available only recently. Here we examine the predictions of the various XRF models for the afterglow emission, and test them against the observations of XRF 030723 and XRGRB 041006, the events with the best monitored afterglow light curves in their respective class. We show that most existing XRF models are hard to reconcile with the observed afterglow light curves, which are very flat at early times. Such light curves are, however, naturally produced by a roughly uniform jet with relatively sharp edges that is viewed off-axis (i.e. from outside of the jet aperture). This type of model self consistently accommodates both the observed prompt emission and the afterglow light curves of XRGRB 041006 and XRF 030723, implying viewing angles $\theta_{obs}$ from the jet axis of $(\theta_{obs}-\theta_0)\sim 0.15\theta_0$ and $\sim \theta_0$, respectively, where $\theta_0\sim 3$ deg is the jet half-opening angle. This suggests that GRBs, XRGRBs and XRFs are intrinsically similar relativistic jets viewed from different angles, corresponding to $\gamma(\theta_{obs}-\theta_0)$ of less than 1, between 1 and a few, and more than a few, respectively, where $\gamma$ is the Lorentz factor. Future observations with Swift could help test this unification scheme in which GRBs, XRGRBs and XRFs share the same basic physics and differ only by their orientation relative to our line of sight.Comment: some references added, small typos corrected, and the important role of HETE II emphasize

Pulsars With Jets May Harbor Dynamically Important Accretion Disks

For many astrophysical sources with jets, there is evidence for the contemporaneous presence of disks. In contrast, pulsars such as the Crab and Vela show jets but have not yet revealed direct evidence for accretion disks. Here we show that for such pulsars, an accretion disk radiating below detectable thresholds may simultaneously account for (1) observed deviations in the braking indices from that of the simple dipole, (2) observed pulsar timing ages, and (3) possibly even the jet morphology via a disk outflow that interacts with the pulsar wind within, collimating and/or redirecting it.Comment: 10 pages, 2 figs., in press, ApJ. Let

Are the therapeutic strategies in anorexia of ageing effective on nutritional status? A systematic review with meta-analysis

BACKGROUND: Anorexia of ageing (AA) may be considered as a risk factor for frailty and has an important impact on quality of life, morbidity and mortality. METHODS: A systematic review and a meta-analysis were performed to summarise the results from several trials on the effectiveness of treatments in AA, as associated with depression, sensory impairment of taste and smell, decreased appetite or early satiety, and disability. Eligible studies were required to report baseline and follow-up values, the mean change (∆-change) from baseline, and/or the mean difference among intervention groups versus control group, concerning food intake (kcal/daily) and/or nutritional outcomes, such as body weight, body mass index, albumin and Mini Nutritional Assessment. RESULTS: The systematic review included 20 papers based on different therapeutic approaches concerning food intake and/or nutritional outcomes. The results of the meta-analysis indicate that the interventions for AA have an important impact on body weight [+1.59 kg; 95% confidence interval (CI) = 1.48-+1.71 kg; P < 0.001) and on energy intake (+56.09 kcal; 95% CI = -54.05 to +166.25 kcal; P = 0.32). Regarding secondary outcomes, it was not possible to meta-analyse the limited amount of data availab le. CONCLUSIONS: The different variants of AA need to be defined because diverse therapeutic approaches are available. A more precise definition of the functional impairments associated with AA may allow a more correct decision about the most appropriate therapy to be prescribed. Moreover, this may allow for a more effective performance of the different therapeutic approaches once they are better targeted to the different scenarios of AA

UVES/VLT high resolution absorption spectroscopy of the GRB080330 afterglow: a study of the GRB host galaxy and intervening absorbers

We study the Gamma Ray Burst (GRB) environment and intervening absorbers by analyzing the optical absorption features produced by gas surrounding the GRB or along its line of sight. We analyzed high resolution spectroscopic observations (R=40000, S/N=3 - 6) of the optical afterglow of GRB080330, taken with UVES at the VLT ~ 1.5 hours after the GRB trigger. The spectrum illustrates the complexity of the ISM of the GRB host galaxy at z = 1.51 which has at least four components in the main absorption system. We detect strong FeII, SiII, and NiII excited absorption lines associated with the bluemost component only. In addition to the host galaxy, at least two more absorbers lying along the line of sight to the afterglow have been detected in the redshift range 0.8 < z < 1.1, each exhibiting MgII absorption. For the bluemost component in the host galaxy, we derive information about its distance from the site of the GRB explosion. We do so by assuming that the excited absorption lines are produced by indirect UV pumping, and compare the data with a time dependent photo-excitation code. The distance of this component is found to be 280+40-50 pc, which is lower than found for other GRBs (1 - 6 kpc). We identify two additional MgII absorbers, one of them with a rest frame equivalent width larger than 1A. The distance between the GRB and the absorber measured in this paper confirms that the power of the GRB radiation can influence the conditions of the interstellar medium up to a distance of at least several hundred pc. For the intervening absorbers, we confirm the trend that on average one strong intervening system is found per afterglow, as has been noted in studies exhibiting an excess of strong MgII absorbers along GRB sightlines compared to quasars.Comment: 8 Pages, 7 ps figures, A&A in pres

Improving Higher Education Attainment for All Students: A National Imperative

Once a world leader, the United States has fallen behind other nations in the educational attainment of its population. Although the percentage of adults age 45 to 54 who hold at least a baccalaureate degree is higher in the United States than in other Organisation for Economic Co-operation and Development (OECD) nations, the United States now ranks below several other nations, including Norway, the Netherlands, Korea, New Zealand, Denmark, and Sweden, in the share of adults age 25 to 34 who hold this credential. While the U.S. invested heavily in the educational attainment of earlier generations, other nations have been investing substantially in their younger populations. Essentially, educational attainment has stalled in the United States, with about 30% of adults in each age cohort holding at least a bachelor\u27s degree. Over this same period, however, educational attainment has been rising dramatically in some other nations. In Korea, for example, 34% of adults age 25 to 34 now hold at least a baccalaureate degree, up from just 17% of adults age 45 to 54.

Comparison of antioxidant compounds in pig meat from Italian autochthonous pig Suino Nero Lucano and a modern crossbred pig before and after cooking

This study aimed to evaluate and compare the antioxidant compounds of raw and cooked Longissimus lumbontm muscles from Suino Nero Lucano (SNL) and a modern crossbred (CG) pig. Vitamin E, phenols, histidine-containing peptides, and superoxide dismutase (SOD) activity have been detected in the raw and cooked meat of both genetic types. Cooking process decreased the content of all considered antioxidant compounds (P &lt; 0.05). The antioxidant compounds of meat were significantly influenced by genetic type (P &lt; 0.001). Autochthonous SNL raw and cooked meat showed a higher endogenous antioxidants content (P &lt; 0.001) and SOD activity (P &lt; 0.02) compared to CG meat. The results of this research highlighted that the pig meat, in particular autochthonous pig meat, showed good concentrations of endogenous antioxidant compounds that could confer functional properties to the product

Maryland\u27s Higher Education Gains at Risk

This Op-Ed described the struggles that Maryland\u27s higher education is currently facing, outlining several solutions